Input: Claim: Proteins can fold into their functional forms due to specific sequences of amino acids. [SEP] Text: 480408MGI:3811072Genetic reagent (Mus musculus)ZP3:CrePMID: 10686600MGI:2176187Genetic reagent (Mus musculus)Dll1Dll1kiPMID: 26801181; PMCID: PMC4788113; DOI: 10. 1534/genetics. 115. 184515MGI:5790945Genetic reagent (Mus musculus)Dll1Dll4kiPMID: 26114479; PMCID: PMC4482573; DOI: 10. 1371/journal. pgen. 1005328MGI:5779556Genetic reagent (Mus musculus)Dll1D1N-E3_D4kithis papermini gene insertion in the Dll1 locusGenetic reagent (Mus musculus)Dll1D1contD4kithis papermini gene insertion in the Dll1 locusGenetic reagent (Mus musculus)HprtDll1ECD_Dll4ICDthis paperinducible insertion into Hprt locusGenetic reagent (Mus musculus)HprtDll4ECD_Dll1ICDthis paperinducible insertion into Hprt locusCell line (Mus musculus)E14TG2aPMID: 26114479; PMCID: PMC4482573; DOI: 10. 1371/journal. pgen. 1005328Cell line (Mus musculus)129Sv/castPMID: 26114479; PMCID: PMC4482573; DOI: 10. 1371/journal. pgen. 1005328Cell line (Homo sapiens)HeLaN1PMID: 9653148; DOI: 10. 1073/pnas. 95. 14. 8108Cell line (Mus musculus)pMP8. CAG-DLL1PMID: 26801181; PMCID: PMC4788113; DOI: 10. 1534/genetics. 115. 184515Cell line (Mus musculus)E14repPMID: 26801181; PMCID: PMC4788113; DOI: 10. 1534/genetics. 115.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Boxes for 28 °C treatments are filled grey, and 31 °C treatments in white. Whiskers denote 1. 5 × the inter-quartile range, and the black line indicates the meanFull size image Gonad histological condition differed amongst treatments (Figs. 5, 6). For the females, there was a marginally significant effect of temperature and the interaction of temperature and pH on the distribution of histological stages (Table 5). Ovaries from urchins maintained in control conditions had abundant mature eggs (Fig. 5) and were in the mature or partly spawned condition. With increased temperature and decreased pH, ovary condition declined with an increase in the number of individuals in the post-spawned or spent condition (Fig. 6). These ovaries had few or no eggs in the lumen, and many had degenerating eggs and accumulations of lipofuscin pigment granules (Fig. 5). No females in the control treatment were in the post-spawned category. Fig. 5Histology of the gonads of female (a–d) and male (e–h) Echinometra sp. A held in experimental treatments for 77 d. The gonads of urchins maintained in control conditions had an abundance of mature gametes (a, e) or were partly spawned (b, f). In the other treatments, the gonads were post-spawned/spent (c, d, g, h) with empty gonad tubules and lipofuscin-like pigment accumulations (e. g. , in centre of c). Scale bars = 100 µmFull size image Fig. 6Histological condition of the female ovaries (top) and male testes (bottom) of Echinometra sp. A maintained in experimental treatments for 77 dFull size image Table 5 Cumulative link model analysis for ordinal data for female (total N = 34) and male (N = 35) Echinometra sp. A Full size table Differences in histological categories were more distinct in the males, with the effect of pH/high pCO2 and the interaction being significant (Table 5). With the exception of the high temperature and low pH/high pCO2 treatment, ~50 % of the testes were mature. Testis condition clearly declined in the low pH treatments (Figs.

Output: corroborate


Input: Claim: Composting food waste has no environmental impact. [SEP] Text: Likewise, the values agreed with those reported in previous studies [1, 16]. Comparing end-product moisture in both treatments there were no statistically significant differences. The values of pH were within the range established by the NTC 5167 for the use of products as soil improvers. The pH was slightly alkaline (around neutral values), which favors their application in acid soils facilitating carbon mineralization, generation of OH− ions and introduction of basic cations such as K+ [43]. The results obtained are similar to those reported for co-composting processes of GW and FW [1, 16]. The smaller values of pH found in this study could be related to the addition of PR, since its dissolution improves the formation of organic acids of low molecular weight and the generation of CO2 during the degradation of organic waste [44]. Furthermore, PR can also reduce the pH for the adsorption of NH3 and cations [5, 45]. Table 3 End-product quality characteristics for both treatments TA (n=3) TB (n=3) NTC 5167 Hernández et al. [16] Oviedo-Ocaña et al. [1] Boldrin et al. [46] Zhang and Sun [6] Moisture % 45. 70 (3. 59) 44. 20 (1. 13) <35 33. 87 54. 6 29 – 44 -- pH Units 7. 39 (0. 17) 7. 34 (0. 57) >4 - <9 7. 51 7. 60 -- 7. 9 Total organic carbon % dw 28. 16 (0. 85) 29. 04 (1. 58) >15 20. 87 23. 1 10 – 19 25 % dw 1. 76 (0. 32) 1. 55 (0. 31) >1 1. 37 2. 35 0. 7 – 0. 9 3. 0 C/N - 15. 97 (4. 09) 18. 68 (7. 19) - 14. 9 -- 11 – 27 -- Cation exchange capacity cmol kg-1 38. 13 (6. 71) 32. 70 (7. 05) >30 32. 77 -- -- -- Electric conductivity dS m-1 0. 93 (0. 23) 0. 62 (0. 14) - 0. 21 1. 66 -- 2. 61 Water retention capacity % 157. 00 (19.

