Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: -19 PreprintsProtocolsVideosJournalsTools & a paperRelationship between and Depth of Estimated from the along the Sea of is a preprint; it has not been peer reviewed by a journal. work is licensed under a CC BY 4. 0 LicenseStatus:Under RevisionVersion 1posted 7You are reading this latest preprint versionAbstractWe found the depth of the seismogenic layer based on D95, the cut-off depth at which 95% of the earthquakes occurred, from the event catalog before the mainshock of five major earthquakes, such as the 2003 Northern Miyagi, the 2004 Chuetsu, the 2008 Iwate-Miyagi, the 2016 Kumamoto, and the 2016 central Tottori earthquakes. Our results show that the main event depth, aftershock distribution, and main slip area are confined above the base of the seismogenic zone. A simple modelling of the geothermal gradient based on surface heat flow shows that the temperature at the base of the seismogenic zone is constrained to a range of 250-450 ºC. We confirmed that mainshock depths for five cases nucleated at the deepest portion of the seismogenic layer, and large rupture areas occurred within the seismogenic layer. Some aftershock streaks of the 2016 Kumamoto earthquake occurred at 5 km deeper than the bottom of seismogenic depth. EarthquakeSeismogenic zoneCrustal temperatureEarthquake HazardCrustal structure2003 northern Miyagi earthquake2004 Chuetsu earthquake2008 Iwate-Miyagi earthquake2016 Kumamoto earthquake2016 Tottori earthquakeFiguresFigure 1Figure 2Figure 3Figure 4Figure 51. IntroductionSeismogenic depth is an important parameter influencing earthquake hazards and crustal mechanical properties. The cut-off depth distribution of seismicity has been interpreted as the brittle-ductile boundary of rock deformation (Kobayashi 1976; Chapman 1986; Ito 1993). Sibson (1982) examined the distribution of heat flow and cut-off depth of seismicity (D90) above which 90% of the shallow earthquakes occur in various continental settings in the and found a correlation between the theoretical frictional to quasi-plastic transition models and the observed cut-off depth.

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: Renal cortex shows muscular artery, there is marked thickening of the tunica intema (I) due to proliferation of intemal cells which encroached upon the arterial lumen. Internal elastic lamina (arrow) and tunica media (arrow head) remained unchanged. Interstitial bleeding (B) is noticed X400. Figure 21 Light micrograph of a kidney section of diabetic rat treated with S. polyanthum extract. H&E staining. Renal cortex shows hemorrhagic blood between renal tubules (arrow). Thickened wall of muscular artery (A) is noticed. Thickened arteriole (T) is also seen near renal corpuscle. Glomerulosclerosis of renal corpuscles is noticed (arrow head) X 200. Figure 22 Light micrograph of a kidney section of diabetic rat treated with S. polyanthum extract. H&E staining. Note that there is an arteriole with thickened wall at the hilum of renal corpuscle (arrow). Glomerulosclerosis of capillary tuft and capillary narrowing is seen inside renal corpuscle (arrow head). Urinary space (U) remains clear X 1000. Figure 23 Light micrograph of a kidney section taken from normal non diabetic rat treated with O. sumatrana. H&E staining. Note the interstitial bleeding (B) between cortical convoluted tubules. Thickened wall muscular artery (arrow) is seen. Glomerulosclerosis of renal corpuscle (arrow head) is noticed. Urinary space (U) is clear X 400. Figure 24 Light micrograph of a section of renal medulla of diabetic animals treated with O. sumatrana extract. H&E staining. Hemorrhagic blood (arrow) is seen in between the collecting ducts (D) X 400. Figure 25 Light micrograph of a section of renal cortex of diabetic rat treated with O. sumatrana extract. H&E staining. Bleeding (B) is noticed between cortical convoluted tubules. Arterioles at hilum of renal corpuscle shows thickened wall (arrow). Glomerulosclerosis of capillaries of glomerular tuft of renal corpuscle is visible (arrow head). Urinary space of renal corpuscle (U) is normal X 1000. Figure 26 Light micrograph of a kidney section taken from normal non diabetic rat treated with H.

Output: pass


Input: Claim: Analysis of hydrothermal vent ecosystems provides clues about life's origins. [SEP] Text: Figures AbstractThe deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts’ functional capabilities. Citation: (2014) of Viruses, Bacteria and Archaea in through Metagenomics. 9(10): e109696. Vladimir N. Uversky, University of College of Medicine, of AmericaReceived: March 25, 2014; Accepted: September 11, 2014; Published: October 3, 2014Copyright: © 2014 Anderson et al. This is an open-access 9452. 3 for the viral metagenome and 4481541. 3 for the cellular metagenome. Funding: Funding for sequencing of the viral metagenome was provided by the Gordon and Foundation. All other funding was provided by a grant through NNA04CC09A to the at the for Science. R. A. was funded by a through NSF grant number DGE-0718124, an grant to the University of Program, and the ARCS Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. IntroductionThe deep subsurface below hydrothermal systems hosts a high diversity of archaea, bacteria, and viruses that must tolerate extremely variable environmental conditions.

Output: corroborate


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: Scholz (1988) proposed a schematic diagram relating the temperature and depth to geologic features, fault rock mechanisms, friction rate behavior, seismic behavior, and strength of the structure for the major geological and seismological features, intended for quartzo-feldspathic rocks. The shallow part is a brittle zone as a seismogenic layer corresponding to temperatures of approximately 300°C. Between 300 and 450°C, it enters a brittle–ductile state and may partially rupture in the transition zone. Islands, Tanaka and Ishikawa (2002) found a correlation between heat flow data and D90 beneath northeastern Japan. Their results follow the thermal structure derived from seismic tomography (Hasegawa et al. 2000). Tanaka (2004, 2009) showed the relationship between the temperature and depth of earthquake nucleation using actual seismic activity and temperature observations. This study indicates that the temperature of 250°C to 450°C corresponds to the D90, assuming a typical heat flow value of silicates. The relationship between the size of earthquakes and thickness of the seismogenic layer has long been discussed. For example, Das and Scholz (1983) reported that large earthquakes tend to nucleate at the base of the seismogenic zone and often rupture the entire brittle seismogenic layer. Ito (1990, 1993) studied thickness of the seismogenic layer beneath the and recognized its local depth variations. He suggested that the cut-off depth of seismicity is closely related to the depth of large crustal earthquakes with magnitudes greater than 7 where the seismic-aseismic boundary sharply changes. Hashimoto and Matsu’ura (2000) and Shibazaki (2002) argued that nucleation of the large earthquakes is determined by the seismic-aseismic boundary, where high gradients in strength and critical weakening displacement on the edges of the base of the seismogenic zone. Studies have recognized the spatial distribution of the thickness of seismogenic layer beneath Japanese Islands. In a recent study, Omuralieva et al. (2012) estimated the spatial distribution of the D90 over the whole of Japan using relocated hypocenters, which eliminated interplate or intraslab events from the geometry of the subducting Pacific and plates. They found that D90 is shallow in volcanic areas, the Kinki district, and the middle of Shikoku district and deep along the coastal area of the Pacific Ocean, with the lateral variation ranging from 5 km to 40 km.

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: polyrhizus. H&E staining. Interstitial bleeding (B) is seen. Thickened muscular artery (arrow) is noticed. Glomerulosclerosis in renal corpuscle is visible (arrow head), urinary space (U) remains clear X 200. Figure 27 Light micrograph of a kidney section taken from normal non diabetic rat treated with H. polyrhizus. H&E staining. Markedly thickened wall of muscular artery in renal cortex is seen due to extensive thickening of the tunica intema (area limited between opposite arrows). This causes narrowing of the lumen of blood vessel X 1000. Figure 28 Light micrograph of a section of renal cortex of diabetic female adult rat treated with H. polyrhizus extract. H&E staining. Extensive bleeding (B) in between renal tubules is seen. Muscular arteries with thickened walls (arrow) are noticed. Glomerulosclerosis of glomerular tuft of capillaries of renal corpuscles is visible (arrow head) X 400. Extensive thickening (sclerosis) in wall of muscular arteries and arterioles of the kidney: Muscular arteries showed marked thickening of the tunica intema due to proliferation of intemal cells which encroached upon the arterial lumen. Internal elastic lamina and tunica media remained unchanged (Figs 19-21, 23, 26-28). Arteriolar damage was presented as dramatic proliferation of their intemal cells (Figs 21, 22, 25). These changes might be the cause of disruption of vascular walls and interstitial bleeding. Renal glomerulosclerosis: Renal corpuscles demonstrated diffuse glomerulosclerosis. This was manifested by uniform and homogeneous thickening of the glomerular capillary basement membrane associated with an increase in mesangial cells and matrix. Urinary space remained clear since there had been no proliferation of podocytes (Figure 19, 21-23,25, 26,28). fruits and vegetables have antioxidant properties. This is due to their contents of vitamins and polyphenols which can eliminate excessive reactive oxygen species through reducing or scavenging activities or through the chelation of transition metals. Transition metals can promote the production of hydroxyl radicals, a most reactive oxygen species, via the Fenton reaction. Much has been published on the beneficial effects on health of a diet rich in fruits and vegetables.

Output: pass


Input: Claim: Analysis of hydrothermal vent ecosystems provides clues about life's origins. [SEP] Text: High-temperature, reduced hydrothermal fluids mix with cold, oxidized seawater both above and below the seafloor to establish strong gradients in temperature, pH, and chemical and mineralogical composition [1]–[5]. Wide variations in environmental parameters can occur over centimeter scales. Constant fluid flux throughout and above the subsurface transports organisms from one region to the next, exposing them to a range of environmental conditions. Gradients that dominate this environment create a highly diverse microbial community consisting of both archaea and bacteria [6]. Physical and chemical parameters vary according to fluid mixing and volcanic activity, leading to niche partitioning in microbial communities across both space [1] and time [7], [8]. Moreover, hyperthermophiles are routinely cultured from fluids that exit at low temperatures (5–30°C) [9], [10], indicating that organisms in vent systems are frequently flushed from their native habitats, most likely from the deep subsurface. Microbial communities in hydrothermal systems are known to form biofilms that coat mineral surfaces, including within high-temperature chimney structures [5]. Such biofilms, which are likely to occur within the subsurface as well, host high-density communities with potentially high contact rates between organisms. The dynamic, diverse and dense nature of this habitat should foster frequent exchange of genes within the microbial community. Previous work with vent samples has shown that the genes responsible for this process, including transposases and integrases, were observed to occur at high frequency in cellular metagenomes from hydrothermal systems as compared to other environments [11], [12]. Analysis of fully sequenced genomes of thermophiles, including many from vent systems, suggests that gene transfers occur more frequently among thermophiles than mesophiles or psychrophiles [13], [14] and that these transfers sometimes cross domains [13]–[15]. The prevalence of horizontal gene transfer in vent systems may expand the functional repertoire of a given species, expanding the pangenome and providing access to different ecological niches. This expanded metabolic flexibility would provide a strong advantage in hydrothermal vent environments where fluid flux and environmental gradients expose communities to wide extremes in temperature, pH, and chemical composition. Here, we use comparative metagenomics to elucidate the role that viruses play in facilitating gene flow and manipulating host genetic potential in hydrothermal systems.

