Input: Task: corroborate the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: The sustainable harvest residuals and thinnings alone are estimated at about 75 million tons/year accordingly to the DOE biomass report [1]. These forest residuals and thinnings could produce the equivalent of 5 billion gallons of lignocellulosic ethanol annually. Woody biomass feedstocks include softwood and hardwood. Various pretreatment methods have been developed for pretreating biomass before an enzymatic conversion of pretreated biomass into monomeric sugars for a biofuel or a bioproduct conversion process. An overview on lignocellulosic biomass pretreatment methods well described that most of the pretreating methods worked well on herbaceous biomass and hardwood biomass while not working well with high lignin content softwood biomass [2]. Thus, softwood biomass is the most recalcitrant biomass to pretreat for enzymatic hydrolysis. To utilize the most recalcitrant lignocellulosic materials, an efficient, scalable and cost effective pretreatment method is needed. Bisulfite pulping was a widely used industrial method for pretreating woody biomass for papermaking industries. In 1867, Tilghman invented the use of calcium bisulfite to pulp wood [3, 4]. The first commercial sulfite process for sulfite pulp production was built in 1874 in Bergvik, Sweden [5]. Due to its effectiveness in lignin sulfonation and lignin removal from wood, bisulfite or sulfite pulping has been used for almost 14 decades in the papermaking industry. In addition, spent sulfite pulping liquor is rich in hemicellulose sugars, such as arabinose, galactose, mannose and xylose. However, the spent sulfite liquor also contains some glucose. Spent sulfite liquor has been a source of hemicellulosic sugar for renewable biofuel fermentation, as demonstrated by Tembec for over two decades [6]. Sulfite pulping sludge has been found highly digestible by enzymes and suitable for producing lignocellulosic ethanol [7–9]. The cost that goes into producing a bleached sulfite pulp, however, is high compared to the price of the sugar that it could replace. [SEP] Justify:

Output: The text corroborates the claim by discussing the use of hemicellulosic sugars derived from spent sulfite pulping liquor as a source for renewable biofuel fermentation, indicating that sugars can indeed be converted into biofuels. Specifically, it details how these sugars, along with lignocellulosic ethanol production, relate to bioengineering applications in the production of biofuels.


Input: Task: contrast the claim using the given text. Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: Response: Added a bar plot of Phyla relative abundances to the PCoA ordination in figure 5 (labeled ‘a’ and ‘b’) and statistical data in the supplementary file (Table S4). DiscussionL354-357. Can you remind here when was the sampled post-mining site restored? Was it at 2007? I wonder if one reason for the lack of photosynthetic potential difference between post-mining and natural biocrusts is because the biocrust in the post-mining site has been already recovered. For example, soil colonization by cyanobacteria can be faster than thought. Response: I mentioned the restoration year in L375. I agree that it is likely that the biocrusts we sampled have a significant cyanobacterial community, however we hypothesize that the recovery of the biocrust differs even within the mining site, emphasizing the importance of microenvironments, where certain areas have more developed biocrusts and others have less developed biocrust even within the same post-mining plot. I referenced this in the discussion (L376 – L383): “…However, in the current study, we sampled post-mining biocrusts at a different location in the Gov mining site (~500 m away from the original plot) due to technical constraints. In the new location we found that the photosynthetic potential of the biocrust in the post-mining plots did not differ from the natural biocrust. These results highlight the importance of microenvironments in shaping the functionality of biocrusts (Garcia-Pichel and Belnap, 1996). The similarities in active communities and photosynthetic potential could be due to more developed biocrusts in the new sampling locations compared to the previous ones. ”L369-370. There is little discussion on the results of the Picrust analysis. It would be nice to compare the results of this study with other studies that have also examined functional genes in biocrusts to see if abundances of the functional genes at this site greatly differ from those of biocrusts of other regions. Response: I added a paragraph addressing the analysis with reference and comparison to a previous study that used to infer functional potential (L395 – L405):“…analysis revealed no significant differences in the abundances of genes within any of the function categories examined (Fig. 6). [SEP] Justify:

Output: The text contrasts the claim by discussing the recovery and photosynthetic potential of biocrusts in post-mining sites and their similarity to natural biocrusts, implicating that plants (or similar organisms) can thrive outside of traditional soil environments. The reference to microenvironments and the ability of certain biological communities to recover and exhibit functionality suggests that growth is not limited to soil alone.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: CircParser also filters out non-informative blast results, such as “uncharacterized”, “clone”, “linkage group” and others from the output table. Figure 1: An overview of the CircParser pipeline. (A) The pipeline includes merging of the circRNAs with overlapping genome coordinates and presents the number of different circRNAs originating from one host gene. (B) CircParser includes the prediction of circRNA structural components using a genome annotation gff/gff3 file. Download full-size image DOI: 10. 7717/peerj. 8757/fig-1 CircParser can also discriminate circular RNAs by their structural components: exonic, intronic, exon-intronic or intergenic using genome annotation gff/gff3 file (-a parameter). In this case, the user should avoid circRNAs coordinate merging (using –np parameter) during the pipeline implementation for correct results (Fig. 1B). Usage: perl CircParser. pl -np -b INPUT_FILE –genome REF_-a. gff However, poor quality of annotation file can lead to errors in the circRNAs structure analysis. implementation of CircParser is available at applied CircParser to twelve merged coordinate files that contained information about joint coordinates for circRNAs predicted using CircExplorer2, miARma-Seq (with CIRI predictor), CIRI2, find_circ, and circFinder. The five different algorithms predicted on average ∼131 (CircExplorer2); ∼501 (CIRI); ∼706 (CIRI2); ∼257 (find_circ), and ∼398 (circFinder) circRNAs per sample, with an insignificant overlap ∼37 circRNAs (Fig. 2; Table S1), similarly to previously published comparisons (Hansen, 2018; Hansen et al. , 2016). Figure 2: Number of circular RNAs that have been predicted by 2, CircExplorer2, find_circ, circFinder, and that are common between all prediction algorithms. Download full-size image DOI: 10. 7717/peerj. 8757/fig-2 To access the host gene of circular RNAs and to reduce false-positive rates, only overlapping circRNAs (Fig. 2) were used in CircParser. [SEP] Justify:

Output: The text is irrelevant to the claim. It discusses the CircParser pipeline for analyzing circular RNAs without mentioning anything about space exploration or the documentation of planets.


Input: Task: corroborate the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: Blastobotrys adeninivorans and B. raffinosifermentans, two sibling yeast species which accumulate lipids at elevated temperatures and from diverse sugars access Published: 20 June 2019 Blastobotrys adeninivorans and B. raffinosifermentans, two sibling yeast species which accumulate lipids at elevated temperatures and from diverse sugars Stéphane Thomas1 na1, Daniel R. A. Sanya1 na1, Florian Fouchard1, Huu-Vang Nguyen1, Gotthard Kunze2, Cécile Neuvéglise1 & …Anne-Marie Crutz-: orcid. org/0000-0001-9111-51851 Show authors Biotechnology for Biofuels 38. 1 ± 1. 6% of its dry-cell weight, and synthesize lipids from various sugar substrates, up to 36. 6 ± 0. 5% when growing in cellobiose. Both species, represented by LS3 and CBS 8244T, could grow with little filamentation in the lipogenic medium from 28 to 45 °C and reached lipid titers ranging from 1. 76 ± 0. 28 to 3. 08 ± 0. 49 g/L in flasks. Under these conditions, the maximum bioconversion yield (YFA/S = 0. 093 ± 0. 017) was obtained with LS3 at 37 °C. The presence of genes for predicted subunits of an ATP citrate lyase in the genome of LS3 reinforces its oleaginous character. ConclusionsBlastobotrys adeninivorans and B. raffinosifermentans, which are known to be xerotolerant and genetically-tractable, are promising biotechnological yeasts of the Saccharomycotina that could be further developed through genetic engineering for the production of microbial oil. To our knowledge, this is the first report of efficient lipid storage in yeast when cultivated at a temperature above 40 °C. This paves the way to help reducing costs through consolidated bioprocessing. BackgroundThe use of renewable feedstocks to produce microbial oil for biodiesel or other applications has become a scientific and environmental issue over the last two decades. [SEP] Justify:

Output: The text corroborates the claim by discussing the ability of two yeast species, Blastobotrys adeninivorans and B. raffinosifermentans, to synthesize lipids from various sugar substrates, which implies the potential for biofuel production. The mention of efficient lipid storage and the potential for genetic engineering to enhance this capability further supports the claim that bioengineered yeast can produce biofuels from sugars.


Input: Task: contrast the claim using the given text. Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: In contrast, a previous study conducted in the Highlands, examined active bacterial communities during a rain and subsequent drying (Baubin et al. , 2021). The results indicated an increase in genes related to photosynthesis, light, and sensing following the rain, while the other function categories did not vary significantly. We note that the identity and abundances of the functional genes in the dry biocrusts detected by Baubin et al. , (2021) and here (Fig. 6) are similar. Therefore, we propose that the similarity between the post-mining and natural biocrust communities (Fig. 5) reflect similar functional potential (Fig. 6). However, low abundance of active ASVs were used to infer the abundances of functional genes (Fig. 6), and large variance between samples in post-mining biocrusts could mask significant differences (Table S5). ”L379-381. It is hypothesized that the low bacterial growth in harsh environments like this one could be because biocrusts prioritize activation and preparation for desiccation over growth. However, this hypothesis cannot be fully demonstrated with the reported results. Could you add 401. Is there any practical experience of the application of cyanobacteria inoculation to restore this mining site in Israel? If so, it would be nice to add a few sentences regarding the potential of this technique to restore biocrust in the current mining site. Response: No, there have not been any active restoration measures in Zin mining sites and no previous scientific studies regarding the mining practices of ICL mining company. I address the need for active restoration measures in Zin mining sites (including cyanobacteria inoculation) in L439 – L444:“…Our results further emphasize the need for active restoration measures in the Zin mines. Such measures include soil inoculation with local cyanobacterial propagules (Acea, 2003, Wang et al. , 2009, Zhao et al. , 2016, et al. , 2017) and increased hydration (Morillas & Gallardo, 2015, Zhang et al. , 2018), which were effective in enhancing biocrust establishment and recovery following disturbances (Antoninka et al. , 2020). ”Table 1. Values should also include the standard deviation. Response: I added SD values to the table (L254 – L254). [SEP] Justify:

