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: 87e-05Nsequence-specific DNA binding (18/39), DNA binding (19/39), zinc ion binding (11/39), regulation of transcription, DNA-templated (19/39), RNA polymerase II transcription factor activity, sequence-specific DNA binding (8/39)6. 21e-04Oregulation of transcription, DNA-templated (53/130), transcription, DNA-templated (50/130), sequence-specific DNA binding (25/130), positive regulation of transcription from RNA polymerase II promoter (26/130), nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (8/130), endocytosis decreased (26/130), invasive growth increased (37/130), cell shape abnormal (15/130)1. 29e-02Pintracellular signal transduction (19/129), protein kinase activity (22/129), protein serine/threonine kinase activity (22/129), kinase activity (24/129), phosphorylation (24/129)3. 34e-06Qextracellular region (33/67), fungal-type cell wall (30/67), cell wall (25/67), anchored component of membrane (20/67), cell wall organization (23/67)1. 01e-20Rpositive regulation of transcription from RNA polymerase II promoter (21/119), DNA binding (32/119), RNA polymerase II core promoter proximal region sequence-specific DNA binding (12/119), transcription factor activity, sequence-specific DNA binding (10/119), transcription, DNA-templated (33/119)1. 55e-02Sintegral component of membrane (59/133), membrane (68/133), fungal-type vacuole membrane (18/133), vacuole (18/133), L-tyrosine transmembrane transporter activity (4/133)5. 48e-03Tstress-activated protein kinase signaling cascade (4/33), regulation of apoptotic process (4/33)3. 57e-02Ucytoskeleton (15/80), spindle (6/80), kinetochore microtubule (3/80)1. [SEP] Justify:

Output: The text is irrelevant to the claim about X-ray crystallography and protein structures. It discusses various biological processes and functions, such as DNA binding and transcription regulation, 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: a Inorganic aragonite precipitation rates at three temperatures as a function of Ω (aragonite saturation state, redrawn from (Burton and Walter 1987)). b Mean coral precipitation (calcification) rates in each seawater pCO2 treatment (Cole et al. 2018) overlaid onto inorganic aragonite precipitation rate contours (in pale grey for different Ω) replotted as a function of temperature. We assume that corals cultured at 400 µatm and 25 °C have a ΩECM = 12 (Sevilgen et al. 2019) and a precipitation rate equivalent to that observed at Ω = 12 and 25 °C in inorganic aragonites (Burton and Walter 1987). We scale linearly all other coral precipitation rates to this valueFull size imageThe role of the skeletal organic matrix in aragonite precipitationIn the above exercise, we assume that coral calcification is only influenced by ΩECM and temperature. However, this is an oversimplification. Corals produce a skeletal organic matrix composed of proteins, sugars, polysaccharides and lipids which controls mineral precipitation (Falini et al. 2015). Observations of modern day Porites spp. corals, growing over a range of seawater Ω, indicate that skeletal density is reduced at low seawater Ω but that linear extension is not affected (Mollica et al. 2018). These variations are not driven by conditions and likely reflect the role of the skeletal organic matrix in skeletogenesis. Aspartic acid, the most common amino acid in the coral skeletal organic matrix (Cuif et al. 1999), inhibits aragonite precipitation at the concentrations inferred to occur at the coral calcification site (Kellock et al. 2020). The degree of inhibition increases at low seawater Ω and at higher [aspartic acid]. Skeletal aspartic acid and total amino acid concentrations in cultured Porites spp. corals are positively correlated with seawater pCO2 (Kellock et al. 2020). Reducing ΩECM and increasing skeletal [aspartic acid], as can occur in corals at high pCO2, both act to increase the degree of aspartic acid inhibition of aragonite precipitation and can contribute to reduced coral calcification rates under ocean acidification. [SEP] Justify:

Output: The text corroborates the claim by discussing the impact of ocean acidification on coral calcification rates. It explains that as seawater aragonite saturation state (Ω) decreases, which is associated with higher pCO2 levels (a factor of ocean acidification), the degree of inhibition of aragonite precipitation by aspartic acid increases. This indicates that coral calcification rates can be reduced under conditions of ocean acidification, aligning with the claim that coral reefs are affected by this phenomenon.


Input: Task: contrast the claim using the given text. Claim: Food waste reduction alone can solve global hunger issues. [SEP] Text: A un anno dalla scadenza per il raggiungimento degli Obiettivi di Sviluppo del Millennio, fissata nel 2015, l’della Fame 2014 offre una prospettiva articolata del problema della fame nel mondo, che porta nuovi spunti al dibattito mondiale rispetto a dove concentrare gli sforzi nella lotta contro la fame e la malnutrizione. Secondo il GHI 2014, lo stato della fame nei Paesi in via di sviluppo è complessivamente migliorato in confronto al 1990, con un calo del 39%. Nonostante i progressi fatti, la situazione mondiale è ancora “grave”, con 805 milioni di persone che continuano a soffrire la fame, secondo le stime dell’Organizzazione delle per l’Agricoltura e l’Alimentazione (FAO). K. von Grebmer, A. Saltzman, E. Birol, D. Wiesmann, N. Prasai, S. Yin, Y. Yohannes, P. Menon, J. Thompson, A. Sonntag. 2014. 2014 Index: of Hidden Hunger. Bonn, Washington, DC, and Dublin: and Concern Worldwide. Alors qu’il ne reste plus qu’une année avant la date d’échéance de la réalisation des Objectifs du Millénaire pour le développement, l’Indice de la faim dans le monde 2014 (GHI) offre une analyse multidimensionnelle de la faim et présente de nouvelles données permettant d’alimenter le débat mondial sur la question de savoir où concentrer les efforts dans la lutte contre la faim et la malnutrition. [SEP] Justify:

Output: The text contrasts the claim by discussing the ongoing global hunger crisis, highlighting that despite a decrease in hunger levels in developing countries since 1990, there are still 805 million people suffering from hunger. It suggests that food waste reduction alone is insufficient to address the complex and multifaceted nature of global hunger and malnutrition, as indicated by the 2014 Global Hunger Index report.


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: 47e-02Vfungal-type vacuole (15/43), mannosylation (7/43), integral component of membrane (28/43), cell wall mannoprotein biosynthetic process (6/43), alpha-1,6-mannosyltransferase activity (4/43)1. 45e-05Wmitochondrion (144/165), mitochondrial inner membrane (57/165), mitochondrial matrix (34/165), oxidation-reduction process (31/165), mitochondrial translation (22/165), respiratory growth decreased rate (81/165), respiratory growth absent (71/165), mitochondrial genome maintenance absent (25/165)3. 15e-15 Table 1—source data 1 Full table of enrichments for Table 1. Download elife-46883-table1-data1-v4. csv Several of the functions that we find enriched within our clusters have been previously associated with molecular features of IDRs, which we recover in our analysis. For example, we find a cluster that is associated with ‘nucleocytoplasmic transporter activity’ (cluster M) that includes IDRs from FG-NUP proteins Nup42, Nup145, Nup57, Nup49, Nup116, and Nup100 that form part of the nuclear pore central transport channel (Alber et al. , 2007). In cluster M, we find molecular features such as increased asparagine content, increased polar residue content, and increased proline and charged residue demixing (‘Omega’; Martin et al. , 2016) in addition to the well-known ‘FG’ repeats that are found in the FG-(reviewed in Terry and Wente, 2009). Another interesting example is cluster O, which contains IDRs from proteins that are enriched for a wide range of annotations such as ‘P-body’, ‘cytoplasmic stress granule’, ‘actin cortical patch’, and ‘DNA binding’. contains IDRs from proteins associated with phase separation and membraneless organelles such as Sup35 (Franzmann et al. , 2018) and Dhh1 (Protter et al. , 2018). [SEP] Justify:

Output: The text is largely irrelevant to the claim regarding X-ray crystallography. It discusses various biological functions, components, and features associated with proteins and their activities but does not mention 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: We know of no reports that constrain the effect of temperature on the skeletal organic matrix, however, changes in the concentration, composition and behaviour of the skeletal organic matrix will influence coral calcification rate. Increasing temperature had no significant effect on pHECM at high pCO2 but reduced pHECM at low seawater pCO2. If reduced pHECM is associated with reduced ΩECM, then this offset between pCO2 treatments may explain why calcification rates remain similar between 25 and 28 °C at low seawater pCO2 (reduced ΩECM enhances any aspartic acid inhibition of aragonite precipitation) but accelerates at high seawater pCO2 (increased ΩECM decreases any aspartic acid inhibition of aragonite precipitation). Insights into controls on pHECM Changes in pHECM between corals and temperatures could reflect changes in calcification (reducing pHECM), in the influx/efflux of relevant solutes to/from the calcification site or in the activity of carbonic anhydrase (CA) enzymes that catalyse the interconversion of CO2 + H2O and HCO3− + H+. Both calcium adenosine triphosphatase (Ca-ATPase) and a bicarbonate anion transporter (BAT) have been localised to the plasma membrane of the calicoblastic cells and remove H+ and add HCO3− to the ECM, respectively (Zoccola et al. 2004, 2015), see Fig. 4. The activities of calcification-related enzymes and solute carriers and the expression of the genes which encode them can be affected by both temperature and seawater pCO2 (Edge et al. 2005; Barshis et al. 2013; Kenkel et al. 2013; Maor-Landaw et al. 2014; Zoccola et al. 2016; Kurihara et al. 2018; Yuan et al. 2018). Temperature increases, below the denaturing threshold, usually promote enzyme activity, e. g. increasing temperature enhances the efficiencies of coral Ca-ATPase (Ip et al. 1991) and coral CAs (Zoccola et al. 2016) over the temperature range studied here (25–28 °C). [SEP] Justify:

Output: The text corroborates the claim by discussing how changes in temperature and seawater pCO2 influence the calcification rates of corals. It explains that while temperature increases typically enhance enzyme activity critical for coral calcification, variations in pHECM and ΩECM due to different pCO2 conditions can affect these processes. This indicates that both ocean acidification (reflected in changes in pCO2) and warming (as temperature rises) have a notable impact on coral reefs.


