Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: The intracellular accommodation of unbranched hyphae (during the early stage) and of arbuscules (at a later stage) is a coordinated developmental process between the plant and the fungal cells: it involves an intricate and largely unexplored signal exchange, intense secretory activity related to the biogenesis of the perifungal membrane and an overall reorganization of the cell architecture. Several plant genes are known to be required for the establishment and functioning of the AM symbiosis. Some of them encode proteins that are components of the so-called 'SYM pathway' and are essential for early signalling and root colonization [10]. Other genes are likely involved in nutrient exchange during arbuscule functioning, such as the Medicago truncatula gene coding for a phosphate transporter (PT4) specifically induced in arbuscule-containing cells [22]. However, despite molecular and cellular evidence of the expression of these genes in arbuscule-containing cells, the corresponding proteins have not been identified through proteomic approaches until very recently [23], most likely because of their accumulation in a small sub-population of root cells, those harbouring the arbuscules, and because of technical difficulties with membrane protein extraction. Whereas the main signal molecules involved in the AM fungus–host plant dialogue have been identified, little information is so far available on the recognition events and on the long-maintenance factors involved in the ECM symbiosis (Garcia et al. 2015), although auxin and ethylene have been identified as some of the signals exchanged between the two partners in ECM [24,25]. By contrast, nothing is known concerning this aspect in the ericoid and the orchid mycorrhiza. The colonization steps have a very different morphology in ECM and AM symbioses. During the symbiotic phase, ECM fungi form a fungal sheath (the mantle) that develops outside the root. From the inner layers of the mantle, some hyphae penetrate between the epidermal and the outer cortical cells to form an intercellular hyphal network (the Hartig net) inside the root tissues [1]. Mycorrhiza-induced small secreted proteins (MiSSPs) are fungal proteins known to be involved during the formation and maintenance of the symbiosis between ECM fungi and their host plant [26,27]. [SEP] Justify:

Output: The text corroborates the claim by detailing the biological processes and interactions involved in the symbiotic relationship between mycorrhizal fungi and plant roots. It describes how fungal structures like arbuscules facilitate these relationships through a coordinated developmental process, involving gene expression and nutrient exchange between the plant and fungi. The mention of several plant genes and their significance in the establishment and functioning of arbuscular mycorrhizal symbiosis directly supports the claim about the symbiotic nature of the relationship.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: When FPA was at its minimum, the cellulose content became almost stable. In accordance with the degradation regularity of cellulose, the peak of xylanase activity on day 120 (293. 5 U/L) corresponded with the increased degradation rate of hemicellulose. After 135 days the total weight loss of bagasse was 51. 6%, in which the losses of lignin, cellulose and hemicellulose were 65. 5%, 62. 8% and 61. 5%, respectively. Figure 2 Inducible lignocellulosic enzymes (laccase, MIP, cellulase and xylanase) (A) and changes of lignocellulose component contents (B) during bagasse degradation by C. cladosporioides Ch2-2 at 28°C. Full size imageThese results indicated that multiple lignocellulosic enzymes of Ch2-2 were an efficient natural synergy system with a clear selective secretion pattern, which was induced by the specific components of bagasse. Even more importantly, it was found that the degradation rate of lignin limited that of the holocellulose to some extent. Ligninase purification and propertiesThe important role of C. cladosporioides Ch2-2 ligninase during the degradation process was mentioned above, which was crucial in order for cellulases and hemicellulases to carry out their roles sufficiently. In order to further analyze the ligninase characteristic, laccase and MIP were purified and studied. The molecular weight of laccase was about 70 kDa as measured by SDS-PAGE (Figure 3A). Its optimal temperature and pH were 15°C and pH 3. 5, respectively (Figure 4A, D). It was stable at a very wide temperature and pH range of 4 to 40°C and pH 2. 0 to 5. 5 (Figure 4B, D). Using ABTS as a substrate, the Km and Vmax for laccase were 2. 8 μM and 57. 9 μmol/min/mg under the optimal conditions. Laccase activity was inhibited by 2 mM of Fe2+ (5. 36%), SDS (27. 2%) and was slightly inhibited by EDTA (74. 6%) at a concentration of 10 mM, and essentially unaffected by 2 mM of EDTA (98. [SEP] Justify:

Output: The text is largely irrelevant to the claim because it discusses the degradation of lignocellulosic materials and the activity of various enzymes, such as laccase and cellulase, in the degradation process. There is no mention of bioengineered yeast or its ability to produce biofuels from sugars, making it not supportive or contrasting to the claim.


Input: Task: pass the claim using the given text. Claim: All bacteria are harmful to human health. [SEP] Text: (2020) Broadly targeted autoreactivity is common in severe SARS-Cov-2 infection. medRxiv. [Crossref] Brawer Ae, (2019) Multiple myeloma presenting with clinical and serological features of systemic lupus erythematosus: a case report. Cases 2: 1-2. Bigazzi PE (1997) Autoimmunity caused by xenobiotics. Toxicology 119: 1-21. [Crossref] (2010) Toxicology of autoimmune disease. Toxicol 23: 455-466. [Crossref] Abou-(2018) Neural autoantibodies in patients with neurological symptoms and histories of chemical/mold exposures. Health 34: 44-53. [Crossref] Brawer AE, (2016) The onset of rheumatoid arthritis following trauma. Rev 8: 77-80. [Crossref] Guengerich FP (2017) Intersection of roles of cytochrome P450 enzymes with xenobiotic and endogenous substrates. Relevance to toxicity and drug interactions. Toxicol 30: 2-12. [Crossref] (2019) A comprehensive review of common polymorphic variants that cause missense mutations in human CYP’s and UGT’s. 111: 983-992. (2014) On the possible interaction between vaccines and drugs. 70: 369-371. Editor-in-Chief 10. 15761/FWH. 1000195 Corresponding author 07740, USA E-mail : bhuvaneswari. bibleraaj@uhsm. nhs. uk No data. [SEP] Justify:

Output: The text does not address the claim about bacteria being harmful to human health. It discusses various medical topics, including autoimmune diseases and toxicology, without mentioning bacteria or their effects on health. Therefore, the text is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: The identification of the key molecular players in mycorrhizal symbioses is mandatory to understand the complex interactions between the symbiotic partners and the ways to improve and fully exploit their symbiotic potential in sustainable crop and forest management. Genome sequences of several mycorrhizal fungal species are now available and provide a great opportunity to increase our knowledge on the mycorrhizal lifestyle, on the metabolic capabilities of these symbioses and on the molecular dialogue between the two symbiotic partners [28]. Advertisement 3. The symbiotic proteomics of mycorrhizal interactionsProteomics is the large-scale study of proteins from a specific proteome in order to understand cellular processes, and includes assessment of protein abundance, protein modifications, along with identification of interacting partners and networks. As the aim of proteomics is the identification of proteins, the molecular components actually taking part in cellular processes, rather than their genetic information, proteomics could be the main technique to unravel the key players of mycorrhizal symbioses. However, when the number of proteomics studies is compared with those using genomics, transcriptomics or microscopy, the gap is very significant (Table 1). One of the reasons is that the methods for protein identification are based, nowadays, mainly on mass spectrometry, a more complex and expensive technology than high-throughput DNA or RNA sequencing. Protein identification is made by matching the peptides masses to corresponding masses calculated by the software on proteins or translated gene sequences available in databases. If sequences are not found in databases, protein identification fails. Over the years, many loopholes have been found, among them the easiest was to use sequences from other species. Concerning the identification of plant proteins, the best-studied and well-sequenced plant is Arabidopsis thaliana. Unfortunately, this plant is not able to form any type of mycorrhizal symbiosis. In the past few years, DNA sequencing has become cheaper and almost a routine technique, allowing the genome sequence of many organisms to become available. Another aspect that has hindered the use of proteomics in the study of mycorrhizal interactions is the fact that the mycorrhizal symbiosis involves a small percentage of plant root cells, that may contain fungal structures at different developmental stages and with different putative roles [29]. [SEP] Justify:

Output: The text corroborates the claim by discussing the importance of understanding the interactions between mycorrhizal fungi and their plant partners, detailing the identification of molecular players in mycorrhizal symbioses. It explicitly states that the research aims to explore the metabolic capabilities of these symbiotic relationships and the molecular dialogue between the symbiotic partners, which underscores the existence of a symbiotic relationship between mycorrhizal fungi and plant roots.


Input: Task: contrast the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Oleaginous yeasts, defined as those that can accumulate lipids to over 20% of their dry-cell weight (DCW), are still being screened and can be found in different taxa. A useful criterion is their ability to grow on pentoses or polysaccharides, which are lignocellulosic sugars. However, although some of these yeasts are immediately suitable for providing useful enzymes (such as sugar hydrolases), their capacity to be custom engineered for specific lipid production will require additional effort. Conversely, known genetically-tractable yeasts may not have yet been tested for their oleaginous potential. Blastobotrys adeninivorans is part of a basal clade of the Saccharomycotina subphylum [1] and diverged long before Saccharomyces cerevisiae. The species was first described in 1984, under the name of Trichosporon adeninovorans [2], and successively reclassified into the genera Arxula (adeninivorans) in 1990 [3] and Blastobotrys in 2007 [1]. A few natural isolates of soil, plant (wood hydrolysate, silage), or animal origin have been described in the literature or deposited in culture collections. Among them, the type strain CBS 8244T and the industrial strain LS3 have been the best studied, LS3 being used to develop auxotrophic recipients for genetic transformation [4, 5]. Since the early 1990s, the species has attracted attention because of its interesting biochemical, physiological, and genetic properties. First, it exhibits a versatile metabolism, indicative of the presence of various degradative enzymes and pathways linked to central metabolism [6]. One to several strains can assimilate a number of sugar substrates, such as d-galactose, d-xylose, l-arabinose, raffinose, sucrose, trehalose, cellobiose, starch, and arbutin, and can also ferment some of them (glucose, sucrose, and starch) [6, 7]. Organic acids (e. g. , pyruvate, acetate, and butyrate), as well as aromatic compounds (e. g. , hydroxybenzoates), may also serve as a growth source [6, 7]. [SEP] Justify:

Output: The text contrasts the claim by detailing that while some oleaginous yeasts can grow on sugars, their custom engineering for high lipid production will require additional effort. This implies that current bioengineering techniques may not yet be fully sufficient to achieve high yields of biofuels, thus challenging the assertion that bioengineered yeast can be easily designed for this purpose.