Output: The text contrasts the claim by discussing active restoration measures such as soil inoculation with cyanobacterial propagules and increased hydration. These methods have been effective in enhancing biocrust establishment and recovery following disturbances, suggesting that plants (or plant-like organisms such as cyanobacteria) can thrive in conditions that do not strictly involve traditional soil. Additionally, the mention of successful methods for biocrust recovery indicates that alternatives to soil methods can indeed support plant growth.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: This pipeline allows the elimination of non-informative outputs (e. g. , contains only chromosome/contig name, number of uncharacterized loci, or name of BAC clone, and etc. ), while keeping more the relevant blast results and retrieving the likely host gene name for the circular RNAs; in the case of impossibility to find identical sequences in the database, this tool mark these sequences as ). CircParser results also allow us to determine the number of circRNA types from one host gene and their minimum and maximum size in base pairs (bp). We showed that our algorithm detected presumable host gene names for the vast majority of predicted circRNAs. Moreover, most of them were related to muscle functions (e. g. , calcium/calmodulin-dependent protein kinase, troponin T3, myocyte-specific enhancer factor 2C, and others), and immune-related genes (MHC class IA antigen), which were consistently found among different individuals (Table S2), despite the relatively low coverage for circRNAs analysis of the sequencing data used (Mahmoudi & Cairns, 2019). An example of circRNA structure analysis for 2, CircExplorer2, find_circ, and circFinder outputs is presented in S3. To estimate the capacity of our pipeline we compared a number of host genes that were predicted by CircExplorer2 and CircParser (CircExplorer2 outputs were used as input files) for the same O. niloticus fast muscle datasets used earlier. As a result, CircParser shows greater efficiency for Nile tilapia, improving the number of predicted host genes up to two-fold (Fig. 3). Figure 3: CircParser capacity: number of host genes that were predicted by CircExplorer2 and CircParser. Download full-size image DOI: 10. 7717/peerj. 8757/fig-3 Another equally important aspect of CircParser concerned the accuracy of this pipeline. The most well-annotated reference genome of zebrafish (assembly GRCz11) and zebrafish muscle transcriptomic dataset (ERR145655) were used for accuracy estimation, i. e. , the agreement between the annotation file and CircParser output. We showed that in this case, CircParser host gene prediction was confirmed in 82. 4% cases. [SEP] Justify:

Output: The text discusses a computational pipeline related to circRNA analysis and does not address planetary exploration or documentation. Therefore, it is irrelevant to the claim about the exploration of planets.


Input: Task: corroborate the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: [17] reported the relative fatty acid (FA) composition of two strains of this species, without however mentioning the total amount of lipid. Several yeast species are well-known lipid producers. Three have attracted most of the research efforts in recent years [18]: Yarrowia lipolytica and Lipomyces starkeyi, belonging to the Saccharomycotina, and Rhodotorula (Rhodosporidium) toruloides, belonging to the Basidiomycota. All three species exhibit a genome size of over 20 Mb [19,20,21]. L. starkeyi and R. toruloides are known for their utilization of a wide range of substrates and their outstanding lipogenic capabilities (up to 70% DCW as lipids) [22,23,24]. L. starkeyi is particularly well suited for rapid and simultaneous utilization of sugar mixtures, reaching a lipid content of 52% DCW and a lipid titer of 13. 3 g/L in a mixture of cellobiose and glucose [25]. Strain diversity or culture conditions may alter lipid production; to maximize lipid production, the synthesis of endopolysaccharides under nitrogen limitation should be avoided [26]. Although progress has been made in recent years, the genetic engineering of these yeasts is still a shortcoming [18]. B. adeninivorans is phylogenetically close to Y. lipolytica [27]. Some strains of Y. lipolytica, as well as other species in the genus, are naturally more prone to store lipids from exogenous hydrophobic compounds than to turn glucose into lipids. Lipid content can easily reach 30% DCW [28] in the former case and generally 6 to 15% DCW in the latter [28, 29]. Metabolic engineering and/or process optimization, as well as strain screening, have been successfully used to increase lipid content above 35% DCW and reportedly up to 90%. Y. lipolytica has also required genetic engineering or specific culture conditions to utilize xylose, cellobiose, or cellulose polymers, which are major components of lignocellulosic materials. [SEP] Justify:

Output: The text corroborates the claim by discussing yeast species like L. starkeyi and Y. lipolytica, which are noted for their lipid production capabilities from substrates such as glucose and other sugars. Specifically, it mentions that L. starkeyi can utilize sugar mixtures and achieve substantial lipid content, indicating a potential for biofuel production. Additionally, it highlights the advancements in metabolic engineering which have enhanced the lipid content even further, supporting the idea that bioengineered yeast can effectively convert sugars into biofuels.


Input: Task: contrast the claim using the given text. Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: of for to & Inclusion Statement/Code of News and this journal Search all journals of for to & Inclusion Statement/Code of News and this journal Search all journals HortDate: 01 Dec 2014 Online ISSN: 2327-9834 Advertisement 10. 21273/. 49. 12. 1506 Free access Download PDF Cite this 0. 05; t test) in biomass production between the plants grown aeroponically and hydroponically. Aeroponically grown plants produced an average of 49. 8 g dried aerial plant material (DW) (sd 20. 7) per plant, whereas hydroponically grown plants produced an average of 57. 6 g DW (sd 16. 0). In contrast, withaferin A content was statistically higher in plants grown hydroponically. These plants contained an average of 7. 8 mg·g−1 DW (sd 0. 3), whereas the aeroponically grown plants contained an average of 5. 9 mg·g−1 DW (sd 0. 6). These results demonstrate that hydroponic techniques are optimal in reproducibly and efficiently generating withaferin A. These findings may be of importance to the natural products industry in seeking to maximize production of biologically active compounds from medicinal plants. Keywords: optimization of plant secondary metabolites synthesis; plant pharmaceuticals; soilless plant culture; natural productsIntensified interest in plant secondary metabolites for anticancer and other disease treatments has led to recent exploration of medicinal plant growth conditions to optimize biomass production and metabolite synthesis (Cragg et al. , 2009; Nagella and Murthy, 2011). Our study compares these variables for Withania somnifera when grown under soilless hydroponic and aeroponic conditions. W. somnifera (L. ) Dunal (Solanaceae) has been used for over 3000 years in the Ayurvedic medical tradition of India (Dalavayi et al. , 2006). Preparations of dried root powder called “ashwagandha” have been administered as a general tonic to increase energy, improve overall health and longevity, and to prevent diseases (Xu et al. , 2009). Currently, considerable attention is focused on the anticancer properties of one of the secondary metabolites, withaferin A (WA), of this medicinal plant (Mishra et al. , 2000). [SEP] Justify:

Output: The text contrasts the claim by providing evidence that plants can thrive in alternative methods like hydroponics and aeroponics. It specifically states that the study compares biomass production between plants grown aeroponically and hydroponically, indicating both methods can be effective for plant growth. Additionally, the text demonstrates that certain plants can produce higher yields and specific metabolite contents using these soilless methods, thereby contradicting the claim that plants can only grow in soil.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: Conclusions Thus, we conclude that CircParser represents a reproducible workflow that enables researchers to effectively predict the host genes for circular RNAs, even in non-model organisms with poorly annotated genome assemblies. Sequencing and quality trimming statistics Number of circular RNAs have been predicted by CircExplorer2, CIRI/ miARma-Seq, CIRI2, find_circ, and circFinder software. The number of common circular RNAs predicted by all methods is also indicated. DOI: 10. 7717/peerj. 8757/supp-1 CircParser pipeline output table for overlapping circRNAas (without structural component analysis) DOI: 10. 7717/peerj. 8757/supp-2 CircParser pipeline output table for overlapping circRNAs (with structural component analysis) DOI: 10. 7717/peerj. 8757/supp-3 We would like to acknowledge Jorge Galindo-Villegas from (Norway) and Tomas B. Hansen from the (Denmark) for their valuable advice. M. O. Fernandes is an for PeerJ. The authors declare there are no competing interests. conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft. conceived and designed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft. Md. analyzed the data, authored or reviewed drafts of the paper, and approved the final draft. analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft. performed the experiments, authored or reviewed drafts of the paper, and approved the final draft. Jorge M. O. Fernandes conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft. DNA following information was supplied regarding the deposition of DNA sequences: Data is available at the database: GSE135811. The following information was supplied regarding data availability: CircParser is available at Github. [SEP] Justify:

Output: The text discusses a workflow for predicting host genes for circular RNAs and mentions various software used in this process. It does not provide any information about the exploration or documentation of planets, making it irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: 5 g/L NH4Cl in YNB medium with 30 g/L carbon source, leading to a mass carbon-to-nitrogen ratio (C/N) of 60 and 90, respectively). Under these conditions, lipogenesis began at the start of growth for all strains. The highest amount of lipids in the cells was reached after 72 h and ranged from 14 to 29% DCW (Figs. 3, 4). Lipogenesis was negligibly better at C/N 90 than C/N 60 (up to 10% better) but it lowered growth and global sugar consumption. Fig. 3Bioconversion of sugars into lipids during the growth of two strains of B. raffinosifermentans in nitrogen-limited YNB-based media. Glucose and xylose were each used as the C source (30 g/L) at two different C/N ratios. Average values and the standard deviation (n = 3) for OD600 (blue line), residual sugar in the medium (g/L, plain green line), cumulative organic acids (g/L, dotted green line), and lipid content (% DCW, orange line) were plotted over time (h)Full size image Fig. 4Bioconversion of sugars to lipids during growth of two strains of B. adeninivorans in nitrogen-limited YNB-based media. Glucose and xylose were each used as the C source (30 g/L)at two different C/N ratios. Average values and the standard deviation (n = 3) for OD600 (blue line), residual sugar in the medium (g/L, plain green line), cumulative organic acids (g/L, dotted green line), and lipid content (% DCW, orange line) were plotted over time (h)Full size image The four strains exhibited different behaviors in terms of growth and metabolism, lipid accumulation, organic acid excretion, and sugar consumption. There were no strict species-specific correlations. CBS 7377 was the slowest and least efficient strain for lipid accumulation, whereas LS3 (of the same species) reached the highest lipid content. Conversely, the OD reached by LS3 in stationary phase was the lowest of all strains. However, different OD may reflect morphological differences between strains rather than differences in biomass production. The results of the strains of B. adeninivorans were more similar to each other. [SEP] Justify:

Output: The text corroborates the claim by discussing the bioconversion of sugars into lipids by yeast strains in nitrogen-limited media. It specifically mentions the use of glucose and xylose as carbon sources, which indicates that sugars are being converted into lipid products, a form of biofuel. This process demonstrates the capability of bioengineered yeast to utilize sugars for biofuel production.