Output: corroborate


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: In this research, we investigated the local variation of D95, the depth above which 95% of the earthquakes occurred, where major inland earthquakes stroked after 2001, such as the 2003 Northern Miyagi, the 2004 Chuetsu, the 2008 Iwate-Miyagi, the 2016 Kumamoto, and the 2016 central Tottori earthquakes. The hypocenter catalog to compute D95 was used as the seismic activity before the mainshock occurred. These events were relocated from the Hi-net earthquake catalog. We then compared the nucleation depth, aftershock area, estimated depths of 250, 300, and 450°C, and seismic velocity structure corresponding to the D95. 2. MethodsWe first calculated D95 for each event region from high-resolution catalog including hypocenters occurred before each mainshock. To justify the meaning of the value of D95, we needed to compare D95 to the depth range of hypocenter of mainshock, aftershocks, rupture area, and crustal temperature for each event region to find whether there is an agreement to D95. Additionally, we estimated the depth of the crustal temperature where it reaches 250 ˚C, 300 ˚C, and 450 ˚C, hereinafter referred to as D250deg, D300deg, D450deg, respectively. In this section, we explain the method to prepare the dataset to calculate D95, D250-450deg and that to compare other seismic parameters. 2. 1 Earthquake event catalog The high-sensitivity seismograph network (Hi-net) operated by the Institute for (NIED) has been under operation since 2000 and has been generating its own earthquake catalog using seismic records from Japanese multiple institutes and universities (Okada et al. , 2004). Because seismometers of Hi-net are installed at the bottom of a borehole at depths of over 100 m at approximately 800 locations nationwide (with 20–25 km mesh) on Japanese Islands, their records contain relatively low noise with dense coverage. These seismic data are open to the public through the website and are heavily used for earthquake research and for monitoring from micro- to mega earthquakes (Obara et al. , 2005; Institute for 2019). Yano et al.

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: Oxidative stress is implicated in the onset, development and progression of diabetes mellitus types 1 and 2; it also enhances development of diabetic complications such as retinopathy, nephropathy, hypertension and atherosclerotic vascular disease. 19‒21 On other hand, hyperglycemia enhances the formation of free radicals such as superoxide anion radicals, NADPH oxidase-induced reactive oxygen species and peroxynitrates. These radicals aggravate glucose auto-oxidation and lipid peroxide formation. 22 In diabetes mellitus, the antioxidant defenses are affected; this impact is expressed as an impairment of glutathione metabolism, alteration in antioxidant enzymes and decreased ascorbic acid levels. 23,24 Thus the antioxidant activity of plant extracts through their radical scavenging effect could help in management of diabetes mellitus. Plants and their extracts are widely used in folk medicine in many countries for management of diseases. Hypoglycaemic effect of natural dietary sources such as garlic, cinnamon extract and black cumin volatile oil had been reported. 25‒27 Amongst the plants with show potential for use in treatment of diabetes mellitus in Malaysia and other Asian countries are S. polyanthum, O. sumatrana and H. polyrhizus. These plants were under investigations in faculty of Pharmacy, UiTM laboratories for the last few years. The high doses of the extracts used in this study were determined on the basis of previous biochemical studies. They were the highest relatively safe and effective doses in terms of antioxidative and antihyperglycaemic activities. This study showed that the plant extract had severely damaged the liver cells (hepatocytes) in diabetic and in normal non diabetic rats. Hepatic damage was associated with infiltration by macrophages. This finding is similar to that shown on the damaging effect of other exogenous toxins on the liver. 14,15 Macrophage infiltration of the liver is expected since it is a normal event that happens following necrosis of hepatocytes. Plant extracts had also damaged the kidney in diabetic and normal non diabetic rats. Their impact was demonstrated as interstitial bleeding, extensive thickening of the wall of muscular arteries and arterioles and glomerulosclerosis of renal corpuscles. Interstitial bleeding was due to damaged arteriole walls.

Output: pass


Input: Claim: Analysis of hydrothermal vent ecosystems provides clues about life's origins. [SEP] Text: This result provides compelling molecular evidence of abundant proviruses in cellular genomes in vents and complements descriptions of high proportions of lysogenic cells in vents and the deep ocean based upon mitomycin C induction experiments [28], [29]. We also analyzed the relative abundance of mobile genetic elements in 40 viral and cellular metagenomes, also selected to represent a range of environments, and controlled for sequencing method. We found a relative enrichment of mobile genetic elements in both the viral and cellular gene pools at Hulk hydrothermal vent (Table 2). Thus, not only do the genomes of archaea and bacteria in vents encode a higher abundance of mobile elements, on average, than genomes native to other habitats, but vent viruses encode a high abundance of mobile elements as well. These data suggest that selection has favored enrichment of mobile elements in these cellular and viral genomes, potentially leading to increased rates of horizontal gene flow among cells and viruses. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 1. Percent of reads in cellular metagenomes matching a protein in the “Prophage” grouping of the database. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 2. Percent of reads in cellular and viral metagenomes matching a mobile element. Evidence of genomic plasticity in vent genomes Having found evidence for gene transfer and viral integration in the genomes of vent cells and viruses, we sought evidence for either lysogenic virus integration or gene transfer events in other hydrothermal vent isolates. Of the 34 available fully sequenced vent genomes, 20 (59%) contain integrated viruses (Table S4). Most of these viruses encode capsid genes or genes such as DNA ligases, which have been identified before as being particularly abundant in the viral fraction of this hydrothermal vent sample [46]. However, identification of auxiliary metabolic genes (AMGs) in these viral genomes is difficult, partly due to the high abundance of unknown genes and partly because the boundaries between the viral and cellular genome are not always clearly delineated. To better identify regions that have been transferred in vent genomes, we compared genomes from bacterial or archaeal isolates with sequences sampled directly from the environment. This strategy can identify potential hypervariable regions, or “genomic islands,” that display lower coverage than the rest of the genome [47]–[49].

Output: corroborate


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: 3 − 9 − 9 2 7–12 0. 01 0. 01 − 9 − 9 1. 00 0. 5 10 10 3 13–18 1. 0 0. 5 − 9 2 0. 01 0. 005 8 5 4 19–24 1. 0 0. 5 6 2 0. 01 0. 005 6 4 5 25–30 1. 0 0. 5 6 0. 5 0. 01 0. 005 6 4 Table 2 Relocation parameters for relocated hypocenter used for D95 and aftershock catalog 2. 2 D95 In this study, D95 was used to estimate the depth corresponding to the seismogenic depth. The seismogenic depth has been thought as the depth of onset of quartz plasticity as well as temperature above 300°C (Scholz 1998), assuming the presence of quartz as a dominant mineral in the crust. Earthquakes were selected from magnitudes larger than M1. 5 from the relocated catalog (see section 2. 1). This selection satisfies the Gutenberg–Richter rule for proper analysis. Only the crustal events, shallower than the depth of 40 km, between 2001 and the time before the mainshock were considered to compute D95. This is because we wanted to verify if any pre-condition can predict the maximum depth of the main event before the mainshock occurred. The final D95 result is available at every grid point, evenly spaced at 0. 1 ° in the latitude and longitude directions. To calculate D95, we first counted the total number of earthquakes that occurred within the depth column. The dimension of this depth column is 0. 02 ° × 0. 02 ° (latitude × longitude) × depth. Then, we resampled by averaging the final grid points evenly spaced at 0. 1 °. The size of grid space is justified by the fact that it is larger than the location uncertainty of the JUICE catalog, 0. 37 km and 0. 85 km in the horizontal and vertical direction, respectively, in the good station coverage. We assumed these uncertainties are compatible with this study because we used similar station combinations and the same technique as the JUICE catalog. D95 was left as an undetermined value if the total number of events within the depth column is less than 50 events due to the insufficient sample size. 2.

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: Thickened wall of muscular arteries and arterioles was the result of extensive thickening of the tunica intema which was produced by proliferation of intemal cells. These arterial thickening encroached upon their lumen and narrowed them, thus ischemia of the kidney and their renal corpuscles would be expected. Similar vascular changes were reported in hypertension and in diabetic nephropathy. 14,15 Dose-dependent thickening of the endometrial blood vessels was also noticed in rats treated with crude methanolic leaf extract of (150 to 300mg/kg body weight, p. o. daily for 30days). 28 Dose-dependent damaging of the kidney was also noticed in rats after treatment with aqueous leaf extract of rinbacin, the renal pathologic changes was manifested by damaged glomeruli and tubules. 16 Glomerulosclerosis of glomerular tuft of capillaries in renal corpuscles was an extension to the changes that happened in arteries and arterioles. Narrowing of glomerular capillaries was due to a uniform and homogeneous thickening of the glomerular capillary basement membrane which was associated with an increase in mesangeal cells and matrix. Urinary space remained clear since there had been no proliferation of podocytes. Such changes were also reported in chronically ischaemic glomeruli and in diabetic nephropathy. 14,15 Three types of controls were compared with animals given the plant extracts, they were normal, normal diabetic and normal non diabetic rats treated with vitamin E, a well known antioxidant. Our data (unpublished) showed the three plant extract to have high antioxidant capacity, thus the use of vitamin E as the control antioxidant. enhanced wound healing in normal and diabetic rats. 29 Its administration in this study did not implicate any effects on rat liver and kidney. The other two controls also showed normal liver and kidney. Little is known of the phytochemical constituents of O. sumatrana. Early studies on S. polyanthum showed it to contain flavonoids, tannins and alkaloids. 30 Other species of the same family, S. commersonii, S. glomeratum and S. mauritianum were shown to contain high levels of phenolic compounds. 31 H. polyrhizus has high content of betacyanins, red-violet pigments from the betalain family.

