Input: Task: corroborate the claim using the given text. Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: Research has shown that HIV can interrupt the way these energy powerhouse structures work, including increasing the release of harmful molecules that can contribute to the progression of HAND. In addition, this energy is needed for effective gene expression within the cell. Studies done by Thangavel’s research group at Texas A&M University have already shed light on the epigenetic changes in the human brain cause energy dysfunction, which can contribute to HAND. Thangavel also suggests that N-terminal acetylation may impact the signalling cascade of gene expression which has been shown to be significantly associated with depressive behaviours, problems with forming memories, and dementia. He proposes that N-terminal acetylation changes induced by viral infections could explain how the virus and body interact. He also explains that if more can be understood about how HIV effects the cell’s energy source, it may be possible to develop therapeutic approaches to prevent HAND, as well as new ways to test for the condition. Improving quality of life Further research is still needed to learn more about the relationship between HIV infection, modifications to proteins via N-terminal acetylation or other mechanisms, and cognitive impairment or behavioural changes. It is likely that epigenetic modifications regulate both gene expression in the energy-producing compartments of a cell, as well as gene expression more broadly. Improved diagnosis and management of cognitive disorders in people with HIV infection, which is well managed through medications, means that overall quality of life can be improved for those living with the virus. How did you first become interested in the impact of HIV infection on the brain? Our research focus is aligned with the global efforts to eliminate the suffering of HIV. Understanding the mechanisms of disease progression is key to developing new therapeutic strategies. In the early phase of my research, there was a lack of knowledge of HIV and its virulent subtypes. Our experiments highlighted the higher virulence of the subtypes found in the US compared to European, Asian, and African subtypes, which trigger neuronal cell death through the excess production of a neurotoxin called quinolinic acid. Neurological impairments caused by the subtypes from the US were also somewhat elevated, which paralleled with the high occurrence of HAND in the US. Disruption of energy homeostasis is one of the features observed in neurodegenerative conditions, including HAND. [SEP] Justify:

Output: The text corroborates the claim by discussing how epigenetic changes in the human brain related to HIV can impact gene expression. It specifically mentions that 'epigenetic modifications regulate both gene expression in the energy-producing compartments of a cell, as well as gene expression more broadly,' which directly supports the idea that environmental factors (in this case, HIV infection) can modify gene expression.


Input: Task: contrast the claim using the given text. Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: Response: I added literature regarding physical trampling and how they might compare to the mining disturbance in the hyper-arid (L358 – L370):…” Previous studies examining the effect of a physical disturbance (repeated trampling) on biocrust communities, revealed a decrease in the amount of extractable DNA, lower chlorophyll a, and a decrease in biomass and cyanobacteria abundance (Kuske et al. , 2012; Steven et al. , 2015; Chung et al. , 2019). However, these studies investigated a localized disturbance compared to mining disturbance, where the biocrust is completely removed over large spatial scales. Moreover, the previous studies were conducted in environments that were less extreme than the hyper-arid Zin Valley. Therefore, we expected the damage to the biocrust in Zin post-mining sites to follow similar patterns but to be more conspicuous than the previously reported disturbed biocrusts (Kuske et al. , 2012; Steven et al. , 2015; Chung et al. , 2019). Our previous report (Gabay et al. , 2022) supported this notion; we demonstrated differences in bacterial communities in natural and post-mining biocrusts, expecting these differences to be reflected in the proliferating communities of these biocrusts. "Similarly, transcriptomic studies that show the genes that are expressed during a wetting pulse and have documented metabolic a physiological changes in the bacterial community in a wetting pulse. These studies show where resources may be going to rather than growth, and should probably be at least mentioned in this text. Response: I added previous studies that showed expression of nitrogen cycling genes and metabolite production following wetting (L417 – L425):…” One study examining microbial nitrogen transformations in biocrusts collected from biome in Namibia and showed that following wetting, nitrogen cycling genes are expressed in biocrust organisms (Maier et al. , 2022). another study examining biocrust samples taken from the in Utah demonstrated a pulse of metabolite release following controlled wetting (Swenson et al. , 2018). Based on these reports (Maier et al. , 2022; Swenson et al. , 2018) and due to the extreme conditions in (Levi et al. , 2021), we suggest that hyperarid biocrust communities prioritize functions such as metabolite production, nutrient cycling and preparation for desiccation over growth. [SEP] Justify:

Output: The text contrasts the claim by discussing biocrust communities that exist in hyper-arid environments, indicating that such communities can grow in conditions that suggest they are not limited to trees as their sole habitat. The mention of studies examining microbial nitrogen transformations and metabolite release in biocrusts suggests a variety of environments, potentially including rocks and soil, where these organisms thrive, contradicting the claim that mosses can only grow on trees.


Input: Task: pass the claim using the given text. Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: Cognitive function in morbidly obese individuals with and without binge eating disorder. Compr Psychiatry. 2012; 53(5): 490–495. 33. Divergent neural substrates of inhibitory control in binge eating disorder relative to other manifestations of obesity. Obesity. 2013; 21(2): 367–377. 34. . Inhibitory control in bulimic-type eating disorders: a systematic review and meta-analysis. PLoS One. 2013; 8(12): e83412. 35. . Neurocircuitry of addiction. Neuropsychopharmacology. 2010; 35(1): 217–238. CrossRef36. . Set-shifting ability across the spectrum of eating disorders and in overweight and obesity: a systematic review and meta-analysis. Psychol Med. 2014; 44(16): 3365–3385. 37. . Model-based influences on humans’ choices and striatal prediction errors. Neuron. 2011; 69(6): 1204–1215. 38. Disorders of compulsivity: a common bias towards learning habits. Mol Psychiatry. 2015; 20(3): 345–352. CrossRef39. -Terpstra, J, Moreno, F. Prefrontal and striatal dopaminergic genes predict individual differences in exploration and exploitation. Nat Neurosci. 2009; 12(8): 1062–1068. CrossRef40. . Biases in the explore-exploit tradeoff in addictions: the role of avoidance of uncertainty. Neuropsychopharmacology. In press. DOI: 10. 1038/n208. 41. Svaldi, J, Tuschen-. Information processing of food pictures in binge eating disorder. Appetite. 2010; 55(3): 685–694. CrossRef42. Impulsivity in binge eating disorder: food cues elicit increased reward responses and disinhibition. PLoS One. 2013; 8(10): e76542. 43. -. Cognitive interference and a food-related memory bias in binge eating disorder. Appetite. 2014; 72: 28–36. 44. Svaldi, J, Bender, C, Tuschen-Caffier, B. Explicit memory bias for positively valenced body-related cues in women with binge eating disorder. J Exp Psychiatry. 2010; 41(3): 251–257. CrossRef45. [SEP] Justify:

Output: The text discusses various studies related to cognitive function and disorders, specifically focusing on eating disorders and their associated biases. However, it does not directly address the broader concept of cognitive biases influencing decision-making in general. Therefore, it is irrelevant to the specific claim being analyzed.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: Oocyte and sperm nuclei fuse resulting in syngamy (Figure 1). The zygote undergoes a series of cleavage divisions, forming two‐cell, four‐cell, eight‐cell morula and blastocyst stages [2] (Figure 1). During cleavage stage divisions, programming of maternal and paternal chromosomes takes place to create the embryonic genome (embryonic genome activation, EGA) and to start the preimplantation embryo development. If the EGA fails, the development does not continue because of the inability of the embryo to have cellular functions [3]. This activation is initiated by the degradation of maternal nucleic acids, specific RNAs stored in oocytes, proteins and other macromolecules [4]. Upon EGA, which starts at the two‐cell stage in mouse and four‐ to eight‐cell stage in human [5], remarkable reprogramming of expression occurs in the preimplantation embryo. These reprogramming events are controlled by DNA methylation, histone acetylation, transcription, translation and miRNA regulation [6]. Therefore, the development of preimplantation embryos includes continuous molecular, cellular and morphological events. These events would eventually form a multilineage embryo that has a capability to implant and continue the foetal development. Figure 1. Schematic diagram outlining the main stages of preimplantation embryo development. Fertilisation followed by syngamy, cleavage divisions results in two, three, four, and so on cell embryos which eventually form the morula and the blastocyst. In this 2. Gene expression and epigeneticsFor a normal developing embryo, the expression of both maternal and paternal genes is required. An intense epigenetic change occurs upon fertilisation to establish pluripotency [7]. Although there are a number of post‐translational modifications within chromatin including acetylation, ubiquitination, SUMOylation and phosphorylation; methylation of histone lysine and arginine residues is the main focus in preimplantation embryos. Methylation and chromatin modification not only play crucial roles in determining the transcriptional state but also are capable of determining the transcriptional repression [8–10]. The mechanism leading to the changes in methylation is not well established, but it has been suggested that the reprogramming takes place by either passive or active demethylation. [SEP] Justify:

Output: The text corroborates the claim by discussing various mechanisms of epigenetic changes that occur during the development of embryos. It mentions that intense epigenetic changes happen upon fertilization, which establish pluripotency and indicate how methylation and chromatin modifications play crucial roles in determining gene expression. The text emphasizes that DNA methylation, histone modifications, and other factors are capable of affecting transcriptional states in developing embryos, thus linking environmental factors to modifications in gene expression, aligning directly with the claim about epigenetics.


