Input: Task: corroborate the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Research has shown that HIV can interrupt the way these energy powerhouse structures work, including increasing the release of harmful molecules that can contribute to the progression of HAND. In addition, this energy is needed for effective gene expression within the cell. Studies done by Thangavel’s research group at Texas A&M University have already shed light on the epigenetic changes in the human brain cause energy dysfunction, which can contribute to HAND. Thangavel also suggests that N-terminal acetylation may impact the signalling cascade of gene expression which has been shown to be significantly associated with depressive behaviours, problems with forming memories, and dementia. He proposes that N-terminal acetylation changes induced by viral infections could explain how the virus and body interact. He also explains that if more can be understood about how HIV effects the cell’s energy source, it may be possible to develop therapeutic approaches to prevent HAND, as well as new ways to test for the condition. Improving quality of life Further research is still needed to learn more about the relationship between HIV infection, modifications to proteins via N-terminal acetylation or other mechanisms, and cognitive impairment or behavioural changes. It is likely that epigenetic modifications regulate both gene expression in the energy-producing compartments of a cell, as well as gene expression more broadly. Improved diagnosis and management of cognitive disorders in people with HIV infection, which is well managed through medications, means that overall quality of life can be improved for those living with the virus. How did you first become interested in the impact of HIV infection on the brain? Our research focus is aligned with the global efforts to eliminate the suffering of HIV. Understanding the mechanisms of disease progression is key to developing new therapeutic strategies. In the early phase of my research, there was a lack of knowledge of HIV and its virulent subtypes. Our experiments highlighted the higher virulence of the subtypes found in the US compared to European, Asian, and African subtypes, which trigger neuronal cell death through the excess production of a neurotoxin called quinolinic acid. Neurological impairments caused by the subtypes from the US were also somewhat elevated, which paralleled with the high occurrence of HAND in the US. Disruption of energy homeostasis is one of the features observed in neurodegenerative conditions, including HAND. [SEP] Justify:

Output: The text corroborates the claim by discussing the relationship between epigenetics and gene expression, particularly in the context of HIV infection. It mentions that 'epigenetic modifications regulate both gene expression in the energy-producing compartments of a cell, as well as gene expression more broadly,' which aligns with the claim that epigenetics involves how environmental factors affect gene expression. The reference to the ongoing research into how factors related to HIV impact these processes further supports the idea that both environmental factors and gene expression are interconnected.


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: After SOU (2020: 4) was published in January 2020, it was sent for referral and more than 100 answers (available at M2020/00166/Kl) came from industry, NGOs, academia and different agencies. Most of the respondents backed the conclusions and most were positive to implement the suggestions the inquiry concluded in relation to BECCS. A view among many answering the referral was that the market should take responsibility for BECCS as far as possible, but that governmental support was key to developing the market. Most respondents to the referral backed the suggestion of holding a negative auction and that it should be conducted as soon as possible. In autumn 2020 the government tasked the Agency with investigating and preparing the formalities for conducting an auction. 2021 the government presented a budget of €40 million per year until 2040 for a first auction during 2022. The central liberal party which needed to support the budget to pass in parliament countered that the budget needed to be extended. The opposition in the parliament has since suggested a budget of €200 million per year and presented developing BECCS as one of the key options for Swedish climate change abatement. A report by the Agency (2021) on the proposed format of the auctioning concluded that the governmental budget of €40 million would result in developments not p. 130 p. 131reaching targets. They also conclude that the potential for BECCS in point sources over 300 kt CO2 per annum is 31. 7 Mt divided by 22. 2 Mt in the pulp and paper industry and 9. 5 Mt in the heat sector (mainly CHP). Using the schematic emission pathway figure from 15 presented in Figure 7. 3, an emission pathway for Sweden can be generated for Figure 7. 6. Compared to the IPCC schematics of Figure 7. 3, only the marginal change in relation to a reference level for the sector is reported to the and the EU commission (FCCC/KP/AWG/2011/INF. 2). About 70% of the land area of Sweden is covered by forests and 58% of the land area is productive managed forests that are part of the forestry sector. Since year 1903 Sweden has had a law in place encouraging regrowth in managed forests. As such, forestry where the outtake of biomass is balanced by replanting of trees is an integral part of the forestry culture. [SEP] Justify:

Output: The text contrasts the claim by discussing the implementation aspects of BECCS (Bioenergy with Carbon Capture and Storage) in Sweden, including government budgets and industry support. It emphasizes existing agreements and plans for auctioning carbon capture efforts, suggesting that there is an active push towards developing such technologies. While it does not provide direct evidence or studies addressing safety concerns, it implies confidence in proceeding with these measures, which contrasts with the claim's suggestion that further study is necessary for safety.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 4a), and the pathways “Glycosphingolipid biosynthesis − globo series” and “Limonene and pinene degradation” were significantly enriched (Additional file 1: Fig. S4c). Additionally, a total of 1122 DEGs, including 593 upregulated and 529 downregulated DEGs, were specifically expressed in QQ-vs-LYQQ (Fig. 4a), but only the “Plant-pathogen interaction” pathway was significantly enriched (Additional file 1: Fig. S4d). Moreover, a total of 2175 DEGs, including 1177 downregulated and 998 upregulated DEGs, overlapped between MZ-vs-LYQQ and MZ-vs-QQ specifically, indicating that these DEGs might be associated with zigzag-shaped stem formation in both QQ and LYQQ. KEGG analysis showed that these DEGs were mainly involved in the “Plant-pathogen interaction”, “Phenylpropanoid biosynthesis”, “Flavonoid biosynthesis” and “Linoleic acid metabolism” pathways (Fig. 4b). GO enrichment analysis showed that these DEGs were significantly enriched in 59 GO terms, of which the most highly enriched components were categorized as catalytic activity (465), metabolic process (381), binding (323), cellular process (322), single-organism process (285) and membrane (274) (Fig. 4c). Identification of key DEGs regulating zigzag-shaped stem formation Based on the changes in expression in the comparisons MZ-vs-QQ and MZ-vs-LYQQ, 76 DEGs potentially involved in zigzag-shaped stem formation were identified (Fig. 5). Among these DEGs, 19 were associated with cell wall synthesis and cell expansion, of which seven, namely, cellulose synthase (TEA032164. 1, TEA030545. 1), expansin (TEA027164. 1), leucine-rich repeat extensin-like protein 1 (XLOC_003301), chitinase-like protein (TEA022978. 1) and pectinesterase (XLOC_003301, and TEA004581. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses gene expression data and pathways related to plant biology, but does not provide any insights regarding 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: Oocyte and sperm nuclei fuse resulting in syngamy (Figure 1). The zygote undergoes a series of cleavage divisions, forming two‐cell, four‐cell, eight‐cell morula and blastocyst stages [2] (Figure 1). During cleavage stage divisions, programming of maternal and paternal chromosomes takes place to create the embryonic genome (embryonic genome activation, EGA) and to start the preimplantation embryo development. If the EGA fails, the development does not continue because of the inability of the embryo to have cellular functions [3]. This activation is initiated by the degradation of maternal nucleic acids, specific RNAs stored in oocytes, proteins and other macromolecules [4]. Upon EGA, which starts at the two‐cell stage in mouse and four‐ to eight‐cell stage in human [5], remarkable reprogramming of expression occurs in the preimplantation embryo. These reprogramming events are controlled by DNA methylation, histone acetylation, transcription, translation and miRNA regulation [6]. Therefore, the development of preimplantation embryos includes continuous molecular, cellular and morphological events. These events would eventually form a multilineage embryo that has a capability to implant and continue the foetal development. Figure 1. Schematic diagram outlining the main stages of preimplantation embryo development. Fertilisation followed by syngamy, cleavage divisions results in two, three, four, and so on cell embryos which eventually form the morula and the blastocyst. In this 2. Gene expression and epigeneticsFor a normal developing embryo, the expression of both maternal and paternal genes is required. An intense epigenetic change occurs upon fertilisation to establish pluripotency [7]. Although there are a number of post‐translational modifications within chromatin including acetylation, ubiquitination, SUMOylation and phosphorylation; methylation of histone lysine and arginine residues is the main focus in preimplantation embryos. Methylation and chromatin modification not only play crucial roles in determining the transcriptional state but also are capable of determining the transcriptional repression [8–10]. The mechanism leading to the changes in methylation is not well established, but it has been suggested that the reprogramming takes place by either passive or active demethylation. [SEP] Justify:

Output: The text corroborates the claim by discussing how epigenetic changes, specifically in the context of preimplantation embryo development, are crucial for establishing gene expression in both maternal and paternal genes. It highlights that intensive epigenetic changes lead to the establishment of pluripotency and that DNA methylation and chromatin modifications are key factors affecting transcriptional states. These processes are manifestations of how gene expression can be influenced, which aligns with the claim regarding epigenetics and its relation to environmental factors across generations.


