Input: Task: contrast the claim using the given text. 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). [SEP] Justify:

Output: The text contrasts the claim by discussing the varying depths of seismic activity, particularly noting that the 2016 Kumamoto earthquake occurred at specific faults related to geological formations. Additionally, it references various depth gradients and thermal structures, indicating that earthquake depths are not uniform, as some regions have shallower isotherms and that aftershocks occur at different depths. This directly opposes the claim that all earthquakes occur at the same depth.


Input: Task: pass the claim using the given text. 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. [SEP] Justify:

Output: The text discusses various compounds extracted from plants and their potential antiviral activities, specifically against SARS-CoV-2. However, it does not mention the relationship between traditional medicines and indigenous cultures, nor does it provide any information to support or negate the claim about traditional medicines being derived from plants used by these cultures. Therefore, the text is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. 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. [SEP] Justify:

Output: The text discusses the role of specific structural motifs, including a β-turn and β-hairpin, in inducing global conformational rearrangements in protein structures, particularly in the context of RNA-binding and helicase activity. The mention of how movement within these structures can lead to translocation of bound RNA supports the claim that mechanical stress can induce conformational changes in proteins, as conformational rearrangements often result from mechanical or biochemical stressors.


Input: Task: contrast the claim using the given text. 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. [SEP] Justify:

Output: The text contrasts the claim by discussing the varying depths of aftershocks following different earthquakes, particularly the 2016 Kumamoto earthquake, where aftershocks occurred 5 km deeper than the seismogenic layer. This demonstrates that earthquakes do not all occur at the same depth and that the depth can vary significantly, debunking the claim.


Input: Task: pass the claim using the given text. 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. . [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses pre-clinical studies and clinical trials involving antiviral candidates and phytochemicals for COVID-19 treatment, rather than addressing the relationship between traditional medicines and their origins in indigenous cultures.


Input: Task: corroborate the claim using the given text. 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. [SEP] Justify:

Output: The text supports the claim by demonstrating that conformational rearrangements occur in the Prp43 protein as a result of ATP hydrolysis. It describes how the Hook-Turn's positioning shifts, indicating that mechanical influences related to ATP hydrolysis lead to changes in the protein structure. The assertion that 'conformational rearrangements at the active site induce global conformational changes in Prp43' bolsters the claim that mechanical stress can induce conformational changes in proteins.


Input: Task: contrast the claim using the given text. 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. [SEP] Justify:

Output: The text contrasts the claim by discussing the variability in earthquake nucleation depths and the observations related to different earthquakes. It states that 'our observation confirmed that large earthquakes nucleated at the base of the deepest portion of the seismogenic layer,' which suggests that earthquakes do not occur at a uniform depth, thereby rebutting the claim that all earthquakes occur at exactly the same depth.


Input: Task: pass the claim using the given text. 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. [SEP] Justify:

Output: The text provides a variety of references related to the antiviral properties of traditional medicinal plants, particularly in the context of COVID-19. However, it does not specifically address the derivation of these traditional medicines from plants used by indigenous cultures. Therefore, the text is not relevant to the claim.


Input: Task: corroborate the claim using the given text. 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. [SEP] Justify:

Output: The text corroborates the claim by discussing how applying large torsional perturbations to individual sidechains can generate large, coherent motions of structural elements in proteins, indicating that mechanical stress can lead to conformational changes. It specifically mentions that these conformational changes can have functional consequences, as certain residues can drive large-scale coherent conformational change, aligning with the assertion that mechanical stress induces such changes in protein structures.


Input: Task: contrast the claim using the given text. Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: ConclusionWe investigated the depth of the seismogenic layer based in D95, the cut-off depth at which 95% of the earthquakes occurred, for five actual cases, such as the 2003 Northern Miyagi, the 2004 Chuetsu, the 2008 Iwate-Miyagi, the 2016 Kumamoto, and the 2016 central Tottori earthquakes. D95 is computed from the relocated event catalog, containing only the background seismicity before the mainshocks occurred. Our results show that for all 5 cases, D95 is deeper or close to the main event depth, and envelops the deeper portion of aftershock distribution and main slip area. A simple modelling of the geothermal gradient based on surface heat flow shows that D95 sits at the crustal temperature of 250-450 ºC. Therefore, we concluded that D95 is a suitable parameter to show the bottom of seismogenic layer. And the crustal temperature of 250-450 ºC corresponds with seismogenic layer. We also witnessed that large earthquakes nucleated at the deepest portion of the seismogenic layer and that the large slip region occurred at shallower than the bottom of seismogenic layer. Some deep aftershocks of the 2016 Kumamoto earthquake, occurred at 5 km deeper than the bottom of seismogenic depth, are similar phenomenon observed in the 1992 M 7. 3 Landers earthquake. Abbreviations D95 Cut-off depth at which 95% of the earthquakes occurred D250deg, D300deg, D450deg Depth of the crustal temperature where it reaches 250 ˚C, 300 ˚C, and 450 ˚for Vp/Vs P-wave to S-wave velocity ratio DeclarationsEthics approval and consent to participate Not applicable. Consent for publication Not applicable. Availability of data and materials (We are planning to prepare the repository on NIED website or present them in the main paper as tables) Competing interests The authors declare that they have no competing interests. study received no specific grant from any funding agency. Contributions TEY conceived and planned the framework of the study and carried out the relocation, D95, and crustal temperature computations, and drafted the manuscript. MM adopted the result of Vp/Vs and Vp structure to the study and also help wrap up the study. [SEP] Justify:

Output: The text contrasts the claim by providing specific research findings about the varying depths at which earthquakes can occur. It mentions that for several studied cases, the depth of significant seismic activity (the cut-off depth or D95) is variable and that large earthquakes often nucleate at the deepest portion of the seismogenic layer, indicating a range of depths rather than all earthquakes occurring at the same depth.


Input: Task: corroborate the claim using the given text. Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: HomeBIJEthnobotany of medicinal plants used to treat malaria by traditional healers from ten indigenous colombian communities located in waupes medio Submit manuscript. . . eISSN: 2575-906X 167. DOI: 10. 15406/bij. 2017. 01. 00022 indigenous communities from possess knowledge in the use of plants to treat their illnesses. This knowledge has been transmitted orally from generation to generation. The present 3. 2billion people remain at risk of malaria. Annually, it produces between 149-303million clinical cases and kills more than 400,000 people. Among those killed, 90% are children under 5years old. 1 America, the transmission of paludism is found in nine countries sharing the amazon forest region and in 8 countries representing the Caribbean and Central America. 2 in 2016, 83 356 cases of malaria were reported to the Institute (INS) through the (Sivigila), and the distribution by species corresponded to 47 497 cases (57%) by P. falciparum, followed by P. vivax with 33 055 cases (39. 7%) and 2 804 cases (3. 3%) of mixed infections (P. falciparum and P. vivax). In addition, 19 deaths were confirmed because of this disease in Colombian territory. 3 These data show the importance of this disease in the panorama of morbidity and mortality at local and global level. Natural or vector borne infection in humans is by six species from the genus Plasmodium: P. falciparum, P. vivax, P. ovale, P. malariae, P. knowlesi,1 and recently P. cynomolgi. 4 This parasite is transmitted to humans by the bite of the Anopheles mosquito. Once inside the organism, the parasite causes clinical symptoms that can range from mild to grave, or even lead to fatal. 5,6 Traditional medicine uses plants to treat different illnesses, and their use is so efficient that the Organization (WHO) estimates that 80% of the world population uses plants as alternative therapy. 7 Since 1670, medical plants like Quina have been used to treat paludic feavers. It was not until 1820 that two French chemists, isolated a metabolite called quinina from this plant. [SEP] Justify:

Output: The text corroborates the claim by highlighting that indigenous communities possess valuable knowledge in the use of plants for treating illnesses, which has been passed down orally over generations. It specifically states that 'traditional medicine uses plants to treat different illnesses,' thus supporting the assertion that many traditional medicines are derived from plants that indigenous cultures have historically utilized.