Output: pass


Input: Claim: Analysis of hydrothermal vent ecosystems provides clues about life's origins. [SEP] Text: Many of the genes in both the first and second genomic islands encode proteins that interact with the environment, including sugar and nitrate membrane transporters, and proteins related to energy metabolism, including hydrogenases (Table S5). Possession of a diverse suite of hydrogenases can enhance metabolic flexibility in variable redox conditions, and has been observed in other Epsilonproteobacteria isolated from hydrothermal vents [52]. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 2. Recruitment plot of metagenomic reads to Caminibacter mediatlanticus TB-2. Cellular metagenomic reads were mapped to the longest contig of the draft genome of C. mediatlanticus TB-2, with percent similarity on the y-axis and base pair numbers on the x-axis (A). Coverage plot of read recruitment is shown per base pair, with blue line showing actual coverage and green line showing a convolution function of the coverage plot using a weighting of 50000 (B). Percent GC plot for the same contig is shown on the same scale, with base pair numbers marked below (C), and are annotated with loci and recombinases or integrases found on the contig. Orange shading shows the location of loci on the genome; green shading shows the location of two metagenomic islands. presence of this hypervariable region indicates that genomic islands from genomes in vent environments encode genes related to environmental interactions and energy metabolism. The genomic island shown here is unique to a vent isolate from the Mid-Atlantic Ridge. The C. mediatlanticus strains present in our sample on the Juan de most likely have genomic islands of their own, though these cannot be identified without a fully sequenced strain from the Juan de Fuca Ridge. None of the sequenced strains from the Juan de had high enough coverage with our metagenome to identify genomic islands. However, the genomic island on C. mediatlanticus provides evidence of horizontal transfer of genes that facilitate metabolic flexibility in an environment that is very similar to the Juan de Fuca Ridge. From this we can hypothesize that genes related to environmental interactions and metabolic activity are transferred in our sample site. Quantification of relative gene enrichment in the viral fraction We next sought to determine whether there were differences in the relative enrichment of gene types in the cellular and viral fractions.

Output: corroborate


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: The result by Tanaka (2009) shows that estimated temperature changes by approximately 50 ˚C due to the uncertainty in the thermal properties of the shallow and deep rocks alone. This result implies that D300deg can change up to about 4 km due to uncertainty in the thermal properties. Another caveat is that it is possible for very hot fluids reaching the surface, crustal structure, climate change, and heat sources can alter the geothermal profile. Further discussion of this caveat is in the discussion session. 2. 4 Vertical cross-sections along the coseismic faults of large earthquakes We obtained the vertical cross-sections along the approximate fault locations which intersect with main aftershocks and mainshocks for the 2003 Northern Miyagi, the 2004 Chuetsu, the 2008 Iwate-Miyagi, the 2016 Kumamoto, and the 2016 central Tottori earthquakes. We then compared (1) the D95 depth with 5 other parameters; (2) patterns of D250-450deg, (3) hypocenters of mainshocks and (4) their aftershocks, (5) their coseismic rupture from results by Honda et al. (2005) for the 2004 Chuetsu earthquake, Suzuki et al. (2010) for the 2008 Iwate–Miyagi earthquake, Kubo et al. (2016) for the 2016 Kumamoto earthquake, and Kubo et al. (2017) for the 2016 central Tottori earthquake, and (6) local velocity structure from Matsubara et al. , 2019. In figures 1-5, D300deg are interpolated from the D300deg result; We used the GMT command “surface” with 0. 5˚ as the search radius and eight maximum iterations to obtain the minimum curvature solutions for the 0. 05 ° grid. D95 in the map view is not interpolated but shown in color corded circle. The color indicates the D95 at the site. Note that the cross-sections are all vertical cut. This means that if a coseismic fault has low-angle dipping, the interpretation from the cross-section figure is needed to be cautious. For our reference, we inserted the F-net CMT solutions. 3. ResultsThe summary of results is shown in Table 3.

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: 11,32,33 Tannins are polyphenols. All plants contain tannins which contribute to the astringent taste of vegetables. The content of tannins in S. polyanthum is expected to be high based on its high content of polyphenols. Food rich in tannins exert a growth depressing effect in rats and chicken. 34 At the high daily doses used in this study (1g/kg for S. polyanthumand O. sumatrana, 3g/kg for H. polyrhizus), treatment of rats for two weeks has resulted in marked pathological changes in their liver and kidney, although the animals exhibited no obvious morbidity or significant loss in body weight. The offending chemical(s) is unknown but the toxicity of tannins and/other polyphenols could not be ruled out. More studies are required to monitor the safe use of the studied plants and their extracts in traditional medicine. work demonstrated the importance of safety studies on herbal extracts. Natural products are not necessarily safe especially at the higher dose range or when an extract is taken for prolonged periods of time. Acknowledgements Prof. Dr. AA. H. Dhiab Al-Nuaimi is most grateful to Prof. Dr. Aishah Adam, Faculty of for her unlimited support and encouragement. He is also indebted to for their support. Conflict of interest The study was supported by a research grant from the Ministry of Science, Technology and Innovation (MOSTI), to whom the author is most grateful. 59. Efferth T, Kain B. Toxicities by herbal medicines with emphasis to traditional chinese medicine. Metab. 2011;12(10):989‒996. . Vegetables, fruit, antioxidants and cancer: a review of Italian studies. Nutr. 2001;40(6):261‒267. . Nutritional sciences from fundamentals to food. 3rd ed. Cengage, USA; 2017. C, Scalbert A. Proanthocyanidins and tannin-like compounds - nature, occurrence, dietary intake and effects on nutrition and health. J Agric. 2000;80(7):1094‒1117. Identification of two polyphenolic compounds with antioxidant activities in longan pericarp tissues. J Chem. 2007;55(14):5864‒5868. Norman J. Spices.

Output: pass


Input: Claim: Analysis of hydrothermal vent ecosystems provides clues about life's origins. [SEP] Text: 83: 324–339 View 2. (2013) The deep viriosphere: Assessing the viral impact on microbial community dynamics in the deep subsurface. Geochemistry 75: 649–675. View 3. (2011) as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage. 77: 120–133. View 4. (1985) Submarine hydrothermal vents and associated gradient environments as sites for the origin and evolution of life. 15: 327–345. View 5. (2003) Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Microbiol 69: 3580–3592 View 6. (2007) Microbial population structures in the deep marine biosphere. Science (80–) 318: 97–100 View 7. (2002) Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat. Microbiol 68: 1585–1594 View 8. (2003) Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption. 43: 393–409 View 9. (1998) Thermophilic and hyperthermophilic microorganisms in 3–30°C hydrothermal fluids following a deep-sea volcanic eruption. 25: 33–41 View 10. Summit M, Baross JA (2001) A novel microbial habitat in the mid-ocean ridge subseafloor. 98: 2158–2163 View 11. (2007) Novel and diverse integron integrase genes and integron-like gene cassettes are prevalent in deep-sea hydrothermal vents. 9: 2298–2312 View 12. (2009) Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J 3: 1420–1424. View 13. (2001) Horizontal gene transfer in prokaryotes: Quantification and classification. Microbiol 55: 709–742 View 14. (2005) Highways of gene sharing in prokaryotes. 102: 14332–14337 View 15. (1999) Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 399: 323–329. View 16.

Output: corroborate


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: D95 and D250-D450degs do not remain constant locally for most cases, rather fluctuate about 4 km and 19 km in depth at most, respectively. Except for some aftershocks that occurred in the southwestern part of the Kumamoto earthquake penetrated 5 km deeper than D95, mainshock hypocenters and their aftershocks nucleated mainly above the D95 and D250-450degs. Therefore, our results indicate that D95 is suitable representation for the base of the seismogenic layer. Isodepth surface of D95 lies within Vp/Vs (the ratio of compressional wave velocity to shear wave velocity) of the range between 1. 68 and 1. 82 and Vp (compressional wave velocity) of the range between 5. 9 and 6. 8 km. For most cases, mainshock occurred in the region between D300deg and D450deg. Except for mainshocks of the Iwate-Miyagi earthquake occurred about 2 km deeper than D450deg and of the Kumamoto earthquake occurred in the range between D250deg and D300deg. Overall patterns of D250-450deg and D95 are compatible particularly to Vp/Vs structure. However, the patterns of D250-450deg for the Iwate-Miyagi earthquake is extremely shallow and for the epicentral region of the Kumamoto earthquake is extremely deep. Table 3 Summary of results for all five study regions 2003 (Fig. 1) 2004 Chuetsu (Fig. 2) 2008 Iwate- Miyagi (Fig. 3) 2016 Kumamoto (Fig. 4) 2016 central Tottori (Fig. 5) 1. D95 (km) 12-13 SW NE 8–18 10–14 13 22 17 1. D450deg (km) 11–18 22 8 3-5 SW NE 7–16 25–30 3–6 3. Mainshock depth (Hi- net/our local relocated catalog) [km] 12. 313. 6 14. 1/14. 8 6. 7 12. 6/12. 2 (4/14) 13. 1/12. 7 (4/16) 11. 6/10. 1 4. Aftershock 5–15 5–20 3–13 Most: 5–15 SW:20 5–15 5. Main slip unknown 3–20 (Honda et al.

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: London: Ltd; 1990. Marks C. The exotic kitchen of Indonesia. New York: M. Evans and Company; 1993. Sayekti S, Muhtadi A, Supriyatna. Aktivitas hipoglikemik daun salam dan herba bulu lutung. CerminDuniaKedokteran. 1994;95:50‒54. Mizrahi Y, Nerd A. Climbing and columnar cacti: New arid land fruit crops. In: Janick J, editor. Perspectives on new crops and new uses. Alexandria: ASHS Press; 1999. p. 358‒366. . Betacyanins in fruits from red-purple pitaya, Hylocereus polyrhizus (Weber) britton and rose. Food Chem. 2002;77(1):101‒106. Beneficial effects of high dietary fiber intake in patients with type 2 diabetes mellitus. N Med. 2000;342(19):1392‒1398. Concentrations of p-synephrine in fruits and leaves of Citrus species (Rutaceae) and the acute toxicity testing of Citrus aurantium extract and p-synephrine. Food ChemToxicol. 2008;46(8):2770‒2775. Basic histopathology, a text and colour atlas. Edinburgh: Churchill Livingstone; 1985. (1998) Pathology, basic and systemic. London: WB Ltd; 1998. Effects of rinbacin extract on rat kidney. Bull. 2002;25(8):1022‒1025. . Effect of Vitamins A, E, C and Omega-3 on in Diabetic Rats. Publ Health. 2007;36(2):58‒63. Protective effect of N2-mercaptopropionylglycine on rats and dogs liver during ischemia/reperfusion process. Arq Gastroenterol. 2003;40(3):177‒180. . Inflammation and neovascularization in diabetic atherosclerosis. Exp Biol. 2007;45(1):93‒102. Free radicals and antioxidants in normal physiological functions and human disease. Biol. 2007;39(1):44‒84. .