Input: Task: pass the claim using the given text. Claim: Ocean carbon capture may mitigate climate change but requires further study for safety. [SEP] Text: , Elia, A. , Boitier, B. , Koasidis, K. , Doukas, H. , Cassetti, G. , Anger-Kraavi, A. , Bui, H. , Campagnolo, L. , De Miglio, R. , Delpiazzo, E. , Fougeyrollas, A. , Gambhir, A. , Gargiulo, M. , Giarola, S. , Grant, N. , Hawkes, A. , Herbst, A. , Köberle, A. C. , Kolpakov, A. , Le Mouël, P. , McWilliams, B. , Mittal, S. , Moreno, J. , Neuner, F. , Perdana, S. , Peters, G. P. , Plötz, P. , Rogelj, J. , Sognnæs, I. , Van de Ven, D. -J. , Vielle, M. , Zachmann, G. , Zagamé, P. and Chiodi, A. (2021) ‘Where is the EU headed given its current climate policy? A stakeholder-driven model inter-comparison’. Science of the Total Environment, 793. )| falseSearch 300. Paltsev, S. , Morris, J. , Kheshgi, H. and Herzog, H. (2021) ‘Hard-to-abate sectors: The role of industrial carbon capture and storage (CCS) in emission mitigation’. Applied Energy, 300. )| falseSearch 109. Smith, E. , Morris, J. , Kheshgi, H. , Teletzke, G. and Herzog, H. (2021) ‘The cost of CO2 transport and storage n global integrated assessment modeling’. of Control, 109. )| falseSearch 34. Tongur, S. and Engwall, M. (2014) ‘The business model dilemma of technology chifts’. Technovation, 34. )| falseSearch 276. Yue, X. , Deane, J. P. , O’Gallachoir, B. and Rogan, F. [SEP] Justify:

Output: The text provided includes a list of authors and references to different studies without addressing the specific claim about ocean carbon capture and its implications for climate change mitigation and safety. Therefore, it does not provide relevant information to corroborate or contrast the claim.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 1), were upregulated, whereas 12, especially xyloglucan endotransglucosylase/hydrolase (XLOC_007313, TEA019643. 1, TEA031643. 1), pectinesterase (TEA026842. 1), reduced wall acetylation 2 (XLOC_021264), expansin (TEA012391. 1), UDP-glycosyltransferase 74B5 (TEA020219. 1) and isoamylase 3 (XLOC_040461), were downregulated in both QQ and LYQQ (Fig. 5a and Additional file 3: Table S3). Eighteen transcription factor genes, including the 13 downregulated genes floral homeotic protein 1 (TEA017728. 1), TIFY (TEA012041. 1), NAC transcription factor 010 (TEA026168. 1), transcription factor 2 (XLOC_053049), -related homeobox 2 (TEA032867. 1), ethylene-responsive transcription factor TINY (TEA027175. 1), transcription factor MYB1R1 (TEA026206. 1), squamosa promoter-binding-like protein (TEA003577. 1), transcription factor HEC1 (TEA030941. 1), transcription factor bHLH18 (TEA000681. 1), transcription factor (TEA006216. 1), growth-regulating factor 1 (TEA022970. 1), and Scarecrow-like protein (TEA030046. 1) and the five upregulated genes transcription factor bHLH041 (TEA031877. 1), transcription factor IBH1-like (TEA009726. 1), WRKY transcription factor 28 (TEA023233. 1), transcription factor (TEA031729. 1) and transcription factor 1 (TEA022287. 1), were identified (Fig. 5b and Additional file 3: Table S3). In addition, 10 DEGs involved in auxin, jasmonic acid, and salicylic acid metabolism and transport were also identified in the list of key DEGs; interestingly, except for jasmonic acid-amido synthetase (TEA020186. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses transcription factors and gene expression rather than the role of fossilized plants in understanding ancient climates and ecosystems. There are no references to fossils, ancient climates, or ecosystems within the provided text.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: CDX2 is extensively expressed in eight‐ and 16‐cell stage and it is expressed only in TE cells of the blastocyst [32]. Although OCT4 and NANOG are also expressed broadly at eight‐ and 16‐cell stage embryos, they are only expressed in ICM in blastocysts [32]. A number of transcription factors are required for blastocyst formation. Embryos lacking CDX2 expression cannot form blastocoel cavity but they have the ability to implant [30]. Lack of OCT4 or NANOG expression causes failure of ICM and the development of these embryos is arrested at the blastocyst stage [31, 32]. TEAD4 is another transcription factor that has a role in blastocyst transition in which the lack of TEAD4 nuclear localisation impairs TE‐specific transcriptional programme in inner blastomeres [33]. Furthermore, the aberrant expression of TCFAP2C transcription factor also leads to embryonic arrest during morula to blastocyst transition [34] and Klf5 mouse‐mutant embryos arrest at the blastocyst stage [35]. The remethylation process starts shortly after implantation [16, 22, 23, 36]. This de novo methylation occurs asymmetrically, such that ICM is hypermethylated possibly due to the Dnmt3b methylase [37], whereas TE remains hypomethylated due to the active demethylation by enzyme catalysis and passive demethylation [11, 14, 22]. Alteration of the methylation profiles in embryos has been shown to cause alterations of ICM and TE differentiation. Variations of the H3 arginine 26 residue (H3R26me) were shown to lead to changes of TE and ICM differentiation of a blastomere [38]. X‐chromosome inactivation is an epigenetic phenomenon in which the activity of X chromosomes is strictly regulated to equalise X‐chromosome expression and gene dosage between males and females and relative to autosome chromosomes [39]. For correct development, X‐chromosome dosage compensation is crucial. The inactivation of X chromosome occurs in at least two phases: initiation and maintenance. X‐inactivation mouse model systems have shown that the inactivation of X chromosome takes place during early embryogenesis of the female embryo by undergoing transcriptional silencing of genes along the X chromosome [40]. [SEP] Justify:

Output: The text corroborates the claim by discussing various epigenetic processes, such as X-chromosome inactivation and methylation, that affect gene expression during embryogenesis. It highlights how changes in methylation profiles can lead to alterations in differentiation of cell types, which is a fundamental aspect of epigenetics influencing gene expression across generations.


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: The CO2 is compressed into a liquid under high pressure and transported through pipelines to sites where it may be stored, in porous sedimentary rock formations containing saltwater, for example, or used for other purposes. The captured CO2 can be injected into the ground to extract oil dregs or used to produce cement and other products. Governments and industry are betting big on such projects. Last year, for example, the British government announced £20 billion (more than $25 billion) in funding for CCUS, often shortened to CCS. States allocated more than $5 billion between 2011 and 2023 and committed an additional $8. 2 billion from 2022 to 2026. Globally, public funding for CCUS projects rose to $20 billion in 2023, according to the Agency (IEA), which works with countries around the world to forge energy policy. Given the urgency of the situation, many people argue that CCUS is necessary to move society toward climate goals. But critics don’t see the technology, in its current form, shifting the world away from oil and gas: In a lot of cases, they point out, the captured CO2 is used to extract more fossil fuels in a process known as enhanced oil recovery. They contend that other existing solutions such as renewable energy offer deeper and quicker CO2 emissions cuts. “It’s better not to emit in the first place,” says Grant Hauber, an energy finance adviser at the Institute for a nonpartisan organization in Lakewood, Ohio. greening of planes, trains and automobiles power heats up Food & to overcome political polarization on climate change What’s more, fossil fuel companies provide funds to universities and researchers — which some say could shape what is studied and what is not, even if the work of individual scientists is legitimate. For these reasons, some critics say CCUS shouldn’t be pursued at all. “Carbon capture and storage essentially perpetuates fossil fuel reliance. It’s a distraction and a delay tactic,” says Jennie Stephens, a climate justice researcher at in Boston. She adds that there is little focus on understanding the psychological, social, economic and political barriers that prevent communities from shifting away from fossil fuels and forging solutions to those obstacles. [SEP] Justify:

Output: The text contrasts the claim by highlighting that while carbon capture and storage (CCUS) may be funded and pursued, critics argue that the current form of the technology does not effectively shift society away from fossil fuel reliance. Critics contend that CCUS is often used in enhanced oil recovery, which contradicts the claim that it is a step toward addressing climate change. Moreover, the text includes perspectives that suggest a need for understanding the broader social and economic barriers to transitioning away from fossil fuels, indicating that more study is indeed necessary before these technologies can be deemed safe or effective.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 1), the remaining genes, especially PIN3 (TEA019069. 1), were downregulated in both QQ and LYQQ (Fig. 5c and Additional file 3: Table S3). Furthermore, seven DEGs involved in protein processing and transportation on the endoplasmic reticulum and vesicles, namely, vesicle-associated membrane protein 714 (XLOC_031693), SEC1 family transport protein, signal peptidase complex catalytic subunit SEC11A (TEA001395. 1), SEC13B (XLOC_004426), SECA2 (XLOC_057225), SEC6 (TEA030236. 1), SEC11A (TEA001395. 1), and SEC22 (XLOC_037235); the three vacuolar protein sorting-related proteins VPS18 (TEA007337. 1), VPS41 (TEA031089. 1) and VSR6 (TEA021222. 1); and the vacuole membrane protein KMS1 (XLOC_036914) were identified from the MZ-vs-QQ and MZ-vs-LYQQ comparisons (Fig. 5d and Additional file 3: Table S3). Among these 18, VPS41, SEC11A and SEC1 were significantly repressed in both QQ and LYQQ. Genes that regulate cell division (cell division cycle 20. 1 and cell division control protein 6 B) and plant development, such as shaggy-related protein kinase, 3 (XLOC_028596), -3 (XLOC_032980), -like (XLOC_028345), -related protein (TEA008751. 1), LAZY protein (TEA031847. 1) and LAZY 1-like (TEA001744. 1), were also identified, and all of these genes were downregulated in both QQ and LYQQ (Fig. 5e and Additional file 3: Table S3). Moreover, the 2 protein (VLN2) and actin-depolymerizing factor 2 (ADF2) were suppressed in both QQ and LYQQ (Fig. 5e and Additional file 3: Table S3). [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the downregulation of various genes in specific conditions (QQ and LYQQ) 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: In human preimplantation embryos, it has been shown that the reduced expression of X chromosomes in females ensures the dosage compensation [41]. expression activates the X‐chromosome inactivation by engaging proteins functioning in chromatin remodelling [3, 42]. With the advanced technologies, including single‐cell RNA sequencing, it has emerged that lncand XIST are expressed on the active X chromosome in the early human preimplantation embryos [43]. Furthermore, the expression of these two RNAs has never been shown to overlap. Introducing XACT into heterologous systems caused the accumulation of Xist RNA in cis and therefore it may be involved in the control of XIST association to chromosome in cis and may temper its ability of silencing. It is also possible that XACT functions in balancing the X‐chromosome inactivation at the early stages of preimplantation embryo development [43, 44]. Recently, the dosage compensation was shown to be driven by a CAG promoter of a new Xist allele (Xist(CAG)) [45]. Furthermore, Xist(CAG) upregulation in preimplantation embryos showed variation depending on the parental origin and the paternal expression was suggested to be preferentially inactivated with the paternal Xist(CAG) transmission [45]. 2. 2. Epigenetic modification of the gametesIn germ cells, methylation is maintained in a sex‐specific manner. Methylation in PGCs diminishes as they migrate to the gonads. Studies suggest that in females, remethylation occurs after birth when the oocytes are in the process of development. When demethylation is completed, the PGCs either enter mitosis in males or arrest at meiosis in females [46]. Reprogramming of the methylation in the embryo is necessary for parent‐specific expression of genes [14]. Gene expression varies during preimplantation embryo development due to these reprogramming events and appropriate gene expression determines the survival of the embryo [6]. Recently, short noncoding RNAs, microRNAs (miRNAs) and long noncoding RNAs (lncRNA) have gained importance in their potential function to affect numerous pathways by targeting multiple genes [47, 48]. Advertisement 3. [SEP] Justify:

Output: The text corroborates the claim by discussing the role of epigenetic modification in gene expression, particularly in human preimplantation embryos and germ cells. It explains how environmental factors such as sex-specific methylation in PGCs and the reprogramming events during embryo development can influence gene expression, thereby demonstrating the relevance of epigenetics in understanding how such influences may propagate across generations.


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: Large-scale CCUS projects currently online or in development are expected to capture more than 400 megatons of CO2 per year by 2030. That’s far short of the more than 1 gigaton of CO2 per year CCUS projects would need to capture by then in order to stay on track with the Agency’s scenario for achieving net-zero emissions by 2050. A recent analysis suggests that at least 5 billion tons annually is achievable. The research, not yet published, limits CCUS growth to an average of 20 percent per year until 2050 for most cases. “That’s a major contribution to climate mitigation,” says Samuel Krevor, an environmental engineer at London and a lead author of the research. Krevor, like many researchers in the field, receives some funding from fossil fuel companies. says the contribution is likely to be minor relative to other climate solutions, including shifting to renewable energy and planting and maintaining forests to help store away CO2 from the atmosphere. Using data from the IPCC, Hauber and colleagues calculate that by 2030, CCUS will provide just 2. 4 percent of all emissions reductions. What’s more, projects rarely meet their stated goals. An analysis by the Institute for of 13 key CCUS projects, published in 2022, found that most failed to reach their targets. Relying on publicly available data, the analysis found, for example, that the facility has underperformed by 36 percent over its lifetime. When there were fewer customers for the captured CO2, the analysis finds, the facility released it into the atmosphere. A facility in Decatur, Illinois, run by Midland, an agribusiness based in Chicago, was nearly 50 percent off its annual target at the end of 2020. An ExxonMobil spokesperson said the company has made progress since the report, noting that the company has expanded CO2 storage capacity at its facility by over 1 million metric tons annually. And a spokesperson for Midland said that how much CO2 it captures and stores depends on how much biofuel it produces. The company’s Decatur facility is looking at different strategies to decarbonize its operations including capturing CO2 produced by a new gas power plant that will provide energy for the company’s biofuel facility. It’s also unclear how much CO2 capacity underground storage sites possess. [SEP] Justify:

Output: The text contrasts the claim by highlighting the limitations and challenges of current carbon capture and storage (CCUS) projects. It mentions that these projects are expected to capture far less CO2 than necessary to stay on track for net-zero emissions, stating they could capture only 2.4 percent of all emissions reductions by 2030. Additionally, it notes that many projects fail to meet their targets and raises concerns about how much CO2 underground storage can realistically accommodate.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Metabolic analysis and key metabolite identification To investigate the metabolic pathways involved in zigzag-shaped stem formation, the metabolites in the stems of and MZ were detected using UPLC-ESI-TOF-MS/MS. In total, 752 metabolites clustered into 97 KEGG pathways were identified from and MZ, and among these metabolites, 75, 84 and 86 metabolites showed significantly different levels in the MZ-vs-QQ, MZ-vs-LYQQ and QQ-vs-LYQQ comparisons, respectively (Additional file 1: Fig. S5). diagram analysis showed that 13 metabolites overlapped between MZ-vs-QQ and MZ-vs-LYQQ, which were our metabolites of interest (Fig. 6a), and the results indicated that these differential metabolites might be associated with zigzag-shaped stem formation in tea plants. Based on their log2 fold change values, these differential metabolites were visualized as a heat map in Fig. 6b. Quercetin O-acetylhexoside, methyl gallate, D-pantothenic acid and L-glutamic acid were upregulated in both QQ and LYQQ, whereas the remaining metabolites, including fustin, 10-formyl-THF, skimmin, LysoPC 20:4, LysoPC 18:1 (2n isomer), LysoPC 18:3 (2n isomer), 2-methylsuccinic acid, 2-isopropylmalate, and caffeine, were significantly downregulated in tea plants with zigzag-shaped shoots. DiscussionPlants are sessile and cannot move freely from their habitat, even if they encounter adverse environments. Generally, plant shoots grow upward, whereas roots grow downward; therefore, shoot architecture is a determinant of plant morphology. In tea plants, the shoots play a substantial role in determining the horticultural characteristics and tea yield, and almost all tea plant cultivars exhibit straight stems. The two tea plants QQ and LYQQ, with zigzag-shaped shoots, were identified and planted previously; however, with advances in research, there is increasing interest in the mechanism by which QQ and LYQQ develop their zigzag-shaped shoots. [SEP] Justify:

Output: The text is largely focused on metabolic analysis related to tea plants and their zigzag-shaped stem formation, and it does not address any aspects of fossilized plants or their role in understanding ancient climates and ecosystems. Therefore, it is irrelevant to the claim.


Input: Task: pass the claim using the given text. Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Expression of miRNAs in preimplantation embryosThe expression of miRNAs in preimplantation embryos has been mainly studied by knock‐out experiments, by cloning experiments and by identifying individual miRNAs by microarray analysis and real‐time polymerase chain reaction [93]. The expression studies have been carried out using animal models and tissues, cultured cells; that is, cancer cells and human embryonic stem cells; and mouse/bovine/human gametes and embryos. Human embryonic stem cells, which are derived from the inner cell mass of an embryo at the blastocyst stage and are characterised by their ability of self‐renewal and multipotency, are the key in gene expression research since the access of human embryos is difficult and these cells are one of the closest representations of human embryos. Studying miRNA expression in stem cells not only gives insight into potential miRNAs expressed in human embryos but also may show the important role of miRNAs in the stem cell functioning [94]. MiRNA expression has been observed as early as oogenesis and spermatogenesis in mouse, bovine and human [95, 96]. Differences in the miRNA expression have been observed between immature and mature oocytes that may represent the natural turnover and indicate that each embryonic stage is defined by a specific miRNA. Similar miRNA expression profiles in mature mouse oocytes and early developing embryos indicate that at these stages the zygote has maternally inherited miRNAs [50]. Similar to oocyte, sperm carries a range of miRNAs. Approximately 20% of these miRNAs are located in the nuclear or perinuclear part of the sperm indicating that these miRNAs are transferred to the zygote at the time of fertilisation [97]. It was suggested that the sperm‐borne miRNAs may down‐regulate the maternal transcripts in mammals. However, when this hypothesis was tested using microarray analysis, it was shown that none of these miRNAs in the sperm have significant importance since all of them were already present in the oocytes (meiosis II) [98]. Multiple miRNAs were involved in the formation of germ cell layers. MiR‐290, which was expressed at different levels during preimplantation embryo development of mouse embryos, had a negative effect on the germ cell and mesoderm differentiation in the mouse ES cells via targeting Nodal inhibitors [99]. [SEP] Justify:

Output: The text does not specifically address the concept of epigenetics or the influence of environmental factors on gene expression across generations. It focuses on the expression of miRNAs in preimplantation embryos and related research methods, which, while related to gene expression, does not directly corroborate or oppose the claim regarding epigenetics.


