Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: Similarly, the distances between two noise distributions of the m images and the m+1 images and two transformation matrix distributions (τ)of the m images and the m+1 images are computed using the Kullback-Leibler (KL) divergence. These are respectively termed C2 and C3. If the weighted average of these three criteria (C1, C2, and C3) falls below a predetermined threshold, this image is regarded as a member of the support set of the initial m images. The procedure for calculating the KL divergence between two MOG distributions is elaborated in 3. After this, the previously described procedure is repeated, and the U and V matrices are updated using the calculated xi∘τik values. This iterative process continues until the predetermined stopping condition is met. The complete procedure is visually depicted in Fig. 2. The main part of the proposed method is the calculation of the low rank matrix, which is shown by the green box in the mentioned figure. A detailed algorithmic representation of this part is provided in Algorithm 5. Figure 2: Overall procedure of proposed method. Download full-size image DOI: 10. 7717/peerj-cs. 1713/fig-2 Experiments and results In this section, we conduct experiments to evaluate the performance of the proposed method on both simulated and real datasets. The obtained results are then compared with the performance of several existing algorithms, namely Two-Stage (Oreifej et al. , 2011), BNLTV (Mao & Gilles, 2012), NDL (Zhu & Milanfar, 2012), HVDKR (Xie et al. , 2016), SGL (Lou et al. , 2013), Centroid (Meinhardt-Llopis & Micheli, 2014), RPCA (Lau, Lai & Lui, 2019b), JSUB (Lau, Lai & Lui, 2019a), PCA-Based (Li, Mersereau & Simske, 2007), Lucky-Region (Aubailly et al. , 2009), and UCSPF (Zhang et al. , 2018). For this purpose, in this section, first, the datasets that were utilized for the experiments, are introduced. Subsequently, we evaluate the proposed method’s performance on these datasets and conduct a comparative analysis of the results with the aforementioned algorithms. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses a computational method involving Kullback-Leibler divergence and performance evaluation of algorithms on datasets, rather than any information regarding the exploration or documentation of planets.


Input: Task: corroborate the claim using the given text. Claim: The discovery of exoplanets has expanded the search for extraterrestrial life. [SEP] Text: Reviews "Bennett describes the search for life beyond the Earth in terms that are accessible to the nonscientist and yet reveal a broad understanding of the evolution of stars, planets, and organisms. The author's optimism is contagious. May it help inspire us to actually accomplish these lofty goals. "—James F. is a rich, slow, and rewarding read. Rich because it is full of some of the most interesting current interdisciplinary science regarding planets and life that you can find, blending astronomy, geology, history, and astrobiology in a single narrative. Slow because each page is so full of interesting content that you don't want to skim. Rewarding because Bennett is simply a fantastic writer and presenter, making the read thoroughly enjoyable. No science expertise required. ---Jennifer Wiseman, Books & CultureBeyond UFOs gives a good impression from the moment you first take it into your hands. It is attractively produced, well written, and very thoroughly proofread. It's an interesting and challenging complement to focused research, and will be particularly enjoyed by anyone who has an appetite for broad science tinged with morals. ---Elizabeth Griffin, The ObservatoryThe old adage 'don't judge a book by its cover' (or, in this case, its title) certainly applies here. While one might expect a book of science fiction, Bennett presents this awe-inspiring topic in a scientifically accurate but personal way. I would recommend it to anyone interested in reading a creative summary of the status of the search for life elsewhere in the universe and would hope that it might provide a starting point to inspire the next generation of astronomers and astrobiologists. ---Lisa Jardine-Wright, EducationParticularly enjoyable is the down-to-earth writing; Bennett, an astrophysicist, author, and educator, tells the reader exactly how he feels about various topics (even the role of God in the scheme of things). Readers may not agree with everything he says, but he does offer food for thought. ---B. R. Parker, ChoiceFinalist for the 2008 Eugene M. walks us through the daunting calculations that lead to the conclusion that the existence of life elsewhere is not only possible, but highly likely. But as we wonder where else life exists and what forms it might take, scientists are forced back to more fundamental questions. What is the nature of life itself? Will we know it if we see it? . . . [SEP] Justify:

Output: The text corroborates the claim by discussing the search for life beyond Earth and indicating that the existence of life elsewhere is not only possible but highly likely. This reflects the broader implications of examining exoplanets, as the search for extraterrestrial life is directly tied to understanding planets outside our solar system.


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 known that in high stress environments, biocrust microorganisms increase nutrient availability and accumulation by resuming carbon and nitrogen fixation upon hydration (Aranibar, 2022). The resulting organic carbon and nitrogen compounds can be consumed during the long desiccation periods (Belnap, 2003; Colesie et al. , 2014). One study examining microbial nitrogen transformations in biocrusts collected from succulent Karoo biome in Namibia and showed that following wetting, nitrogen cycling genes are expressed in biocrust organisms (Maier et al. , 2022). Another study examining biocrust samples taken from the in Utah demonstrated a pulse of metabolite release following controlled wetting (Swenson et al. , 2018). Based on these reports, and due to the extreme conditions in (Levi et al. , 2021), we suggest that hyperarid biocrust communities prioritize functions such as metabolite production, nutrient cycling, and preparation for desiccation over growth. Natural recovery of biocrusts has been long debated and is generally estimated to be a slow process, especially in arid sites that experience very short activity periods for biocrust development, such as the hyperarid Zin mining site (Kidron et al. , 2020; Weber et al. , 2016). The time and trajectory of recovery depend on many factors relating to local climatic conditions and site properties (Belnap and Lange, 2003). One such factor that greatly affects establishment and restoration of biocrusts is the proximity, availability, and dispersal timing of biocrust propagules (Bowker, 2007; Walker et al. , 2007). Thus, the low proliferation rates we observed, particularly in post-mining biocrusts, suggest that restoration processes might be much slower than previously estimated. The topsoil from a stockpile is used to cover the mining pits. This soil may not contain a biocrust seed bank because it was probably destroyed and buried during the mining processes. Further increase in bacterial biomass might highly depend on the dispersal of biocrust propagules to the site from adjacent natural areas by wind or water. 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. [SEP] Justify:

Output: The text contrasts the claim by discussing the recovery and growth mechanisms of biocrusts in extreme environments. While it centers on soil health, it implies that growth and survival can be enhanced in environments with microbial interventions and nutrient cycling, suggesting that alternative methods such as hydroponics or aeroponics could be effective in providing the necessary nutrients, rather than the sole reliance on soil indicated in the claim.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: evaluation of the proposed method encompasses both simulated and real datasets. The real datasets consist of the Chimney, Building, Moon-surface, and Water-tower sets, each of which includes corresponding ground truth images (Zhu & Milanfar, 2012). Meanwhile, the simulated datasets encompass the Car-front (Lau, Lai & Lui, 2019a) and Road (Lau, Lai & Lui, 2019a) sets. The simulated dataset is generated using two distinct approaches. The first method involves warping through a Gaussian deformation vector and introducing blurring through Gaussian noise. This dataset is referred to as the Gaussian simulated dataset. The second approach employs inter-modal and spatially correlated Zernike coefficients (Chimitt & Chan, 2020). This dataset is referred to as the Zernike simulated dataset. Further comprehensive information about these datasets is available in 1. The free parameters can be classified into six distinct groups. The first group encompasses the convergence criteria of the EM method. This parameter involves a trade-off between runtime and algorithm accuracy. Given that turbulence removal is not a real-time computation but rather an offline problem, the chosen value strikes a balance between achieving satisfactory accuracy and ensuring a reasonable runtime. The intention is to avoid an excessively stringent threshold that could lead to impractical computation times while still maintaining attainable levels of accuracy. The second group of parameters pertains to the calculation of Δτ matrices and includes α, Wmin, and Wmax,, which are utilized in determining the size of the sliding window. Additionally, β is employed to identify outlier ∆τ. These parameter values were chosen through a process of trial and error, involving thorough examination of the datasets. It is important to note that the value of Wmin should be chosen small enough to encompass local transformation information, while Wmax should not be too large, as it might include a substantial portion of the image, causing the estimated transformation to become out of locality. The third group of free parameters is used to determine the optimal value of ∆τ through the ADMM method. This group comprises parameters ρandεtolerance with their values set to the ones according to the recommendations of He et al. (2014). The fourth group of free parameters pertains to the number of MOG models used in noise and distortion estimation. This group encompasses the maximum number of models and the threshold for model integration, determined through a trial-and-error process. [SEP] Justify:

Output: The text is irrelevant to the claim about the exploration and documentation of planets. It discusses the evaluation of proposed methods that involve datasets for image processing and noise estimation, which does not relate to planetary exploration.