Output: pass


Input: Claim: Analysis of hydrothermal vent ecosystems provides clues about life's origins. [SEP] Text: (2012) Marine Viruses: Truth or Dare. 4: 425–448 View 17. (1998) Gene transfer by transduction in the marine environment. Microbiol 64: 2780–2787. View 18. (2010) High frequency of horizontal gene transfer in the oceans. Science (80–) 330: 50. View 19. (2007) Exploring the vast diversity of marine viruses. Oceanography 20: 135–139. View 20. (2005) Photosynthesis genes in marine viruses yield proteins during host infection. Nature 438: 86–89. View 21. (2007) Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature 449: 83–86 View 22. (2006) Transcription of a “photosynthetic” T4-type phage during infection of a marine cyanobacterium. 8: 827–835 View 23. -(2008) Efficient phage-mediated pigment biosynthesis in oceanic cyanobacteria. 18: 442–448. View 24. (2011) Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. 108: E757–64 View 25. (1996) Lysogenic conversion by a filamentous phage encoding cholera toxin. Science (80–) 272: 1910–1914 View 26. Paul JH (2008) Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? ISME J 2: 579–589 View 27. (2005) High abundances of viruses in a deep-sea hydrothermal vent system indicates viral mediated microbial mortality. 52: 1515–1527. View 28. ölfe MG (2003) Lysogeny and virus-induced mortality of bacterioplankton in surface, deep, and anoxic marine waters. 48: 1457–1465. View 29. (2008) Lysogenic virus-host interactions predominate at deep-sea diffuse-flow hydrothermal vents. ISME J 2: 1112–1121. View 30. Meyer F, Paarmann D, D’ (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386 View 31.

Output: corroborate


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: , 2005) 2–6 (Suzuki et al. , 2010) 0–15 (Kubo et al. , 2016) 4–13 (Kubo et al. , 2016) 6. Vp (km/s), Vp/Vs 6. 2–6. 4, 1. 68–1. 76 6. 1–6. 8, 1. 76–1. 82 6. 0–6. 3, 1. 70–1. 78 5. 9–6. 4, 1. 68–1. 74 6. 2–6. 3, 1. 72–1. 74 3. 1 Case 1. The 2003 earthquake D95 was undetermined due to a lack of sufficient background seismicity events before the mainshock listed in the Hi-net catalog (Figure 1 (a, d)). Instead, D95 of 12-13 km estimated in the northern extension of the study region was used for this study case. We confirmed that the mainshock occurred near D95 by comparing the depth of D95 as 12-13 km to the depth of mainshock nucleated is at 12. 3 km according to Hi-net catalog; and 13. 6 km in JUICE catalog (Yano et al. , 2017). D250-450deg are the range of 7 and 18 km (Figure 1 (b, e))). Isotherm along the cross-section is deep in the southern part and shallower by 5 km in the northern part. Aftershocks mainly occurred within the range of 5 to 15 km. The mainshock and main aftershock were located within the D300-D450deg between 11-18 km, apparently within a depth of D250-450deg. Vp along the cross-section in Figure 1 (g) is nearly layered structure as well as Vp/Vs except there were two low Vp/Vs zones in the epicentric region and its northern extension (Figure 1 (h)). The distribution of seismicity is mainly above these two low Vp/Vs zone. D95, D250-450deg, and Vp gently lean southward to deeper. D95 laid within the narrow Vp range between 6. 2 and 6. 4 km/s and within the Vp/Vs range between 1. 68 and 1. 76. 3. 2 Case 2.

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: Pharmacotherapy for diabetic retinopathy-it is not just a dream. Diabetologia Croatica. 2008;37(3):57‒66. . Diabetes, oxidative stress, antioxidants: a review. J Toxic. 2003;17(1):24‒38. . Effect ofseed kernel on antioxidant defense system in streptozotocin-induced diabetes in rats. Life Sci. 2004;75(22):2717‒2731. Anti-diabetic activity of fruits of Terminalia chebula on streptozotocin induced diabetic rats. Journal of health science. 2006;52(3):283‒291. . Cinnamaldehyde-A potential antidiabetic agent. Phytomedicine. 2007;14(1):15‒22. Hypoglycaemic property of nutraceuticals. J Pharm Sci. 2007;6(2):105‒107. M. Herbs and spices: cinnamon's link to diabetes control. Today’s dietitian. 2015;17(11):12. Toxic effects of methanolic extract of Aspilia africanaleaf on estrous cycle and uterine tissues of Wistar rats. Morphol. 2007;25(3):609‒614. Effect of vitamin E on plasma malondialdehyde, antioxidant enzyme levels and the rates of wound closures during wound healing in normal and diabetic rats. J Clin Nutr. 2002;11(7):448‒451. . A review of natural products and plants as potential antidiabetic drugs. J Ethnopharmacol. 1989;27(3):243‒275. Characterisation of the phenolic constituents in Mauritian endemic plants as determinants of their antioxidant activities in vitro. J Plant Physiol. 2006;163(8):787‒799. Betacyanins from vine cactus Hylocereus polyrhizus. Phytochemistry. 2001;58(8):1209‒1212. Minor betalains in fruits of Hylocereus species. Phytochemistry. 2007;68(2):251‒259. Reed JD. Nutritional toxicology of tannins and related polyphenols in forage legumes. J Anim Sci. 1995;73(5):1516‒1528. ©2018 Al-Nuaimi.

Output: pass


Input: Claim: Lunar ice deposits may harbor ancient microorganisms from Earth's early history. [SEP] Text: Минералого-геохимическая специфика разновозрастных орогенных месторождений золотаВремя формированияМеталлогенический стильМеталлы-индикаторыРудные минералыЖильные минералыПримерыместорожденийИсточникиАрхейМафическийAu/Ag ˃ 5As, W, ± Пирит, арсенопирит, галенит, пирротин, сфалерит, халькопирит, тетраэдрит-теннантит, сульфосоли, антимонит, Au, Ag, Pb и Bi теллуриды и сульфотеллуриды и др.

Output: pass


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: The 2004 Chuetsu earthquake Overall D95 pattern in this region (Figure 2 (a)) tend to be deeper, compare to those in the other study areas. D95 varies from about 17 km to 22 km in depth and appears to deepen northward in the cross-section (Figure 2 (d)). Particularly, the deepest D95 is located at about 10 km southwest of the mainshock. Focal depth of the mainshock, as 14. 1 km according to the Hi-net event catalog and 14. 8 km in JUICE catalog (Yano et al. , 2017) are shallower than the D95. Majority of aftershocks occurred between 5 and 15 km in depth, with the sprinkling deep events. Main coseismic slip was estimated around 3-20 km in depth (Honda et al. , 2005). Therefore, D95 lies deeper than the hypocenter of the mainshock, majority of aftershocks, and area of large coseismic slips. D250deg is about 4-10 km in depth and D450deg is about 8-22 km (Figure 2 (b, e)). D250, 300, 450deg are shallow in the northeastern area and deep in the southwestern area. This pattern is similar to D95 curve. zone and Vp/Vs can be seen around 20 km in depth at southwest from the mainshock (Figure 2 (g, h)). This high Vp zone and Vp/Vs location is compatible to the region where D95 and D250-450deg both be deeper. D95 laid within the Vp range of between 6. 1 and 6. 8 km/s and within the Vp/Vs range of between 1. 76 and 1. 82. 3. 3 Case 3. The 2008 Iwate-Miyagi earthquake D95 is relatively within a narrow range between 9-11 km in depth near the mainshock hypocenter (Figure 3 (a, d)), whereas its northeastern part is extremely deep to 18 km. Hypocenter of the mainshock lies at a depth of 6. 7 km.

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: is Open Access? is an initiative that aims to make scientific research freely available to all. To date our community has made over 100 million downloads. It’s based on principles of collaboration, unobstructed discovery, and, most importantly, scientific progression. As PhD students, we found it difficult to access the research we needed, so we decided to create a new publisher that levels the playing field for scientists across the world. How? By making research easy to access, and puts the academic needs of the researchers before the business interests of publishers. are a community of more than 103,000 authors and editors from 3,291 institutions spanning 160 countries, including winners and some of the world’s most-cited researchers. Publishing on IntechOpen allows authors to earn 10. 5772/intechopen. 98322 this 1. Choose citation style Select style to clipboard Get citation 2. Choose citation style Select format Bibtex RIS Download citation IntechDrugs from by Hany El-the from by Hany A. El-purchase hard copies of this book, please contact the representative in India: CBS Publishers & Distributors Pvt. Ltd. www. cbspd. com | customercare@cbspd. com 1. Choose citation style Select style to clipboard Get citation 2. Choose citation style Select format Bibtex RIS Download citation Impact of this 1. IntroductionMedicinal plants produce various secondary metabolites in their normal metabolic pathways and these metabolites play an important role for providing the activities of different therapeutic benefits. Medicinal plants have been considered for many years as an essential source of drugs such as morphine, digoxine, quinine, taxol, galantamine, artemisinine etc. for the treatment of several diseases and these natural products are still popular main stream stage for researchers to discovery of novel bioactive compounds with recent advancement in science and technology. Furthermore, FDA-approved antiviral drugs (famciclovir, ganciclovir, sorivudine, zidovudine, didanosine, zalcitabine, stavudine and ivermectin) are originally modeled on a natural product parent. The potential utilization of plant extracts and their secondary metabolites to combat the development of antiviral agents is considered to be one of the most important approaches toward effective therapy for viral infections by inhibiting the replication cycle of various DNA and RNA viruses.

Output: pass


Input: Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: The Prp43•U7-RNA•ADP•BeF3-complex unveils the structural basis of why Prp43 can bind RNA in a sequence-independent manner. The Prp43•ADP•BeF3- structures illustrate how Prp43 binds and releases complex RNA substrates due to massive rearrangements of the C-terminal domains which affect an opening of the interior RNA-binding tunnel which is formed by the two RecA-like and the C-terminal domains. The hydrolysis of an ATP molecule induces conformational rearrangements of the RecA-like domains which, in turn, allow the translocation of the RNA through the interior tunnel via the so far unrecognized RF motif present in a β-turn of all DEAH-box helicases. According to our results, the translocation mechanism of MLE is very unlikely to be compatible for Prp43. All proposed functional mechanisms of Prp43 are strengthened by functional analyses of structure-based mutants in this study. structure of Prp43 with bound RNA in an active state In order to overcome the lack of crystal structures of DEAH-box helicases in an active state, we crystallized Prp43 in the presence of the non-hydrolysable ATP-analog ADP•BeF3- as well as a U16-RNA. For these crystallization approaches, an N-terminally truncated version of Prp43 from C. thermophilum was used (ctPrp43ΔN), which lacks the first 60 amino acids (Figure 1a). Previously, we already demonstrated that this truncated ctPrp43 variant is fully capable of replacing its yeast ortholog in spliceosome disassembly assays (Tauchert et al. , 2016). Crystals of ctPrp43ΔN•ADP•BeF3- in the presence of the U16-RNA were obtained in the space group P6122 and diffracted up to 2. 62 Å. In addition to the ADP•BeF3- and a central magnesium ion at the active site, seven out of the 16 nucleotides of the RNA as well as one additional phosphate group were traceable in the electron density (for an omit map of the RNA see Figure 1—figure supplement 1a).