Input: Task: contrast the claim using the given text. Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: ”Minor concerns:Title: I am not sure the comma is needed between hyperarid and phosphateResponse: I removed the commaLine 210: picrust should be 2Response: corrected (L208). Line 214: I think this should be spelled out more completely. It just sends the reader to a reference. This is a specialized set of functional annotations. I think it would help the reader interpret Figure 6 and where the annotations are coming from. Response: I added a description of the referenced study and explained the source of the functional annotations (L213 – L218):“…The function categories were chosen based on Meier et al. (2021). In their study, Meier et al. collected biocrusts from the Negev and analyzed bacterial metagenomes in the biocrusts to evaluate the distribution of metabolic potential among bacterial populations. To compare functional potential between various bacterial phyla, they selected metabolic genes encoded in the metagenomic-assembled genomes and grouped them into 10 function categories. ” Citation: RC2: 'Comment on egusphere-2022-1510', #2, 04 Mar 2023 This study is interesting as it identifies which bacteria proliferate in biocrusts from natural and postmining areas and examines functional gene abundances unlike previous studies that have focused on characterizing the microbial community composition of natural and post-mining biocrusts. This, I consider the approach novel. Nonetheless, I have a few comments that should be addressed:AbstractL19-23. I recommend deleting this sentence because it refers to a previous study, and the abstract should focus on the objectives and results of the present study. Then, in the Introduction or the Discussion, it is fine if mention to previous results is done. M&ML103-105. It is not clear the predominant p109. Add a short description of the biocrust sampled (thickness, cover, composition, …. ). Were there differences in the biocrust from natural and post-mining sites? ResultsRegarding the results of the proliferated bacterial community composition, it would be nice to include a figure with the relative abundances of the different bacteria phylum for natural and post-mining biocrusts to make the results clearer. DiscussionL354-357. Can you remind here when was the sampled post-mining site restored? Was it at 2007? [SEP] Justify:

Output: The text contrasts the claim by discussing a study that analyzes bacterial metagenomes in biocrusts, indicating that certain bacterial communities can proliferate in natural and post-mining areas, which implies a broader habitat potential for biocrusts that includes not just trees but also potentially other substrates like rocks or soil. The context around biocrusts suggests a diversity of growth environments, contrasting with the claim that mosses are restricted to trees alone.


Input: Task: pass the claim using the given text. Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: Effects of the mu-opioid receptor antagonist GSK1521498 on hedonic and consummatory eating behaviour: a proof of mechanism study in binge-eating obese subjects. Mol Psychiatry. 2013; 18(12): 1287–1293. 46. Neural and behavioral effects of a novel mu opioid receptor antagonist in binge-eating obese people. Biol Psychiatry. 2013; 73(9): 887–894. 47. Effects of mu opioid receptor antagonism on cognition in obese binge-eating individuals. Psychopharmacology (Berl). 2012; 224(4): 501–509. 48. . Acute effects of morphine on distinct forms of impulsive behavior in rats. Psychopharmacology (Berl). 2009; 205(3): 489–502. 49. Wiskerke, J, Schetters, D, van Es, IE, et al. mu-Opioid receptors in the nucleus accumbens shell region mediate the effects of amphetamine on inhibitory control but not impulsive choice. J Neurosci. 2011; 31(1): 262–272. [SEP] Justify:

Output: The text is irrelevant to the claim as it focuses on the effects of mu-opioid receptor antagonists on eating behavior and cognition in obese individuals, without mentioning cognitive biases or their influence on decision-making.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: Indirect pathways of demethylation are associated with DNA repair [11–14]. Two main stages, PGCs and preimplantation embryos, are important in the regulation by methylation. 2. 1. Epigenetic modification of the zygote and the preimplantation embryosIn mammals (human, bovine, rat, pig and mouse), the zygote undergoes genome‐wide demethylation [15–17] with the exception of imprinted genes [18]. The male pronucleus of the zygote undergoes selective demethylation due to the loss of DNA replication leading to asymmetric methylated sister chromatids [15, 16, 19, 20]. These events start following the sperm decondensation in humans and in mouse with some variations [17, 21, 22]. The female pronucleus of the zygote remains highly methylated at this stage [17, 21, 22]. Demethylation of the maternal genome starts with the first cleavage divisions [19, 23, 24]. By the morula stage, the mouse preimplantation embryos become undermethylated. Polarisation and compaction of individual blastomeres start at around eight‐cell stage of the developing embryo. Many factors are involved in these processes including E‐cadherin (CDH1), partitioning defective homologue 3 (PARD3), PARD6B and protein kinase C zeta [25–27]. The blastocyst stage embryo has a fluid‐filled cavity and two cell populations consisting of inner cell mass (ICM) and trophectoderm (TE). All the blastomeres are believed to be totipotent in cleavage embryos until four‐ to eight‐cell stage since these cells form both the ICM and TE lineage [28]. ICM develops into epiblast, whereas TE forms the extraembryonic tissues such as placenta. ICM is composed of pluripotent cells that have the capacity to develop into any cell type of the foetus. Transcriptional and epigenetic events strictly regulate these differentiation events. A number of transcriptional factors play a crucial role in blastocyst formation. These include caudal type homeobox 2 (CDX2) for TE specification, octamer 3/4 (OCT4) and NANOG for the establishment of ICM pluripotency [29–31]. [SEP] Justify:

Output: The text corroborates the claim by discussing epigenetic modifications during crucial stages of embryo development, specifically highlighting how DNA methylation and demethylation processes can influence gene expression. It mentions that transcriptional and epigenetic events regulate differentiation, which aligns with the claim that environmental factors can modify gene expression through epigenetics.


Input: Task: contrast the claim using the given text. Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: Response: I added a description of the biocrusts in Gov mining site (L106 – L109):“…Biocrusts were sampled either from the post-mining site or the adjacent natural area. The biocrusts in Gov are thin (between 1. 5 - 2. 5 mm deep), and smooth. The site is characterized by areas covered in biocrusts or desert pavement. In each sampling site, we sampled along a 100 m strip at approximately 10 m intervals (Fig. 1). ”ResultsRegarding the results of the proliferated bacterial community composition, it would be nice to include a figure with the relative abundances of the different bacteria phylum for natural and post-mining biocrusts to make the results clearer. Response: Added a bar plot of Phyla relative abundances to the PCoA ordination in figure 5 (labeled ‘a’ and ‘b’) and statistical data in the supplementary file (Table S4). DiscussionL354-357. Can you remind here when was the sampled post-mining site restored? Was it at 2007? I wonder if one reason for the lack of photosynthetic potential difference between post-mining and natural biocrusts is because the biocrust in the post-mining site has been already recovered. For example, soil colonization by cyanobacteria can be faster than thought. Response: I mentioned the restoration year in L375. I agree that it is likely that the biocrusts we sampled have a significant cyanobacterial community, however we hypothesize that the recovery of the biocrust differs even within the mining site, emphasizing the importance of microenvironments, where certain areas have more developed biocrusts and others have less developed biocrust even within the same post-mining plot. I referenced this in the discussion (L376 – L383): “…However, in the current study, we sampled post-mining biocrusts at a different location in the Gov mining site (~500 m away from the original plot) due to technical constraints. In the new location we found that the photosynthetic potential of the biocrust in the post-mining plots did not differ from the natural biocrust. These results highlight the importance of microenvironments in shaping the functionality of biocrusts (Garcia-Pichel and Belnap, 1996). [SEP] Justify:

Output: The text contrasts the claim by discussing the presence of biocrusts in various environments, including post-mining sites and natural areas. It indicates that these biocrusts, which could contain mosses, are found on surfaces like desert pavement and soil, contradicting the assertion that mosses can only grow on trees.


Input: Task: pass the claim using the given text. Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: Skip to main content Intended for healthcare professionals Search this journalSearch all journalsEnter search terms. . . Searchsearch Enter search terms. . . Searchsearch Search Access/ProfileAccessView access optionsView profileCreate profile Cart 0 by discipline Select discipline: All disciplines All disciplines Life & & Sciences & HumanitiesSelect subject: All subjects All subjects Cardiology & Medicine & Endocrinology & -legal & Orthopaedics & Medicine & & & & Methods & & & & & Criminology & Economics & & & Management & Marketing & & & & & & & & PlanningBrowse journals Sage publishes a diverse portfolio of fully journals in a variety of disciplines. you can explore our Disciplines Hubs, including: Journal portfolios in each of our subject areas. Links to Books and content from across Sage. for/ Reviewers SocietiesFrequently asked questions In this journal : 3. 1 5-Factor: 3. 3 email alertsYou are adding the following journal to your email alertsNew contentMakingCreate email alert Restricted accessReview 10. 1177/0272989X14547740ContentsAbstract2013. Predefined exclusion criteria were used to identify 213 studies. During data extraction, information was collected on type of bias or heuristic studied, respondent population, decision type, study type (actual or hypothetical), study method, and study conclusion. Results. Of the 213 studies analyzed, 164 (77%) were based on hypothetical vignettes, and 175 (82%) were conducted with representative populations. Nineteen types of cognitive biases and heuristics were found. Only 34% of studies (n = 73) investigated medical personnel, and 68% (n = 145) confirmed the presence of a bias or heuristic. Each methodological quality criterion was satisfied by more than 50% of the studies, except for sample size and validated instruments/questions. Limitations are that existing terms were used to inform search terms, and study inclusion criteria focused strictly on decision making. Conclusions. Most of the studies on biases and heuristics in medical decision making are based on hypothetical vignettes, raising concerns about applicability of these findings to actual decision making. Biases and heuristics have been underinvestigated in medical personnel compared with patients. Get full access to this 1. . Uncertainty: Heuristics and Biases. 1st ed. New York: Press; 1982. Crossref2. Kahneman D, Tversky A. [SEP] Justify:

Output: The text primarily provides information about the methodological aspects of a study on cognitive biases and heuristics but does not explicitly address or support the claim regarding the influence of cognitive biases on decision-making. The discussion mainly encompasses study design and results rather than making a direct connection to decision-making effects.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: CDX2 is extensively expressed in eight‐ and 16‐cell stage and it is expressed only in TE cells of the blastocyst [32]. Although OCT4 and NANOG are also expressed broadly at eight‐ and 16‐cell stage embryos, they are only expressed in ICM in blastocysts [32]. A number of transcription factors are required for blastocyst formation. Embryos lacking CDX2 expression cannot form blastocoel cavity but they have the ability to implant [30]. Lack of OCT4 or NANOG expression causes failure of ICM and the development of these embryos is arrested at the blastocyst stage [31, 32]. TEAD4 is another transcription factor that has a role in blastocyst transition in which the lack of TEAD4 nuclear localisation impairs TE‐specific transcriptional programme in inner blastomeres [33]. Furthermore, the aberrant expression of TCFAP2C transcription factor also leads to embryonic arrest during morula to blastocyst transition [34] and Klf5 mouse‐mutant embryos arrest at the blastocyst stage [35]. The remethylation process starts shortly after implantation [16, 22, 23, 36]. This de novo methylation occurs asymmetrically, such that ICM is hypermethylated possibly due to the Dnmt3b methylase [37], whereas TE remains hypomethylated due to the active demethylation by enzyme catalysis and passive demethylation [11, 14, 22]. Alteration of the methylation profiles in embryos has been shown to cause alterations of ICM and TE differentiation. Variations of the H3 arginine 26 residue (H3R26me) were shown to lead to changes of TE and ICM differentiation of a blastomere [38]. X‐chromosome inactivation is an epigenetic phenomenon in which the activity of X chromosomes is strictly regulated to equalise X‐chromosome expression and gene dosage between males and females and relative to autosome chromosomes [39]. For correct development, X‐chromosome dosage compensation is crucial. The inactivation of X chromosome occurs in at least two phases: initiation and maintenance. X‐inactivation mouse model systems have shown that the inactivation of X chromosome takes place during early embryogenesis of the female embryo by undergoing transcriptional silencing of genes along the X chromosome [40]. [SEP] Justify:

Output: The text corroborates the claim by discussing various transcription factors and their influence on gene expression during embryonic development. It highlights processes such as remethylation and X-chromosome inactivation, which are epigenetic mechanisms that show how gene expression can be modified by environmental factors. For example, it notes that 'the aberrant expression of TCFAP2C transcription factor also leads to embryonic arrest,' indicating a link between environmental influences (in this case, transcription factor expression) and gene expression changes.