Input: Task: corroborate the claim using the given text. Claim: The discovery of exoplanets has expanded the search for extraterrestrial life. [SEP] Text: Bennett offers a host of lessons here not only about global warming and environmental degradation, but our place in the universe as well. ---by planet, moon by moon, [Beyond UFOs] explores the possibility of life elsewhere in this solar system. It then speculates about other solar systems in our galaxy where, according to the prevailing scientific view, simple life almost surely exists and intelligent life is plausible. For the most part, Bennett's search for extraterrestrial life adds up to a very satisfying package. . . . At its core, this book delivers a combination that is hard to beat: solid yet highly speculative science plus accessible prose that add up to an out-of-this-world reading experience. ---Fred Bortz, Seattle TimesIn cogent and entertaining language, astrophysicist and popular writer Bennett explains that the determining factor in whether we can locate intelligent life elsewhere in the universe is whether such a civilization--and our own--can continue long enough to develop the highly sophisticated technology needed for interstellar travel. . . Bennett does a wonderful job of explaining the conditions necessary for simple life, how we might discern its existence and where we should be looking. He then does the same thing for intelligent life. While he is fair to those who believe life is incredibly rare, he makes a compelling case that life is likely to be abundant. "Precise, accurate, lucid, and engaging. This is popular-science writing at its best. I enjoyed reading this book. "—"This is a fascinating book about the living universe, well-written and timely. "—David Morrison, coauthor of System and Voyages to the PlanetsThis is a highly readable and enjoyable book that centers on astrobiology--a discipline that melds astronomy, biology, geology--and a little bit of luck--to explore the prospect of life on other worlds. . . . Bennett is an excellent writer, taking the reader on an exploration quest to find alien life, and how difficult solar system sleuthing can be, such as on Mars, Jupiter's Europa, or on Saturn's Titan. You'll also find an excellent treatment on current activities surrounding the on-going search for extraterrestrial intelligence. Winner of the 2010 US Review of Books's in Culture"With the possible exception of the God question, I can think of no subject that has inspired such wide-eyed wonder and speculation as the matter of whether or not we are alone in the cosmos. [SEP] Justify:

Output: The text corroborates the claim by discussing the search for life beyond our planet and the scientific speculation surrounding it. The mention of exploring conditions for life on other worlds ties directly into the broader theme of exoplanet discovery expanding our understanding of potential extraterrestrial life, echoing the sentiment that the search has indeed broadened due to these discoveries. Additionally, it highlights that Bennett's exploration includes both our solar system and others, suggesting that recent advancements have sparked more interest and research into this area.


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: , 2017) and increased hydration (Morillas and Gallardo, 2015; Zhang et al. , 2018), which were effective in enhancing biocrust establishment and recovery following disturbances (Antoninka et al. , 2020). 5 proliferation of biocrust bacteria was detected after wetting, suggesting prolonged recovery times of biocrusts following major mechanical disturbances such as mining. Furthermore, recovery largely depends on site conditions and the ability of biocrust propagules to disperse to post-mining sites. Further research is needed to confirm our hypothesis of low proliferation and thus restoration rates in hyperarid biocrust bacterial communities. Code and data availability All data produced in this study and scripts used for community analysis, functional predictions, and chlorophyll a estimation plot are available at (Gabay, 2023). The raw 16S sequences are available in the NCBI database under 906925 and accession numbers SAMN31937891–SAMN31937900 ( last access: 30 November 2022). supplement related to this 10. 5194/soil-9-231-2023-supplement. Author contributions TG: conception, sample collection, incubation, chlorophyll a and DNA extraction, statistical analysis, visualization, and writing (original draft preparation, reviewing, and editing). EP: DNA-SIP assay, DNA quantification, and PCR amplification. OG and YZ: conception, writing (reviewing and editing), investigation, and supervision. RA: conception, statistical analysis, visualization, supervision, and writing (reviewing and editing). All authors read and approved the paper. Competing interests The contact author has declared that none of the authors has any competing interests. Disclaimer Publisher's note: remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. thank from ICL-Rotem for coordinating sample collection and providing Zin factory maps and meteorological data, for her assistance in sample collection, and for suggestions on statistical analyses. Lastly, we thank ICL-Rotem for their support and funding of this research. Financial support Funding for this research was provided by ICL-Rotem. was supported by the Foundation (grant no. 19-24309Y) and was supported by the of and Sport (SoResearch (grant no. EF16_013/0001782)). Review statement This paper was edited by and reviewed by two anonymous referees. 10. 3389/fmicb. 2015. [SEP] Justify:

Output: The text does not directly address the claim about plants growing only in soil. Instead, it discusses research related to biocrust bacteria and their recovery under various conditions, including disturbances. There is no mention of hydroponics or aeroponics, making the relevance to the claim cold and contrasting with the notion by implying there are other growth conditions discussed, although not explicitly stated.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: When selecting the value of the integration threshold, ensure that it is not too small, which would preserve similar models, and not excessively large, as it might lead to the merging of dissimilar models. The fifth group of free parameters encompasses the parameters: the parameter m represents the minimum number of images required for the algorithm to function accurately. Through the examination of the datasets, it has been determined that the proposed method can effectively remove turbulence with a set of 25 images. Therefore, the parameter m has been set to 25. Within this group, a threshold value is defined for the purpose of identifying the support set. If the weighted mean of the three criteria introduced in selecting a subset of images using the method section becomes lower than this threshold, the current image is regarded as a member of the support set of the initial set of m images. The value of this threshold is also determined through trial and error. The stopping criteria for the EM method (Algorithm 1), method (Algorithm 4), and calculating low rank matrix (Algorithm 5) are the number of iterations, which are set to 40, 10, and 100 iterations, respectively. The sixth group of free parameters involves the λ parameter applied in the WALS method. The determination of this parameter value was achieved through an iterative process of trial and error, conducted specifically on the applied datasets. Table 1: Free parameters of the proposed method and their values, which have been used in all experiments. name Parameter group MaxIter=40 Number of iterations EM convergence criteria (Algorithm 4) α=0. 56 The ratio of entropy of each window w. r. t. the entropy of the whole image Calculation of Δτ Wmin=max(7,120min(width,height)) Minimum size of sliding window Wmax=max(19,18min(width,height)) Maximum size of sliding window β=1. 3 Coefficient of selecting outlier transformation matrix ρ=2 Penalty amount Finding the optimal value of Δτ by the ADMM method εtollerance=10−7 Threshold of determination of convergence condition ε=0. 15 Merge threshold Number of MOG models in estimating distortion and noise Maxk=10 Number of primary Gaussian models m=25 Number of data choices method C=10 Number of iterations εRansac= 0. 5 Similarity threshold for selecting support set λ = 0. 0001 Regularization parameter WALS method DOI: 10. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses technical parameters and algorithms related to image processing methods rather than providing any information about the exploration and documentation of planets.


Input: Task: corroborate the claim using the given text. Claim: The discovery of exoplanets has expanded the search for extraterrestrial life. [SEP] Text: The search for extraterrestrial intelligence today has almost theological status in terms of its implications, and yet it is a rigorous science conducted by world-class scientists. Jeffrey Bennett's book is one of the finest primers on this burgeoning new field. And even though this can be a technically daunting science, Bennett's highly readable prose invites everyone into the dome to gaze through the telescope to have a look for themselves, for this is a journey we are all on together. "—Michael Shermer, publisher of Skeptic and columnist for Scientific American[Jeffrey Bennett] has taken a break from the treadmill of updating his textbook and has written a popular book instead, bringing the rest of us up to date on our extraordinary new and expanded universe--and on who else might live in it. . . Beyond UFOs is crammed with neat analogies, startling imagery and mind-blowing illustrations of astronomical concepts. If you want to understand the universe and our place in it, you will not find a better primer. The first diagram alone--which shows how Earth's 10,000-kilometre span of real estate fits into a supercluster of galaxies a billion trillion kilometers across--bear a good 10 minutes of study. This truth is astonishing, and humbling--and Beyond UFOs is a great place to find it. ---Michael Brooks, New ScientistWinner of the 2009 in Cosmology/New ScienceThis exploration of potential alien life is a timely work, just as the steadily increasing discoveries of extra-solar planets makes the possibility of finding alien life more plausible. . . . [Beyond UFOs] is a fully rounded examination of the subject, accessible to all. I guarantee that after reading this book you will be watching space probe results that much more closely. And maybe, you will be watching the skies too! ---and i ix xi 1. Worlds beyond 1 2. It Science? 22 3. Know about 41 4. Life? 62 5. 87 6. of a 111 7. Life in the 137 8. Life among the 161 9. for 184 10. Everybody? 197 207 Afterword to the 209 221 (Deutsch) Share this book Twitter Linkedlogin or register with to order this product. in Language: English Publisher: year: 2011 Edition: With a New afterword by the author Audience: Professional and scholarly;College/higher education; content: 248 Illustrations Other: 8 color illus. 25 halftones. [SEP] Justify:

Output: The text corroborates the claim by discussing the steadily increasing discoveries of extra-solar planets, indicating that these discoveries make the possibility of finding alien life more plausible. It emphasizes the implications of exoplanets on the search for extraterrestrial life, thereby directly supporting the claim.