Input: Task: contrast the claim using the given text. Claim: Food waste reduction alone can solve global hunger issues. [SEP] Text: Selon le GHI 2014, les niveaux de faim dans les pays en développement pris dans leur ensemble se sont améliorés depuis 1990, diminuant de 39%. Malgré les progrès enregistrés, le niveau de la faim dans le monde demeure « grave » avec 805 millions de personnes qui continuent de souffrir de la faim, selon des estimations de l’Organisation des pour l'alimentation et l'agriculture (FAO). This book includes Synopsis that is translated into German and French: von Grebmer, Klaus; Saltzman, Amy; Birol, Ekin; Wiesmann, Doris; Prasai, Nilam; Yin, Sandra; Yohannes, Yisehac; Menon, Purnima; Thompson, Jennifer and Sonntag, Andrea. 2014. Synopsis of 2014 Global hunger index: The challenge of hidden hunger. 83. Bonn, Germany; Washington, D. C. and Dublin, Ireland: Welthungerhilfe; Institute (IFPRI); and Concern Worldwide. von Grebmer, Klaus; Saltzman, Amy; Birol, Ekin; Wiesmann, Doris; Prasai, Nilam; Yin, Sandra; Yohannes, Yisehac; Menon, Purnima; Thompson, Jennifer and Sonntag, Andrea. 2014. Synopse Welthunger-Index 2014: Herausforderung verborgener Hunger. 83. Bonn, Germany; Washington, D. C. and Dublin, Ireland: Welthungerhilfe; Institute (IFPRI); and Concern Worldwide. von Grebmer, Klaus; Saltzman, Amy; Birol, Ekin; Wiesmann, Doris; Prasai, Nilam; Yin, Sandra; Yohannes, Yisehac; Menon, Purnima; Thompson, Jennifer and Sonntag, Andrea. 2014. Synthèse l’Indice de la faim dans le monde 2014: Le défi de la faim invisible. 83. Bonn, Germany; Washington, D. C. [SEP] Justify:

Output: The text contrasts the claim by highlighting that despite improvements in hunger levels in developing countries, an estimated 805 million people still suffer from hunger. This suggests that food waste reduction alone is insufficient to resolve the complexity of global hunger issues, indicating that additional measures are required.


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 evolutionary signatures for the IDRs in this cluster include features that are typically associated with so-called ‘prionogenic’, low complexity disordered regions, such as increased mean polyglutamine repeats (Alberti et al. , 2009), but also indicate that there are other relevant molecular features for this set of disordered regions (Figure 4A). For example, in these regions, the variance of the net charge is reduced, and charged residues are depleted during evolution. These sequence features are illustrated in Figure 4B, where we compare the presence of glutamine and charged residues in an example disordered region from this cluster (Ccr4; a protein that is known to accumulate in P-bodies; Teixeira and Parker, 2007) to an example from the corresponding simulation (Figure 4B). Taken together, these results indicate that our analysis captures molecular features that have been previously associated with IDR functions, and suggests additional molecular features in these IDRs that may be important for their functions. Figure 4 Download asset Open asset Evolutionary signatures in cluster O contain some molecular features that are typically associated with IDRs as well as some that are not. (A) Pattern of evolutionary signatures in cluster O. (B) Example disordered region from cluster O, Ccr4, with a subset of highlighted molecular features compared between its real set of orthologs and an example set of simulated orthologous IDRs. Species included in phylogeny in order from top to bottom are S. cerevisiae, Saccharomyces mikatae, Saccharomyces kudriavzevii, Saccharomyces uvarum, Candida glabrata, Kazachstania naganishii, Naumovozyma castellii, Naumovozyma dairenensis, Tetrapisispora blattae, Tetrapisispora phaffii, Vanderwaltozyma polyspora, Zygosaccharomyces rouxii, Torulaspora delbrueckii, Kluyveromyces lactis, Eremothecium (Ashbya) cymbalariae, Lachancea waltii. [SEP] Justify:

Output: The text is irrelevant to the claim because it discusses evolutionary signatures and molecular features related to intrinsically disordered regions (IDRs) of proteins, without mentioning X-ray crystallography or its application in determining 3D protein structures.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Ca-ATPase uses ATP as an energy source for Ca2+ transport; however, respiration rates did not change significantly between 25 and 28 °C in the corals cultured at 750 µatm pCO2 (Cole et al. 2018) implying that the corals are maintaining a steady energy expenditure (Fig. 4). Ca-ATPase is only one component of the energy budget and temperature-driven increases in the activities of other biological processes (reducing their energy demand) could offset any increase in energy demand by Ca-ATPase. In contrast, respiration rates in corals cultured at 180 µatm pCO2 were significantly lower (two-tailed paired t test, p = 0. 03) at 28 °C (by ~ 20%) than at 25 °C (Cole et al. 2018). This implies that coral metabolic costs, including calcification, are reduced at the higher temperature although individuals maintain similar calcification rates at 25 and 28 °C in spite of this. In this case, the reduction in energy expenditure, e. g. reducing synthesis of calcification-based enzymes and carriers, could be balanced by temperature enhancement of the activities of the enzyme and solute carriers which are present coupled with the temperature promotion of aragonite precipitation. This hypothesis is consistent with evidence that temperature-driven increases in enzyme activity may even offset gene downregulation in response to ocean acidification (Zoccola et al. 2016). Fig. 4Summary of key processes affecting pHECM and the impact of the 3 °C temperature increase on coral physiological processes and pHECM. Solutes can be supplied to the ECM either paracellularly, passing along junctions between cells, or transcellularly, passing across cells (Allemand et al. 2011). H+ (Zoccola et al. 2004) and HCO3− transport (Zoccola et al. 2015) serve to increase and decrease pHECM, respectivelyFull size imageSeawater acidification increases the permeability of the coral tissue and could accelerate the paracellular transport of ions (H+, DIC species, Ca2+) along concentration gradients to and from the calcification site (Venn et al. 2020). Increasing temperature in that study had no effect on paracellular permeability. [SEP] Justify:

Output: The text corroborates the claim by discussing the effects of ocean acidification on coral physiology. It mentions that seawater acidification increases coral tissue permeability and may influence ion transport concerning calcification. Additionally, the impact of temperature changes on respiration and metabolic costs supports the idea that warming, in conjunction with acidification, affects coral reefs' physiological processes, such as calcification and energy expenditure.


Input: Task: contrast the claim using the given text. Claim: Food waste reduction alone can solve global hunger issues. [SEP] Text: and Dublin, Ireland: Welthungerhilfe; Institute (IFPRI); and Concern Worldwide. This record includes the 2014 Global hunger index by severity, an infographic related to the 2014 Global hunger index: (GHI) is based on three equally weighted indicators: > Undernourishment: the proportion of undernourished people as a percentage of the population (reflecting the share of the population with insufficient caloric intake); > Child underweight: the proportion of children younger than age five who are underweight (that is, have low weight for their age, reflecting wasting, stunted growth, or both), which is one indicator of child undernutrition; and > Child mortality: the mortality rate of children younger than age five (partially reflecting the fatal synergy of inadequate food intake and unhealthy environments). This book includes the following synopsis, translated into German and French: von Grebmer, Klaus; Saltzman, Amy; Birol, Ekin; Wiesmann, Doris; Prasai, Nilam; Yin, Sandra; Yohannes, Yisehac; Menon, Purnima; Thompson, Jennifer and Sonntag, Andrea. 2014. Synopsis of 2014 Global hunger index: The challenge of hidden hunger. 83. Bonn, Germany; Washington, D. C. and Dublin, Ireland: Welthungerhilfe; Institute (IFPRI); and Concern Worldwide. The 2014 Index (GHI) report—the ninth in an annual series—presents a multidimensional measure of national, regional, and global hunger. It shows that the world has made progress in reducing hunger since 1990, but still has far to go, with levels of hunger remaining “alarming” or “extremely alarming” in 16 countries. This year’s report focuses on a critical aspect of hunger that is often overlooked: hidden hunger. Also known as micronutrient deficiency, hidden hunger affects more than an estimated 2 billion people globally. The repercussions of these vitamin and mineral deficiencies are both serious and long-lasting. Where hidden hunger has taken root, it not only prevents people from surviving and thriving as productive members of society, it also holds countries back in a cycle of poor nutrition, poor health, lost productivity, persistent poverty, and reduced economic growth. [SEP] Justify:

Output: The text contrasts the claim by discussing the complexity of hunger and highlighting issues like 'hidden hunger,' which is not solely addressed by food waste reduction. The 2014 Global Hunger Index shows persistent issues such as micronutrient deficiencies affecting over 2 billion people, indicating that merely reducing food waste does not tackle the root causes of hunger effectively.


