Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: Unlike some studies, our ring-width temperature reconstructions show no increased persistence in temperature anomalies following eruptive events compared to the climate model ensemble (Fig. 6). Ring widths from conifers therefore appear suitable for volcanic investigations. high-altitude and high-latitude trees predominantly used to determine the temperature impacts of volcanic eruptions contain higher biological persistence than the chronologies we used in our temperature reconstructions, influencing their post-eruption response. For example, the average first-order autocorrelation of our predictor chronologies is 0. 53 (range 0. 15–0. 87; SD 0. 15) compared to Arctic sites with an average of 0. 62 (range 0. 15–0. 93; SD 0. 13; Cropper and Fritts, 1981). Nevertheless, several species do show a lagged volcanic response (Figs. 3 and S7) that is not present in the final temperature reconstructions. Methodological decisions play an important role in the persistence of tree-ring-based temperature reconstructions (Büntgen et al. , 2021). In our reconstructions, pre-whitening of both the tree-ring predictors and the temperature data, including significant lagged predictors, and the selection of predictors from multiple species all contribute to the responses we identified. 5 few studies have considered whether volcanic signals are identifiable in tree-ring chronologies from the Southern Hemisphere. We investigated whether volcanic events could be identified in tree rings using data from eight dendrochronological species. In doing so, we set out to answer the following three questions. First, can volcanic signals be identified in the Southern Hemisphere? Second, are there species-level differences in volcanic signal strength? Finally, does chronology selection impact the magnitude of post-volcanic cooling in temperature reconstructions from tree rings? In answering the first two questions, we found that dendrochronological species are reliable recorders of volcanic cooling but that response varies across species. The magnitude and persistence of the species-wide volcanic response can be broadly linked to plant life history traits. The larger magnitude and more immediate responses are recorded by the “fast-responder” species, such as mountain beech and kauri, and more delayed but persistent responses are recorded by the “stress-tolerator” species, such as silver pine.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Comparable findings were observed across the entire TCGA-KIRC cohort and the external validation set (Figs. 3D–3I). Additionally, the distributions of risk scores, survival status, and gene expression of the model genes for each dataset were presented, further substantiating the robustness and accuracy of the risk model. The baseline characteristics for each dataset are provided in Table 1. Figure 3: Validation of models in TCGA-KIRC testing set and entire TCGA-KIRC cohort and external independent cohort. (A–C) Validation of the risk model in the TCGA-KIRC testing set (KM curve, ROC curve, risk plot). (D–F) Validation of the risk model in the entire TCGA-KIRC cohort (KM curve, ROC curve, risk plot). (G–I) Validation of the risk model in the external validation set ICGC-RECA-EU cohort (KM curve, ROC curve, risk plot). Download full-size image DOI: 10. 7717/peerj. 16927/fig-3 Table 1: Baseline for each dataset. Type TCGA--RECA-EU Entire set Testing set Training set p-value Age <=65 348 (65. 78%) 165 (62. 5%) 183 (69. 06%) 0. 1342 63 (69. 2%) >65 181 (34. 22%) 99 (37. 5%) 82 (30. 94%) 28 (30. 7%) 185 (34. 97%) 101 (38. 26%) 84 (31. 7%) 0. 1361 39 (42. 8%) MALE 344 (65. 03%) 163 (61. 74%) 181 (68. 3%) 52 (57. 1%) T T1 269 (50. 85%) 139 (52. 65%) 130 (49. 06%) 0. 7243 54 (59. 3%) T2 69 (13. 04%) 36 (13. 64%) 33 (12. 45%) 13 (14. 3%) T3 180 (34. 03%) 84 (31. 82%) 96 (36. 23%) 22 (24. 2%) T4 11 (2. 08%) 5 (1. 89%) 6 (2. 26%) 2 (2. 2%) M M0 420 (79. 4%) 209 (79. 17%) 211 (79. 62%) 0.

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: rate enhanced shoot accumulation of P, Ca, Fe, and B (Fig. 2C). Effects of AMF or P rate on shoot accumulation of other nutrients were a result of the effects of AMF and P rate on biomass. In general, AMF inoculation accounted for a greater proportion of variation in shoot N (ηA2 > 0. 27), K (ηA2 > 0. 18), S (ηA2 > 0. 23), B (ηA2 > 0. 38), Fe (ηA2 > 0. 27), and Zn (ηA2 > 0. 19) content than P rate (ηP2 not shown). P rate accounted for a greater proportion of variation in shoot P (ηP2 > 0. 64), Ca (ηP2 > 0. 23), Mg (ηP2 > 0. 28), Cu (ηP2 > 0. 11), and Mn (ηP2 > 0. 7) content than AMF inoculation (ηA2 not shown). Nutrient accumulation in roots. Root S, Mg, B, Cu, and Fe concentrations (Table 2) were greater than leaf concentrations (data not shown). and Mn concentrations were similar or greater than average plant concentrations (Table 2). Root N, P, and Ca were less than average plant concentrations. In general, ‘Red Rubin’ had the greatest root N, P, Cu, Fe, and Zn concentrations (Table 2) and accumulated the least root nutrient content (content data not shown). ‘Cinnamon’ had the greatest root K and Mn concentrations and root and Zn content. ‘Sweet Dani’ had the greatest root Mg concentrations and root Mg and Fe content. ‘Siam Queen’ had the greatest root Cu concentration and content. Variation among cultivars accounted for greater than 70% of variation in root N, K, Mg, and Fe concentrations (ηC2 > 0. 70) and between 50% and 68% of the variation in root concentrations of other nutrients. Variation among cultivars in root nutrient content was generally smaller than variation in root nutrient concentrations (data not shown). Inoculation with AMF enhanced root accumulation of N, K, S, and Zn (Fig. 1E).

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: In general, volcanic events can be more readily observed in the ring widths of fast-responder species, which should be prioritised for future regional or hemispheric studies. Unfortunately, the paucity of information on the ecology of many species limits our understanding of how species allocate resources to processes other than cambial growth in response to short-term changes in climatic conditions. The volcanic response of trees is complex, with positive, negative, and neutral responses identified sometimes within the same species group. For subalpine sites, this finding is not dissimilar to previous studies of temperate-zone species. We found that site-related factors have greater control over displayed volcanic responses than species and presented a suite of plausible, testable hypotheses explaining the results. The altitude of the site with respect to the species altitudinal limit and exposure to prevailing conditions are factors thought to determine whether a tree-ring volcanic response could be identified. In some cases, sites near the lower altitudinal limit of the species were also strong responders, suggesting a reduction in summer moisture stress could also be an important factor in post-volcanic growth. Our results indicate that studies intending to utilise tree rings to investigate regional volcanic cooling should carefully consider the characteristics of the sample site. While valid for all dendrochronological studies, it is particularly important for identifying volcanic signals, as we find that the range of temperature-sensitive sites is greater than the range of volcanically sensitive sites. In answer to the last question, we developed two new reconstructions of summer temperature to investigate whether chronology selection impacted the magnitude of post-volcanic cooling. There was little difference in the post-event anomalies, suggesting that limiting the predictor pool for volcanic sensitivity is unnecessary when targeting average growing-season temperatures in New Zealand. Both reconstructions showed temperature anomalies remarkably consistent with studies based on instrumental temperature and the ensemble mean response of CMIP5 climate models. Based on these results, ring widths are reliable indicators of regional volcanic climate response. More broadly, the findings of this study have important implications for the development of future tree-ring or multiproxy hemispheric temperature reconstructions from the Southern Hemisphere, which often incorporate species-specific “master” chronologies (i. e. composite chronologies developed from across many sites) into their predictor pool. As shown in this study, the compositing process can result in reduced volcanic signals when more than one type of response (i. e.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: 8822 81 (89. 0%) M1 79 (14. 93%) 38 (14. 39%) 41 (15. 47%) 9 (9. 9%) Unknow 30 (5. 67%) 17 (6. 44%) 13 (4. 91%) 1 (1. 1%) N N0 239 (45. 18%) 129 (48. 86%) 110 (41. 51%) 0. 3733 79 (86. 8%) N1 16 (3. 02%) 11 (4. 17%) 5 (1. 89%) 2 (2. 2%) Unknow 274 (51. 8%) 124 (46. 97%) 150 (56. 6%) 10 (11%) Grade G1 13 (2. 46%) 10 (3. 79%) 3 (1. 13%) 0. 0555 G2 228 (43. 1%) 117 (44. 32%) 111 (41. 89%) G3 205 (38. 75%) 90 (34. 09%) 115 (43. 4%) G4 75 (14. 18%) 41 (15. 53%) 34 (12. 83%) Unknow 8 (1. 51%) 6 (2. 27%) 2 (0. 75%) I 263 (49. 72%) 134 (50. 76%) 129 (48. 68%) 0. 7915 Stage II 57 (10. 78%) 31 (11. 74%) 26 (9. 81%) Stage III 123 (23. 25%) 58 (21. 97%) 65 (24. 53%) Stage IV 83 (15. 69%) 40 (15. 15%) 43 (16. 23%) Unknow 3 (0. 57%) 1 (0. 38%) 2 (0. 75%) DOI: 10. 7717/peerj. 16927/table-1 Development and validation of nomogram and PCA analysis Nomograms were employed to validate the clinical applicability and utility of the risk models. Specifically, nomograms were developed to predict OS at 1, 3, and 5 years by integrating various clinical parameters, including age, gender, pathological stage, histological grade, and risk score (Fig. 4A). Calibration plots were utilized to assess the predictive accuracy of the nomogram prediction model, demonstrating similar trends to the ideal model in predicting patients’ OS at 1, 3, and 5 years, affirming a good fit between the predicted values of the risk model and the actual outcomes (Fig. 4B).

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: rate enhanced root accumulation of P, Mg, and Fe and suppressed root accumulation of S and Cu (Fig. 2E). Significant effects of AMF on root accumulation of other nutrients were a result of the effects of AMF on biomass. In general, AMF inoculation accounted for a greater proportion of variation in root N (ηA2 > 0. 53), P (ηA2 > 0. 14), K (ηA2 > 0. 10), S (ηA2 > 0. 25), Ca (ηA2 > 0. 16), Mg (ηA2 > 0. 17), B (ηA2 > 0. 13), Fe (ηA2 > 0. 15), and Zn (ηA2 > 0. 07) content than P rate (ηP2 not shown). P rate accounted for a greater proportion of variation in root Cu (ηP2 > 0. 15) content than AMF inoculation (ηA2 not shown). Phenolic production. In general, ‘Red Rubin’ had the greatest average plant ACY and P2-P4 concentrations (Table 3) and the greatest whole plant ACY and P4 content production (content data not shown). ‘Cinnamon’ had the greatest average plant concentrations and production of P6 and P8; ‘Sweet Dani’ had the greatest average plant concentrations of P5 and P7 and production of P3, P5, and P7; and ‘Siam Queen’ had the greatest average plant concentrations of TP, P9–P11, and MPP and production of P10 and P11. Variation among cultivars accounted for greater than 90% of variation in average plant P10 concentrations (ηC2 > 0. 90); between 61% and 79% of variation in average plant TP, P7, and P11 concentrations; and 49% to 60% of the variation in average plant concentrations of other measured phenolics. In general, variation among cultivars in TP, P2, P3, P6, P8, and P11 production was generally greater than variation among cultivars in average plant concentrations and variation among cultivars in P5, P7, P9, and P10 production was smaller than variation among cultivars in average plant concentrations (data not shown). Table 3.

