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 total conversions of glucan and xylan were 87. 8% and 89. 6%, respectively (Fig. 3). When the substrate (7%) was fed four times to reach a final solids loading of 40%, the yields of glucose and xylose decreased to 73. 3% and 55. 8%, respectively, which were significantly (P < 0. 05) lower than those from the batch hydrolysis. Cello-oligosaccharides and xylo-oligosaccharides reached 17. 9 g/L and 27. 2 g/L as a maximum, respectively. The total conversions of glucan and xylan decreased to 83. 6% and 87. 4%, respectively (Fig. 3). Cello-oligosaccharides and xylo-oligosaccharides have been identified as strong inhibitors of cellulase [22,23,24, 39]. Here, the accumulation of oligosaccharides probably contributed to the significant decline in the monosaccharides yields. The time course of sugar evolutions during the fed-batch hydrolysis demonstrated that most of the sugars were released within 72 h even if the substrate was fed four times (Additional file 2). Table 2 Results of fed-batch enzymatic hydrolysis with different feeding times and the chemical compositions of the solid residues after enzymatic hydrolysisFull size table Fig. 3Sugars yields of the fed-batch enzymatic hydrolysis at solids loadings varying from 12 to 40% (w/v). a yields of glucose and cello-oligosaccharides. b yields of xylose and xylo-oligosaccharides. *The enzyme blend was fed four times simultaneously with the substrateFull size image The chemical composition of the residues was analyzed and the results are presented in Table 2. Interestingly, the glucan and xylan contents of the residues after the batch hydrolysis at 12% (w/v) solids loading were reduced significantly (P < 0. 05) to 14. 4% and 7. 8%, respectively, compared to the pretreated corn stover. In contrast, the lignin and ash contents dramatically increased (Table 2, Entry 1). This was primarily attributed to the degradation of the carbohydrate polymers within corn stover. [SEP] Justify:

Output: The text does not address the claim regarding bioengineered yeast producing biofuels from sugars. Instead, it discusses the outcomes of enzymatic hydrolysis and the conversion rates of glucan and xylan in a fed-batch system, which is unrelated to the claim about yeast modification for biofuel production.


Input: Task: corroborate the claim using the given text. Claim: Many investors see cryptocurrency as a hedge against inflation. [SEP] Text: (2000), Cai et al. (2001) and Elder et al. (2012). In contrast, the limited studies focusing on cryptocurrencies find that CPI release has a negligible impact on Bitcoin prices (e. g. , Corbet, Larkin, Lucey, et al. , 2020; Pyo & Lee, 2020) with Lyocsa et al. (2020) noting that exchange hacking announcements have a much larger influence on price volatility. We seek to find answers to two related questions. First, does Bitcoin, or cryptocurrency more generally, offer a potential hedge to heightened inflation expectations? If so, is this dependent on particular levels of inflation or inflation expectations? Second, does cryptocurrency offer protection against surprises emanating from monthly scheduled CPI announcements? In both cases, we contrast the cryptocurrency response with that of gold. In doing so, we contribute to the continuing discussion on the utility of cryptocurrencies and their value within a diversified portfolio. Our measures of inflation expectations include inflation swap rates and the break-even inflation rates (BEIR) inferred from Treasury markets. We incorporate both short-term (5-year) and long-term (10-year) inflation expectations, along with a set of control variables for credit conditions, the term structure and uncertainty in cryptocurrency, economic policy and financial markets. Although we do include a brief discussion relating to monthly actual and survey measures of inflation, we focus on inflation expectations derived from financial instruments as they are available at a daily frequency and provide estimates of ‘revealed’ rather than ‘stated’ inflation beliefs. In addition, as the cryptocurrency market has developed, other coins have gained some prominence and Bitcoin's market dominance has fallen. We reflect this by expanding our sample to include other cryptocurrencies and find that they share similar inflation hedge properties to Bitcoin. In demonstrating that cryptocurrency prices have some capacity to respond to innovations in inflation expectations, we also contribute to the literature that demonstrates crypto markets have become more efficient over time (e. g. , Bariviera, 2017; Blau, 2017; Nadarajah & Chu, 2017; Tiwari et al. , 2018; Urquhart, 2016; Vidal-Tomas & Ibanez, 2018). We extend the sample period used in the earlier literature to evaluate the cryptocurrency return–inflation relationship during a complete monetary policy cycle. [SEP] Justify:

Output: The text supports the claim by discussing the potential for cryptocurrencies, specifically Bitcoin and others, to act as a hedge against inflation. It mentions studies that focus on the relationship between cryptocurrency prices and inflation expectations, indicating that they have 'some capacity to respond to innovations in inflation expectations.' Additionally, the text reflects on the evolving nature of the cryptocurrency market, suggesting that as it has developed, cryptocurrencies have demonstrated inflation hedge properties similar to Bitcoin.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Figures AbstractGut bacterial communities of bumble bees are correlated with defense against pathogens. Further understanding this host-microbe association is vitally important as bumble bees are currently experiencing global population declines, potentially due in part to emergent diseases. In this study, we used pyrosequencing and community fingerprinting (ARISA) to characterize the gut microbial communities of nine bumble species from across the Bombus phylogeny. Overall, we delimited 74 bacterial taxa (operational taxonomic units or OTUs) belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, Actinobacteria, Flavobacteria and Alphaproteobacteria. Each bacterial community was taxonomically simple, containing an average of 1. 9 common (relative abundance per sample > 5%) bacterial OTUs. The most abundant and prevalent (occurring in 92% of the samples) bacterial OTU, based on 16S rRNA sequences, closely matched that of the previously described Betaproteobacteria species Snodgrassella alvi. Bacteria that were first described in bee-related external environments dominated a number of gut bacterial communities, suggesting that they are not strictly dependent on the internal gut environment. data showed a correlation between bacterial community structures and the geographic locations where the bees were sampled, suggesting that at least a subset of the bacterial species may be transmitted environmentally. Using light and fluorescent microscopy, we demonstrated that the gut bacteria form a biofilm on the internal epithelial surface of the ileum, corroborating results obtained from Apis mellifera. Citation: Lim HC, Chu C-(2015) of Communities of Bee Species. 10(3): e0118566. Editor: Fabio S. Nascimento, Universidade de São Paulo, Faculdade de Filosofia Ciências e Letras de Ribeirão : November 6, 2014; Accepted: January 17, 2015; Published: March 13, 2015Copyright: © 2015 Lim et al. This is an open access 2155. Funding: The work was supported by a U. S. Department of Agriculture, of Food and Agriculture grant (#2010-65104-05992) to SAC and by a U. S. Department of Agriculture, of Food and Agriculture grant grant (#2009-35505-06012) to MJS. [SEP] Justify:

Output: The text contrasts the claim by detailing the importance of diverse gut bacteria in bumble bees, which support their defense against pathogens. It suggests that a more diverse microbial community is beneficial, as indicated by the correlation between bacterial communities and defense against emergent diseases. The mention of various bacterial taxa and their functioning in the gut ecosystem implies that complete sterility may not confer the same health advantages as a diverse microbiota.


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: When the feeding times rose from 1 to 4, the glucan and xylan contents of the residues increased gradually, while the lignin and ash contents decreased on a continued basis (Table 2, Entries 2–5), which was accordant with the continued decline of the hydrolytic yields (Fig. 3), implying that stronger products inhibition occurred with the increase in solids loadings. Effects of enzyme supplementation modes on fed-batch enzymatic hydrolysisThe effects of enzyme supplementation modes on the hydrolysis yields were investigated and compared during the fed-batch hydrolysis process. The enzyme cocktail was either added completely at the start of the hydrolysis or separately supplemented with the substrate. The fed-batch process was initiated at 12% (w/v) solids loading, and fed four times to reach 40% (w/v) solids loading. As depicted in Fig. 4, more sugars were released when the enzyme was added in a whole within the first 36 h. It was likely more loaded enzyme contributed as a single boost of a higher enzymatic hydrolysis rate. This phenomenon was consistent with the previous reports that cellulase added in a whole facilitated the release of glucose and xylose [16]. However, the rates of sugars release became inferior to those of the fed-batch enzyme supplementation mode after 12 h (Fig. 4), suggesting that the enzymatic activity diminished gradually as the enzymatic hydrolysis proceeded. Interestingly, more sugars were observed when the hydrolysis reaction was extended to 48 h or longer when the required enzyme was added concomitantly with the substrate. It was probably due to a higher enzymatic activity at the later stage of hydrolysis. The maximal concentrations of glucose and xylose were 146. 7 g/L and 58. 7 g/L, respectively, when the substrate and the enzyme cocktail were both fed separately (Table 2, Entry 6). These data resulted 8. 7% and 4. 8%, respectively, higher than those with the enzyme added in a whole. The fed-batch addition mode of the enzyme cocktail caused the glucan and xylan contents of the residues to decrease, which was in agreement with the results of the higher sugars concentrations (Table 2, Entry 5 vs Entry 6). Cello-oligosaccharides and xylo-oligosaccharides slightly decreased by 12. 8% and 4. [SEP] Justify:

Output: The text does not address the claim directly or indirectly. It discusses the effects of enzyme supplementation on hydrolysis yields and sugar release rates during the hydrolysis process, but it does not mention bioengineered yeast or its potential to produce biofuels from sugars.