Input: Task: contrast the claim using the given text. Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: & & & & &Aa : español español& & caption full caption right caption left caption center &A expert &A expert 1 Slide 2 Slides 3 Slides 4 Slides 5 Slides 6 Slides 7 full width center : capture, utilization and storage technologies are expected to play a role in cutting CO2 emissions and limiting global warming, but some critics say they are costly and divert attention from more effective strategies. help with climate change, carbon capture will have to evolve The technologies are a useful tool to reduce CO2 levels but have yet to move us away from fossil fuels Gilbert 07. 09. 2024 sound science and smart storiesHelp us make scientific knowledge accessible to allDonate today More than 200 kilometers off Norway’s coast in the sits the world’s first offshore carbon-capture-and-storage project. Built in 1996, the Sleipner project strips carbon dioxide from natural gas — largely made up of methane — to make it marketable. But instead of releasing the CO2 into the atmosphere, the greenhouse gas is buried. The effort stores around 1 million metric tons of CO2 per year — and is praised by many as a pioneering success in global attempts to cut greenhouse gas emissions. Last year, total global CO2 emissions hit an all-time high of around 35. 8 billion tons, or gigatons. At these levels, scientists estimate, we have roughly six years left before we emit so much CO2 that global warming will consistently exceed 1. 5 degrees Celsius above average preindustrial temperatures, an internationally agreed-upon limit. (Notably, the global average temperature for the past 12 months has exceeded this threshold. )Phasing out fossil fuels is key to cutting emissions and fighting climate change. But a suite of technologies collectively known as carbon capture, utilization and storage, or CCUS, are among the tools available to help meet global targets to cut CO2 emissions in half by 2030 and to reach net-zero emissions by 2050. These technologies capture, use or store away CO2 emitted by power generation or industrial processes, or suck it directly out of the air. Panel on (IPCC), the body charged with assessing climate change science, includes carbon capture and storage among the actions needed to slash emissions and meet temperature targets. Carbon capture, utilization and storage technologies often capture CO2 from coal or natural gas power generation or industrial processes, such as steel manufacturing. [SEP] Justify:

Output: The text contrasts the claim by highlighting that while carbon capture technologies, such as those used in the Sleipner project, are significant for reducing CO2 emissions, they are not presented as a definitive solution to all climate change problems. The text notes that some critics argue these technologies are costly and may divert attention from more effective strategies to combat climate change, emphasizing that phasing out fossil fuels is key to reducing emissions. It states that while CCUS is a useful tool in the broader context of climate action, it is not sufficient on its own to address all challenges related to climate change.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Zigzag-shaped shoots, which occasionally appear in garden plants, are an unusual trait in woody plants, but there is relatively little information regarding this feature. Similarly, in Arabidopsis, zig mutant stems elongate in a zigzag fashion, curve upward at the internodes and, interestingly, exhibit abnormal gravitropism in hypocotyls and shoots [8-11]. To understand the cause of this anomalous zigzag-shaped morphology, we observed stem sections using optical microscopy. There were no aberrations in the main tissue structures (Fig. 1). However, differences in cell arrangement and shape were observed between the zigzag-shaped stems of QQ and LYQQ and the MZ stems, including the arrangement of cortex cells, which were disordered and loosely arranged, and the cells in the cortex and pith exhibited aberrant shapes (Fig. 1). Consistent with our findings, similar cell shapes and arrangements were found in the zig-1 mutant stems of Arabidopsis [8]; however, different cell shapes and arrangements were observed in the epidermal layer and pith of Arabidopsis than in the cortex and pith of tea plants; this may represent a difference between woody plants and Arabidopsis. Thus, zigzag-shaped stems might be caused by the anomalous shape, arrangement and expansion of cells in tea plants. To investigate the molecular mechanism of zigzag-shaped stem formation in tea plants, shoots were collected, and transcriptome sequence analysis was performed. In total, 46. 06 million clean reads were generated, and 6232, 7212 and 6930 DEGs were identified from MZ-vs-QQ, MZ-vs-LYQQ and QQ-vs-LYQQ, respectively (Additional file 2: Table S1 and Fig. 3b). These DEGs were mainly enriched in several pathways, such as ‘Biosynthesis of secondary metabolites’, ‘Plant-pathogen interaction’, and ‘Stilbenoid, diarylheptanoid and gingerol biosynthesis’, indicating that these pathways might be associated with differences among cultivars (Fig. 3b). [SEP] Justify:

Output: The text discusses zigzag-shaped shoots in woody plants and their cellular characteristics but does not address fossilized plants or their role in understanding ancient climates and ecosystems. Therefore, it is 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: Furthermore, HPAT5 was shown to interact with let‐7 family of miRNAs [110]. Implantation of embryos involves complex mechanisms and many different genetic and physiological factors are involved during the process. Developing preimplantation embryo must have a good coordinated interaction with the maternal uterine endometrium. LncRNAs were shown to be differentially expressed in endometrial tissues obtained from pigs with pregnancy and non‐pregnancy with two lnc_01729386 and TCONS_01325501, with potential roles in implantation [111]. Advertisement 5. Gene expression and assisted reproductive technologiesworld, approximately 1% of children are born with assisted reproductive technology (ART) treatments. The infertile couples have the best possibility to conceive a child with these treatments. Although these techniques have been considered to be safe in terms of foetal and post‐natal development [112, 113], there is an increased risk for morbidities, especially imprinting disorders [114]. Furthermore, the global gene expression profiles vary due to in vitro culture of zygotes [115, 116] and in vitro fertilisation processes [117]. Following in vitro culture, apoptotic and morphogenetic pathways have shown to be altered [118]. Intra‐cytoplasmic sperm injection (ICSI), one of the widely used ART techniques, provides infertile couples with sperm motility problems a great chance to have a baby. ICSI is a unique process in which the sperm is injected into the ooplasm [119]. However, ICSI bypasses a number of physiological processes that would normally take place. These embryos derived from ICSI were shown to be cleaved at a slower rate. Furthermore, a reduced number of embryos become hatched with a fewer number of cells and the calcium oscillations are shorter with different patterns [120]. Mice embryos generated by ICSI were shown to be obese and have anomalies of the organs [121]. Advertisement 6. ConclusionNormal development of preimplantation embryos involves complex mechanisms. For a normal developing embryo, the expression of both maternal and paternal genes is required. Several factors are involved in the regulation of parental genes in preimplantation embryos. Epigenetic modifications are one of the most important factors that are involved in the regulation of gene expression during preimplantation embryos. Extensive research studies have been performed throughout the years to establish the methylation profiles of the mammalian gametes and embryos. [SEP] Justify:

Output: The text corroborates the claim by discussing how 'epigenetic modifications are one of the most important factors that are involved in the regulation of gene expression during preimplantation embryos.' This indicates that epigenetics plays a crucial role in gene expression, aligning with the claim that environmental factors can influence this expression across generations.


Input: Task: contrast the claim using the given text. Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: The CO2 is compressed into a liquid under high pressure and transported through pipelines to sites where it may be stored, in porous sedimentary rock formations containing saltwater, for example, or used for other purposes. The captured CO2 can be injected into the ground to extract oil dregs or used to produce cement and other products. Governments and industry are betting big on such projects. Last year, for example, the British government announced £20 billion (more than $25 billion) in funding for CCUS, often shortened to CCS. States allocated more than $5 billion between 2011 and 2023 and committed an additional $8. 2 billion from 2022 to 2026. Globally, public funding for CCUS projects rose to $20 billion in 2023, according to the Agency (IEA), which works with countries around the world to forge energy policy. Given the urgency of the situation, many people argue that CCUS is necessary to move society toward climate goals. But critics don’t see the technology, in its current form, shifting the world away from oil and gas: In a lot of cases, they point out, the captured CO2 is used to extract more fossil fuels in a process known as enhanced oil recovery. They contend that other existing solutions such as renewable energy offer deeper and quicker CO2 emissions cuts. “It’s better not to emit in the first place,” says Grant Hauber, an energy finance adviser at the Institute for a nonpartisan organization in Lakewood, Ohio. greening of planes, trains and automobiles power heats up Food & to overcome political polarization on climate change What’s more, fossil fuel companies provide funds to universities and researchers — which some say could shape what is studied and what is not, even if the work of individual scientists is legitimate. For these reasons, some critics say CCUS shouldn’t be pursued at all. “Carbon capture and storage essentially perpetuates fossil fuel reliance. It’s a distraction and a delay tactic,” says Jennie Stephens, a climate justice researcher at in Boston. She adds that there is little focus on understanding the psychological, social, economic and political barriers that prevent communities from shifting away from fossil fuels and forging solutions to those obstacles. [SEP] Justify:

Output: The text contrasts the claim by presenting arguments that suggest ocean carbon capture and storage (CCUS) technology is not a comprehensive solution to climate change. Critics argue that while projects are being funded and supported, CCUS often perpetuates reliance on fossil fuels rather than reducing emissions. For instance, the text cites concerns that captured CO2 is frequently used in enhanced oil recovery, which contradicts the idea that CCUS will solve climate problems. Additionally, experts advocate for transitioning to renewable energy sources that can provide quicker and deeper emissions reductions, indicating that CCUS alone will not resolve the issues related to climate change.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: To gain insights into the DEGs that specifically regulate zigzag-shaped stem development, we made a Venn diagram of cultivar comparisons and identified 2175 overlapping DEGs between MZ-vs-QQ and MZ-vs-LYQQ, which were mainly enriched in the “Plant-pathogen interaction”, “Phenylpropanoid biosynthesis”, “Flavonoid biosynthesis” and “Linoleic acid metabolism” pathways (Fig. 4). Among these pathways, the “Phenylpropanoid biosynthesis” pathway serves as a source of metabolites in plants, is involved in the biosynthesis of lignin, flavonoids, coumarins and lignans, and plays a fundamental role in plant structural support [29, 30]. It has been found that, in Arabidopsis, mutation of the genes encoding cinnamate 4-hydroxylase (C4H) and hydroxycinnamoyl-coenzyme A shikimate:quinate hydroxycinnamoyl-transferase (HCT) involved in this pathway resulted in changes in the structural, developmental, and reproductive phenotypes of Arabidopsis plants [31-33]. Interestingly, the flavonols quercetin and kaempferol have been shown to inhibit polar auxin transport and to enhance consequent localized auxin accumulation [34-36]. Recently, Kuhn, et al. [34] suggested that flavonols could modulate auxin transport by modifying the antagonistic kinase/phosphatase equilibrium. Therefore, flavonols could affect auxin transport in zigzag-shaped shoots. On the other hand, Ramos, et al. [37] found that the concentration of quercetin in the upper half of longitudinally dissected 45-degree-inclined radiata pine seedlings was higher than that in the lower half and than that in non-inclined seedlings when seedlings were inclined for one month, indicating that quercetin can accumulate in inclined shoots such as the internodes of zigzag-shaped shoots. Consistently, we observed that a C4H gene (TEA016772. [SEP] Justify:

Output: The text does not address the claim about fossilized plants and their role in understanding ancient climates and ecosystems. Instead, it focuses on the genetic and biochemical processes related to plant development and metabolism. Since there is no mention of fossilization or ancient climates, the text is 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: CpGs were classified as unmethylated (below the first quartile of the total distribution; CpGs, dark red) or methylated (above the third quartile of the total distribution; me-CpGs, light blue) for muscle and for testis. The expression of genes measured as log2-transformed count per million (cpm) values is shown in the upper panel depending on the type of CpGs these genes contained in their first intron. In the lower panel, the relative distance of the CpGs and me-CpGs from the first exon-first intron boundary was calculated as distance from nucleotide 0 (bp)/width of the intron (bp). The sequences of the four enriched TF-binding motifs that contained CpGs are also shown. rank sum test with continuity correction was used to test for statistical differences of gene expression and relative distance between CpGs and me-CpGs, which are reported with the following equivalence: ***p < 0. 001; *p < 0. 05Full size image Table 1 Effects on gene expression of the methylation status and the relative distance of the CpGs inside the four transcription factor binding motifs enriched in the first intronsFull size table The DNA methylation of the first intron associates with the upstream features and is independent of its lengthIn order to test whether there is association of the methylation state of two gene features, we calculated the odds ratio (OR) as representative of the odds that a gene feature A is also methylated when gene feature B is methylated. In both tissues, there was strong evidence for statistically significant association of the DNA methylation of the promoter, the first exon and the first intron (Fig. 5), since the 99. 9% confidence intervals (CIs) were far from overlapping the value 1. The gene body methylation, including all exons and introns of a gene, showed strong association with the DNA methylation of all gene features tested, while the methylation of the rest of exons and the rest of introns was also associated. In testis, the methylation of the first intron was associated with the methylation of the rest of exons as well. Fig. 5Association of DNA methylation between pairs of gene features as measured by odds ratio. [SEP] Justify:

Output: The text corroborates the claim by discussing the association between DNA methylation—a key epigenetic mechanism—and gene expression. It highlights that DNA methylation status can significantly affect gene features and expression, thus illustrating the influence of environmental factors on genetic expression. The mention of statistical significance in the association of methylation states with gene features underscores the role of these environmental factors in shaping gene expression, which reinforces the core idea of epigenetics.


Input: Task: contrast the claim using the given text. Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: According to the Global CCS Institute, an industry-led think tank headquartered in Melbourne, Australia, of the 41 commercial projects operational as of July 2023, most were part of efforts that produce, extract or burn fossil fuels, such as coal- and gas-fired power plants. That’s true of the Sleipner project, run by the energy company Equinor. It’s the case, too, with the world’s largest CCUS facility, operated by ExxonMobil in Wyoming, in the United States, which also captures CO2 as part of the production of methane. Granted, not all CCUS efforts further fossil fuel production, and many projects now in the works have the sole goal of capturing and locking up CO2. Still, some critics doubt whether these greener approaches could ever lock away enough CO2 to meaningfully contribute to climate mitigation, and they are concerned about the costs. Others are more circumspect. Sally Benson, an energy researcher at Stanford University, doesn’t want to see CCUS used as an excuse to carry on with fossil fuels. But she says the technology is essential for capturing some of the CO2 from fossil fuel production and usage, as well as from industrial processes, as society transitions to new energy sources. “If we can get rid of those emissions with carbon capture and sequestration, that sounds like success to me,” says Benson, who codirects an institute that receives funding from fossil fuel companies. Annual global carbon dioxide emissions need to be cut in half by 2030, or by about 20 gigatons, to achieve net-zero emissions by 2050. Carbon capture, utilization and storage technologies, called CCUS or CCS, are estimated to contribute less to emissions reductions than some other climate mitigation strategies, including shifting to renewable energy or restoring ecosystems. CCUS can also be more expensive; costs here are expressed as additional costs relative to the existing technology or status quo effort. Born from the oil industryCCUS technology was not conceived as a climate solution. It dates to the 1970s and 1980s, when oil production in the began to decline. Oil companies started using a process called enhanced oil recovery that injects CO2 (or water) into sedimentary rocks to recover hard-to-reach dregs of oil, a precursor to today’s CCUS. [SEP] Justify:

Output: The text contrasts the claim by highlighting significant challenges and limitations associated with carbon capture and storage (CCUS) technologies. While some advocates believe in the potential of CCUS for climate mitigation, critics express doubt about the ability of these technologies to meaningfully reduce CO2 emissions and are concerned about their associated costs. It notes that CCUS has historically been linked to fossil fuel production, which raises skepticism about its effectiveness as a standalone climate solution. The mention of other strategies, like shifting to renewable energy, being more effective further reinforces the contrast to the claim that ocean carbon capture will solve all climate change problems.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 1) was significantly differentially expressed between MZ-vs-QQ and MZ-vs-LYQQ; moreover, we found that skimmin (pmf0295) expression was reduced in the MZ-vs-QQ (log2 FC: -0. 995) and MZ-vs-LYQQ (log2 FC: -3. 52) comparisons. Therefore, the zigzag-shaped stems of tea plants might be partially related to flavonoids, especially flavonol-mediated auxin transport. It is well recognized that a zigzag-shaped inflorescence stem results from the mutation of zig (zigzag)/sgr4, which encodes VPS10 interacting 11 (VTI11), a Qb-SNARE involved in vesicle transport between the trans-Golgi network and vacuole that causes abnormal gravitropism in Arabidopsis when mutated [8, 10, 11, 38, 39]. SNAREs play an important role in membrane fusion at the vacuole and are involved in the regulation of amyloplast sedimentation in response to gravity and in cell shape development [11, 39]. ZIG can form a complex with other types of SNARE proteins, including SYP22/SGR3/VAM3, SYP5, and VAMP727, most likely at the prevacuolar compartment and vacuole [11, 40-42]. Although ZIG and the other SGR genes were not significantly expressed, 11 genes mainly involved in vesicular trafficking were identified (Fig. 5d and Additional file 3: Table S3). Among these genes, both vacuolar protein sorting-associated protein genes (VPS18 and VPS41) were repressed in QQ and LYQQ, whereas the expression levels of vesicle-associated membrane protein 714 (VAMP714) and vacuolar-sorting receptor 6 (VSR6) were increased in QQ and LYQQ. It has been established that the phenotype of zig-1 could be partially suppressed by mutations in the zig suppressor1 (ZIP1), ZIP2, ZIP3 and ZIP4 genes in Arabidopsis [38, 43, 44]. Niihama, et al. [SEP] Justify:

Output: The text discusses the genetic and molecular biology aspects of plant traits, particularly focusing on the expression of genes in Arabidopsis and does not provide any evidence or information regarding fossilized plants or their relevance to ancient climates and ecosystems. As a result, it is 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: The vast majority of the highest expressed genes in both tissues had DNA methylation below 10% (89. 5% of genes in muscle and 84. 9% in testis). However, in the lowest expressed genes, DNA methylation was more equally distributed to the two extremes, with the 75. 2% of genes in the muscle and the 48. 2% of genes in the testis having less than 10% methylation, and the 24. 8% of genes in the muscle and the 51. 8% of genes in the muscle having more than 90% methylation. More genes contain tDMRs in their first intron than in other gene featuresIn general, there were distinct patterns between the tissue-specific genes and the non-tissue-specific genes that were obvious from the gene expression data. Therefore, we focused on tDMRs between testis and muscle and explored the relationships between differential DNA methylation and differences in gene expression. Both directions of correlation were evident between DNA methylation and gene expression. There was strong negative correlation (ρ = − 0. 73, p < 0. 001) for up-regulated genes, in either testis or muscle that contained hypo-methylated tDMRs inside their gene body or 4 kb upstream of the TSS or downstream of the 3′ UTR (squares in Fig. 6). Nonetheless, there was also weaker positive correlation (ρ = 0. 26, p < 0. 001) for up-regulated genes, in either testis or muscle that contained hyper-methylated tDMRs (circles in Fig. 6). The same two categories of genes showing either negative or positive correlation between DNA methylation and gene expression were obvious in genes that contained tDMRs only in the promoter, first exon or first intron (Fig. 6). There were 187 genes that contained tDMRs in their first intron, while there were fewer genes that contained tDMRs in their promoter (47) and the first exon (75). The majority of the tDMRs in the first intron were located in proximity to the first exon-first intron boundary (Additional file 1: Fig. S7). Fig. 6Differentially expressed genes with differentially methylated regions (tDMRs) between tissues. [SEP] Justify:

Output: The text corroborates the claim by discussing the relationships between differential DNA methylation (a key epigenetic mechanism) and gene expression in different tissues. It specifically mentions how DNA methylation correlates with gene expression, indicating that environmental factors that might cause changes in DNA methylation can influence gene expression, which aligns with the broader scope of epigenetics that explores these influences across generations.