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: positive, negative, or neutral) is recorded by a single species. However, as most species-level composites show significant volcanic responses, temperature reconstructions based on composite chronologies should also show the influence of volcanic eruptions. Data availability All data and software used in this study are publicly available. Zealand “seven-station” temperature series was downloaded from NIWA at (last access: 4 July 2021; NIWA Research, 2021). time series was sourced from (last access: 7 August 2021; Trenberth and for Staff, 1984). The raw tree-ring width series can be downloaded from the Bank at (last access: 13 March 2021; NCEI, 2022). Superposed epoch analysis was undertaken using R code published on with (Rao et al. , 2019a). The two new temperature reconstruction series can be accessed through the NOAA/Service for Paleoclimatology archives ( (last access: 6 February 2022; NOAA, 2022). supplement related to this 10. 5194/cp-18-1169-2022-supplement. Author contributions PAH and JGP conceptualised this study, JGP curated the data, and PAH undertook the analysis. PAH wrote the manuscript with contributions from all authors. Competing interests The contact author has declared that neither they nor their co-authors have any competing interests. Disclaimer Publisher's note: remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Special issue statement This 10. 1038/nature02101, 2003. Allen, K. J. : A of Phyllocladus, University of Tasmania, PhD thesis, 343 pp. , 1998. . , Francey, R. , and Baker, P. J. : Lack of cool, not warm, extremes distinguishes late 20th Century climate in 979-year Tasmanian summer temperature reconstruction, Environ. Res. Lett. , 13, 034041, 2018. Blake, S. A. P. , Palmer, J. G. , Björklund, J. , Harper, J. B. , and Turney, C. S. M. : Palaeoclimate potential of Manoao colensoi (silver pine) tree rings using Blue-Intensity (BI), Dendrochronologia, 60, 125664, 2020. Biondi, F.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Similarly, consistent trends were observed in the TCGA-KIRC testing set, the entire TCGA-KIRC cohort, and the external validation set (Figs. 4C–4H). The PCA scatter plot results across various cohorts indicated the risk model’s ability to distinctly differentiate between low- and high-risk patients (Figs. 4I–4L). Collectively, these indications suggest the accuracy and clinical applicability of the risk model. Figure 4: Nomograms and PCA analysis of the risk model. (A and B) Nomograms and calibration plots constructed in the TCGA-KIRC training set to predict OS at 1, 3, and 5 years. (C and D) Nomograms and calibration plots constructed in the TCGA-KIRC testing set to predict OS at 1, 3, and 5 years. (E and F) Nomograms and calibration plots constructed in the entire TCGA-KIRC cohort to predict OS at 1, 3, and 5 years. (G and H) Nomograms and calibration plots constructed in the external validation set to predict OS at 1, 3, and 5 years. (I–L) PCA scatter plots of risk models for high- and low-risk groups in (I) the TCGA-KIRC training set, (J) the TCGA-KIRC testing set, (K) the entire TCGA-KIRC cohort, and (L) the external validation set. Download full-size image DOI: 10. 7717/peerj. 16927/fig-4 Immune landscape between the low-risk and high-risk groups Initially, we evaluated the tumor microenvironment within the entire TCGA-KIRC cohort using the method. The analysis revealed substantially higher estimated and immune scores in the high-risk group compared to the low-risk group (p < 0. 001) (Fig. 5A). Subsequently, we employed the algorithm to determine the distribution of 22 immune cell types within the TCGA-KIRC cohort. The composition of these immune cell types was visualized as a histogram, depicting the relative proportions of distinct immune cells in each sample (Fig. S4). We further utilized the “ggplot2” R package to calculate correlations between risk scores and immune cells.

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: Phenolic composition in whole plants and shoots (stems and leaves) of 16-week-old, greenhouse-grown ‘Cinnamon’ (CN), ‘Sweet Dani’ (SD), ‘Siam Queen’ (SQ), and ‘Red Rubin’ (RR) basil plants. Inoculation with AMF increased ACY (‘Red Rubin’ only; data not shown), P2, P4–P7, and MPP production (Fig. 1B). rate enhanced ACY (‘Red Rubin’ only; data not shown), P3, P6–P9, and MPP production and suppressed P5 production (Fig. 2B). Significant effects of AMF or P rate on production of other phenolics was a result of the effects of AMF and P rate on plant biomass. In general, AMF inoculation accounted for a greater proportion of variation in P4 (ηA2 > 0. 13), P5 (ηA2 > 0. 17), P7 (ηA2 > 0. 12), and MPP (ηA2 > 0. 16) production than P rate (ηP2 not shown). P rate accounted for a greater proportion of variation in P3 (ηP2 > 0. 22) and P8 (ηP2 > 0. 18) than AMF inoculation (ηA2 not shown). Phenolic accumulation in shoots. Specific phenolics were only detected in shoots (e. g. , P2, P3, and P6–P9; Table 3). Leaf phenolic concentrations were two to six times greater than stem concentrations (data not shown). Shoot TP, P4, P8–P10, and MPP concentrations were similar or greater than average plant concentrations (Table 3). Shoot P5 and P11 concentrations were less than average plant concentrations. In general, ‘Red Rubin’ had the greatest shoot concentrations (Table 3) of ACY, P2, and P4 and accumulated the most shoot ACY, P2, and P4 content (content data not shown). ‘Cinnamon’ had the greatest shoot concentrations of P6 and P7 and shoot P6–P9 content.

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: and Qeadan, F. : Inequality in paleorecords, Ecology, 89, 1056–1067, 2008. Boswijk, G. , Fowler, A. , Lorrey, A. , Palmer, J. , and Ogden, J. : Extension of the kauri (Agathis australis) chronology to 1724 BC, The Holocene, 16, 188–199, 2006. . , Jones, P. D. , Karlen, W. , Schweingruberll, F. H. , and Zetterberg, P. : A 1,400-year tree-ring record of summer temperatures in Fennoscandia, Nature, 346, 434–439, 1990. Briffa, K. R. , Jones, P. D. , and Osborn, T. J. : Influence of volcanic eruptions on summer temperature over the past 600 years, Nature, 393, 2–7, 1998. Buckley, B. , Ogden, J. , Palmer, J. , Fowler, A. , and Salinger, J. : Dendroclimatic interpretation of tree-rings in Agathis australis (kauri). 1. Climate correlation functions and master chronology, J. Roy. Soc. New Zeal. , 30, 263–276, 2000. Büntgen, U. , Arseneault, D. , Boucher, É. , Churakova (Sidorova), O. V. , Gennaretti, F. , Crivellaro, A. ,. ,. , McCormick, M. , Myglan, V. S. , Nicolussi, K. , Piermattei, A. , Oppenheimer, C. , Reinig, F. , Sigl, M. , Vaganov, E. A. , and Esper, J. : Prominent role of volcanism in climate variability and human history, Dendrochronologia, 64, 125757, 2020. Büntgen, U. , Allen, K. , Anchukaitis, K. J. , Arseneault, D. , Boucher, É. , Bräuning, A. , Chatterjee, S. , Cherubini, P.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: The analysis demonstrated significant positive associations between risk scores and specific immune cell populations, including CD8+T cells, activated CD4+ memory T cells, and Tregs (Fig. 5B). Moreover, we examined the relationship between the expression levels of prevalent immune checkpoint molecules and the risk score. Our findings revealed a robust correlation between the risk score and these immune checkpoints (p < 0. 05). Notably, CTLA4, LAG3, 1, 9, and LILRB1 exhibited significantly higher expression levels in high-risk KIRC patients compared to low-risk patients (p < 0. 001) (Fig. 5C). Additionally, our analysis revealed a correlation between high-risk status and heightened immune-related functions, including APC_co_stimulation, T_cell_co-stimulation, and inflammation promotion (Fig. 5D). Furthermore, we investigated the association between TMB and the risk score. The findings indicated a higher TMB in high-risk patients compared to low-risk patients (p = 0. 023). Additionally, we noted that individuals exhibiting both high TMB and high risk displayed the poorest prognosis, whereas those with low TMB and low risk exhibited the most favorable prognosis (Figs. 5E–5G). Figure 5: Immune landscape and tumor mutation load in low- and high-risk groups of the entire TCGA-KIRC cohort. (A) Differential analysis of the tumor microenvironment in low- and high-risk groups. (B) Differential analysis of immune cells in low- and high-risk KIRC groups. (C) Differential analysis of immune checkpoints between low- and high-risk groups. (D) Analysis of differences in immune-related functions between low- and high-risk groups. (E) Correlation of risk score with TMB. (F) KM curve showing survival difference between high and low TMB patients. (G) KM curve showing survival difference analysis of patients with combined analysis of TMB and risk score. *p < 0. 05; **p < 0. 01; ***p < 0. 001. Download full-size image DOI: 10. 7717/peerj.

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: ‘Sweet Dani’ had the greatest shoot P7 concentration and shoot P3, P5, P7, and MPP content. ‘Siam Queen’ had the greatest shoot TP, P9–P11, and MPP concentrations and shoot TP, P10, and P11 content. Variation among cultivars accounted for greater than 72% of variation in shoot TP, P10, and P11 concentrations (ηC2 > 0. 72); between 49% and 61% of variation in shoot P2–P9 concentrations; and 35% of variation in shoot MPP concentrations. Variation among cultivars in shoot TP, P7, and P9–P11 content was generally smaller than variation in shoot concentrations and variation among cultivars in shoot P2–P3, P5, P6, P8, and MPP content was generally greater than variation in shoot concentrations (data not shown). Inoculation with AMF enhanced shoot accumulation of ACY (‘Red Rubin’ only; data not shown), P2, P4–P7, and MPP (Fig. 1D). rate enhanced shoot accumulation of ACY (‘Red Rubin’ only; data not shown), P3, P6–P9, and MPP (Fig. 2D). Significant effects of AMF or P rate on shoot accumulation of other phenolics were a result of the effects of AMF and P rate on biomass. In general, AMF inoculation accounted for a greater proportion of variation in shoot P4 (ηA2 > 0. 11), P5 (ηA2 > 0. 09), P7 (ηA2 > 0. 12), and MPP (ηA2 > 0. 21) content than P rate (ηP2 not shown). P rate accounted for a greater proportion of variation in shoot TP (ηP2 > 0. 15), P3 (ηP2 > 0. 22), P8 (ηP2 > 0. 18), P9 (ηP2 > 0. 09), and P11 (ηP2 > 0. 11) content than AMF inoculation (ηA2 not shown). Phenolic accumulation in roots. Root TP, P5, and P10 concentrations (Table 3) were greater than leaf concentrations (data not shown).