Input: Task: pass the claim using the given text. Claim: All bacteria are harmful to human health. [SEP] Text: At the base of the cilia are the basal bodies, which are responsible for ciliary assembly (Dutcher and O'Toole, 2016). Other features of the cell include a centrally located nucleus, a proteinaceous cell wall, Golgi bodies within the cup-shaped region formed by the chloroplast, and mitochondria. Image credit: Debbie Maizels. Various features make C. reinhardtii an excellent laboratory species. It grows vegetatively as a haploid, which allows mutant phenotypes to be expressed immediately. Under optimal conditions, C. reinhardtii grows so rapidly that its numbers can double approximately every 8 hours (Harris, 2001). The fact that it can grow in the dark on acetate-containing medium while retaining a functional photosynthetic apparatus, has allowed even light-sensitive photosynthesis mutants to be isolated (Levine, 1969; Spreitzer and Mets, 1980). The motile cilia of this photosynthetic eukaryote share the same structure and many of the same constituent proteins as those of mammals, and so research into its motility prompted studies that greatly advanced our understanding of cilium dysfunctions in humans (Brown and Witman, 2014). Furthermore, C. reinhardtii can be induced to sexually reproduce in the laboratory, making it easy to introduce multiple traits into a single haploid strain (e. g. to generate double or triple mutants). The power of C. reinhardtii as a model organism was further elevated by the advent of genetic transformation (Boynton et al. , 1988; Kindle, 1990; Remacle et al. , 2006), the establishment of a full nuclear genome sequence (Merchant et al. , 2007), the construction of a genome-wide library of mapped, indexed insertional mutants (Li et al. , 2016) and -mediated targeted gene disruptions (Ferenczi et al. , 2017 and 1. Taxonomic and laboratory history of C. reinhardtii Based on traditional taxonomic criteria, the genus Chlamydomonas (sensu lato) contains more than 500 species. In the course of taxonomic revisions, which are still in progress, Chlamydomonas (sensu stricto) is comprised of three species (Pröschold et al. , 2018). Accordingly, the taxonomy of some species mentioned in this 0. [SEP] Justify:

Output: The text is irrelevant to the claim that 'All bacteria are harmful to human health.' It discusses various scientific features of Chlamydomonas reinhardtii, a eukaryotic organism, and does not reference bacteria or their effects on human health. Thus, it does not provide information that supports or contradicts the claim.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: For example, arbuscules are limited to the root cortical cells in the AM symbiosis, a tissue where not all plant cells are colonized. In addition, the majority of key proteins are likely to be membrane proteins. Taken together, this means that protein extraction from AM roots will lead to a very small percentage of proteins expressed in symbiosis. This ‘dilution effect’ has made it very hard to identify the key proteins directly involved in plant–fungus interactions. In summary, the lack of sequence databases of reference organisms and the difficulties in protein extraction have characterized the first decade of proteomics applications to mycorrhizal symbiosis, and explain the limited results obtained. Advertisement 4. Proteomics in actionThe first proteomic investigation of the plant–mycorrhizal fungus symbiosis was published by Dumas et al. (1990) and used mono-dimensional polyacrylamide gel electrophoresis (PAGE) to separate soluble proteins from non-mycorrhizal roots and from roots infected by different AM fungi [30]. After this pioneering study, and because of improvements in sample extraction, sample purification and in the technological performance of the equipment, many studies have aimed to identify the key players involved in mycorrhizal interactions (Figure 3). Many strategies have been set up, depending on the target mycorrhizal type, on the symbiotic stage of interest and subcellular localization [30]. Figure 3. The figure represents different approaches that can be used to collect biological material for AM roots proteomics. (A) Collection of the whole root is the easiest and quickest approach, but it has a drawback due to the fact that the amount of proteins involved in the symbiosis is a very small percentage of the all extracted proteins. The visual enrichment approach allows the collection only of the roots in contact with the fungus. (B) The root organ culture system allows to study the early stages of colonization by following the root and hypha growth until they contact each other and then collect only the root pieces reached by the hyphae. (C) By microscope inspection, roots with the higher percentage of fungal hyphae in contact can be selected. [SEP] Justify:

Output: The text corroborates the claim by discussing the symbiotic relationship between arbuscular mycorrhizal (AM) fungi and plant roots. It highlights the interactions involved in this symbiosis, noting that studies have investigated protein expressions related to mycorrhizal interactions. The mention of techniques to study the early stages of colonization and the focus on roots that are in contact with the fungus further supports the idea of a symbiotic relationship, affirming the claim.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Although the separation of pretreated slurry into liquid and solid fraction is also an energy-consuming process, it could nevertheless be essential, mainly for three reasons: (1) to use the liquid fraction to cultivate and adapt the yeast prior to SSF; (2) to reduce the inhibitor concentration in the solid fraction, which can then be used as substrate for SSF, and (3) to increase the WIS content in the solid fraction, which gives flexibility to operate the process with more than 20% (w/w) WIS content, which is not possible with the whole slurry obtained with the pretreatment method used in the study unless evaporation is employed. Figure 2Evaluation of fermentation performance of Thermosacc in the liquid fraction of pretreated slurry. Glucose (diamonds), mannose (triangles), and galactose (squares) consumption, and ethanol (circles) production in anaerobic fermentation of liquid fraction diluted to 90% (v/v) (solid lines) and 60% (v/v) (dotted lines) with 3 g L-1 of yeast loading. The graph represents the mean of two biological replicates. Error bars are omitted for the sake of clarity. Full size imageTable 1 Composition of spruce slurry and non-washed solids used in simultaneous saccharification and fermentation (SSF) Full size tableSSF with the solid fractionHigh WIS content in batch SSF causes inhomogeneityThe solid fraction obtained after centrifugation of pretreated slurry contained increased WIS content of 30% (w/w) and reduced concentration of inhibitors (Table 1) compared to the pretreated slurry with a WIS content of 20% (w/w). The fermentability of the solid fraction was assessed in batch SSF at 20% (w/w) WIS content. One of the major problems encountered during the batch SSF was difficulty in mixing, and as a result, local variations in temperature (35 ± 4°C) were encountered. Sampling was unconventionally done during the batch SSF by opening the fermenter lid and manually mixing the contents with a spatula, and a small portion was then withdrawn. There was a 40-h delayed onset of glucose consumption and after 96 h, only free glucose and mannose present in the solid fraction were consumed and the ethanol concentration reached 9. [SEP] Justify:

Output: The text does not directly address the claim regarding bioengineered yeast and its ability to produce biofuels. Instead, it discusses the process of separating pretreated slurry and the properties of the liquid and solid fractions for fermentation; while it mentions yeast and ethanol production, it does not support or contrast the specific claim about designing yeast for high yields of biofuels.


Input: Task: pass the claim using the given text. Claim: All bacteria are harmful to human health. [SEP] Text: are also commonly found in the pelagic zone of lakes, where they sometimes form spring blooms (Similä, 1988; Krivtsov et al. , 2000). The term 'pelagic zone' refers to the water column of lakes and oceans not on or near the lake or ocean bottom. Chlamydomonas spp. are usually motile, and although this has an energetic cost, it gives them a competitive advantage in lakes that have stratified into distinct layers as a consequence of seasonal changes in temperature (Striebel et al. , 2009). Under conditions of stratification, motile algae often ascend toward the lake surface during the day to optimize their exposure to sunlight. During the night, they tend to descend to access the nutrient-rich environment below the surface. Indeed, this pattern of vertical movement has been observed for the population of Chlamydomonas sp. in a small Finnish lake (Jones, 1988). Environmental conditions and the availability and distribution of natural resources differ substantially in soils and lakes (Sommer et al. , 2012; Coleman et al. , 2017). Phosphorous, for example, is likely to be limiting to the growth of organisms in lakes and geologically old soils, while nitrogen limitation is more common in young soils (Schindler, 1977; Vitousek and Howarth, 1991). Light availability and grazing pressure by predators represent additional key environmental differences between soil and lake habitats. Consequently, these two habitats require distinct adaptations and life history strategies to optimize fitness, and it is still an open question as to whether specific pelagic strains of C. reinhardtii exist in lakes (Box 2). Chlamydomonas spp. other than C. reinhardtii are adapted to a wide range of habitats. For example, Chlamydomonas eustigma is an acidophilic species isolated from acid mine drainage (Hirooka et al. , 2017), Chlamydomonas euryale is found in temperate marine environments (Burch et al. , 2015), Chlamydomonas spp. have been isolated from Antarctic ice (Liu et al. , 2006), and some members of the genus Chlamydomonas are carotenoid-rich organisms present on the surface of snow, giving it a red appearance (Remias et al. , 2005). A Chlamydomonas sp. [SEP] Justify:

Output: The text is irrelevant to the claim as it focuses on the ecological and biological characteristics of Chlamydomonas species in aquatic environments without mentioning bacteria or their impact on human health. It discusses aspects such as nutrient availability, environmental adaptations, and the presence of different Chlamydomonas species in diverse habitats, thus failing to address or support the claim regarding bacteria.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: (D–E) Using a laser microdissection (LMD) approach, it is possible to select non-colonized cells (D) and colonized cells (E) from root sections, and to collect them separately, thus avoiding the dilution effect caused by the heterogeneous situation of a mycorrhizal root. 4. 1. Proteomics on the early stages of the mycorrhizal symbiosisThe studies on the early stages of the symbiosis coincide with the earlier studies in symbiotic proteomics. Burgess and collaborators set up a complex experiment to identify proteins either induced, enhanced or inhibited during the early stages of ECM development [31]. They compared, over a time-course, the profiles of proteins expressed in roots inoculated with three different isolates of Pisolithus tinctorius showing different degrees of root colonization: isolate H2144 exhibited a very high infectivity, isolate 441 showed moderate infectivity, while isolate H506 was not able to induce ECM [31]. They used two-dimensional electrophoresis (2DE)-PAGE, a gel electrophoresis technique introduced in the middle 1970s by O'Farrell and Klose and able to separate with high-resolution proteins by two orthogonal properties: iso-electrical point and molecular weight [32]. With this approach, Burgess et al. (1995) found that the morphological changes observed in the inoculated plant roots were linked with massive changes in protein composition, and claimed that these changes commenced at the time of contact between the two partners [31]. It was later discovered [33,34] that these morphological changes during the establishment of ECM were not caused by the contact between plant and fungus, because molecular signals released in the rhizosphere were sufficient to trigger them. The work by Burgess et al. (1995) was nevertheless important because it revealed some plant and fungal symbiosis-related polypeptides and demonstrated that their upregulation was tightly correlated with fungal infectivity. Five years later, another paper on the early stage of the ECM symbiosis was published by Laurent et al. (1999). They used the same methodological approach, 2DE-PAGE separation, but they focused their attention on the cell wall polypeptides, in order to identify cell surface proteins involved in ECM symbiosis development. [SEP] Justify:

Output: The text corroborates the claim by discussing the establishment of mycorrhizal symbiosis, including details about how morphological changes in plant roots correlate with fungal infectivity and protein composition changes. The references to 'symbiosis-related polypeptides' and how they correlate with fungal infectivity directly support the idea that mycorrhizal fungi form symbiotic relationships with plant roots.