Input: Task: contrast the claim using the given text. Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: It is therefore important to determine how to increase plant biomass and WA production by comparing outcomes from traditional, in-soil growing conditions with soilless hydroponic and aeroponic conditions in controlled greenhouse environments. Growing plants in controlled environments (greenhouses), using hydroponic and aeroponic conditions, reduces exposure to pests, permits application of reproducible growth conditions, and allows for year-round biomass production (Muro et al. , 1997). These benefits are then associated with increased yield and quality of secondary metabolites used as potential pharmaceuticals. Because biomass production and especially secondary metabolites (like WA) may be related to the plant's defense mechanisms, it is possible that “over”-controlling the growing conditions in the greenhouse may actually reduce the plant's synthesis of these parameters. In future studies, we plan to include stressors such as heat, salt load, and partial dehydration to test how these stressors affect WA synthesis. Controlling other factors (in the greenhouse) would therefore allow us to isolate the particular stressor that specifically improves secondary metabolite (WA) production while optimizing other growth conditions. In hydroponics, the roots of the plants are maintained in a static, continuously aerated, or discontinuously flowing nutrient liquid solution (Jones, 2004; Souret and Weathers, 2000). In aeroponics, water and nutrients are supplied through a fine mist that deposits droplets of nutrient solution on the roots (Souret and Weathers, 2000; Zobel et al. , 1976). These soilless methods are optimal for medicinal plant research and production because they eliminate soilborne pests, prevent contamination through field-grown plant species, and afford a more rigorously controlled, year-round growing environment. Materials and MethodsSeeds of Withania somnifera were obtained from the Center (NPC; University of Arizona) stock collection (6 months old, stored at 4 °C). They were germinated in 1-inch Grodan rockwool cubes in a germination chamber kept at 28 °C with 16 h of fluorescent lighting. After ≈5 weeks (late summer), seedlings with an aerial length of ≈5 cm were transferred to a float system [deep water culture containing 50% modified Medium (Hoagland and Arnon, 1950); see composition in Table 1] in the greenhouse [25 °C, 45% relative humidity (RH) and a light shadecloth to protect from direct sunlight]. [SEP] Justify:

Output: The text contrasts the claim by providing detailed information on how plants can successfully grow using hydroponics and aeroponics, which are soilless growing methods. It highlights the advantages of these methods, such as reduced exposure to pests and the ability to control growth conditions, thereby supporting the notion that plants can thrive outside of traditional soil environments. The text explicitly states, "These soilless methods are optimal for medicinal plant research and production" and describes how these techniques can lead to year-round biomass production, which directly counters the claim.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: Availability and implementation: implementation of CircParser is available at study has received funding from the Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 683210) and from the of Norway under the Toppforsk programme (grant agreement no 250548/F20). was supported by the RFBR (for Basic Research) Grant no 19-54-54004. This work was partially carried out in for and supported by Ministry of Science and of Russian Federation, grant #075-15-2019-1659. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 2019. miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data. Methods 152:31-40. 2019. circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs. Bioinformatics 36(2):539-545. 2012. Transcriptome-wide discovery of circular RNAs in Archaea. Research 40:3131-3142 Ekblom R, Wolf JB. 2014. A field guide to whole-genome sequencing, assembly and annotation. 7:1026-1042. 2018. CircView: a visualization and exploration tool for circular RNAs. Briefings in Bioinformatics 19:1310-1316. 2015. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. 16:4. 2018. Circular RNA identification based on multiple seed matching. Briefings in Bioinformatics 19:803-810 Hansen TB. 2018. Improved circRNA identification by combining prediction algorithms. Frontiers in Cell and 6:20. 2016. Comparison of circular RNA prediction tools. Research 44:e58. 2018. Molecular roles and function of circular RNAs in eukaryotic cells. Cellular and Science 75:1071-1098. 2019. Identification of virus-encoded circular RNA. Virology 529:144-151 -. 2016. salmon genome provides insights into rediploidization. Nature 533:200-205 Mahmoudi E, Cairns MJ. 2019. Circular RNAs are temporospatially regulated throughout development and ageing in the rat. 9:2564 Marcel M. 2011. [SEP] Justify:

Output: The text is irrelevant to the claim because it discusses various studies and research funding related to circular RNAs and bioinformatics, and does not provide any information about planets or their exploration.


Input: Task: corroborate the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: Overall, both species cultivated in low-nitrogen medium reached a lipid content above 20%. Sugar uptake was more efficient for LS3 than for other strains in all media (Figs. 3, 4). With few exceptions, < 75% of the initial sugar was consumed by the end of experiment, leaving room for optimization of the medium and culture conditions. Within the time of the experiment, B. raffinosifermentans LS3 reached the highest lipid content among all four strains, whereas B. adeninivorans CBS 8244T accumulated lipid more slowly and probably did not reach its maximum. The excretion of organic compounds is a well-known competing sink for lipid production, particularly that of citric acid, both an intermediate of the TCA cycle and a precursor for acetyl-CoA in oleaginous yeasts. In our shake-flask experiments, we found two different organic acids to be excreted into the medium: citric acid and acetic acid. Globally, their cumulative concentration in the medium (Figs. 3, 4) tended to steadily rise over time and reached 3. 4 ± 0. 2 g/L (CBS 7766 cultivated in xylose C/N 90) to 10. 1 ± 0. 6 g/L (LS3 cultivated in xylose C/N 90) by the end of experiment. LS3 was unique concerning the excretion of organic acids, both in terms of their total concentration, which did not increase after 50 to 60 h of cultivation in some media, and the relative proportion of acetic to citric acid. Although acetic acid was the most abundant organic acid excreted by all other strains, excretions of citric acid was equivalent or more abundant in LS3 (Additional file 1: Figure S3). In glucose media, in particular, the final concentration of acetic acid was no more than half that of citric acid for this strain. This lower final concentration of acetic acid was due to reaching the plateau early (C/N 90, Additional file 1: Figure S3) or clear reuptake of this compound (C/N 60, Additional file 1: Figure S3), whereas glucose was not exhausted. [SEP] Justify:

Output: The text corroborates the claim by discussing the lipid content produced by bioengineered yeast strains cultivated under different conditions. The mention of efficient sugar uptake and lipid production directly supports the concept that bioengineered yeast can transform sugars into biofuels, as lipids are potential biofuel sources.


Input: Task: contrast the claim using the given text. Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: The nutrient medium (NM) was stone-aerated using an air pressure pump (EcoAir 5) for 1 min every 5 min to promote aerial plant and root growth. When the plants reached an aerial height of 10 to 15 cm (≈6 weeks) (in early fall), they were transferred to an aeroponics box measured 1. 0 m × 1. 0 m × 1. 5 m (width × length × height) or to a hydroponic system (nutrient film technique with drip irrigation using a 5″ × 5″ × 10″ polyvinyl chloride pipe). Both systems were located in the same greenhouse. There were seven plants in the aeroponics box and seven plants in the hydroponics system. In both environments, the interplant distance was the same at 20 cm. In the aeroponics system, plants were arranged on the periphery of a square platform, whereas in the hydroponic system, the plants were arranged linearly. Therefore, in both systems, the plant density was similar. Plants in the aeroponics system were irrigated with NM for 1 min every 4 min and in the hydroponics system for 1 min every 10 min. The hydroponic system contained a small volume of nutrient film in the pipe so that the roots were exposed to nutrients even when irrigation was off. For both systems, the NM was sourced from the same reservoir containing the NM with a pH of 5. 9 and electroconductivity (EC) of 1. 85 dS·m−1. Table 1. Composition of nutrient medium (NM). z Plant growth was assessed by measuring the height of all plants and calculating the weekly averages for both systems. In addition, the surface area of one average-sized leaf of six randomly chosen plants per system was measured every week and weekly averages were calculated. This was done by tracing the leaf (while remaining on the plant) on a plain paper and cutting it out on paper. This paper was weighed and the surface area determined by using a predetermined surface area of paper-to-weight ratio. To measure plant biomass production, all plants were harvested at the flowering stage (8 weeks after transfer to the two growth conditions), and both wet and dry weights were recorded for aerial and root segments. The aerial parts were weighed individually per plant and the roots were measured as a total for each system. [SEP] Justify:

Output: The text contrasts the claim by detailing experiments conducted in both aeroponic and hydroponic systems, demonstrating that plants can not only grow but thrive in these alternative methods. The text explains how plants were transferred to an aeroponic box and a hydroponic system, with specific measurements of growth and nutrient systems indicating successful plant development outside of traditional soil.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: Skip to Content eLife home page your research Search by keyword or author Reset form my search to Genetics and 10. 7554/eLife. 46922 Open access Copyright information Version of RecordSeptember 24, 2019 Open annotations (there are currently 0 annotations on this page). 12,314 views 1,028 downloads 124 6922. Copy to clipboard Download BibTeX Download. RIS Full text Figures and data Peer review Side by side Additional files 10 figures, 2 tables and 6 additional files 1 with 2 supplements Download asset Open asset Estimating the rate of germline mutation using multigenerational CEPH/Utah pedigrees. (a) The CEPH/Utah dataset comprises 33 three-generation families. Summaries of sequencing coverage for CEPH/Utah individuals are presented in Figure 1—figure supplement 1. After identifying candidate de novo mutations in the second generation (e. g. , the de novo ‘T’ mutation shown in the second-generation father), it is possible to assess their validity both by their absence in the parental (first) generation and by transmission to one or more offspring in the third generation. (b) Total numbers of DNMs (both SNVs and indels) identified across second-generation CEPH/Utah individuals and stratified by parental gamete-of-origin. Boxes indicate the interquartile range (IQR), and whiskers indicate 1. 5 times the IQR. Diagrams of phasing strategies for germline DNMs are presented in Figure 1—figure supplement 2. Figure 1—figure supplement 1 Download asset Open asset Distribution of sequencing coverage in CEPH/Utah samples (a) The fraction of bases greater than or equal to the specified coverage in the second generation, (b) third generation, (c) first-generation parents sequenced to 30X coverage, and (d) first-generation parents re-sequenced to 60X coverage. Figure 1—figure supplement 2 Download asset Open asset Determining the parent-of-origin for de novo mutations using transmission. (a) We phased de novo mutations observed in the second generation by transmission to a third generation. We first searched ±200 kilobase pairs from the de novo allele (shown in red) for informative sites (shown in blue) present in one of the two first-generation parents of the second-generation individual. [SEP] Justify:

Output: The text does not address the claim regarding the exploration and documentation of planets. It primarily discusses research related to genetic mutations and sequencing coverage in a specific dataset, which is irrelevant to the topic of planetary exploration.


