Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: The study did not require ethical approval or consent, as no endangered or protected plant species were involved. Consent for publication Not applicable. Availability of data and materials All data generated or analysed during this study were included in this published 289. Roychoudhry S,Kepinski S. Shoot and root branch growth angle control—the wonderfulness of lateralness. Plant Biol. 2015;23:124-131. Morita MT. Directional gravity sensing in gravitropism. Plant Biol. 2010;61:705-720. . Arabidopsis thaliana: A model for the study of root and shoot gravitropism. Arabidopsis Book. 2002;1:e0043. . Growth-mediated plant movements: hidden in plain sight. Plant Biol. 2018;41:89-94. . Input and signal conversion of gravity in plant gravitropism. J Exp Bot. 2019;70(14):3495-3506. . Plant responses to gravity. Dev Biol. 2019;92:122-125. . SGR2, a phospholipase-like protein, and ZIG/SGR4, a SNARE, are involved in the shoot gravitropism of Arabidopsis. Plant Cell. 2002;14(1):33-46. . Role of endodermal cell vacuoles in shoot gravitropism. J Regul. 2002;21(2):113-119. . Involvement of the vacuoles of the endodermis in the early process of shoot gravitropism in Arabidopsis. Plant Cell. 2002;14(1):47-56. . complex containing SGR3/AtVAM3 and ZIG/VTI11 in gravity-sensing cells is important for Arabidopsis shoot gravitropism. . 2003;100(14):8589-8594. Weijers D,Wagner D. Transcriptional responses to the auxin hormone. Plant Biol. 2016;67:539-574. Zhao Y. Auxin biosynthesis and its role in plant development. Plant Biol. 2010;61:49-64. Adamowski M,Friml J. PIN-dependent auxin transport: action, regulation, and evolution. Plant Cell. 2015;27(1):20-32. [SEP] Justify:

Output: The text is irrelevant to the claim because it discusses various aspects of plant gravitropism and related studies without addressing fossilized plants or their implications for understanding ancient climates and ecosystems.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Once silencing expression patterns are established by DNA methylation, epigenetic inheritance patterns are further solidified by small non-coding RNAs (miRNAs) that ensure regional silencing through degradation of unwanted mRNAs, stunting mRNA maturation or blocking promoter areas associated with mRNA to be silenced. Citation1,Citation17,Citation43 miRNAs can also influence the epigenome itself. This is exemplified by the fact that GpG islands are often occupied by miRNAs that specifically degrade mRNA transcripts that encode for proteins involved in silencing or histone constriction, such as MeCP2, and EZH2Citation44 (all of which are discussed further below). In other words, methylation patterns control transcription of non-coding miRNAs, which, in turn, may assist in silencing by destroying any potential mRNA that may have eluded repression. Methyl-CpG-binding proteins. Once CpG methylation patterns are established, silencing is continually reinforced by a series of methyl-CpG-binding proteins that directly dock to CpGs through their methyl-CpG binding domains (MBD). Citation45,Citation46 In humans, MBD proteins include MBD1, MBD2, MBD3, MBD4 and MeCP2. The basic function of MBD proteins is to secure a primary attachment to methylated CpG and a secondary attachment to the surrounding histone scaffolding in order to enable constriction by further docking of DNMTs, histone methyltransferases, HDACs and ATPase chromatin remodeling complexes. These components work together to compress chromatin into heterochromatin at transcription start sites throughout the genome. Citation47MBD1. MBD1 forms a primary attachment to methylated CpG sites, a secondary attachment to histone constriction enzymes such as SETDB1/Suv39 h1, which methylates H3K9, a tertiary attachment to DNMT1, and a quaternary attachment to a TRD protein. Citation48 As a complex, MBD1-TRD further recruits HP1, HDACs and MCAF1. [SEP] Justify:

Output: The text corroborates the claim by discussing mechanisms such as DNA methylation and small non-coding RNAs (miRNAs) that influence gene silencing and expression patterns. It highlights how established methylation patterns and the actions of miRNAs can affect gene expression, which is consistent with the idea of epigenetics exploring environmental influences on gene activity across generations.


Input: Task: contrast the claim using the given text. Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: Given the distribution of households over resource endowment classes (Table 1a), and the average farm size and allocation of crops per class (Table 1b), we estimated that 36% of the total arable land was cultivated with climbing bean in the 2011A season, highlighting the importance of climbing bean in this region. Table 1. (a) household classes, and the distribution of all 1018 households in Gafuka Cell, Kinoni, Burera over the household classes provided by the local government. (b) Average farm size, livestock ownership, and allocation of land to crops for the different classes observed in the detailed farm characterisation with minimum and maximum values in parentheses. * Other crops include banana, sweet potato and vegetables. Yield and responses to fertiliser as affected by resource endowment and gender Rainfall was evenly distributed over the season with no major dry spells (Figure 2) and stable maximum (19. 8–26. 7°C) and minimum (7. 2–15. 3°C) day temperatures. An average yield of 1. 87 t climbing bean grain and 4. 69 t residue biomass ha−1 was recorded in the farm characterisations. Yields varied greatly between fields: from 0. 63 to 4. 23 t ha−1 grain, and 2. 91 and 6. 89 t ha−1 of stover biomass. Poorer households had significantly smaller grain yields than richer households (Fpr = 0. 039) (Table 2a). There was no significant effect of household class on stover yield. Figure 2. Accumulated rainfall at Musanze weather station in the 2012A season and the main planting period and harvest period (dry beans) of climbing bean in the demo trial in northern Rwanda. Table 2. Climbing bean yields (a) observed in the detailed farm characterisation averaged by household class; (b) observed in the demo plots without and with DAP fertiliser as well as the response to DAP fertiliser, averaged by District and Sector, by household class, and by gender of the farmer (t ha−1). In the demo trial, grain yield ranged from 0. 14 to 6. 9 t ha−1 with an overall average yield of 1. 69 t ha−1: close to the average yield observed in the farm characterisations. Yield in the demo trial was strongly affected by the Sector where the trial was located (Fpr< 0. [SEP] Justify:

Output: The text contrasts the claim by providing specific data on crop yields from traditional farming in a specific region, indicating variability based on household resource endowment. The mention of an average yield of climbing beans and the significant differences in yields between poorer and richer households demonstrates that productivity can differ greatly and is not uniformly the same across different types of agriculture.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Haswell ES. Gravity perception: How plants stand up for themselves. Curr Biol. 2003;13(19):R761-R763. . Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity. Curr Biol. 2016;26(22):3026-3032. . A core regulatory pathway controlling rice tiller angle mediated by the LAZY1-dependent asymmetric distribution of auxin. Plant Cell. 2018;30(7):1461-1475. . 1 family plays a key role in gravity signaling within statocytes and in branch angle control of roots and shoots. Plant Cell. 2017;29(8):1984-1999. . AtLAZY1 is a signaling component required for gravitropism of the Arabidopsis thaliana inflorescence. Plant J. 2013;74(2):267-279. . Architecture1, an protein involved in shoot gravitropism, regulates plant architecture in rice. Plant Physiol. 2013;161(1):317-329. . Maize LAZY1 mediates shoot gravitropism and inflorescence development through regulating auxin transport, auxin signaling, and light response. Plant Physiol. 2013;163(3):1306-1322. Yoshihara T,Iino M. Identification of the gravitropism-related rice gene LAZY1 and elucidation of LAZY1-dependent and -independent gravity signaling pathways. Physiol. 2007;48(5):678-688. . Loss of a highly conserved sterile alpha motif domain gene (WEEP) results in pendulous branch growth in peach trees. . 2018;115(20):E4690-E4699. . Genetic divergence between Camellia sinensis and its wild relatives revealed via genome-wide SNPs from RAD sequencing. PloS One. 2016;11(3):e0151424. Chen L,Yamaguchi S. RAPD markers for discriminating tea germplasms at the inter-specific level in China. Plant Breeding. 2005;124(4):404-409. . Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality. . 2018;115(18):4151-4158. . [SEP] Justify:

Output: The text does not provide any information or evidence relevant to the claim regarding fossilized plants and their role in understanding ancient climates and ecosystems. Instead, it discusses various studies related to plant growth, gravitropism, and genetic divergence among plant species, which do not address the claim directly.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: These include: (1) BAZ2A/TIP5 and BAZ2B; (2) KMT1F/CLLD8, KMT1E/SETDB1 and (3) KIAA1461/MBD5 and KIAA1887/MBD6. Citation45,Citation71 Little is known about the function of BAZ2B. There is evidence to suggest that it can dock to methylated DNA through its primary MBD domain, also having a secondary DNA-binding homeobox and different transcription factor domain, a tertiary tandem C4HC3 zinc-fingerlike domain and a quaternary AT hook domain, which is capable of binding to DNA, also being part of the N-CoR complex. BAZ proteins are likely to be involved in the recruitment of HDAC1, DNMTs and ISWI-ATPase nucleosomal constriction machinery close to DNA promoter regions targeted for silencing. Citation72,Citation73In the case of KMT1F/CLLD8, co-existence of a MBD domain on pre-SET/SET brings together constrictive methylase SETDB1 in conjunction with Suv39 h1. Citation45,Citation74–Citation76 MBD5 is unique in that it harbors a secondary proline-tryptophan-tryptophan-proline domain, which can allow direct docking to chromatin, and is generally concentrated in areas with DNMT3a/3b, suggesting a role in newly established patterned heterochromatin. Citation71 All of these studies clearly show the importance of MBD proteins in bringing together methylated CpGs and reinforcements that ultimately model and shape the histone scaffold to constrict around methylated areas of DNA targeted for silencing. Mutations or defects in any of the above mentioned processes, including DNMTs or MBPs, can lead to developmental disorders such as Rett syndrome (MeCP2),Citation77 Angelman syndrome, defects in brain development, autism (MBD1),Citation78,Citation79 or immunodeficiency-centromeric instability and facial anomalies syndrome (DNMT3b). [SEP] Justify:

Output: The text corroborates the claim by discussing the role of proteins like MBD5 and BAZ2 proteins in gene expression mechanisms, particularly how they interact with methylated DNA and histone modification. It mentions that mutations or defects in these processes can lead to developmental disorders, suggesting that environmental factors influencing gene expression can have significant hereditary implications.


