Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: Efficient induction of transgene-free human pluripotent stem cells using a vector based on Sendai virus, an RNA virus that does not integrate into the host genome. Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 85, 348–362. CrossrefPubMed2010. Amniotic fluid cells are more efficiently reprogrammed to pluripotency than adult cellsCell. Reprogram. 12117-125. Galende, E. , Karakikes, I. , Edelmann, L. , et al. (2010). Amniotic fluid cells are more efficiently reprogrammed to pluripotency than adult cells. Cell. Reprogram. 12, 117–125. CrossrefPubMed2009. Chd1 regulates open chromatin and pluripotency of embryonic stem cellsNature460863-868. Gaspar-Maia, A. , Alajem, A. , Polesso, F. , et al. (2009). Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature 460, 863–868. CrossrefPubMed2009. Generation of induced pluripotent stem cells from human cord blood using OCT4 and SOX2Cell5353-357. Giorgetti, A. , Montserrat, N. , Aasen, T. , et al. (2009). Generation of induced pluripotent stem cells from human cord blood using OCT4 and SOX2. Cell 5, 353–357. CrossrefPubMed2009. Klf4 reverts developmentally programmed restriction of ground state pluripotencyDevelopment. 1361063-1069. Guo, G. , Yang, J. , Nichols, J. , et al. (2009). Klf4 reverts developmentally programmed restriction of ground state pluripotency. Development. 136, 1063–1069. CrossrefPubMed1962. The developmental capacity of nuclei taken from intestinal epithelium cells of feeding tadpolesJ. Embryol. Exp. Morphol. 10622-640. Gurdon, J. B. (1962). The developmental capacity of nuclei taken from intestinal epithelium cells of feeding tadpoles. J. Embryol. Exp. Morphol. 10, 622–640. [SEP] Justify:

Output: The text corroborates the claim by discussing the process of reprogramming cells, specifically mentioning that 'Amniotic fluid cells are more efficiently reprogrammed to pluripotency than adult cells.' This indicates that the concept of using cell reprogramming techniques to achieve pluripotency is valid, supporting the claim that scientists employ these methods to convert non-pluripotent cells into pluripotent stem cells.


Input: Task: contrast the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: Подчеркнем, что ВИЭ в сельском хозяйстве однозначно не следует рассматривать только в контексте модной повестки дня, их использование должно найти свою нишу в сельскохозяйственном производстве и в обеспечении жизни людей в сельских районах только в тех случаях, когда это действительно востребовано (например, отсутствие доступа сельских территорий к устойчивому энергоснабжению) и является экономически и экологически обоснованным (или в перспективе мо� [SEP] Justify:

Output: The text contrasts the claim by stating that renewable agriculture techniques (ВИЭ) should not be viewed solely as a fashionable agenda, but rather should find their place in agricultural production based on actual needs and economic and ecological justification. This implies that relying solely on these techniques may not address all soil depletion issues.


Input: Task: pass the claim using the given text. Claim: Climate change is causing shifts in species distributions and ecosystem dynamics. [SEP] Text: To account for possible spatial autocorrelation in model coefficients, we spatially-kriged the residuals of each distribution model using inverse-distance squared weightings and creating new distribution models with same sub-sampled distribution data, but with this variable included as an autocovariate39. The results provided in the main text are from a final probabilistic weighted (by cross-validation ) ensemble distribution of the 60 distributions for each species and period, constructed using the Biomod2 package40 for R26. Additionally, we investigated whether our results could be caused by 100m resolution models, based only on data from the Lizard, underestimating species’ full climate envelope. To do so, we used the models derived from the two sets of macroclimate data to project species distributions using the 100m climate data. Model validation We independently evaluated the ensemble models by computing sensitivity and specificity and determining the number of times they correctly predicted establishments and extinctions between time periods. Probabilistic projections of species distributions were thus converted to binary outputs using a predicted probability of occurrence threshold set separately for each model and species, that ensured that 90% of observe presences occurred in grid cells with suitable climate. To account for incomplete observer coverage, and hence the likelihood that an apparent absence in either period is a false absence, we computed the number of cells in which establishment, extinction, persistence and absence (in both periods) were predicted by each ensemble model. We then generated an equivalent number of each possibility randomly and assessed model performance in the same way. The randomisation process was repeated 10,000 times, and the proportion of times the model performed better than random assessed. To ensure our results were robust to the method for thresholding suitable climate, we re-ran our analysis using 0. 5 for all species, and found qualitatively similar results. Distribution shifts To calculate the distance over which species must move to keep pace with climate, we again converted the probabilistic projections of species distributions to binary output. European projections of probability of occurrence were resampled to a UTM equal area projection prior to calculation. Then, for each historically occupied grid cell, we calculated the centre-to-centre distance between that grid cells and the nearest location with climatically suitable location under present day conditions, setting this distance at zero if the grid cell was to be occupied in both periods. 10. 5065/D6W957CT (2015). [SEP] Justify:

Output: The text provides an extensive description of the methods used to model species distributions and assess changes in their spatial patterns, but it does not directly address or support the claim that climate change is causing these shifts. Instead, it focuses on the technical aspects of modeling without explicitly linking the results to climate change impacts on species distributions.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: PubMed1975. The developmental capacity of nuclei transplanted from keratinized skin cells of adult frogsJ. Embryol. Exp. Morphol. 3493-112. Gurdon, J. B. , Laskey, R. A. , and Reeves, O. R. (1975). The developmental capacity of nuclei transplanted from keratinized skin cells of adult frogs. J. Embryol. Exp. Morphol. 34, 93–112. PubMed2003. Nuclear reprogramming and stem cell creationProc. Natl. Acad. Sci. USA10011819-11822. Gurdon, J. B. , Byrne, J. A. , and Simonsson, S. (2003). Nuclear reprogramming and stem cell creation. Proc. Natl. Acad. Sci. USA 100, 11819–11822. CrossrefPubMed2009. Generation of induced pluripotent stem cells by reprogramming mouse embryonic fibroblasts with a four transcription factor, doxycycline inducible lentiviral transduction systemJ. Vis. Exp. 331447. Hamilton, B. , Feng, Q. , Ye, M. , et al. (2009). Generation of induced pluripotent stem cells by reprogramming mouse embryonic fibroblasts with a four transcription factor, doxycycline inducible lentiviral transduction system. J. Vis. Exp. 33, 1447. PubMed2011. Generation of induced pluripotent stem cells from bovine embryonic fibroblast cellsCell Res. 211509-1512. Han, X. , Han, J. , Ding, F. , et al. (2011). Generation of induced pluripotent stem cells from bovine embryonic fibroblast cells. Cell Res. 21, 1509–1512. CrossrefPubMed2007. Treatment of sickle cell anemia mouse model with iPS cells generated from autologous skinScience3181920-1923. Hanna, J. , Wernig, M. , Markoulaki, S. , et al. (2007). Treatment of sickle cell anemia mouse model with iPS cells generated from autologous skin. Science 318, 1920–1923. CrossrefPubMed2002. [SEP] Justify:

Output: The text provides several references to the process of nuclear reprogramming, including studies on induced pluripotent stem cells (iPSCs) generated from adult cells. For example, it mentions the generation of iPSCs from mouse embryonic fibroblasts and bovine embryonic fibroblast cells, demonstrating that cell reprogramming is being utilized to convert adult cells into a pluripotent state. This aligns with the claim, affirming that scientists indeed use cell reprogramming techniques to achieve this transformation.


Input: Task: contrast the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: Причем использование ВИЭ в сельском хозяйстве обостряет проблему сокращения площадей земель сельскохозяйственного назначения, включая сельскохозяйственные угодья, за счет размещения энергетических объектов17. 16. Горюнова Н. Н. , Огунлана А. О. Возобновляемые источники энергии как основа реализации Парижского соглашения по снижению выбросов парниковых газов в России/ Общество: политика, экономика, право. 2017. № 2. С. 34 - 37. 17. См. об этом, напр. : Краснова И. [SEP] Justify:

Output: The text contrasts the claim by stating that the use of renewable energy sources in agriculture exacerbates the problem of reducing agricultural land area. This suggests that reliance solely on renewable agriculture techniques does not resolve all soil depletion issues.


Input: Task: pass the claim using the given text. Claim: Climate change is causing shifts in species distributions and ecosystem dynamics. [SEP] Text: 30 & Jarvis, A. Very high resolution interpolated climate surfaces for global land areas. International journal of Climatology 25, 1965-1978 (2005). 31 Bennallick, I. et al. Book for Cornwall and the Isles of Scilly. 2 edn, (Croceago Press, Praze-an-Beeble, 2009). 32 Preston, C. D. , Pearman, D. & Dines, T. D. of the British & Irish flora. (Press, 2002). 33 Kurtto, A. , Sennikov, A. & Lampinen, R. Atlas florae europaeae. (for Mapping the Flora of Europe & Fennica Vanamo. 2016). 34 Pearson, R. G. & Dawson, T. P. Predicting the impacts of climate change on the distribution of species: are bioclimate envelope models useful? and Biogeography 12, 361-371 (2003). 35 Petitpierre, B. , Broennimann, O. , Kueffer, C. , Daehler, C. & Guisan, A. Selecting predictors to maximize the transferability of species distribution models: Lessons from cross‐continental plant invasions. and Biogeography 26, 275-287 (2017). 36 Phillips, S. J. & Dudík, M. Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography 31, 161-175 (2008). 37 Hastie, T. J. & Tibshirani, R. J. Models. Vol. 43 (CRC Press, 1990). 38 Breiman, L. Random forests. 45, 5-32 (2001). 39 F Dormann, C. et al. Methods to account for spatial autocorrelation in the analysis of species distributional data: a review. Ecography 30, 609-628 (2007). 40 Thuiller, W. , Georges, D. , Engler, R. , Georges, M. D. & Thuiller, C. W. Package ‘biomod2’. (2012). Additional DeclarationsThere is NO Competing Interest. Supplementary FilesSuppInfoFinal. [SEP] Justify:

