Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Rapid selection and identification of Miscanthus genotypes with enhanced glucan and xylan yields from hydrothermal pretreatment followed by enzymatic hydrolysis access Published: 03 August 2012 Rapid selection and identification of Miscanthus genotypes with enhanced glucan and xylan yields from hydrothermal pretreatment followed by enzymatic hydrolysis Taiying Zhang1, Wyman1,2, Katrin Jakob3 & …Bin Yang1,4 Show authors Biotechnology for Biofuels 17. 5 min followed by co-hydrolysis in a multi-well batch reactor identified two varieties out of 80 that had significantly higher sugar yields from pretreatment and enzymatic hydrolysis than others. The differences in performance were then related to compositions of the 80 varieties to provide insights into desirable traits for Miscanthus that enhance sugar yields. ConclusionsHigh throughput pretreatment and co-hydrolysis (HTPH) rapidly identified promising genotypes from a wide range of Miscanthus genotypes, including hybrids of Miscanthus sacchariflorus/M. sinensis and Miscanthus lutarioriparius, differentiating the more commercially promising species from the rest. The total glucan plus xylan content in Miscanthus appeared to influence both mass and theoretical yields, while lignin and ash contents did not have a predictable influence on performance. BackgroundWorld petroleum reserves are being depleted at an accelerating rate and production rates are slowing. In fact, Kerr reported that conventional oil production might have already reached its peak instead of plateauing between 2015 and 2020 as predicted earlier [1–3]. In addition, a move from fossil to renewable fuels is vital if we hope to slow the impacts of carbon dioxide accumulation on global climate. Against this background, production of fuels from cellulosic biomass is one promising option for large-scale and low-cost sustainable production of liquid fuels with low greenhouse gas emissions. Crops planted for the specific purpose of energy production are expected to play an essential role in meeting the of 2007 in the United States. In the recent report entitled “U. S. update: for Bioenergy and Bioproducts Industry” jointly released by DOE and USDA, energy crops were predicted to become dominant at prices above $50 per dry ton after 2022 with the baseline about 37% of total biomass at $60 per dry total [4]. [SEP] Justify:

Output: The text primarily discusses the rapid selection and identification of Miscanthus genotypes with enhanced sugar yields and does not directly reference bioengineered yeast or the production of biofuels from sugars, making it irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: The phenotyping analysis of mutant plants showed reduced Rubisco content, photosynthetic rates, and biomass accumulation. In this study, it has been shown that it is possible to produce superior non-native Rubisco enzymes by multiplex gene editing withCas9 in polyploid species. The function of the OsPMEI12 gene, which belongs to the pectin methylesterase inhibitors (OsPMEI) gene family for growth, cell wall development, and response to phytohormone and heavy metal stress, was elucidated by mutating it in rice (Oryza sativa L. ) [17]. It has been revealed that the OsPMEI12 gene plays a role in the regulation of methyl esterification during growth, thus pectin status is controlled by hormones and cadmium stress. Discovery of genetic male sterility (GMS) genes will allow to unravel the molecular mechanism of anther development and to develop male sterility systems for crop breeding and hybrid seed production. Therefore, the researchers focused on elucidating the roles of the transcription factors genes (bHLH, band LBD gene families) responsible for the GMS agronomic trait in highly heterosis maize [18]. Mutation of transcription factor gene families with yielded the following results; that ZmbHLH51 and ZmbHLH122 are necessary for male fertility, ZmTGA10 has affected anther dehiscence. ZmMYB84 is essential for maize pollen development. ZmPHD11 is responsible for the formation of anther cuticle and Ubisch bodies. Two MYB33 paralogs are important for GMS. ZmLBD27 has an impact on the reduced ratio of normal pollen grains. ZmPHD11/27 influenced viable pollen formation. Two homologous genes (Bra018924 and Bra014296) of PP2A, a 55 kregulatory subunit (PR55/B), were edited through theCas9 system to develop self-compatible lines controlled by type 2A serine/threonine protein phosphatases (PP2As) in Chinese cabbage [19]. The PR55/B gene knock-out line did not show self-incompatibility and produced seeds, suggesting that the PR55/B gene was responsible for the self-incompatibility. 2. [SEP] Justify:

Output: The text corroborates the claim by detailing how gene editing techniques, such as multiplex gene editing with Cas9, can lead to the production of superior traits in crops. Specifically, it discusses the role of the OsPMEI12 gene in growth and stress response, and how mutation of transcription factor gene families impacts male fertility and pollen development in maize. These findings imply an enhancement of growth traits, which supports the idea that gene editing can improve crop yields.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: While their use provides the theoretical opportunity to dissect the host genetic component of the host-microbiome interacting system, it represents a rather brute force approach as these deficient strains present dysbiotic states per se. which hinders the use of proper negative controls. The approach we propose could be employed alone or jointly with germ-free, knock-out, and (or) gnotobiotic approaches to reproducibly and effectively advance the science of host-microbial mutualism. For instance, our approach should allow the detection of links between the activity of different modules of gut immunity and the abundance or activity of particular groups of bacteria. Supporting informationS1 Fig. Top 20 enriched IPA pathways in caecum after Ectromelia virus infection. Significant and differentially expressed genes from ECTV infected samples compared to control uninfected were used in a pathway enrichment analysis using IPA software (Ingenuity). Top 20 most enriched pathways and their corresponding p-values are shown. Lines connect overlapping pathways sharing at least 5 genes. S1 Mat. Results from the Analysis. 1. Pflughoeft KJ, (2012) Human microbiome in health and disease. Pathol 7: 99–122. pmid:21910623 View 2. - (2007) Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell 131: 33–45. pmid:17923086 View 3. (2003) Viral mimicry of cytokines, chemokines and their receptors. Immunol 3: 36–50. pmid:12511874 View 4. (2006) Anti-immunology: evasion of the host immune system by bacterial and viral pathogens. Cell 124: 767–782. pmid:16497587 View 5. (2005) Ectromelia virus: the causative agent of mousepox. J 86: 2645–2659. pmid:16186218 View 6. (2008) Correlates of protective immunity in poxvirus infection: where does antibody stand? Biol 86: 80–86. pmid:17923850 View 7. (2011) CD94 is essential for NK cell-mediated resistance to a lethal viral disease. Immunity 34: 579–589. pmid:21439856 View 8. [SEP] Justify:

Output: The text contrasts the claim by discussing the importance of microbial diversity in terms of 'dysbiotic states' and the relationship between gut immunity and bacterial diversity. The phrase 'deficient strains present dysbiotic states' indicates that a lack of diversity (suggestive of a 'sterile gut') is not necessarily healthy and may hinder proper immune functionality. Thus, the text suggests that a diverse microbiome may support better health outcomes.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Among various potential perennial energy crops, Miscanthus, which is native to Asia and the Pacific Islands, has been selected and studied as one of the most promising energy crops for Europe over the past two decades [5–8]. Based on Miscanthus field trials at different locations in Europe, a growth model towards more robust yield predication on the basis of different climatic and soil condition was developed in Europe [9]. has been successfully produced with high yields over a wide range of climatic conditions in Europe, it also became of interest as a dedicated biomass crop in the US, and first field trials were planted in Illinois and Arkansas [10–14]. It has been reported that the average productivity of Miscanthus x giganteus was 30 t/ha-year and the maximum productivity was as high as 61 t/ha-year over a 3 year period in side-by-side trials while the productivity of switchgrass, one of the most studied energy crops in the United States, was reported to be 15. 8 t/ha-year in upland and 12. 6 t/ha-year in lowland varieties [10]. Thus, Miscanthus could potentially reduce the land requirements to support U. S. biofuels production [11, 12]. Further study on the effects of management on Miscanthus x giganteus productivity in different environments based on four locations in the provided more insights on how to improve the productivity of Miscanthus x giganteus and its capacity as a stable and reliable biomass feedstock [13]. In addition to high productivity, Miscanthus could be very important for the relatively high carbohydrate content (>60%) of some genotypes. genus in general, and Miscanthus x giganteus in particular, have been identified as prime candidates for biomass energy crops because of an array of other attributes including high photosynthetic efficiency, strong stress tolerance, perennial growth, low nutrient requirements, and high carbon content [5, 14]. For biological processing to ethanol and other products, it is particularly beneficial to identify genotypes that are most easily processed into sugars. As with other types of lignocellulosic biomass, pretreatment is essential to disrupt the natural recalcitrance of Miscanthus to release fermentable sugars with high yields with the fungal enzymes typically used. [SEP] Justify:

Output: The text focuses on the productivity of the Miscanthus x giganteus as a biomass crop for biofuels and discusses its attributes and requisite processing for sugar production. However, it does not mention bioengineered yeast or its design for biofuel production, making it irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: 2 ResistancePlant diseases are a significant threat to crop productivity, with losses estimated to cost billions of dollars annually. Genome editing can be used to enhance the resistance of crops to diseases by editing genes that encode for disease resistance. MicroRNAs act as regulators of the plant immune system by silencing the genes involved in pathogen virulence or by regulating the expression of target genes. MicroRNAs belonging to the miRNA482/2118 superfamily targeted R-genes of the class NBS-LRR (nucleotide-binding site-leucine rich repeat). In tomato, knockout mutants for SlymiR482e-3p gene, a member of the miR482/2118 family, were generated to detect its role against tomato wilt disease resistance [Fusarium oxysporum f. sp. lycopersici (race 2) (Fol)] [20]. The results showed that SlymiR482e-3p gene negatively regulated the resistance to wilt disease. In another study with miR482 gene family in tomato, mutations in the two genes (miR482b and miR482c) were generated [21]. The expression levels of their target NBS-LRR genes were increased, followed by reduced late blight, caused by Phytophthora infestans, disease symptoms in mutant plants. Interestingly, it was concluded that knocking out these two genes could lead to expression perturbation of other miRNAs, suggesting cross-regulation between miRNAs. In cotton (Gossypium hirsutum L. ), the MIR482 mutant collection was obtained by knocking out MIR482 genes in miR482 gene family with dozens of members usingCas9. This mutant collection allow us to examine the role of individual MIR482 genes against pathogen response and to identify miR482-NLR module(s) that respond to, particularly fungal pathogen Verticillium dahliae agent for Verticillium wilt and other pathogens. It has also been reported that this collection may be a useful genetic resource for the development of new disease-resistant cotton varieties [22]. 2. 3 Improved QualityQuantitative trait loci (QTLs) are genomic regions that are associated with complex traits such as crop quality. QTLs can be used to improve crop quality by identifying genomic regions associated with desirable traits. [SEP] Justify:

Output: The text corroborates the claim by discussing how genome editing can enhance crop resistance to diseases, which is a factor that indirectly contributes to improving crop yields. The discussion of specific genes and traits, such as the role of microRNAs in disease resistance and improvements in crop quality through quantitative trait loci (QTLs), supports the assertion that gene editing can lead to better growth traits and subsequently higher yields.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Log in or to journalnew issue alertsGet alerts Enter your Email address: Subscribe to e2018. | DOI: 10. 1249/FIT. 0000000000000421 It! Encourage clients to include whole fruits, vegetables, grains, and beans and legumes in their diet over fruit juices, sweetened beverages, energy drinks, and more processed foods. Encourage the inclusion of fermented and higher fiber foods in the diet to assure a healthy gut. Select healthy foods first over supplements. is not uncommon for active individuals to experience gastrointestinal (GI) distress, upper respiratory symptoms (URS), and other illnesses associated with sport participation. Research in endurance athletes shows that 30% to 50% report some type of GI distress associated with exercise (1). In addition, URS are common among athletes. In the three months before the 2016 summer Olympics, URS were the most common illness (48%) reported by 132 athletes participating in the games, especially those involved in prolonged, intense activity and during competitions (2). Of those reporting URS, 95% reported being unable to participate in sport. In this same sample, 21% reported GI distress during the same period, with 79% of these athletes being unable to participate in sport. You don’t have to be an Olympic athlete to have GI symptoms associated with exercise. Even recreational and fitness athletes experience GI issues or concerns associated with training or competition. No one wants to run to the bathroom, throw up, or quit a sporting event because of GI distress. Although GI symptoms associated with sport are typically mild to moderate, when they occur, they can derail performance or prevent participation in exercise and sports. It is well established that gut health is closely linked to immune health and the prevention of illness (3). Thus, a healthy intestinal microbiota (defined in the following section) translates into a healthier immune system and decreased susceptibility to illness or disease (3). Part of having a healthy gut means having a healthy microbiota. In the following section, we address key steps to help you maintain a healthy gut, improve your overall immune system, and reduce your risk of illness. . The human gut contains thousands of bacterial species plus many other microorganisms that are collectively known as the gut microbiota (4). The number of microorganisms inhabiting the gut plays a significant role in regulating host immunity, protecting against pathogens, strengthening gut integrity, synthesizing vitamins, and producing energy, especially short chain fatty acids (SCFA). [SEP] Justify:

Output: The text contrasts the claim by stating that a healthy intestinal microbiota is crucial for immune health and prevention of illness. It emphasizes that having a diverse population of microorganisms in the gut plays a significant role in regulating immunity and provides various health benefits, suggesting that a sterile gut would not provide these advantages.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Conventional pretreatment and enzymatic hydrolysis methods are very labor intensive and time consuming, making it very expensive and/or slow to screen large numbers of plants to find those that display enhanced sugar yields. However, high throughput methods have been recently developed that allow rapid screening of large numbers of combinations of plants, pretreatment conditions, and enzyme loadings and formulations to narrow the field to those with high sugar release or other desirable features [28–34]. These methods can also handle much smaller amounts of samples than conventional approaches, thereby allowing characterization of sugar release from different anatomical fractions [30]. Such rapid screening methods have been applied to a sorghum diversity panel [32], a high-throughput microplate for enzymatic hydrolysis of lignocellulosic biomass [33], and high-throughput screening of cellulose following ionic liquid treatment [34]. Recent rapid screening studies of enzymatic hydrolysis using different glycosyl hydrolases were employed to compare AFEX and dilute acid pretreatment of corn stover [35, 36]. Studer et al. developed a higher temperature, high throughput method appropriate for hydrothermal and other thermochemical pretreatments based on the 96 well-plate format and employing a custom made steam chamber for rapid heating and cool down of multiple reaction vessels [29]. Results for poplar without liquid–solid separation after pretreatment in the multi-well plate system were shown to be statistically identical to those from standard pretreatment and hydrolysis methods with liquid–solid separation and solid washing [29]. Advantage has also been taken of the ability to process small sample sizes to determine variations in sugar release among tree growth rings and to identify promising traits in poplar as well as the high throughput determination of glucan and xylan fractions in lignocelluloses developed by Selig et al. [28, 31, 37]. In this study, the previously established HTPH system was applied to screen Miscanthus genotypes with the goal of identifying those that displayed enhanced release of glucan and xylan from the coupled operations of hydrothermal pretreatment and enzymatic hydrolysis. Conventional hydrothermal pretreatment in tubular batch reactors followed by enzymatic hydrolysis was applied first to identify baseline conditions that gave the highest total sugar yields from Miscanthusx giganteus cv. Illinois planted in Illinois. [SEP] Justify:

Output: The text is irrelevant to the claim because it focuses on methods for screening and optimizing sugar yields from different plant sources and treatments, but does not mention bioengineered yeast or its application in producing biofuels. It discusses various pretreatment and hydrolysis techniques applied to biomass, without connecting them to bioengineering yeast specifically.


Input: Task: corroborate the claim using the given text. Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: Many genes in QTLs have been targeted with genome editing. Starch branching enzymes (SBEs) are involved in the biosynthesis of starch in plants and there have been several studies on the use of genome editing SBE genes in crops to modify starch content and properties. For example, one study used -Cas9 RNP-method to induce mutations in SBE genes to develop a unique potato starch lacking branching [23]. Another study usedCas9 to generate high-amylose rice by targeting SBEI and SBEIIb genes [24]. napus, an oilseed plant that is the raw material for both cooking oil and biodiesel production, loss-of function of the BnLPAT2 and BnLPAT5 genes belonging to lysophosphatidic acid acyltransferase (LPAT) family allowed to lay out their precise roles in oil biosynthesis. That is, the oil content decreased, the size of oil body increased in mutant lines [25]. The results of this study illustrated that these genes could be used for oil production improvement. In order to prevent enzymatic browning, negatively affecting tubers during harvest and post-harvest procedures, researchers targeted the (PPOs) gene family and mutated the StPPO2 gene in Solanum tuberosum L. [26]. A lower PPO causing oxidation of polyphenols (natural antioxidants) in tuber was observed in mutant lines and enzymatic browning was reduced. Another study with the polyphenol oxidases (PPOs) gene family was carried out in eggplant (Solanum melongena L. ) [27]. In this study, the researchers stated that it would be possible to develop eggplant varieties that retain a high polyphenol content beneficial to human health in the berries during harvest and post-harvest processes by knocking out the three genes (SmelPPO4, SmelPPO5, SmelPPO6). 2. 4 ContentGenome editing can also be used to enhance the nutritional content of crops by increasing the levels of essential nutrients, such as oil, phenolic acid, vitamins and minerals [4]. This is particularly important in developing countries, where nutrient deficiencies are prevalent and access to a diverse diet is limited. [SEP] Justify:

Output: The text corroborates the claim by discussing how genome editing has been used to target various genes that influence crop traits, such as starch content, oil production, and nutritional value. Specific examples include using Cas9 to modify SBE genes for enhanced starch properties in potatoes and rice, as well as altering genes related to oil biosynthesis in oilseed plants. Furthermore, it mentions that genome editing can enhance the nutritional content of crops, addressing nutrient deficiencies, which collectively supports the idea that gene editing can indeed improve crop yields through enhanced growth traits.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: The SCFA (propionate, butyrate, and acetate) are produced when nondigestible carbohydrates (e. g. , dietary fiber) or other food components are metabolized by the gut bacteria (4). These SCFA are now recognized as key metabolic and immune mediators and have an anti-inflammatory role. Thus, anything that disrupts the gut microbiota, such as pathogens or antibiotics, has the potential to significantly impact the health of the host. How do we keep our gut microbiota healthy? Diet has a major impact on the gut microbiota. The ability of the gut bacteria to metabolize indigestible proteins and carbohydrates, especially those found in dietary fiber, contributes to the health of the gut microbiota. Thus, extremes in dietary behaviors, such as high animal-based diet versus plant-based diet, can result in a wide range of alterations in the gut microbiota in humans. Low-fiber diets will mean lower production of SCFA and the benefits these metabolites play in providing energy to the gut and keeping it healthy. The specific dietary factors that play a role in improving gut health are discussed as follows. How do we keep our gut microbiota healthy? Diet has a major impact on the gut microbiota. The ability of the gut bacteria to metabolize indigestible proteins and carbohydrates, especially those found in dietary fiber, contributes to the health of the gut microbiota. Thus, extremes in dietary behaviors, such as high animal-based diet versus plant-based diet, can result in a wide range of alterations in the gut microbiota in humans. Healthy Diet. There are a number of dietary steps you can take to help maintain a healthy gut. Probiotics. One way to maintain the beneficial bacteria in the gut is to consume foods that contain probiotics. (5) has defined a probiotic as a “live microorganism which, when administered in adequate amounts, confer a health benefit to the host. ” There are thousands of fermented foods consumed worldwide by every culture. These foods are generally defined as foods or beverages made through a controlled microbial growth (e. g. , bacteria are added to the product) and enzymatic conversions of major or minor food components to simpler components (e. g. , enzymatic digestion of lactose to its simple sugars) (6). Some of the more common fermented foods in the American diet include dairy foods, such as yogurt and kefir. [SEP] Justify:

Output: The text contrasts the claim by emphasizing the importance of gut bacteria and their role in health. It discusses how short-chain fatty acids (SCFA) produced by gut bacteria are key metabolic and immune mediators, highlighting that a healthy gut microbiota is crucial for health. The text suggests that disruptions to this microbiota, such as through pathogens or antibiotics, can negatively impact health, implying that a diverse gut microbiome is essential rather than a sterile one. Additionally, the mention of probiotics and fermented foods further supports the idea that maintaining a diverse set of gut bacteria is beneficial.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Then the HTPH system was applied to 80 different Miscanthus varieties to screen for those that gave the highest sugar release and identify the most promising genotypes based on baseline conditions determined from conventional pretreatment results. As reported in a companion paper (in preparation), a flowthrough reactor system was then applied to follow release of sugars and other biomass components and gain new insights into biomass deconstruction patterns that favour high sugar yields based on hydrothermal pretreatment. Results and discussionMiscanthus compositionsAs the most widely cultivated biomass genotype currently available, Miscanthus x giganteus cv. Illinois was selected as the reference material for identification of pretreatment conditions that gave the highest total glucose plus xylose release from conventional pretreatment and subsequent enzymatic hydrolysis in the batch tubes. This genotype contained 42. 87 ± 0. 64% glucan, 22. 02 ± 0. 32% xylan, 19. 67 ± 0. 01% lignin, 2. 33 ± 0. 10% ash, 3. 21% water extractives, and 5. 80% ethanol extractives. The average moisture content of Miscanthus x giganteus cv. Illinois was determined to be 7. 37 ± 0. 11% based on 10 tests. The data reported for the 80 Miscanthus genotypes (provided as the Additional file 1: Table S1 and Additional file 2: Table S2) include averages, minimum and maximum contents of glucan, xylan, the total glucan plus xylan as carbohydrates, and lignin. The average compositions of all 80 Miscanthus genotypes were 40. 74% glucan, 21. 01% xylan, 24. 03% lignin, and 2. 83% ash. However, the 80 Miscanthus genotypes showed significant diversity in compositions, with glucan levels ranging from 27. 7% to 48. 6%, xylan from 19. 6% to 27. 1%, lignin from 15. 5% to 27. 8%, and ash from 1. 10% to 7. 37%. Thus, these samples were expected to enable the study of how composition affects sugar release from pretreatment and hydrolysis and aid in the selection of desirable traits to target for improvements. The total glucan and xylan content, which was important to establish the maximum possible ethanol yield, ranged from 48. 6% to 72. 8%. [SEP] Justify:

Output: The text does not specifically mention bioengineered yeast or its application in producing biofuels from sugars. Instead, it focuses on the screening and characterization of Miscanthus genotypes for sugar release and composition. Therefore, it is irrelevant to the claim about bioengineered yeast.


Input: Task: corroborate the claim using the given text. Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: The oleic acid content of soybean seeds was modulated by knocking out GmFAD2-1A and GmFAD2 genes belonging to the fatty acid desaturase (FAD2) family [28]. The loss of function of these genes has paved the way for cultivating soybean genotypes with high oleic acid content. miltiorrhiza, the SmLACs genes of the laccase family, which has 29 family members with high homology, were multiplex silenced by targeting their conserved sequences to reveal their role in the production of medicinal phenolic acid compounds [29]. It has been concluded that SmLACs play a role in lignin formation and phenolic acid biosynthesis in the roots due to decreased expression of target genes and delayed hairy root development, larger and looser xylem cells, low RA and SAB accumulation, and very low lignin content in edited lines compared to wild types. By knocking out six genes (. 2,. 1, BBLe) belonging to the berberine bridge enzyme-like (BBL) family using a single sgRNA, a nicotine-free tobacco variety was developed and the amount of nicotine was reduced [30]. In this way, the use of nicotine-free tobacco by smokers may protect their health. The genes in α- and γ-gliadin gene families were silenced using six sgRNAs, and a less allergenic bread wheat variety containing gluten with fewer immunogenic epitopes, which would be beneficial in the diet of coeliac patients, was obtained [31]. A less allergenic durum wheat variety was produced [32]. The multiplex editing of CM3 and CM16 genes belonging to α-amylase/trypsin inhibitors (ATI) family subunit U form was carried out using seven gRNAs targeting the two genes of interest. The editing of these genes decreased the amount of ATI transcripts. It was reported that this might have happened due to nonsense-mediated mRNA decay. Interestingly, it was noted that ATI 0. 28 pseudogene were activated after knocking out CM3 and CM6 genes. 3 Challenges of in Crop ImprovementDespite its potential benefits, genome editing in crops also faces several challenges. One of the biggest challenges is the regulatory landscape. [SEP] Justify:

Output: The text corroborates the claim by providing specific examples of gene editing techniques used to enhance various traits in crops. It mentions the modulation of oleic acid content in soybean seeds through knocking out specific genes, which can improve the quality of the crop. It also discusses the development of a less allergenic bread wheat variety by silencing certain genes, indicating that gene editing can result in beneficial traits that can potentially enhance crop yields and meet consumer health needs. Overall, the text demonstrates the application of gene editing in improving crop traits, which supports the claim.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: These foods contain the bacteria necessary to begin the fermentation process, but also can contain additional healthy bacteria added to increase the health benefit of the product. A variety of other fermented foods contain healthy bacteria such as kimchi or sauerkraut, kombucha, tempeh, miso, natto, cheese, sour cream, cultured buttermilk, wine, beer, sourdough bread, olives, pickled vegetables, salami, and soy sauce. Tempe, miso, and natto are made from fermented soybeans, whereas kimchi is a fermented cabbage popular in Korea, and kombucha is a fermented sweet tea. When selecting fermented foods, remember they can be high in added salt and sugar, so read the labels. The processing of these products also is important because exposure to high temperatures will kill the healthy bacteria. If you have never tried some of these fermented foods, make a point of stepping out and trying something new. Prebiotics. The bacteria of the gut need to be maintained; thus, they require their own sources of energy and nutrients. The prebiotic concept was developed when researchers realized the health benefit of nondigestible carbohydrates (e. g. , dietary fibers) on the gut. Thus, a probiotic adds healthy bacteria to the gut, whereas a prebiotic provides the energy and nutrition (e. g. , dietary fiber) the bacteria need for growth. However, it is important to remember that although all prebiotics are fiber, not all fibers are prebiotics. To be considered a prebiotic, a fiber must be resistant to absorption, be fermentable in the gut, and provide nourishment to the gut bacteria. These indigestible carbohydrates reach the colon and undergo various degrees of degradation or fermentation by the gut bacteria. Fibers with a higher degree of fermentation produce energy and other byproducts, such as SCFA, which enhance microbial growth and gut health and improve overall immune function (7,8). Thus, the high-fiber foods recommended in the next section, especially those soluble and fermentable fibers, are considered prebiotics. High-fiber foods. Based on national survey data, adults in the consume only half the recommend adequate intake for dietary fiber per day (men = 38 g/d women = 25 g/d) (8). [SEP] Justify:

Output: The text contrasts the claim by highlighting the importance of diverse bacteria in the gut, emphasizing that healthy gut bacteria are necessary for health and that consuming fermented foods adds beneficial bacteria to the gut. It states that prebiotics provide energy for these bacteria, indicating that maintaining a diverse microbial population is essential for gut health. The overall message is that diversity in gut bacteria is beneficial, opposing the idea that a completely sterile gut would be healthier.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: The genotypes with the highest total glucan and xylan content of 48. 6% glucan and 24. 2% xylan also had the highest glucan content and could realize a theoretical ethanol yield of 127 gallons from glucan and xylan per dry ton of feedstock, as calculated by the [38]. The theoretical ethanol yield of Miscanthus x giganteus cv. Illinois was 113 gallons ethanol per dry ton feedstock. Therefore, Miscanthus has excellent potential for high ethanol yields. Batch pretreatment and enzymatic hydrolysisFigure 1 summarizes glucan and xylan sugar yields from batch hydrothermal pretreatment (Stage 1) of Miscanthus x giganteus cv. Illinois in tube reactors at 180°C, 200°C, and 220°C and from subsequent enzymatic hydrolysis of the washed solids (Stage 2) at the conditions noted. Soluble xylan and glucan yields in Stage 1 increased with pretreatment time at 180°C and 200°C to peak values after 35 and 11. 4 minutes, respectively, before dropping with longer times due to xylose degradation becoming more rapid than xylan hydrolysis to xylose. However, the glucan plus xylan based sugar yields in Stages 1 and 2 combined dropped from 69. 7% to 45. 6% as reaction time increased from 4. 6 min to 18. 5 min at 220°C because xylan degradation became very rapid and pronounced in Stage 1. Figure 1Glucan plus xylan yields vs. pretreatment time from hydrothermal pretreatment of Miscanthus x giganteus cv. Illinois. Hydrothermal pretreatments at 180°C, 200°C and 220°C followed by enzymatic hydrolysis with 60 FPU/g(glucan + xylan) at 50°C for 72 hours. Full size image2, glucan plus xylan yields reached peak values of 64. 2 and 61. 9% after 28 and 11. 4 minutes for pretreatment at 180°C and 200°C, respectively, but sugar yields continually dropped with increasing pretreatment times at 220°C for the range of times tested. Sugar yields from enzymatic hydrolysis of pretreated solids were relatively high, ranging from 73. 5 to 93. 1% over the range of pretreatment temperatures tested. [SEP] Justify:

Output: The text primarily discusses the glucan and xylan content from the feedstock Miscanthus x giganteus and its theoretical ethanol yields, but does not specifically mention bioengineered yeast or its ability to produce biofuels. Thus, it is irrelevant to the claim about bioengineered yeast.


