Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: However, the number of species that can survive at these low saturation conditions is limited compared with the species richness of the surrounding area. These findings are generally consistent with those of Fabricius et al. (2011) from CO2 vents in Guinea, where the diversity and abundance of structurally complex corals was reduced threefold at low pH, yet Porites corals were still found at pH below 7. 7 and aragonite saturation of 2. 9. Morelos, the conditions are more extreme as the water is often undersaturated or has much lower saturation values than 2. 9, yet Porites astreoides and Siderastrea radians corals are still abundant. Therefore, the site demonstrates that certain coral species may tolerate extreme acidification events and still maintain their ability to calcify. While we did not measure calcification rates during this study, we note that the ojos are part of a complex and elaborate underground conduit system that has developed over millennia in this karstic terrain. The seepage at these sites has therefore been continuous for an extended period of time compared with the average age of coral colonies. Thus, the corals settled, calcified, and the colonies grew within the plume of low-pH groundwater discharge. This is different than the more ephemeral volcanic vent sites, and therefore the ojos represent areas where the ecosystem had ample time to adapt and evolve exposed to low-pH conditions. Although the coral species found at the ojo sites (S. radians, P. astreoides, and P. divaricata) all occur on reef structures, they are rarely major contributors to the framework of the Meso-Reef: thus, while their presence is encouraging when considering the future of these specific scleractinian species, there are severe implications for the future of reef ecosystems and the many organisms that rely on structurally complex corals to build the reef framework. Specifically, our data suggest that as seawater saturation nears 2. 5, today’s larger, dominant, framework-building corals of the Meso-(e. g. , Acropora and Montastraea), may be replaced by smaller, patchily distributed colonies of only a few species. While only a limited number of coral species live in areas exposed to the low-pH groundwater, their presence in undersaturated waters raises interesting questions. [SEP] Justify:

Output: The text corroborates the claim by detailing how low pH conditions, indicative of ocean acidification, significantly affect coral species diversity and abundance. It reports that 'the diversity and abundance of structurally complex corals was reduced threefold at low pH', aligning with the claim that coral reefs are impacted by ocean conditions. Moreover, it discusses the implications for reef ecosystems as seawater saturation decreases, suggesting that the conditions due to ocean acidification could lead to changes in dominant coral species, thereby supporting the claim further.


Input: Task: contrast the claim using the given text. Claim: All sustainable buildings are completely carbon-neutral. [SEP] Text: This paper has shown that despite having clean hydroelectricity, if Bhutan follows the 2014 BAU energy-economy pathway, the GHG emissions arising from it will exceed the sink capacity by as early as 2037 under high economic growth due to its industry and transport GHG. Low growth will mean the CN goal is easier to maintain but it will not achieve other goals. The model however does show that all three goals of increased wealth and happiness can be achieved and at the same time maintaining carbon neutrality, through greater electrification of industry and transport. This shows that the integration of CN with economic growth and the SDG’s can be achieved by other developing nations, a message of great hope as we approach the future. Nevertheless, such general conclusions require more detailed and nuanced policy directions in any one location. In this case the LEAP model suggests Bhutan can leapfrog existing carbon intensive technologies by adopting efficient technologies and fuel switching options to curb its rising carbon emissions especially in the industry and transport sectors. But the model runs for the various scenarios show that energy system changes in Bhutan are possible to maintain its CN status though there are additional costs that may make this difficult, except under the CN_NDC Plan scenario where Bhutan will achieve both financial savings as well as sufficient emissions reduction to maintain CN. However, this is not the high growth scenario that is more likely due to Bhutan’s aspiration and policy of becoming a middle-income nation by 2023 and its policy of maintaining its fairness, sufficiency and well-being as measured by GNH. Under these high growth pressures Bhutan will need to rapidly electrify their industry and transport as part of its economic growth strategy. The costs are not prohibitive, just 2% of GDP, and the results achieve GNH and GDP commitments. Disruptive innovations in transport and industry may make this even easier as reduced cost solutions for electric transport and industry electrification suggested for Bhutan are likely to be part of the agenda of economic growth in all emerging nations under growth pressures [55]. Such approaches have been called regenerative development as a way of showing that reducing impacts is not enough when a net zero outcome is required [56]. This study therefore recommends detailed planning by any emerging nation as it approaches the future under such growth pressures whilst needing to adapt their economies to the net zero Paris agenda. [SEP] Justify:

Output: The text contrasts the claim by discussing how maintaining carbon neutrality (CN) can be complex and dependent on various factors, including growth scenarios and economic strategies. It indicates that Bhutan faces challenges in maintaining CN while aiming for economic growth. The mention of increased GHG emissions if the 2014 BAU energy-economy pathway is followed underlines that not all sustainable approaches guarantee complete carbon neutrality, especially in the context of high economic growth. Therefore, while carbon neutrality is a goal, achieving it completely in sustainable buildings is contingent on numerous factors, which counters the absolute nature of the claim.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Further, stabilizing selection stands in contrast to purifying selection on individual residues, the major evolutionary mechanism thought to preserve function in stably folded regions of the proteome (Taylor and Raes, 2004). Thus, we propose that these two major biophysical classes of protein regions (IDRs vs. folded regions) also evolve under two different functional regimes. Materials and methods Multiple sequence alignments and visualization Request a detailed protocol We acquired orthologs of Saccharomyces cerevisiae from the (Byrne and Wolfe, 2005) and made multiple sequence alignments using MAFFT (Katoh and Standley, 2013) with default settings, as previously described (et al. , 2014; et al. , 2012). We visualized multiple sequence alignments using Jalview (Waterhouse et al. , 2009). Quantification of evolutionary divergence of IDRs and ordered regions of the proteome Request a detailed protocol We identified IDRs in the S. cerevisiae proteome using 3 (Jones and Cozzetto, 2015) and filtered them to include only those that are 30 amino acids or longer. We identified the non-disordered regions of the proteome as the inverse subset of the IDRs, and again only included regions that are 30 amino acids or longer. Using the multiple sequence alignments constructed for these protein regions (as above), and only including those proteins for which there at least 10 species in the alignment and at least 10 amino acids for each species, we calculated evolutionary distances for each region using PAML (Yang, 2007) using the WAG model, with an initial kappa of 2, initial omega of 0. 4, and clean data set to 0. We used the sum of branch lengths for each region to estimate the evolutionary divergence, and plotted the distribution of this metric for IDRs and non-IDRs in the S. cerevisiae proteome in Figure 1—figure supplement 1. Quantification of IDR overlap with pfam annotations Request a detailed protocol We obtained the list of Pfam (El-Gebali et al. , 2019) domain coordinates for S. cerevisiae from the Database (SGD) (Cherry et al. , 2012). We included domain coordinates that had e-values less than or equal to 1, and which occurred in more than one protein in the S. cerevisiae proteome. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses stabilizing selection, purifying selection, and evolutionary analysis of proteins, without mentioning X-ray crystallography or its application in determining protein structures.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Physiological and/or genetic adaptations allowing corals and other calcifying organisms to persist under low saturation, low-pH conditions are largely unknown and are currently under investigation. One suggestion is that the energy allocated to calcification in such conditions may come at the expense of other metabolic activities and result in lower growth rates (Atkinson et al. 1995; Jokiel et al. 2008; Cohen and Holcomb 2009); another idea is that high nutrient concentrations could provide energetic resources that may offset deleterious effects of high CO2 (Jokiel et al. 2008; Cohen and Holcomb 2009). Laboratory experiments with Astrangia, Occulina, Porites, Montipora, and Favia sp. show that while calcification rates were reduced under low saturation (Ω ~ 1. 5) conditions, the addition of inorganic nutrients or food under the same low saturation conditions enabled the corals to maintain 75–100% of their calcification rates (Langdon and Atkinson 2005; Ries et al. 2009; Cohen and Holcomb 2009; Holcomb et al. 2009). These ideas are consistent with our field observations that certain coral species may survive in undersaturated waters when nutrient concentrations are high (ojo waters had 2–10 times higher nutrient concentrations than surrounding water). The interplay of nutrient availability, low saturation conditions, and calcification in corals should be further investigated under natural conditions as this may be important for predicting future coral distribution and survival. Another potential explanation for the survival of some coral species in the immediate vicinity of the ojos is that daily or seasonal fluctuations in discharge may periodically expose the corals to ambient waters with high saturation levels. Our samples were taken on three field trips over a 15-month period and were monitored continuously over 2 months, and pH levels were nearly always low at ojo sites, where the three tolerant scleractinian species were present (Hofmann et al. 2011). However, it is possible that the groundwater discharge fluxes do vary over time scales we have not captured, and that these corals experience intermittent relief from low-pH, low aragonite saturation waters. Semi-permanent sensors installed over a whole year will enable us to determine the consistency of saturation levels around the corals. If fluctuations in discharge do impact saturation conditions, we will be able to estimate possible response thresholds for the coral species living nearest to the ojo centers (e. g. [SEP] Justify:

Output: The text corroborates the claim by discussing the physiological and genetic adaptations of corals under low saturation and low pH conditions, which directly relates to ocean acidification. It notes that calcification rates are reduced in these conditions, which indicates an effect of ocean acidification on coral reefs. Additionally, the text mentions the importance of nutrient availability in the context of low pH waters and highlights field observations on coral survival under varying saturation levels, supporting the claim that coral reefs are influenced by factors associated with ocean acidification and warming.