Output: corroborate


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: Aftershocks are located between 3 to 12 km in depth and can be subdivided into two segments based on their spatial patterns; in a southern segment, aftershock clouds exhibit concave up between 3 and -12 km, whereas they appears more flat in a northern segment between 9 and 4 km (Figure 3 (e)). D95 encloses most of these deeper portion aftershocks distributions. Main coseismic slip was estimated around 2-6 km in depth (Suzuki et al. , 2010). Therefore, D95 lies below the hypocenter of the mainshock, and the deeper bound of where majority of aftershocks and coseismic rupture occurred. In contrast to other cases, D250-450deg is very shallow at a depth of 1-5 km (Figure 3 (b, e)). D250-450deg is much shallower than D95. There are low Vp/Vs zones around 10 km away in both strike directions from the mainshock (Figure 3 (h)). High Vp/Vs zone penetrates about 3 km deeper just beneath the mainshock. This concave pattern of high Vp/Vs is comparable to the pattern of aftershock distribution and D95. D95 lies within the Vp between 6. 0 and 6. 3 km/s (Figure 3 (g)) and within the Vp/Vs between 1. 7 and 1. 78. 3. 4 Case 4. The 2016 Kumamoto earthquake Except epicentric area, shallower D95 and D300deg of about 10 km in depth lies along a wide range of the Beppu-Shimabara graben where our cross-section runs (Figure 4 (a, b)). D95 tend to be slightly deeper about 3 km at southwest than northeast along the cross-section (Figure 4 (a, c)). Cloud of background seismicity before the mainshock appear to be shallower around Mt. Aso area (Figure 4 (d)). Majority of aftershocks occurred down to 13 km and becomes shallow in the vicinity of Mt. Aso. This pattern is similar to D95. There are less aftershocks southwest of Mt. Aso region. Some streaks of aftershocks penetrated about 5 km deeper than D95. Mainshocks occurred on April 14 2016 and April 16 2016 had depths of 12. 6 km (12.

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: Among the viral infections, Virus type 1 (HIV-1) and 2 (HIV-2) as genetic variabilities that causes Syndrome (AIDS) which is one of the most dangerous infectious disease all over the world and has led to the death of many people. The anti-HIV potential of the 717 plant species belonging to 151 families were summarized for 206 HIV-reverse transcription (HIV-RT), 254 HIV-protease (HIV-PR) and 43 species as HIV-integrase (HIV-IN); among them Calendula officinalis, Justicia gendarussa and Sceletium tortuosum might be useful potential sources for new lead compounds in the development of new candidates with anti-HIV properties of therapeutic interest reported by Salehi et al. [1]. 16 ethanolic extracts of Turkish medicinal plants were evaluated for their antiviral activities against Virus (HSV) and Sindbis virus (SINV); according to results, the extracts of Galanthus elwesii and Rheum ribes showed the most potent anti-HSV activities as well as Galanthus elwesii and Leucojum aestivum were found to be the most potent anti-SINV [2]. Moreover, 14 herbal products with confirmed clinical safety features were attractive starting material for the identification of new antiviral activities and their identified compounds for the eradication of viral diseases were also reported [3]. Coronavirus 2 (SARS-CoV-2), Virus (IAV), and (NV) are highly pathogens that affected the health of the worldwide community. SARS-CoV-2 is an enveloped RNA virus (genus Betacoronavirus, subgenus Sarbecovirus) that was originated in December 2019 in patients with infectious pneumonia in Wuhan, China. Despite of intense efforts relevant to experimental and clinical studies since the start of the COVID-19 pandemic, no disease-specific drug is available, yet. Several treatment strategies including already known antiviral drugs, interpherons, interleukin inhibitors, and other drugs acting through different mechanims are being implemented in COVID-19 patients. Moreover, the traditional medicines can serve as the source of potential new drug candidates and initial research focuses on the isolation of antiviral lead compounds.

Output: pass


Input: Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: ADP•BeF3- is shown at the binding cleft between the two RecA-like domains in ball-and-stick mode. (c) Superposition of ctPrp43ΔN•ADP•BeF3-(HR) (orange) and ctPrp43ΔN•ADP•BeF3-(LR) (blue) with ctPrp43ΔN•U7•ADP•BeF3- (green). Structures were superimposed via their helicase core (RecA1 and RecA2 domains) and are shown in ribbon representation. In comparison to the ctPrp43ΔN•U7•ADP•BeF3- complex structure, the conformation of the two RecA-like domains in the ctPrp43ΔN•ADP•BeF3- complex is almost identical and they superpose very well with r. m. s. d. values of 0. 34 Å (312 Cα) in case of ctPrp43ΔN•ADP•BeF3-(HR) and with 0. 39 Å (318 Cα) for the ctPrp43ΔN•ADP•BeF3-(LR) structure (Figure 2c). However, a large rearrangement of the C-terminal domains is seen in both ctPrp43ΔN•ADP•BeF3- complex structures (Figure 3), which leads to the disruption of the interaction between two β-hairpin loops from the RecA2 domain and the OB-fold. As a consequence, the RNA-binding tunnel of ctPrp43ΔN•U7•ADP•BeF3- is opened and transformed into a shallow groove. In the closed state, the C-terminal domains of the ctPrp43ΔN•U7•ADP•BeF3- complex and of ctPrp43ΔN•ADP superpose well (r. m. s. d. of 0. 55 Å for 267 Cα). Figure 3 Download asset Open asset Conformational changes between the ctPrp43ΔN•ADP complex structure (5d0u) (Tauchert et al.

Output: corroborate


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: 2 km in Yano and Matsubara, 2007) and 13. 1 (12. 7 km in Yano et al. , 2007) km respectively. Main co-seismic slip was estimated around 0-15 km in depth (Kubo et al. , 2016). Therefore, D95 lies below the hypocenter of the mainshock, and the bases of where majority of aftershocks occurred, and on the deeper limit of co-seismic rupture. D250deg, D300deg, and 450deg vary in wide range about between 3 km and 14 km, between 6 km and 18 km, and between 8 km and 30 km in depth, respectively (Figure 4 (d)). Particularly, deepest depths of all D250-450deg are at about 10 km to the southwest from the mainshock along the cross-section. D450deg appears to enclose the deep streaks of aftershocks. There is a shallower kink in the pattern at the southwest from Mt. Aso region in the same area of less aftershock activity. Depths of mainshocks are on or slightly above the D300deg. Layered structure of Vp and Vp/Vs can be seen generally except Mt. Aso region (Fig. 4 (e,f)). layer stretching out the surface along the cross-section depresses about 10 km in depth around Mt. Aso region. Low Vp/Vs zone rises to shallower depth about 5 km than underneath Mt. Aso region. D95 lies within the Vp between 5. 9 and 6. 4 km/s and within the Vp/Vs between 1. 68 and 1. 74. 3. 5 Case 5. The 2016 central Tottori earthquake D95 gives a constant value about 13 km in depth along the cross-section near the source region of the 2016 central Tottori earthquake (Figure 5 (a, c)). Hypocenter of the mainshock was located at a depth of 11. 6 km according to the Hi-net catalog (10. 1 km in the local relocated catalog). Background seismicity before the mainshock was slightly active in the vicinity of mainshock hypocenter (Figure 5 (c)). Clouds of aftershocks can be seen mainly in the southeast of the cross-section at a depth of shallower than 15 km (Figure 5 (d)).

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: This review particularly presents a survey of recent studies on traditional medicines, medicinal plants and phytoconstituents that have indicated antiviral activity for SARS-CoV-2 infection. Advertisement 2. Traditional medicinesTraditional medicine is being frequently used all over the world. Treatment with traditional medicine is still esteemed highly, particularly by those who have no access to modern health-care. Traditional medicine is to be understood as the total of the knowledge, practices based on theories and experiences indigenous to different cultures used to maintain and improve health, to prevent and diagnose illnesses. Traditional medicine can be included in medical systems and folk medicine along with health knowledge. The numbers of medicinal plants from various medical systems like etc. could be taken into consideration as an inspiring source for bioactive phytochemicals as drug designing as well as nutraceuticals and functional foods for wellness. Based on Lipinski factors and lower binding energies, numbers of compounds from medicinal plants were analyzed for their pharmacological and biological characteristics. Some selected bioactives were found to have lower toxicity with a higher gastrointestinal absorption rate and potent anti-inflammatory and anti-viral activities against targets of COVID-19 which is an infectious pandemic caused by the SARS-CoV-2 virus. The critical target components of SARS-CoV-2 are the Spike protein (S-protein) and the Main protease (Mpro). Mpro is required for the maturation of the various polyproteins involved in replication and transcription. S-protein helps the SARS-CoV-2 to enter the host cells through the Angiotensin-2 (ACE-2). Since ACE-2 is required for the binding of SARS-CoV-2 on the host cells, ACE-2 inhibitors and blockers have got wider attention, in addition to S-protein and Mpro modulators as potential therapeutics for COVID-19. So far, no specific drugs have shown promising therapeutic potential against COVID-19. Therfeore, several studies were undertaken to evaluate the therapeutic potential of traditional medicinal plants against COVID-19. 2. 1 medicineBased on the frequency of appearance of each medicinal herb and their corresponding pharmacological activities from Medicines (TCM), one of the TCM formula was reconstructed with the potential of treating COVID-19 infection.

Output: corroborate


Input: Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: The ctPrp43ΔN•ADP•BeF3-(HR) structure is in a marginally more closed conformation, hence the ctPrp43ΔN•ADP•BeF3- complex structures are not completely identical. They represent two slightly different snapshots of Prp43 which both might exist in solution and presumably are favored by the different crystallization conditions or different crystal packing. These two states of ctPrp43ΔN•ADP•BeF3- might also give a hint at how Prp43 switches into the closed conformation since in the ctPrp43ΔN•ADP•BeF3-(HR) complex structure one inter-domain contact is present between the RecA2 (Asp 486) and the ratchet-like domain (Lys 605). These interactions between sequentially distal residues might trigger the switching from the open into the closed conformation after the binding to RNA. The circumstance that both structures of the ctPrp43ΔN•ADP•BeF3- complex are in a similar, open conformation strongly suggests the possibility that the complex structures presented reflect the main conformation of Prp43 in an active state in solution. Owing to the fact that Prp43•ADP•BeF3- crystallized in different space groups and in divergent crystallization conditions, the open conformation in crystallo is highly unlikely to be a crystallization artefact. This assumption is additionally supported by the low number of crystal contacts for the ctPrp43ΔN•ADP•BeF3-(HR) (355. 3 Å² of buried surface/1. 1% of the total surface) and the ctPrp43ΔN•ADP•BeF3-(LR) (1524. 3 Å²/4. 7%) complex structure. To further strengthen the hypothesis that the opening of the tunnel by the displacement of the C-terminal domains is crucial for the helicase function of Prp43, we designed a mutant of Prp43 which allows us to trap the closed conformation by the introduction of an internal disulfide bond (ctPrp43-IDSB).

