Input: Task: corroborate the claim using the given text. Claim: Climate change affects crop yields due to changes in temperature and precipitation patterns. [SEP] Text: When the analysis results of monthly average air temperature data of Turkey are examined, it is detected that 6% of Turkey has a decreasing trend, 67% has an increasing trend, and 27% has no trend. In addition, 22% of the regions with increasing trend tendency were found to be in the fifth degree risk, 12% in the fourth degree risk, 8% in the third degree risk, 17% in the second degree risk, and 9% in the first degree risk increasing trend region. It was concluded that 1% of the regions with a decreasing trend tendency were in the decreasing trend tendency with a fifth degree risk, 1% with a fourth degree risk, 1% with a third degree risk, 1% with a second degree risk, and 1% with a first degree risk. Ciftci and Sahin stated in their study that the most striking change in Turkey's average air temperature occurred in the summer months, with an increase of 1. 56 °C. In addition, extreme air temperature indices indicate that summer is the season with the highest temperature change (Ciftci & Sahin 2023). Therefore, these results gave similar results to the analysis results of air temperature parameter of this study. Bahadır stated that the increase in temperature in the region of Turkey was 0. 3 °C, and the increase in temperature in the Mediterranean region was 0. 5–0. 6 °C. These results showed that similar results were obtained in the analysis results of these regions of the study, especially in the GIS maps in November and December (Bahadır 2011). Serkendiz et al. evaluated Turkey's drought in their study. As a result of the analysis using both precipitation and evaporation data, they stated that drought has generally increased in most parts of Turkey according to the MK method. In the analysis results of this study, an increasing trend in precipitation was observed in some regions and a decreasing trend in some regions. However, increasing trends in temperatures have been observed across the country. Therefore, it can be seen that the analysis results are similar (Serkendiz et al. 2024). When standard deviation analysis results of monthly average air temperature data are examined, it is detected that 43% of Turkey has a decreasing trend, 46% has an increasing trend, and 11% has no trend. [SEP] Justify:

Output: The text corroborates the claim by providing data on the trends in air temperature and precipitation in Turkey. It mentions that 67% of Turkey has an increasing trend in temperature, and discusses the changes in precipitation patterns contributing to drought conditions. These findings support the claim that climate change, reflected in temperature and precipitation fluctuations, impacts agricultural production and crop yields.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Bacteria and treatment preparations DSM from stock was cultured or donated by BioGaia (Stockholm, Sweden) and its μV isolated as described in Al-Nedawi et al (2015). Bacteria were diluted in Krebs to a working concentration of 108 x CFU/mL. Bacteria used for isolation of μV were cultured for 72-hr reaching final concentration of 1012 x CFU/mL. Bacteria were subsequently centrifuged at 1900 g (3000 rpm) (8R) for 30 min at 4°C. The supernatant was filtered through a 0. 2 μm filter. Some supernatant media (CM) was saved for future analysis. The remaining culture medium was centrifuged at 42,000 rpm (Type 45 Ti rotor) for 6-hr at 4°C and the supernatant collected and subsequently tested as the conditioned medium minus the μV (CM- μV). Remaining media was cultured and determined to be free of bacteria since no growth occurred over 48 hours. The pellet was collected in phosphate-buffered saline (PBS) washed 3 times and centrifuged for 3-hr at 42,000 rpm (Type 70. 1 Ti rotor). The remaining μV (pellet) were re-suspended in PBS at a concentration roughly equivalent to 1012 CFU/mL and stored at -80°C until use. Microvesicles were diluted to a working concentration roughly equivalent to that generated by bacteria at a final concentration of 108 CFU/mL. Nanop3. 1, build 3. 1. 54; Malvern Panalytical) with a detection threshold of 5. ResultsDSM and the products of its cultivation were applied intraluminally to in vitro preparations of mouse jejunum and colon to determine whether μV could replicate the effect of the parent bacteria on intestinal motility (Fig 1A). The μV were characterized via NTA as described in the methods. The isolated microvesicles had an average size of 156. 3 ± 2. 1 nm and the modal size was 139. 3 +/- 7. 6 nm (+/- SEM) (Fig 1B). The remaining conditioned media after the μV and bacteria had been removed (CM-μV) was then administered intraluminally to the tissue. As a negative control, the growth media used to culture the bacteria (broth) was applied separately. [SEP] Justify:

Output: The text contrasts the claim by detailing an experimental procedure that emphasizes the use of specific bacteria and their microvesicles in studying intestinal motility. It highlights that bacteria were cultured and isolated, aiming to understand their effects on gut function. This suggests that a diverse bacterial presence, rather than sterility, is crucial for proper gut health as it is focused on the manipulation and examination of bacterial effects.


Input: Task: pass the claim using the given text. Claim: Mechanical stress can induce conformational changes in protein structures. [SEP] Text: 1038/nsmb986 of Science®6582. 10. 1021/bi012159+ of Science®5194. 10. 1093/emboj/18. 19. 5187 of Science®1429. 10. 1093/nar/gkh287 of Science®95. CAS48. 10. 1002/1097-0134(20010101)42:1<38::AID-PROT50>3. 0. CO;2-3 of Science®2. 5 Å resolution. Biochemistry 41: 9015–9020. 10. 1021/bi026054y of Science®136. CAS1. 7 A crystal structure of the apo form of the soluble quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus reveals a novel internal conserved sequence repeat. J 289: 319–333. 10. 1006/jmbi. 1999. 2766 of Science®322. 10. 1016/S0969-2126(03)00023-6 of Science®1479. PubMedWeb of Science®2. 1) protein is under redox regulation in vitro. Biol 13: 4609–4617. 10. 1128/MCB. 13. 8. 4609 of Science®665. 10. 1089/152308603770310338 of Science®374. 10. 1146/annurev. 0180. 002013 CASWeb of Science®1114. 10. 1073/pnas. 0611636104 of Science®1373. 10. 1093/pcp/pcm108 of Science®7456. 10. 1158/0008-5472. CAN-08-0565 of Science®885. 10. 1016/j. jmb. 2004. 04. 024 of Science®2816. 10. 1016/S0021-9258(18)45951-0 of Science®1092. 10. 1107/S174430910604200593. CASPubMed98. 10. 1038/nsmb876 of Science®540. 10. 1038/nsb945 CAS656. CAS3764. 10. 1073/pnas. 0611577104 of Science®127. 10. 1159/000089616 of Science®7153. [SEP] Justify:

Output: The text provided does not address or relate to the claim regarding mechanical stress inducing conformational changes in protein structures. Instead, it consists of a series of DOI references and citations without meaningful context or information relevant to the specific claim.


Input: Task: corroborate the claim using the given text. Claim: Climate change affects crop yields due to changes in temperature and precipitation patterns. [SEP] Text: In addition, 8% of the regions with increasing trend tendency are in the fifth degree risk, 11% in the fourth degree risk, 14% in the third degree risk, 11% in the second degree risk, and 2% in the first degree risk increasing trend region. It was concluded that 10% of the regions with a decreasing trend tendency were in the fifth degree risk, 10% in the fourth degree risk, 11% in the third degree risk, 11% in the second degree risk, and 1% in the first degree risk decreasing trend tendency. study aims to investigate variability in monthly total precipitation and monthly average air temperature data of all provinces in Turkey. The strongest aspect of the study is that it analyzes the entire country and applies the ITPAM method to meteorological data across the country for the first time. However, the use of precipitation and air temperature parameters in the study and the lack of use of other hydro-meteorological parameters (such as lakes, streams, etc. ) are stated as a weakness. In this study, both average and standard deviation analyses of 30-year precipitation and air temperature data between 1991 and 2020 were carried out with the ITPAM method, one of the most up-to-date trend methods. As a result of the study, trend analysis results of precipitation and air temperature data of 81 provinces in Turkey were obtained, interpreted separately, and Turkey precipitation-air temperature trend maps were obtained. As a result, it is concluded that monthly average air temperature data of Turkey has a largely increasing trend. It is also recommended that all future climate change studies and action plans to be prepared on these issues should take into account the recommendations listed below. Water management should be planned within the framework of a holistic approach and developed in line with this principle. In degree to monitor water resources, systems that track the use of water resources should be made widespread. Awareness projects should be prepared and supported to ensure and promote water conservation. Incentives should be provided for rainwater collection systems to ensure efficient use of rainwater by the public. Water waste in agriculture should be prevented by applying new technologies in irrigation systems. New designs of water structures should be applied to minimize this situation by taking into account the decreases in surface water through evaporation and evaporation with the decreases in precipitation and increases in air temperature levels. Increasing these meteorological parameters and investigating the changes in water resources (such as lakes, streams, etc. [SEP] Justify:

Output: The text corroborates the claim by discussing the increasing trend of monthly average air temperatures and analyzing precipitation trends across Turkey. It emphasizes the importance of these climatic elements in relation to water management in agriculture, which is directly linked to crop yields.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: coli K1 infection in neonates [22], and improved acute alcohol-induced liver injury and intestinal permeability [23]. Culture supernatants from L. acidophilus and LGG produced an anti-inflammatory response, inhibiting gene expression of the matrix metalloproteinase (MMP) MMP-9, expression of which has been noted in inflammatory disease [24]. Conditioned media from L. plantarum inhibited NF-κB binding activity and proteasome function [25]. We have recently shown that culture supernatants from Saccharomyces cerevisiae and boulardii yeasts reverse acute stress-induced dysmotility in the gut and reproduce the effects seen with the yeasts themselves [26]. Although the presence of μV in these studies was not tested, these results support the suggestion that bioactive molecules or components produced or secreted by yeasts and bacteria are capable of therapeutic effects independent of the parents. As interest in the various roles of μV grows, research into their capability to produce effects on the GI tract, has emerged. μV produced by L. casei BL23 contain proteins that have been previously identified as mediators of the effect of Lactobacillus probiotics; p40, p75, and LCABL_31160 [27]. Particularly p40 and p75 produced by L. casei BL23 bind to mucin, collagen, and cultured epithelial cells [28]. We previously showed that JB-1 μV reproduced the same immune and neuronal effects caused by the whole bacteria [9]. Proteomic analysis of JB-1 and its μV showed that GroEL an analogue of heat shock protein, could independently reproduce immune activities of the bacteria [9]. Introduction of JB-1 into the gut lumen decreased the amplitude of neuronally dependent colonic migrating motor complexes subsequently referred to as PCC and this was reproduced by the μVs alone [9]. Microvesicles from L. plantarum WCFS1 increased survival of C. elegans infected with E. faecium (vancomycin resistant enterococci) [10]. These results support the role of μV in gut Lactobacillus bacterial signaling and their significance in the mechanisms of communication with mammalian hosts within the microbiome-gut-brain axis. [SEP] Justify:

Output: The text contrasts the claim by discussing the therapeutic effects of diverse gut bacteria and yeast, specifically highlighting the roles of Lactobacillus and Saccharomyces species. It emphasizes that the presence of these microorganisms and their bioactive molecules produces positive outcomes, such as improved gut health and reduced inflammation, suggesting that a diverse microbiome is beneficial rather than a completely sterile gut.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography allows for the visualization of complex biomolecules at atomic resolution. [SEP] Text: search IUhome archive editors for authors for readers submit open access journal menu home archive editors for authors for readers submit open access Issue contents Download PDF of 1. Introduction 2. H/D exchange and perdeuteration 3. Neutron instrumentation at reactor neutron sources 4. Neutron instrumentation at spallation neutron sources 5. Neutron cryo-crystallography 6. Structural refinement options for neutron diffraction data 7. Recent instrumentation development for sub-atomic resolution X-ray structures 8. Redox biology: from supply to utilization of electrons 9. Neutron diffraction data collection and processing for AcNiR 10. Molecular sensing: heme-based gas sensors 11. Neutron diffraction data collection and processing for AxCytCp 12. information 1. Introduction 2. H/D exchange and perdeuteration 3. Neutron instrumentation at reactor neutron sources 4. Neutron instrumentation at spallation neutron sources 5. Neutron cryo-crystallography 6. Structural refinement options for neutron diffraction data 7. Recent instrumentation development for sub-atomic resolution X-ray structures 8. Redox biology: from supply to utilization of electrons 9. Neutron diffraction data collection and processing for AcNiR 10. Molecular sensing: heme-based gas sensors 11. Neutron diffraction data collection and processing for AxCytCp 12. information 10. 1107/S2052252515011239 | access Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential Matthew P. Blakeley,a Samar S. Hasnainb and Svetlana V. Antonyukb* aLarge-Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France, and bGroup, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, UK*Correspondence e-mail: s. antonyuk@liverpool. ac. uk Edited by V. T. [SEP] Justify:

Output: The text does not address the claim directly. It contains information about various neutron and X-ray crystallography topics but lacks specific statements regarding the capability of X-ray crystallography to visualize complex biomolecules at atomic resolution. Therefore, it is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Climate change affects crop yields due to changes in temperature and precipitation patterns. [SEP] Text: Close mobile search navigation 42. 42. doi: Download citation file: Ris (Zotero) accurate grasp of the influence of precipitation and temperature changes on the variation in both the magnitude and temporal patterns of runoff is crucial to the prevention of floods and droughts. However, there is a general lack of understanding of the ways in which runoff sensitivities to precipitation and temperature changes are associated with the CMIP5 scenarios. This paper investigates the hydrological response to future climate change under CMIP5 RCP scenarios by using the Capacity (VIC) model and then quantitatively assesses runoff sensitivities to precipitation and temperature changes under different scenarios by using a set of simulations with the control variable method. The source region of the (SRYR) is an ideal area to study this problem. The results demonstrated that the precipitation effect was the dominant element influencing runoff change (the degree of influence approaching 23%), followed by maximum temperature (approaching 12%). The weakest element was minimum temperature (approaching 3%), despite the fact that the increases in minimum temperature were higher than the increases in maximum temperature. The results also indicated that the degree of runoff sensitivity to precipitation and temperature changes was subject to changing external climatic conditions. climatic change, control variable method, delta method, runoff sensitivities, source region of the Yellow River, VIC model recent years, a broad consensus has developed that the global hydrological cycle will be affected by future global climate change (Bates et al. 2008; Gosling & Arnell 2016; Zarch et al. 2017). Under the condition of limited water resources, an accurate understanding of the law of space-time change in water resources is indispensable to the establishment of an effective management mechanism and to develop policies to adapt to this environmental change. The use of different kinds of global climate model (GCM) scenarios is extremely useful for projecting trends of future global climate changes and for understanding a range of possible runoff changes (Dosio & Panitz 2016; Pourmokhtarian et al. 2017). However, there is a general lack of understanding of the ways in which precipitation and temperature changes influence runoff at spatial and temporal scales under climate change scenarios. Climate change may change land surface forcing including precipitation, temperature and other climate variables and may further result in changes in runoff (Andrews et al. 2015). Currently, there are two methods used in research to determine the impact of climate change on runoff. [SEP] Justify:

Output: The text corroborates the claim by discussing the impacts of precipitation and temperature changes on runoff, which is a crucial component influencing crop yields. It highlights that climate change alters key climate variables, such as precipitation and temperature, thus affecting the hydrological cycle, which directly relates to agricultural outputs. The mention of 'the precipitation effect was the dominant element influencing runoff change' supports the idea that changing climate conditions can significantly affect agricultural productivity, ultimately supporting the claim regarding crop yields.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Figures AbstractThe host genotype has been proposed to contribute to individually composed bacterial communities in the gut. To provide deeper insight into interactions between gut bacteria and host, we associated germ-free C3H and C57BL/10 mice with intestinal bacteria from a C57BL/10 donor mouse. Analysis of microbiota similarity between the animals with denaturing gradient gel electrophoresis revealed the development of a mouse strain-specific microbiota. Microarray-based gene expression analysis in the colonic mucosa identified 202 genes whose expression differed significantly by a factor of more than 2. Application of bioinformatics tools demonstrated that functional terms including signaling/secretion, lipid degradation/catabolism, guanine nucleotide/guanylate binding and immune response were significantly enriched in differentially expressed genes. We had a closer look at the 56 genes with expression differences of more than 4 and observed a higher expression in C57BL/10 mice of the genes coding for Tlr1 and Ang4 which are involved in the recognition and response to gut bacteria. A higher expression of Pla2g2a was detected in C3H mice. In addition, a number of interferon-inducible genes were higher expressed in C3H than in C57BL/10 mice including Gbp1, Mal, Oasl2, Ifi202b, Rtp4, Ly6g6c, Ifi27l2a, Usp18, Ifit1, Ifi44, and Ly6g indicating that interferons may play an essential role in microbiota regulation. However, genes coding for interferons, their receptors, factors involved in interferon expression regulation or signaling pathways were not differentially expressed between the two mouse strains. Taken together, our study confirms that the host genotype is involved in the establishment of host-specific bacterial communities in the gut. Based on expression differences after colonization with the same bacterial inoculum, we propose that Pla2g2a and interferon-dependent genes may contribute to this phenomenon. Citation: (2013) Differences in Expression in the Colon of after Colonization with Bacteria. 8(8): e72317. Markus M. Heimesaat, Charité, Franklin, GermanyReceived: April 15, 2013; Accepted: July 10, 2013; Published: August 9, 2013Copyright: © 2013 Brodziak et al. [SEP] Justify:

Output: The text contrasts the claim by highlighting that the host genotype influences the establishment of specific bacterial communities in the gut. It indicates that individual differences in gene expression in response to gut bacteria suggest that diversity in the gut microbiota may be beneficial for the host's immune response. The mention of various genes that are significantly expressed in relation to gut bacteria implies that a healthy gut is associated with diverse bacteria rather than being completely sterile.


Input: Task: corroborate the claim using the given text. Claim: X-ray crystallography allows for the visualization of complex biomolecules at atomic resolution. [SEP] Text: Forsyth, Institut Laue-Langevin, France, and Keele University, UK (Received 6 March 2015; accepted 9 June 2015; online 30 June 2015) Year of Crystallography saw the number of macromolecular structures deposited in the Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i. e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i. e. ≤0. 7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm3 crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H+) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. [SEP] Justify:

Output: The text supports the claim by stating that 'the number of X-ray structures determined to sub-atomic resolution (i. e. ≤1 Å) has passed 600', which demonstrates that X-ray crystallography is capable of achieving atomic resolution in macromolecular structures. Furthermore, it mentions that 'sub-mm3 crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins,' reinforcing the ability of X-ray crystallography to visualize complex biomolecules at specified resolution levels.