Output: The text is largely composed of references and does not provide any information that addresses the claim regarding climate change and its effects on species distributions and ecosystem dynamics. Therefore, it is considered irrelevant (pass) to the claim.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: Monoclonal mice generated by nuclear transfer from mature B and T donor cellsNature4151035-1038. Hochedlinger, K. , and Jaenisch, R. (2002). Monoclonal mice generated by nuclear transfer from mature B and T donor cells. Nature 415, 1035–1038. CrossrefPubMed797. Huangfu, D. , Maehr, R. , Guo, W. , et al. (2008a). Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat. Biotechnol. 26, 795–797. CrossrefPubMed1275. Huangfu, D. , Osafune, K. , Maehr, R. , et al. (2008b). Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2. Nat. Biotechnol. 26, 1269–1275. CrossrefPubMed2011. Copy number variation and selection during reprogramming to pluripotencyNature47158-62. . , et al. (2011). Copy number variation and selection during reprogramming to pluripotency. Nature 471, 58–62. CrossrefPubMed2005. Generation of cloned mice by direct nuclear transfer from natural killer T cellsCurr. Biol. 151114-1148. Inoue, K. , Wakao, H. , Ogonuki, N. , et al. (2005). Generation of cloned mice by direct nuclear transfer from natural killer T cells. Curr. Biol. 15, 1114–1148. CrossrefPubMed2008. Stem cells, the molecular circuitry of pluripotency and nuclear reprogrammingCell132567-582. Jaenisch, R. , and Young, R. (2008). Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132, 567–582. CrossrefPubMed2010. A nonviral minicircle vector for deriving human iPS cellsNat. Methods7197-199. Jia, F. , Wilson, K. D. , Sun, N. , et al. (2010). A nonviral minicircle vector for deriving human iPS cells. Nat. [SEP] Justify:

Output: The text corroborates the claim by discussing multiple studies and findings related to the induction of pluripotent stem cells. It mentions specific research where pluripotent stem cells were derived from various adult somatic cells, such as mature B and T cells and primary human fibroblasts, using defined factors and techniques in cell reprogramming. This directly supports the assertion that scientists use cell reprogramming to achieve pluripotency in adult cells.


Input: Task: contrast the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: О. Зарубежный опыт правового регулирования использования возобновляемых источников энергии/ Экологическое право. 2019. № 4. С. 23–29. Экономистами и другими исследователями неоднократно отмечались недостатки использования ВИЭ. Так, Н. Н. Горюнова и А. О. Огунлана заключают: «К существенным недостаткам ВИЭ можно отнести нестабильность выработки энергии, относительно низкий КПД, высокую стоимость установки. [SEP] Justify:

Output: The text contrasts the claim by highlighting the disadvantages of renewable energy sources (ВИЭ), suggesting that relying solely on these techniques may not adequately address soil depletion issues due to their instability, low efficiency, and high installation costs.


Input: Task: pass the claim using the given text. Claim: Biodiversity loss can negatively impact ecosystem resilience and function. [SEP] Text: You are encouraged to refer to the final revised version. Preprint (738 KB) Download & links The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version. Preprint (738 KB) revised paper 10. 5194/bg-21-1629-2024, 2024 Short summary Co-editor-in-chief Short summary Rate-of-change records based on compositional data are ambiguous as they may rise irrespective of the underlying trajectory of ecosystems. We emphasize the importance of characterizing both the direction and the rate of palaeoecological changes in terms of key features of ecosystems rather than solely on community composition. Past accelerations of community transformation may document the potential of ecosystems to rapidly recover important ecological attributes and functions. Hide Co-editor-in-chief Ecosystems are, in many ways, changing more rapidly than they have in the past. Rapid past ecological changes can provide critical insight into how to best understand ecosystem function to improve ecological restoration, but a historic focus on community composition in the paleoecological literature can obscure the causes of these changes, making mechanisms unclear. The authors demonstrate a path forward using pollen and diatom records from a lake in the to construct a narrative of terrestrial and aquatic ecosystem changes that combines well-established vegetation changes with rapid changes to water management changes to explore how rapidly the ecosystem responds to perturbations, and how aquatic function has been restored after pollution events. Doing so provides new insight into how to use the paleoecological record to understand restoration success and the time scales upon which ecosystem changes occur. örer, and Interactive discussion Status: closed Comment types: AC – author | RC – referee | CC – community | EC – editor | CEC – chief editor | : Report abuse RC1: 'Comment on egusphere-2023-2623', #1, 22 Dec 2023 The manuscript "Rates of palaeoecological change can inform ecosystem restoration" focuses on data analysis for the past 150 years from di Avigliana lake. This is a very well written manuscript dealing with relevant environmental concerns, such as biodiversity and its restoration. I think that one of the relevant messages that makes this paper very interesting is the documentation of past acceleration of community transformation and the use of palaeoecological indicators. I would also like to highlight that the authors made an effort to include policy context. [SEP] Justify:

Output: The text provides a detailed discussion regarding ecological changes and restoration processes but does not directly address the claim about biodiversity loss impacting ecosystem resilience and function. While it mentions relevant topics like past ecological transformations, the restoration of ecosystems, and the importance of biodiversity, it does not explicitly connect these ideas to the negative impact of biodiversity loss. Therefore, it is deemed irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: Methods 7, 197–199. CrossrefPubMed2009. Virus free induction of pluripotency and subsequent excision of reprogramming factorsNature458771-775. Kaji, K. , Norrby, K. , Paca, A. , et al. (2009). Virus free induction of pluripotency and subsequent excision of reprogramming factors. Nature 458, 771–775. CrossrefPubMed2005. LIF/STAT3 controls ES cell self-renewal and pluripotency by a Myc-dependentDevelopment132885-896. Kanakura, P. , McLean, C. , Sheppard, A. , et al. (2005). LIF/STAT3 controls ES cell self-renewal and pluripotency by a Myc-dependent. Development 132, 885–896. CrossrefPubMed1977. Studies of the developmental potential of 4- and 8-cell stage mouse blastomeresJ. Exp. Zool. 200365-376. Kelly, S. J. (1977). Studies of the developmental potential of 4- and 8-cell stage mouse blastomeres. J. Exp. Zool. 200, 365–376. CrossrefPubMed2008. An extended transcriptional network for pluripotency of embryonic stem cellsCell1321049-1061. Kim, J. , Chu, J. , Shen, X. , et al. (2008). An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132, 1049–1061. CrossrefPubMed476. Kim, D. , Kim, C. H. , Moon, J. I. , et al. (2009a). Generation of human induced pluripotent stem cells by direct delivery of reprogramming proteins. Cell 4, 472–476. CrossrefPubMed653. Kim, J. B. , Greber, B. , Arauzo-Bravo, M. J. , et al. (2009b). Direct reprogramming of human neural stem cells by OCT4. Nature 461, 649–653. CrossrefPubMed2010. Epigenetic memory in induced pluripotent stem cellsNature467285-290. Kim, K. , Doi, A. , Wen, B. , et al. (2010). [SEP] Justify:

Output: The text corroborates the claim by referencing multiple studies and articles that discuss methods of inducing pluripotency in cells, including the generation of induced pluripotent stem cells through reprogramming processes. For instance, it mentions 'Generation of human induced pluripotent stem cells by direct delivery of reprogramming proteins,' indicating that scientists are actively reprogramming cells to achieve pluripotency.


Input: Task: contrast the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: Несмотря на условную “экологическую чистоту” ВИЭ, их использование сопровождается также некоторыми негативными эффектами: изъятием значительных площадей земель, изменениями в ландшафте, шумовым загрязнением, воздействием на флору и фауну»16. [SEP] Justify:

Output: The text contrasts the claim by indicating that despite the 'ecological cleanliness' of renewable energy sources (ВИЭ), their use also comes with negative effects such as land extraction, landscape changes, noise pollution, and impacts on flora and fauna. This suggests that renewable agriculture techniques alone do not resolve all soil depletion issues.


Input: Task: pass the claim using the given text. Claim: Biodiversity loss can negatively impact ecosystem resilience and function. [SEP] Text: Overall, the paper is clear, well-structured, methodologically robust, and with an excellent quality. However, there are some minor aspects that to me requires a bit of improvement. 1) why the authors focused on di Avigliana requires a bit more of explanation. I'm assuming that might be for the quality of the chronology and available data (some information on the section called "context"). However, to me, the manuscript could improve if the authors include a paragraph justifying the choice of study site and also why the results from this lake have the potential to help improving our understanding on restoration of ecosystems. 2) I found methods a bit short and limited in detail. How about including some of the information currently placed in the 10. 5194/egusphere-2023-2623-RC1 AC1: 'Reply on RC1', Walter Finsinger, 19 Jan 2024 Dear RC1,Many thanks for the overall positive assessment of our manuscript. We send you a detailed response to each of your comments in the attached document. Best regards,and co-authors. Citation: RC2: 'Comment on egusphere-2023-2623', Alistair W. R. Seddon, 08 Jan 2024 The paper explores ideas related rate-of-change (RoC) analysis, using a published diatom and pollen dataset from the to move beyond RoC analysis of palaeoecological assemblages and towards ecological properties. They extend ideas of RoC analysis to look at the amount of change relative to baseline conditions. The main point is that whilst RoC analyses on assemblages can detect points of assemblage shifts, they can mask other important details (e. g. whether the changes are positive or negative in the context of management/ conservation). In moving towards temporal analysis of ecological properties the authors are also making a small step towards acknowledging palaeoecology’s potential contribution to assessing Variables (EBVs). I think the paper makes an important contribution since RoC curves (e. g. Mottl et al 2021) should always be assessed in the context of the ecological changes that are underlying them and this paper helps emphasise this point. The move towards highlighting the relevance of of palaeoecology for IPBES and EBVs is also very welcome. One important caveat is that even some derived ecosystem properties (e. g. [SEP] Justify:

Output: The text does not address the claim directly. While it discusses aspects of a scientific paper related to ecological analysis and the importance of understanding ecological properties, it does not provide information on biodiversity loss or its effects on ecosystem resilience and function. Therefore, it is deemed irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: Epigenetic memory in induced pluripotent stem cells. Nature 467, 285–290. CrossrefPubMed1964. Multipotentiality of single embryonal carcinoma cellsCancer Res. 241544-1551. Kleinsmith, L. J. , and Pierce, G. B. Jr. (1964). Multipotentiality of single embryonal carcinoma cells. Cancer Res. 24, 1544–1551. PubMed2006. Myc influences global chromatin structureEMBO J. 252723-2734. (2006). Myc influences global chromatin structure. EMBO J. 25, 2723–2734. CrossrefPubMed2000. Cell-fate conversion of lymphoid-committed progenitors by instructive actions of cytokinesNature407383-386. Kondo, M. , Scherer, D. C. , Miyamoto, T. , et al. (2000). Cell-fate conversion of lymphoid-committed progenitors by instructive actions of cytokines. Nature 407, 383–386. CrossrefPubMed2011. Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in cultureCell8106-118. Laurent, L. C. , Ulitsky, I. , Slavin, I. , et al. (2011). Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture. Cell 8, 106–118. CrossrefPubMed2009. Modelling pathogenesis and treatment of familial dysautonomia using patient-specific iPSCsNature461402-406. Lee, G. , Papapetrou, E. P. , Kim, H. , et al. (2009). Modelling pathogenesis and treatment of familial dysautonomia using patient-specific iPSCs. Nature 461, 402–406. CrossrefPubMed2009. Generation of rat and human induced pluripotent stem cells by combining genetic reprogramming and chemical inhibitorsCell416-19. Li, W. , Wei, W. , Zhu, S. , et al. (2009). Generation of rat and human induced pluripotent stem cells by combining genetic reprogramming and chemical inhibitors. [SEP] Justify:

Output: The text corroborates the claim by discussing various studies related to induced pluripotent stem cells (iPSCs), which are created through cell reprogramming. Specifically, it mentions the generation of induced pluripotent stem cells through genetic reprogramming and highlights their potential in modeling pathogenesis and treatment, thus indicating the utility of such reprogramming techniques in developing pluripotent stem cells.