Input: Task: contrast the claim using the given text. Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: Distribution of female and male farmers participating in the demo trial over household classes (%). DAP fertiliser increased bean grain yields strongly: from 1. 36 to 2. 02 t ha−1 on average (Table 2b) (Fpr< 0. 001). The response to fertiliser differed significantly affected among Sectors (Fpr = 0. 022), and household resource classes (Fpr = 0. 006) with poorer households having weaker responses, but not by gender of the farmer or by District (Table 2b). Response to DAP also varied strongly among sites (Figure 2c). In a few cases, yields were smaller with fertiliser than without. Soil characteristics In the demo trial, average soil characteristics observed in Burera and clearly differed (Fpr< 0. 001 for all soil parameters), whereas differences between Sectors within Districts were small and not significant (Table 4). Soils in Burera were relatively fertile with more soil C, soil N and available P, and pH that were unlikely to limit bean productivity. Soils in Gakenke were less fertile on average with lower pH, C and N concentrations, a lower C/N ratio, less available P and less silt and clay than in Burera. Soil characteristics observed in the farm characterisations (Table 4) were comparable with those in the demo trial in Kinoni (Burera), with the exception of available P concentrations, which were larger in the demo trial. Table 4. Soil characteristics in the detailed farm characterisation and the demo trial averaged by district and sector. The first latent vector of a to distinguish Sectors based on soil characteristics from trial sites accounted for 95% of the variation and provided an almost perfect segregation of sites between the two Districts (Figure 4), even though District was not used as a dependent variable. C and N concentration had strong loadings in the first vector, indicating that these variables differed more consistently between the two Districts than, for example, silt and clay or available P. was in fact negatively associated with the first vector, which is unexpected given that sites in Burera had large values on the first vector and large average soil available P concentrations, which suggests that available P was not useful in distinguishing sites from different Districts. The second vector accounted for only 4% of the variation and only partially distinguished sites from different Sectors within Districts. Figure 4. [SEP] Justify:

Output: The text contrasts the claim by providing evidence that the effectiveness of DAP fertiliser and the crop yields varied significantly among different sectors and household resource classes. It states that responses to fertiliser were not uniform: poorer households demonstrated weaker responses, and in some cases, yields with fertiliser were smaller than without. Additionally, soil characteristics differed significantly between demo trial sites, impacting productivity outcomes. This indicates that crop productivity in desert agriculture cannot be said to be equivalent to traditional farming across all locations, as both agricultural methods are influenced by varying environmental and economic factors.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis. Mol Plant. 2017;10(6):866-877. Yao M,Chen L: Tea germplasm and breeding in China. In: Breeding. Edited by. Berlin, Heidelberg: Springer; 2012: 13-68. Vogt T. Phenylpropanoid biosynthesis. Mol Plant. 2010;3(1):2-20. Fraser CM,Chapple C. The phenylpropanoid pathway in Arabidopsis. Arabidopsis Book. 2011;9:e0152-e0152. . Flavonoid accumulation in Arabidopsis repressed in lignin synthesis affects auxin transport and plant growth. Plant Cell. 2007;19(1):148-162. . Mutations in the cinnamate 4-hydroxylase gene impact metabolism, growth and development in Arabidopsis. Plant J. 2009;60(5):771-782. . The growth reduction associated with repressed lignin biosynthesis in Arabidopsis thaliana is independent of flavonoids. Plant Cell. 2010;22(5):1620-1632. . Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Sci Rep. 2017;7:41906. . Flavonols accumulate asymmetrically and affect auxin transport in Arabidopsis. Plant Physiol. 2011;156(2):585-595. Hernandez I,Munne-Bosch S. Naringenin inhibits seed germination and seedling root growth through a salicylic acid-independent mechanism in Arabidopsis thaliana. Biochem. 2012;61:24-28. Ramos P, Guajardo J, Moya-León MA,Herrera R. A differential distribution of auxin and flavonols in radiata pine stem seedlings exposed to inclination. Genomes. 2016;12(3):42. . Conversion of functional specificity in Qb-1 homologues of Arabidopsis. Curr Biol. 2005;15(6):555-560. -Pierce M. [SEP] Justify:

Output: The text discusses various aspects of plant genomics and biochemical pathways in Arabidopsis, focusing on tea flavor, flavonoid accumulation, and auxin transport. However, it does not mention fossilized plants or their role in understanding ancient climates and ecosystems, making it irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Citation25 It is also reported that, in some cases, histone residues can be modified in ways that promote transcription or silencing, as in the case of H3K9, which can be trimethylated (to promote gene repression) or acetylated (to promote transcriptionally active genes). Citation86 Additionally, a number of other modifications such as sumoylation of H4 and biotinylation of H4K8 and H4K12 are generally believed to be associated with transcriptional repression, although this may not always be the case and needs to be investigated further. Citation87,Citation88Nucleosomal PositioningThe nucleosomal structure is predicted by the characteristics of the collective assembly of individual histone octamers that circumscribe 146 base pairs of DNA, which are further adjoined by a piece of 15 base pairs of DNA woven through the connective linker histone H1. Constricted nucleosomes are packaged tightly around DNA, serving as a multi-composite mechanical barricade by which transcription initiation complexes are denied access to DNA. Citation57 In the opposite manner, expansive, nucleosome-free, non-methylated CpG islands are associated with active gene expression. In these regions, biochemical forces eject nucleosomes (by sliding and twisting) away from DNA to ensure an open unmethylated loop of DNA is highly accessible by transcriptional complexes and at 5′ promoter gene regions. Citation48 The three most recognized events associated with how nucleosomes twist and slide involve (1) the stability of the histone cores H2A/H2B; (2) the integrity of the H1 linker and (3) the supporting tortional movement enabled by the ATPase-driven chromatin remodeling machinery. Histone core stability. Nucleosomal ejection is initiated by a destabilized H2A histone core that occurs through an exchange process with an unstable dimer. The unstable dimer is collapsible, highly acetylated and enables chromatin expansion and nucleosome ejection at areas of unmethylated DNA targeted for active expression. Citation89 Unstable histone variants such as H2A. [SEP] Justify:

Output: The text corroborates the claim by discussing mechanisms of gene expression regulation through histone modifications and nucleosomal positioning, which are crucial aspects of epigenetics. It highlights how different modifications to histone proteins can impact transcription, indicating that environmental factors can lead to changes in gene expression, which supports the essence of the claim.


Input: Task: contrast the claim using the given text. Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: Scatter plot of scores of trial sites on the 1st (x-axis) and 2nd (y-axis) vector of a Discriminant Analysis, as well as the eigen values, the percentage of variation accounted for, and the loadings of the vectors. Several characteristics of the soils sampled during the farm characterisation were significantly related to household class with bean fields from wealthier households having soils higher in pH with greater available P, CEC and exchangeable Ca2+ and Mg2+ (Table 5). Exchangeable K+ levels were generally high and unrelated to household type (Table 5). In a first analysis of the soils from the demo trial which did not consider potential confounding of trial sites within Sector, soil C, N, available P and silt and clay concentrations increased progressively with resource endowment across the household classes (Table 5). The fields of wealthier households had higher pH, greater soil C, N, available P and silt and clay. In the demo trial, none of the soil parameters was significantly related to household class if confounding effects of Sector were accounted for. Thus, poorer households were more frequently located in Sectors with poorer soils. Female farmers in the demo trial had a significantly higher C/N ratio than male farmers, while other soil parameters did not differ between female and male farmers (Table 5). Table 5. Soil fertility characteristics in the detailed farm characterisation (Kinoni only) and the demo trial (average of sectors) as affected by household class and gender, and the significance of the differences between classes. * Compensated for confounding effects of Sector in the demo trial. † Not compensated for confounding effects of Sector. Impact of soil and crop management characteristics on yield and response to fertiliser In the farm characterisations, exchangeable Mg2+ and CEC were significantly positively associated with grain yield (Fpr = 0. 009 for Mg2+ and 0. 044 for CEC), whereas none of the other soil parameters, nor organic input rates were. Staking density and height were strongly associated with both grain (Fpr < 0. 001 for density and Fpr = 0. 005 for height) and stover yield (Fpr = 0. 010 and 0. 016) (Figure 5), as also indicated by the relatively strong correlation coefficients, given these data were collected in highly variable farmers’ fields. [SEP] Justify:

Output: The text contrasts the claim by discussing how various soil characteristics and management practices significantly affect yield. Specifically, it states that in the farm characterizations, exchangeable Mg2+ and CEC were positively associated with grain yield, indicating that the success of agriculture may vary based on soil types and management rather than being uniform across different farming practices, particularly in desert agriculture compared to traditional methods.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Wortmannin-induced vacuole fusion enhances amyloplast dynamics in Arabidopsis zigzag1 hypocotyls. J Exp Bot. 2016;67(22):6459-6472. Zheng H, von. The plant vesicle-associated 1a likely mediates vesicle transport from the trans-Golgi network to the prevacuolar compartment. Cell. 1999;10(7):2251-2264. . complex unique to seed plants is required for protein storage vacuole biogenesis and seed development of Arabidopsis thaliana. Plant Cell. 2008;20(11):3006-3021. . Vacuolar/pre-vacuolar compartment Qa-3/SYP22 and PEP12/SYP21 have interchangeable functions in Arabidopsis. Plant J. 2010;64(5):864-873. . Loss-of-function mutations of retromer large subunit genes suppress the phenotype of an Arabidopsis zig mutant that lacks Qb-11. Plant Cell. 2010;22(1):159-172. . ZIP genes encode proteins involved in membrane trafficking of the TGN-PVC/vacuoles. Physiol. 2009;50(12):2057-2068. Wickner W,Rizo J. A cascade of multiple proteins and lipids catalyzes membrane fusion. Cell. 2017;28(6):707-711. . Sec17 can trigger fusion of trans-SNARE paired membranes without Sec18. . 2015;112(18):E2290-E2297. . LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res. 2007;17:402. . Out of shape during stress: a key role for auxin. Sci. 2018;23(9):783-793. Ljung K. Auxin metabolism and homeostasis during plant development. Development. 2013;140(5):943-950. . Transcriptional and hormonal regulation of gravitropism of woody stems in Populus. Plant Cell. 2015;27(10):2800-2813. . VLN2 regulates plant architecture by affecting microfilament dynamics and polar auxin transport in rice. Plant Cell. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses various aspects of plant biology and genetic studies in Arabidopsis, such as vacuole fusion and auxin transport, without mentioning fossilized plants or their role in understanding ancient climates and ecosystems.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Citation32 SWI/1 and hare typically associated with gene expression and reportedly present in the vicinity of unmethylated CpG islands and heavily acetylated histone tails. BAF type remodeling proteins contain BRDs, which bind to acetylated lysines with high specificity. Citation119 It is now becoming more apparent that the human genome encodes for dozens of BRD-containing proteins, many of which play a role in promoting transcription. These include the HAT enzymes PCAF and GCN5, the Tip60 acetyltransferase, the co-activator CBP, the transcriptional protein TAF1, BRD2, 2L4, BAZ2A, BAZ2B, and the nuclear proteins Sp100, Sp110 and Sp140. Citation119–Citation121 Moreover, many proteins that contain BRDs also have other domains including -box type zinc finger, Ring finger, zinc finger, helicase, 40 repeat and MBDs. Citation119 The complexity of BRD-containing proteins role in the regulation of gene expression can be exemplified by the BRDs in human SWI/1 and hwhich have dynamic capacity to bind H3K14ac, H4K8ac, H4K5ac and H4K122ac, as well as DNA, via AT-hook or zinc finger binding motifs. Citation122–Citation125 This is also exemplified by the Brg-1 component of remodeling complex BAF, which contains two bromodomains (BD1 and BD2) with capacity to trigger transcription through association with transcription factor E2F, transcription mediators such as CDK8 and TRAP220, 119 and with ability to dock to acetylated histone tails. Citation126 Other human BRD proteins, such as Brd4, are also recruited to acetylated H3/H4 tails or phosphorylated H3S10 and, in turn, recruit enzymes that phosphorylate and recruit P-TEFb to transcriptional start sites. [SEP] Justify:

Output: The text corroborates the claim by detailing the roles of BRD-containing proteins and their interaction with acetylated histone tails, demonstrating a link to gene expression regulation. This aligns with the claim's assertion that environmental factors can influence gene expression, as these modifications can be affected by environmental context and potentially passed across generations.


Input: Task: contrast the claim using the given text. Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: Wealthier households used more stakes per unit area than poorer households (Fpr = 0. 044) (Figure 5), but staking height did not differ significantly with household class. Figure 5. Scatter graph of stake density (left) and stake height (right) and climbing bean yield for the two poorest and the two wealthiest household classes as observed in the detailed farm characterisation. ‘r’ represents Pearsons correlation coefficient. In the demo trial, differences in yield among Sectors (Table 2b) poorly reflected differences in soil fertility (Table 4). with good average soil characteristics (e. g. Nemba) reported relatively poor yields and vice versa (e. g. Rwaza). It is therefore unsurprising that none of the soil parameters contributed significantly to explain yield variability. Among the agronomic factors (planting density, emergence rate, planting date, timing of first weeding, organic manure applications), only organic manure application rate was significantly positively associated with yield (Fpr = 0. 022). Sites that received more organic inputs tended to give larger bean yields. Almost all farmers (96%) applied the same amount of organic manure to both plots, while the amount applied varied massively from < 300 kg ha−1 to 67 t ha−1. A separate analysis for plots without and with fertiliser indicated that the application rate of organic inputs was highly significantly associated with yield in plots without fertiliser (Fpr < 0. 001), but not in plots with fertiliser, which suggests that the additional N and/or P supplied through organic inputs improved yield in plots without fertiliser. Gender of the farmer or household class were not related to the rate of organic manure application. Stake number or length was not measured in the demo trial. The response to fertiliser was not significantly influenced by any of the soil or agronomic characteristics. Bean yield in the control plot however was positively correlated with yield response (tpr < 0. 001). A similar pattern was observed at Sector level with the largest average response to fertiliser observed in Kinoni where control yields were largest and smallest in Cyabingo where control yields were small (Table 2b). Strong responses to DAP fertiliser (a yield increase of more than 1. [SEP] Justify:

Output: The text contrasts the claim by highlighting that yield variability can be affected by multiple factors including soil fertility and the application of organic manure, which suggests that crop productivity is not consistent across different farming practices or areas. Specifically, it states that 'the differences in yield among Sectors poorly reflected differences in soil fertility,' indicating that productivity is not uniform and can vary significantly depending on agronomic practices, which contradicts the idea that desert agriculture yields the same crop productivity as traditional farming universally.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 2015;27(10):2829-2845. . Auxin, microtubules, and vesicle trafficking: conspirators behind the cell wall. J Exp Bot. 2017;68(13):3321-3329. Majda M,Robert S. The role of auxin in cell wall expansion. Mol Sci. 2018;19(4). . (DRIF) also interacts with WOX and KNOX proteins associated with wood formation in Populus trichocarpa. Plant J. 2018;93(6):1076-1087. -H, Fujioka S, Lin W-. Antagonistic HLH/bHLH transcription factors mediate brassinosteroid regulation of cell elongation and plant development in rice and Arabidopsis. Plant Cell. 2009;21(12):3767-3780. . HEC of a job regulating stem cells. Devel Cell. 2014;28(4):349-350. . A regulatory framework for shoot stem cell control integrating metabolic, transcriptional, and phytohormone signals. Dev Cell. 2014;28(4):438-449. . PkMADS1 is a novel MADS box gene regulating adventitious shoot induction and vegetative shoot development in Paulownia kawakamii. Plant J. 2002;29(2):141-151. . PpeTAC1 promotes the horizontal growth of branches in peach trees and is a member of a functionally conserved gene family found in diverse plants species. Plant J. 2013;75(4):618-630. . A brachytic dwarfism trait (dw) in peach trees is caused by a nonsense mutation within the gibberellic acid receptor PpeGID1c. New Phytol. 2016;210(1):227-239. . Phases of dormancy in Yam tubers (Dioscorea rotundata). Ann Bot. 2006;97(4):497-504. . A novel integrated method for large-scale detection, identification, and quantification of widely targeted metabolites: application in the study of rice metabolomics. Mol Plant. 2013;6(6):1769-1780. . KEGG for linking genomes to life and the environment. Res. 2008;36:480-484. . [SEP] Justify:

Output: The text does not address the claim regarding fossilized plants providing insights into ancient climates and ecosystems. It primarily discusses various topics related to plant biology, development, and gene regulation without mentioning fossilization or climate insights.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Citation32 The nuclear lamina itself is a type of glue that secures heterochromatin organization into position and in organized fashion to sustain gene silencing. Lamins directly interact with H3K9me3 and MeCP2/Sin3A, which bind to lamin B, HP1γ and HP1α. Citation55,Citation157 Lamins also adhere to lamin-associated polypeptides and, at the inner membrane, bind with emerin, Sun1 and Sun2, which anchor nesprin-3 on the outer side, where it binds to cytoskeletal actin via a Klarsicht/ANC-1/Syne homology domain. Moreover, on the outside membrane, nesprin-2 forms complexes with kinesin-1 motor protein apparatus by associating with and recruiting KLC1 to the outer nuclear membrane, which requires lamin A and C. Ultimately, the kinesin-1/nesprin-2/SUN complex spans the entire nuclear envelope in order to anchor cytoskeletal structures to nuclear lamina. Citation158Given the important role of lamins in these processes, it is not surprising that lamin A and lamin C mutations are associated with severe disorganization of chromatin and degenerative diseases, collectively termed as laminopathies. One example is the Hutchinson-Gilford progeria syndrome, which corresponds to a loss of coordinated transcriptional control of the progerin protein. Citation157,Citation159 In addition, more than 200 pathogenic mutations are associated with the LMNA gene, most of which result in developmental disorders of skeletal, heart, muscle and neurological systems, such as Emery-Dreifuss muscular dystrophies, AD-limb girdle muscular dystrophy, lipodystrophy, neuropathy, cardiomyopathy, dermopathy, Syndrome, hepatic stenosis, hyperpigmentation, fertility problems and accelerated aging syndromes. Citation160,Citation161SummaryWhile there are few absolutes in the field of epigenetics, a general line of thought to simplify a very complex matter could include the following. Epigenetics may be conceptualized as control over how genomic DNA is expressed. This control is initiated by DNMTs that methylate CpGs, which are then tagged by MBD proteins attached to potent repression complexes. [SEP] Justify:

Output: The text corroborates the claim by discussing aspects of epigenetics, specifically mentioning that epigenetics can be conceptualized as 'control over how genomic DNA is expressed.' This aligns with the idea that environmental factors can influence gene expression, as epigenetics often involves mechanisms like methylation that can be affected by external conditions.