Input: Task: corroborate the claim using the given text. Claim: Climate change affects crop yields due to changes in temperature and precipitation patterns. [SEP] Text: One method is based on the concept of the climate elasticity of runoff, with results obtained directly from historical meteorological elements and runoff time series (Schaake 1990; Yang & Yang 2011; Brikowski 2015; Fan et al. 2017). Another more commonly used method is the hydrological modelling approach (Dibike & Coulibaly 2005; Immerzeel et al. 2010; Teklesadik et al. 2017). Since climate and hydrological phenomena are significantly different in their spatial scales, a physics-based distributed hydrological model has been recognized as extremely effective at identifying temporal and spatial variability in runoff at the river-basin scale (Bhatti et al. 2016; Gregoretti et al. 2016; Huziy & Sushama 2017). In this approach, climate input variables of interest, such as precipitation and temperature, can be considered separately, and hydrological processes and fluxes (such as runoff and evaporation) can be simulated under conditions of climate change and changes in other drivers. Therefore, this approach can also be used to study the sensitivity of runoff to climate change. Compared to assumed climate change scenarios, global climate models have a clear physical meaning, are more readily used by the scientific community and are suitable for the hydrological modelling approach. Substantial research on assessing the sensitivity of runoff to precipitation and temperature changes is being carried out worldwide. Nijssen et al. (2001) focused on the problem of climate change in macro-scale river basins (including the and Yenisei Rivers) around the world and found that the annual mean runoff decreased whenever temperatures increased. Tang et al. (2012) evaluated runoff changes/sensitivity when temperatures increased in the Basin; the results also show that temperature increases generally lead to a decrease in runoff. Rasouli et al. (2014) provided the linearly scaled meteorological forcing inputs necessary to study model sensitivity in climate change scenarios. Their results showed that runoff, peak runoff, and the timing of peak runoff clearly have a sensitivity to both warming and precipitation changes. Bosshard et al. (2014) assessed the impact of climate change on the hydrology of the Rhine basin by using the hydrological model and utilizing regional climate model data. Their results suggested that temperature effects are of prime importance for the Alpine tributaries, while precipitation effects dominate in the lower portion of the Rhine basin. [SEP] Justify:

Output: The text corroborates the claim by discussing various studies that examine the sensitivity of hydrological processes, including runoff, to changes in temperature and precipitation—both of which are critical factors influencing crop yields. For example, it notes that temperature increases generally lead to a decrease in runoff, which can directly impact water availability for crops. Furthermore, the text mentions significant research that evaluates the sensitivity of runoff to these climate variables, emphasizing their importance under climate change scenarios.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: The majority of these genes grouped in biological processes involved in water transport across the gut wall and immune responses. Since mainly immunoglobulin-associated genes were identified in the “defense/immunity protein activity molecular function cluster”, it can be assumed that presence of microbiota influenced adaptive immune responses in this model [34]. The category “immune responses” was also enriched in differentially expressed genes when mucosal gene expression in our experimental animals was evaluated with bioinformatics approaches. We had a closer look at single genes whose expression differed by a factor of greater than 4. Amongst these genes, we found higher expression in C57BL/10 than in C3H mice of toll-like receptor 1 (TLR1, 4-fold) and angiogenin 4 (Ang4, 33-fold). Direct effects of these two genes on colonic microbiota composition have so far not been demonstrated. However, differences in Ang4 expression have been reported between germ-free mice and mice monoassociated with Bacteroides thetaiotaomicron [35]. The antibacterial peptide Ang4 is very effective against Gram positive bacteria including Enterococcus faecalis and Listeria monocytogenes. Gram negative bacteria such as Bacteroides thetaiotaomicron and Escherichia coli are less sensitive. Interestingly, intestinal Ang4 mRNA expression is induced by complex microbiota and by B. thetaiotaomicron alone in previously germ-free mice [23]. In contrast to Ang4, phospholipase A2, group IIA (Pla2g2a), guanylate nucleotide binding protein 1 (Gbp1), and cluster of differentiation 14 (Cd14) were higher expressed in C3H than in C57BL/10 mice. The same observation has been reported in C3H and C57BL/6 mice and was associated with a strain-specific susceptibility to microbiota-driven colitis: interleukin 10-deficient mice with a C3H background are susceptible whereas the C57BL/6 background renders the mice colitis resistant [22]. The latter strain shares a considerable proportion of its genetic background with the C57BL/10 mice that were used in our experiment because C57BL/6 and C57BL/10 are sub-strains of C57BL origin. [SEP] Justify:

Output: The text contrasts the claim by discussing the influence of microbiota on immune responses and gene expression in the gut. It suggests that the presence of beneficial bacteria, such as Bacteroides thetaiotaomicron, can positively affect immune functions, indicating that a diverse gut microbiota may confer health benefits as opposed to a completely sterile gut.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography allows for the visualization of complex biomolecules at atomic resolution. [SEP] Text: This is of particular significance since, despite all the advances in X-ray detectors and data collection protocols, radiation damage can still occur at 100 K (Liebschner et al. , 2013; Kekilli et al. , 2014). This is particularly evident for redox centres in metalloproteins (Kekilli et al. , 2014; Suga et al. , 2015) and carboxylic-acid-containing residues, Asp and Glu, since X-rays cause CO2 elimination, precluding determination of Asp and Glu protonation states (Gerstel et al. , 2015). We note that, despite the large number of X-ray structures in the Bank (PDB), there is still a scarcity of genuine `damage-free' structures of redox systems at ambient temperatures. The application of neutron crystallography for the location of H atoms in macromolecules has historically been restricted to the study of small unit-cell systems (cell edges <30 Å) for which large crystals of several mm3 could be grown. Even then, long data collection times of several months were required due to the lack of optimized instrumentation (Schoenborn, 2010). This is no longer the case, with neutron crystallography expanding beyond its traditional boundaries, to address larger and more complex problems, with smaller samples and shorter data collection times. The origin of this transformation can be found in a number of advances including the development of quasi-Laue (Blakeley et al. , 2010; Meilleur et al. , 2013) and monochromatic (Kurihara et al. , 2004; ) diffractometers with cylindrical image-plate detectors at nuclear reactor neutron sources, time-of-flight (TOF) Laue diffractometers at spallation neutron sources (Langan et al. , 2004; Coates et al. , 2010; Kusaka et al. , 2013), centralized facilities for sample deuteration and new computational tools for structural refinement (Afonine et al. , 2010; Gruene et al. , 2014). Of the 83 neutron structures in the PDB, more than half (49/83) were deposited since 2010 (Fig. 1). Many of these illustrate the complementarity of combining X-ray and neutron crystallography in order to locate important H-atom positions to improve our understanding of macromolecular structure and function. [SEP] Justify:

Output: The text discusses the limitations and advancements in both X-ray and neutron crystallography but does not provide direct information on the capability of X-ray crystallography to visualize complex biomolecules at atomic resolution. Hence, it is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Climate change affects crop yields due to changes in temperature and precipitation patterns. [SEP] Text: However, to date, most of these studies are aimed at the average temperature (Chang & Jung 2010). Only a few works discuss the runoff sensitivities to changes in meteorological elements associated with the CMIP5 models of various global climate change scenarios, which may not be sufficient for reliable estimates of the influence of temperature on runoff. Runoff in the hydrological system is affected by the change in average temperature. In addition, the susceptibility of runoff to the maximum and minimum temperatures accounted for a fairly large proportion of impacts, especially in areas of high altitude and large temperature differences (Zhang et al. 2014). The scientific programs behind this work are in accordance with the traditional hydro-meteorological observations as well as global climate models, together with climate change and the physically based hydrological model. The goal of this study is to objectively and comprehensively investigate the sensitivity of runoff to precipitation and temperature changes by separating the possible impacts of meteorological elements under the different climate change scenarios. Under the condition of global warming, temperatures in high-altitude areas increase considerably more than temperatures in low altitude areas. This scenario exacerbates climate change-related problems in the region (Li et al. 2017b). Plateau, a sensitive and vulnerable region to climate warming, is the world's highest plateau. Recently, the rate of temperature rise over the Tibetan Plateau, which has a cold plateau climate, has been much higher than that of the surrounding areas (Zhou & Huang 2012). This region is also called the ‘water tower of Asia’. As the origin of many rivers in Asia, the has the headwaters of several world-class rivers, such as the in South Asia; the Brahmaputra River, the Salween River, and the in Southeast Asia; and the and the in China. In this study, the source region of the (SRYR) is taken as the case study area. It is located in the northeastern and covers only 15% of the whole basin but contributes to more than one-third of the total runoff. In recent years, climate changes have taken place in the Basin, which are expected to continue in the future, inevitably leading to the appearance of progressive complex changes in the water resources of the region (Gao et al. 2016; Ren et al. 2016; Qin et al. 2017). [SEP] Justify:

Output: The text corroborates the claim by discussing how runoff, which is influenced by temperature and precipitation changes, plays a significant role in the hydrological system. The mention of sensitivity to temperature changes, especially in high-altitude areas, aligns with the assertion that climate change impacts crop yields through alterations in temperature and precipitation patterns. The reference to progressive changes in water resources due to climate changes further supports the idea that these alterations can affect agricultural outputs.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: For Cd14, which is involved in the detection of lipopolysaccharides by TLR4, it was later demonstrated that a higher expression by gut epithelial cells is responsible for a lower colitis susceptibility in IL-10-/- mice with a C3H than with a C57BL/6 background [36]. Whether or not differences in intestinal Cd14 expression are also involved in the selection of resident gut bacteria remains to be clarified. The high genetic homogeneity that can be assumed for C57BL/6 and C57BL/10 mice suggests that our experimental mice were affected by a known frameshift mutation in exon 3 of the Pla2g2a gene in C57BL/6 mice which results in a defective gene product [25]. This would have been the most plausible explanation for a more than 70-fold higher expression of this gene in C3H mice. However, gene sequence and Southern blot analyses revealed that this mutation was absent in our experimental animals. Differences in intestinal Pla2g2a activities have been shown for different mouse strains with the wild-type alleles. It has been proposed in one study that nucleotide substitutions and resulting amino acid changes may influence the substrate binding properties of the enzyme [37]. In conjunction with the fact that Pla2g2a gene expression is equal in germ-free and conventional mice [23], these findings suggest that this gene is a good candidate for genetically fixed host factors that may influence microbiota composition. In fact, Pla2g2a exerts strong antibacterial effects against Gram positive and to a lesser extend against Gram negative bacteria and there is evidence that it plays an important role in the intestinal defense against pathogenic bacteria [38]. The expression in human bronchioepithelial and nasal epithelial cells of type IIA phospholipase A2 is up-regulated by IFN-gamma [39] indicating that interferons may regulate the expression of genes with possible functions in host-microbe interactions. This notion is supported by the fact that many interferon (IFN)-inducible genes were > 4-fold higher expressed in C3H than in C57BL/10 mice. [SEP] Justify:

Output: The text contrasts the claim by discussing the role of various genes and their expressions in influencing microbiota composition, particularly highlighting that gene expression is equal in germ-free and conventional mice, suggesting the importance of a diverse microbiota. Additionally, the text mentions that Pla2g2a plays an important role in intestinal defense against pathogenic bacteria, indicating that a lack of bacterial diversity (as implied by a completely sterile gut) could be detrimental rather than healthier.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography allows for the visualization of complex biomolecules at atomic resolution. [SEP] Text: Figure 1 Neutron and joint X-ray/neutron structures of macromolecules deposited in the PDB since 2010, including data collection details and crystallographic parameters for each. The structures are ordered in terms of the ratio of the crystal volume to the asymmetric unit volume, from lowest to highest. Those with the lowest ratios can be considered the most challenging. Highlighted in red is the study of HIV-1 protease with the antiretroviral drug amprenavir bound (Weber et al. , 2013) that has the lowest ratio of the crystal volume to the asymmetric unit volume. Highlighted in orange is the study of inorganic pyrophosphatase from Thermococcus thioreducens (I-PPase; Hughes et al. , 2012) that currently is the largest unit cell and asymmetric unit volume to be studied. Highlighted in blue is a study of rubredoxin from Pyrococcus furiosus (RdPf; Munshi et al. , 2012) that is the fastest data collection to date at 14 h. Highlighted in green is another study of RdPf (Cuypers et al. , 2013) which is currently the highest resolution study at 1. 05 Å. Highlighted in purple are neutron cryo-crystallography studies performed at 100 K for cytochrome c peroxidase (MW ∼34 kDa) (Casadei et al. , 2014) and β-lactamase (MW ∼28 kDa) (Coates et al. , 2014), and highlighted in yellow are the studies of Cu nitrite reductase (MW ∼37 kDa) from Achromobacter cycloclastes (AcNiR) and cytochrome c′ (MW ∼14 kDa) from Alcaligenes xylosoxidans (AxCytCp) presented here. 2. H/D exchange and perdeuteration In neutron macromolecular crystallography, the replacement of H by D is advantageous for two main reasons. Firstly, H has an anomalously large incoherent scattering cross section, while that of D is ∼40 times lower (Table 1). [SEP] Justify:

Output: The text does not address the claim directly about X-ray crystallography and its ability to visualize complex biomolecules at atomic resolution. Instead, it discusses neutron and joint X-ray/neutron structures, specific studies related to various macromolecules, and technical details about crystal volume ratios and data collection. As such, it is irrelevant to the claim about the visualization capability of X-ray crystallography.


Input: Task: corroborate the claim using the given text. Claim: Climate change affects crop yields due to changes in temperature and precipitation patterns. [SEP] Text: Most of the previous works focused on analyzing the hydrological process under changes in the climate and land use, but few of them attempted to investigate the runoff sensitivity under the different climate-change scenarios. Therefore, this paper seeks to address the aforementioned issues by pursuing the following objectives: (1) to investigate the hydrological response to future climate change by using the Capacity (VIC) model; (2) to quantitatively assess the sensitivities of runoff to precipitation and temperature changes under different climate scenarios by using a set of simulations with the control variable method, based on identifying the separate and interacting effects of changes in precipitation and temperature on runoff to find the most sensitive elements and seasons that influence runoff; and (3) to conduct a study on the influence of external climatic conditions on the degree of runoff sensitivities to precipitation and temperature changes, with a quantification of the range in variation. region study region SRYR is located in the northeast (95. 5–103. 5°E and 32–36. 5°N), with the Tangnaihai hydrological station as the control outlet of the basin. The region is located in central Eurasia and has a cold plateau climate (Figure 1). The region has an obvious northwest–southeast inclined terrain, with most of the area at an altitude of 3,000 m above sea level, and a large temperature difference between day and night. The region serves as the source of the and plays an important role in grain production and social development for the entire region. Figure 1View largeDownload slideMap of the SRYR and the location of hydrologic and meteorological stations. Figure 1View largeDownload slideMap of the SRYR and the location of hydrologic and meteorological stations. Close modal A temporal and spatial sequence of meteorological elements and a spatial distribution of vegetation coverage and soil are necessary for most physically based hydrological models. The observations included meteorological data from 18 national basic weather stations in China, in and around the SRYR. These data cover the period from 1966 to 2005. The vegetation data were taken from 1-km global land-cover products provided by the University of Maryland. For soil parameters, information from the (NOAA) soil classification was used. In addition to the model input data, hydrological modelling was performed by comparing observed runoff to simulated runoff (Singh et al. 2017). [SEP] Justify:

Output: The text corroborates the claim by discussing the investigation of hydrological responses, specifically assessing the sensitivities of runoff to changes in precipitation and temperature due to climate change scenarios. This aligns with the claim that climate change impacts crop yields as it addresses how alterations in temperature and precipitation affect runoff, which is a crucial component in water availability for crops.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: In addition to the aforementioned Gbp1, these genes included Mal, Oasl2, Ifi202b, Rtp4, Ly6g6c, Ifi27l2a, Usp18, Ifit1, Ifi44, and Ly6g. Interestingly, the interferon regulatory factor 9-encoding gene (IRF9) was 2-fold higher expressed in C3H mice. It may therefore well be that IFN-dependent epithelial responses towards gut bacteria differ in a host-specific manner. However, whether individual IFN-dependent immune responses are the cause or the consequence of differences in intestinal microbiota composition remains elusive. On the one hand mouse strain specific Gbp1 expression has been demonstrated. Among the 46 inbred strains tested, mice with a C3H but not with a C57BL background displayed IFN-inducible GBP-1 synthesis [40]. The importance of genes that are regulated by interferon-alpha or interferon-beta has been concluded from experiments with IRF9-deficient mice. These mice with an impaired IFN-alpha and IFN-beta signaling show higher temporal variations in and lower individuality of intestinal microbiota composition than wild-type control mice and STAT1-deficient mice with defective IFN-gamma signaling [41]. On the other hand intestinal bacteria influence the expression of IFN-inducible genes. For instance, differential expression profiles of IFN-responsive genes in response to monoassociation with Bacteroides thetaiotaomicron and Bifidobacterium longum have been observed in mice. Based on gene interaction network analysis it has been concluded that host responses to B. thetaiotaomicron are centered on tumor necrosis factor alpha triggered gene expression but that the gene expression network associated with Bifidobacterium longum is centered on INF-gamma responsive genes [42]. Taken together, there is good indication that interferons are important players in host-bacteria interactions. However, we did not observe differences between C3H and C57BL/10 mice in the expression of genes coding for interferons, their receptors or for molecules involved in interferon signaling. [SEP] Justify:

Output: The text contrasts the claim by discussing the influence of gut bacteria on the expression of interferon-inducible genes and the variability in intestinal microbiota composition among different mouse strains. It suggests that diversity in gut bacteria has biological implications, indicating that a diverse gut microbiota is important for proper immune responses, as shown by experiments with IRF9-deficient mice who exhibited higher variations in microbiota composition compared to wild-type mice. This suggests that a completely sterile gut, lacking such diversity, would not necessarily be healthier.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography allows for the visualization of complex biomolecules at atomic resolution. [SEP] Text: Since the historical bottleneck for successful neutron crystallographic studies has been the need for sufficiently large crystal volumes, perhaps most importantly perdeuteration permits data collection from much smaller crystal volumes (cf. D-exchanged samples) (Howard et al. , 2011; Weber et al. , 2013), making larger unit-cell systems more accessible to study. Furthermore, neutron map cancellation effects are avoided, allowing all D atoms to be readily visualized (at 2. 5 Å resolution), including those attached to carbon atoms (e. g. CD2, CD3 groups) (Fisher et al. , 2014). Neutron facilities throughout the world have now developed dedicated laboratories for deuteration, such as the at the Institut Laue-Langevin (ILL) and the Bio-at (ORNL). 3. Neutron instrumentation at reactor neutron sources In recent years, great progress has been made in developing new and improved instrumentation for neutron macromolecular crystallography. At reactor neutron sources, the use of cylindrical neutron-sensitive image-plate (NIP) detectors that completely surround the sample and provide large coverage of reciprocal space (>2π steradian) have been incorporated into the design of instrumentation, such as the LADI-III diffractometer (Blakeley et al. , 2010) at the ILL high-flux reactor, the BioDIFF diffractometer ( ) at the II research reactor (FRM II), the BIX-3 and BIX-4 diffractometers (Tanaka et al. , 2002; Kurihara et al. , 2004) at the JRR-3M reactor at the (JAEA) and the diffractometer (Meilleur et al. , 2013) at the (HFIR) at ORNL. In order to reduce the volumes of the crystals required, the LADI-III and diffractometers utilize quasi-Laue methods for data collection, in which a narrow-wavelength band pass (e. g. δλ/λ = 30%) is extracted from the original broadband spectrum of wavelengths (white beam). Quasi-Laue methods provide large gains in flux relative to monochromatic methods, while reducing background scattering and reflection overlap compared with the use of the full white beam. [SEP] Justify:

Output: The text discusses advances in neutron crystallography, specifically improvements in instrumentation and crystal volume requirements. It does not mention X-ray crystallography or its capabilities with regard to visualizing biomolecules at atomic resolution. Therefore, the text is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Climate change affects crop yields due to changes in temperature and precipitation patterns. [SEP] Text: Precipitation critically influences the spatial distribution of hydrological fluxes, especially in runoff. In summer and winter, the spatial variability of the runoff yield is more obvious than that of precipitation. Figure 4View largeDownload slideThe spatial distribution meteorological elements in the historical period (1966–2005). Figure 4View largeDownload slideThe spatial distribution meteorological elements in the historical period (1966–2005). Close modal Precipitation changes results demonstrate that the evaluated climate change projections of precipitation clearly differ from the GCMs or scenarios. Even where the models agree on the direction of precipitation change, there are considerable differences in magnitude. Compared to two other GCMs, on the basis of the absolute value of regional precipitation changes in the peak and valley of each season, the BCC-CSM1. 1 model has the smallest peak-valley difference and therefore has less regional differences. In addition, the difference between present and future precipitation projected by BCC-CSM1. 1 was significantly smaller than that projected in absolute numbers by MIROC-ESM and MIROC-ESM-CHEM. The ensemble mean changes (the average of all GCMs) in average annual precipitation are +8. 7% for RCP4. 5 and +9. 7% for RCP8. 5 at the control area of the Maqu station and +7. 0% for RCP4. 5 and +7. 7% for RCP8. 5 at the control area of the Tangnaihai station. In this significantly water-scarce basin, projected increasing precipitation may help to both mitigate the harm caused by continuous droughts and have a positive effect on the social ecosystem. Our results also indicate that climate change projections of precipitation vary distinctly with region and season (see Figure 5). Compared with other seasons, in winter, precipitation increases significantly, with an increase greater than 50% in some areas under the MIROC-ESM and MIROC-ESM-CHEM models. In the projections of precipitation changes for spring and winter, all models except for BCC-CSM1. 1 project a significant increase in P for the whole study region. In summer, precipitation increases in the study area in BCC-CSM1. 1, but the other two models have a negative P change signal from the northern region. [SEP] Justify:

Output: The text corroborates the claim by discussing the influence of precipitation on hydrological fluxes and how climate change projections indicate significant changes in precipitation. It highlights that the evaluated climate change projections of precipitation differ depending on the region and season, which can ultimately impact crop yields. Increased precipitation, particularly in certain seasons, is noted as potentially beneficial for mitigating drought impacts, aligning with the claim that climate change, through alterations in precipitation, can affect agricultural outputs.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Differentially expressed genes with functions in the immune system included SLPI encoding the secretory leucocyte protease inhibitor (28-fold higher expressed in C3H) and Mep1a coding for meprin 1 α (8-fold higher expressed in C57BL/10). SLPI expression is up-regulated by bacterial antigens and under inflammatory conditions. The protein protects the tissue from immune cell-derived proteases and is implicated in the priming of innate immunity and tissue repair. It also acts as an antibacterial protein and is active against both Gram positive and Gram negative bacteria [43]. Meprins have been implicated in dysregulated immune responses towards gut bacteria in chronic gut inflammation because the expression of meprins is down-regulated in patients with ileal Crohn’s disease. Pre-treatment with meprin α and meprin β decreased the ability of E. coli to bind to host receptors and to induce the expression of pro-inflammatory IL-8 [44]. These findings suggest that SLPI and meprin 1 α may act as microbiota regulators. The intestinal mucus layer in the colon consists of a dense inner bacteria-free and a loose outer layer that is colonized by commensal bacteria. The mucins that form this layer are mainly composed of the densely O-glycosylated mucus protein MUC2. The glycans may serve as substrates and, in addition as adhesion sites for gut bacteria. Therefore, different mucin glycosylation pattern may be involved in the selection of a host specific microbiota [45]. Interestingly, a recent study clearly demonstrated that intestinal expression of β-1,4-N-acetylgalactosaminyltransferase 2 (B4galnt2) which may contribute to mucin decoration with N‑acetylgalactosamine influences gut microbiota in mice [46]. Using a 16S rRNA gene sequencing approach, the authors identified numerous bacterial taxa or operational taxonomic units that were influenced by B4galnt2 expression. Since closely related bacterial species appeared to replace each other in B4galnt2-/- and B4galnt2+/+ mice, respectively, it is difficult to interpret whether B4galnt2-induced changes influence microbiota function. Interestingly, Helicobacter spp. [SEP] Justify:

Output: The text contrasts the claim by discussing several biological functions and regulatory roles of bacteria within the gut environment. It highlights that the intestinal mucus layer is an important structure containing a loose layer colonized by commensal bacteria, which indicates that a diverse bacterial presence is integral to gut health rather than a completely sterile environment. Additionally, the text mentions that bacterial antigens up-regulate immune responses and protect tissue, suggesting that some bacterial diversity supports immune function and gut health.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography allows for the visualization of complex biomolecules at atomic resolution. [SEP] Text: In 2012, the LADI-III diffractometer was relocated to a new guide (H143) closer to the ILL reactor. The new end-position provides an improved band-pass profile (due to the lack of instruments upstream) and most importantly a four-fold increase in flux at the sample position (cf. previous H142 position). Owing to these recent improvements, LADI-III is further extending the limits of the field. Currently the 2. 0 Å resolution structure (PDB code: 4JEC ) of perdeuterated HIV-1 protease (MW ∼21 kDa) with amprenavir bound (Weber et al. , 2013) has the lowest ratio (33) for the crystal volume used for data collection (0. 2 mm3) to the asymmetric unit volume of the macromolecule studied (60000 Å3). Moreover, the 2. 5 Å resolution structure (PDB code: 3Q3L ) of inorganic pyrophosphatase (I-PPase, MW ∼125 kDa) has the largest asymmetric unit volume (a = 106. 1 Å, b = 95. 5 Å, c = 113. 7 Å, β = 98. 1°/C2) deposited thus far (Hughes et al. , 2012). This structure was determined using data from a 5 mm3 D-exchanged crystal of I-PPase; however, more recently data have been collected to ∼2. 5 Å resolution using the LADI-III diffractometer but from a dramatically smaller (0. 32 mm3) perdeuterated crystal of I-PPase, illustrating the huge benefits of perdeuteration (Ng/Garcia-Ruiz, unpublished results). The 1. 05 Å resolution neutron structure (PDB code: 4AR3 ) of the oxidized form of perdeuterated rubredoxin from Pyrococcus furiosus (RdPf, MW ∼6 kDa) is to the highest resolution of any of the structures deposited thus far (Cuypers et al. , 2013). These data were collected from a 6. 9 mm3 perdeuterated crystal of RdPf using the monochromatic thermal neutron diffractometer D19 at the ILL. [SEP] Justify:

Output: The text does not directly address the claim regarding X-ray crystallography and its ability to visualize complex biomolecules at atomic resolution. Instead, it discusses the LADI-III diffractometer and recent developments in neutron diffraction and crystal structures without explicitly linking these advancements to the capabilities of X-ray crystallography.


Input: Task: corroborate the claim using the given text. Claim: Climate change affects crop yields due to changes in temperature and precipitation patterns. [SEP] Text: For autumn, all model results show an increase in P for almost the whole study region, apart from some areas that have so much rainfall that they probably appear in the negative P change signal from the southern region. Figure 5View largeDownload slideThe relative change (%) in predicted average precipitation from the historical data for different scenarios. Figure 5View largeDownload slideThe relative change (%) in predicted average precipitation from the historical data for different scenarios. Close modal Maximum and minimum temperatures changes has a much higher degree of consistency in its spatial pattern trends than precipitation. All GCM model results show a temperature increase in all seasons throughout the year, but there were obvious changes in the magnitude of the variation in different seasons using the same GCM and using different GCMs for the same season. Moreover, for all models, the temperature increase in the RCP8. 5 scenario is greater than that in the RCP4. 5 scenario. For example, in the case of the control area in the Tangnaihai station, the magnitudes of increases in minimum temperature are approximately 1. 60 and 1. 98 °C (RCP4. 5 and RCP8. 5, respectively), whereas for the maximum temperature, the increases in temperature are approximately 1. 36 and 1. 69 °C, respectively. This result is consistent with the ranking of the changes for the representative concentration path scenarios setting. Analysis of the spatial distribution of the maximum and minimum temperature produced a variety of trends (see Figure 6). The maximum and minimum spatial distribution variations in temperature in the study region are clearly different under different GCM scenarios and sometimes even totally opposite in the northwest part, during winter. In the projections of seasonal temperature changes, all models agree on the phenomenon that the increase in the minimum temperature is greater than that of the maximum temperature. The increase in the magnitude of the maximum and minimum temperatures is larger in spring and autumn, and the increase in the magnitude of the temperature in the upstream station (Maqu) was significantly higher than that of the downstream station (Tangnaihai). Figure 6View largeDownload slideThe spatial variations of predicted temperature (°C) from the historical data for different scenarios. (a) the Tmin results of scenarios; (b) the Tmax results of scenarios. Figure 6View largeDownload slideThe spatial variations of predicted temperature (°C) from the historical data for different scenarios. (a) the Tmin results of scenarios; (b) the Tmax results of scenarios. [SEP] Justify:

Output: The text corroborates the claim by detailing how climate change leads to increased temperatures and changes in precipitation patterns. It states that all model results show an increase in precipitation for almost the entire study area and that there's a consistent temperature increase in all seasons. These findings support the assertion that climate change impacts crop yields through alterations in both temperature and precipitation.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Figures AbstractThe spread of antibiotic resistance, originating from the rampant and unrestrictive use of antibiotics in humans and livestock over the past few decades has emerged as a global health problem. This problem has been further compounded by recent reports implicating the gut microbial communities to act as reservoirs of antibiotic resistance. We have profiled the presence of probable antibiotic resistance genes in the gut flora of 275 individuals from eight different nationalities. For this purpose, available metagenomic data sets corresponding to 275 gut microbiomes were analyzed. Sequence similarity searches of the genomic fragments constituting each of these metagenomes were performed against genes conferring resistance to around 240 antibiotics. Potential antibiotic resistance genes conferring resistance against 53 different antibiotics were detected in the human gut microflora analysed in this study. In addition to several geography/country-specific patterns, four distinct clusters of gut microbiomes, referred to as ‘Resistotypes’, exhibiting similarities in their antibiotic resistance profiles, were identified. Groups of antibiotics having similarities in their resistance patterns within each of these clusters were also detected. Apart from this, mobile multi-drug resistance gene operons were detected in certain gut microbiomes. The study highlighted an alarmingly high abundance of antibiotic resistance genes in two infant gut microbiomes. The results obtained in the present study presents a holistic ‘big picture’ on the spectra of antibiotic resistance within our gut microbiota across different geographies. Such insights may help in implementation of new regulations and stringency on the existing ones. Citation: (2013) Analysis of Genes in the of Individuals from and Age-Groups. 8(12): e83823. Niyaz Ahmed, University of Hyderabad, IndiaReceived: August 10, 2013; Accepted: November 10, 2013; Published: December 31, 2013Copyright: © 2013 Ghosh et al. This is an open-access 1. Detection of Genes in (A) Gut metagenomes of and Chinese individuals. The presence of homologs of various antibiotic resistance genes in these gut microbiomes was checked by performing BLASTx searches of the corresponding contigs against the ARDB database [25]. One of the key aspects of this step was to identify an appropriately stringent set of thresholds of BLAST parameters (e. g. [SEP] Justify:

Output: The text contrasts the claim by discussing the presence of antibiotic resistance genes within gut microbiomes, suggesting that a diverse gut flora can harbor significant problems such as antibiotic resistance. This implies that having a completely sterile gut, while unhealthy due to lack of beneficial bacteria, might be preferable to having a diverse but resistant gut microbiome, which presents a potential health threat.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography allows for the visualization of complex biomolecules at atomic resolution. [SEP] Text: Although more commonly used for diffraction studies in structural chemistry, the D19 diffractometer is capable of collecting data to atomic (and potentially sub-atomic) resolution from small macromolecules (cell edges <50 Å) and to medium resolution (1. 8–2. 5 Å) from larger macromolecules (cell edges <100 Å), provided that sufficiently large crystals of several mm3 are available. This has been demonstrated in recent years by the ensemble of neutron studies of xylose isomerase (MW ∼43 kDa) (Kovalevsky et al. , 2010, 2012; Langan et al. , 2014). 4. Neutron instrumentation at spallation neutron sources At spallation neutron sources, neutrons produced by proton pulses are `time-stamped' such that, by recording TOF information, the corresponding energy and wavelength of each neutron can be calculated. TOF techniques in combination with large position-sensitive detectors (PSDs) allow wavelength-resolved Laue patterns to be collected using all the available neutrons (Langan et al. , 2004). The TOF Laue method therefore has all of the advantages of quasi-Laue methods employed at reactor sources, but does not suffer in the same way from reflection overlap and a build up of background scattering over the wavelength range. In the last few years, two new TOF Laue diffractometers dedicated to macromolecular crystallography have been constructed; MaNDi (Coates et al. , 2010) at the Source (SNS) at ORNL and iBIX (Kusaka et al. , 2013) at the Complex (J-PARC). Table 2 provides details of diffractometers currently in operation at reactor and spallation neutron sources. Table 2Neutron diffractometers currently in operation at reactor and spallation neutron sources BIX-3 and BIX-4 have been offline since 2011, but will be online again towards the end of 2015 once the JRR-3M reactor restarts. Instrument name Neutron source and power Detector type Data collection method LADI-58 -Laue (δλ/λ = 30%, λrange options; 2. 6–3. 4, 3. 2–4. 2, 3. 8–5. 0, 4. 1–5. [SEP] Justify:

Output: The text does not address the claim directly regarding X-ray crystallography or its ability to visualize biomolecules at atomic resolution. Instead, it focuses on neutron diffraction techniques and specific instruments used in macromolecular crystallography, without giving information that corroborates or contradicts the claim about X-ray crystallography.


Input: Task: corroborate the claim using the given text. Claim: Climate change affects crop yields due to changes in temperature and precipitation patterns. [SEP] Text: Figure 8View largeDownload slideRelative changes in seasonal precipitation, maximum and minimum temperature, and runoff. Figure 8View largeDownload slideRelative changes in seasonal precipitation, maximum and minimum temperature, and runoff. Close modal Runoff sensitivity to precipitation and temperature changes schemes results section assesses the sensitivity of runoff to precipitation and temperature changes under the different climate change scenarios and identifies the separate and interacting effects of changes in meteorological elements of runoff. Simulation results are shown for each scheme in a 40-year time series of simulated daily runoff using the VIC model (Table 3). Table 3Comparison of the mean annual runoff for the Tmax, Tmin and P effect schemes program with the initial program (scheme I) Station. GCM. Scenario. Simulation scheme (%). II. III. IV. V. VI. VII. VIII. Maqu BCC-CSM1. 1 RCP4. 5 13. 4 −9. 7 −2. 9 10. 4 3. 2 −12. 9 −0. 8 RCP8. 5 17. 6 −12. 3 −2. 9 14. 6 4. 2 −15. 9 −0. 3 MIROC-4. 5 24. 7 −10. 6 −4. 1 19. 5 12. 3 −15. 7 8. 7 RCP8. 5 26. 4 −11. 1 −4. 1 20. 8 13. 3 −16. 2 9. 6 MIROC-ESM-4. 5 28. 9 −10. 7 −4. 2 23. 5 15. 9 −16. 1 11. 5 RCP8. 5 31. 1 −12. 5 −4. 3 25. 2 15. 7 −18. 4 11. 6 Tangnaihai BCC-CSM1. 1 RCP4. 5 14. 6 −10. 8 −2. 3 12. 2 3. 1 −13. 5 −0. 4 RCP8. 5 19. 5 −13. 7 −2. 0 17. 4 4. 5 −16. 7 0. 6 MIROC-4. 5 25. 1 −12. 0 −3. 3 20. 8 11. 4 −16. 4 8. 3 RCP8. 5 25. 5 −13. 1 −3. 2 20. 9 10. 7 −17. 6 7. [SEP] Justify:

Output: The text corroborates the claim by analyzing the sensitivity of runoff to changes in precipitation and temperature due to climate change. It details how different climate scenarios have varying effects on runoff, which is integral for understanding how changes in these meteorological elements can impact agricultural systems, aligning with the idea that climate change affects crop yields through alterations in temperature and precipitation.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Only those antibiotic resistance genes were considered which had at least 70% of their lengths being mapped by these sequences. Sequences mapping to these genes were retained for the next steps. Step 2: For each shortlisted antibiotic resistance gene (as obtained in the previous step), the phylum level taxonomic affiliation of each metagenomic sequence mapping to it was obtained [19]. Based on these affiliations, the sequences were grouped into phylum level bins. Sequences assigned only at the level of Bacteria or Archaea were placed in separate bins. Step 3: In this step, for each shortlisted antibiotic resistance gene (as in Step 1), a given phylum bin was first selected. Sequences belonging to this bin were then assembled using the CAP3 assembly program [27], along with the sequences belonging to the corresponding superkingdom bins (either Bacteria or Archaea). Sequences belonging to all other phylum bins were assembled separately one at a time, along with the unassembled sequences belonging to the corresponding superkingdom bins. Step 4: Finally the antibiotic resistance genes encompassed by the contigs obtained above were profiled as described for the other gut metagenomes (refer to preceding section). The steps 1–3 of this workflow are further summarized in Figure S1. in the Diversity and abundance of antibiotic resistance genes. For a given metagenome, the detected antibiotic resistance genes in each contig were tagged with a resistance profile (i. e. the antibiotic(s) to which the given gene products confer resistance to) of the corresponding antibiotic resistance gene in ARDB. The total number of resistance genes identified in the underlying gut microbial community was then obtained by collating the above information for the entire metagenome. Subsequently, the antibiotic resistance profiles corresponding to each of these genes was obtained. The abundance of antibiotic resistance genes in each metagenome was calculated as the total number of antibiotic resistance genes detected per million base pairs of the corresponding metagenome. The gut microbiota of individuals exposed to a wide variety of antibiotic resistant organisms are expected to have resistance against a much larger array of antibiotics as compared to the gut microbiome of individuals having relatively lesser exposure. This is likely to be reflected in the overall diversity of antibiotic resistance in the corresponding microbiomes, i. e. the number of different antibiotics for which the resistance genes are detected per sequence volume of the corresponding metagenomes. [SEP] Justify:

Output: The text contrasts the claim by discussing the gut microbial community's relationship with antibiotic resistance. It suggests that exposure to a wider variety of antibiotic-resistant organisms can lead to increased resistance against a larger array of antibiotics, highlighting the importance of diversity in the gut microbiome. This implies that a completely sterile gut, lacking this diversity, may not be healthier and may lack the necessary resilience against various antibiotics.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography allows for the visualization of complex biomolecules at atomic resolution. [SEP] Text: 5 Å) -II, 20 (λ choice from 2. 4−5. 6 Å) BIX-3 JRR-3M, 20 (λ = 2. 9 Å) BIX-4 JRR-3M, 20 (λ = 2. 6 Å) 84 -Laue (λrange options, Δλ ≃ 1 Å; 2−3, 2. 8−4, 3. 3−4. 5 Å, plus 2. 8–3. 0 with δλ/λ ≃ 7%) D19 ILL, 58 (λ choice from 0. 8−2. 4 Å) 0. 1 Megawatts Time-sensitive PSD Pulsed (20 Hz) white TOF Laue (λrange 0. 6−7 Å) 2 Megawatts 30 Anger cameras Pulsed (60 Hz or 30 Hz) white TOF Laue; adjustable λ range (Δλ ∼ 2. 16 Å at 60 Hz, Δλ ∼ 4. 32 Å at 30 Hz) iBIX J-PARC, 1 Megawatt 30 λ-shifting fibre detectors Pulsed (25 Hz) white TOF Laue (λrange = 0. 7−7. 8 Å); adjustable λ range (Δλ ∼4. 0 Å) 5. Neutron cryo-crystallography As neutrons of the energies used for crystallographic experiments do not cause any radiation damage, data collection is generally performed at room temperature. Nevertheless, the ability to collect data at cryogenic temperatures is of interest. Since, the reduction of dynamic disorder at cryogenic temperatures lowers atomic displacement parameters (ADPs), this leads to improvements in the nuclear scattering density definition (Blakeley et al. , 2004) and permits the use of smaller crystals [cf. room temperatue (RT)] to achieve equivalent or potentially higher resolution data. In addition, certain crystals are unstable at RT and so the ability to cryo-cool crystals for data collection increases the array of feasible experiments. Moreover, comparison of structures determined at different temperatures can be made. This is important since protonation states can change due to the pKa dependence on temperature. [SEP] Justify:

Output: The text does not directly address the claim regarding X-ray crystallography's ability to visualize biomolecules at atomic resolution. Instead, it discusses various parameters and techniques related to neutron cryo-crystallography and the effects of temperature on data collection, which is unrelated to directly visualizing complex biomolecules.