Input: Task: contrast the claim using the given text. Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: CCUS technologies are now capturing CO2 from a variety of operations — including at traditional power plants that burn coal or other fossil fuels; in nontraditional plants where energy is produced from biofuels such as ethanol; and during the production of ammonia, which is used in fertilizer. All such efforts complement other practices that turn to natural processes to remove carbon from the atmosphere to help reach net zero, such as planting forests or locking CO2 in soils using sustainable farming practices. The strongest criticisms are lobbed at using CCUS to extract fossil fuels. Today nearly three-quarters of the carbon captured through CCUS projects is used to extract more oil from dregs. The largest CCUS operation, ExxonMobil’s $656 million facility in Wyoming, aims to capture around 8 million tons of CO2 each year from methane extracted from the nearby LaBarge gas fields. ExxonMobil sells the captured CO2 for enhanced oil recovery. Though the effort cuts emissions because some of the CO2 remains in the ground, the burning of the additional fossil fuels it helps extract still releases CO2. Just 12 of the 41 existing projects included in the Global CCS Institute database inject CO2 with the exclusive aim of storing it underground, thus keeping its climate-warming effects at bay. Half of those 12, including the Sleipner project, are involved in methane production — and methane releases carbon dioxide into the atmosphere when burned. Cement manufacturing and iron and steel manufacturing are also desirable targets for CCUS, because each produces around 6 percent to 9 percent of global CO2 emissions, and both processes are difficult to clean up in other ways. Only one project, run by the Company, is capturing CO2 emissions from iron and steelmaking. There are no projects up and running to capture CO2 from cement manufacturing. ’s database includes just a single fully operational, large-scale project that is currently sucking CO2 directly from the air and storing it underground. That project, in Hellisheiði, Iceland, is run by the Swiss company Climeworks. Another, bigger Climeworks project recently started operations but is not yet completed. But the database omits direct air capture projects that are doing other things with the CO2, including one that is sealing it in concrete, and omits smaller-scale and pilot projects that are online or coming online. [SEP] Justify:

Output: The text contrasts the claim by outlining the limitations and criticisms of Carbon Capture, Utilization, and Storage (CCUS) technologies. Although CCUS is being implemented in various sectors to capture CO2, the text highlights that much of the captured carbon is used to extract more fossil fuels, which ultimately contributes to CO2 emissions rather than solving climate issues. Furthermore, it mentions that only a fraction of projects aim to store CO2 underground without further emissions, indicating that CCUS alone will not resolve climate change problems.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: [44] reported that ZIP2, which encodes an AtVPS41/AtVAM2 protein, is involved in protein sorting to the vacuole in Arabidopsis, and the zip2 mutation is a missense mutation. These results indicate that zigzag-shaped stem formation is mainly related to abnormal gravitropism responses mediated by membrane trafficking. Additionally, we also found that six SEC family genes were significantly expressed in the MZ-vs-QQ and MZ-vs-LYQQ comparisons (Fig. 5d and Additional file 3: Table S3); these genes are crucial for SNARE complex assembly and preprotein translocation [45, 46]. Interestingly, we found that both LAZY genes (TEA031847. 1, TEA001744. 1) were markedly repressed in QQ and LYQQ (Fig. 5d and Additional file 3: Table S3). It is well known that loss-of-function mutation of LAZY1 enhances polar indole-3-acetic acid (IAA) transport and reduces shoot gravitropism and therefore regulates the growth angle of lateral branches in rice, Arabidopsis and maize [17-19, 21, 47]; however, the function of LAZY in woody plants remains to be elucidated. Therefore, we propose that the development of zigzag-shaped stems in tea plants might be associated with a change in the shoot gravitropism response, especially one affecting the disruption of membrane trafficking to vacuoles, although the ZIG/SGR4 gene did not exhibit a significant change in expression. The plant hormone auxin is important for organ growth and cell morphogenesis. In this study, seven DEGs involved in auxin metabolism, transport and signalling were identified by comparison of the MZ-vs-QQ and MZ-vs-LYQQ sets, and all of the genes were downregulated in QQ and LYQQ (Fig. 5c and Additional file 3: Table S3). Numerous studies have suggested that polar auxin transport, which is primarily determined by polar localization of PIN auxin efflux carriers, controls plant tropism in roots and shoots and plays essential roles in plant growth [13, 48, 49]. Gerttula, et al. [SEP] Justify:

Output: The text does not address the claim about fossilized plants and their insights into ancient climates and ecosystems. Instead, it discusses genetic and molecular mechanisms related to plant growth and gravitropism, focusing on specific genes and their roles in Arabidopsis, rice, and other plants. Therefore, it is 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: DiscussionIn this study, we present an inverse correlation of the DNA methylation in the first intron and gene expression, which is conserved in tissues with different levels of cellular complexity and across vertebrates. Furthermore, we detect CpGs in enriched TF-binding sites close to the first exon–first intron boundary indicative of gene expression and tDMRs the methylation of which correlates with gene expression. Recent studies on the relationship between DNA methylation and gene expression have revealed a key role for the region from + 0. 5 to + 2. 5 kb downstream of the TSS in transcriptional regulation of different human tissues [37, 38]. In addition, the methylation of the first exon was shown in mammalian cell lines to be negatively correlated to gene expression, in a more pronounced way than the promoter region [9]. In parallel, the methylation of the first intron has been shown by functional studies to have both positive and negative correlation with gene expression in specific genes in cancer cell lines, fetal and adult tissues [39], CD4+ cell lines isolated from mice [40], during lineage specification in T cells [41], in multiple myeloma cell lines [42], in leukocytes of patients with schizophrenia [43] and in blood samples isolated from children [44]. Furthermore, it has been suggested that the first intron contains distinct properties from the rest of introns and that is linked to transcriptional regulation [45, 46]. These properties may be linked to the closer proximity of the first intron to the TSS, since in many species the CpG-rich regions expand from the CGI promoter to the surrounding sequences [47]. Other active chromatin marks are enriched in conserved parts of the human first intron [48]. However, to the best of our knowledge, an association at the genome-wide scale of the methylation of the first intron as an outlined gene feature has not been demonstrated to date. In two complex tissues of a phylogenetically distant species, we present the same pattern previously observed in humans. In the European sea bass genome, the median methylation of the first intron showed, consistently in both tissues, the most clear inverse relationship with gene expression among all gene features. [SEP] Justify:

Output: The text corroborates the claim by discussing the relationship between DNA methylation and gene expression, indicating how factors like methylation levels can influence gene expression across different tissues and species. It illustrates epigenetic mechanisms by describing how methylation of specific gene features, such as the first intron, has correlations with gene expression, which can be shaped by various environmental factors.


Input: Task: contrast the claim using the given text. Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: A decade ago in a paper in the of Environment and Resources, Benson and Heleen de Coninck, a climate change researcher at the of Technology and in the Netherlands, wrote that, to help mitigate climate change, CCUS needs to serve more than fossil fuel companies seeking to extract oil. In the decade since, Benson notes, CCUS has been slow to expand into other areas largely because of a lack of public policies supporting the technologies, such as government subsidies for new projects or a tax on CO2 emissions that would make it cheaper to sequester than to emit it. However, she notes, this is now changing. When it is fully operational, Climeworks’ Mammoth project will be the world’s largest facility pulling CO2 directly from the air and burying it underground. The project, in Hellisheiði, Iceland, follows another, smaller Climeworks project called Orca. : © 2024 to the futureCCUS may be poised to turn a corner. As of July 2023, 351 new commercial-scale CCUS projects were in the works, according to the Global CCS Institute. Many of these forthcoming projects will capture CO2 with the exclusive goal of burying it underground rather than using it to squeeze out more oil. Around 22 of the projects are aimed at capturing CO2 at cement plants and five will capture CO2 directly from the air and store it underground. Still, a connection with fossil fuels remains: Around 30 will serve methane production, and others are planned for carbon capture at coal- and gas-fired power plants. Even with this new bloom of projects, it’s not clear that the technology has a large part to play in solving our climate woes, says Sean O’Leary, a senior researcher in energy and economics at the Valley Institute, a clean-energy think tank based in Johnstown, Pennsylvania. Current and future projects are unlikely to capture carbon in sufficient quantities to make much of a dent on global emissions, O’Leary says. Estimates suggest that existing projects could capture around 50 million tons of CO2 annually — cutting the more than 35 billion tons of gross global carbon emissions by around 0. 14 percent. Once all 392 projects are online, they could capture a few hundred million tons — about 1 percent of carbon emissions. Estimates of how much carbon CCUS needs to capture to help achieve climate goals vary widely between 1 billion and 30 billion tons annually by 2050. [SEP] Justify:

Output: The text contrasts the claim by stating that despite an increase in carbon capture and storage (CCUS) projects, experts like Sean O’Leary argue that the technology is unlikely to capture enough carbon to significantly impact global emissions. O’Leary estimates that even when all projects are operational, they could only capture about 1 percent of carbon emissions, which suggests that CCUS will not soon solve all problems related to climate change.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: [50] proposed that PIN expression in different cambium cells results in auxin transport towards the cambium in the top and bottom of the stem to trigger wood formation in response to gravity in woody stems. Consistent with this finding, we found that the expression of was repressed in QQ and LYQQ (Fig. 5c and Additional file 3: Table S3); these changes in expression in QQ and LYQQ might alter the polar transport of auxin and then affect the auxin gradients between stem sides; therefore, the shoots exhibit bending. Wu, et al. [51] reported that rice VLN2, a type of actin-binding protein involved in microfilament regulation, affects the recycling of PIN2 and polar auxin transport, and vln2-defective mutant plants exhibited a hypersensitive gravitropic response and twisted roots and shoots at the seedling stage. In this study, we also found that VLN2 (TEA030753. 1) was markedly repressed in QQ and LYQQ (Fig. 5e and Additional file 3: Table S3), suggesting that zigzag-shaped stems in tea plants might be related to polar auxin transport and the gravitropism response. Moreover, cell expansion might exert a compressive force, leading to bending of the stem. Our results showed that genes involved in cell expansion and cell wall synthesis, such as expansin, and xyloglucan endotransglucosylase/hydrolase protein, were differentially expressed (Fig. 5a and Additional file 3: Table S3), resulting in alteration of cell expansion and elongation. In addition, wall-associated kinase (WAK) genes were also differentially expressed in MZ-vs-QQ and MZ-vs-LYQQ, suggesting that WAK-mediated cell expansion and signalling pathways might be required for zigzag-shaped stem formation in tea plants. It is possible that cell expansion in the stems can produce a force that can lead to zigzag-shaped shoots. Importantly, cell expansion and differentiation predominantly rely on auxin [12, 52, 53]; thus, the mechanism of auxin regulation in zigzag-shaped shoot development needs to be studied precisely in the different tissue sides of zigzag-shaped stems. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the expression of certain genes involved in auxin transport and their implications for stem development in tea plants. It does not provide any information or insights related to fossilized plants, ancient climates, or 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: We further show that the inverse relationship between DNA methylation of the first intron and gene expression is conserved across vertebrate species, since it is evident in the model fish Tetraodon, in the model frog Xenopus and two healthy human tissues. This does not seem to hold in invertebrates, which actually exhibit distinct mechanisms of DNA methylation and extreme diversity [49, 50]. In general, across vertebrates, several characteristics of the sequences related to DNA methylation, like the CpG density, are conserved around the TSSs. These characteristics slightly differ for fish, where there is higher CpG density, but still signatures of CGI promoters [47]. Nevertheless, even though the CpG density differs, conserved mechanisms of regulation are present as reflected in this study. Overall, there seems to be a conserved role for the DNA methylation of the first intron across tissues, vertebrates and developmental stages. The classic promoter methylation–gene expression model seems to hold only in extreme cases and specific genes, while a “triple-inverse” model was suggested, where the methylation of the promoter and the gene body exerts separate influences on gene expression [51]. The variability of DNA methylation in the first intron from 0 to 100% independently of the expression level could be linked to the more variable and larger length of the intron and suggestive of a more complex role of this methylation. In our case, a general pattern would be a negative association of the methylation of the first intron with gene expression in the majority of genes, which is clearest at the extremes of the gene expression range. Nevertheless, subclasses of genes escape this rule and exhibit positive correlations. Indeed, at the genome-wide level there are clusters of genes, each one showing different DNA methylation patterns associated with gene expression [38, 52]. DNA methylation in positive correlation with gene expression has been suggested to appear either as cause or consequence of transcription [53]. Our results also suggest a permissive state of gene expression linked with low methylation, but not a linear inhibitory link with high methylation. These observations are in support of the increasing evidence of a far more complex relationship of the epigenetic modifications—including histone and DNA modifications and noncoding RNAs—with gene expression at a spatiotemporal scale [52]. [SEP] Justify:

Output: The text corroborates the claim by discussing the intricate connections between DNA methylation and gene expression. It indicates that DNA methylation can have conservation across vertebrate species, suggesting a relationship influenced by external factors. The mention of a 'permissive state of gene expression linked with low methylation' highlights how epigenetic modifications can influence gene expression, aligning with the concept of environmental factors impacting genetic expression over generations.


Input: Task: contrast the claim using the given text. Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: Large-scale CCUS projects currently online or in development are expected to capture more than 400 megatons of CO2 per year by 2030. That’s far short of the more than 1 gigaton of CO2 per year CCUS projects would need to capture by then in order to stay on track with the Agency’s scenario for achieving net-zero emissions by 2050. A recent analysis suggests that at least 5 billion tons annually is achievable. The research, not yet published, limits CCUS growth to an average of 20 percent per year until 2050 for most cases. “That’s a major contribution to climate mitigation,” says Samuel Krevor, an environmental engineer at London and a lead author of the research. Krevor, like many researchers in the field, receives some funding from fossil fuel companies. says the contribution is likely to be minor relative to other climate solutions, including shifting to renewable energy and planting and maintaining forests to help store away CO2 from the atmosphere. Using data from the IPCC, Hauber and colleagues calculate that by 2030, CCUS will provide just 2. 4 percent of all emissions reductions. What’s more, projects rarely meet their stated goals. An analysis by the Institute for of 13 key CCUS projects, published in 2022, found that most failed to reach their targets. Relying on publicly available data, the analysis found, for example, that the facility has underperformed by 36 percent over its lifetime. When there were fewer customers for the captured CO2, the analysis finds, the facility released it into the atmosphere. A facility in Decatur, Illinois, run by Midland, an agribusiness based in Chicago, was nearly 50 percent off its annual target at the end of 2020. An ExxonMobil spokesperson said the company has made progress since the report, noting that the company has expanded CO2 storage capacity at its facility by over 1 million metric tons annually. And a spokesperson for Midland said that how much CO2 it captures and stores depends on how much biofuel it produces. The company’s Decatur facility is looking at different strategies to decarbonize its operations including capturing CO2 produced by a new gas power plant that will provide energy for the company’s biofuel facility. It’s also unclear how much CO2 capacity underground storage sites possess. [SEP] Justify:

Output: The text contrasts the claim by detailing limitations of carbon capture, utilization, and storage (CCUS) technologies, highlighting that they are expected to capture far less CO2 than is needed to mitigate climate change effectively. It emphasizes that CCUS will contribute only 2.4 percent of the necessary emissions reductions by 2030, suggesting that reliance on this method alone will not solve climate change. Additionally, it notes that several CCUS projects have historically failed to meet their targets, reinforcing the argument that ocean carbon capture will not be a complete solution to climate problems.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: In this study, 20 transcription factors (TFs) belonging to different TF families, including two ARFs, were differentially expressed in MZ-vs-QQ and MZ-vs-LYQQ, and most of these TFs were significantly repressed in QQ and LYQQ (Fig. 5b and Additional file 3: Table S3). Almost all of these genes had homologues associated with plant growth and developmental regulation in other plants. For instance, (TEA031729. 1), a MYB-type TF, could interact with WOX to control wood formation in poplar [54]; overexpression of IBH1 causes erect leaves in rice and dwarfism in Arabidopsis [55]; and HEC1 coordinates with WUS to promote stem cell proliferation in the shoot meristem [56, 57]. kawakamii, antisense suppression of PkMADS1, a regulator of shoot morphogenesis, resulted in zigzag-shaped shoots [58]. Interestingly, in some transformants of antisense PkMADS1, the main shoot apex appeared to be used up early during leaf formation, and then, the axillary bud of the youngest leaf took over the function of the apical meristem, resulting in the formation of one leaf per node and the zigzag-shaped growth habit for the stem, indicating that central and lateral meristem fates regulated by a variety of TFs may relate to zigzag-shaped shoot formation. Recently, several genes that regulate architectural phenotypes in woody plants, such as 2 (ARK2) in Populus [50] and 1C (GID1C), Control 1 (TAC1) and WEEP in peach [23, 59, 60], have been isolated; however, most of these genes are related to the plant gravitropic response, and none of these genes encode TFs. Additionally, among the nine SGR genes, SGR1 and SGR7 encode scarecrow (SCR) and GRAS family TFs, respectively. We found that the SCR gene (TEA030046. 1) was markedly repressed in QQ and LYQQ (Fig. 5b and Additional file 3: Table S3). [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 various transcription factors and their roles in plant development, which is unrelated 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: The function of the inverse relationship between DNA methylation of the first intron and gene expression could be partially explained by the presence of intronic enhancers interacting with the promoters of their corresponding genes. Indeed, the intron-mediated enhancement is a well-described phenomenon [48, 54, 55]. Silencing of intragenic enhancers is considered to play a role even more significant than promoter methylation in the silencing of their target genes [7]. In addition, intronic enhancers present tissue-specific methylation status associated with gene expression [56, 57]. Our results also revealed enriched TF-binding motifs common between tissues. Moreover, the unmethylated CpGs tend to be located closer to the beginning of the first intron and associated with higher gene expression levels, while the methylated CpGs tend to be further downstream and associated with lower gene expression levels. Therefore, the methylation status of the CpGs at shorter or greater distances from the beginning of the first intron which belong to a TF-binding motif is indicative of the gene expression level. Taken together, these results further support a regulatory role for the DNA methylation in the first intron region, although further experiments are needed to demonstrate the mechanistic relationships at the functional level. tDMRs located in the whole gene showed both positive and negative correlation with gene expression as in human tissues [11]. Here, in addition to confirm this in a phylogenetically distant species, we partition the genomic localization of tDMRs in three important gene features: promoter, first exon and first intron. tDMRs are distributed across all these gene features and exhibit both directions of correlation, but no enrichment of positive or negative correlation depending on the location. This is in accordance with the latest findings in human tissues [11] and in contrast to the standard model of gene regulation by DNA methylation. However, in the first intron, there are more tDMRs, in agreement with our finding of the importance of the first intron in the regulation of gene expression by DNA methylation. In human macrophages after bacterial infection, the majority of gene body DMRs were also located in the first introns of genes [58]. Taken together, these results suggest an overlooked role for the DNA methylation of the first intron in the tissue-specific regulation of gene expression. [SEP] Justify:

Output: The text corroborates the claim by discussing the role of DNA methylation and intronic enhancers in regulating gene expression, highlighting the influence of specific tissue environments on gene expression levels. It mentions that 'the methylation status of the CpGs... is indicative of the gene expression level,' which suggests that environmental factors can impact gene regulation. The details about tissue-specific regulation and the implications for evolutionary biology support the overarching theme of epigenetics influencing gene expression across generations.