Input: Task: corroborate the claim using the given text. Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: , 44, 2664–2682. Liao, S. Qin, X. Luo, L. Han, Y. Wang, X. Usman, B. Nawaz, G. Zhao, N. Liu, Y. & Li, R. (2019). /Cas9-induced mutagenesis of semi-rolled leaf1, 2 confers curled leaf phenotype and drought tolerance by influencing protein expression patterns and ROS scavenging in rice (Oryza sativa L. ). Agronomy, 9, 728. Liu, L. , Zhang, J. , Xu, J. , Li, Y. , Guo, L. , Wang, Z. , Zhang, X. , Zhao, B. , Guo, Y. D. & Zhang, N. (2020). /Cas9 targeted mutagenesis of SlLBD40, a lateral organ boundaries domain transcription factor, enhances drought tolerance in tomato. Plant Sci. , 301,110683. Liu, Q. , Kasuga, M. , Sakuma, Y. , Abe, H. and Miura S. , Yamaguchi-Shinozaki K. & Shinozaki K. (1998). Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought and low temperature responsive gene expression, respectively, in Arabidopsis. Plant Cell, 10, 1391– 1406. Liu, S. , Li, C. , Wang, H. , Wang, S. , Yang, S. , Liu, X. , Yan, J. , Li, B. , Beatty, M. & Zastrow-Hayes, G. (2020). Mapping regulatory variants controlling gene expression in drought response and tolerance in maize. Genome Biol. , 21, 163. Liu, S. , Li, C. , Wang, H. , Wang, S. , Yang, S. , Liu, X. , Yan, J. , Li, B. , Beatty, M. , Zastrow-Hayes, G. & et al. (2020). Mapping regulatory variants controlling gene expression in drought response and tolerance in maize. Genome Biol. , 21,163. Ma, X. , Zhu, Q. [SEP] Justify:

Output: The text provides examples of gene editing (specifically Cas9-induced mutagenesis) being used to enhance traits such as drought tolerance in various crops like rice and tomato. By referencing the enhancement of traits involved in plant growth, it suggests that gene editing techniques can directly improve crop yields.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Dietary fiber recommendations can be normalized based on energy intake, so that 14 g of fiber per 1000 kcals will meet the recommended intake for most adults consuming adequate energy. Dietary fibers are primarily made up of a large class of nondigestible carbohydrates, which can be further subdivided by their characteristics such as solubility, fermentability, and viscosity (9). Foods most beneficial to the gut bacteria are those that contain fibers that are soluble (oats, barley, beans, peas, and fruits like apple and citrus) and fermentable (fruits and vegetables). Thus, foods such as whole grains, fruits, and vegetables, and beans and legumes, contain a variety of fibers in varying quantities. To meet the dietary fiber recommendations, an individual needs to replace low-fiber foods with those higher in fiber. This means consuming whole fruits and vegetables instead of fruit and vegetable juices, selecting whole grains (e. g. , brown rice, quinoa, faro, oats, barley, wheat) instead of lower fiber options like white bread, rice, and pasta and eating more nuts, beans, and legumes. 1 for a list of high-fiber food options. Select breads, pasta, cereals, and crackers that provide at least 2 to 3 g of fiber per serving. Learning to read food labels will help you identify those foods higher in fiber. Eat beans and legumes more frequently because they provide the highest amount of fiber per serving. TABLE 1: Common High-Foods to limit: There are a number of foods that individuals will say they “like,” but the foods do not “like” them. These foods seem to bother some people and cause GI distress. For example, individuals may complain of chocolate, citrus foods, spicy foods, coffee, or alcohol causing GI distress. For others, foods or beverages containing high fructose, such as sweetened beverages and sugar-free candy or gums can cause gas due to poor fructose absorption. Carbonated drinks can cause bloating and gas. Finally, highly processed foods that are frequently high in sugar and/or fat provide little benefit to the gut microbiota. Adding more nutrient- and fiber-dense foods to the diet will improve gut health. To meet the dietary fiber recommendations, an individual needs to replace low-fiber foods with those higher in fiber. [SEP] Justify:

Output: The text contrasts the claim by emphasizing the importance of dietary fiber and diverse foods in promoting gut bacteria health. It specifically mentions that 'adding more nutrient- and fiber-dense foods to the diet will improve gut health,' indicating that a diversity of food which supports various gut bacteria is healthier than a completely sterile gut.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Total glucan plus xylan yields from pretreatment (Stage 1) at 180°C combined with enzymatic hydrolysis (Stage 2) increased from 79. 5% to 86. 9% as pretreatment time was increased from 17. 5 min to 35 min and then dropped slowly with extended pretreatment time. At 200°C, overall glucan plus xylan yields from Stage 1 plus Stage 2 increased from 78. 0% to 85. 9% as pretreatment time increased from 7. 2 min to 11. 4 min and then dropped. Increasing the temperature to 220°C resulted in a maximum overall glucan plus xylan yield of 69. 7% from the two stages combined at the shortest sampling time of 4. 6 min with a rapid drop after that, suggesting that the rapid degradation of xylose resulted in overall sugar loss at 220°C. Thus, similar high total sugar yields of about 85% were obtained at 180°C and 200°C for Miscanthus x giganteus cv. Illinois pretreatment followed by enzymatic hydrolysis, while sampling times were not short enough to capture high sugar yields at 220°C. Because such short times would be impractical to implement commercially, additional experiments were not run to determine if yields would improve at shorter times. Thus, pretreatment times to achieve the highest overall glucan plus xylan yields from the two stages for Miscanthus x giganteus cv. Illinois were 35 min at 180°C and 11. 4 min at 200°C, corresponding to similar pretreatment severities (logR0) [39] of 3. 9 and 4. 0, respectively. The maximum glucan plus xylan yields for hydrothermal pretreatment followed by enzymatic hydrolysis were very similar to those reported in the literature for AFEX and ethanol organosolv pretreatments of Miscanthus, as shown in Table 1. In addition, as a result of the higher carbohydrate content of Miscanthus compared to other biomass listed in Table 1, the overall mass sugar yield of 55. 7 g glucan plus xylan per 100 g of dry Miscanthus x giganteus cv. Illinois was greater than mass yields from application of hydrothermal pretreatment to other feedstocks listed in Table 2, such as 40. 8 g glucan + xylan per 100 g dry corn stover [24] and 52. [SEP] Justify:

Output: The text discusses the yields of glucan and xylan from pretreatment and enzymatic hydrolysis of Miscanthus x giganteus but does not address bioengineered yeast or its capability to produce biofuels. Therefore, it is irrelevant to the claim about yeast and biofuel production.


Input: Task: corroborate the claim using the given text. Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: Nunez-Munoz, L. , Vargas-Hernandez, B. , Hinojosa-Moya, J. , Ruiz-Medrano, R. & Xoconostle-Cazares, B. (2021). Plant drought tolerance provided through genome editing of the trehalase gene. Plant Signal. Behav. 16, 1877005. Ogata, T. , Ishizaki, T. , Fujita, M. & Fujita, Y. (2020). /Cas9-targeted mutagenesis of OsERA1 confers enhanced responses to abscisic acid and drought stress and increased primary root growth under nonstressed conditions in rice. 15, 0243376. Orvar, B. L, Sangwan, V. , Omann, F. & Dhindsa, R. S. (2000). Early steps in cold sensing by plant cells: the role of actin cytoskeleton and membrane fluidity. Journal, 23, 785–794. Osakabe, Y. & Osakabe, K. (2015). Genome editing with engineered nucleases in plants. Plant and Cell Physiology, 56 (3), 389–400. Osakabe, Y. & Osakabe, K. (2017). to in Plants. in Elsevier: Amsterdam, The Netherlands, 149, 99–109. Osakabe, Y. , Watanabe, T. , Sugano, S. S. , Ueta, R. , Ishihara, R. , Shinozaki, K. & et al. (2016). Optimization ofCas9 genome editing to modify abiotic stress responses in plants. Sci. Rep. 6, 26685. doi: 10. 1038/srep26685. Park, J. J. , Dempewolf, E. , Zhang, W. & Wang, Z. Y. (2017). RNA-guided transcriptional activation viadCas9 mimics overexpression phenotypes in Arabidopsis. 12, e0179410. Piatek, A. , Ali, Z. , Baazim, H. , Li, L. , Abulfaraj, A. & Al-Shareef, S. (2015). RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors. [SEP] Justify:

Output: The text corroborates the claim by providing examples of research that highlights the use of genome editing to enhance plant traits such as drought tolerance and stress response, which are crucial for improving crop yields. For instance, it mentions genome editing of the trehalase gene to provide drought tolerance, which directly relates to enhancing growth traits that can lead to better crop performance.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: This means consuming whole fruits and vegetables instead of fruit and vegetable juices, selecting whole grains (e. g. , brown rice, quinoa, faro, oats, barley, wheat) instead of lower fiber options like white bread, rice, and pasta and eating more nuts, beans, and legumes. are many other reasons an individual may have GI distress. Some foods and beverages, such as alcohol, caffeine, or compounds in these products, can irritate the gut causing GI distress or increasing esophageal reflux. If the frequency of reflux is high, the condition is called gastroesophageal reflex disease (GERD) (Table 2). GI distress may be due to a particular food that is not well tolerated because of the inability to digest a specific food component (e. g. , gluten or lactose intolerance) or having an allergy to a food component (e. g. , allergy to milk protein). There can be more severe gut issues, such as irritable bowel syndrome (IBS) or Celiac disease. Any of these issues can disrupt health and derail an athlete’s ability to exercise and train optimally. Table 2 lists some of these GI issues, their definitions, diet and lifestyle approaches for management, and links to more information. Until these gut issues are identified and appropriate dietary or medical measures taken, being physically active can be difficult. Many of these issues require seeking medical help and visiting a dietitian for dietary advice to help relieve or improve symptoms. TABLE 2: GI Issues and the Dietary or for gut is the largest immune organ in the body. Thus, part of staying healthy is providing the gut with the energy and nutrients needed. Keep the gut healthy by consuming fermented foods that contain healthy bacteria (probiotics), such as yogurt, kefir or fermented soy products, and eating a diet high in unprocessed, high-fiber foods (prebiotics) (whole fruits, vegetables, grains, and legumes). These foods provide indigestible carbohydrates that help maintain the gut bacteria and produce byproducts that help keep the body healthy. now know that the gut is our largest immune organ. Thus, keeping the gut healthy will help keep us healthy and resistant to illness and disease. Diet plays a major role in maintaining a healthy gut by providing both prebiotics and probiotics. [SEP] Justify:

Output: The text contrasts the claim by emphasizing the importance of maintaining gut health through a diverse diet that includes fermented foods and high-fiber options, which support healthy gut bacteria. It specifically notes that the gut is the largest immune organ and that consuming diverse, unprocessed foods leads to a healthier gut environment. This indicates that a completely sterile gut, lacking in diverse bacteria, would be counterproductive to health.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: 6 g glucan + xylan per 100 g dry wheat straw [26]. Although pretreatment temperatures and solids loadings were different for these five feedstocks, the log of the pretreatment severities at the highest overall glucan and xylan yields were in the range from about 3. 9 to 4. 0 for Miscanthus x giganteus cv. Illinois, corn stover, and poplar. However, both corn stover and poplar studies used higher solids loadings and achieved higher xylan yields but lower glucan yields [24, 40]. This suggests that corn stover and poplar require more severe hydrothermal pretreatment to disrupt the cellulose structure enough to gain higher glucan yields in Stage 2. Wheat straw was reported to require more severe pretreatment (logR0 of 4. 15) to achieve the highest overall glucan and xylan yield, while the highest glucan yield of 91% (mainly in Stage 2) was obtained with relatively low enzyme loading of 15 FPU Celluclast plus 15 IU Novozym 188 per gram dry substrate (about 39. 7 FPU cellulase per gram glucan) [25]. Table 2 Comparison of Miscanthus and other selected biomass feedstocks Full size tableHigh throughput pretreatment and co-hydrolysis (HTPH) of system was applied to 80 Miscanthus genotypes with different characteristics to rapidly measure overall glucan and xylan yields from hydrothermal pretreatment at 180°C for 0, 17. 5, and 35 min followed by enzymatic hydrolysis of the entire pretreated slurry (180°C for 35 min is the optimal condition based on our previous batch tube experiments, data unpublished). A scatter matrix S(x) of compositions and HTPH sugar yields (mass yields, g/100 g raw Miscanthus) for the 80 Miscanthus genotypes is presented in Additional file 3: Figure S1 (selected data with R^2 > 0. 5 are shown in Figure 2) X = (x1x2 x10)’ to provide a statistical estimate of the covariance matrix of the multivariate normal distribution and allow determination of whether the variables are correlated and whether the correlation is positive or negative. The data in Figure 2 and Additional file 3: Figure S1 were normalized by the average values of 80 Miscanthus genotypes. [SEP] Justify:

Output: The text discusses the pretreatment and enzymatic hydrolysis of biomass feedstocks, particularly Miscanthus and other materials, to yield glucan and xylan but does not address the production of biofuels using bioengineered yeast specifically. Therefore, it is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: Plant Biotechnology, 13, 578–589. Que, Z. , Lu, Q. , Liu, T. , Li, S. , Zou, J. & Chen, G. (2020). The rice annexin gene OsAnn5 is a positive regulator of cold stress tolerance at the seedling stage. Res. Sq. ; in press. Rath, D. , Amlinger, L. , Rath, A. & Lundgren, M. (2015). -Cas immune system: biology, mechanisms and applications, Biochimie, 117, 119–128. Roca. , Lourenco-de Almeida-Engler, J. & Grossi-de-Sa, M. F. (2019). Improved drought stress tolerance in Arabidopsis bydCas9 fusion with a Transferase. Sci. Rep. , 9, 8080. Ruelland, E. , Vaultier, M. N. , Zachowski, A. & Hurry V. (2009). Cold signalling and cold acclimation in plants. Advances in Botanical Research. , 49, 35–150. . & Singh, N. (2011). Engineering cold stress tolerance in crop plants. Curr. Genom. , 12, 30. Shakesphere, S. , Sivaji, M. & Sathish raj, R. (2022). Promises and Potentiality of in Crop Improvement. Vijyan Varta, 3 (7), 80-86. Shen, C. , Que, Z. , Xia, Y. , Tang, N. , Li, D. , He, R. & Cao, M. (2017). Knock out of the annexin gene OsAnn3 viaCas9-mediated genome editing decreased cold tolerance in rice. J. Plant Biol. , 60, 539–547. Shi, J. , Gao, H. , Wang, H. ,. , Hakimi, S. M. , Mo, H. , & Habben, J. E. (2017). ARGOS 8 variants generated by -Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnol. J. , 15, 207–216. Siddiqui, K. S. & Cavicchioli, R. (2006). [SEP] Justify:

Output: The text describes various studies and breakthroughs in plant biotechnology that demonstrate how gene editing can enhance traits such as cold stress tolerance and drought tolerance in crops. For instance, it mentions that 'ARGOS 8 variants generated by -Cas9 improve maize grain yield under field drought stress conditions.' This explicitly supports the claim, highlighting that gene editing technologies have the potential to improve crop yields by enhancing specific growth traits.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Dietary steps to a healthy gut include consuming whole grains, fruits, and vegetables and beans/legumes, which are high in dietary fiber and are used by the gut bacteria for energy and nutrients. The gut bacteria also produce byproducts important to our health. The inclusion of fermented foods in the diet will help maintain the concentration of healthy bacteria in the gut. 1. . : a preliminary strategy to reduce gastrointestinal distress in athletes. Sports Exerc. 2018;50(1):116–23. doi: 10. 1249/mss. 0000000000001419. : 00005768-201801000-00015. | Text | PubMed | CrossRef 2. Prevalence of illness, poor mental health and sleep quality and low energy availability prior to the 2016 Games. Sports Med. 2018;52(1):47–53. doi: 10. 1136/bjsports-2017-098208. | Text | PubMed | CrossRef 3. . Nutrition strategies for gut health and immune function—what do we know and what are the gaps? Exchange. 2017;28(179):1–5. 4. Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474(11):1823–36. doi: 10. 1042/BCJ20160510. : 28512250. | PubMed | CrossRef 5. Organization. Probiotics in food. Health and nutritional properties and guidelines for evaluation. 2001. 6. Health benefits of fermented foods: microbiota and beyond. Biotechnol. 2017;44:94–102. doi: | PubMed | CrossRef 7. Dietary prebiotics: current status and new definition. . 2010;7(1):1–19. 8. Sweat W, Manore MM. Dietary fiber: simple steps for managing weight and improving health. . 2015;19(1):9–16. | Text | CrossRef 9. Institute of Medicine (IOM); Food and Nutrition Board. Intakes for Energy, Carbohydrate, Fiber, Fat, Fatty acids, Cholesterol, Protein, and Amino Acids. Washington (D. C. ): Academies Press; 2005. Keywords:Gut Microbiota; Prebiotic; Probiotic; Dietary Fiber; © 2018 of Sports Medicine. View full 2018. [SEP] Justify:

Output: The text contrasts the claim by emphasizing the importance of dietary diversity and gut bacteria for health. It suggests that consuming whole grains, fruits, vegetables, and fermented foods is beneficial because these foods provide nutrients and energy to gut bacteria, which are crucial for maintaining a healthy microbiota. This indicates that having a diverse microbiota is important for gut health, which opposes the idea that a completely sterile gut is healthier.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: The 10 components in the scatter matrix (4 compositional variables plus 6 sugar yields for three different pretreatment times followed by co-enzymatic hydrolysis) were assumed independent so that the regular covariance matrix would be a diagonal matrix. The diagonal in Additional file 3: Figure S1 was filled with the variables (xi) of the scatter matrix for each column, and the results and discussion focuses on the lower left part in Additional file 3: Figure S1. Additional file 3: Figure S1 included all the scatter plots with ellipse matrix (xi’) and linear fit applied at the 95% confidence level with the adjusted R-square between any of ten variables in order to reveal correlations. For example, the first column (x1) (K-lignin column) showed the scatter plots of other nine variables (xi, i = 2-9) as listed in each row in the diagonal versus K-lignin content with ellipse matrix and linear fit with the adjusted R-square to investigate the correlations. No obvious correlation was found between sugar yields from enzymatic hydrolysis of raw Miscanthus and lignin contents, but a negative correlation was observed between sugar yields and lignin contents following hydrothermal pretreatment for 17. 5 and 35 min, consistent with recently reported findings for poplar [28]. Figure 2Normalized scatter matrix of 80 Miscanthus HTPH glucan and xylan mass yields. HTPH glucan and xylan mass yields (g/100 g dw raw Miscanthus) from hydrothermal pretreatment at 180°C in 0, 17. 5 min, and 35 min. Full size imageIn the second left column (glucan content column) in Additional file 3: Figure S1, a positive correlation was found between glucan and xylan contents (the third row) in raw Miscanthus, suggesting a structural correlation between them. A negative correlation was observed between glucan contents and sugar yields for enzymatic hydrolysis without pretreatment, suggesting cellulose in raw biomass was a strong contributor to recalcitrance [15, 19, 25]. However, overall mass sugar yields (g sugar/100 g biomass) following pretreatments at 17. 5 and 35 min in the HTPH system were positively correlated to glucan content, which simply emphasized that high glucan content was one of the vital criteria for cellulosic feedstocks. [SEP] Justify:

Output: The text discusses various correlations between sugar yields and lignin contents in Miscanthus, as well as the contributions of glucan and xylan to sugar yields, but it does not directly address bioengineered yeast or support the claim regarding its capability to produce biofuels. Thus, the information is not relevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell, 6, 251– 264. Yang, W. , Chen, S. , Cheng, Y. , Zhang, N. , Ma, Y. ,Wang, W. , Tian, H. , Li, Y. , Hussain, S. , & Wang, S. (2020). Cell wall/vacuolar inhibitor of fructosidase 1 regulates ABA response and salt tolerance in Arabidopsis. Plant Signal. Behav. , 15,1744293. Yu, J. , Ge, H. , Wang, X. , Tang, R. , Wang, Y. , Zhao, F. , Lan, W. , Luan S. and Yang, L. (2017). Overexpression of pyrabactin resistance-like abscisic acid receptors enhances drought, osmotic, and cold tolerance in transgenic poplars. Sci. , 8, 1752. 3389/fpls. 2017. 01752 Yue, E. Cao, H. & Liu, B. (2020). OsmiR535, a potential genetic editing target for drought and salinity stress tolerance in Oryza sativa. Plants, 9, 1337. Yue, Y. , Zhang, M. , Zhang, J. , Duan, L. & Li, Z. (2012). SOS1 gene overexpression increased salt tolerance in transgenic tobacco by maintaining a higher K+/Na+ ratio. J. Plant Physiol. , 169, 255–261. Zargar, S. M. , Nagar, P. , Deshmukh, R. , Nazir, M. , and Rakwal, R. (2017). Aquaporins as potential drought tolerance inducing proteins: Towards instigating stress tolerance. J. Proteom. , 169, 233–238. Zeng, Y. , Wen, J. , Zhao, W. , Wang, Q. and Huang, W. (2020). Rational improvement of rice yield and cold tolerance by editing the three genes OsPIN5b, GS3, and OsMYB30 with the –Cas9 system. Front. Plant Sci. , 10, 1663. [SEP] Justify:

Output: The text supports the claim by referencing genetic editing in plants, specifically through the expression of genes that enhance drought tolerance and cold tolerance. For example, it mentions the 'rational improvement of rice yield and cold tolerance by editing the three genes OsPIN5b, GS3, and OsMYB30 with the –Cas9 system.' This indicates that gene editing can directly affect crop yields, corroborating the claim about enhancing growth traits.