Input: Task: contrast the claim using the given text. Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: The similarities in active communities and photosynthetic potential could be due to more developed biocrusts in the new sampling locations compared to the previous ones. ”L369-370. There is little discussion on the results of the Picrust analysis. It would be nice to compare the results of this study with other studies that have also examined functional genes in biocrusts to see if abundances of the functional genes at this site greatly differ from those of biocrusts of other regions. Response: I added a paragraph addressing the analysis with reference and comparison to a previous study that used to infer functional potential (L395 – L405):“…analysis revealed no significant differences in the abundances of genes within any of the function categories examined (Fig. 6). In contrast, a previous study conducted in the Highlands, examined active bacterial communities during a rain and subsequent drying (Baubin et al. , 2021). The results indicated an increase in genes related to photosynthesis, light, and sensing following the rain, while the other function categories did not vary significantly. We note that the identity and abundances of the functional genes in the dry biocrusts detected by Baubin et al. , (2021) and here (Fig. 6) are similar. Therefore, we propose that the similarity between the post-mining and natural biocrust communities (Fig. 5) reflect similar functional potential (Fig. 6). However, low abundance of active ASVs were used to infer the abundances of functional genes (Fig. 6), and large variance between samples in post-mining biocrusts could mask significant differences (Table S5). ”L379-381. It is hypothesized that the low bacterial growth in harsh environments like this one could be because biocrusts prioritize activation and preparation for desiccation over growth. However, this hypothesis cannot be fully demonstrated with the reported results. Could you add 401. Is there any practical experience of the application of cyanobacteria inoculation to restore this mining site in Israel? If so, it would be nice to add a few sentences regarding the potential of this technique to restore biocrust in the current mining site. Response: No, there have not been any active restoration measures in Zin mining sites and no previous scientific studies regarding the mining practices of ICL mining company. [SEP] Justify:

Output: The text contrasts the claim by discussing the growth and functional potential of biocrusts, which includes communities of organisms potentially on soils and rocks. There is no mention of a limitation on mosses being found only on trees, indicating that they may also be found on other substrates, including soils and rocks, which directly challenges the claim.


Input: Task: pass the claim using the given text. Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: New York: HarperOne; 2012. 20. Chapman GB. Time discounting of health outcomes. In: eds. Time and Decision: Economic and on Intertemporal Choice. New York: Foundation; 2003. p 395–418. 21. Croskerry P. The importance of cognitive errors in diagnosis and strategies to minimize them. Acad Med. 2003;78(8):775–80. CrossrefPubMedWeb of Science22. Reporting guidelines for survey research: an analysis of published guidance and reporting practices. PLoS Med. 2011;8(8):e1001069. CrossrefWeb of Science23. . of Reporting (CORE) index identifies important deficiencies in observational study conference abstracts. J Clin Epidemiol. 2008;61(12):1241–9. Crossref24. Meyrick J. What is good qualitative research? A first step towards a comprehensive approach to judging rigour/quality. J Health Psychol. 2006;11(5):799–808. CrossrefPubMedWeb of Science25. . The influence of positive affect on clinical problem solving. Making. 1991;11(3):221–7. CrossrefPubMedWeb of Science26. Myers RE. Decision counseling in cancer prevention and control. Health Psychol. 2005;24(suppl 4):S71–7. CrossrefPubMedWeb of Science27. Sharman SJ. Current negative mood encourages changes in end-of-life treatment decisions and is associated with false memories. Cogn Emot. 2011;25(1):132–9. CrossrefPubMedWeb of Science28. . Affect, framing, and persuasion. J Market Res. 2003;40(1):54–64. CrossrefWeb of Science29. Action tendency emotions evoked by memorable breast cancer messages and their association with prevention and detection behaviors. Health Commun. 2010;25(8):737–46. CrossrefPubMedWeb of Science30. Fox CR, Tversky A. Ambiguity aversion and comparative ignorance. In: Kahneman D, Tversky A, eds. Choices, Values, and Frames. New York: 2000. p 528–42. Crossref31. . Attitudes of obstetricians and gynecologists toward hormone replacement therapy. Making. 1998;18(4):406–11. CrossrefPubMedWeb of Science32. [SEP] Justify:

Output: The text does not directly address the claim regarding the influence of cognitive biases on decision-making. Instead, it includes a series of citations and references to various studies and articles, without articulating a specific viewpoint or evidence that supports or opposes the claim.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: In human preimplantation embryos, it has been shown that the reduced expression of X chromosomes in females ensures the dosage compensation [41]. expression activates the X‐chromosome inactivation by engaging proteins functioning in chromatin remodelling [3, 42]. With the advanced technologies, including single‐cell RNA sequencing, it has emerged that lncand XIST are expressed on the active X chromosome in the early human preimplantation embryos [43]. Furthermore, the expression of these two RNAs has never been shown to overlap. Introducing XACT into heterologous systems caused the accumulation of Xist RNA in cis and therefore it may be involved in the control of XIST association to chromosome in cis and may temper its ability of silencing. It is also possible that XACT functions in balancing the X‐chromosome inactivation at the early stages of preimplantation embryo development [43, 44]. Recently, the dosage compensation was shown to be driven by a CAG promoter of a new Xist allele (Xist(CAG)) [45]. Furthermore, Xist(CAG) upregulation in preimplantation embryos showed variation depending on the parental origin and the paternal expression was suggested to be preferentially inactivated with the paternal Xist(CAG) transmission [45]. 2. 2. Epigenetic modification of the gametesIn germ cells, methylation is maintained in a sex‐specific manner. Methylation in PGCs diminishes as they migrate to the gonads. Studies suggest that in females, remethylation occurs after birth when the oocytes are in the process of development. When demethylation is completed, the PGCs either enter mitosis in males or arrest at meiosis in females [46]. Reprogramming of the methylation in the embryo is necessary for parent‐specific expression of genes [14]. Gene expression varies during preimplantation embryo development due to these reprogramming events and appropriate gene expression determines the survival of the embryo [6]. Recently, short noncoding RNAs, microRNAs (miRNAs) and long noncoding RNAs (lncRNA) have gained importance in their potential function to affect numerous pathways by targeting multiple genes [47, 48]. Advertisement 3. [SEP] Justify:

Output: The text corroborates the claim by discussing various aspects of epigenetics in relation to gene expression. It illustrates how modifications in gene expression occur under specific conditions, such as the methylation changes in primordial germ cells (PGCs) during migration and development. The text states, 'Reprogramming of the methylation in the embryo is necessary for parent‐specific expression of genes,' indicating that environmental factors can influence gene expression patterns. Furthermore, it highlights the role of noncoding RNAs, which can affect multiple gene pathways, suggesting that these epigenetic modifications are indeed responsive to environmental conditions.


Input: Task: contrast the claim using the given text. Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: I address the need for active restoration measures in Zin mining sites (including cyanobacteria inoculation) in L439 – L444:“…Our results further emphasize the need for active restoration measures in the Zin mines. Such measures include soil inoculation with local cyanobacterial propagules (Acea, 2003, Wang et al. , 2009, Zhao et al. , 2016, et al. , 2017) and increased hydration (Morillas & Gallardo, 2015, Zhang et al. , 2018), which were effective in enhancing biocrust establishment and recovery following disturbances (Antoninka et al. , 2020). ”Table 1. Values should also include the standard deviation. Response: I added SD values to the table (L254 – L254). Citation: Report abuse × Please provide a reason why you see this comment as being abusive. You might include your name and email but you can also stay anonymous. Please provide a reason why you see this comment as being abusive. Please confirm reCaptcha. Comment* Name: Email: discussion Status: closed Comment types: AC – author | RC – referee | CC – community | EC – editor | CEC – chief editor | : Report abuse RC1: 'Comment on egusphere-2022-1510', #1, 03 Feb 2023 The manuscript “Only a minority of bacteria grow after wetting in both natural and post-mining biocrusts in a hyperarid, phosphate mine” presents the results of a H2-18-O stable isotope probing assay of the growing community members in hyperarid biocrusts that have been disturbed, or not, by mining activities. Overall, the manuscript is well conceived, written, and presented. The conclusions are sound and justified. I do have a concern that the authors have missed a swath of the literature that reports the response of biocrusts to physical disturbances, such as chronic physical trampling. These data show that physical disturbances differ from other disturbances and may affect the recovery of the biocrust community. I think some of this literature should be discussed in the context of what these authors see, and how it may be unique in these hyperarid sites. Similarly, transcriptomic studies that show the genes that are expressed during a wetting pulse and have documented metabolic a physiological changes in the bacterial community in a wetting pulse. [SEP] Justify:

Output: The text contrasts the claim by discussing biocrusts and active restoration measures that involve soil inoculation. The mention of soil inoculation implies that organisms, potentially including mosses, can grow in soil, thereby contradicting the claim that mosses cannot grow on soil.