Input: Task: corroborate the claim using the given text. Claim: Many investors see cryptocurrency as a hedge against inflation. [SEP] Text: We then use a structural break occurring in March 2020, identified in our initial regression tests, to separate the sample into pre-COVID and post-COVID periods and illustrate a significant change in the reported correlations. Pre-COVID (Panel B) we find that Bitcoin returns are not significantly correlated with stock returns or inflation expectations, while gold returns are negatively correlated (at the 1% level) with both stock returns and inflation expectations. Post-COVID (Panel C) Bitcoin returns are significantly positively correlated with gold, stocks and inflation expectations, and the gold correlations switch from negative to positive. 3 empirical analysis utilises an OLS regression model of the form: R t = α + β 1 % ∆ IE t + ∑ j = 2 3 4 5 β j Control j t + β 6 R t − 1 + ε t (1)where Rt is the daily return for gold or cryptocurrency, Rt–1 is the lagged daily return, and %ΔIEt is the daily percentage change in inflation expectations. A set of four control variables is included to represent the state of the economy and market uncertainty at time t. Economic policy uncertainty is captured by the EPU index (Baker et al. , 2016), financial market uncertainty is encapsulated by the CBOE implied volatility index (VIX), the TED spread (TED) provides a measure of credit risk, and the difference between 2- and 10-year Treasury yields represents the term premium (TERM). Newey-West standard errors correct for heteroscedasticity. 3. 1 Baseline regression 3 (Panel A), we report the baseline univariate coefficient estimates, where the return is regressed on a measure of inflation expectation. We initially focus on Bitcoin returns as they offer the longest sample period and Bitcoin continues to constitute a significant portion of the overall cryptocurrency market. We identify a statistically significant positive relationship between inflation expectations and returns in gold and Bitcoin markets. When we include both 5- and 10-year estimates in the same regression model, the short-term (5-year) expectations appear to dominate. However, the high variance inflation factors relating to those models mean that we are reluctant to focus on models with both terms to avoid multicollinearity issues. TABLE 3. The relationship between inflation expectations and daily returns of Bitcoin and Gold. [SEP] Justify:

Output: The text corroborates the claim by identifying a statistically significant positive relationship between inflation expectations and returns in Bitcoin markets. This suggests that as inflation expectations increase, Bitcoin returns also increase, indicating that many investors may be viewing cryptocurrency as a hedge against inflation.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Both grants supported the expenses for pyrosequencing, DNA fingerprinting, and materials/reagents used in this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. IntroductionRecent studies have shown that bacterial symbionts of animals play significant roles in shaping the physiology, ecology and evolution of their hosts [1,2]. In insects, these symbionts allow specialization on particular diets, such as termites on wood and aphids on phloem, even to the extent that some host and bacterial genomes have become complementary and compensatory with respect to genes that underlie biosynthesis pathways [3,4]. Moreover, resident gut bacteria may protect hosts against invasion by microbial pathogens through production of antimicrobial compounds, stimulation of host-immune systems or competition for space and nutrients [5–7]. Such colonization resistance conferred by resident microbiota has been documented in a wide variety of insects, including flies [8], caterpillars [9], termites [10], and locusts [11] and bumble bees [12]. Recent studies of gut microbiota in bees belonging to the corbiculate clade (honey bees [Apini], bumble bees [Bombini], stingless bees [Meliponini] and orchid bees [Euglossini]) have advanced understanding of the taxonomic composition and structure of microbial communities [13–15], elucidated important health effects and roles in defense against host enemies [12,16–19] and revealed ecological factors, such as host species, and environmental chemical substances that affect bacterial communities [20,21]. Understanding the contributions of intestinal microbiota to host fitness of bees is important and timely as many species of these globally important pollinators are currently under threat from disease [22–25], agrochemicals [26,27], habitat degradation [28,29] or a combination of these factors [30,31]. To date, most studies of bumble bees (Bombus), which are much more speciose than honey bees (Apis), have focused on specific bacterial lineages [32] of only a few host species [15], often relying on 16S rRNA sequencing of a small number of molecular clones, limiting the scope of our knowledge of the microbial diversity and structure of their gut microbiota [33]. [SEP] Justify:

Output: The text contrasts the claim by discussing the significant roles of bacterial symbionts in shaping host physiology and ecology. It emphasizes that diverse gut bacteria contribute positively to the health of various insects, including providing protection against microbial pathogens through mechanisms such as antimicrobial compound production and stimulation of host-immune systems. This suggests that a sterile gut, which lacks this diversity and protective function, would not 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: 8%, while the total conversions of glucan and xylan increased to 89. 5% and 88. 5%, respectively (Fig. 3). Surprisingly, these conversions were only marginally lower than those from the batch hydrolysis at 12% (w/v) solids loading without significant differences (P > 0. 05). According to the mass balance analysis, 432. 9 kg glucose, 173. 2 kg xylose, 46. 0 kg cello-oligosaccharides, and 76. 4 kg xylo-oligosaccharides, respectively, could be obtained from 1000 kg of the pretreated corn stover (Fig. 5). These data strongly supported that the enzyme blend added separately during the fed-batch hydrolysis facilitated higher sugars concentrations and yields. Fig. 4Effects of enzyme supplementation modes on the release of glucose, xylose, and TRS during the fed-batch enzymatic hydrolysis. The fed-batch hydrolysis was initiated at 12% (w/v) solids loading, and 7% fresh substrate was fed four times (3, 6, 24, and 48 h) to reach 40% (w/v) solids loading. The enzyme supplementation modes were as follows: a The enzyme blend (based on the final solids loading, 40%, w/v) was added completely at the beginning of the hydrolysis (hollow symbols). b The enzyme blend was fed simultaneously with the pretreated corn stover at each time point of feeding to maintain an identical final enzyme dosage (solid symbols)Full size image Fig. 5Corn stover to fermentable sugars mass balance analysis. The analysis was based on the fed-batch enzymatic hydrolysis of the SMs-pretreated corn stover. The hydrolysis was initiated at 12% (w/v) solids loading, and 7% substrate was fed four times (3, 6. 24, and 48 h) to reach a final solids loading of 40% (w/v). The enzyme cocktail was fed simultaneously with the substrate at each feeding time point. The hydrolysis was held at 50 °C, pH 4. [SEP] Justify:

Output: The text does not address or provide information specifically related to bioengineered yeast or its capability to produce biofuels. Instead, it focuses on enzymatic hydrolysis processes and the conversion of corn stover into fermentable sugars, thus making it irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Gene editing technologies like CRISPR can help create pest-resistant crops. [SEP] Text: Anti-proteins could help put the brakes on gene editing Scientists are exploring the proteins’ potential as a way to control and reduce off-target effects by Charles Q. Choi, special to C&EN June 6, 2021 | A version of this story appeared in Issue 21 Popular in Rwanda identifies index case for current Marburg virus outbreak Periodic Graphics: Porphyria and the vampirism myth Scientists reject a binary view of human sex at NIH symposium Delta-8-THC craze concerns chemists Cannabis industry gets crafty with terpenes Credit: Adapted from Sci. Adv. A cryo-electron microscopy reconstruction shows the anti-protein AcrIIA4 binding to a complex consisting of the Cas9 enzyme and a guide RNA. the technology behind the 2020 in Chemistry, has revolutionized the life sciences. The method offers a cheap, fast, and easy way to make edits in precise spots in genomes and could be game changing for treating genetic disorders and cancer and for other applications. faces safety concerns because scientists have only limited ways to control the technique. Now researchers have found that a dazzling variety of naturally occurring proteins, known as anti-could offer ways to exercise that control. These proteins could potentially be delivered after gene therapy to stave off harmful side effects or help direct therapies to the right parts of the body. Anti-could also play a role in efforts to spread beneficial genes through a population—to control insects, for example. And they have several advantages over other control methods; for example, they can be genetically encoded into a cell. Related: 2-in-1 base editors make two DNA edits at once (clustered regularly interspaced short palindromic repeats) are segments of bacterial DNA that are part of ancient microbial defense systems. Bacteria use RNA molecules derived from segments, along with a number of Cas (-associated) enzymes, to identify foreign DNA and slice it apart. In 2012, scientists revealed a way to apply and the Cas9 enzyme to cut the DNA in a cell’s genome in a precise spot (Science, DOI: 10. 1126/science. 1225829). Essentially, all one needs is to introduce Cas9 and a guide RNA—which directs the enzyme where to cut—into cells. But the longer a system remains active in cells, the more likely it is to edit parts of a genome other than its intended target, yielding potentially dangerous side effects. [SEP] Justify:

Output: The text corroborates the claim by indicating that anti-proteins could be employed in efforts to spread beneficial genes through a population, which aligns with the idea of using gene editing technologies like CRISPR to create pest-resistant crops. It discusses how these techniques can be game-changing for various applications, including the potential to control insects, which further supports the assertion that gene editing can assist in agricultural advancements.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: 20 [standard deviation, SE]) while the average number of OTUs with relative abundance above 5% was 1. 92 ± 0. 95 (S1 Table). Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFig 2. Heatmap showing relative abundance of each bacterial OTU (rows) in each of the pyrosequencing sample (columns). On the left is a cladogram showing phylogenetic relationships of the OTUs (tip labels = representative sequence ID). The IDs of the OTUs are abbreviated by only keeping their unique, last five characters (e. g. , HUSOE0I01BDDRB to BDDRB). On the right are classifications of the OTUs at two taxonomic levels, if available. For clarity, only labels for OTUs with relative abundance > 10% are shown. Atop the heatmap, a cladogram indicates phylogenetic relationships of the bee species investigated. The bars at the bottom of the graph indicate the phylogenetic clade in which each bee species falls. MD = Mendacibombus (subgenus). See S4 Fig. for fully labeled tips. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 3. Sequencing depth and number of OTUs detected for each pyrosequencing sample. Gut bacterial taxa Sequencing of all 13 pyrosequencing samples revealed bacteria from only six classes: Actinobacteria, Alphaproteobacteria, Bacilli, Betaproteobacteria, Flavobacteria and Gammaproteobacteria (Table 2). Overall, Betaproteobacteria was the most dominant class, accounting for 52. 7 ± 42. 2% of the bacterial sequences when abundance was averaged across 13 pyrosequencing samples. This was followed by Bacilli (18. 5 ± 36. 0%) and Gammaproteobacteria (13. 5 ± 24. 9%) (Fig. 3, S1 Table). The number of OTUs found in each class varied widely; it ranged from 20 each in Bacilli and Betaproteobacteria, to two in Alphaproteobacteria. containing OTUs with high abundance included Neisseriales (Betaproteobacteria), Lactobacillales (Bacilli) and Enterobacteriales (Gammaproteobacteria). [SEP] Justify:

Output: The text contrasts the claim by providing detailed information on the diversity of bacterial taxa found in the gut. It reports that sequencing revealed bacteria from six classes with specific abundance percentages, indicating a diverse microbial community. The existence of multiple operational taxonomic units (OTUs) in different classes suggests that a sterile gut, which would lack this diversity, may not be healthier. The dominance of certain bacterial classes and their relative abundance also highlights the role that diverse gut bacteria play in 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: 8, and 200 rpm for 120 hFull size image The results of enzymatic hydrolysis on various lignocellulosic materials at high solids loadings under different hydrolysis modes obtained in previous studies and in this project are summarized in Table 3. Some pretreatments remove lignin and hemicellulose while retaining and concentrating cellulose in the regenerated solids, as an approach favorable to high glucose concentrations with the fed-batch enzymatic hydrolysis (Table 3, Entries 1 and 2). However, the high glucose concentration exerts a substantial inhibitory effect on cellulase, which could affect the hydrolysis efficiency of cellulose [28]. For example, the total conversion was merely 60. 0%, when the fed-batch enzymatic hydrolysis of corn stover was performed at 30% (w/v) solids loading (Table 3, Entry 2). Xylose and oligosaccharides have been directly used for the production of biofuels [31, 32]. Some microorganisms are capable to metabolize a broad spectrum of substrates and can grow on a medium containing glucose and other sugars such as xylose, cello-oligosaccharides, and xylo-oligosaccharides. Here, the total conversions of glucan and xylan reached approximately 89% taking into account the oligosaccharides released. The SMs pretreatment can detain a majority of the sugar polymers including cellulose and hemicelluloses [33]. Here, the oligosaccharides released from corn stover were up to 41. 5 g/L, which contributed to the high conversions of glucan and xylan (Table 3, Entry 5). The total sugar conversions were slightly higher than the monomeric sugar yields achieved by the batch hydrolysis with the assistance of mechanical stirring (Table 3, Entry 3). Overall, the fed-batch enzymatic hydrolysis strategy was promising for hydrolyzing alkaline organosolv-pretreated corn stover into fermentable sugars with high concentrations and yields. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses enzymatic hydrolysis of lignocellulosic materials and conversion efficiency, but does not mention bioengineered yeast or its ability to produce biofuels. It focuses on the processes involved in converting sugars rather than bioengineering organisms to achieve high yields.


Input: Task: corroborate the claim using the given text. Claim: Gene editing technologies like CRISPR can help create pest-resistant crops. [SEP] Text: is Open Access? is an initiative that aims to make scientific research freely available to all. To date our community has made over 100 million downloads. It’s based on principles of collaboration, unobstructed discovery, and, most importantly, scientific progression. As PhD students, we found it difficult to access the research we needed, so we decided to create a new publisher that levels the playing field for scientists across the world. How? By making research easy to access, and puts the academic needs of the researchers before the business interests of publishers. are a community of more than 103,000 authors and editors from 3,291 institutions spanning 160 countries, including winners and some of the world’s most-cited researchers. Publishing on IntechOpen allows authors to earn 10. 5772/intechopen. 85499 this 1. Choose citation style Select style to clipboard Get citation 2. Choose citation style Select format Bibtex RIS Download citation Intech by Yuan-From the - Technologies and by Yuan-and Shiu-purchase hard copies of this book, please contact the representative in India: CBS Publishers & Distributors Pvt. Ltd. www. cbspd. com | customercare@cbspd. com 1. Choose citation style Select style to clipboard Get citation 2. Choose citation style Select format Bibtex RIS Download citation Impact of this 1. IntroductionGene editing is a type of genetic engineering in which DNA is inserted, deleted, modified, or replaced in the genome of a living organism. Unlike traditional methods that randomly insert genetic material into a host genome, current gene editing technologies target and change the specific genome locations. Zinc finger nucleases (ZFNs), transcription activator-like effectors nucleases (TALENs), and clustered regularly interspaced short palindromic repeats ()/Cas9 nuclease system are the three common gene editing technologies. These technologies have been widely used in genome engineering to enable a broad range of mutation by inducing DNA breaks that stimulate error-prone repairs such as homologous recombination (HR) or nonhomologous end joining (NHEJ). They successfully make it possible to achieve site-specific editing, modification, and manipulation at specific genomic sites (Table 1) [1]. [SEP] Justify:

Output: The text corroborates the claim by describing gene editing technologies, including CRISPR, and explaining their capabilities in specifically targeting and modifying genomic locations. It mentions that these technologies are widely used in genome engineering, which can relate to creating crops that are resistant to pests by enabling precise genetic modifications.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: At the opposite end of the spectrum, bacterial orders with OTUs with low overall abundance included Burkholderiales (Betaproteobacteria), Oceanospirillales (Gammaproteobacteria) and Bifidobacteriales (Actinobacteria) (Table 2). Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFig 3. Relative abundance (averaged across 13 pyrosequencing samples) of different bacterial classes. The average number of sequences obtained from each pyrosequencing sample was 15,170. only six bacterial OTUs from five different classes were found to be dominant across all 13 samples (i. e. , OTUs possessing the highest relative read abundance in each pyrosequencing sample, range: 47. 3%−99. 3%). Based on BLASTn results, five of these OTUs have sequences that were highly similar (98. 7%−100%) to named bacteria known either from the gut of bees, flowers or the immediate environment of bees (e. g. , bee bread) (Table 4). The most prevalent of these dominant OTUs matched Snodgrassella alvi, found in 12 pyrosequencing samples. Further, it was the most dominant OTU in eight sequencing samples (Fig. 2, S4 Fig. ). The other five dominant OTUs matched sequences of Saccharibacter floricola, Fructobacillus tropaeoli, Lactobacillus kunkeei, Gilliamella apicola, and an unnamed bacterium belonging to (Table 4). Other than the dominant OTUs, we uncovered some OTUs that were less dominant (rarely accounting for more than 5% of the reads in a sample), such as one classified as phylotype firm-5 (HUSOE0I01BP7S6, detected in seven bee species) and a Bifidobacteriales OTU (HUSOE0I01AJO2K, detected in five Bombus species) (S1 Table). At the level of individual pyrosequencing samples, the group of OTUs comprising phylotype beta (or S. alvi) appeared to be particularly diverse. Each sample that contained HUSOE0I01A3N3V (the most abundant of the beta/S. [SEP] Justify:

Output: The text contrasts the claim by detailing the diversity of bacterial orders and emphasizing that a variety of bacterial operational taxonomic units (OTUs) are present in the gut environment. The mention of dominant and less dominant OTUs, along with the high similarity of OTUs to those found in the gut of bees, suggests that a diverse bacterial community is prevalent, which may imply that a completely sterile gut is not preferable 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: Table 3 The results of enzymatic hydrolysis on various lignocellulosic materials at high solids loadings using different hydrolysis modesFull size table Conversion of the monosaccharides and oligosaccharides within the hydrolysates into microbial lipids using a fed-batch fermentation modeFed-batch fermentation is a promising culture mode for the industrial-scale lipid production [36]. In this study, cell growth and lipid accumulation were severely repressed when the TRS concentration of the hydrolysate was 150 g/L during batch fermentation. More severely inhibitory effect occurred at even higher sugar concentration (Additional file 3). Thus, a fed-batch culture was investigated to assess the potential of sugars consumption and lipid production by C. oleaginosum. The fed-batch culture was held at 30 °C, 200 rpm for 264 h. Sugar evolution profiles of the fed-batch culture are shown in Fig. 6. When glucose concentration was higher than 20 g/L, glucose was assimilated firstly, whereas xylose was assimilated at quite a slow rate without significant consumption (P < 0. 05) (Fig. 6a). It was suggested that C. oleaginosum exhibited a diauxic growth with a strong preference over glucose. A similar phenomenon was observed when glucose and xylose coexisted, suggesting the occurrence of glucose repression [40]. As shown in Fig. 6a, the other TRS (subtraction of glucose and xylose from the TRS) were consumed slowly. It was worth mentioning that 87. 8% of them were assimilated at the end of the fed-batch culture. The main components of these TRS were arabinose, galactose, mannose, soluble oligosaccharides, etc. Interestingly, both cello-oligosaccharides and xylo-oligosaccharides were assimilated by C. oleaginosum (Fig. 6b). The overall consumption of these two types of sugars was 74. 1% and 68. 3%, respectively (Table 4). Only 3. 1 g/L cello-oligosaccharides and 5. 8 g/L xylo-oligosaccharides were not consumed, likely being soluble oligosaccharides with higher degree of polymerization [31]. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the results of enzymatic hydrolysis on lignocellulosic materials and the consumption of various sugars during a fed-batch fermentation process without specifically mentioning bioengineered yeast or their ability to produce biofuels. The focus is on microbial lipids production by C. oleaginosum rather than the direct relationship between yeast and biofuel production from sugars.