Input: Task: pass the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: genomics is probably the splitting of the database by order. This might make fast. genomics less effective for selfish genetic elements that can move between distantly related bacteria. Still, the main (genus-level) database can quickly indicate which orders frequently contain the protein of interest. To ensure that presence/absence analyses give reliable results, fast. genomics includes only high-quality genomes; but this means that much of the diversity visible in metagenomes is missing from fast. genomics. For instance, of the 20,739 genera in GTDB, only about a third (6,377) are included in fast. genomics. Including low-quality metagenome-assembled genomes might allow analysts to identify more conserved gene neighborhoods. Still, the fast. genomics main database includes 1,418 genomes from uncultivated genera, of which 1,368 are metagenome-assembled genomes. And most prokaryotic proteins do have homologs in the main database: for instance, for random proteins from its database, fast. genomics finds at least one potential ortholog (at least 30% identity and 50% coverage) for 94% of queries. Fast. genomics does not support iterative searches to find distant homologs (homologs that are too distant to be found using pairwise methods such as BLAST). In this case, we recommend using the HMMer web server [34] for iterated searches against reference proteomes, or using a tool such as AnnoTree [15] for predefined families. Comparisons to other comparative genomics websites As far as we know, the other fast websites for comparative genomics of bacteria and archaea all rely on pre-computed orthology groups, such as eggNOG. Above, we assessed the accuracy of ortholog groups for finding homologs. Here, we give an example of how tools that rely on ortholog groups can fail. Consider the TonB-dependent transporter BT2172. We previously proposed, based partly on comparative genomics evidence, that this transporter functions together with another protein, BT2173, belonging to the uncharacterized family DUF4249 [35]. Fast. genomics shows that these proteins form a conserved operon, and that this subfamily of TonB-dependent transporters is almost always encoded next to a DUF4249 protein, across dozens of genera. [SEP] Justify:

Output: The text is irrelevant to the claim, as it discusses topics related to genomics and comparative genomics of bacteria without addressing the health implications of gut sterility versus bacterial diversity. No part of the text provides information supporting, contrasting, or contextualizing the claim about gut health.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Correlations between xylan content and other compositions and sugar yields (the third left column (xylan content column) in Additional file 3: Figure S1) were similar to correlations found for glucan content, except that sugar yields from enzymatic hydrolysis of raw Miscanthus were less negatively correlated to xylan content, undoubtedly due to the lower recalcitrance of xylan than glucan. Correlations between ash content and other compositions and sugar yields are shown in the fourth left column (ash content column) in Additional file 3: Figure S1. Although a negative correlation was found between K-lignin content and ash content in raw Miscanthus, glucan content and xylan content were not obviously related to ash content. This indicated that the small amount of ash did not appear to affect structural carbohydrates content. Sugar yields did not show any significant correlation to ash content for pretreatment times of 0, 17. 5, and 35 min followed by enzymatic hydrolysis. Besides the correlations of the composition variables and sugar yields, glucan and xylan yields for three different pretreatment times showed interesting and most significant correlations (Figure 2). The strongest positive correlations were found between HTPH glucan and xylan yields with R^2 values of 0. 5772, 0. 7888, and 0. 7959 for the pretreatments at 0 min, 17. 5 min and 35 min, respectively (Figures 2a, 2b, and 2c). These results suggested a strong correlation of glucan and xylan yield for the HTPH system and followed the sugar yield patterns observed for application of HTPH to poplar [28]. However, the glucan or xylan yields without pretreatment did not show correlations (with R^2 less to 0. 05) to those glucan and xylan yields for the pretreatment at 17. 5 min and 35 min ( Additional file 3: Figure S1). These results suggested that sugar yields from direct enzymatic hydrolysis of raw lignocellulosic biomass without pretreatment were not suitable predictors of sugar yields from enzymatic hydrolysis of pretreated biomass. However, the glucan yields for pretreatment at 17. 5 min showed a very strong positive correlation (with R^2 of 0. 757) to glucan yields for pretreatment at 35 min (Figure 2d). The correlation (with R^2 of 0. [SEP] Justify:

Output: The text discusses various correlations between xylan, glucan content, and sugar yields in the context of enzymatic hydrolysis of lignocellulosic biomass, but it does not mention bioengineered yeast or their capacity to produce biofuels. Therefore, the text is irrelevant to the claim about bioengineered yeast and their role in biofuel production.


Input: Task: corroborate the claim using the given text. Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: Zhang, A. , Liu, Y. , Wang, F. , Li, T. , Chen, Z. , Kong, D. Bi, J. , Zhang, F. , Luo, X. and Wang, J. (2019). Enhanced rice salinity tolerance viaCas9-targeted mutagenesis of the OsRR22 gene. Mol. Breed. , 39, 47. Zhang, A. , Liu, Y. , Wang, F. , Li, T. , Chen, Z. , Kong, D. , Bi, J. , Zhang, F. , Luo, X. , Wang, J. , et al. (2019). Enhanced rice salinity tolerance viaCas9-targeted mutagenesis of the OsRR22 gene. Mol. Breed. , 39, 47. Zhang, H. Zhang, J. Wei, P. Zhang, B. Gou, F. Feng, Z. Mao, Y. Yang, L. Zhang, H. Xu, N. et al. (2014). /Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol. J. 12, 797–807. Zhang, X. , and Thomashow M. F. (2004). Freezing sensitive tomato has a functional CBF cold response pathway, but a CBF regulon that differs from that of freezing tolerant Arabidopsis. Journal, 39, 905– 919. Zhao, C. Z. , Zhang, Z. J, Xie, S. J, Si, T. , Li, Y. Y. & Zhu, J. K. (2016). Mutational evidence for the critical role of CBF transcription factors in cold acclimation in Arabidopsis. Plant Physiology. , 171, 2744– 2759. Zhao, Y. , Zhang, C. , Liu,W. , Gao,W. , Liu, C. , Song, G. , Li, W. X. , Mao, L. , Chen, B. & Xu, Y. (2016). An alternative strategy for targeted gene replacement in plants using a dual-sgRNA/Cas9 design. Sci. Rep. , 6, 23890. Zhu, L. , Chen, S. , Alvarez, S. [SEP] Justify:

Output: The text provides multiple scholarly references that illustrate the application of gene editing techniques, specifically Cas9-targeted mutagenesis, to enhance traits such as salt tolerance in rice and suggest that such modifications can lead to improved crop resilience and potentially yield. This supports the claim that gene editing can enhance growth traits, thereby likely improving crop yields.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Figures AbstractThe human GI tract is a complex and still poorly understood environment, inhabited by one of the densest microbial communities on earth. The gut microbiota is shaped by millennia of evolution to co-exist with the host in commensal or symbiotic relationships. Members of the gut microbiota perform specific molecular functions important in the human gut environment. This can be illustrated by the presence of a highly expanded repertoire of proteins involved in carbohydrate metabolism, in phase with the large diversity of polysaccharides originating from the diet or from the host itself that can be encountered in this environment. In order to identify other bacterial functions that are important in the human gut environment, we investigated the distribution of functional groups of proteins in a group of human gut bacteria and their close non-gut relatives. Complementary to earlier global comparisons between different ecosystems, this approach should allow a closer focus on a group of functions directly related to the gut environment while avoiding functions related to taxonomically divergent microbiota composition, which may or may not be relevant for gut homeostasis. We identified several functions that are overrepresented in the human gut bacteria which had not been recognized in a global approach. The observed under-representation of certain other functions may be equally important for gut homeostasis. Together, these analyses provide us with new information about this environment so critical to our health and well-being. Citation: Dobrijevic D, Abraham A-L, Jamet A, Maguin E, van de (2016) of Bacteria from the Non-Reveals the Importance of Conjugation and a Paucity of Motility and in the Gut Environment. 11(7): e0159030. Francesco Cappello, University of : April 15, 2016; Accepted: June 24, 2016; Published: July 14, 2016Copyright: © 2016 Dobrijevic et al. This is an open access 3. 3 million human gut microbial genes has been established in 2010 [1], and more recently an extensive update of this catalogue was published, combining data from different sources and containing nearly 10 million genes [2]. Apart from metagenomics projects, data derive from sequencing efforts targeting the genomes of specific bacteria from the human gut. So far, sequences of 778 gut-associated bacterial genomes are available through the Project [3], thus giving access to an independent complementary line of investigation of the human gut microbiota. [SEP] Justify:

Output: The text contrasts the claim by discussing the complex and diverse microbial communities that inhabit the human GI tract, highlighting the importance of a diverse gut microbiota for health and homeostasis. It emphasizes the co-existence of gut bacteria and their roles in essential functions, which suggests that a sterile gut would lack these critical interactions necessary for health.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: 5907) between xylan yields for 17. 5 min pretreatment and glucan yields for 35 min pretreatment (Figure 2f) was not as strong as that between glucan yields (Figure 2d) although positive correlations were found between xylan yields for 17. 5 min pretreatment and glucan for 35 min pretreatment (R^2 of 0. 5907, Figure 2f), and between xylan yields for 17. 5 min and for 35 min pretreatment (R^2 of 0. 5794, Figure 2g). Figures 3 and 4 show overall glucan yields (Stage 1+ Stage 2) versus original glucan content and overall xylan yields (Stage 1+ Stage 2) versus original xylan content for each Miscanthus sample to further investigate impacts of carbohydrate contents on glucan and xylan yields. The percent theoretical glucan yields based on original glucan content in raw Miscanthus (g/g original glucan) in Figure 3 ranged from 3. 1% to 26. 4% with averages of 13. 3% for no pretreatment, from 36. 8% to 71. 3% with an average of 52. 9% for 17. 5 min pretreatment, and from 48. 6% to 90. 6% with an average of 69. 3% for 35 min pretreatment. These HTPH results showed that theoretical glucan yields generally decreased as glucan content increased in raw Miscanthus. However, glucan mass yields (g/100 g dry weight Miscanthus), calculated as a percent of the total dry weight of raw Miscanthus tended to increase with glucan content of raw Miscanthus (in Additional file 3: Figure S1, glucan yields in column A7 for a 17. 5 min pretreatment and in column A9 for a 35 min pretreatment). In other words, as glucan content in raw Miscanthus increased, it became more difficult to degrade glucan into glucose through pretreatment and enzymatic hydrolysis by HTPH under the experimental conditions applied even though the quantity of released glucose generally increased due to the greater amount. This negative effect became more significant when the pretreatment time was increased from 0 to 17. 5 min and further to 35 min. The mechanism can be a combination of various factors and requires further investigation. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses glucan and xylan yields from Miscanthus and their relationship with pretreatment times. It does not mention bioengineered yeast or its ability to produce biofuels, thereby failing to support or contradict the claim.


