Input: Task: pass the claim using the given text. Claim: Saturn’s rings are composed primarily of ice particles and rocky debris. [SEP] Text: Edges of Saturn’s rings are fractal access Published: 01 April 2015 Edges of Saturn’s rings are fractal Jun Li1 & Martin Ostoja-Starzewski2 SpringerPlus 1981. Using three box-counting methods, we determine the fractal dimension of edges of rings seen here to be consistently about 1. 63 ~ 1. 78. This clarifies in what sense Saturn’s rings are fractal. BackgroundThe images recently sent by the Cassini spacecraft mission (available on the NASA website show the complex and beautiful rings of Saturn. Beginning with (Mandelbrot, 1982; Avron and Simon, 1981; Fridman and Gorkavyi, 1994), there have been conjectures that radial cross-sections of Saturn’s rings are Cantor sets, but, to the best of our knowledge, no convincing fractal analyses of actual images ever appeared. Of the 87 Cassini images, in Figure 1 (a) we reproduce slide #42 bearing the title “in Saturn’s Rings,” in Figure 1 (b) the slide #54 titled “Scattered Sunshine,” in Figure 1 (c) we reproduce slide #66 taken two weeks before the planet’s August 2009 equinox, and in Figure 1 (d) slide #68 showing edge waves raised by Daphnis on the Keeler Gap. The first of these is a false-color image of Saturn’s main rings made by combining data from multiple star occultations using the Cassini ultraviolet imaging spectrograph. In the second of these, Saturn’s icy rings shine in scattered sunlight, from about 15° above the ring plane. In the third image, a part of the Cassini Division, between the B and the A rings, appears at the top of the image, showing ringlets in the inner division, while in the fourth Daphnis cruises through the Keeler Gap, raising edge waves in the ring material as it passes. The first two photographs show the curved geometry of Saturn’s main rings with a low opening angle, while the latter two reflect the details of a part of the rings. Finally, in Figure 1 (e), we reproduce the image sent by ‘Voyager 2’ spacecraft in 1981 ( The selected set of images represent Saturn’s rings from a variety of view angles and regions. [SEP] Justify:

Output: The text provides detailed information about the fractal nature and imagery of Saturn's rings, particularly focusing on the geometric and fractal characteristics observed in the images captured by the Cassini spacecraft. However, it does not address the composition of the rings, which is the main aspect of the claim regarding whether they are made up mostly of ice and rocky materials. Therefore, the text is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: At BBCH 62, the percentage of root length containing arbuscules and AM fungal root colonization was significantly improved by inoculation (-M vs + M, arbuscules: 26% vs 41%; AM fungal root colonization: 43. 9% vs 60. 3%) (Fig. 3b; Table S3). At BBCH 89, inoculation with F. mosseae significantly increased percentage of AM fungal root colonization and of root length containing vesicles (80% and 7. 8%, respectively) compared with S. sinuosa (67% and 5%, respectively) (Fig. 3c; Table S3). Moreover, the occurrence of vesicles in the roots of tomato was significantly increased by AM fungal inoculation (-M vs + M: 5. 5% vs 7. 1). Finally, an inter-family variability was detected: the occurrence of vesicles was promoted in the roots of tomato inoculated with isolates belonging to the family Gigasporaceae compared with the ones inoculated with the isolates belonging to the family Glomeraceae (7. 8% vs 6. 4%). In Fig. 2e the image of a not inoculated root of tomato var. at transplanting (i. e. , BBCH 22), while in Fig. 2f-l images of AM fungal structures within the roots of inoculated plants sampled at transplanting and at BBCH 62 and BBCH 89. Effect of AM fungal inoculation on tomato yield and fruit nutrient concentrations In 2019, AM fungal inoculation significantly increased total fruit yield of tomato var. Pisanello accumulated during the productive phase by 32%(+ M vs – M: 1452. 6 g plant− 1 vs 1098. 3 g plant− 1) (Fig. 4a; Table S2). Moreover, there was a difference between the members of Gigasporaceae: tomato plants inoculated with S. pellucida showed higher total yield (+ 27%) than plants inoculated with G. gigantea (1614. 1 g plant− 1 vs 1269. 5 g plant− 1). Details about yield (mean ± SE) at each harvest are given in Fig. S3. In 2020, at BBCH 22, AM fungal inoculation increased by 115% shoot dry weight (SDW) of var. (+ M vs -M: SDW: 0. [SEP] Justify:

Output: The text corroborates the claim by providing evidence that arbuscular mycorrhizal (AM) fungal inoculation increases root colonization and fruit yield in plants, particularly in nutrient-poor conditions. It details the percentage increase in arbuscular colonization and vesicle occurrence in the roots of tomato plants, thereby indicating improved nutrient uptake associated with mycorrhizal fungi.


Input: Task: contrast the claim using the given text. Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: 1071/wf181606305. Tree-ring anatomy and carbon isotope ratio show both direct and legacy effects of climate on bimodal xylem formation in Pinus pinea. 38(8):1098–1109. Variations of wood anatomy and δ13C within-tree rings of coastal pinus pinaster showing intra-annual density fluctuations. IAWA J 28(1):61–74524. Water uptake by plants: perspectives from stable isotope composition. Plant, 15(9):1073–1082. D13C and tree-ring width reflect different drought responses in Quercus ilex and Pinus halepensis. Oecologia 137(4):512–518. N, Linares JC, Castro-Díez P, Sass-(2015) Contrasting secondary growth and water-use efficiency patterns in native and exotic trees co-occurring in inner spain riparian forests. 24(1). Combining d13C and d18O analyses to unravel competition, CO2 and O3 effects on the physiological performance of different-aged trees. Plant, 30:1023–1034317. Impact of drought on temporal dynamics of wood formation in Pinus Sylvestris. 30:490–50128. ML (1981) Fire and succession in the conifer forest of northern North America. In: (eds) Forest succession: concepts and application. Springer, New York, pp 374–4052. 01. Palisades, NY: and (SEDAC). (2005) Association between tree-ring and needle δ 13 C and leaf gas exchange in pinus halepensis under semi-arid conditions. Oecologia 144(1):45–54. Elsevier, Oxford, pp 2296–230817. H, Flexas J, Galmés J (2009) Variability in water use efficiency at the leaf level among Mediterranean plants with different growth forms. 317(1–2):17–29. A (2009) Lack of direct evidence for the carbon-starvation hypothesis to explain drought-induced mortality in trees. of Am 106(26). Physiological mechanisms of drought-induced tree mortality are far from being resolved. 186(2):274–281. Explaining global increases in water use efficiency: why have we overestimated responses to rising atmospheric CO2 in natural forest ecosystems? [SEP] Justify:

Output: The text contrasts the claim by describing various studies that investigate the relationships between tree-ring data and environmental factors. It mentions aspects of tree-ring anatomy and carbon isotope ratios that are critical in understanding climate influences and responses, thereby indicating that tree rings can indeed provide insights into past environmental disturbances, which directly challenges the claim that they cannot be used for such studies.


Input: Task: pass the claim using the given text. Claim: Saturn’s rings are composed primarily of ice particles and rocky debris. [SEP] Text: Figure 1 (a,b,c,d,e): The original images of the Cassini and Voyager missions. Full size image Results and discussionAs is well known (Mandelbrot, 1982), the fractal dimension D comes from estimation of the slope of log(n)-log(r) in n ∝ r − D, where n is the number of boxes with size r needed to cover the region of interest. The local slopes of log(n)-log(r) are also acquired to determine optimal cut-offs of box sizes. The cut-offs are specified where the local slope varies strongly. The log(n)-log(r) plots of the three box counting methods for images of Figure 1 (a), (d), and (e) are shown in Figures 2, 3 and 4, respectively. Since the plots for Figures 1 (b) and (c) are very similar to the others, they are not shown here in order to save space. Note that, for modified box counting, r denotes the ratio of image size to box size, unlike power 2 or divider box counting, where r is the box size. Figure 2 Results of box counting method to estimate the fractal dimension of image (a) in Figure 1 : (a) Modified box counting; (b) Power 2 box counting; (c) Divider box counting. Full size image Figure 3 Results of box counting method to estimate the fractal dimension of image (d) in Figure 1 : (a) Modified box counting; (b) Power 2 box counting; (c) Divider box counting. Full size image Figure 4 Box counting method to estimate the fractal dimension of image (e) in Figure 1 : (a) Modified box counting; (b) Power 2 box counting; (c) Divider box counting. Full size image Note that these images were projections of Saturn’s rings from different angles and regions. Following the arguments presented in (Maggi 2008; Meakin 1998), given the fact that the rings’ thickness is extremely small compared to their radii, the projection onto the plane of the photograph does not affect the fractal dimension. Besides, the self-similarity of fractals indicates that the fractal dimension of a part is same as that of the whole. Overall, the box counting results of all images are given in Table 1. [SEP] Justify:

Output: The text is irrelevant to the claim since it focuses on the methods for estimating fractal dimensions based on images of Saturn’s rings, without providing any information about the composition of the rings themselves.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: 30 g plant− 1 vs 0. 14 g plant− 1) (Fig. 4b; Table S3). In addition, significant differences (+ 75%) were observed between the SDW of plants inoculated with S. sinuosa compared with those inoculated with F. mosseae (SDW: 0. 34 g plant− 1 and 0. 20 g plant− 1, respectively). In 2020, total yield of var. was increased by 38% following AM fungal inoculation (+ M vs -M: 1432. 2 g plant− 1 vs + 1036. 85 g plant− 1), whereas no differences were recorded among and within families (Fig. 4b; Table S3). In 2019, at first harvest, AM fungal inoculation significantly increased N concentration and decreased Zn concentration in fruits of var. Pisanello, as compared to controls (Fig. 5a; Table S4). Fruits of plants inoculated with F. mosseae had higher values of both N and Cu concentration than those inoculated with S. sinuosa. In addition, inoculation with S. pellucida increased Cu concentration compared to G. gigantea. At the second harvest, AM fungal inoculation, although decreasing Ca concentration in fruits, increased P, Mg, Cu, and Mn concentration compared with controls (Fig. 5a; Table S4). An inter-family variability was recorded, and Mg and Mn concentration in fruits increased in plants inoculated with members of Gigasporaceae compared with those inoculated with Glomeraceae. Moreover, within Glomeraceae, the inoculation with F. mosseae, similarly to the first harvest, increased K, Mg and Mn concentration as compared to the inoculation with S. sinuosa. Large differences were reported also in fruit content of all studied nutrients of var. Pisanello at first harvest according to inoculation with members of both Gigasporaceae and the Glomeraceae, with the exception of the Mn content in fruits of plants inoculated with isolates belonging to Gigasporaceae (Table S5 and S6). Moreover, inter-family differences were recorded in fruit content of K and Ca, which was also increased by the inoculated treatments compared with the controls. Similarly, at the second harvest, some inter-family differences were observed in nutrient content of fruits (i. e. [SEP] Justify:

Output: The text corroborates the claim by detailing various beneficial impacts of AM fungal inoculation on nutrient uptake in plants. Specifically, it mentions how AM fungal inoculation led to increased nitrogen (N), phosphorus (P), magnesium (Mg), copper (Cu), and manganese (Mn) concentrations in fruits, indicating improved nutrient uptake capabilities. Moreover, it describes yield increases and nutrient content improvements across different varieties, which supports the assertion that mycorrhizal fungi enhance nutrient uptake for plants, particularly in potentially nutrient-poor conditions.