Input: Task: corroborate the claim using the given text. Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: As molecular dynamics is generally accepted to accurately model the motion of proteins, the promise is that a long enough simulation will generate all the motions of a given protein structure. Unfortunately, current systems run too slowly to simulate all but the smallest motions. To overcome this computational limit, we have developed a molecular-dynamics perturbation method that induces large changes in a protein structure in very short simulation times. The changes correspond to large motions of specific structural elements on the surface of the protein that corroborate well with the canonical motions of several well-characterized proteins. This bodes well for our method to identify, for any given protein structure, structural elements on the surface that might bind drugs, regulate signals, undergo chemical modifications, or become unstructured. Citation: (2009) Probing the Flexibility of Changes in through Local Perturbations. PLoS 5(4): e1000343. of AmericaReceived: October 8, 2008; Accepted: February 27, 2009; Published: April 3, 2009Copyright: © 2009 Ho, Agard. This is an open-access 1. Structures with intermediate-scale motions. (A) (TIM) has a mobile loop that covers the active site (orange). The mobile loop has been crystallized in both an open [8tim] (green) and closed [1TPH] (blue) conformations. (B) (DHFR) pos-sesses the Met20-loop that has been crystallized in three different states - open [1RA2] (green), closed [1RX2] (blue) and occluded [1RX7] (purple). There is experimental evidence that the Met20-loop interacts with the adenosine-binding loop, the F–G loop and the G–H loop. (C) α-Lytic protease (αLP) [1SSX] is the control as it is a kinetically-stable protease (catalytic triad in orange) that does not possess any mobile loops. (D) Receptor (ER) has a highly mobile Helix-12 that covers the ligand (red) binding site. ER has been crystallized in a closed [1QKU] (blue) and open [1QKT] (green) conformation. [SEP] Justify:

Output: The text corroborates the claim by discussing a 'molecular-dynamics perturbation method that induces large changes in a protein structure in very short simulation times.' This indicates that mechanical or simulated stress is effectively causing conformational changes in proteins, as these changes correspond to significant motions in specific structural elements of proteins. The emphasis on the ability to identify structural elements that may bind drugs or undergo modifications also supports the idea that conformational changes are a critical aspect of protein behavior under stress.


Input: Task: contrast the claim using the given text. Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: TM provides available crustal heat flow data and compute crustal temperature of new results for 3 earthquake areas of, the northern Miyagi, the Chuetsu, and the Iwate-Miyagi earthquakes. TI provided local geology of 5 study areas and their insight relate to seismic activity. All authors read and approved the final manuscript. presented in this paper were printed using the Tools (GMT) software by Wessel and Smith (2009). 10. 1126/science. 1163113. Chapman DS (1986) Thermal gradients in the continental crust, in of the Crust, edited by J. B. Dawson et al. London 24:1986 Cristensen NI (1996) Poisson's ratio and crustal seismology, J 101:3139–3156. Das S, Scholz CH (1983) Why large earthquakes do not nucleate at shallow depths. bNature 305:621–623. Fowler CMR (2005) The solid Earth, 2nd ed. Press, 685 pp. Fukuyama, E. , S. Ishida, D. S. Dreger and H. Kawai (1998) Automated seismic moment tensor determination by using on-line broadband seismic waveforms, Zisin (J. Seismol. Soc. Jpn) Ser. 2, 51, 149-156 (in Japanese with English abstract). Hasegawa A. , Yamamoto A. , Umino N. , Miura S. , Horiuchi S. , Zhao D. , Sato H. (2000) Seismic activity and deformation process of the overriding plate in the northeastern Japan subduction zone. Tectonophysics 319:225–239. Hashimoto C, Matsu’ura M (2000) 3-D of Processes at Boundaries. pure 157:2125–2147. Honda. R. , Aoi, S. , Morikawa, N. , Sekiguchi, H. , Kunugi, T. , and Fujiwara, H. (2005) Ground motion and rupture process of the 2004 Prefecture earthquake obtained from strong motion data of K-NET and KiK-net. Space 57, 527-532. Ishii, T. , Y. Yanagisawa, S. Yamaguchi, A. Sangawa, and K. [SEP] Justify:

Output: The text contrasts the claim by discussing the variations in earthquake characteristics in different regions such as northern Miyagi and the Chuetsu area. It references studies that indicate differences in seismic activity and crustal temperature, suggesting that earthquakes do not all occur at the same depth, since their occurrence is related to local geological conditions and varying seismic processes.


Input: Task: pass the claim using the given text. Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: 56 hectares located within the town of Mitú, the Capital of the Department of Vaupés Medio, in the Vaupés Medio zone, was chosen as the study area (Figure 1). This area includes 10 indigenous communities with 1260 inhabitants distributed as demonstrated in Table 1. According to the Holdridge classification, this region is located within the Forest life system zone, between 185 to 205 meters above sea level, with an average temperature of 25. 7°C, 3000mm maximum annual rain fall, relative humidity is always above 80%, and the sun shines on average 1,255 hours annually. 15 Figure 1 Geographical location of the study area. of Inhabitants* Number and % of Vista del Tuy 85 0°43'25. 29'' N and 70°54'50" O 2 (6. 06) 2 57 0°50'24. 86" N and 70°56'47. 98" O 4 (12. 12) 6 105 0°48'11. 09'' N and 70°57'. 16. 20' O 9 (27. 27) 19 San José de Ñamú 186 0°55'44. 89'' N and 70°33'. 24. 80' O 2 (6. 06) 6 Yuruparí 240 0°51'56. 68'' N and 70°59'. 56. 68'' O 6 (18. 18) 13 de los Cerros 84 0°52'46. 24'' N and 70°43'18. 19'' O 2 (6. 06) 4 de Mandí 171 1°05'59. 17'' N and 70°43'10. 31'' O 2 (6. 06) 4 del Ti 127 0°48'05. 68'' N and 70°42'01. 97'' O 1 (3. 03) 0 de Lima 84 0°57'35. 61'' N and 70°4345,55'' O 1(3. 03) 1 Nazaret del Ti 121 0°51'24. 50'' N and 70°41'31. 46'' O 3 (9. 09) 2 Total 33(100) 57 Table 1 Geographical characteristics of the ten communities in the Middle Vaupes. *Data reported by Felipe Rodriguez, the indigenous president of the Association of () in 2010. Altitude (m. s. n. m): 180. [SEP] Justify:

Output: The text is irrelevant to the claim as it focuses on geographical and demographic details about the indigenous communities in the Vaupés Medio zone without mentioning anything related to traditional medicines or their derivation from plants used by these cultures.


Input: Task: corroborate the claim using the given text. Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: (E) The N-terminal domain of the chaperone HSP90 (HSP90) has a 23 amino acid lid [2IOR] (green) that undergoes a large conformational change to bind ADP [2IOQ] (blue). (RIP) Previous efforts to induce local perturbations used generic heat baths to apply the perturbation to an individual residue [33],[34]. While sufficient for inducing small-scale changes, we wished to explore applicability to larger perturbations. In our experience, the application of a high-temperature heat bath propagates most of the energy along the backbone, which invariably unfolds the backbone at the point of perturbation. In contrast, the Perturbation (RIP) circumvents the problem of the backbone unfolding by exclusively perturbing the χ angles, generating motions orthogonal to the backbone degrees of freedom. In the RIP method, the protein is first stripped of ligands and waters, energy minimized, and pre-equilibrated without constraints to 300 K over 10 ps using Amber with GB/SA implicit solvent [35]. To avoid having to modify the Amber source code, the actual RIP calculations are performed by running sets of constant energy 100 fs simulations, which allow the rotamer perturbations to develop, with no other restraints applied. Between each interval, the instantaneous rotational velocity is calculated for each χ angle of the residue being perturbed. The bond and bond angle vibrations are suppressed, and a pure χ rotational velocity of the desired magnitude is applied to the atomic velocities and then the next 100 fs interval begins. Because of the reduced degrees of freedom, imposing a sidechain rotamer kinetic energy of 300 K results in far greater rotational velocities than those in a standard 300 K MD simulation. The direction of rotation is maintained until it exceeds a limit of ±60° from the initial χ angle, upon which the direction of rotation is reversed. This limit restricts the sidechain to exploring the basin surrounding a single rotamer, and allows long sidechains such as MET to effectively explore the landscape of a single rotamer. The resultant motion is that of the sidechain rotating back-and-forth around the initial χ angle. If there are no collisions with other residues, no energy gets transferred. But if there is a collision, a large displacement may be induced in another part of the protein. [SEP] Justify:

Output: The text corroborates the claim by discussing how the application of perturbations can induce changes in protein structure. Specifically, it mentions that the RIP method generates motions orthogonal to the backbone degrees of freedom, indicating that mechanical stress applied to the χ angles can lead to conformational changes in the protein. Additionally, the text states that a collision can induce a 'large displacement' in another part of the protein, further supporting the idea that mechanical stress can impact the protein's conformation.