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: , Churakova (Sidorova), O. V. , Corona, C. , Gennaretti, F. , Grießinger, J. , Guillet, S. , Guiot, J. , Gunnarson, B. , Helama, S. , Hochreuther, P. , Hughes, M. K. , Huybers, P. ,. , Meier, W. J. H. , Myglan, V. S. , Nicolussi, K. , Oppenheimer, C. , Reinig, F. , Salzer, M. W. , Seftigen, K. , Stine, A. R. , Stoffel, M. , St. George, S. , Tejedor, E. , Trevino, A. , Trouet, V. , Wang, J. , Wilson, R. , Yang, B. , Xu, G. , and Esper, J. : The influence of decision-making in tree ring-based climate reconstructions, Nat. Commun. , 12, 3411, 2021. Christiansen, B. : Volcanic eruptions, large-scale modes in the Northern Hemisphere, and the El Niño-Southern Oscillation, J. Climate, 21, 910–922, 2008. Cook, E. R. and Kairiukstis, L. A. (Eds. ): Methods of dendrochronology: applications in the environmental sciences, Publishers, Amsterdam, 394 pp. , 1990. Cook, E. R. , Bird, T. , Peterson, M. , Barbetti, M. , Buckley, B. , D'Arrigo, R. , and Francey, R. : Climatic change over the last millennium in Tasmania reconstructed from tree-rings, Holocene, 2, 205–217, 1992. and Cleaveland, M. K. : Drought reconstructions for the continental United States, J. Climate, 12, 1145–1163, 1999. . , and D'Arrigo, R. D. : A multi-millennial palaeoclimatic resource from Lagarostrobos colensoi tree-rings at. Change, 33, 209–220, 2002. Cook, E. R. , Seager, R.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: 16927/fig-5 Biological functions of hub genes To investigate the biological functions of hub genes, we performed a PPI analysis of hub genes and their interacting genes using and the network illustrates that the four genes are enriched in DNA damage response, potassium channel complex, cell cycle checkpoint, microtubule polymerization, transmembrane transporter complex, regulation of ion transmembrane transport, detection of chemical stimulus, etc. , (Fig. 6A). Then, we further performed GSEA pathway enrichment analysis for each gene in the low and high-risk groups of the entire TCGA-KIRC cohort. In the high-risk group, the top five GO terms were considered to be significantly enriched representatives. The results showed that hub genes were involved in immunoglobulin complex, humoral immune response mediated by circulating immunoglobulin, complement activation, phagocytosis recognition, and humoral immune response (Fig. 6B). The top five KEGG pathways in the high-risk group showed that hub genes were involved in complement and coagulation cascades, cytokine receptor interaction, retinol metabolism, oxidative phosphorylation, and drug metabolism cytochrome p450 (Fig. 6C). Figure 6: Expression validation and biological functions of hub genes and drug screening. (A) PPI network presentation of hub genes by portal. (B) The top five GO terms in the high-risk group. (C) The top five KEGG pathways in the high-risk group. (D) Expression of hub genes in GEO-COVID-19 cohort. (E) Expression of hub genes in TCGA-KIRC cohort. (F–I) Detection of hub gene expression in renal cancer cell lines by qRT-PCR. *p < 0. 05, **p < 0. 01, ***p < 0. 001. Download full-size image DOI: 10. 7717/peerj. 16927/fig-6 Expression validation of hub genes Analysis of public databases revealed significant overexpression of hub genes in both COVID-19 and KIRC (Figs. 6D and 6E). Additionally, qPCR results demonstrated variable degrees of overexpression of the four hub genes in RCC cell lines (Figs. 6F–6I). These findings further substantiate the accuracy and reliability of the risk model.

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: Root P5 and P11 were similar or greater than average plant concentrations (Table 3). Root TP, P4, P8–P10, and MPP concentrations were less than average plant concentrations. Only ‘Red Rubin’ roots contained detectable amounts of ACY. In general, ‘Sweet Dani’ had the greatest root concentrations (Table 3) and P5 and MPP content (data not shown). ‘Cinnamon’ had the greatest P4, P10, P11, and TP content. Variation among cultivars accounted for greater than 24% of variation in root TP, P5, and MPP (ηC2 > 0. 24). Variation among cultivars in root phenolic content was generally greater than variation in root phenolic concentrations (data not shown). Inoculation with AMF enhanced root accumulation of P4 and P5 in roots and suppressed root accumulation of P11 (Fig. 1F). rate enhanced root accumulation of P4 and suppressed root accumulation of P5 and MPP (Fig. 2F). Significant effects of AMF on root accumulation of other phenolics were a result of the effects of AMF on biomass. In general, AMF inoculation accounted for a greater proportion of variation in root P4 (ηA2 > 0. 17) content than P rate (ηP2 not shown). P rate accounted for a greater proportion of variation in root TP (ηP2 > 0. 13), P5 (ηP2 > 0. 17), P10 (ηP2 > 0. 07), P11 (ηP2 > 0. 10), and MPP (ηP2 > 0. 12) content than AMF inoculation (ηA2 not shown). Relationships between nutrient uptake and phenolics. Inoculation with AMF enhanced P2, P4–P7, and MPP production and N, K, S, B, Fe, and Zn uptake (Fig. 1A–B). Enhanced P2 and P6 production in AMF-inoculated plants was related to enhanced N uptake; enhanced P4 production was related to enhanced N and Fe uptake; enhanced P5 production was related to enhanced S, B, and Fe uptake; enhanced P7 and MPP production was related to enhanced K, B, and Fe uptake (Table 4).

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: , Cane, M. A. , and Stahle, D. W. : drought: Reconstructions, causes, and consequences, Earth-Sci. Rev. , 81, 93–134, 2007. Cook, E. R. , Seager, R. ,. , and Woodhouse, C. : Megadroughts in North America: Placing IPCC projections of hydroclimatic change in a long-term palaeoclimate context, J. Quaternary Sci. , 25, 48–61, 2010. Cropper, J. P. and Fritts, H. C. : Tree-ring width chronologies from the. , 13, 245–260, 1981. Crowley, T. J. and Unterman, M. B. : Technical details concerning development of a 1200 yr proxy index for global volcanism, Earth Syst. Sci. Data, 5, 187–197, 2013. D’and Wagner, W. S. : Temperature-sensitive tree-ring width chronologies of pink pine (Halocarpus biformis) from Stewart Island, New Zealand, Palaeogeogr. Palaeoclimatol. Palaeoecol. , 119, 293–300, 1996. D’. , Krusic, P. J. , Buckley, B. M. , and Villalba, R. : Tree-ring records from New Zealand: Long-term context for recent warming trend, Clim. Dynam. , 14, 191–199, 1998. D'Arrigo, R. , Wilson, R. , and Tudhope, A. : The impact of volcanic forcing on tropical temperatures during the past four centuries, Nat. Geosci. , 2, 51–56, 2009. D'Arrigo, R. , Wilson, R. , and Anchukaitis, K. J. : Volcanic cooling signal in tree ring temperature records for the past millennium, J. Geophys. Res. -Atmos. , 118, 9000–9010, 2013. Dang, H. , Jiang, M. , Zhang, Q. , and Zhang, Y. : Growth responses of subalpine fir (Abies fargesii) to climate variability in the Qinling Mountain, China, Forest Ecol. Manag.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Drug screening To identify potential drugs for the treatment of COVID-19 and KIRC co-morbidity, we conducted drug target enrichment analysis with four hub genes (GTSE1, 4, HECW2, and KCNMA1) as genetic targets associated with the construction of risk models via cellMiner and DsigDB databases (Tables S3, S4). The results revealed that Etoposide, Fulvestrant and Topotecan were significantly positively correlated with the expression level of the four hub genes (Table 2). These drugs serve as important 0. 0096 0. 0092 0. 3335 4, GTSE1 Methotrexate 0. 0104 0. 0101 −0. 3295 GTSE1, HECW2 Fulvestrant 0. 0388 0. 0005 0. 4364 4, GTSE1 Vinblastine 0. 0446 0. 0402 −0. 2657 GTSE1, KCNMA1 Topotecan 0. 0491 0. 0112 0. 3255 KCNMA1 Melphalan 0. 0546 0. 0147 0. 3135 4, HECW2 Raloxifene 0. 0722 0. 0003 0. 4530 4, KCNMA1 Tamoxifen 0. 1510 0. 0034 −0. 3718 KCNMA1 Irinotecan 0. 2312 0. 0191 0. 3019 4, GTSE1 Camptothecin 0. 2700 0. 0099 0. 3305 4, GTSE1 DOI: 10. 7717/peerj. 16927/table-2 recent research has uncovered the participation of several coronavirus receptor genes in the advancement of KIRC (Choong et al. , 2023; Tang et al. , 2021; Hossain, Akter & Uddin, 2021; Tripathi et al. , 2020), their mechanisms of action remain unclear. Thus, it is significant to evaluate the expression, prognosis, immune function, and other characteristics of COVID-19-related genes in KIRC tissues. These genes can not only function as prognostic biomarkers and drug targets for both COVID-19 and KIRC but also offer novel insights into the underlying pathogenic mechanisms shared by these two diseases.

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: rate enhanced P3, P6–P9, and MPP production and P and Ca uptake (Fig. 2A–B). Enhanced P3 and P6 production was related to enhanced P uptake; enhanced P7, P8, and MPP production was related to enhanced P and Ca uptake (Table 4). Enhanced P9 production in HP plants was not correlated to P-enhanced uptake of any nutrient measured. Table 4. Relationships between nutrient uptake and phenolic production of 16-week-old, greenhouse-grown basil plants. Inoculation with AMF enhanced accumulation of P4 and P5 in shoots and roots and MPP in shoots (Figs. 1D and 1F). AMF-enhanced P4 accumulation in shoots was related to enhanced N and Fe uptake and enhanced P4 accumulation in roots was related to enhanced Fe uptake (Table 4). AMF-enhanced P5 accumulation in shoots was related to enhanced S, B, and Fe uptake and enhanced P5 accumulation in roots was related to enhanced S and B uptake. AMF-enhanced MPP accumulation in roots was related to enhanced B and Fe uptake. rate enhanced accumulation of P11 and MPP in shoots and P4 in roots (Figs. 2D and 2F). Enhanced MPP accumulation in shoots of HP plants was related to enhanced P and Ca uptake (Table 4). Enhanced P11 accumulation in shoots and P4 accumulation in roots of HP plants were related to enhanced Ca uptake. DiscussionRoot colonization. Root colonization by AMF in our study was 10% to 30% higher than that reported for other basil cultivars (e. g. , ‘Genovese’, ‘Purple Petra’) inoculated with the same isolate of AMF or with different species [e. g. , Funneliformis (formerly Glomus) mosseae (Nicolson & Gerd. ) Walker & Schüßler, Gigaspora rosea Nicolson & Schenck, Gi. margarita Becker & Hall] (Copetta et al. , 2006; Lee and Scagel, 2009; Toussaint et al. , 2007). Methods used to quantify AMF can yield different results, particularly when quantifying colonization of different AMF species (McGonigle et al. , 2006), and AMF colonization can increase over time (Copetta et al. , 2006).