Input: Task: pass 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: : Distribution of Mixotrophy and Mechanisms across in an Community, mSystems, 6, e00786-20, 2021. . , Schrempf, D. , Woodhams, M. D. , von Haeseler, A. , and Lanfear, R. : IQ-TREE 2: for in the Genomic Era, Mol. Biol. Evol. , 37, 1530–1534, 2020. Morillas, L. and Gallardo, A. : Biological soil crusts and wetting events: Effects on soil N and C cycles, Appl. Soil Ecol. , 94, 1–6, 2015. Parada, A. E. , Needham, D. M. , and Fuhrman, J. A. : Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples, Environ. Microbiol. , 18, 1403–1414, 2016. Pepe-Ranney, C. , Koechli, C. , Potrafka, R. , Andam, C. , Eggleston, E. , Garcia-Pichel, F. , and Buckley, D. H. : Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation, ISME J. , 10, 287–298, 2016. Rajeev, L. , da Rocha, U. N. , Klitgord, N. , Luning, E. G. , Fortney, J. , -Pichel, F. , Brodie, E. L. , Northen, T. R. , and Mukhopadhyay, A. : Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust, ISME J. , 7, 2178–2191, 2013. Ritchie, R. J. : of Equations for Acetone, Methanol and Ethanol Solvents, Photosyn. Res. , 89, 27–41, 2006. Schwartz, E. , Hayer, M. , Hungate, B. A. , and Mau, R. L. [SEP] Justify:

Output: The text provided does not address the claim about plant growth in soil versus alternative methods like hydroponics or aeroponics. Instead, it appears to be a list of scientific references and articles that focus on soil ecosystems and other related topics but does not clearly support or contrast the claim regarding plant growth methods.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: 7717/peerj-cs. 1713/table-1 Compare the results of the proposed method with the existing methods As mentioned, the results of the proposed method are compared with the results of the other eleven methods. The results of the Gaussian simulated dataset are compared with the Two-and JSUB methods, and the results of the Chimney and Building image sequences are compared with the PCA-Based, Lucky Region, Two-and UCSPF methods. These comparative results are presented in Tables 2 and 3, respectively. The results of the proposed method on the sequences of the Moon-surface and Water-tower images are provided in 15. 3815 19. 9009 16. 7093 19. 5172 24. 0959 20. 9223 25. 1344 SSIM 0. 5448 0. 8136 0. 6801 0. 8163 0. 9137 0. 8375 0. 9460 Road PSNR 26. 58 27. 4061 23. 9782 30. 03 33. 8682 32. 1232 32. 0174 SSIM 0. 7822 0. 8036 0. 7638 0. 8608 0. 9063 0. 9005 0. 9226 Mean PSNR 20. 9807 23. 6535 20. 3437 24. 7736 28. 9820 26. 5227 28. 5759 SSIM 0. 6635 0. 8086 0. 7219 0. 8385 0. 91 0. 869 0. 9343 DOI: 10. 7717/peerj-cs. 1713/table-2 Note: The best result in each row is shown in bold. Table 3: The results of the proposed method and other existing methods based on PSNR (first rows) and SSIM (second rows) criteria on the chimney and building sequences. PCA-baced Lucky region Two-stage 16. 2921 31. 0421 30. 6152 31. 4314 31. 0052 32. 0103 28. 4552 24. 0133 31. 0484 30. 8352 SSIM 0. 0539 0. 1137 0. 1193 0. 112 0. 1075 0. 1632 0. 9065 0. 8736 0. 9155 0. 9231 Building PSNR 14. 346 24. 0679 25. 0724 24. 808 26. 2145 26. 4822 15. 8501 24. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the results of comparative methods without addressing the exploration or documentation of planets. There is no connection between the details provided regarding proposed methods and any planetary exploration.


Input: Task: corroborate the claim using the given text. Claim: The discovery of exoplanets has expanded the search for extraterrestrial life. [SEP] Text: downloadDownload free _right2013 – Life is a : The “Search for Water” evolves into the “Search for Life”Bill SmithThe 2013 data from the gives a current estimate of the number of Earth-like planets in the habitable zone of sun-like stars in the Galaxy, as 144 billion. We propose that this estimate has caused a consciousness change in human belief in the probability of life off Earth. This seems to have affected NASA's public statements which are now leaning to the more visionary mission goal of the " Search for Life " rather than the 1975-2012 focus of the " Search for Water ". We propose that the first confirmed Earth-like planet, expected to be announced later this year, be called " " in honour of the visionary USA scientist Bill Borucki, the father of the Kepler Mission. We explore the 2013 status of the Hoyle-of Panspermia, its hypothesis, propositions, experiments and evidence. We use the model for scientific hypotheses(1). Finally we explore Hoyle's vision of a planetary microbe defense system we call the Hoyle Shield. We explore the subsystem components of the shield and assess some options for these components using breakthrough technologies already available. downloadDownload free _rightSee full preview is currently unavailable. You can download the paper by clicking the button above. Loading PreviewSorry, preview is currently unavailable. You can download the paper by clicking the button above. Related papersin the Ointment: Homochirality & Extraterrestrial Origin-Of-Life TheoriesTimothy GordondownloadDownload free _rightLectures in astrobiologyAndreas CorzodownloadDownload free _rightScience and Boarddr padownloadDownload free _rightOf Life: Astrobiologylucian gleiserArxiv preprint arXiv:0811. 1291, 2008downloadDownload free _rightis the Code? A Question of ExtraTerrestrial OriginsTzipe Govezensky2010downloadDownload free _rightof Explorationian crawfordAstrobiology, 2010downloadDownload free _rightOrigin of LifeJoshue EspindownloadDownload free _rightLife's chirality from prebiotic environmentslucian gleiserof Astrobiology, 2012downloadDownload free _rightfrom the Ancient Ironfree _rightDid life come from another world? [SEP] Justify:

Output: The text corroborates the claim by discussing the estimation of Earth-like planets in the habitable zone, and how this has shifted human belief regarding the probability of life beyond Earth. It suggests that this consciousness change has influenced NASA's focus towards the 'Search for Life,' indicating a clear link between exoplanet discoveries and the search for extraterrestrial life.


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: : Probing of Microorganisms in with H218O, in: Probing, Springer, 129–136, 2019. Sengupta, M. : Environmental impacts of mining: monitoring, restoration, and control, 2nd Edn. , 1 pp. , 2021. Steven, B. , Kuske, C. R. , Gallegos-Graves, L. V. , Reed, S. C. , and Belnap, J. : in. Environ. Microbiol. , 81, 7448–7459, 2015. Štovícek, A. and Gillor, O. : of Communities to Hydration and in Ecosystems, in: Microbiology of Hot Deserts, edited by: Ramond, J. -B. and Cowan, D. A. , Publishing, Cham, 244, 319–339, 2022. Sultana, N. , Zhao, J. , Zheng, Y. , Cai, Y. , Faheem, M. , Peng, X. , Wang, W. , and Jia, Z. : Stable isotope probing of active methane oxidizers in rice field soils from cold regions, Biol. Fertil. Soils, 55, 243–250, 2019. Swenson, T. L. , Karaoz, U. , Swenson, J. M. , Bowen, B. P. , and Northen, T. R. : Linking soil biology and chemistry in biological soil crust using isolate exometabolomics, Nat. Commun. , 9, 19, 2018. R Team: R: A language and environment for statistical computing, Vienna, Austria, (last access: 1 December 2022), 2013. . , Strong, C. L. , Bullard, J. , Webster, R. , and Lan, S. : Soil biocrusts affect metabolic response to hydration on dunes in west Queensland, Australia, Geoderma, 405, 115464, 2022. Velasco Ayuso, S. , Giraldo Silva, A. , Nelson, C. , Barger, N. N. , and Garcia-Pichel, F. : Production of High-Biomass for Restoration of Soils, Appl. Environ. Microbiol. , 83, e02179-16, 2017. [SEP] Justify:

Output: The text contrasts the claim by mentioning various studies and research in environmental microbiology and soil health, implying a broader understanding of plant growth conditions that could include methods beyond traditional soil. Even though the text does not assert hydroponics or aeroponics directly, the emphasis on environmental impacts and biological interactions suggests alternative methods could be viable for plant growth.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: 0312 25. 3721 28. 4178 SSIM 0. 1858 0. 3271 0. 3882 0. 3855 0. 4857 0. 5137 0. 6449 0. 7214 0. 7926 0. 8802 Mean PSNR 15. 3190 27. 555 27. 8438 28. 1197 28. 6098 29. 2462 22. 1526 24. 0222 28. 2102 29. 6265 SSIM 0. 1198 0. 2204 0. 2537 0. 2487 0. 2966 0. 3384 0. 7757 0. 7975 0. 8540 0. 90165 DOI: 10. 7717/peerj-cs. 1713/table-3 Note: The best result in each row is shown in bold. Table 4: The results of the proposed method based on PSNR (first rows) and SSIM (second rows) criteria on Zernike simulated datasets. Proposed Car-front PSNR 23. 0173 SSIM 0. 9208 Road PSNR 31. 7254 SSIM 0. 9167 Mean PSNR 27. 3714 SSIM 0. 9188 DOI: 10. 7717/peerj-cs. 1713/table-4 Figures 3–6 provide visual representations of the restored images obtained from the proposed method and the results of the previous methods. It is evident from these images that the -and UCSPF methods yield higher visual quality in terms of the final restored image compared to the other methods. Figure 3: (A) The reference image of the car-front sequence (B) one observed image, and the qualitative results of (C) the proposed method, (D) NDL, (E) SGL, (F) centroid, (G) RPCA, (H) JSUB, and (I) two-stage, on this sequence. Photo credit: Pui Anantrasirichai. Download full-size image DOI: 10. 7717/peerj-cs. [SEP] Justify:

Output: The text is irrelevant to the claim as it contains numerical data and references to visual representations of image restoration methods, which do not address the exploration or documentation of planets. No mention or discussion of planets is found in the provided content.