Input: Task: pass the claim using the given text. Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: CrossrefWeb of Science45. Kahneman D, Tversky A. Introduction judgment under uncertainty: Heuristics and biases. In: eds. Judgment under Uncertainty: Heuristics and Biases. New York: Press; 1982. Crossref46. . Early adoption of BRCA1/2 testing: who and why. Genet Med. 2003;5(2):92–8. CrossrefPubMedWeb of Science47. Parental angst making and revisiting decisions about treatment of attention-deficit/hyperactivity disorder. Pediatrics. 2009;124(2):580–9. CrossrefPubMedWeb of Science48. . Barriers to physician adherence to nonsteroidal anti-inflammatory drug guidelines: a qualitative study. Ther. 2008;28(6):789–98. CrossrefPubMedWeb of Science49. -Degnan D, Normand S-LT, Soumerai SB. Impact of adverse events on prescribing warfarin in patients with atrial fibrillation: matched pair analysis. BMJ. 2006;332(7534):141–5. CrossrefPubMed50. Cioffi J. A study of the use of past experiences in clinical decision making in emergency situations. Nurs Stud. 2001;38(5):591–9. CrossrefPubMedWeb of Science51. . Can induced anxiety from a negative earlier experience influence vascular surgeons’ statistical decision-making? A randomized field experiment with an abdominal aortic aneurysm analog. J Surg. 2006;203(5):642–52. CrossrefPubMedWeb of Science52. -. Narratives that address affective forecasting errors reduce perceived barriers to colorectal cancer screening. Med. 2010;71(1):45–52. CrossrefPubMedWeb of Science53. . The cognitive structuring of patient delay in breast cancer. Med. 2006;63(12):3137–49. CrossrefPubMedWeb of Science54. . How underlying patient beliefs can affect physician-patient communication about prostate-specific antigen testing. Pract. 2002;5(3):120–9. PubMed55. -Tsao G. What do patients consider when making decisions about treatment for hepatitis C? Med. 2005;118(12):1387–91. CrossrefPubMedWeb of Science56. . [SEP] Justify:

Output: The text does not provide any direct information regarding the influence of cognitive biases on decision-making. It contains citations and references to various studies and topics but does not engage with the claim itself, rendering it irrelevant.


Input: Task: pass the claim using the given text. Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: Gene expression and small noncoding RNAs: microare a large family of short noncoding RNAs between 17 and 25 nucleotides (nt) in length [49]. MiRNAs were first identified in Caenorhabditis elegans over two decades ago [50] and since then many have been identified in multiple organisms, such as worms, flies, fish, frogs, mammals and plants, by molecular cloning and bioinformatics [51]. Most miRNA sequences are conserved among a wide range of mammalians [52], though there are some that differ from each other only by a single nucleotide [53]. The conserved miRNA sequences among different species can be distinguished by the nomenclature such that when only the first three letters differ this indicates the same sequence in different species, that is, hsa‐miR‐145 in Homo sapiens and mmu‐miR‐145 in Mus musculus [54]. MiRNAs have been shown to be of great importance in a wide variety of biological processes involving cell cycle regulation, apoptosis, cell differentiation, imprinting, homeostasis and development, including limb development [55], morphogenesis of lung epithelial [56], embryonic angiogenesis [57], formation of hair follicle and proliferation of T‐cell [58, 59]. They play key roles in regulating transcriptional and post‐transcriptional gene silencing in many organisms by targeting mRNAs for translational inhibition, cleavage, degradation or destabilisation [53, 60–64]. Each miRNA has multiple mRNA targets that may regulate up to 30% protein‐coding genes and shape protein production from hundreds to thousands of genes [65–67]. MiRNAs recognise their targets through base pairing of the complementary sequence of their seed sequence (2–8 nt of miRNAs) within the open reading frame (ORF) and 3′untranslated region (UTR) of target mRNA [68]. Although the targets of miRNAs are not fully known, bioinformatics studies show a range of possible target genes [69]. The functional activities and the predicted/observed targets of miRNAs can be identified using miRNA databases. These databases can be accessed using the following URL: ( and MiRNA biogenesisMiRNA biogenesis involves multiple important steps. [SEP] Justify:

Output: The text provides detailed information about microRNAs (miRNAs) and their role in gene expression regulation. However, it does not specifically address how gene expression can be modified by environmental factors, which is central to the claim about epigenetics. Therefore, while the text is related to gene expression, it does not corroborate or contrast with the claim effectively.


Input: Task: contrast the claim using the given text. Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: These studies show where resources may be going to rather than growth, and should probably be at least mentioned in this text. Minor concerns:Title: I am not sure the comma is needed between hyperarid and phosphateLine 210: picrust should be 2Line 214: I think this should be spelled out more completely. It just sends the reader to a reference. This is a specialized set of functional annotations. I think it would help the reader interpret Figure 6 and where the annotations are coming from. Citation: AC1: 'Reply on RC1', Talia Gabay, 20 Mar 2023 The manuscript “Only a minority of bacteria grow after wetting in both natural and post-mining biocrusts in a hyperarid, phosphate mine” presents the results of a H2-18-O stable isotope probing assay of the growing community members in hyperarid biocrusts that have been disturbed, or not, by mining activities. Overall, the manuscript is well conceived, written, and presented. The conclusions are sound and justified. I do have a concern that the authors have missed a swath of the literature that reports the response of biocrusts to physical disturbances, such as chronic physical trampling. These data show that physical disturbances differ from other disturbances and may affect the recovery of the biocrust community. I think some of this literature should be discussed in the context of what these authors see, and how it may be unique in these hyperarid sites. Response: I added literature regarding physical trampling and how they might compare to the mining disturbance in the hyper-arid (L358 – L370):…” Previous studies examining the effect of a physical disturbance (repeated trampling) on biocrust communities, revealed a decrease in the amount of extractable DNA, lower chlorophyll a, and a decrease in biomass and cyanobacteria abundance (Kuske et al. , 2012; Steven et al. , 2015; Chung et al. , 2019). However, these studies investigated a localized disturbance compared to mining disturbance, where the biocrust is completely removed over large spatial scales. Moreover, the previous studies were conducted in environments that were less extreme than the hyper-arid Zin Valley. [SEP] Justify:

Output: The text contrasts the claim by discussing biocrust communities, which include mosses and are found in hyper-arid environments. The mention of previous studies indicating that mosses and other organisms like cyanobacteria can exist in disturbed environments, such as biocrusts, directly contradicts the assertion that mosses can only grow on trees and not on rocks or soil. The exploration of biocrust communities and their response to disturbances demonstrates that mosses thrive in varied substrates beyond just trees.


Input: Task: pass the claim using the given text. Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: JAMA. 2010;304(11):1198–203. CrossrefPubMedWeb of Science68. . Stage of adoption of the human papillomavirus vaccine among college women. Prev Med. 2009;48(5):420–5. CrossrefPubMedWeb of Science69. Parental attitudes about influenza immunization and school-based immunization for school-aged children. Dis J. 2010;29(8):751–5. CrossrefPubMedWeb of Science70. . The simultaneous analysis of patient, physician and group practice influences on annual mammography performance. Med. 1996;43(3):315–24. CrossrefPubMedWeb of Science71. Influenza among healthy young children: changes in parental attitudes and predictors of immunization during the 2003 to 2004 influenza season. Pediatrics. 2006;117(2):e268–77. CrossrefPubMedWeb of Science72. Misperceptions about influenza vaccination among parents of healthy young children. (Phila). 2007;46(5):408–17. CrossrefPubMedWeb of Science73. . The importance of social norms for uptake of catch-up human papillomavirus vaccination in young women. Sex Health. 2011;8(3):330–7. CrossrefPubMedWeb of Science74. Duffett-. Cervical cancer screening practices among university women. J Neonatal Nurs. 2008;37(5):572–81. CrossrefPubMedWeb of Science75. Seasonal and 2009 H1N1 influenza vaccine uptake, predictors of vaccination, and self-reported barriers to vaccination among secondary school teachers and staff. Hum Vaccin. 2011;7(1):89–95. CrossrefPubMed76. Zikmund-. “I’ll do what they did”: social norm information and cancer treatment decisions. Couns. 2011;85(2):225–9. CrossrefPubMedWeb of Science77. Croskerry P. Achieving quality in clinical decision making: cognitive strategies and detection of bias. Med. 2002;9(11):1184–204. CrossrefPubMedWeb of Science78. Fagerlin A, Zikmund-. Cure me even if it kills me: p9. CrossrefPubMedWeb of Science79. . What makes a tumor diagnosis a call to action? [SEP] Justify:

Output: The text does not provide any information that directly supports or refutes the claim regarding cognitive biases and their influence on decision-making. Instead, it appears to list various studies and resources related to health, vaccination, and medical decision-making without discussing cognitive biases specifically. As such, it is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: Furthermore, HPAT5 was shown to interact with let‐7 family of miRNAs [110]. Implantation of embryos involves complex mechanisms and many different genetic and physiological factors are involved during the process. Developing preimplantation embryo must have a good coordinated interaction with the maternal uterine endometrium. LncRNAs were shown to be differentially expressed in endometrial tissues obtained from pigs with pregnancy and non‐pregnancy with two lnc_01729386 and TCONS_01325501, with potential roles in implantation [111]. Advertisement 5. Gene expression and assisted reproductive technologiesworld, approximately 1% of children are born with assisted reproductive technology (ART) treatments. The infertile couples have the best possibility to conceive a child with these treatments. Although these techniques have been considered to be safe in terms of foetal and post‐natal development [112, 113], there is an increased risk for morbidities, especially imprinting disorders [114]. Furthermore, the global gene expression profiles vary due to in vitro culture of zygotes [115, 116] and in vitro fertilisation processes [117]. Following in vitro culture, apoptotic and morphogenetic pathways have shown to be altered [118]. Intra‐cytoplasmic sperm injection (ICSI), one of the widely used ART techniques, provides infertile couples with sperm motility problems a great chance to have a baby. ICSI is a unique process in which the sperm is injected into the ooplasm [119]. However, ICSI bypasses a number of physiological processes that would normally take place. These embryos derived from ICSI were shown to be cleaved at a slower rate. Furthermore, a reduced number of embryos become hatched with a fewer number of cells and the calcium oscillations are shorter with different patterns [120]. Mice embryos generated by ICSI were shown to be obese and have anomalies of the organs [121]. Advertisement 6. ConclusionNormal development of preimplantation embryos involves complex mechanisms. For a normal developing embryo, the expression of both maternal and paternal genes is required. Several factors are involved in the regulation of parental genes in preimplantation embryos. Epigenetic modifications are one of the most important factors that are involved in the regulation of gene expression during preimplantation embryos. Extensive research studies have been performed throughout the years to establish the methylation profiles of the mammalian gametes and embryos. [SEP] Justify:

Output: The text corroborates the claim by stating that 'epigenetic modifications are one of the most important factors that are involved in the regulation of gene expression during preimplantation embryos.' This indicates that epigenetics plays a key role in modifying gene expression, which aligns with the claim regarding the influence of environmental factors.