Input: Task: contrast the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Full size imageAlthough the substrate feed improved the mixing and cell feed improved the cell viability, the highest observed ethanol yield was only 53% of the theoretical maximum despite the fact that a large fraction of cells remained viable even after 96 h of fed-batch SSF (Figure 4). The concentration levels of hexose sugars including glucose, mannose and galactose remained below 0. 3 g L-1 after 96 h, indicating that there were no fermentable monomeric sugars. This likely indicates that enzymatic hydrolysis could be a possible limiting factor affecting the overall ethanol yield. It has previously been shown that at increasing solids concentration, the proportion of adsorbed cellulase decreased because of adsorption inhibition, the mechanism of which remains elusive [31]. Also, there is previous evidence that xylose and xylooligomers with a concentration as low as 1. 67 g L-1 can decrease enzymatic hydrolysis rates and yields [32]. In our study xylose was not fermentable by Thermosacc and the existence of xylose at a significant concentration of 15 g L-1 in the SSF can hinder enzymatic hydrolysis. Besides, softwoods, such as spruce, contain relatively high lignin content [13], which can cause increased nonspecific adsorption of cellulases to lignin [32] especially at high WIS content. Evidence also suggests that the simple and oligomeric phenolics generated during pretreatment, cause inhibition and precipitation of enzymes, even at low concentrations [6, 33]. Furthermore, the operation of SSF at suboptimal temperature of enzymes combined with other aforementioned factors are some of the areas that need improvement to further increase the ethanol yields to make the process economically feasible. ConclusionWe here demonstrated that the cultivation of yeast in a continuous culture wherein the outflow of cell suspension was fed to the SSF reactor, can significantly enhance cell viability and contribute to overall increase in ethanol yield. We also show that it is possible to work at a high WIS content of 20% (w/w) in conventional bioreactors using a well-designed fed-batch SSF process. Furthermore, we demonstrated the production of high ethanol-concentration (40 g L-1), which is the minimal requirement for an economical distillation process. [SEP] Justify:

Output: The text contrasts the claim by detailing the limitations observed in the production of ethanol from sugars using bioengineered yeast. It states that the highest observed ethanol yield was only 53% of the theoretical maximum, and discusses factors such as low sugar concentration and suboptimal conditions that hinder the overall yield, indicating challenges in achieving high yields of biofuels.


Input: Task: pass the claim using the given text. Claim: All bacteria are harmful to human health. [SEP] Text: has even been identified in the air at 1,100 meters above the ground: this and other algae can be dispersed by wind over extended distances (Brown et al. , 1964). Taken together, several reports provide information on the biogeographical distribution of C. reinhardtii and other Chlamydomonas spp. However, there is little knowledge of the abundance and variations of Chlamydomonas spp. in different soil types, the dynamics of these natural populations over daily or seasonal cycles, and their physiological capabilities. chloroplast and mitochondrial genomes of C. reinhardtii have been sequenced and are 206 and 15. 8 kb, respectively (Vahrenholz et al. , 1993; Maul et al. , 2002; Gallaher et al. , 2018). Since the sequence of the nuclear genome was first published (Merchant et al. , 2007), the scientific community has focused some effort on elevating the quality of the genome sequence and improving its assembly and annotation (Blaby et al. , 2014). The current version 5. 5 nuclear genome is 111 Mb, which is similar in size to the genome of the model land plant Arabidopsis thaliana (Blaby et al. , 2014). Recently, whole-genome sequences for more than 50 additional laboratory strains and field isolates were generated (Flowers et al. , 2015; Gallaher et al. , 2015). The sequences of 12 field isolates confirmed earlier reports that with a nucleotide diversity (π) of ~3%, the C. reinhardtii genome is among the most polymorphic of all eukaryotes (Flowers et al. , 2015). The field strains, isolated from various locations in the and Canada, genetically group into three distinct populations, with gene flow between populations sufficiently low to allow the populations to adapt to their local environments. The low ratio of genome-wide non-synonymous to synonymous substitutions (0. 58) further indicates that natural selection efficiently eliminates C. reinhardtii alleles of low fitness (Flowers et al. , 2015). Whole-genome and epigenome sequencing has also been used to examine adaptation in the laboratory under changing environmental conditions (Kronholm et al. , 2017). Life cycle and its role in nature Forming zygotes likely allows C. reinhardtii to survive when conditions become harsh (Harris, 2001; Goodenough et al. [SEP] Justify:

Output: The text does not address the claim regarding the harmfulness of bacteria to human health. Instead, it discusses the biogeographical distribution, genomic sequencing, and adaptation of the alga C. reinhardtii, which is not related to bacteria or their impact on human health. Thus, it is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: It was a huge sampling effort not only because they analyzed the early stage of the symbiosis but also because they had to enrich samples for cell wall polypeptides (CWP). One of the main results was the observation of the enhanced synthesis of several immunologically related 31- and 32-kDa fungal polypeptides, called symbiosis-regulated acidic polypeptides (SRAPs) [35]. As gene expression studies were also carried out, these proteomic data also highlighted the fact that expression of SRAP-32 was regulated at transcriptional level, suggesting that the synthesis of new hyphal proteins is an important process during symbiosis formation [35]. In AM symbiosis, the phase between the first contact and the formation of the first arbuscule, a period ranging between few hours and 1–2 weeks after inoculation, is normally considered as an early stage of the interaction [36]. Focus on this particular phase is important to understand the cross-talk between the partners and how the proteomes of the two organisms change during the colonization events. A study by the group of Dumas-Gaudot [37] focused on the early stages of the AM symbiosis in three different genotypes of the model plant M. truncatula: the wild-type (J5), a mycorrhiza-defective (TRV25, dmi3) and an autoregulation-defective (TR122, sunn) genotype. The study was aimed at investigating changes in the root proteome elicited in response to appressorium formation by Glomus intraradices. For this purpose, the authors compared by 2DE-PAGE the root proteome from non-inoculated roots and from roots synchronized for appressorium formation by G. intraradices. The authors showed that proteins that responded to appressorium formation were differentially expressed in different genotypes. This paper was important because it also reported, for the first time, the identification of plant root proteins involved in mycorrhizal symbioses by matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry. This technique revealed appressorium-responsive proteins that were previously unknown on the basis of transcriptome analyses, demonstrating that proteomics and transcriptomics are complementary approaches [37]. [SEP] Justify:

Output: The text corroborates the claim by detailing the processes and studies that investigate the symbiotic relationship between mycorrhizal fungi and plant roots. It discusses the early stages of arbuscular mycorrhizal (AM) symbiosis, highlighting the interaction of Glomus intraradices with the roots of Medicago truncatula, which supports the existence of a symbiotic relationship. Additionally, the mention of identifying root proteins that are involved in mycorrhizal symbioses further reinforces the claim.


Input: Task: contrast the claim using the given text. Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: In batch SSF, the concentration of fermentable sugars is kept very low during most of the process, which could result in yeast starvation. This could be circumvented by performing prehydrolysis prior to SSF, in order to increase the concentration of fermentable sugars. However, high sugar concentrations can lead to high osmotic pressure in the fermentation medium, which is known to stress the yeast. The incubation of yeast in a medium containing high concentrations of different fermentable sugars has been shown to increase the fermentation ability of the yeast [19]. Thus, high initial concentrations of fermentable sugar as a result of prehydrolysis prior to SSF may influence the fermentation step in the process in various ways. Performing prehydrolysis at 45-48°C prior to SSF of steam-pretreated spruce, and other lignocellulosic materials, at low solids loadings has not shown any positive effect on ethanol yield, and in some cases even resulted in lower ethanol yields than SSF without prehydrolysis [5, 20, 21]. Manzanares et al. [12] reported no increase in ethanol yield from dilute-acid-pretreated olive tree prunings, even at solids concentrations up to 23% dry matter (DM), whereas they observed an increase in overall ethanol yield from 11 to 50% in SSF of hot-water-pretreated olive prunings with 23% DM when SSF was preceded by prehydrolysis. Prehydrolysis of hot-water-pretreated olive prunings at lower solids concentrations did not increase the ethanol yield [12]. It thus appears that including prehydrolysis prior to SSF does not always improve the overall ethanol yield of SSF and the presence of fiber in SSF might have an effect on the ethanol yield. Previous studies also suggest that not only the initial WIS content influences the overall ethanol yield in SSF. Also, the pretreatment method used prior to SSF has an influence on the overall ethanol yield in SSF [12]. This is partly due to different degrees of degradation of the biomass during pretreatment. Lignocellulosic biomass is further degraded and chemically altered during a prehydrolysis step, which might influence the ethanol yield in the following enzymatic hydrolysis and fermentation. [SEP] Justify:

Output: The text contrasts the claim by indicating that while high concentrations of fermentable sugars can increase yeast fermentation ability, various factors including prehydrolysis and the concentration of sugars can negatively affect ethanol yield, suggesting that bioengineered yeast may not always produce high yields of biofuels from sugars as the process is heavily influenced by method and conditions.