Input: Task: contrast the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: Причем использование ВИЭ в сельском хозяйстве обостряет проблему сокращения площадей земель сельскохозяйственного назначения, включая сельскохозяйственные угодья, за счет размещения энергетических объектов17. Экономистами и другими исследователями неоднократно отмечались недостатки использования ВИЭ. Так, Н. Н. Горюнова и А. О. [SEP] Justify:

Output: The text contrasts the claim by indicating that the use of renewable energy sources (ВИЭ) in agriculture exacerbates the problem of reducing agricultural land, suggesting that renewable agriculture techniques alone are insufficient to address soil depletion issues.


Input: Task: pass the claim using the given text. Claim: Biodiversity loss can negatively impact ecosystem resilience and function. [SEP] Text: in this instance, tree cover inferred from arboreal pollen percentages) are also context dependent. Whilst increases in tree cover (i. e. ‘positive’ rates of change) might be viewed favourably in the context of the ecological restoration for this alpine ecosystem, in other locations (e. g. grasslands) increases in tree cover might not necessarily be representative of a positive change in terms of restoration (e. g. Veldmann et al. 2019, DOI: 10. 1126/science. aay7976). Thus, some derived ecosystem properties are likely to be as context dependent as the pollen/ diatom assemblages themselves. This is an important point to make if the approaches used on ecosystem properties are further generalized and I think this should be emphasized in the discussion. A second critique, particularly from the pollen data, is that there are obvious potential representation preservation issues that are not taken into account when RoCs on pollen assemblages are analysed, which can be addressed by correction by pollen production values and through methods such as modelling. If palaeoecology is going to move towards EBVs then I think here would be as good a place as any to at least reference this critique in reference to recently published RoC analysis and the analysis of the ecological properties derived in this specific study. The methods are quite brief in the main text, but even if I understand the papers is limited on space, I think you should move the paragraph about which baseline periods were selected from the 10. 5194/egusphere-2023-2623-RC2 AC2: 'Reply on RC2', Walter Finsinger, 19 Jan 2024 Dear Prof. Alistair W. R. Seddon, Many thanks for the in-depth assessment of our manuscript. We send you a detailed response to each of your comments in the attached document. Best regards, and co-authors. 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. [SEP] Justify:

Output: The text does not address the claim directly regarding biodiversity loss's impact on ecosystem resilience and function. Instead, it discusses the context-dependency of tree cover changes and critiques related to the analysis of pollen data. Since it focuses on specific methodologies and critiques rather than the claim about biodiversity loss and its effects on ecosystems, the text is deemed irrelevant.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: Cell 4, 16–19. CrossrefPubMed2011. Reprogramming of sheep fibroblasts into pluripotency under a drug-inducible expression of mouse-derived defined factorsPLoS One6e15947. Li, Y. , Cang, M. , Lee, A. S. , et al. (2011). Reprogramming of sheep fibroblasts into pluripotency under a drug-inducible expression of mouse-derived defined factors. PLoS One 6, e15947. CrossrefPubMed2005. Murine embryonic stem cell differentiation is promoted by SOCS-3 and inhibited by the zinc finger transcription factor Klf4Blood105635-637. Li, Y. , McClintick, J. , Zhong, L. , et al. (2005). Murine embryonic stem cell differentiation is promoted by SOCS-3 and inhibited by the zinc finger transcription factor Klf4. Blood 105, 635–637. CrossrefPubMed2009. A chemical platform for improved induction of human iPSCsNat. Methods6805-808. Lin, T. , Ambasudhan, R. , Yuan, X. , et al. (2009). A chemical platform for improved induction of human iPSCs. Nat. Methods. 6, 805–808. CrossrefPubMed2012. Generation and characterization of reprogrammed sheep induced pluripotent stem cellsTheriogenology77338-346. Liu, J. , Balehosur, D. , Murray, B. , et al. (2012). Generation and characterization of reprogrammed sheep induced pluripotent stem cells. Theriogenology 77, 338–346. CrossrefPubMed2008. Generation of induced pluripotent stem cells from adult rhesus monkey fibroblastsCell3587-590. Liu, H. , Zhu, F. , Yong, J. , et al. (2008). Generation of induced pluripotent stem cells from adult rhesus monkey fibroblasts. Cell 3, 587–590. CrossrefPubMed2012. Generation of patient-specific induced pluripotent stem cell-derived cardiomyocytes as a cellular model of arrhythmogenic right ventricular cardiomyopathyJ. . Ma, D. , Wei, H. , Lu, J. [SEP] Justify:

Output: The text corroborates the claim by describing various studies and research that involve the reprogramming of adult cells, such as sheep fibroblasts and rhesus monkey fibroblasts, into pluripotent stem cells. For instance, it mentions the generation of induced pluripotent stem cells (iPSCs) and discusses methods to induce pluripotency, thus supporting the assertion that scientists utilize cell reprogramming for this purpose.


Input:
Task: contrast the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: Причем использование ВИЭ в сельском хозяйстве обостряет проблему сокращения площадей земель сельскохозяйственного назначения, включая сельскохозяйственные угодья, за счет размещения энергетических объектов17. 16. Горюнова Н. Н. , Огунлана А. О.  Возобновляемые источники энергии как основа реализации Парижского соглашения по снижению выбросов парниковых газов в России/ Общество: политика, экономика, право. 2017. № 2. С. 34 - 37.

17. См. [SEP] Justify:

Output: The text contrasts the claim by stating that the use of renewable energy sources in agriculture exacerbates the problem of land area reduction for agricultural purposes. This indicates that relying solely on renewable agriculture techniques does not address the broader issue of soil depletion and may even contribute to it.


Input: Task: pass the claim using the given text. Claim: Biodiversity loss can negatively impact ecosystem resilience and function. [SEP] Text: 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-2023-2623', #1, 22 Dec 2023 The manuscript "Rates of palaeoecological change can inform ecosystem restoration" focuses on data analysis for the past 150 years from di Avigliana lake. This is a very well written manuscript dealing with relevant environmental concerns, such as biodiversity and its restoration. I think that one of the relevant messages that makes this paper very interesting is the documentation of past acceleration of community transformation and the use of palaeoecological indicators. I would also like to highlight that the authors made an effort to include policy context. Overall, the paper is clear, well-structured, methodologically robust, and with an excellent quality. However, there are some minor aspects that to me requires a bit of improvement. 1) why the authors focused on di Avigliana requires a bit more of explanation. I'm assuming that might be for the quality of the chronology and available data (some information on the section called "context"). However, to me, the manuscript could improve if the authors include a paragraph justifying the choice of study site and also why the results from this lake have the potential to help improving our understanding on restoration of ecosystems. 2) I found methods a bit short and limited in detail. How about including some of the information currently placed in the 10. 5194/egusphere-2023-2623-RC1 AC1: 'Reply on RC1', Walter Finsinger, 19 Jan 2024 Dear RC1,Many thanks for the overall positive assessment of our manuscript. We send you a detailed response to each of your comments in the attached document. Best regards,and co-authors. Citation: RC2: 'Comment on egusphere-2023-2623', Alistair W. R. Seddon, 08 Jan 2024 The paper explores ideas related rate-of-change (RoC) analysis, using a published diatom and pollen dataset from the to move beyond RoC analysis of palaeoecological assemblages and towards ecological properties. They extend ideas of RoC analysis to look at the amount of change relative to baseline conditions. [SEP] Justify:

Output: The text is irrelevant to the claim as it primarily focuses on discussing a manuscript regarding palaeoecological change and its analysis without directly addressing the effects of biodiversity loss on ecosystem resilience and function.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: , et al. (2012). Generation of patient-specific induced pluripotent stem cell-derived cardiomyocytes as a cellular model of arrhythmogenic right ventricular cardiomyopathy. J. doi: 10. 1093/eurheartj/ehs226. Crossref2012. Generation of human-induced pluripotent stem cells by a nonintegrating RNA Sendai virus vector in feeder-free or xeno-free conditionsInt. . Macarthur, C. C. , Fontes, A. , Ravinder, N. , et al. (2012). Generation of human-induced pluripotent stem cells by a nonintegrating RNA Sendai virus vector in feeder-free or xeno-free conditions. Int. doi: 10. 1155/2012/564612. CrossrefPubMed2007. Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contributionCell155-70. Maherali, N. , Sridharan, R. , Xie, W. , et al. (2007). Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell 1, 55–70. CrossrefPubMed2008. A high-efficiency system for the generation and study of human induced pluripotent stem cellsCell3340-345. Maherali, N. , Ahfeldt, T. , Rigamonti, A. , et al. (2008). A high-efficiency system for the generation and study of human induced pluripotent stem cells. Cell 3, 340–345. CrossrefPubMed2009. Transgenic mice with defined combinations of drug-inducible reprogramming factorsNat Biotechnol27169-171. Markoulaki, S. , Hanna, J. , Beard, C. , et al. (2009). Transgenic mice with defined combinations of drug-inducible reprogramming factors. 27, 169–171. CrossrefPubMed1981. Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cellsProc. Natl. Acad. Sci. USA787634-7638. Martin, G. R. (1981). [SEP] Justify:

Output: The text corroborates the claim as it discusses the generation of human-induced pluripotent stem cells, highlighting a method used in cell reprogramming. It refers to techniques involving reprogramming factors and the resulting pluripotent stem cells, thus supporting the assertion that scientists employ cell reprogramming for this purpose.