Input: Task: corroborate the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: In terms of their FA composition, Blastobotrys strains synthesized and stored four main FAs during the 96 h of cultivation, accounting for more than 96% of total FA content: C18:1 (43 to 52%, depending on the strain and medium), C16:0 (23 to 27%), C18:2 (11 to 20%), and C18:0 (4 to 11%) (Additional file 1: Figure S4). C16 and C18 FAs are typically the most abundant FAs in a wide range of yeasts and fungi [60, 61]. However, the relative proportion varies depending on the yeast and culture/media conditions. The FA fraction was particularly poor in mono unsaturated C16:1. This feature was also noted for B. adeninivorans CBS 8244T in a comparative study of the FA composition of Saccharomycotina yeasts cultivated in YPD [62]. We found consistent but only very low levels of C17 chain-length FA (< 4 mg/g DCW). Indeed, yeast are not known to naturally synthesize large amounts of such odd-chain FAs, unless provided, for example, with odd-carbon precursors or benzoate [63,64,65]. Olstorpe et al. [17] reported FA profiles for CBS 8244T and CBS 7377 cultured in YPD medium, which were unexpectedly poor in oleic acid (3 to 11% of total FA at 30 °C) and rich in C17:1 (20 to 29% of total FA at 30 °C). The reason for these uncommon profiles is unknown, especially since Froissard et al. [62] reported the same four main FAs in B. adeninivorans CBS 8244T cultivated in YPD at 28 °C as those observed here. Lipid synthesis from various carbon sourcesSugars found in plants as reserve sugars or constituting lignocellulosic fibers, as well as the industrial by-product glycerol, are attractive substrates for microbial oil production. We tested the LS3 strain, our best lipid producer, for its ability to accumulate lipids while growing in various hexoses, polysaccharides, or glycerol. [SEP] Justify:

Output: The text supports the claim by mentioning that 'lipid synthesis from various carbon sources, sugars found in plants as reserve sugars or constituting lignocellulosic fibers... are attractive substrates for microbial oil production.' This indicates that bioengineered yeast can utilize sugars for lipid production, which aligns with the broader context of producing biofuels.


Input: Task: contrast the claim using the given text. Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: The plants were dried in a dark and warm drying room (39 °C, 17% RH) for 14 d. All data were statistically analyzed to determine the mean, sd, and statistical parameters (t test) using Microsoft ExcelTM (Microsoft Inc. , Redmond, WA). We are aware that there is a division of opinion in the plant science research community concerning the validity of using statistical analysis in studies such as ours, where true sample replication was not undertaken and where, instead, the process of pseudoreplication of samples was used (South and Somers, 2009; Wilson, 2007). As far as costs, timing, and inherent additional concerns resulting from replication in the greenhouse, we chose not to repeat the experiments described here but to rely on the strength of differences in the various parameters which we measured (biomass, WA production), especially as evidenced from statistical analysis. Air-dried foliage was combined for each growing condition and pulverized (Wiley Mill, Model No. 2). Three representative samples of 1. 0 g each were extracted with 10. 0 mL 60% aqueous methanol and subjected to 2 h of ultrasonic vibration and stored at room temperature for 1 week. The extracts were then filtered and washed twice with 2 mL of 60% aqueous methanol (MeOH). The solvent was evaporated to dryness using a Buchi rotavapor (water bath at 40 °C). The remaining residues were re-dissolved in 2. 0 mL MeOH and filtered through cotton. Each solution was diluted 1:10 with MeOH and subjected to HPLC on a Kromasil C18 RP column (250 × 4. 6 mm, 5 μm, 0. 7 mL·min−1 flow rate) with gradient elution using 40% to 100% aqueous MeOH and ultraviolet-Vis detection at 229 nm. An external standard curve method was used to calculate the concentrations of WA in all samples. ResultsSeed germination rate was 34% (data not shown). Plant growth analysis showed trends but no statistically significant differences between the aeroponically and hydroponically grown plants (Figs. 1 and 2), although during the first 3 weeks, aeroponically grown plants developed faster. [SEP] Justify:

Output: The text contrasts the claim by providing evidence that plants were analyzed for growth in alternative methods, specifically aeroponics and hydroponics. It notes that plant growth analysis showed trends, indicating that plants can thrive in these methods, even if there were no statistically significant differences noted. The statement about aeroponically grown plants developing faster during the first 3 weeks further supports that they can indeed grow and thrive outside of soil.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: If the second-generation individual’s spouse does not possess these informative alleles, we can look in the children of the second-generation individual to see if they have inherited both the de novo allele and the nearby informative alleles. This pattern of inheritance is only possible if the de novo allele and informative alleles are on the same haplotype; thus, in this example, we see that the de novo allele is on the maternal grandfather’s haplotype, and is paternal in origin. (b) A toy sample of paired-end sequencing reads is shown for each member of a trio (mother, father, and child). In this strategy, we identify informative alleles (shown in blue) that are present in one of the two parents, and within a read length (500 bp) of the de novo allele in the child (shown in red). Then, we identify individual sequencing reads that span the de novo and informative alleles. If the de novo allele is always present in the same read as the informative allele, then we can phase the de novo allele to the parent with the informative allele, and vice versa. Figure 2 with 2 supplements Download asset Open asset Effects of parental age and sex on autosomal DNM counts and mutation types in the second generation. (a) Numbers of phased paternal and maternal de novo variants as a function of parental age at birth. Poisson regressions (with 95% confidence bands, calculated as 1. 96 times the standard error) were fit for mothers and fathers separately using an identity link. Germline mutation rates, as a function of both paternal and maternal ages, are presented in Figure 2—figure supplement 1. (b) Mutation spectra in autosomal DNMs phased to the paternal (n = 3,584) and maternal (n = 880) haplotypes. Asterisks indicate significant differences between paternal and maternal fractions at a false-discovery rate of 0. 05 (Benjamini-Hochberg procedure), using a Chi-squared test of independence. P-values for each comparison are: C > G: 0. 719, T > G: 4. 93e-3, T > A: 8. 60e-2, T > C: 8. 02e-2, C > A: 0. 159, C > T: 7. 65e-6, indel: 8. [SEP] Justify:

Output: The text is irrelevant to the claim about the exploration of planets. It discusses genetic inheritance patterns, sequencing methods, and mutation rates without any mention of planets or their exploration.


Input: Task: corroborate the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: The FA fraction of the cells was characterized after 72 and 96 h of culture at 28 °C in YNB-based medium with the C source at 30 g/L and 0. 75 g/L NH4Cl. After 96 h, lipids accumulated to above 30% DCW in all substrates, except galactose, starch, and glycerol (Fig. 5). Maximum lipid synthesis and storage was obtained for some of the sugars (i. e. , cellobiose, glucose, sucrose, or fructose), likely rapidly assimilated, after 96 h in our shake-flask cultures since the rise between 72 and 96 h was less than 5. 5% (Additional file 2: Table S1). In contrast, glycerol appeared to be the least favorable substrate for bioconversion into lipids (total FAs reached only 16. 1 ± 0. 4% DCW), probably because of its slow assimilation, which also affected the OD reached at 96 h: 11. 4 ± 1. 0% in glycerol instead of 16. 8 ± 0. 4% in cellobiose. We also observed small differences in the composition of FA profiles relative to that obtained in glucose, especially when LS3 was grown in starch or glycerol (Additional file 2: Table S1). Such variations that depend on the culture conditions have already been reported for other oleaginous yeasts [66]. In all cases, however, C18:1 was the main FA, followed in decreasing proportion by C16:0, C18:2, and C18:0 (Additional file 2: Table S1). In conclusion, all tested substrates, from simple to complex, could be turned into lipids by strain LS3, although with varying efficiency. Fig. 5Bioconversion of various sugars into lipids. LS3 was cultivated for 72 h in nitrogen-limited YNB-based medium (0. 75 g/L NH4Cl) supplemented with the indicated sugars at 30 g/L. a Lipid content (% DCW) is presented as a bar with the average value and mean deviation (n = 2) and a color code indicating the nature of the carbon source: green, C5 monosaccharide; light blue, C6 monosaccharide; blue, disaccharide; gray, polysaccharide; red, polyol. [SEP] Justify:

Output: The text supports the claim by stating that the tested substrates, including various sugars like cellobiose, glucose, sucrose, and fructose, can be converted into lipids by the yeast strain LS3. This shows that bioengineered yeasts are able to utilize sugars for lipid production, which is a critical step in biofuel generation.