Input: Task: pass the claim using the given text. Claim: All bacteria are harmful to human health. [SEP] Text: How common are dormant zygospores in the environment, and where do they occur? Are zygospores typical overwintering forms, and do they also have an increased resistance to challenging biotic interactions? What are the most common biotic interactions of C. reinhardtii in the environment (competing photosynthetic microbes, grazers, bacteria, fungi)? In what ways does C. reinhardtii communicate with its neighbors (e. g. infochemical signals)? What is the metabolic significance of these interactions? How often and under what situations do cells shed their cilia in nature? Is there a selective advantage of deciliation in response to stress? Does C. reinhardtii associate with biofilms on soil p10. 7554/eLife. 39233. 004 Figure 2 Download asset Open asset Life cycle of C. reinhardtii. Haploid (n) vegetative cells occur as two mating types, mt+ and mt-, that divide by mitosis (“Asexual reproduction”; Harris, 2001, Goodenough et al. , 2007). Gametogenesis can be induced by nitrogen starvation (-N) in the presence of light, and gametes of opposite mating types can fuse to form diploid (2n) zygotes (“Sexual reproduction”). Within a few hours of fertilization, zygotes resorb their four cilia to become immotile. Over the course of several days these zygotes are remodeled into highly resistant, dormant zygospores. In this process, a strong, multilayered cell wall is formed, and chlorophyll is degraded (Harris, 2001; Goodenough et al. , 2007). As a result, mature zygospores appear orange, which reflects their carotenoid content (Lohr, 2009). When environmental conditions improve, the zygote undergoes meiosis to release four haploid cells (sometimes 8 and 16 when mitosis also occurs within the zygote wall; “Germination”). The haploid cells then resume vegetative growth. In the laboratory, zygote germination is induced by the addition of nitrogen (+N) to the medium in the light (Harris, 2001); nitrogen also causes reprogramming of gametes to vegetative cells (Pozuelo et al. , 2000). Image credit: Debbie Maizels. [SEP] Justify:

Output: The text is irrelevant to the claim regarding bacteria's harmfulness to human health as it does not discuss bacteria's impact on health but instead focuses on the life cycle and behavior of C. reinhardtii, a type of green algae. There is no mention of harmful effects of bacteria, and therefore it does not support or refute the claim in any way.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: The early stage of the mycorrhizal symbiosis represents a challenging, but also a very attractive, stage for proteomics. The sampling time and sampling method are crucial for the experiment’s outcome, and synchronization of the root colonization events would enrich root samples in the proteins of interest. Lopez-Meyer and Harrison (2006) first proposed a system to synchronize AM fungal spore germination and root penetration events [38]. Despite this technical improvement, the amount of proteins involved in the plant response to the AM fungus and in the PPA formation, as compared to the amount of proteins in the whole root, is expected to be very low and at the limit of detectability. Therefore, new strategies for sample preparation and experimental designs are required to reveal the key components of this fundamental phase of the mycorrhizal symbiosis. 4. 2. Proteomics on late stageLate stage of the AM symbiosis commonly indicates the phase in which the fungus has already build up the arbuscules. In nature, the symbiosis is highly dynamic and very complex because, while arbuscules are forming, new penetration events occur. Bestel-Corre et al. [39] reported the first mass spectrometry (MS)-based identification of mycorrhiza-related proteins. These authors studied the response of M. truncatula inoculated either with the AM fungus Glomus mosseae (current name Funneliformis mosseae) or with the nitrogen-fixing bacterium Sinorhizobium meliloti. Proteins were separated by 2DE-PAGE and image analyses, with precise quantification of spots volume performed to identify differentially expressed protein spots. Those spots were excised from the gels and analyzed by mass spectrometry. Notably, only plant or bacterial proteins were identified, may be due to difficulties in extracting fungal proteins. The authors identified several proteins related to defence responses, root physiology and respiratory pathway. However, none seemed to be a key protein in the mycorrhizal symbiosis. The proteomic analysis of the late stage of the AM symbiosis using the whole root system as starting material never allowed very good results. To overcome this problem, many studies on the late stage of the symbiosis focused their attention on a specific sub-cellular compartment. [SEP] Justify:

Output: The text corroborates the claim by discussing the dynamic nature of mycorrhizal symbiosis, mentioning that during the late stage of the symbiosis, the fungi form structures called arbuscules in the plant roots. This information supports the idea that mycorrhizal fungi indeed establish a symbiotic relationship with plant roots, as it highlights the interaction and structural formation that occurs during this symbiosis.


Input: Task: pass the claim using the given text. Claim: Chassis organisms like E. coli are commonly used for synthetic gene construction. [SEP] Text: LacI/P T7lac was also quite tightly regulated although it generated the highest background expression for GFP (Figure 4, Panel C). The ratio between the induced and the uninduced expression levels was protein dependent with relatively small induction windows for svFv173-2-5-AP (1. 2-25) and large for luciferase (60–3,000). In strain ER2566, XylS/Pm and LacI/P T7lac displayed the highest induction windows, while LacI/P trc was by far the least inducible system (0. 1-0. 2 times compared to XylS/Pm). In DH10B, induction ratios for AraC/P BAD were 1. 3-27 times higher than the ratios of XylS/Pm and XylS/Pm ML1-17. These results are consistent with a previous report documenting that the induction ratio in the AraC/P BAD system can reach up to 1,200-fold when functionally compared for the phoA reporter gene [11]. As for XylS/Pm[24, 25], the induction level can also be modulated over a wide concentration range by varying the inducer concentration. In addition, uninduced levels can be even further reduced by the presence of glucose, which represses the expression in this system [47]. The main disadvantage of the AraC/P BAD system is that the inducer can be metabolized in most strains of E. coli. The predicted translational efficiencies of the ribosomal binding sites vary over a wide rangeThe DNA region corresponding to the 5′-UTR plays a central role in regulation of gene expression [48–50]. It covers the untranslated nucleotides at the 5′ end of the mRNA [51, 52], including the ribosome binding site (RBS) that together with the translational start site influence expression [28, 49, 53]. One program frequently used to analyse the expected efficiency of these nucleotide sequences is the RBS calculator [54]. We applied its reverse engineering function on the various 5′-UTR-gene combinations used in the study and determined the translation initiation rate (TIR) values of the respective expression systems. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses specific details about gene expression systems, induction ratios, and regulation without mentioning the use of chassis organisms like E. coli in synthetic gene construction. It focuses on the performance of various expression systems rather than supporting or contrasting the claim.


Input: Task: pass the claim using the given text. Claim: All bacteria are harmful to human health. [SEP] Text: Following gamete fusion, a pair of homeodomain transcription factors initiates the genetic program for zygote development (Kurvari et al. , 1998; Lee et al. , 2008). The first zygote-specific genes are induced within minutes of gamete fusion, with hundreds of additional genes activated over the next few hours (Lopez et al. , 2015; Joo et al. , 2017). A gene encoding a polyketide synthase is induced two days after zygote formation and is critical for the zygote-to-zygospore transition, probably because it participates in the biosynthesis of the cell wall lipid polymer (Heimerl et al. , 2018). Several stages of the sexual cycle, including gamete formation and maintenance and zygote germination, depend on light and involve regulation by three different photoreceptors (Huang and Beck, 2003; Müller et al. , 2017; Zou et al. , 2017). Similar to Saccharomyces cerevisiae (Liti, 2015), we know little about the life cycle of C. reinhardtii in its natural environment. For example, there is no quantitative data on the frequency of sexual reproduction relative to vegetative growth. Yet, nitrogen is thought to become limited more commonly in soils than lakes (Schindler, 1977; Vitousek and Howarth, 1991; Coleman et al. , 2017). This notion is congruent with nitrogen limitation being a major cue for zygospore formation in nature, but we are not aware of any data on zygospore induction in natural soil environments. The occurrence of clonal cultures of opposite mating types that are derived from a single zygospore isolated from dry soil provides additional evidence for a critical role of zygospores during desiccation (Harris, 2009). Freezing resistance of zygospores and their more efficient germination under long-day conditions compared to short-day conditions suggests that zygospore formation is an overwintering strategy (Suzuki and Johnson, 2002). If true, the question arises as to whether or not nitrogen limitation and day length are adequate cues to herald the approach of winter, or whether, for example, a decrease in soil moisture content or temperature can also induce zygospore formation in C. reinhardtii. Physiological and metabolic capabilities C. [SEP] Justify:

Output: The text provided discusses various biological processes and the life cycle of C. reinhardtii, which is a type of green algae, and does not mention bacteria nor comment on their effects on human health. Therefore, it is irrelevant to the claim regarding all bacteria being harmful.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: With this approach, the same group published two other papers few years later, using sub-cellular fractionation methods, reporting more remarkable results described in the next paragraphs. Mycorrhizal systems different from ECM and AM have been seldom investigated with proteomic approaches. However, recent results have been published for orchid mycorrhiza by Valadares et al. (2014). For orchids, the association with symbiotic fungi is required for seed germination and seedling development, when the plant relies on the fungus also for carbon supply (a strategy termed mycoheterotrophy). Recently, 2D-LC-MS/MS (two-dimensional liquid chromatography MS/MS) coupled to isobaric tagging for relative and absolute quantification has been used to identify proteins with differential accumulation in the orchid species Oncidium sphacelatum at different stages of plant development after seed inoculation with a Ceratobasidium sp. fungal isolate. Eighty-eight proteins, including proteins putatively involved in energy metabolism, cell rescue and defence, molecular signalling and secondary metabolism, have been identified and quantified. These results suggest profound metabolic changes during the development of mycorrhizal orchids, likely related to a switch from the fully mycoheterotrophic to the photosynthetic stages [40]. 4. 3. Proteomics on sub-cellular compartmentAlthough 30% of naturally occurring proteins are predicted to be embedded in biological membranes [41], comprehensive membrane proteomics is technically difficult due to the hydrophobicity, heterogeneity and lower abundance of membrane proteins. In mycorrhizal symbioses, membrane proteins are very important because they likely include the receptors that control the fungal–plant dialogue as well as the transporters that mediate nutrient exchange. For these reasons, many authors have focused on membrane proteins using different enrichment protocols. The first study on sub-cellular fractionation of membrane proteins was conducted by Benabdellah et al. (1998). They isolated the microsomal protein fraction from colonized tomato roots, where they found several differentially expressed proteins [42]. Few years later, the same group identified for the first time a protein related to mycorrhizal symbiosis by Edman N-terminal sequencing, after plasma membrane enrichment and 2DE-PAGE protein separation [43]. [SEP] Justify:

Output: The text corroborates the claim by discussing the symbiotic relationship between orchids and mycorrhizal fungi. It states that 'the association with symbiotic fungi is required for seed germination and seedling development,' emphasizing that the plants depend on the fungi for carbon supply. This clearly supports the claim that mycorrhizal fungi form symbiotic relationships with plant roots.