Input: Task: contrast the claim using the given text. Claim: All sustainable buildings are completely carbon-neutral. [SEP] Text: The modelling of Bhutan’s future suggests it will need to develop a CN strategy that can avoid the structural path dependence and lock-in of carbon intensive infrastructure by enabling new CN technologies for simultaneous growth in GDP and GNH with reductions in GHG. Such changes may require concerted efforts to identify potential barriers to deploy these options and seek access to finance [57]. Such development issues are central to the future planning of any emerging nation and this study shows that it is possible to maintain CN status under both low and high growth pressures. study undertaken here is a high level demonstration of how developing and developed nations, can avoid the lock-in of structural path dependence on carbon intensive activities whilst growing economically and socially. But the particular context of each place will need to be addressed so that growth pressures can be adapted to achieve these simultaneous goals. MethodsThis study used the Long-range Planning (LEAP) model to conduct an integrated energy system analysis of Bhutan through scenario modelling. LEAP is an energy system model developed by the Institute (SEI), which is flexible, user-friendly and free for emerging economies [58]. The objective function of LEAP is cost minimisation from a societal perspective. LEAP can support combinations of top-down and bottom-up approaches to energy system modelling [59], and it is capable of modelling issues beyond technological choices and thus is useful for capacity building applications [60] and to assess Goal issues [59, 61]. The LEAP model is increasingly being used for low emission development (LED) studies, notably in emerging economies [59, 60, 62,63,64,65,66,67,68]. In building the LEAP Bhutan model, its optimisation capability was used for electricity generation expansion alongside its simulation features. The simulation model gives more flexibility to the user to incorporate practical issues. Scope and limitationsIn this study, discussions and analysis are limited to those topics which are deemed pertinent to understanding the overall energy mix, the associated cost and GHG emissions purely from a CN perspective. For this reason, the trend and implications of local air pollutants, are not analysed as the focus is primarily on GHG emissions represented by carbon dioxide equivalent (CO2e) consisting of carbon dioxide (CO2), methane (CH4) and Nitrous oxide (N2O). The study also does not incorporate embodied carbon emissions, or costs associated with infrastructure, houses and buildings including retrofits, which can reduce energy demand. [SEP] Justify:

Output: The text contrasts the claim by indicating that the study focuses on achieving carbon-neutral (CN) status while recognizing the complexities involved. It notes barriers in deploying CN technologies and emphasizes that the context of each location must be considered to adapt growth pressures, suggesting that not all sustainable buildings can be assumed to be completely carbon-neutral. Moreover, the study explicitly states that it does not analyze embodied carbon emissions or costs associated with infrastructure, implying that achieving full carbon neutrality is not guaranteed in all cases.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: We then computed the percentage overlap of each IDR (coordinates determined as above) with the Pfam domain coordinates, and plotted the distribution of percent overlap values for all predicted IDRs in the S. cerevisiae proteome in Figure 1—figure supplement 2. Evolutionary analysis of diverged disordered regions Request a detailed protocol Evolutionary analysis of diverged disordered regions was performed as in Zarin et al. (2017), with some modifications to facilitate proteome-wide analysis. Briefly, we sought to simulate evolution of disordered regions while being agnostic to the conservation of molecular features that we tested. Using the multiple sequence alignments of S. cerevisiae IDRs and species branch lengths (as described above), we used the previously described phylo-HMM software (et al. , 2014; et al. , 2012) to obtain maximum likelihood estimates of the site-specific (i. e. ‘column’) and ‘local’ rate of evolution for each amino acid. The phylo-HMM exploits preferential conservation of SLiMs in disordered regions to predict them by comparing these site-specific rates to the ‘local’ rates of evolution. Because indels are frequently found in disordered regions, the phylo-HMM software models sequence evolution as a probabilistic evolutionary process that considers amino acid substitutions according to a standard continuous time markov process framework (Durbin et al. , 1998) and generation of indels with power-law distribution (Cartwright, 2006). For our set of data, we used the default parameters of the software, that is the parameters used in the original study on a similar set of data (for example, we used a window size of 31 alignment columns to estimate the ‘local’ rate of evolution). Having predicted these rates of evolution and conserved SLiMs for each IDR, we simulated 1000 orthologous sets of IDRs for each IDR. We did this using a previously described disordered region evolution simulator (et al. , 2014; et al. , 2012) that preserves SLiMs and evolves disordered regions according to a disordered region-specific substitution matrix, but is agnostic to other molecular features. We used the S. cerevisiae sequence as the root for the simulator. [SEP] Justify:

Output: The text is irrelevant to the claim because it discusses the analysis of intrinsically disordered regions (IDRs) and evolutionary simulations in the context of S. cerevisiae proteome rather than mentioning or supporting the use of X-ray crystallography for determining the 3D structures of proteins.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: , minimum duration or fraction of time spent in supersaturated conditions required for corals to survive). In natural environments, it is not possible to entirely exclude the impact of other variables, and for the ojos specifically the impact of lower salinity, on the observed coral distribution. However, previous studies suggest that many species are able to withstand osmotic stress with limited harmful effects when exposed to lower than ambient salinities (Coles and Jokiel 1978; Hoegh-Guldberg and Smith 1989; Xiubau et al. 2009). In fact, Coles and Jokiel (1978) showed that salinities as low as 25 ppt in themselves were insufficient to have any negative impacts on Montipora sp. , a coral found in abundance along the coast. Here, we only present data from ojos with salinities consistently above 25 ppt. and many other corals were commonly observed at the control sites, yet not within the low saturation zones, this suggests that salinity itself is insufficient to explain the observed distribution patterns. While the impact of multiple stressors (i. e. , high temperature, light, and/or sedimentation) can compound the salinity factor and cause negative responses across species (Coles and Jokiel 1978; Hoegh-Guldberg and Smith 1989; Lirman and Manzello 2009; Xiubau et al. 2009), these discharge sites actually experience lower than ambient temperatures while light and sedimentation levels remain the same at the ojos and at the control sites. Therefore, by only including data from ojos that have salinities consistently higher than 25 ppt, we have attempted to control for, if not entirely negate, the impact of salinity on coral distribution found at Puerto Morelos. This work illustrates that while the effects of ocean acidification on coral reefs and other calcifying organisms may be severe, the impacts will differ considerably across various species and ecosystems and some calcifying corals given the right condition will continue to grow and calcify. It is possible, therefore, that the ocean acidification scenario will result in an ecosystem shift along the Reef, in which today’s frame-building colonies are replaced by more tolerant species such as Porites and Siderastrea. The decrease in species richness observed when Ωarag < 2. [SEP] Justify:

Output: The text corroborates the claim by discussing how ocean acidification impacts coral reefs and other calcifying organisms. It notes that 'the effects of ocean acidification on coral reefs... may be severe,' indicating that these factors indeed affect coral ecology. Furthermore, it suggests potential shifts in the ecosystem as a result of these stressors, supporting the claim regarding the impact of ocean acidification on coral reefs.


Input: Task: contrast the claim using the given text. Claim: All sustainable buildings are completely carbon-neutral. [SEP] Text: This study specified four aggregated measures based on data availability, suitability to Bhutan’s context and the emerging global vision shown in Table 4 with detail descriptions provided in 5. 3). Selection of the mitigation measuresThe mitigation measures outlined in Table 4 above were then deployed one by one onto the BAU scenario to obtain the cost of mitigating a tonne of GHG through the cost-benefit summary report in the LEAP model. It was observed that none of the measures except for the F8050 were effective enough on their own to keep the GHG emissions within the sink capacity, despite some of the measures being no-regret options (i. e. options with no cost or negative cost, meaning they save money). Given these limits, the mitigation measures were combined to form groups of cost-effective CN measures to hold the emission level within the sink capacity at the lowest cost of mitigation during the planning period. The process of moving from one combination to the next is based on the cost of mitigation shown in Fig. 5. The cheaper options (e. g. 1st and 2nd lowest) were combined first to see if the emissions level remains within the sink capacity, if not, then the 1st is combined with the 3rd lowest and so on. If the combination of any two measures failed to keep the emission levels within the sink capacity, then the combination of three measures were applied onto the scenario under investigation. This leads to the formation of scenarios. Fig. 5The cost of aggregated carbon neutral measures (US$/tCO2e)Full size image– carbon neutral scenariosrepresents the BAU scenario, which includes the two mitigation measures ‘IS + ATECH’ that form the least cost option in holding the emissions level within the sink capacity. Similarly, CN_NDCPlan represents the scenario with ‘IS + MF30’ as the combined measures. represents the high economic growth (high GDP) scenario with ‘IS + MF30 + F8050’ as the combined measures. Under the LGDP scenario, the emissions level remains well below the sink capacity, thus application of the mitigation measures does not arise. Low growth may not be an effective policy, however, as economic and social goals are largely pushing the country towards a high growth future based on the need to create opportunities and growth provides these. [SEP] Justify:

Output: The text contrasts the claim by highlighting that while mitigation measures were applied to control GHG emissions, the outcome showed that not all measures were effective enough on their own to maintain emissions within the sink capacity. Specifically, it states that 'none of the measures except for the F8050 were effective enough on their own,' suggesting that the complete carbon neutrality claimed is not universally achievable or guaranteed in all sustainable buildings.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: The simulator uses a model similar to the phylo-HMM where amino acids can either mutate or generate an indel according to the specified rates of evolution. In contrast to the phylo-HMM, the substitution matrix used in the simulator was obtained using the stationary frequencies of the 20 amino acids derived from predicted disordered regions in the S. cerevisiae proteome, and exchangeability between pairs of amino acids was inferred from closely related species S. cerevisiae, Saccharomyces paradoxus, S. mikatae, and Saccharomyces bayanus (as in et al. , 2014; et al. , 2012). Therefore, as evolutionary time increases, sequences diverge from the initial S. cerevisiae sequence according to the phylogenetic tree and tend towards the equilibrium stationary frequencies of disordered amino acids. This simulator requires a scaling factor to convert evolutionary distances from substitutions per site as obtained from PAML (Yang, 2007). We chose the scaling factor such that the average distance between S. cerevisiae and S. uvarum over all the IDR alignments equals 1. Sequences and trees were read into R using the ‘seqinr’ (Charif and Lobry, 2007) and ‘ape’ (Paradis and Schliep, 2019) packages, respectively. Sequences were parsed in R using the ‘stringr’ (Wickham, 2010) and ‘stringi’ (Gagolewski, 2019) packages. We calculated all the sequence features for the real and simulated set of IDR orthologs using custom functions in R except for isoelectric point, which was computed using the computePI function in seqinr (Charif and Lobry, 2007), as well as ‘Omega’ (Martin et al. , 2016), ‘Kappa’ (Das and Pappu, 2013), and Wootton-Federhen complexity (Wootton and Federhen, 1993), which were calculated using the localCider program (Holehouse et al. , 2017) called through R using the ‘rPython’ package (Bellosta, 2015). [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses a simulator and methods related to evolutionary distances and sequence features in a programming context using R. It does not mention X-ray crystallography or provide any information about determining the 3D structures of proteins.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: AbstractOcean acidification (OA) is a major threat to marine calcifying organisms. This manuscript gives an overview of the physiological effects of acidification on reef-building corals from a cellular to population scale. In addition, we present the first review of the indirect effects resulting from altered species interactions. We find that the direct effects of acidification are more consistently negative at larger spatial scales, suggesting an accumulation of sub-lethal physiological effects can result in notable changes at a population and an ecosystem level. We identify that the indirect effects of acidification also have the potential to contribute to declines in coral cover under future acidified conditions. Of particular concern for reef persistence are declines in the abundance of crustose coralline algae which can result in loss of stable substrate and settlement cues for corals, potentially compounding the direct negative effects on coral recruitment rates. In addition, an increase in the abundance of bioeroders and bioerosive capacity may compound declines in calcification and result in a shift towards net dissolution. There are significant knowledge gaps around many indirect effects, including changes in herbivory and associated coral–macroalgal interactions, and changes in habitat provision of corals to fish, invertebrates and plankton, and the impact of changes to these interactions for both individual corals and reef biodiversity as structural complexity declines. This research highlights the potential of indirect effects to contribute to alterations in reef ecosystem functions and processes. Such knowledge will be critical for scaling-up the impacts of OA from individual corals to reef ecosystems and for understanding the effects of OA on reef-dependent human societies. Similar content being viewed by others Bioerosion and Growth: A 0. 1 unit decline in oceanic pH since the industrial revolution and is likely to cause up to an additional 0. 3–0. 32 unit decline by the end of the century (IPCC 2014; Gattuso et al. 2015). Changes in pH also result in a change in the concentrations of carbonate and bicarbonate ions in seawater which can affect fundamental organism physiology, such as calcification (Erez et al. 2011). As a result, OA is widely recognised to be a pervasive threat to marine biodiversity (Garrard et al. 2013; Harvey et al. 2013). [SEP] Justify:

Output: The text corroborates the claim by mentioning that ocean acidification (OA) is a major threat to marine calcifying organisms, particularly reef-building corals, and discusses the direct negative effects of acidification on coral physiology and population dynamics. It emphasizes that these effects can lead to notable changes at the ecosystem level, thus confirming the impact of ocean acidification on coral reefs.


Input: Task: contrast the claim using the given text. Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: A retrospective towards a biodegradable material concept for future Indonesian sustainable architecture 1. Hence, to support a better economic condition, equipped with an assurance of an environmentally friendly setting, Indonesia must generate a competitive yet dynamic development, including global appreciation of green building and sustainable city. The research aims to find the concept of biodegradable materials for the future sustainable architecture of Indonesia from local natural materials typical of Indonesia. Understanding the context, following the global trend in biodegradable material while respecting local resources shall be the main agenda for developing green development in Indonesia, especially by advancing its tropical architecture. Fig. 1Source: BP-REDD + Indonesia, 2015 (BP-REDD+, 2015), www. reddplus. go. id downloaded on March 28, 2020Environmental issues are illustrated by deforestation and forest degradation mapping in Indonesia. Full size imageMaterial and methodsTheoretical approachThe idea of new sustainability has risen since the third millennium; the 2000 year has influenced a cultural significant around the world, contributing to the idea of a utopian future as the year has created a sense of the beginning of a new century. Climate change reports and global warming news have spread worldwide, stimulating more serious actions from reducing gas emissions to heatwaves’ control across the continents. More progressive movements are growing to shift the traditional perspective on green living towards a new sustainable generation (McLennan 2004). After two decades, the new sustainability has claimed that the future lies in regeneration. The action includes restoring ecosystems, rebalancing our climates, and rebuilding economies (Greene 2019). The landscape of innovation has set the idea of contemporary sustainability (Almy and Benedikt 2007) and work on: integrating nature with technology (Aziz and Sherif 2016), reinventing tradition for sustainability, less waste (Mostafa et al. 2018), edible products, re-use/recycle, and researching for new materials (Greene 2019). Despite varied, these actions are going towards an integrated ecosystem, respecting the process of sustainable activities, and expecting immediate results towards achieving zero waste, as illustrated by Fig. 2. When it comes to product innovation, the worlds are curious to invest in creative and scientific materials. The reborn of the renaissance is in demand; the idea of revisiting tradition, redefining classic, rethinking timeless, exploring philosophy, yet reinterpreting art bridge the gap between nature and humanity (McLennan 2004). [SEP] Justify:

Output: The text contrasts the claim by discussing the broader context of sustainability and biodegradable materials in architecture. It emphasizes the research focus on 'biodegradable materials for the future sustainable architecture of Indonesia' but does not conclude that all materials used in sustainable architecture are biodegradable. Instead, it implies a selective approach towards biodegradable materials, suggesting that while some may be biodegradable, not every material in sustainable architecture necessarily is.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: We calculated the mean and log variance of each feature for each real set of orthologous IDRs and each of the 1000 sets of orthologous IDRs. Because simulations sometimes lead to the deletion of the IDR, we did not include those IDRs that had fewer than 950 non-empty simulations. To obtain a random expectation for Figure 1C, we quantified the number of significant (p<0. 01) molecular features in a set of randomly chosen simulated IDRs (one for each real IDR). To summarize the difference between each real set of orthologous IDRs and its corresponding 1000 simulated sets of orthologous IDRs, we used a standard Z-score (Z) where we subtracted the mean of the simulations (μ) from the real value (x) and divided by the standard deviation of the simulations (σ). The formula for the Z-score is as follows: Z=x- μσ Strain construction and growth conditions Request a detailed protocol All strains (Supplementary file 1 - Table S4) were constructed in the S. cerevisiae BY4741 background. IDR transformants were constructed using the in vivo site-directed mutagenesis method (Storici et al. , 2001). Ste50 IDR mutants were constructed in the ssk22Δ0::HisMx3 ssk2Δ0 background as in Zarin et al. (2017). Genomic changes in transformed strains were confirmed by Sanger sequencing. For mitochondrial strains, starting strains were acquired from the GFP collection (Huh et al. , 2003). The Fus1pr-GFP reporter was constructed as in Zarin et al. (2017) using Gibson assembly (Gibson et al. , 2009), integrated at the HO locus using a selectable marker (URA3), and confirmed by PCR. All experiments were done on log-phase cells grown at 30°C in rich or synthetic complete media lacking appropriate nutrients to maintain selection of markers, unless otherwise stated. Two percent (wt/vol) glucose was used as the carbon source. Confocal microscopy and image analysis Request a detailed protocol We acquired all images with a 8 microscope using standard, uncoated glass slides with a 100x objective. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses statistical methods for analyzing data and experimental protocols in yeast, specifically focusing on IDRs (intrinsically disordered regions) and microscopy. There is no mention or implication regarding X-ray crystallography or its use in determining the 3D structures of proteins.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: While the effects of OA are ubiquitous, they are of particular concern for calcifying organisms such as scleractinian corals, which use carbonate ions to build their skeleton (Hofmann et al. 2010). This potential for OA to reduce calcification in corals has identified coral reefs as one of the most vulnerable ecosystems to OA (Council 2010). The change in calcification and a suite of other physiological effects on corals have the potential to result in indirect effects through altered interactions with other reef organisms. This paper provides a short overview of the direct physiological effects alongside a detailed review of the indirect effects of OA on shallow water tropical and temperate corals, to gain new insights about how corals and coral communities may be affected under future acidified conditions. Specifically we aim to: (1) review the direct, physiological effects of OA on reef building corals across different levels of biological organisation; (2) identify the indirect effects of OA through changes to ecological interactions and provide evidence of how these manifest at an ecosystem level; (3) identify priority areas for future research on indirect effects. While we acknowledge the importance of symbionts and microbial communities in influencing coral responses to environmental change, this review focuses on the responses of, and impacts on, the coral host. MethodsWe completed a literature search on ISI Web of Science for studies that identified the direct and indirect effects of ocean acidification on corals (completed October 2021). We focused primarily on tropical shallow water corals with some temperate corals included to capture research from naturally acidified field sites in temperate regions. Deep water corals were excluded from this review on the basis that other variables such as temperature and light that also change with depth would confound comparisons of OA effects. To review the literature on the physiological effects of acidification on corals, papers were selected using search terms for ocean acidification (‘ocean acidification’, ‘pCO2’, ‘pH’, ‘carbon dioxide’), ‘coral’ and a direct, physiological metric. These metrics were the eight broad headings presented here (Fig. [SEP] Justify:

Output: The text corroborates the claim by discussing the effects of ocean acidification (OA) on coral reefs, particularly highlighting that calcifying organisms such as scleractinian corals are especially vulnerable. It notes that OA can reduce calcification in corals, which supports the assertion that coral reefs are affected by ocean acidification. The text aims to provide insights into both the direct physiological effects of OA and their indirect effects on coral ecosystems, validating the claim about the susceptibility of coral reefs to changes in ocean conditions.