Input: Task: contrast the claim using the given text. Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: A power outage occurred 30 d after the plants had been transplanted to their systems (during Week 5) resulting in a temperature rise to 50 °C and disabling the pumps supplying NM to both systems for ≈4 h. As a result of this event, the growth rate of aeroponically grown plants decreased to less than 1 cm/week and the growth rate of hydroponically grown plants reduced to ≈3 cm/week. 1, the effect of the power outage is seen in Week 5, because plant heights remained almost the same. The trend lines show aeroponic plants with a slightly steeper growth slope, signifying a faster growth rate on average. Additionally, the surface area of the leaves in each system varied largely and yielded only weak trends without statistically significant differences. This can be seen in Figure 3, where the leaves of the aeroponically grown plants were somewhat larger than in the hydroponically grown plants. Size Fig. 1. Aerial plant size grown aeroponically and hydroponically. Vertical bars represent 95% confidence interval. Diamonds and squares represent weekly averages (n = 7) and lines represent linear best fit. Citation: HortScience horts 49, 12; 10. 21273/. 49. 12. 1506Download FigureDownload figure as PowerPoint slide Size Fig. 2. Plant growth rates in aeroponics and hydroponics. Vertical bars represent 95% confidence interval. Diamonds and squares represent weekly averages (n = 7). Citation: HortScience horts 49, 12; 10. 21273/. 49. 12. 1506Download FigureDownload figure as PowerPoint slide Size Fig. 3. Leaf surface areas for aeroponics and hydroponics. Vertical bars represent 95% confidence interval. Diamonds and squares represent weekly averages (n = 6). Citation: HortScience horts 49, 12; 10. 21273/. 49. 12. 1506Download FigureDownload figure as PowerPoint slideAs shown in Table 2, aeroponically grown plants produced an average of 49. 8 g DW (sd 20. 7). Hydroponically grown plants produced an average of 57. 6 g DW (sd 16. 0). Therefore, there was no significant difference (P > 0. 05) in aerial biomass production between the two growing methods. The percent DW column (Table 2) indicates what percentage of the wet weight corresponds to actual plant material. [SEP] Justify:

Output: The text contrasts the claim by providing evidence that plants can thrive in hydroponic and aeroponic systems. It discusses the growth rates of plants grown in these alternative methods, indicating that aeroponically grown plants had a faster growth rate on average compared to hydroponically grown plants. Additionally, the data shows that both methods produced significant plant biomass, with hydroponically grown plants producing an average of 57.6 g DW. This indicates that plants can indeed grow effectively outside of soil, directly contradicting the claim.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: 01e-2, CpG >TpG: 0. 835. Mutation spectra stratified by parental ages are presented in Figure 2—figure supplement 2. Figure 2—figure supplement 1 Download asset Open asset Contribution of maternal and paternal age to de novo mutation rates. For (a) second- and (b) third-generation individuals in the CEPH/Utah cohort, plotted points show the relationship between paternal and maternal age at birth. Each point is colored by the autosomal SNV mutation rate in the individual; these rates were calculated by dividing the autosomal count in each child by that child’s autosomal callable fraction. Colors indicate the magnitude of the mutation rate (blue = lower, red = higher). Black lines indicate the trend for a 1:1 relationship between paternal and maternal age. Figure 2—figure supplement 2 Download asset Open asset Comparison of mutation spectra in children born to older or younger parents. Second-generation children were divided into two groups based on the ages of their parents at birth, and autosomal mutation spectra were compared between the two groups. In all panels, no significant differences were found at a false-discovery rate of 0. 05 (Benjamini-Hochberg procedure), using a Chi-squared test of independence. (a) Comparison of DNMs in children born to fathers younger (n = 2,182) or older (n = 2,360) than the median paternal age of 29. 2 years. P-values for each comparison are: C > G: 0. 304, T > G: 0. 140, T > A: 0. 306, T > C: 0. 248, C > A: 0. 8. 81e-2, C > T: 0. 444, indel: 6. 89e-2, CpG >TpG: 0. 810. (b) Comparison of DNMs in children born to mothers younger (n = 2,225) or older (n = 2,317) than the median maternal age of 25. 7 years. P-values for each comparison are: C > G: 0. 580, T > G: 0. 659, T > A: 0. 554, T > C: 0. 697, C > A: 0. 918, C > T: 0. 990, indel: 0. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses mutation spectra and the influence of parental ages on mutation rates in children, with no mention of planets or their exploration.


Input: Task: corroborate the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: toruloides thermotolerant mutant, a temperature increase from 30 to 37 °C, while stimulating lipid production, drastically raised the relative proportion of C18:1, which reached 86% of total FA [32]. In conclusion, lipid metabolism of the LS3 and CBS 8244T strains was robust at temperatures from 28 to 45 °C. Temperature had a moderate impact on the final amount and nature of total cellular FAs, although LS3 showed optimal lipid production at 37 °C. Such robustness of lipid metabolism to differences in temperature is not shared across all yeasts. For example, the lipid content of L. starkeyi DSM 70295 reportedly decreased by 57% when the culture temperature was raised from 10 to 20 °C [70]. In the thermophilic species Kluyveromyces marxianus, 11 wild-type strains recently screened for lipogenesis (the best strain reportedly reached 10% DCW, mainly stored as free FAs) had a much lower FA content at 30 than 42 °C [42]. ConclusionsHarnessing microbial lipid metabolism to produce oils or other chemicals of interest is a promising alternative to petroleum or plant oil. However, limitations in the use of yeast have been encountered, such as the poor utilization of certain types of substrates, weak xerotolerance, limited yields for lipid conversion in competition with other metabolic pathways, or difficult culturing in bioreactors (filamentation, foaming). We believe that the availability of a set of various oleaginous microorganisms adapted to different types of applications could be useful. Elevated temperatures may help reduce the costs of the process and participate in the solubilization of substrates. B. adeninivorans and B. raffinosifermentans exhibit many advantageous traits for biotechnological processes and, as reported here, were able to synthesize and store lipids at high temperatures, up to 45 °C. Among four tested strains, LS3 was the best lipid-producing one. Although it showed a temperature dependence for growth, glucose consumption, and lipid storage, its native performance in the tested range of 28 to 45 °C is a good starting point (24 to 30% DCW from glucose). As for other oleaginous yeasts, strain screening, process optimization, and/or metabolic engineering is likely to be successful. [SEP] Justify:

Output: The text corroborates the claim by discussing the potential of oleaginous microorganisms, specifically strains like LS3, to produce lipids from glucose. The text indicates that these yeasts can convert sugars into oils or other chemicals of interest, positioning them as viable candidates for biofuel production. It highlights that LS3 was capable of producing 24 to 30% dry cell weight (DCW) from glucose, reinforcing the idea that bioengineered yeast can indeed produce biofuels from sugars.


Input: Task: contrast the claim using the given text. Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: Data in this column show that all plant materials were dried to the same extent. Table 2. Measured plant biomass for aeroponics and hydroponics. z Chemical analysis of the plant materials indicated that the hydroponically grown plants contained significantly higher concentrations of WA (P < 0. 05). As shown in Table 3, hydroponically and aeroponically grown plants contained an average of 7. 8 mg·g−1 DW (sd 0. 3) and 5. 9 mg·g−1 DW (sd 0. 6) WA, respectively. Table 3. content in dried plant materials for aeroponics and hydroponics. z DiscussionBecause multiple factors influence plant biomass production, we controlled all feasible environmental conditions (timing of transplanting, temperature, light, nutrient medium, RH, location in the greenhouse, etc. ) to reduce variability and to allow more precise comparison of plant growth under the two specified conditions. Additionally, the experiment comprised seven pesudoreplicates in each growing condition to attain accurate results. In previous studies, Solanum lycopersicum (tomatoes) have been found to produce higher yield in hydroponics and aeroponics than in traditional soil culture (Gysi and Von Allmen, 1997). Additionally, Solanum lycopersicum var. cerasiforme (cherry tomatoes), grown aeroponically, produced higher yields when compared with plants grown hydroponically. The improved yield was attributed to enhanced root aeration (Cho et al. , 1996; Soffer and Burger, 1988). In a recent study (Kindscher et al. , 2014) the authors discuss the effects of experimental manipulations of nutrients in the soil in which Physalis longifolia were grown. The authors found negligible differences in WA and other withanolides production as a function of these manipulations. However, the authors stress the importance of using genetic isolates of plants to provide for homogeneity so as to reduce secondary metabolite variability. In our study we used seeds from an isolated stock previously grown for several generations at NPC. We suggest, therefore, that genetic variability contributed minimally to the differences in secondary metabolite production in this study such that the differences we found can be more strongly attributed to the growing conditions. In this study, similar growth patterns and biomass yields of Withania somnifera were observed for both growing conditions. [SEP] Justify:

Output: The text contrasts the claim by providing evidence that plants can thrive in hydroponics and aeroponics, citing that previous studies found higher yields of Solanum lycopersicum (tomatoes) in these methods compared to traditional soil culture. Additionally, it mentions improved yields for Solanum lycopersicum var. cerasiforme (cherry tomatoes) grown aeroponically, indicating that plants do grow and can thrive in these alternative growing methods.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: 371, CpG >TpG: 0. 678. (c) Comparison of DNMs in children born to fathers in the 25th percentile of youngest (n = 1,120) or oldest (n = 1,165) paternal ages (26. 4 or 34 years). P-values for each comparison are: C > G: 1. 73e-2, T > G: 0. 428, T > A: 0. 872, T > C: 0. 979, C > A: 0. 943, C > T: 7. 77e-2, indel: 0. 788, CpG >TpG: 0. 706. (d) Comparison of DNMs in children born to mothers in the 25th percentile of youngest (n = 1,169) or oldest (n = 1,121) maternal ages (22. 5 or 31. 4 years). P-values for each comparison are: C > G: 0. 327, T > G: 9. 92e-2, T > A: 0. 841, T > C: 0. 975, C > A: 0. 963, C > T: 0. 940, indel: 0. 598, CpG >TpG: 0. 780. Figure 3 with 2 supplements Download asset Open asset Parental age effects on autosomal germline mutation counts vary significantly among CEPH/Utah families. Illustrations of pedigrees exhibiting the smallest (family 24_C, panel a) and largest (family 16, panel b) paternal age effects on third-generation DNM counts demonstrate the extremes of inter-family variability. Diamonds are used to anonymize the sex of each third-generation individual. The method used to separate CEPH/Utah pedigrees into unique groups of second-generation parents and third-generation children is presented in Figure 3—figure supplement 1. Third-generation individuals are arranged by birth order from left to right. The number of autosomal DNMs observed in each third-generation individual is shown within the diamonds, and the age of the father at the third-generation individual’s birth is shown below the diamond. The coloring for these two families is used to identify them in panels c and d. [SEP] Justify:

Output: The text is irrelevant to the claim concerning the exploration and documentation of planets. It discusses parental age effects on germline mutation counts in children, presenting statistical data and comparisons that do not relate to planetary exploration.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: AbstractIn 2010, our group announced the discovery of two cellodextrin transporter families from the cellulolytic fungus, Neurospora crassa. Furthermore, we demonstrated the utility of these transporters in the production of lignocellulosic biofuels. This discovery was made possible by a decision to systematically study cell wall degradation by N. crassa. The identified transport pathway has opened up a new way of thinking about microbial fermentation of hexoses as well as pentoses derived from plant cell walls. Integrating this pathway with the endogenous metabolism and signaling networks of S. cerevisiae is now a major goal of our group. Developing methods to convert the sugar-rich cell walls of plants to fuel is a major societal goal,Citation1 and has become the focus of intense research. Citation2 Present methods for conversion are limited by the evolved recalcitrance of plant cell walls to depolymerization into constituent sugars, and deficiencies in the traits of microbes used to ferment these sugars to fuels such as ethanol. Citation3 It is our philosophy that fundamental breakthroughs addressing both of these limitations will be made through the study of model organisms. Hence, we study the mechanisms by which the filamentous fungus, Neurospora crassa, degrades and metabolizes plant cell walls. N. crassa has been studied since the 1920s,Citation4 and features a wealth of resources including a high quality genome,Citation5 facile methods for genetic manipulation,Citation6 an almost complete set of gene knockouts,Citation7 and an international community of researchers. In the wild, N. crassa is commonly found growing upon recently burned plant matter,Citation8 and in 1977 was reported to secrete cellulases in response to specific inducers. Citation9 However, until 2009 N. crassa was largely ignored as a model biomass degrader; research focused instead on the related fungus, Trichoderma reesei (Hypocrea jecorina). T. reesei is now favored by industry for its ability to secrete large quantities of cellulases used to deconstruct plant biomass. Citation10Biomass degradation by N. crassa was revisited in 2009, with the report of a systematic study of plant cell wall degradation by this fungus. [SEP] Justify:

Output: The text does not address the claim directly as it primarily discusses the research on Neurospora crassa and its role in degrading plant cell walls for biofuel production. While it mentions the challenges of converting plant biomass into sugars, it does not specifically corroborate or contrast the claim regarding bioengineered yeast producing biofuels from sugars. Thus, it is considered irrelevant to the claim.


Input: Task: contrast the claim using the given text. Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: Initially, aeroponically grown plants showed a growth rate that was statistically not different from hydroponically grown plants. As mentioned, a power outage causing a sharp rise in greenhouse temperature combined with irrigation pump failure resulted in reduced plant growth rates in both systems. As expected, this reduction, accompanied by partial wilting, was initially more pronounced in aeroponically grown plants whose roots did not receive any moisture or nutrients during the outage. All plants recovered in both conditions (Figs. 1 to 3) and resumed growth within 1 week. The pump failure, which was experienced in our study, may be considered a plant stressor, which therefore may have contributed to an increase in secondary metabolites (WA) production. Because this stress (lack of fertigation) would have been more pronounced in the aeroponics system, one would expect WA synthesis to be higher than in the hydroponic system because in the latter, some nutrient medium continued to bathe the plant roots. Because we found that WA production was larger in hydroponics, it amplifies the significance of our results. Plants generally display variations in biomass production (likely as a result of genetics and uncontrolled “hidden” environmental factors). To take such variations into account, we removed apparent outlier plants (H4 and A5) from the data analysis (not shown), which resulted in identical statistical results as data analysis, which included the outliers. These analyses showed that both soilless growing conditions yielded the same biomass per plant. In contrast, however, WA content analysis showed statistically significant differences. Plants growing in their natural habitat showed large variations of WA content (Kumar et al. , 2007; Mirjalili et al. , 2009). For example, naturally occurring plants in Iran were found to contain concentrations of WA ranging from 2. 2 to 32. 5 μg·g−1 DW (corresponding to 0. 0002% to 0. 00325%) (Mirjalili et al. , 2009), whereas in India, the leaves of naturally occurring plants were reported to contain 0. 192 to 1. 312 g/100 g DW (corresponding to 0. 192% to 1. 312%, but mostly less than 1%) WA (Kumar et al. , 2007). We report here that the aerial parts of our plants grown hydroponically contained an average of 7. 8 mg·g−1 DW (0. [SEP] Justify:

Output: The text contrasts the claim by demonstrating that plants can indeed grow and thrive in alternative methods like hydroponics and aeroponics. It explains that aeroponically grown plants showed growth rates comparable to those grown hydroponically, with no significant differences noted under normal conditions. Additionally, the text discusses recovery from stress in both systems, further emphasizing that these soilless growing conditions can support plant growth effectively.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: (c) The total number of autosomal DNMs is plotted versus paternal age at birth for third-generation individuals from all CEPH/Utah families. Regression lines and 95% confidence bands indicate the predicted number of DNMs as a function of paternal age using a Poisson regression (identity link). Families are sorted in order of increasing slope, and families with the least and greatest paternal age effects are highlighted in blue and red, respectively. (d) A Poisson regression (predicting autosomal DNMs as a function of paternal age) was fit to each family separately; the slope of each family’s regression is plotted, as well as the 95% confidence interval of the regression coefficient estimate. The same two families are highlighted as in (a). A dashed black line indicates the overall paternal age effect (estimated using all third-generation samples). Families are ordered from top to bottom in order of increasing slope, as in (c). A random sampling approach was used to assess the robustness of the per-family regressions to possible outliers; the results of these simulations are shown in Figure 3—figure supplement 2. Figure 3—figure supplement 1 Download asset Open asset Defining unique families in the CEPH/Utah dataset. The pedigree for a single family (family ID 19) is depicted. In this family, the third-generation individuals are first cousins and share a pair of grandparents. However, for the purposes of the inter-family variability presented in Figure 3, we defined ‘families’ as the unique groups of second-generation parents and their third-generation children. Thus, family ID 19 would be split into two unique families (19_A and 19_B), designated by the red boxes. Figure 3—figure supplement 2 Download asset Open asset Paternal age effect ranks of CEPH/Utah families are robust to outlier samples. For each CEPH/Utah family (i. e. , unique set of second-generation and third-generation individuals), we randomly sampled 75% of the third-generation individuals in the family, fit a regression predicting autosomal DNM counts as a function of paternal age at birth, and calculated the ‘rank’ of that family’s paternal age effect (out of 40 total families). We then plotted the distribution of ranks across 100 trials for each family. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the analysis of autosomal de novo mutations (DNMs) related to paternal age within a specific dataset, without any mention or indication of planetary exploration or documentation.


Input: Task: corroborate the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: Citation11 Transcriptomic, proteomic and phenotypic data showed: (1) that the core cellulases of N. crassa are similar to those of T. reesei; (2) that N. crassa transcriptionally upregulates ∼2% of genes in response to pure cellulose or plant cell walls; (3) that there is a large amount of functional redundancy to the cellulase system of N. crassa, as only a cellobiohydrolase(I) deletion strain had a significant deficiency in its capacity to degrade pure cellulose. Interestingly, the set of cellulose-induced genes identified in this study included 10 major facilitator superfamily transporters. The strong induction of these transporters during biomass degradation led to a hypothesis that they have a key role in this process. In addition to the transporters, we noticed that N. crassa induced the expression of a putative intracellular β-glucosidase, an enzyme that cleaves the β (1 → 4) glycosidic bond in short cellodextrin chains. Cellodextrins are β (1 → 4) linked oligosaccharides of glucose, and are the product of cellulose depolymerization by fungal cellulases. Citation12 We therefore reasoned that a likely substrate for some of these transporters were cellodextrins. In 2010, we showed that two transporters, CDT-1 and CDT-2, indeed mediate the uptake of cellodextrins by N. crassa, and that following uptake cellodextrins are hydrolyzed intracellularly to glucose by a β-glucosidase. Citation13 A number of transcriptomic studies have shown that orthologs of these transporters are transcriptionally upregulated in response to plant cell wall material or cellobiose in diverse fungi, suggesting they are fundamental to the strategies used by fungi to interact with plants. Citation14–Citation16 The identification of these genes confirmed reports of cellodextrin permeasesCitation17 and intracellular β-glucosidasesCitation18 in T. reesei. The importance of these transporters to biomass degradation by N. crassa and other fungi inspired us to engineer the transport pathway into the yeast, Saccharomyces cerevisiae. S. [SEP] Justify:

Output: The text corroborates the claim by discussing the engineering of transport pathways into the yeast Saccharomyces cerevisiae, which is a significant step in enhancing its ability to process substrates like cellodextrins. These cellodextrins are derived from cellulose, a sugar source, which links directly to the claim that yeast can produce biofuels from sugars. The engineering of yeast to improve its transport and degradation of these sugars supports the notion that bioengineered yeast can effectively convert sugars into biofuels.