Input: Task: contrast the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: Полагаем, что вид используемого возобновляемого источника энергии с учетом существующих технологий может усложнять этот выбор вплоть до возникновения конфликта целей и интересов (использование энергии солнца предполагает занятие генераторами энергии земельных участков большой площади одновременно пригодных, скажем, для растениеводства; ветрогенераторы могут создавать проблемы для ведения животноводства и др. ). [SEP] Justify:

Output: The text contrasts the claim by suggesting that the type of renewable energy source used can complicate agricultural choices, potentially leading to conflicts between solar energy generation and land use for agriculture. This indicates that renewable agriculture techniques alone may not resolve all soil depletion issues, as other factors must be considered.


Input: Task: pass the claim using the given text. Claim: Biodiversity loss can negatively impact ecosystem resilience and function. [SEP] Text: The main point is that whilst RoC analyses on assemblages can detect points of assemblage shifts, they can mask other important details (e. g. whether the changes are positive or negative in the context of management/ conservation). In moving towards temporal analysis of ecological properties the authors are also making a small step towards acknowledging palaeoecology’s potential contribution to assessing Variables (EBVs). I think the paper makes an important contribution since RoC curves (e. g. Mottl et al 2021) should always be assessed in the context of the ecological changes that are underlying them and this paper helps emphasise this point. The move towards highlighting the relevance of of palaeoecology for IPBES and EBVs is also very welcome. One important caveat is that even some derived ecosystem properties (e. g. in this instance, tree cover inferred from arboreal pollen percentages) are also context dependent. Whilst increases in tree cover (i. e. ‘positive’ rates of change) might be viewed favourably in the context of the ecological restoration for this alpine ecosystem, in other locations (e. g. grasslands) increases in tree cover might not necessarily be representative of a positive change in terms of restoration (e. g. Veldmann et al. 2019, DOI: 10. 1126/science. aay7976). Thus, some derived ecosystem properties are likely to be as context dependent as the pollen/ diatom assemblages themselves. This is an important point to make if the approaches used on ecosystem properties are further generalized and I think this should be emphasized in the discussion. A second critique, particularly from the pollen data, is that there are obvious potential representation preservation issues that are not taken into account when RoCs on pollen assemblages are analysed, which can be addressed by correction by pollen production values and through methods such as modelling. If palaeoecology is going to move towards EBVs then I think here would be as good a place as any to at least reference this critique in reference to recently published RoC analysis and the analysis of the ecological properties derived in this specific study. The methods are quite brief in the main text, but even if I understand the papers is limited on space, I think you should move the paragraph about which baseline periods were selected from the 10. [SEP] Justify:

Output: The text does not directly address the claim regarding the negative impact of biodiversity loss on ecosystem resilience and function. Instead, it discusses the analysis of ecological properties and the context-dependent nature of ecosystem metrics without making clear connections to how these factors relate to biodiversity loss and its consequences on ecosystems.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc. Natl. Acad. Sci. USA 78, 7634–7638. CrossrefPubMed2007. Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouseNat. Cell Biol. 9625-635. Masui, S. , Nakatake, Y. , Toyooka, Y. , et al. (2007). Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse. Nat. Cell Biol. 9, 625–635. CrossrefPubMed2004. Specific knockdown of Oct4 and beta2-microglobulin expression by RNA interferenceStem Cells22659-668. . , et al. (2004). Specific knockdown of Oct4 and beta2-microglobulin expression by RNA interference. 22, 659–668. CrossrefPubMed1992. Derivation of pluripotential embryonic stem-cells from murine primordial germ-cells in cultureCell70841-847. Matsui, Y. , Zsebo, K. , and Hogan, B. L. M. (1992). Derivation of pluripotential embryonic stem-cells from murine primordial germ-cells in culture. Cell 70, 841–847. CrossrefPubMed2007. Direct reprogramming of genetically unmodified fibroblasts into pluripotent stem cellsNat. Biotechnol. 251177-1181. Meissner, A. , Wernig, M. , and Jaenisch, R. (2007). Direct reprogramming of genetically unmodified fibroblasts into pluripotent stem cells. Nat. Biotechnol. 25, 1177–1181. CrossrefPubMed2008. Dissecting direct reprogramming through integrative genomic analysisNature349-55. Mikkelsen, T. S. , Hanna, J. , Zhang, X. , et al. (2008). Dissecting direct reprogramming through integrative genomic analysis. Nature 3, 49–55. Crossref1976. Pluripotent teratocarcinoma-thymus somatic cell hybridsCell945-55. Miller, R. A. [SEP] Justify:

Output: The text corroborates the claim by providing information about the direct reprogramming of genetically unmodified fibroblasts into pluripotent stem cells. It specifically mentions the method of converting adult cells (fibroblasts) into pluripotent stem cells, which aligns with the claim regarding cell reprogramming.


Input: Task: contrast the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: Полагаем, что вид используемого возобновляемого источника энергии с учетом существующих технологий может усложнять этот выбор вплоть до возникновения конфликта целей и интересов (использование энергии солнца предполагает занятие генераторами энергии земельных участков большой площади одновременно пригодных, скажем, для растениеводства; ветрогенераторы могут создавать проблемы для ведения животноводства и др. ). [SEP] Justify:

Output: The text contrasts the claim by suggesting that the choice of renewable energy sources could complicate agricultural practices, leading to potential conflicts of goals and interests. It indicates that adopting renewable energy, such as solar or wind, might not solely resolve soil depletion issues if these techniques interfere with agriculture or livestock operations.


Input: Task: pass the claim using the given text. Claim: Biodiversity loss can negatively impact ecosystem resilience and function. [SEP] Text: 5194/egusphere-2023-2623-RC2 AC2: 'Reply on RC2', Walter Finsinger, 19 Jan 2024 Dear Prof. Alistair W. R. Seddon, Many thanks for the in-depth assessment of our manuscript. We send you a detailed response to each of your comments in the attached document. Best regards, and co-authors. Citation: Peer review completion AR: Author's response | RR: Referee report | ED: Editor decision | EF: Editorial file upload ED: Reconsider after major revisions (21 Jan 2024) by Petr Kuneš Thank you for your responses to comments raised by both reviewers. They both think, and I share their ideas, that this is an important contribution to exploring the ecosystem rate of change with high significance for ecosystem restoration and further practices in conservation and is worth publishing as BG Letters. I invite you to submit the revised version following your answers to the raised issues, which will be further evaluated. Hide ED: Reconsider after major revisions (21 Jan 2024) by (Co-editor-in-chief) I agree with the Associate Editor's decision to reconsider the manuscript after major revisions and I likewise feel confident that the authors can address all recommended changes to further improve the manuscript. by on behalf of the Authors (22 Jan 2024) Author's response Author's tracked changes Manuscript ED: Publish subject to technical corrections (25 Jan 2024) by Petr Kuneš Thank you for submitting your revised manuscript. Before publication, I would like to point out a few minor comments to consider: L. 129: It would be fair, according to policies, to also acknowledge the constituent databases of Neotoma, either the EPD or (or both if applicable). This also applies to l. 391. L. 130: “. . . datasets were treated with custom-coded functions in the R environment…” - is this really necessary here? L. 131–132: This sentence could be merged with the previous to avoid text duplication and to shorten the text. Perhaps something like this: “The format of pollen and diatom datasets was adapted for the R-Ratepoll package (Mottl et al. , 2021b), where the rate of palaeoecological change (hereafter RoC) scores were calculated in regular time bins. [SEP] Justify:

Output: The text does not provide any direct information regarding biodiversity loss or its impacts on ecosystem resilience and function. Instead, it focuses on the peer review process and communication between authors and reviewers regarding a manuscript. As such, it is irrelevant to the claim being analyzed.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: , and Ruddle, F. H. (1976). Pluripotent teratocarcinoma-thymus somatic cell hybrids. Cell 9, 45–55. CrossrefPubMed1977. friend erythroleukemia cell hybrids resemble their pluripotent embryonal carcinoma parentDev. Biol. 56157-173. Miller, R. A. , and Ruddle, F. H. (1977). friend erythroleukemia cell hybrids resemble their pluripotent embryonal carcinoma parent. Dev. Biol. 56, 157–173. CrossrefPubMed2003. The homeoprotein Nanog is required for maintenance of pluripotency in mouseCell113631-642. Mitsui, K. , Tokuzawa, Y. , Itoh, H. , et al. (2003). The homeoprotein Nanog is required for maintenance of pluripotency in mouse. Cell 113, 631–642. CrossrefPubMed2009. Variation in the safety of induced pluripotent stem cell linesNat. Biotechnol. 27743-745. Miura, K. , Okada, Y. , Aoi, T. , et al. (2009). Variation in the safety of induced pluripotent stem cell lines. Nat. Biotechnol. 27, 743–745. CrossrefPubMed2012. Generation of feeder free pig induced pluripotent stem cells without Pou5f1Cell Transplant21815-825. Montserrat, N. , de Onate, L. , Garreta, E. , et al. (2012). Generation of feeder free pig induced pluripotent stem cells without Pou5f1. 21, 815–825. CrossrefPubMed2008. Regulatory networks define phenotypic classes of human stem cell linesNature455401-405. . , et al. (2008). Regulatory networks define phenotypic classes of human stem cell lines. Nature 455, 401–405. CrossrefPubMed2009. Upping the ante: Recent advances in direct reprogrammingMol. Ther. 17947-953. Muller, L. U. W. , Daley, G. Q. , and Williams, D. A. (2009). Upping the ante: Recent advances in direct reprogramming. Mol. [SEP] Justify:

Output: The text corroborates the claim by referencing advances in inducing pluripotent stem cells and mentions 'induced pluripotent stem cell lines,' suggesting that scientists are effectively using cell reprogramming techniques to create pluripotent stem cells from adult cells. This aligns with the claim that cell reprogramming is utilized for converting adult cells into pluripotent stem cells.