Output: corroborate


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: Main coseismic slip was estimated around 4-13 km in depth (Kubo et al. , 2016). Therefore, D95 lies below the hypocenter of the mainshock and coseismic rupture and on or near the deeper limit of the cloud of aftershock. D250deg, D300deg, and 450deg run between 3 and 8 km, between 4 and 10 km, and between 7 and 16 km in depth, respectively (Figure 5 (b, d)). They commonly have a trend to become deeper toward the southeast along the cross-section. While aftershocks occurred much deeper than the D250-450deg in the northwest the mainshock nucleated between D300deg and D450deg. D95 lies within the Vp between 6. 2 and 6. 3 km/s and within the Vp/Vs between 1. 72 and 1. 74 (Figure 5 (e,f)). 4. Discussion 4. 1 Case 1. The 2003 earthquake The 2003 Northern-Miyagi earthquake occurred at the eastern edge of the Miocene northern Honshu rift system (Sato et al. , 2004a), and the damaged area is the boundary between the Neogene rocks and the Paleozoic and Mesozoic rocks of the (Kato et al. , 2004). sedimentary rocks spread widely in the Asahiyama and Sue Hills. basin fill is subdivided into two units; the Matsushima-wan Group composed of mainly syn-rift sediments such as volcanic rocks, fluviolucastrine sediments and marine-interbedded sandstone and siltstone in ascending order and the composed of post-rift sediments such as a shallow marine sandstone (Ishii et al. , 1982; Kato et al. , 2004). Hypocenters are located at downward extension of a west-dipping, inverted reverse fault (Sue fault) (Umino et al, 2003; Nishimura et al. , 2003; Kato et al. , 2004; Kimura and Okamura, 2009). Both the Sue fault was originally formed in the extensional stress field during the Miocene opening Sea of Japan and reactivated in the compression stress field due to the subduction of the Pacific plate during Quaternary (Sato et al. , 2004b).

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: Some parameters like drug-likeness, pharmacokinetics, and toxicity were also determined to ensure the safety and efficacy of active constituents. Based on the findings amarogentin, eufoliatorin, α-amyrin, caesalpinins, kutkin, β-sitosterol, and belladonnine were found the top ranked molecules have the highest affinity toward both the spike glycoprotein and ACE-2 [10]. Further, fourthy-one plant-derived compounds from Indian medicinal plants were screened for their inhibitory effect on Main protease (Mpro) of SARS-CoV-2 using the molecular docking approach. Among them amentoflavone, lectin, glycyrrhizic acid, hypericin and torvoside H exhibited high binding energy. Amentoflavone isolated from Torreya nucifera showed the highest binding energy of 10. 0 kcal/mol with the SARS-CoV-2 Mpro [11]. Furthermore, free energy calculations on these compounds performed by using the molecular docking procedure. The results suggested that amentaflavone, hypericin, and respectively complexed with SARS-CoV-2 Mpro show better binding with stabilizing interactions and provided valuable information in developing new, novel and natural anti-viral drugs for COVID-19 [9]. In addition, taraxerol isolated from Clerodendrum species has shown potential antiviral activities with desirable pharmacological features [12]. active constituent of ayurvedic herb from Withania somnifera has shown promising antiinfluenza properties by targeting neuraminidase of H1N1 Influenza as well as the highest binding affinity with S-protein and ACE-2 receptor [13]. of Health, India, has recommended the use of the aqueous extract of Withania somnifera as a preventive and prophylactic for treating COVID-19 infection. Withametelin isolated from Datura innoxia plant, has shown a better binding affinity against Mpro, S-protein and ACE-2. However, the pharmacological analysis revealed its toxicity to health. Other compound known as Daturaolone also isolated from Datura innoxia, has shown lower toxicity and potent antiviral and anti-inflammatory activities.

Output: pass


Input: Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: The remaining helicase activity of the mutant is most likely caused by the fraction of ctPrp43-IDSB which does not contain the internal disulfide bond. The activity of ctPrp43 and the ctPrp43-IDSB mutant were also analyzed for a physiological and more complex substrate RNP by using the S. cerevisiae ILS disassembly assays (Figure 5 and Figure 5—figure supplement 1). In previous work it was shown that ctPrp43 is capable of functionally replacing scPrp43 in the spliceosome (Tauchert et al. , 2016). ctPrp43 can release about 60% of intron-lariat RNA from scILS in the presence of ATP and scNtr(1•2) and dissociate the remaining spliceosomal RNP core into the free U6 snRNA, 18S U5 and 20S U2 snRNP (Figure 5c). This is close to the 65% efficiency of recombinant scPrp43 (Figure 5b). In case of the ctPrp43-IDSB mutant, these assays were performed in the presence and absence of DTT, which can reduce the disulfide bridge between the RecA1 and ratchet-like domain and thus free ctPrp43-IDSB from its locked conformation. Without DTT, the efficiency of ILS disassembly by ctPrp43-IDSB is clearly impaired compared to the wild-type protein since only 10% of all ILSs are dissociated which equals the amount of the negative control (Figure 5a and d). In the presence of DTT, the ILS dissociation efficiency of ctPrp43-IDSB can be fully restored to the wild-type activity level of 60% (Figure 5e). This clearly hints at the fact that locking Prp43 in the closed conformation distinctly influences its activity as deduced from the crystal structures of ctPrp43ΔN•ADP•BeF3- and thus proving the importance of adopting the open conformation for the helicase activity of Prp43 also in the spliceosome (Video 1). Figure 4 with 3 supplements see all Download asset Open asset Helicase activity and RNA-binding assays of ctPrp43 and mutants.

Output: corroborate


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: Background seismicity before the mainshock was relatively quiet so that D95 was undetermined due to a lack of sufficient data. However, there were at least three major historical earthquakes occurred in 1861, 1900, and 1962 in the north extension of the study region. We assumed that these historical earthquakes and the 2003 earthquake are related to each other, so that we borrowed D95 value from the north extension region. The mainshock depth and D95 turn out to be compatible in this case, however, D250-450deg in this seismically inactive area is going to be critical to understand the seismogenic depth. We re-estimated D250-450deg from latest method (Matsumoto et al. , 2022), which included a careful analysis for climate change correction and crustal thermal structure based on the sedimentary layers, rather than a uniform subsurface structure model, the temperature dependence of thermal conductivity, and the difference in heat generation by lithology. D300deg maps in both Figure 1 (b) and Figure 1 (c) show similar patterns with D95 (Figure 1 (a)) being shallower toward to the west. However, a new D300deg shows better fit with D95 than the original result, particularly more moderate change in depth towards the northwestern region. D250-450deg cross-sections in both Figure 1 (e) and (f) appear compatible with Vp/Vs and aftershocks patterns as relatively a flat and constant depth. However, because of new D250deg-450deg (Figure 1 (f)) and high Vp/Vs (around 1. 8) being shallower in the south than the north, new result is better fit with the Vp/Vs pattern. Because the new D450deg (Figure 1 (f)), in the epicentral region, is shallower about 5 km than the original result (Figure 1 (e)), the location of the mainshock falls onto D450deg isotherm. The kinks in the D250-450deg isotherms at about 12 km to the north from the epicenter may be artifact since it is due to the one extreme value at the temperature measurement point. 4. 2 Case 2 The 2004 Chuetsu earthquake The 2004 Chuetsu earthquake occurred in the that is filled by > 6km thick sedimentary and volcaniclastic rocks (Government, 2000).

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: The twenty alkaloids and terpenoids with high binding affinities to the SARS-CoV-2 3CLpro were further docked to the 3CLpro of SARS-CoV by comparing with the reference inhibitors (Lopinavir and Ritonavir). From them, 10-hydroxyusambarensine, cryptoquindoline, 6-oxoisoiguesterin and 22-hydroxyhopan-3-one showed potent activity against SARS-CoV-2 3CLpro [31]. 2. 6. 2 Nigerian medicinal plantsmedicinal plants and their 9 phytoconstituents were investigated against symptoms related to COVID-19. Their specific therapeutic actions are administered to combat the key players in the pathogenesis of the disease [32]. 2. 6. 3 Moroccan medicinal plantsThe molecular docking studies on sixtyseven phytoconstituents from Moroccan medicinal plants were evaluated for their in vitro and in vivo antiviral activity against SARS-COV-2 Main protease before clinical trial. The results of molecular docking studies showed that three compounds (crocin, digitoxigenin, and β-eudesmol) were proposed as inhibitors against the coronavirus based on the energy types of interaction between these compounds and studied protein [33]. 2. 6. 4 medicinal plantsTwentynine phytoconstituents isolated from commonly used traditional medicinal plants were examined against SARS-CoV-2 using molecular docking and molecular dynamics. Molecular docking identified arabic acid from Acacia senegal and L-canavanine found in Sutherlandia frutescens were determined as a potential inhibitor 3C-Like main protease (3CLpro) of SARS-CoV-2. Similarly, hypoxoside isolated from Hypoxis hemerocallidea and uzarin from Xysmalobium undulatum were also identified as a potential inhibitor of SARS-CoV-2 receptor binding domain and SARS-CoV-2 RNA-dependent polymerase (SARS-CoV-2 RdRp). In addition, these compounds exhibited favorable binding orientations characterized by strong molecular interactions within respective inhibitors binding pockets of the target enzymes [34]. 2. 7 Traditional medicinal plants of countriesUncaria tomentosa (cat’s claw) is traditionally used medicinal plant in countries.

Output: pass


Input: Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: Conformational rearrangements at the helicase core To investigate the effect of ATP hydrolysis on the Prp43 conformation, the structures of the ADP and the ADP•BeF3- bound state were compared. Since the conformations of the RecA-like domains of the three structures ctPrp43ΔN•U7•ADP•BeF3-, ctPrp43ΔN•ADP•BeF3-(HR) and ctPrp43ΔN•ADP•BeF3-(LR) are very similar, the analysis of the conformational switches was restricted to the comparison of ctPrp43ΔN•ADP•BeF3-(HR) with the previously published ctPrp43ΔN•ADP structure. The individual RecA-like domains of ctPrp43ΔN•ADP and ctPrp43ΔN•ADP•BeF3-(HR) superimpose well with r. m. s. d. values of 0. 36 Å (139 Cα) for the RecA1 domains and 0. 44 Å (142 Cα) for the RecA2 domains. Superimposing the helicase cores consisting of both RecA-like domains shows that the RecA1 and RecA2 domains are rotated by ca. 4˚ and ca. 14˚, respectively. There is also a slight translational displacement of the RecA2 domain by a 2. 7 Å shift of its center of mass with regard to the RecA1 domain. Depending on the ADP/ATP state, conformational changes of several of the conserved SF2 helicase motifs, most strikingly of those in the RecA2 domain are observed (Figure 6). The conformations of the motifs I, Ia, Ib and II, which are all located in the RecA1 domain, are similar between the ATP-bound and the ADP-bound state of Prp43. This ATP-bound state, mimicked by the bound ADP•BeF3-, also allows to deduce how Prp43 does hydrolyze ATP.

