Input: Task: pass the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: Thus, we are unable to answer whether there is continuous distribution of haplotype frequencies with a clinal transition between geographic extremes, whether there are two allopatric ranges separated by a distinct geographic gap, or whether the ranges meet at a distinct zone of parapatry or sympatry. Because of the extent of the genetic dissimilarity, we are rather skeptical about the first alternative. Rather, we expect that clades I and II are entities separated at species level. We propose a separate species status for the two clades as per the genetic species concept [20–22] which sets a cutoff based on empirical data (cytochrome b in the order Chiroptera) of about 5% of corrected sequence divergence [e. g. [23, 24]]. These two groups have almost double that divergence with 9% corrected divergence. (ii) Within the clade II, a divergence of about 3% separates African and Asian haplotypes of R. hardwickii. Within the African group, our genetic data contradict the groupings proposed by previous studies [see [8, 9, 17] and [25]], which stress a separate status for the populations of the central Sahara (including that of Upper Egypt). The genetic relatedness of these small bats to the largest form in Libya suggests an unexpected degree of phenotypic plasticity in these bats, apparently driven by temporary local conditions rather than by the genotypic backgrounds of the respective populations. Here, the selection pressures of the extreme conditions of desert habitats may have played a key role. A similar pattern of morphological bimodality has been observed in other desert or semi-desert species of bats [16, 25, 26], such as Taphozous nudiventris Cretzschmar, 1830, Rhinolophus clivosus Cretzschmar, 1828, Asellia tridens (Geoffroy, 1813), or Pipistrellus kuhlii (Kuhl, 1817), and such an explanation could be also invoked with respect to the smaller Arabian form, Rhinopoma microphyllum asiriensis Nader and Kock, 1983. (iii) Our study has revealed that the morphospecies R. muscatellum is composed of two distinct clades: clade III in Yemen and clade IV in Iran and, supposedly, in Oman. [SEP] Justify:

Output: The text does not address or provide any information related to the claim about fossils offering insights into evolutionary history. Instead, it discusses genetic divergence and species classification within specific bat populations, which is irrelevant to the topic of fossils and their significance in understanding evolution.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: 17. Bonfante P, Genre A. Arbuscular mycorrhizal dialogues: do you speak ‘plantish’ or ‘fungish’? Sci 2015;20:150-4. 18. Maillet F, Poinsot V, André O, Puech-Pagès V, Haouy A, Gueunier M, et al. Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza. Nature 2011;469:58–63. 19. -Pagès V, Novero M, Rey T, et al. Short-chain chitin oligomers from arbuscular mycorrhizal fungi trigger nuclear Ca2+ spiking in Medicago truncatula roots and their production is enhanced by strigolactone. 2013;198:179–89. 20. . Arbuscular mycorrhizal fungi elicit a novel intracellular apparatus in Medicago truncatula root epidermal cells before infection. 2005;17:3489–99. 21. . Life histories of symbiotic rhizobia and mycorrhizal fungi. 2011;21:R775–85. 22. . A phosphate transporter from Medicago truncatula involved in the acquisition of phosphate released by arbuscular mycorrhizal fungi. 2002;14:2413–29. 23. The membrane proteome of Medicago truncatula roots displays qualitative and quantitative changes in response to arbuscular mycorrhizal symbiosis. J Proteomics 2014;108:354–68. 24. Raudaskoski M, Kothe E. Novel findings on the role of signal exchange in arbuscular and ectomycorrhizal symbioses. Mycorrhiza 2014;25:1–10. 25. . Truffles regulate plant root morphogenesis via the production of auxin and ethylene. 2009;150:2018–29. 26. Plett JM, Martin F. Blurred boundaries: lifestyle lessons from ectomycorrhizal fungal genomes. 2011;27:14–22. 27. [SEP] Justify:

Output: The text provides multiple references that support the claim that mycorrhizal fungi have a symbiotic relationship with plant roots. For instance, it discusses 'Short-chain chitin oligomers from arbuscular mycorrhizal fungi trigger nuclear Ca2+ spiking in Medicago truncatula roots' and 'A phosphate transporter from Medicago truncatula involved in the acquisition of phosphate released by arbuscular mycorrhizal fungi', which both highlight interactions between mycorrhizal fungi and plant roots, confirming their symbiotic relationship.


Input: Task: contrast the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: Consequently, more of the neuron types needed to make their MB are available to these embryos, likely making these insects less dependent on appropriating other neurons to temporarily function in the larval MB. A higher number of MB neurons persisting from the larva to adult increases the likelihood that a memory trace could persist from one stage to the other. Metamorphic changes of the larval neurons Although there are examples of neurons that change their neuropeptides during postembryonic life (Veverytsa and Allan, 2012), our study did not find any neuron that changed its small molecule transmitter. The neurons did, though, show a great range of morphological changes. At one end of the spectrum were neurons like DAN-d1/PPL1 03 (Figure 3B) and MBON-j1/MBON 02 (Figure 4B), whose larval and adult forms are very similar. At the other end of the spectrum are MBIN-b/PAL-OL and MBON-g/LALs-NO2i. b (Figure 4B), which trans-differentiate into adult neurons that bear no similarity to their larval forms. Neurons possessing the same form in both the larval and adult stages are like those of direct developing insects because they undergo their full developmental trajectory during embryogenesis and achieve their mature form at hatching. Other larval neurons have a morphology that appears to be based on pausing their developmental trajectory at an intermediate step and using this intermediate form as the basis for their larval morphology. The larval octopaminergic cells, OAN-a1 and -a2, fit this pattern. Their larval neurons stop at the MB calyx but in their adult form (OA-VUMa2), they extend beyond the calyx to form major arbors in the lateral horn neuropils (Busch et al. , 2009). A similar strategy occurs for thalamic neurons in the developing mammalian visual system (Kanold et al. , 2003). These early-born neurons arrive at the cortical subplate prior to the birth of their granule cell targets in the visual cortex. They assume an intermediate phenotype, synapsing with the subplate neurons, but after the granule cells are born, they lose these temporary connections and grow into the cortex to find their final targets. [SEP] Justify:

Output: The text contrasts the claim by discussing the developmental processes of neurons in relation to insects and their metamorphism. It states that 'neuron types needed to make their MB are available to these embryos,' which implies less dependence on the larval stages and suggests that metamorphic changes in their neurons could lessen the characteristic metamorphosis observed in other insects. The text focuses on the morphology changes of the neurons, which may indicate alternative evolutionary strategies rather than a complete metamorphosis as traditionally understood in the context of insect development.


Input: Task: pass the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: Evolutionary historyThe evolutionary history of Rhinopomatidae is a subject of particular interest, one which makes the group one of the most enigmatic clades of chiropterans. In the traditional view, Rhinopomatidae were regarded as the most primitive group of extant bats, the closest to the common ancestor of microbats and megabats [12, 14]. Indeed, compared to other families of Yangochiroptera and Yinpterochiroptera, the family Rhinopomatidae exhibits a set of unique plesiomorphies: (i) the trochiter of the humerus (tuberculum minor) is small and does not permit the scapulo-humeral lock found in other bats; (ii) the wing tip index has the lowest value of all Chiroptera; (iii) medial phalanx of the second wing finger is complete and well-ossified; (iv) the last cervical and first throracic vertebrae are free (not fused as in other bats); (v) individual sacral vertebrae have distinct boundaries; (vi) the uropatagium is incomplete; (vii) the calcar is absent; (viii) tail is long and mouse-like, not entirely integrated to the uropatagium; (ix) the premaxillae are not attached to each other or to maxillae; and (x) the premaxillae are developed at the palatal plane only. A few of these characteristics (i, iv, vii) are shared with Craseonycteridae, while the others are unique among both Yangochiroptera and Rhinolophoidea, partly resembling the condition in Pteropodidae (i, iii, iv, v, vi, ix, partly vii, viii, x). In contrast to the major clades of Yinpterochiroptera [cf. [3, 15]], Rhinolophidae (1 genus, ca. 77 species), Hipposideridae (9 genera, ca. 81 species), and Pteropodidae (42 genera, ca 184 species), the family Rhinopomatidae is much less diversified [15]. [SEP] Justify:

Output: The text does not specifically address the role of fossils in providing insights into evolutionary history. Instead, it discusses the evolutionary history of the family Rhinopomatidae and its characteristics compared to other bat families without mentioning fossils. Therefore, it is considered irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and represses jasmonic acid (JA) responsive genes. 2014;111:8299–304. 28. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. 2015;47:410–5. 29. Balestrini R, Gómez-. Application of to plant pathogenic and symbiotic interactions. J 2009;4:81–92. 30. Recorbet G, Dumas-Gaudot E. Proteomics of biotrophic plant–microbe interactions: symbioses lead the march. : & Sons, Inc; 2008. p. 764. 31. . Effect of fungal-isolate aggressivity on the biosynthesis of symbiosis-related polypeptides in differentiating eucalypt ectomycorrhizas. Planta 1995;195:408–17. 32. O'Farrell PH. High resolution two-dimensional electrophoresis of proteins. J 1975;250:4007–21. 33. Felten J, Martin F, Legué V. Signalling in Ectomycorrhizal Symbiosis. In: Perotto S, Baluška F. (eds. ) Signaling and Communication in Plant Symbiosis. Berlin, Heidelberg: Heidelberg; 2012. 42. 34. Ditengou FA, Müller van Doorn MM, et al. Volatile signalling by sesquiterpenes from ectomycorrhizal fungi reprogrammes root architecture. 2014;6:6279–9. 35. de A novel class of ectomycorrhiza-regulated cell wall polypeptides in Pisolithus tinctorius. 1999;12:862–71. 36. Bonfante P, Genre A. Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis. 2010;1:1–11. 37. -Gaudot E. Mutations in DMI3 and SUNN modify the appressorium-responsive root proteome in arbuscular mycorrhiza. 2006;19:988–97. 38. Lopez-Meyer M, Harrison MJ. [SEP] Justify:

Output: The text corroborates the claim by providing insights into the mechanisms and interactions involved in mycorrhizal symbiosis. It discusses mutualistic fungi, such as Laccaria bicolor, and highlights the importance of various proteins and signaling involved in plant-fungus interactions, which supports the idea that mycorrhizal fungi form beneficial relationships with plant roots.