Input: Task: contrast the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: Полагаем, что вид используемого возобновляемого источника энергии с учетом существующих технологий может усложнять этот выбор вплоть до возникновения конфликта целей и интересов (использование энергии солнца предполагает занятие генераторами энергии земельных участков большой площади одновременно пригодных, скажем, для растениеводства; ветрогенераторы могут создавать проблемы для ведения животноводства и др. ). [SEP] Justify:

Output: The text contrasts the claim by suggesting that the choice of renewable energy sources can complicate agricultural decisions and create conflicts of interest, indicating that renewable agriculture techniques alone may not address all soil depletion issues.


Input: Task: pass the claim using the given text. Claim: Biodiversity loss can negatively impact ecosystem resilience and function. [SEP] Text: ” Hide ED: Publish subject to minor revisions (review by editor) (29 Jan 2024) by (Co-editor-in-chief) Thank you for addressing the recommended revisions, I agree with Dr. Kuneš that the revised manuscript is much improved. Please address the remaining minor comments in a brief letter addressed to me and I won't hesitate to recommend that the subsequent manuscript with further improvement be accepted by BG Letters. by on behalf of the Authors (30 Jan 2024) Author's response Author's tracked changes Manuscript ED: Publish as is (30 Jan 2024) by Thank you for considering the additional recommended changes, particularly as they involve data accessibility. The revised manuscript is publishable in BG Letters. Sincerely, Paul C. ED: Publish subject to technical corrections (06 Feb 2024) by (Co-editor-in-chief) Please do not use red and green in figures at the same time and please replace all instances with a colorblind-friendly color scheme. Hide AR by on behalf of the Authors (13 Feb 2024) Author's response 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: 10. 5194/bg-21-1629-2024, 2024 Short summary Co-editor-in-chief Short summary Rate-of-change records based on compositional data are ambiguous as they may rise irrespective of the underlying trajectory of ecosystems. We emphasize the importance of characterizing both the direction and the rate of palaeoecological changes in terms of key features of ecosystems rather than solely on community composition. Past accelerations of community transformation may document the potential of ecosystems to rapidly recover important ecological attributes and functions. Hide Co-editor-in-chief Ecosystems are, in many ways, changing more rapidly than they have in the past. Rapid past ecological changes can provide critical insight into how to best understand ecosystem function to improve ecological restoration, but a historic focus on community composition in the paleoecological literature can obscure the causes of these changes, making mechanisms unclear. [SEP] Justify:

Output: The text does not address the claim about biodiversity loss affecting ecosystem resilience and function. Instead, it discusses aspects of ecological changes and the rate of transformation within ecosystems without directly linking it to biodiversity or the negative impacts of its loss.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: Ther. 17, 947–953. CrossrefPubMed2011. Induced pluripotent stem cell lines derived from equine fibroblastsRev. 7693-702. Nagy, K. , Sung, H. K. , Zhang, P. , et al. (2011). Induced pluripotent stem cell lines derived from equine fibroblasts. Rev. 7, 693–702. CrossrefPubMed2008. Generation of induced pluripotent stem cells without Myc from mouse and human fibroblastsNat. Biotechnol. 26101-106. Nakagawa, M. , Koyanagi, M. , Tanabe, K. , et al. (2008). Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts. Nat. Biotechnol. 26, 101–106. CrossrefPubMed2012. New windows to enhance direct reprogramming of somatic cells towards induced pluripotent stem cellsBiochem. Cell Biol. 90115-123. Nakhaei-Rad, S. , Bahrami, A. R. , Mirahmadi, M. , et al. (2012). New windows to enhance direct reprogramming of somatic cells towards induced pluripotent stem cells. Biochem. Cell Biol. 90, 115–123. CrossrefPubMed2010. Differentiation of mesenchymal stem cells to insulin-producing cells and their impact on type 1 diabetic ratsJ. Physiol. Biochem. 66181-187. Neshati, Z. , Matin, M. M. , Bahrami, A. R. , et al. (2010). Differentiation of mesenchymal stem cells to insulin-producing cells and their impact on type 1 diabetic rats. J. Physiol. Biochem. 66, 181–187. CrossrefPubMed2012. Generation of virus-free induced pluripotent stem cell clones on a synthetic matrix via a single cell subcloning in the naïve statePLoS One7e38389. Nishishita, N. , Shikamura, M. , Takenaka, C. , et al. (2012). Generation of virus-free induced pluripotent stem cell clones on a synthetic matrix via a single cell subcloning in the naïve state. [SEP] Justify:

Output: The text corroborates the claim by discussing the generation of induced pluripotent stem cell lines from fibroblasts, which implies the use of cell reprogramming techniques to convert adult cells into pluripotent stem cells. Specifically, references to the generation of induced pluripotent stem cells from mouse and human fibroblasts and equine fibroblasts support the concept of reprogramming adult cells.


Input: Task: contrast the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: Государства – участники Конференции заявили также о необходимости поощрять, расширять и поддерживать такое сельское хозяйство, которое, в частности, позволяет повышать уровень продовольственной безопасности и искоренять голод и является экономически жизнеспособным, обеспечивая сохранение земельных и водных ресурсов, растений и зоогенетических ресурсов, биологического разнообразия и экосистем (п. 111). [SEP] Justify:

Output: The text contrasts the claim by stating the need to promote agricultural practices that enhance food security and eradicate hunger without implying that renewable agriculture techniques alone are sufficient to address all soil depletion issues. It emphasizes the importance of various resources, sustainability, and biodiversity, which suggests a broader approach rather than solely relying on renewable agriculture techniques.


Input: Task: pass the claim using the given text. Claim: Biodiversity loss can negatively impact ecosystem resilience and function. [SEP] Text: Preprints AbstractDiscussion © Author(s) 2024. This work is distributed under the Attribution 4. 0 License. © Author(s) 2024. This work is distributed under the Attribution 4. 0 License. Preprints AbstractDiscussionMetrics 20 Feb 2024 | 20 Feb 2024 Crowd-sourced trait data can be used to delimit global biomes Simon Scheiter, Sophie Wolf, and Abstract. Biomes and their biogeographic patterns have been derived from a large variety of variables including species distributions, bioclimate or remote sensing products. Yet, whether plant trait data are suitable for biome classification has rarely been tested. Here, we aimed to assess systematically which traits are most suitable for biome classification. We derived patterns of 33 different traits by combining crowd-sourced species distribution data and trait data from the TRY database. Using supervised cluster analyses, we developed biome classification schemes using these traits and 31 different biome maps. A sensitivity analysis with randomly sampled combinations of traits was performed to identify traits and biome maps that are most appropriate for biome classification and achieved the highest data-model agreement. Due to gaps in the trait data, species distribution models were used to obtain biome maps at the global scale. We showed that traits can be used for biome classification and that the most appropriate traits are conduit density, rooting depth, height, and different leaf traits, including specific leaf area and leaf nitrogen. Data-model agreement was maximized when biome maps used to inform cluster analyses were based on biogeographic zonation and species distributions, in contrast to biome maps derived from optical reflectance. The availability of crowd-sourced trait data is heterogeneous and large data gaps are prevalent. Nonetheless, it is possible to derive biome classification schemes from these data to predict global biome patterns with good agreement. Filling data gaps is essential to further improve trait-based biome maps. How to cite. Scheiter, S. , Wolf, S. , and Kattenborn, T. : Crowd-sourced trait data can be used to delimit global biomes, EGUsphere [preprint], 2024. Received: 30 Jan 2024 – Discussion started: 20 Feb 2024 Publisher's note: remains neutral with regard to jurisdictional claims made in the text, published maps, institutional affiliations, or any other geographical representation in this preprint. The responsibility to include appropriate place names lies with the authors. [SEP] Justify:

Output: The text is irrelevant to the claim as it focuses on biome classification using trait data and does not discuss biodiversity loss or its impacts on ecosystem resilience and function.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: PLoS One 7, e38389. CrossrefPubMed2000. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cellsNat. Genet. 24372-376. Niwa, H. , Miyazaki, J. , and Smith, A. (2000). Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat. Genet. 24, 372–376. CrossrefPubMed2007. Generation of germline-competent induced pluripotent stem cellsNature448313-317. Okita, K. , Ichisaka, T. , and Yamanaka, S. (2007). Generation of germline-competent induced pluripotent stem cells. Nature 448, 313–317. CrossrefPubMed2008. Generation of mouse induced pluripotent stem cells without viral vectorsScience322949-953. Okita, K. , Nakagawa, M. , Hyenjong, H. , et al. (2008). Generation of mouse induced pluripotent stem cells without viral vectors. Science 322, 949–953. CrossrefPubMed2011. Immunogenicity of induced pluripotent stem cellsCirc. Res. 109720-721. Okita, K. ,Nagata, N. , and Yamanaka, S. (2011). Immunogenicity of induced pluripotent stem cells. Circ. Res. 109, 720–721. CrossrefPubMed2010. Advances in reprogramming somatic cells to induced pluripotent stem cellsRev. 6367-380. Patel, M. , and Yang, S. (2010). Advances in reprogramming somatic cells to induced pluripotent stem cells. Rev. 6, 367–380. CrossrefPubMed2008. Disease-specific induced pluripotent stem cellsCell134877-886. Park, I. , Arora, N. , Huo, H. , et al. (2008). Disease-specific induced pluripotent stem cells. Cell 134, 877–886. CrossrefPubMed2009. Clone and gene-specific aberrations of parental imprinting in human induced pluripotent stem cellsStem Cells. 272686-2690. [SEP] Justify:

Output: The text corroborates the claim by referencing various studies, such as the generation of induced pluripotent stem cells (iPSCs) from somatic cells without viral vectors. This indicates that cell reprogramming techniques are indeed used to transform adult cells into pluripotent stem cells, supporting the claim.


Input: Task: contrast the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: Государства – участники Конференции заявили также о необходимости поощрять, расширять и поддерживать такое сельское хозяйство, которое, в частности, позволяет повышать уровень продовольственной безопасности и искоренять голод и является экономически жизнеспособным, обеспечивая сохранение земельных и водных ресурсов, растений и зоогенетических ресурсов, биологического разнообразия и экосистем (п. 111). [SEP] Justify:

Output: The text contrasts the claim by stating that agriculture must not only focus on renewable techniques but also on increasing food security and eradicating hunger, as well as maintaining land and water resources and biodiversity, implying that soil depletion issues cannot be solved solely by renewable techniques alone.