Input: Task: contrast the claim using the given text. Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: Therefore, we expected the damage to the biocrust in Zin post-mining sites to follow similar patterns but to be more conspicuous than the previously reported disturbed biocrusts (Kuske et al. , 2012; Steven et al. , 2015; Chung et al. , 2019). Our previous report (Gabay et al. , 2022) supported this notion; we demonstrated differences in bacterial communities in natural and post-mining biocrusts, expecting these differences to be reflected in the proliferating communities of these biocrusts. "Similarly, transcriptomic studies that show the genes that are expressed during a wetting pulse and have documented metabolic a physiological changes in the bacterial community in a wetting pulse. These studies show where resources may be going to rather than growth, and should probably be at least mentioned in this text. Response: I added previous studies that showed expression of nitrogen cycling genes and metabolite production following wetting (L417 – L425):…” One study examining microbial nitrogen transformations in biocrusts collected from biome in Namibia and showed that following wetting, nitrogen cycling genes are expressed in biocrust organisms (Maier et al. , 2022). another study examining biocrust samples taken from the in Utah demonstrated a pulse of metabolite release following controlled wetting (Swenson et al. , 2018). Based on these reports (Maier et al. , 2022; Swenson et al. , 2018) and due to the extreme conditions in (Levi et al. , 2021), we suggest that hyperarid biocrust communities prioritize functions such as metabolite production, nutrient cycling and preparation for desiccation over growth. ”Minor concerns:Title: I am not sure the comma is needed between hyperarid and phosphateResponse: I removed the commaLine 210: picrust should be 2Response: corrected (L208). Line 214: I think this should be spelled out more completely. It just sends the reader to a reference. This is a specialized set of functional annotations. I think it would help the reader interpret Figure 6 and where the annotations are coming from. Response: I added a description of the referenced study and explained the source of the functional annotations (L213 – L218):“…The function categories were chosen based on Meier et al. (2021). In their study, Meier et al. [SEP] Justify:

Output: The text provides information about biocrusts, including those that exist in extreme environments, and discusses their microbial communities and functions. This is relevant to the claim as it implies that these communities—including possibly mosses—can thrive in conditions outside of trees, which contradicts the idea that mosses can only grow on trees and not on rocks or soil.


Input: Task: pass the claim using the given text. Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: CrossrefPubMedWeb of Science91. . The influence of default options on the expression of end-of-life treatment p10. CrossrefPubMedWeb of Science92. . The veil of experience: do consumers prefer what they know best? Health Econ. 2000;9(3):267–70. CrossrefPubMedWeb of Science93. Baron J, Ritov I. Reference points and omission bias. Process. 1994;59(3):475–98. CrossrefWeb of Science94. . Violence risk assessment and risk communication: the effects of using actual cases, providing instruction, and employing probability versus frequency formats. Behav. 2000;24(3):271–96. CrossrefPubMedWeb of Science95. Timmermans DRM, Ockhuysen-Vermey CF, Henneman L. Presenting health risk information in different formats: the effect on participants’ cognitive and emotional evaluation and decisions. Couns. 2008;73(3):443–7. CrossrefPubMedWeb of Science96. Tversky A, Griffin D. Endowments and contrast in judgments of well-being. In: Kahneman D, Tversky A, eds. Choices, Values, and Frames. New York: 2000. p 709–25. Crossref97. . “I know just how you feel”: the validity of healthy women’s perceptions of breast-cancer patients receiving treatment. J Psychol. 2002;32(1):110–23. CrossrefWeb of Science98. . It must be awful for them: perspective and task context affects ratings for health conditions. Mak. 2006;1(2):146–52. Web of Science99. . Ignorance of hedonic adaptation to hemodialysis: a study using ecological momentary assessment. J Exp Psychol. 2005;134(1):3–9. Crossref100. Attitudes to chemotherapy: comparing views of patients with cancer with those of doctors, nurses, and general public. BMJ. 1990;300(6737):1458–60. CrossrefPubMed101. Slot KB, Berge E. Thrombolytic treatment for stroke: patient p22. CrossrefPubMedWeb of Science102. . [SEP] Justify:

Output: The text does not directly address the claim about cognitive biases influencing decision-making. Instead, it lists various references and studies without providing specific insights or conclusions related to cognitive biases or decision-making processes.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: In the more recent years, the importance of noncoding RNAs in the regulation of genes has become clear. A handful of studies have been performed to analyse the expression of microRNAs, which have been shown to regulate mRNAs that encode up to 30% human protein‐coding genes. The expression of miRNAs has been observed in mouse, bovine and human gametes and embryos. Furthermore, in the last couple of years, expression of long noncoding RNAs and their roles in embryonic development and implantation have been investigated. The extensive research studies have provided crucial understanding of the development of preimplantation embryos and the regulation of gene expression, and with the advancing technologies more molecular studies will help to comprehend the mechanisms better. 1. Jaroudi, S. and SenGupta, S. , DNA repair in mammalian embryos. Mutat Res, 2007. 635(1): 77. 2. William, L. , Human Embryology. New York. Vol. 2nd edition. 1997. 3. Schultz, R. M. , The molecular foundations of the maternal to zygotic transition in the preimplantation embryo. Update, 2002. 8(4): 31. 4. Moore, K. , Persaud, T. V. N. , Human. 6th ed. Philadelphia:Saunders Company;1998. 5. Telford, N. A. , Watson, A. J. , and Schultz, G. A. , Transition from maternal to embryonic control in early mammalian development: a comparison of several species. Dev, 1990. 26(1): 100. 6. Bell, C. E. , Calder, M. D. , and Watson, A. J. , Genomic RNA profiling and the programme controlling preimplantation mammalian development. Reprod, 2008. 14(12): 701. 7. McClay, D. W. and Clarke, H. J. , Remodelling the paternal chromatin at fertilisation in mammals. Reproduction, 2003. 125(5): 33. 8. Tamaru, H. and Selker, E. U. , A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature, 2001. 414(6861): 83. 9. Jackson, J. P. , et al. , Control of methylation by the histone H3 methyltransferase. [SEP] Justify:

Output: The text corroborates the claim by discussing the regulation of gene expression through noncoding RNAs and their roles in embryonic development and implantation, indicating that the expression of these RNAs can be influenced by various factors, which aligns with the concept of epigenetics modifying gene expression.


Input: Task: contrast the claim using the given text. Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: collected biocrusts from the Negev and analyzed bacterial metagenomes in the biocrusts to evaluate the distribution of metabolic potential among bacterial populations. To compare functional potential between various bacterial phyla, they selected metabolic genes encoded in the metagenomic-assembled genomes and grouped them into 10 function categories. ” Citation: RC2: 'Comment on egusphere-2022-1510', #2, 04 Mar 2023 This study is interesting as it identifies which bacteria proliferate in biocrusts from natural and postmining areas and examines functional gene abundances unlike previous studies that have focused on characterizing the microbial community composition of natural and post-mining biocrusts. This, I consider the approach novel. Nonetheless, I have a few comments that should be addressed:AbstractL19-23. I recommend deleting this sentence because it refers to a previous study, and the abstract should focus on the objectives and results of the present study. Then, in the Introduction or the Discussion, it is fine if mention to previous results is done. M&ML103-105. It is not clear the predominant p109. Add a short description of the biocrust sampled (thickness, cover, composition, …. ). Were there differences in the biocrust from natural and post-mining sites? ResultsRegarding the results of the proliferated bacterial community composition, it would be nice to include a figure with the relative abundances of the different bacteria phylum for natural and post-mining biocrusts to make the results clearer. DiscussionL354-357. Can you remind here when was the sampled post-mining site restored? Was it at 2007? I wonder if one reason for the lack of photosynthetic potential difference between post-mining and natural biocrusts is because the biocrust in the post-mining site has been already recovered. For example, soil colonizacion by cyanobacteria can be faster than thought. L369-370. There is little discussion on the results of the Picrust analysis. It would be nice to compare the results of this study with other studies that have also examined functional genes in biocrusts to see if abundances of the functional genes at this site greatly differ from those of biocrusts of other regions. L379-381. [SEP] Justify:

Output: The text contrasts the claim as it discusses biocrusts, bacterial metagenomes, and microbial communities in natural and post-mining areas, indicating that mosses and other organisms can thrive in environments besides trees, such as biocrusts found in soil and on rocks, thus suggesting that mosses may not be restricted to growing only on trees.