Input: Task: pass the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: No fertilised eggs or embryos have been sequenced, individual tissues derived from juvenile fish were used for the genome annotation and whole larval fish for the developmental analysis. We will specify in the figures and text that the results shown are from whole larvae, and add more detail to the material and methods section about which type of sample was analysed in which way. The bioinformatic processing, especially of the assemble and annotation, is very poorly described. This is also a sensitive topic, as illustrated by the numerous "assemblathon" and "annotathon" initiatives to evaluate tools and workflows. Importantly, providing configuration files and in-depth description of workflows and parameter settings is highly recommended. This can be made available through data store services and documents even benefit from DOIs. This provides others with more information to evaluate the resolution of this work. No doubt that it is well done,but especially in the field of genome assembly and annotation, high resolution is VERY cost and time-intensive. Not surprisingly, most projects are conditioned by trade-offs between cost, time, and labor. The authors should provide others with the information needed to evaluate this. We will upload the code used to assemble and annotate this genome to a public repository or add it to the supplementary material. The genome assembly did not use a specific workflow (e. g. , nextflow), but was done with a simple command and standard parameters in IPA. Scaffolding was carried out by using their standardised proprietary workflow, of which a detailed description provided by can be found in the supplementary material. The annotation workflow has been described in a previous publication already, but an in-depth description can also be found in the Material and methods section, including parameters used for specific steps. The RNA-seq mapping and analysis part has also been described in the Material and Methods section, including parameters and models for DESEq2. Quantifications of T3 and T4 levels look fairly low and not so convincing. The work would clearly benefit from a discussion about why the signal is so low and what are the current technological limitations of these quantifications. This would really help (general) readers. We will add a comment on this in the manuscript as suggested. Basically, the T3/T4 levels are consistent with other published work in fish. In the present manuscript for grouper we have a peak level of 1. 2 ng/g (1,200 pg/g) of T4 and 0. [SEP] Justify:

Output: The text is irrelevant to the claim about insects undergoing complete metamorphosis. It discusses genome assembly and annotation and does not mention insects, larvae, or metamorphosis. Therefore, it does not provide any supporting or contrasting information related to the claim.


Input: Task: pass the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: The fact that the phenotype of Rhinopomatidae (similarly as in Craseonycteridae) is composed almost exclusively of the ancestral characters not affected by adaptive rearrangements common in other chiropteran families, in contrast to other chiropteran families [42], suggests that (i) the clade was established at a very early stage of chiropteran radiation (prior to the first appearances of modern families, in the or earlier), and (ii) that rhinopomatids were relatively little affected by the same adaptive processes that affected other all bat families, which all evolved under constant competitive pressure from other microbat clades. The latter could happen only under conditions of long-term isolation of rhinopomatids from other bats. An analogous case is the extinct clades of Palaeochiropterygidae and Hassianycteridae, which extensively diversified in during geographic isolation of that region in the Early and [43, 44]. These endemic groups were radically replaced by modern bat families soon after their invasion during the "grand coupure" [33]. The respective modern clades, Hipposideridae, Rhinolophidae, modern Emballonuridae, Vespertilionidae, Molossidae [comp. [29, 31]], arrived either from Africa and or Asia, and their early radiations most probably took place there (comp. also [3] for molecular support to that hypothesis). The complete absence of rhinopomatids in the fossil record and the lack of coevolutionary influence on their phenotype suggest that this group was absent in Europe and probably also in Africa and Asia. Of course, Tanzanycterididae with Tanzanycteris mannardi from the (46 Ma) of Tanzania [45] may ultimately be shown to be closely related to Rhinopomatidae. Unfortunately the characters available in the specimen of Tanzanycteris provide only tentative support for such a possibility (e. g. enlarged cochlea, a lack of scapulo-humeral lock which is, common to all other Eocene bats). The first appearance datum of Megadermatidae s. str. is nearly synchronous with dramatic rearrangements of the European mammalian fauna, with the appearance of the Asiatic elements (e. g. [SEP] Justify:

Output: The text does not directly address the claim regarding fossils providing insights into evolutionary history. Rather, it discusses details about the phenotype and evolutionary characteristics of specific bat families without specifically relating this information to fossil evidence or the broader context of evolutionary insights.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: An experimental system to synchronize the early events of development of the arbuscular mycorrhizal symbiosis. In: Sánchez F, Quinto C, López-Lara IM, Geiger O. (eds. ) Molecular Plant–Microbe Interactions. Saint Paul: for Plant-Microbe Interactions; 2006. 551. 39. Bestel-Corre G, Dumas--F, van Tuinen D, et al. Proteome analysis and identification of symbiosis-related proteins from Medicago truncatula Gaertn. by two-dimensional electrophoresis and mass spectrometry. Electrophoresis 2001;23:122–37. 40. . Proteome changes in Oncidium sphacelatum (Orchidaceae) at different trophic stages of symbiotic germination. Mycorrhiza 2014;24:349–60. 41. . Membrane proteins and membrane proteomics. 2008;8:3924–32. 42. Benabdellah K, Azcón-Aguilar C, Ferrol N. Soluble and membrane symbiosis-related polypeptides associated with the development of arbuscular mycorrhizas in tomato (Lycopersicon esculentum). 1998;140:135–43. 43. Benabdellah K, Azcon-Aguilar C, Ferrol N. Alterations in the plasma membrane polypeptide pattern of tomato roots (Lycopersicon esculentum) during the development of arbuscular mycorrhiza. J 2000;51:747–54. 44. -Gaudot E. Identification of membrane-associated proteins regulated by the arbuscular mycorrhizal symbiosis. Biol 2005;59:565–80. 45. Maldonado-van. Methods to estimate the proportion of plant and fungal RNA in an arbuscular mycorrhiza. Mycorrhiza 2002;12:67–74. 46. -Gaudot E. A mass spectrometric approach to identify arbuscular mycorrhiza-related proteins in root plasma membrane fractions. 2006;6(Suppl 1):S145–55. 47. . [SEP] Justify:

Output: The text corroborates the claim by detailing various studies and experimental setups that investigate the development of arbuscular mycorrhizal symbiosis, which is a specific type of symbiotic relationship between mycorrhizal fungi and plant roots. It references 'symbiosis-related proteins,' 'development of arbuscular mycorrhizas in tomato,' and the identification of proteins in the context of mycorrhizal symbiosis, all of which support the idea that mycorrhizal fungi form beneficial relationships with plant roots.


Input: Task: contrast the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: Such morphological changes have already been associated as corresponding to metamorphosis in groupers (et al 1998) as they occur during TH level increase, and they also happen to be under the control of TH in grouper (et al 1998). Based on this study but also on studies (conducted on many other teleost species) showing that the increase of TH levels is always associated with an activation of TH pathway genes and morphological and pigmentation changes we concluded that metamorphosis of E. malabaricus occurs between D32 and juvenile stage. We will improve the clarity of the manuscript to make sure that our conclusion is based on our transcriptomic and morphological data plus the available literature. (2) We clearly observed another activation of TH related gene earlier in the development (between D1 and D10, with a surge of trhrs, tg and tpo at D3. As this activation was very unexpected for us, we decided to focus the analysis of TH levels between D1 and D10 and very interestingly we observed high level of T4 at D3 indicating that THs are instrumental very precociously in the larval development of the malabar grouper which has never been shown before. We declared line 195 that our “data reinforce the existence of two distinct periods of TH signalling activity, one early on at D3 and one late corresponding to classic metamorphosis at D32”. However, we agree that we could have been clearer and clearly explained that this early activation was very intriguing for us and that we wanted to investigate hormonal levels around that period. However, we never claimed anywhere in the manuscript that this early developmental period corresponds to metamorphosis. Something else is occurring and both TH and cortisol seem to be involved but further experiments need to be conducted to understand their role and their possible interaction. (3) Finally, regarding the comment about cortisol enhancing or participating in TH driven metamorphosis, our data clearly showed an activation of the corticoid pathway genes around metamorphosis (between D32 and juvenile stage) suggesting a potential implication of corticoids in metamorphosis, but we agree with the reviewer that further experiment are needed to test that. We never claimed that cortisol was enhancing or participating in metamorphosis, on the contrary we are “suggesting a possible interaction between TH and corticoid pathway during metamorphosis”. [SEP] Justify:

Output: The text contrasts the claim by discussing metamorphosis in a different species (the malabar grouper), focusing on the role of TH and cortisol, and indicating that the authors did not claim that early developmental stages correspond to metamorphosis. They explicitly state that 'we never claimed anywhere in the manuscript that this early developmental period corresponds to metamorphosis,' suggesting that their findings do not support the notion of complete metamorphosis as understood in the context of insects.


Input: Task: pass the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: Based on the above discussion, we proposed the following biogeographic hypothesis (Figure 5):Figure 5Palaeogeographic situation of the Indian-region in the Late Eocene/(35 My) and in the Miocene (20 My), with expected expansion pathways of three major lineages (sensu [9]) of the family. The paleogeographic background maps were compiled by Ron Blakey, Department of Geology, University, Flagstaff [66]. Printed with permission. Full size image(i) Rhinopomatidae originated during the Eocene from the early diversification of rhinolophoid bats that remained isolated from competitive pressure of other chiropteran clades somewhere in the archipelago south of the seaway or in India. (ii) The group evolved in isolation until the Oligocene when the marine barrier between the Mediterranean and provinces disappeared. Endemic adaptation to major chiropteran foraging strategies in ancient rhinolophoids produced clades whose ecomorphological design was much different corresponding foraging specialists on neighbouring continents. Some of those ancient clades survive now: rhinopomatids as aerial foragers, craseonycterids as foragers of small prey in cluttered habitats, and megadermatids as ground gleaners. (iii) The land between Iran and western India, uplifted during the Oligocene, was subsequently invaded by rhinopomatids and became the key location of their early Neogene radiation. The westward invasion was from the south, then to Arabia (which came in contact with the Iran belt some 20 Ma ago) with the R. muscatellum lineage, and perhaps later to the northern part of the Iran and to the Mediterranean with the R. hardwickii lineage. The paleobiogeographic analyses of rodents [52] suggest that the respective westward migrations may begun even much earlier – in the late Eocene and early Oligocene via archipelagos south of the seaway. (iv) Extension of the paleogeographic and paleoenvironmental rearrangements of the during the Vallesian and Turolian stage, ca. 11 Ma [compare with [53–55]], fixed the already established divergences among the clades within both R. hardwickii and R. muscatellum lineages. [SEP] Justify:

Output: The text is irrelevant (pass) to the claim as it discusses a biogeographic hypothesis and paleogeography concerning specific bat lineages, rather than addressing fossils or their insights into evolutionary history. It does not mention fossils or their role in understanding evolution, and focuses instead on migration patterns and adaptations of certain bat species.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: Live-cell imaging reveals periarbuscular membrane domains and organelle location in Medicago truncatula roots during arbuscular mycorrhizal symbiosis. 2009;151:809–19. 48. A H+-ATPase that energizes nutrient uptake during mycorrhizal symbioses in rice and Medicago truncatula. 2014;26:1818-30. 49. Kobae Y, Hata S. Dynamics of periarbuscular membranes visualized with a fluorescent phosphate transporter in arbuscular mycorrhizal roots of rice. Physiol 2010;51:341–53. 50. . truncatula half-ABC transporters are essential for arbuscule development in arbuscular mycorrhizal symbiosis. 2010;22:1483–97. 51. Rhizobium-legume symbiosis shares an exocytotic pathway required for arbuscule formation. 2012;109:8316–21. 52. -M. Mass spectrometry-based label-free quantitative proteomics. J 2010;2010:1–6. 53. Dumas---Arnaud M, Fontaine B, et al. Proteomics as a way to identify extra-radicular fungal proteins from Glomus intraradices-RiT-DNA carrot root mycorrhizas. Ecol 2004;48:401–11. 54. Recorbet G, Rogniaux H, Gianinazzi-Pearson V, Dumasgaudot E. Fungal proteins in the extra-radical phase of arbuscular mycorrhiza: a shotgun proteomic picture. 2009;181:248–60. 55. . rhizogenes pRi TL-DNA segment as a gene vector system for transformation of plants. Genet 1987;207:251–5. 56. . A homologue of the cell cycle check point TOR2 from Saccharomyces cerevisiae exists in the arbuscular mycorrrhizal fungus Glomus mosseae. Protoplasma 2000;212:89–98. 57. -Hill Y, Lammers PJ. Expression in an arbuscular mycorrhizal fungus of genes putatively involved in metabolism, transport, the cytoskeleton and the cell cycle. In:. (eds. [SEP] Justify:

Output: The text corroborates the claim by discussing various studies related to arbuscular mycorrhizal symbiosis in plant roots, specifically mentioning Medicago truncatula and other species. It highlights the presence and functions of structures like the periarbuscular membrane and arbuscule development indicative of a symbiotic relationship. For example, it notes that certain transporters and ATPases are crucial for nutrient uptake during these mycorrhizal symbioses, directly supporting the idea that mycorrhizal fungi form beneficial associations with plant roots.


Input: Task: contrast the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: We have improved the clarity of the manuscript in several places to make sure that our conclusion is based on our transcriptomic and morphological data plus the available literature. (2) We clearly observed another activation of TH related gene earlier in the development between D1 and D10, with a surge of trhrs, tg and tpo at D3. As this activation was very unexpected for us, we decided to focus the analysis of TH levels between D1 and D10 and very interestingly we observed high level of T4 at D3 indicating that THs are instrumental very precociously in the larval development of the malabar grouper which has never been shown before. We declared lines 224-225 that our “data reinforce the existence of two distinct periods of TH signalling activity, one early on at D3 and one late corresponding to classic metamorphosis at D32”. However, we agree that we could have been clearer and clearly explained that this early activation was very intriguing for us and that we wanted to investigate hormonal levels around that period. However, we never claimed anywhere in the manuscript that this early developmental period corresponds to metamorphosis. Something else is occurring and both TH and cortisol seem to be involved but further experiments need to be conducted to understand their role and their possible interaction. We have added corresponding statements in the abstract (lines 39-43) and discussion (lines 447 to 449). (3) Finally, regarding the comment about cortisol enhancing or participating in TH driven metamorphosis, our data clearly showed an activation of the corticoid pathway genes around metamorphosis (between D32 and juvenile stage) suggesting a potential implication of corticoids in metamorphosis, but we agree with the reviewer that further experiment are needed to test that. We never claimed that cortisol was enhancing or participating in metamorphosis, on the contrary we are “suggesting a possible interaction between TH and corticoid pathway during metamorphosis”. And we also say that our “results brought a first insight into the potential role of corticoids in the metamorphosis of E. malabaricus and call for functional experiments directly testing a possible synergy. ” Nonetheless, we agree that some parts of our manuscript can be confusing in regards of cortisol synthesis during metamorphosis as we did not measure cortisol levels between D32 and juvenile stage. We have therefore made changes throughout the Introduction and Discussion to make this clearer. [SEP] Justify:

Output: The text contrasts the claim by stating that the authors did not claim that the early developmental period corresponds to metamorphosis. They emphasize that their focus was on the activation of certain gene pathways and hormonal levels during larval development, without establishing that an actual metamorphosis occurred. The authors mention that something else is happening during the early development, indicating a clear distinction between larval development and metamorphosis.


Input: Task: pass the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: (v) The extension of the range of the large-sized Indian R. microphyllum may have appeared quite late after these events, possibly even during the Quaternary under the influence of more pronounced seasonality in the climate [53]. ConclusionThis first genetic study dealing with the family Rhinopomatidae has enabled us to put forward phylogenetic hypotheses that differ considerably from the concepts resulting of previous morphological studies. Contrary to what was expected, we found deep allopatric genetic divergences within the R. hardwickii and R. muscatellum lineages, which suggests a separate species status for the Afro-Arabian branch of R. hardwickii (i. e. R. cystops) and for the Yemeni branch of R. muscatellum. In contrast, we found a surprisingly high genetic homogeneity in R. microphyllum (0. 5% of genetic distance over 3,400 km of geographic distance). Morphological polymorphism in the genetically uniform R. cystops and R. microphyllum and the characteristics of the fossil taxon suggests plasticity of body size in this group. Considering information on the Recent and past ranges and the genealogy of the group, we expect that history of the family included (i) an early isolation in archipelago south of seaway or in India, (ii) a northward- and westward spread into Mediterranean after disappearance of the marine barrier in the and (iii) retreat from there after the Miocene climatic optimum. MethodsTaxonomic samplingWe examined both museum specimens and individuals collected during our field excursions. The material examined for morphometric analysis (n = 252) covered all parts of the range (except East Asia), included nearly all nominal taxa, and included the holotypes of R. hardwickii Gray, 1831, R. lepsianum Peters, 1859, R. kinneari Wroughton, 1912, R. cystops Thomas, 1903, R. arabium Thomas, 1913, R. muscatellum Thomas, 1903, R. seianum Thomas, 1913, R. pusillum Thomas, 1920, and R. macinnesi Hayman, 1937. The molecular analyses were undertaken with 26 specimens representing three nominal species, namely R. microphyllum, R. hardwickii, and R. [SEP] Justify:

Output: The text does not relate to the claim about fossils providing insights into evolutionary history. Instead, it discusses genetic studies and the phylogenetic hypotheses of certain species being examined, which do not mention or connect to the role of fossils in understanding evolution.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: ) Diversity and Integration in Mycorrhizas. Dordrecht: Springer Netherlands; 2002. 148. 58. Secretome of the free-living mycelium from the ectomycorrhizal basidiomycete Laccaria bicolor. J 2012;11:157–71. 59. Proteomic analysis of Pteris vittata fronds: two arbuscular mycorrhizal fungi differentially modulate protein expression under arsenic contamination. 2010;10:3811–34. 60. Effects of heavy metals and arbuscular mycorrhiza on the leaf proteome of a selected poplar clone: a time course analysis. 2012;7:e38662. 61. Cangahuala--M, Manga A, van TD, Henry C, et al. Arbuscular mycorrhizal symbiosis elicits proteome responses opposite of P-starvation in SO4 grapevine rootstock upon root colonisation with two Glomus species. Mycorrhiza 2011;21:473–93. 62. -Pearson V, et al. On the mechanisms of cadmium stress alleviation in Medicago truncatula by arbuscular mycorrhizal symbiosis: a root proteomic study. 2009;9:420–33. 63. Fester T, Hause G. Accumulation of reactive oxygen species in arbuscular mycorrhizal roots. Mycorrhiza 2005;15:373–9. 64. . Evolutionary adaptation to Zn toxicity in populations of Suilloid fungi. 2004;162:549–59. 65. Turnau K. The influence of industrial dust on the mycoflora of Pino-Quercetum forest near Cracow. III. The influence of industrial dust on the mycorrhiza of Vaccinium myrtillus. Acad 1988;226:135–45. 66. Specific regions in the Sod1 locus of the ericoid mycorrhizal fungus Oidiodendron maius from metal-enriched soils show a different sequence polymorphism. Ecol 2011;75:321–31. 67. Perotto S, Actis-Perino E, Perugini, Bonfante P. Molecular diversity of fungi from ericoid mycorrhizal roots. [SEP] Justify:

Output: The text corroborates the claim by discussing various studies and findings related to mycorrhizal fungi, such as 'Arbuscular mycorrhizal symbiosis elicits proteome responses' and other references that indicate a focused study on the symbiotic relationship between fungi and plant roots. Specifically, it notes the effects of different mycorrhizal fungi like Glomus species on plant responses, reinforcing the idea of a symbiotic relationship.


Input: Task: contrast the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: Data were further examined with Perseus, and annotated to gene ontology (GO) terms and of Genes and Genomes (KEGG) pathways by evaluating the GO terms, KEGG pathway enrichment, and mRNA expression of differentially expressed proteins (DEPs) to assess the shell formation, body torsion, changes in feeding habits, and metamorphosis of B. areolata larvae through proteomics analysis, and to explore the larval development and metamorphosis mechanisms based on proteomics. This study could provide reference data for related studies of other marine gastropods from a proteomics perspective. Resultsof Larval DevelopmentThree groups of larval B. areolata at different developmental stages including the middle veliger stage before attachment (ZRZ-III), later veliger stage (velum atrophy) (ZRZ-V), and juvenile stage (ZRZ-VI) were used. Each group was replicated three times. The three stages of larval development are shown in Fig. 1a–c. The early veliger stage is distinguished by the appearance of the velum, feet, and shell. The middle veliger stage is a pelagic life for 1–2 d and the average shell height of the middle veliger larvae is about 520 μm, and the late veliger stage is characterized by a more rapid heartbeat and larger and elongated foot (Fig. 1a). After 10–12 d, the late veliger stage sinks to the substratum and leads a benthic life, the velum gradually degenerates and atrophies, after which the veliger completes its metamorphosis (Fig. 1b) and enters the juvenile snail stage (Fig. 1c). Figure 1Embryonic development of Babylonia areolata. (a) Veliger before attachment (b) Veliger at the later metamorphosis stage (velum atrophy) (c) Juvenile B. areolata, the feeding habits change from phytophagy to sarcophagy. Full size imageSodium dodecyl sulfate polyacrylamide gel electrophoresis of the extracted proteinsThe determined protein concentration of the sample is shown in Table 1. The extracted proteins were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The samples at the three developmental stages showed clear protein bands (Fig. [SEP] Justify:

Output: The text contrasts the claim by discussing the metamorphosis of B. areolata larvae, which is a marine gastropod and not an insect. Specifically, it mentions the transition through various developmental stages (e.g., early veliger, middle veliger, and late veliger stages) leading to a juvenile stage, but it does not address whether insects can also undergo such metamorphosis. Thus, while it provides insight into the larval development of a specific organism, it does not support the claim regarding insects.