Input: Task: pass the claim using the given text. Claim: Biodiversity loss can negatively impact ecosystem resilience and function. [SEP] Text: Download & links Preprint (PDF, 4886 KB) Supplement (2526 KB) Download & links Preprint (4886 KB) Metadata XML Supplement (2526 KB) and Status: closed Comment types: AC – author | RC – referee | CC – community | EC – editor | CEC – chief editor | : Report abuse RC1: 'Comment on egusphere-2024-276', Peter van Bodegom, 02 Apr 2024 Scheiter et al present an interesting approach to delineate biomes based on traits information. They use a combination of a number of extensive databases and interesting approaches. Even so, I have a number of major and minor comments. Major comments:- A main concern is that some components of the methods do not logically link to each other, which does not help the story line. This specifically applies to two analyses; analyses described in section 2. 4 and 2. 6. a. The aim of the analysis in 2. 4 and how it contributes to the story line remains unclear to me. You create, for each of the four cases (? ) a trait set to work with. First of all, I don’t understand why that is needed because you already tested the performance of different complete trait sets in 2. 3. So, why would you continue working with subsets of traits if you already know how the entire combination of traits works? Now, you seem to throw away most of the information presented in 3. 1 instead of building upon them. That does not only seem unnecessary, but also creates biases (because subsets of traits are used; an argument you make yourself in l. 275). Moreover, given the different selection criteria and procedure for different trait sets/cases, interpretation of these results is made even harder (not possible). Also, I don’t see the need for doing it. You use it in 2. 5 (but then only for the case 4), but I think that also could have been done directly on the best performing trait sets from 2. 3. To me, that would have been a much more direct way to test it and with fewer biases. b: I don't understand why the analysis in 2. 6 is useful to do given that you started with using trait maps to fit biome distributions based on complete biome maps. Why would you then derive additional trait maps, using a different procedure with other input data than used elsewhere in the paper. [SEP] Justify:

Output: The text does not address the claim regarding biodiversity loss and its impacts on ecosystem resilience and function. Instead, it focuses on a critique of a scientific paper's methodologies and analyses without mentioning biodiversity or ecosystem functionality.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: Pick, M. , Stelzer, Y. , Bar-Nur, O. , et al. (2009). Clone and gene-specific aberrations of parental imprinting in human induced pluripotent stem cells. Stem Cells. 27, 2686–2690. CrossrefPubMed2007. Lin-28 binds IGF-2 mRNA and participates in skeletal myogenesis by increasing translation efficiencyGenes Dev. 211125-1138. Polesskaya, A. , Cuvellier, S. , Naguibneva, I. , et al. (2007). Lin-28 binds IGF-2 mRNA and participates in skeletal myogenesis by increasing translation efficiency. Genes Dev. 21, 1125–1138. CrossrefPubMed2007. Direct generation of ES-like cells from unmodified mouse embryonic fibroblasts by Oct4/Sox2/Myc/Klf4Cell Res. 17959-962. Qin, D. , Li, W. , and Zhang, J. (2007). Direct generation of ES-like cells from unmodified mouse embryonic fibroblasts by Oct4/Sox2/Myc/Klf4. Cell Res. 17, 959–962. CrossrefPubMed2009. Gene silencing in human embryonic stem cells by RNA interferenceBiochem. Biophys. Res. Commun. 3901106-1110. Rassouli, F. B. , and Matin, M. M. (2009). Gene silencing in human embryonic stem cells by RNA interference. Biochem. Biophys. Res. Commun. 390, 1106–1110. CrossrefPubMed2009. Disease-corrected haematopoietic progenitors from Fanconi anaemia induced pluripotent stem cellsNature46053-59. Raya, A. , Rodriguez-Piza, I. , Guenechea, G. , et al. (2009). Disease-corrected haematopoietic progenitors from Fanconi anaemia induced pluripotent stem cells. Nature 460, 53–59. CrossrefPubMed2011. Generation of hircine-induced pluripotent stem cells by somatic cell reprogrammingCell Res. 21849-853. Ren, J. , Pak, Y. , He, L. , et al. [SEP] Justify:

Output: The text corroborates the claim by referencing processes like 'Clone and gene-specific aberrations of parental imprinting in human induced pluripotent stem cells' and 'Direct generation of ES-like cells from unmodified mouse embryonic fibroblasts by Oct4/Sox2/Myc/Klf4,' which indicate the use of cell reprogramming techniques to derive pluripotent stem cells from adult cells.


Input: Task: contrast the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: Государства – участники Конференции заявили также о необходимости поощрять, расширять и поддерживать такое сельское хозяйство, которое, в частности, позволяет повышать уровень продовольственной безопасности и искоренять голод и является экономически жизнеспособным, обеспечивая сохранение земельных и водных ресурсов, растений и зоогенетических ресурсов, биологического разнообразия и экосистем (п. 111). 22 25 сентября 2015 г. [SEP] Justify:

Output: The text contrasts the claim by stating that sustainable agriculture must also address food security, eliminate hunger, and ensure the conservation of land and water resources among other factors. This implies that addressing soil depletion cannot be accomplished solely through renewable agriculture techniques.


Input: Task: pass the claim using the given text. Claim: Biodiversity loss can negatively impact ecosystem resilience and function. [SEP] Text: Moreover, you already have 31 biome maps to test performance against. So, why create another one? I would say the study is about understanding biome distributions based on traits (a story already told by the kappa values) and not about predicting/extrapolating biome distributions. In other words, the aim and position of this analysis in the story line is not clear to me. - Another methodological issue is that I do not understand why the authors thought it important to first use the traits in combination with species distribution models to make trait maps and then to couple those to the biome maps instead of using the locations of the trait observations (g. using the original TRY data, possibly aggregated to the 0. 5 degree pixels of the locations) directly? Coupling individual locations can be done to calibrate and validate biome models and avoid the major uncertainties involved in creating/ extrapolating the trait maps, i. e. i don't see that necessity. I wonder to which extent these uncertainties contributed to the low Kappa-values of the predictions. - I had hoped that the authors would have focused more on the ecological interpretation, rather than on the methodological aspects. a. : This already starts from the presentation of the data. With slightly different analyses and visualization, potentially a lot more ecological insights might have been gained. For instance, fig 7 presents the mean trait values for some biomes. However, these are individual traits while you tested how different trait combinations allow distinguishing among biomes. However, nowhere we learn about those combinations (their synergies and their redundancies). For instance, I would have liked a so-called confusion matrix to see how for a given trait set, biomes were predicted properly or not and whether this is consistent among the different (best-performing) trait sets: which trait combinations (in addition to single traits) lead to the best predictions? Is that consistent between trait sets? Which trait combinations allow distinguishing e. g. ‘’subtropical forest’’ (just to name one) from other forests? Is that consistent through different trait sets? I think the analysis has the potential to bring such answer and thus ecological understanding, but that remains unexplored. [SEP] Justify:

Output: The text does not address or relate to the claim about biodiversity loss and its impacts on ecosystem resilience and function. Instead, it discusses methodological concerns regarding biome distributions, trait maps, and their interpretations. The focus is primarily on data presentation and analysis rather than the ecological consequences of biodiversity loss.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: (2011). Generation of hircine-induced pluripotent stem cells by somatic cell reprogramming. Cell Res. 21, 849–853. CrossrefPubMed2002. Human feeders support prolonged undifferentiated growth of human inner cell masses and embryonic stem cellsNat. Biotechnol. 20933-936. Richards, M. , Fong, C. Y. , Chan, W. K. , et al. (2002). Human feeders support prolonged undifferentiated growth of human inner cell masses and embryonic stem cells. Nat. Biotechnol. 20, 933–936. CrossrefPubMed2004. The transcriptome profile of human embryonic stem cells as defined by 2251-64. Richards, M. , Tan, S. P. , Tan, J. H. , et al. (2004). The transcriptome profile of human embryonic stem cells as defined by SAGE. 22, 51–64. CrossrefPubMed2002. Correction of a genetic defect by nuclear transplantation and combined cell and gene therapyCell10917-27. Rideout, W. , Hochedlinger, K. , Kyba, M. , et al. (2002). Correction of a genetic defect by nuclear transplantation and combined cell and gene therapy. Cell 109, 17–27. CrossrefPubMed2005. Transcriptional regulation of Nanog by OCT4 and SOX2J. Biol. Chem. 28024731-24737. Rodda, D. , Chew, J. , Lim, L. , et al. (2005). Transcriptional regulation of Nanog by OCT4 and SOX2. J. Biol. Chem. 280, 24731–24737. CrossrefPubMed2008. A combined chemical and genetic approach for the generation of induced pluripotent stem cellsCell2525-528. Shi, Y. , Do, J. T. , Desponts, C. , et al. (2008). A combined chemical and genetic approach for the generation of induced pluripotent stem cells. Cell 2, 525–528. CrossrefPubMed2008. Advances in the study on induced pluripotent stem cellsChin. Sci. Bull. 53709-717. Shuang, L. , and EnKui, D. (2008). [SEP] Justify:

Output: The text corroborates the claim by discussing the generation of induced pluripotent stem cells, which is a result of somatic cell reprogramming. Specifically, it mentions 'Generation of hircine-induced pluripotent stem cells by somatic cell reprogramming,' indicating that adult cells are being reprogrammed to become pluripotent.


Input: Task: contrast the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: </strong><strong> следует обеспечить создание устойчивых систем производства продуктов питания и внедрить методы ведения сельского хозяйства, которые позволяют повысить жизнестойкость и продуктивность и увеличить объемы производства, способствуют сохранению экосистем. Цель 7, закрепленная в том же документе, предполагает обеспечение всеобщего доступа к недорогим, надежным, устойчивым и современным источникам энергии для всех. [SEP] Justify:

Output: The text contrasts the claim by discussing the need for creating sustainable food production systems and implementing agricultural methods that improve resilience and productivity, suggesting that solutions to soil depletion involve more than just renewable agriculture techniques. It emphasizes the importance of ecosystem preservation and access to reliable energy sources, indicating a multifaceted approach rather than a sole reliance on renewable methods.