Input: Task: corroborate the claim using the given text. Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: June 6, 2023 Cut of the crop: High-yields of non-browning eggplant via genome editing Eggplant is cultivated globally – but its production is fraught with issues affecting the crop’s overall yield and post-harvest properties. The fruit can be less appealing when damaged or cut due to the enzymatic browning of tissues. Cultivating high-yielding yet non-browning eggplants is an area of ongoing research at the for and Biotechnology, UAE. The researchers have improved the fruit’s properties by genome editing a key enzyme, polyphenol oxidase. As a result of tweaking a single gene, eggplants produce more fruit that is also non-browning. Eggplant is a popular edible crop. Despite its vast global production, significant eggplant yield loss can occur due to attacks by disease-causing pathogens or adverse weather conditions. As well as selecting plants for enhanced stress resistance, fruit quality and nutritive value of the crop are also important characteristics for eggplant breeders. Recent technological advances are making it possible to quickly breed bountiful and desirable crops. Kottackal and colleagues at the for and Biotechnology (KCGEB) are making strides in this area. A leading institute in the Emirates, the KCGEB is under Court and affiliated with the UAE University. Here, researchers have recently developed a new genome edited eggplant variety with superior quality and high yields. Non-edited eggplant Eggplant: what’s in a name? Also known as aubergine, eggplant is a fruit crop and member of the Solanaceae family. The purple colouration of eggplant is caused by the compound anthocyanin, a powerful antioxidant that can remove harmful free radicals from the body. It’s also high in fibre, making it good for digestion. Eggplant breeding across the world aims to generate varieties that can better resist or tolerate different pests, pathogens, and environmental stresses, as well as improve post-harvest organoleptic qualities (its sensory appeal – eg, taste, texture, and smell). Location, oxidation, discolouration! One unappealing property of eggplant is its susceptibility to browning when cut or damaged, affecting its flavour and nutritional properties. These undesirable traits also reduce the fruit’s post-harvest value. [SEP] Justify:

Output: The text corroborates the claim by providing evidence that genome editing has led to the development of high-yielding, non-browning eggplants. It states that researchers have used genome editing to tweak a single gene, which has resulted in eggplants that produce more fruit and possess desirable qualities. This directly supports the claim that gene editing can enhance growth traits to improve crop yields.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: More than 90% of gut bacteria are members of only two phyla, Bacteroidetes and Firmicutes, the relative proportions of which exhibit a continuous gradient within the human population [4, 5]. Within the borders of these phyla the microbiota composition is highly individual-specific, showing high variability at the species and strain levels. In contrast to this taxonomic diversity however, functional profiles are far less variable across healthy individuals [1, 6, 7], confirming the existence of a well-balanced host-microbial symbiosis. The results of functional analyses of the human gut metagenome showed that the proteome of the human gut microbiota is enriched in proteins involved in carbohydrate metabolism, energy metabolism and storage, generation of short-chain fatty acids, amino acids metabolism, biosynthesis of secondary metabolites and metabolism of cofactors and vitamins [1, 4, 6–8]. In particular, the human gut microbiota provides a broad and diverse array of carbohydrate-active enzymes, many of which are not present in the human glycobiome [9]. Similar observations were made during genome analysis of some of the human gut-associated bacteria, such as Bacteroides fragilis, Bacteriodes thetaiotaomicron or Methanobrevibacter smithii [10, 11]. Additionally, many yet uncharacterized or completely novel protein families were shown to be specific to the human gut, suggesting that many unknown and uncharacterized processes are yet to be discovered in this environment [12]. The formentioned catalogue containing 3. 3 million non-redundant microbial genes from the intestinal tract of 124 individuals [1] provided an opportunity to differentiate bacterial functions necessary for a bacterium to thrive in the gut environment, and therefore present in every gut bacterial species, from those involved in the homeostasis of the whole gut ecosystem, encoded across many bacterial species. Qin et al. referred to these functions as (bacterial) "minimal gut genome" and "minimal gut metagenome", respectively [1]. The minimal gut metagenome includes functions known to be important to the host—bacterial interaction, such as the capacities to metabolize complex polysaccharides and to synthesize short-chain fatty acids, indispensable amino acids and vitamins. It also includes a considerable fraction of functions (~45%) that were present in less than 10% of earlier sequenced, mainly non-gut, bacterial genomes. [SEP] Justify:

Output: The text contrasts the claim by emphasizing the importance of gut microbiota diversity and the functional role of bacteria in human health. It discusses how a 'well-balanced host-microbial symbiosis' exists and outlines various 'bacterial functions necessary for a bacterium to thrive in the gut environment,' which are crucial for metabolism and overall health. This indicates that a completely sterile gut would likely lack these essential functions provided by diverse gut bacteria.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: A plausible explanation is inhibition of cellulases by higher concentrations of sugars released during HTPH from Miscanthus genotypes that contained higher amounts of glucan and/or xylan, especially when higher xylan yields were obtained as the pretreatment time was increased. It was reported recently that not only glucose but also xylose and particularly oligomeric xylan are strong inhibitors of cellulases [41, 42]. Another possible mechanism would be greater amounts of cellulose presenting a more structured obstacle to enzyme action. Figure 3HTPH glucan yields 80 Miscanthus vs. glucan contents in raw Miscanthus at 3 different pretreatment times. HTPH glucan yields on basis of original glucan content in raw Miscanthus of 80 Miscanthus. Full size imageFigure 4HTPH Xylan yields of 80 Miscanthus vs. glucan contents in raw Miscanthus at 3 different pretreatment times. HTPH xylan yields on basis of original glucan content in raw Miscanthus of 80 Miscanthus. Full size imageThe percent of theoretical xylan yields ranged from 3. 3% to 16. 2% with an average of 9. 3% for no pretreatment, from 45. 5% to 79. 1% with an average of 62. 6% for 17. 5 min pretreatment, and from 54. 7% to 86. 1% with an average of 72. 9% for 35 min pretreatment (Figure 4). Xylan content in raw Miscanthus did not significantly affect xylan yields calculated on basis of the original xylan content of raw Miscanthus. Xylan content had more negative effects on theoretical xylan yields for unpretreated Miscanthus (0 min) than those for 17. 5 min and 35 min pretreatments at 180°C. With hydrothermal pretreatment at 180°C for 17. 5 min and 35 min, HTPH results for 80 Miscanthus genotypes indicated that pretreatment conditions had a greater impact on xylan hydrolysis than xylan content in raw Miscanthus genotypes, in contrast to the findings for glucan yields in Figure 3. The negative impacts of lignin on glucan and xylan mass yields (g/100 g raw Miscanthus) are shown in Additional file 3: Figure S1. [SEP] Justify:

Output: The text does not address the claim about bioengineered yeast or its capabilities. Instead, it focuses on the inhibition of cellulases by sugars released during hydrothermal pretreatment from Miscanthus genotypes, detailing the impacts of various factors on glucan and xylan yields. This information is unrelated to the design or production capabilities of bioengineered yeast for biofuels.


Input: Task: corroborate the claim using the given text. Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: Instead, they are carried through to the next generation – resulting in an altered trait. Mutations give rise to variations in any species, resulting in different colours, behaviour, and survival of its progeny. Plant breeders have more recently used chemicals and irradiation techniques to induce random mutations in seeds that alter the function of specific proteins, therefore, altering traits. By altering genes in different plant varieties, this form of plant breeding has given rise to the vast selection of crops with desirable characteristics that we consume today. However, this method of plant breeding is a long process, requiring at least six generations of selectively bred plants before the final variety with desirable characteristics is produced. Moreover, the mutations can be randomly introduced throughout the plant. Precision breeding using genome editing Now, new tools have been identified over the last decade that dramatically reduce the time needed for breeding crops with superior characteristics, introducing desirable traits quickly and precisely by more accurately controlling the desired genetic mutations. Techniques and tools have been developed to alter the sequences of genes at specific locations in a plant’s genome (complete set of genetic material in its DNA). The most well-known tool, called -Cas9, uses a concept naturally occurring in bacteria. It involves molecular components that can locate target sequences in a genome and cut the DNA at specific locations. Natural repair mechanisms in the plant cells would usually repair these changes successfully, but sometimes the plant fails to, and a mutation is introduced. In their research, Kottackal and colleagues have altered the enzymatic browning in cut eggplant fruits using genome editing. Specific genes can be targeted using the method to be edited to introduce precise mutations. The introduced mutation would be identical to one that could have arisen from traditional or mutational plant breeding, except that there is only a single precise mutation, instead of several thousand random ones. Genome editing significantly shortens the time required for selective plant breeding from roughly a decade to only a few years. Remarkably, scientists have also developed methods by which no foreign DNA is left behind in the edited plant, only the desired mutation. This method of precision breeding has led to several research studies in recent years that demonstrate its efficiency in rapidly improving plant traits. -Cas9-based editing of an eggplant’s enzyme reduces enzymatic browning and results in increased and longer-lasting yields of fruits. [SEP] Justify:

Output: The text corroborates the claim by providing detailed information on how genome editing techniques, such as -Cas9, can introduce precise mutations in plants, leading to improved traits. It specifically mentions that this precision breeding method significantly reduces the time required for breeding crops with superior characteristics and has been shown to increase and prolong yields, as exemplified by the example of reducing enzymatic browning in eggplants.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: majority of the 153 overrepresented bactNOGs have no known function, or a function involved in energy production, DNA metabolism, transcription or translation (Fig 4, S1 Table). Individual bactNOG descriptions reveal a number of functions that have earlier been associated with the gut environment, such as the degradation of conjugated bile acids (bactNOG15678, Choloylglycine hydrolase), cobalamin (vitamin B12) biosynthesis (bactNOG85989, Cobyrinic acid a, c-diamide synthase) [21] or iron acquisition (bactNOG99581, bactNOG38121, Ferric uptake regulator protein) [22, 23], emphasizing the importance of these processes in the gut environment. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFig 4. Functional composition of gut species bactNOG datasets. BactNOGs represented in one or more of the 23 gut bacterial species in this study were attributed to one of three groups: overrepresented or underrepresented compared to non-gut species (see text for details), or neither over nor underrepresented (indicated by *). Within each of these groups, the number of different BactNOGSs attributed to a functional category is indicated as a percentage of the total number of BactNOGs in the group. Functional category descriptions are short forms of the full descriptions presented in tables “S1” and “S2” Tables. less than 4 of the overrepresented bactNOGs point to an important role of conjugation in the gut environment (bactNOGs 07070, 26309, 08200, 44258), a function that had not been recognized as such in the earlier global approach to the identification of bacterial functions that are important in the gut environment described in [1]. [SEP] Justify:

Output: The text contrasts the claim by emphasizing the importance of diverse gut bacteria and their various functional roles in the gut environment. It mentions that overrepresented bactNOGs are involved in crucial processes such as energy production, DNA metabolism, and the degradation of bile acids, thereby suggesting that a diverse gut microbiome contributes to essential functions that a completely sterile gut would lack.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: In order to further investigate the impact of lignin content on overall glucan and xylan yields, the overall percent theoretical glucan and xylan yields based on original glucan and xylan contents are plotted versus lignin content of raw Miscanthus for 80 Miscanthus samples following hydrothermal pretreatment at 180°C for 0 min, 17. 5 min, and 35 min and subsequent enzymatic hydrolysis of the pretreated whole slurry in the HTPH system in Figure 5. The high scatter and significant deviation of glucan and xylan yields from a linear fit to lignin content show that lignin content was not a dominant factor in controlling hydrolysis through hydrothermal pretreatment followed by enzymatic hydrolysis of the whole slurry at a high enzyme loading of 75 mg of cellulase plus 25 mg of xylanase protein/g of total glucan plus xylan in the raw biomass. Figure 5HTPH glucan and xylan yields of 80 Miscanthus samples vs. lignin contents in raw Miscanthus. HTPH glucan and xylan yields on basis of glucan + xylan content in raw Miscanthus of 80 Miscanthus samples. Full size imageTable 3 summarizes the 80 Miscanthus genotypes according to sample numbers provided by showing the highest and lowest sugar yields in terms of both mass yield (g of 100 g dry weight raw Miscanthus) and percentage of theoretical yield (g sugar per gram of original glucan and xylan contents in raw Miscanthus) for no pretreatment and for a pretreatment time of 35 min as measured by HTPH. Overall, the genotypes with the highest or lowest sugar yields through pretreatment were different from those with the highest or lowest sugar yields without pretreatment. The genotypes showing the highest mass yields were totally different from those with the highest theoretical yields, indicating that genotypes less resistant to HTPH did not necessarily release the highest quantity of sugars. The genotypes with the highest glucan plus xylan yields on the basis of both total mass and percentage of theoretical yields were similar to those with highest glucan yields because of the higher glucan content. The genotypes showing the highest glucan or glucan plus xylan yields without pretreatment contained lignin contents as low as 15. 5% and 17. 7%. [SEP] Justify:

Output: The text discusses lignin content and its impact on glucan and xylan yields from Miscanthus samples, focusing on hydrothermal pretreatment and enzymatic hydrolysis. However, it does not address bioengineered yeast or their capability to produce biofuels from sugars, thus making it irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: Professor Amiri, Director of explains, ’Gene editing has a high potential for practical applications in agriculture, and contributes to global food security. The science of gene editing – a faster strategy than standard breeding – is making waves in agriculture by improving the traits of interest in a precise way. These accurate genome changes enable the improvement of a wide range of crop plants which can reinforce food security, especially in countries with less arable land. ’ Eggplant editing Genome editing has been used as a tool recently to alter the enzymatic browning of cut eggplant fruits. As part of ongoing research, Kottackal and colleagues published results from their recent study to show how -Cas9-based editing of the eggplant’s PPO enzyme reduces the amount of enzymatic browning and results in an increased (by 10%) and long-lasting yield of fruits in the edited plants. This is the first ever trial of genome-edited eggplant in field conditions. With the knowledge that PPO regulates the degree of browning in cut fruits, the research team targeted one of the genes encoding this enzyme, PPO2, in eggplants. In particular, they targeted this enzyme’s copper ion A binding site (a conserved region across PPO genes in different species). The researchers used the -Cas9 genome-editing system to mutate the corresponding location on the gene. The image shows the browning of juice from non-edited eggplant (left), with little browning of juice from the edited eggplant (two tubes on right). Kodackattumannil, P, et al, (2023), Reports, CC BY 4. 0. The study confirmed that no random mutations were introduced into the plants, and gene-edited eggplants that contained mutated PPO2 were identified. Surprisingly, the researchers discovered that mutation of this specific region of PPO2 resulted in multiple phenotypes in the progeny across generations. These included early seed germination, higher yield of eggplants, fewer seeds, decreased activity of the PPO enzyme, and reduced or no browning of the cut fruits harvested. Next-generation eggplants The discovery of the pleiotropic nature of this gene is novel and of immense benefit to a plant breeder, given that different traits can be enhanced by mutating the same target. This ongoing research is now focused on field trials of the same edited crop. [SEP] Justify:

Output: The text corroborates the claim by providing evidence that gene editing has 'high potential for practical applications in agriculture' and can specifically improve crop yields. It notes that the genome editing of eggplants resulted in an 'increased (by 10%) and long-lasting yield of fruits in the edited plants.' Additionally, the text discusses how the mutation of the PPO2 gene led to 'higher yield of eggplants' along with other beneficial traits. This supports the assertion that gene editing can improve crop yields through the enhancement of growth traits.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: It can be cleaved from host glycans by multiple fucosidases produced by gut commensals such as Bacteroides thetaiotaomicron, resulting in a high availability in the intestinal lumen where it can be used as a carbon source by B. thetaiotaomicron itself [31] or by other resident bacteria such as Escherichia coli [32] or Roseburia intestinalis [33]. A certain number of functions that were detected as overrepresented in the single bactNOG comparisons do not appear as such in the analysis by groups of bactNOGs. Some group functions even appear in the list of overrepresented single bactNOGs (S1 Table) as well as in the list of underrepresented single bactNOGs (see below, S2 Table). This is for example the case for the function "Ferric uptake regulator protein" (represented by bactNOGs 38121 and 99581 in the list of overrepresented bactNOGs and by bactNOG31290 in the list of underrepresented bactNOGs). This type of result suggests that closely related gut and non-gut bacteria use distinct proteins for the same function or, alternatively, that the proteins represented by different bactNOGs in spite of identical descriptions exert different functions of which some are more important in the gut environment. Gut adaptation through functional paucity The direct comparison of closely related bacteria from the gut and other environments also provides a unique opportunity to focus on underrepresented functions, which may be equally informative of the functioning of the gut ecosystem. In contrast to the overrepresented functions, underrepresented functions included far less bactNOGs with unknown functions (Fig 4, S2 Table). Remarkably, one third of the underrepresented bactNOGs is involved in motility and signal transduction, including several chemotaxis related functions. Another remarkable underrepresented function is the Pur operon repressor protein (bactNOG16918), identified in only one of the 23 gut bacteria as opposed to 21 of the 23 non-gut bacteria. This repressor controls the transcription of the pur operon for purine biosynthetic genes, and its absence would be expected to result in the constitutive transcription of the operon. [SEP] Justify:

Output: The text contrasts the claim by detailing the roles of various gut commensals, indicating that a diverse microbiome contributes significantly to gut health and functionality. It discusses how gut bacteria like Bacteroides thetaiotaomicron and Escherichia coli perform important functions in the gut ecosystem, suggesting that a sterile gut would lack these essential interactions and functions.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: However, the lignin contents of the genotypes realizing the highest glucan or glucan plus xylan yields with pretreatment ranged from 21. 7% to 22. 6%, slightly higher than the 21. 0% average lignin content of all 80 Miscanthus genotypes. 112 (M. sacchariflorus/M. sinensis) and 229 (Miscanthus lutarioriparius) showed similarly high glucan and xylan theoretical yields even though they had much different lignin contents. These results suggest that not only lignin content but also lignin composition impacted sugar yields, similar to results for a study of populus variants [28]. The lowest sugar yields were from two genotypes: 1) Sample 33 (M. sinensis) with a glucan plus xylan content of 70. 1% had the lowest glucan and glucan plus xylan theoretical yields without pretreatment and 2) Sample 140 (M. sacchariflorus/M. sinensis) with a glucan plus xylan content of 60. 9% had the lowest glucan, xylan, and glucan plus xylan theoretical yields following pretreatment for 35 min. Thus, these two samples displayed strong recalcitrance even though both glucan and xylan content were close to the average values. In addition, the same genotypes maintained the highest and lowest glucan or xylan theoretical yields as the pretreatment time was extended from 17. 5 to 35 min at 180°C, and these varieties were not the same as those showing the highest or lowest theoretical yields without pretreatment. This trend indicated that enzymatic hydrolysis of raw Miscanthus without pretreatment would not be effective for rapidly identifying varieties with high yield potential. Table 3 Summary of HTPH results for Miscanthus genotypes displaying highest and lowest sugar yields Full size tableOverall, these 80 genotypes represented similarity of cellulosic biomass samples as well as diversity according to the range of the compositional data and fermentable sugars results. The compositional data for dry Miscanthus samples ranged from 27. 6% to 48. 8% glucan with an average of 40. 8% and a standard deviation of 3. 8%, from 18. 6% to 28. 0% xylan with an average of 24. 1% and a standard deviation of 2. 0%, and from 15. 4% to 27. [SEP] Justify:

Output: The text discusses various genotypes of Miscanthus and their lignin and sugar yields, but it does not mention bioengineered yeast or its capability to produce biofuels. Therefore, it is irrelevant to the claim about bioengineered yeast's potential for high biofuel yields from sugars.