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: , 240, 143–150, 2007. Dee, S. G. , Cobb, K. M. , Emile-geay, J. ,. , and Charles, C. D. : No consistent ENSO response to volcanic forcing over the last millennium, Science, 367, 1477–1481, 2020. Ding, C. and He, X. : K-means Clustering via Analysis, in: Proceedings of the 21st on Machine Learning, Banff, Alberta, Canada, 4–8 July 2004, 29–38, 2004. Duncan, R. P. , Fenwick, P. , Palmer, J. G. , McGlone, M. S. , and Turney, C. S. M. : Non-uniform interhemispheric temperature trends over the past 550 years, Clim. Dynam. , 35, 1429–1438, 2010. Dunwiddie, P. W. : Dendrochronological studies of indigenous trees, New Zeal. J. Bot. , 17, 251–266, 1979. Emile-Geay, J. , Seager, R. , Cane, M. A. , Cook, E. R. , and Haug, G. H. : Volcanoes and ENSO over the past millennium, J. Climate, 21, 3134–3148, 2008. Esper, J. , Schneider, L. , Krusic, P. J. , Luterbacher, J. , Büntgen, U. , Timonen, M. , Sirocko, F. , and Zorita, E. : European summer temperature response to annually dated volcanic eruptions over the past nine centuries, B. Volcanol. , 75, 1–14, 2013. Fatichi, S. , Pappas, C. , Zscheischler, J. , and Leuzinger, S. : Modelling carbon sources and sinks in terrestrial vegetation, New Phytol. , 221, 652–668, 2019. Fenwick, P. : Reconstruction of past climates using pink pine (Halocarpus biformus) tree-ring chronologies, Lincoln University, PhD thesis, 2003. Fowler, A. M. , Palmer, J. , Salinger, J.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: In this study, we identified 156 shared genes between the COVID-19 and KIRC cohorts and selected four hub genes (GTSE1, 4, HECW2, and KCNMA1) as the foundation for developing a risk model. By conducting a comprehensive statistical analysis, we validated the model’s accuracy, robustness, and clinical relevance in predicting the prognosis of KIRC. All four genes exhibited notable overexpression in both COVID-19 and KIRC cohorts. Specifically, GTSE1 and 4 were identified as risk factors for KIRC prognosis, whereas HECW2 and KCNMA1 served as protective factors. GTSE1 is a protein that is specifically expressed during the G2 and S phases of the cell cycle and is involved in the progression and metastasis of various cancers (Monte et al. , 2000; Guo et al. , 2016; Liu et al. , 2019; Xu et al. , 2018). Research has demonstrated the significant overexpression of GTSE1 in KIRC tissue. Depletion of GTSE1 expression has been found to suppress the proliferation and invasion of KIRC cells and induce apoptosis both in vitro and in vivo (Chen et al. , 2022). Notably, the depletion of GTSE1 leads to the upregulation of KLF4, a tumor suppressor in KIRC (Song et al. , 2013). Intriguingly, certain studies have reported that the depletion of KLF4 in lung epithelial cells results in an upregulation of ACE2 expression (Mastej et al. , 2022). Therefore, we speculated that there may be a potential connection between GTSE1 and ACE2. 4, a constituent of the carcinoembryonic antigen family, is frequently overexpressed in cancer and often signifies tumor invasion (Wakabayashi-Nakao et al. , 2014). 4 exhibits high expression in KIRC and can potentially serve as an independent prognostic marker associated with sunitinib resistance and immune infiltration (Peng et al. , 2021). HECW2, a member of the E3 ubiquitin ligase family, plays a pivotal role in kidney development (Qiu et al. , 2016). Investigations have revealed the upregulation of HECW2 in colon and cervical cancer, suggesting its potential involvement in tumorigenesis (Lu et al.

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: AMFs have been previously reported to increase or have no influence on total growth of basil and differentially affect growth of specific structures (Copetta et al. , 2006; Lee and Scagel, 2009; Toussaint et al. , 2007). Decreased total plant biomass and increased root growth is a common plant response to low P availability in the growing substrate (Veresoglou et al. , 2012). In our study, there was no significant interaction between AMF and P rate treatments on biomass or biomass allocation. Inoculation with AMF increased biomass but had no influence on biomass allocation. In contrast, P rate increased biomass and altered biomass allocation. Additionally, AMF inoculation accounted for a greater proportion of variation in root, stem, and total plant biomass than P rate. These results suggest that the influence of AMF on growth may not be completely related to plant P status. Nutrient uptake and allocation. rate increased biomass, P concentration, and P content of basil and there was no interaction between P rate and AMF inoculation on biomass, P concentration, and P content. These results indicate that non-mycorrhizal and AMF plants grown with the low P rate were P-deficient compared with high P plants and increasing P rate enhanced P uptake (e. g. , plants were more efficient at P uptake). In contrast, AMF inoculation increased biomass and P content but not P concentration indicating that AMF only increased P accumulation in the plant and not the ability of basil to absorb P. Araim et al. (2009) reported that AMF inoculation increased P concentration of shoots but not roots of coneflower [Echinacea purpurea (L. ) Monech. ]. Mycorrhizal fungi are reported to improve P uptake in low P growing conditions, primarily because the fungi’s extraradical hyphae increase access to P by extending beyond the P-depletion zone around the root system (Smith et al. , 2003). When there is no response to AMF in terms of P uptake, it has been assumed that the mycorrhizal uptake pathway is not functioning and that all of the plant P is absorbed directly through P transporters in the root epidermis and root hairs. Increased growth or success of AMF-colonized plants is then attributed to other benefits of the symbiosis.

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: , and Ogden, J. : Dendroclimatic interpretation of tree-rings in Agathis australis (kauri): 2. Evidence of a significant relationship with ENSO, J. Roy. Soc. New Zeal. , 30, 277–292, 2000. Fowler, A. M. , Lorrey, A. , and Crossley, P. : Seasonal growth characteristics of kauri, Tree-Ring Res. , 61, 3–19, 2005. Fowler, A. M. , Boswijk, G. , Gergis, J. , and Lorrey, A. : ENSO history recorded in Agathis australis (kauri) tree rings. Part A: kauri's potential as an ENSO proxy, Int. J. Climatol. , 28, 1–20, 2008. Fritts, H. C. : and Climate, Academic Press, 582 pp. , ISBN 978-0122684500, 1976. Gao, C. , Robock, A. , and Ammann, C. : Volcanic forcing of climate over the past 1500 years: An improved ice core-based index for climate models, J. Geophys. Res. -Atmos. , 113, D23111, 2008. Garrison, C. S. , Kilburn, C. R. J. , and Edwards, S. J. : The 1831 eruption of that never happened: has the source of one of the largest volcanic climate forcing events of the nineteenth century been misattributed? , J. Appl. Volcanol. , 7, 8, 2018. Grime, J. P. : & Sons, Ltd. , Chichester-New York-Brisbane-Toronto, 222 pp. , ISBN 978047199695, 1979. Grissino-Mayer, H. D. : Accuracy: A Manual and Tutorial for the -Ring Res. , 57, 205–221, 2001. Gu, L. , Baldocchi, D. D. , Wofsy, S. C. , William Munger, J. , Michalsky, J. J. , Urbanski, S. P. , and Boden, T. A.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: , 2013). KCNMA1, a constituent of the renal K channel, is implicated in the regulation of renal potassium metabolism (Welling, 2016). Extensive research has highlighted the involvement of KCNMA1 in diverse tumor processes. Specifically, it is upregulated in breast cancer, prostate cancer, glioblastoma, and cervical cancer, while downregulated in gastric and colon cancer (Ma et al. , 2017; Basile et al. , 2019; Du et al. , 2016; Bury et al. , 2013). The immune system serves as the primary defense against viral infections, and its decline heightens susceptibility to SARS-CoV-2 (et al. , 2020). Functional enrichment analysis of shared and hub genes in both diseases reveals significant enrichment of genes associated with immune functions. Immune functional correlation analysis also indicates heightened immune-related functions in the high-risk group of KIRC patients, highlighting the close relationship between shared genes of these diseases and immune function. The high-risk group exhibits notably higher estimated scores and immune scores, with higher estimated scores being linked to lower tumor purity (Yoshihara et al. , 2013). Tumors with low purity are associated with a poor prognosis but have a higher likelihood of benefiting from immunotherapy (Gong, Zhang & Guo, 2020). CTLA4, LAG3, 1, 9, and LILRB1 are all common and promising immunotherapy targets (Zhou et al. , 2020; Chao, Weissman & Majeti, 2012; Li et al. , 2020). The more targets there are, the better the expected effect of cancer immunotherapy will be. Therefore, the effect of immunotherapy in high-risk group will be better than that in low-risk group. Comparatively, the high-risk group demonstrates elevated proportions of CD8+ T cells, activated CD4+ memory T cells, and Tregs, which serve as effector T cells, fostering tumor immune activation and cytotoxicity against tumor cells, thereby favoring positive clinical outcomes for patients (Dunn et al. , 2002). However, Tregs function as immune suppressive cells that inhibit tumor immune responses and secrete various immune suppressive factors, facilitating tumor immune evasion (Lei et al. , 2020). These findings imply that four key genes in KIRC may be involved in immune regulation.

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: In a container, extraradical hyphae may not improve physical access to P beyond that of non-mycorrhizal roots; however, Smith et al. (2003) believe that AMFs are a dominant route for plant P supply, even when overall growth or P uptake remains unaffected. AMF inoculation and increased P rate had different effects on nutrient uptake in basil. AMF inoculation of basil enhanced N, K, S, B, Fe, and Zn uptake suggesting that AMF-inoculated plants were either more efficient at uptake of these nutrients or had a higher demand for these nutrients. In our study, AMF increased accumulation or enhanced uptake of all nutrients. In contrast, increased P rate enhanced uptake of fewer nutrients and even suppressed uptake of Cu and S. Mycorrhizal fungi have been reported to improve uptake of several nutrients, including N, P, K, S, Ca, and Zn (Azcón et al. , 2003; Clark and Zeto, 2000). Reports of enhanced nutrient uptake in AMF-inoculated plants are not always substantiated by analyses of total plant nutrient uptake (e. g. , only leaf concentrations are measured) and even when total plant uptake is calculated, concentration data are not always used to distinguish whether nutrient uptake was enhanced (e. g. , increased concentration and content) or just increased as a result of greater biomass in AMF-inoculated plants. and Ca uptake in high P plants compared with low P plants resulted in enhanced accumulation of these nutrients as well as B and Fe in shoots and Fe and Mg in roots. Additionally, increased P rate suppressed accumulation of S and Cu in roots. These results indicate P availability alters nutrient accumulation patterns in basil and suggest that P rate alters the ability of plants to use nutrients for growth and metabolic processes. Plants adapt their morphology and metabolism in response to P-limiting growing conditions (Rausch and Bucher, 2002). These adaptive changes strive to increase P availability in the rhizosphere, enhance P uptake, and maintain metabolic efficiency. In our study, P availability influenced biomass allocation so it is not surprising that it also influenced allocation of nutrients within the plant.