Input: Task: contrast the claim using the given text. Claim: Beauveria bassiana is a fungal pathogen that can effectively control locust populations. [SEP] Text: bassiana in wheat root tissues was found to be necessary to improve our knowledge of the endophytic colonization of B. bassiana. Also, there are studies based on increasing nematode development of B. bassıana. Hanel (1994) hypothesized that the increased nematode numbers after the application of B. bassiana to the soil were due to the indirect effect of B. bassiana. He noted these indirect effects as higher nutrient supply for plant nematodes, changes in soil microflora, and increased nutrient availability for plants. Mwaura et al. (2017) found that ten ml of a B. bassiana spore suspension at a concentration of 5 × 107 inoculated tuber and soil together with Ditylenchus destructor and D. dipsaci in the greenhouse caused a higher nematode reproduction in potatoes. Yerukala et al. (2021) reported that B. bassiana in Rutgers tomato cultivar increased the number of gall and egg masses formed by M. incognita in the roots. Additionally, few studies with different plant-parasitic nematode species support the nematicidal effect of B. bassiana (Ghayedi and Abdollahi 2013; Kepenekçi et al. 2017; Youssef et al. 2020; Karabörklü et al. 2022). The present study results showed that 108 and 107 spores/ml of BIM-001 and BY2 isolates negatively affected P. thornei soil and root density according to control. However, the most effective concentration on P. thornei was 108 spore/ml in both isolates. While the reproduction rate of P. thornei was found to be 5. 8 in the control, the reproduction rates of BIM-001 and BY2 isolates in 108 spore/ml concentration were found to be 3. 9 and 3. 6, respectively. Although nematode reproduction rate was not suppressed at a highly, these results showed that B. bassiana, an entomopathogenic fungus, could control P. thornei infection on wheat to a certain extent. Maybe the effect on nematode control will be higher when working with higher concentrations. In addition, Göze Özdemir et al. (2022) found that P. thornei mortality rate was 75. 5 and 64. [SEP] Justify:

Output: The text contrasts the claim as it focuses on the effects of Beauveria bassiana on nematodes and their reproduction rates, rather than on locust populations. The mention of its ability to control nematodes and the effects observed in different plant species does not provide evidence for the claim regarding locusts.


Input: Task: pass the claim using the given text. Claim: All bacteria are harmful to human health. [SEP] Text: Such studies could then be extended to include analyses performed under controlled laboratory conditions that closely align with conditions encountered in the field, using innovative methods such as microfluidics to mimic conditions of the soil and other complex environments (Stanley et al. , 2016). Add a comment + Open annotations. The current annotation count on this page is being calculated. 1756. PubMed 223. 401. PubMed 680. PubMed 543. 1538. PubMed 585. PubMed 1137. PubMed 334. 429. PubMed 247. PubMed 1136. 886. PubMed 150. PubMed 452. PubMed 574. 666. PubMed 392. PubMed 624. PubMed 549. 1575. PubMed 337. PubMed 18. PubMed 127. PubMed 3572. 2369. PubMed 162. PubMed 2352. PubMed 565. PubMed 2018. PubMed 538. PubMed 361. PubMed 1669. 112. PubMed 406. PubMed 176. PubMed 281. PubMed 3211. PubMed 8313. 98. PubMed 6274. PubMed 185. PubMed 87. 332. PubMed 448. 105. 1232. PubMed 1430. PubMed 5523. PubMed 184. 2306. PubMed 1980. PubMed 840. PubMed 540. 552. PubMed 387. PubMed 5835. 198. 817. 2743. PubMed 72. 5963. PubMed 2679. PubMed 251. PubMed 207. PubMed 312. 428. PubMed 273. 201. PubMed 948. PubMed 83. 4167. 718. PubMed 19. 292. PubMed 2931. PubMed 1610. PubMed 38. 69. 1192. PubMed 4776. PubMed 268. 230. PubMed 263. 773. 138. 240. PubMed 262. PubMed 0646. PubMed 76. 0744. PubMed 1507. 448. 115. 241. 80. 1752. 220. PubMed 377. 286. 888. PubMed 246. 577. 15. 8-kb genome suggests mechanisms for DNA replication 24:241–247. PubMed 364. 115. 1555. PubMed 503. PubMed 1347. and and that it is possibly not even a single species. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses research methods in the context of studying bacteria in controlled laboratory conditions but does not address whether bacteria are harmful or beneficial to human health. It mentions innovative methods to analyze soil conditions and does not provide any information that supports or contrasts the claim about the harmfulness of all bacteria.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: These parameters are measured for individual LC-MS/MS or LC/LC-MS/MS runs and changes in protein abundance are calculated via a direct comparison between different analyses [52]. The spectral counting strategy used by Abdallah et al. (2014) suggests that accommodation of AM fungi within root cortical cells implies both a dynamic reorganization of the root membrane proteome and the de novo synthesis of AM-related proteins [23]. This study, beside the identification of proteins corresponding to key genes already identified in mycorrhizal symbiosis, also reported new proteins, many of which support the importance of membrane trafficking during mycorrhiza colonization. In summary, sub-cellular and peptide fractionations led to the identification of many key proteins involved in AM symbiosis. Despite the recent contributions of proteomics to the study of the plant–fungus mycorrhizal interactions were substantial, the role of many of them as actors in the symbiosis is still to be fully understood. 4. 4. Proteomics to identify fungal proteinsMost proteomic studies on the AM interaction have focused on plant proteins. Identification of fungal proteins is more challenging due to the impossibility to grow AM fungi in axenic cultures, to the lower amount of fungal biomass, as compared to plant material, and to the more scanty sequence information. However, pioneering studies have been carried out in France by Dumas-Gaudot and Recorbet [53,54]. Dumas-Gaudot et al. (2004) used the root organ culture method [55] to enrich for proteins expressed in the extra-radical mycelium of the AM species G. intraradices. They successfully produced, for the first time, a 2DE reference map for the extra-radical proteome of an AM fungus. After the selection of the most intense protein spots, they tried to identify them by mass spectrometry. Unfortunately, only very few proteins from filamentous fungi were known and present in public databases, and the only available genome sequence, at that time, was from Neurospora crassa, phylogenetically very far from Glomeromycota. In spite of that, identification was possible for 8 proteins out of the 14 analyzed, and homologies were found for 4 of them. Few years later, the same group attempted again the identification of fungal proteins expressed in the AM association [54]. [SEP] Justify:

Output: The text corroborates the claim by discussing the role of arbuscular mycorrhizal (AM) fungi in the symbiotic relationship with plant roots. It notes that accommodation of AM fungi within root cortical cells suggests a dynamic interaction and highlights the importance of mycorrhiza colonization. This suggests a symbiotic relationship, as the identification of key proteins involved in AM symbiosis further supports the concept of these fungi working closely with plant roots to facilitate this mutual association.


Input: Task: contrast the claim using the given text. Claim: Beauveria bassiana is a fungal pathogen that can effectively control locust populations. [SEP] Text: 1%, respectively, at a concentration of 108 spore/ml of B. bassiana BY2 and BIM-001 isolates after 72 h in vitro. The high nematicidal effect found as a result of the study carried out in vitro, unfortunately, could not be found in the experiment carried out on wheat under controlled conditions. It should not be overlooked that there was no direct contact between P. thornei and B. bassiana in the soil as in the in vitro study. Consequently, B. bassiana 108 and 107 spores/ml concentration applications reduced the reproduction of P. thornei on wheat than in the control. It was determıned that these isolates showed nematicidal effect on P. thornei. This may be due to secondary metabolites of B. bassiana during the infection (Amobonye et al. 2020). Another result of the study, when B. bassiana was applied to the soil contaminated with P. thornei at concentrations of 108 and 107 spores/ml, it was determined that the height and fresh weight of wheat plants and roots increased than the control. B. bassiana isolate (MARD 92) was identified to have endophytic property which enables it to be established within plant tissues and increases its field efficacy in controlling some pests (Khudhair et al. 2016). Beserra et al. (2019) reported that B. bassiana application in soybean positively affected vegetative development and reduced parasitism of P. brachyurus in roots. According to Kepenekci et al. (2017), tomato growth and yield increased with increasing dose applications of B. bassiana (F-56 and F-63) isolates in tomato roots infected with M. incognita. ConclusionsIn the present study, the application of native B. bassiana isolates BIM-001 and BY2 inoculum density was found important for biocontrol efficacy. Also, as concentration densities above 108 spore/ml are considered more promising in control to root lesion nematodes, reassessment with different concentrations can be done. B. bassiana BIM-001 and BY2 isolates may be used in the control of root lesion nematode on wheat which is an important plant parasitic nematode group in Turkey and the world. Therefore, detailed research is needed on the factors responsible for the pathogenicity of P. [SEP] Justify:

Output: The text contrasts the claim as it discusses the application of Beauveria bassiana isolates in controlling root lesion nematodes and its effects on wheat rather than directly addressing locust populations. It emphasizes the effectiveness of B. bassiana on plant health and nematodes, indicating a potential biocontrol mechanism but does not support the specific claim regarding locusts.