Input: Task: contrast the claim using the given text. Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: Matsuno (1982) Geology of the Matsushima district, with Map at 1:50,000, of Japan, 121 pp. (in Japanese with English abstract). (1990) of the of Seismicity in the Crust and to -Earthquakes. J 38:223–250. (1993) Cutoff depth of seismicity and la 379 rge earthquakes near active volcanoes in Japan. Tectonophysics 217:11–21. Agency (2021) The seismological bulletin of Japan. Accessed 30 Sep 2021 Kato, N. , Sato, H. , Imaizumi, T. , Ikeda, Y. , Okada, S. , Kagohara, K. , Kawanaka, T. , Kasahara, K. (2004) Seismic reflection profiling across the source fault of the 2003 earthquake (Mj 6. 4), NE Japan: basin inversion of Miocene back387 arc rift, Space, 56, 1369-1374. Kato, N. , Sato, H. and Umino, N. (2006) Fault reactivation and active tectonics on the fore-arc side of the back-arc rift system, NE Japan. J Struct Geol, 28, 2011-2022. Kimura, H. , Okamura, Y. (2009) Construction of a fault model based on 3-dimensional structure of fault-related folds in the source area of the 2003 earthquake (Mj = 6. 4) in NE Japan, on 9, 65-78. (1976) A relationship between the distribution of focal depth of micro395 earthquakes and surface heat flow in the southwestern Japan and central Japan. Proc. Symp. Research, 184-193, Natl. Comm. Geophys. Seismol. Soc. , Jpn. , (in Japanese with English abstract) Kubo, H. , Suzuki, W. , Aoi, S. (2016). Source rupture processes of the 2016 Kumamoto, Japan, earthquakes estimated from strong-motion waveforms. Space 68, 161. Kubo, H. , Suzuki, W. , Aoi, S. (2017) Source rupture process of the 2016 central Tottori, Japan, earthquake (M JMA 6. 6) inferred from strong motion waveforms. Space 69, 127. [SEP] Justify:

Output: The text contrasts the claim by discussing various studies related to seismicity, fault models, and the relationship between earthquake characteristics and geological factors. By highlighting different research papers and findings, the text implies that earthquakes do not uniformly occur at the same depth, contradicting the claim.


Input: Task: pass the claim using the given text. Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: The rainy season is between March and July, with monthly precipitations that oscillate between 250 and 300 mm. The least rainy period occurs between August and October and is called “Indian summer or time of the worm”. The dry period occurs between November and February. The indigenous communities studied can be found between tributaries of the creeks Ti and Tui on the shores of the Vaupés river, known specifically as the Vaupés Medio. In this region located between Pucarón and Yacayacá, there are 22 indigenous communities with approximately 2684 inhabitants, belonging mostly to the ethnic groups: and Tukano. Additionally, there are small populations of ethnic groups representing the Siriano, Yurutí, Barazano, Makuna, Pisamira, Taiwano, and Desanos peoples, as well as non-indigenous people, all members of the Association of Vaupés Medio (). The majority of these ethnic groups are not found within their ancestral territories, displaced from other Amazonian territories due to the phenomenon of rubber harvesting (Felipe Rodriguez, Personal communication, 2006. ). The indigenous economy in this zone is subsistence, coming from agricultural activities known as “chagras” or small plantations, fishing, hunting and collection of wild species. 16 Ethics Initially, the researchers informed the community of the objectives and expectations of the study and invited the traditional healers to participate. The key informants who offered to participate read the informed consent, if they could not read; it was translated to Cubeo and read to them. The translator is the first author of this work, is indigenous Cubeo and is knowledgeable of some dialects spoken in the zone. Subsequently, the informed consent was signed and in the case of those who did not know how to sign, their finger print was used. The informed consent had the approval of the from the Institute within the of the University of Antioquia. Coordination with the community At the 2007 congress of the indigenous organization of Vaupés Medio, the first contact with the communities in this zone was made. Attending were approximately 70 people, among them leaders and inhabitants from the community, permitting a space for discussion and knowledge sharing. Additionally, consent for the collection of information for the study was obtained. During this event the study design and proposal was presented to traditional authorities. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the geography, climate, and the socio-economic aspects of indigenous communities in the Vaupés region without providing any information about traditional medicines or their plant origins. It primarily focuses on community interactions and the ethical considerations of the research conducted with these communities, without addressing anything related to medicinal plants or their use.


Input: Task: corroborate the claim using the given text. Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: As an example, applying RIP to Glu128, a residue located near the mobile loop of TIM, results in a Cα RMSD deformation response with one large peak at residue 175 (Figure 3A). By overlaying the 10th ps conformation of the RIP simulation over the crystal structures (Figure 3B), it can be seen that the peak of large conformational change at residue 175 corresponds to the ligand-binding loop at residues 167–177. There is also a displacement of the helix near Glu128. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 3. RIP-induced conformation changes of TIM. (A) the Cα RMSD response to the perturbation of RIP on Glu128 (red arrow) shown after 2 ps (blue) and at the end of the 10 ps simulation (green). (B) The 10th ps conformation (red) of the TIM structure due to RIP on Glu128 (red spheres), overlaid over the closed state (blue) and open state (green) of the crystal structures. (C) The frequency distribution of Cα RMSD for all residues from the entire set of perturbations of RIP over every residue in TIM. global map of deformability in TIM can be constructed by applying RIP to every residue along the entire length of the protein. Each column in the RIP deformation map represents the 10 ps Cα RMSD response to a perturbation of RIP on the residue with sequential numbering on the X-axis (Figure 4A). To facilitate visualization, the actual response is shown on the map only if the responding residue is perturbed by more than a defined threshold. The threshold was chosen by analyzing the probability distribution (Figure 3C) of the Cα RMSD responses in the set of RIP simulations applied to every residue in TIM. This distribution has an average of 1. 5Å, a σ of 1. 2 Å. The peak of Cα RMSD at 0. 8 Å corresponds to the residual motion from the initial pre-equilibration of 300 K. Using a cutoff of 6Å (mean+3. 75σ) results in a sparse global map consisting of mostly contiguous segments of deformation (Figure 4A). Lower thresholds result in noisier maps, showing many single-residue deformations. [SEP] Justify:

Output: The text corroborates the claim by providing a specific example of how applying RIP (a form of mechanical stress) to Glu128 induces conformational changes in the TIM protein structure. It describes the Cα RMSD deformation response and illustrates that certain residues, including residue 175, experience significant conformational changes due to mechanical perturbations, thereby supporting the assertion that mechanical stress can lead to alterations in protein conformations.


Input: Task: contrast the claim using the given text. Claim: All earthquakes occur at exactly the same depth beneath the Earth’s surface. [SEP] Text: Stein CA (1995) Heat flow of the Earth. In: “Physics, A Handbook of Physical Constants,” T. J. Ahre. Am. Geophys. Union, pp 144–158 Suzuki, W. , Aoi, S. , Sekiguchi, H. (2010) of the 2008 Iwate–Miyagi Nairiku, Japan, from Near-Source Strong-Motion Records. Bulletin of the of America 100 (1): 256–266. doi: Takemura, M (2005) Re-evaluation of Magnitude and of the 1900 in Japan :Comparison with the 1962 and the 2003 Events, Jishin. Vol 58, Num 1, pp 41-53. (2004) Geothermal gradient and heat flow data in and around Japan (II): Crustal thermal structure and its relationship to seismogenic layer. Earth, 56:1195–1199. (2009) Structure : One of Depth of Earthquakes. Zisin 61:239–245. Japanese with English abstract). Tanaka A, (2002) Temperature distribution and focal depth in the crust of the northeastern Japan. Earth, 54:1109–1113. Tanaka A, (2005) Crustal thermal regime inferred from magnetic anomaly data and its relationship to seismogenic layer thickness: islands case study. 152:257–266. Turcotte DL, (1982) Geodynamics applications of coninuum physics to gelogic problems. and Sons. Ukawa M, Ishida M, Matsumura 508 S, (1984) Hypocenter determination method of the Kanto-Tokai observational network for microeathquakes. . 53:1–88. Umino, N. , Okada, T. , Nakajima, J. , Hori, S. , Kono, T. , Nakayama, T. , Uchida, N. , Shimizu, J. , Suganomata, J. , Gamage, S. S. N. , Hasegawa, A. , Asano, Y. (2003) Hypocenter and focal mechanism distributions of aftershocks of July 26 2003 M6. 4 northern Miyagi, NE Japan, earthquake revealed by temporary seismic observation, Space, 55, 719-730. [SEP] Justify:

Output: The text contrasts the claim by discussing various studies and findings related to earthquake depth, suggesting that earthquake depths are not uniform but vary based on specific conditions and regions, particularly in Japan. This is inferred from phrases such as 'structure: One of Depth of Earthquakes,' which indicates variability in depths.