Input: Task: contrast the claim using the given text. Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: 78%), whereas the aeroponic plants contained an average of 5. 9 mg·g−1 DW (0. 59%). These results show that hydroponically grown plants contained a significantly higher concentration of WA than plants grown aeroponically. As noted in “Methods,” our study does not comprise true replication (repeating the same experiment) but rather relies on analysis from pseudoreplicates. There is an almost equal division of opinion as to the validity of the latter approach with the conclusion that mitigating circumstances often prevent true replication in plant science research. Being aware of this situation, and using the results of our statistical analysis conservatively, we suggest that our findings indicate that WA synthesis using hydroponics is a more efficient system than using aeroponics (Hurlbert, 1984). Further research is needed to explore the mechanism(s) responsible for the increase in WA production we report here. Still, our findings are likely to have implications for the growing conditions of other medicinal plants where a secondary metabolite is the target compound. Our results indicate that hydroponics (NFT system) is the more effective method for growing Withania somnifera with the goal of reproducibly generating withaferin A. In addition, hydroponics is more suitable for commercial applications because it is less susceptible to problems (e. g. , resulting from pump failure). Plants grown hydroponically are also more economically grown and harvested as a result of the ability to customize the layouts of the systems compared with traditional field culture. The soilless conditions also eliminate soilborne pests and prevent contamination by field-growing plants. The results we report in this study suggest that other medicinal plants may also synthesize higher concentrations of metabolites in hydroponic conditions, which may be of pharmaceutical interest. Further studies should be undertaken to find the most effective nutrient medium composition, including adjustments to the sources of nutrients as well as changes to pH and EC, all known to affect biomass production and secondary metabolite synthesis (Hoagland and Arnon, 1950; Nagella and Murthy, 2011). Literature & Shin, G. H. 1996 Effects of culture systems on growth and yield of cherry tomatoes in hydroponics RDA J. Agr. Sci. 38 563 5671996Effects of culture systems on growth and yield of cherry tomatoes in hydroponicsRDA J. Agr. Sci. 38563567)| falseSearch 347. [SEP] Justify:

Output: The text contrasts the claim by providing evidence that plants can indeed thrive in alternative growing methods, specifically hydroponics. It highlights that hydroponically grown plants contained a significantly higher concentration of a target compound compared to those grown aeroponically, indicating that hydroponics is an effective method for growing certain plants. Additionally, it mentions that soilless conditions eliminate soilborne pests, further supporting the idea that plants can grow outside traditional soil environments.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: Families’ density plots are ordered along the y-axis by the original ranks of each family (as determined using the full dataset, and originally shown in Figure 3d, where a rank of 1 corresponds to the smallest age effect, and a rank of 40 corresponds to the largest). Figure 4 Download asset Open asset Identification of post-PGCS germline mosaicism in the second generation. (a) Mosaic variants occurring during or after primordial germ cell specification (PGCS) were defined as DNMs present in multiple third-generation siblings, and absent from progenitors in the family. (b) Comparison of mutation spectra in autosomal single-nucleotide germline mosaic variants (red, n = 288) and germline de novo variants observed in the third generation (non-shared) (blue, n = 22,644). Asterisks indicate significant differences at a false-discovery rate of 0. 05 (Benjamini-Hochberg procedure), using a Chi-squared test of independence. P-values for each comparison are: C > G: 6. 84e-2, T > G: 0. 169, T > A: 0. 236, T > C: 1. 51e-2, C > A: 4. 31e-3, C > T: 0. 385, CpG >TpG: 2. 26e-6. (c) For each third-generation individual, we calculated the number of their DNMs that was shared with at least one sibling, and plotted this number against the individual’s paternal age at birth. The red line shows a Poisson regression (identity link) predicting the mosaic number as a function of paternal age at birth. (d) We fit a Poisson regression predicting the total number of germline single-nucleotide DNMs observed in the third-generation individuals as a function of paternal age at birth, and plotted the regression line (with 95% CI) in blue. In red, we plotted the line of best fit (with 95% CI) produced by the regression detailed in (c). (e) For each third-generation individual, we divided the number of their DNMs that occurred during or post-PGCS in a parent (i. e. [SEP] Justify:

Output: The text is irrelevant to the claim regarding the exploration of planets. It discusses density plots, germline mosaicism, and related statistical analyses without any connection to planetary exploration or documentation.


Input: Task: corroborate the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: cerevisiae is the current organism of choice for fermenting glucose and sucrose to ethanol, but lacks the capacity to ferment cellodextrins. Citation19 Strains engineered to express cdt-1 or cdt-2 along with an intracellular β-glucosidase (gh1-1) grew with cellodextrins as a sole carbon source, and fermented cellobiose to ethanol efficiently. Multiple reports preceded ours in describing cellodextrin consumption or fermentation by engineered strains of S. cerevisiae. As early as 1986, Kohchi and Toh-e reported the consumption of cellobiose by S. cerevisiae expressing a secreted β-glucosidase from Candida pelliculosa. Citation20 They did not measure its fermentative capacity, however. Then, in 1988 Machida et al. reported cellobiose fermentation by S. cerevisiae expressing secreted β-glucosidases from Saccharomycopsis fibuligera. Citation21 Subsequent studies have repeated this feat both in labCitation22–Citation29 and industrial strains of S. cerevisiae,Citation30,Citation31 and in other yeast species. Citation32 All of these strains rely on extracellular hydrolysis of cellobiose to glucose by secreted β-glucosidases followed by uptake via the endogenous S. cerevisiae hexose transporters. In contrast, the first step in the pathway we described is the import of cellodextrins into the cytosol of S. cerevisiae, only then does hydrolysis to glucose occur. Other yeasts in nature have been shown to ferment cellobiose, but the molecular basis for this capability was not determined. Citation33–Citation36There are two main distinctions between cellodextrin fermentation mediated by transport and one mediated by extracellular hydrolysis to glucose: (1) cellodextrin transporters have a relatively high affinity for cellodextrins; (2) cellodextrins are hydrolyzed intracellularly. Both may be important during the fermentation of plant cell wall derived sugars. [SEP] Justify:

Output: The text corroborates the claim by discussing the fermentation of various sugars, including cellobiose, to produce ethanol by engineered strains of Saccharomyces cerevisiae. This aligns with the idea that bioengineered yeast can convert sugars into biofuels, as it highlights the capabilities of yeast to ferment carbohydrates to produce ethanol, which is a type of biofuel.


Input: Task: contrast the claim using the given text. Claim: Modern agriculture can function without water or sunlight as long as the right technology is used. [SEP] Text: , Watanabe, H. , Cho, J. , An, N. , & Lee, B. (2014). Photodegradation of Butachlor and Pyrazosulfuron-ethyl in Water under Natural Sunlight. of Environmental Agriculture, 33(2), 134-137. 2014, “Photodegradation of Butachlor and Pyrazosulfuron-ethyl in Water under Natural Sunlight”, of Environmental Agriculture, vol. 33, no. 2, 137. Available from: doi:10. 5338/KJEA. 2014. 33. 2. 134 Ok, Junghun et al. “Photodegradation of Butachlor and Pyrazosulfuron-ethyl in Water under Natural Sunlight. ” of 33. 2 (2014): 134-137. 1. . Photodegradation of Butachlor and Pyrazosulfuron-ethyl in Water under Natural Sunlight. of [Internet]. 2014;33(2): 134-137. Available from: doi:10. 5338/KJEA. 2014. 33. 2. 134. and Byungmo Lee. “Photodegradation of Butachlor and Pyrazosulfuron-ethyl in Water under Natural Sunlight. ” of 33, no. 2 (2014): 134-137. doi: 10. 5338/KJEA. 2014. 33. 2. 134. Journal of p-ISSN 1225-3537e-ISSN 2233-4173 > Archives > 10. 7585/kjps. 2022. 26. 4. 330 Close 2014. Vol. 33. No. 2. 10. 5338/KJEA. 2014. 33. 2. [SEP] Justify:

Output: The text discusses the photodegradation of chemicals like Butachlor and Pyrazosulfuron-ethyl in water under natural sunlight, highlighting the importance of sunlight in agricultural practices. This information contrasts the claim by implying that sunlight is necessary for certain agricultural processes, thereby suggesting that modern agriculture cannot fully function without water or sunlight, even with technology.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: , that were shared with a sibling) by their total number of DNMs (germline +germline mosaic), and plotted this fraction of shared germline mosaic DNMs against their paternal age at birth. Figure 5 with 1 supplement Download asset Open asset Identification of gonosomal mutations in the second generation. (a) Gonosomal post-zygotic variants were identified as DNMs in a second-generation individual that were inherited by one or more third-generation individuals, but exhibited incomplete linkage to informative heterozygous sites nearby. (b) Comparison of mutation spectra in single-nucleotide gonosomal DNMs that occurred on the paternal (n = 249) or maternal (n = 226) haplotypes. No significant differences were found at a false-discovery rate of 0. 05 (Benjamini-Hochberg procedure), using a Chi-squared test of independence. P-values for each comparison are: C > G: 3. 05e-2, T > G: 0. 972, T > A: 0. 858, T > C: 0. 148, C > A: 3. 31e-2, C > T: 2. 66e-2, indel: 0. 247, CpG >TpG: 0. 932. (c) Comparison of mutation spectra in autosomal single-nucleotide germline DNMs observed in the second-generation (non-gonosomal) (n = 4,542) and putative gonosomal mutations (n = 475) in the second generation. Asterisks indicate significant differences at a false-discovery rate of 0. 05 (Benjamini-Hochberg procedure), using a Chi-squared test of independence. P-values for each comparison are: C > G: 0. 517, T > G: 0. 800, T > A: 2. 32e-3, T > C: 0. 255, C > A: 0. 129, C > T: 0. 805, indel: 0. 446, CpG >TpG: 0. 212. (d) Numbers of phased gonosomal variants as a function of parental age at birth. Poisson regressions (with 95% confidence bands) were fit for the mutations phased to the maternal and paternal haplotypes separately using an identity link. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses mutations and genetic analyses, without any mention of planets, exploration, or documentation. Thus, it does not provide any information related to the claim about planetary exploration.