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 also find functions associated with our clusters that have not been previously associated with molecular features of IDRs. For example, cluster D (Figure 5A) is associated with DNA repair, and its evolutionary signature contains increased mean ‘Kappa’ (Das and Pappu, 2013) and decreased mean ‘Decoration’ (SCD) (Sawle and Ghosh, 2015), both of which indicate that there is an increased separation of positive and negatively charged residues in these IDRs compared to our null expectation. This is illustrated by the IDR from Srs2, a protein that is known to be involved in DNA repair (Aboussekhra et al. , 1989; Yeung and Durocher, 2011), and shows high charge separation compared to an example corresponding simulation (Figure 5B). The evolutionary signature for this cluster also reveals an increased mean fraction of charged residues and negatively charged residues in particular (Figure 5A), which is also clear in the comparison between the real Srs2 orthologs and the simulation (Figure 5B). Although acidic stretches have been associated with IDRs in histone chaperones (Warren and Shechter, 2017), to our knowledge, the separation of oppositely charged residues has not been associated with the wider functional class of DNA repair IDRs. Figure 5 Download asset Open asset contains disordered regions associated with DNA repair. (A) Pattern of evolutionary signatures in cluster D. (B) Example disordered region from cluster D, Srs2, with a subset of highlighted molecular features compared between its real set of orthologs and an example set of simulated orthologous IDRs. Species included in phylogeny in order from top to bottom are S. cerevisiae, S. mikatae, S. kudriavzevii, S. uvarum, C. glabrata, Kazachstania africana, K. naganishii, N. castellii, N. dairenensis, T. phaffii, Z. rouxii, T. delbrueckii, K. lactis, Eremothecium (Ashbya) gossypii, E. cymbalariae, Lachancea kluyveri, Lachancea thermotolerans, L. waltii. [SEP] Justify:

Output: The text is irrelevant to the claim about X-ray crystallography and its use in determining the 3D structures of proteins. Instead, the text discusses evolutionary signatures of intrinsic disordered regions (IDRs) in proteins related to DNA repair without mentioning any methods, including X-ray crystallography, for determining protein structures.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: The [H+]sw-[H+]ECM gradient in the current study is much higher at low seawater pCO2 (Venn et al. 2013, 2019; Schoepf et al. 2017) regardless of temperature indicating that any increased paracellular permeability is offset by enhanced H+ transport out of the ECM. Strong inverse correlations were observed between [H+]sw-[H+]ECM and coral calcification in Porites spp. cultured at 25 °C (Cole et al. 2018) suggesting that the [H+]sw-[H+]ECM gradient may provide an indication of the energy budget available to meet the demands of calcification, i. e. for solute transport and for the synthesis of the skeletal organic matrix (Allison et al. 2018). In this study, corals exhibit similar inverse correlations at 25 °C but more mixed relationships at 28 °C (Fig. 2). The breakdown of these correlations implies that [H+]sw-[H+]ECM alone does not provide a good indication of the potential of the coral to calcify at higher temperatures. Other factors, e. g. the ability of the coral to synthesise the organic matrix used to mediate aragonite precipitation, may also be important. We observe no significant relationships between net photosynthesis rates (reported in Cole et al. 2018) and either [H+]sw-[H+]ECM or pHECM in any coral colony at either temperature (Supplementary figs. 1 and 2). Further resolution of the relationships between temperature, calcification and metabolism requires observations over a greater range of temperatures (as in Coles and Jokiel 1977). Implications for coral reefs under future climate changeThis study was conducted under laboratory conditions, and there were no diurnal variations in light availability and seawater DIC chemistry as observed on natural reefs (Dai et al. 2009). Furthermore, we do not know the typical seawater pH of the reef site in which the corals grew and were acclimated before collection. However, our study yields insights into the likely interactions of seawater pH and temperature in massive Porites spp. corals. At 750 µatm pCO2, calcification rates at 28 °C exceed those at 25 °C (Cole et al. [SEP] Justify:

Output: The text corroborates the claim by discussing the effects of different seawater pCO2 levels on coral calcification, which is directly related to ocean acidification and temperature. It highlights that at increased pCO2 levels, coral calcification rates vary with temperature, suggesting that both acidification and warming impact coral health and ability to calcify. The mention of observations regarding coral behavior under different temperature conditions also aligns with the claim about the effects of climate change on coral reefs.


Input: Task: contrast the claim using the given text. Claim: Food waste reduction alone can solve global hunger issues. [SEP] Text: von Grebmer, Klaus; Saltzman, Amy; Birol, Ekin; Wiesmann, Doris; Prasai, Nilam; Yin, Sandra; Yohannes, Yisehac; Menon, Purnima; Thompson, Jennifer and Sonntag, Andrea. 2014. Synopse Welthunger-Index 2014: Herausforderung verborgener Hunger. 83. Bonn, Germany; Washington, D. C. and Dublin, Ireland: Welthungerhilfe; Institute (IFPRI); and Concern Worldwide. Der Welthunger-Index (WHI) 2014 stellt die nationale, regionale und weltweite Hungersituation zum neunten Mal in jahrlicher Folge multidimensional dar. Er zeigt, dass bei der globalen Hungerbekampfung seit 1990 Fortschritte erzielt werden konnten, jedoch angesichts sehr ernster oder gar gravierender Hungerwerte in 16 Landern noch immer groser Handlungsbedarf besteht. dieses Berichts liegt auf einem entscheidenden Aspekt des Hungers, der haufig ubersehen wird, dem verborgenen Hunger. – auch Mikronahrstoffmangel genannt – betrifft Schatzungen zufolge mehr als zwei weltweit. an Vitaminen und Mineralstoffen kann ernste und langfristige Folgen haben. Wo verborgener Hunger verbreitet ist, gefahrdet er nicht nur das Uberleben und beschrankt die Entfaltung der Menschen als produktive Mitglieder ihrer Gesellschaft, sondern halt ganze Lander gefangen in einem Kreislauf aus unzureichender Ernahrung, schlechter Gesundheit, Produktivitatsverlusten, fortdauernder Armut und vermindertem wirtschaftlichen Wachstum. [SEP] Justify:

Output: The text contrasts the claim by highlighting that despite progress in combating hunger since 1990, significant issues still persist, particularly regarding hidden hunger, or micronutrient deficiency, which affects more than two billion people worldwide. The mention of serious hunger values in 16 countries and the multifaceted nature of hunger suggests that food waste reduction alone is insufficient to address these complex issues, emphasizing the need for comprehensive solutions.


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: Our analysis also indicates that there is not necessarily a 1:1 mapping between IDRs with shared evolutionary signatures and current protein functional annotations. For example, we find three clusters associated with ribosome biogenesis (clusters A, C, F) that cannot be distinguished based on their enriched GO terms. The largest of these is cluster A, where 201/295 proteins have a ‘nucleus’ annotation, and 110/295 are essential proteins (‘inviable’ deletion phenotype). This cluster is also enriched for several phenotypes associated with RNA accumulation (Table 1, cluster A; see supplementary data for full list of significant enrichments). contains highly acidic IDRs with CKII phosphorylation consensus sites. CKII has been previously associated with nucleolar organization (Louvet et al. , 2006), and a previous analysis of non-conserved consensus phosphorylation sites found ribosome biogenesis as strongly enriched in predicted CKII targets (Lai et al. , 2012). In contrast, cluster C shares neither of these molecular features with cluster A, and cluster F shares only highly acidic residue content. Interestingly, cluster C contains increased mean polylysine repeats, and is significantly enriched for proteins that have been experimentally verified as targets for lysine polyphosphorylation (Bentley-DeSousa et al. , 2018) (p=2. 7×10−3, hypergeometric test). Overall, although the IDRs in these clusters share different evolutionary signatures, they are all found in proteins associated with ribosome biogenesis. We hypothesize that these different signatures point to different functions relating to ribosome biogenesis, but we have no indication of what these might be based on current protein annotations (see Discussion). We find similar observations in multiple clusters that have distinct evolutionary signatures enriched for terms associated with regulation of transcription (clusters ). These clusters are not clearly separable based on mechanistic steps of transcription (such as sequence-specific DNA binding, chromatin remodeling, etc. ). Some of these clusters exhibit molecular features that have been associated with different classes of transcriptional activation domains that are based on amino acid composition (reviewed in Frietze and Farnham, 2011). For example, clusters J, O and N have increased glutamine residue content, and cluster N has increased proline residue content. [SEP] Justify:

Output: The text does not address the claim regarding X-ray crystallography or its application in determining the 3D structures of proteins. Instead, it discusses protein clusters related to ribosome biogenesis and their evolutionary signatures without mentioning X-ray crystallography. 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: 2018) suggesting that temperature increases, below the thermal stress threshold, can at least partially offset the impact of ocean acidification. Future increases in seawater temperatures may offset ocean acidification effects in individuals of this genus living below their upper thermal stress limits. However, elevating seawater temperature beyond the stress threshold reduced both calcification and pHECM in the branching corals Stylophora pistillata and Pocillopora damicornis over a wide range of seawater pH (Guillermic et al. 2021). Thermally induced bleaching may also decrease pHECM (Dishon et al. 2015). spp. are relatively resilient to high seawater pCO2 (Fabricius et al. 2011; Crook et al. 2012) compared to other corals, and the implications of this study for other species are less clear. Temperature had little effect on skeletal δ11B (reflecting pHECM) in Acropora spp. cultured at ambient and high pCO2 (Reynaud et al. 2004; Dissard et al. 2012) although increasing temperature at high seawater pCO2 acted to significantly decrease calcification in Acropora intermedia (Anthony et al. 2008). While some coral species may acclimatise or adapt to climate change (IPCC 2019), seawater temperature increases are unlikely to benefit the majority of corals which are already living close to their maximum thermal tolerance limits. Coral reefs are predicted to decline greatly at even a 2 °C temperature increase compared to pre-industrial levels (IPCC 2019). [SEP] Justify:

Output: The text corroborates the claim by discussing the effects of both temperature increases and ocean acidification on coral species. It states that while temperature increases below certain thresholds may offset some impacts of ocean acidification, overall, 'seawater temperature increases are unlikely to benefit the majority of corals which are already living close to their maximum thermal tolerance limits.' Furthermore, it cites predictions that coral reefs 'are predicted to decline greatly at even a 2 °C temperature increase compared to pre-industrial levels,' highlighting the detrimental effects of warming and acidification on coral reefs.


Input: Task: contrast the claim using the given text. Claim: Food waste reduction alone can solve global hunger issues. [SEP] Text: von Grebmer, Klaus; Saltzman, Amy; Birol, Ekin; Wiesmann, Doris; Prasai, Nilam; Yin, Sandra; Yohannes, Yisehac; Menon, Purnima; Thompson, Jennifer and Sonntag, Andrea. 2014. Synthèse l’Indice de la faim dans le monde 2014: Le défi de la faim invisible. 83. Bonn, Germany; Washington, D. C. and Dublin, Ireland: Welthungerhilfe; Institute (IFPRI); and Concern Worldwide. Le rapport de l’Indice de la faim dans le monde 2014 – neuvieme edition – propose une mesure multidimensionnelle de la faim au niveau national, regional et mondial. Le GHI 2014 montre les progres effectues en matiere de reduction de la faim depuis 1990, mais des efforts restent a faire, le niveau de la faim restant alarmant voire extremement alarmant dans 16 pays. Cette annee, le GHI se concentre sur un aspect particulier de la faim souvent neglige : la faim invisible. Egalement connue sous la forme de carences en micro-nutriments, la faim invisible touche plus de 2 milliards de personnes dans le monde. Les consequences de ces carences en vitamines et en mineraux sont a la fois graves et perennes. La faim invisible n’empeche pas seulement les personnes qui en sont affectees de survivre et de devenir des membres actifs de la societe, elle ramene egalement les pays dans des cycles de malnutrition, de mauvaise sante, de pertes de productivite, de pauvrete persistante et de croissance economique reduite. [SEP] Justify:

Output: The text contrasts the claim by highlighting that hunger is a multidimensional issue that cannot be solved by food waste reduction alone. It specifically refers to the concept of 'invisible hunger,' which includes micronutrient deficiencies affecting over 2 billion people, suggesting that merely addressing food waste does not encompass the broader challenges of hunger and malnutrition.