Input: Task: pass the claim using the given text. Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: Campuzano-Zuluaga G, Alvarez-Sánchez G, Escobar-Gallo GE, et al. Design of malaria diagnostic criteria for the Sysmex XE-2100 hematology analyzer. Hyg. 2010;82(3):402‒411. Bermúdez ázquez D. La investigación etnobotánica sobre plantas medicinales: una revisión de sus objetivos y enfoques actuales. Interciencia. 2005;30(8):453‒459. Rieckmann KH, Antuñano FJL. Chloroquine resistance of Plasmodium falciparum in Brazil detected by a simple in vitro method. Health Organ. 1971;45(2):157‒167. Tang W, Eisenbrand G. Chinese drugs of plant origin. Chemistry, pharmacology, and use in traditional and modern medicine. Springer-Verlag. 1992. . Qinghaosu. The Lancet. 1993;341(8845):603‒608. Gentry AH. Tree species richness of upper Amazonian forests. . 1988;85(1):156‒159. Gari J. Biodiversity and indigenous agroecology in Amazonia: The indigenous people of Pastaza. Etnoecologica. 2001;5(7):21‒37. Guevara Garzón J. En busca de un modelo de salud para los pueblos indígenas. La experiencia del Vaupés. Mitú: de salud del Vaupés, Ministerio de salud. 1998. Bodnar Y. Pueblos indígenas de Colombia: apuntes sobre la diversidad cultural y la información sociodemográfica disponible. afrodescendientes de América Latina y el Caribe: información sociodemográfica para políticas y programas. 2006. p. 135‒154. IGAC. Instituto Geográfico Agustín Codazzi. Diccionario geográfico de Colombia, Colombia; 1996. Correa F. [SEP] Justify:

Output: The text provides a list of references and citations related to various studies and topics, but it does not provide any information about traditional medicines being derived from plants used by indigenous cultures. Therefore, it is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 4. The global Cα RMSD response of TIM to RIP. (A) Each column corresponds to the perturbation of the residue marked by the X-value. Intensity represents Cα RMSD deviation for the 10th ps of simulation above background (>6. 0 Å). (B) Perturbation strength histogram and structural linchpins. Structural linchpins are defined if the number of residues with Cα RMSD >6Å induced by a residue is greater than 3σ above the mean. The structural linchpins are mapped onto the structure as sticks. Scale is 0 (white) to 30+ (red). (C) Conversely, local regions that are highly susceptible to perturbation can be identified via a local flexibility histogram and mapped onto the structure. Scale is 0 (white) to 15+ (red). first point to note is that there is no systematic response along the diagonal in the RIP deformation map. Residues adjacent to the perturbed residue are not automatically disturbed. This demonstrates the key property of the RIP method: perturbing a sidechain does not systematically disturb the local backbone, unless there is a specific interaction of the perturbed sidechain to the backbone. Consequently, if deformations are observed then they can be directly attributed to the perturbing sidechain. As is evident from the deformation map, perturbing some residues can induce large changes in the protein while others have virtually no effect. The magnitude of the perturbation inducible by a particular residue can be quantitated by counting the number of residues that respond significantly to the perturbation (above the 6Å threshold). Residues capable of inducing significant perturbations will be referred to as structural linchpins (Figure 4B). While structural linchpins are generally larger amino acids, some smaller amino acids also show up. Another way of extracting useful information from the RIP deformation map is to quantify the susceptibility of each residue to local perturbation (Figure 4C) by summing the number of above-threshold deformations horizontally across the deformation map (Figure 4A). Unlike the perturbation strength defined above, this local flexibility is a global property based on the entire set of perturbations along the protein chain. [SEP] Justify:

Output: The text corroborates the claim by discussing how perturbing certain residues in a protein can induce significant deformations and conformational changes, which supports the assertion that mechanical stress can cause changes in protein structure. The reference to residues capable of inducing significant perturbations and the definition of structural linchpins shows a direct relationship to the claim about mechanical stress and conformational changes.


Input: Task: contrast the claim using the given text. Claim: Seismic waves can travel through space. [SEP] Text: g. Aki et al. , 1977). Models obtained with this technique using regional arrays are typically confined to the upper mantle. For the Alpnetwork the lower bound is around 600 km depth. Assuming a spherical chunk with a lateral extension similar to that of the seismic array (up to ∼10∘), below this depth only about one-fourth of the horizontal area spanned by this chunk is penetrated by intersecting rays, leading to smearing of anomalies along the rays within the remaining area (e. g. Sandoval et al. , 2004). Lateral resolution is limited by the station spacing of the array. The method is mainly sensitive to volumetric perturbations of seismic velocity and does not give constraints on the location of internal discontinuities. It has been used in many studies on mantle structure, for example Koulakov et al. (2002), Lippitsch et al. (2003), and Piromallo and Morelli (2003). A method which reaches beyond teleseismic tomography is full waveform inversion (FWI), where entire or partial waveforms are inverted for velocity and also density perturbations (e. g. Mora, 1987; Tromp et al. , 2005; Fichtner et al. , 2009; Zhu et al. , 2012, 2015; Butzer et al. , 2013; Schumacher et al. , 2016). Predictions of waveforms for given velocity models are obtained by full 3D numerical forward modelling, making the method very expensive with regard to storage requirements and computation time. When applied to teleseismic body waves, hybrid approaches are invoked to make the method numerically tractable (e. g. Monteiller et al. , 2013; Tong et al. , 2014a, b): full 3D forward modelling is only done in a regional box below the array while wave propagation from the distant earthquake to this box is done by less expensive methods which, however, assume laterally homogeneous or axially symmetric earth structure. One basic preparatory step for both methods is the determination of travel times. While the need for travel times is obvious for travel-time tomography, teleseismic full waveform inversion can also benefit from travel times in two different ways. First of all, FWI requires a good (ideally 3-D) starting model to ensure that the inversion converges to the global minimum. [SEP] Justify:

Output: The text contrasts with the claim by discussing the limitations of seismic wave modeling and the fact that it primarily focuses on the Earth's interior. Statements like 'the method is mainly sensitive to volumetric perturbations of seismic velocity' imply that seismic waves are concerned with geological structures rather than traveling through the vacuum of space, thus contradicting the claim.


Input: Task: pass the claim using the given text. Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: 1993;31(4):255‒258. Antiprotozoal activities of Colombian plants. J Ethnopharmacol. 2001;78(2‒3):193‒200. Oga S, Sertié JA, Brasile AC, et al. Antiinflammatory effect of crude extract from Guarea guidonia. Planta Med. 1981;42(3):310‒312. . Analysis of the from Leaves of Specimens of Guarea guidonia (L. ) Sleumer (Meliaceae). Journal of Research. 2005;17(3):271‒273. . Terpenoids from Guarea guidonia. Phytochemistry. 2002;60(4):333‒338. . 16,17-Seco- and 2,3:16,17-di-Seco-pregnanes from Guarea guidonia. J Soc. 2008;19(6):1073‒1077. LC-ESI-MS determination of quassinoids isobrucein B and neosergeolide in Picrolemma sprucei stem infusions. J Soc. 2009;20(6):1065‒1070. de Andrade- In vitro inhibition of Plasmodium falciparum by substances isolated from Amazonian antimalarial plants. Oswaldo Cruz. 2007;102(3):359‒365. Biological activity of neosergeolide and isobrucein B (and two semi-synthetic derivatives) isolated from the Amazonian medicinal plant Picrolemma sprucei (Simaroubaceae). Oswaldo Cruz. 2009;104(1):48‒56. Struwe L, Albert VA. A monograph of Neotropical potalia aublet (Gentianaceae: Potalieae). Systematic botany. 2004;29(3):670‒701. Duke J, R Vasquez. Dictionary. FL: 1994. Roumy V, Garcia-Pizango G, Gutierrez-Choquevilca AL, et al. Amazonian plants from Peru used by Quechua and Mestizo to treat malaria with evaluation of their activity. J Ethnopharmacol. 2007;112(3):482‒489. Gentry AH. Bignoniaceae, in Flora de Colombia, IdC Naturales. [SEP] Justify:

Output: The text is largely a list of scientific publications and studies concerning the properties and activities of various plants, specifically relating to their medicinal uses. However, it does not explicitly discuss the derivation of traditional medicines from plants used by indigenous cultures, therefore making it irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: In TIM, there are two segments with significant local flexibility (Figure 4C). One of the segments of large local flexibility corresponds to a striking horizontal band of deformations at residue 75 in the deformation map (Figure 4A). This segment corresponds to the dimer-interface loop. As deformation of the dimer-interface loop occurs independently of the location of the applied perturbation, a reasonable interpretation is that the dimer-interface loop is an intrinsically mobile loop in the monomer state. In contrast, there is a scattered band of flexibility in the segment corresponding to the ligand-binding loop at residue 175. Flexibility in the ligand-binding loop is induced only by the cluster of structural residues that surround it (Figure 4B). This can be interpreted as the ligand-binding loop being conditionally flexible, i. e. , large fluctuations of neighboring residues can readily displace the mobile loop. To illustrate the range of motion induced by the RIP method in the mobile loop of TIM, the entire ensemble of the final conformations of each perturbation is shown (Figure 5A). The range of motion generated by RIP is far greater than the differences between the open and closed conformations of the mobile loop found in the crystal structures (Figure 1A). Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 5. Ensemble of the last conformation of the trajectories of perturbations induced by RIP for (A) TIM, (B) DHFR, (C) αLP, (D) ER, (E) HSP90. Red corresponds to an RMSD deviation of 15 Å or more. These ensembles are used to generate the flexibility histograms. in (DHFR) catalyzes the reduction of dihydrofolate by NADP. The protein binds both ligands through the Met20 loop. Crystallography of the enzyme with different ligands has defined three states for the Met20 loop (Figure 1B) suggesting that loop dynamics may be functionally important: i) a closed state where the Met20 loop covers both dihydrofolate and NADP; ii) an occluded state where the Met20 loop packs against the dihdyrofolate but blocks NADP; and iii) an open state where the loop may be disordered in solution (Sawaya and Kraut 1997). [SEP] Justify:

Output: The text corroborates the claim by discussing how mechanical perturbations lead to significant local flexibility and motion in protein structures, particularly in the dimer-interface loop of the TIM protein. It describes how the deformation of this loop occurs independently of the applied perturbation location, indicating that mechanical stress can induce conformational changes.


Input: Task: contrast the claim using the given text. Claim: Seismic waves can travel through space. [SEP] Text: In contrast to that, travel-time uncertainty increases above the highly complex structures in the Alpine arc where the P wave fronts are significantly altered by the strongly heterogeneous subsurface. This decreases their correlation with the waveforms on other stations of the array and to the stacked reference trace. It is also likely that uncertainty increases due to local site effects which can be significant in narrow valleys where anthropogenic activities such as traffic are harder to evade. These influences should be visible on single stations which show a high daytime noise level. We expect those effects to be present equally in both the high- and the low-frequency dataset. However, most of the station outliers we see in one dataset are not present in the other. Figure 7Maps of the median uncertainty of all picks for the high-frequency (a) and the low-frequency (b) dataset. Symbol sizes correlate with number of picks per station, colour shows the average travel-time uncertainty and symbol shapes indicate the average pick class on each station. Inset shows OBS stations only with symbol size increased by a factor of 2. 5. Travel-time uncertainty gets higher for db0. 5 in areas strongly influenced by deep subsurface structures, e. g. orogenic roots as well as strong heterogeneities close to the surface. Coverage in terms of measurement duration is best in the northern Alpine foreland, central Alps and Apennines. Complementary experiments are salient, as their measuring duration (i. e. number of total picks) is limited in contrast to other stations. The EASI experiment can be seen as a straight line of smaller-sized symbols on a north–south-directed profile, spatially (but with no overlap in time) cutting through the SWATH-D experiment in the central Alps above the Tauern Window. The latter has a higher station density compared to the rest of the array. Ocean bottom seismometers are characterised by a lower number of picks (smaller symbol size) as well as by a higher average uncertainty as a consequence of their noisy measuring environment. travel-time uncertainty distribution pattern of the lower-frequency dataset db0. 1 (Fig. 7b) shows a shape comparable to the high-frequency one with the lowest uncertainty in the northeastern parts of the array. However, overall uncertainty is higher, and the contrast between regions of high and low uncertainty is decreased. [SEP] Justify:

Output: The text contrasts with the claim by discussing the complexities of seismic wave propagation specifically within terrestrial environments, such as the Alpine arc, and how travel-time uncertainty increases due to various geological factors. The reference to travel-time uncertainty and local site effects suggests that there are limitations to how seismic waves can be accurately measured or modeled in certain conditions, indicating that their behavior is not straightforward and may not support the notion of traveling through space.


Input: Task: pass the claim using the given text. Claim: Many traditional medicines are derived from plants used by indigenous cultures. [SEP] Text: In: Forero E, Betancur J, editors. de Colombia, Bogotá DC, Colombia; 2009. p. 1‒462. . de la Amazonía Peruana. Perú: Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Peru; 1997. Cayón E, Aristizabal S. Etnobotánica Chamí. Cespedesia. 1980;9(33‒34):5‒114. Roig JT. Plantas medicinales de y su folclore. UC Rica, editor. San José, Costa Rica, 1988. p. 103‒104. Ayensu ES. of the West Indies. Algonac, Michigan, USA; 1981. p. 282. Díaz JL. Usos de las plantas medicinales de México. éxico; 1977. p. 345. Morton JF. Atlas of of Middle America: Bahamas to Yucatan. Thomas CC, 1980. p. 1448. Escobar N. Flora Tóxica de Panamá. U. Panamá, Panama. 1972. Figueroa H. Enfermedades de los conquistadores. Ibarra JdP, Antigua, Guatemala. 1983. Guzmán DJ. Especies útiles de la flora Salvadoreña. Md Educación, San Salvador, El Salvador. 1975. Barrett B. of Nicaragua’s Atlantic Coast. Economic Botany. 1994;48(1):8‒20. Agarwal K, Popli S. The constituents of Crescentia cujete leaves. Fitoterapia 1992;63(5):476. of the Popoluca, Mexico: A botanical systematical perspective. Economic Botany. 2003;57(2):218‒230. Isolation of cytotoxic metabolites from targeted peruvian amazonian medicinal plants. J Nat Prod. 2008;71(1):102‒105. . Leishmanicidal and trypanocidal activities of Bolivian medicinal plants. J Ethnopharmacol. 1994;41(1‒2):19‒37. Menachery MD. 1996. p. 269‒302. Boster JS. [SEP] Justify:

Output: The text does not offer any specific information or evidence that relates to the claim regarding traditional medicines derived from indigenous plant use. Instead, it consists largely of citations and references to various works related to plants and medicinal uses without directly addressing the claim.


Input: Task: corroborate the claim using the given text. Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: Using the RIP analysis, the results of the perturbations can be used to generate a RIP deformation map of DHFR (Figure 6A). From this map, potential structural linchpins can be identified (Figure 6B), and the local flexibility calculated (Figure 6C). The RIP deformation map displays many regions of large conformational changes, dispersed in sequence space. Regions of significant local flexibility (Figure 6C) map to the Met20 loop, the adenosine-binding loop, the F–G loop, and the G–H loop. Experiments suggests that all these loops couple to the activity of the Met20 loop [37],[38]. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 6. RIP perturbations of (DHFR). (A) RIP deformation map. (B) Structural linchpins and perturbation strength histogram. (C) Local flexibility mapped on structure and in histogram. Colors are as in Figure 4. Stability of α-α-Lytic protease (αLP) (Figure 1C) is a kinetically stable protein shown by experiment to be highly resistant to unfolding [39] and to have extraordinarily high hydrogen-exchange protection factors (>1010) throughout its large hydrophobic core. The reduced dynamics and absence of mobile segments is believed to be functionally important for minimizing proteolytic destruction [40]. Reflecting these properties, αLP is also found to be extremely stable in standard MD calculations [33], where loops separating secondary structural elements appear to be firmly held by interaction with the body of the protein. This provides a good test for the RIP method, as any large-scale predictions of flexibility would likely be erroneous. In agreement with the known dynamics of αLP, the deformation map for αLP (Figure 7) is remarkably empty; there are only scattered segments of limited deformation, indicating that αLP is particularly insensitive to single residue perturbations and thus, conformationally very stable. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 7. RIP perturbations of α-lytic Protease (αLP). (A) RIP deformation map. (B) Structural linchpins and perturbation strength histogram. (C) Local flexibility mapped on structure and in histogram. Colors are as in Figure 4. [SEP] Justify:

Output: The text corroborates the claim by describing the RIP deformation map and highlighting the presence of large conformational changes in specific protein loops, such as the Met20 loop and others. It notes that these regions of significant local flexibility are indicative of how mechanical perturbations could impact protein structures, thereby supporting the assertion that mechanical stress can induce such conformational changes.