Input: Task: pass the claim using the given text. Claim: Biodiversity loss can negatively impact ecosystem resilience and function. [SEP] Text: b: Also the discussion section is now almost entirely focused on the methods instead of the question why the analysis is a useful thing to do and what we learn from it: I would be interested in seeing an ecological interpretation for how and why the results of the analysis help global ecological understanding of biome distribution and functioning. That would have led to a much more interesting story. In the current set-up, the discussion section does not provide much insight. Minor comments:The abstract does not help to tell the story. The method applied is not clearly explained, i. e. which steps were taken. Also the role of the 31 biome maps was unclear (in the abstract it seemed an input, while it is used to train the data. Also, a clear take home message is missing: ‘’we can make biome maps’’, but it is not explained why that is important or what is the added value of this study. I would have appreciated an explanation/argumentation on why choosing these trait maps instead of other maps, i. e. what is the conceptual advantage to these maps? (Also in light of the discussion section where it Is mentioned that different trait maps could have led to different outcomes) With some self-advertisement; Verheijen et al. NewPhytol 209: 563-575 also evaluated which traits could be used best to distinguish among biomes, albeit which is much smaller dataset and fewer traits (And a different method). Interestingly, similar traits popped up as important. At some parts in the methods section it is unclear whether all individual 31 biome maps were tested independently or whether an aggregate was used. It seems that you tested each map individually, but a better explanation throughout the methods on this would have been appreciated. The role and use of PFTs is confusing to me. You derive different trait maps depending on growth form/PFT and clustered them into four cases in 2. 2. Then, it seems that trait clusters were made for each of those four cases (if I understand the methods correctly) in 2. 3. Then, later in 2. 3 you seem to continue with the outcomes of case4 only. This is not clearly described and also the reason why you do this, remains unclear to me. Also the role and use of PFTs is confusing to me. [SEP] Justify:

Output: The text does not address the claim about biodiversity loss and its impact on ecosystem resilience and function. Instead, it discusses concerns regarding the clarity of a study's methods and the interpretation of biome maps without mentioning biodiversity, ecosystem resilience, or related impacts.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: Advances in the study on induced pluripotent stem cells. Chin. Sci. Bull. 53, 709–717. Crossref2008. Promotion of reprogramming to ground state pluripotency by signal inhibitionPLoS Biol. 6e253. Silva, J. , Barrandon, O. , Nichols, J. , et al. (2008). Promotion of reprogramming to ground state pluripotency by signal inhibition. PLoS Biol. 6, e253. CrossrefPubMed2010. Chromatin-remodeling components of the BAF complex facilitate reprogrammingCell141943-955. Singhal, N. , Graumann, J. , Wu, G. , et al. (2010). Chromatin-remodeling components of the BAF complex facilitate reprogramming. Cell 141, 943–955. CrossrefPubMed2009. Parkinson's disease patient-derived induced pluripotent stem cells free of viral reprogramming factorsCell136964-977. Soldner, F. , Hockemeyer, D. , Beard, C. , et al. (2009). Parkinson's disease patient-derived induced pluripotent stem cells free of viral reprogramming factors. Cell 136, 964–977. CrossrefPubMed2007. Epigenetic signatures of stem-cell identityNat. Rev. Genet. 8263-271. Spivakov, M. , and Fisher, A. G. (2007). Epigenetic signatures of stem-cell identity. Nat. Rev. Genet. 8, 263–271. CrossrefPubMed2009. Role of the murine reprogramming factors in the induction of pluripotencyCell136364-377. Sridharan, R. , Tchieu, J. , Mason, M. J. , et al. (2009). Role of the murine reprogramming factors in the induction of pluripotency. Cell 136, 364–377. CrossrefPubMed2009. Without a trace? . PiggyBac-ing toward pluripotencyNat. Methods6329-330. Stadtfeld, M. , and Hochedlinger, K. (2009). Without a trace? PiggyBac-ing toward pluripotency. Nat. [SEP] Justify:

Output: The text discusses advances in induced pluripotent stem cells and various studies on reprogramming factors integral to converting adult cells into pluripotent stem cells. It specifically mentions roles of various components (e.g., chromatin-remodeling components) and factors that promote reprogramming to pluripotency. This supports the claim that scientists use cell reprogramming for this purpose.


Input: Task: pass the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: № 261-ФЗ «Об энергосбережении и о повышении энергетической эффективности и о внесении изменений в отдельные законодательные акты Российской Федерации»30 в составе показателей оценки эффективности деятельности органов исполнительной власти субъектов Российской Федерации, органов местного самоуправления городских округов и муниципальных районов утверждаются показатели энергосбережения и повышения энергетической эффективности. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses energy conservation and efficiency measures within Russian legislation and does not mention soil depletion or renewable agriculture techniques. Thus, it does not provide any supporting or contrasting information related to the claim.


Input: Task: pass the claim using the given text. Claim: Biodiversity loss can negatively impact ecosystem resilience and function. [SEP] Text: In general, i don't think you tested different combinations of PFTs, but trait maps of woody vs non-woody vegetation. I understand you have a personal interest to compare to aDGVM2 results, but to me those comparisons do not add much to the story. The title of section 4. 2 is strange and seems wrong. I am surprised that the kappa does not go beyond 0. 6. I had hoped that higher kappas would be feasible. This is not discussed, but I would be interested (e. g. instead of the current 4. 3) if such aspects of model performance would be discussed and interpreted With respect to figure 3; what does it tell us if ranks of certain traits vary with number of traits (while ranks of other don't)? i. e. what is the message/understanding this figure gives? Citation: AC1: 'Reply on RC1', Simon Scheiter, 07 May 2024 The comment was uploaded in the form of a supplement: Citation: CC1: 'Comment on egusphere-2024-276', Bianca Rius, 17 Apr 2024 Scheiter et al. delve into the utilization of crowd-sourced trait data for defining global biomes, investigating the suitability of trait data for biome classification and identifying the most relevant traits for this purpose. While the study is intriguing and significant, I have some comments to offer. Major comments:The findings presented in this study offer valuable insights into the fundamental ecological mechanisms driving plant biogeography and global distribution strategies. However, while the results are intriguing and significant, the interpretation from an ecological perspective could be further emphasized. Additionally, it would be beneficial for the authors to underscore the importance of their study and the implications of their findings, particularly in informing our understanding of global biome classification and its ecological implications. Strengthening the ecological context and emphasizing the practical implications of the findings would significantly enhance the impact and relevance of the study. The findings regarding the differences in trait distribution and occurrence between biomes are indeed intriguing, but they have been explored somewhat superficially in the manuscript. understand that this topic is complex, questions 2 and 4 require a more in-depth exploration throughout the manuscript. As a reader, I was expecting these interesting questions to be thoroughly addressed. For instance, the observed tendency of tropical forests to have plants with greater height could be explored in more detail in the discussion section. [SEP] Justify:

Output: The text is largely irrelevant to the claim as it discusses comments and feedback regarding a scientific study on plant traits and biome classification without directly addressing the impact of biodiversity loss on ecosystem resilience and function. While it touches on ecological mechanisms and traits, it does not provide any clear evidence or argument related to the claim about biodiversity loss.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: Methods 6, 329–330. CrossrefPubMed2010. Induced pluripotency: History, mechanisms, and applicationsGenes Dev. 242239-2263. Stadtfeld, M. , and Hochedlinger, K. (2010). Induced pluripotency: History, mechanisms, and applications. Genes Dev. 24, 2239–2263. CrossrefPubMed894. Stadtfeld, M. , Brennand, K. , and Hochedlinger, K. (2008a). Reprogramming of pancreatic beta cells into induced pluripotent stem cells. Curr. Biol. 18, 890–894. CrossrefPubMed949. Stadtfeld, M. , Nagaya, M. , Utikal, J. , et al. (2008b). Induced pluripotent stem cells generated without viral integration. Science 322, 945–949. CrossrefPubMed2010. A reprogrammable mouse strain from gene-targeted embryonic stem cellsNat. Methods753-55. Stadtfeld, M. , Maherali, N. , Borkent, M. , et al. (2010). A reprogrammable mouse strain from gene-targeted embryonic stem cells. Nat. Methods 7, 53–55. CrossrefPubMed1982. Recurrent germ-line transmission of the teratocarcinoma genome from the METT-1 culture line to progeny in vivoJ. Exp. Zool. 224465-469. Stewart, T. A. , and Mintz, B. (1982). Recurrent germ-line transmission of the teratocarcinoma genome from the METT-1 culture line to progeny in vivo. J. Exp. Zool. 224, 465–469. CrossrefPubMed2010. Human iPS cell-based therapy: considerations before clinical applicationsCell Cycle9880-885. Sun, N. , Longaker, M. T. , and Wu, J. C. (2010). Human iPS cell-based therapy: considerations before clinical applications. 9, 880–885. CrossrefPubMed2010. Efficient generation of functional dopaminergic neurons from human induced pluripotent stem cells under defined conditionsStem Cells281893-1904. Swistowski, A. , Peng, J. [SEP] Justify:

Output: The text corroborates the claim as it discusses 'induced pluripotency,' which refers to the process of reprogramming adult cells into induced pluripotent stem cells. Several references are made to techniques and studies related to generating induced pluripotent stem cells, indicating that scientists are indeed applying cell reprogramming methods for this purpose.


Input: Task: pass the claim using the given text. Claim: All soil depletion issues are solved solely by using renewable agriculture techniques. [SEP] Text: Именно таким образом трактуется, в частности, понятие производственной инфраструктуры в приказе Росстата от 29 февраля 2016 г. № 101 «Об утверждении Основных методологических и организационных положений по подготовке и проведению Всероссийской сельскохозяйственной переписи 2016 года», в котором в составе производственной инфраструктуры, технических средств и технологий сельскохозяйственных производителей учитывается применение ВИЭ (как современных технологий). [SEP] Justify:

Output: The text discusses the definition of production infrastructure and the inclusion of renewable energy sources (VER) in agricultural technology without addressing soil depletion issues or renewable agriculture techniques specifically. Hence, it does not support or contrast the claim.