Output: contrast


Input: Claim: Proteins can fold into their functional forms due to specific sequences of amino acids. [SEP] Text: 184515Cell line (Mus musculus)N1repPMID: 26801181; PMCID: PMC4788113; DOI: 10. 1534/genetics. 115. 184515Cell line (Mus musculus)N2repPMID: 26801181; PMCID: PMC4788113; DOI: 10. 1534/genetics. 115. 184515Bacterial strain (E. coli)SW106PMID:15731329Transfected construct (Mus musculus)pMP8. CAG-DLL4this paperprogenitor: pMP8. CAGTransfected construct (Mus musculus)pMP8. CAG-D1ECD _D4ICDthis paperprogenitor: pMP8. CAGTransfected construct (Mus musculus)pMP8. CAG-D1N- E3_D4this paperprogenitor: pMP8. CAGTransfected construct (Mus musculus)pMP8. CAG-D1N- E2_D4this paperprogenitor: pMP8. CAGTransfected construct (Mus musculus)pMP8. CAG- D1N-D_D4this paperprogenitor: pMP8. CAGTransfected construct (Mus musculus)pMP8. CAG- D4ECD_D1ICDthis paperprogenitor: pMP8. CAGTransfected construct (Mus musculus)pMP8. CAG- D4N-E3_D1this paperprogenitor: pMP8. CAGTransfected construct (Mus musculus)pMP8. CAG- D4N-E2_D1this paperprogenitor: pMP8. CAGTransfected construct (Mus musculus)pMP8. CAG- D4N-D_D1this paperprogenitor: pMP8. CAGTransfected construct (Mus musculus)pMP8. CAG- D1contD4this paperprogenitor: pMP8. CAGTransfected construct (Mus musculus) pMP8. CAG- D4contD1this paperprogenitor: pMP8.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: 5, 6), and most distinctly so in the high temperature low pH treatment, where no mature gonads were detected. The latter finding agrees with the significant interaction between the two stressors seen with statistical analysis, suggesting a synergistic effect. Coelomic fluidThe pH of the coelomic fluid was lower than in the external treatment water of the aquaria. Although the coelomic fluid from Echinometra sp. A from the control pH 8. 1 treatment was higher (mean pH = 7. 56, SD = 0. 05) than that from the urchins kept at pH 7. 9 (mean pH = 7. 52, SD = 0. 07), this effect was not statistically significant (Table 6). Temperature had also no measurable effect on coelomic fluid pH (Table 6). Table 6 Analysis of variance pH and ion concentrations in the coelomic fluid of Echinometra sp. A in two temperature and two pCO2 treatmentsFull size table There was less variation in the ion concentration of samples from the aquarium water (Fig. 7) compared to the concentration in the coelomic fluid samples. No significant difference between water samples of the treatments was detected for any of the four ions measured (2-factor ANOVA, p > 0. 1 for each factor and the interaction term). Compared to the external medium, calcium, magnesium and sodium were significantly decreased (indicated by non-overlapping standard deviations, Fig. 7). Potassium was in the same range in the coelomic fluid and in the aquarium water. Fig. 7Ion concentration in the coelomic fluid of Echinometra sp. A. Treatment levels (Temperature/pH) are listed on the horizontal axes. Boxes for 28 °C treatments are filled grey and, 31 °C white. Horizontal lines represent the mean (solid line) and standard deviation (dashed line) of the average aquarium water, and exact values for these were 413 mg L−1 (1 SD = 5 mg L−1) for Ca, 389 mg L−1 (1 SD = 5 mg L−1) for K, 1,323 mg L−1 (1 SD = 11 mg L−1) for Mg, 1. 07 mg L−1 (1 SD = 0.