Input: Task: corroborate the claim using the given text. Claim: Gene editing technologies like CRISPR can help create pest-resistant crops. [SEP] Text: 1 Genetic cloning of living organismsFor conventional genetic cloning of animals, plants, and microbes, the target genes in the specific genome are cut using restriction enzymes. It usually takes lots of work and long time to clone and screen for the desired ones. Current gene editing technologies can be used to achieve the desired clones both quickly and accurately, without the limitation of restriction site availability [11]. 2. 1. 2 Establishment of animal modelsGenetic cloning, gene knock-in, and gene knockout are the most common methods to make induced or experimental animal models. The efficient approaches include andCas9. By these new gene editing technologies, specific animal models of many diseases for which there are no animal models available previously have been established with unprecedented efficiency and precision [12, 13, 14]. 2. 1. 3 Development of testing tools and reagents/Cas9 can be optimized by bacterial genotypes to be more adaptive to the variation of food pathogens, compared with traditional methods. locus of different bacterial species show high variance to be an ideal basis for genotyping [15]. /Cas12a(Cpf1) (DNA endonuclease targeted trans reporter) system can be used to diagnose gene mutations, cancers, and microbial infections and test microbial antibiotic resistance by analyzing specimens [16]. 2. 1. 4 Discovery of drugsThe screening and identification of target sites are critical to drug discovery; thus, excellent and suitable platforms are needed. Gene editing technologies can work for the editing of functional genes and the screening of target sites. For example,Cas9 was used to target the exons encoding functional protein domains. A screen of 192 chromatin regulatory domains in murine acute myeloid leukemia (AML) cells identified 6 known drug targets and 19 additional dependencies [17]. 2. 2 Nonhuman therapeutics2. 2. 1 Agricultural productsThe gene editing technology can be used to produce agricultural products in accordance with the need of humans. For example, crops were produced with high yield and resistant to diseases, insects, herbicides, and harsh environment [18, 19]; domesticated animals (pig, buffalo) were produced with double muscle phenotype [20]; and aquatic products (catfish) were produced with high level myostatin (MSTN) gene expression [21]. 2. 2. 2 FoodWe can make food more productive or have longer shelf-life by gene editing technologies. [SEP] Justify:

Output: The text corroborates the claim by stating that 'crops were produced with high yield and resistant to diseases, insects, herbicides, and harsh environment' using gene editing technologies. This directly supports the idea that CRISPR and similar methods can create pest-resistant crops, as they describe the successful application of these technologies in agriculture to enhance crop resistance.


Input: Task: pass the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: alvi OTUs) generally also contained at least two other closely related beta OTUs. Most of these rarer beta OTUs were unlikely to be variants caused by sequencing errors because they have non-trivial abundance (> 5 reads) and were found in more than one sample. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 4. Taxonomic assignments of six OTUs based on naïve Bayesian classification of 16S rRNA sequence. Community distinctiveness based on phylogenetic distances among bacteria Based on the UniFrac “all environments together” test, there was an overall significant difference among the pyrosequencing samples, a difference that was based on a combination of their community composition and the phylogenetic distances among the OTUs within the communities (P ≤ 0. 01, after correcting for multiple comparisons). This difference was primarily driven by pyrosequencing samples “_FL”, “” and “” (Table 5). The distinctiveness of these microbial communities was supported by NMDS and jackknife hierarchical clustering (Fig. 4 and S5 Fig. ). The sample “” was dominated by three bacterial OTUs, all of which were either absent or present at very low abundance in other pyrosequencing samples. These three OTUs included two closely related taxa belonging to the order of Lactobacillales (relative abundance = 50. 3% and 37. 5%, respectively) and one belonging to Oceanospirillales (11. 2%) (Fig. 2, S4 Fig. ). The sample “” was dominated by a member of Lactobacillales (relative abundance = 99. 3%), which occurred in significant abundance in only one other pyrosequencing sample (“_ARG”). The third highly distinctive pyrosequencing sample was “_FL”. It contained two principal OTUs, belonging to Flavobacteriales (76. 2%) and Enterobacteriales (17. 1%), respectively. Both of these OTUs occurred in significant abundance in only 1–2 other gut bacterial communities (Fig. 2, S4 Fig. ). [SEP] Justify:

Output: The text is largely focused on the analysis and description of specific microbial communities present in various samples. It discusses different operational taxonomic units (OTUs) and their relative abundances, which relate to the diversity of bacterial communities. However, it does not provide any information supporting or contrasting the claim that a completely sterile gut is healthier than one with diverse bacteria. Thus, it is deemed irrelevant to the claim.


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% (w/w) solids loading although the commercial enzymes mixtures were loaded [21]. In this study, 16. 8% of the total soluble sugars within the hydrolysate were oligosaccharides when the fed-batch enzymatic hydrolysis was conducted at the final solids loading of 40% (w/v), although the enzyme blend contained very high cellobiase activity (253. 0 CBU/gds). The accumulation of oligosaccharides is expected to be lower when the enzyme cocktail is optimized. However, it is difficult and uneconomical to completely avoid the release of oligosaccharides during the enzymatic hydrolysis. Development of oligosaccharides assimilation strains will be particularly advantageous as a sizeable portion of sugars in the hydrolysate are oligomers. Here, the oligosaccharides could be co-fermented with the monosaccharides (glucose and xylose), evidencing that the sugar loss can be avoided. In addition, extra enzymes were not deemed necessary during the hydrolysis process, which is conducive to the techno-economics of the enzymatic hydrolysis technology. High sugar concentrations and yields of fermentable sugars were reached using the fed-batch hydrolysis with a high enzyme dosage (15 mg protein/g glucan). The high enzyme cost severely impedes the commercial success. Nguyen and coworkers have reported that simultaneous saccharification and fermentation (SSF) of corn stover at high solids loadings achieved high ethanol titers with significantly reduced enzyme dosages [44, 45]. The integration of the fed-batch enzymatic hydrolysis and lipid fermentation has the opportunity to reach high lipid yield with significantly lower enzyme loadings. Lipid samples produced by C. oleaginosum using the fed-batch culture were transmethylated, and the resulting FAMEs were analyzed by GC. The major composition of fatty acids was long-chain fatty acids with 16 and 18 carbon atoms including myristic acid (0. 7 ± 0. 0%), palmitic acid (27. 5 ± 0. 4%), stearic acid (12. 0 ± 0. 3%), oleic acid (49. 0 ± 0. 2%), and linoleic acid (9. 6 ± 0. 2%). [SEP] Justify:

Output: The text does not directly address the claim regarding bioengineered yeast and its ability to produce biofuels from sugars. Instead, it discusses processes related to enzymatic hydrolysis and sugar extraction, along with the challenges of enzyme costs and the production of fatty acids. As a result, it is considered irrelevant to the specific claim.


Input: Task: corroborate the claim using the given text. Claim: Gene editing technologies like CRISPR can help create pest-resistant crops. [SEP] Text: For example,Cas9 was used to edit thermophilic bacteria Streptococcus thermophilus as a bacteriophage-insensitive mutant to improve the product (e. g. , yogurt, cheese) yield by refraining from the infection of phages [22]. The white button mushroom Agaricus bisporus was engineered to resist browning usingCas9. The effect was achieved by targeting to knock out the genes that encodes polyphenol oxidase—an enzyme that causes browning [23]. 2. 2. 3 Industrial products/Cas9 has been used to establish marine algae (e. g. , diatoms) as useful in industrial applications as the carbon neutral synthesis of fuels, pharmaceuticals, health foods, biomolecules, materials related to nanotechnology, and bioremediations of contaminated water [24, 25]. /Cas9 was used to encode the pixel values of black and white images and a short movie into the living bacterial genomes. /Cas9, the technical limits of this information storage system can be optimized to be minimal. /Cas9 can capture and stably store many real data within the genomes of living cells [26]. 2. 2. 4 Environmental protectionMarine microalgae are in charge of about 40% of primary production on earth and capture more CO2 than rain forests. Diatoms are the most important unicellular eukaryotic microalgae and have dominant ecological significance. /Cas9 can be used to modify the diatom genome to achieve more effects in reducing the global warming [25]. 2. 2. 5 Restoration of extinct animalsWoolly mammoths are different from current living elephants by adapting to the extreme cold environment. The mammoth TRPV3 gene, which encodes a temperature-sensitive transient receptor potential (thermoTRP) channel involved in thermal sensation and hair growth, could be achieved by modifying genes of Asian elephants [27]. The mammoth may be restored usingCas9, if the modified embryo can be successfully transferred into the uterus of living elephants. 2. 3 Human therapeutics2. 3. 1 Medicine screeningThe therapeutic strategies of Parkinson’s disease (PD) are quite variable including drug and nondrug treatment. Therefore, it is necessary to find a suitable strategy to treat PD safely, efficiently, and quickly. [SEP] Justify:

Output: The text corroborates the claim by providing an example of how the Cas9 gene editing technology has been utilized to engineer the white button mushroom (Agaricus bisporus) to resist browning. This demonstrates the capability of gene editing technologies, such as CRISPR, in modifying crops for desired traits, which aligns with the claim regarding the creation of pest-resistant crops.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: results showing that not only species but also geographic location of the host affects its gut bacterial community, again supports existing evidence that at least some members of the gut microbial community appear to be environmentally transmitted [60–63]. This may explain the relatively different gut microbial communities found between populations of same Bombus species collected in different geographic regions, such as the microbiota of B. terrestris from France and Argentina (Fig. 4 and S5). European colonies of B. terrestris were shipped to for commercial pollination and became naturalized since the 1990s. The species then spread to Argentina, and may have been exposed to environmental resources considerably different to those in Europe [64,65]. In identifying common bacteria found in the gut of bumble bees, we can rely on previously conducted in vivo and in vitro studies (often focusing on related bacteria in honey bees) to infer the roles they play in contributing to colony and individual health. Outside of the gut, bacteria such as L. kunkeei and S. floricola may benefit bumble bees by producing weak acids that aid in the fermentation and preservation of stored pollens in the nest [66,67]. The gut is likely to be an important source of these bacteria because worker bumble bees first moisten collected pollen with regurgitated nectar before packing it onto the hind leg pollen-carrying structure (corbicula) [59,68]. In the ileum, bacteria may enhance nutrient absorption by helping to break down food molecules. This is supported by a functional genomics study that found that the gut microbiome of honey bees (which share a number of gut bacterial species with bumble bees) was enriched for genes associated with carbohydrate breakdown (including those involved in pectin breakdown) and transport [17]. In addition to nutrition, evidence is mounting that gut bacteria benefit their bee hosts by contributing to the latter’s defenses against non-native bacteria and protistan enemies. For example, Vasquez et al. [19] found that lactic acid bacteria (Lactobacillus spp. and Bifidobacterium spp. ) isolated from honey bees have inhibition properties on microorganisms such as yeasts and other bacteria (including Melissococcus plutonius, the causative agent of European foulbrood), with L. kunkeei (dominant in “” and “_ARG”) showing the strongest effects. [SEP] Justify:

Output: The text contrasts with the claim by emphasizing the importance of a diverse gut microbiome in maintaining health. It demonstrates that gut bacteria enhance nutrient absorption and contribute to the host's defenses against pathogens, indicating that having a variety of bacteria is beneficial rather than promoting sterility. Furthermore, it states that certain gut bacteria play essential roles in fermentation and preservation, which supports the idea that a diverse gut is advantageous 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: Specifically, oleic acid was the most abundant one, followed by palmitic, stearic, and linoleic acid, and these four fatty acids accounted for over 98% of the total fatty acids. The lipid samples presented a fatty acid profile similar to those of vegetable oils, demonstrating that the microbial lipid could be explored as a potential feedstock for biodiesel production [46]. ConclusionThe fed-batch enzymatic hydrolysis of alkaline organosolv-pretreated corn stover was promising for obtaining high concentrations and yields of fermentable sugars. The total conversions of glucan and xylan reached 89. 5% and 88. 5%, respectively, at a high solids loading of 40% (w/v), when the oligosaccharides released were taken into account. High lipid content and yield were realized under a fed-batch culture mode. Oligosaccharides were co-assimilated with monosaccharides by C. oleaginosum, which played a crucial role in minimizing the loss of oligosaccharides and improving the lipid production. This work provides valuable information facilitating the design of a more cost-effective lignocellulose-to-lipid route. MethodsRaw materials, enzymes, and chemicalsCorn stover used in this study was purchased from Zhengzhou (Henan, China). It was chopped by a high-speed shredder (HC-3000, Co. , Ltd. , Jinhua, China) before sieving through 1-mm-sized screen. Then, the samples were washed for three times with water to remove the adhering dirt, stones, and metals, oven-dried at 105 °C until the weight was constant, and stored in a desiccator for long-term storage. The raw corn stover contained 35. 9% glucan, 21. 7% xylan, 22. 1% total lignin, and 2. 3% ash (Table 1, Entry 1). The other materials were proteins, non-structural sugars, organic acid, inorganics, crude fat, waxes, coloring material, etc. Specifically, there were 8. 7% water extractives and 4. 5% ethanol extractives, respectively, in the raw corn stover. [SEP] Justify:

Output: The text is irrelevant to the claim as it does not provide any information regarding bioengineered yeast or its ability to produce biofuels from sugars. Instead, it focuses on the fatty acid profile from lipid samples and the conversion rates of glucan and xylan from corn stover, which does not directly relate to the assertion about bioengineered yeast.


Input: Task: corroborate the claim using the given text. Claim: Gene editing technologies like CRISPR can help create pest-resistant crops. [SEP] Text: These are important advancements that have benefits, not only for producers, but also consumers and, more broadly, the planet. If we can harness gene editing to improve upon ways to make agriculture more sustainable and edit plants so that they are more adaptable to turbulent climactic changes, the abilities for smallholder farmers to be more productive on the land with fewer pesticides and/or fertilizers can provide a more regionally stable food source. The major challenges lie in getting these technologies into the market, and to the people who can benefit from them the most, without being financially prohibitive. This is where harmonization of regulatory frameworks, even on a regional basis, as is the case in Latin America, and potentially in sub-will be key. The complexity of the patent and licensing landscape further deters progress in the area of proliferation. At this point, there does not appear to be any consensus among patent and/license holders on how to proceed. Europe could be a game changer if the decides to regulate gene edited agrifoods differently than GMOs. The uncertainty surrounding the EU remains a major limitation to the applicability of -Cas systems in Europe’s agricultural sectors (Cardi et al. , 2023: 18). But we have yet to see whether the recent EU proposal moves forward at the member-state level or is rejected. As discussed in Sect. 5. 3, there are varying expert opinions on which direction the EU will go. Rejecting the new breeding techniques proposal may disadvantage the EU in terms of global competitiveness in agricultural products and the ability to address agricultural sustainability and climate change. The eventual direction the EU chooses will have implications for its trading partners, especially those in African countries like Uganda, Kenya and Tanzania that are in the process of finalizing their regulatory frameworks for gene edited agrifoods. Informant 19 (a private sector representative) said of smallholders in sub-Saharan Africa, …much of the activism against modern technologies is really out of touch with what farmers are facing. Farmers are not looking for GMOs. Farmers are not looking for gene edited technologies. Farmers are like, ‘I’m grappling with this pest. Do you know any solution that can help? ’ I wish there was a model that would just allow farmers to have the opportunity to choose. [SEP] Justify:

Output: The text corroborates the claim by discussing the potential benefits of gene editing in agriculture, particularly in helping smallholder farmers deal with pests and making agriculture more sustainable. It highlights how gene editing can enhance the adaptability of plants and reduce reliance on pesticides and fertilizers, with a direct reference to farmers searching for solutions to pest problems. This aligns with the claim that gene editing technologies like CRISPR can contribute to the creation of pest-resistant crops.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Similarly, studies have shown that bacteria cultures from honey bee crops or larvae inhibited the growth of bacterial pathogens of bees [69,70]. As one of the few studies that focused on bumble bee protistan parasites, Koch and Schmid-Hempel [12] showed that bees first treated with antibiotics then subsequently fed with feces from nest mates have lower parasite load (Trypanosomatidae: Crithidia bombi) compared to bees not given viable bacterial inoculation. While the study was groundbreaking, the mechanisms by which gut bacteria exert their protective functions against enteric protists are not entirely clear. Similar to honeybees, we found that bacteria in the ileum of the bumble bee species B. impatiens forms biofilms on the inside surface of the gut epithelium (Fig. 6). This suggests that bumble bee gut microbiotas may have specific functions in their hosts, such as providing nutritional benefits or defense against intestinal pathogens. Future research in these areas will have important implications for the conservation of corbiculate bees worldwide, as numerous species and populations are purportedly threatened by invasive parasites or deficient nutrition [71–73]. In addition to the dominant bacterial OTUs, we also uncovered numerous rare ones. It is possible that these could be the result of sequencing errors despite our stringent computational pipeline, removal of singletons and the clustering of sequences into OTUs. The inflation of microbial diversity as a result of sequencing errors is a recognized methodological artifact of next-generation sequencing [74]. Nonetheless, several of the rare OTU appear authentic and likely have important functions because of their ubiquity or moderate abundance in a small number of samples. Rare OTUs classified under beta/S. alvi are particularly interesting because a number of them always coexist with the dominant beta/S. alvi OTU when the latter is present. A similar situation was reported in honey bees in which a number of closely related S. alvi genomes coexisted at the level of colony, if not at the level of individual bees [17]. Given that gene content of bacteria can differ significantly even when their 16S rRNA sequences are very similar [75], these minor beta/S. alvi variants may play complementary functional roles to the dominant bacterial strains. Supporting InformationS1 Fig. Phylograms (Bayesian consensus trees) based on 16S rRNA alignment. [SEP] Justify:

Output: The text contrasts the claim by discussing the functional roles of gut bacteria in bumble bees, indicating that diverse microbiotas may provide nutritional benefits and defense against intestinal pathogens. It highlights that the presence of bacteria can inhibit the growth of pathogens and may have important functions in the host's gut, which suggests that a completely sterile gut would not be healthier due to the lack of these protective and beneficial bacterial interactions.


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: Cellic® CTec2, a commercial enzyme blend containing aggressive cellulases, high level of β-glucosidase, and hemicellulase [47], was purchased from Novozymes (Tianjin, China). The total protein concentration of the enzyme blend was determined to be 116. 2 mg/mL. The filter paper activity and β-glucosidase activity were 247. 1 FPU/mL (filter paper units per milliliter of enzyme solution) and 4167 CBU/mL (cellobiase units per milliliter of enzyme solution), respectively, as assayed by the published procedures [48, 49]. The chemical reagents used in this study were of analytical grade and purchased locally. Alkaline organosolv pretreatment procedureThe SMs pretreatment of corn stover at high solids loading was conducted according to our previous published method with some modifications [33]. Specifically, NaOH (4. 0 g) and methanol (80 mL) of analytical grades were mixed in a 500-mL red cap glass bottle (Duran, Schott, Germany) to obtain a homogeneous solution. 40 g of the raw corn stover was added into the bottle and mixed thoroughly with the solution by stirring with glass rods. Then, the bottle was sealed and immersed in a water bath (80 °C) for 1 h. When the pretreatment was complete, the slurry was cooled below 50 °C by water instantly, filtrated through a Buchner funnel, and washed for three times with 400 mL of water to a weak alkalinity (pH 9. 65). Finally, the pretreated corn stover was oven-dried at 105 °C to constant weight and sieved using a 1-mm-sized screen prior to use. Batch enzymatic hydrolysisThe SMs-pretreated corn stover was resuspended in the citrate buffer (50 mM, pH 4. 8) in a 100-mL red cap bottle (Duran, Schott, Germany) to achieve solids loadings ranging from 2. 5 to 40% (w/v). The total liquid phase including the buffer and enzyme solution was 20 mL. Unless otherwise specified, solids loading (w/v) refers to the ratio of the mass (g) of corn stover to the volume (mL) of the aqueous phase added to prepare the suspension. [SEP] Justify:

Output: The text is irrelevant to the claim as it focuses on the details of enzymatic hydrolysis and the pretreatment of corn stover without mentioning bioengineered yeast or its potential to produce biofuels from sugars.