Input: Task: contrast the claim using the given text. Claim: Seismic waves can travel through space. [SEP] Text: These distortions are shifted to the NE for the waves arriving from the SSW in Fig. e. The associated residuals exhibit large-scale coherent patterns of negative and positive residuals but are again different in various regions. For example, residuals are generally positive in southeastern France for the waves arriving from SSW while they are normal to negative for the event from WNW. This is again an indication of heterogeneous mantle structure to be resolved by tomography later. 5. 2 Stacked residuals Although travel-time residuals differ with epicentral distance and event back-azimuth as waves move through high- or low-velocity zones from different angles before reaching the surface, there are certain features which tend to occur for a large number of events. The most prominent ones are the negative residuals along the Apenninic and Alpine chain. We stacked residuals for all analysed events to identify regions of stable negative or positive travel-time residuals. It is important to understand that after stacking of the demeaned travel-time residuals, the resulting residuals are relative to an unknown one-dimensional earth model defined by all events used for stacking and not to the standard earth model used to calculate travel-time differences in the first place (e. g. Aki et al. , 1977). Hence, negative or positive residuals indicate higher or lower velocities, respectively, relative to this average model and not relative to a standard earth model. Figure 10Stacked travel-time differences for 370 events of the high-frequency dataset db0. 5 corrected for crustal influences. Circle sizes correlate with number of back-azimuth bins for each station (maximum=12). Blue colours point to subsurface structures with vp values higher than average, red colours to structures with vp values lower than average. Travel times are binned calculating the mean travel time for all events within 30∘ bins to balance out directional influences. Standard deviation of the azimuthal influence on each station is marked by crosses; e. g. small crosses mark stations residuals mostly independent of variations in back-azimuth. A travel-time correction is applied for the station elevation using a constant near-surface velocity estimate of 5. 5 km s−1. [SEP] Justify:

Output: The text contrasts the claim because it discusses travel-time residuals of seismic waves as they move through the Earth's crust and mantle. It emphasizes that seismic waves are affected by geological structures and travel at specific velocities within the Earth, indicating that they do not propagate through the vacuum of space as the claim suggests.


Input: Task: pass the claim using the given text. Claim: Curcumin, found in turmeric, has anti-inflammatory properties. [SEP] Text: Plant material, processing and extraction processturmeric (LKD) rhizomes were collected from the Lakadong region in Meghalaya, India (Location: 25° 11′ 0" North, 92° 17′ 0" East). The plant material was authenticated at the of India, Shillong, Meghalaya (India) and a voucher specimen (Specimen number. GIPS/2018/003) was preserved for future reference at the of. The rhizomes were cleaned, dried, and ground into coarse powder. The homogeneous powdered material (1 kg) was subjected to successive extraction for 72 h using solvents (2. 5 L) of increasing polarity (hexane, chloroform, ethyl acetate, and methanol) in a Soxhlet apparatus. The extracts obtained were filtered, concentrated using reduced pressure and labeled as hexane extract (LKDHE), chloroform extract (LKDCH), ethyl acetate extract (LKDEA), and methanol extract (LKDME). Residual solvents in extracts by gas chromatographyThe collected extracts were analyzed for residual solvent content using (GC) with a Headspace system (Clarus 690 Perkin Elmer). The injection Volume sampling rate was maintained at 12,50000pts/s with initial oven temperature at 40̊ C for 2 min followed by GC run (Ramp 1 at 5. 0 deg/min to 100 deg/min hold for 1 min and Ramp 2 10. 0 deg/min to 150 deg/min with hold time of 0. 00 min), offset at 100 µV. Extract samples were placed in vials, and the GC run was executed following the specified procedure (Fig. 1). The outcomes are displayed in Additional file 1: Fig. S1. Fig. 1Phytochemical evaluation of LKD extracts and characterization of curcumin. [SEP] Justify:

Output: The text provides detailed information about the processing and extraction methods of turmeric rhizomes but does not mention or address the anti-inflammatory properties of curcumin. Therefore, it is irrelevant to the claim regarding the health benefits of curcumin.


Input: Task: corroborate the claim using the given text. Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: Motion of Helix-12 of the Receptor belongs to a family of nuclear receptors that are ligand-inducible transcription factors [15]. The ligand binds in a hydrophobic pocket in the ligand-binding domain of the (ER) that is covered by Helix-12, so that in the bound state the ligand is completely buried. Not only does Helix-12 need to be displaced for ligand entry and exit, but it is also the key allosteric transducer. Crystal structures of ER with bound agonists and antagonists (Figure 1D) reveal that Helix-12 responds to the bound ligand by occupying one of several conformations that serve to either support or block binding of the downstream transcriptional co-activator protein [16]. Clearly, Helix-12 is a functionally-critical mobile segment of the protein although there is no information about the timescale of its motion. The RIP deformation map of ER (Figure 8A) calculated in the absence of ligand, shows a very limited set of responding distortions with the exception of a horizontal band at residue 162. The horizontal band corresponds to a short loop between the α-helices (Figure 8C). Apart from a large conformational change of a long segment at the C-terminus (residues 232–250), ER appears to be very stable. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 8. RIP perturbations of (ER). (A) RIP deformation map. (B) Structural linchpins and perturbation strength histogram. (C) Local flexibility mapped on structure and in histogram. Colors are as in Figure 4. large conformational change in the C-terminus is induced by Trp83, which is the only residue that would qualify as a structural linchpin (Figure 8B). Trp83 has been found to be a highly conserved residue in the nuclear receptor family with the greatest change in the solvent accessible surface area between the apo and holo structures [41], indicating a possible key role in binding Helix-12. The conformation induced by RIP on Trp83 reveals a dramatic cooperative motion in Helix-12, where the α-helix remains intact but moves by 13 Å (red in Figure 9). [SEP] Justify:

Output: The text supports the claim by detailing how Helix-12 of the nuclear receptor ER responds to ligand binding, indicating that its motion is critical for functionality. It discusses how 'the conformation induced by RIP on Trp83 reveals a dramatic cooperative motion in Helix-12,' suggesting that not only is there movement in the protein structure, but that this motion is induced by the binding process, consistent with the claim that mechanical stress can lead to conformational changes.


Input: Task: contrast the claim using the given text. Claim: Seismic waves can travel through space. [SEP] Text: , 2008), which was compiled for the correction of crustal influences on seismic studies that analyse deeper structures such as a teleseismic tomography. The layer model contains information on sediment thickness and upper and lower crustal average velocity and thickness (and thus Moho depth) discretised on a 15′×15′ regular grid. It was created from various seismic reflection, refraction and receiver function studies. For the Alpine region, we improve information on the Moho depth using a more recent study of Spada et al. (2013). Lastly, for the western and central Alpine region, we replace this model with the more detailed, fully 3D regional tomographic model of Diehl et al. (2009a, hereafter referred to as D09a). We use the information on the model resolution supplied to us by D09a to assess which model to favour at a certain point in space. To only account for crustal influences in our dataset, we remove velocity perturbations associated with the uppermost mantle below the suggested Moho proxy by D09a of 7. 25 km s−1. The resulting travel-time differences (calculated by assuming a planar, vertically incident wave front passing through the crust) between our crustal 3-D model and the crustal minimum 1D model of D09a can be found in Fig. A2 in the 7. 5∘ E to 46∘ N, 14. 5∘ E (Fig. ). For later reference and interpretation, we group these residuals into three major anomalies: a western negative anomaly (W) following the Alpine mountain chain to the east and bending south towards the Po plain, which can be clearly discerned from a large zone of positive residuals to the west; a central negative anomaly (C) attached to anomaly W in the south but following a very different strike; and an eastern anomaly (E) bending circularly to the south towards the Dinarides, whose separation from anomaly C an be recognised by virtue of the travel-time residuals observed on the very dense SWATH-D array (inset in Fig. ). In addition, we define anomaly A located at the western Italian coast and penetrating into central Italy with a strike of 130∘. 5. 3 Azimuthal dependence We already showed travel-time residuals for individual wave fields. [SEP] Justify:

Output: The text contrasts the claim by discussing seismic studies and models focused on crustal structures rather than addressing the ability of seismic waves to travel through space. It emphasizes crustal influences and travel-time differences within the Earth without mentioning their behavior in the vacuum of space, suggesting a limitation to terrestrial conditions rather than an affirmation of the claim.