Input: Task: contrast the claim using the given text. Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: 2 t ha−1) were seen where soil available P was more limiting (in most cases less than 10 mg kg−1), likely because bean yield in control plots were limited by P shortages (Figure 6a). No relationship between soil N and response to DAP fertiliser was observed (Figure 6b), which suggests that available N was not limiting bean yield. At many sites, yield was not or only slightly improved by fertiliser application, despite small soil N or P concentrations observed at these sites (Figure 5a and 5b). In these cases, factors other than N and P availability presumably overrode any benefit from DAP. So two, contrasting tendencies could be observed in the responses. The strongest responses to DAP were observed in fields with small soil available P concentrations, whereas larger responses were generally observed in fields with good control yields. Figure 6. Response of climbing bean grain yield to the application of DAP fertiliser as a function of (a) plant available P and (b) soil N in the demo trials. endowment and gender explain yields of climbing beans and their response to fertiliser The combination of two complementary approaches: farming systems analysis and multi-locational on-farm trials gave good insights into the factors affecting both current production of climbing beans and the opportunities for sustainable intensification. Given the strong co-variation among variables that indicate resource endowments and the influence of resource endowment, both in terms of current availability and in terms of past management, it is difficult to unravel the precise role of different factors. Household resource endowment and gender of the farmer played a key role in determining the grain yield of climbing beans. Both the farm characterisations and the demo trial provided evidence that poorer households farmed on poorer soils (Table 5), as observed elsewhere in SSA (Franke et al. , Reference Franke, van den Brand and Giller2014; Tittonell et al. , Reference Tittonell, Vanlauwe, Leffelaar, Rowe and Giller2005). The differences among household classes in pH, CEC, exchangeable Ca2+ and Mg2+ in the farm characterisations, and in total C and N and available P in the demo trial were most probably caused by differences in crop management in the past, especially the past use of organic manures and mineral fertiliser. [SEP] Justify:

Output: The text contrasts the claim by highlighting that crop yield responses in desert agriculture are influenced by various factors, including soil nutrient availability and farmer resource endowments. It mentions that yields were not significantly improved by fertilizer application in many cases, indicating that environmental conditions and management practices play a critical role in determining productivity, which can vary from traditional farming methods. This suggests that desert agriculture might not achieve the same productivity levels as traditional farming universally.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36. Li B,Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323. . Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010;11(2):R14. . Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics. 2005;21(19):3787-3793. . Expression patterns of alpha-amylase and beta-amylase genes provide insights into the molecular mechanisms underlying the responses of tea plants (Camellia sinensis) to stress and postharvest processing treatments. Planta. 2019(250):281-298. . Analysis of relative gene expression data using real-time quantitative PCR and the 2(-C(T)) Method. Methods. 2001;25(4):402-408. . Identification and evaluation of reliable reference genes for quantitative real-time PCR analysis in tea plant (Camellia sinensis (L. ) O. Kuntze). Mol Sci. 2014;15(12):22155-22172. LegendsAdditional file 1: Fig. S1 Growth architectures of MZ (a and d), QQ (b and e) and LYQQ (c and f) in a natural tea garden. The shoots of QQ and LYQQ exhibit a zigzag shape. Fig. S2 Stem morphology (a) and inter-node length (b) analysis of and QQ. Mature stems were collected on February 2020. The length of the inter-node between the third and fourth nodes (red lines) was determined (n=5). ** indicates a significant difference at the 0. 01 level. Fig. S3 GO enrichment analysis of DEGs identified from the comparisons MZ-vs-QQ (a), MZ-vs-LYQQ (b), and QQ-vs-LYQQ (c). Fig. [SEP] Justify:

Output: The text does not address the claim regarding fossilized plants and their role in providing insights into ancient climates and ecosystems. Instead, it discusses various topics related to RNA-Seq data, gene expression, and tea plants, which are irrelevant to the claim about fossilized plants.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Repression complexes, in turn, control modifications to histones H3 and H4 tails, which perpetuate constriction and make stable modifications to the histone cores H2A and H2B to prevent histone unit ejection/nucleosomal displacement. These collective events are associated with stabilized tension of the histone H1 linker. HP1α and HP1β proteins tether silencing elements—from methylated CpGs to ATPase remodeling machinery—together, in order to tightly crowd methylated DNA close to the nucleosomes, thereby blocking transcription elements. The positioning of silenced heterochromatin along the nuclear envelope is carried on by lamins; centrally positioned euchromatin remaining transcriptionally active. Within euchromatin, unmethylated CpG islands remain open to transcription initiation complexes by opposing processes such as hyperacetylation of histone tails, H2A core variant exchange, HMG proteins binding, which disrupt the H1 linker, and the FACT complex and ATPase reposition machinery, which promotes continual nucleosomal expansion. Silencing and transcription patterns are altered by environmental cues and the transmittance of epigenetic information is heritable through mitosis and meiosis. While this describes a very basic model, the complexities of epigenetic control in regulating the phenotype seem infinite. [SEP] Justify:

Output: The text corroborates the claim by stating that "silencing and transcription patterns are altered by environmental cues" and that "the transmittance of epigenetic information is heritable through mitosis and meiosis." These statements indicate that environmental factors can influence gene expression, which aligns with the definition of epigenetics as stated in the claim.


Input: Task: contrast the claim using the given text. Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: In addition, the greater silt and clay content of fields belonging to wealthier households in the demo trial (Table 5) suggests they were located on soils with better inherent fertility. In the demo trial, these differences in soil fertility between household classes were confounded by geographic location, but similar patterns were observed in the farm characterisations in which geographic confounding was not an issue. We return to this issue below. Women play an important role in farming in Rwanda: they are more frequently engaged in farm activities, and control a larger part of the land and harvest than men (Franke and de Wolf, and de Wolf2011). Yet, in the demo trial women farmers achieved poorer yields than men in both treatments with and without fertiliser (Table 3, Figure 3). We found no evidence that female farmers belonged more frequently to poorer households (Table 3). This suggests that the poorer yields achieved by female farmers were related to differences in access to resources within the household. The only soil characteristic that clearly differed was the higher C:N ratio of the soil from fields of female farmers in the demo trial which could indicate less use of organic inputs in the past. Interviews with the farmers indicated that women farmers primarily rely on compost as organic manure, while male farmers own most of the animals and have access to animal manure richer in N. There was no significant relationship between soil C:N ratio, nor in fact any other soil characteristic measured, and bean yield. Other possible explanations for the poorer yields on the fields of female farmers include: (i) women usually do not own tree plantations and therefore may use poorer quality stakes in climbing bean; (ii) women may face more labour constraints due to their other responsibilities (e. g. fetching water and firewood, household chores) and (iii) women were more likely to pick green immature pods from the demo trial before final harvest to feed the family. Poorer households in the farm characterisations used fewer stakes per unit area and stakes of poorer quality, which in turn was associated with smaller yield (Figure 5). Poor households prefer sticks made of Napier grass (Pennisetum purpureum) due to their low costs, while richer households prefer Eucalyptus and other wooden stakes for their durability (Klapwijk, Reference Klapwijk2011). Cutting stakes from trees; however, may entail environmental costs. [SEP] Justify:

Output: The text contrasts the claim by detailing differences in crop yields related to gender and socioeconomic status among farmers in Rwanda, indicating that variations in yields are influenced by factors such as access to resources, which suggests that productivity is not uniform across different demographics or conditions. This directly opposes the notion that desert agriculture has the same productivity levels as traditional farming overall.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: -19 PreprintsProtocolsVideosJournalsTools & a 10. 21203/rs. 2. 20459/v3This work is licensed under a CC BY 4. 0 LicenseStatus:Published04 Mar, 2020Read the published version in BMC →Version 3posted 2You are reading this latest preprint versionShow more versionsAbstractBackground: Shoot orientation is important for plant architecture formation, and zigzag-shaped shoots are a special trait found in many plants. Zigzag-shaped shoots have been selected and thoroughly studied in Arabidopsis however, the regulatory mechanism underlying zigzag-shaped shoot development in other plants, especially woody plants, is largely unknown. Results: In this study, tea plants with zigzag-shaped shoots, namely, Qiqu (QQ) and Lianyuanqiqu (LYQQ), were investigated and compared with the erect-shoot tea plant Meizhan (MZ) in an attempt to reveal the regulation of zigzag-shaped shoot formation. Tissue section observation showed that the cell arrangement and shape of zigzag-shaped stems were aberrant compared with those of normal shoots. Moreover, a total of 2175 differentially expressed genes (DEGs) were identified from the zigzag-shaped shoots of the tea plants QQ and LYQQ compared to the shoots of MZ using transcriptome sequencing, and the DEGs involved in the “Plant-pathogen interaction”, “Phenylpropanoid biosynthesis”, “Flavonoid biosynthesis” and “Linoleic acid metabolism” pathways were significantly enriched. Additionally, the DEGs associated with cell expansion, vesicular trafficking, phytohormones, and transcription factors were identified and analysed. Metabolomic analysis showed that 13 metabolites overlapped and were significantly changed in the shoots of QQ and LYQQ compared to MZ. Conclusions: Our results suggest that zigzag-shaped shoot formation might be associated with the gravitropism response and polar auxin transport in tea plants. This study provides a valuable foundation for further understanding the regulation of plant architecture formation and for the cultivation and application of horticultural plants in the future. [SEP] Justify:

Output: The text is irrelevant to the claim as it does not address fossilized plants or their role in providing insights into ancient climates and ecosystems. Instead, it discusses zigzag-shaped shoot development in tea plants and related genetic research.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Slice numbers represent residue positions. Green denotes histone marks typically associated with gene activation; red represents histone marks generally associated with transcriptional repression. Modifications are denoted at specific histone residues as Bio+, biotinylated; Ac+, acetylated; Me+, methylated (variable methylation can include me1, me2, me3); Ac-, de-acetylated and SUMO, sumoylated. Display full size2. 8 Å resolutionSource: and consequences of histone modifications. Source: Elsevier BVAcetylation by Tip60 for at DNA LesionsSource: for the Advancement of Science (AAAS)Methyl-CpG binding domain 1 (MBD1) interacts with the Suv39h1-HP1 heterochromatic complex for DNA methylation-based transcriptional repressionSource: Elsevier BVCan our understanding of epigenetics assist with primary prevention of congenital defectsSource: of Histone H3, Expression of G9a (Kmt1c) and Suv39h1 (Kmt1a), and DNA Methylation of in Liver and BrainSource: Elsevier BVEnvironmental signals and transgenerational epigeneticsSource: LtdNon-coding RNAs, epigenetics and complexity. Source: Elsevier BVArtificial light at night: melatonin as a mediator between the environment and epigenome. Source: SocietyCurrent and potential anticancer drugs targeting members of the UHRF1 complex including epigenetic modifiers. Source: Publishers Ltd. Early environmental regulation of forebrain glucocorticoid receptor gene expression: implications for adrenocortical responses to stress. Source: S. [SEP] Justify:

Output: The text corroborates the claim by discussing how environmental signals can impact gene expression, specifically mentioning 'transgenerational epigenetics,' which suggests that environmental factors can indeed influence gene activity across generations. This is directly aligned with the claim regarding the role of environmental factors in epigenetics.