Input: Task: corroborate the claim using the given text. Claim: Climate change affects crop yields due to changes in temperature and precipitation patterns. [SEP] Text: An analysis of the P effect under different external environmental conditions shows that: (1) with the Tmin changes, all seasons except summer exhibit a slight decrease in the P effect in comparison with the historical condition; (2) with the Tmax changes, all seasons except spring exhibit a significantly decreased P effect, and the range of the decrease for the Maqu station is far higher than that for the Tangnaihai station; (3) with the Tmax and Tmin changes, it can be seen that all seasons have decreased to the lowest P effect; and (4) the gap in the P effect between the stations differs significantly and shows volatile fluctuation in autumn, and there is the smallest gap in the summer season. Compared with the other seasons, in the spring, the P effect is very different and even appears to grow under the condition of Tmax. Figure 11View largeDownload slideThe influence of external climatic conditions on the levels of runoff sensitivities to precipitation and temperature changes. The style of the abscissa is ‘A-B’. The abscissa measures how much of the projected changes are explained by a single effect (Tmax, Tmin or P) when converted to the ‘A’ situation in the context of the ‘B’ situation. Figure 11View largeDownload slideThe influence of external climatic conditions on the levels of runoff sensitivities to precipitation and temperature changes. The style of the abscissa is ‘A-B’. The abscissa measures how much of the projected changes are explained by a single effect (Tmax, Tmin or P) when converted to the ‘A’ situation in the context of the ‘B’ situation. Close modal The results of the analysis of the Tmax effect under different external environment conditions show that: (1) compared with the P and Tmin effects, the Tmax effect of the regional external environment fluctuated greatly; (2) under the condition of P changes, all seasons except spring exhibit a significant decrease in the Tmax effect in comparison with the historical environment; and (3) under the condition of Tmin changes, spring exhibits a significant increase in the Tmax effect. The other seasons show a slight decrease compared with the historical environment; (4) under the condition of P and Tmin changes, it can be seen that all seasons except spring show the lowest Tmax effect. [SEP] Justify:

Output: The text corroborates the claim by analyzing the effects of changes in temperature (Tmax and Tmin) and precipitation on the P effect, which is linked to crop yields. It discusses how different temperature changes (Tmax and Tmin) impact seasonal effects, indicating that climate change is directly influencing these factors and subsequently crop yields.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: In addition, results also indicate (Tables S2 and S3), a majority of genes conferring resistance to the poly−/glycopeptide-based antibiotic vancomycin and bacitracin could only be assigned at the level of phylum (i. e. , the similarity observed between the identified genes with those present in the ARDB was relatively low). While the resistance against bacitracin (the genes bcra and baca) seemed to primarily originate from the phylum Firmicutes, followed by Bacteroidetes and Proteobacteria, the majority of genes conferring resistance to vancomycin (predominantly the genes vanug, vang, vanrg) were observed to belong to the phylum Firmicutes. These results indicate a predominance of antibiotic resistance genes originating from hitherto unknown organisms in the analyzed gut microbiomes. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 1. Number of gut metagenomes containing genes resistant to various antibiotics. of the identified antibiotic resistance genes in the analyzed gut microbial communities were observed to confer resistance to more than one antibiotic. These multi-antibiotic resistance profiles (referred here as wide-spectrum resistance profile) and the corresponding nomenclature codes used are listed in Table S4. Among them, genes having the profile F3H8F5 (conferring resistance to lincosamide, streptogramin B and macrolide) were detected in 182 out of the 275 microbiomes. Thus, apart from genes conferring resistance to single antibiotics, multi-antibiotic resistance genes were also observed to be present in the gut microflora across various nationalities. Geography-specific Patterns in the of Genes in interesting patterns were observed when the diversities of the antibiotic resistance were compared across the gut microbiomes of adult individuals belonging to different nationalities (Table S5, Figure 2, Figure 3). The abundances of antibiotic resistance genes as well as the diversity of antibiotic resistance in the individuals (Spanish, French and Italian) were observed to be significantly higher as compared to the American and Danish individuals (two tailed t-test P<0. 01). This indicated that the gut microbiota of populations have resistance to a wider array of antibiotics as compared to the American and Danish individuals. A similar trend was also observed by Forslund et al. [20]. [SEP] Justify:

Output: The text contrasts the claim by discussing the presence and diversity of antibiotic resistance genes in gut microbiomes. It suggests that a diverse gut microbiota, which includes a wider array of antibiotic resistance genes observed across different populations, is associated with higher genetic diversity and resilience to multiple antibiotics. This diversity undermines the idea that a completely sterile gut, devoid of bacteria, would be healthier.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography allows for the visualization of complex biomolecules at atomic resolution. [SEP] Text: 1 (46. 8) (Å2) 6. 3 Raniso (%) 12. 3 Rfree_aniso (%) 13. 9 Number of protein atoms 3639 Multiple occupancy side/main chains 42/15 Water molecules 674 Partial waters 94 Cu ions 2 Sulfate ions 0. 4 Acetate ions 3 Malonate ions 2 Visible/expected H atoms 1649/2700 PDB access number 5akr Rsym = Σ|I − 〈I〉|/ΣI, where I is the observed intensity and 〈I〉 is the average intensity of multiple symmetry-related observations of that reflection. Rcryst = Σ||Fp obs| − |Fp calc||/Σ|Fp obs|. Rfree = Σ||Fp obs| − |Fp calc||/Σ|Fp obs| where |Fp obs| is from a test set not used in the structural refinement. Raniso and Rfree_aniso are as Rcryst and Rfree, except with anisotropic atomic displacement parameter refinement. Figure 3 Left: the X-ray structure of AcNiR (from Achromobacter cycloclastes), showing the number of H atoms visible (1649) in the electron density maps at 0. 87 Å resolution. Right: the same X-ray structure of AcNiR but showing all 2700 expected H atoms in the structure; 61% of expected H atoms are observed in this 0. 87 Å resolution X-ray structure. Figure 4 The type 2 Cu site of AcNIR with nitrite bound at 0. 87 Å resolution. The catalytically important residue Asp98 is seen in multiple conformation with two distinct conformations visible. The 2Fo − Fc electron density map (in cyan) is contoured at the 1. 5σ level and the Fo − Fc hydrogen omit map (in red) is contoured at the 2. 0σ level. 9. Neutron diffraction data collection and processing for AcNiR The largest crystal available of AcNiR with volume ∼0. 3 mm3 (0. 8 × 0. 7 × 0. 6 mm) was soaked in D2O buffers one month prior to neutron data collection, in order to exchange labile H atoms for D atoms. [SEP] Justify:

Output: The text does not directly address the claim about X-ray crystallography and its ability to visualize biomolecules at atomic resolution. Instead, it contains specific data related to a structural analysis including various mathematical formulations and details about a specific protein structure without explicitly confirming or denying the claim.


Input: Task: corroborate the claim using the given text. Claim: Climate change affects crop yields due to changes in temperature and precipitation patterns. [SEP] Text: Even for spring, the magnitude of growth decreases compared to the condition of Tmin. However, the Tmax effect shows a small increase under the condition of changes in P. The results of analysing the Tmin effect under different external environment conditions show that: (1) under the condition of P changes, all seasons exhibit a slight decrease in the Tmin effect compared with the historical environment; (2) under the condition of Tmax changes, all seasons except spring agree on a significant decrease in the Tmin effect compared with the historical environment, with spring showing a significant increase; (3) under the condition of P and Tmax changes, it can be seen that all seasons except spring show the lowest Tmin effect. Even for spring, the magnitude of growth decreases, compared to the condition of Tmax changes. In other words, Tmax and Tmin weaken the power of each other in spring, under the condition of P changes. this paper, we investigate the hydrological response to future climate change in a case study of the SRYR, where the water resources system is very sensitive to climate change, using the VIC model with the delta change method with different CMIP5 RCP scenarios. Based on the changing characteristics of hydrological elements, as well as meteorological elements including precipitation (P), the minimum and maximum temperature (Tmin and Tmax) are obtained from nine modelling schemes with the control variable method that uses the same parameters of the model over the baseline period (1966–2005) with CMIP5 RCP scenarios in RCP4. 5 and RCP8. 5. The contribution of changes in meteorological factors to runoff at seasonal scales are then quantified. Through the assessment of the amount of runoff change under different schemes, we determined the most sensitive element and season that influences the runoff, and we then quantitatively evaluated their levels of sensitivity. Furthermore, to better understand the influence of external climatic conditions on the levels of runoff sensitivities to precipitation and temperature changes, we also conducted a comparative study on the amount of runoff change under combined meteorological element schemes. The results show that the projected precipitation suggests a general increase, with a larger level either in summer or winter depending on the GCMs used. All scenarios show clearly warming trends in each season, with a larger level in winter, noting particularly that the minimum temperature warming rate is higher than that of the maximum temperature. [SEP] Justify:

Output: The text corroborates the claim by discussing how changes in temperature (Tmin and Tmax) and precipitation (P) influence crop yields and hydrological responses. It specifically mentions that the magnitude of growth decreases under the changing conditions of Tmin and Tmax, thereby indicating that temperature changes are affecting crop yields. Furthermore, the assessment of the hydrological response to future climate change directly relates to how these meteorological changes can impact agricultural outcomes.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Similarly, the diversity of antibiotic resistance as well as the abundances of resistance genes of the Japanese individuals was observed to be significantly higher as compared to the Danish and American populations (two tailed t-test P<0. 02). Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 2. Abundances of antibiotic resistance (indicated in a color coded format) identified in the adult gut metagenomes from seven different nationalities. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 3. Diversity and Abundance of antibiotic resistance genes across nationalities. Diversity of antibiotic resistance genes across nationalities are shown in (A) and, the Abundances of antibiotic resistance genes, in the gut of individuals from various nationalities are shown in (B). Details of the gut microbiomes obtained from individuals belonging to various nationalities (indicated in the figure) are provided in Table S1. Chinese individuals were observed to have significantly higher abundances of antibiotic resistance genes as compared to those of other nationalities (two tailed t-test P<1e-12) (Figure 3). This result is also in line with those obtained by Hu et al [21]. However, the diversity of antibiotic resistance in the Chinese populations was observed to be significantly lower than those in other nationalities. The above results thus indicate that the Chinese individuals have higher number of genes conferring resistance to the same antibiotic as compared to those from other geographies. Within the 267 adult gut microbiomes, the diversity of antibiotic resistance was observed to have a rough correlation with the age of the individuals (R = 0. 22, P<0. 003) (Figure 4). This observation indicates that the reservoir of antibiotic resistance genes in the gut microbiome is likely to increase with the age of the individual. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 4. Variation of the antibiotic resistance diversity (in the 267 adult gut microbiomes) with the age of the individuals. Details on the names of the different gut microbiomes indicated in the figure are provided in Table S1. antibiotic resistance genes were detected only in the Chinese population. Among the 157 antibiotic resistance genes whose homologs were detected in the current study, 35 were observed to be present only in the Chinese gut metagenomes (Table S6). [SEP] Justify:

Output: The text contrasts the claim by discussing the correlation between diversity of antibiotic resistance genes and the populations studied. It indicates that the diversity of gut microbiomes, including their antibiotic resistance profiles, varies across different nationalities and suggests that higher diversity (like that found in some populations) may be associated with different health indices. This implicitly challenges the idea that a completely sterile gut, which would lack such diversity, is healthier.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography allows for the visualization of complex biomolecules at atomic resolution. [SEP] Text: Using exposures from 12 to 24 h, diffraction data at RT were collected from the D-exchanged crystal to 2. 3 Å resolution (Fig. 5) over a period of 15 days using LADI-III. Data were indexed and integrated using (Campbell et al. , 1998), wavelength-normalized using (Arzt et al. , 1999) and scaled and merged using the CCP4 program SCALA (Winn et al. , 2011). Data-collection and processing statistics for the neutron data are given in Table 4. Structural refinement using the neutron data is currently in progress and will be reported elsewhere. In addition, perdeuterated AcNiR has since been produced in the at the ILL, and larger crystals of ∼1 mm3 have been grown (Fig. 6). In summer 2015, we hope to collect a complete data set using LADI-III on these larger perdeuterated AcNiR crystals, with the aim to extend the resolution of the diffraction data such that the visibility of all H atoms (as D atoms) in the proton pathways will be enhanced. Table 4Neutron data-collection and processing statistics for AcNiR Values in parentheses are for the highest-resolution shell. Neutron source, instrument -III Space group P213; No. 198 Unit-cell parameters a = 96. 3 Å, b = 96. 3 Å, c = 96. 3 Å, α = 90°, β = 90°, γ = 90° Wavelength range (Å) 3. 13–4. 05 Number of images 16 Angle between images (°) 7 Average exposure time (min) 1365 Resolution (Å) 40–2. 3 (2. 42–2. 3) Total number of reflections 61260 (4095) Unique reflections 10414 (1273) Completeness (%) 78. 2 (66. 0) Multiplicity 5. 9 (3. 2) I/σ(I) 8. 6 (5. 7) Rmerge 0. 182 (0. 219) Rp. i. m 0. 062 (0. 112) Figure 5 Left: a neutron quasi-Laue diffraction pattern from a D-exchanged crystal of AcNiR (volume = 0. 3 mm3) collected using the quasi-Laue LADI-III diffractometer. [SEP] Justify:

Output: The text provides detailed information about neutron diffraction data collection and processing related to a specific crystal but does not mention or support the claim about X-ray crystallography or its ability to visualize biomolecules at atomic resolution. Therefore, it is deemed irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Climate change affects crop yields due to changes in temperature and precipitation patterns. [SEP] Text: According to the results of statistical analysis, the magnitude of runoff changes depends considerably on the GCMs (Xu et al. 2009). These results are in good agreement with those by Zhang et al. (2017), and they also provide a detailed analysis of the seasonal scale. A large increase in precipitation and rapidly warming temperature are the prominent reasons for the runoff changes (Tang et al. 2012). We found that there is an obvious difference in the impact that the meteorological elements have on the runoff. The effect of precipitation changes determines the changes in seasonal runoff to a large degree (consistent with previous studies), with a 23% degree of influence relative to baseline period runoff, followed by the effects of maximum temperatures (approaching 12%) and the minimum temperatures (approaching 3%). The effect of maximum temperature changes is outclassed by that of the minimum temperature changes (Liu et al. 2017), despite the fact that the magnitude of increase in the minimum temperature is greater than that of the maximum temperature. Winter is the season that displays the greatest sensitivity of runoff to precipitation and maximum temperature change; but for the minimum temperature change, spring is the most sensitive season. The levels of runoff sensitivities to precipitation and temperature changes vary with different external climatic conditions. The gap in the P effect between the stations differs significantly and shows volatile fluctuation in autumn, with the smallest gap occurring in the summer season. Tmax and Tmin weaken the power of each other in spring under the condition of P changes. Great efforts have been made to fully assess runoff sensitivities to precipitation and temperature changes in this study; however, further research is required on the impact of frozen ground degradation on runoff and other indirect effects caused by temperature increases (Li et al. 2017a; Wang et al. 2018). A series of limitations exists in the process of hydrological modelling simulations (Mockler et al. 2016; Trudel et al. 2017), although previous studies have shown that GCMs are the most important factor of uncertainty in hydrological simulation. However, other uncertainty factors such as downscaling methods and types of hydrological models have also been found to have great significance in hydrological simulations (Teutschbein et al. 2011; Srivastava et al. 2014; Yuan et al. 2017). Although three GCMs and two emission scenarios were used in this study, other uncertainties were not taken into account. [SEP] Justify:

Output: The text corroborates the claim by detailing how changes in precipitation and temperature, specifically maximum and minimum temperatures, significantly influence runoff, which relates to crop yields. It indicates that a large increase in precipitation and warming temperatures are key factors affecting hydrological responses, which in turn could affect agricultural productivity. The sensitivity of runoff to these climatic changes supports the assertion that these variables are critical in understanding how climate change may impact crop yields.


Input: Task: contrast the claim using the given text. Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Antibiotic resistance genes in the gut microbiome of Japanese infants. An extremely high abundance of antibiotic resistance genes was observed in the gut microflora of two Japanese infants (JP-IN-1 aged 4 months and JP-IN-4 aged 7 months). The gut microbial communities in these two infants were observed to harbor resistance genes against 21 different antibiotics (Tables S2 and S5). However, the microbial groups containing the genes resistant to these antibiotics were observed to be different in these two samples. and Enterobacter genera accounted for most of the antibiotic resistance genes in the JP-IN-1 sample, a majority of these genes in the JP-IN-4 sample were observed to originate from the genus Escherichia and uncharacterized organism(s) belonging to Proteobacteria phylum. The over-abundance of antibiotic resistance genes in the gut microflora of these two infants is alarming. across Figure 5 depicts the ranked abundances of the resistance profiles corresponding to different antibiotic across the gut metagenomes. Based on the similarities in their resistance profiles, the antibiotics could be clustered into four groups, with resistance profile to fosmidomycin having abundance pattern distinct from the remaining four groups (Figure 5). The first group G1 contained the antibiotics vancomycin and bacitracin, the resistances to which were observed to be present across all gut microbiomes (but were relatively less abundant in the Chinese gut microbiomes). The group G2 contained the antibiotics F3H8F5 (conferring resistance to lincosamide, macrolide andstreptogramin B), tetracycline and cephalosporin. Resistance to these three antibiotics, although detected across all geographies, were observed to have a relatively higher abundance in the Chinese gut metagenomes. Amongst the non-Chinese gut microbiomes, while resistance to cephalosporin was observed to be higher in the American individuals, the resistance to F3H8H5 was observed to be higher in French/Italian/Japanese and certain Spanish individuals. [SEP] Justify:

Output: The text contrasts the claim by discussing the presence of antibiotic resistance genes in the gut microbiome of infants, suggesting that a diverse gut microbiome may play a role in the abundance of these resistance genes. The observation of different microbial groups and their resistance profiles indicates that a completely sterile gut, likely lacking in microbial diversity, might not be healthier, particularly given the alarming over-abundance of resistance genes in the subjects discussed.