Input: Task: corroborate the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: The high-affinity of CDT-1 and CDT-2 for cellodextrins could be particularly important during the simultaneous saccharification and fermentation (SSF) of plant cell walls to fuel. SSF, in which fermenting microbes are included in the depolymerization reaction, increases the efficiency of conversion by relieving product inhibition upon cellulases. Citation37 With a KM of ∼5 µM, cellodextrin transporters may be capable of reducing sugar concentrations below levels obtainable by the inclusion of extracellular β-glucosidases, which generally have a KM of 100–1,000 µM. Citation38 This idea has not been rigorously tested and further studies applying and validating models of SSF using cellodextrin-transporting strains are necessary. Citation39,Citation40Relocating hydrolysis of cellodextrins from outside to inside the cell may seem like a trivial change, but it has a profound advantage. Specifically, transport of cellodextrins followed by intracellular hydrolysis to glucose facilitates the cofermentation of cellulose-derived glucose and hemicellulose-derived xylose. Citation41,Citation42 The inability of S. cerevisiae to coferment glucose and xylose is a barrier to efficient lignocellulosic biofuel production. Both glucose and xylose enter S. cerevisiae through the endogenous S. cerevisiae hexose transporters, but glucose is vastly preferred to xylose. Citation43,Citation44 Thus, xylose will not be taken up until all glucose is consumed. This sequential fermentation of glucose and xylose leads to lower ethanol yields and productivities. Citation45 Cellodextrin transport represents an alternate route for glucose to enter yeast, leaving the endogenous hexose transporters unoccupied and capable of transporting xylose. Strains containing the cellodextrin transport pathway from N. crassa and an efficient xylose fermentation pathway coferment cellobiose and xylose at high rates and with high yields. Citation41,Citation42Intracellular hydrolysis of cellodextrins does have associated problems, however. Yeast set metabolic and growth rates to match the perceived abundance of nutrients. [SEP] Justify:

Output: The text corroborates the claim by discussing how strains of yeast can utilize cellodextrins and coferment glucose and xylose to improve biofuel production. It highlights the role of cellodextrin transport in allowing sugars to enter yeast cells, which is essential for enhancing the efficiency of lignocellulosic biofuel production.


Input: Task: contrast the claim using the given text. Claim: Modern agriculture can function without water or sunlight as long as the right technology is used. [SEP] Text: 134 Number of citation : 1 of Butachlor and Pyrazosulfuron-ethyl in Water under Junghun Ok1*, Hirozumi Watanabe2, Junglai Cho1, Nanhee An1, Byungmo Lee1 1Division, of Agricultural Sciences, Suwon, Gyeonggi-do 441-707, Korea 2of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan *교신저자(Corresponding author): Phone: +82-10-4541-1629; Fax: +82-31-290-0507; E-mail: junghunok@gmail. com This is an Open-Access 3. 0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. : Dissipation of herbicides in paddy water varies significantly, being dependent on environmental conditions such as sunlight. The photodegradation under natural sunlight may be one of natural degradation routes of herbicides dissipation. Therefore, the aim of this study was to monitor the degradation of butachlor and pyrazosulfuron-ethyl in paddy water under natural sunlight. : The 12 water sample bottles of treatment were covered by quart glass plates, which allow about 90% of UV radiation (280-2000 nm) to pass through, to minimize the UV attenuation. The other 12 water sample bottles of the control were covered by glass lids and wrapped with aluminum foils to prevent the sunlight. The concentration of butachlor and pyrazosulfuron-ethyl in paddy water samples bottles was monitored under ambient conditions with and without natural sunlight. The concentration of butachlor and pyrazosulfuron-ethyl for treatment decreased from 355. 3μg/L to 37. 8μg/L and from 10. 5μg/L to 3. 9μg/L, respectively, during consecutive 21 days after herbicide application under natural sunlight. : The concentration of butachlor in paddy water decreased quickly under ambient conditions with natural sunlight. The degradation of butachlor in paddy water was enhanced by the natural sunlight. However, the degradation of pyrazosulfuron-ethyl was insignificant under natural sunlight. [SEP] Justify:

Output: The text contrasts the claim by detailing the significant impact of sunlight on the degradation of herbicides in paddy water. It states that the degradation of butachlor was enhanced by natural sunlight, indicating that sunlight plays a crucial role in agricultural processes related to herbicide degradation. This suggests that modern agriculture cannot entirely function without sunlight, which directly contradicts the claim.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: A diagram of an identification strategy for post-zygotic gonosomal DNMs (using only two generations) is presented in Figure 5—figure supplement 1. Figure 5—figure supplement 1 Download asset Open asset Strategy for identifying post-zygotic DNMs using two generations. (a) Diagram of an example two-generation pedigree structure that is amenable to the post-zygotic detection strategy. In this example, the child has a de novo ‘T’ allele that is <= 500 bp downstream of a heterozygous ‘G’ allele. Question marks in the parents indicate that the child could have inherited the ‘G’ allele from either parent; unlike the read tracing strategy (Figure 1—figure supplement 2), a particular parent does not need to be ‘informative. ’ (b) In the child’s reads, only two possible sets of linked haplotypes should be seen, assuming the de novo allele occurred in the germline of a parent. The presence of three distinct haplotypes, demonstrating incomplete linkage of the de novo and heterozygous alleles, indicates that the de novo ‘T’ allele is post-zygotic. Author response image 1 Download asset Open asset Lack of correlation between read depth and mutation rates in CEPH/Utah samples. For each second- or third-generation CEPH/Utah sample, we calculated mean read depth across all autosomal base pairs covered by >=12 reads in all members of the trio. We then assessed whether there was a correlation between mean read depth and the autosomal mutation rate in these samples. For each generation, we fit a linear model predicting read depth as a function of autosomal mutation rate, and do not find a significant association in either generation at a p-value threshold of 0. 05 (second-generation p = 0. 92, third-generation p = 0. 073). Author response image 2 Download asset Open asset Anti-correlation between slope and intercept. For each CEPH/Utah family, we fit a linear model predicting DNM counts as a function of paternal age (see Figure 3). We then assessed whether the slopes and intercepts of these regressions were correlated; overall, slope and intercept point estimates are negatively correlated in CEPH/Utah families (p < 2. 2e-16). [SEP] Justify:

Output: The text is irrelevant to the claim about planetary exploration and documentation. It discusses a genetic identification strategy and mutation rates without any mention or relation to planets or exploration. Therefore, it does not support, refute, or provide any relevant information concerning the claim.


Input: Task: corroborate the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: 69 for pdc (Additional file 1: Table S1B); therefore, the acetolactate decarboxylase (AldC) to be engineered should have a strong affinity for the substrate acetolactate to compete with ZMO1141, thus ensuring carbon flux toward acetoin and 2,3-BDO. Construct heterologous 2,3-BDO pathway in Z. mobilis and optimize flask fermentation conditionsThe gene expression cassettes containing the sequences of three codon-optimized 2,3-BDO pathway genes (als, aldC, and bdh) from B. licheniformis and E. cloacae as well as wild-type version from E. cloacae were then designed and synthesized (Table 2). As discussed above, Z. mobilis has three als gene homologs, but does not have the aldC and bdh genes needed for 2,3-BDO production. Additionally, since Z. mobilis Pdc is a very abundant and efficient enzyme with low Km (<0. 31 mM) and high k cat (>100 1/s), a strong als gene may be needed to divert carbon flux from ethanol production to 2,3-BDO. We, therefore, constructed several pathways with either two genes (aldC and bdh) or three genes (als, aldC, and bdh). These genes were assembled using the Biobrick-based metabolic pathway engineering strategy and cloned into the minimized shuttle vector pEZ (Table 1). The results indicated that the three-gene pathways produced more 2,3-BDO than did the two-gene pathways (Table 2; Fig. 2). Table 2 The source and components of the 2,3-BDO pathway constructed and the corresponding 2,3-BDO titer (g/L) after 24-h post-inoculation in Z. mobilis 8bFull size table Fig. 2Biomass (OD600 nm), acetoin, 2,3-BDO, and ethanol titers after 24-h post-inoculation in either a Z. [SEP] Justify:

Output: The text corroborates the claim by describing the engineering of a metabolic pathway within the yeast Zymomonas mobilis to produce biofuels, specifically 2,3-BDO, from sugar substrates. It mentions the construction of specific genes (als, aldC, and bdh) to optimize the fermentation process for biofuel production, indicating that bioengineered yeast can indeed convert sugars into biofuels.


Input: Task: contrast the claim using the given text. Claim: Modern agriculture can function without water or sunlight as long as the right technology is used. [SEP] Text: Keyword Butachlor,Natural sunlight,Paddy water,Photodegradation,Pyrazosulfuron-ethyl are widely used in rice paddies, golf courses and other types of fields. The acetanilide herbicide butachlor and the sulfonylurea herbicide pyrazosulfuron-ethyl are pre-emergence herbicide to control weeds of transplanted rice paddy fields (Chen and Chen,1979; Zheng et al. , 2008). Previous study investigated herbicide behavior and its dissipation in rice paddy environment (Ok et al. , 2012), however, the influence factor on herbicide degradation in paddy water was imprecise. Many environment factors related to the degradation and dissipation of herbicides including temperature, pH, sunlight, microbe, and soil properties (Chen and Chen, 1979; Samanta et al. , 1999; Sarmah and Sabadie, 2002; Vulliet et al. , 2004, Zheng et al. , 2008). Degradation of herbicides in paddy water also varies significantly, being dependent on environmental conditions such as sunlight (Chen and Chen, 1979; Sarmah et al. , 2000). The photodegradation under natural sunlight may be one of natural degradation routes of herbicides dissipation. Several studies reported that photodedegradation of butachlor were the major routes of herbicides dissipation from paddy fields in summer days (Chen and Chen, 1979). Chen and Chen (1979) reported that the half-life of butachlor in aqueous solution were 5. 4 hr after exposure to sunlight. In addition, the photolysis of pyrazosulfuron-ethyl was observed to enhance in aqueous condition (Zheng et al. , 2008). However, the photodegradation of butachlor have been investigated solely under controlled laboratory conditions, and only few studies for pyrazosulfuron-ethyl has been referred to their photochemical degradation in paddy water. Therefore, the aim of this study was to monitor the degradation of butachlor and pyrazosulfuron-ethyl in paddy water under natural sunlight. Materialsandanalytical grade solvents (acetonitrile, acetone, acetic acid, methanol, phosphoric acid) were purchased from (2011, Tokyo, Japan). [SEP] Justify:

Output: The text contrasts the claim by emphasizing the importance of both water and sunlight in the agricultural process, particularly in relation to the degradation of herbicides in rice paddies. It discusses how environmental factors, including sunlight, are crucial for herbicide behavior and dissipation in paddy water, indicating that modern agriculture cannot function without these elements.