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: : Response of a deciduous forest to the eruption: Enhanced photosynthesis, Science, 299, 2035–2038, 2003. Harper, J. L. : Population biology of plants, Academic Press, New York, 892 pp. , ISBN 9780123258502, 1977. Haurwitz, M. W. and Brier, G. W. : A Critique of the Analysis Method: to Solar-Weather Relations, Mon. Weather Rev. , 109, 2074–2079, 1981. Holmes, R. L. : Computer-Control in Tree-and Measurement, Tree-Ring Bulletin, 43, 69–78, 1983. and Zhang, X. : The effect of volcanic eruptions on global precipitation, J. Geophys. Res. -Atmos. , 118, 8770–8786, 2013. Khodri, M. , Izumo, T. , Vialard, J. , Janicot, S. , Cassou, C. , Lengaigne, M. , Mignot, J. , Gastineau, G. , Guilyardi, E. , Lebas, N. , Robock, A. , and McPhaden, M. J. : Tropical explosive volcanic eruptions can trigger El Ninõ by cooling tropical Africa, Nat. Commun. , 8, 1–12, 2017. Krakauer, N. Y. and Randerson, J. T. : Do volcanic eruptions enhance or diminish net primary production? Evidence from tree rings, Global Biogeochem. Cy. , 17, 1118, 2003. and Drew, L. G. : Tree-ring chronologies of the 3. New Zealand, Laboratory of Tree-Ring Research, University of Arizona, Tucson, Arizona, 1979. Manson, B. R. : The life history of silver beech (Nothofagus menziesii), Proc. New Zeal. Ecol. Soc. , 21, 27–31, 1974. . , and Wilmshurst, J. M. : Palynology and the ecology of the conifers, Front. Earth Sci. , 5, 1–23, 2017. McGregor, S. , Timmermann, A. , and Timm, O. : A unified proxy for ENSO and PDO variability since 1650, Clim.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: The expression levels of immune checkpoints serve as an indicator of tumors’ response to immune checkpoint inhibitors, with overexpression of immune checkpoints leading to immune suppression and evasion (Qin et al. , 2019). Our observations reveal significantly higher expression levels of CTLA4, LAG3, 1, 9, and LILRB1 in high-risk KIRC patients compared to low-risk patients. Previous studies have established a positive association between higher TMB in tumor cells and increased benefits from immunotherapy (Rizvi et al. , 2015). In our study, we found that high-risk KIRC patients exhibited higher TMB compared to their low-risk counterparts. We hypothesize that the poorer prognosis in high-risk patients may stem from immune suppression and evasion triggered by immune checkpoint overexpression. Conversely, high-risk patients may derive greater benefits from immune therapies, including immune checkpoint blockade. These results illustrate the existence of a link between these four hub genes that may be associated with immune function and the predictive potential of immunotherapy effects. The treatment of patients with both KIRC and COVID-19 presents a challenging task (Ged, Markowski & Pierorazio, 2020). In our study, we identified a total of 3 drugs. Etoposide, a potent topoisomerase II poison, not only functions as an inducer of cancer cell death but also shows promise in treating immune-mediated inflammatory diseases associated with cytokine storm syndrome (Bailly, 2023). Some studies have speculated that etoposide may be a viable option for addressing COVID-19-induced cytokine storms (Delgado-López et al. , 2021; Hamizi, Aouidane & Belaaloui, 2020; Lovetrue, 2020). Fulvestrant, a steroid anti-estrogen, has gained approval for treating hormone receptor-positive metastatic breast cancer (Howell, Johnston & Howell, 2004). Research indicates that fulvestrant can significantly inhibit the growth and invasion of RCC cells (Song et al. , 2018). Moreover, it enhances the sensitivity of Sunitinib in RCC (Gu et al. , 2020), offering a potential new therapy for metastatic RCC (Song et al. , 2018). Joshi and Sanjeev et al (Jani et al. , 2021; Nayarisseri et al. , 2020).

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: To our knowledge, our results are the first report of AMF enhancing production of caftaric and feruloyl tartaric acids in basil. Caftaric acid is produced in several plants, including coneflower and basil (Lee and Scagel, 2010). Araim et al. (2009) reported that inoculation with R. intraradices decreased caftaric acid in shoots and increased caftaric acid in roots of coneflower. Caftaric acid was not detected in roots of basil, but AMF increased shoot production of caftaric acid. Toussaint et al. (2007) reported that inoculation with G. calendonium (Nicolson & Gerd. ) Trappe & Gerd. and F. mosseae increased caffeic acid concentrations in ‘Genova’ shoots and inoculation with R. intraradices has no influence on shoot caffeic acid concentrations. Araim et al. (2009) reported that AMF increased production of most phenolics in roots and suggested that mycorrhizae could play an important role in optimizing the growth of coneflower by inducing the production of secondary phytomedicinal metabolites. Plants produce several phenolics in response to biotic and abiotic factors (Bennett and Wallsgrove, 1994; Chalker-Scott, 1999). Chitin, a component of fungal cell walls, can induce production of secondary metabolites in basil (Kim et al. , 2003). Little is known about signaling compounds such as chitin and the role of secondary metabolism in the interactions between plants and mycorrhizae (Strack and Fester, 2006; Strack et al. , 2003). Relationships between nutrient uptake and phenolics. Positive relationships between certain nutrients and phenolic production were a function of growth or allocation. For example K and Zn uptake was related to rosmarinic acid production, and AMF increased K and Zn uptake; however, AMF only enhanced rosmarinic acid accumulation in shoots not roots. Correlations between nutrient uptake and phenolics do not imply direct linkage between nutrients and phenolic production; however, these relationships can give insight into how nutrient management may impact product qualities. Nguyen et al.

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: : Tree-from Conifers 1800-30, in: without a summer? : World climate in 1816, edited by: Harington, C. R. , of Nature, Ottawa, 510–515, 1992. Palmer, J. G. and Xiong, L. : climate over the last 500 years reconstructed from Libocedrus bidwillii Hook. f. tree-ring chronologies, The Holocene, 14, 282–289, 2004. Palmer, J. G. , Lorrey, A. , Turney, C. S. M. , Hogg, A. , Baillie, M. , Fifield, K. , and Ogden, J. : Extension of kauri (Agathis australis) tree-ring chronologies into Stage (OIS) 3, J. Quaternary Sci. , 21, 779–787, 2006. . , Allen, K. , Fenwick, P. , Cook, B. I. , O'Donnell, A. , Lough, J. , Grierson, P. , and Baker, P. : Drought variability in the eastern Australia and summer drought atlas (1500-2012) modulated by the Oscillation, Environ. Res. Lett. , 10, 124002, 2015. Phipps, R. : Comments on interpretation of climatic information from tree rings, eastern North America, Bull. , 42, 11–22, 1982. Pieper, H. , Heinrich, I. , Heußner, K. U. , and Helle, G. : The influence of volcanic eruptions on growth of central European lowland trees in NE-Germany during the last millennium, Palaeogeogr. Palaeoclim. , 411, 155–166, 2014. Raible, C. C. , Brönnimann, S. , Auchmann, R. , Brohan, P. , Frölicher, T. L. , Graf, H. F. , Jones, P. , Luterbacher, J. , Muthers, S. , Neukom, R. , Robock, A. , Self, S. , Sudrajat, A. , Timmreck, C. , and Wegmann, M.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Utilized artificial intelligence and machine learning algorithms, concluding that fulvestrant may be an effective treatment for COVID-19. Topotecan, a topoisomerase I (TOP1) inhibitor, has demonstrated efficacy in preventing SARS-CoV-2-induced fatal inflammation (Ho et al. , 2021). Furthermore, clinically relevant concentrations of topotecan induce apoptosis more effectively than 5-FU in RCC cell lines (Ramp et al. , 2001). Previous studies have demonstrated that the combination of Suberoylanilide hydroxamic acid with topotecan can effectively inhibit the growth of renal cancer cells (Sato et al. , 2011). Additionally, topotecan in combination with various drugs may represent a novel treatment for inducing apoptosis in otherwise unresponsive RCC cells (Déjosez et al. , 2000; Sato et al. , 2009; Sato et al. , 2008). These drugs serve as valuable 10. 7717/peerj. 16927/supp-1 map showing differentially expressed genes in the COVID-19 cohort. DOI: 10. 7717/peerj. 16927/supp-2 map showing differentially expressed genes in the entire TCGA-KIRC cohort. DOI: 10. 7717/peerj. 16927/supp-3 results of WGCNA for the COVID-19 cohort of differentially expressed genes. (A) Demonstration of scale independence and mean connectivity of WGCNA, choosing a soft threshold of 13 and a scale-free topological fit index of 0. 9 resulted in relatively balanced scale independence and mean connectivity of WGCNA; (B) Systematic tree diagram and trait correlation heat map of genes. DOI: 10. 7717/peerj. 16927/supp-4 showing the relative proportion of immune cells in high- and low-risk samples. DOI: 10. 7717/peerj. 16927/supp-5 COX regression results for the training set. DOI: 10. 7717/peerj. 16927/supp-6 genes generated after LASSO regression. DOI: 10. 7717/peerj. 16927/supp-7 analysis results based on cellMiner database. DOI: 10. 7717/peerj. 16927/supp-8 analysis results based on DSigDB database.

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: Plant nutrient status can significantly influence or have little or no effect on production secondary metabolites (Areias et al. , 2000; Fanasca et al. , 2006; Mogren et al. , 2006; Nell et al. , 2009). Our results suggest that conflicting reports of the influence of nutrition on phenolic production may be a result of the specific phenolics measured, the impact of nutrition on growth and allocation, and the use of making inferences from data derived from only aerial portions of a plant. In conclusion, our results indicate fertilizer management can be used to alter phenolic composition of basil plants and AMF inoculation may provide an additional strategy for optimizing basil composition quality beyond benefits obtained from just altering plant nutrient status or growth. For example, improving N, S, Mg, and B nutrition by AMF inoculation may enhance accumulation of caftaric, feruloyl tartaric, and caffeic acids. In contrast, improving P and Ca nutrition by altering P rate may enhance accumulation of cinnamyl malic acid and caffeic acid derivative (P8). Our results also indicate that increasing P rate or AMF inoculation may enhance accumulation of chicoric acid; however, the effects of P rate and AMF on enhanced accumulation of chicoric acid was not related to enhanced uptake of similar nutrients. Literature CitedAraim, G. , Saleem, A. , Arnason, J. T. & Charest, C. 2009 Root colonization by an arbuscular mycorrhizal (AM) fungus increases growth and secondary metabolism of purple coneflower, Echinacea purpurea (L. ) Monech. J. Agr. Food Chem. 57 2255 2258Araim,G. Saleem,A. Arnason,J. T. Charest,C. 2009Root colonization by an arbuscular mycorrhizal (AM) fungus increases growth and secondary metabolism of purple coneflower, Echinacea purpurea (L. )Monech. J. Agr. Food Chem. 5722552258)| falseSearch 1. 1: Polyphenolics: Determination of total phenolics, p. 1–4. In: Wrolstad, R. E. (ed. ). Current protocols in food analytical chemistry. &. & Herrmann, K.

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: : Tambora 1815 as a test case for high impact volcanic eruptions: Earth system effects, WIREs Clim. Change, 7, 569–589, 2016. Rao, M. , Cook, E. , Cook, B. , Anchukaitis, K. , D'Arrigo, R. , Krusic, P. , and LeGrande, A. : “Data for: A double bootstrap approach to Analysis to evaluate response uncertainty”, V1 [data set], 2019a. 'Arrigo, R. D. , Krusic, P. J. , and LeGrande, A. N. : A double bootstrap approach to Analysis to evaluate response uncertainty, Dendrochronologia, 55, 119–124, 2019b. Robock, A. : Cooling following large volcanic eruptions corrected for the effect of diffuse radiation on tree rings, Geophys. Res. Lett. , 32, 1–4, 2005. Rozas, V. , García-González, I. , Pérez-De-Lis, G. , and Arévalo, J. R. : Local and large-scale climatic factors controlling tree-ring growth of Pinus canariensis on an oceanic island, Clim. Res. , 56, 197–207, 2013. Salinger, M. J. : Climate: 1. Precipitation Patterns, Mon. Weather Rev. , 108, 1892–1904, 1980. Salinger, M. J. : Climate: The instrumental record, of Wellington, Wellington, New Zealand, 357 pp. , 1981. Salinger, M. J. : Climate: of Eruptions, Weather Clim. , 18, 11–19, 1998. and Briffa, K. R. : Reconstruction of climate indices back to AD 1731 using dendroclimatic techniques: Some preliminary results, Int. J. Climatol. , 14, 1135–1149, 1994. Santoso, A. , Mcphaden, M. J. , and Cai, W. : Characteristics of ENSO Extremes and the Strong 2015/2016 El Niño, Rev. Geophys. , 55, 1079–1129, 2017. Scuderi, L.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: DOI: 10. 7717/peerj. 16927/supp-9 Download MIQE checklist. All essential information (E) must be submitted with the manuscript. Desirable information (D) should be submitted if available. If using primers obtained from RTPrimerDB, information on qPCR target, oligonucleotides, protocols and validation is available from that source. DOI: 10. 7717/peerj. 16927/supp-10 Download Primer-. DOI: 10. 7717/peerj. 16927/supp-11 of abbreviations RCC renal cell carcinoma KIRC kidney renal clear cell carcinoma SARS-CoV-2 severe acute respiratory syndrome coronavirus 2 ACE2 angiotensin-converting enzyme-2 fold change FDR false discovery rate DEGs differentially expressed genes WGCNA weighted correlation network analysis LASSO least absolute shrinkage and selection operator of Genes and Genomes GO qPCR real-time fluorescent quantitative PCR amplification ROC receiver operating characteristic curve AUC the area under the curve OS overall survival PCA principal component analysis TMB tumor mutation burden PPI protein-protein interaction -The authors sincerely thank all participants involved in this study. authors declare that they have no competing interests. conceived and designed the experiments, performed the experiments, prepared figures and/or tables, and approved the final draft. performed the experiments, prepared figures and/or tables, and approved the final draft. analyzed the data, authored or reviewed drafts of the 2023. Etoposide: a rider on the cytokine storm. Cytokine 168:156234. 2019. KCNMA1 expression is downregulated in colorectal cancer via epigenetic mechanisms. Cancers 11(2):245 Bury M, Girault A, Mégalizzi V, Spiegl-. 2013. Ophiobolin a induces paraptosis-like cell death in human glioblastoma cells by decreasing BKCa channel activity. & Disease 4(3):e561 Cairns P. 2010. Renal cell carcinoma. 9(1–6):461-473. 2012. The CD47-SIRPα pathway in cancer immune evasion and potential therapeutic implications. in Immunology 24(2):225-232. 2022.