Input: Task: pass the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: muscatellum (Table 2, column 1; Figure 1). Species identification followed the criteria summarized by [9] and Corbet and Hill [56], aided by direct comparisons with other material included in morphometric comparisons. Voucher specimens have been deposited in the collections of the National Museum, and the Department of Zoology, Faculty of Science, Charles University, both Prague, Czech Republic. Specimens were selected in order to provide a reliable geographic and taxonomic coverage of the range, and include the holotype material of R. microphyllum, R. kinneari, R. cystops, R. arabium, and R. pusillum. For further details concerning the specimens (including the morphometrical data), see [16, 17]. Fossils reported in this paper are deposited in the collections of Department of Zoology, in Prague [see Additional file 2]. Table 2 Specimen and sequence informationFull size tableThe present paper is the first molecular assay on taxonomy of Rhinopomatidae. All other studies on this group (as well as a preliminary routine identification of our own material) have been based on results of morphometric comparisons. Rhinopomatid taxa have been traditionally diagnosed by morphometric specificities, and distinguish these morphology-based taxa from genetic grouping by denoting them as "morphospecies". Molecular analysisWe extracted total genomic DNA from ethanol-preserved tissues and sequenced 402 bp of the 5'-end of the cytochrome b gene (according protocols published in [5]). Accession nos. [GenBank: DQ337480 – DQ337502, EF443165 – EF443167]. As multiple outgroup, we used representatives of the clade et al. , 2005: Hipposideros bicolor [AF358131], Rhinolophus hipposideros [AF044660], Rousettus leschenaulti [AF044662] and Epomophorus wahlbergi [AF044642]. The sequences were aligned by eye and the dataset was processed in PAUP 4. 0b10 [57]. We tested the cladistic information content and saturation level [58] by saturation tests [59]. We have inferred the model of sequence evolution in Modeltest 3. 7 [60] using a hierarchical likelihood ratio test. [SEP] Justify:

Output: The text discusses specimen identification, molecular assays, and taxonomic analysis of certain species, but it does not provide information relevant to the claim regarding fossils and their role in understanding evolutionary history.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: 1996;5:123–31. 68. The genome portal of the Department of Genome Institute. Res 2012;40:D26–32. 69. MycoCosm portal: gearing up for 1000 fungal genomes. Res 2014;42:D699–704. 70. Martin F, Aerts A, Ahrén The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 2008;452:88–92. 71. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 2010;464:1033–8. 72. Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. 2013;110:20117–22. 73. -Gaudot E. Proteomic studies of arbuscular mycorrhizal associations. Chem 2013;2013:48–58. 74. . Arbuscule-containing and non-colonized cortical cells of mycorrhizal roots undergo extensive and specific reprogramming during arbuscular mycorrhizal development. 2012;69:510–28. 75. Picotti P, Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. 2012;9:555–66. 76. . Selected reaction monitoring to determine protein abundance in Arabidopsis using the Arabidopsis proteotypic predictor. 2014;164:525–36. 77. . Single-cell imaging mass spectrometry. 2013;17:854–9. 78. van Remoortere A, van. Peptide and protein imaging mass spectrometry in cancer research. J Proteomics 2010;73:1921–44. 79. -M, Howes-Podoll M, et al. MALDI mass spectrometry-assisted molecular imaging of metabolites during nitrogen fixation in the Medicago truncatula–Sinorhizobium meliloti symbiosis. 2013;75:130–45. information 1. Introduction2. Plant–symbiotic fungi interactions3. The symbiotic proteomics of mycorrhizal interactions4. Proteomics in action5. Mycorrhizal fungi and heavy metals6. Conclusion and future perspective 1. Choose citation style Select style to clipboard Get citation 2. [SEP] Justify:

Output: The text corroborates the claim as it discusses 'plant-symbiotic fungi interactions' and includes references to mycorrhizal associations and the developmental changes in mycorrhizal roots. This directly supports the idea of mycorrhizal fungi having symbiotic relationships with plant roots.


Input: Task: pass the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: An expression stability measure for all genes in both assays was performed using the GeNorm program ( according to Vandesompele et al. [18]. The most stable pair of genes was used to normalize the gene expression levels of the GOI in (2007) using the Geomean function (Table 1). Further interrogation of the data was undertaken by normalisation using three of the most stable genes in every assay (Figure S1) and results compared with those from the pair of stable genes. For data analysis, only samples with at least two technical repeats and coefficient of variation percentage (%CV) lower than 25% were considered. Statistical analyses were conducted using Kruskal–Wallis (non-parametric one way analysis of variance by ranks) followed by multiple comparisons of mean ranks for all groups with version 10. 0 (StatSoft, Tulsa, OK). Percentage differences of those genes that were differentially regulated from control were calculated. Further, data were analysed by principal component analysis (PCA) with PAST [19]. All PCA's were performed on a variance-covariance matrix, as all variables were measured in the same units, and without any group assumptions. PCA score plots are presented with convex hulls highlighting groupings and showing PC1 and PC2. of minimum exposure times of larvae to cues to elicit settlement or metamorphosis without attachment The minimum exposure time to elicit larval responses varied among the different cues. Visible signs of early metamorphosis (flattening into discs and development forming floating polyps) occurred 4 hpi with J010-E, whereas complete metamorphosis without attachment of 98±2% of larvae occurred 6 hpi. In order to sample swimming larvae prior to any observable morphogenetic changes, they were collected 1-3 hpi with J010-E (Table 1). While no behavioural or developmental response was recorded during the first 2 hpi with HOorg and HOaq, initial attachment was observed after 3 hpi, and complete metamorphosis with attachment was observed 16 hpi (settlement rates of 94±5% (HOorg) and 70±8% (HOaq), respectively). To reduce any variation in the assays and to ensure that all larvae were sampled at the same developmental phase, larvae were collected 1 hpi with HOorg or HOaq (Table 1). [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses gene expression analysis and statistical methods in experimental biology without addressing insect metamorphosis or any related biological processes such as larval stages. It does mention terms related to larvae and metamorphosis, but does not provide any support or contrast concerning the claim about insects and their metamorphosis.


Input: Task: pass the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: The resulting model was used to correct distances and for maximum likelihood and Bayesian analyses. We performed distance analyses to quantify genetic gaps within the clade. We computed pairwise p-distances (Table 3, lower triangle, values used in the text to demonstrate genetic distances) and corrected distances among ingroup haplotypes. We used GTR (model fitting best our data according to Modeltest; Table 3, upper triangle) and K2P (distance used in previous studies on bat species [e. g. [23, 24, 61]]) corrections. The results of both corrected distance analyses were almost identical. The data were ordered by computing trees using several approaches: neighbor-joining, maximum parsimony (heuristic search with 100 random-addition sequences and the TBR branch-swapping algorithm; Figure 3a) and maximum likelihood (Figrue 3b). For the Bayesian analysis (performed in MrBayes 3. 1 [62]; Figure 3c) we used GTR + I + G model, flat priors and random starting tree. We ran four chains in MCMC analysis with 10,000,000 generations and sampled trees every 100 generations. The stationary was inspected via log probability plots and the convergence diagnostics for model parameters and burn-in was used to discard first 1,000,000 generations. We repeated the Bayesian run to test for convergence. The robustness of the topologies obtained was tested by bootstrap using 1,000 replicates, and by computing posterior probabilities. We estimated the approximate dates of divergences (Figure 3d) using the linearized tree approach [63]. The difference in log-likelihoods (2 [log L -log Lclock], [64]) of non-clock like (log L = -1867. 36) and clock-like (logLclock = -1884. 45) trees compared against χ2 distribution (df = Ntaxa - 2) was not significant at the 5% level (19. 50), and thus the molecular clock could not be rejected. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses genetic distance analyses, model corrections, and Bayesian analyses without making any reference to fossils or their role in understanding evolutionary history.


Input: Task: corroborate the claim using the given text. Claim: Some mushrooms can bioaccumulate heavy metals from the soil. [SEP] Text: Biosorption and Bioaccumulation of Metals by Isolated from Soil in Basra Governorate- Jaafar1, Amin Al-Sulami1, Asaad Al-Taee2*, Faris Aldoghachi3 and Suhaimi Napes4 1College of Education for 23College of Science, Basra University, Basra, Iraq 4College of : Asaad Al-of Basrah, environmental development, Basra, 61001, Iraq Tel: 009647801405715 E-mail: amraltaee@yahoo. com Received date: June 06, 2015; Accepted date: July 13, 2015; Published date: July 20, 2015 Citation: Jaafar R, Al-Sulami A, Al-(2015) Biosorption and Bioaccumulation of Metals by Isolated from Soil in Basra Governorate- Iraq. J 5:190. doi:10. 4172/2155-952X. 1000190 Copyright: © 2015 Jaafar R, et al. This is an open-access 0. 33 mgg-1), while the lowest accumulation was in concentration 5 mgl-1 (0. 029 mgg- 1) at 2h of incubation. the results showed maximum accumulation at 24h for concentration 100 mgl-1 then decreased at 48 h. The results of biosorption experiment showed that D. radiodurans has a good ability to absorption both Pb and Cd in considering to the metals concentrations and times. This which can be clarified from the elevated percentage of Pb absorption (63. 46%) in concentration 50 mgl-1 and during 2h. For biosorption of Cd the was decreased with the increasing time and the high biosorption noticed during 2h at concentration 50 mgl-1 (31. 23%). radiodurans Heavy metals; Minimum inhibitory concentration; Bioaccumulation; D. radiodurans is one of the most known radiation resistant organisms. It can live in cold, dehydration, vacuum and acid, and is therefore known as a polyextremophile. It is found in habitats rich in organic materials, such as soil, feces, meat, or sewage, in addition to that, it’s isolated from dried foods, room dust, medical instruments and textiles [1]. [SEP] Justify:

Output: The text corroborates the claim by discussing the bioaccumulation of metals by certain organisms, specifically mentioning D. radiodurans, which demonstrates an ability to absorb heavy metals such as Pb and Cd from the environment. This implies that similar mechanisms may exist in mushrooms, supporting the claim regarding their potential to bioaccumulate heavy metals from soil.