Input: Task: contrast the claim using the given text. Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: In this sense, more designers are willing to revisit traditional materials, fusing them with dynamic new functionality (Ripley and Bhushan 2016), combining contrast ideas to create a hybrid while reducing environmental impacts (Cecchini 2017). Thus, cross-fields and multi-discipline projects offer a potency of sharing and networking, whether in inspiration, technique, and development, encouraging hybridization of biodegradable material. Fig. 2Source: downloaded on March 28, 2020Various materials and shapes in zero experimental waste packaging by Austeja Platukyte. Full size imageDue to serious environmental issues in Indonesia, more movements are raised locally and globally to make Indonesian realize the impacts. From pollution to garbage management, Indonesia was ranked 133 out of 180 countries in 2018 according to the Index (EPI 2018). This country is considered as the lowest rank amongst others located in the Asia–Pacific region. Plenty of researchers have considered Indonesia as being ignorant of the severe effects caused by irresponsible environmental activities. Therefore, more involvement and participation are stimulated to address unreduced emissions, temperature rise, and waste cycle (Mostafa et al. 2018). Architects, urban planners, developers, contractors, and designers are willing to explore new engagement; currently, it is being initiated by developing cassava plastic, bamboo textile, pineapple fibers, tapioca bags, and seaweed packaging. (Hernandha 2017). Extended research is required to perfect this biodegradable material capability to be more systematic, architectural, and degrade naturally in the environment during a time frame (Chang et al. 2017). Moreover, these varieties of biodegradable material are still only produced for smaller-scale items and targeted for selected communities, as displayed by Fig. 3. In this sense, Architecture as a medium potentially serves a bigger audience and functions for more extended periods (Krzemińska et al. 2017). Research and development of biodegradable building material may directly impact the city yet to the country (Group 2017). Nevertheless, most Indonesians still use more conventional materials and methods, driven mainly by economic aspects (Sassi 2006). Although, one must bear in mind that these users also demand to use familiar materials and methods if the new biodegradable building material is expected to hit the market successfully. [SEP] Justify:

Output: The text contrasts the claim by stating that while there is a push for biodegradable materials in architecture, many Indonesians still rely on conventional materials and methods. Specifically, it mentions that 'most Indonesians still use more conventional materials and methods, driven mainly by economic aspects,' implying that not all materials used in sustainable architecture are biodegradable.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: For all GFP images, seven evenly spaced z-slices covering ~6 microns in the z plane were collected for each field of view, and maximum projections of these slices were quantified for Figure 2B, or presented as micrographs in Figure 6C. To quantify basal Fus1pr-GFP expression, single cells in micrographs were segmented using YeastSpotter ( (Lu et al. , 2019). The segmented masks and corresponding fluorescent images were imported into R using the ‘EBImage’ package (Pau et al. , 2010), and GFP intensity for each cell was quantified using base R functions (example available on To assay shmooing, log phase cells were inoculated with 1 uM alpha factor for 2 hr at 30°C (as in Kompella et al. , 2016), at which point they were imaged in brightfield as above. We repeated each microscopy experiment at least twice on different days, and present representative results from one of those days in Figure 2B, C and Figure 6. Clustering of proteome-wide evolutionary signatures Request a detailed protocol Hierarchical clustering was performed using the Cluster 3. 0 program (de Hoon et al. , 2004). The evolutionary signature data was first filtered to include only those IDRs that had at least one Z-score with an absolute value of 3 or more, and with at least 95% data present for the 164 features. This resulted in 4646 IDRs (filtered from the initial 5149) that were then clustered using uncentered correlation distance and average linkage, with ‘cluster’ and ‘calculate weights’ options selected for ‘genes’ (i. e. IDRs), but not for arrays (i. e. molecular features). Clusters were picked manually for further analysis. The full clusterplot is available in supplementary data. In order to ensure that the clustering was not simply due to sequence similarity between the disordered regions, for each cluster, we compared the pairwise distance of the IDRs in each cluster to that of the IDRs outside that cluster, and calculated the percent of disordered regions in each cluster that fell in the top 1% of pairwise distance in all the clusters. This metric is presented for each cluster in Supplementary file 1 - Table S2. [SEP] Justify:

Output: The text does not address the claim regarding X-ray crystallography and instead focuses on methods involving microscopy, fluorescent imaging, and clustering of evolutionary signatures in protein data. Therefore, it does not provide any information supporting or refuting the claim.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: 1): ‘tissue biomass’ OR ‘lipid’ OR ‘protein’; ‘calcification’; ‘photosynthesis’; ‘survival’ OR ‘mortality’; ‘growth’ OR ‘skeletal density’ OR ‘porosity’; ‘reproduction’; ‘abundance’; and ‘species richness’ OR ‘species diversity’ OR ‘community composition’. Where possible, all relevant studies found in the search were included with the exception of calcification and photosynthesis due to the vast body of literature on these metrics which have already been the subject of several reviews and meta-analyses (e. g. Erez et al. 2011; Kornder et al. 2018). Therefore, for these metrics, we focused on papers published in the last 10 years. To ensure there was no bias in the data from this particular selection of publications, additional observations of calcification under OA were recorded from studies focusing on another metric where calcification was also measured. Observations were excluded if they considered variations in other environmental variables (e. g. temperature, nutrients, light), although if possible, we included comparisons between ‘ambient’/‘control’ conditions with the acidified treatment/s. Fig. 1A summary of the physiological effects of ocean acidification from a cell to community scale. Pie charts summarise the proportion of observations taken from the literature showing a significant decrease (green), no significant change (blue) or a significant increase (purple) in response to elevated pCO2. From within any study, only sequential, non-overlapping pCO2 step comparisons are presented. Number within each pie chart denotes the number of observations for that metric. N = 902 observations from 93 studiesFull size imageFor every study selected, the statistical outcomes of comparisons between acidification treatments for each metric were recorded as ‘significant increase’, ‘significant decrease’, or ‘no significant change’. Effects which were not statistically analysed were excluded. Many studies used pCO2 treatments or field sites with acidification levels well beyond that expected in the near future (i. e. , up to 5000 µatm). [SEP] Justify:

Output: The text corroborates the claim by discussing the impacts of ocean acidification on various physiological metrics related to coral reefs and other marine organisms. It describes how studies measure effects like calcification and photosynthesis under elevated pCO2, which directly relates to how ocean acidification affects coral reefs. Additionally, the mention of significant decreases, increases, or no changes in response to elevated pCO2 supports the idea that such environmental changes affect coral reef health and survivability.


Input: Task: contrast the claim using the given text. Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: By understanding the situation, it is now our opportunity to reinvent Indonesian building material developed by crisscrossing borders between different fields (Özdamar and Ateş 2018), neglecting superficial transformation while moving forward towards global impacts (Ripley and Bhushan 2016). Hence, although traditional resources and techniques are suggested to create a familiar atmosphere for biodegradable material development in Indonesia, collaboration, proliferation, and improvisation shall stimulate innovation and creativity. A biodegradable material concept is defined as an abstract idea or a general notion to design property of a substance that enables it to be decomposed by microorganisms (Harper 2001). The aim is to create a material that can degrade naturally in the actual environment (Wahyuningtiyas and Suryanto 2017), resulting in decay in stable conditions to reduce pollution (Sassi 2006). Although biodegradable is associated with natural matter, artificial material shall be understood as an intellectual product that can transform both raw yet waste materials into a contemporary product design (Todor et al. 2018). It shall contain calculation, strategy, and planning to adapt better to the environment while improving the way of life (Ahmed 2015). Although some industrial materials are derived from natural resources, their transformation process may not always be concerned with biodegradability. Hence, to push forward a new modern yet biodegradable building material, the industry shall be encouraged to create a more advanced natural product for building construction (Özdamar and Ateş 2018) without ignoring its biodegradability in the natural environment (Mittal and Dogne 2016). Practically, there are four standard categories of biodegradable materials, namely: minimal processing (timber, bamboo), bonded material (mixtures like carpet and board), compounds (adhesives and polymers), and synthetics (like plastics). These techniques can be implemented as building elements or components and applied during installation or construction (Sassi 2006). Thus, a biodegradable material concept in this research means a general idea to transform Indonesian natural material into building elements or components by considering its biodegradability. Though generic and regular material can be the resource, specific techniques and quality control must set a new standard for delivering a higher grade in biodegradable production. With generally traditional architecture and research on Indonesian natural materials are dominated respectively by (Fig. [SEP] Justify:

Output: The text contrasts the claim by stating that while biodegradable materials are important, there are also artificial materials that do not adhere to biodegradability requirements. It notes that 'Although biodegradable is associated with natural matter, artificial material shall be understood as an intellectual product that can transform both raw yet waste materials into a contemporary product design,' indicating that not all materials used in sustainable architecture can be guaranteed to be biodegradable.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: For example, the cluster with the highest amount of sequence similarity according to this threshold (top 1% similarity) is cluster Q, with 8. 9% of IDRs in this cluster having high sequence similarity according to this threshold. However, the vast majority of the clusters are comprised of IDRs with negligible sequence similarity; for example, 17/23 clusters have less than 1% IDRs with high sequence similarity. In order to calculate pairwise distances, we made pairwise global alignments (with gap opening penalty of 0 and gap extension penalty of 1) and calculated distances using the 62 matrix (this was done using the ‘stringDist’ function in the package; Pagès et al. , 2018). Tests for enrichment of annotations Request a detailed protocol Annotations for (GO) terms, phenotypes, and literature were acquired from SGD (Cherry et al. , 2012) for the S. cerevisiae proteome. We included GO terms that applied to a maximum of 5000 genes in the S. cerevisiae proteome. A test for enrichment of annotations was done using the hypergeometric test for each cluster against all the proteins in the clustering analysis. To obtain Q-values, p-values were corrected using the Benjamini-Hochberg method. Q-values below an FDR of 5% were retained. Because there is not a 1-to-1 correspondence between IDRs and annotations, which are based on proteins, we also calculated Q-values using permutation tests. To do so, we uniformly sampled 1000 clusters of IDRs for each cluster from the 4646 IDRs included in our clusterplot, and obtained the sum of the top ten – log Q-values associated with each test for enrichment, as above. We compared this test statistic to the observed sum of top ten – log Q-values for each cluster, and reported the difference as a standard Z-score in Supplementary file 1 - Table S2. In order to understand how our evolutionary signatures compare to information obtained only from amino acid frequencies, we computed vectors of Z-scores for each IDR that represented their amino acid frequencies normalized to the proteome-wide average. We clustered these vectors using k-means (K = 25) with the Cluster 3. 0 program (de Hoon et al. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses various aspects of data analysis related to intrinsically disordered regions (IDRs) in proteins and mentions methods such as pairwise global alignments and enrichment tests without mentioning X-ray crystallography or its application in determining 3D structures of proteins.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Finally, we review the effects of acidification on the abundance and diversity of corals at naturally acidified reef sites (Table 2), as well as evidence of any indirect effects at such sites (Table 3). Observations of coral abundance and diversity were only taken from one study per site to avoid over-representation of a limited set of intensively studied locations within the data set. We focus on the effect of pCO2 as a ‘catch-all’ measure of OA effects. However, we note that other measures of water chemistry, such as aragonite saturation (Ω) and the relative abundance of carbonate (CO32−) and bicarbonate (HCO3−) ions, are correlated with pCO2 and that OA effects encompass changes in all of these variables. Direct effects of OA on coralCorals employ a range of biological responses to counteract the adverse effects of acidification. These stress responses can manifest at multiple levels of biological organisation ranging from molecular or cellular processes to whole organism responses (Edmunds et al. 2016). The cumulative effect of these physiological responses can translate into effects on populations by altering key demographic rates. This includes population growth through reproduction, recruitment, and colony growth, and population shrinkage through mortality. Ultimately, these demographic parameters then affect coral communities through changes in coral cover, and altered community composition and species diversity. At the molecular and cellular level, corals have a variety of processes that allow them to survive and grow under acidified conditions. While mechanisms such as the ability to internally regulate pH (McCulloch et al. 2012, 2017) allow corals to adjust to acidic conditions, they are thought to be energetically costly (Allison et al. 2018). However, increased pCO2 does not always result in depletion of energy reserves (measured via tissue biomass; e. g. Strahl et al. 2016) (Fig. 1). This suggests that at least some coral species can maintain growth under OA via regulating pH at the site of calcification (see: Comeau et al. 2022). At the ‘whole colony’ level, both calcification and photosynthesis can be affected by ocean acidification. For photosynthesis, effects of OA are highly variable among studies (Fig. 1). The majority of observations considered here showed no significant changes in the rates or efficiency of photosynthesis under OA (e. g. [SEP] Justify:

Output: The text corroborates the claim by discussing the effects of ocean acidification (OA) on coral communities. It details observations of coral abundance and diversity in relation to acidification and mentions direct effects of OA on coral physiology, which can impact population growth, mortality, and community composition. It specifically notes that both calcification and photosynthesis in corals can be affected by ocean acidification, aligning with the claim that coral reefs are impacted by changing oceanic conditions.


Input: Task: contrast the claim using the given text. Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: 4); (1) timber; (2) bamboo; (3) thatch; and 4) fiber; The state of the art for this research concentrates on constructing a new kind of fiber as less dominated material in Indonesian building material industry. It is created by using the edible source as a contrast to common historic building materials, which traditionally may be categorized as natural, organic, and degradable but may not yet be categorized as biodegradable according to the interpretation of the modern standard. Edible materials tend to offer a better contribution in terms of degradability, allergy reaction, safe effect, efficient production, yet consumption. Hence, by understanding the concept above, the design criteria for this research are: (1) Natural and organic; (2) Traditionally inspired; (3) Durability for 1–5 years; (4) Cross-disciplines; (5) Multi-products. Fig. 4Source: downloaded on June 26, 2021in Architecture. Full size imageThe architecture of Indonesia does not only reflect its biodiversity but also representing the culture. architecture has been built as natural yet temporary, sot is being associated with sustainability and resilience (Mittal and Dogne 2016). Indonesian architecture illustrates the mixture of various foreign influences like Indian, Chinese, Arab, and European. culture, the house is the center of Indonesian customs, social relations, traditional laws, taboos, myths, and religions that bind humans with nature (Hays 2015). The earliest structures of the Indonesian vernacular house are constructed by using flexible nail-less joints and non-load bearing walls; before bricks, iron and mortar are found. In the tropical climate of Indonesia, Indonesian vernacular houses are made from traditional materials. They are produced by using various techniques like sun-drying, burned, smoked, and mostly considered hand-made. Especially in ancient times, fewer materials are initiated by neither mixture nor using machines. In the current situation, advanced technology may be found within the industry, while the practically rural community is still eager to preserve its traditional technique with minor transformation nor advanced method (Özdamar and Ateş 2018), as demonstrated by Fig. 5. Hence, there is a gap for producing a new form of biodegradable material based on Indonesian tradition, though method and technique shall be planned to match the existing craftsmanship. [SEP] Justify:

Output: The text contrasts the claim by discussing various materials, such as timber and bamboo, that may be categorized as natural and organic but do not necessarily meet the modern standard of being biodegradable. It explicitly states that while traditional materials can be degradable, they may not be categorized as biodegradable. This highlights a distinction between being environmentally friendly and meeting the specific criteria of biodegradability.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: , 2004) We performed a similar permutation test (as above), where the sample of 1000 clusters was not uniform, but drawn to create 1000 random clusters of IDRs with similar amino acid composition for each cluster. For example, for each IDR in a cluster, we found the cluster that it fell into in the amino acid frequency clusterplot, and sampled from that cluster to replace the IDR in our evolutionary signature clusterplot. We did this 1000 times for each cluster, and used the same test statistic as the above-described permutations to report the difference in enriched annotations between our clusterplot based on evolutionary signatures and the clusterplot based on amino acid frequencies (Supplementary file 1 - Table S2). Identification of highly disordered proteins with unknown function Request a detailed protocol We identified proteins whose biological role is unknown according to their SGD annotation (Cherry et al. , 2012). We quantified the percent of residues that were predicted to be disordered in each protein with unknown function, and present the top ten most disordered proteins in Table 2. Add a comment + Open annotations. The current annotation count on this page is being calculated. Data availability The analysis is based on publicly available sequence data from the (YGOB). Source data has been included as supplementary data. 1739. PubMed 7219. PubMed 395. PubMed 982. PubMed 2256. PubMed 3174. PubMed 553. PubMed 701. PubMed 158. PubMed 298. PubMed 1138. PubMed 14. PubMed 26. PubMed 3439. PubMed 66. 110. PubMed 621. PubMed 1461. PubMed 12. 1. 0-2: A to the R Project for Devoted to Retrieval and Analysis In:. E, Vendruscolo M, editors. to Sequence Evolution: Molecules, Networks, Populations. Berlin: Springer. 232. 887. PubMed 898. PubMed 705. 3030. PubMed 3397. PubMed 288. PubMed 281. PubMed 1454. PubMed 191. PubMed 839. PubMed 967. PubMed 432. 121. PubMed 1499. PubMed 5654. PubMed 277. 1126. 1026. PubMed 905. PubMed 345. PubMed 3086. PubMed 8317. PubMed 25. PubMed 1351. PubMed 3802. [SEP] Justify:

Output: The text does not address the claim regarding X-ray crystallography and its ability to determine the 3D structures of proteins. Instead, it discusses a permutation test used in protein analysis without providing any information on X-ray crystallography, thus making it irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Bedwell-Ivers et al. 2017; Bahr et al. 2018), nor in the density of symbionts or the chlorophyll within each symbiont (e. g. Bedwell-Ivers et al. 2017; Rivest et al. 2017). Changes in photosynthetic acquisition of energy under OA are therefore unlikely to be the limiting factor for coral persistence in the future. The effect of acidification on calcification is the most widely recognised threat to corals and there is a substantial body of research showing declines in calcification (Erez et al. 2011; Chan and Connolly 2013; Kornder et al. 2018), as well as some evidence of increased dissolution (e. g. Fine and Tchernov 2007; Kline et al. 2019). However, calcification responses are highly variable, and both species and colony specific (e. g. Sekizawa et al. 2017; Bahr et al. 2018), with the overall majority of observations showing no significant effect of acidification (e. g. Carbonne et al. 2021) (Fig. 1). Furthermore, corals continue to calcify and grow in naturally acidified reefs (e. g. Inoue et al. 2013; Camp et al. 2017) (Fig. 1) under conditions far more acidic than the theoretical limits for calcification and net carbonate accretion (560 ppm atmospheric CO2, Silverman et al. 2009; 2. 3 to 3. 5 Ω aragonite, Kline et al. 2019) (Table 2). At the population level, negative effects of OA are more apparent (Fig. 1) suggesting that small changes in multiple aspects of physiology might accumulate to comprise a significant impact when summed across all individuals in the population. There is some evidence of a shift in growth strategies under acidification, with some corals maintaining linear extension by building less dense, more porous, skeletons (Mollica et al. 2018; Teixidó et al. 2020). This strategy is unlikely to drive changes in coral cover under acidification; however, there may be significant indirect effects through increased vulnerability to breakages in weaker skeletons (Hennige et al. 2015). In contrast, other colonies maintain skeletal density/porosity at the expense of linear extension (Enochs et al. [SEP] Justify:

Output: The text supports the claim by discussing the effects of ocean acidification (OA) on coral calcification and growth, detailing how acidification is a recognized threat to corals. It mentions that there is substantial research showing declines in calcification due to acidification and that small physiological changes across individual corals may accumulate to create significant impacts at the population level, corroborating the idea that coral reefs are affected by acidification. Additionally, the text describes growth strategy shifts under acidification that could further imply indirect impacts on corals, aligning with the claim regarding the effect of ocean conditions on coral reefs.


Input: Task: contrast the claim using the given text. Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: It delivers smooth and causing less alienation, and a new material shall be created by respecting retrospection: using Indonesian natural material executed by advanced traditional technique. Execution shall be encouraged by focusing on creating contrasts or differences, neglecting monotonous and homogeneous that is often problematic in traditional and conventional productions. Fig. 5Source: and on March 28, 2020at Prihal Exhibition. Full size imageMethod of researchThis research investigates a retrospective to find a biodegradable material concept for future Indonesian sustainable architecture through the bibliographic coupling method to identify the relationship between one another based on the subject’s proximity (Rupadha 2016; Glänzel and Czerwon 1996; Kessler 1963, 1965). A comparison study on local and global trends is highlighted to contrast a unique Indonesian perspective on the biodegradable material concept based on local inspiration taken from its culture and biodiversity. It is followed by experimental methods to determine the effect of specific treatments on others under controlled conditions (Sugiyono 2014; Sukardi 2011), carried out in the laboratory using natural materials suitable for producing biodegradable building materials. The research is presented as follows; (1) Understanding local–global trends in biodegradable architecture; (2) Indonesian potency on biodegradable materials; (3) A biodegradable material concept as an alternative perspective for Indonesian sustainable architecture. A new concept is proposed as an open-ended perspective by using local materials such as Tea and Indonesian Coffee; it is presented as an inspiration to initiate the development of contemporary Indonesian biodegradable building material. By understanding the bigger picture, a more sustainable architecture is expected to be constructed by respecting local craftsmanship, exploring available local materials, and presenting techniques for a greener environment. Hence, this research suggests unusual inspiration for developing a concept of green building biodegradable material by using familiar Indonesian resources. Results and discussionUnderstanding local–global trends in biodegradable architectureMore researchers and designers around the world are currently engaged in nature-inspired objects; whether it is developed as a method, form, structure, and even function. These new items are proliferated to mimic nature to bring design closer to the actual environment. Using technology, such as 3D printing, transplantation, fermentation, and other techniques involving nature, researchers believe that parametric design, biomimicry, or genetically modified species may improve humans’ relationships and habitat. [SEP] Justify:

Output: The text contrasts the claim by discussing the exploration of biodegradable materials for sustainable architecture, highlighting the use of natural local materials such as Tea and Indonesian Coffee. While it presents these materials as part of a concept for biodegradable building materials, it does not assert that every material in sustainable architecture is biodegradable, suggesting a more nuanced view that acknowledges the potential for both biodegradable and non-biodegradable materials in the field.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Skip to Content eLife home page your research Search by keyword or author Reset form my search to Research 10. 7554/eLife. 03430 Open access Copyright information Version of RecordNovember 3, 2014 Accepted ManuscriptSeptember 25, 2014 Open annotations (there are currently 0 annotations on this page). 15,701 views 2,776 downloads 421 3430. Copy to clipboard Download BibTeX Download. RIS Full text Figures and data Peer review Side by side Additional files 7 figures, 1 table and 7 additional files 1 with 1 supplement Download asset Open asset Co-evolution of residues across protein complexes from the evolutionary sequence record. (A) Evolutionary pressure to maintain protein–protein interactions leads to the co-evolution of residues between interacting proteins in a complex. By analyzing patterns of amino acid co-variation in an alignment of putatively interacting homologous proteins (left), evolutionary couplings between co-evolving inter-protein residue pairs can be identified (middle). By defining distance restraints on these pairs, the 3D structure of the protein complex can be inferred using docking software (right). (B) Distribution of E. coli protein complexes of known and unknown 3D structure where both subunits are close on the bacterial genome (left), allowing sequence pair matching by genomic distance. For a subset of these complexes, sufficient sequence information is available for evolutionary couplings analysis (dark blue bars). As more genomic information is created through on-going sequencing efforts, larger fractions of the E. coli interactome become accessible for EVcomplex (right). A detailed version of the workflow used to calculate all E. coli complexes currently for which there is currently enough sequence information is shown in Figure1—figure supplement 1. Figure 1—figure supplement 1 Download asset Open asset Details of the EVcomplex Pipeline. Figure 2 with 8 supplements Download asset Open asset Evolutionary couplings capture interacting residues in protein complexes. (A) Inter- and Intra-EC pairs with high coupling scores largely correspond to proximal pairs in 3D, but only if they lie above the background level of the coupling score distribution. To estimate this background noise a symmetric range around 0 is considered with the width being defined by the minimum inter-EC score. For the protein complexes in the evaluation set, this distribution is compared to the distance in the known 3D structure of the complex that is shown here for the methionine transporter complex, MetNI. [SEP] Justify:

Output: The text discusses the concept of co-evolution of residues across protein complexes and the analysis of protein interactions using evolutionary couplings but does not mention X-ray crystallography or its role in determining the 3D structures of proteins. Therefore, it is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: 2015a), which can reduce lifetime reproductive because slower growth means corals are more likely to die before reaching the largest, most fecund, colony sizes. For reproduction metrics, the effect of acidification is again variable among studies. Overall, the early stages of reproduction (production of gametes, fertilisation, and larval development, growth and survival) appear to largely be unaffected by acidification (e. g. Rivest et al. 2018; Pitts et al. 2020). Conversely, the later stages of reproduction (settlement, metamorphosis, recruit growth and survival) show more consistent negative effects (e. g. Jiang et al. 2018; Yuan et al. 2018), suggesting that recruits are more vulnerable to acidification than gametes or larvae. This is of concern because even a moderate (20%) decline in recruitment was estimated to reduce coral cover by 15% over 7 year period (Evensen et al. 2021). However, declines in recruitment are estimated to potentially rise as high as 52% by mid-century conditions (~ 560 µatm), and 73–91% by end of century conditions (~ 800 µatm) (Albright et al. 2010; Fabricius et al. 2017). Such reductions are therefore likely to present a significant threat to the persistence of corals and coral communities under acidified conditions. Finally, despite the described physiological effects, increased pCO2 does not consistently reduce adult colony survival, under acute experimental or naturally acidified conditions. Rather, OA appears to result in sub-lethal effects, defined here as “physiological effects that reduce coral fitness (e. g. , cause slower growth or lower reproductive output) but do not result in mortality”. The accumulation of such sub-lethal effects on growth and reproduction may suppress population growth rates in the future, contributing to changes in abundance, species richness and/or diversity, and community composition at an ecosystem level. Overall, we find the direct effects of acidification on corals are highly variable. This variation may result from differences in experimental methodology or pCO2 levels; however, it is also likely to represent the significant variation both between individuals, species and sites. In total across all scales 52% of observations included here found no significant difference with acidification (Fig. 1). [SEP] Justify:

Output: The text corroborates the claim by discussing how ocean acidification affects the reproductive stages of corals. It mentions that while earlier stages of reproduction may be largely unaffected by acidification, later stages show consistent negative effects, indicating a significant threat to coral populations. Furthermore, it highlights how reductions in recruitment due to acidification are likely to harm coral communities, suggesting that ocean acidification is indeed impacting coral reefs.