Input: Task: pass the claim using the given text. Claim: Curcumin, found in turmeric, has anti-inflammatory properties. [SEP] Text: A: TLC chromatogram of LKD successive extracts; B, C, D: HPTLC fingerprinting of isolated curcumin from fingerprinting of purified LKD curcumin F MS spectra G 1H NMR of purified LKD curcumin H 13C NMR of purified LKD curcuminFull size imagePhysical evaluations and phytochemical studies of the LKD successive extractsPhysical properties of the LKD successive extractsVarious physical parameters were evaluated on the extracts including testing for organoleptic characters, nature of the extract, percentage yield; pH and solubility testing were determined [13]. Phytochemical evaluations and analytical process of curcumin from LKDPreliminary phytochemical screening, thin layer chromatography and quantification of total phenolic contentPhytochemical screening of the LKD successive extracts was conducted to identify various classes of phytochemicals [14]. Prominent phytochemical classes that produced positive test results underwent further verification using Thin-(TLC) methods. For extracts abundant in curcuminoids, TLC analysis was executed following established protocols [15]. The procedure encompassed preparing sample extracts for analysis, selecting the stationary phase, optimizing the mobile phase, developing the chromatogram, and spotting detection, all in accordance with established guidelines. The stationary phase for TLC employed pre-coated silica gel 60 F254 aluminum sheets (Merck Ltd. ), while the mobile phase was composed of a mixture of chloroform and methanol in a 9:1 ratio. Subsequently, the TLC plates were observed using short UV light (264 nm), long UV light (366 nm), and visible light, both before and after applying the detecting reagent. Furthermore, the optimization of High-Performance Thin-(HPTLC) fingerprinting and the analysis of the curcumin-rich crude fraction after isolation via column chromatography were performed using equipment, which included the sample applicator, visualizer, and 4 software. Furthermore, based on the results of the preliminary phytochemical screening and TLC analysis, further studies were conducted for the total phenolic and tannin content estimation using a UV–Visible spectrophotometer (Shimadzu-AA6300). The total phenolic content and total tannin content were determined using the Folin-Ciocalteu method with certain modifications [16]. [SEP] Justify:

Output: The text is mainly focused on the analytical methods and procedures for evaluating curcumin extracts, such as TLC and HPTLC fingerprinting, and does not provide information about the anti-inflammatory properties of curcumin. Therefore, the text is irrelevant to the claim regarding curcumin's anti-inflammatory effects.


Input: Task: corroborate the claim using the given text. Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: Although it doesn't move to the same location found in the crystal structure (green in Figure 9), perhaps due to the short simulation, we do see a hinge motion about the same pivot point (blue and green in Figure 9) observed in the crystal structures. Notably, this conformational change does not result in a significant distortion along Helix-12. The ability to generate this kind of large cooperative motion is due in part to the removal of the ligand normally found in the crystal structure for the simulations. In the absence of ligand, Helix-12 covers a cavity and is only weakly bound to the body of the protein. Thus the collisions generated by the perturbation on Trp83 are sufficient to induce the entire helix to move cooperatively. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 9. Conformational change in Helix-12 of the ligand-binding domain. (A) Overlay of the crystal structures showing Helix-12 in the closed conformation (blue) and the open conformation (green), which indicates the pivot point between the two structures. In the RIP simulations, perturbation on Trp-83 (red spheres) induces a large conformational change in Helix-12 (red), from the starting conformation of the closed structure (blue), where the hinge of the perturbed motion corresponds to the pivot point of the crystal structures. of the Chaperone HSP90 Th N-terminal ligand-binding domain of the chaperone HSP90 [42] consists of a active-site lid that is 30 amino acids in length (Figure 1E). The lid is involved in ATP/ADP binding that is associated with the conformational changes of HSP90. The motion of the lid corresponds to an intermediate-scale motion of the lid independent of the body of the protein, as revealed by crystal structures of HSP90 in different ligand-bound states. The RIP deformation map of the HSP90 ligand-binding domain (Figure 10A) in the ADP-bound state, calculated in the absence of ligand, clearly identifies the lid as a highly flexible region. The conformational ensemble of the perturbed structures show large conformational changes in the lid comparable with the scale of motion found in the crystal structures (Figure 5D). [SEP] Justify:

Output: The text corroborates the claim by explaining that perturbations in protein structures, such as those on Trp-83, can induce significant conformational changes. It details how a mechanical stress (perturbation) results in a hinge motion of Helix-12, indicating that mechanical stress is indeed capable of inducing these conformational alterations.


Input: Task: contrast the claim using the given text. Claim: Seismic waves can travel through space. [SEP] Text: Teleseismic waves can be considered as planar waves propagating through the subsurface and accumulating travel-time residuals on their way to the surface. Lags or advances of travel time due to velocity perturbations in the mantle are transported by the ray to the surface where they finally appear as travel-time residuals. The lateral shift between the location of the velocity perturbation and its associated travel-time residual at the surface depends on the incidence angle of the ray. This angle is not constant but, owing to the increase in seismic velocity with depth in the earth, decreases successively as the waves approach the surface. Thus, for velocity perturbations at shallow mantle depths and hence subvertical rays we expect small lateral shifts while we expect large lateral shifts for deep seated perturbations. On top of that, variations of the location of travel-time residuals with azimuth allow some inferences on the dip of a velocity perturbation. For example, a dipping slab will produce a maximum travel-time residual for teleseismic waves entering it along the updip direction. Based on these considerations, we conclude that travel-time residuals that stack coherently over all azimuths must be caused by velocity perturbations located in the shallow mantle. Thus, the anomalies W, C, E and A appearing in the overall stack in Fig. hint at fast shallow mantle probably associated with the lithospheric slabs below the western, central and eastern Alps and the Apennines. In particular, the strike of anomaly A correlates well with the strike of the Apenninic mountain chain, forming a narrow band along the western Italian coast in the north and then opening up into a broad band below central Italy. The large lateral shift of anomaly A with azimuth (Fig. 10) indicates that the Adriatic slab below the Apennines extends deep into the upper mantle. The same applies to anomaly E, associated with the eastern Alpine slab, which also exhibits a considerable lateral shift depending on azimuth. Lateral shifts of anomalies C and W are not that strong, implying that the central and western Alpine slabs terminate at shallower depths compared to the Adriatic slab below the Apennines and eastern Alpine ones. The fact that anomalies C and E appear strongest for waves arriving from the NE hint at a NE-ward dip of the associated slabs. [SEP] Justify:

Output: The text contrasts the claim by focusing on the propagation of teleseismic waves specifically through the earth's subsurface, emphasizing their behavior and characteristics related to velocity perturbations, rather than their ability to travel through the vacuum of space. The mention of planar waves accumulating travel-time residuals indicates a terrestrial context and does not support the notion that seismic waves can exist or propagate through the vacuum of space.


Input: Task: pass the claim using the given text. Claim: Curcumin, found in turmeric, has anti-inflammatory properties. [SEP] Text: Sampling was done by preparing all the successive extracts at concentration of 1 mg/mL. A series of dilution in the concentration range of 0. 02–0. 10 mg/mL was prepared for tannic acid (1 mg/mL stock solution) taken as reference standard. The total phenolics (TP), total simple phenolics (TSP) and total tannin content (TC) were estimated using the reported methods. All estimations were performed in triplicates and were statistically expressed as Mean ± S. E. M using linear regression equation. Isolation and characterization of curcumin from LKDThe analysis of the chloroform extract (LKDCH) through TLC and HPTLC confirmed a notable presence of curcumin. Consequently, an attempt was undertaken to isolate curcumin from this extract, employing a column chromatography approach. The wet packing method was adopted, wherein the column was packed with silica gel (#60–120 mesh, column grade, Merck Ltd. ), combined with exceptionally pure chloroform. LKDCH (50 g) was absorbed in chloroform and introduced into the column. The elution process was executed by employing a gradient mixture of methanol (MeOH) and chloroform (CHCl3), with a progressively increasing proportion of MeOH within CHCl3. The gradient levels were as follows: 1%, 2. 5%, 5%, 7. 5%, 10%, 15%, 20%, 40%, 60%, 80%, and finally, 100%. The eluates were collected in 25 mL fractions. values led to the pooling of corresponding eluates, which were subsequently concentrated using a rotary evaporator. The procedure yielded 105 fractions. Notably, fractions 50–55 exhibited distinct yellow single spots of curcumin, which were then combined and subjected to concentration. To enhance its purity, curcumin was purified through recrystallization in 100% acetone and stored at room temperature. The characterization and interpretation of the structure of the isolated curcumin was analyzed by sophisticated spectrometric techniques including FTIR (Bruker Alpha), 1HNMR and 13CNMR (Neo 500 MHz FT-NMR spectrometer), Mass spectrometer (-spectrometer) [17]. [SEP] Justify:

Output: The text does not provide evidence related to curcumin's anti-inflammatory properties. Instead, it describes a method for isolating and purifying curcumin using various techniques. The text mainly focuses on the procedures and results of curcumin extraction and characterization, which are unrelated to the claim about its anti-inflammatory effects.