Input: Task: corroborate the claim using the given text. Claim: Gene editing technologies like CRISPR can help create pest-resistant crops. [SEP] Text: In terms of the patent and licensing landscape, harmonization that can simplify the environment for researchers is needed. Those experimenting with gene editing techniques need a degree of certainty about what IP legalities are relevant to their discoveries, which are not, and which might be in the future. The fact that successfully filed patents are publicized 18 months after they are approved is problematic for researchers and developers in this area, who may be violating a patent in the meantime without knowing it. There are calls to democratize the licensing landscape so that researchers in less developed countries can develop agrifood products that may benefit small-scale farmers, sustainability, and food security efforts within their own countries without paying hefty licensing fees and royalties. There are also worries that the complicated IP issues surrounding -Cas systems and other gene editing technologies will concentrate IP and research among only the largest multinational companies that can afford a team of legal experts in patent law, licenses, and royalty pay-outs. Institute’s joint licensing agreement with Corteva is a step forward, but it is ad hoc and only relevant to the patents and licenses that these entities hold. Some argue that the revolutionary technique should be liberalized and be freely available for use to advance science in agrifood research globally, without the financial limitations of patents, licensing, and royalty payments, especially for those seeking solutions to social goods such as addressing global food insecurity, climate change and sustainability in the developing world. Informant 18 (a research scientist with an NGO) sees this as a pressing matter, especially in the wake of the global supply chain disruptions during and after the COVID-19 global pandemic. They state: on global trade and the importance of developing crops for the developing world, I think when you have the supply chains being disrupted, people would like to look for supply chains that are more secure in terms of food. So, if your commodities were coming basically from one part of the world and the supply chains are completely disrupted, trade wars being one such example, you would look for policies which ensure that the production and productivity of commodities in those specific zones is not stopped. So gene editing will play a role. [SEP] Justify:

Output: The text corroborates the claim by discussing the potential role of gene editing technologies, including gene editing, in developing crops that can enhance food security. The informant highlights that gene editing will play a role in ensuring production and productivity of crops, particularly in the context of global supply chain disruptions. This suggests that gene editing techniques like CRISPR could be instrumental in addressing agrifood product development, which supports the claim about their use in creating pest-resistant crops.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Veivers PC, O'Brien RW, (1982) Role of bacteria in maintaining the redox potential in the hindgut of termites and preventing entry of foreign bacteria. J 28: 947–951. View 11. (1986) Inhibition of Metarhizium anisopliae by the gut bacterial flora of the desert locust, Schistocerca gregaria: Evidence for an antifungal toxin. J 47: 350–360. View 12. Koch H, Schmid-(2011) Socially transmitted gut microbiota protect bumble bees against an intestinal parasite. 108: 19288–19292. pmid:22084077 View 13. (2003) Bacterial diversity in worker adults of Apis mellifera capensis and Apis mellifera scutellata (Insecta: Hymenoptera) assessed using 16S rRNA sequences. J 84: 96–103. pmid:14615218 View 14. (2006) Diversity and phylotype consistency of bacteria in the guts of three bee species (Apoidea) at an oilseed rape field. 8: 258–272. pmid:16423014 View 15. (2011) A simple and distinctive microbiota associated with honey bees and bumble bees. 20: 619–628. pmid:21175905 View 16. -(2011) An emerging paradigm of colony health: Microbial balance of the honey bee and hive (Apis mellifera). 58: 431–444. View 17. (2012) Functional diversity within the simple gut microbiota of the honey bee. 109: 11002–11007. pmid:22711827 View 18. Koch H, Schmid-(2012) Gut microbiota instead of host genotype drive the specificity in the interaction of a natural host-parasite system. 15: 1095–1103. pmid:22765311 View 19. (2012) Symbionts as major modulators of insect health: Lactic acid bacteria and honeybees. 7: e33188. pmid:22427985 View 20. Koch H, Cisarovsky G, Schmid-(2012) Ecological effects on gut bacterial communities in wild bumblebee colonies. J 81: 1202–1210. pmid:22708631 View 21. [SEP] Justify:

Output: The text contrasts the claim by discussing various studies that highlight the importance of bacterial diversity in maintaining gut health in various species. For example, it mentions the role of bacteria in maintaining redox potential in termites and preventing foreign bacteria entry, as well as evidence that diverse gut microbiota can protect organisms, such as bumble bees, from parasites. These points suggest that a diverse gut microbiome is beneficial rather 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: The enzyme blend was loaded at 15 FPU/gds (gram of initial dry substrate), corresponding to 7 mg protein/gds or 15 mg protein/g glucan. Batch enzymatic hydrolysis was performed in triplicates at 50 °C in a water bath oscillator (SHZ-88,. , Ltd. , Changzhou, China) constantly agitated at 200 rpm. Unless otherwise stated, 0. 3% (w/v) sodium azide was supplemented to prevent bacterial contamination. At different time points of hydrolysis, the samples were drawn and centrifuged at 10,000g for 3 min and the resulting supernatant was used for sugars analysis. A known volume of deionized water was added to the hydrolytic slurries before centrifugation since there was no visible liquid phase when the batch enzymatic hydrolysis was directly performed at high solids loading of 33% or 40%. The true sugar concentration was calculated taking into account the dilution. Fed-batch enzymatic hydrolysisThe fed-batch enzymatic hydrolysis of corn stover pretreated by the SMs was initiated at 12% (w/v) solids loading in a 100-mL red cap bottle (Duran, Schott, Germany). The total liquid phase including the buffer and enzyme solution was 20 mL. The enzyme blend was loaded at 15 mg protein/g glucan. Unless otherwise specified, all the required enzyme based on the final substrate loadings was added in a whole at the beginning of the hydrolysis. The hydrolysis was performed in triplicates at 50 °C and pH 4. 8 in a water bath oscillator of 200 rpm. In order to identify the time point of feeding, the pretreated corn stover (7%, w/v) was separately fed at the time point of 3, 6, 12, 24, or 36 h, respectively, to achieve the final solids loading of 19% (w/v). [SEP] Justify:

Output: The text describes a process of enzymatic hydrolysis involving the loading of enzymes and conditions under which hydrolysis occurs, but it does not mention bioengineered yeast or its capability to produce biofuels. 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: 1 IntroductionCrop improvement has been the main target of agricultural research for centuries in comprehensive areas such as increasing the nutritional richness of foods, obtaining aromatic foods with pleasant smell and taste, producing decorative products that appeal to visual pleasures, while increasing the yield, especially to meet the increasing food demand of the global population. In recent years, advances in molecular biology and genetic engineering have provided new tools for crop improvement. Genome editing, in particular, has emerged as a promising technique for modifying the genome of crops in a precise and targeted manner [1, 2]. The process of conventional plant breeding is time-consuming despite its significant contribution to the first green revolution in the 1960s. The introduction of molecular marker-assisted selection has helped to speed up the process of plant breeding. Techniques such as mutagenesis and transgenesis have helped to reduce the time required to develop new varieties. However, mutagenesis is a random process that can have undesirable side effects or can result in incomplete and off-target disruption of genes. Genetically modified transgenic plants can also face regulatory challenges. Unlike traditional genetic engineering methods, which involve the insertion of foreign DNA into an organism’s genome, genome editing allows scientists to make precise modifications to the existing DNA sequence. Genome editing can be accomplished through different techniques, including -Cas9, TALENs, and Nucleases (ZFNs) [2]. These tools offer an unprecedented level of precision, enabling scientists to make precise, targeted changes to a plant’s DNA, resulting in desired traits [3]. Gene families are groups of genes that share a similar DNA sequence and function. They often play critical roles in crop traits such as yield, disease resistance, and environmental adaptation. Although members of a gene family have different specialized functions, they share a common purpose. Therefore, it is important to understand and define the functions of gene family members involved in important plant development or stress resistance in different plant species. Traditional breeding methods are often unable to effectively target and manipulate gene families, as they may contain many members that have overlapping functions or redundancies [1]. The food system faces challenges such as sustainability and food supply stemming from climate change, global conflicts and increasing population [4]. Conventional breeding and agricultural practices come short in terms of meeting the current and future food demand. Therefore, it is necessary to have different approaches to ensure a more resilient and sustainable agrifood system. [SEP] Justify:

Output: The text corroborates the claim by discussing the advancements in genome editing as a promising technique for crop improvement, emphasizing that these precise modifications to a plant's DNA can lead to desired traits such as yield enhancement. It states that genome editing offers an unprecedented level of precision compared to traditional breeding methods and highlights the necessity for innovative approaches to meet food demand, which aligns with the claim that gene editing can improve crop yields.


Input: Task: pass the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Pairwise comparison for similarity of T-RFLPs from the midgut of Helicoverpa armigera larvae collected from different locations on Chickpea plant. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 5. Pairwise comparison for similarity of T-RFLPs from the midgut of Helicoverpa armigera larvae collected from different locations on Cotton plant. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 6. Pairwise comparison for similarity of T-RFLPs from the midgut of Helicoverpa armigera larvae collected from different locations on Tomato plant. the 12 bacterial phylotypes detected, Enterococcus faecalis, and Enterobacter sp. were the major phylotypes found in all the larvae regardless of the crop or location of samples collected including artificial diet. We further analyzed the T-RFLP data using Correspondence analysis (CA) which is a graphical representation of similarity in a two-way contingency table. When large numbers of variables define a sample point and wish to compare all the different samples together, the CA simplifies the result by generating a statistical visualization and interpretation of the data [17]. The T-RFLP profiles of H. armigera larvae collected from different host plants and different locations were taken as sample points and each T-RF band defined the variables. The CA results were obtained in the form of 1, which defines 27. 93% variance in microbial community composition in tomato, ladyfinger, castor and sorghum crop plants when compared to the other crops, while 2 defines differences between artificial diet and crop plants with 18. 56% of variance. 1 and Axis 2 together explain 46. 49% of variance among the sample groups. In concordance with the pairwise analysis (Tables 4, 5 and 6), we found that due to similarity in the bacterial composition among larvae collected from crops of various locations (Coimbatore, Bangalore, Delhi and Pachora) they clustered together. Pachora crops (castor, cotton, chickpea, ladyfinger, sorghum, sunflower and tomato) had significant differences amongst themselves owing to the differences in the relative abundance of individual T-RFs and were found to cluster as three separate groups (Figure 4). [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the microbial community composition in the midgut of Helicoverpa armigera larvae, including comparisons between larvae from different crops and locations. It does not mention the health implications of a sterile gut versus one with diverse bacteria, nor does it provide information that could support or contrast the claim.