Input: Task: pass the claim using the given text. Claim: Biodiversity loss can negatively impact ecosystem resilience and function. [SEP] Text: One possible explanation for this phenomenon could be light competition. It would be valuable to delve deeper into why the identified distinguishing traits are significant and what they represent in terms of plant strategies and ecological functions. Hence, you can offer insights into their ecological relevance and their role in shaping biome characteristics. Specifically, you could discuss how these traits contribute to plant adaptation to specific environmental conditions, resource acquisition strategies, and ecosystem functioning. While you have begun to address this topic, emphasizing the ecological significance of the identified traits and highlighting avenues for future research would strengthen the overall argument and underscore the importance of your findings. It's essential to clarify the methodology, especially in section 2. 4, to improve understanding for readers. The conclusion and a significant portion of the discussion focusing on models may seem disconnected from the main purpose of the paper as outlined in the abstract and manuscript title. As a reader, I felt somewhat puzzled. Notably, none of the four questions posed at the end of the introduction mention the theme of modeling. To mitigate this discrepancy, you could consider clarifying from the outset that modeling will be a significant aspect of the study. Alternatively, you may choose to shift the focus of the discussion to emphasize other aspects that were highlighted earlier in the manuscript, aligning more closely with the stated objectives and questions. Minor comments:- In the abstract the use of the “31 different biome maps” is not clear, is it used to perform the supervised cluster analyses or it is used to evaluate the results from this analyses? - Enhancing the fluidity of the introduction by providing more ecological context and emphasizing the significance of generating this type of map would improve the transition to the research questions. - l58 and l59 are more appropriate for Materials and Methods section- It's not clear in the methods why you “created three different maps for each trait” and why you filtered the observations according to PFTs before spatially aggregating the trait values. - In section 2. 2 I didn’t understand the difference between 3) and 4). - In section 2. 3, specifying the total number of traits considered would enhance clarity. don’t miss anything, it is only specified in the abstract. - It is unclear why the analysis described in section 2. 4 was performed if the most important traits were identified in section 2. 3. - Fig. [SEP] Justify:

Output: The text does not directly address the claim about biodiversity loss and its impact on ecosystem resilience and function. Instead, it discusses specific methods and needs for clarification in the research, focusing on plant traits and ecological functions without mentioning the implications of biodiversity loss.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: , Liu, Q. , et al. (2010). Efficient generation of functional dopaminergic neurons from human induced pluripotent stem cells under defined conditions. 28, 1893–1904. CrossrefPubMed2001. Nuclear reprogramming of somatic cells by in vitro hybridization with ES cellsCurr. Biol. 111553-1558. Tada, M. , Takahama, Y. , Abe, K. , et al. (2001). Nuclear reprogramming of somatic cells by in vitro hybridization with ES cells. Curr. Biol. 11, 1553–1558. CrossrefPubMed2006. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factorsCell126663-676. Takahashi, K. , and Yamanaka, S. (2006). Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676. CrossrefPubMed2007. Induction of pluripotent stem cells from adult human fibroblasts by defined factorsCell1311-12. Takahashi, K. , Tanabe, K. , Ohnuki, M. , et al. (2007). Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 1–12. Crossref1992. Human Oct3 gene family: cDNA sequences, alternative splicing, gene organization, chromosomal location, and expression at low levels in adult tissuesRes. 204613-4620. Takeda, J. , Seino, S. , and Bell, G. I. (1992). Human Oct3 gene family: cDNA sequences, alternative splicing, gene organization, chromosomal location, and expression at low levels in adult tissues. Res. 20, 4613–4620. CrossrefPubMed2011. Functionality and transduction condition evaluation of recombinant Klf4 for improved reprogramming of iPS cellsCell. Reprogram. 1399-112. Tang, Y. , Lin, C. J. , and Tian, X. C. (2011). Functionality and transduction condition evaluation of recombinant Klf4 for improved reprogramming of iPS cells. Cell. Reprogram. 13, 99–112. CrossrefPubMed2005. [SEP] Justify:

Output: The text corroborates the claim by referencing the induction of pluripotent stem cells from adult fibroblasts by defined factors in the study by Takahashi et al. (2007), which illustrates the process of cell reprogramming to convert adult cells into pluripotent stem cells.


Input: Task: contrast the claim using the given text. Claim: All encryption methods will become obsolete with the rise of quantum computers. [SEP] Text: To guarantee that the decrypting party applies respective conjugates of the same permutation matrices that were used to encrypt plaintext, the two communicating parties pre-share a secret key using some asymmetric key exchange scheme. This secret key is used to create the Permutation Pad, consisting of permutations, as well as the Pad, consisting of the Hermitian conjugates of the permutations used for the encryption. Permutation matrices can be efficiently implemented in a quantum circuit using and SWAP gates [27]. Moreover, permutation matrices can be used to specify Qiskit operator objects using row-by-row matrix description, thus making it possible to implement QPP in the IBM Quantum systems. On the other hand, permutation matrices can be converted into arrays, to be implemented in classical systems. To the best of our knowledge, QPP is the first ever hybrid quantum-classical scheme. It will require further examination to determine whether there are advantages to using the quantum implementation of QPP as opposed to a classical implementation, for instance, we would expect that the quantum implementation is more efficient than the classical implementation. However, one of the main attributes of QPP is that it can be implemented in both classical and quantum devices. Previous implementations of QPP have shown that it is lightweight and can be run today on a free-of-charge IBM Quantum system as well as any classical computer, unlocking the potential of being widely used for quantum encryption in classical systems, quantum systems, as well as hybrid systems, with significant potential use-cases such as quantum internet [19–21, 24–26]. Having a hybrid encryption scheme reduces the limitations and vulnerabilities of a scenario where two different schemes are used on quantum and classical devices, and therefore we continue advancing QPP to ensure that both quantum and classical QPP implementations are efficient and secure. In this work, we present a fully-functioning implementation of the QPP algorithm used to encrypt superposition states with Qiskit in IBM Quantum systems. We were curious to examine whether QPP is limited to basis states, and also explore whether there are any security benefits brought about by introducing superposition states. This work goes beyond academic interest and exhibits potential to be used in the future quantum internet where the states of quantum systems may generally be superposition states transmitted over a quantum channel [28, 29]. This paper builds on and extends our previous research [24–26]. [SEP] Justify:

Output: The text contrasts the claim by discussing the Quantum Permutation Pad (QPP), which is both a hybrid quantum-classical encryption scheme and a potential solution for secure encryption in both types of systems. It highlights that QPP can be implemented in classical systems as well as quantum systems, with significant potential use-cases for quantum encryption, thereby suggesting that certain encryption methods, like QPP, can continue to be viable and effective even in the era of quantum computing.


Input: Task: pass the claim using the given text. Claim: Biodiversity loss can negatively impact ecosystem resilience and function. [SEP] Text: 3: Parallel coordinates plots are already complex visualizations to comprehend, and as it stands, I don't think the figure adds much value, unless it is thoroughly explored and contextualized in the text. - Fig. 5: The background color (gray) on the map is too similar to the light blue, making it difficult to interpret the figure. - Why is there such an extensive comparison with the results from aDGVM2? This was not anticipated based on the main questions posed in the Introduction section. - 4. 2, you briefly touch on the importance of examining trait covariation, highlighting its significance compared to focusing solely on individual traits. However, given that some of your results seem to directly address this aspect, it would be beneficial to delve deeper into this topic and explicitly connect it with the obtained results. - acknowledge that analyzing the occurrence and abundance of traits in each biome may not be the primary focus of your manuscript, it presents an opportunity for a valuable complementary analysis. By examining the diversity of traits within each biome, specifically by assessing the variance in their distribution, you can provide additional insights into the functional composition and ecological characteristics of these biomes. This analysis could help elucidate patterns of trait diversity across different environmental gradients and provide a deeper understanding of the ecological processes driving biome differentiation. Writing errors: I believe a parenthesis is missing for the reference in the following sentences: ”Biomes are commonly used to represent major vegetation formations and to map their biogeographic distributions. Multiple biome maps were developed based on a variety of different data sources Beierkuhnlein and Fischer (2021). ” “Despite the increasing availability of trait data in databases such TRY (Kattge et al. , 2020) and extrapolated global biome maps Wolf et al. (2022); Boonman et al. (2020), a systematic assessment of the performance of traits for biome classification and an identification of the most appropriate traits remain elusive. ” Citation: AC3: 'Reply on CC1', Simon Scheiter, 07 May 2024 The comment was uploaded in the form of a supplement: Citation: RC2: 'Comment on egusphere-2024-276', Bianca Rius, 18 Apr 2024 Scheiter et al. delve into the utilization of crowd-sourced trait data for defining global biomes, investigating the suitability of trait data for biome classification and identifying the most relevant traits for this purpose. [SEP] Justify:

Output: The text does not address the specific claim regarding biodiversity loss and its impact on ecosystem resilience and function. Instead, it focuses on the complexities of visualizations in scientific analysis, discussions about trait covariation, and references to data sources for biome classification. Thus, it is irrelevant to the claim presented.


Input: Task: corroborate the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: Induction of dedifferentiation, genomewide transcriptional programming, and epigenetic reprogramming by extracts of carcinoma and embryonic stem cellsMol. Biol. Cell165719-5935. Taranger, C. K. , Noer, A. , Sorensen, A. L. , et al. (2005). Induction of dedifferentiation, genomewide transcriptional programming, and epigenetic reprogramming by extracts of carcinoma and embryonic stem cells. Mol. Biol. Cell 16, 5719–5935. CrossrefPubMed2010. The efficient generation of induced pluripotent stem (iPS) cells from adult mouse adipose tissue-derived and neural stem cellsCell Transplant. 19525-536. Tat, P. A. , Sumer, H. , Jones, K. L. , et al. (2010). The efficient generation of induced pluripotent stem (iPS) cells from adult mouse adipose tissue-derived and neural stem cells. Cell Transplant. 19, 525–536. CrossrefPubMed1998. Embryonic stem cell lines derived from human blastocystsScience2821145-1147. Thomson, J. A. , Itskovitz-Eldor, J. , Shapiro, S. S. , et al. (1998). Embryonic stem cell lines derived from human blastocysts. Science 282, 1145–1147. CrossrefPubMed2008. Derivation of human skin fibroblast lines for feeder cells of human embryonic stem cellsCurr. Protoc. Biol. 7. Unger, C. , Felldin, U. , Nordenskjold, A. , et al. (2008). Derivation of human skin fibroblast lines for feeder cells of human embryonic stem cells. Curr. Protoc. Biol. 7. PubMed2009. Sox2 is dispensable for the reprogramming of melanocytes and melanoma cells into induced pluripotent stem cellsJ. Cell Sci. 1223502-3510. Utikal, J. , Maherali, N. , Kulalert, W. , et al. (2009). Sox2 is dispensable for the reprogramming of melanocytes and melanoma cells into induced pluripotent stem cells. J. Cell Sci. 122, 3502–3510. [SEP] Justify:

Output: The text corroborates the claim by discussing the efficient generation of induced pluripotent stem (iPS) cells from adult mouse adipose tissue-derived and neural stem cells, directly supporting the idea that scientists can reprogram adult cells to become pluripotent.