Input: Task: corroborate the claim using the given text. Claim: The discovery of exoplanets has expanded the search for extraterrestrial life. [SEP] Text: Hostname: page-component-788cddb947-jbjwg Total loading time: 0 Render date: 2024-10-08T15:12:34. 214Z Has data issue: false hasContentIssue false Home >Books >in the Universe >for in the print or eBook [Opens in a new window] Book contents in the Life in the page Acknowledgements1 for Extraterrestrial Life2 Where in the Universe to Look? 3 Evolution – Here and Elsewhere4 Concept of Habitability5 Life in the Solar System6 Life in Systems7 of Extraterrestrial Life8 Intelligence – Here and of 10. 1017/9781009207355. 003 [Opens in a new window] Publisher: publication year: 2022 a Privileged Generation? For many millennia, humans have gazed up in wonder at the night-time sky. The full panoply of the is an awesome sight. The scale of space is immense. Is there life out there somewhere? If so, where, and what form does it take? In the space of a couple of sentences, we’ve already gone from generalized wonder to specific questions. The next step is from questions to hypotheses, or, in other words, proposed answers. Here are two such hypotheses that I’ll flesh out as the book progresses: first, life exists on trillions of planets in the universe; second, it usually follows evolutionary pathways that are broadly similar to – though different in detail from – those taken on Earth. Going from cosmic wonder to questions about alien life and on to hypothetical answers has been possible for a long time. But the final steps – from hypothetical answers to testing the hypotheses to arriving at an understanding of reality – have so far proved beyond humanity’s grasp. That may be about to change. We may be on the threshold of being able to answer the age-old question ‘are we alone in the universe? ’ with a resounding ‘no’. But what is the basis of this claim? The short answer is advancing technology, and in particular advancing design of telescopes. We’ll get to that topic soon. But first, let me reassure you that I’m not alone in my optimism about the imminent discovery of evidence for alien life. [SEP] Justify:

Output: The text corroborates the claim by discussing humanity's long-standing curiosity about life beyond Earth and how advancements in technology, particularly in telescope design, are paving the way for potential discoveries regarding alien life. It emphasizes that we may be on the 'threshold of being able to answer' questions about extraterrestrial life, which indicates that these discoveries, including those of exoplanets, have a significant role in our search for life beyond our planet.


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: Preprints AbstractDiscussion © Author(s) 2023. This work is distributed under the Attribution 4. 0 License. © Author(s) 2023. This work is distributed under the Attribution 4. 0 License. Preprints AbstractDiscussionMetrics 09 Jan 2023 | 09 Jan 2023 Only a minority of bacteria grow after wetting in both natural and post-mining biocrusts in a hyperarid, phosphate mine and Abstract. Biological soil crusts (biocrusts) are key contributors to desert ecosystem functions; therefore, biocrust restoration following mechanical disturbance is imperative. In the hyperarid regions, phosphate mining has been practiced for over 60 years, destroying soil habitats, and fragmenting the landscape. To understand the effects of mining activity on soil health, we previously characterized the biocrust communities in four phosphate mining sites over spatial (post-mining and natural plots) and temporal (2–10 years since restoration) scales. We showed that bacterial abundance, richness, and diversity in natural plots were significantly higher than in post-mining plots, regardless of temporal scale. In this study, we selected one mining site and used DNA stable isotope probing (DNA-SIP) to identify which bacteria grow in post-mining and natural biocrusts. Since biocrust communities activate only after wetting, we incubated the biocrusts with H218O for 96 hours under ambient conditions. We then evaluated the physicochemical soil properties, chlorophyll a concentrations, activation, and functional potential of the biocrusts. The DNA-SIP assay revealed low bacterial activity in both plot types and no significant differences in the proliferated communities’ composition when comparing post-mining and natural biocrusts. We further found no significant differences in the microbial functional potential, photosynthetic rates, or soil properties. Our results suggest that growth of hyperarid biocrust bacteria after wetting is minimal. We hypothesize that due to the harsh climatic conditions, during wetting bacteria devote their meager resources to prepare for the coming drought, by focusing on damage repair, and organic compound synthesis and storage rather than on growth. These low growth rates contribute to the sluggish recovery of desert biocrusts following major disturbances such as mining. Therefore, our findings highlight the need for implementing active restoration practices following mining. How to cite. Gabay, T. , Petrova, E. , Gillor, O. [SEP] Justify:

Output: The text contrasts the claim by discussing the role of biological soil crusts and the growth of bacteria in hyperarid environments, which suggests that alternative growth methods such as biocrust restoration following mechanical disturbances may be effective. The focus on soil health and the minimal bacterial growth after wetting indicates that plants and microorganisms can interact and potentially thrive in conditions that differ from traditional soil growth, thereby providing context against 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: 1713/fig-3 Figure 4: (A) The reference image of the road sequence, (B) one observed image, and the qualitative results of (C) the proposed method, (D) NDL, (E) SGL, (F) centroid, (G) RPCA, (H) JSUB, and (I) two-stage, on this sequence. Download full-size image DOI: 10. 7717/peerj-cs. 1713/fig-4 Figure 5: (A) The reference image of the chimney sequence, (B) one observed image, and the qualitative results of (C) the proposed method, (D) lucky region, (E) two-stage, (F) BNLTV, (G) NDL, (H) HVDKR, (I) SGL, (J) centroid, (K) UCSPF, and (L) PCA-based, on this sequence. Photo credit: Chiman Kwan. Download full-size image DOI: 10. 7717/peerj-cs. 1713/fig-5 Figure 6: (A) The reference image of the building sequence, (B) one observed image, and the qualitative results of (C) the proposed method, (D) lucky region, (E) two-stage, (F) BNLTV, (G) NDL, (H) HVDKR, (I) SGL, (J) centroid, (K) UCSPF, and (L) PCA-based, on this sequence. Photo credit: Chiman Kwan. Download full-size image DOI: 10. 7717/peerj-cs. 1713/fig-6 method exhibits a restored image with lower quality compared to other methods. Despite the restoration of the geometric structure, the resulting image appears blurry and overly brightened due to the effects of temporal averaging. The RPCA method, lacking a mechanism to effectively remove distortion, primarily focuses on selecting a subset of turbulent images with minimal distortion and maximal sharpness during the subsampling stage. As a result, the restored image obtained using the RPCA method continues to exhibit some degree of distortion. [SEP] Justify:

Output: The text discusses various methods for restoring images and the quality of those restorations, mentioning specific techniques such as the RPCA method. It does not address the claim regarding the exploration and documentation of planets, making it irrelevant to the argument presented.


Input: Task: corroborate the claim using the given text. Claim: The discovery of exoplanets has expanded the search for extraterrestrial life. [SEP] Text: A 2021 paper in the leading scientific journal Nature, by the American physicist and his colleagues, began with the following sentence: ‘Our generation could realistically be the one to discover evidence of life beyond Earth. ’ Its authors clearly share my optimism in this respect. Of course, there’s a question-mark hanging over the meaning of ‘our generation’, as the six authors are varied in age, and their readers even more so. But that’s a small uncertainty in the grand scheme of things. The key point is that many scientists suspect that the first evidence of life beyond Earth will be forthcoming on a timescale of years to decades, not centuries. Even if it takes five decades to acquire the first conclusive evidence, a reasonable proportion of those alive today (regrettably not including me! ) will still be here to see it. In the previous paragraph, I used the phrase ‘many scientists’. But scientists of what type? Science is a broad endeavour, and some parts of it are more relevant to the search for life than others. However, that said, many scientific disciplines have a role to play. They include cosmology, astronomy, astrophysics, planetary science, atmospheric science, geology, ecology, evolutionary biology, genetics, molecular biology, and organic chemistry – and that is far from being an exhaustive list. The principal discipline is astrobiology, which is a mix of some or all of the above, with the exact mix depending on the astrobiologist concerned. Astrobiologists of my generation weren’t trained as such, as there were no courses in the subject, so we’ve migrated towards it from various starting points – in my case evolutionary biology. But there’s a younger cohort of astrobiologists who have indeed been trained in this discipline. Importantly, the ‘many scientists’ who suspect that the first evidence of alien life will be found on the years-to-decades timescale include specialists in all of the disciplines mentioned above, and indeed others too. So this optimism isn’t a passing fad in one particular narrow branch of science. [SEP] Justify:

Output: The text corroborates the claim by expressing optimism about discovering evidence of life beyond Earth and emphasizing the role of various scientific disciplines, including those related to the study of exoplanets. The mention of many scientists believing that evidence of extraterrestrial life will likely be found in the near future ties directly to the exploration of exoplanets and how that pursuit has spurred interest in the search for life outside Earth.


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: I added literature regarding physical trampling and how they might compare to the mining disturbance in the hyper-arid (L358 – L370):…” Previous studies examining the effect of a physical disturbance (repeated trampling) on biocrust communities, revealed a decrease in the amount of extractable DNA, lower chlorophyll a, and a decrease in biomass and cyanobacteria abundance (Kuske et al. , 2012; Steven et al. , 2015; Chung et al. , 2019). However, these studies investigated a localized disturbance compared to mining disturbance, where the biocrust is completely removed over large spatial scales. Moreover, the previous studies were conducted in environments that were less extreme than the hyper-arid Zin Valley. Therefore, we expected the damage to the biocrust in Zin post-mining sites to follow similar patterns but to be more conspicuous than the previously reported disturbed biocrusts (Kuske et al. , 2012; Steven et al. , 2015; Chung et al. , 2019). Our previous report (Gabay et al. , 2022) supported this notion; we demonstrated differences in bacterial communities in natural and post-mining biocrusts, expecting these differences to be reflected in the proliferating communities of these biocrusts. "Similarly, transcriptomic studies that show the genes that are expressed during a wetting pulse and have documented metabolic a physiological changes in the bacterial community in a wetting pulse. These studies show where resources may be going to rather than growth, and should probably be at least mentioned in this text. Response: I added previous studies that showed expression of nitrogen cycling genes and metabolite production following wetting (L417 – L425):…” One study examining microbial nitrogen transformations in biocrusts collected from biome in Namibia and showed that following wetting, nitrogen cycling genes are expressed in biocrust organisms (Maier et al. , 2022). another study examining biocrust samples taken from the in Utah demonstrated a pulse of metabolite release following controlled wetting (Swenson et al. , 2018). Based on these reports (Maier et al. , 2022; Swenson et al. , 2018) and due to the extreme conditions in (Levi et al. , 2021), we suggest that hyperarid biocrust communities prioritize functions such as metabolite production, nutrient cycling and preparation for desiccation over growth. [SEP] Justify:

Output: The text contrasts the claim by discussing studies related to biocrust communities and their responses to wetting pulses and disturbances. It indicates that biocrust organisms, which are not traditional soil plants, can express nitrogen cycling genes and produce metabolites, showing a form of thriving in environments that do not resemble standard soil conditions. This indirectly supports the idea that plants or plant-like organisms can survive outside of traditional growing mediums such as soil, suggesting alternative methods like hydroponics or aeroponics may also allow for plant growth.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: Nonetheless, due to its emphasis on the selection of a subset of sharp images and using the appropriate energy function to merge these subsampled images, coupled with the application of the blind deconvolution method, the restored image has little blur. The JSUB method closely resembles the RPCA method except that its energy function uses TV regularization, the L2 norm, and adaptive Gaussian noise for joint subsampling. This method also lacks a blind deconvolution step, resulting in a mildly distorted but blurred image. The Two-Stage method’s deficiency caused by from the generation of an unsuitable reference image through the averaging process, leading to errors during the registration stage and ultimately resulting in a blurred final image. Similar to the Two-Stage method, the NDL method also suffers from the impact of the erroneous reference image generated through the averaging process. This issue substantially affects the performance of the registration stage, and even though the method employs the blind deconvolution technique, the resulting image lacks clarity in terms of capturing image details. HVDKR uses the RPCA method to generate a reference image with reduced blur and distortion. This approach then further enhances the reference image using a variational model. Employing deformation-guided fusion the method not only models and mitigates the impact of the image but also effectively reduces blurriness in the final restored image. But since it is a step-by-step process, the interaction between the two factors of blur and distortion has not been taken into account. As a result, while the output images may exhibit relatively improved sharpness, the overall restored image tends to retain some level of blurriness and distortion, and also the fine details in the image are not well-defined. In the UCSPF method, by separating the phase and magnitude components in the frequency domain, structural information and brightness intensity are separated to process the two distortion and blur factors separately. Through multiscale and multidimensional operations applied to these distinct components, the UCSPF method effectively produces an output image characterized by reduced levels of distortion and blur. Moreover, this approach facilitates the preservation of sufficient image details. Nonetheless, the processing conducted in the frequency domain lacks access to spatial information. For this reason, frequency-domain processing, although well-restored in detail in high-energy areas, has caused fluctuations in the brightness intensity in smooth regions. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses image processing techniques and methods for restoring blurry images. It does not mention planets or their exploration, making the content unrelated to the claim about the thorough exploration and documentation of planets.


Input: Task: corroborate the claim using the given text. Claim: The discovery of exoplanets has expanded the search for extraterrestrial life. [SEP] Text: Telescopes of Galileo’s day were great for astronomy – especially when compared with the naked eye – but they weren’t much use for astrobiology. In contrast, today’s telescopes have the capability of addressing hypotheses about alien life. For example, we can now use telescopes to examine the atmospheres of distant exoplanets. We can search for signs of oxygen, which is regarded as a biosignature. In particular, it may be a signature of photosynthesis by microbes and plants. It’s true that oxygen may come to exist in planetary atmospheres by abiotic means. However, as we’ll see in 3. 7 centimetres, Newton’s (in 1668) 2. 5 centimetres. They’re not directly comparable because Galileo’s was a refractor (a telescope that uses lenses) while Newton’s was a reflector (a telescope that uses mirrors), but they were both tiny by current standards. Today’s large telescopes have mirrors with diameters measured in metres rather than centimetres. For example, the Canarias, situated on the Spanish island of La Palma, has an aperture of 10. 4 metres. The increase in telescope size has been continuous from the 1600s to the 2000s, though it has speeded up significantly since 1900. The largest telescope in the world at the end of the nineteenth century was the Leviathan of Parsonstown in County Offaly, Ireland, which had a diameter of 1. 83 metres. This size was exceeded in 1917 with the construction of the on in southern California, with a diameter of 2. 5 metres. So the last 100 years have seen the largest increase – more than 8 metres between the early twentieth and early twenty-first centuries. However, these measurements in metres don’t quite suffice to explain just how much more powerful modern telescopes are than their ancient forerunners. The light-collecting capability of a telescope scales not with the diameter of its primary mirror but with its surface area. So, in terms of functionality, a 10-metre mirror is not 10 times as good as a 1-metre mirror; rather it’s better by a factor of 100. [SEP] Justify:

Output: The text corroborates the claim by discussing modern telescopes' capabilities to examine the atmospheres of distant exoplanets and search for biosignatures, such as oxygen, which could indicate the presence of extraterrestrial life. This directly supports the idea that the discovery of exoplanets, facilitated by advanced telescopes, enhances the search for life beyond Earth.


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: 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 colonizacion by cyanobacteria can be faster than thought. 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. L379-381. It is hypothesised 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. Table 1. Values should include also the standard deviation. Citation: AC2: 'Reply on RC2', Talia Gabay, 20 Mar 2023 This study is interesting as it identifies which bacteria proliferate in biocrusts from natural and postmining areas and examines functional gene abundances, unlike previous studies that have focused on characterizing the microbial community composition of natural and post-mining biocrusts. This, I consider the approach novel. Nonetheless, I have a few comments that should be addressed: AbstractL19-23. I recommend deleting this sentence because it refers to a previous study, and the abstract should focus on the objectives and results of the present study. Then, in the Introduction or the Discussion, it is fine if mention to previous results is done. Response: I removed the section from the abstract. M&ML103-105. It is not clear the predominant p109. Add a short description of the biocrust sampled (thickness, cover, composition, …. ). Were there differences in the biocrust from natural and post-mining sites? [SEP] Justify:

Output: The text contrasts the claim by discussing the growth potential of biocrusts, specifically mentioning microbial communities in post-mining and natural areas. It implies that plant-like microbial life can proliferate in environments lacking traditional soil, thereby suggesting that plants or similar organisms can thrive without conventional soil conditions.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: Despite the visually satisfactory quality of the final images, it is noteworthy that the computed PSNR and SSIM values are lower than expected. As evident in Figs. 3–6, the resulting images from the proposed method exhibit sharper edges and finer details in comparison to those generated by other methods. The smooth regions within the ground truth images are returned as smoothly in the output images. The distortion is removed as much as possible, but the brightness of the output image in the Chimney sequence produced by the proposed method appears slightly darker compared to the corresponding ground truth image. Figure 7 presents the restored images generated by the proposed method on the Zernike turbulence dataset. A visual comparison of both Gaussian and Zernike turbulence images reveals that blurring is more obvious than distortion in the Zernike images. While the proposed method effectively restores Zernike turbulence images with notable accuracy, as evident in Fig. 7F, it is worth noting that the details of the asphalt road are not fully restored to their original quality. Figure 7: (A) The reference image of the car-front sequence (B) one Zernike simulated image, and (C) the qualitative results of the proposed method, (D) the reference image of the road sequence (E) one Zernike simulated image (F) the qualitative results of the proposed method. Photo credit: Pui Anantrasirichai. Download full-size image DOI: 10. 7717/peerj-cs. 1713/fig-7 Indeed, conventional images typically exhibit characteristics of low-frequency signals, rendering them low rank. Distortion, characterized by sudden change in the signal changes, introduces high-frequency components that elevate the signal’s rank. The time-varying blur in an image sequence from a single scene results in images that are distinct from one another. Consequently, the overall diversity of the image sequence increases. This phenomenon elevates their temporal rank. Turbulence images, caused by both distortion and spatiotemporal varying blur, possess high ranks. Consequently, by generating a low-rank matrix, it becomes possible to obtain an image that encompasses all high-rank images derived from it. This image aims to closely resemble the reference (turbulence-free) image. Consequently, the creation of a low-rank matrix can be used to eliminate turbulence. Accordingly, the LRMF method was adopted for this particular objective. [SEP] Justify:

Output: The text discusses image processing methods and the quality of image restoration in the context of Zernike turbulence datasets, but it does not mention planets or any exploration of them. Therefore, it is irrelevant to the claim about the thorough exploration and documentation of all planets.


Input: Task: corroborate the claim using the given text. Claim: The discovery of exoplanets has expanded the search for extraterrestrial life. [SEP] Text: You compare graphs of amount of light received versus wavelength for the two occasions (Figure 1. 1). Dips in the amount of light at particular wavelengths when the planet is in front of the star are interpreted as resulting from absorption of light by gases in the planet’s atmosphere. Since different gases have different characteristic patterns of absorption, you can identify them. Figure 1. 1 Detecting gases in exoplanet atmospheres. Left: amount of light received by a space telescope when the planet is ‘off to one side’ from our perspective. Right: amount of light received when the planet is in a direct line between its host star and the Earth. Note the dip in the amount of light received at a particular wavelength in the right-hand panel. If instead of looking at this graph you were looking at the light itself, after it had been split into its various colours by a prism, you would see a dark band at the wavelength (= colour) concerned. Such a dip (or band) is interpreted as the result of absorption by a particular gas in the planet’s atmosphere, and is known as an absorption band. Since different gases have different patterns of absorption centred on different wavelengths – in other words different ‘signatures’ – they can be identified. Some gases, notably oxygen, are regarded as biosignatures. As we will see later (in 2020. It gave its name to the famous Arecibo message broadcast by it into space in 1974. There are also large arrays of radio telescopes – for example ASKAP (Pathfinder), located about 700 kilometres north of the city of Perth, which started observing the sky in 2012. A of are about to feel the multidisciplinary nature of the search for extraterrestrial life that I mentioned at the outset, because we are about to move from the astronomical realm to its biological counterpart. In particular, we are going to move from the telescopes used in the search for habitable planets – and ultimately the life that’s on some of them – to the search for a workable definition of life. How can we search for life if we can’t define it? And yet the task of defining life is not an easy one – even in the restricted context of planet Earth (are viruses alive? ). It’s more difficult again to attempt a definition that will work in a cosmic context. But an imperfect definition is better than nothing – so here goes. [SEP] Justify:

Output: The text corroborates the claim by discussing the techniques used to detect gases in exoplanet atmospheres and noting that certain gases, such as oxygen, are regarded as biosignatures. This suggests that the study of exoplanets not only aims to discover new planets but also to investigate their potential to support life, thereby expanding the search for extraterrestrial life.