Input: Task: contrast the claim using the given text. Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: 10. 5194/cp-18-1169-2022 © Author(s) 2022. This work is distributed under the Attribution 4. 0 License. Special issue: Interdisciplinary studies of volcanic impacts on climate and. . . © Author(s) 2022. This work is distributed under the Attribution 4. 0 License. 10. 5194/cp-18-1169-2022, 2022. Received: 02 Dec 2021 – Discussion started: 17 Dec 2021 – Revised: 04 Apr 2022 – Accepted: 13 Apr 2022 – Published: 24 May 2022 1 from large volcanic eruptions are a key source of temperature and hydroclimate variability on interannual to decadal timescales (Robock, 2005; Iles et al. , 2013; Sigl et al. , 2015). As few large volcanic eruptions have occurred during the instrumental era, much of our knowledge about volcanic impacts on climate, particularly regional and global temperature, comes from proxy records spanning centuries to millennia (Tejedor et al. , 2021; Wilson et al. , 2016; D'Arrigo et al. , 2013). These records are predominantly high-altitude or high-latitude tree-ring proxies from the (e. g. Briffa et al. , 1998; D'Arrigo et al. , 2009; Pieper et al. , 2014). In comparison, there are very few proxy-based characterisations of the temperature response to volcanic events from the (Tejedor et al. , 2021; Neukom et al. , 2014). The limited number of studies considering tree-ring proxies have generally not found significant impacts following what are considered “large” volcanic eruptions (Krakauer and Randerson, 2003; Palmer and Ogden, 1992; Allen et al. , 2018; Cook et al. , 1992). Two eruptions (in 1902 CE and Agung in 1963 CE) have been identified in tree-ring sites spanning South America, but the impacts of other eruptions on growth have proved less conclusive (Villalba and Boninsegna, 1992). Discovering whether the hemispheres have contrasting sensitivities to volcanic eruptions is vital to understanding future climate projections (Neukom et al. , 2014). [SEP] Justify:

Output: The text contrasts the claim by providing evidence that tree-ring proxies are utilized to study the impacts of large volcanic eruptions on climate and hydroclimate variability. It states that much of the understanding regarding volcanic impacts on climate comes from proxy records, which include high-altitude or high-latitude tree-ring proxies. The text mentions specific instances and studies indicating that tree rings have indeed been used to identify the temperature response to volcanic eruptions, citing research that highlights their relevance in studying such environmental disturbances.


Input: Task: pass the claim using the given text. Claim: Saturn’s rings are composed primarily of ice particles and rocky debris. [SEP] Text: Table 1 Box counting results Full size table ConclusionsAll the images analyzed in this paper yield fractal dimensions in the range 1. 63 to 1. 78. This is a consistent estimate of the fractal dimension of the rings’ edges, regardless of the various image sources we utilized. Indeed, the fact that the rings’ edges are fractal provides one more hint to developing models of the intricate mechanics and physics governing these structures of granular matter. Interestingly, somewhat related studies (Feitzinger and Galinski 1987; de la Fuente and de la Fuente 2006a, b) found average fractal dimension ~1. 7 for the projected fractal dimension of the distribution of star-forming sites (HII regions) in a sample of 19 spiral galaxies. MethodsUsing the box counting method, we determine the fractal dimension of edges of those rings. First, various edge detection methods are performed and compared to optimally identify ring boundaries: ‘Sobel’, ‘Robert’, ‘Laplacian of Gaussian’, ‘Canny’ and ‘Zero-Cross’ edge functions in the Processing Toolbox. Furthermore, the morphology operation functions of ‘bridge’, ‘close’, ‘thicken’, ‘thin’ and ‘skel’ are employed to connect some isolated pixels and also remove redundant pixels on the boundaries from consideration of physical reality. It was found that the option of ‘Laplacian of Gaussian’ edge function with ‘close’ and ‘thin’ morphology operation produced optimal appearance of ring boundaries. The resulting edge images are displayed in Figure 5 (a-e), respectively, for the five original images we displayed in Figure 1 (a-e). Figure 5 (a,b,c,d,e): Images processed, respectively, from Figure 1 (a,b,c,d,e) to capture the ring edges. Full size image We perform three box counting methods to estimate fractal dimensions of the above processed black-white images of Saturn rings, so as to take into account the influences of the sizes and shapes of covering boxes: 1. Modified box counting using boxes with shape being self-similar to the global image. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the fractal dimensions of the edges of Saturn's rings and the methods used to analyze images of those edges. It does not provide any information about the composition of Saturn's rings or mention ice particles and rocky debris.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: , K, Mg, Zn and Mn: Gigasporaceae > Glomeraceae) as well as differences in Ca content between inoculated treatments and controls. In 2020, at the second harvest, AM fungal inoculation increased P, K, Zn, Fe, Cu and Mn concentration in fruits of var. compared with controls (Fig. 5b; Table S4). In addition, the concentration of N, K, Zn, Cu and Mn in fruits of plants inoculated with members of Gigasporaceae was higher than in fruits of plants inoculated with Glomeraceae. Conversely, Ca concentration in fruits of plants inoculated with Gigasporaceae was lower compared with with Glomeraceae. Finally, significant differences were recorded within Glomeraceae: F. mosseae increased Zn concentration in fruits, whereas S. sinuosa increased K concentration. In var. Rio Grande, at the second harvest, nutrient content was not modified by inoculation treatments, with the exception of Ca content in fruits that was higher in plants inoculated with Glomeraceae (Table S7 and S8). To summarize the effect of AM fungal inoculation on plant physiological traits and AM fungal root colonization patterns, showed a significant response in total yield and fruit nutrient concentration, as well as in AM fungal traits, in both Pisanello and tomato varieties (Fig. 6; Table S9). In the PCO biplots, the first two principal coordinates explained 30. 2 and 39. 0% of the total variance in the varieties Pisanello and Rio Grande, respectively (Fig. 6). Pairwise tests highlighted significant differences between F. mosseae and mock-inoculated control (-M) and between G. gigaspora and -M in the var. Pisanello (Table S9). Moreover, significant differences were detected between F. mosseae and -M, G. gigaspora and -M, S. pellucida and -M, as well as between F. mosseae and G. gigaspora, and between G. gigaspora and S. sinuosa (Table S9). [SEP] Justify:

Output: The text corroborates the claim by detailing how AM fungal inoculation significantly increased the concentrations of essential nutrients (P, K, Zn, Fe, Cu, and Mn) in fruits when compared to control groups. The findings indicate that mycorrhizal fungi, such as those from Gigasporaceae and Glomeraceae, positively influence nutrient content in plants, supporting the assertion that these fungi enhance nutrient uptake in nutrient-poor soils.


Input: Task: contrast the claim using the given text. Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: The muted volcanic impact in proxy reconstructions could be due to a maritime dampening effect on post-eruption cooling and/or the distribution of landmasses toward the Equator (Raible et al. , 2016; Krakauer and Randerson, 2003; Allen et al. , 2018). Such explanations suggest that the magnitude of cooling is too small to be reliably recorded in tree-ring archives. However, climate models show a clear volcanic signal via reduced mean surface air temperatures (Neukom et al. , 2014, 2018). There are several potential explanations for the discrepancy between proxy reconstructions and climate models in the Southern Hemisphere. These include the underestimation of the moderating effects of the ocean on post-eruption cooling in climate models, changes to the hydrological cycle in response to volcanic cooling, uncertainties in volcanic forcing data, and/or proxy noise and spatial distribution (Neukom et al. , 2018; Zhu et al. , 2020). The question remains as to whether proxies – specifically tree rings – do record volcanic events. To our knowledge, no studies have explored the factors which influence whether (or not) volcanic signals can be identified using tree-ring data from the Southern Hemisphere. Tree growth depends on a range of environmental and biological factors, and thus careful site and tree selection is necessary to ensure that a specific influence of interest can be studied (Norton and Ogden, 1987). tree-ring studies are predominantly from high latitudes or mid-latitude alpine treeline sites where tree growth is temperature limited (Scuderi, 1990). Around 80 % of chronologies from such sites show significant growth reductions following large eruptions due to unusually low growing-season temperatures (Krakauer and Randerson, 2003). For high-latitude sites, decreased light availability after eruptions also contributes to the strong growth reduction (Tingley et al. , 2014). Tree-ring studies from mid-latitude lowland sites have shown that volcanic response is less clear, as temperate-zone trees are less temperature-limited and have more complex relationships with multiple climate variables (Pieper et al. , 2014; Wilson et al. , 2016). Exploring possible responses to volcanic eruptions, Pieper et al. [SEP] Justify:

Output: The text contrasts the claim by discussing various aspects of how tree rings may indeed represent responses to volcanic events. It highlights that studies have documented significant growth reductions in tree-ring records following large eruptions, suggesting that tree rings can reflect volcanic activity. Specifically, it states that 'around 80% of chronologies from such sites show significant growth reductions following large eruptions,' which supports the notion that tree rings can be used to study past volcanic activity, directly opposing the claim.