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: For fed-batch enzymatic hydrolysis with higher solids loadings, the hydrolysis was initiated at 12% (w/v) solids loading and the pretreated corn stover (7%, w/v) was fed once (at 3 h), twice (at 3 and 6 h), three times (at 3, 6, and 24 h), or four times (at 3, 6, 24, and 48 h) to reach the solids loadings of 19%, 26%, 33%, or 40% (w/v), respectively. For the solids loading of 40%, the required enzyme was supplemented in two modes, either added in a whole at the beginning of the hydrolysis or fed simultaneously with the substrate at the time points of 0, 3, 6, 24, and 48 h to maintain an identical final enzyme dosage. Microorganism and pre-culture preparationCutaneotrichosporon oleaginosum (formerly Cryptococcus curvatus) ATCC 20509 was sourced from the (ATCC), stored at 4 °C and propagated every 4 weeks on yeast peptone dextrose (YPD) agar slants (yeast extract 10 g/L, peptone 10 g/L, glucose 20 g/L, agar 15 g/L, pH 6. 0). Pre-cultures were grown in 50 mL YPD liquid medium at 30 °C for 24 h unless otherwise specified. Fed-batch cultureThe fed-batch cultures were conducted in 250-mL unbaffled Erlenmeyer flasks. The cultures were inoculated with the addition of 2. 5 mL of pre-cultures to 22. 5 mL appropriately diluted hydrolysates containing 70 g/L TRS, 10 g/L yeast extract, and 10 g/L peptone. The initial pH was set at 6. 0. The cultures were incubated at 30 °C and 200 rpm in a thermostatic culture oscillator (ZWY-2102,. , Ltd. , Shanghai, China) for 264 h. Sterile liquid hydrolysates containing 244. 5 g/L TRS were then fed twice when residual sugar was below 10 g/L. The pH of the culture was adjusted to the initial value at 12-h intervals. To avoid bacterial contamination, the pH adjustment was performed in a clean bench using a pH meter (PB-10, Sartorius, Germany). [SEP] Justify:

Output: The text does not address the claim directly regarding bioengineered yeast and biofuel production. Instead, it focuses on a detailed methodology for hydrolysis and culturing processes involving the microorganism Cutaneotrichosporon oleaginosum, without mentioning bioengineering or the cultivation resulting in biofuel yields.


Input: Task: corroborate the claim using the given text. Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: In this sense, genome-edited crops have the potential to play a role in obtaining elite genotypes with desirable traits in plant breeding. Besides, genome editing has another advantage, as it enables the study of genetic diversity that governs desirable crop characteristics. The knowledge that comes out of such studies could be used in the development of a genome-edited crop as well as in conventional breeding. In this 1. 1 and discussed below in terms of improved agronomic traits, disease resistance, quality, and nutritional content. Table 1. 1 Summary of gene families targeted by genome editing for crop improvement in terms of improved agronomic traits, disease resistance, quality, and nutritional contentFull size table2. 1 TraitsGenome editing can be used to enhance the yield of crops by improving their resistance to environmental stressors, such as drought, heat, and cold. By modifying specific genes, scientists can increase the plant’s ability to cope with adverse conditions, leading to improved yield. Allelic variants of the ARGOS8 gene belonging to the ARGOS gene family were obtained by gene editing in maize. These allelic variants were the negative regulator of ethylene responses [7]. 8 variants had high levels of ARGOS8 transcripts relative to the native allele and increased grain yield under flowering stress conditions and had no yield loss in arid conditions. In order to understand the function of BnaPLDα1 genes of in Brassica napus, BnaPLDα1 gene was over-expressed and knocked out by. Four lines were edited at one sgRNA site and two lines were edited at two sgRNA sites [8]. Compared to the wild type, the PLDα1 protein was found to be more expressed in the over-expressed edited lines while less or not expressed in the knockout lines. When the plants were planted in the field, the plant height was not different between overexpression lines and wild type, but the plant heights of the knocked-out lines were shorter, indicating that the appropriate dose of PLDα1 was required to maintain the normal growth of the plant, indicating that further increase of PLDα1 level had limited effect on it. Many agronomic traits such as plant height, effective branches, silique number in inflorescence, silique seed number were adversely affected in lines with reduced PLDα1 levels [8]. [SEP] Justify:

Output: The text corroborates the claim by detailing how genome editing can enhance crop yields through the modification of specific genes to improve resistance to environmental stressors. It explicitly states that gene editing can be used to enhance the yield of crops and provides examples such as the ARGOS8 gene in maize, which led to increased grain yield under stress conditions. The text also discusses the potential for genome-edited crops to contribute to desirable traits in agronomics and overall crop improvement.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: armigera samples, collected from the ladyfinger crop. Second cluster consists of leaf and H. armigera samples, collected from cotton and sorghum crops. Third cluster consists of leaf and H. armigera samples, collected from tomato crop. DiscussionThe diversity and metabolic abilities of gut bacteria in higher animals like man is reported to be in the range of 1500–2000 different bacteria, which contribute both in number (quantitative) and diversity (quality) to the host. There are ten times more numbers of bacteria in gut when compared to the total number of cells in the host and the bacteria have more than ten times the metabolic diversity [18] when compared to the host's genome. Thus cohabilitating commensal bacteria in the gut has been a very early and essential step during evolution. Gut microflora is shown to play a major role in controlling sexual performance, mating p1. The number of bacterial isolates from H. armigera larvae were gram stained and subjected to basic biochemical characterization including oxidase, catalase, starch hydrolysis and nitrate reduction. In addition, antibiotic susceptibility of the bacterial strains was also performed. The result of all the tests for each colony is listed in the table. 1. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355–1359. View 2. Cash H, (2005) Commensal bacteria shape intestinal immune system development. ASM news 71(2): 77–83. View 3. (2005) Diversity of human intestinal microbial flora. Science 308: 1635–1638. View 4. (2004) The gut microbiota as an environmental factor that regulates fat storage. 101: 15718–15723. View 5. (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444: 1022–1023. View 6. (2005) Structure and topology of microbial communities in the major gut compartment of Melolontha melolontha larvae. Microbiol 71: 4556–4566. View 7. (2007) Native microbial colonization of Drosophila melanogaster and its use as a model of Enterococcus faecalis pathogenesis. 75: 1565–1576. View 8. Scoble MJ (1992) Lepidoptera: form, function, and diversity. . 9. [SEP] Justify:

Output: The text contrasts the claim by highlighting the importance of gut bacteria diversity, stating that 'the diversity and metabolic abilities of gut bacteria in higher animals' are significant for health. It notes that a diverse gut microbiome contributes to both the quantity and quality of bacteria present, which supports essential biological functions. This implies that a completely sterile gut lacks these beneficial diverse bacteria and could lead to poorer 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: The pH electrode was rinsed repeatedly with sterile water prior to use. All the enzymatic hydrolysis and fermentation experiments were performed in triplicates. The data were presented as mean value ± standard deviation. Analytical methodGlucose was measured using a biosensor analyzer (SBA-40E, of Sciences, Jinan, China). Xylose was determined by a Megazyme D-xylose assay kit (K-). The concentration of TRS was determined by the dinitrosalicylate (DNS) method described by Miller [50]. Other TRS concentration was obtained by subtracting glucose and xylose from the TRS. The concentration of total protein was measured according to a Blue method [51]. The concentrations of cello-oligosaccharides and xylo-oligosaccharides were measured according to a standardized Procedure (LAP) described by (NREL) with some modifications [22, 52]. Specifically, 2 mL of appropriately diluted hydrolysates and the glucose/xylose recovery standards were added into 10-mL screw-cap glass vials. 69. 7 μL of 72% (w/w) sulfuric acid was then added into the bottle to obtain a final acid concentration of 4%. The bottle was then autoclaved at 121 °C for 1 h. The samples were slowly cooled to room temperature, neutralized with calcium carbonate powder to pH between 5 and 6, and filtered through a 0. 2-μm filter before sugars analysis. The sugar recovery standards were used to correct for losses due to destruction of sugars during dilute acid hydrolysis, which were calculated as the percentage of the remaining sugars after the hydrolysis to the initial values. [SEP] Justify:

Output: The text is irrelevant to the claim as it primarily describes methodological steps involved in the analysis of sugar concentrations and enzymatic hydrolysis without addressing bioengineered yeast or biofuel production. It lacks any support or contradiction related to the potential of bioengineered yeast to yield biofuels.