Output: corroborate


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: Structural analyses and stratigraphy of Neogene strata in this region suggest that reverse faults and fault-related folds have grown in the last 2 to 3 million years due to EW compression (Sato, 1992). We re-estimated D250-450deg from latest method (Matsumoto et al. , 2022), which included a careful analysis for climate change correction and crustal thermal structure based on the sedimentary layers, rather than a uniform subsurface structure model, the temperature dependence of thermal conductivity, and the difference in heat generation by lithology. D95 in Figure 2 (a) and D300deg maps for both Figure 2 (b) and Figure 2 (c) show similar patterns as being deeper toward Sea of Japan. Particularly, D95 reaches deeper than 30 km near the Sea of Japan. D250-450deg in both Figure 2 (e) and (f) appears compatible with Vp/Vs and aftershocks patterns as deeper in the southwest. However, new D250deg-450deg in Figure 2 (f) shows better fit with D95 (Figure 2 (a)), particularly aftershocks and Vp/Vs are having a concave upward pattern in the southwest from the mainshock. 4. 3 Case 3 The 2008 Iwate-Miyagi earthquake The 2008 Iwate-Miyagi earthquake struck with a magnitude of 7. 2 near the volcanic front in the eastern flank of the Ranges in Northern Japan. It recorded over 4G at the ground surface in the source region (Aoi et al. , 2008). The epicenter was located to the northeast of Mt. Kurikoma, a Quaternary active volcano, and this event caused many landslides, debris flows and landslide dams. Similar to the 2003 earthquake which occurred in the south from the 2008 Iwate-Miyagi earthquake, this earthquake occurred near the eastern edge of the Miocene failed rift (Sato, 1994). In the source region of this earthquake, there are many west-dipping Miocene normal faults reactivated as reverse faults under the EW compressional stress field since Pliocene (Kato et al. , 2006). The basement rocks of the source region are Cretaceous granitoids (Sasada, 1985). We re-estimated D250-450deg from latest method (Matsumoto et al.

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: Twentysix phytoconstituents of Uncaria tomentosa were docked on the binding interface of the ACE-2 and SARS-CoV-2 spike protein of novel corona virus. From these compounds namely Proanthocyanidin C1, 3-isodihydrocadambine, and Uncaric acid had a good predicted binding affinity for interface of the ACE-2 as compared to the sulfated Heparin OctaSaccharide (HepOS). Likewise, 3-dihydrocadambine, Proanthocyanidin B4, Proanthocyanidin B2 and Proanthocyanidin C1 had the highest docking score on SARS-CoV-2 spike glycoprotein in their open state. Virtual prediction ADME revealed that Speciophylline, and Uncaric acid presented values of drug ability according to Lipinski rule, demonstrating their potential bioavailability as likely orally active antiviral. Uncaria tomentosa can be performed as an herbal supplement with the safety and efficacy parameters at both preclinical and clinical stages to evaluate its effectiveness in the treatment of novel coronavirus disease (COVID-19) [18]. Thirty-nine herbal medicinal plants known in the America and Europe for the management of respiratory conditions, mainly regarding the symptoms cough, pain and fever were studied for their therapeutic potential alongwith the limitations for their use and possible risks. For five out of the 39 herbal drugs a positive benefit/risk assessment was determined. The level of evidence for Althaea officinalis, Commiphora molmol, Glycyrrhiza glabra, Hedera helix and Sambucus nigra are suggested a potential clinical use as adjuvants in the treatment of early/mild cases of COVID-19. Another twelve herbal medicines were classified as promising plant species [19]. Advertisement 3. Various phytoconstituentsVarious phytoconstituents occured in living organisms in a high structural diversity have antiviral activities by inhibiting different stages in the replication of various viruses. Their different antiviral mechanisms like virus adsorption, virus-cell fusion, reverse transcription, protease and integrase inhibition have been reported in recent studies [20, 21].

Output: pass


Input: Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: The RecA1 domain is colored in light gray, the RecA2 domain in dark gray, carbon atoms of the ADP in yellow, oxygen in red, nitrogen in blue, phosphorus in orange, beryllium in chartreuse, fluoride in light blue, magnesium in light green and water molecules in pale pink. Nucleotide-interacting motifs are shown in blue, nucleic acid-binding motifs in ruby and motif III, which couples ATP hydrolysis to RNA unwinding, in green. Residues, which are involved in base-stacking with the adenine moiety, are presented in light orange. Residues from motif I, which are involved in Mg2+ coordination (Thr 126), and from motif II, which coordinate water molecules at the active site (Asp 218 and Glu 219), are presented as sticks. The water molecule 388 is perfectly positioned for the nucleophilic attack on the γ-phosphate and thus its hydrolysis. The conserved SF2 helicase motifs I-VI are numbered according to convention. (a, Right panel) Schematic representation of the active site in ctPrp43ΔN•ADP•BeF3-(HR). Motifs and residues are labeled as introduced in the left panel. Water molecules are numbered according to the PDB entry. Stacking interactions are shown by double lines, polar interactions between ADP•BeF3- and Prp43 via red dotted lines, interactions between Prp43 and water molecules via light blue lines and the coordination of the central Mg2+ by dark green lines. (b) Active site of Prp43 with bound ADP (PDBid: 5d0u) (Tauchert et al. , 2016). (Left and right panel) Labeling and numbering according to a. Numerous rearrangements and conformational changes are noticeable between the ATP- and ADP-bound state. In the course of NTP hydrolysis, the loop harbouring the conserved motif III, which is known to couple ATPase and unwinding activity (Schwer and Meszaros, 2000; Banroques et al. , 2010; Fitzgerald et al. , 2016), also undergoes a pronounced rearrangement.

Output: corroborate


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: , 2022), which included a careful analysis for climate change correction and crustal thermal structure based on the sedimentary layers, rather than a uniform subsurface structure model, the temperature dependence of thermal conductivity, and the difference in heat generation by lithology. Isotherms of D250deg-450deg are much shallower than D95 (Figure 3). These extremely shallow isotherms may be affected by active volcanoes close to this region. D300deg maps in both Figure 3 (b) and Figure 3 (c) show similar patterns with D95 (Figure 3 (a)) being shallower at the epicentric region and the southwest from the epicenter. However, a new D300deg in Figure 3 (c) shows better fit with D95 than the original result (Figure 3 (b)), particularly concentrated shallow depth in the volcanic region. D250-450deg cross-sections in both Figure 3 (e) and Figure 3 (f) appear compatible with the pattern of high Vp/Vs (around 1. 8) as relatively a flat depth while they are not alike to the aftershock’s patterns. Mainshock hypocenter is below the D450deg. Although new D250deg-450deg (Figure 3 (f) in the northeast give deeper depth which are slightly closer to the aftershocks in the area, new method for D250deg-450deg is not dramatically improve the original result. This result confirmed that an active volcanic region is challenging and need more consideration to estimate the seismogenic depth by heat flow data. 4. 4 Case 4 the 2016 Kumamoto earthquake The 2016 Kumamoto earthquake occurred at the Futagawa and Hinagu faults located at the topographic boundary between the Kumamoto and Yatsushiro plain and the foothills composed of Cretaceous accretionary complex and Jurassic metamorphic rocks. Aftershocks occurred along the Beppu-Shimabara graben and the southern side of the graben (of Science and Technology, 2016a).

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: Lycorine, hypericin, emodin, tylophorine, ouabain, mycophenolate mofetil, silvestrol, myricetin and scutellarein were also reported for their inhibitory effects against SARS-CoV-2 and other human coronaviruses [22]. Some phytoconstituents such as myricitrin, methyl rosmarinate, 5,7,3′,4′-tetrahydroxy-2′-(3,3-dimethylallyl) isoflavone, 3,5,7,3′,4′,5′-hexahydroxy flavanone-3-β-D-glucopyranoside, (2S)-eriodictyol 7-O-(6′′-O-galloyl)-β-D-glucopyranoside, calceolarioside B, myricetin, 3-O-β-D-glucopyranoside, licoleafol, and amaranthin were reported as potential lead candidates to develop novel anti-SARS-CoV-2 drugs [23]. Moreover, anthraquinone derivatives were screened on the basis of binding energy against N-(NTD) of SARS-CoV-2. Emodin, Anthrarufin, Alizarine, Aloe- emodin, and Dantron showed the good binding affinity at three different active sites of N-of SARS-CoV-2 nucleocapsid phosphoprotein. These compounds prevent the assembly of virus p4. ConclusionPlants and their secondary metabolites provide valuable leads for the development into drugs for the novel antiviral activities. Ivermectin is the FDA approved drug and inhibited the replication of SARS-CoV-2 [35]. Although there is an increase in the use of traditional medicine worldwide, researches in traditional medicines are insufficient. Assessments of the quality, safety, and efficacy of traditional medicines are needed to provide scientific information that regulations need. In the present review, antiviral activity mainly against coronaviruses of traditional medicines along with their phytoconstituents through the literature data relevant to their enzyme and receptor interactions given by different assays.

Output: pass


Input: Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: The transition of this motif might be required to induce the global conformational rearrangements leading to the rotation of the RecA domains. The rotation leads to a movement of a β-turn in the RecA1 domain and of a β-hairpin in the RecA2 domain, which both are directly located at the RNA-binding tunnel and thus might be involved in RNA translocation (Figure 7a, Video 2). The β-turn in the RecA1 domain consists of the amino acids Arg 180 and Phe 181, and the β-hairpin of the RecA2 domain is composed of the amino acids Tyr 348, Gly 349 and Thr 350. Interestingly, this second loop has previously been identified to be crucial for the helicase activity of the DExH-box helicase MLE (Prabu et al. , 2015). In this study by Prapu and co-workers, a triple-mutant of the MLE was generated in which all residues located in this loop were mutated to glycine residues. This loop was termed Hook-Loop as it hooks between the bases of the bound RNA. It was assumed that in the course of NTP hydrolysis the movement of this loop causes the translocation of the bound RNA. Replacing the wild-type Hook-Loop sequence by GGG led to a complete loss of the helicase activity of MLE. Notably, in contrast to MLE the corresponding residues of the Prp43 Hook-Loop do not contact the bound RNA. In order to analyze the impact of both β-hairpin loops on RNA unwinding, several mutants of Prp43 were generated. In the Hook-Turn mutant (ctPrp43-HT), the amino acids 180–181 were mutated to GG and in the Hook-Loop mutant (ctPrp43-HL) the residues 348 and 350 were replaced by glycines. In addition to this, a double mutant in which both, the Hook-Turn and the Hook-Loop, contain the glycine substitutions (ctPrp43-HT&HL), was also analyzed. Figure 7 with 1 supplement see all Download asset Open asset Position of the Hook-Turn and Hook-Loop in ctPrp43.