Input: Task: pass the claim using the given text. Claim: Saturn’s rings are composed primarily of ice particles and rocky debris. [SEP] Text: This method is well suited for generally rectangular images (Xu and Lacidogna 2011), where the boxes are rectangles self-similar to the whole image. The selection of the ratio of image size to box size is in powers of 2 for optimal log(n)-log(r) regression. When the ratio does not give an integer box size, the box size was chosen to be the closest integer at that ratio. 2. Power 2 box counting using boxes with sizes as powers of 2, possessing optimal log(n)-log(r) regression. Here the partial boarder effects are evident generally when the image size was not powers of 2. In this case the image was embedded in an empty image with size being powers of 2 closest to the original image size. The box counting was then performed on the ‘enlarged’ image. 3. Divider box counting using boxes with sizes being the dividers of the image size. Subsequent box size may be too close for log(n)-log(r) regression, while the border effects can be eliminated. In particular the cut-offs of box sizes are considered by examining the local slopes of log(n)-log(r). Figure 6 shows an example of the local slope of log(n)-log(r) for power 2 box counting applied to Figure 1 (a) with r = 2 to r = b/2, where b denotes the image size (after extended to powers of 2). The fine box size r = 2 tends to be below the average spacing of ring p4. Figure 6 An example of the local slope of log(n)-log(r) for power 2 box counting applied to Figure 1 (a) with r=2 to r=b/2, where b denotes the image size (extended to powers of 2). Full size image 10. 1051/0004-6361:20054552220. 454:473–80, Doi:10. 1051/0004-6361:200547760940. Author informationAuthors and AffiliationsDivision of Engineering and Applied Science, of Technology, 91125, of & Engineering, Institute for Theory and Beckman Institute, University of Illinois at Urbana-Champaign, 61801, -StarzewskiAuthorsJun LiView author publicationsYou can also search for this author in PubMed 4. [SEP] Justify:

Output: The text is irrelevant to the claim about Saturn's rings as it discusses methods for image analysis, specifically box counting and log(n)-log(r) regression, without any mention of Saturn, its rings, or their composition.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: Effect of AM fungal inoculation on litter decomposition and bacterial and fungal abundance in soil A significant interaction between AMF inoculation (AMF inoc) and time of field exposure (Time) was observed for litter bags weight (% of remaining mass) and decomposition rate (expressed as a first-order decay constant, k) (P < 0. 001; Fig. 7). As expected, for all treatments, the percentage of remaining mass decreased with time, showing the highest values at 40 days and the lowest at 79 days in G. gigantea and in S. sinuosa, respectively (Fig. 7a). At 40 days from litter bag deposition, lower percentages of remaining mass were recorded in all treatments as compared with G. gigantea, whereas at 52 days S. sinuosa showed a significantly lower remaining mass than all the treatments including the not inoculated control (-M) (Fig. 7a). In the S. pellucida treatment, litter bags weights significantly decreased at each sampling time, while in the other treatments a more variable trend was recorded (Fig. 7a). At the latest sampling time, 86 days from litter bag deposition, -M and F. mosseae showed similar percentage of remaining mass (mean: 8. 5%) in comparison with the other AM fungal inoculated treatments (mean: 1. 3%). The decomposition rate per day, during the starting period of litter bag deposition (1–40 days), was similar among all AM fungal inoculated treatments and -M, whereas during the following 12 days (between 40 and 52 days from litter bag deposition) S. sinuosa strongly promoted the decomposition rate compared to the other treatments (Fig. 7b). In the third period (the following 15 days), S. pellucida determined a faster decomposition as compared to the other treatments, whereas during the fourth period (the latest 15 days), G. gigantea, S. pellucida and S. sinuosa showed higher values of decomposition rate per day compared to -M and F. mosseae. Total bacterial and fungal abundances as well as fungal:bacterial ratios in the rhizospheric soil of both tomato varieties significantly increased under AM fungal inoculation (Fig. 7c,d; Table S10 and S11). [SEP] Justify:

Output: The text corroborates the claim by indicating that AM fungal inoculation significantly affects litter decomposition and alters bacterial and fungal abundance in the soil. Specifically, it mentions that total bacterial and fungal abundances, as well as the fungal:bacterial ratios, significantly increased under AM fungal inoculation. This suggests that mycorrhizal fungi (AMF) play a role in enhancing soil microbial communities, which is likely linked to improved water and nutrient uptake for plants, thereby supporting the claim.


Input: Task: contrast the claim using the given text. Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: (2014) proposed three modes for tree growth in temperate regions: (1) growth reduction due to decreased growing-season temperature, resulting in narrow rings, (2) neutral or no response if the climate sensitivity to volcanic eruptions is insufficient to influence tree growth, and (3) enhanced growth due to an increase in the diffuse light fraction and reduced water stress, resulting in wide rings. Temperate-zone trees from the are also likely to display similar mixed volcanic signals, depending on their relative sensitivity mode and the magnitude of the regional cooling effect. Understanding these factors will help elucidate the proxy archive contribution to the model–data discrepancy. This knowledge will benefit future studies of hemispheric temperatures and help identify which species and/or regions should be prioritised for future proxy development. Our goal in this study is to assess whether tree rings record past volcanic events using a multispecies network of high-quality, replicated tree-ring chronologies from New Zealand. This country is a long, narrow, archipelagic landscape stretching from 34 to 47∘ S. Climatically, the northern part protrudes into the warm sub-tropical ridge, whereas the southern end is embedded in the cool southwesterlies (Salinger, 1980). Island and axial ranges, which rise to 3764 m, are a significant barrier to east–west airflow, leading to strong regionalisation of precipitation anomalies (Salinger, 1980). Land clearing has resulted in the loss of forests from most lowland areas and nearly all of the eastern drylands. The most common remaining forest types are wet conifer–broadleaved forests and montane to alpine forests dominated by southern beech (Nothofagaceae) (McGlone et al. , 2017). Tree-ring chronologies have been developed from locations widely distributed throughout New Zealand. Since the initial dendrochronological studies undertaken by LaMarche et al. (1979), records have been generated from nine endemic species, of which seven are conifers and two are Nothofagaceae (Table 1). Five main species have been used to develop multi-centennial tree-ring chronologies: kauri (Agathis australis), pink pine (Halocarpus biformis), silver pine (Manoao colensoi), cedar (Libocedrus bidwillii), and silver beech (Lophozonia menziesii). [SEP] Justify:

Output: The text contrasts the claim by discussing the potential for tree rings to reflect past volcanic activity through three modes of tree growth influenced by volcanic eruptions. It mentions that temperate-zone trees may exhibit mixed volcanic signals and highlights a study aiming to assess if tree rings record past volcanic events, which directly opposes the claim.


Input: Task: pass the claim using the given text. Claim: Bioinformatics combines biology, computer science, and information technology. [SEP] Text: Most of the results provided in this section rely on estimating the number of substitutions in tandem repeat sequences. We note that the algorithm only provides estimates for duplication events. Furthermore, due to its efficiency, SMTR is more appropriate for large-scale data analysis. We use the Database (TRDB) [28], which provides the set of tandem repeats in each chromosome, as identified by the Finder (TRF) algorithm, and related information such as the length of the repeat unit and indel (insertion/deletion) percentage. As a preprocessing step, among overlapping repeats, we keep only one. We also remove repeats with unknown (N) bases and those with copy number less than 2. Finally, we discard repeats whose indel percentage is nonzero, as our model does not include insertion and deletion mutations. We note however that the indel percentage is an approximate value for the number of apparent insertions and deletions. Excluding repeats with non-zero indel percentages does not guarantee that there will be no insertions or deletions in the remaining repeats. Another limitation is that our method assumes substitutions are unbiased, and so it cannot take into account different transition and transversion probabilities, or the effect of GC content. As an example of the preprocessing step, the number of repeat sequences in chromosome 1 reduces from 93,626 to 38,628 as a result of preprocessing. We applied the SMTR algorithm to tandem repeats in each chromosome to study the role of tandem duplication and substitution mutations in their formation. The results for chromosome X are given in Fig. 3a. Each point in this plot corresponds to a tandem repeat sequence. The position of each point is determined by the estimated number of tandem duplications and substitutions that occurred to create the sequence. It can be observed that tandem repeat sequences can roughly be divided into two clusters with different behaviors: one dominated by tandem duplication mutations and the other by substitution mutations. This difference in behavior matches well with the classification of tandem repeats as microsatellites and minisatellites, with pattern lengths of 1–10 and 11–100 bases, respectively. Other chromosomes exhibit behavior similar to chromosome X illustrated here. Among all chromosomes, the minimum Kendall tau correlation coefficient between the rankings of repeats based on length of the pattern and based on the fraction of mutations that are substitutions was 0. 5160. [SEP] Justify:

Output: The text does not address the claim directly and instead provides detailed information about the SMTR algorithm and its application to tandem repeat analysis in chromosomes. It discusses aspects related to preprocessing and mutation analysis without mentioning the intersection of biology, computer science, and information technology, making it irrelevant to the specific claim about the field of bioinformatics.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: Moreover, fungal abundance and fungal:bacteria ratio increased in the rhizospheric soil of var. Pisanello under Gigasporaceae compared with Glomeraceae (Fig. 7c; Table S10 and S11). Similarly, in the rhizospheric soil of var. Rio grande, bacterial and fungal abundance and fungal:bacteria ratio increased under Gigasporaceae compared with Glomeraceae (Fig. 7d; Table S10 and S11). The fungal:bacterial ratio was higher under G. gigaspora compared with S. pellucida. Finally, we found a significant relationship between the matrix of percentages of remaining mass of litter bags at the four sampling times and the matrix of soil fungal and bacterial abundances, as demonstrated by the analysis (ρ = 0. 241). DiscussionThe present study showed that: (i) AM fungal inoculation increased AM fungal colonization traits at flowering as well as total yield and fruit nutrient concentration (e. g. , P, Cu, and Mn) in the tomato varieties Pisanello and Rio Grande; (ii) in the var. AM fungal inocula belonging to Gigasporaceae positively affected the occurrence of arbuscules and vesicles at transplanting and fruit maturity, respectively; (iii) overall Gigasporaceae promoted the concentration of nutrients in tomato fruits in comparison with Glomeraceae; (iv) a variability of AM fungal colonization and fruit nutrient concentration occurred within members of Glomeraceae in both tomato varieties; (iv) within Gigasporaceae, S. pellucida increased the yield of var. compared to G. gigantea; (v) in var. the inoculation with F. mosseae determined a litter degradation similar to controls and lower than S. sinuosa and the two species belonging to Gigasporaceae; (vi) in both tomato varieties AM fungal inoculation promoted total bacterial and fungal abundances as well as fungal:bacterial ratios as compared to control; (vii) Gigasporaceae increased fungal:bacterial ratios as compared to Glomeraceae, irrespective of tomato variety. mycorrhizal infection potentials (MIPs) of the field experimental soil sampled in 2019 and of 2020 were low. [SEP] Justify:

Output: The text corroborates the claim by providing evidence that arbuscular mycorrhizal (AM) fungal inoculation increases nutrient concentrations (such as P, Cu, and Mn) in tomato fruits and enhances AM fungal colonization traits. Specifically, it mentions that Gigasporaceae, a type of mycorrhizal fungus, positively affects nutrient uptake and the health of the plants, thus supporting the idea that mycorrhizal fungi improve nutrient uptake in nutrient-poor soils.


Input: Task: contrast the claim using the given text. Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: Most chronologies are primarily sensitive to austral summer temperatures, with temperature reconstructions developed from beech (Norton et al. , 1989), silver pine (Cook et al. , 2002), cedar (Palmer and Xiong, 2004), pink pine (Duncan et al. , 2010), and multispecies networks (Salinger et al. , 1994). Thus, New Zealand, with its wide latitudinal and altitudinal range, regionalised climate zones, and wide distribution of tree-ring chronologies from multiple species – including some instances of multiple species from the same site – is ideal for studying tree-ring sensitivities to past volcanic events. Using the dendrochronological dataset, we aim to answer the following specific questions. Can we identify volcanic signals in high-quality tree-ring series from the Southern Hemisphere? Are there differences in the expression of volcanic signals amongst the species? Does chronology selection impact the magnitude of post-volcanic cooling in tree-ring-based temperature reconstructions? 2 Data and methods 2. 1 Tree-ring chronologies Zealand tree-ring chronologies analysed in this study were collated to develop the (Palmer et al. , 2015; Fig. 1). Palmer et al. (2015) identified chronologies from the Bank and personal collections, screened the tree-ring measurements for dating problems using the software program (Holmes. , 1983; Grissino-Mayer, 2001), and developed site “master” chronologies from the raw ring widths using the “signal-free” method of standardisation (Melvin and Briffa, 2008). The metadata for all chronologies are provided in Table S1 in the Supplement. As only a single chronology has been developed from mountain toatoa (Phyllocladus alpinus), it was excluded from the study, leaving a pool of 96 chronologies from eight dendrochronological species for volcanic response analysis. Figure 1Distribution of tree-ring chronologies in New Zealand. Elevation data sourced from the and licensed for reuse under CC BY 4. 0. Table 1Distribution, reported climate sensitivities, and key 0. 04 (blue) and 0. 08 (red). Known eruptions are labelled. [SEP] Justify:

Output: The text contrasts the claim by providing evidence that tree-ring chronologies are, in fact, sensitive to volcanic events and can be used to identify volcanic signals. It explicitly states that New Zealand is ideal for studying tree-ring sensitivities to past volcanic activity, indicating that tree rings can provide valuable data on historical environmental disturbances.


Input: Task: pass the claim using the given text. Claim: Bioinformatics combines biology, computer science, and information technology. [SEP] Text: Given the large number of tandem repeats in each chromosome, such high correlation coefficients lead to p-values that are practically zero (as computed with ). Fig. 3The mutation profile of tandem repeats in chromosome X (a) and mutation variation across chromosomes in microsatellites (pattern length ≤10): Mean of the ratio of the number of substitutions to the length of the tandem repeat sequence (b) and mean of the total number of mutations per tandem repeat sequence for each chromosome (c)Full size image We now turn our attention to evaluating the variation of mutation rates across chromosomes. Through comparison with the chimpanzee genome [29–31], it is known that mutation rates vary across chromosomes. To see whether this variation can also be observed in repeated regions, we study the number of mutations in tandem repeat sequences across chromosomes. Since our model represents replication slippage, we only consider tandem repeats with short patterns. Specifically, for tandem repeats with pattern length ≤10, we estimate the number of substitution and duplication mutations. As a measure of mutation activity, we find the average of the ratio of the the number of substitutions to the length of the tandem repeat sequence for each chromosome (Fig. 3b). The top five chromosomes that have the highest substitution rates are Y, 21, 22, 19, and 16. Based on comparison with the chimpanzee genome [31], the five chromosomes with highest mutation activity are Y, 21, 19, 22, and 16. Thus the top five chromosomes are the same based on the two approaches (p-value=0. 00002). We repeated this analysis for repeats with maximum pattern lengths of 8, 9, 11, and 12, and in all cases, at least four of the top five matched the result from comparison with chimpanzee [31]. We also considered the average number of mutations per tandem repeat for each chromosome (Fig. 3c). On average, tandem repeats in chromosome 21 have a higher number of mutations than other autosomes. The average number of duplication mutations is estimated to be higher in chromosome 21 than in the Y chromosome. The higher number of mutations in chromosome 21 compared to other autosomes is also observed if we set the upper bound on the length of the patterns at 8, 9, 11, and 12. DiscussionFigure 1 demonstrates that compared to the proposed method, SMTR, is both more accurate and faster. The efficiency of SMTR allows it to be applied at the genome scale. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses mutation rates in tandem repeats and comparisons with the chimpanzee genome rather than addressing the interdisciplinary nature of bioinformatics or its components.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: The values are consistent with the low MIPs recorded in agricultural soils located in the same area (Bedini et al. 2013; et al. 2013; Pellegrino et al. 2011a,b). This supports AM fungal inoculation and confirms how agricultural practices damage soil AM fungal inoculum potential and impair native AM fungal community with putatively adverse effects on growth and yield of crops (Gosling et al. 2006; Johnson 1993; Plenchette et al. 2005). On the other side, the AM fungal species utilised as inocula in our study showed values of MIP similar among each other and higher than the field experimental soil. This suggested a potentially fast and early colonization of the inoculated AMF that is crucial for their adaption and development and for a beneficial effect on plant growth and nutrient uptake (Smith et al. 1992), in accordance to the site-specificity of AM fungal inoculants establishment and persistence (Kokkoris et al. 2019). flowering, irrespective of AM fungal species, AM fungal inoculation increased percentages of AM fungal root colonization and of root length containing arbuscules of both tomato varieties compared with controls. These results are in accordance with the positive effect recorded on mycorrhizal colonization parameters assessed at different sampling times (i. e. , transplanting, flowering and harvest) in some tomato varieties (TC 2000, PKM-1, Rio Grande, Roma and Perfect Peel) inoculated at nursery by a crude inoculum composed by five AM fungal species and by single inocula (i. e. , Funneliformis mosseae and Rhizophagus intraradices) (Bona et al. 2017; Njeru et al. 2017; Subramanian et al. 2006). However, the positive effect on mycorrhizal colonization, assessed on tomato plants collected at fully ripening in comparison with controls (Bona et al. 2017; Njeru et al. 2017), was not confirmed by our study on Rio Grande. This inconsistency might be due to differences in soil AM fungal native inoculum potential linked to soil texture, in the responsiveness of the host genotype or to differences in the adopted agricultural systems (conventional vs organic). In addition, under high N and K mineral fertilization and no P application, AM fungal inoculum of R. [SEP] Justify:

Output: The text corroborates the claim by providing evidence that AM fungal inoculation provides a beneficial effect on plant growth and nutrient uptake. It mentions that the inoculated AM fungi exhibit faster colonization which is essential for adaptation and development, implying enhanced nutrient uptake in plants. The positive effects on mycorrhizal colonization parameters and the relationship with root length and ARbuscular mycorrhizae further support the direct impact of mycorrhizal fungi on nutrient uptake, especially in nutrient-poor soils.


Input: Task: contrast the claim using the given text. Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: Table 1 summarises the distribution, average climate responses, and main wood properties (average annual ring growth and temporal correlation or persistence) of the species, as described by the studies documenting the development of the chronologies. In addition, the response of each species to average monthly temperatures, calculated for this study, is also summarised. All species show significant (p < 0. 05) relationships with average temperatures (Salinger, 1981; Mullan, 2012) during individual months of the current growing season, except toatoa (Table 1, Figs. S1–S6 in the Supplement). Tree growth is only weakly correlated with average monthly temperatures, with |r| < 0. 3 for most chronologies. Pink pine shows stronger correlations with summer temperatures, with r values of 0. 4–0. 6. Pine pink is also significantly correlated to temperatures over the entire growing season, whereas the other species are seasonally restricted with significant correlations to peak summer temperatures only. Most species are positively correlated to current season temperatures, with wider ring widths associated with warm years; however, kauri and beech show an inverse relationship to temperature, with warm temperatures restricting growth. Cedar, silver pine, mountain beech, and both Phyllocladus species show stronger sensitivities to prior than current season temperatures (Figs. S1–S6). 2. 2 Selection of volcanic events Event selection is a significant source of uncertainty in tree-ring studies of volcanic cooling. The choice of volcanic events can greatly influence the magnitude of average regional cooling identified (Esper et al. , 2013; Wilson et al. , 2016). In addition, for many events that occurred before instrumental records, the timing, location, and size of eruptions are uncertain (Timmreck et al. , 2021; Garrison et al. , 2018). For this analysis, we are interested in those events which would likely have reduced growing-season temperatures over and thus be identifiable as ring-width anomalies. Therefore, we selected events using a regional volcanic dimming threshold rather than an eruption magnitude. Prior to the instrumental era, we picked events from the Greenland and Antarctic ice core sulfate aerosol analysis of Toohey and Sigl (2017) based on peak stratospheric atmospheric aerosol depth (SAOD). We averaged SAOD, modelled using the Aerosol module (Toohey et al. [SEP] Justify:

Output: The text contrasts the claim by detailing how tree-ring studies can identify volcanic events and their impacts on growing-season temperatures. It explicitly states that tree rings can be used to recognize ring-width anomalies caused by volcanic cooling, indicating that tree rings are indeed a valuable resource in studying past volcanic activity.