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: I added a description of the biocrusts in Gov mining site (L106 – L109):“…Biocrusts were sampled either from the post-mining site or the adjacent natural area. The biocrusts in Gov are thin (between 1. 5 - 2. 5 mm deep), and smooth. The site is characterized by areas covered in biocrusts or desert pavement. In each sampling site, we sampled along a 100 m strip at approximately 10 m intervals (Fig. 1). ”ResultsRegarding the results of the proliferated bacterial community composition, it would be nice to include a figure with the relative abundances of the different bacteria phylum for natural and post-mining biocrusts to make the results clearer. 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). [SEP] Justify:

Output: The text contrasts the claim by discussing the recovery of biocrusts, particularly emphasizing that biocrusts can be found and are functional in post-mining sites, highlighting that certain environments influence their capacity for photosynthesis. The mention of cyanobacterial communities and the microenvironment's role implies that plants or plant-like organisms, which may not strictly require soil, can thrive in alternative conditions, thus disputing the claim's assertion.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: Through the iterative integration of these two techniques within the LRMF method, a comprehensive framework has been established. This framework is capable of generating turbulence-free images while minimizing the presence of turbulence. The performance of the proposed method was assessed in terms of the PSNR and SSIM criteria using the t-test statistical method. To accomplish this, the maximum values obtained from the previous methods were compared with those of the proposed method. The outcome of the PSNR-based t-test indicated a 50% similarity, signifying that the proposed method’s accuracy is on par with the best outcomes of the previous methods. Conversely, the t-test conducted based on the SSIM yielded a result of 95%, underscoring the superior accuracy of the proposed method in comparison to the preceding previous methods. Since the PSNR criterion is based on MSE, even slight changes in the image’s brightness can lead to a decrease in the numerical values of this criterion. Therefore, the relative darkening observed in the results of the proposed method might contribute to the decrease in the numerical values of this criterion. On the other hand, SSIM is a perception-based criterion that, like the human visual system, considers structural, luminance, and contrast similarities between the two images. Therefore, higher numerical values of this criterion in the results of the proposed method indicate a high perceptual similarity between the resultant images and the reference images. Further detailed evaluation of the proposed method is provided in 10. 7717/peerj-cs. 1713/supp-1 Code and Dataset. DOI: 10. 7717/peerj-cs. 1713/supp-2 Download (A) The reference image of the Water tower sequence, (B) one observed image, and the qualitative results of (C) the proposed method, (D) Centroid, (E) NDL, (F) RPCA, (G) SGL, and (H) Two-Stage, on this sequence. DOI: 10. 7717/peerj-cs. 1713/supp-3 Download (A) The reference image of the Moon surface sequence, (B) one observed image, and the qualitative results of (C) the proposed method, and (D) NDL, on this sequence. DOI: 10. 7717/peerj-cs. 1713/supp-4 of different turbulence impact on Desert sequence. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses a method for generating images and evaluating their quality using different statistical criteria, specifically PSNR and SSIM. There is no mention of planets or their exploration in the provided text.


Input: Task: corroborate the claim using the given text. Claim: The discovery of exoplanets has expanded the search for extraterrestrial life. [SEP] Text: Second, a group of questions that I think of as being about the biology of alien life. These are questions about the nature of life forms, wherever they are found. For example: Is life usually (or always) based on carbon? Is it usually dependent on water? Is life usually made of cells or cell-like units? Are large life forms common, and do they usually arise from the evolution of multicellularity rather than by some other means? Are there features of large multicellular life forms that are to be expected to occur widely across multiple planets, for example skeletons? How does intelligent life arise from unintelligent beginnings, and are there parallels in the evolution of intelligence from one planet to another? Although these two groups of questions are reasonably distinct from each other, they are not without overlap and interaction, as I mentioned earlier. For example, by now we are fairly sure that, Earth aside, there are no multicellular life forms in the solar system, even though the possibility of microbial life having evolved on some local body – for example Jupiter’s moon Europa or Saturn’s moon Enceladus – remains a possibility, as we’ll see in 5. In contrast, it seems highly probable that there are plenty of rocky bodies scattered across our galaxy that have large life forms as well as microbes. Some authors have argued against this – notably the American scientists in their 2000 book Rare Earth. These authors argued that Earth possessed a combination of unique features that was unlikely to be replicated elsewhere. However, that was before the discovery of Earth-like exoplanets, and their argument no longer seems tenable. As we proceed, these two groups of questions – about the geography and biology of alien life – will always both be at least in the background. In particular 1. 1 Detecting gases in exoplanet atmospheres. Left: amount of light received by a space telescope when the planet is ‘off to one side’ from our perspective. Right: amount of light received when the planet is in a direct line between its host star and the Earth. Note the dip in the amount of light received at a particular wavelength in the right-hand panel. If instead of looking at this graph you were looking at the light itself, after it had been split into its various colours by a prism, you would see a dark band at the wavelength (= colour) concerned. [SEP] Justify:

Output: The text supports the claim by discussing how the discovery of Earth-like exoplanets challenges previous arguments against the possibility of life elsewhere. It states that the argument presented by scientists in the book 'Rare Earth' that Earth possesses unique features unlikely to be replicated was made before the discoveries of such exoplanets. The mention that many rocky bodies across the galaxy may have life forms, alongside the questions regarding the biology of alien life, illustrates a direct connection to expanding the search for extraterrestrial life.


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: 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). Citation: Report abuse × Please provide a reason why you see this comment as being abusive. You might include your name and email but you can also stay anonymous. Please provide a reason why you see this comment as being abusive. Please confirm reCaptcha. Comment* Name: Email: discussion Status: closed Comment types: AC – author | RC – referee | CC – community | EC – editor | CEC – chief editor | : Report abuse RC1: 'Comment on egusphere-2022-1510', #1, 03 Feb 2023 The manuscript “Only a minority of bacteria grow after wetting in both natural and post-mining biocrusts in a hyperarid, phosphate mine” presents the results of a H2-18-O stable isotope probing assay of the growing community members in hyperarid biocrusts that have been disturbed, or not, by mining activities. Overall, the manuscript is well conceived, written, and presented. The conclusions are sound and justified. I do have a concern that the authors have missed a swath of the literature that reports the response of biocrusts to physical disturbances, such as chronic physical trampling. These data show that physical disturbances differ from other disturbances and may affect the recovery of the biocrust community. I think some of this literature should be discussed in the context of what these authors see, and how it may be unique in these hyperarid sites. Similarly, transcriptomic studies that show the genes that are expressed during a wetting pulse and have documented metabolic a physiological changes in the bacterial community in a wetting pulse. [SEP] Justify:

Output: The text contrasts the claim by discussing the effectiveness of alternative methods in enhancing biocrust establishment and recovery in disturbed mining sites. The reference to 'active restoration measures' and 'increased hydration' suggests that plants can thrive in conditions other than soil, indicating that alternative methods may be viable for plant growth.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: (A) Desert sequence reference image, (B) a weak turbulence sample, and (C) a severe turbulence sample DOI: 10. 7717/peerj-cs. 1713/supp-5 effect of the turbulence rate on the accuracy of the proposed method (PSNR). Sequences with the smaller number represent the images with weaker turbulence. DOI: 10. 7717/peerj-cs. 1713/supp-6 effect of the alpha parameter on the accuracy of the proposed method. DOI: 10. 7717/peerj-cs. 1713/supp-7 effect of putting aside the (A) distortion factor, (B) blurring factor, and (C) on the performance of the proposed method on the Car-front sequence. DOI: 10. 7717/peerj-cs. 1713/supp-8 of symbols and variables. DOI: 10. 7717/peerj-cs. 1713/supp-9 Simulation Parameters. DOI: 10. 7717/peerj-cs. 1713/supp-10 information about the datasets employed in experiments. DOI: 10. 7717/peerj-cs. 1713/supp-11 results of the proposed method on the Moon-surface and Water-tower sequences. DOI: 10. 7717/peerj-cs. 1713/supp-12 comparison of the results of the proposed method by putting aside different components on the Car-front sequence based on the SSIM and PSNR criteria. DOI: 10. 7717/peerj-cs. 1713/supp-13 Information and authors declare that they have no competing interests. conceived and designed the experiments, performed the experiments, analyzed the data, performed the computation work, prepared figures and/or tables, authored or reviewed drafts of the 2018. Key challenges and resolutions for atmospheric turbulence effect removal. of Grid and 11(11):39-52. 2009. Automated video enhancement from a stream of atmospherically-distorted images: the lucky-region fusion approach. . 2004. Convex optimization. Cambridge: Press. . 2011. Distributed optimization and statistical learning via the alternating direction method of multipliers. Delft: Inc. . 2021. Subsampled turbulence removal network. Mathematics, Computation and Geometry of Data 1(1):1-33 Chimitt N, Chan SH. 2020. [SEP] Justify:

Output: The text does not address or relate to the claim that all planets have been thoroughly explored and documented. Instead, it focuses on various aspects of atmospheric turbulence and methods related to video enhancement, which are unrelated to planetary exploration.