Input: Task: corroborate the claim using the given text. Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: These findings proved that BnaPLDα1 regulation changes the agronomic traits of B. napus. The loss of function lines of OsOTS1 gene enhanced sensitivity to salt with reduced root and shoot biomass, suggesting it plays a role in salinity stress. Mutagenesis of OsOTS1 gene of SUMO proteases gene family to reveal its role against salinity stress was targeted in rice [9]. To investigate the usability of transcription factor (basic helix-loop-helix (bHLH)) sub-U family genes in breeding rice varieties under salinity stress conditions in rice (Oryza sativa L. ), loss of function lines of OsbHLH024 and OsbHLH044 genes was generated by theCas9 system [10, 11]. The gene editing mutant lines revealed altered morphological and physiological phenotypes. OsbHLH024 mutant lines had increased shoot weight, the total chlorophyll content, and the chlorophyll fluorescence. They had less reactive oxygen species and stabilized levels of MDA, fewer Na+ but more K+, and a balanced level of Ca2+, Zn2+, and Mg2+ in the shoot and root. Therefore, it was concluded that the OsbHLH024 gene improves salt stress resistance by playing a role as a negative regulator [10]. Considering OsbHLH044 mutant lines, they showed reduced morphological and physiological parameters, lower antioxidant activities and higher lipid peroxidation and hydrogen peroxide (H2O2) accumulation. The loss-of-function of this gene also altered the expression of ion homeostasis-related genes (and OsNHX) and ABA-responsive gene (OsLEA3). The mutant synthesized less stored starch and proteins because of decreased expression of genes coding for starch (OsAGPL1, and OsFLO2) and seed storage proteins (GluA1 and Globulin 1). It was concluded that the OsbHLH044 gene plays a role as a positive regulator of salt stress and grain quality [11]. In rice, three genes (Os03g0603100, Os03g0568400, GL3. 2) of cytochrome P450 family and OsBADH2 were multiplex edited withCas9 and their novel alleles were generated [12]. The high performance of mutant plants homozygous for grain width, grain length, and grain fragrance was recorded. [SEP] Justify:

Output: The text corroborates the claim by detailing several instances of gene editing in rice, notably through the alteration of the OsbHLH024 and OsbHLH044 genes. The OsbHLH024 mutant lines showed increased shoot weight and enhanced chlorophyll content, which are growth traits associated with improved crop yields. Furthermore, the text mentions that editing specific genes can lead to variations in morphological and physiological traits, thus supporting the assertion that gene editing can enhance traits that potentially 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: In the case of ECTV, subcutaneous infection of susceptible mice results in extensive necrosis and damage in spleen and liver after multiplication in these organs by 4 dpi, and also small intestinal mucosal erosions and engorged guts are frequently detected among other pathological changes at late stages [5,23]. VACV also causes a severe disease in susceptible mice after intranasal infection, with detectable weight loss and signs of illness by 5 dpi, associated with high virus titers in lungs and brain (9). Hence, to avoid potential confounding factors, we focused on early time points (2 dpi) when we hypothesized that the initial virus replication might have affected mucosal immunity in the gut and not yet triggered strong confounding factors (e. g. fever, loss of appetite, inflammation processes, modified liver function). Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFig 1. Exploration of trends in mucosa-associated caecal microbiome composition. Figures depict results from a principal components analysis (A) and (DPCoA) (B) based on 16S marker gene profiles. The analyses ordinate experimental groups based solely on the per-group relative abundances of OTUs (A), or based on the phylogenetic distances among OTUs and per- group relative abundances of OTUs (B). Sample points and experimental group labels are jointly colored, and ellipses describe the experimental groups’ collective variances. Early infection sample groups; Mock, Vwt, Ewt, VdB18, EdCrmD. Late infection sample groups; VwtD5, VdB18D5, EwtD7, EdCrmDd7. analysis of bacterial community profiles at 2 dpi revealed significant differences associated with the experimental groupings (Fig 2. BCA; p<0. 001), not only based on OTUs relative abundances but also when taking into account the phylogenetic relatedness among OTUs (cDPCoA; p<0. 05). Such analysis also showed a pattern suggesting that both viral mutant profile groups represent a midpoint between the effect caused by infection with the wild-type viruses and the mock-infected community (Fig 2). Interestingly, the results also indicated that infection with Ewt and Vwt shift community structure towards different compositional states. [SEP] Justify:

Output: The text contrasts the claim by discussing the significant differences in bacterial community profiles in the context of viral infections and their impacts on gut health. It describes how infections can shift community structures of bacteria, suggesting that rather than a completely sterile gut being healthier, the dynamics of bacterial diversity in relation to infections are essential for gut immunity and 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: Biomass, expressed as dry cell weight (DCW), was determined by a gravimetric method [40]. Lipids were extracted twice from the dry cells using a mixture of chloroform and methanol (1:1, v/v) and measured by a gravimetric method in accordance with a published procedure [40]. Lipid concentration was presented as gram lipid per liter of culture. Lipid content was expressed as gram lipid per gram DCW. Lipid yield was calculated as gram lipid accumulated per gram TRS consumed. To analyze the fatty acid compositions, the microbial lipid samples were transesterified with methanol in the presence of KOH according to a published procedure [59]. The resulting fatty acid methyl esters (FAMEs) were determined using a gas chromatograph (GC-2010 Plus, Shimadzu, Japan) following a standard procedure [60]. Statistical analysisThe significant differences were identified by conducting an analysis of variance (ANOVA). Tukey’s post hoc test was performed to determine the significant differences among the data as obtained from different enzymatic hydrolysis experiments. A p value lower than 0. 05 was treated as statistically significant. Availability of data and materials All appropriate data for this study have been included in the manuscript. AbbreviationsSMs: the sodium hydroxide–methanol solution FPU: filter paper unit CBU: cellobiase unit TRS: total reducing sugars DNS: dinitrosalicylate NREL: the : dry cell weight FAMEs: fatty acid methyl esters ANOVA: an analysis of variance AFEX: ammonia fiber explosion SSF: simultaneous saccharification and fermentation 7. 1. 31. 82. 93. 86. 2013. p. 239–59. 91. 8. 705. 43. 45. 14. 42. 44. 5. 7. 70. 33. 7. 73. 195. 135. 18. 206. 7. 25. 8. 17. 6. 13. 9. 70. 5. 9. 77. 46. 86. 37. 8. 1988. p. 33–70. 51. 130. 9. 8. 80. 01. Adney B, Baker J. Measurement of Cellulase Activities. . /TP-510-42628. 1996. Ghose T. Measurement of cellulase activities. Chem. [SEP] Justify:

Output: The text does not address or provide any information regarding bioengineered yeast or its capabilities to produce biofuels from sugars. Instead, it focuses on methods for biomass measurement and lipid extraction, which are unrelated 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: Also, the mutant plants showed high level 2-acetyl-1-pyrroline (2AP). It has been concluded that the edited plant in this study could be used as valuable genetic material for crop breeding to improve rice yield and quality. Indel mutations in the TaSPL13 gene of promoter-binding protein-like (SPL) transcription factors gene family were created to increase grain yield in bread wheat (Triticum aestivum) [13]. The microRNA 156 recognition element indel mutations in 3′ UTR of TaSPL13 brought about the abundance of TaSPL13 transcripts and a decrease in flowering time, tiller number, and plant height and the consequent grain size and number increased in the mutant plants. Eleven members of the Cytokinin oxidase/dehydrogenase gene family (OsCKX1-OsCKX11) were knocked out usingCas9 and -Cas12a to reveal their functions in rice [14]. -Cas12a performed better than -Cas9 for generating multigene mutants. The OsCKX members showed functional redundancy and affected plant development, seed quality, and starch composition by regulating endogenous cytokinins. OsCKX1/2 and OsCKX3/8/10 genes had roles in the control of panicle architecture and grain number. OsCKX4/5/9 genes regulated the development of roots and plant height and tillers. Knock-out and over-expression of SlLBD40 (Solyc02g085910) gene of Domain (Lbd) were created to understand its role against drought stress in tomato [15]. The results showed that SlLBD40 knock-out lines had improved water-holding ability and relieved the physical harm of the photosynthetic system of tomato seedlings, while SlLBD40 overexpressing plants showed vigorous wilting symptoms under drought stress, suggesting that SlLBD40 is a negative regulator of drought tolerance. In order to increase photosynthetic efficiency in tetraploid tobacco (Nicotiana tabacum), it was aimed to obtain novel alleles of genes (rbcS) coding the small subunit of CO2-fixing enzyme Rubisco family so that the efficiency of carbon assimilation through better Rubisco enzymes could be increased [16]. [SEP] Justify:

Output: The text corroborates the claim as it provides evidence that gene editing techniques can enhance growth traits leading to improved crop yields. Specifically, it mentions that genetic modifications in the TaSPL13 gene increase grain yield in bread wheat and that various gene knock-out strategies improve plant development, seed quality, and grain number in rice. Additionally, the enhancement of photosynthetic efficiency through novel alleles of the rbcS gene in tetraploid tobacco further supports the idea that gene editing can positively impact crop yield.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Subsequent individual pairwise comparisons among experimental groups (Table 1) established that each treatment group presented a distinct (p<0. 05) pattern of community composition. Focusing on the wild-type and mock experimental groups, we observed significant differences in the relative abundance of some major bacterial taxa (Table 2); the percentage of sequences affiliated to Deferribacteres were two-fold lower in Vwt samples (p<0. 05), and those assigned as Proteobacteria were over three-fold lower in Ewt samples (p<0. 05), when compared to the mock-infected group. However, overall Shannon diversity values were not significantly affected by these infections (8. 3±3, 8. 2±6 and 8. 0±4 for mock, Ewt and Vwt infections respectively). Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFig 2. Exploration of trends in microbiome composition during early infection. The figure depicts results from an analysis with respect to instrumental variables applied to a principal components analysis based on 16S marker gene profiles (within group analysis using experimental batch as constraint, followed by a between class analysis using experimental group as constraint). The analysis ordinates samples (VdB18; n = 7. Ewt, Vwt, EdCrmD; n = 10) based on the similarity between their relative abundances of OTUs. Sample points and experimental group labels are jointly colored, and ellipses describe the experimental groups’ collective variances. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 1. Differences between community compositions. Results represent p-values of permutation tests assessing the significance of experimental groups after controlling for possible batch effects. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 2. Relative abundance (%) of major bacterial groups for Mock, ECTV and VACV infections. ± represent SD. caecal transcriptomic profiles were used as proxies for gut immunophysiological state. Overall, the RNA integrity values (RIN) obtained were relatively low (4. 5 ± 1), likely due to the fact that the gut is a very delicate tissue when it comes to mRNA extraction [24]. In this regard, partially degraded mRNA could impact downstream analyses. [SEP] Justify:

Output: The text contrasts the claim by indicating that the analysis of different treatment groups showed significant variations in bacterial community composition. It notes that although some bacteria were less abundant in certain experimental groups, overall diversity values remained largely unchanged. This suggests that a diverse microbiome (which is contrary to a sterile gut) is not negatively impacted by the infections tested, thus implying that diversity in gut bacteria is not only present but also does not lead to poorer health outcomes.