Input: Task: pass the claim using the given text. Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: Health Psychol. 2012;31(1):114–21. CrossrefPubMedWeb of Science149. . The impact of counseling with a practical statistical model on patients’ decision-making about treatment for epilepsy: findings from a pilot study. Epilepsy Res. 1993;16(3):207–14. CrossrefPubMedWeb of Science150. . Framing effects in younger and older adults. . 2005;60(4):P215–8. CrossrefPubMedWeb of Science151. Monitoring styles in women at risk for cervical cancer: implications for the framing of health-relevant messages. Med. 1999;21(1):27–34. CrossrefPubMedWeb of Science152. . Acceptability of the H1N1 vaccine among older adults: the interplay of message framing and perceived vaccine safety and efficacy. Health Commun. 2012;27(6):559–68. CrossrefPubMedWeb of Science153. O’Connor AM. Effects of framing and level of probability on patients’ p26. CrossrefPubMedWeb of Science154. Park S-Y. The effects of message framing and risk perceptions for HPV vaccine campaigns: focus on the role of regulatory fit. Q. 2012;29(4):283–302. CrossrefPubMed155. . Message framing and pap test utilization among women attending a community health clinic. J Health Psychol. 2005;10(1):65–77. CrossrefPubMedWeb of Science156. . Persuading physicians to test their patients’ level of kidney functioning: the effects of message frame and point of view. Health Commun. 2010;25(2):107–18. CrossrefPubMedWeb of Science157. The effects of message framing and ethnic targeting on mammography use among low-income women. Health Psychol. 2001;20(4):256–66. CrossrefPubMedWeb of Science158. . Need for cognition and choice framing effects. J Mak. 1996;9(4):283–90. CrossrefWeb of Science159. Van ‘t,. Self-efficacy moderates message-framing effects: the case of skin-cancer detection. Psychol Health. 2010;25(3):339–49. CrossrefPubMedWeb of Science160. Van ‘t. Preaching to the choir? [SEP] Justify:

Output: The text provided contains multiple references to studies and research articles related to health communication and decision-making but does not explicitly discuss cognitive biases or their influence on decision-making. Therefore, the text is irrelevant to the claim regarding cognitive biases.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: Nature, 2002. 416(6880): 60. 10. Fuks, F. , et al. , The methyl‐CpG‐binding protein MeCP2 links DNA methylation to histone methylation. J Biol Chem, 2003. 278(6): 40. 11. Morgan, H. D. , et al. , Epigenetic reprogramming in mammals. Genet, 2005. 14 1: pp. R47–58. 12. Zhu, B. , et al. , 5‐Methylcytosine DNA glycosylase activity is also present in the human MBD4 (G/T mismatch glycosylase) and in a related avian sequence. Res, 2000. 28(21): 65. 13. Hardeland, U. , et al. , The versatile thymine DNA‐glycosylase: a comparative characterization of the human, Drosophila and fission yeast orthologs. Res, 2003. 31(9): 71. 14. Dean, W. , Lucifero, D. , and Santos, F. , DNA methylation in mammalian development and disease. 2005. 75(2): 111. 15. Oswald, J. , et al. , Active demethylation of the paternal genome in the mouse zygote. Curr Biol, 2000. 10(8): 8. 16. Mayer, W. , et al. , Demethylation of the zygoticpaternal genome. Nature, 2000. 403. 2. 17. Beaujean, N. , et al. , Non‐conservation of mammalian preimplantation methylation dynamics. Curr Biol, 2004. 14(7): pp. R266–7. 18. Reik, W. , Dean, W. , and Walter, J. , Epigenetic reprogramming in mammalian development. Science, 2001. 293(1089): 93. 19. Rougier, N. , et al. , Chromosome methylation patterns during mammalian preimplantation development. Genes Dev, 1998. 12(14): 13. 20. Dean, W. , et al. , Conservation of methylation reprogramming in mammalian development: aberrant reprogramming in cloned embryos. 2001. 98(24): 8. 21. Santos, F. and Dean, W. [SEP] Justify:

Output: The text corroborates the claim by providing references to research that discusses DNA methylation and epigenetic reprogramming, which are central concepts in the study of how environmental factors can influence gene expression. For instance, several studies are mentioned, such as those on DNA methylation dynamics during development and demethylation processes in zygotes, all of which imply that epigenetics encompasses how gene expression is altered by external factors.


Input: Task: contrast the claim using the given text. Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: It is hypothesised that the low bacterial growth in harsh environments like this one could be because biocrusts prioritize activation and preparation for desiccation over growth. However, this hypothesis cannot be fully demonstrated with the reported results. Could you add 401. Is there any practical experience of the application of cyanobacteria inoculation to restore this mining site in Israel? If so, it would be nice to add a few sentences regarding the potential of this technique to restore biocrust in the current mining site. Table 1. Values should include also the standard deviation. Citation: AC2: 'Reply on RC2', Talia Gabay, 20 Mar 2023 This study is interesting as it identifies which bacteria proliferate in biocrusts from natural and postmining areas and examines functional gene abundances, unlike previous studies that have focused on characterizing the microbial community composition of natural and post-mining biocrusts. This, I consider the approach novel. Nonetheless, I have a few comments that should be addressed: AbstractL19-23. I recommend deleting this sentence because it refers to a previous study, and the abstract should focus on the objectives and results of the present study. Then, in the Introduction or the Discussion, it is fine if mention to previous results is done. Response: I removed the section from the abstract. M&ML103-105. It is not clear the predominant p109. Add a short description of the biocrust sampled (thickness, cover, composition, …. ). Were there differences in the biocrust from natural and post-mining sites? Response: I added a description of the biocrusts in Gov mining site (L106 – L109):“…Biocrusts were sampled either from the post-mining site or the adjacent natural area. The biocrusts in Gov are thin (between 1. 5 - 2. 5 mm deep), and smooth. The site is characterized by areas covered in biocrusts or desert pavement. In each sampling site, we sampled along a 100 m strip at approximately 10 m intervals (Fig. 1). ”ResultsRegarding the results of the proliferated bacterial community composition, it would be nice to include a figure with the relative abundances of the different bacteria phylum for natural and post-mining biocrusts to make the results clearer. [SEP] Justify:

Output: The text contrasts the claim by discussing biocrusts, which are thin layers of biological material typically found on the soil or rocks. It implies that biological communities, including cyanobacteria, can proliferate in harsh environments like post-mining sites, suggesting that these organisms, which may include mosses, do grow on surfaces other than trees. The discussion of biocrusts and their characteristics indicates that mosses are not limited to trees, thus refuting the claim.


Input: Task: pass the claim using the given text. Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: The influence of personal relevance on the effects of gain- and loss-framed health-promoting messages. J Health Psychol. 2011;17(5):712–23. CrossrefPubMedWeb of Science161. . Decisional strategy determines whether frame influences treatment p94. CrossrefPubMedWeb of Science162. . Gain versus loss framing in adherence-promoting communication targeting patients with chronic diseases: the moderating effect of individual time perspective. Health Commun. 2012;27(1):75–85. CrossrefPubMedWeb of Science163. . Breast screening in response to gain, loss, and empowerment framed messages among diverse, low-income women. J Poor Underserved. 2007;18(3):550–66. CrossrefPubMedWeb of Science164. Fahy A, Desmond DM. Irish mothers’ intentions to have daughters receive the HPV vaccine. Med Sci. 2010;179(3):427–30. CrossrefPubMedWeb of Science165. Han K-H, Jo S. Does culture matter? A cross-national investigation of women’s responses to cancer prevention campaigns. Women Int. 2012;33(1):75–94. CrossrefPubMedWeb of Science166. Lauver D, Rubin M. Message framing, dispositional optimism, and follow-up for abnormal Papanicolaou tests. Health. 1990;13(3):199–207. CrossrefPubMedWeb of Science167. Llewellyn-. Cancer patients’ decision making and trial-entry p12. CrossrefPubMedWeb of Science168. . The effects of framing and action instructions on whether older adults obtain flu shots. Health Psychol. 2002;21(6):624–8. CrossrefPubMedWeb of Science169. O’. Framing effects on expectations, decisions, and side effects experienced: the case of influenza immunization. J Clin Epidemiol. 1996;49(11):1271–6. CrossrefPubMedWeb of Science170. . A randomized evaluation of loss and gain frames in an invitation to screening for type 2 diabetes: effects on attendance, anxiety and self-rated health. J Health Psychol. 2010;15(2):196–204. CrossrefPubMedWeb of Science171. . [SEP] Justify:

Output: The text does not address cognitive biases or their influence on decision-making directly. Instead, it mentions various studies regarding message framing in health communications, which may relate to decision-making but does not explicitly support or contradict the claim about cognitive biases.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: , Epigenetic reprogramming during early development in mammals. Reproduction, 2004. 127(6): 51. 22. Santos, F. , et al. , Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev Biol, 2002. 241(1): 82. 23. Monk, M. , Boubelik, M. , and Lehnert, S. , Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development, 1987. 99(3): 82. 24. Howlett, S. K. and Reik, W. , Methylation levels of maternal and paternal genomes during preimplantation development. Development, 1991. 113(1): 27. 25. De Vries, W. N. , et al. , Maternal beta‐catenin and E‐cadherin in mouse development. Development, 2004. 131(18): 45. 26. VB, A. , Cell polarity regulator PARD6B is essential for trophectoderm formation in the preimplantation mouse embryo. Biol Reprod, 2010. 83(3): 58. 27. Ducibella, T. , et al. , Changes in cell surface and cortical cytoplasmic organization during early embryogenesis in the preimplantation mouse embryo. J Cell Biol. , 1977. 74(1): 67. 28. Kelly, S. J. , Studies of the developmental potential of 4‐ and 8‐cell stage mouse blastomeres. J Exp Zool. 1977. 200(3): 76. 29. Chambers, I. , et al. , Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell, 2003. 113(5): 55. 30. Strumpf, D. , et al. , Cdx2 is required for correct cell fate specification and differentiation of trophectoderm in the mouse blastocyst. Development, 2005. 132(9): 102. 31. Nichols, J. , et al. , Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell, 1998. 95(3): 91. 32. Dietrich, J. E. and Hiiragi, T. [SEP] Justify:

Output: The text provides various studies focusing on developmental processes in mammals which implicitly support the claim regarding epigenetics. While it does not explicitly mention environmental factors, the mention of DNA methylation and changes in cell organization during early development suggests examination of gene expression modifications via varying biological conditions. Therefore, it can be interpreted as corroborating the claim of epigenetics.