Input: Task: contrast the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: verreauxi were determined at five larval rearing phases, early-phyllosoma stages (instars 1–6, culture days ≈ 0–36; (S1), mid-phyllosoma stages (instars; 7–12, culture days ≈37–150; S2), late-phyllosoma stages (instars 13–17, culture days ≈151–220; S3), metamorphosis (culture days ≈220; S4) and puerulus stage (culture days ≈221–242; S5). Phyllosoma survival measures were determined at routine density reductions at the mid- and late-phyllosoma stages and during isolation of final instar phyllosoma before metamorphosis. Early and mid-phyllosoma survival was determined by volumetric counts of larval numbers whereby five subsamples of larvae were counted and the average used to determine the total number of animals being cultured. Late stage phyllosoma were counted individually when removed from mass rearing vessels for metamorphosis. Metamorphosis survival was defined as survival from final phyllosoma instar (instar 17) to 2 days’ post metamorphosis. For each family cohort a minimum of three culture vessels were monitored for survival and the mean survival between the vessels indicated cohort survival. Body weight of all individually tagged female broodstock was recorded using a digital scale following the annual moult cycle and before egg extrusion. The survival data at the five time points (S1 to S5) during the larval rearing was treated as binary characteristics and analysed using both linear and threshold mixed models (section 2. 5). Development of new microsatellite markers, genotyping and parentage verificationA set of eleven microsatellite markers with consistent PCR amplification, clear allelic variation, and clarity of electrophoretic signatures were used to construct the pedigree. These highly polymorphic markers were developed using information from the transcriptome sequences of two S. verreauxi individuals [25]. [SEP] Justify:

Output: The text provides detailed information on the various larval stages of the species S. verreauxi including early, mid, and late phyllosoma stages, but it focuses specifically on this species and its survival measures rather than making a general statement about certain insects undergoing complete metamorphosis. As it describes the specific stages of the phyllosoma without clearly indicating that this process applies to insects in general, it contrasts the claim by implying that this metamorphosis may not represent the complete metamorphosis process as understood in other insect contexts.


Input: Task: pass the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: Figures AbstractFibrillarin (FIB), a methyltransferase essential for life in the vast majority of eukaryotes, is involved in methylation of rRNA required for proper ribosome assembly, as well as methylation of histone H2A of promoter regions of rRNA genes. RNA viral progression that affects both plants and animals requires FIB proteins. Despite the importance and high conservation of fibrillarins, there little is known about the evolutionary dynamics of this small gene family. We applied a phylogenomic microsynteny-network approach to elucidate the evolutionary history of FIB proteins across the Tree of Life. We identified 1063 non-redundant FIB sequences across 1049 completely sequenced genomes from Viruses, Bacteria, Archaea, and Eukarya. FIB is a highly conserved single-copy gene through Archaea and Eukarya lineages, except for plants, which have a gene family expansion due to paleopolyploidy and tandem duplications. We found a high conservation of the FIB genomic context during plant evolution. Surprisingly, FIB in mammals duplicated after the Eutheria split (e. g. , ruminants, felines, primates) from therian mammals (e. g. , marsupials) to form two main groups of sequences, the FIB and FIB-like groups. The FIB-like group transposed to another genomic context and remained syntenic in all the eutherian mammals. This transposition correlates with differences in the expression patterns of FIB-like proteins and with elevated Ks values potentially due to reduced evolutionary constraints of the duplicated copy. Our results point to a unique evolutionary event in mammals, between FIB and FIB-like genes, that led to non-redundant roles of the vital processes in which this protein is involved. Author summary Fibrillarins are a small group of proteins known to be essential for eukaryotic life as they are involved in several process in the cell. Changes in the amount of fibrillarins in cells can lead to incorrect translation of proteins, and is associated with various types of cancer as well as bacterial and viral responses. To date, no formal analysis of the evolution of fibrillarins through different groups of organisms such as prokaryotes, fungi, plants, and animals exists. [SEP] Justify:

Output: The text does not directly relate to the claim about fossils providing insights into evolutionary history. Instead, it discusses fibrillarins, their functions, and their evolutionary dynamics across different organisms, but does not address fossils or their role in understanding evolutionary history.


Input: Task: corroborate the claim using the given text. Claim: Some mushrooms can bioaccumulate heavy metals from the soil. [SEP] Text: The manufacturing of energy from nuclear power factories, uranium mining, nuclear weapons production and nuclear accidents are the major cause of release of radionuclide's into the environment. The nuclear wastes typically contain inorganic and organic contaminants that include radionuclide's, heavy metals, acids/base and solvents. The high radiation level, in combination with the chemical hazards cause intensive damage to ecosystem and living organisms. The clean –up of nuclear waste by physiochemical methods is impractical and the cost is prohibitive. As a result a less costly in situ bioremediation technology is being investigated as a potential substitute method for treating such contaminated sites. The development of bioremediation strategies using Deinococcus spp, is therefore vital for the clean up of contaminated sites with radioactive waste. As these sites rarely contaminated by a single chemical, it is necessary to developed strain to be multi- resistant to various toxic agents [2]. Bioremediation is a natural process which depends on bacteria, fungi, and plants to altering pollutants as these organisms perform their normal life functions. These organisms have the ability of exploiting chemical contaminants as an energy source in their metabolic processes. Therefore, bioremediation affords alternative tool to destroy or reduce the risky contaminants through biological activity and this method has an effective cost [3]. Among the different methods, bioaccumulation and biosorption are potential for the removal of metals [4]. The active mode of metal accumulation of living cells is in most cases referred to bioaccumulation which relys on intrinsic biochemical and structural properties, physiological and genetic adaptation, environmental modification of metal specification, availability and toxicity [5]. Bioaccumulation is defined as the uptake of toxicant by living cells and transports it into the cell [6] and is a growth dependent process mediated only by living biomass [7]. The process of biosorption is possible by both living and dead biomasses [8]. The ability of certain species of bacteria in accumulating heavy metals was investigated inclusively [9,10]. Hence the natural organisms, either indigenous or extraneous can be used for bioremediation of heavy metals [11]. The present study aimed to isolate Deinococcus radiodurans from soil and identifying it biochemically and molecularly, in addition to determining their ability to remediation Pb and Cd through bioaccumulation and biosorption processes. [SEP] Justify:

Output: The text corroborates the claim as it discusses bioaccumulation, specifically in the context of bioremediation involving living organisms such as bacteria and fungi, which can accumulate heavy metals from contaminated environments. It explains that bioaccumulation is a process by which living cells uptake toxicants and transport them into the cell, directly supporting the idea that some organisms, including potentially mushrooms, can bioaccumulate heavy metals from the soil.


Input: Task: pass the claim using the given text. Claim: Insects make up the majority of animal diversity on Earth. [SEP] Text: Todas se declararam como sendo do gênero feminino, e é importante destacar que essa pergunta não era eliminatória, ou seja, todas as mulheres seriam consideradas na pesquisa independentemente do gênero declarado. No que diz respeito à formação das entrevistadas, o curso com maior representatividade foi Ciência da Computação, com sete mulheres formadas, seguido por Tecnologia em Jogos Digitais, com seis respondentes. Análise e Desenvolvimento de Sistemas ou Sistemas da Informação aparece em terceiro lugar, com cinco respostas, e, por fim, a área das Engenharias, com quatro respostas. Dentro das Engenharias, 75% das respostas se concentraram em Engenharia da Computação. Quando questionadas sobre a motivação para escolha do curso, a maioria afirma sempre ter gostado de computadores, tecnologia, jogos e matemática. A escola com ensino médio técnico em tecnologia aparece como fator determinante para três mulheres, assim como feira de profissões para outras quatro, que não consideravam um curso nas áreas STEM e acabaram mudando de escolha após se informarem mais sobre as possibilidades de carreira, o que ilustra o papel fundamental das escolas como propulsoras da entrada de mulheres em cursos STEM. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the motivations and educational backgrounds of women in STEM fields, without mentioning anything related to insects or animal diversity. Therefore, it does not provide any corroboration or contrast to the claim.


Input: Task: pass the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: Next-generation sequencing enhances the accessibility of great number of genome sequences from different organisms. The aim of this work is to detect the sequence stability of the fibrillarin gene copies on distant related organisms, and whether it could be associated to the changes on the organization of their genome structures. We applied a novel methodology to detect rearrangements on genomes and found evidence of evolutionary forces on plants that keep the genome region where fibrillarin is located conserved. Also, we observed that a duplication of fibrillarin occurred in mammals which led to novel or specific functions of fibrillarin duplicates. Citation: Pereira-Santana A, Gamboa- (2020) Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin. PLoS 16(10): e1008318. Sergei L. : January 31, 2020; Accepted: September 7, 2020; Published: October 19, 2020Copyright: © 2020 Pereira-Santana et al. This is an open access 15. 5ka proteins, and one of several C/D box small nucleolar RNAs (snoRNA); the latter guides the whole complex to the target rRNA for methylation [1, 4, 5]. Archaeal FIB proteins can form a similar RNP complex with L7Ae, Nop5, and a guide RNA to methylate pre-rRNA sequences [6]. Also, FIB can independently carry out the methylation of histone H2A in ribosomal promoters [7–9]. FIB proteins have been studied extensively in different model organisms and have gained attention in the scientific community due to their essential roles in cell survival, cancer therapy, stress tolerance, and nucleolar dynamics [1, 10, 11]. An early experiment in yeast identified impaired ribosomal processing, including impaired rRNA methylation, in thermos-sensitive FIB-deficient mutants [12]. Recently, a novel ribonuclease function was described for FIB; this activity is dependent on the GAR domain and is impaired by phospholipids [13]. Specific localization in the nucleoli and Cajal bodies of cells has made it possible to use it as a nucleolus marker. [SEP] Justify:

Output: The text discusses next-generation sequencing and its application in genome studies across different organisms, particularly focusing on the fibrillarin gene and its evolutionary implications, but it does not mention fossils or provide insights related to them. Therefore, it is irrelevant to the claim about fossils providing insights into evolutionary history.