Input: Task: contrast the claim using the given text. Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: Access to good quality staking materials (number of stakes, height and durability) is a major challenge limiting productivity and the wider adoption of climbing beans (Musoni et al. , and Blomme2014; Reckling, Reference Reckling2011). A relatively small amount of DAP fertiliser (70 kg DAP ha−1 containing 12. 6 kg N and 14 kg P ha−1) in the demo trial provided a high average yield response of 0. 66 t ha−1. Although other P fertilisers that do not contain N may be preferable as basal application to legumes such as common bean, DAP was the only option available in Rwanda. Organic manure also increased yields, at least in plots without fertiliser applications, and may be seen as a substitute for mineral fertiliser. Assuming that DAP fertiliser input cost 102 US$ ha−1, labour and opportunity costs of fertiliser application were 20 US$ ha−1 and bean grain fetches US$ 0. 47 kg−1, a response of 0. 52 t ha−1 is required to achieve a value to cost ratio of 2, which is often considered the threshold to make an investment economically attractive. While the observed average response to DAP was above this threshold of 0. 52 t ha−1, it was not achieved by roughly half of the farmers (Figure 2c). Thus approaches are needed to predict the likelihood of substantial crop response to reduce the economic risk of using fertiliser. None of the measured soil or crop management parameters were significantly related to the response to DAP fertiliser. While the strongest responses to fertiliser were observed on soils with low available P concentrations, this was not consistent (Figure 5a). The only two measured variables for which we could find a statistically significant relationship with response to fertiliser were household class and yield in the control plot. This suggests that wealthier households and well-managed fields had a stronger chance of achieving an economically worthwhile response to DAP fertiliser application in bean. The poor responses to fertiliser in fields with very poor control yields suggest the existence of what have been termed poorly or non-responsive soils where a range of factors limit yield (Tittonell and Giller, and Giller2013). [SEP] Justify:

Output: The text contrasts the claim by highlighting that the productivity of climbing beans, influenced by various factors such as the quality of staking materials and the effectiveness of fertiliser application, varies significantly among farmers in Rwanda. It specifically mentions poor responses to fertiliser in fields with low control yields and refers to 'poorly or non-responsive soils,' indicating that factors influencing productivity are not uniformly present, thereby contradicting the idea that desert agriculture yields the same crop productivity as traditional farming everywhere.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: and MorphologyBiology and Geneticsauxin transportgravitropism responsestem developmenttea plantzigzag-shaped stemFiguresFigure 1Figure 2Figure 3Figure 4Figure 5Figure 6BackgroundIn higher plants, the morphology of the plant mainly depends on the development and orientation of the shoots; therefore, plant shoots, which are usually negatively geotropic, play a crucial role in morphological architecture formation in many plants, such as landscape plants, fruit trees and other plants of economic interest. The growth and development of shoots are regulated by diverse factors, including light, temperature and phytohormones [1, 2], but gravitropism is important for the upward growth of shoots and is a determinant of the form and posture of plants [3-5]. However, the molecular mechanism by which shoot architecture formation in woody plants is mediated by gravitropism remains largely unknown. In plants, gravity is sensed by specialized cells called statocytes, and then, a signal is transported to the elongation zone, leading to differential cell growth in the elongation zone to reorient organ growth in response to the gravity signal [6]. It is thought that sedimentable amyloplasts play a critical role in gravity perception and that endodermal cells containing sedimented amyloplasts function as statocytes in plant shoots [3, 7]. In Arabidopsis, shoot responsiveness to gravitropism is regulated by a group of (SGR) genes, of which at least nine SGR genes have been isolated and functionally studied [3]. It has been established that mutant sgr genes could reduce the plant gravitropism response by regulating endodermal cell development, starch accumulation and amyloplast movement [7-11]. Kato, et al. [8] and Morita, et al. [10] found that both SGR2 and zigzag (ZIG)/SGR4 were involved in the formation and function of the vacuole, suggesting that vacuolar integrity participates in shoot gravitropism. Interestingly, ZIG/SGR4 encodes Qb-11, which is involved in membrane trafficking between the trans-Golgi network and the vacuole, and the stems of zig/sgr4 mutants elongate in a zigzag fashion [8, 10, 11]. [SEP] Justify:

Output: The text is irrelevant to the claim as it mainly discusses the morphology, development, and genetic factors affecting higher plants, particularly related to gravitropism. There is no mention of fossilized plants, ancient climates, or ecosystems, which are central to the claim.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Source: Elsevier BVEpigenetic modifications and human pathologies: cancer and CVDSource: Press (CUP)from Xenopus laevis: Elsevier BVInhibition of apoptosis by MAD1 is mediated by repression of the PTEN tumor suppressor geneSource: WileyHistone H1 binding is inhibited by histone variant H3. 3Source: WileyMBD family proteins: reading the epigenetic codeSource: of BiologistsEpigenetics and SignalsSource: Press (OUP)A of Benign and in the Third GenerationSource: (Health)HMGN5/NSBP1: A new member of the HMGN protein family that affects chromatin structure and functionSource: Elsevier BVComputational Epigenetics: the new scientific paradigm. Source: Biomedical InformaticsComparative study of methyl-CpG-binding domain proteinsSource: and epigenetic landscape of Alzheimer's diseaseSource: and interaction of NSBP1/HMGN5 with nucleosomes in euchromatin counteracts linker histone-mediated chromatin compaction and modulates transcription. Source: Elsevier BVAging by epigenetics--a consequence of chromatin damage? Source: Elsevier BVGcn5 regulates the dissociation of SWI/SNF from chromatin by acetylation of Swi2/Snf2Source: Harbor LaboratoryKeeping things quiet: Roles of NuRD and Sin3 co-repressor complexes during mammalian developmentSource: Elsevier BVby CHRAC and ISWI without Disruption or trans-Displacement of the Histone OctamerSource: Elsevier BVControl of DNMT1 Abundance in by Acetylation, Ubiquitylation, and the Histone CodeSource: of chromatin structure and function by HMGN proteins. Source: Elsevier BVAcf1, the largest subunit of CHRAC, regulates ISWI-induced nucleosome remodelling. Source: WileySequence-specific recognition of methylated DNA by human zinc-finger proteinsSource: Press (OUP)Expansion of with in BAF53-depleted Interphase CellsSource: for (ASCB)Duality in bromodomain-containing protein complexes. Source: IMR PressMaternal epigenetics and methyl supplements affect agouti gene expression in Avy/a miceSource: provided by 10. 1016/j. gene. 2007. [SEP] Justify:

Output: The text corroborates the claim by mentioning 'Maternal epigenetics and methyl supplements affect agouti gene expression in Avy/a mice,' which suggests that environmental factors like maternal diet can indeed influence gene expression across generations. This aligns with the claim's focus on environmental influences over genetic expression.


Input: Task: contrast the claim using the given text. Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: Among the 40 sites with a poor yield in the control plot (< 600 kg grain ha−1), 23 sites (21% of all sites) had a poor response to DAP fertiliser application (< 300 kg ha−1) and could be considered non-responsive in our trial. Among the ‘Very Poor’, ‘Poor’, ‘Well-off’ and ‘Rich’ households, 25%, 24%, 17% and 0% of the sites, respectively, could be classified as non-responsive. Reflections on the methods used Working within a large ‘development to research’ project such as N2Africa (Giller et al. , de Wolf, Woomer, Vanlauwe, Vanlauwe, van Asten and Blomme2013) facilitated the collection of data on climbing bean across a wide heterogeneity of farmers’ biophysical conditions and crop management practices, which in turn reflect differences in socio-economic conditions in northern Rwanda. It allowed us to assess the large variability in yield and responses to a technology, under conditions more representative of farmers’ conditions than trials replicated at only a few sites. It thus provided important information on which proportion and which type of farmers and households could benefit from an innovation and the potential risks associated with adoption. Yet this mode of working also imposes constraints on experimental designs and sampling strategies. First, it was only possible to compare a small number of treatments, given that trial implementation and data collection were primarily in the hands of the farmers and rural development agents. Second, researchers had limited control over the selection of participating farmers and sites. Ideally, a stratified random selection approach of farmers would have been followed, in our case with the key factors Sector, socio-economic class of the household, and gender of the farmer as strata. The farm characterisations provided detailed data from a few farms at a single site and backed up some of the findings from the demo trial and represented actual farmers’ practices. Apart from the responses to fertiliser application, a great deal of the observations in the demo trial could have been made through observations in farmers’ fields as done in the detailed farm characterisation as well, but would require a larger number of farms to be assessed. In the demo trial, the differences among household classes, soil properties, common bean yield and response to fertiliser were confounded by geographic location. [SEP] Justify:

Output: The text contrasts the claim by highlighting the variability in crop yields and responses to agricultural practices under different conditions. It indicates that among various types of households and farming conditions, there are significant differences in yield and responsiveness, suggesting that agricultural productivity is not uniform across different settings. The observations from the trial demonstrate that desert agriculture does not yield the same productivity as traditional farming everywhere, given the specific local conditions and variability in effectiveness.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Plant shoot architecture formation is regulated by plant hormones, especially auxin gradients, which are integrated into almost all aspects of plant growth and development [12, 13]. Shoot curvature is controlled by auxin, and increased auxin levels promote cell elongation at the bottoms of reoriented shoots, resulting in upward bending. Therefore, the genes involved in auxin transport and response, especially the polarly localized PIN-(PIN) auxin efflux carriers, play crucial roles in plant shoot formation [13, 14]. PIN-mediated polar auxin transport has been well recognized as being involved in the plant gravity response [3, 7, 15]. For example, after gravistimulation, PIN3 and PIN7 are relocalized towards the gravity vector and trigger changes in auxin flux [16]. Recently, several individual genes, such as LAZY1, LPA1, and WEEP, have been characterized and recognized as new factors involved in plant architecture regulation; these genes also depend on auxin and gravity signalling [17-23], indicating that gravity response and polar auxin transport play primary roles in plant architecture development. However, previous reports have mainly focused on model plants, and the mechanism of architecture development in woody plants remains largely unknown. The tea plant (Camellia sinensis (L. ) O. Kuntze), which is native to southwestern China, is a perennial evergreen woody plant in the family Theaceae [24, 25]. Its tender leaves and buds are processed as a beverage for drinking because tea leaves contain secondary metabolites that are healthy for humans, and tea plants are currently cultivated in over 60 countries around the world [26, 27]. Numerous studies have examined secondary metabolism and stress-response mechanisms in tea plants; conversely, tea plant growth and development processes, such as architecture formation, which is one of the key regulators of tea yield [28], tea processing and even ornamental value, remain to be revealed. Two tea plant cultivars, namely, C. sinensis var. Qiqu (QQ) and C. sinensis var. Lianyuanqiqu (LYQQ), both with zigzag-shaped shoots, were selected and planted more than 80 years ago and described in a previous study [28], but the molecular mechanism of zigzag-shaped shoot formation remains unknown. [SEP] Justify:

Output: The text is irrelevant to the claim as it primarily discusses the regulation of plant shoot architecture by hormones without mentioning fossilized plants, ancient climates, or ecosystems. There is no connection made to how fossilized plants can provide insights into ancient conditions.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: of the main mechanisms of epigenetic control is post translational modification of histones, and one of the relatively less characterized, yet functionally important histone modifications is monoubiquitylation, which is reversed by histone deubiquitinases. In Arabidopsis, only two of such enzymes are known to date. One of them, OTLD1, deubiquitylates histone 2B and functions as a transcriptional repressor. But, could the same deubiquitinase act both as a repressor and an activator? Here, we addressed this question. Using gain-of-function and loss-of-function Arabidopsis alleles, we showed that OTLD1 can promote expression of a target gene. This transcriptional activation activity of OTLD1 involves occupation of the target chromatin by this enzyme, deubiquitination of monoubiquitylated H2B within the occupied regions, and formation of the euchromatic histone acetylation and methylation marks. Thus, OTLD1 can play a dual role in transcriptional repression and activation of its target genes. In these reactions, H2B ubiquitylation acts as both a repressive and an active mark whereas OTLD1 association with and deubiquitylation of the target chromatin may represent the key juncture between two opposing effects of this enzyme on gene expression. : Chromatinchromatin remodelingepigeneticshistone modifications IntroductionEpigenetic regulation of gene expression involves imposition of two altering functional states, i. e. , active, euchromatic and repressive, heterochromatic, on the target chromatin. One of the main mechanisms of epigenetic control is post translational modification of histones, which includes over a hundred of specific modification sites, the studies of many of which are still in their infancy. Citation1-3 Among such relatively less characterized, yet functionally important histone modifications, is monoubiquitylation. Citation4-6 In plant chromatin, monoubiquitylation is found both on histones 2A (H2A) and 2B (H2B),Citation7 with H2B monoubiquitylation being better characterized and shown to affect diverse aspects of the plant life cycle, such as cell cycle, photomorphogenesis, root growth, leaf shape, flowering time, and seed dormancy. [SEP] Justify:

Output: The text corroborates the claim by discussing epigenetic regulation as it relates to gene expression, particularly noting that modifications like monoubiquitylation in histones can result in alterations in gene expression. It mentions how these modifications affect various biological processes, which suggests a relationship between environmental factors and changes in gene expression that can be passed across generations.


Input: Task: contrast the claim using the given text. Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: The wealthier households have better yields in general and achieved stronger response to fertiliser. In addition, wealthier ‘well-off’ and ‘rich’ households were more market-oriented and more likely to afford investments in fertiliser than poorer households. However, also among wealthier households we found sites giving a poor response to fertiliser, presumably because of poorly fertile (non-responsive) soils or highly fertile soils that provided sufficient P to the crop. This suggests that the targeting of fertilisers may be substantially improved if soil fertility status, for instance as indicated by yields in the past or by soil fertility parameters, can also be taken into account. If fertiliser for common bean would be primarily targeted to the ‘well-off’ and ‘rich’ farmers, who comprise 34% of the rural households in (Table 1a), an obvious question is: what can be offered to support the other 66% of households? Innovations that reduce staking costs or improve staking quality, such as the use of plastic or Sisal strings, could substantially help to lower costs of production and increase bean productivity, also for the poorer households (Musoni et al. , and Blomme2014). It is well known that resource poor households are in a weak position to adopt new technologies and tend to make only marginal changes in their farming practices, and transforming their farming practices requires knowledge intensive research and extension approaches taking the local context into account (Kristjanson et al. , and Coe2012). Rwanda's rural sector policies have been criticised as too oriented to economic growth with little attention for pro-poor strategies leading to a growing inequality and the poor being by-passed (Ansoms, Reference Ansoms2008). Our results underpin the need for research and extension to pay special attention to the needs of women farmers (Manfre et al. , and Akeredolu2013). Women-headed households are in many respects in a disadvantaged position to adopt innovations (FAO, 2011). In our study, women achieved smaller average yields than men irrespective of the resource endowment of the household or the gender of the household head, suggesting that targeting women-headed households alone will not close the gender gap. [SEP] Justify:

Output: The text contrasts the claim by discussing how wealthier households achieve better yields and are more responsive to fertilisers compared to poorer households. It highlights that different households experience varying productivity levels based on factors like resource availability, soil fertility, and knowledge about farming practices. This directly challenges the notion that desert agriculture yields the same productivity everywhere, indicating that productivity is context-dependent and varies significantly across different socioeconomic groups.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: In this study, the stems of tea plants with zigzag-shaped (QQ and LYQQ) and erect (C. sinensis var. Meizhan, MZ) shoots were collected and investigated for structural differences, transcription and metabolic regulation using section observation, transcriptome sequencing and metabolite detection, respectively, for the first time. In total, 46. 06 million reads were generated from nine samples, and the differentially expressed genes (DEGs) were identified and compared. A total of 2175 DEGs, including 998 upregulated and 1177 downregulated genes, were identified from the zigzag-shaped shoots of QQ and LYQQ compared to the erect shoots of MZ. The candidate DEGs, including genes associated with vesicular trafficking, cell expansion, transcription factors, and phytohormones and diverse genes involved in the regulation of plant growth and development, were seemingly related to zigzag-shaped shoot formation in tea plant. The results will contribute greatly to an improved understanding of the molecular regulatory mechanism of zigzag-shaped shoot formation in woody plants. ResultsPhenotypic characterization and stem ultrastructure analysis of tea plants with erect and zigzag-shaped shoots Under natural conditions, the trees of MZ, QQ and LYQQ can grow upward uniformly (Additional file 1: Fig. S1). The leaves of MZ and QQ are flat, while those of LYQQ are folded inwards. In the MZ plant, the stems grew straight up, exhibiting normal shoot morphology; however, the shoots of both QQ and LYQQ tended to bend at each node and elongate in a zigzag fashion (Fig. 1a-c). Additionally, plants with zigzag-shaped shoots had shorter stems and fewer leaves than erect plants (Additional file 1: Fig. S2a), and the internode distance (between two nodes) in plants with zigzag-shaped shoots was significantly shorter than that in erect plants (Additional file 1: Fig. S2b). To precisely investigate the differences in zigzag-shaped stems at the ultrastructure level, we longitudinally dissected the stems of the and MZ tea plants. Observation of the stem longitudinal sections showed that the tissues were basically normal, but the cell arrangement and shape differed between zigzag-shaped and erect stems (Fig. [SEP] Justify:

Output: The text discusses an investigation into the structural differences of tea plants with zigzag-shaped and erect shoots, focusing on genetic and morphological characteristics rather than fossilized plants or their implications for ancient climates and ecosystems. Thus, it does not provide relevant information to support or contrast the claim.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: For example, in mammals, UBP44, a member of the UBP/USP family of deubiquitinases, deubiquitylates H2Bub at its target gene promoter and represses transcriptionCitation28 whereas H2Bub deubiquitylation at the target gene promoter by a different member of this enzyme family, UBP42, activates transcription. Citation29 Also in mammals, on the genome-wide level, H2Bub negatively correlates gene induction. Citation30 In yeast, H2Bub deubiquitylation by Ubp10 is involved in transcriptional repression,Citation27 and H2Bub deubiquitylation by Ubp8 is required for transcriptional activation,Citation31 and these histone deubiquitinases target H2Bub in different chromatin domains. Citation32 Also, in yeast, H2B ubiquitylation in quiescent promoters inhibits transcription and in active gene bodies promotes transcription elongation. Citation33The notion that the same histone deubiquitinase can associate with the chromatin of its target genes and directly control their transcription via both activating and repressive regulatory pathways has not been examined. We addressed this question using OTLD1, one of the two known plant histone deubiquitinases. Our data suggest that OTLD1 can play a dual role in transcriptional repression and activation. This idea is illustrated in Fig. 5 using OSR2 as an example of an OTLD1-repressed geneCitation17 and AN3 as an example of an OTLD1-activated gene. OTLD1 can associate with the chromatin of the promoter regions of both genes and deubiquitylate H2Bub in both promoters. After these two “common” steps, the effects of OTLD1 on both genes diverge, and the OSR2 chromatin loses its euchromatic histone modification marks whereas the AN3 chromatin acquires them, ultimately resulting in transcription repression or activation, respectively. In this scenario, H2B ubiquitylation would act as both a repressive and an active mark. Thus, OTLD1 association with and deubiquitylation of the target chromatin may represent the key juncture between two opposing effects of this enzyme on gene expression. [SEP] Justify:

Output: The text corroborates the claim by discussing the role of histone deubiquitinases, like OTLD1, in regulating transcription through deubiquitylation of H2Bub at gene promoters. This demonstrates how molecular processes can influence gene expression, aligning with the notion that environmental or genetic factors could affect expression across generations. It emphasizes the regulatory pathways that can either activate or repress gene expression, supporting the broader concept of epigenetic influence.


Input: Task: contrast the claim using the given text. Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: This approach also offers greater precision, enabling farmers to target specific areas of their farms that require attention and reduce the use of chemicals and fertilizers (Figure 1) [5]. Figure 1. Smart farming using artificial intelligence on farm for the improvement in agriculture production. Advertisement 2. The evolution of farming: from traditional to smart farmingThe evolution from traditional to smart farming can be traced back to the early 1990s when precision agriculture (PA) was first introduced. PA is a farming approach that involves using technology to target specific areas of the farm that require attention, such as soil moisture levels or nutrient deficiencies. This approach uses data analysis tools to optimize inputs and minimize waste, resulting in higher crop yields and reduced costs [1]. Over the years, smart farming has evolved to include a range of advanced technologies. For example, drones equipped with cameras and sensors can provide detailed images and data on crop health and yield. Soil sensors can measure soil moisture, temperature, and nutrient levels, providing insights into the health of the soil and enabling farmers to make informed decisions about fertilization and irrigation [6]. Another technology that has revolutionized smart farming is the IoT. IoT-enabled sensors and devices can be placed throughout the farm to monitor environmental conditions, track crop growth, and optimize irrigation and fertilizer applications. This data is transmitted to a central platform, where it is analyzed and used to generate insights that can help farmers make informed decisions [7]. Advertisement 3. The benefits of smart farming3. 1 Increased productivitySmart farming allows farmers to collect data on crop health, soil quality, and other key indicators in real time. This data can be analyzed to optimize inputs such as fertilizers, water, and pesticides, resulting in higher crop yields. By targeting specific areas of the farm that require attention, farmers can also reduce waste and ensure that resources are used efficiently [8]. 3. 2 SustainabilitySmart farming promotes sustainable farming practices by minimizing the use of resources such as water, fertilizers, and pesticides. By using precision agriculture techniques, farmers can reduce the amount of chemicals used on crops, resulting in a more environmentally friendly approach to farming. In addition, smart farming can help farmers adapt to climate change by providing insights into weather patterns and enabling them to adjust farming practices accordingly [9]. 3. 3 Cost savingsBy optimizing inputs and reducing waste, smart farming can lead to significant cost savings for farmers. [SEP] Justify:

Output: The text contrasts the claim by discussing the advancements in smart farming and precision agriculture, which optimize inputs and practices to achieve higher crop yields. It indicates that the effectiveness of agriculture can significantly vary based on the use of technology and practices, suggesting that desert agriculture may not yield the same productivity as traditional farming universally.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 1d-f). In QQ and LYQQ, the cortex cells tended to be disordered and arranged loosely, and the cells in both the cortex and pith exhibited aberrant shapes (Fig. 1g-i). RNA sequencing, reference genome alignment and new gene annotation To investigate the regulation of zigzag-shaped stem formation in tea plants at the transcriptional level, we utilized RNA-Seq technology to analyse DEGs in the stems of MZ, QQ and LYQQ plants. In total, 46. 06 million clean reads were generated from nine samples, and the sequence data were deposited in the (SRA accession: PRJNA559220). After removing adaptor sequences, duplicate sequences, ambiguous reads and low-quality reads, a total of 16. 37, 13. 28, and 15. 48 million high-quality clean reads were generated for MZ, QQ and LYQQ, respectively (Additional file 2: Table S1). The average amount of clean reads per sample was 5. 2 million. The Q20 values ranged from 97. 39% to 98. 55%, and the Q30 values ranged from 92. 26% to 95. 07%. All the transcripts were aligned to the reference genome, and the average proportion of samples mapped to the genome was 76. 38%. The new genes were then aligned to the Nr and KEGG databases for protein functional annotation. In total, 34248, 34374 and 33598 genes were identified from MZ, QQ and LYQQ, respectively, and 28021 (82. 58%), 27441 (80. 87%) and 27982 (82. 46%) genes were annotated as known genes in MZ, QQ and LYQQ, respectively (Additional file 2: Table S2). These results indicated that the obtained high-quality transcriptomic data could be used for further analysis. Validation of differential expression data To validate the reliability of the RNA-Seq results, 16 DEGs were randomly selected from the RNA-Seq data and examined using qRT-PCR. The qRT-PCR data exhibited similar expression patterns to the RNA-Seq data among the cultivars (Fig. 2), suggesting that our transcriptomic data are reliable and valid. [SEP] Justify:

Output: The text does not address the claim regarding fossilized plants and their insights into ancient climates and ecosystems. Instead, it focuses on RNA sequencing and gene annotation in tea plants, which is irrelevant to the context of fossilized plants.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Breaking the code: How changes in gene expression can cause complications in HIV/AIDS Health & 23, 2023 HIV and AIDS are major global healthcare concerns. Advances in anti-retroviral therapy mean that people with HIV infection live longer, which is leading to new health concerns, such as neurological complications. Thangavel at Texas A&M University, USA, aims to understand the mechanisms behind cognitive changes in HIV infection. His research shows that alterations in gene expression and protein modifications are likely behind the changes seen in the immune cells of the brain. Every day, 4,000 people become infected with human immunodeficiency virus (HIV), and it remains a leading cause of death in many countries. In 2021, someone died from acquired immune deficiency syndrome (AIDS) every minute, equating to around 650,000 AIDS-related deaths. Around 75% of people who carry the virus responsible for have access to anti-retroviral treatment. This prevents the condition from progressing and has improved overall life expectancy. However, researchers are still learning about how living with HIV infection can impact health in the long term. A paradigm shift is happening in the research arena towards enhancing the quality of life for people living with HIV infection. Neurological complications of attacks the body’s immune system, including white blood cells. The virus hijacks the cellular machinery and causes epigenetic changes which alter gene expression. HIV infection can also affect cells of the central nervous system, leading to inflammation that can impair brain function. The collection of cognitive changes associated with HIV infection is known as NeuroAIDS. A paradigm shift is happening in the research arena towards enhancing the quality of life for people living with HIV infection. One type of a NeuroAIDS disorder is HIV-associated neurocognitive disorder (HAND), which includes symptoms such as behaviour changes, depression, and memory loss. Specialist methods have been used to characterise some of the changes in the brain resulting from HAND and showed that alterations in genes and proteins are associated with metabolic pathways, neurodegenerative disorders, and dementia. The exact mechanism of HAND is unclear. However, we do know that HIV does not directly infect neurons; instead, it indirectly leads to disrupted glial function (glial cells support and protect neurons), neuronal dysfunction, or death. Despite effective anti-retroviral therapy, around 50% of people with HIV may have HAND. [SEP] Justify:

Output: The text corroborates the claim by discussing how HIV infection leads to epigenetic changes that alter gene expression. It mentions that the virus hijacks cellular machinery and causes epigenetic changes, indicating a mechanism through which environmental factors (such as the presence of the virus) can influence gene expression. This supports the idea that epigenetics involves the interaction between environmental factors and gene expression.