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: usGuidelines to authorRole of ethicsRole of Authors6. 80SJR 0. 3910. 8 (2024)Frequency :Monthly (and December):(Scopus and Embase), 10. 18805/LRF-698Cite 1413. doi: 10. 18805/LRF-698. : Optimum plant nutrition with various organic and inorganic fertilizers such as synthetic fertilizer, compost, mycorrhiza and bacterial isolations have a pivotal role in agricultural production. This study was laid out to observe the combined impact of mycorrhiza and vermicompost treatments on plant growth and nutrient uptake of cowpea. Methods: The experiment was laid out under controlled greenhouse conditions at Tokat Gaziosmanpaþa University in 2021. Arbuscular mycorrhizal fungi and vermicompost treatments were used in the experiment. The experiment was laid out in split-plot randomized complete design with three replications. Result: Individual performance of vermicompost amendment was more effective on nutrient uptake and seedling growth compared with alone mycorrhizal treatment and control. However, the combined application of mycorrhiza and vermicompost exhibited a remarkable synergistic impact on each other. In particular, combined application of vermicompost and mycorrhizal fungi induced leaf phosphorus content up to 72% over control seedlings. In conclusion, vermicompost both increased effectiveness of mycorrhizal fungi and also promoted nutrient uptake, dry matter accumulation and seedling growth in cowpea. treatmentOrganic fertilizerPlant nutritionSynergistic impactVigna unguiculatamycorrhizal fungi (AMF), which has a ubiquitous distribution in known global ecosystems, uses the plant-fixed carbon which is provided by the host plant, in return, it induces plant growth by rising water and nutrients via extraradical and intraradical hyphae and the root apoplast interface (Parniske, 2008). Indeed, while the primary beneficial role of AMF is considered as nutrient supply in particular poor soils, secondary roles of them are thought to a reduction of root invasion by soil-borne microbial plant pathogens, protection of plants from phytotoxic impacts of heavy metals, enhancing water balance under stress conditions (Abeer et al. , 2015) and decreasing of insect herbivory (Neumann and George, 2010).

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: A. : Tree-ring evidence for climatically effective volcanic eruptions, Quaternary Res. , 34, 67–85, 1990. Sigl, M. , McConnell, J. R. , Toohey, M. , Curran, M. , Das, S. B. , Edwards, R. , Isaksson, E. , Kawamura, K. , Kipfstuhl, S. , Krüger, K. , Layman, L. , Maselli, O. J. , Motizuki, Y. , Motoyama, H. , Pasteris, D. R. , and Severi, M. : Insights from Antarctica on volcanic forcing during the Common Era, Nat. Clim. Change, 4, 693–697, 2014. Sigl, M. , Winstrup, M. ,. , Ludlow, F. , Büntgen, U. , Caffee, M. , Chellman, N. , Dahl-Jensen, D. , Fischer, H. , Kipfstuhl, S. , Kostick, C. , Maselli, O. J. , Mekhaldi, F. , Mulvaney, R. , Muscheler, R. ,. , Schüpbach, S. , Steffensen, J. P. , Vinther, B. M. , and Woodruff, T. E. : Timing and climate forcing of volcanic eruptions for the past 2,500 years, Nature, 523, 543–549, 2015. Stewart, G. H. : Structure and canopy tree species regeneration requirements in indigenous forests, Westland, New Zealand, Department of 66, 1–33, 2002. Tejedor, E. , Steiger, N. , Smerdon, J. E. , Serrano-Notivoli, R. , and Vuille, M. : Responses to in the Last Millennium, Paleoceanogr. Paleocl. , 36, 1–17, 2021. Timmreck, C. , Toohey, M. , Zanchettin, D. , Brönnimann, S. , Lundstad, E. , and Wilson, R. : The unidentified eruption of 1809: a climatic cold case, Clim.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: GTSE1 promotes tumor growth and metastasis by attenuating of KLF4 expression in clear cell renal cell carcinoma. 102(9):1011-1022 ärmander A, Waldenström öm K, Johansson ME. 2023. SARS-CoV-2 replicates and displays oncolytic properties in clear cell and papillary renal cell carcinoma. 18(1):e0279578 Déjosez. 2000. Sensitivity to TRAIL/APO-2L-mediated apoptosis in human renal cell carcinomas and its enhancement by topotecan. and Differentiation 7(11):1127-1136 ć. 2020. cell activation, senescence, exhaustion and skewing towards TH17 in patients with COVID-19 pneumonia. 11(1):3434 Delgado-López PD, Buzón-Martín L, Montero-Baladia M, Astigarraga I. 2021. Etoposide for cytokine storm because of coronavirus disease 2019. Chest 159(4):1678-1679. 2016. BKCa promotes growth and metastasis of prostate cancer through facilitating the coupling between αvβ3 integrin and FAK. Oncotarget 7(26):40174-40188. 2002. Cancer immunoediting: from immunosurveillance to tumor escape. 3(11):991-998. 2020. Advanced renal cell carcinoma and COVID-19-a personal perspective. Urology 17(8):425-427 Goeman J. 2010. L1 penalized estimation in the Cox proportional hazards model. 52(1):70-84. 2020. Tumor purity as a prognosis and immunotherapy relevant feature in gastric cancer. 9(23):9052-9063. 2017. Tumor mutational burden as an independent predictor of response to immunotherapy in diverse cancers. Therapeutics 16(11):2598-2608. 2020. Baseline characteristics and outcomes of 1591 patients infected with SARS-CoV-2 admitted to ICUs of the Lombardy region, Italy. JAMA 323(16):1574-1581. 2020.

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: Besides, to the best of our knowledge, combined application of AMF with various organic and biological amendments induces effectiveness of AMF (Cavagnaro, 2015; Sagar et al. , 2021). Vermicompost is an innovative technology in the sustainable agricultural perspective due to the decomposition and conversion of organic residues into rich and eco-friendly organic manure by the special earthworms. The basic difference that distinguishes vermicompost from other organic amendments is exposure to the action of some enzymes and microorganisms while passing through the digestive system of earthworm (Ravindran et al. , 2016). Vermicompost treatment promotes germination and seedling growth (Ceritoglu et al. , 2021), improves crop yield and quality (Joshi et al. , 2015) and enhances soil physiological, chemical and biological properties (Arancon and Edwards, 2011), reduces pathogenic infections (Yatoo et al. , 2021). Besides, vermicompost has also many direct and indirect effects on plants and soil such as improving soil structure, increasing organic matter and carbon content, porosity and water retention reducing bulk density, promoting microbial biomass and activity, suppressing plant diseases, and inducing various enzymatic activities, i. e. , dehydrogenase, nitrogenase, phosphatase (Singh et al. , 2020). Beneficial and synergistic influences of vermicompost on the promotive effect of AMF were already stated by various researchers (Pireh et al. , 2017). However, the information about the combined application of vermicompost and AMF in cowpea production is limited. Cowpea is a major crop for human and animal feed in particular places in which malnutrition is widely seen such as the African continent (Omomowo and Babalola, 2021). Therefore, improving cowpea growth through sustainable strategies constitutes a part of food security in the world. arbuscular mycorrhizal fungi and soil Three cowpea cultivars (Akkiz, Karagöz, Karnikara) belonging Vigna unguiculata were used in the experiment. Cow manure-based vermicompost was supplied from the commercial company. Physio-chemical properties of vermicompost were given in Table 1. Mycorrhizal bio-material was supplied by BioGlobal commercial company.

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: Past, 17, 1455–1482, 2021. Tingley, M. P. , Stine, A. R. , and Huybers, P. : Temperature reconstructions from tree-ring densities overestimate volcanic cooling, Geophys. Res. Lett. , 41, 7838–7845, 2014. Toohey, M. and Sigl, M. : Volcanic stratospheric sulfur injections and aerosol optical depth from 500 BCE to 1900 CE, Earth Syst. Sci. Data, 9, 809–831, 2017. Toohey, M. , Stevens, B. , Schmidt, H. , and Timmreck, C. : Aerosol (EVA v1. 0): an idealized forcing generator for climate simulations, Geosci. Model Dev. , 9, 4049–4070, 2016. Trenberth, K. and for Staff (Eds. ): [data set], slp-soi (last access: 7 August 2021), 1984 (updated regularly). Villalba, R. and Boninsegna, J. A. : Changes in American Tree-following Eruptions between 1750-1970, in: without a summer? : World climate in 1816, edited by: Harington, C. R. , of Nature, Ottawa, 493–509, 1992. Wardle, J. : The ecology of Nothofagus solandri, New Zealand, New Zeal. J. Bot. , 8, 609–646, 1970. Wardle, P. : Plant communities of Park (New Zealand) and neighbouring lowland and coastal areas, New Zeal. J. Bot. , 15, 323–398, 1977. Wilson, R. , Anchukaitis, K. , Briffa, K. R. , Büntgen, U. , Cook, E. , D'Arrigo, R. , Davi, N. , Esper, J. , Frank, D. , Gunnarson, B. , Hegerl, G. , Helama, S. , Klesse, S. ,. , Osborn, T. J. , Rydval, M. , Schneider, L. , Schurer, A. , Wiles, G. , Zhang, P.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Targeting the ERβ/Angiopoietin-2/Tie-2 signaling-mediated angiogenesis with the FDA-approved anti-estrogen Faslodex to increase the Sunitinib sensitivity in RCC. & Disease 11(5):367. 2016. Silencing GTSE-1 expression inhibits proliferation and invasion of hepatocellular carcinoma cells. and Toxicology 32(4):263-274. 2020. Etoposide-based therapy for severe forms of COVID-19. 142:109826 --. 2021. TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation. Cell 184(10):2618-32. e17. 2021. Emerging role of Neuropilin-1 and angiotensin-converting enzyme-2 in renal carcinoma-associated COVID-19 pathogenesis. Reports 13(4):902-909. 2004. The use of selective estrogen receptor modulators and selective estrogen receptor down-regulators in breast cancer. & Endocrinology & Metabolism 18(1):47-66. 2021. An insight into the inhibitory mechanism of phytochemicals and FDA-approved drugs on the ACE2-Spike complex of SARS-CoV-2 using computational methods. Chemicke zvesti 75(9):4625-4648 University and Medicine. 2023. COVID-19 dashboard by the center for systems science and engineering (CSSE) at johns hopkins university (JHU) January 10. Kellum JA, van. 2020. Targeting acute kidney injury in COVID-19. Nephrology, Dialysis, Transplantation 35(10):1652-1662 Kilpinen H, Barrett JC. 2013. How next-generation sequencing is transforming complex disease genetics. Trends in Genetics: TIG 29(1):23-30. 2020. Immune cells within the tumor microenvironment: biological functions and roles in cancer immunotherapy. 470:126-133. 2020. LILRB4 ITIMs mediate the T cell suppression and infiltration of acute myeloid leukemia cells. Cellular & 17(3):272-282. 2019.