Input: Task: contrast the claim using the given text. Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: Response: Added a bar plot of Phyla relative abundances to the PCoA ordination in figure 5 (labeled ‘a’ and ‘b’) and statistical data in the supplementary file (Table S4). DiscussionL354-357. Can you remind here when was the sampled post-mining site restored? Was it at 2007? I wonder if one reason for the lack of photosynthetic potential difference between post-mining and natural biocrusts is because the biocrust in the post-mining site has been already recovered. For example, soil colonization by cyanobacteria can be faster than thought. Response: I mentioned the restoration year in L375. I agree that it is likely that the biocrusts we sampled have a significant cyanobacterial community, however we hypothesize that the recovery of the biocrust differs even within the mining site, emphasizing the importance of microenvironments, where certain areas have more developed biocrusts and others have less developed biocrust even within the same post-mining plot. I referenced this in the discussion (L376 – L383): “…However, in the current study, we sampled post-mining biocrusts at a different location in the Gov mining site (~500 m away from the original plot) due to technical constraints. In the new location we found that the photosynthetic potential of the biocrust in the post-mining plots did not differ from the natural biocrust. These results highlight the importance of microenvironments in shaping the functionality of biocrusts (Garcia-Pichel and Belnap, 1996). The similarities in active communities and photosynthetic potential could be due to more developed biocrusts in the new sampling locations compared to the previous ones. ”L369-370. There is little discussion on the results of the Picrust analysis. It would be nice to compare the results of this study with other studies that have also examined functional genes in biocrusts to see if abundances of the functional genes at this site greatly differ from those of biocrusts of other regions. Response: I added a paragraph addressing the analysis with reference and comparison to a previous study that used to infer functional potential (L395 – L405):“…analysis revealed no significant differences in the abundances of genes within any of the function categories examined (Fig. 6). [SEP] Justify:

Output: The text contrasts the claim by discussing the recovery of biocrusts in post-mining sites, highlighting the presence of cyanobacterial communities and the functionality of biocrusts in varied microenvironments. The mention of biocrusts and their ecological importance implies that these communities, which can include mosses, can develop in soil and possibly on rocks, challenging the assertion that mosses exclusively grow on trees.


Input: Task: pass the claim using the given text. Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: Age differences in treatment decision making for breast cancer in a sample of healthy women: the effects of body image and risk framing. Forum. 2005;32(4):799–806. CrossrefPubMedWeb of Science172. . What do I have to lose? Effects of a psycho-educational intervention on cancer patient preference for resuscitation. J Behav Med. 2007;30(6):533–44. CrossrefPubMedWeb of Science173. . Effects of outcome framing on treatment decisions in the real world: impact of framing on adjuvant breast cancer decisions. Making. 1989;9(4):262–71. CrossrefPubMedWeb of Science174. Van den. Elective single-embryo transfer: persuasive communication strategies can affect choice in a young British population. Online. 2011;23(7):838–50. CrossrefPubMedWeb of Science175. Welkenhuysen M, Evers-Kiebooms G, d’Ydewalle G. The language of uncertainty in genetic risk communication: framing and verbal versus numerical information. Couns. 2001;43(2):179–87. CrossrefPubMedWeb of Science176. Witting M, Boere-. Predicting participation in ultrasound hip screening from message framing. Health Commun. 2012;27(2):186–93. CrossrefPubMedWeb of Science177. . Framing of outcome and probability of recurrence: breast cancer patients’ choice of adjuvant chemotherapy (ACT) in hypothetical patient scenarios. Res Treat. 2000;60(1):9–14. CrossrefPubMedWeb of Science178. . Omission and commission in judgment and choice. J Psychol. 1991;27(1):76–105. CrossrefWeb of Science179. . Omission bias and decision making in pulmonary and critical care medicine. Chest. 2005;128(3):1497–505. CrossrefPubMedWeb of Science180. Omission bias and pertussis vaccination. Making. 1994;14(2):118–23. CrossrefPubMedWeb of Science181. Omission bias and vaccine rejection by parents of healthy children: implications for the influenza A/H1N1 vaccination programme. Vaccine. 2010;28(25):4181–5. CrossrefPubMedWeb of Science182. . How do physicians weigh iatrogenic complications? [SEP] Justify:

Output: The text provided does not directly address the claim regarding cognitive biases influencing decision-making. Instead, it presents a series of studies and references related to treatment decision-making in breast cancer and risk communication, without explicitly discussing cognitive biases. Therefore, the text is deemed irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: , Stochastic patterning in the mouse pre‐implantation embryo. Development, 2007. 134(23): 31. 33. Home, P. , et al. , Altered subcellular localization of transcription factor TEAD4 regulates first mammalian cell lineage commitment. . , 2012. 109(19): 7. 34. Paul, S. and Knott, J. G. , Epigenetic control of cell fate in mouse blastocysts: the role of covalent histone modifications and chromatin remodeling. Dev. , 2014. 81(2): 82. 35. Lin, S. C. , et al. , Klf5 regulates lineage formation in the pre‐implantation mouse embryo. Development, 2010 137(23): 63. 36. Davis, T. L. , et al. , The H19 methylation imprint is erased and re‐established differentially on the parental alleles during male germ cell development. Genet, 2000. 9(19): 94. 37. Watanabe, D. , et al. , Stage‐ and cell‐specific expression of Dnmt3a and Dnmt3b during embryogenesis. Mech Dev, 2002. 118(1–2): 90. 38. Torres‐Padilla, M. E. , et al. , Histone arginine methylation regulates pluripotency in the early mouse embryo. Nature, 2007. 445(7124): 8. 39. Disteche, C. M. , Dosage compensation of the sex chromosomes and autosomes. Dev Biol, 2016. 56: 18. 40. Namekawa, S. H. , et al. , Two‐step imprinted X inactivation: repeat versus genic silencing in the mouse. Biol, 2010. 30(13): 205. 41. Petropoulos, S. , et al. , Single‐cell RNA‐Seq reveals lineage and X chromosome dynamics in human preimplantation embryos. Cell, 167(1): p. 285. 42. McHugh, C. A. , et al. , lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature, 2015. 521: 236. 43. Vallot, C. , et al. , XACT noncoding RNA competes with XIST in the control of X chromosome activity during human early development. Cell. [SEP] Justify:

Output: The text provides various references that focus on epigenetic mechanisms such as 'covalent histone modifications' and 'chromatin remodeling' which are integral in understanding how environmental factors can affect gene expression. The mention of studies on 'pluripotency' and differential methylation during development aligns with the claim that epigenetics examines modifications in gene expression influenced by environmental conditions.


Input: Task: contrast the claim using the given text. Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: In contrast, a previous study conducted in the Highlands, examined active bacterial communities during a rain and subsequent drying (Baubin et al. , 2021). The results indicated an increase in genes related to photosynthesis, light, and sensing following the rain, while the other function categories did not vary significantly. We note that the identity and abundances of the functional genes in the dry biocrusts detected by Baubin et al. , (2021) and here (Fig. 6) are similar. Therefore, we propose that the similarity between the post-mining and natural biocrust communities (Fig. 5) reflect similar functional potential (Fig. 6). However, low abundance of active ASVs were used to infer the abundances of functional genes (Fig. 6), and large variance between samples in post-mining biocrusts could mask significant differences (Table S5). ”L379-381. It is hypothesized that the low bacterial growth in harsh environments like this one could be because biocrusts prioritize activation and preparation for desiccation over growth. However, this hypothesis cannot be fully demonstrated with the reported results. Could you add 401. Is there any practical experience of the application of cyanobacteria inoculation to restore this mining site in Israel? If so, it would be nice to add a few sentences regarding the potential of this technique to restore biocrust in the current mining site. Response: No, there have not been any active restoration measures in Zin mining sites and no previous scientific studies regarding the mining practices of ICL mining company. I address the need for active restoration measures in Zin mining sites (including cyanobacteria inoculation) in L439 – L444:“…Our results further emphasize the need for active restoration measures in the Zin mines. Such measures include soil inoculation with local cyanobacterial propagules (Acea, 2003, Wang et al. , 2009, Zhao et al. , 2016, et al. , 2017) and increased hydration (Morillas & Gallardo, 2015, Zhang et al. , 2018), which were effective in enhancing biocrust establishment and recovery following disturbances (Antoninka et al. , 2020). ”Table 1. Values should also include the standard deviation. Response: I added SD values to the table (L254 – L254). [SEP] Justify:

Output: The text contrasts the claim by discussing biocrusts and bacterial communities without mentioning mosses specifically. The focus on cyanobacteria inoculation and biocrust restoration implies that there are other environments, such as soil, where beneficial organisms can exist, thereby indirectly disputing the absolute nature of the claim that mosses are restricted to trees.


Input: Task: pass the claim using the given text. Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: p 473–88. Crossref194. Berndsen M, van der Pligt J. Time is on my side: optimism in intertemporal choice. (Amst). 2001;108(2):173–86. CrossrefPubMedWeb of Science195. . Extent and determinants of error in doctors’ prognoses in terminally ill patients: prospective cohort study. BMJ. 2000;320(7233):469–72. CrossrefPubMed196. The distinct role of comparative risk perceptions in a breast cancer prevention program. Med. 2011;42(2):262–8. CrossrefPubMedWeb of Science197. -P. Prognosis or “curabo effect? ” Physician prediction and patient outcome of surgery for low back pain and sciatica. Spine. 2005;30(12):1448–53. CrossrefPubMedWeb of Science198. . Discrepancies between patient and physician estimates for the success of stem cell transplantation. JAMA. 2001;285(8):1034–8. CrossrefPubMedWeb of Science199. . Ego bias, reverse ego bias, and physicians’ prognostic. Med. 1991;19(12):1533–9. CrossrefPubMedWeb of Science200. Loewenstein G, Prelec D. P2000. p 565–96. Crossref201. . Order of information: impact on perceived level of functional independence. Health Care. 2005;18(4):1–12. CrossrefPubMed202. . Clinical reasoning about new symptoms despite preexisting disease: sources of error and order effects. Fam Med. 1995;27(5):314–20. PubMed203. . Clinical diagnosis and the order of information. Making. 1998;18(4):412–7. CrossrefPubMedWeb of Science204. . Order of information affects clinical judgment. J Mak. 1996;9(3):201–11. CrossrefWeb of Science205. . Primacy effects in clinical judgments of contingency. Making. 1988;8(3):216–22. CrossrefPubMedWeb of Science206. . How the manner of presentation of data influences older patients in determining their treatment p8. CrossrefPubMedWeb of Science207. ’N, Unwin A. [SEP] Justify:

Output: The text provided lists various studies and references related to medical prognoses and clinical judgment but does not specifically discuss cognitive biases or their influence on decision-making. Therefore, it is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: Javascript is disabled in your browser. Please enable Javascript to view PeerJ. Related research -of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors View 10. 7717/peerj. 10 Published 2013-02-12 Accepted 2012-12-31 Received 2012-11-13 regulatory networks, Statistical network inference, Gene expression data, Experimental design, Interventional data Copyright © 2013 Emmert-This is an open access 2013. Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors. PeerJ 1:e10 inference of gene regulatory networks gained within recent years a considerable interest in the biology and biomedical community. The purpose of this paper is to investigate the influence that environmental conditions can exhibit on the inference performance of network inference algorithms. Specifically, we study five network inference methods, Aracne, BC33NET and MRNET, and compare the results for three different conditions: (I) observational gene expression data: normal environmental condition, (II) interventional gene expression data: growth in rich media, (III) interventional gene expression data: normal environmental condition interrupted by a positive spike-in stimulation. Overall, we find that different statistical inference methods lead to comparable, but condition-specific results. Further, our results suggest that non-steady-state data enhance the inferability of regulatory networks. than ten years after the completion of the Project (Consortium, 2004; Lander et al. , 2001; Venter et al. , 2001) it is nowadays generally acknowledged that in order to obtain a functional understanding of organisms and the emergence of their phenotypes it is not sufficient to study sequence data alone. Instead, within recent years there are increasing attempts to infer genome-scale molecular interactions from high-throughput data to tackle this problem. Depending on the applied technology, this resulted in the construction of protein–protein interaction networks, metabolic networks or transcription regulatory networks (Blais & Dynlacht, 2005; Förster et al. , 2003; Lee et al. , 2002; Ma et al. , 2004; Palsson, 2006; Yu et al. , 2008). These networks can be considered as phenomenological networks because each interaction within these networks is based on the measurement of the corresponding biochemical binding between genes or gene products. [SEP] Justify:

Output: The text corroborates the claim by discussing research on the influence of environmental factors on gene expression and the inference of gene regulatory networks. It highlights that different experimental conditions affect the inferability of regulatory networks, which aligns with the study of epigenetics and how gene expression can be modified by environmental influences.


Input: Task: pass the claim using the given text. Claim: Sign languages have their own unique grammatical structures, different from the spoken languages in the same region. [SEP] Text: 3 Syllable and Mora SJ has a cross-linguistically common canonical syllable structure (C)(G)V(C) where V may be a long vowel or a diphthong, as inka/ ‘mosquito’,kya. ku/ ‘guest’,kai. ko/ ‘silkworm’, etc. The same canonical syllable structure is observed across most Mainland dialects, although some dialects show conspicuous divergence from this, as in Shiiba (Shimoji and Hirosawa, this volume) where there is a double glide sequencewy/, which is phonetically realized as a non-syllabic (i. e. glide) version of the rounded front vowel [ʏ], as inwyaata/ [ʏaːta] ‘boiled’ orhwyaa/ [ʏ̥aː] ‘fly’. Ryukyuan languages often have a more complex syllable structure with an onset cluster CC and/or with a special pre-onset slot which is filled only by a laryngeal ˀ. In Miyako, for example, there is a wide range of consonants which may form an onset geminate CC with the first C being a moraic onset, as inffa/ [fːa] ‘child’,ssan/ [sːaŋ] ‘not know’,vva/ [ʋːa] ‘2sg’,mma/ [mːa] ‘mother’, etc. (see Wang, this volume). It is a controversial issue whether onset geminates can be moraic (cf. Hayes 1989), but the Ryukyuan data suggests that they may be moraic in some languages (and other languages such as Trukese, Topinzi 2008). Miyako further has a rich array of syllabic consonants, and some of them may even carry an onset, as inpztu/ [ps̩tu] ‘person’ (CC̩. CV), etc. The mora plays a central role in most Japonic languages in such a way that the length contrast between long and short vowels and between singleton and geminate consonants is phonemic. [SEP] Justify:

Output: The text discusses the syllable structures and phonemic contrasts in various Japonic languages, but does not address sign languages or their grammatical structures. Thus, it is irrelevant to the claim about sign languages having unique grammatical systems.


Input: Task: pass the claim using the given text. Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: The impact of information order on intentions to undergo predictive genetic testing: an experimental study. J Health Psychol. 2010;15(7):1082–92. CrossrefPubMedWeb of Science208. . Presenting risks and benefits to patients. J Med. 2002;17(8):612–7. CrossrefPubMedWeb of Science209. Einhorn HJ. Learning from experience and suboptimal rules in decision making. In: eds. Judgment under Uncertainty: Heuristics and Biases. New York: Press; 1982. p 268–86. Crossref210. . Risk as feelings in the effect of patient outcomes on physicians’ future treatment decisions: a randomized trial and manipulation validation. Med. 2012;75(2):367–76. CrossrefPubMedWeb of Science211. Mazzocco K, Cherubini P. The effect of outcome information on health professionals’ spontaneous learning. Med Educ. 2010;44(10):962–8. CrossrefPubMedWeb of Science212. . What influences participants’ treatment preference and can it influence outcome? Results from a primary care-based randomised trial for shoulder pain. Gen Pract. 2004;54(499):93–6. PubMedWeb of Science213. . Absolutely relative: how research results are summarized can affect treatment decisions. Med. 1992;92(2):121–4. CrossrefPubMedWeb of Science214. Bhandari M, Tornetta P. Communicating the risks of surgery to patients. Trauma. 2004;30(3). Crossref215. . Completeness of reporting trial results: effect on physicians’ willingness to prescribe. Lancet. 1994;343(8907):1209–11. CrossrefPubMedWeb of Science216. . Influence of method of reporting study results on decision of physicians to prescribe drugs to lower cholesterol concentration. BMJ. 1994;309(6957):761–4. CrossrefPubMed217. How should the impact of different presentations of treatment effects on patient choice be evaluated? A pilot randomized trial. PLoS One. 2008;3(11):e3693. CrossrefPubMedWeb of Science218. The effect of alternative summary statistics for communicating risk reduction on decisions about taking statins: a randomized trial. PLoS Med. 2009;6(8):e1000134. [SEP] Justify:

Output: The text is largely a list of references and does not directly address or provide evidence regarding cognitive biases or their influence on decision-making. As such, it does not support or refute the claim but rather is irrelevant to it.


Input: Task: corroborate the claim using the given text. Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: In this paper, we study an aspect of the experimental design of gene expression data in the particular context of inferring gene regulatory networks from such data. Specifically, we investigate the influence of environmental conditions on the inference performance of five popular network estimation algorithms, namely, Aracne (Margolin et al. , 2006), BC3NET (de & Emmert-Streib, 2012), CLR (Faith et al. , 2007), C3NET (Altay & Emmert-Streib, 2011; Altay & Emmert-Streib, 2010) and MRNET (Meyer, Kontos & Bontempi, 2007; Meyer, Lafitte & Bontempi, 2008). The rational behind our study is the fact that the information stored in the DNA is not sufficient to explain the phenotypic characteristics of an organism. Instead, there are genotype-environment interactions that have an important influence on this (Falconer & Mackay, 1996; Lynch & Walsh, 1998). For similar reasons studying the expression of genes without considering the environmental conditions of the cells under investigation is fragmented. In order to study the influence of environmental conditions on the gene expression, and ultimately on the inference performance of network inference algorithms, we focus on two important, biologically relevant conditions. The first environmental condition we study corresponds to the placement of cells into a rich media. This leads to an increased proliferation of the cells due to the surplus of nutrition. The second environmental condition corresponds to a positive spike-in stimulation of cells as induced, e. g. , by the administration of drugs. Here by spike-in stimulation we mean that the influence of a drug starts abruptly and lasts only for a short period of time. In addition to these two environmental conditions, we contrast the inference performance for data generated under these two conditions with results for data that correspond to a normal condition, where we do not assume an environment influence. For conducting these investigations we simulate gene expression data because this allows us controlling the corresponding conditions and simultaneously guarantees the availability of sufficiently large sample sizes to enable robust statistical findings that can be utilized to advance the experimental design of future gene expression studies aiming to infer gene regulatory networks. Specifically, for our study we generate 6600 different data sets and infer a total of 33,000 different regulatory networks. [SEP] Justify:

Output: The text corroborates the claim by discussing how environmental conditions influence gene expression and the importance of considering these conditions in gene regulatory network inference. It explicitly states that 'the information stored in the DNA is not sufficient to explain the phenotypic characteristics of an organism,' which aligns with the concept of epigenetics as it relates to the modification of gene expression by environmental factors.


Input: Task: pass the claim using the given text. Claim: Sign languages have their own unique grammatical structures, different from the spoken languages in the same region. [SEP] Text: In Kyoto, a lexeme is specified for tone and prominence (accent), with both having a contrastive function. In Kagoshima, a word is specified for tone only, and a post-lexical and non-contrastive rule determines which syllable/mora is accented to realize the lexically specified tone (Falling or Level). For example, in Kagoshima Japanese, the wordonago/ ‘woman’ has a Falling tone (/onago/[F]) while the wordotoko/ ‘man’ has a Level tone (/otoko/[Lv]). A post-lexical rule then determines where the fall occurs (penultimate syllable), with the output foronágo/[F] becoming [ònágò]. In the case of the level tone, the final syllable is assigned H by a post-lexical rule. type is especially common in Kyūshū and Ryukyuan languages (see Kato, Tamamoto, Carlino and Urabe, this volume). 5 A few Japonic languages have a characteristic typically associated with a stress language, i. e. a foot-based metrical structure. This is true, for example, the Aoya dialect of Tottori (Western Japanese, Matsumori 2012), the Maisaka dialect of Shizuoka (Eastern Japanese, Poppe 2016), the Nakijin dialect of (Lawrence 1990), the Nagahama dialect of Irabu (Miyako, Southern Ryukyuan), etc. However, such languages are much less well documented than tone-like pitch accent languages as noted above. 6 2. 2 section discusses the morphosyntactic features of Japonic. From a broad range of topics pertaining to morphosyntax, this section focuses on the number category, adjectival expressions and alignment systems, since these in particular exhibit a surprising amount of internal diversity, are well documented in our volume, and are worth the special attention of theoretical linguists and typologists. There are of course many more typologically interesting topics which are not covered in this section simply due to limitations of space, and the reader is referred to § 3 of the present 2. 2. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses tonal specifications and morphosyntactic features of Japonic languages. It does not address sign languages or their grammatical structures, therefore not providing any information that corroborates or contrasts with the claim regarding the uniqueness of sign languages.