Input: Task: pass the claim using the given text. Claim: Herbal remedies can replace all pharmaceuticals. [SEP] Text: SearchSearch in: to Occom, herbal remedies and letter fragment Author Occom, Samson Date1754 ms number754900. 2 abstractHerbal remedies and a letter fragment. handwritingOccom's hand is largely clear and legible; however, within the context, many letters and words are difficult to decipher. paperSeveral small sheets folded into a booklet and bound with thread are in good condition, with light-to-moderate staining and wear. inkBrown ink is faded on some pages. There is some spattering that occasionally makes it difficult to differentiate between ink spots and punctuation. noteworthyWhen Occom's intention regarding a word or abbreviation is uncertain, the word or abbreviation has been left unmodified in the modernized transcription. Lines separating each numbered section of the herbal remedies have not been transcribed. The contents of the letter fragment are very similar to those of manuscript 756900. 2. layoutThe journal fragment is, relative to one recto, written upside-down and meant to be read from the back of the booklet. About this preserves the author's original text, including abbreviations and historical notation Modernizedversion expands abbreviations and historical notation within the author's original text to produce a modern reading copy. Technicalversion shows transcription markup and includes a summary of metadata captured in the document text. Page 1r of Aſhes — good for Pluracy 6 good for Sore mouth 7 geepbiyanbuſ[illegible][illegible] good for ^young^ Children that are inclining to fits, Start[illegible][guess: l]ed 8 — Cowachink good for Cole 9 witch Root good for Bait for Muſk 11 Page 1v wehſuc. [SEP] Justify:

Output: The text is largely about the documentation of herbal remedies and their historical context but does not provide any evidence or argument that supports or refutes the claim. It describes the condition and transcription of a document related to herbal remedies without addressing the efficacy of these remedies in comparison to pharmaceuticals. Therefore, it is deemed irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: They maintained the same experimental system, but they used the GeLC-MS/MS method and could identify 92 different fungal proteins. GeLC-MS/MS approach combines a mono-dimensional gel (1D-PAGE) and a nano-scale capillary liquid chromatography-MS/MS. Briefly, after the 1D-PAGE separation, the mono-dimensional gel is cut in several pieces; in-gel digestion results in different protein fractions that are separated and analyzed by LC-MS/MS. Using the MetaCyc database, a collection of more than a thousand metabolic pathways [57], these authors grouped those proteins in 11 pathways that span energy, metabolism and cell rescue processes. These data, together with previous identifications of putative homologues of cell-cycle gene in G. mosseae and G. intraradices [56,57], suggest that signalling pathways known in model species may also operate in AM fungi. Although the GeLC-MS/MS strategy opened the possibility to large-scale proteomics of mycorrhizal fungi, no further data have been published with this technique. Secreted fungal proteins play key roles in host plant colonization and symbiosis development in ECM interactions. Vincent et al. (2012) have identified the extracellular proteins secreted in the growth medium by the free-living mycelium of the ECM fungus L. bicolor using 2-DE, IPG-IEF shotgun (IPG strip was cut into fractions and tryptic peptides were eluted from the each fraction) and SDS-PAGE shotgun, with the aim to validate predicted secreted proteins and identify putative novel effectors of the symbiosis. Among the 224 proteins identified, there were carbohydrate-active enzymes (CAZymes), probably involved in cell wall remodelling during hyphal growth, as well as secreted proteases. Additionally, the involvement of some of these proteins in the establishment of the mycorrhizal symbiosis was supported by transcriptomic analyses of ECM roots [58]. Advertisement 5. Mycorrhizal fungi and heavy metalsIn plants, stress tolerance to soil pollution can be increased by their interaction with mycorrhizal fungi [59]. [SEP] Justify:

Output: The text corroborates the claim by discussing the roles of mycorrhizal fungi in forming symbiotic relationships with plants. It mentions that secreted fungal proteins play key roles in host plant colonization and symbiosis development in ECM (Ectomycorrhizal) interactions, which directly supports the claim that mycorrhizal fungi establish symbiotic relationships with plant roots.


Input: Task: contrast the claim using the given text. Claim: Beauveria bassiana is a fungal pathogen that can effectively control locust populations. [SEP] Text: However, extrapolation to microbe-plant association may be misleading. When microbes attempt to colonize plants, they are recognized by the plant immune system, including the salicylic acid (SA) pathway. Plant SA alters the composition and assembly of the plant microbiome, and plants expressing constitutive production of SA show slower fungal colonization (11, 12). Low spore attachment can result in reduced penetration of the root tissue, causing minimal activation of the SA pathway and potentially allowing for more robust endophyte establishment by B. bassiana. A comprehensive examination of plant immune activation upon B. bassiana colonization (i. e. , the SA-dependent systemic acquired resistance) is needed and will provide critical information on B. bassiana growth dynamics within the host plants. Furthermore, like other fungal endophytes, B. bassiana has the potential to bypass the activation of plant SA-dependent systemic acquired resistance by producing a (fungal) salicylate hydrolase. This enzyme potentially would enable the fungus to grow endophytically without causing drastic changes in plant immunity. Unique and understudied aspects of endophytic colonization by B. bassiana are (i) any impacts on arthropod pests feeding on colonized plants, (ii) the extent to which B. bassiana may safeguard plants from plant pathogens, and (iii) the degree and conditions driving growth promotion and increased plant abiotic stress tolerances (Fig. 2). While several studies have shown these various benefits, little is known concerning the underlying genetic and biochemical mechanisms involved. Although some attention has been directed toward examining the potential protective effects of endophytic B. bassiana against insect pests, this research remains limited and often shows contradictory results. Current hypotheses include that B. bassiana might protect plants from phytophagous arthropods directly (e. g. , parasitism or production of toxic compounds) and/or indirectly by deterring arthropods from ovipositing on or colonizing the plant. B. bassiana can be found as a natural epiphyte on many plants, which supports potential direct parasitism via topical acquisition of fungal spores from the plant canopy. Alternatively, Cry-like toxins and enterotoxins could be produced in planta during fungal endophytic growth, providing plants with direct systemic protection against insect pests, an idea we are currently exploring. [SEP] Justify:

Output: The text contrasts the claim by discussing the complexities and ambiguities surrounding the role of Beauveria bassiana in plant and pest interactions. While it acknowledges some potential benefits of B. bassiana in protecting plants from arthropod pests, it emphasizes that the research is limited and often shows contradictory results. The statement 'this research remains limited and often shows contradictory results' indicates that there is no conclusive evidence supporting the effectiveness of B. bassiana in controlling locust populations specifically.


Input: Task: pass the claim using the given text. Claim: Herbal remedies can replace all pharmaceuticals. [SEP] Text: �]t boild togather — good for Conſumtion 35 Page 4r Prickly Leav’d and moſt of the thorn. [SEP] Justify:

Output: The text is irrelevant to the claim as it does not provide any information about herbal remedies replacing pharmaceuticals. Instead, it appears to mention a specific herbal preparation without addressing the claim directly.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: Six out of ten of the most polluted soils in the world are contaminated by heavy metals [60], and mycorrhizal symbioses have been found to reduce metal toxicity to the host in soils with potentially toxic amounts of soluble and insoluble metals. Phytoremediation, the plant-mediated reclamation of polluted soils, is receiving increasing attention as a natural method to restore the biological features of the soil. Mycorrhizal fungi can have an important part in this process. Many studies have been carried out on the benefits of mycorrhizal plant–fungus interaction in heavy-metals-polluted soils, but only few of them have used a proteomic approach to identify the key proteins potentially involved in mycorrhiza-mediated stress tolerance. Researches on this topic have analyzed different plant organs, like leaves or root, but also focused on the symbiotic fungus. Bona et al. (2010) studied the leaf proteome of the arsenic hyperaccumulator fern Pteris vittata inoculated with two fungi (Glomus mosseae and Gigaspora margarita), with and without arsenic treatment [59]. The symbiosis with both fungi decreased arsenic concentration compared with non-mycorrhizal plants, indicating the protective effect of mycorrhizal fungi. Interestingly, the plant protein expression profile was different when the plant was inoculated with G. mosseae or G. margarita. Although they studied a different biological system, Cangahuala-Inocente and colleagues (2011) identified instead a core of 25 proteins, supporting the existence of conserved plant responses to Glomus irregulare and Glomus mosseae, at least in a woody perennial species such as grapevine [61]. A study on root proteomics has been conducted by Aloui et al. [62]. They reported, using a 2DE approach followed by MS/MS, the protective effect conferred by G. intraradices to the model legume M. truncatula in the presence of Cd. They identified 36 mycorrhiza-related proteins, but only 6 displayed changes in abundance upon Cd exposure. [SEP] Justify:

Output: The text corroborates the claim by discussing the protective effects of mycorrhizal fungi in various scenarios, including their role in reducing metal toxicity to host plants in polluted soils. It highlights specific studies that demonstrate how these fungi interact with plant roots, such as the decreased arsenic concentration in plants inoculated with mycorrhizal fungi compared to non-mycorrhizal plants, confirming the symbiotic relationship.


Input: Task: contrast the claim using the given text. Claim: Nosema ceranae is a microsporidian parasite affecting honeybee health and productivity. [SEP] Text: For instance, clear X580 haplotypes were GTAAA and AATGG, and if both are present in an isolate they will produce the RWWRR genotype, found in a number of isolates. and GTWRR haplotypes were also found, indicating that AAAAA and GTTGG must also exist (these inferences are detailed in Table 5 and additional examples can be seen in Fig. 1). Table 5 Inferences from the genotypic nature of single spores and isolatesFull size table Moreover, the X639 clones analyzed provide even clearer evidence for recombination. Four clean genotypes were obtained from the Australian samples and genotype 11, the one with most double peaks, was selected for cloning. This genotype could correspond to a mix of genotypes 2, 3 and 4 and the 38 clones sequenced produced 15 different haplotypes: four clones had one of the genotypes 2, 3, or 4; nine were other different recombinants of these and unexpectedly, two clones had a genotype 1. This latter genotype apparently did not exist in the original sample, at least with sufficient prevalence as to produce identifiable peaks in the chromatograms. Thus, direct sequencing from the original isolates highlights the haplotypes existing at considerable frequencies, while minority sequences may not be detected unless many clones are analyzed. Indeed, an earlier analysis of a series of clones indicated that the true allelic richness was most probably underestimated [23]. Strong LD has been found for short reads but those below 200 bp may be too short to identify breaking haplotypes, and LD may decay over larger distances [26]. In fact, our findings support that hypothesis: for example, a pair of nucleotides 27 bp apart is always CC or TT, yet all possible combinations exist with respect to the C or T 291 bp downstream (shadowed in Fig. 2). Thus, to detect recombination longer undivided DNA fragments must be analyzed. In summary, it appears that N. ceranae does not fit into the model of strict asexual reproduction outlined above but rather, the data obtained support the existence of a cryptic sexual cycle. Ploidy and diversity in N. ceranae Whatever the mechanisms creating genotype heterogeneity, the fact that all the isolates except one appeared to be mixed or heterozygous for the different markers raises a number of fundamental questions. genus is binucleate and recent studies even suggest a possible polyploidy for N. [SEP] Justify:

Output: The text contrasts the claim by discussing the genetic characteristics and genotypic diversity of N. ceranae, highlighting that it does not conform to strict asexual reproduction. Instead, it suggests that the data supports the existence of a cryptic sexual cycle, which implies a complexity beyond the claim's assertion that it simply affects honeybee health and productivity.