Input: Task: contrast the claim using the given text. Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: Most global estimates suggest that between 10,000 billion and 30,000 billion tons of underground storage is available. Some estimates put it as a high as 55,000 billion tons. Greig, a chemical engineer at who previously worked on a CCUS project for the fossil fuel industry, notes that those volumes could be way off. Assessments are based on estimates of the pore space in different geologic formations — those pores provide open spaces that can hold CO2 — which gives only a rough picture, he says: “Subsurface storage is by nature uncertain. ”Such uncertainties have caused projects to veer off course, including a $2. 7 billion project to separate CO2 from methane in gas fields in In Salah, Algeria, and store it 1. 9 kilometers underground. The energy company Equinor and its partners started injecting CO2 there in 2004 with the aim of storing 1. 1 million tons annually. But it suspended operations because of limits in underground capacity, according to an Equinor spokesperson. There were concerns that the gas was escaping up toward the cap rock, which acts as a final safety net sealing the CO2 in place. On top of the uncertainty, money is a problem. Some skeptics say that the costs of building and operating CCUS projects ultimately make them unviable. According to 2019 data from the IEA, the costs of capturing CO2 range from $15 to $120 per ton, depending on how dilute the gas stream is. Cost estimates for capturing CO2 directly from the air, where it is very dilute, typically vary between $225 and $500 per ton, with some estimates as high as $1,000 per ton. Multiply that price tag by even a small portion of the 1 billion tons of CO2 that the IPCC says needs to be removed from the atmosphere by 2050, and the costs quickly add up. Stay in the KnowSign up for the newsletter todaySome experts point out that these costs will likely go down as the technologies mature and if the market increases, though not necessarily on the same scale as the dramatic costs reductions seen for solar and wind power technology. For example, the IEA notes that costs for CO2 capture from coal-fired power plants dropped from over $100 per ton in 2014 to $65 per ton in 2017, and it estimates that in projects built from 2025 to 2027, the cost will be around $45 per ton. [SEP] Justify:

Output: The text contrasts the claim by highlighting the uncertainties and financial challenges associated with carbon capture and storage (CCUS). Greig, a chemical engineer, points out that current estimates of geological storage capacity may be overly optimistic and notes that subsurface storage is inherently uncertain. The text also references a failed CCUS project in In Salah, Algeria, due to concerns about gas escaping and the limits of underground capacity. Additionally, it discusses the high costs of implementing CCUS technologies, which some skeptics argue make them unviable. This evidence implies that ocean carbon capture is unlikely to soon resolve all climate change issues due to technical and economic hurdles.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Plant growth and development are directed by a TF-mediated complex network integrated with plant hormones, enzymes and other cellular components; therefore, as-yet-unknown TFs may be involved in the regulation of plant architectural phenotypes. ConclusionIn the current study, we investigated the mechanism of zigzag-shaped shoot formation in tea plants using comparative transcriptomics and metabolomic analysis. The results showed that zigzag-shaped stem development in tea plants might be regulated by a complex network involving vesicular trafficking, phytohormones, cell expansion, secondary metabolism, and diverse transcription factors. Importantly, zigzag-shaped shoot formation might be closely related to alterations in the gravitropic response and polar auxin transport in tea plants. Our findings provide insights into zigzag-shaped shoot formation in tea plants and serve as a valuable foundation for further investigations of architecture formation in woody plants. MethodsPlant materials The tender stems (between the first and third leaves from the apical bud) of tea plants with erect (C. sinensis var. Meizhan, MZ) and zigzag-shaped (C. sinensis var. Qiqu, QQ; C. sinensis var. Lianyuanqiqu, LYQQ) shoots were collected from the germplasm resource garden of in October 2018. A portion of each sample was immediately frozen in liquid nitrogen and then stored at -80°C until use for transcriptome sequencing and metabolite analysis. The remaining samples were fixed in cold fixative solution (4°C) for section observation. All samples were examined in triplicate and used as biological replicates. Tissue section observation Longitudinal stem sections were sliced and stained as previously described by Ile, et al. [61] with minor modifications. At least seven stems from each tea plant cultivar were cut into fragments (<0. 5 cm) and fixed in fixative solution over 72 h at 4°C. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the mechanisms of shoot formation in tea plants and the methodologies used for analyzing plant samples. It does not address 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: We used RRBS to assess DNA methylation and RNA-seq to measure the gene expression levels in the European sea bass genome which is one of the best annotated teleost genomes [31]. Nevertheless, the precision of the annotation of genes and their regulatory elements is not comparable to model species, like human or mouse. Therefore, we defined promoters as the region − 1000 kb upstream the predicted TSSs, as commonly arbitrarily defined [59,60,61,62,63,64], but without excluding the possibility of alternative TSSs or variable promoter lengths. The limitations of the sea bass genome annotation may influence also the gene expression data, where the analysis could only be performed at the gene level, based on the current annotation. RRBS allows for enrichment of the standard relevant parts of the genome for DNA methylation, e. g. , promoters and CpG islands, and requires only a modest amount of sequencing [65, 66], making it a cost-effective alternative to WGBS which is considered generally inefficient since only 20–30% of the reads provide relevant information [67, 68]. Our RRBS results, including the genome representation and the actual methylation values, are comparable to other teleost fish, like the stickleback [69], the Atlantic salmon [70] and the zebrafish [71]. Regardless of the limitations of this study related to the main species in question and the techniques used, our key results were confirmed in other vertebrate species, corroborating the general trends shown in the sea bass, even accepting the possibility that some genes may be not well annotated. ConclusionsOur integrative analyses clearly reveal the important and conserved role of the methylation level of the first intron and its inverse association with gene expression regardless of tissue and species. Notably, the first intron exhibits a tissue-independent enrichment for TF-binding motifs and the methylation of the CpGs they contain is indicative of the gene expression level. Furthermore, the first intron presents a higher number of tDMRs than other gene features, suggestive of a regulatory role in tissue-specific expression. These findings not only contribute to our basic understanding of the epigenetic regulation of gene expression but also identify the first intron as an informative gene feature regarding the relationship between DNA methylation and gene expression where future studies could be focused, e. g. [SEP] Justify:

Output: The text corroborates the claim by discussing the role of DNA methylation in gene expression, highlighting how environmental factors, in this case, affect gene expression levels. It mentions that 'the methylation level of the first intron and its inverse association with gene expression' are important, thus directly connecting environmental epigenetic factors to gene expression across species, which aligns with the fundamentals of epigenetics.


Input: Task: contrast the claim using the given text. Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: Partly because of the costs, CCUS should be prioritized for cases where there are no other reasonable approaches to reducing CO2 emissions, says Sabine Fuss, a climate economist at the Institute on and at of Berlin. She does, though, see a potential role for direct air capture despite its expense. And while researchers are divided on the feasibility of direct air capture, Fuss thinks it needs to be funded regardless. If the world overshoots its climate targets, she says, we will likely need this technology to reach net-zero emissions and forestall even worse effects of climate change. How big a role CCUS will eventually need to play is up to us and what we do now, Fuss says. But given the uncertainties, we can’t continue to burn fossil fuels and release carbon and count on CCUS to clean it up afterward. “We have to do all that we can to reduce emissions in the short to medium term rather than rely on CO2 removals in the longer run,” she says. 10. 1146/knowable-070924-2 is a freelance reporter based in Washington, DC, who covers the environment, agriculture and sustainability. She’s a good listener, a keen observer and a bit of a cynic. Check out her work at bynatashagilbert. com or @ngreports. [SEP] Justify:

Output: The text contrasts the claim by suggesting that while carbon capture, utilization, and storage (CCUS) might have a role in mitigating climate change, it should not be relied upon as a primary solution. Sabine Fuss emphasizes the importance of reducing emissions in the short to medium term rather than relying on CCUS interventions to rectify emissions after the fact, indicating that it is not a comprehensive solution to climate change.


Input: Task: pass the claim using the given text. Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: The stems were dehydrated by transferring them sequentially through a series of increasing concentrations of ethanol (75 to 100% absolute ethanol), followed by 100% ethanol, ethanol:xylene (2:1), ethanol:xylene (1:1), ethanol:xylene (1:2), pure xylene, pure xylene (each for 1 h), xylene:Paraplast (1:1) for 24 h, and molten Paraplast (melting point 65°C) for 48 h and finally embedded in freshly molten Paraplast. Central longitudinal sections of 5 μm thickness per stem were cut using a disposable-blade rotary microtome (RM2016, Leica, Shanghai, China), allowed to stand overnight and dried at 40°C for 4 h. Sections were dewaxed in xylene, hydrated gradually in decreasing concentrations of ethanol (from 100 to 70%) and stained with safranine (1. 0% for 2. 5 h) followed by (1. 0% for 8 s) in ethanol. After staining, the stem sections were observed under a Leica DMi8 inverted microscope (Leica, Shanghai, China). UPLC-ESI-MS/MS analysis and differential metabolite identification A total of 100 mg of powder from crushed freeze-dried samples was weighed and extracted overnight at 4°C with 1. 0 ml of 70% aqueous methanol containing 0. 1 mg/L lidocaine as an internal standard. Following centrifugation at 10,000 ×g for 10 min, the supernatant was absorbed and filtered (SCAA-104, 0. 22-μm pore size; ) before liquid chromatography-tandem mass chromatography (LC-MS/MS) analysis. Quality control samples were mixed with all the samples to ensure the reproducibility of the entire experiment. The extracted compounds were analysed using an ultra performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS) system (UPLC, Shim-pack 30A; MS/MS, 6500 QTRAP) [62]. For compounds separation, column, mobile phases, and operation parameters were chosen or set following the description by Xu et al. [63]. [SEP] Justify:

Output: The text is irrelevant to the claim as it primarily describes a detailed procedure for the preparation and analysis of plant stems using various chemical methods and instruments. It does not mention fossilized plants, ancient climates, or ecosystems, thus failing to provide support or contradiction to the claim.