Input: Task: contrast the claim using the given text. Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: Whether producing a new generation of products, applications, or robots, various institutions are exploring more intuitive and communicative materials that interact, correspond, and decompose within their environment. Wired fabrics, compostable plastic, disposable technology are going to be trending for daily life soon. The sustainability idea in the global world now puts more concern about the overall impact that happened to the earth. A green action can now be calculated precisely and generate more participation from households to government regulation, especially becoming more common in the most developed countries. In Indonesia, the idea of sustainability is still in an initiation process, progressing towards a more advanced phase. Mostly, the initiation is an introduction of an experimental product to replace daily utensil that harms the environment. The action can be varied like replacing plastic, garbage management, and introducing re-use/recycle activity. Although there is a wide gap between local and global actions, most activities in Indonesia are inspired by international movements while finding a suitable way to be implemented in Indonesia. Indonesian are having difficulties being mindful of its richness and fortune. The act of preserving and conserving its environment is still in progress due to the overall level of education. Moreover, Indonesian rich culture and biodiversity shall not only be preserved and conserved but developed to ensure that its nature can be passed down in a more excellent way to the next generation. In this sense, regeneration must be understood as taking part in the sustainability process, elevating tradition while strengthening Indonesian cultural identity by advancing the production process. Despite resilient, resourceful, and diverse, Indonesian architecture reflects the core of cultural values. Well-known as conservative, refined, and delicate, Indonesian must be encouraged to face the competitive world with more open-minded paradigms while preserving what they believe best. Indonesian culture emphasizes the philosophy of living in harmony, believing in subjugation to nature. However, to be progressive in sustainability, Indonesian must now be ready to question the tendency always to feel comfortable in common systems and ideology; this includes how Indonesian architecture is perceived. Despite superstitious, having a strong belief in the power of objects and events, undeniably, Indonesian has always had a solid connection to nature. It is an excellent foundation yet an open opportunity to introduce a new way of living based on essential human nature: to live harmoniously with the environment. However, to move forward, the sustainable action shall focus on an entire transformation process of developing a biodegradable material. [SEP] Justify:

Output: The text contrasts the claim by indicating that there is a focus on introducing new materials, including biodegradable ones, but it suggests that sustainable action must encompass the entire transformation process of developing biodegradable materials, which implies that not all materials in sustainable architecture are currently biodegradable.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: (Plots for all complexes in the evaluation set are shown in Figure 2—figure supplement 1 and 2. ) (B) A larger distance from the background noise (ratio of EC score over background noise line) gives more accurate contacts. Additionally, the higher the number of sequences in the alignment the more reliable the inferred coupling pairs are which then reduces the required distance from noise (different shades of blue). Residue pairs with an 8 Å minimum atom distance between the residues are defined as true positive contacts, and precision = TP/(TP + FP). The plot is limited to range (0,3) which excludes the histidine kinase—response regulator complex (HK–RR)—a single outlier with extremely high number of sequences. (C) To allow the comparison across protein complexes and to estimate the average inter-EC precision for a given score threshold independent of sequence numbers, the raw couplings score is normalized for the number of sequences in the alignment, resulting in the EVcomplex score. In this work, inter-ECs with an EVcomplex score ≥0. 8 are used. Note: the shown plot is cut off at a score of 2 in order to zoom in on the phase change region and the high sequence coverage outlier HK-RR is excluded. (D) For complexes in the benchmark set, inter-EC pairs with EVcomplex score ≥0. 8 give predictions of interacting residue pairs between the complex subunits to varying accuracy (8 Å TP distance cutoff). All predicted interacting residues for complexes in the benchmark set that had at least one inter-EC above 0. 8 are shown as contact maps in Figure 2—figure supplement 3–8. Figure 2—figure supplement 1 Download asset Open asset Distribution and accuracy of raw EC scores for all complexes in evaluation set. Figure 2—figure supplement 2 Download asset Open asset Distribution and accuracy of raw EC scores for all complexes in evaluation set (2). Figure 2—figure supplement 3 Download asset Open asset Contact maps of all complexes with solved 3D structure with inter-ECs above EVcomplex score of 0. 8. Predicted coevolving residue pairs with an EVcomplex score ≥0. 8 and all inter-ECs up to the rank of the last include inter-EC are visualized in complex contact maps (red dots: inter-ECs, green and blue dots: intra-ECs for monomer 1 and 2, respectively). [SEP] Justify:

Output: The text does not address the claim directly. It discusses metrics for evaluating protein complexes and their inferred coupling pairs but does not mention X-ray crystallography or its application in determining 3D structures of proteins. Therefore, it is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Interestingly however, it appears that consistently negative effects are more often seen at a population level (26% of 274 observations), rather than cell (10% of 80 observations) or colony level (16% of 388 observations). This suggests that while the acidification has largely sub-lethal physiological effects on individuals, coral populations and communities may still be altered. We therefore stress the importance of researching the effects of acidification on coral populations and communities in addition to effects on individual coral colonies. Indirect effects of OA on coralsIndirect effects are defined here to be a change in an ecological interaction between species. This may occur when a physiological or behavioural change affects either the extent or outcome of an interaction with another species or taxon. Indirect effects can occur as a result of physiological changes to one or both of the interacting taxa, changes to the interaction itself or changes in environment in which the interaction occurs and, consequently predicting indirect effects is challenging, and requires knowledge of both the stressor and all individuals involved (Connell et al. 2011; Sunday et al. 2016). In the following section we review the indirect effects of OA for reef-building corals, including interactions between corals, and between corals and other taxa (see Table 1). Table 1 Published studies which consider, or raise the potential for, indirect effects of acidification on corals and coral communities. ‘−’ negative effect, ‘ = ’ neutral or no effect, ‘ + ’ positive effectFull size tableCompetitionFor sessile benthic organisms, competition is primarily for resources such as space and light (Lang and Chornesky 1990) and helps to structure communities and determine species distributions (e. g. Connell et al. 2004). OA may affect competition dynamics through; (1) a change in the frequency of competition as coral cover changes, resulting in either intensification or competitive release (Hofmann et al. 2010); (2) a change in the identity of competitors as species composition changes; (3) an altered outcome of an existing competitive interaction, resulting from differences in the magnitude to which different species are affected by OA; (4) an altered outcome of an existing competitive interaction due to changes in availability of resources, or; (5) novel competitive interactions as a result of shifting distributions (e. g. Alexander et al. 2016). [SEP] Justify:

Output: The text corroborates the claim by discussing the effects of ocean acidification (OA) on coral populations and communities, highlighting both direct and indirect impacts. It notes that while individual corals may experience sub-lethal physiological effects, the broader ecological interactions at the population level are more significantly altered due to OA. This aligns with the claim that coral reefs are affected by both ocean acidification and warming.


Input: Task: contrast the claim using the given text. Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: It is best, if accompanied by easy-to-digest information and user-friendly application primarily to be delivered at home as the house is the center of Indonesian society. Biodegradable material that can be produced and applied to most houses in Indonesia means a higher level of applicability and acceptance to the broader audience. offering many natural resources that can be found throughout the archipelago, the best initiation is easily found in the surrounding living environment, whether the resource comes from the house, garden, park, and market. ; whether it is a familiar building material, food ingredients, fabrics, or herbs, as long as it offers a familiarity directly to the end-user. In addition, developing natural and organic fiber at home and the surrounding environment is more visible because of its availability and affordability. Indonesian potency on biodegradable materialsAccording to the stagnancy of technology and application of homogeneous material in the existing setting; a biodegradable material concept as an alternative for Indonesian sustainable architecture must highlight the importance of a new method, advancing the final product for moving from only preserving and conserving a raw traditional building material to the advanced ones. A superficial transformation shall be shifted to the exploration of complex material and technique. This action needs to completely change the overall formation, structure, function, or even genetics of the designed materials. Crosschecking with the latest global trends: fish scale, skin waste, crustacean exoskeleton, eggshell, algae, ground coffee beans, rice husk, fruit peel, corn husks, wool, yogurt pots, tree cellulose, fungus, yeast, fermented farm waste, food waste, animal skin, sunflower seeds also bee wax can be developed as biodegradable materials. It is almost every natural thing that can be converted and transformed into biodegradable building material. It means Indonesian exploration of biodegradable does not need to be afraid to explore different bio things, moving forward from one or two popular material choices as in the current situation is dominated by limited types. Also, the exploration may be continued by the advancement of different techniques like fermentation, yeast, distillation, brew, inspired by various traditional methods rather than repeating common methods, as exemplified by Fig. 6. Although these traditional methods are common in Indonesia, especially for the home industry, implementation is relatively stagnant or steady than embracing diversity. [SEP] Justify:

Output: The text contrasts the claim by suggesting that not every material used in sustainable architecture is biodegradable. It emphasizes the potential of biodegradable materials in Indonesian architecture and discusses the exploration of various natural resources, but it also describes a stagnancy in the current use of traditional materials, implying that the existing options are limited. The exploration of 'different bio things' indicates that while many materials, like 'fish scale, skin waste, crustacean exoskeleton, eggshell, ...' can be converted into biodegradable materials, this does not support the claim that all materials are biodegradable.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Top left and bottom right quadrants: intra-ECs; top right and bottom left quadrants: inter-ECs. Inter- and intra-protein crystal structure contacts at minimum atom distance cutoffs of 5/8/12 Å are shown as dark/middle/light gray dots, respectively; missing data in the crystal structure as shaded blue rectangles. Figure 2—figure supplement 4 Download asset Open asset Contact maps of all complexes with solved 3D structure with inter-ECs above EVcomplex score of 0. 8 (2). Figure 2—figure supplement 5 Download asset Open asset Contact maps of all complexes with solved 3D structure with inter-ECs above EVcomplex score of 0. 8 (3). Figure 2—figure supplement 6 Download asset Open asset Contact maps of all complexes with solved 3D structure with inter-ECs above EVcomplex score of 0. 8 (4). Figure 2—figure supplement 7 Download asset Open asset Contact maps of all complexes with solved 3D structure with inter-ECs above EVcomplex score of 0. 8 (5). Figure 2—figure supplement 8 Download asset Open asset Contact maps of all complexes with solved 3D structure with inter-ECs above EVcomplex score of 0. 8 (6). Figure 3 with 1 supplement Download asset Open asset Blinded prediction of evolutionary couplings between complex subunits with known 3D structure. Inter-ECs with EVcomplex score ≥0. 8 on a selection of benchmark complexes (monomer subunits in green and blue, inter-ECs in red, pairs closer than 8 Å by solid red lines, dashed otherwise). The predicted inter-ECs for these ten complexes were then used to create full 3D models of the complex using protein–protein docking. For the fifteen complexes for which 3D structures were predicted using docking, energy funnels are shown in Figure 3—figure supplement 1. Figure 3—figure supplement 1 Download asset Open asset Comparison of Interface RMSD to score. scores of docked models are plotted against their iRMSDs to the bound complex crystal. Gray data points correspond to models created without any ECs as unambiguous restraints whereas blue dots correspond to model created using all inter-couplings with EVcomplex score ≥0. 8. [SEP] Justify:

Output: The text does not provide any direct information about X-ray crystallography or its capability to determine the 3D structures of proteins. Instead, it discusses various aspects of protein structures and the relationship between evolutionary couplings and structural predictions without referencing X-ray crystallography specifically. Therefore, this text is considered irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: While the effect of competition on growth suggests there is a greater physiological cost of competition under OA, the lack of impact on competitive ability potentially indicates a change in allocation of resources to maintain competitive ability. However, while Evensen and Edmunds (2018) focused on mesenterial filaments, these are only one of a number of competitive mechanisms corals use, and the effect of OA on other competitive methods has not been considered as yet. How the effects of competition under acidification scale up to an ecosystem level is largely unknown. Early evidence of the effect of competition at an ecosystem level found that recovery on coral reefs under the combination of OA and competition reduced recovery an additional 14% compared to OA alone (Evensen et al. 2021). However, competition was found to be less important than coral growth in recovery. Therefore, to understand how OA-induced changes to coral–coral interactions play out at an ecosystem level requires additional research on the extent to which corals compete, their competitive ability or aggression, and the impacts of competition on colony growth and survival. Competition between hard and soft coralsIn general, soft corals appear to be more resistant to high pCO2 than hard corals (Gabay et al. 2014) suggesting that soft corals could win more competitive interactions with hard corals in the future. Under recent historical ambient conditions, adult soft corals were often the subordinate competitors (Dai 1990), although chemical defences used by soft corals have been shown to affect hard corals through inhibiting recruitment (Atrigenio and Alino 1996) and growth, as well as causing significant tissue necrosis and mortality (Sammarco et al. 1983). However, ambient oceanic pCO2 has increased dramatically since these studies were published and it is not known whether these interactions still occur or result in the same outcome under today’s or future pCO2 conditions. Only one study has experimentally tested the physiological effects of competition between hard and soft corals under high pCO2 conditions. This study found that the presence of a soft coral competitor had a negative effect on photosynthesis but not growth of the hard coral (Porites cylindrica), and negligible changes in competitive ability in response to changing pCO2 conditions (Brien et al. 2016; Table 1). In contrast, the cytotoxicity of the soft coral Sarcophyton spp. [SEP] Justify:

Output: The text corroborates the claim by discussing the impacts of ocean acidification (OA) on coral reefs and competition among coral species. It mentions that 'the effect of competition at an ecosystem level found that recovery on coral reefs under the combination of OA and competition reduced recovery an additional 14% compared to OA alone,' indicating a direct impact of OA on coral recovery. Furthermore, the discussion of how soft corals appear more resistant to high pCO2 compared to hard corals reinforces the idea that ocean acidification affects coral species differently, impacting the coral reef ecosystem.


Input: Task: contrast the claim using the given text. Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: Exploration shall be encouraged to demonstrate different, contrast, distinction, and divergence in terms of color, texture, size, the process even performance for achieving the advancements. Fig. 6Source: downloaded on March 28, 2020Potency of Material; Left to Right: Soybean cake, Red soy oil-cake, Solid fermented glutinous rice, Black soy oil-cake, Fermented cassava, Buffalo milk yogurt, Nata de coco, Kombucha, Enrekang cheese. Full size imageHowever, to represent the Indonesian-ness, one shall choose a natural resource or method locally and globally recognized as Indonesian, although a total rework needs to be planned to advance the invention. Hence, in this sense, the research highlights the unlimited potentials of Indonesian biodiversity as the concept for biodegradable architecture material to address the stagnant inspiration. Also, to address current problems on developing global biodegradable material, the following Indonesian projects need to be perfected by ensuring its capability to decay smoothly to the actual environment. Also, the research shall be extended to be more architecture as the option for biodegradable building material is still considered scarce. Simulation, calculation, and prediction are needed to be encouraged to generate a greener biodegradable material, presenting a better future for a more sustainable environment. Despite unlimited inspiration that can be found from Indonesian resources, the problem remains the same and is dominated by orthodoxies. The gap and the real challenge are where the Indonesian-ness must be interpreted as the new output. A biodegradable material concept as an alternative perspective for Indonesian sustainable architectureTwo inspirations are selected for experimenting with traditional materials and techniques. Elaborations and proliferation are considered for presenting various colors, textures, sizes, and characters by using a variety of types, concentrations, intensification. However, the resource of material and techniques remain conventional. This home experimentation leads to producing different biodegradable materials related to green buildings and is chosen because of the availability and affordability of Indonesia’s general public. Two familiar materials have been investigated for 2 years in this experimentation; tea and coffee as the main ingredients. The first one is intended for creating sheets, and the other as insulation or filler. First initiation using kombucha tea generally leads to vegan leather, fusuma, wallpaper sheet, bioplastic, and translucent materials. [SEP] Justify:

Output: The text contrasts the claim by indicating that, although there is an exploration of biodegradable materials for sustainable architecture, the discussion emphasizes that options are still considered scarce and that traditional materials and techniques are predominantly used. This suggests that not every material used in sustainable architecture is necessarily biodegradable, as it acknowledges a reliance on conventional resources.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: score outliers with scores >100 are not shown, and any model with an iRMSD >35 Å is displayed as iRMSD = 35 Å for visualization purposes. Figure 4 Download asset Open asset Evolutionary couplings give accurate 3D structures of complexes. EVcomplex predictions and comparison to crystal structure for (A) the methionine-importing transmembrane transporter heterocomplex MetNI from E. coli (PDB: 3tui) and (B) the gamma/epsilon subunit interaction of E. coli ATP synthase (PDB: 1fs0). Left panels: complex contact map comparing predicted inter-ECs with EVcomplex score ≥0. 8 (red dots, upper right quadrant) and intra-ECs (up to the last chosen inter-EC rank; green and blue dots, top left and lower right triangles) to close pairs in the complex crystal (dark/mid/light gray points for minimum atom distance cutoffs of 5/8/12 Å for inter-subunit contacts and dark/mid gray for 5/8 Å within the subunits). Inter-ECs with an EVcomplex score ≥0. 8 are also displayed on the spatially separated subunits of the complex (red lines on green and blue cartoons, couplings closer than 8 Å in solid red lines, dashed otherwise, lower left). Right panels: superimposition of the top ranked model from 3D docking (green/blue cartoon, left) onto the complex crystal structure (gray cartoon) and close-up of the interface region with highly coupled residues (green/blue spheres). Figure 5 with 3 supplements Download asset Open asset Evolutionary couplings in complexes of unknown 3D structure. Inter-ECs for five de novo prediction candidates without E. coli or interaction homolog complex 3D structure (Subunits: blue/green cartoons; inter-ECs with EVcomplex score ≥0. 8: red lines). For complex subunits which homomultimerize (light/dark green cartoon), inter-ECs are placed arbitrarily on either of the monomers to enable the identification of multiple interaction sites. Contact maps for all complexes with unsolved structures are provided in Figure 5—figure supplement 1 and 2. [SEP] Justify:

Output: The text does not directly relate to the claim about X-ray crystallography; it mainly discusses evolutionary couplings and complex structures without mentioning X-ray crystallography's role in determining 3D protein structures. Thus, it is considered irrelevant to the claim.