Input: Task: corroborate the claim using the given text. Claim: Some mushrooms can bioaccumulate heavy metals from the soil. [SEP] Text: Bioaccumulation of heavy metals by were grown in TGY broth containing different concentrations of lead (5, 10, 25, 50) mgl-1 and for cadmium 10, 20, 50, 100 mgl-1 for 2, 4, 6, 24 and 48 h and incubated at 30ºC in a shaker incubator at 180 rpm. Two replicates for each concentration have been done plus, one as a control. The bacterial cells were harvested by centrifugation at 6000 rpm for 15 min and suspended in 1 ml of distilled water, oven - dried and weighed. The dried biomass were then digested as follow: 100 ml beaker containing the dried cells, 5 ml concentrated nitric acid was added; the beaker was placed on a hot plate, stirred continuously, and heated initially at a medium rate for 5 min. Then, the beaker was heated on maximum setting until nitrogen oxide fumes were given off for a short time and a white residue was left. The beaker was left to cool for about 2 min and digestion was repeated with an additional 2 ml of concentrated nitric acid; this time it was heated until brown nitrogen oxide fumes almost ceased to appear. The beaker was cooled again for about 2 min and then 2 ml of 1:1 hydrochloric acid (35- 37%) was added. The mixture was heated at a medium rate for 3 min. After that it was cooled to room temperature and made up to 25 ml or bigger volume with distilled water. Metal concentrations were measured by an atomic absorption spectrophotometer (ICE 3000 ) [16]. The metals accumulation then calculated using this equation: E. Con. = A*B/D Where E. Con = the concentration of heavy metals in (mg/g) A= Concentration of heavy metals from calibration curve B= final concentration of sample (mg/l) D= dry weight of sample (gram) Biosorption experiment The equilibrium, kinetics data of the biosorbent D. radiodurans were obtained by performing batch experiments. The experiments were carried out in 250 ml flasks to which 100 ml of single ion metals solution of Cd and Pb, and l ml of biomass (exponential phase) was added. [SEP] Justify:

Output: The text corroborates the claim by detailing an experiment that studies bioaccumulation of heavy metals, specifically lead and cadmium, by bacterial cells. While it explicitly discusses bacterial cells rather than mushrooms, it indicates a scientific inquiry into the accumulation of heavy metals typical in organisms, supporting the claim regarding bioaccumulation in fungi like mushrooms.


Input: Task: contrast the claim using the given text. Claim: Perennial plants can provide year-round yields and stabilize soil. [SEP] Text: Un des champs a été transformé en culture annuelle par application de désherbant, coupe et labourage; le champ voisin, servant de témoin, a été fauché lui aussi, mais on en a laissé les plantes repousser. L’écart entre la productivité nette des deux champs provient surtout de la diminution de la productivité primaire brute, relevée dans le champ traité; la respiration de l’écosystème était similaire dans les deux cas. Quand le bilan du carbone prend en compte la biomasse retirée et les applications d'engrais, on constate que le champ traité a perdu 149 g de C par m2 alors que le champ témoin en a séquestré 96 g, pour un écart net de 245 g de C par m2, de juin à décembre (210 jours). On en déduit que le passage des graminées vivaces à une culture annuelle peut entraîner la perte d'une plus grande quantité de carbone que celle séquestrée par les graminées vivaces, en une saison. Anthropogenic activities have altered the global carbon cycle causing an increase in the atmospheric carbon dioxide (CO2) concentration. As a greenhouse gas, CO2 increases the amount of energy retained by the atmosphere, causing an increase in global average temperature (Forster et al. 2007). Since the original conversion of native vegetation to agricultural land, a large decrease in soil organic carbon and a subsequent decline in soil fertility have been observed in Canada (Smith et al. 2000). However, soils remain a substantial global pool of carbon (1500 Pg C), containing about twice the amount of the atmospheric pool (780 Pg C) (Janzen 2005). Restoring soils by sequestering atmospheric carbon could reduce atmospheric CO2 while enhancing soil fertility, increasing yields, improving food security and improving agricultural sustainability (Lal 2007; Lal et al. 2007). This makes sequestering carbon in soils an attractive option for mitigation of rising atmospheric CO2 levels. [SEP] Justify:

Output: The text contrasts the claim by discussing the negative impact of converting perennial grasslands to annual crops, specifically highlighting that this conversion leads to a loss of soil organic carbon and a potential decline in soil fertility. It states that the treated field lost more carbon than was sequestered, suggesting that the presence of perennial plants could stabilize soil and maintain carbon levels, opposing the claim that annual crops offer comparable benefits.


Input: Task: pass the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: Fibrillarin can act as a sensor of cellular stress and change its localization to the cytoplasm [14]. Due to its role in aiding rRNA processing of ribosomal p1. In this context, FIB functions as a negative transcriptional regulator of immune responsive genes, including PR1 [17]. Despite the vital role of FIB for organisms and extensive molecular and biochemical studies on their functions [12, 18, 19], there are no comprehensive studies on its evolutionary history across the Tree of Life. No complete evolutionary history across the Tree of Life can exclude the viral world [20]. Viruses transfer genetic material to living organisms and therefore have a high impact on biodiversity [21]; certain lineages of viruses present a strong correlation with specific lineages of the Tree of Llife (e. g. , Archaea are host of dsDNA/ssDNA viruses but not RNA viruses while ssRNA(+) viruses are widespread across Eukarya [20]). Giant viruses that can harbor up to 2500 protein coding sequences, present an expanded metabolic diversity (e. g. , components of glycolysis, gluconeogenesis, TCA cycle, among other metabolic pathways), and present genome sizes up to 2. 5 Mb [21–25]. A comparative genomic study of FIB protein across multiple lineages would facilitate our understanding of its molecular evolution and current functional dynamics. The reconstruction of evolutionary history requires the selection and comparison of a set of genomes to each other and outgroup species, homology-based protein detection among different lineages, the connection between compared genes and their biological function, and the genomic context, both ancient and recent rearrangements [26]. Thanks to the rapid increase in the number of fully sequenced genomes, more resolution of genomic evolutionary processes are known at smaller genome scales (e. g. , gene loss and gene duplication) and entire genome-scale (ancient whole-genome duplication and triplication, WGD/WGT, or paleopolyploidy). These duplication events create genetic novelty and provide the raw material for evolution and biological diversity [27–31]. In comparative genomics, synteny analysis has proven to be a powerful tool for understanding genome rearrangements on both small and entire genome scales. Syntenic genes referred to as syntelogs, onhologs, or syntenic homologous genes, are genes that share the same genomic context. [SEP] Justify:

Output: The text does not address the claim regarding fossils and their role in providing insights into evolutionary history. Instead, it discusses topics such as the role of Fibrillarin in cellular stress, genomic studies, and evolutionary processes based on genomic data, but does not specifically relate these points to fossil evidence or the evolutionary history as revealed by fossils.


Input: Task: corroborate the claim using the given text. Claim: Some mushrooms can bioaccumulate heavy metals from the soil. [SEP] Text: 33± 0. 0007 mgg-1, while the lowest was 0. 029 ± 0. 268 mgg-1 after 2h. In addition to that, the rising of incubation period may reduce the accumulation for all concentrations. Figure 1: Bioaccumulation of Pb by D. radiodurans at different incubation period and different concentrations. LSD (0. 0049). The accumulation of Cd increase in parallel with the increasing of concentration for all studying time (Figure 2). The figure clarifies increasing in Cd accumulation with the times (2, 4 and 6 h) for concentrations 10, 20 and 50 mgl-1, then decrease during 24 and 48h. For concentration 100 mgl-1, accumulation increase within 2, 4, 6, and 24h, then decrease with 48h. The analysis of variance of bioaccumulation of Pb and Cd between time and concentration was significant (P<0. 05) in all treatments as show by LSD value. Figure 2: Bioaccumulation of Cd by D. radiodurans at different incubation period and different concentrations. LSD (0. 0341). The results of Pb and Cd accumulation showed that, this bacterium was able to accumulate high amounts of Cd 36. 86 ± 0. 007 mgg-1 in comparison to 0. 33 ± 0. 0007 mgg-1 for Pb. This may be due to difference in toxicity of these metals to this bacterium and to its intrinsic properties which help it in occupying varying tolerance, also the history of pollution of the soils from which bacterium isolated by these metals play critical tool in development ability of these bacteria to deal with such contaminations, this which agrees with the results of the present study where it show high MIC value for Cd than this for Pb for this bacterium. From the results the accumulation increase with time, then start decreasing over specific time. This agrees with Ray et al. [24] who reported that, the accumulation of Pb by B. cereus increased with time, then starts decreasing. It may be concluded that, metal binding sites became saturated after specific time. The maximum accumulation of both of metals by this bacterium occurs in the highest concentration of metals then start decreasing with increasing of the time, this observed by Tunali et al. [SEP] Justify:

Output: The text corroborates the claim by providing specific evidence of bioaccumulation of heavy metals, such as lead (Pb) and cadmium (Cd), by a bacterium. It mentions that the accumulation of Cd increases with time and concentration, and discusses the capacity of certain organisms to accumulate these metals from contaminated soils. While it primarily focuses on a bacterium, the principles of bioaccumulation can be generalized to mushrooms as they also have the capability to uptake heavy metals from the soil.