Input: Task: pass the claim using the given text. Claim: Bioinformatics combines biology, computer science, and information technology. [SEP] Text: Such large-scale analyses enable statistically studying hypotheses about the formation of tandem repeats. We studied the relationship between the length of the pattern in a tandem repeat and number of substitution and duplication mutations. A clear difference emerges between minisatellites and microsatellites, as shown in Fig. 3a. The different mutation profiles suggest that these two types of tandem repeats may result from different mutation mechanisms. This is compatible with previous findings, where polymerase slippage is thought to give rise to microsatellites while unequal recombination is believed to cause the heterogeneity observed in minisatellites [32]. Our method is only designed to model slippage and not recombination. The fact that it generally estimates the number of substitutions to be higher for minisatellites than microsatellites can be the result of higher raw heterogeneity that is observed in microsatellites and/or caused by model mismatch. The results of this analysis suggests that it is possible to design statistical tests to decide the origin of tandem repeat sequences, as a means of classifying them, rather than relying on classification merely based on pattern length. Figure 3b presents the normalized number of substitutions in tandem repeats, averaged for each chromosome. As discussed, the five chromosomes with the highest rates in Fig. 3b are the same as the five chromosomes with the highest mutation rates, as obtained by [31] based on comparison with chimpanzee genome. This suggests a strong relationship between substitutions in repeated regions and overall mutation activity in chromosomes. On the other hand, the results are not exactly aligned. For example, while chromosome X has the smallest divergence from chimpanzee, it does not have the smallest normalized number of substitutions. Overall, our results suggest estimation of mutation activity based on tandem repeats can be a powerful tool in studying mutations since unlike existing methods it relies on a single genome rather than on comparison of genomes from different species. In Fig. 3c, the reason that tandem repeats in chromosome 21 exhibit a higher number of mutations is unknown to us but it is interesting to note that individuals with trisomy 21 can survive into adulthood, which suggests that mutations in chromosome 21 are relatively better tolerated. It is also observed that 3 of the 5 chromosomes with the highest total number of mutations in microsatellites, Y, 21, and 22, match the result from [31]. This further suggests a higher mutation activity in these chromosomes. [SEP] Justify:

Output: The text discusses specific analyses and findings related to tandem repeats and mutations in chromosomes without mentioning bioinformatics as a field or how it integrates biology, computer science, and information technology. Therefore, it does not provide relevant information regarding the claim.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: However, while the potential influence of vesicles on plant productivity and nutrient acquisition is currently unknown (van der Heijden and Scheublin 2007), the higher rate of arbuscules found in roots of tomato inoculated with Gigasporaceae can be associated to the distinctive trait of this family to improve plant nutrient acquisition. Accordingly, periarbuscular membrane-localised proteins, such as PT4 and AMT2, are required for phosphate and ammonium transport, respectively (Luginbuehl and Oldroyd 2017). Moreover, in pot cultures, roots inoculated with Gigasporaceae were reported to show a higher persistence of total arbuscules than Glomeraceae (et al. 2005). Finally, the Glomeraceae intra-family variability in AM fungal root colonization of both tomato varieties supports previous studies that detected significant differences in AM fungal root colonization among closely related AM fungal species belonging to the same family and colonizing different plant genotypes (Klironomos 2000; Maherali and Klironoms 2012). Indeed, host-specificity and functional diversity in AMF was supported by the opposite trend in the AM fungal root colonization of F. mosseae and S. sinuosa detected in the varities Pisanello and Rio Grande. Nevertheless, further studies with a larger number of AM fungal isolates would better elucidate both inter- and intra-family variability in mycorrhizal colonization traits, since in the field the interactions between inoculated AMF and native microbial community can be an additional factor adding complexity in the outcome of the symbiosis. accordance with the overall increases of AM fungal colonization in tomato roots following nursery inoculation, total yield was improved by an average of 35% in both inoculated varieties. Our results are in agreement with the yield increase (22%) detected, in a clay-loam soil, on tomato var. TC 2000 inoculated at nursery by a mixture of five AM fungal species (Bona et al. 2017). These authours also reported larger fruit diameters following AM fungal inoculation as well as a strong increase in number of marketable fruits (125%) and a two-fold higher percentage of dry pulp. By contrast, Subramanian et al. (2006) did not find any effect of nursery AM fungal inoculation by R. intraradices on fruit yield of tomato var. [SEP] Justify:

Output: The text corroborates the claim by discussing how the Gigasporaceae family of mycorrhizal fungi improves plant nutrient acquisition, which is indicative of their role in nutrient uptake for plants in nutrient-poor soils. Furthermore, it mentions an increase in yield of inoculated tomatoes by an average of 35%, supporting the notion that mycorrhizal fungi contribute positively to plant productivity and nutrient absorption.


Input: Task: contrast the claim using the given text. Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: , 2016), over the latitudinal range of (30 to 50∘ S). The SAOD magnitude corresponding to a substantial temperature response is unknown before analysis. However, selecting a magnitude post-analysis based on the observed response risks biasing the results (Haurwitz and Brier, 1981). Therefore, the following two different SAOD thresholds were used: SAOD > 0. 08, which resulted in 10 eruptions for analysis between 1400 and 1900 CE, and SAOD > 0. 04, resulting in 18 eruptions for the same period (Fig. 2). Between 1900 and 1990 CE, we selected the three largest tropical eruptions, which have been shown to have significant impacts on instrumental temperatures in (Salinger, 1998). At each methodological step, the analysis was carried out using both the 13 (10 pre-1900 CE events plus 3 post-1900 CE) and 21 (18 pre-1900 CE events plus 3 post-1900 CE) event lists separately. Full details of all selected eruptions are provided in Table S2 in the Supplement. 2. 3 Superposed epoch analysis We tested whether a volcanic signal can be identified in tree-ring chronologies using superposed epoch analysis (SEA; Haurwitz and Brier, 1981), a statistical technique widely used to determine the impacts of volcanic eruptions on climate (Rao et al. , 2019b; Adams et al. , 2003; Scuderi, 1990; Salinger, 1998; Tejedor et al. , 2021). The composite response of individual chronologies to the 13 largest eruptions and the 21 full eruption list between 1400 and 1990 CE was studied 0–5 years post-event, with anomalies calculated by subtracting the average of the nearest 5 year background period undisturbed by volcanic forcing (Table S2; Büntgen et al. , 2020). Species-level responses were then tested using a composite chronology produced by simple averaging of annual values across sites (Cook and Kairiukstis, 1990). Volcanic responses were categorised as positive or negative if the anomalies exceeded the 5th or 95th percentile response of 10 000 random samples of years undisturbed by volcanic forcing or neutral if they fell between these bounds. 2. 4 Temperature reconstructions To investigate the influence of chronology selection on the identification of volcanic signals in temperature reconstructions, we report two new reconstructions of summer temperatures (December–February). [SEP] Justify:

Output: The text contrasts the claim by explaining that tree-ring chronologies can be used to identify volcanic signals through a statistical technique known as superposed epoch analysis (SEA). The analysis investigates the impacts of volcanic eruptions on climate using tree rings, thereby providing evidence that tree rings are indeed useful for studying past volcanic activity.


Input: Task: pass the claim using the given text. Claim: Bioinformatics combines biology, computer science, and information technology. [SEP] Text: However, care should be taken in interpreting results about mutation counts that are not normalized by the length of the sequence. The opportunity for mutation increases with length and copy number. In particular, increased copy number may increase the probability of misalignment during replication [33]. Another factor that can affect the number of mutations in a complex manner is the interplay between substitution mutations and tandem duplication mutations: if many substitutions occur, the copies become more heterogeneous, which may decrease the possibility of misalignment. This interaction is not taken into account in our model and left to future work. ConclusionIn this paper, we introduced a new stochastic model for tandem duplication and substitution mutations, and analyzed it via stochastic approximation. In particular, we fully characterized the limit set of the stochastic process described by the model. In addition to enabling us to predict the behavior of a sequence that undergoes tandem duplication and substitution mutations, this characterization allowed us to derive a minimization problem whose solutions are estimates of the conditional mutation probabilities for tandem duplication and substitution. We showed further that it is possible to estimate the total number of mutations. Finally, we evaluated the estimation method via simulation by generating random sequences and comparing the estimated probabilities with the true values and also applied it to the human genome, where it demonstrated the differing behavior of micro- and mini-satellites as well as the variability of mutation activity across chromosomes. Advantages of our method include its scalability and the fact that it relies on a single sequence to infer occurrences of mutations. While with this method, we can learn only about mutations in tandem repeat regions, our results show that the findings may be applicable to surrounding regions and can be of use in forming hypotheses about mutation activity, for example, about factors that increase or decrease activity. There still exist many open problems in stochastic modeling and estimation for tandem repeats. For example, the model presented here does not take into account deletions nor the fact that the level of heterogeneity may affect the probability of tandem duplication. Neither does the model consider bias in substitution mutations. For example, it cannot reflect different transversion and transition probabilities. Incorporating such biases will make the method more appropriate, for instance, for GC rich repeats. Further, we only analyzed it in the asymptotic regime and left finite-time behavior to future work. [SEP] Justify:

Output: The text is irrelevant to the claim, as it discusses mutation counts, stochastic models for mutations, and the behaviors of sequences related to mutations without addressing the combination of biology, computer science, and information technology as described in the claim.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: PKM-1, under well watered conditions over a two-year experiment. Similarly, Njeru et al. (2017), nursery inoculating three varities of tomato (Roma, ), did not find fruit yield changes during a three-year experiment. Nevertheless, during the third year of the study following no cover crops, var. inoculated with a mixture of F. mosseae IMA1 and R. intraradices IMA6 showed 54% higher fruit yield compared with controls. The incosistencies in field outcome of the AM fungal inoculation highlight the importance of performing multi-year experiments and verifying the effects on all harvests, taking into consideration the scalability of the tomato fruit ripening. Indeed, Conversa et al. (2013) detected relevant yield increases at some harvest times during the two-year experiment on tomato var. Ercole (1st year: +11% and + 29% at 75 and 99 days after transplating (DAT); 2nd year: +83% and + 15% at 43 and 105 DAT). Other factors that can affect the field outcome of AM fungal inoculation can be the variability in compatibility between plant genotype and AM fungal isolate, soil water/nutrient availability and soil AM fungal inoculum potential (Hart and Reader 2002; Klironomos 2000; Subramanian et al. 2006). Very few studies explored in the field the effect of AM fungal inoculation on nutrients in tomato fruits and they focused only on N and P uptake (Bowles et al. 2016; Conversa et al. 2013). In line with the increases detected in the present study on fruit P concentration following AM fungal inoculation and no P fertilization, Conversa et al. (2013) reported P increases at 0 and 60 kg P2O5 fertilizer rates, respectively. It is worth pointing out that this effect can be of key importance for tomato production, since it is known that high P uptakes are needed for maximizing tomato growth and development (Zhu et al. 2018). Similarly to Bowles et al. (2016), reporting increases in fruit N content by 22% in MYC + plants compared with the mutant nonmycorrhizal tomato genotype rmc, we found a promotion of fruit N concentration in var. Pisanello at 1st harvest. [SEP] Justify:

Output: The text corroborates the claim by providing evidence that AM fungal inoculation (symbiotic relationship with mycorrhizal fungi) leads to increased nutrient uptake, specifically noting a 22% increase in fruit nitrogen content and improved phosphorus concentration in plants. This suggests that mycorrhizal fungi can enhance nutrient uptake for plants, which aligns with the claim that they improve water and nutrient uptake in nutrient-poor soils.


Input: Task: contrast the claim using the given text. Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: The volcanic response in tree-ring reconstructions of temperature was also tested using SEA and the two sets of volcanic eruption years. Further, variation in the temperature response to different volcanic events was estimated by calculating the 90th percentile bootstrap confidence interval from 1000 replicates drawn without replacement from the event list (Rao et al. , 2019b). In each iteration, approximately two-thirds (9 of 13 or 15 of 21) of the volcanic events were selected. The confidence interval provides some indication of how eruptions of different sizes, locations, and seasonality may impact the SEA results. To further assess how event selection may have affected the SEA results, the analysis was repeated using volcanic events selected from the ice core analysis of Crowley and Unterman (2013), using a Southern Hemisphere-wide average threshold of SAOD > 0. 08 and SAOD > 0. 04 rather than a regional threshold (Table S3). We compared the volcanic response seen in our multispecies reconstructions to the ensemble mean DJF response of seven climate models from the 5 (CMIP5) suite with (past1000, 850–1850 CE) simulations. The CMIP5 models were forced with either the Gao et al. (2008) or Crowley and Unterman (2013) volcanic forcing series (see Table S4). Data from the historical simulations were appended to extend the dataset from 1850 to 2005 CE. Figure 3Mean chronology departures 5 years before and 5 years after the 13 largest eruption years (year 0), separated by tree species. The chronologies contributing to the species-wide composite are shown in black, with the number of chronologies indicated in parentheses. The sensitive chronology composite in shown in blue and the number of contributing chronologies is shown in brackets. Significance bands (dotted grey lines) are the 1st, 5th, 95th, and 99th percentile of 10 000 random samples of non-event years from the species-wide composite. Download 3 Results 3. 1 Overall species volcanic responses The results of the superposed epoch analysis for the 13 largest volcanic eruptions between 1400 and 1990 CE are shown in Fig. 3. Two composite responses are shown for each species: the response averaged across all sites (“all chronology composite”) and the response calculated only from the site chronologies that individually showed a significant (either positive or negative) response to volcanic eruptions (“sensitive chronology composite”). [SEP] Justify:

Output: The text contrasts the claim by providing evidence of the use of tree-ring reconstructions to study the volcanic response and environmental disturbances associated with volcanic eruptions. Specifically, it discusses the analysis of temperature responses to significant volcanic events and the methodology behind such studies, which directly refutes the assertion that tree rings cannot be used for this purpose.


Input: Task: pass the claim using the given text. Claim: Bioinformatics combines biology, computer science, and information technology. [SEP] Text: Finite-time analysis will enable us to analytically quantify the accuracy of the presented estimation method as a function of the number n of mutations and to devise improved estimation algorithms. Finally, further work is needed to accurately model mutations other than DNA slippage that cause duplication, especially those that lead to minisatellite repeats. AbbreviationsODE: Ordinary differential equation NRMSE: Normalized root mean square error 921. 61. Accessed 09 Mar 2018. 65. Accessed 22 June 2017. 63. PubMed 71. TH, Cantor C. Evolution of protein molecules In: Munro H, editor. Metabolism. New York: Academic Press: 1969. p. 132. 20. Accessed 18 July 2017. 255. Accessed 25 June 2018. 304. Accessed 25 June 2018. 721. Accessed 08 June 2018. 8. 31. Accessed 08 Dec 2017. 62. Accessed 09 Oct 2018. 16. Accessed 09 Oct 2018. 1999. Heidelberg. p. 44–53. . Zinc finger gene clusters and tandem gene duplication. J Comput Biol. 2002; 9(2):429–46. 2005. Chap. 8. 2008. . A stochastic model for genomic interspersed duplication. In: Proc. on (ISIT2015), : 2015. p. 904–8. Elemento O, Gascuel O. An efficient and accurate distance based algorithm to reconstruct tandem duplication trees. Bioinformatics. 2002; 18(suppl. 2):92–99. 87. Accessed 06 Mar 2018. . Differences and similarities between various tandem repeat sequences: Minisatellites and microsatellites. Biochimie. 1997; 79(9):577–86. Furthermore, the authors would like to thank anonymous reviewers for their insightful comments and valuable suggestions, which helped us improve the paper. research was supported by Foundation grants CCF-1317694 and CCF-1755773, and by a – (BSF) grant no. 2017652. Availability of data and materials The datasets analyzed in the current study are available from the Database ( [28] under organism: Homo sapiens HG38. [SEP] Justify:

Output: The text does not mention bioinformatics or the integration of biology, computer science, and information technology. Instead, it focuses on the analysis of mutations and estimation algorithms, which is irrelevant to the claim about the nature of bioinformatics.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: This is also supported by the higher N content previously detected in roots and shoots of tomato under field AM fungal inoculation (Subramanian et al. 2006). Among the other seven minerals (and Mg) analysed in tomato fruits, positive responses to AM fungal inoculation were detected for Mg, Cu, and Mn in var. Pisanello and for K, Zn, Fe, Cu and Mn in var. at 2nd harvest, whereas negative responses were detected in var. Pisanello for Zn and Ca at 1st and 2nd harvest, respectively. There is well-documented proof in literature of positive changes in fruit, shoot and root Zn concentration of different plant types (i. e. , grass, annual and perennial herbs and woody) following AM fungal inoculation (13%, 18% and 32%, respectively) (Lehmann et al. 2014). However, the opposite response to inoculation we detected for var. Pisanello and var. Rio Grande, might be explained by edaphic factors, such as soil Zn availabilities, as well as plant type which have been shown to affect AM fungal mediated crop Zn nutrition. As regards Cu, Fe, and Mn concentration, in accordance with our results, there are evidences for positive changes in fruit, shoot and root Cu concentration (34%, 26% and 41%, respectively) as well as fruit and root Fe concentration (8% and 18%, respectively) and fruit Mn concentration (19%) following AM fungal inoculation of annual and perennial plants (i. e. , woody, herb and grass) (Lehmann and Rillig 2015). Moreover, Watts-Williams and Cavagnaro (2014) reported in the wild-type tomato genotype positive changes in shoot and root Cu concentration at low P and Zn availability and in shoot at high P and Zn availability. They also reported positive changes in root Fe and Mn concentration at low P availability. Furthermore, the negative change in Ca fruit concentration and the opposite Mg pattern found in var. Pisanello is not supported by the previously reported no changes in shoot and root under low P availability (Watts-Williams and Cavagnaro 2014). Finally, the increase of K in fruits of the inoculated tomato var. is in line with Liu et al. (2002) who detected higher K concentrations in AM fungal inoculated plants of maize. [SEP] Justify:

Output: The text corroborates the claim by providing evidence of positive changes in nutrient concentrations (Zn, Cu, Fe, Mn, and K) in plants following AM fungal inoculation, indicating that mycorrhizal fungi enhance nutrient uptake in tomato and other applicable plant species. The references to increased mineral content, such as the higher N content in roots and shoots and positive responses detected for various minerals, supports the assertion that mycorrhizal fungi improve nutrient uptake, particularly in nutrient-poor soils.