Output: corroborate


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: While the most of the aftershocks occurred within the seismogenic layer, we found an exception in the aftershock distribution pattern during the 2016 Kumamoto earthquake below the southwestern strand of the Futagawa fault near the junction with the Hinagu fault (Figure 4); aftershocks apparently extend 5 km deeper than D95, which are significant considering that uncertainty of the hypocenter locations from the JUICE catalog is about 1 km in the depth direction. The estimated temperature of aftershock area is between 300°C and 450°C. The isotherm in this region is significantly deeper than that in the other part of the Futagawa Fault. This deep isotherm is constrained by the temperature data from station #1129 at Azumimachi, Uto (Sakagawa et al. , 2005). The temperature profile taken from 100 m to 900 m for every 100 m in depth shows that subsurface temperature increases nearly linearly, indicating that the effect of local heat source on the data is apparently minimal. However, because the simple method we used in this analysis has limitation to estimate the crustal temperature in the complex system of extremely active groundwater flow region, extremely deep D250-450deg around a depth of 30 km may not be significant. and Vp/Vs values in the region where deep aftershocks occurred are approximately 6. 5 km/s and 1. 7, respectively (Matsubara et al. 2019). These ranges are not extra ordinary to be in the seismogenic zone since they are within the range in the other cases. Immediate deepening from pre-earthquake level was also recognized by the 1992 M 7. 3 Landers earthquake. The seismic-aseismic transition changes to shallower as much as 3 km over the course of 4 years (Rolandone et al. , 2004). They claimed that the brittle-ductile transition became deeper after Landers due to high postseismic stress and strain rates at the base of the seismogenic zone. The time-dependent changes of depth relation of the postseismic seismicity of Kumamoto earthquake may be important to monitor to understanding the mechanical behavior of rocks in the crust. 4. 5 Case 5 the 2016 central Tottori earthquake The mainshock and aftershocks of the 2016 central Tottori earthquake occurred where pre-Neogene basement rocks mainly composed by late Cretaceous and Paleogene granitic rocks are extensively exposed.

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: Pre-clinical studies would provide deep insight into mechanism of actions and also drug ability of the antiviral candidates for the treatment of COVID-19 infection. Besides, vast range of double-blinded clinical studies with strict protocols is required to estimate the accurate potential of antiviral phytochemicals against COVID-19 with the aim of ensuring the fulfillment of international acceptable standards. Therefore, phytoconstituents will play an important role and continue to support in developing potential drugs against SARS-CoV-2. of interestThe authors declare no conflict of interest. 1. -Rad M, Kılıc -Rad J. Medicinal plants used in the treatment of human immunodeficiency virus. Int. J. Mol. Sci. 2018;19(5):1459-1519. DOI: 10. 3390/ijms190514592. . Antiviral activities in extracts of Turkish medicinal plants. Pharm. Biol. 2000;38:171-175. DOI: 10. 1076/1388-0209(200007)3831-SFT1713. Sener B. Antiviral activity of natural products and herbal extracts. J. 2020;31:474-477. 4. . herbal medicine at the forefront battle against COVID-19: Clinical experience and scientific basis. Phytomedicine 2020;80:153337. DOI: 0. 1016/j. phymed. 2020. 1533375. -L. Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. J. Pharm. Anal. 2020;10:313e319. DOI: 10. 1016/j. jpha. 2020. 03. 0096. . Saxifraga spinulosa-derived components rapidly inactivate multiple viruses including SARS-CoV-2. Viruses. 2020;12:699. DOI: 10. 3390/v120706997. Bahramsoltani R, Rahimi R. An evaluation of traditional Persian medicine for the management of SARS-CoV-2. Front. Pharmacol. 2020;11:571434. DOI: 10. 3389/fphar. 2020. 5714348. .

Output: pass


Input: Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: (a) The localization of the Hook-Turn in the RecA1 domain and of the Hook-Loop in the RecA2 domain in the ctPrp43ΔN•U7•ADP•BeF3- complex structure is shown. Domains are colored according to Figure 1a. (b) Superpositions of the RecA1 and RecA2 domains of the ctPrp43ΔN•U7•ADP•BeF3- and the ctPrp43ΔN•ADP (PDB 5d0u) complexes for the Hook-Turn and Hook-Loop, respectively. The superpositions indicate that the Hook-Loop remains in a highly similar conformation after ATP hydrolysis in contrast to the Hook-Turn which is shifted towards the RNA in the ADP-bound state. Video 2 Download asset This video cannot be played in place because your browser does support HTML5 video. You may still download the video for offline viewing. Download as MPEG-4 Download as WebM Download as conformational rearrangements at the active site induce global conformational changes in Prp43 which are coupled with the unwinding activity. The morphing between the ctPrp43ΔN•U7•ADP•BeF3- (PDBid: 5lta) complex structure and ctPrp43ΔN•ADP (PDBid: 5d0u) reveals conformational rearrangements in the course of ATP hydrolysis, mainly of the Hook-Turn, which is in close spatial proximity to the RNA. Prp43 translocates RNA via its Hook-Hook-Turn and Hook-Loop mutants were tested for their dsRNA unwinding capabilities. As shown in Figure 4a, the ctPrp43-HT (0. 68 nM/min) and the ctPrp43-HT&HL (0. 88 nM/min) mutants exhibit a strongly impaired RNA unwinding activity compared with wild-type ctPrp43 (60. 03 nM/min) which corresponds to an almost complete loss of function as seen for the negative control (0. 46 nM/min). Intriguingly, the ctPrp43-HL (61. 87 nM/min) mutant shows an activity being almost equal to the wild-type protein.

Output: corroborate


Input: Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: While there are some minor active faults which are striking NE-SW and NW-SE, orthogonal to NE-SW, recognized around the mainshock (RGAFJ, 1991) and no major fault is known at the mainshock and aftershock region (of Science and Technology, 2016b). 4. 6 Relationship between D95 and aftershock area, seismogenic layer, nucleation, and rupture process Both background seismicity before mainshocks and seismicity after the mainshock tend to be occurred at Vp/Vs in the green color region (1. 7-1. 8) in Figure 1-5. Therefore, the analysis of Vp/Vs pattern is also shed light on understanding the seismogenic depth and forecasting the future aftershock regions. Our observation confirmed that large earthquakes nucleated at the base of the deepest portion of the seismogenic layer (e. g. , Sibson 1984) The nucleation depths for the main shocks and the deepest portion of the main co-seismic rupture are near or shallower than D95 for all 5 cases. Therefore, our results support that D95 is indeed a significant index for the base depth of the seismogenic layer. For the solid crust, climate change correction and the temperature dependence of thermal conductivity and the difference in heat generation by lithology should be precisely applied in the equation at each study site. These parameters in equation 1 can be arguable since a continental crust, especially complicated island arcs as Japanese Islands, may not be suitable to estimate the crustal temperature. We partially applied the latest temperature models (Matsumoto et al, 2022) to the 2003 northern Miyagi, the 2004 Chuetsu, and the 2008 earthquakes (Figure 1 (c and f), Figure 2 (c and f), Figure 3 (c and f)). These models are obtained by a crustal structure model that considers the temperature dependence of thermal conductivity, the difference in heat generation due to lithology, and local climate differences. New version of isotherms tends to fit better with Vp/Vs patterns and aftershock distributions. 5.

Output: contrast


Input: Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: Traditional medicinal plants against replication, maturation and transmission targets of SARS-CoV-2: Computational investigation. J. Biomol. Struc. Dyn. 2020;5:1-18. DOI: 10. 1080/07391102. 2020. 18422469. . Structural basis for the inhibition of SARS-CoV2 main protease by Indian medicinal plant-derived antiviral compounds. J. Biomol. Struc. Dyn. 2020;1-9. DOI: 10. 1080/07391102. 2020. 183445710. . Antiviral activity of traditional medicinal plants from Ayurveda against SARS-CoV-2 infection. J. Biomol. Struc. Dyn. 2020;19:1-17. DOI: 10. 1080/07391102. 2020. 18327711. . Natural compounds as potential inhibitors of novel coronavirus (COVID-19) main protease: An in silico study. Research Square. DOI: 21203/rs. 3. rs-22839/v112. Sharma K, Zafar, R. Occurrence of taraxerol and taraxasterol in medicinal plants. Pharmacog. Rev. 2015;9:19-23. DOI: 10. 4103/0973-7847. 15631713. . Promising anti-influenza properties of active constituent of Withania somnifera Ayurvedic herb in targeting neuraminidase of H1N1 influenza: Computational study. Biophys. 2015;72(3):727-739. DOI: 10. 1007/s12013-015-0524-914. . Ethnomedicines of Indian origin for combating COVID-19 infection by hampering the viral replication: Using structure-based drug discovery approach. J. Biomol. Struc. Dyn. 2020;1-16. DOI: 10. 1080/07391102. 2020. 177853715. . Plants-derived biomolecules as potent antiviral phytomedicines: New insights on ethnobotanical evidences against coronaviruses. Plants. 2020;9:1244. DOI: 10. 3390/plants909124416.

Output: pass


Input: Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: Figures AbstractProtein conformational changes and dynamic behavior are fundamental for such processes as catalysis, regulation, and substrate recognition. Although protein dynamics have been successfully explored in computer simulation, there is an intermediate-scale of motions that has proven difficult to simulate—the motion of individual segments or domains that move independently of the body the protein. Here, we introduce a molecular-dynamics perturbation method, the Perturbation (RIP), which can generate large, coherent motions of structural elements in picoseconds by applying large torsional perturbations to individual sidechains. Despite the large-scale motions, secondary structure elements remain intact without the need for applying backbone positional restraints. Owing to its computational efficiency, RIP can be applied to every residue in a protein, producing a global map of deformability. This map is remarkably sparse, with the dominant sites of deformation generally found on the protein surface. The global map can be used to identify loops and helices that are less tightly bound to the protein and thus are likely sites of dynamic modulation that may have important functional consequences. Additionally, they identify individual residues that have the potential to drive large-scale coherent conformational change. Applying RIP to two well-studied proteins, which possess functionally-relevant mobile loops that fluctuate on the microsecond/millisecond timescale, the RIP deformation map identifies and recapitulates the flexibility of these elements. In contrast, the RIP deformation map of α-lytic protease, a kinetically stable protein, results in a map with no significant deformations. In the N-terminal domain of HSP90, the RIP deformation map clearly identifies the ligand-binding lid as a highly flexible region capable of large conformational changes. In the ligand-binding domain, the RIP deformation map is quite sparse except for one large conformational change involving Helix-12, which is the structural element that allosterically links ligand binding to receptor activation. RIP analysis has the potential to discover sites of functional conformational changes and the linchpin residues critical in determining these conformational states. Many proteins undergo large motions to carry out their biological functions. The exact nature of these motions is typically inferred from the crystal structures of the protein trapped in different states, which normally constitutes a difficult series of experiments.

Output: corroborate