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: However, clusters I and R have no amino acid composition bias, while cluster N has increased proline-directed phosphorylation consensus sites, suggesting post-translational modifications. This indicates that our analysis reveals new sub-classifications of transcription-associated IDRs. While we hypothesize that these IDRs have different functions, once more we have no indication of what these functions could be based on current protein annotations (see Discussion). A cluster of evolutionary signatures is associated with N-terminal mitochondrial targeting signals One of our clusters of intrinsically disordered regions is exceptionally strongly associated with the mitochondrion (144/165 proteins in the cluster) and other annotations that are related to mitochondrial localization and function (for example, 81/165 proteins in the cluster have shown a decreased respiratory growth phenotype) (Table 1, cluster W; see supplementary data for full list of significant enrichments). The vast majority of mitochondrial proteins are synthesized with N-terminal pre-sequences (Maccecchini et al. , 1979) (also known as N-terminal targeting signals) that are cleaved upon import (Vögtle et al. , 2009) and are thought to sample dynamic structural configurations (Saitoh et al. , 2011; Saitoh et al. , 2007) (Figure 6A). Since 145/165 of the disordered regions in this cluster are N-terminal, we hypothesized that this cluster contains disordered regions that are associated with mitochondrial targeting signals (Vögtle et al. , 2009). In line with this hypothesis, we find previously described sequence features of mitochondrial N-terminal targeting signals in our evolutionary signatures; for example, these IDRs are depleted of negatively charged residues, have an abundance of positively charged residues, and are much more hydrophobic than our null expectation (Figure 6—figure supplement 1A) (Garg and Gould, 2016; Vögtle et al. , 2009). Examples of disordered regions in this cluster include those of the synthase Cox15 and the mitochondrial inner membrane ABC (ATP-binding cassette) transporter Atm1 (Figure 6—figure supplement 1B). In order to test our hypothesis that this cluster of evolutionary signatures identifies mitochondrial N-terminal targeting signals, we used a recently published tool that scores the probability that a sequence is a mitochondrial targeting signal (Fukasawa et al. , 2015). [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the analysis of intrinsically disordered regions (IDRs) in proteins and their association with mitochondrial targeting signals. There is no mention of X-ray crystallography or its application in determining the 3D structures of proteins, thus making the content unrelated to the claim.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: AbstractRising atmospheric CO2 and its equilibration with surface ocean seawater is lowering both the pH and carbonate saturation state (Ω) of the oceans. Numerous calcifying organisms, including reef-building corals, may be severely impacted by declining aragonite and calcite saturation, but the fate of coral reef ecosystems in response to ocean acidification remains largely unexplored. Naturally low saturation (Ω ~ 0. 5) low pH (6. 70–7. 30) groundwater has been discharging for millennia at localized submarine springs (called “ojos”) at Puerto Morelos, México near the Mesoamerican Reef. This ecosystem provides insights into potential long term responses of coral ecosystems to low saturation conditions. In-situ chemical and biological data indicate that both coral species richness and coral colony size decline with increasing proximity to low-saturation, low-pH waters at the ojo centers. Only three scleractinian coral species (Porites astreoides, Porites divaricata, and Siderastrea radians) occur in undersaturated waters at all ojos examined. Because these three species are rarely major contributors to Caribbean reef framework, these data may indicate that today’s more complex frame-building species may be replaced by smaller, possibly patchy, colonies of only a few species along the Reef. The growth of these scleractinian coral species at undersaturated conditions illustrates that the response to ocean acidification is likely to vary across species and environments; thus, our data emphasize the need to better understand the mechanisms of calcification to more accurately predict future impacts of ocean acidification. Use our pre-submission checklist Avoid common mistakes on your manuscript. IntroductionAtmospheric CO2 is currently on the rise, and its equilibration with surface seawater is expected to reduce the pH of the surface oceans by approximately 0. 4 pH units by year 2100 (Caldeira and Wickett 2005; Orr et al. 2005; Doney et al. 2009). Numerous calcifying organisms, including reef-building corals, may be severely impacted by this reduction in pH, which will lower the aragonite and calcite saturation state (Ω) and make skeletal and shell formation for many organisms more difficult (Fine and Tchernov 2007; Anthony et al. 2008; Doney et al. 2009). [SEP] Justify:

Output: The text corroborates the claim by detailing how rising atmospheric CO2 leads to lower pH levels and reduced carbonate saturation in the oceans, which severely impacts reef-building corals. It highlights that these changes can affect coral species richness and colony size, indicating that coral reefs are indeed affected by ocean acidification.


Input: Task: contrast the claim using the given text. Claim: All sustainable buildings are completely carbon-neutral. [SEP] Text: Carbon neutral Bhutan: sustaining carbon neutral status under growth pressures paper Open access Published: 15 February 2023 Carbon neutral Bhutan: sustaining carbon neutral status under growth pressures : orcid. org/0000-0002-0969-37931, Vanessa Rauland2 & Peter Newman1 Reviews 1. The figure shows the interacting mechanism at a high-level of what Bhutan is attempting to do and is a unique way for a developing country to have reduced these complex issues down to three key indicators. No other country has developed a Happiness set of indicators. It is why Bhutan is worth being seen as a case study of a globally significant approach. Fig. 1The 3G mechanism. Adapted from [11]. (GDP – gross domestic product; GNH – gross national happiness; GHG – greenhouse gas)Full size imageThe following sections provide a brief overview of why Bhutan is unique from a geography perspective before providing a synthesis on the relationship between economic growth, carbon emissions, energy use and social wellbeing. It then highlights Bhutan’s energy system, the context of earlier studies conducted on energy modelling and emissions reduction, then gives the results from seven economic scenarios created to examine the nexus growth pressures and their policy recommendations. A separate Methods section shows the scenario storylines and how the modelling was done as well as the scope and limitations of the study. Regional characteristics of BhutanBhutan is a small land-locked developing country nested between China and India in the eastern Himalaya range (see Fig. 2) with a population of less than a million people having a per capita GDP of USD 3372 [13]. Being in the Himalayas, Bhutan is a mountainous country with altitude reaching up to 7500 m above sea level in some places. 71% of Bhutan’s land area is covered by forest, which is the cornerstone for Bhutan’s carbon neutrality. The popular religion in Bhutan is Buddhism, which has influenced the GHN-based development paradigm with it’s leaders cautiously crafting their national development pathways at the intersection of economic growth, human wellbeing and nature conservation. Fig. 2Location of Bhutan [12]Full size imageCarbon emissions, energy use and socio-economic wellbeingWhile the relationship between carbon emissions, energy use and economic growth appear simple, they are in fact complex, intertwined and evolving. [SEP] Justify:

Output: The text contrasts the claim by discussing Bhutan's approach to carbon neutrality, which is complex and contingent on various factors including economic growth and social well-being. It highlights that Bhutan's carbon neutrality is a result of specific geographical and cultural contexts rather than suggesting that all sustainable buildings achieve this status universally.


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: Using this tool, we find that the IDRs in cluster W have a much higher probability of being mitochondrial targeting signals than any other cluster with enriched annotations in our analysis (Bonferroni-corrected p≤6. 5×10−11, Wilcoxon test) (Figure 6B, red box). Interestingly, the adjacent cluster V (Figure 6B, purple box), which we hypothesize to contain targeting sequences for the endoplasmic reticulum, is distinct from cluster W in this analysis. Figure 6 with 4 supplements see all Download asset Open asset is associated with mitochondrial N-terminal targeting signals. (A) Schematic (not to scale) showing the path of a mitochondrial precursor peptide (with N-terminal targeting sequence in red) from the cytosol, where it is translated, to the mitochondrial matrix, where the peptide folds and targeting sequence is cleaved. (B) Violin plots (median indicated by black dot, thick black line showing 25th-75th percentile, and whiskers showing outliers) show distributions of mitochondrial presequence probability scores for all IDRs in each cluster. The cluster that we predict to contain mitochondrial N-terminal targeting signals is outlined in red, while the cluster that we predict to contain endoplasmic reticulum targeting signals is outlined in purple. (C) Micrographs of S. cerevisiae strains in which Cox15 is tagged with GFP, with either the wildtype Cox15 IDR, deletion of the Cox15 IDR, replacement of the Cox15 IDR with the Atm1 IDR (also in the mitochondrial targeting signal cluster), or replacement of the Cox15 IDR with the Emp47 IDR (from the endoplasmic reticulum targeting signal cluster). If the specificity of the function of the IDRs in this cluster is strong, we predict that swapping an IDR from cluster W with that of a verified mitochondrial targeting sequence would result in correct localization to the mitochondria, while swapping an IDR from a different cluster would not. Mitochondrial precursor peptides that are not correctly targeted to the mitochondria are thought to be degraded (Mårtensson et al. , 2019; Weidberg and Amon, 2018). [SEP] Justify:

Output: The text does not address the claim directly and instead discusses analyses related to mitochondrial targeting signals and their identification through clustering, as well as the localization of mitochondrial precursor peptides. There is no mention of X-ray crystallography or its application in determining 3D structures of proteins, making this text 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: Recent field studies in the Mediterranean and Guinea have demonstrated strong impacts of low pH related to volcanic CO2 vents on both individual organisms and community structure (Hall-Spencer et al. 2008; Cigliano et al. 2010; Dias et al. 2010; Rodolfo-Metalpa et al. 2010; Fabricius et al. 2011). However, additional field studies under different natural conditions are necessary to ascertain a wider range of potential long-term impacts of ocean acidification on communities and ecosystem processes (Doney et al. 2009; Riebesell et al. 2010). Along the eastern coast of the Yucatán Peninsula, México (. 1S), nearshore springs, referred to locally as “ojos,” discharge naturally low-pH, low carbonate saturation groundwater (Ω = [Ca2+][CO3 2−]/K’sp). These highly localized springs are a natural feature of the karst terrain, have been continuously discharging water for millennia (Beddows et al. 2002), and have been the focus of many studies since the early 1990s (van Tussenbroek 1995; Ruiz-Renteria et al. 1998; Carruthers et al. 2005). Discharge from these “ojos” is markedly more acidic (pH = 6. 70–7. 30 total scale) and less saturated (Ωarag = 0. 30–0. 97 at ojo centers) than the surrounding ocean water (Ωarag = 3. 60), and they occur in close proximity to one of the Caribbean’s largest coral reef ecosystems (the Reef). Thus, the ojos of the Yucatán Peninsula provide a natural laboratory for examining the long-term impacts of low saturation waters on specific organisms and the coastal ecosystem. Specifically, much can be learned from this site about the response of calcifying organisms exposed to reduce saturation states over time scales much longer than the life span of individual organisms. The conditions creating low-pH seawater at the ojos differ from those of the ocean acidification scenario: specifically, the discharging water at the ojos is derived from high CO2 concentrations associated with brackish water that has interacted with soil and limestone. [SEP] Justify:

Output: The text corroborates the claim by detailing the impacts of low pH and ocean acidification on coral reefs, specifically mentioning studies that investigate the effects of volcanic CO2 vents on individual organisms and community structures. It also highlights the significant ecological conditions, such as the low-pH waters from the 'ojos' on the Yucatán Peninsula, which serve as a natural laboratory for understanding the consequences of ocean acidification on coral reef ecosystems. The mention of low carbonate saturation demonstrates a direct link to the effects 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 is demonstrated by the volumes of research uncovering issues of coupling and decoupling phenomena among these variables [14] and others that explore energy and economic system decarbonisation for a net zero transition [15], which is the new term for carbon neutrality. The complexity intensifies when the social dimension is included due to many indirect ways that energy is consumed; for Bhutan, the social is primarily considered through its GNH index (see Table 1). It is not hard to see that in the GNH Index there are indicators that traditionally would have led to increased energy consumption such as ‘economic development’, ‘living standard’ and even ‘health’ and ‘education’, though decoupling all of these is now part of the UN agenda to achieve the SDG’s and the at the same time. Table 1 Components of GNH IndexFull size tableThere are different approaches and methods to analyse and understand the nexus between all these GNH and GDP variables that can help us to understand their implications for carbon neutrality in Bhutan. Some approaches use qualitative methods, others use econometric techniques, and some others use spatial-based land-use planning and integrated energy-economy models, which are either top-down, bottom-up or hybrid. These will be briefly explained before showing how they were used in this paper. Qualitative approaches, such as through a social ecological lens, assist with understanding the high level need to transform political and cultural dimensions among others beyond techno-economic fixes, for example on the need for drastic emission reduction towards carbon neutrality [17]. A social ecological lens was also used to inform spatial-based emission modelling for urban development [18, 19] that can bring out high emission spots. Econometric techniques show that the GDP-emission relationship is non-linear and varies across countries and their socio-economic structures as well as by the functional form used in the analysis [20]. Econometric analysis of the GDP-emission nexus mostly illuminates the presence or absence of the Curve (EKC). This shows an inverted U-shaped curve indicating that economic growth can lead to reductions in emissions after a certain development level is reached. Energy-economy models enable quantitative and holistic assessment of climate policy [21] and they can be applied to design a low carbon society [22]. [SEP] Justify:

Output: The text contrasts the claim by discussing the complexities of achieving carbon neutrality and the challenges related to various factors such as economic development, living standards, and education. It highlights that while aiming for carbon neutrality is part of an agenda (the UN's), achieving this goal is complicated by various indirect energy consumption factors and socio-economic dynamics. This suggests that not all sustainable buildings can be claimed to be completely carbon-neutral due to these intricate relationships.


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: To test this, we first used the (uncharacterized) disordered region from Atm1 that falls into cluster W to replace that of Cox15, which also falls into cluster W and is an experimentally verified mitochondrial targeting sequence (Vögtle et al. , 2009) (Figure 6C). In accordance with our hypothesis, we find that GFP-tagged Cox15 correctly localizes to the mitochondria when its disordered region is swapped with that of Atm1, but does not localize correctly when its disordered region is deleted (Figure 6C; full micrographs in Figure 6—figure supplement 2). We also repeated this experiment with another protein that has an experimentally verified N-terminal mitochondrial targeting sequence, Mdl2, and found the same results (Figure 6—figure supplement 3). Next, we replaced the Cox15 IDR with the disordered region of Emp47, which has an evolutionary signature that we predict to be associated with targeting signals for the endoplasmic reticulum (cluster V). In this case, as we predicted, we found no mitochondrial localization of Cox15-GFP. For strains where there was no discernible localization to the mitochondria (and no presence of GFP), we wanted to rule out that these were caused by the transformation process. Therefore, we restored the wildtype N-terminal IDR in the strains in which the Cox15 IDR was replaced with Emp47 or knocked out (Figure 6—figure supplement 4). Because we were able to rescue the mitochondrial localization with the restored wildtype IDR, we conclude that the absence of mitochondrial GFP expression is directly linked to the mutations we made in the N-terminal IDR of each strain. Importantly, these putative targeting signals have no detectable similarity when their primary amino acid sequences are aligned, and we therefore suggest that the similarity in their molecular features is preserved by stabilizing selection (see Discussion). These results confirm that IDRs with similar evolutionary signatures can rescue subcellular targeting functions, and suggest that the evolutionary signatures are specific enough to predict function of at least some IDRs. Evolutionary signatures of function can be used for functional annotation of fully disordered proteins A major challenge to proteome-wide analysis of IDRs is the limited applicability of homology-based sequence analysis. [SEP] Justify:

Output: The text discusses experimental results related to protein localization and the evolutionary signatures of disordered regions in proteins. However, it does not mention X-ray crystallography or its role in determining protein structures. Therefore, the text 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: It is thus characterized by low pH, high Ca2+ (salinity normalized), high dissolved inorganic carbon (DIC), and high total alkalinity (TA). However, the organisms residing at the ojos have been exposed to low-pH and low aragonite saturation, as is predicted for future ocean acidification (Table 1), but the organisms are also exposed to high nutrients, high dissolved inorganic carbon, and high alkalinity that are not necessarily predicted in future oceans subjected to acidification. Yet, these environments provide an opportunity to study in situ community impacts on corals exposed to low carbonate saturation conditions and often extreme drops in pH for extended time intervals. Table 1 Chemical measurements and calculations at centers of ojo dischargeFull size table At least thirteen ojos lie approximately 500 m offshore within the Park at Puerto Morelos, in a shallow lagoon approximately 5 m deep (ESM Fig. 1S). The ojos range from 10-m long “fractures” to small circular depressions (seeps) only a few centimeters across (ESM Fig, 2S). Based on monitoring over two and a half years (April 2008 to September 2010), discharge from the ojos is continuous with a combined discharge flux (estimated using excess 224Ra measurements) reaching as high as ~800,000 m3 h−1 (Derse et al. 2008). Discrete water samples taken during three different sampling events (June 2009, November 2009, and September 2010) indicate that the pH (and other water chemical characteristics) at each ojo center varied on tidal time scales. However, the water discharged at the ojo center remained undersaturated during all sampling events (Table 1). Continuous pH monitoring over 2 months using a SeapHOx sensor supports this conclusion (Hofmann et al. 2011). The relationship between water chemistry and benthic biota (identity, density, and size) was investigated at 10 ojos dominated by rocky substrates and characterized by similar temperature, salinity, light, and pH conditions over the three different sampling events. We report the calculated saturation states (Pierrot et al. 2006) based on measured DIC, TA, and nutrient concentrations for each discrete sample using CO2Sys. For samples with higher than expected Ca2+ concentrations, conservative aragonite saturation values were calculated based on measured Ca2+ concentrations (Table 1). [SEP] Justify:

Output: The text corroborates the claim by discussing the characteristics of low pH environments and the exposure of organisms to low carbonate saturation conditions, predicting scenarios aligned with future ocean acidification. It highlights how these conditions impact coral communities, supporting the assertion that coral reefs are indeed affected by ocean acidification.


Input: Task: contrast the claim using the given text. Claim: All sustainable buildings are completely carbon-neutral. [SEP] Text: Energy-economy models have been deployed to assess different techno-economic options to reach an emission reduction target [23, 24]. This study also uses an energy-economy model called LEAP – Long-range Planning – which is now re-named as Analysis Platform, designed especially for emerging countries, to investigate the future of carbon neutral Bhutan (see the Methods section). Net zero transition and carbon neutral challengeAgreement requires a net zero transition by 2050 for a 1. 5 °C world. However, the sum of the nationally determined contributions (NDCs) are nowhere close to achieving this and every nation must now ratchet up their commitments as part of the Agreement. Modelling such as in this paper is required to ascertain how each country can move towards carbon neutrality. Moreover the pathways to a net zero transition are multiple, contested and disruptive [25] and how the underlying drivers interact and evolve are context-specific and place-based. Thus place-based studies such as that for Bhutan undertaken in this research can demonstrate how to resolve such complexity, and thereby contribute to expanding the knowledge base required globally to address this critical problem. Net zero transition for a country like Bhutan means carbon neutrality that does not impede the growth in its other goals towards happiness and being a middle-income country – these are the growth pressures that are part of every nation’s approach to the future. The broadly accepted intention of CN is to balance the carbon going into the atmosphere with the inputs and outputs of any economic activities and requires the measurement, reduction, and finally offsetting of emissions [26, 27]. Birchall [28] considers CN as an extension of long- term climate policy and GHG mitigation strategies that should be applied at the national level. While there is an 14,067:2018 for the carbon footprint of products, there is no universal definition or framework for CN at the national level and many of the countries that have pledged carbon neutrality have not clearly defined it, although in some cases broader strategies for achieving it have been outlined [29, 30]. Several countries have pledged to become CN [30], though Bhutan is one of the very few that have actually achieved this status. Carbon neutrality has many definitions but the one Bhutan has used is based on neutralizing greenhouse gas emissions with forest-based carbon sequestration [11] – taking a territorial approach. The definition used here is the simplest for developing policy scenarios. [SEP] Justify:

Output: The text contrasts the claim by explaining that carbon neutrality (CN) is a complex goal that varies by context and is not universally defined. It indicates that achieving carbon neutrality involves balancing emissions with inputs and outputs of economic activities, highlighting that many countries have pledged carbon neutrality without clear definitions. It specifically mentions Bhutan's approach to carbon neutrality, indicating that while Bhutan has achieved this status, it relies on forest-based carbon sequestration, rather than implying all sustainable buildings must inherently be carbon-neutral.