Input: Task: contrast the claim using the given text. Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: Dr Marília Chiavegato – with Productivity in Crop and Animal FarmingOct 13, 2021 | 0 Reddit +1 0 LinkedIn 0 Email Vdemand on agricultural systems to increase the food supply has risen sharply as the global population continues to grow. However, as agricultural systems increase productivity, they also emit more greenhouse gases and exacerbate climate change. Simultaneously meeting food supply demands and reducing environmental impact in agricultural settings is one of the most important issues of our time. Dr Marília Chiavegato of has dedicated her career to studying the ecological components of agricultural ecosystems, called ‘agroecosystems’. Her team’s findings will aid the development of management practices that not only boost productivity, but also lower the environmental impact associated with conventional agriculture. Agroecosystem ManagementSimultaneously addressing the global food crisis and climate change requires that we look at agroecosystems through a new lens. Though agricultural settings are human-made, they are still complex and dynamic ecosystems. Thus, just as in natural systems, all components of the ecosystem such as the soil structure, plant diversity and animal populations, interact with one another to modify the landscape and any associated ecological services. These components can have a large influence on agricultural output, such as livestock meat yields, and significant environmental impacts, such as the amount of greenhouse gas emissions. Moreover, there are social, political, and economic considerations that influence agroecosystems that are typically not encountered in natural ecosystems. Additionally, climate change will undoubtedly impact agricultural settings, reducing our ability to grow food, and forcing us to change how we manage land. An increase in flooding, drought and depleted soil all need to be considered when planning for the future. Therefore, it is important that agroecosystems are resilient to the shocks and stressors of a changing climate, while also maintaining high levels of productivity. Prior to making land management decisions, we must increase our knowledge of the mechanisms underpinning agroecosystems, and how these might change with a warming planet. Dr Marília Chiavegato and her lab at have used methods based on a systems approach, in which management strategies are monitored on farms rather than simulated, to begin to tackle these important questions and address prominent knowledge gaps. [SEP] Justify:

Output: The text contrasts with the claim by discussing the complexities of agricultural ecosystems and the importance of managing them in the face of climate change. It highlights that agricultural settings, including desert agriculture, are dynamic ecosystems with various interacting components that affect productivity. By emphasizing that managing agroecosystems must take into account environmental impacts and the resilience to climate change, the text suggests that uniform productivity across all farming types, including desert agriculture, is not valid.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Identification of DEGs and pathways in cultivar comparisons The DEGs in each cultivar pair were then determined according to the parameters p value≤0. 01 and |log2FC|≥1. In total, 6232 DEGs, including 2969 upregulated and 3263 downregulated DEGs, were detected in MZ-vs-QQ (Fig. 3a). GO enrichment analyses showed that most of the DEGs were enriched in the terms ‘catalytic activity’, ‘metabolic process’, ‘cellular process’, ‘binding’, ‘single-organism process’, and ‘membrane’ (Additional file 1: Fig. S3). The DEGs were also subjected to KEGG pathway enrichment analyses, which showed that the pathways ‘Biosynthesis of secondary metabolites’, ‘Plant-pathogen interaction’, ‘Phenylpropanoid biosynthesis’, ‘Stilbenoid, diarylheptanoid and gingerol biosynthesis’, ‘Monoterpenoid biosynthesis’, ‘Biosynthesis of unsaturated fatty acids’, ‘alpha-Linolenic acid metabolism’, and ‘Flavonoid biosynthesis’ were significantly enriched. Additionally, we found that the zeatin biosynthesis pathway was enriched (Fig. 3b). In the MZ-vs-LYQQ comparison, a relatively high number of DEGs (7212), including 4002 upregulated and 3210 downregulated DEGs, were identified (Fig. 3a). All the DEGs could be mapped to 132 KEGG pathways, and the pathways ‘Phenylpropanoid biosynthesis’, ‘Cutin, suberine and wax biosynthesis’, ‘Plant-pathogen interaction’, ‘Stilbenoid, diarylheptanoid and gingerol biosynthesis’, ‘Flavonoid biosynthesis’, ‘Biosynthesis of secondary metabolites’, ‘Monoterpenoid biosynthesis’, ‘Glutathione metabolism’, and ‘Arginine and proline metabolism’ were significantly enriched (Fig. 3b). [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses differential expression genes (DEGs) and pathways in cultivar comparisons without mentioning fossilized plants or their role in understanding ancient climates and ecosystems.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Epigenetic mechanisms Thangavel at Texas A&M University, USA, aims to understand more about HAND progression. He explains that HIV may alter the normal functions of cells by changing gene expression – in other words, whether a gene within the cell is turned on or off. When a gene is switched on, this means that the instructions in our DNA can be converted into an end product, for example a particular protein. In particular, Thangavel is interested in an aspect of gene modification called epigenetics. Epigenetics is a reversible change in the way that genes are read, caused by your behaviours and environment. For example, some epigenetic changes increase the risk of developing cancer, as they alter the way that a certain gene functions. While gene expression may change, the underlying DNA sequence remains the same. N-terminal acetylation might explain how the HIV virus interacts with the human body. Epigenetic mechanisms can include the addition of a chemical group to one end of a protein, a process called N-terminal acetylation. Protein synthesis within the cell happens in ribosomes, cellular machines that link smaller building bricks together to form larger proteins. Sometimes proteins are altered, or modified, during this stage of production. HIV can modify immune cells Thangavel is particularly interested in N-terminal acetylation within an important cell type in the brain, the microglia. Microglia cells are often known as the immune cells of the central nervous system, and play important roles in brain infections, such as HAND. During infection with HIV, the microglia are unable to carry out their normal protective roles and this can promote inflammatory responses within the brain. Thangavel proposes that N-terminal acetylation changes could explain how the virus and body interact. Alterations to proteins within the microglia cells through N-terminal acetylation can have a number of consequences, such as impairment of the mitochondrial energy-production and metabolic functions in the microglia, which cause misfolded or degraded proteins, or alterations to signalling pathways within the cell. There may also be issues with oxidative stress and redox imbalance, meaning an imbalance between oxidants and antioxidants. This is likely to affect energy resources and metabolic fuel within the microglia. Many of these changes have already been linked to the development of neurodegenerative disorders. [SEP] Justify:

Output: The text corroborates the claim by explaining that epigenetics involves reversible changes in the way genes are expressed due to behaviors and environmental factors. It specifically mentions that 'Epigenetics is a reversible change in the way that genes are read, caused by your behaviours and environment,' which directly supports the idea that environmental influences can affect gene expression.


Input: Task: contrast the claim using the given text. Claim: Ocean carbon capture may mitigate climate change but requires further study for safety. [SEP] Text: But, when using fossil fuels, carbon is taken from the geosphere and introduced to the atmosphere. If these emissions are captured, the carbon is returned to the geosphere and never enters the atmosphere. was to be used, as suggested by the fossil industry representative, the flow of carbon would still exist and require reductions. If what was captured through DACCS close to the chimney was counted to counter other hard-to-abate emissions, the flow of CO2 from the chimney would still need to be stopped or countered by other CDRs under a net zero target. As a result, as illustrated in Figure 7. 2, fossil CCS can never be CDR and used as a means to counter other hard-to-abate emissions. 6 WG3 the following is stated: CCS helps reduce gross emissions but does not remove CO2 from the atmosphere, unless combined with bioenergy (BECCS). (6 WG3, 2022, 4. 41) 7. 2 Difference between carbon dioxide removal (CDR) and fossil carbon capture and storage (CCS) Download FigureDownload figure as PowerPoint slide A point must be highlighted though. The fact that fossil CCS is not CDR does not reduce its importance in climate change abatement. A recent study of scenarios for cutting emissions in Europe concluded that deep emission cuts and level of CCS deployment were tightly intervened (Nikas et al. , 2021). Figure 7. 3 from 15 (2018) provides a schematic overview of how the emission pathways work and how different sectors contribute to different climate change abatement p. 120 p. 121targets. Reduced emissions through fossil CCS are illustrated in orange while the negative emissions through technological CDR technologies such as BECCS are illustrated in yellow. The amount of CO2 released to the atmosphere reaches net zero when the uptake from CDR equals the remaining emissions. In the figure, CDR from AFOLU (agriculture forestry and other land use) is illustrated in brown. net contributes to GHG today, changed practices could lead to net uptake of CO2. 7. 3 Schematic explanation of the contribution of different sectors to global CO 2 emissions Source: 15 (2018). Reproduced with permission of IPCC. Download FigureDownload figure as PowerPoint slide 3. 1 options for creating CDR exist where all have their respective strengths and weaknesses. 6 WG1 2. [SEP] Justify:

Output: The text contrasts the claim by clarifying that while fossil CCS can reduce gross emissions, it does not equate to removing CO2 from the atmosphere unless combined with bioenergy practices. It states, 'the fact that fossil CCS is not CDR does not reduce its importance in climate change abatement', suggesting that further study is necessary to understand its true impact on carbon capture and emission reduction.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: A total of 6930 DEGs, including 3932 upregulated and 2998 downregulated DEGs, were detected in the QQ-vs-LYQQ comparison (Fig. 3a) and mapped to 132 pathways. The DEGs in the pathways ‘Plant-pathogen interaction’, ‘Cutin, suberine and wax biosynthesis’, ‘Biosynthesis of secondary metabolites’, ‘Phenylpropanoid biosynthesis’, ‘Stilbenoid, diarylheptanoid and gingerol biosynthesis’, ‘Brassinosteroid biosynthesis’ and ‘Monoterpenoid biosynthesis’ were significantly enriched (Fig. 3b). Identification of DEGs and pathways involved in zigzag-shaped stem formation in tea plants We generated a Venn diagram to compare the different cultivars and showed that 1082 DEGs overlapped among the MZ-vs--vs-QQ, and QQ-vs-LYQQ comparisons (Fig. 4a). These DEGs were significantly enriched in the pathways of “Plant-pathogen interaction”, “Stilbenoid, diarylheptanoid and gingerol biosynthesis”, “Phenylalanine metabolism”, and “Tryptophan metabolism” (Additional file 1: Fig. S4a). In addition, a total of 1255 DEGs, including 527 downregulated and 728 upregulated DEGs, were specifically detected in the MZ-vs-LYQQ comparison (Fig. 4a). Among the top 20 pathways, “Cysteine and methionine metabolism”, “Cutin, suberine and wax biosynthesis”, “Taurine and hypotaurine metabolism”, and “Other types of O-glycan biosynthesis” were markedly enriched (Additional file 1: Fig. S4b). Unexpectedly, the number of DEGs in the MZ-vs-QQ set (949, including 494 downregulated and 455 upregulated) was lower than that in MZ-vs-LYQQ (Fig. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses differential expression genes (DEGs) and biochemical pathways in tea plants, which does not provide any insights or information related to fossilized plants or their significance in understanding ancient climates and ecosystems.