Input: Task: contrast the claim using the given text. Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: Analysis was repeated for the full set of 21 eruptions with SAOD > 0. 04, with similar (but weaker) results for most species, suggesting that not all events had a measurable climatic impact over (Fig. S7). The species-wide response to volcanic events varied widely between dendrochronological species. Three out of eight species, i. e. silver pine, mountain beech, and tānekaha, recorded a composite neutral response. Tānekaha is only weakly correlated to average temperatures (Fig. S6b), which may explain its subdued response. However, compared to other species, mountain beech and silver pine both show relatively strong temperature sensitivities (Figs. S1a and S4). As many mountain beech chronologies extend only to the mid-1700s, the species composites were tested against a smaller subset of volcanic events, which may contribute to this result. Of the remaining five species, one recorded a positive response, while four recorded a negative response. Kauri (Fig. 3a) was the only species to show a composite positive response to volcanic events, maximal in year t+1. Kauri showed a consistent response across sites, with all except two chronologies showing a positive anomaly following an event, although only 8 of the 17 positive responses were significant at p < 0. 05. The sensitive chronology composite recorded a very strong t+1 response, indicating that at these eight sites, kauri receives a significant growth benefit from the climatic changes following a volcanic eruption. This response is coherent with the predominant kauri temperature sensitivity, which is an inverse response to current summer temperatures (Fig. S3). However, as most kauri chronologies are only weakly correlated to monthly temperatures, the strong volcanic response suggests climatic changes other than temperature also contribute to the post-event growth benefit. Pink pine, cedar, silver beech, and toatoa show lagged negative responses to volcanic events, with peak negative anomalies recorded in years t+2 or t+3 (Fig. 3b, c, e, and g). The pink pine response is consistent across sites. All except one pink pine chronology recorded a negative response in t+2, which was significant for most of the chronologies (14/21; p < 0. 05). This response is coherent with the pink pine's broad sensitivity to temperatures over the current growing season (Fig. [SEP] Justify:

Output: The text contrasts the claim by providing evidence that tree rings, specifically from various species such as kauri and mountain beech, can indeed reflect responses to volcanic events. The analysis shows that kauri recorded a significant growth response following eruptions, indicating that tree rings can reveal information about past volcanic activity and environmental changes, which directly contradicts the claim.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Javascript is disabled in your browser. Please enable Javascript to view PeerJ. Differentially expressed serum proteins in children with or without asthma as determined using isobaric tags for relative and absolute quantitation proteomics All reviews of published 2023. Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the 2020. The first revision was submitted on August 1st, 2020 and was reviewed by 2 reviewers and the Academic Editor. A further revision was submitted on August 26th, 2020 and was reviewed by the Academic Editor. The 2020. Version 0. 3 (accepted) · Aug 26, 2020 · changes you have made in the manuscript have improved the manuscript. Congratulations! ! [# PeerJ - this decision was reviewed and approved by Vladimir Uversky, a PeerJ covering this Section #] 0. 3 (PDF) Download author's response letter - submitted Aug 26, 2020 Version 0. 2 · Aug 11, 2020 · Please address the comments of the reviewers and submit a revised manuscript. · Aug 8, 2020 Basic reporting No comment. Experimental design No comment. Validity of the findings No comment. Additional comments Asthma is one of the most common chronic noncommunicable diseases, which is a chronic inflammatory disease of the lower airway that is commonly encountered by the otolaryngologist. Asthma is a serious global health issue and asthma guidelines recommend a stepwise approach to management with goals to achieve control and minimize future risk. It is a good idea to investigate the protein composition and expression levels in serum samples obtain from children with or without asthma. In this manuscript, Dr. Fang and colleagues looked at the role of the differentially expressed proteins (DEPs) identified by using isobaric tags for relative and absolute quantitation (iTRAQ) combined with liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses in the pathogenesis of childhood asthma. The study provides the conclusion, which showed that numerous DEPs that may play important roles in the pathogenesis of childhood asthma. Those proteins may be novel biomarkers of childhood asthma and may provide new clues for the early clinical diagnosis and treatment of childhood asthma. After the modification, the data quality and language description are improved. [SEP] Justify:

Output: The text discusses a specific study related to differentially expressed serum proteins in children with asthma but does not mention or confirm the broader definition of proteomics as the study of the entire set of proteins expressed in a cell. Therefore, it does not support or contrast the claim, making it irrelevant.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: 2020), as well as by the intra-family AM fungal functional variability (Avio et al. 2006; Munkvold et al. 2004). The intra-family variability was supported by the higher total yield found in the var. Pisanello inoculated with S. pellucida compared with G. gigantea, together with the higher shoot dry weight found in the var. inoculated with S. sinuosa compared with F. mosseae. The hypothesis that members of Gigasporaceae, due to their colonization strategy, would have had a stronger effect on nutrient uptake of fruits compared with members of Glomeraceae, was instead confirmed by our results on fruit nutrient concentrations. Indeed, the concentration of several nutrients were higher in fruits inoculated with Gigasporaceae (var. Pisanello: Mg and Mn; var. Rio Grande: N, K, Zn, Cu, Mn), with the only exception of Ca showing higher concentration in fruits of tomato var. inoculated with members of Glomeraceae. Thus, this detected beneficial functional trait of Gigasporaceae can be of great importance in nursery/field inoculation programmes in order to improve tomato quality by enhancing macro- and micro-nutrient concentration in fruits, especially in the scenario of increased atmospheric CO2, which is reported to lower mineral nutrient uptake by almost all crops (Dong et al. 2018; Gojon et al. 2022; Pimenta et al. 2022; Tripp et al. 1991). Previously, Maherali and Klironomos (2007) reported that inoculation with Gigasporaceae correlated with enhanced P concentration in shoots, whereas inoculation with Glomeraceae determined the opposite response. Accordingly, Powell et al. (2009) found that evolution of increased soil colonization is positively correlated with shoot P content. Indeed, members of Gigasporaceae have a mycelium that lacks in infective, runner hyphae, but that forms many absorptive hyphae per infection unit and intrahyphal anastomoses (De la Providencia et al. 2005; Friese and Allen 1991; Hart and Reader 2005). On the other side, members of Glomeraceae form extra-radical mycelia differentiating absorptive and runner hyphae from hyphal bridges and forming anastomoses between different hyphae. [SEP] Justify:

Output: The text supports the claim by discussing the beneficial effects of mycorrhizal fungi, particularly Gigasporaceae, on nutrient uptake in plants. It specifically notes that inoculation with Gigasporaceae correlates with enhanced nutrient concentrations, such as phosphorus (P) and other macro- and micro-nutrients, which are crucial for plant growth, particularly in nutrient-poor soils. Furthermore, the mention of increased nutrient uptake under conditions like elevated atmospheric CO2 indicates their role in overcoming nutrient deficiencies.


Input: Task: contrast the claim using the given text. Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: S2), i. e. cooler spring–summer–autumn temperatures suppress growth across most pink pine sites. Similarly, the negative silver beech response is coherent with its current season temperature sensitivity (Fig. S1b), although neither the temperature correlation nor the volcanic response is particularly strong. All four toatoa chronologies recorded a significant negative response in t+3. However, as toatoa shows only weak lagged correlation with monthly temperatures (Fig. S6a), the link between temperature sensitivity and volcanic response is not easily elucidated. In contrast, cedar does not show a consistent species-wide response. Both significant negative and positive responses were recorded in 13 of the 26 chronologies, with the rest showing a neutral response. This is despite a largely consistent within-species temperature sensitivity, which is an inverse response to prior season temperatures (Fig. S5). 3. 2 Within-species variability in volcanic response The overall muted species response of cedar masks very different individual chronology responses. Cedar ring-width series respond differently to volcanic events depending on their location, with both very negative and very positive responses recorded. The other species do not show similar variation. The cedar chronologies have the widest geographical distribution of any species, and thus geographical factors may influence the variability in response. We used k-means clustering via principal component analysis (Ding and He, 2004) to investigate whether within-species variation could be explained by obvious factors like regional climate or elevation. Principal component analysis (PCA) was applied to the longest common time interval of the chronologies (1732–1976 CE), and the first four principal components were retained. Figure 4(a) Results of k-means clustering of cedar chronologies. (b–f) Mean chronology departures 5 years before and after eruption years (year 0), separated by cluster, and the 95th and 99th significance levels calculated by generating 10 000 random samples of non-event years from the group composite. The map in (a) was made with free vector map data, which are available at (last access: 17 November 2021). Five chronology groups were identified via clustering (Fig. 4a), broadly corresponding to differences in region and altitude. chronologies were distributed in two groups. [SEP] Justify:

Output: The text contrasts the claim by discussing various tree species' responses to past volcanic activity, specifically highlighting that cedar ring-width series can show significant variability in response to volcanic eruptions depending on geographical factors. The mention of the variability in responses and the study conducted through principal component analysis (PCA) indicates that tree rings, specifically from certain species, can indeed provide insights into past environmental disturbances related to volcanic events.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Although there are still some deficiencies (sample size is small) in this study, there are few relevant explorations in this field. This study is a good case worthy of publication and guidance for further research. Cite this review as (2020) #1 of "Differentially expressed serum proteins in children with or without asthma as determined using isobaric tags for relative and absolute quantitation proteomics (v0. 2)". PeerJ Reviewer 2 · Aug 11, 2020 Basic reporting no comment Experimental design no comment Validity of the findings no comment Additional comments Some minor issues need to be corrected by the author. 1. Please describe the clustering method used in the cluster analysis in Materials and Methods. 2. CCL5 should be chemokine (C-C motif) ligand 5 or C-C motif chemokine ligand 5. Please read the 3. Symbol of Complement component 1s should be C1S. Please pay attention to the wording of gene names to distinguish different species. Cite this review as (2020) #2 of "Differentially expressed serum proteins in children with or without asthma as determined using isobaric tags for relative and absolute quantitation proteomics (v0. 2)". PeerJ 0. 2 (PDF) Download author's response letter - submitted Aug 1, 2020 Version 0. 1 (original submission) · May 22, 2020 · Please address the reviewer's comments on a point by point basis and submit your revised manuscript. [# PeerJ Staff Note: Please ensure that all review comments are addressed in a rebuttal letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. It is a common mistake to address reviewer questions in the rebuttal letter but not in the revised manuscript. If a reviewer raised a question then your readers will probably have the same question so you should ensure that the manuscript can stand alone without the rebuttal letter. Directions on how to prepare a rebuttal letter can be found at: #] · May 10, 2020 Basic reporting Please have a look at Minor concerns: 1 to 3. Experimental design Please have a look at Major concerns: 1 to 5. Validity of the findings No comment. Additional comments Asthma is one of the most common chronic noncommunicable diseases, which is a chronic inflammatory disease of the lower airway that is commonly encountered by the otolaryngologist. [SEP] Justify:

Output: The text does not address or provide information directly relevant to the claim about proteomics studying the entire set of proteins expressed in a cell. Instead, it discusses a specific study relating to differentially expressed serum proteins in children with or without asthma, along with comments on the review process and methodological considerations. Therefore, it is considered irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: The fact that Gigasporaceae family allocates a larger fungal biomass in soil compared with Glomeraceae was confirmed by our results on the higher F:B ratios in inoculated soil in both tomato varieties. In addition within Gigasporaceae, the higher F:B ratios found in soil of var. inoculated with G. gigantea compared with S. pellucida can be due to a larger dimension of the spores and a greater mycelium development (Dalpè et al. 2005; Dood et al. 2000). Nevertheless, our hypothesis that inoculation with Gigasporaceae, associated with a high soil fungal:bacterial ratio, would have determined a lower litter degradation, and that Glomeraceae, associated with a low soil fungal:bacterial ratio, would have determined a higher litter degradation, was not fully confirmed. Indeed, both members of Gigasporaceae and S. sinuosa showed high decomposition rates per day at the latest sampling. However, the positive relationship found between fungal and bacterial abundances and percentages of remaining mass suggests a good predictivity of the microbial traits for litter decomposition dynamics. ConclusionsOur work highlights the importance of understanding the plant responses to AM fungal functional traits in order to better exploit AM fungal inoculants for sustainable agricultural biofertilizer programs targeted to the production of high-quality food. Overall Gigasporaceae, accelerating litter decomposition, might be of great relevance for the absorbtion and traslocation of several macro- and micro-nutrients to tomato fruits and should be taken into consideration in order to develop AM fungal inocula for the enhancement of the nutritional value of tomato under organic farming systems. Moreover, due to the absence of stability and/or uniformity characteristic of environmental conditions, host benefit could be greater with the application of communities having AMF with diverse life-history stategies. Therefore, we suggest that future studies should perform field inoculation with mixtures of members of Gigasporaceae and Glomeraceae families to improve our knowledge on the significance of AM fungal functional groups for host plant nutrient response. [SEP] Justify:

Output: The text corroborates the claim by highlighting the importance of arbuscular mycorrhizal fungi (specifically Gigasporaceae) in enhancing the absorption and translocation of macro- and micro-nutrients to tomato fruits. It suggests that understanding fungal functional traits can lead to better exploitation of AM fungal inoculants for sustainable agriculture, thereby supporting the assertion that mycorrhizal fungi improve nutrient uptake in plants, especially in nutrient-poor soils.


Input: Task: contrast the claim using the given text. Claim: Tree rings cannot be used to study past volcanic activity or environmental disturbances. [SEP] Text: All chronologies are from montane to subalpine areas above 800 m, with groups differentiated between coastal (G1) and inland (G2) locations. A single chronology from the north of the was included in G2. Chronologies from the western coast of the were also distributed in two groups, differentiating between lowland (G3) and montane (G4) forest. The final grouping (G5) includes three chronologies from the dry eastern lowlands. Strong – but opposing – volcanic responses are identified via clustering. Significant lagged post-eruption growth reduction is identified in groups G1 and G2 from montane to subalpine sites from the North Island, including Takapari (Fig. S8c), and the southernmost grouping, G5. Group three (G3), which includes lowland chronologies from the northwestern coast of the South Island, including Ahaura and (Fig. S8d and e), receives a growth benefit in the 2 years following an eruption similar to that observed in kauri. In cedar, we observed all three of the proposed temperate-zone tree responses to volcanic events – positive, negative, and neutral growth – all within a single species, highlighting the importance of site-based factors in determining tree response in temperate zones. 3. 3 Calibration and validation of the temperature reconstructions The peak summer period was selected as the seasonal reconstruction target, as the largest number of chronologies across species showed significant correlations with temperatures between December and February (Table 1). Selecting only those chronologies correlated at p < 0. 1 with average DJF temperatures resulted in a predictor pool of 45 chronologies for reconstruction NZall, of which 25 showed significant volcanic impacts and were used to produce the reconstruction NZsens. Figure 5average DJF temperature reconstructions. Unfiltered (black) and filtered (20-year spline; blue) mean DJF reconstruction with 90 % uncertainty interval (grey) between 1400 and 2018 CE for (a) NZall and (b) NZsens. Reconstruction fit to instrumental temperature (red) over the full calibration period 1911–1990 CE for (c) NZall and (d) NZsens. The 90 % uncertainty interval was calculated from 300 maximum entropy bootstrap replications. average temperature reconstructions are shown in Fig. 5 alongside their instrumental fit over the 1911–1990 CE calibration period. [SEP] Justify:

Output: The text contrasts the claim by detailing how tree-ring chronologies (from montane to subalpine areas) provide insights into volcanic responses, including 'significant lagged post-eruption growth reduction' and positive growth responses observed across different groups of trees. This evidence indicates that tree rings are indeed valuable for studying past volcanic activity and environmental disturbances.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Asthma is a serious global health issue and asthma guidelines recommend a stepwise approach to management with goals to achieve control and minimize future risk. It is a good idea to investigate the protein composition and expression levels in serum samples obtain from children with or without asthma. In this manuscript, Dr. Fang and colleagues looked at the role of the differentially expressed proteins (DEPs) identified by using isobaric tags for relative and absolute quantitation (iTRAQ) combined with liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses in the pathogenesis of childhood asthma. The study provides the conclusion, which showed that numerous DEPs that may play important roles in the pathogenesis of childhood asthma. Those proteins may be novel biomarkers of childhood asthma and may provide new clues for the early clinical diagnosis and treatment of childhood asthma. Although, the current study is interesting and well but there are some major concerns that need to be addressed. Major concerns: 1. “Experimental design & Validity of the findings” In general, the research idea of this manuscript is novelty. However, the biggest defect is the lack of sample quantity, which makes it difficult to judge whether the conclusion is universal or not. If the authors increase each group of samples to 10, where possible, the results should be more applicable. However, considering the high cost of iTRAQ technology, I recommend that the author select 1 or 2 from the 37 DEPs for ELISA verification, and expand the samples to about 50+, which may significantly improve the impact of this study. 2. “Materials & Methods – Clinical information and serum sample collection” Line 103-112. “The included samples were collected from four children with asthma (experimental group) and four children without asthma (control group). ” When grouping, did the authors take into account factors such as age, gender, and body mass index (BMI) of patients in the balance between the two groups? Because the physiological factors mentioned above also have a certain influence on serum protein, considering the small sample size of this study, these factors must be matched to exclude the relevant influence, please explain in the 3. “Materials & Methods – LC-MS/MS analysis” Line 147-150. “Protein fold changes (FC) of at least 1. 5 were obtained, and P < 0. 05 was considered a statistically significant difference. [SEP] Justify:

Output: The text discusses a study related to asthma and the analysis of differentially expressed proteins (DEPs) but does not explicitly support or contest the claim regarding proteomics. It mentions protein composition and expression levels, suggesting a focus on specific proteins in a particular context rather than the overarching concept of proteomics as the study of all proteins expressed in a cell.


Input: Task: corroborate the claim using the given text. Claim: Mycorrhizal fungi improve water and nutrient uptake for plants in nutrient-poor soils. [SEP] Text: Agronomy 11:1116. (2012) Impact of arbuscular mycorrhizal fungi (AMF) and atmospheric CO2 concentration on the biomass production and partitioning in the forage legume alfalfa. Symbiosis 58:171–181. (2009) Reaping the benefits: science and the sustainable intensification of global agriculture. (2013) Mycorrhizal activity and diversity in a long-term organic Mediterranean agroecosystem. Soils 49:781–790. (2018) Ancient tomato (Solanum lycopersicum L. ) varieties of tuscany have high contents of bioactive compounds. Horticulturae 4:51. ’(2017) Arbuscular mycorrhizal fungi and plant growth-promoting pseudomonads improve yield, quality and nutritional value of tomato: a field study. Mycorrhiza 27:1–11. Bowles TM, Barrios-(2016) Effects of arbuscular mycorrhizae on tomato yield, nutrient uptake, water relations, and soil carbon dynamics under deficit irrigation in field conditions. Environ 566:1223–1234. (1999). Glomalean mycorrhizal fungi from tropical Australia. Mycorrhiza 8:305–314. Brundrett MC, (2018) Evolutionary history of mycorrhizal symbioses and global host plant diversity. 220:1108–1115. (2019) Conceptual differences lead to divergent trait estimates in empirical and taxonomic approaches to plant mycorrhizal trait assignment. Mycorrhiza 29:1–11. -(2021) Direct transfer of zinc between plants is channelled by common mycorrhizal network of arbuscular mycorrhizal fungi and evidenced by changes in expression of zinc transporter genes in fungus and plant. 23:5883–5900. (2006) Mycorrhizas and tropical soil fertility. Environ 116:72–84. (2018) Bioactivities of phytochemicals present in tomato. J Technol 55:2833–2849. (2012) Arbuscular mycorrhizal fungi increase organic carbon decomposition under elevated CO2. Science 337:1084–1087. (2015) Getting started with v7. [SEP] Justify:

Output: The text provides multiple references and studies that highlight the role of arbuscular mycorrhizal fungi (AMF) in enhancing nutrient and water uptake in various plant species. For instance, studies mentioned, like Bowles TM et al. (2016), show that arbuscular mycorrhizae improve nutrient uptake and water relations in tomato under deficit irrigation conditions. This aligns with the claim that mycorrhizal fungi improve water and nutrient uptake for plants, particularly in nutrient-poor soils.