Input: Task: contrast the claim using the given text. Claim: Herbal remedies can replace all pharmaceuticals. [SEP] Text: boild in about 3 Quarts of water till Conſumd to a Quart — good for Heart born 36 An herb good for green wound a Stalk with Buſhee top 37 another wead Somew[illegible]hat Like the other herb good for Cauſed by Cold with a So[illegible][guess: r]e heated Put upon the hinder part the Neck 38 Page 4v water take and boil and take the Rt after it is boil’d and Pound it fine to mLay upon f[illegible][guess: a]x Sore and [illegible]ce of the water of for it is good for it 39 Sweet flag good for 40 Augeet good for buſt take the Rt and Pound it in hot water and lett about a jill at once twice a Day 41 A little Sort of India^n^ flax for a Perſon to take 2 Days together that has Page 5r and then take Saſarfax and milk wead and Pound them together 2 thrids of the firſt and third of the Laſt 42 the Docter muſt kake an herb and Rub his hands with it wile he is Dreſſing the Patien 43 Muſk, with Some his fat and Furr wMixt togather good for Ear ake 44 Page 5v Wauhtouwox and Sap good for flme over the Eye 45 another herb and Saſſar‐fax heart and Speccle beans Good for 46 Herb good ^to^ heal brocken bones fingers and ^about the^ ^[below]foot^ 47 Budes and Small wiled but 2 third of the togeg — good for young Women whoſe Flowers are Stopt by weakneſs of Nature 48 Page 6r Dears horn [illegible] and Mut [illegible][guess: ly youbuck], but the horn ſhoud be gated mak about a jill and boil it in about 6 jills of water and Let it boil away half then the other into it goo for When their Monthly Sickneſs over flows 49 an herb boild in 2 gallon of water and boil it about half away and then Cool it. [SEP] Justify:

Output: The text lists several herbal remedies and their uses for various ailments, suggesting that these remedies are alternatives to pharmaceuticals rather than replacements for all pharmaceutical treatments. By detailing specific herbs and their medicinal properties ('good for green wound', 'good for heart', 'good for ear ache'), the text implies that while herbal remedies have uses, they do not encompass the entirety of medical treatment that pharmaceuticals provide, thus contrasting with the claim that they can replace all pharmaceuticals.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: In the past few years, a specialized fungal genomics portal, called MycoCosm ( has been created by the US Department of Energy (DOE) Institute (JGI), offering an access point to the data from all the sequencing genome project managed by the [68,69]. Starting from the three first genome projects on Laccaria bicolor, Tuber melanosporum and Rhizophagus intraradices [70,71,72], several more genomes from symbiotic fungi, including ECM, AM, orchid and ericoid fungi, have been recently sequenced, with the aim to determine the diversity of the molecular processes involved in the interaction [28]. Despite the more powerful techniques and wider reference datasets for protein identification, current limitations exist in the application of proteomics to the study of plant–microbe interactions. In particular, new extraction methods, microsomal studies, sub-cellular enrichment, gel-free separation methods, pre-fractioning separations and new mass spectrometry are still far from being fully explored [73]. In order to identify proteins from a very small subset of target cells, Gaude et al. (2012) combined laser capture microdissection (LCM) and LC-MS/MS [74]. Laser microdissection permits the rapid isolation, from sections of a heterogeneous tissue, of a selected cell population in a manner compatible with the extraction of or proteins [29]. Using LCM, arbuscule-containing cortical cells and cortical cells from non-mycorrhizal M. truncatula roots were isolated. Proteomic analyses on these cells revealed a number of proteins involved in lipid metabolism, most likely related to the synthesis of the PAM. This targeted analysis on a specific subset of colonized cells, those harbouring the arbuscules, curiously did not identify known PAM marker proteins, thus suggesting that either sample preparation or instrument capability were not sensitive enough. Although this first use of LCM in the proteomic investigation of the AM mycorrhizal symbiosis did not identify known marker proteins, it highlighted the PAM as an important carbon sink. The LCM technique coupled with MS/MS techniques could be a powerful combination to investigate the protein profiles of specific cells at specific time-points. Moreover, LCM can help to overcome the problem of asynchronous fungal development and arbuscule maturation in mycorrhizal roots. [SEP] Justify:

Output: The text corroborates the claim by discussing the interactions between mycorrhizal fungi and plant roots, specifically mentioning the arbuscule-containing cortical cells in mycorrhizal roots and highlighting the role of the PAM (arbuscular mycorrhizal) as an important carbon sink. This implies a symbiotic relationship where the fungi and plant roots mutually benefit from this interaction.


Input: Task: contrast the claim using the given text. Claim: Nosema ceranae is a microsporidian parasite affecting honeybee health and productivity. [SEP] Text: Therefore, a nutritional context is essential when interpreting any responses of the bacterial community toward parasite challenges. In our data, parasites negatively affected the relative abundance of all 15 studied gut bacteria, leading to interrupted food digestion and nutrient absorption. It remains unclear whether gut bacteria can actively defend the integrity of the gut tissue in bees. However, microbes can be regulated by diet to protect the gut integrity and support pathogen resistance in other organisms [34]. In prior work, honey bee pathogens have shown negative correlations with S. alvi [35, 36]. From our data, the levels of F. perrara and S. alvi were significantly enhanced with the reduction of N. ceranae. It remains unclear why N. ceranae negatively affected gut bacteria. Even though sugar was the only food resource in our studied bees, the chance is low that N. ceranae directly competes for this food resource with bacteria, as N. ceranae proliferates within epithelia cells and bacteria live in the lumen. Tissue destruction caused by infection might lead to the deterioration of the gut lumen, thus impacting bacteria. Although microbial treatments provide a promising chemical-free strategy to control pathogen infection [37], caution is required, as improper probiotic supplements can lead to dysbiosis of gut microbes and susceptibility toward pathogens [38]. In our study, the relationship between N. ceranae and the studied microbes was correlative. However, the siRNA Dicer treatment and the reduced N. ceranae level was causative. We provided novel insights into interactions between gut parasites and other microbes over the entire life cycle of the parasite. Our study is limited to mid-gut tissues of newly-emerged workers. It will be interesting to screen N. ceranae and bacterial interactions in older forager bees, and in bees collected during different seasons. ConclusionsLevels of N. ceranae are negatively correlated with levels of gut bacteria. Gut bacteria were not independent with each other and were co-regulated. The relative abundance between the gut bacteria and N. ceranae was negatively correlated. MethodsEthics statementThree apiaries (with 10, 10, and 20 colonies in each apiary, respectively) for bee sample collection were established at the USDA-. No specific permits were required for the described studies. Studies involved the European honey bee (Apis mellifera mellifera), which is neither an endangered nor protected species. [SEP] Justify:

Output: The text contrasts the claim by detailing the negative effects of N. ceranae on gut bacteria in honeybees, indirectly suggesting detrimental effects on bee health and productivity. It specifically mentions that 'Levels of N. ceranae are negatively correlated with levels of gut bacteria,' indicating an adverse impact of the parasite on the gut microbiome, which is crucial for the overall health and digestion in honeybees.


Input: Task: pass the claim using the given text. Claim: Herbal remedies can replace all pharmaceuticals. [SEP] Text: and then Put about 3 Qurts of Pound it flax Seed good fror to Eaſe women that are ^in^ Traval 40 ^50^ Page 6v S[illegible][guess: uqee]t and [illegible] Sp[illegible][guess: ec]knand and healing wead, that are buſhee sgood to heal brocken bones about and arms 51 41 Page 7r Blank page. Page 7v Blank page. Page 8r Blank page. Page 8v Blank page. Page 9r Blank page. Page 9v Blank page. Page 10r Blank page. Page 10v Blank page. Page 11r Blank page. Page 11v Blank page. Page 12r Blank page. Page 12v Blank page. Page 13r Blank page. Page 13v Blank page. Page 14r Blank page. Page 14v Blank page. Page 15r Blank page. Page 15v ye 13 the[illegible][guess: ſe] far from my thoughts Page 16r Blank page. [SEP] Justify:

Output: The text provides a description of herbal remedies, such as flax seed for easing women's travel. However, it does not make a definitive claim about replacing all pharmaceuticals. Instead, it simply lists traditional uses, making it irrelevant to the assertion that herbal remedies can wholly replace pharmaceuticals.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: An evidence-based consensus for the classification of arbuscular mycorrhizal fungi (Glomeromycota). Mycorrhiza 23:515-31). The ability to analyze a single-cell proteome is exciting, but also extremely challenging. The first difficulty is the sensitivity, both correlated with the sample itself and with the mass spectrometry detection capability. Every single cell can contain proteins in a range of few to million copies per cell. However, mass spectrometers are now really powerful, and even with an attomole detection limit, only the most abundant proteins are detectable [78]. The estimated number and concentration of proteins in a single mammalian cell is 33 attomole/cell for the most abundant and 830 yotomole/cell for the less abundant [77]. The second challenge is the inherent limitation associated with the imaging modality itself. Even if further development is needed to obtain the combined resolution and sensitivity required, IMS stands up as a very promising technique to analyze specific cell types or conditions. By employing IMS, Ye et al. (2013) detected a large array of organic acids, amino acids, sugars, lipids, flavonoids in roots and root nodules of M. truncatula during nitrogen fixation [79]. They demonstrated that IMS can obtain unique information on the identity and spatial distribution of plant metabolites, although high-resolution MALDI-MS is required to fully resolve the metabolic differences in nodule chemistry. In conclusion, similarly to other ‘omics’ approaches, proteomics has also made rapid progress in the recent year, thus making this approach a very useful one to complement information on gene expression in mycorrhizal tissues. At this speed of technological developments, methods that allow us to easily assign proteins up-regulated during symbiosis to specific cell types and sub-cellular compartments may not be too far ahead. These proteomic techniques will be powerful tools to unravel the molecular component involved in plant–mycorrhizal fungal interactions. 1. . Mineral nutrition, toxic element accumulation and water relations of arbuscular mycorrhizal plants. Mycorrhizal Symbiosis. 3rd edn. Academic Press, London, 2008. 148. 2. Markmann K, Parniske M. Evolution of root endosymbiosis with bacteria: how novel are nodules? Sci 2009;14:77–86. [SEP] Justify:

Output: The text corroborates the claim by discussing the symbiotic interactions between mycorrhizal fungi and plants. It mentions that proteomic techniques are being developed to analyze the interactions specifically during symbiosis, which supports the understanding that mycorrhizal fungi engage in beneficial partnerships with plant roots.