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: The 50 ml of AMF solution per viol (~20-25 spores g- soil) was injected into the rhizosphere of cowpea seedlings four days after emergence. The 50 ml of distilled water was given to each non-AMF applied viol at the same time. Seedlings were irrigated with the Hoagland nutrient solution. The EC of Hoagland solution was adjusted as 1. 4 mmhos cm- until seedlings achieve 14-days of age and after this period EC was set as 1. 8 mmhos cm-2. The experiment was conducted at the end of the 40th day. Morphological observations and nutrient uptake At the final of the experiment, ten plants were randomly selected from each viol. Plants were cut by scissors and separated root and shoot parts. Plant height (PH) was measured by a scale. Stem diameter (SD) was measured at 1 cm above the soil surface using an electronic digital caliper (Mitutoyo 500-182-30 digital caliper, Co. Ltd. , Japan) to investigate seedling growth and robustness. Root fresh weight (RFW) and shoot fresh weight (SFW) were determined and samples were placed in the oven at 68°C until not any differences between the last two observations, therefore, shoot dry weight (SDW) and root dry weight (RDW) were observed. The samples were ground and sieved by 2 mm for the determination of macronutrient contents. Kjeldahl method was used to determine leaf nitrogen content (LNC) of samples (Saez-Plaza et al. , 2013). Modified Vando-molybdate phosphoric yellow color method was used to observe leaf phosphorus content (LPC) and Leaf potassium content (LKC) was determined by flame photometric method (Jackson, 1973). Statistical analysis The test of Shapiro and Wilks was used to investigate the normality of the data. The results were subjected to analysis of variance using JMP (V. 5. 0. 2) according to split-plot randomized complete design. The means were grouped by Tukey’s multivariate test. to analysis of variance, cowpea cultivars caused statistically significant differences at the level of P<0. 01 in the and LPC while it led to significant differences (P<0. 05) in RDW and LNC.

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: , and Zorita, E. : Last millennium summer temperatures from tree rings: Part I: The long term context, Quaternary Sci. Rev. , 134, 1–18, 2016. Xiong, L. and Palmer, J. G. : Tree-ring Chronologies in New Zealand, Tree-Ring Bulletin, 56, 1–16, 2000. Xiong, L. , Okada, N. , Fujiwara, T. , Ohta, S. , and Palmer, J. G. : Chronology development and climate response analysis of different pink pine (Halocarpus biformis) tree-ring parameters, Can. J. Forest Res. , 28, 566–573, 1998. Zhu, F. , Emile-Geay, J. , Hakim, G. J. , King, J. , and Anchukaitis, K. J. : Resolving the Differences in the Simulated and Response to Volcanism, Geophys. Res. Lett. , 47, 1–12, 2020. Zweifel, R. , Sterck, F. , Braun, S. , Buchmann, N. , Eugster, W. , Gessler, A. , Häni, M. , Peters, R. L. , Walthert, L. , Wilhelm, M. , Ziemińska, K. , and Etzold, S. : Why trees grow at night, New Phytol. , 231, 2174–2185, 2021.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Overexpression of G2 and S phase-expressed-1 contributes to cell proliferation, migration, and invasion via regulating p53/FoxM1/CCNB1 pathway and predicts poor prognosis in bladder cancer. of 123:322-334 Lovetrue B. 2020. The AI-discovered aetiology of COVID-19 and rationale of the irinotecan+ etoposide combination therapy for critically ill COVID-19 patients. 144:110180. 2013. The HECT type ubiquitin ligase NEDL2 is degraded by anaphase-promoting complex/cyclosome (APC/C)-Cdh1, and its tight regulation maintains the metaphase to anaphase transition. Journal of 288(50):35637-35650. 2017. KCNMA1 cooperating with PTK2 is a novel tumor suppressor in gastric cancer and is associated with disease outcome. 16(1):46. 2022. A requirement for Krüppel like factor-4 in the maintenance of endothelial cell quiescence. Frontiers in Cell and 10:1003028 McKee M, Stuckler D. 2020. If the world fails to protect the economy, COVID-19 will damage health not just now but also in the future. 26(5):640-642. 2000. Cloning, chromosome mapping and functional characterization of a human homologue of murine gtse-1 (B99) gene. Gene 254(1–2):229-236. 2020. Shape-based machine learning models for the potential novel COVID-19 protease inhibitors assisted by molecular dynamics simulation. in 20(24):2146-2167. 2015. Robust enumeration of cell subsets from tissue expression profiles. 12(5):453-457. 2021. Key sunitinib-related biomarkers for renal cell carcinoma. 10(19):6917-6930. 2020. Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses. Biochemical and Communications 526(1):135-140. 2019. Novel immune checkpoint targets: moving beyond PD-1 and CTLA-4. 18(1):155. 2016. NEDL2 regulates enteric nervous system and kidney development in its Nedd8 ligase activity-dependent manner.

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: However, cultivars did not significantly affect SD and LKC. Treatments and their interaction with cowpea cultivars caused statistically significant differences (P<0. 01) in all traits (Table 2). Table 2: Analysis of variance belonging to investigated morphological and chemical characteristics depending on cowpea cultivars and treatments including vermicompost and arbuscular mycorrhizal fungi. The PH depending on cultivars and treatments changed between 22. 3-24. 8 and 20. 9-25. 0, respectively. The highest pH was in Akkýz and the lowest one was in Karnýkara. The highest PH depending on treatments was obtained by T8 treatment which promoted the PH up to 25% compared with control (Fig 1). All cultivars were in the same statistical group in terms of SD, however, treatments were effective. Depending on treatments, SD varied between 2. 48-3. 56 mm. The highest SD was observed in T8 treatment whereas the lowest one was determined by control seedlings (Fig 2). The highest SFW was obtained by T8 treatment with Karnýkara and Karagöz, respectively, following T8 treatment with Akkýz. Rising vermicompost applications induced both SFW and the effectiveness of AMF (Fig 3). Differences and fluctuation between treatments were higher in SFW compared with SDW due to holding water in plant metabolism. The T8 treatment led to observing the highest dry matter accumulation in shoots. However, T8 treatment promoted dry matter accumulation over control up to 31. 8%, 28. 0% and 18. 2% in Karnikara, Akkiz and Karagöz, respectively. The effectiveness of AMF in these promotive impacts was about 5% in all cultivars (Fig 4). RFW and RDW were similarly affected by treatments and the highest RFW and RDW were obtained by the T8 treatment in Akkiz (Fig 5 and 6). The highest LNC was determined with T8 treatment in Akkýz while the lowest one was observed in control of Karnikara seedlings (Fig 7). In particular, the effectiveness of 45% vermicompost and its synergistic relationship with nitrogen uptake was remarkable since the T5 and T8 treatments increased the LNC compared with control up to 11. 7% and 28. 5%, respectively (Fig 10).

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: navigation Apply for support FAQ Be involved toggle overview Mission statement PAGES logos fellows Meeting minutes us Supporters and partners Supporters and partners organization Scientific partners -of involved Be involved mailing lists Apply to be on the SSC Write for and education Stakeholder engagement Stakeholder engagement Engaging with stakeholders guidelines Endorsed and affiliated Former initiatives and groups Data stewardship Data guidelines PAGES databases External databases webinars PAGES awardees PAGES awardees Scholarship recipients Early-Guest scientists -Menu layer 3 left side Menu layer 3 right side the volcanic signal in tree rings Alexander R. Stine, M. P. Tingley and P. Huybers >Access contents of this issue >Download this 10. 22498/pages. 23. 2. 62 Alexander R. Stine1, M. P. Tingley2 and P. Huybers3 Comparison of the signature of volcanism in tree rings with thermometers indicates that tree rings overestimate volcanic cooling. The timing and spatial expression of the tree-ring response indicate that decreased light availability contributes to the tree-ring response to volcanism. Volcanic eruptions that loft aerosols into the stratosphere offer natural experiments by which to explore the response of the climate system to short-term changes in radiative forcing. In the one to two years following the largest volcanic eruptions of the past century, we observe a decrease in the solar radiation received at the Earth’s surface, as well as cooler than usual surface temperatures (Robock et al. 2007). Volcanic eruptions also offer an opportunity to explore the response of tree-ring proxies to changes in solar radiation and temperature. Most tree-ring chronologies from temperature-limited high-northern latitude regions show a decrease in tree-ring width or density following a major explosive volcanic eruption. This response has historically been interpreted as an exclusive result of the cooler summertime temperatures that are observed following such eruptions – a cooling that is understood to be induced by scattering from volcanic aerosols in the stratosphere that reduce the amount of shortwave radiation reaching the Earth’s surface. An emerging line of evidence supports the hypothesis that high-latitude tree-ring growth also responds to variability in light, independent of the influence of light on temperature (Stine and Huybers 2014; Tingley et al. 2014).

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Oncotarget 7(21):31440-31453. 2001. Topotecan (Hycamtin) responsiveness in human renal carcinoma cell lines of the clear cell and papillary types. 21(5):3509-3517 R Core Team. 2022. R: A language and environment for statistical computing Version 4. 2. 2. 2015. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 348(6230):124-128. 2011. Antitumor effect of suberoylanilide hydroxamic acid and topotecan in renal cancer cells. 19(5):217-223. 2009. A potential novel combination therapy targeting survivin in renal cancer cells: inhibition of survivin expression by topotecan and hexamethylene bisacetamide. Reports 2(3):423-428. 2008. Topotecan and small interfering RNA suppress survivin expression synergistically in Caki-1 renal cancer cells: direct suppression of survivin and enhancement of transfection efficiency by topotecan. of Oncology 32(1):171-176. 2009. CellMiner: a relational database and query tool for the NCI-60 cancer cell lines. BMC Genomics 10(1):277. 2018. Targeting newly identified ERβ/TGF-β1/SMAD3 signals with the FDA-approved anti-estrogen Faslodex or an ERβ selective antagonist in renal cell carcinoma. 12(12):2055-2071. 2013. Attenuation of krüppel-like factor 4 facilitates carcinogenesis by inducing g1/s phase arrest in clear cell renal cell carcinoma. 8(7):e67758. 2005. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the of Sciences 102(43):15545-15550. 2021. Global cancer statistics 2020: estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: A for Clinicians 71(3):209-249. 2021. Downregulation of ACE2 expression by SARS-CoV-2 worsens the prognosis of KIRC and KIRP patients via metabolism and immunoregulation. of 17(8):1925-1939. 2020.