Input: Task: contrast the claim using the given text. Claim: Perennial plants can provide year-round yields and stabilize soil. [SEP] Text: However, the measurements were on soils with high surface organic carbon content and carbonate rich sub-soils, so caution should be used when extrapolating these results to other locations. For example, the highest soil organic carbon stocks reported at long-term agricultural plots in western Canada are about 8. 5 kg C m−2 in the top 15 cm (VandenBygaart et al. 2010), whereas the 0 to 30 cm soil organic carbon content of our fields is about twice this amount. The carbon emissions from the Treatment field following conversion were similar to the losses from established annual crops, and the carbon gains observed on the Control field were similar to other established grassland sites measured elsewhere. The loss of 149 g C m−2 observed from the Treatment field was of a similar magnitude to that observed from annual cropping systems not undergoing cropping system conversion events. For example, Glenn et al. (2010) observed a mean net loss of 106±51 g C m−2 yr−1 from a 3-yr annual rotation south of Winnipeg, and all annual European rotations investigated by Kutsch et al. (2010) were net carbon sources with a mean of 95 ±87 g C m−2 yr−1. The carbon gains from the Control field (96 g C m−2) are similar to other grassland sites: 126±14 g C m−2 yr−1 (Ferlan et al. 2011), 118±36 g C m−2 yr−1 (Meyers 2001), and 147±130 g C m−2 yr−1 (Ammann et al. 2007). However, Ammann et al. (2007) also reported a non-significant loss of 57 (+110 or −130) g C m−2 yr−1 from a grassland site. Conversion of grassland to forest in Germany had a differential carbon loss of about 38 g C m−2 yr−1 in the first year only, but this afforested site had greater NEP in subsequent years (Don et al. 2009). Soil carbon sequestered with perennial crops may be lost relatively quickly by periodic inclusion of annual crops in rotation (Janzen et al. 1998). Under these conditions crediting or otherwise giving producers incentives to convert annual cropland to perennial grasslands for the purpose of removing carbon from the atmosphere may be most beneficial if grasslands remain under perennial management for long periods. [SEP] Justify:

Output: The text contrasts the claim by indicating that soil carbon sequestered with perennial crops may be lost relatively quickly when annual crops are included in the rotation. This suggests that the inclusion of annual crops could undermine the stability and benefits typically attributed to perennial plants in soil management.


Input: Task: pass the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: We sought to identify FIB-like proteins in 47 proteomes of viruses that: infect Bacteria and Archaea; derive from ancient symbiotic viruses; and belong to several species of giant viruses from different lineages such as Pandoravirus, Pithoviridae, Megaviricetes (Phycodnaviridae, Mimiviridae, and Marseillevirus), Faustovirus, Pacmanvirus; as well as some giant uncultured marine viruses from environmental samples (S1 Table). No significant match against viruses was detected. Similarly, no FIB sequences were detected in any of the 212 bacterial genomes analyzed (182 well described bacteria [WDB] [36] and 30 species from the candidate phyla radiation [CPR] group [36, 37]; S2 Table), consistent with previous reports [2, 3]. Among CPR bacteria, we detected 20 different families from the MTase superfamily, but none were significant against our HMM-FIB model for FIB proteins (S3 Table). Searching for the 15. 5k protein (L7Ae homolog in Archaea) and the NOP56 protein (NOP5 homolog in Archaea) across Bacteria proteomes did not result in any significant hit against this lineage (S4 Table). These proteins are essential for the recruitment of fibrillarin in the RNP complex. We identified 1063 non-redundant FIB sequences spanning all major clades from Archaea and Eukarya (S5–S9 Tables). The analyzed homologous sequences include: 143 in Archaea (from 148 analyzed genomes), 103 in protists (from 75 genomes), 170 in fungi (from 157 genomes), 328 in plants (from 153 genomes), and 319 in animals (from 257 genomes; Fig 1A and 1B). We then inferred the phylogenetic gene tree from the alignment of the 1063 retrieved sequences (Fig 1C; S1 Fig; S10 Table). Based on the tree, almost all analyzed sequences formed monophyletic groups according to their taxonomic affiliation. Notably, mammalian FIBs formed into two separate monophyletic groups (and B). Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFig 1. Overview of inspected taxonomic groups and distribution of FIB protein sequences through the three domains of life. [SEP] Justify:

Output: The text does not address the claim directly as it focuses on the identification of FIB-like proteins across various viruses and the construction of a phylogenetic gene tree. While it involves analysis across different domains of life, it does not specifically discuss fossils or their role in understanding the evolutionary history of life.


Input: Task: corroborate the claim using the given text. Claim: Some mushrooms can bioaccumulate heavy metals from the soil. [SEP] Text: The high sorption noticed after 2h at concentration 50 mgl-1. This is similar to Anzeze et al. [29], who reported that, the rate of adsorption of Cd by Eichhornia crasippes was very fast at first and over 95 % of total biosorption of Cd (II) ions occurs in the first 5 minutes and thereafter it proceeds at a slower rate and finally no further significant adsorption is noted beyond 20 minutes of contact time. For effect of metal concentration on biosorption, results show increases in Cd sorption with increasing metal concentration. The initial concentration provides an important driving force to overcome all mass transfer resistance of metal between the aqueous and solid phases [30]. The increasing amount of metal adsorbed by the biomass will be increased with initial concentration of metals. Optimum percentage of metal removal can be taken at high initial metal concentration. Thus, at a given concentration of biomass, the metal uptake increases with increase in initial concentration [31]. 224. éni S, Khwaldia K, et al. (2012) Isolation and characterization of a novel Micrococcusstrain for bioremediation of strontium in radioactive residues. MicrobiolRes 64: 851-858. Volesky B, Holan ZR (1995) Biosorption of heavymetals. BiotechnolProg 11: 235-250. (1995) Metal cation uptake by yeast: areview. ApplMicrobiolBiotechnol 43: 579-584. (2004) Metalbioremediationthrough growing cells. 30: 261-278. (1996) Bioaccumulation and biosorption of CO2+ by neurospora crassa. BiotechnolLett 18: 1205-1208. (1994) Biosorption of heavymetal cations by non- viable yeastbiomas. 15: 429-438. (2002) Uranium accumulation by a bacteriumisolated from electroplating effluent. 18: 295-302. (2008) Novel metalaccumulator and proteasesecretor microbes from Wetland. BiochemBiotechnol 4: 255-264. (2002) Microbiology. (5th Edn. ), McGraw-Hill, New York. Murray RGE (1992) The familyDeinococcaceae. [SEP] Justify:

Output: The text corroborates the claim by discussing the biosorption and bioaccumulation of metals, specifically mentioning heavy metals and their uptake by biomass. It provides evidence of how factors like concentration affect metal uptake, which is relevant to the claim concerning the ability of mushrooms (and other organisms) to accumulate heavy metals from the environment.


Input: Task: contrast the claim using the given text. Claim: Perennial plants can provide year-round yields and stabilize soil. [SEP] Text: It is likely that carbon sequestration benefits increase with the length of the perennial grassland rotation but it may not be reasonable to maintain pastures indefinitely. It may be possible to minimize carbon losses following perennial to annual conversions by using management practices such as reduced intensity tillage (Jabro et al. 2008) or delaying tillage until the soil is cool (Reicosky 1998), which will help reduce the fallow proportion of the growing season and reduce ER following the conversion events. Extending the perennial phase of a crop rotation with respect to the annual phase may make slow, long-term increases in soil organic carbon possible. overall effect of conversion seems to be most strongly related to the relative length of the cropped and fallow periods within the growing season because the difference between the fields following conversion was mainly in GPP while ER was affected relatively little. The ER remained relatively constant for each field throughout the season but there was an inherent difference between the fields, even before the conversion was imposed. The perennial system gained 96 g C m−2 and the transitional system lost 149 g C m−2, even though about 200 g C m−2 was added as manure. The net effect of conversion from a perennial to annual cropping system in the year of conversion was the loss of more than 245 g C m−2. It is likely that perennial root decomposition will contribute additional carbon losses from the converted field over future years, but it will be difficult to distinguish this from the dynamics of future annual crops. When it is not possible to maintain perennial grassland rotations indefinitely, it may be possible to minimize losses with beneficial management practices and increase the relative length of the perennial grassland phase in crop rotations. thank the Council of Canada (NSERC), the Program (MSAPP) and the (AGGP) of Agriculture and Agri-for funding this project. We also acknowledge the Program (CCP) and the University of Manitoba's Faculty of for providing conference travel funding. We thank for providing the fields and site data, and Zoran Nesic, Biometeorology and Group, University of British Columbia, for supplying the temperature controlled housings, software, excellent technical support and advice. of the at Food and provided a great deal of soil carbon analysis. We thank and for technical help. Thanks to and who provided advice. 1957. Reconnaissance soil survey of Report #7. Survey1953. [SEP] Justify:

Output: The text contrasts the claim by indicating that while maintaining perennial grassland rotations can enhance soil carbon levels, it also highlights that it may not be feasible to maintain these systems indefinitely. The conversion from perennial to annual systems results in significant carbon losses, suggesting that the stability and long-term benefits of perennial plants are limited by these management practices and conversion events.


Input: Task: pass the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: a) Depiction of the major taxonomic groups analyzed in this study. FIB sequences were sought across a total of 1002 genomes from the three domains of life (212 Bacteria, 148 Archaea, and 642 Eukarya). Graph dimensions are not to scale. b) The number of FIB sequences (purple bars) per analyzed genome are grouped according to major taxa in a species phylogenetic tree. Concentric circles indicate the number of FIB sequences. c) Unrooted phylogenetic tree of the total 1063 FIB proteins found in Archaea and Eukarya, colored by main taxonomic groups. order to identify amino acid conservation of the FIB domain across lineages, (S2 Fig) was built an alignment by Clustal-O with default parameters using representative sequences from different lineages chosen to encompass different phyla and classes across the five major analyzed groups (e. g. , for animals we used representative sequences of porifera, cnidaria, mollusca, artropoda, tardigrada, nematoda, fish, coelacanth, amphibia, reptiles, and mammals). Overall, FIB domain composition is well conserved from Archaea to lineages of Eukarya, specifically on the MTase domain (S2 Fig). FIB proteins from archaeal organisms are shorter than those from most eukaryotic organisms, but several well conserved amino acids were identified even in distant eukaryotic lineages (red shaded columns in S2 Fig). The GAR domain was not present in Archaea FIB proteins, suggesting acquisition during early eukaryotic evolution. Three different Models (HMM) for RG-rich regions reported in [13] were used identify whether other RG-rich regions (like the GAR domain in FIB) were present in other proteins from Bacteria and Archaea, we had examined; no significant match was found against the proteomes of prokaryotes (S4 Table). In Archaea, we detected FIB homologs in 140 of 148 species (95%), showing evidence of independent gene losses in eight organisms (5% S5 Table) during evolution, or due to genome annotation errors or missing data. [SEP] Justify:

Output: The text does not address the claim regarding fossils and their connection to evolutionary history. Instead, it discusses the analysis of FIB sequences across various taxa and the conservation of certain protein domains, which does not directly relate to fossil evidence or provide insights into evolutionary processes driven by fossil records.