Input: Task: corroborate the claim using the given text. Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 10. RIP perturbations of HSP90. (A) RIP deformation map. (B) Structural linchpins and per-turbation strength histogram. (C) Local flexibility mapped on structure and in histogram. Colors are as in Figure 4. Comparison of the Flexibility of RIP to There are other systems that calculate protein flexibility from a crystal structure. To compare RIP to these methods (Figure 11), we have calculated the flexibility using the Model (ANM) [43] and [32]. We chose ANM as a representative of contact-based network models that generate domain-level motions, where ANM generates a theoretical B-factor for each residue from the sum of the contribution of the lowest modes of oscillations. We chose as a representative of local instability methods, where calculates an RMSDf fluctuation (RMSDf is the averaged Cα RMSD over different conformations of the same structure) at each residue from an ensemble generated from a monte-carlo simulation of the protein using distance constraints derived from a standard force-field. Both methods were chosen largely due to the easy availability of the software implementation. Finally, we compare these flexibilities to various experimental data. For the four proteins with large conformational changes. In the case of TIM, for example, the RMSDf was calculated from the position of the Cα atoms between the open and closed structures (Figure 11A) after they were aligned with the weighted superposition program Theseus [44]. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 11. Comparison of the calculated flexibilities to various experimental data. For each graph, an experimental measure (grey) is compared to the flexibility calculated from a structure (labeled on the top left of graph) using RIP (blue), ANM (red) or (green). RMSDf is calculated as the mean of the Cα RMSD of the crystal structures if they are found in different states as shown in Figure 1. (A) Flexibility of TIM in the open conformation compared to the RMSDf. (B) Flexibility of TIM in the closed conformation. [SEP] Justify:

Output: The text corroborates the claim by discussing the calculations of protein flexibility and conformational changes, specifically noting that large conformational changes in proteins such as TIM are compared using RMSDf calculations from open and closed structures. This implies that mechanical stress, which could lead to these conformational changes, is being analyzed.


Input: Task: contrast the claim using the given text. Claim: Seismic waves can travel through space. [SEP] Text: MCS ionograms were also observed at Kaliningrad, Russia, and Sodankylä, Finland, after the 2012 Sumatra earthquake (epicentral distances \(\sim\)9000 km) (Yusupov and Akchurin 2015)Full size image Numerical simulationsThe numerical study on the sensitivity of ionograms to atmosphere–ionosphere perturbation induced by ground motion followed two steps. The simulation of acoustic wave propagation and associated electron density perturbation was first conducted. Then ionograms were synthesized from the perturbed electron density distribution. The calculations were conducted for \(I=45\) and \(72^\circ\) corresponding to Yamagawa and Kazan, respectively. The unperturbed electron density profile prior to the application of acoustic waves was obtained by integrating the plasma equation set (1) and (2) with a fixed local time, 1500 LT, until the equilibrium state was attained. This process ensures that the background electron density distribution does not change during the simulation of acoustic wave propagation. Because our major purpose is to examine the effect of magnetic inclination at two locations with different dip angles, background atmospheric parameters and solar zenith angles for both calculations were chosen to be the same as those at Yamagawa when coseismic disturbances were observed after the M9. 0 Tohoku-Oki earthquake in 2011, and only \(I\) was changed with the locations. In actual situations, the ionosphere and thermosphere vary widely depending on the local time, latitude, season, solar activity, etc. A key parameter for the detection of MCS in ionograms is the \(f_oF_1\) (Maruyama et al. 2012), which is a measure of the vertical electron density gradient in the lower F region. The \(f_oF_1\) in the two cases (Kazan and Yamagawa) were very similar (4–5 MHz). It is possible to include the above factors in the numerical calculations, but an essential physical mechanism will be obscure. Figure 6 shows the resultant unperturbed density profiles for \(I= 45\) and \(72^\circ\) by the green and orange lines, respectively. [SEP] Justify:

Output: The text contrasts the claim by discussing acoustic wave propagation and ionograms generated from electron density perturbations due to ground motion, but it does not support the idea that seismic waves travel through space. In fact, it specifically focuses on the propagation of acoustic waves in the atmosphere rather than the ability of seismic waves to move through the vacuum of space.


Input: Task: pass the claim using the given text. Claim: Curcumin, found in turmeric, has anti-inflammatory properties. [SEP] Text: Differential scanning calorimetry (DSC)The DSC 3 instrument (Mettler Toledo; Model no-ME-5140313) was employed to examine the melting point behavior of both the isolated and purified curcumin, as well as the standard curcumin. Samples were positioned in aluminum pans and subjected to scanning at a rate of 10 °C per minute within the temperature range of 20 °C to 300 °C under an inert nitrogen gas environment. For confirming the identity and purity of the isolated curcumin, a comparison was made between the endothermic peak of the isolated curcumin and that of the standard curcumin [18]. HPLC analysis for determination of the purity of isolated curcuminThe purity of isolated Curcumin from extracts was determined by HPLC (). consisted of a chromatographic pump, Injector, and UV detector. For HPLC separation, a reversed-phase C-18 column was used. The mobile phase was composed of acetonitrile-acidic Water (pH 3 adjusted by acetic acid) (80:20v/v) at a flow rate of 1 m/min. The run time was 10 min and the detection wavelength was set at 425 nm. The mobile phase was filtered using a 0. 2 nm millipore membrane filter. The sample injection volume was set at 20 μl. The purity was determined by comparing it with a chromatogram of the standard curcumin from SRL, India (95% Purity) [8]. The result is shown in Fig. 2. Fig. 2HPLC chromatogram of curcumin. A: Curcumin standard; B: Curcumin in LKDCH and purity of isolated curcumin from LKDCH; C: Curcumin standard; D Curcumin isolated from size imageNuclear magnetic resonance (NMR)The chemical identity of the LKCH isolated curcumin was further confirmed by proton NMR spectrum usingMultinuclear FT-NMR Spectrometer (ECX400 -Jeol 400 MHz, Japan). The samples were dissolved in dimethyl sulfoxide d6 (DMSO d6) as solvent. 20 µl of tetramethylsilane (TMS) was added to the sample solution as the internal reference. [SEP] Justify:

Output: The text is irrelevant to the claim because it focuses on the analysis and purity assessments of curcumin using techniques like differential scanning calorimetry (DSC) and high-performance liquid chromatography (HPLC). There is no mention or discussion of curcumin's anti-inflammatory properties.


Input: Task: corroborate the claim using the given text. Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: Rex measurements for DHFR identify microsecond dynamics in the Met20 loop, the F–G loop, the adenosine-binding loop and the G–H loop (Figure 11E), suggesting that in the case of DHFR, there is significant overlap between the nanosecond and microsecond dynamics. Coupling between these loops have also been identified in nanosecond MD simulations through cross-correlation and quasi-harmonic analysis [21]–[24]. The large conformational change in Helix-12 of ER, as evident in the large RMSDf values (Figure 11F), provide a difficult challenge for these models of flexibility. There are elevated values of RMSDf in short loops near residue 35 and 165 (Figure 11F), where all three flexibilities finds elevated flexibility. None of the flexibilities identify Helix 12 as a highly flexible region. However, with RIP we can identify one large conformational change by examining the deformability map (Figure 8A), where the conformational change is consistent with the crystal structures (Figure 9). Both ANM and identify elevated flexibility at residue 195, which do not correspond to elevated RMSD values. The conformational changes in HSP90 is dominated by the motion of the lid, indicated by the large values of RMSDf at residue 110 (Figure 11G). This large conformational change is not identified by ANM but both RIP and identify the lid region as flexible. One advantage with RIP over is that by examining the conformational ensemble of perturbed structures generated by RIP (Figure 5E), we can see that the generated motions are of the order of the RMSDf observed in the crystal structures. and ANM identifies a region of elevated flexibility at residue 60 that does not correspond to any elevated region of RMSDf and the large RMSDf in the N-terminal that is involved with inter-domain interactions does not correspond to any calculated flexibility. In conclusion, we find that the flexibility of RIP identifies only loop motions that correspond to large conformational changes of intermediate-scale motions. In contrast, identifies more regions as flexible, where there is some overlap with the regions identified as flexible by RIP. ANM performs poorly for intermediate-scale motions. DiscussionMolecular dynamics (MD) is generally accepted to be an accurate representation of biochemical processes on the molecular level [45]. [SEP] Justify:

Output: The text supports the claim by discussing conformational changes in protein structures in detail. Specifically, it refers to conformational changes in various loops of DHFR and how these changes are identified through methods like RMSDf values and dynamics simulations. The mention of large conformational changes and flexibility in regions of the protein suggests that mechanical stress influences the protein structure at a molecular level, thus corroborating the claim.