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: The consortium of vermicompost and the mycorrhizal was more effective on phosphorus uptake than nitrogen (Fig 8). Promoting rate of the LPC belonging to cultivars by treatments varied between 4-72% and the highest increment was observed in T8 treatment. Although individual AMF treatment was not very effective on P uptake, it has a remarkable impact when used with vermicompost (Fig 10). The highest LKT (1. 69%) was determined with T8 treatment in Karagöz while the lowest LKT was observed with control seedlings of Karnýkara. The LKC varied between 1. 41-1. 69% depending on cultivars and treatments. Treatments induced potassium uptake by 2. 1-15. 3%. The highest increment was determined with T7 treatment following T8 (Fig 9). Fig 1: Influence of vermicompost and mycorrhizal applications on plant height of three cowpea cultivars. Fig 2: Influence of vermicompost and mycorrhizal applications on stem diameter of three cowpea cultivars. Fig 3: Influence of vermicompost and mycorrhizal applications on shoot fresh weight of three cowpea cultivars. Fig 4: Influence of vermicompost and mycorrhizal applications on shoot dry weight of three cowpea cultivars. Fig 5: Influence of vermicompost and mycorrhizal applications on root fresh weight of three cowpea cultivars. Fig 6: Influence of vermicompost and mycorrhizal applications on root dry weight of three cowpea cultivars. Fig 7: Influence of vermicompost and mycorrhizal applications on the leaf nitrogen content of three cowpea cultivars. Fig 8: Influence of vermicompost and mycorrhizal applications on the leaf phosphorus content of three cowpea cultivars. Fig 9: Influence of vermicompost and mycorrhizal applications on the leaf potassium content of three cowpea cultivars. Fig 10: Alterations in nutrient uptake depending on the individual and combined application of vermicompost and arbuscular mycorrhizal fungi compared with non-amended control plants. The AMF facilitates nutrient uptake under optimum and stress conditions.

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: The notion that large-scale tree-ring growth may respond to changes in photosynthetic light availability is not new (Briffa et al. 1998). Indeed, the well-established Vaganov-Shashkin (VS) model of tree-ring growth includes a term whereby the growth rate is proportional to variations in daily average light intensity (Vaganov et al. 2006). Here we discuss two lines of evidence for a direct tree-ring response to volcanic dimming. Each relies on aggregating the tree-ring response to large volcanic eruptions over distinct regions of the Arctic, so as to isolate the effects of reduced light from the effects of cooler temperatures (Stine and Huybers 2014; Tingley et al. 2014). Evidence that light affects trees Figure 1: Comparison of the volcanic cooling recorded by boreal tree rings with volcanic cooling recorded by thermometers. Tree rings are calibrated into temperature units using a Bayesian approach (Tingley et al. 2014). Top row shows response for 1912 Novarupta eruption and bottom row for 1883 Krakatoa eruption. (A and B) Comparison for relatively strongly, and (C and D) for relatively weakly light-limited boreal regions. (E and F) The bias in the tree-ring response from regions of relatively strong (blue) and weak (orange) light-limitation compared with the anomaly in atmospheric transmissivity inferred from contemporary pyrheliometers (green; Kimball 1918). One line of evidence that tree rings respond to changes in the light environment is provided by comparing the volcanic temperature response inferred from tree rings to that measured by thermometers. Consider the response to the 1883 Krakatoa and 1912 Novarupta eruptions - the two largest eruptions that occurred late enough to be reasonably well-monitored by instrumental thermometers, but early enough to be unaffected by the late-20th century decline in Arctic tree-ring width and density relative to temperature referred to as the divergence phenomenon (Briffa et al. 1998). and Novarupta resulted in strong reductions in atmospheric transmissivity, leading to a reduction in surface solar radiation intensity which was recorded by contemporary pyrheliometer measurements (Kimball 1918). In both cases, post-eruption temperature anomalies inferred from tree-ring densities show a larger amplitude response than is consistent with the degree of cooling found in thermometer measurements (Fig.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Renal carcinoma is associated with increased risk of coronavirus infections. Frontiers in 7:579422 Wakabayashi-. 2014. Carcinoembryonic antigen-related cell adhesion molecule 4 (4) is specifically expressed in medullary thyroid carcinoma cells. 35(4):237-242. 2020. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. JAMA 323(11):1061-1069 Warde-. 2010. prediction server: biological network integration for gene prioritization and predicting gene function. Research 38(suppl_2):W214-W220 Weiss SR, Navas-Martin S. 2005. Coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus. Microbiology and Reviews: MMBR 69(4):635-664 Welling PA. 2016. Roles and regulation of renal K channels. of Physiology 78(1):415-435. 2018. High G2 and S-phase expressed 1 expression promotes acral melanoma progression and correlates with poor clinical prognosis. 109(6):1787-1798. 2020. Development and validation of a tumor mutation burden-related immune prognostic model for lower-grade glioma. Frontiers in Oncology 10:1409. 2015. DSigDB: drug signatures database for gene set analysis. Bioinformatics 31(18):3069-3071 Yoshihara K, Shahmoradgoli M, Martínez -Garcia W, Treviño -. 2013. Inferring tumour purity and stromal and immune cell admixture from expression data. 4(1):2612. 2020. Identification of a three-long noncoding RNA prognostic model involved competitive endogenous RNA in kidney renal clear cell carcinoma. International 20:319. 2020. High RPS3A expression correlates with low tumor immune cell infiltration and unfavorable prognosis in hepatocellular carcinoma patients. of 10(9):2768-2784. 2020. A novel coronavirus from patients with pneumonia in China. Journal of Medicine 382(8):727-733 a question Learn more about Q&A a link Alert Loading. . . Just enter your email Tools & info history 12. 0MB) Save to in download will start in a moment. . .

Output: pass


Input: Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: AMF treatment increased PH, SFW and SDW, induced dry matter accumulation in all parts and enhanced the and LKC in seedlings, therefore, the findings are in agreement with previous experiments (Etesami et al. , 2021). On the whole, the primary contribution of AMF is considered as increasing the supply of nutrients to plants, in particular, ionic forms of poor-mobility ones such as ammonium, phosphate, copper and zinc (Barea et al. , 2005). Neuman and George (2010) indicated that AMF both directly contributes to nutrient uptake by symbiotic pathway, and also indirectly influences it via alteration of the root system and functioning and soil properties of mycorrhizosphere. It is considered that AMF hyphae may be able to achieve in smaller soil pores due to their thin diameter, thereby, they can exhibit better competition against soil microbes for nutrient resources. Moreover, AMF might enhance the chemical mobilization of nutrients via activation of inorganic phosphate and ammonium transporters, as well as, plant morphological growth (Banasiak et al. , 2021). Thus, AMF applications promoted nitrogen, phosphorus and potassium uptake and transportation to aboveground parts of plants and enhanced morphological growth of roots and shoots in all cultivars. Besides, individual and combined application of vermicompost caused a remarkable promotion of nutrient uptake and seedling growth. It is considered to be caused by alteration of soil carbon and nutrient pools depending on vermicompost doses. Sarma et al. , (2018) denoted that vermicompost application led to increasing soil organic carbon, C-mineralization and soil respiration. So, these changes promote C transportation to AMF, nutrient uptake by hype and transmit to plant roots and increase seedling growth and development. Ceritoglu et al. , (2018) pointed out that vermicompost enhances soil nutrient pool, promotes microbial activity and improves physiological properties. This experiment also presented that N-P-K uptake gradually increased by individual application of vermicompost and continued to increase by the synergistic influence of AMF. In particular, the LPC increased from 28% to 40% depending on individual vermicompost doses, however, it achieved 72% with AMF treatment. The findings are in agreement with Etesami et al. , (2021) who reviewed the effectiveness of AMF on phosphorus uptake.

Output: corroborate


Input: Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: 1; Tingley et al. 2014). Furthermore, the cold bias is larger in magnitude in high-latitude regions where photosynthesis is inferred to be more limited by light (Nemani et al. 2003), supporting the hypothesis that trees respond directly to decreases in light availability. Pyrheliometer measurements indicate that the atmospheric transmissivity was reduced for substantially longer following Krakatoa (~3 years) than following Novarupta (~1 years; Kimball 1918). In both cases the tree-ring cold bias persists for a period similar to the period of reduced atmospheric transmissivity (Fig. 1e,f). Figure 2: Comparison of the tree-ring density response to volcanic eruptions of the last 700 years with local estimates of light limitation and spatial variability in the response to global dimming (Stine and Huybers 2014). (A) Volcanic response in strongly (blue) and weakly (orange) light-limited regions. (B) Volcanic response in regions with strong (blue) and weak (orange) decline in density relative to temperature during period of global dimming. Comparison of volcanic tree-ring response to (C) light limitation and to (D) global dimming across the boreal region. Whereas the instrumental period contains only a small number of eruptions with a clear response in both the instrumental and tree ring records, 32 major eruptions were recorded in the northern hemisphere ice-core record in just the last 700 years (Gao et al. 2007). Across the high-northern latitudes a close correspondence exists between the magnitude of the tree-ring response to volcanism and estimates of the relative importance of light availability in limiting plant growth (Fig. 2c; Nemani et al. 2003). The reduction in tree-ring density following the major volcanic eruptions of the last 700 years was, on average, twice as large in high-northern latitude regions where light-limitation on photosynthesis is strong, compared with regions where light limitation on photosynthesis is weaker (Fig. 2a). Similar results are found for tree-ring widths (Stine and Huybers 2014). The concordance between the volcanic response and patterns of light limitation to growth suggests that, in the boreal regions that are more strongly light limited, tree growth responds directly to both the reduction in temperature and the reduction in photosynthetically available radiation.

Output: contrast


Input: Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: -19 PreprintsProtocolsVideosJournalsTools & a 10. 21203/rs. 3. rs-4117423/v1This work is licensed under a CC BY 4. 0 LicenseStatus:Under RevisionVersion 1posted 7You are reading this latest preprint versionAbstractwith diabetes are at risk of developing diabetic keratopathy (DK). The pathophysiological mechanisms of DK and associated biomarkers remain unclear. However, tear analysis provides crucial insights into DK. Thus, we conducted a quantitative proteomic analysis of tears from DK patients to identify differentially expressed proteins and potential pathways associated with DK. prospective case-controlled study included patients admitted to between October 2022 and February 2023. We examined 22 eyes with DK and 11 control eyes without DK. General characteristics and dry eye-related features were recorded, including those observed using ocular surface analysis, conjunctival impression cytology, and tear ferning tests. Tear fluid was collected using Schirmer strips after ensuring group similarity in confounders. Proteins were analysed through four-dimensional label-free mass spectrometry. Differential proteins were subjected to analyses of of Genes and Genomes. A protein–protein interaction network map was constructed. the 2733 proteins identified, 313 (156 upregulated and 157 downregulated) differentially expressed proteins were screened. analysis revealed that these differentially expressed proteins mainly participated in mRNA decay, nuclear transcription, and receptor-mediated endocytosis. of Genes and Genomes analysis showed that these differentially expressed proteins could be involved in pathways, such as arginine biosynthesis, extracellular matrix-receptor interactions, and lysosome-related processes. biosynthesis and extracellular matrix-receptor interactions may be involved in DK pathogenesis. These findings may enhance the understanding of DK among ophthalmologists. Biological sciences/Biological techniques/Analytical biochemistryHealth sciences/Diseases/Eye diseases/Corneal diseasesBiological sciences/Cell biology/Mechanisms of diseaseFiguresFigure 1Figure 2Figure 3Figure 4Figure 5IntroductionDiabetic keratopathy (DK), first described in 1981,1 is characterised by xerophthalmia, recurrent corneal epithelial erosion, persistent corneal epithelial defects, recurrent corneal ulcers, and corneal hypoesthesia.

Output: pass