Input: Task: corroborate the claim using the given text. Claim: Proteins can fold into their functional forms due to specific sequences of amino acids. [SEP] Text: (C) Parts of the MNNL and DSL sequences showing the contact amino acids (boxed), the divergent amino acids of DLL1 (red) and DLL4 (blue), and the sequence of ligands with amino acid exchanges (complete sequences of the changed MNNL and DSL domains are shown in Figure 1—figure supplement 1B). The N-glycosylation site at residue N109 of DLL4 is indicated in green. (D) N1/N2 activation ratios of ligands with exchanged N1 contact amino acids. D1contD4 does not show changes in receptor selectivity compared to DLL1. Replacing the contact residues of DLL4 with those of DLL1 only reduces N1/N2 activation ratio to ~13. Elimination of the N-glycosylation site of DLL4 with the N109G mutation (the corresponding amino acid of DLL1) does not change DLL4 receptor selectivity. Each dot represents the mean of N1 (relative luciferase units; Figure 5—source data 1)/N2 (relative luciferase units; Figure 5—source data 2) of n ≥ 3 measurements per clone of a given ligand construct. Bars represent the Mean ± SD of n ≥ 3 clones per construct (Figure 5—source data 3). Figure 5—source data 1 Raw data (RLUs) of luciferase activity in co-cultures with N1rep cells used to generate the graph in Figure 5—figure supplement 1A. Values represent relative luciferase activity (units) after subtraction of E14 background RLUs. Download elife-40045-fig5-data1-v2. xlsx Figure 5—source data 2 Raw data (RLUs) of luciferase activity in co-cultures with N1rep cells used to generate the graph in Figure 5—figure supplement 1B. Values represent relative luciferase activity (units) after subtraction of E14 background RLUs. Download elife-40045-fig5-data2-v2. xlsx Figure 5—source data 3 N1/N2 activation ratios. Values represent N1/N2 activation ratio. Values were used for generation of graphs in Figure 5A and D. [SEP] Justify:

Output: The text discusses specific amino acid sequences and their role in ligand activation ratios and receptor selectivity, which supports the claim that proteins fold into functional forms based on their amino acid sequences. It emphasizes the importance of contact amino acids and their exchanges in modulating functionality.


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: These studies show where resources may be going to rather than growth, and should probably be at least mentioned in this text. Minor concerns:Title: I am not sure the comma is needed between hyperarid and phosphateLine 210: picrust should be 2Line 214: I think this should be spelled out more completely. It just sends the reader to a reference. This is a specialized set of functional annotations. I think it would help the reader interpret Figure 6 and where the annotations are coming from. Citation: AC1: 'Reply on RC1', Talia Gabay, 20 Mar 2023 The manuscript “Only a minority of bacteria grow after wetting in both natural and post-mining biocrusts in a hyperarid, phosphate mine” presents the results of a H2-18-O stable isotope probing assay of the growing community members in hyperarid biocrusts that have been disturbed, or not, by mining activities. Overall, the manuscript is well conceived, written, and presented. The conclusions are sound and justified. I do have a concern that the authors have missed a swath of the literature that reports the response of biocrusts to physical disturbances, such as chronic physical trampling. These data show that physical disturbances differ from other disturbances and may affect the recovery of the biocrust community. I think some of this literature should be discussed in the context of what these authors see, and how it may be unique in these hyperarid sites. Response: I added literature regarding physical trampling and how they might compare to the mining disturbance in the hyper-arid (L358 – L370):…” Previous studies examining the effect of a physical disturbance (repeated trampling) on biocrust communities, revealed a decrease in the amount of extractable DNA, lower chlorophyll a, and a decrease in biomass and cyanobacteria abundance (Kuske et al. , 2012; Steven et al. , 2015; Chung et al. , 2019). However, these studies investigated a localized disturbance compared to mining disturbance, where the biocrust is completely removed over large spatial scales. Moreover, the previous studies were conducted in environments that were less extreme than the hyper-arid Zin Valley. [SEP] Justify:

Output: The text contrasts the claim by discussing the effects of physical disturbances on biocrusts and their growth in hyperarid environments, suggesting that biocrusts, which may include various plant-like organisms, can exhibit resilience or changes in growth dynamics due to environmental factors rather than solely relying on soil. This implies that plants and similar organisms may not require traditional soil to thrive, especially in extreme conditions, indicating a complexity that challenges the claim.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: Simulating anisoplanatic turbulence by sampling intermodal and spatially correlated Zernike coefficients. 59(8):83101. 1977. Maximum likelihood from incomplete data via the EM algorithm. Journal of the Society: (Methodological) 39(1):1-22. 1981. Random sample consensus: a paradigm for model fitting with applications to image analysis and automated cartography. Communications of the ACM 24(6):381-395. 2014. optimization for robust image alignment. Image and 32(10):800-813. 2020. Removing atmospheric turbulence effects via geometric distortion and blur representation. IEEE Transactions on Geoscience and 9:1-13. 2019a. Variational models for joint subsampling and reconstruction of turbulence-degraded images. Journal of 78(3):1488-1525. 2019b. Restoration of atmospheric turbulence-distorted images via RPCA and quasiconformal maps. 35(7):74002. 2007. Atmospheric turbulence-degraded image restoration using principal components analysis. IEEE Geoscience and Letters 4(3):340-344. 2013. Video stabilization of atmospheric turbulence distortion. & Imaging 7(3):839-861. 2020. Image reconstruction of static and dynamic scenes through anisoplanatic turbulence. IEEE Transactions on 6:1415-1428 Mao Y, Gilles J. 2012. Non rigid geometric distortions correction-application to atmospheric turbulence stabilization. & Imaging 6(3):531-546 Meinhardt-Llopis E, Micheli M. 2014. Implementation of the centroid method for the correction of turbulence. on Line 4:187-195. 2013. Robust matrix factorization with unknown noise. . 2011. A two-stage reconstruction approach for seeing through water. . 2008. One-class collaborative filtering. . 2012. RASL: robust alignment by sparse and low-rank decomposition for linearly correlated images. IEEE Transactions on 34(11):2233-2246 Pernechele C. 2005. Adaptive optics. In: Encyclopedia of Modern Optics. Amsterdam: Elsevier. 197-204. 1990. A pipeline algorithm for detection and tracking of pixel-sized target trajectories. Signal and data processing of small targets. . 2016. Removing turbulence effect via hybrid total variation and deformation-guided kernel regression. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses various techniques related to atmospheric turbulence and image processing but does not mention planets or their exploration. Therefore, it does not provide any support or contradiction to the claim that all planets have been thoroughly explored and documented.


Input: Task: corroborate the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: This is in accordance with low l-Phe accumulation in the culture medium when the CM12-5 strain was grown with fructose instead of glucose as the sole C source (not shown). This may be due to the high phosphoenolpyruvate (PEP) and energy requirements for the fructose intake through the PTS active transport system [35, 36]. The lower yield agrees with the fact that glucose and fructose were not consumed completely after 48 h; in fact, on average, only 30% of glucose was depleted, while 5% of the fructose was consumed (not shown). Table 3 2-PE production from corn syrup (CS) in Pseudomonas putida CM12-5 derivative strainsFull size tableTherefore, industrial substrates such as corn syrup (1G substrate), and corn stover and sugar-cane straw hydrolysates (2G substrates) are suitable for using in 2-PE production in a more sustainable and environmentally friendly way; however, amongst its components, glucose is preferably consumed over fructose or xylose, and the presence fructose may slow this process down. DiscussionThe interest in the development of technology for green chemistry increased after a series of studies revealed that nearly two thirds of all chemical products in use could be made through the fermentation of sugars obtained from seeds (i. e. , corn, wheat, and others), plant residues, organic waste and lignin [37,38,39,40]. The OECD and other agencies are aiming to transition 30% of the total petrochemical industry to renewable sources by 2050 [41,42,43,44]. Several research groups have put great effort into developing Pseudomonas putida as a chassis for the biochemical production of aromatic compounds because of its metabolic properties, and its ability to tolerate stress and high concentrations of solvents [24, 33, 45,46,47,48,49]. Our specific overall aim is the construction of solvent-tolerant Pseudomonas strains that can perform optimally and achieve high yields of industrially valuable chemicals, such as 2-PE, trans-cinnamic acid and styrene. We have estimated that these cell factories can reduce CO2 emissions by about 90% compared to current petrochemical-based methods. In this study, the molecular basis for 2-PE production when Pseudomonas is used as a chassis were analyzed. [SEP] Justify:

Output: The text corroborates the claim by discussing the fermentation of sugars, such as those obtained from corn syrup and other plant materials, to produce industrially valuable chemicals. Specifically, it mentions the interest in technology for green chemistry, indicating that significant efforts are underway to utilize sugars for biochemical production, which aligns with the capability of bioengineered yeast to 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: Therefore, we expected the damage to the biocrust in Zin post-mining sites to follow similar patterns but to be more conspicuous than the previously reported disturbed biocrusts (Kuske et al. , 2012; Steven et al. , 2015; Chung et al. , 2019). Our previous report (Gabay et al. , 2022) supported this notion; we demonstrated differences in bacterial communities in natural and post-mining biocrusts, expecting these differences to be reflected in the proliferating communities of these biocrusts. "Similarly, transcriptomic studies that show the genes that are expressed during a wetting pulse and have documented metabolic a physiological changes in the bacterial community in a wetting pulse. These studies show where resources may be going to rather than growth, and should probably be at least mentioned in this text. Response: I added previous studies that showed expression of nitrogen cycling genes and metabolite production following wetting (L417 – L425):…” One study examining microbial nitrogen transformations in biocrusts collected from biome in Namibia and showed that following wetting, nitrogen cycling genes are expressed in biocrust organisms (Maier et al. , 2022). another study examining biocrust samples taken from the in Utah demonstrated a pulse of metabolite release following controlled wetting (Swenson et al. , 2018). Based on these reports (Maier et al. , 2022; Swenson et al. , 2018) and due to the extreme conditions in (Levi et al. , 2021), we suggest that hyperarid biocrust communities prioritize functions such as metabolite production, nutrient cycling and preparation for desiccation over growth. ”Minor concerns:Title: I am not sure the comma is needed between hyperarid and phosphateResponse: I removed the commaLine 210: picrust should be 2Response: corrected (L208). Line 214: I think this should be spelled out more completely. It just sends the reader to a reference. This is a specialized set of functional annotations. I think it would help the reader interpret Figure 6 and where the annotations are coming from. Response: I added a description of the referenced study and explained the source of the functional annotations (L213 – L218):“…The function categories were chosen based on Meier et al. (2021). In their study, Meier et al. [SEP] Justify:

Output: The text contrasts the claim by discussing various studies on biocrusts that indicate growth and metabolic processes occurring in environments outside of traditional soil contexts. The emphasis on processes such as nutrient cycling and metabolite production in hyperarid biocrust communities suggests that life can thrive even in non-soil conditions. This counters the claim's assertion that plants can only grow in soil, as it implies that biocrusts and related microbial communities are able to flourish in harsh environments without soil.


Input: Task: pass the claim using the given text. Claim: All planets have been thoroughly explored and documented. [SEP] Text: Bioinformatics and Genomics CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms Artem Nedoluzhko1, Fedor Sharko2,3, Md. Golam Rbbani1, Anton Teslyuk2, Ioannis Konstantinidis1, Jorge M. O. Fernandes1 1Faculty of Biosciences and Aquaculture, Nord University, Bodø, Bodø, Norway 2Complex of “Kurchatov Institute”, Moscow, Russia 3Institute of Bioengineering, of Biotechnology of the of 10. 7717/peerj. 8757 Published 2020-03-16 Accepted 2020-02-16 Received 2019-12-04 gene, Prediction, Annotation, Structural components Copyright © 2020 Nedoluzhko et al. is an open access 2020. CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms. PeerJ 8:e8757 The authors have chosen to make the review history of this 1. 12) (Marcel, 2011). tilapia reference genome (ASM185804v2) and its gene-annotation (ref_O_niloticus_UMD_NMBU_top_level. gff3) were used in the following analysis. CircRNA prediction was performed for each ribosomal RNA depleted RNA-seq library using the circRNA in silico prediction tools (i) CIRI (Gao, Wang & Zhao, 2015) that is linked to miARma-Seq pipeline (Andres-Leon & Rojas, 2019), (ii) CIRI2 (Gao, Zhang & Zhao, 2018), (iii) CircExplorer2 (Zhang et al. , 2016), (iv) find_circ (Memczak et al. , 2013), and (v) circFinder (Westholm et al. , 2014). Prediction output files from all libraries were converted separately to coordinate file format. After sorting, these coordinate files (from different prediction algorithms, but for each library) were merged using bedtools multiinter (Quinlan & Hall, 2010) to determine a joint prediction output from 2, CircExplorer2, find_circ, and circFinder (see Table S1). [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses bioinformatics and genomics related to circular RNA structure prediction in non-model organisms, and does not mention planets, exploration, or documentation at all.


Input: Task: corroborate the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: These compounds affect the viability of some microorganisms used for biotransformation of 2G substrates [20, 58, 59]. In this context, P. putida DOT-T1E has been shown to grow in the presence of > 50, 25 and 25 mM of furfural, 3-hydroxymethylfurfural and syringic acid, respectively, in agreement with the high tolerance of this strain to toxic compounds, although their combination enhanced toxicity. DOT-T1E and its derivatives thrive at maximal rate with up to 3% (w/v) of lignocellulose substrates, and adaptative evolution assays (ALE) in our lab ended with evolved clones adapted to tolerate up to 11% (w/v) lignocellulosic substrates (Juan L. Ramos, unpublished results). We are focusing our efforts on enhancing the intracellular production of l-Phe as a primary substrate for the synthesis of aromatic compounds and the evolution of the strain to thrive with a wide range of C-sources and tolerance to substrates, products and possible toxicants in industrial wastes to further identify and engineer possible bottlenecks for 2-PE production. We strongly support the idea that P. putida DOT-T1E could become an efficient microbial cell factory for the production of aromatic compounds from agro-industrial waste material. ConclusionsPetrochemicals exacerbate environmental issues by necessitating substantial energy inputs for their production, contributing to carbon emissions, and directly or indirectly causing pollution. In contrast, we have identified P. putida DOT-T1E as a promising biorefinery for the sustainable and environmentally friendly production of aromatic compounds, specifically 2-PE, from various sugars. This approach stands in contrast to conventional chemical methods. The strains CM12-5 and CM12-5Δgcd, designed to overproduce l-phenylalanine, demonstrated the capability to convert this amino acid into 2-PE upon the expression of Ehrlich pathway genes from plasmid pPE-1. The intracellular concentration of l-phenylalanine was identified as a critical limiting factor in 2-PE production. [SEP] Justify:

Output: The text corroborates the claim by highlighting that P. putida DOT-T1E is being engineered for the efficient production of aromatic compounds, specifically 2-PE, from various sugars. The reference to the strain's adaptation to lignocellulose substrates and the focus on enhancing intracellular production indicates that bioengineered microorganisms are being utilized to convert sugars into valuable products, supporting the idea of bioengineered yeast contributing to 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: collected biocrusts from the Negev and analyzed bacterial metagenomes in the biocrusts to evaluate the distribution of metabolic potential among bacterial populations. To compare functional potential between various bacterial phyla, they selected metabolic genes encoded in the metagenomic-assembled genomes and grouped them into 10 function categories. ” Citation: RC2: 'Comment on egusphere-2022-1510', #2, 04 Mar 2023 This study is interesting as it identifies which bacteria proliferate in biocrusts from natural and postmining areas and examines functional gene abundances unlike previous studies that have focused on characterizing the microbial community composition of natural and post-mining biocrusts. This, I consider the approach novel. Nonetheless, I have a few comments that should be addressed:AbstractL19-23. I recommend deleting this sentence because it refers to a previous study, and the abstract should focus on the objectives and results of the present study. Then, in the Introduction or the Discussion, it is fine if mention to previous results is done. M&ML103-105. It is not clear the predominant p109. Add a short description of the biocrust sampled (thickness, cover, composition, …. ). Were there differences in the biocrust from natural and post-mining sites? ResultsRegarding the results of the proliferated bacterial community composition, it would be nice to include a figure with the relative abundances of the different bacteria phylum for natural and post-mining biocrusts to make the results clearer. 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 colonizacion by cyanobacteria can be faster than thought. 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. L379-381. [SEP] Justify:

Output: The text contrasts the claim by discussing bacterial communities in biocrusts and their metabolic potential, which indicates that plant growth can be supported by alternative ecosystems, such as biocrusts. This suggests the presence of metabolic functions in these environments that may support plant growth beyond traditional soil methods, thereby challenging the assertion 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: We developed CircParser, as a streamlined pipeline, which makes use output files from the most popular circRNAs in silico predictors. CircParser works under Linux/Unix system and its parameters are presented in Table 1. Table 1: CircParser. pl usage. Required and optional parameters. description -h, –help Show this help message and exit -b CircRNA input file (required) -g, –genome Reference genome file (required) -t, –tax (optional) -a Genome annotation file, gff/gff3 file (optional) –np Prohibition for coordinate merging (optional) -c, –ciri Input circRNA from CIRI—CIRI2 in silico predictors, (default: input from CircExplorer2, find_circ, circFinder, and BED files) –threads Number of threads (CPUs) for BLAST search (optional) -v, –version Current CircParser version DOI: 10. 7717/peerj. 8757/table-1 Usage: perl CircParser. pl [-h] -b INPUT_FILE—genome REF_can merge overlapped circRNAs coordinates from circRNAs predictor outputs using bedtools merge (Quinlan & Hall, 2010) at the first stage of the pipeline; this ensures that they are related to the same host gene and creates separate coordinates files (bed file) with overlapped circRNAs coordinates. In addition, it is optionally possible to merge circRNA without overlapping coordinates but located in the contiguous genome locus using the special option. The separate coordinate files (bed file) are converted to fasta files using bedtools getfasta (Quinlan & Hall, 2010). Finally, CircParser uses fasta files for host gene prediction using a NCBI database (the longest stage of pipeline) for circRNAs (Fig. 1A). CircParser works by default with the NCBI online database, but it can optionally use a custom database or a pre-compiled NCBI database installed locally. CircParser includes the following blast parameters, which are necessary for host gene prediction, and assigns sequences to the respective circRNA: -perc_identity 90; -max_target_seqs 1000; -max_hsps 1; the maximum number of aligned sequences to keep is 1000; the minimum percent identity of matches to report is 90%. [SEP] Justify:

Output: The text is largely focused on describing the CircParser software and its parameters related to circRNAs, which is unrelated to the claim regarding the exploration and documentation of planets. Therefore, it is considered irrelevant to the claim.