Input: Task: contrast the claim using the given text. Claim: Nosema ceranae is a microsporidian parasite affecting honeybee health and productivity. [SEP] Text: ceranae infection induces an energetic stress in honeybees that results in a higher food intake by infected individuals40,41. As proposed by Alaux et al. 32, such a boost in food intake implies an increase in insecticide oral exposure, potentiating the effect of the later on honeybee mortality. However in this work, N. ceranae-infected and uninfected honeybees consumed a similar quantity of sucrose (Fig. 3). This result indicates that the increased food intake is unlikely to occur systematically during a N. ceranae infection and should not be considered as a specific symptom of nosemosis. Thereby, the highest mortality observed for honeybees treated with N. ceranae-fipronil combinations was not due to an increase in insecticide uptake. In parasite-insecticide interactions, the parasite development and transmission success can be modified in intoxicated organisms42,43. It is known that insect detoxification system can act on a parasite development, disrupting or enhancing it44. On one hand, the deployment of insecticide detoxification may lead to physiological modifications that render the host toxic to parasites. For example, the development of the filaria Wuchereria bancrofti larvae is affected in insecticide-resistant Culex quinquefasciatus mosquitoes, probably due to an increase in esterase activity resulting in a change in the redox potential of the tissues hosting the parasite45. On the other hand, it can be hypothesized that the production of large amounts of detoxifying enzymes could deplete the resource pool through resource-based trade-offs, limiting the host’s immune abilities, therefore favouring the parasite development44. It has been previously stated that thiacloprid may increase N. ceranae spore production, while fipronil and, to a lesser extent, imidacloprid would decrease it32,33. In our experimental conditions, fipronil exposure seemed to have no precise impact on the parasite development. Indeed, fipronil exposure only had a significant but slight impact on N. ceranae development success when applied for 7 days starting from the 7th day after emergence (Fig. 3). Interestingly, fipronil slightly increased or decreased spore production depending on the day of infection. However, our results concern a unique time point in the experiment and a specific parasite development stage (mature spores). [SEP] Justify:

Output: The text contrasts the claim by discussing various aspects of N. ceranae infection, particularly emphasizing that the infection does not lead to systematic increased food intake nor relates directly to specific symptoms of nosemosis. The findings suggest that fipronil exposure has a minimal and variable effect on the development of N. ceranae, which questions its impact on honeybee health and suggests that other factors may influence the interaction between the parasite and honeybee productivity.


Input: Task: pass the claim using the given text. Claim: Herbal remedies can replace all pharmaceuticals. [SEP] Text: Page 16v Look upon my Self of all Creatures moſt InDebtted to god in that he has Diſtinguiſhing Favours to me in giving [illegible]greater advantages to me, to know him and his ways, Stir‐ing up the Hearts of many of his People, to take notice of me with an Eye of Pity and Compaſsion, in that they have received me in their Favour and have manifeſted their Pity to me, in Endleſs Inſtances amongſt [illegible][guess: which] which your Self is on ^one^ of the Page 17r and Shall always Look upon my Self ^[illegible]^ Greatly beholden to you, [illegible]Even as Long as I Shall have my wright Sinces about me, for the Book and Money that you have Sent me by the Hands of the Wheelock of Lebanon, may god Reward you out of his Emence Treaſure of Spiritua^l^ Rewards and gifts, the Psal^[illegible]^ Says, Beleſsed is he that Conſidereth the Poor — and Since you have Favou^r^ to me, have an In‐truſt in your addreſses at the T^h^rone of grace Page 17v Blank page. as PDF/Documents in from regular to full widthexpandcompress Dock and shrink or undock and expand viewer from right hand sideright_panel_closeright_panel_open × Lebanon is a town located in the state of Connecticut southwest of the town of Hartford. The land that became Lebanon was inhabited at least 10,000 years ago based on the archeological record. By the 1600s, the land was permanently inhabited by the Mohegan Indians, who used the area primarily for hunting. Lebanon was officially formed in 1700 when English settlers consolidated a number of land tracts, including several land grants by the Assembly and lands purchased from the Mohegans. However, these purchases were controversial. In 1659, the Mohegans entrusted their reserve land to Mason, and in the following year, Mason transferred this land to the Connecticut colonial government with the understanding that there would be enough land left for the Mohegans to farm. [SEP] Justify:

Output: The text provided does not address the claim about herbal remedies and pharmaceuticals. It discusses historical acknowledgments of gratitude and provides information about the town of Lebanon and its history, which is unrelated to the claim regarding the efficacy of herbal remedies in place of pharmaceuticals.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi form symbiotic relationships with plant roots. [SEP] Text: 3. . Mycorrhizal fungi: their habitats and nutritional strategies. In:. (ed. ) Environmental and (The Mycota). 2nd ed. Springer; 2015. 256. 4. . Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages. Mycorrhiza 2009;20:217–63. 5. LePage BA. The evolution, biogeography, and palaeoecology of the Pinaceae based on fossil and extant representative. 2003;615:29–52. 6. . Evolutionary studies of ectomycorrhizal fungi: recent advances and future directions. Bot 2004;82:1122–32. 7. . Mycorrhizal Symbiosis. 2nd ed. San Diego, California: Academic Press, 1997. p. 605. 8. . Proteome analysis of an ectomycorrhizal fungus Boletus edulis under salt shock. 2007;111:939–46. 9. A higher-level phylogenetic classification of the Fungi. 2007;111:509–47. 10. Parniske M. Arbuscular mycorrhiza: the mother of plant root endosymbioses. Nature 2008;6:763–75. 11. -Hill Y. Carbon metabolism and transport in arbuscular mycorrhizas. 2000;124:949–58. 12. Yang S-Y, Grønlund Nonredundant regulation of rice arbuscular mycorrhizal symbiosis by two members of the phosphate transporter1 gene family. 2012;24:4236–51. 13. . Roles of arbuscular mycorrhizas in plant nutrition and growth: new paradigms from cellular to ecosystem scales. 2011;62:227–50. 14. Gutjahr C, Parniske M. Cell and developmental biology of arbuscular mycorrhiza symbiosis. Biol 2013;29:593–617. 15. . Fungal endophytes in a 400-million-yr-old land plant: infection pathways, spatial distribution, and host responses. 2006;174:648–57. 16. . Fossil arbuscular mycorrhizae from the early Devonian. Mycologia 1995;87:560. [SEP] Justify:

Output: The text corroborates the claim by referencing various studies and findings that detail the relationships and symbiotic roles of mycorrhizal fungi with plants. Parniske's work emphasizes the importance of arbuscular mycorrhiza as a foundational type of symbiosis with plant roots, indicating a synergy in their interactions. Additionally, references to the roles of arbuscular mycorrhizas in plant nutrition and growth further support the existence of these beneficial relationships.


Input: Task: contrast the claim using the given text. Claim: Entomopathogenic nematodes can be used as biological control agents against soil pests. [SEP] Text: am wrong here, this issue needs to be addressed. The issue of replication is an important one. It is be important to clearly state all sample sizes: how many colonies, and how many times each treatment was repeated, etc. I would personally like to see a discussion of whether the concentrations of nematodes used in the experiment are reasonable with respect to field conditions. In the discussion, the authors mention that "the conclusions of scientists advising the European regulatory body OECD in 1996 were that entomopathogenic nematodes were safe for wildlife: however, potential effects insect pollinators were not specifically considered (Ehlers and Hokkanen, 1996". However, the effect described in the manuscript are not obviously pollinator-specific. So, why do your results differ so much from earlier recommendations? Is it because bumblebees are particularly sensitive? Minor point: After referring to a latin name for an organism, it is customary abbreviate the genus (e. g. , B. terrestris). · Sep 15, 2015 Basic reporting In this ms the authors report the effect of entomopathogenic nematodes (Steinernema spp. and Heterorhabditis sp. ) on Bombus terrestris. They reported that both nematode products caused ≥ 80% mortality in bees within the 96 hours at the recommended field concentration. Since the paper focus on Entomopathogenic nematodes as a new threat to bees? . I think they need to validate these findings with care. Nevertheless i commend the work of authors and is not posing any doubt about their finding. The most serious concern is there is no report of these nematodes being infective to bombus, although they have coevolved a way back and present in soil. The author must check it. Of course i agree that may be that very few studies have been undertaken which would reveal the extent of such a phenomenon. The basic findings on Koch postulates, infective mode and proliferation of each species of nematode must be adhered before it get attention and made a subject of debate. Experimental design My another concern about the paper is that author stated that Individual bees were captured at the hive entrance and cold anaesthetised to facilitate transfer into the treatment boxes. How, it was ensured that these bees were already not carrying natural infection of nematodes or latent one. May be these bees have been used already in the area. The author must clarify. [SEP] Justify:

Output: The text contrasts the claim by discussing concerns regarding the effects of entomopathogenic nematodes on Bombus terrestris, suggesting that these nematodes may pose a threat to bees rather than being beneficial biological control agents for soil pests. It raises questions about the safety of these nematodes for pollinators, which implies potential negative impacts rather than promoting their use in pest control.