Input: Task: corroborate the claim using the given text. Claim: Certain fungi can decompose organic matter, contributing to nutrient cycling. [SEP] Text: IntroductionCocoa (Theobroma cacao L. ) is an important perennial crop, whose mode of cultivation is currently at large scale converted from agroforestry to monoculture systems given higher yields under the latter (Armengot et al. 2016; Niether et al. 2020). Because of its dependence on fertile forest soil, cocoa monoculture causes deforestation and CO2 emissions (Gockowski and Sonwa 2011) while cocoa agroforests are known to conserve biodiversity (Asase and Tetteh 2010) and sequester carbon (Nijmeijer et al. 2018). In these cocoa agroforestry systems, cycling of litterfall and decomposition acts as an input-output system for organic matter sustenance (Fontes et al. 2014). Due to reduction in biodiversity when cocoa agroforests are converted into monocultures, this matter cycling is reduced (Schneidewind et al. 2019). This is problematic especially in where nutrient reserves on heavily leached soils are low and nutrient exports in the harvest are rarely replaced by application of mineral fertilizers. Litterfall in cocoa agroforests is estimated to amount to 10 t ha−1 yr−1 (Dawoe et al. 2010; Saj et al. 2021) whereby its distribution throughout the year depends on climatic conditions. It is generally higher in the dry than in the wet season (Saj et al. 2021), however, thunderstorms and high wind speeds in the rainy season may cause occasional peaks (Becker et al. 2015). Litterfall chemistry, such as nutrient concentrations, in cocoa agroforestry systems is influenced greatly by climate and shade tree diversity (Saj et al. 2021; Sari et al. 2022). In a cocoa agroforestry system in Mexico, magnesium (Mg) concentrations were higher in litterfall during the rainy season, whereas phosphorus (P) and calcium (Ca) concentrations were higher in dry season litter (Pérez-Flores et al. 2018). The decomposition of litter biomass releases carbon and nutrients, whose turnover and plant availability is greatly influenced by climate, soil organisms, and litter chemistry (Aerts 1997). In most agroecosystems, initial N, P, lignin, cellulose, and polyphenols are important regulators of litter decomposition (Dawoe et al. [SEP] Justify:

Output: The text corroborates the claim by discussing the decomposition of litter biomass in cocoa agroforestry systems, noting that 'the decomposition of litter biomass releases carbon and nutrients,' which indicates a similar role in nutrient cycling that fungi would contribute. The emphasis on litter cycling and its impact on organic matter sustenance supports the idea that certain organisms, such as fungi, play a crucial role in this process.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: 87x Rb. Amsterdam 14 december 2022, ECLI:NL:RBAMS:2022:7520 (DPA Group), r. o. 5. 14. Het is voor de minderheidsaandeelhouder bijna onmogelijk om te ontsnappen aan het bereik van het billijke prijsvermoeden, omdat slechts in uitzonderlijke situaties niet aan het 90%-criterium wordt voldaan. Als er niet aan het 90%-criterium wordt voldaan, zal alsnog vaak bij de biedprijs worden aangesloten op grond van het jurisprudentieel vermoeden. Het leerstuk van het billijke prijsvermoeden heeft volgens mijn analyse enige aanscherping en duidelijkheid nodig. De toets voor de vraag of de biedprijs een billijke prijs is, is de overweldigende steun door aanmeldende maatman-aandeelhouders. Om de integriteit en betrouwbaarheid van de ratio achter het billijke prijsvermoeden te garanderen, moeten alle correcties op het billijke prijsvermoeden plaatsvinden wanneer wordt vastgesteld of voldaan is aan het 90%-criterium en niet daarna. Ik heb uiteengezet welke ruimte daarvoor bestaat door het introduceren van de maatman-aandeelhouder en de WAP-aandeelhouder. Dit brengt met zich dat er geen situatie denkbaar is waarin het prijsvermoeden weerlegd kan worden zodra eenmaal is voldaan aan het 90%-criterium. De systematiek van het prijsvermoeden en de ratio daarachter lijken mij daar niet geschikt voor. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses legal principles related to shareholder rights and pricing assumptions related to financial transactions. There is no mention of legends, creatures, or cultural narratives that would corroborate or contrast with the claim regarding Bigfoot or the Loch Ness Monster.


Input: Task: pass the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: Genomes from three Euryarchaeota species contained FIB duplicates: Archaeoglobales archaeon ex4484_92, Aciduliprofundum boonei T469, and Halonotius sp. J07HN4 (S5 Table). Significant hits were found in the vast majority of the 148 analyzed proteomes from Archaea for the 15. 5k protein (142 significant hits) and the NOP56 protein (145 significant hits); at least one well conserved copy per specie was identified for each protein (S4 Table). In protists, we detected 103 FIB homologs in 73 of 75 (96%) analyzed species (S6 Table). Fifty-three of 75 species (73%) contained only one FIB sequence per genome (Fig 2A). Sixteen of 75 species (23%) contained FIB duplicates ranging from 2 to 7 paralogs per genome (S6 Table). Species from Stramenopiles and Alveolata also contained more than one FIB per genome (Fig 2A). The phylogenetic analysis of protist FIBs was congruent with the major phylogenetic groups; however, the Alveolata FIBs were separated into several clades, mainly Apicomplexa and Oligohymenophorea, indicating higher divergence (S3 Fig). Interestingly, the FIB sequence SymiT_OLP95976. 1 from the ancestral dinoflagellate Symbiodinium microadriaticum (clustered within the Apicomplexa clade, sister to dinoflagellates) contained up to 53 exons (S3 Fig). Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFig 2. Depiction of the number of FIB proteins detected in Eukarya. a) FIB proteins detected in the protist group. b) FIB proteins detected in Fungi. c) FIBs detected in Plant genomes. d) FIBs detected in invertebrates. e) FIBs detected in vertebrates. Each circle represents the number of FIBs per species (y-axis). Each taxonomic group is presented in a unique color (dots and strips under the x-axis) consistently throughout the text and figures. [SEP] Justify:

Output: The text passes in relevance to the claim as it focuses on genomic and proteomic data from various species, without addressing fossils or their role in understanding evolutionary history. It discusses FIB duplicates and phylogenetic analysis among various organisms but does not provide any insight related to fossils.


Input: Task: corroborate the claim using the given text. Claim: Certain fungi can decompose organic matter, contributing to nutrient cycling. [SEP] Text: On average, 19 kg N ha−1, 3 kg P ha−1, 30 kg K ha−1, 4 kg Ca ha−1 and 4 kg Mg ha−1 exported via annual harvest (cocoa pod husk and beans) represented 5%, 7%, 29%, 2%, and 4%, respectively, of the annual nutrient stocks recycled in total litterfall (Table 4). Table 4 Carbon and nutrient stocks of the annual litterfall components, cocoa bean and pod husk of cocoa agroforests under conventional and organic management in Suhum Municipality, of GhanaFull size tableDecomposition of cocoa leafWithin the first 2 months, 50% of the initial litter DM disappeared under organic and conventional management (Fig. 3a). After 1 month of cocoa leaves placement, P and Ca release under conventional management were 20% and 21%, respectively, higher (p < 0. 05) than under organic management (Fig. 3c and e). Similarly, Mg release at months one and two after cocoa leaves placement were 24% and 10%, respectively, lower (p < 0. 05) under organic management than under conventional management (Fig. 3f). At the end of the 12 months study period, on average 15% of the initial litter remained in the litterbags. Potassium was rapidly released from litter leading to the disappearance of 98% of the initial content. Although DM disappearance and N release rates were 35% greater under organic management compared with conventional management, these differences were not statistically significant (Table 5). Phosphorus, K, and Ca release rates were 13%, 33%, and 41%, respectively, higher in conventional farms than organic farms, but these differences were not significant. For P, K, Ca, and Mg 93–100% of nutrients belong to the labile fraction of the cocoa leaves. Among the nutrient release rates, it was only Mg that under conventional management was significantly (51%) greater than under organic management. Fig. 3Decay and nutrient release patterns of cocoa leaves during 12 months in cocoa agroforests under conventional (Con) and organic (Org) management in Suhum Municipality, of Ghana. Error bars indicate +/− one standard error of the mean. * and ** above the error bars indicate significant differences at p = 0. 05 and 0. [SEP] Justify:

Output: The text corroborates the claim by discussing the decomposition of cocoa leaves and the subsequent release of nutrients such as nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg). It explains how the decomposition of organic matter contributes to nutrient cycling within the cocoa agroforests, supporting the idea that fungi play a role in breaking down organic matter to facilitate nutrient release. The mention of nutrient stocks recycled in litterfall further emphasizes the role decomposers play in nutrient cycling.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: Daarnaast is het ook in het belang van het proces om alle omstandigheden mee te nemen in de vraag of aan het 90%-criterium wordt voldaan. Uit die aangescherpte systematiek wordt per definitie duidelijk of voldoende maatman-aandeelhouders het bod steunen omdat zij de biedprijs een billijke prijs vinden. Daarna staat wat mij betreft vast dat de biedprijs kwalificeert als billijke prijs. Dit kan het gevolg hebben dat de bijzondere uitkoopprocedure iets duidelijker wordt én dat de bestudering daarvan overzichtelijker wordt. Kortom, het billijke prijsvermoeden is de jure een weerlegbaar bewijsvermoeden, maar de facto een onweerlegbaar bewijsvermoeden. Afwijken van het billijke prijsvermoeden is daarom ook echt het monster van Loch Ness. De kans dat we Nessie ooit gaan zien, is nihil. Noten * De auteur bedankt en voor hun commentaar tijdens het schrijfproces. 1 Art. 2:359c BW. 2 Zijn er verschillende soorten aandelen, dan kan de vordering slechts worden ingesteld ten aanzien van de soort waarvan eiser of eiseres ten minste 95% van het geplaatste kapitaal verschaft en 95% van de stemrechten vertegenwoordigt, vgl. art. 2:359c lid 2 BW. 3 Art. 2:359c lid 6 BW, eerste zin. 4 Art. 2:359c lid 6 BW, tweede zin. [SEP] Justify:

Output: The text is irrelevant to the claim, as it discusses legal criteria and processes without mentioning any legends or cultural beliefs about creatures like Bigfoot or the Loch Ness Monster. Therefore, it does not support, contrast, or have any relation to the claim.