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: Proteins with a mixture of disordered regions and structured domains can be assigned function based on homology to their structured domains, but fully disordered proteins are much more difficult to classify (reviewed in van der Lee et al. , 2014). We therefore asked whether hypotheses about functions of fully disordered proteins could be generated using evolutionary signatures. We identified ten yeast proteins of unknown function that are predicted to be most disordered (see Materials and methods). To predict function according to our clustering analysis, we simply assigned them the annotation of the cluster in which they fell (Table 2). For example, Rnq1 has been extensively studied as a ‘yeast prion’, but there is no clear function associated with this protein under normal conditions (Kroschwald et al. , 2015; Sondheimer and Lindquist, 2000; Treusch and Lindquist, 2012). Interestingly, Rnq1 falls into our cluster of disordered regions that are associated with nucleocytoplasmic transport (cluster M) and the nuclear pore central transport channel. While Rnq1 is annotated with a cytosolic localization, an RNQ1 deletion was recently shown to cause nuclear aggregation of the polyQ-expanded huntingtin exon1 (Httex1) in a model of Huntington’s disease (Zheng et al. , 2017). Therefore, we propose a role for Rnq1 in nucleocytoplasmic transport. For some of these largely disordered proteins, we obtain large disordered segments falling into multiple clusters (indicated by more than one cluster ID in Table 2), suggesting more than one possible function for the protein (see Discussion). To estimate the predictive power of this approach, we also identified the ten most disordered yeast proteins with known functions based on their gene descriptions in SGD (Cherry et al. , 2012). We found that predictions of function based on our cluster annotations clearly matched the gene description of the proteins in 5 of 10 cases, suggesting a predictive power of at least 50% (Supplementary file 1 - Table S3, see Discussion). This analysis illustrates how evolutionary signatures can be used to generate hypotheses of function for fully disordered proteins. [SEP] Justify:

Output: The text is irrelevant to the claim regarding X-ray crystallography and the determination of protein structures. Instead, it discusses the classification of fully disordered proteins and their functions without mentioning any methods to elucidate their three-dimensional structures or the use of X-ray crystallography.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Materials and methodsThe area of influence of the low-pH waters was determined by direct measurement of physiochemical parameters either in situ (temperature, salinity, and pH) or from discrete water samples (DIC, TA, salinity, and nutrients). In the case of circular seeps (see Fig. 1e), water samples were collected at 0. 25-m intervals along transects placed at right angles and intersecting over the center of each ojo: transects were at least 4 m from the ojo center in all directions. In the case of fractures (see Fig. 1a, d), samples were taken along one long transect (up to 10 m) following the fracture line, and samples were also collected at 5 or more cross-transect lines perpendicular to the main fracture. Divers collected the water in syringes that were immediately transported to a waiting boat for filtration, poisoning (for DIC and TA), and storage using standard operating procedures outlined by Dickson et al. (2007). Fig. 1Saturation state distribution along select transects in the vicinity of three different ojos with pictures of corals situated around the ojo centers. The saturation state (Ωarag) is shown as a contour image (plotted in Surfer®), and the colors represent the range of saturation levels from blue (low saturation) to red (supersaturation). The contour image gives a visual representation of what the saturation state may look like along a sample transect line. The saturation (Ωarag) values were determined based upon discreet water samples taken at 0. 25-m intervals (up to 36 samples per transect). Distance along the transect line is noted in the contour image in meters (X axis), and the Y axis represents 0. 25 cm. The coral images give examples of where the corals were found along these transect lines. a (Ojo Laja) and d (Ojo Fractura) are examples of large “fractures,” while e (Ojo de Agua) is a large circular “seep”. Calcifying coral species including Siderastrea radians (b) and Porites astreoides (c, f) were found in undersaturated and low saturation water at all 10 ojos sampled. [SEP] Justify:

Output: The text corroborates the claim by detailing the process of measuring physiochemical parameters in specific areas, indicating that low-pH waters, which are related to ocean acidification, were measured and found to impact calcifying coral species. By discussing findings along transects that include corals in undersaturated and low saturation water, the text supports the assertion that coral reefs are indeed affected by ocean acidification.


Input: Task: contrast the claim using the given text. Claim: All sustainable buildings are completely carbon-neutral. [SEP] Text: While some may argue that it should include the export of renewable hydropower (to India), this would imply that the import of embedded carbon in many consumer items was well understood, which it is not and is in fact very complex. This paper will therefore be examining scenarios that fit within the carbon neutralizing sink capacity provided by Bhutan’s current and growing forests. can remain CN in perpetuity is uncertain. [31] expressed concern over the rising GHG emissions in Bhutan. Yangka [32] also cast doubt on the long-term carbon neutrality of Bhutan based on the extrapolation of carbon emission levels from 2005 to 2050. Thus, the challenge for Bhutan is how it can remain CN under social and economic growth pressures [11]. Energy system of BhutanBhutan is endowed with 24,000 MW of hydropower potential and 71% forest cover. It lacks fossil fuel reserves except for a limited sub-bituminous coal [33]. This pattern of natural resource endowment provides a natural advantage for Bhutan in upholding its CN declaration in a carbon constrained world. However, Bhutan also has very energy intensive and highly polluting industry sectors such as the cement, iron and steel, calcium carbide and ferrosilicon industries. Despite its small economy, Bhutan was also listed, along with eleven other countries around the world, as a key economy for silicon production [34]. Bhutan also has a very rigid transportation system, in which commuters do not have the choice of different modes of transportation, since there are no railways and waterways and limited air transport, relying predominantly therefore on the surface road transport system based on trucks, cars and motorbikes. This is dependent on 100% imported diesel and gasoline from India. In 2014, the base year of this study, both the transport and the industry sectors contributed 30% each to the total GHG emissions, which is expected to increase substantially over the planning period of this study. Total energy demand in Bhutan increased from 402 ktoe in 2005 [35] to 650 ktoe in 2014 [36] leading to an increase in the per capita energy consumption from 0. 63 toe to 0. 87 toe. Between these two periods, energy consumption in the transport and industry sectors witnessed a growth of 200% [36]. In 2014, fossil fuels (petroleum and coal) formed the largest share at 37%, followed by biomass at 36% and hydropower at 28%. [SEP] Justify:

Output: The text contrasts the claim by discussing Bhutan’s uncertain status regarding carbon neutrality (CN) despite being endowed with resources like hydropower and forests. It highlights concerns about rising greenhouse gas (GHG) emissions linked to the dominant industry sectors and transportation, which contribute significantly to total emissions. Moreover, it points out that achieving and maintaining carbon neutrality under social and economic pressures is complex, thus challenging the notion that all sustainable buildings can be fully carbon-neutral.


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: Table 2 Evolutionary signatures of function can be used for functional annotation of previously uncharacterized proteins and IDRs. IDNameDescription% 028WRNQ1Protein whose biological role is unknown; localizes to the cytosol96M: Nucleocytoplasmic transport YKL105CSEG2Protein whose biological role is unknown; localizes to the cell periphery92P: Signal transduction YGR196CFYV8Protein whose biological role is unknown; localizes to the cytoplasm in a large-scale study89A: Ribosome biogenesis R: Transcription YGL023CPIB2Protein whose biological role is unknown; localizes to the mitochondrion in a large-scale study86R: Transcription YOL036WProtein whose biological role and cellular location are unknown84P: Signal transduction R: Transcription YNL176CTDA7Protein whose biological role is unknown; localizes to the vacuole83Q: Cell wall organization YFR016CProtein whose biological role is unknown; localizes to both the cytoplasm and bud in a large-scale study83A: Ribosome biogenesis YBL081WProtein whose biological role and cellular location are unknown82M: Nucleocytoplasmic transport YBR016WProtein whose biological role is unknown; localizes to the bud membrane and the mating projection membrane82O: Sup35-like YOL070CNBA1Protein whose biological role is unknown; localizes to the bud neck and cytoplasm and colocalizes with ribosomes in multiple large-scale studies81Does not fall into annotated cluster; close to ribosome biogenesis cluster this work, we tested for evolutionary constraints on highly diverged intrinsically disordered regions proteome-wide. In contrast to the relative lack of constraint on primary amino acid sequence alignments (compared to folded regions, Brown et al. , 2002; Tóth-Petróczy and Tawfik, 2013), we find that the vast majority of disordered regions contain molecular features that deviate in their evolution from our null expectation (a simulation of disordered region evolution; et al. , 2014; et al. , 2012). [SEP] Justify:

Output: The text does not address or provide information related to X-ray crystallography or its use in determining the 3D structures of proteins. Instead, it discusses evolutionary signatures and annotations of uncharacterized proteins and intrinsically disordered regions, which is not relevant to the claim about X-ray crystallography.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: , Ωarag < 1), and low saturation conditions (i. e. , Ωarag < 2. 5) were seen close to the discharge area. Saturation values increased rapidly with distance from the ojo center (Fig. 1). While waters generally reached saturation (Ωarag = 1) within 0. 5 m of the center of discharge, saturation values below 2. 5 were observed up to 2 m from the ojo (ambient Ω in the lagoon was 3. 60; see Fig. 1). Salinities at the ojo center were always lower than ambient due to the brackish discharge, but not lower than 25. Despite these low salinities, Ca2+ concentrations were generally somewhat higher than expected from simple dilution of seawater to the measured salinities, because Ca2+ was added to the groundwater from the dissolution of limestone (ESM Fig. 3S). DIC and TA concentrations were highest at the center of discharge and decreased with distance from the discharge site. TA and DIC were correlated (R 2 = 0. 86) (ESM Fig. 4S). Dissolved nutrient (nitrate, ammonium, phosphate, and silica) concentrations ranged from approximately 2–10 times ambient (Derse et al. 2008). Calcifying organisms such as corals, coralline algae, and calcifying macroalgae were often present in undersaturated or low saturation waters close to the ojos. Here, we focus on calcifying corals, which were present where Ωarag < 2. 5 at all 10 ojos sampled. Only three scleractinian species (Porites astreoides, Porites divaricata, and Siderastrea radians) and one hydrozoan “fire coral” (Millepora alcicornis) were observed where Ωarag < 2. 5. All of these species have aragonitic skeletons. Another six scleractinian coral species (Diploria, Montipora, Montastraea, Agaricia, Porites, and Favia) were present near the ojos, but only where the water saturation was above 2. 5 (Ωarag > 2. 5). These distributions may be evidence that certain calcifying coral species are more tolerant of low saturation waters than other species, with potential implications for differential survival under future CO2 projections. [SEP] Justify:

Output: The text corroborates the claim by discussing the presence of calcifying corals in waters with varying aragonite saturation states (Ωarag), indicating that coral species are encountered in undersaturated or low saturation waters. It highlights that certain coral species are affected by saturation levels, specifically noting that some are present only when Ωarag is above 2.5, which suggests a direct relationship to the conditions related to ocean acidification and potential warming due to increased CO2 projections.


Input: Task: contrast the claim using the given text. Claim: All sustainable buildings are completely carbon-neutral. [SEP] Text: At the sector level, industry and transport together formed 56% of the total energy consumption. Energy-economy modelling for Bhutan’s carbon neutral assessmentThere are many studies on emissions reduction using an energy-economy modelling framework, but they are primarily to examine how to reach a desired emission reduction target without necessarily leading to carbon neutrality. Most carbon neutral studies are at city or other sub-national level [17, 37] and a few are at global level [15] with only limited studies at national level [21]. The fundamental difference between a generic emission reduction and a carbon neutral study is that the latter includes carbon offsetting, which for Bhutan is the forest-based carbon sequestration. But for Bhutan there are only limited studies covering long term integrated energy-economy modelling and policy analyses let alone studies on carbon neutral issues (see Yangka and Newman [38]). Shrestha, et al. [39] highlighted a number of options to reduce GHG emissions, while Yangka and Diesendorf [40] quantified the benefits of expanding electric cooking in terms of reduction in the emissions of CO2 and other local air pollutants. Strategy for Bhutan [5] discusses CN in Bhutan. [5] was developed using a based model without a cost module whilst assuming a low GDP growth rate of 5. 7%. The analyses assumed saturation of travel demand and industrial output by 2020. Such assumptions invariably lead to lower emission levels, thereby overlooking the need to foresee the challenges of CN development and the subsequent policy implications as the country grows (see also the ‘Scope and Limitations’ section). Similarly, national documents on low emissions roadmaps and strategies including Bhutan’s Communication to the [41] do not include a cost module. Only one study provides information on the probable costs of Bhutan’s CN pathway into the future [38] but does not have the full scenarios outlined here. The method in this study is based on the LEAP model, enabling the nexus between carbon neutral, happiness and economic development goals to be analysed under various growth pressures. Methods of analysis and the different scenarios are outlined in a separate Methods section below with further details provided in the 3. Table 3 CO2e emissions (MT-million tonnes) under each scenarioFull size tableA scenarios are not very encouraging. The CN sink capacity of 6. [SEP] Justify:

Output: The text contrasts the claim by explaining that while there are studies on emissions reduction and carbon neutrality, achieving carbon neutrality does not mean that all sustainable buildings are completely carbon-neutral. It highlights the fundamental difference between emissions reduction and carbon neutrality, emphasizing that carbon neutrality involves more complex factors like carbon offsetting and does not solely depend on building construction features. Additionally, it mentions limitations in studies assessing the carbon neutrality pathways which imply that not all sustainable buildings automatically achieve complete carbon neutrality.


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: Our discovery that highly diverged disordered regions contain (interpretable) molecular features that are under evolutionary constraint provides researchers with testable hypotheses about molecular features that could be important for function in their proteins of interest. Furthermore, in principle, our framework for the analysis of diverged disordered regions can be extrapolated to proteins from other species. Importantly, our choice of features was based on previous reports of important sequence features in IDRs that could be easily calculated for protein sequences and scaled to millions of simulated sets of orthologous IDRs. Thus, our evidence for constraint must represent a lower bound on the total amount of functional constraint on highly diverged IDRs: there are very likely to be sequence characteristics that were not captured by our features. Further, even when we do find evidence for constraint on a feature, we do not know whether our feature represents the actual feature required for IDR function, or is simply correlated with it. For example, we found IDRs that show constraint on glycine and arginine content, but these may reflect the real constraint on planar-pi interactions (Vernon and Forman-Kay, 2019) and are not fully captured by either of these features. In the future, we could exhaustively search for protein sequence features that best explain the evolutionary patterns as was done for features of activation domains that explain reporter activity (Ravarani et al. , 2018). Another important element to consider is that many of our features are correlated with each other. For example, net charge is correlated with the fraction of acidic and/or basic residues in a given IDR. Due to the non-independence of molecular features that comprise the ‘evolutionary signatures’, it is difficult to quantify similarity between these evolutionary signatures using standard distance metrics that assume independence. We use a weighted uncentred correlation distance (de Hoon et al. , 2004) in the clustering analysis, which limits the impact of correlated features. However, we caution against a quantitative comparison of individual evolutionary signatures. Despite our choice of molecular features, we found strong evidence that groups of disordered regions share evolutionary signatures, and that these groups of IDRs are associated with specific biological functions. To demonstrate the association of evolutionary signatures with previously known functions, we associated IDRs with protein function, and indeed showed that we could generate hypotheses about protein function for fully disordered proteins. [SEP] Justify:

Output: The text does not address X-ray crystallography or provide any information related to determining 3D structures of proteins. Instead, it discusses evolutionary constraints and molecular features of disordered regions in proteins, which is not relevant to the claim about X-ray crystallography.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: A goodness-of-fit analysis indicates that the number of species (i. e. , species richness) increased significantly as saturation values increased with distance from the ojo centers (P < 0. 0001; Fig. 2). Fig. 2 a Number of species as a function of saturation state. No “other hard corals” (Diploria, Montipora, Montastrea, Agaricia, Porites, and Favia sp. ) were found in low saturation or undersaturated (Ω < 2. 5) waters. Species richness increased significantly (P < 0. 001) with increasing saturation state. b Coral size as a function of saturation state for the different species. Average values for each group are reported, and error bars indicate standard error. Corals were grouped into 3 classes based on the saturation of the water in which they were observed: Ω < 1 (n = 31); 1 < Ω < 2. 5 (n = 72); or Ω > 2. 5 (n = 172). No significant differences in size were observed in colonies of Siderastrea radians; however, colonies of Porites astreoides were significantly larger in supersaturated (Ω > 2. 5) water when compared to Porites astreoides colonies in low saturation and undersaturated water (P = 0. 05). Porites divericata colonies were omitted due to the rarity of their occurrence in both undersaturated and supersaturated water. Although comparing coral colony size for assemblages composed of different species is complicated by species-related morphology and growth rates, we also report the average size of all species found in supersaturated waters to provide qualitative information regarding coral growth outside of the springs. We note that the average size of all species found in supersaturated waters was significantly larger (P < 0. 03) than the average size of corals found where Ω < 2. 5. c Number of coral colonies per unit area as a function of saturation state. Results are normalized to per unit area (0. 25 m2) to account for differences in area sampled between groups. The total (i. e. , all species combined) number of coral colonies per unit area increased significantly with saturation state (P < 0. [SEP] Justify:

Output: The text corroborates the claim by presenting data on coral species richness and growth in relation to saturation state, which is influenced by ocean acidification. For instance, it states that 'No “other hard corals” were found in low saturation or undersaturated (Ω < 2. 5) waters,' and that species richness increased significantly with increasing saturation state (P < 0. 001). This suggests that the health and biodiversity of coral reefs are impacted by the levels of saturation, which are directly related to ocean acidification and warming.


Input: Task: contrast the claim using the given text. Claim: All sustainable buildings are completely carbon-neutral. [SEP] Text: 3 MT’s of CO2e is exceeded in most of the scenarios especially BAU, but also even in the NDC plan scenario. The emissions level exceeds the sink capacity by 2037 under the HGDP scenario, by 2044 under the BAU scenario and by 2047 under the NDC plan scenario. These results suggest the need for intervention to limit the carbon emissions within the CN sink capacity. Reducing carbon emissions inadvertently contributes to strengthening the environmental dimension of the GNH since socio-environmental sustainability forms the core premise for GNH and measuring and minimising carbon emissions is a must for climate policy and the SDGs. Without mitigation measures, the emissions level remains below the sink capacity only under the low economic growth outlook. Bhutan does not envision such a lean horizon, as like most emerging nations the Bhutanese dream of improving their living standard in the twenty-first century when humanity moves out of poverty towards a more sustainable and comfortable livelihood as suggested by the Goals. Thus, these set of scenarios (Group A) do not work and other scenarios are needed to demonstrate how to resolve the conflicts between these three core goals of increasing wealth, improving happiness, and maintaining carbon neutrality. B Scenarios show what mitigation measures can do to keep Bhutan within its forest sink capacity and thus sustain its carbon neutral status going into the future and thus will be analysed in more depth. The results show that there are measures that can keep the emissions within the carbon sink capacity but at varying mitigation costs as explained further in the next section. The results are summarised with their CN counterpart in Fig. 3a, b and c. Footnote 1Fig. 3scenarios under different growth pressures. a BAU and its carbon neutral counterpart. b NDC Plan and its carbon neutral counterpart. c HGDP and its carbon neutral counterpartFull size imageThe total CO2e emissions steadily rose in all the scenarios, however, as can be seen, the rise is lower in the corresponding CN scenarios (orange colour in figures) due to fuel switching and energy efficiency measures. Figure 4 shows the role of reducing carbon intensity in three key scenarios; although the total emissions increase, the carbon intensity of the Bhutanese economy steadily improves from 2. 67 kgCO2e/US$ in the base year to 0. 41kgCO2e/US$ by the end of the planning horizon in the scenario. [SEP] Justify:

Output: The text contrasts with the claim by stating that carbon emissions often exceed the sink capacity under various scenarios and suggests that complete carbon neutrality is not always achievable without intervention. It states that 'the emissions level exceeds the sink capacity' in most scenarios and emphasizes the need for mitigation measures to maintain sustainability. This suggests that while some measures can assist in achieving carbon neutrality, it is not guaranteed for 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: However, many proteins contain multiple IDRs. In these proteins, the IDRs may perform different functions (just as multiple folded domains may perform independent functions), thus complicating the mapping of molecular functions to molecular features of IDRs. We are currently developing more well-defined statistical approaches to predict function for IDRs based on evolutionary signatures. Systematic data at the level of individual IDRs would greatly facilitate future progress in this area. Another challenge in associating specific functions with individual IDRs is that current bioinformatics predictions of IDRs at the proteome level often lead to arbitrary breaks (or merging) of IDRs, as IDR boundaries are very difficult to define precisely (even with sensitive experimental approaches; Jensen et al. , 2013). Whether or not IDRs serve as distinct functional units across a linear peptide sequence, and where the boundaries for these regions lie on a proteome-wide scale, is an area for further research. In our cluster analysis, we find that the vast majority of IDRs in multi-IDR proteins fall into different clusters, and that this matches our expectation from random chance. A small minority of IDRs from very large (>1500 amino acid) disordered proteins cluster together, suggesting that they are ‘broken up’ pieces of larger units. Despite the caveat of IDR boundaries in proteome-wide analyses, evolutionary signatures of selection on molecular features represent a new way to assign function to the large numbers of currently enigmatic IDRs that have been identified based on protein sequences. This approach is complementary to current bioinformatics approaches to predict IDR function that are based on presence (Edwards et al. , 2007) or conservation of SLiMs (Beltrao and Serrano, 2005; Davey et al. , 2012; Lai et al. , 2012; et al. , 2012), prediction of interactions (MoRFs) (Fuxreiter et al. , 2004; Lee et al. , 2012; Mohan et al. , 2006; Oldfield et al. , 2005; Vacic et al. , 2007), or prediction of phase separation (Vernon and Forman-Kay, 2019). Our evolutionary analysis addresses challenges in assigning function to highly diverged intrinsically disordered regions whose presence is conserved in orthologs. Although there are examples of slowly evolving disordered regions (Ahrens et al. , 2016; Ahrens et al. [SEP] Justify:

Output: The text discusses issues related to intrinsically disordered regions (IDRs) in proteins, their functions, and challenges in predicting those functions based on current bioinformatics approaches. It does not provide any information or evidence regarding X-ray crystallography or its use in determining the 3D structures of proteins, 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: 0001, N = 275)Full size image To determine whether saturation state affected the sizes of coral colonies living near the ojos, we compared colony sizes (measured as the plane area) of the three scleractinian species in undersaturated (Ωarag < 1) plus low saturation (1 < Ωarag < 2. 5) waters with sizes of the same species at control sites in supersaturated waters where Ωarag > 2. 5 (close to, but outside the influence of discharge). The size of Siderastrea radians colonies did not differ significantly between the saturation levels; however, Porites astreoides colonies in undersaturated and low saturation waters near ojos were significantly smaller than Porites astreoides colonies in supersaturated water (= 0. 05; Fig. 2). We then compared the sizes of all colonies present where Ω < 2. 5 to the sizes of all coral species found in supersaturated waters and found that the colonies in less saturated waters were also significantly smaller (= 0. 03; Fig. 2). We note that this last comparison provides only a qualitative analysis, as the comparison is across species with different morphologies. Combined, our data suggest that as saturation levels approached maximum ambient values, both the number of species present and the average size of individual colonies of Porites astreoides increased significantly and that in general the coral colonies tend to be larger away from the ojo. When abundances (number of colonies) of Porites astreoides and Siderastrea radians in low saturation (Ωarag < 2. 5) and supersaturated (Ωarag > 2. 5) waters were compared, the densities (number of colonies per 0. 25 cm2) of these individual species did not vary with saturation state. However, for all species combined, the densities were significantly greater away from the ojos (goodness-of-fit; P < 0. 001; Fig. 2). This is attributed to the increase in species number as supersaturation was reached. DiscussionEcological surveys at the ojo sites indicate that certain scleractinian coral species can grow in undersaturated conditions. Thus, these species may be more tolerant of low-pH and low aragonite saturation conditions, and hence more resistant than other species when exposed to changing oceanic pH and carbonate saturation. [SEP] Justify:

Output: The text corroborates the claim by discussing how coral species are affected by their living conditions, specifically focusing on saturation states. It indicates that some coral colonies are found in undersaturated and low saturation waters, which relate to lower pH and conditions linked to ocean acidification. It also highlights that certain scleractinian coral species may be more resilient to these changing conditions, thus confirming the relationship between coral growth and the impacts of ocean acidification.


Input: Task: contrast the claim using the given text. Claim: All sustainable buildings are completely carbon-neutral. [SEP] Text: Furthermore, Bhutan will need its hydropower-based electricity system to expand deeper into various energy end-uses, as is being expounded by many expert studies on how to remove fossil fuels from the economy by becoming more electric [44, 53, 54]. this means greater use of electricity in the transport and industry sectors. The LEAP model shows this where carbon neutral scenarios lead to larger increases in electricity demand compared to non-carbon neutral counterparts as shown in Table 6. For example, under the HGDP and scenarios per capita annual average electricity consumption increases at 7. 0 and 7. 8%. Table 6 Electricity demand under different scenarios (Billion kWh)Full size tableImplications for GNH from the scenariosThe above discussion around carbon emission reduction, economic growth, and access to modern and clean energy with concurrent increase in energy demand provides a basis for an initial attempt to assess their plausible implications at a high level on the domains of GNH. This is shown in Table 7. Table 7 Plausible impact of emissions reduction, energy access and economic growth on GNHFull size tableOn assessing the likely impacts, the indicators associated with each of the nine domains were considered. A tick mark attached to a GNH domain under energy, emission or GDP does not necessarily show unequivocal and unilateral positive impacts on all the indicators under that domain. For example, the time use domain has work and leisure as the two indicators, but the tick mark for the time use domain is attributed to ‘work’ only. Economic growth entails production and consumption, which inadvertently leads to ecological damage and ecological diversity is beyond emissions reduction and clean energy. Table 7 highlights the need for more extensive future research (e. g. through surveys, interviews or focussed group meetings) to analyse any potential deeper implications of the plausible impacts shown here. A carbon neutral economic growth fuelled by hydropower and other clean energy sources alongside energy efficient technologies can lead to an overall enhancement of GNH as shown by several plausible positive impacts on the nine domains of GNH. ConclusionsThis study adds to the literature on CN development at the national level, using long term energy-economy modelling for the case of Bhutan. The study has shed light on some key concerns for Bhutan if it intends to sustain its CN status under growth pressures. [SEP] Justify:

Output: The text contrasts the claim by discussing the complexities of achieving carbon neutrality in Bhutan's energy systems. It states that while efforts are underway to reduce carbon emissions and promote clean energy, economic growth can lead to ecological damage, indicating that not all energy-efficient and sustainable practices lead to complete carbon neutrality. Specifically, it mentions that 'economic growth entails production and consumption, which inadvertently leads to ecological damage,' suggesting that the ideal of complete carbon neutrality in sustainable buildings cannot be universally applied.


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: , 2018; Brown et al. , 2002), these reflect a minority of IDRs, and pose less of a challenge for standard protein sequence analysis methods. Because we take the evolutionary rate of IDRs into account in our analysis, we do not identify constrained molecular features for these slowly evolving IDRs, as they would not be significantly different in our simulated IDRs. Furthermore, although there are examples of IDRs that are lost or gained through evolution (Ahrens et al. , 2017; Montanari et al. , 2011), the presence of IDRs is conserved across orthologs in the vast majority of cases (Bellay et al. , 2011; Chen et al. , 2006a; Chen et al. , 2006b; Colak et al. , 2013). Widespread evidence for shared functions in the highly diverged portions of IDRs also has several evolutionary implications. The lack of homology between most IDRs with similar evolutionary signatures suggests that the molecular features are preserved in each IDR independently. For example, the more than 150 IDRs that we believe represent mitochondrial N-terminal targeting signals share similar constraints on their molecular features, yet these signals have been preserved independently over very long evolutionary time as mitochondrial genes were transferred individually to the nuclear genome (Adams and Palmer, 2003). The preservation of molecular features over long evolutionary time, despite accumulation of amino acid divergence, is consistent with a model of stabilizing selection (Bedford and Hartl, 2009; Hansen, 1997; Lande, 1976), where individual amino acid sites are under relatively weak functional constraints (Landry et al. , 2014). In this view, single point mutations are unlikely to dramatically impair IDR function, and therefore large evolutionary divergence can accumulate. This also suggests that disease-causing mutations in disordered regions are more likely to cause gain of function, consistent with at least one recent study (Meyer et al. , 2018). Although current models for the evolution of short linear motifs (well-characterized functional elements in IDRs) also implicate stabilizing selection (Koch et al. , 2018; Landry et al. , 2014), these motifs represent only a minority of the residues in disordered regions (et al. , 2012). Our observation of shared evolutionary signatures associated with specific functions in highly diverged IDRs suggests that this evolutionary mechanism is shaping the proteome on a much wider scale than currently appreciated. [SEP] Justify:

Output: The text does not address the claim about X-ray crystallography and its use in determining the 3D structures of proteins. Instead, it discusses the evolutionary aspects of intrinsically disordered regions (IDRs) in proteins and their molecular features, which is irrelevant to the claim at hand.