Output: corroborate


Input: Claim: Composting food waste has no environmental impact. [SEP] Text: 26) 141. 53 (11. 99) >100 237. 4 -- -- -- Density g cm-3 0. 50 (0. 11) 0. 46 (0. 04) < 0,6 -- -- -- -- % dw 4. 75 (2. 81) 4. 19 (0. 44) >1 0. 56 0. 8 0. 15 – 0. 23 0. 3 Ash % dw 52. 10 (4. 09) 55. 40 (7. 92) < 60 51. 60 -- 72 – 79 -- Lignin % dw 30. 30 (2. 28) 28. 60 (1. 67) -- -- -- -- -- Note: n: number of samples; dw. dry weight; Standard deviation is in parenthesis; all means (compared in the same row) are statistically similar at p < 0. 05 Regarding TOC, both treatments showed higher values compared to those required by the as soil improver [26]. These higher values could be connected to the carbon content still available to transform due to the presence of lignocellulosic compounds in the GW. Similar values were reported in previous studies from the authors [1, 16]. The products did not have a statistical significant differences. Therefore, it is not possible to attribute this smaller content as an influence of TSC in the process. Nitrogen had values higher than 1% in both treatments, which is favorable for product use in agricultural activities. There was a smaller concentration of N in TB compared to TA, but lacked of statistical significance. This smaller concentration is possibly linked to a higher N volatilization during the first two phases of the process. This is evident in the high temperatures in TB during the first 10 days combined with alkaline pH that promotes NH3 volatilization during turning [34]. On the other hand, relatively high values of N in both treatments could be connected to the high porosity that PR could provide to absorb NH3 and improve N conservation during the process [47, 48]. Ash content was lower than 60% in both treatments, according to the requirements of the NTC 5167, and lacked significant statistical differences comparing TA and TB. However, TB had relatively higher values compared to TA which can be linked to the intense organic matter degradation during the first 10 days, which are reflected in mass loss in the form of CO2 [49].

Output: contrast


Input: Claim: Proteins can fold into their functional forms due to specific sequences of amino acids. [SEP] Text: CAGTransfected construct (Mus musculus)pMP8. CAG- D4N109Gthis paperprogenitor: pMP8. CAGTransfected construct (Mus musculus)pMP8. CAG-Stop -D1ECD_D4ICDthis paperprogenitor: pMP8. CAGTransfected construct (Mus musculus)pMP8. CAG-Stop- D4ECD_D1ICDthis paperprogenitor: pMP8. CAGTransfected construct (Mus musculus)D1N-E3_D4-targetingthis paperbased on Dll1Dll1ki targetingTransfected construct (Mus musculus)D1contD4-targetingthis paperbased on Dll1Dll1ki targetingTransfected construct (Mus musculus)pLexM-Avi-Histhis paperprogenitor: pLexMTransfected construct (Mus musculus)pLexM-D1N-E5-Avi-Histhis paperprogenitor: pLexMTransfected construct (Mus musculus)pLexM-D4N-E5-Avi-Histhis paperprogenitor: pLexMTransfected construct (Mus musculus)pLexM-D1N-E3_D4-E5-Avi-Histhis paperprogenitor: pLexMTransfected construct (Mus musculus)pLexM-D4N-E3_D1-E5-Avi-Histhis paperprogenitor: pLexMTransfected construct (Mus musculus) pLexM-D1contD4-E5-Avi-Histhis paperprogenitor: pLexMTransfected construct (Mus musculus)pLexM-D4contD1-E5-Avi-Histhis paperprogenitor: pLexMTransfected construct (Mus musculus)pLexM-D4N109G-E5-Avi-Histhis paperprogenitor: pLexMAntibodyRat anti-DLL1PMID: 17664336; PMCID: PMC2064846; DOI: 10. 1083/jcb.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: 01 mg L−1) for NaFull size image Internal concentrations of calcium, magnesium and sodium exhibited no differences between temperature or pH treatments (Table 6; Fig. 7). ANOVA for potassium had a marginally significant interaction term between temperature and pH, with values at the 28/7. 9 and 31/8. 1 treatments elevated above the other treatments (Fig. 7). However, values within these groups are also more variable, and averages only vary by a small amount (7–8 %) between treatments. DiscussionOur experiments showed that some of the basic metabolic parameters (growth, respiration, ammonium excretion) of the ecologically important sea urchin Echinometra sp. A responded to temperature and/or pH changes. Growth at the high temperature/high pCO2 treatment was reduced, whereas respiration and ammonium excretion increased in that treatment compared to the ‘present-day’ control. Our initial hypothesis that the interaction of increased temperature and pCO2 at levels expected by the end of this century under most representative concentration pathways (Meinshausen et al. 2011) leads to higher stress than the individual stress alone can thus be accepted. However, our study also illustrated that the effects on adults are not large, at least over the 10-week time scale of our study, and in several cases only marginally significant. Echinometra sp A. and other shallow-water reef species are acclimatised to the large (nearly from 250 to 1,300 µmol) daily changes in pCO2 that they experience over the tidal cycle. However, during less extreme tides and in deeper water, fluctuations in pCO2 were much smaller. MetabolismWe previously showed that the growth of Echinometra sp. A (addressed as E. mathaei) subtly decreased in response to decreased pH/increased pCO2 (Uthicke et al. 2013), which was in agreement with other data on Echinometra species in Japan (Shirayama and Thornton 2005). Although the response to increased pCO2/decreased pH is not always linear, all four other echinoid species thus far investigated can be expected to exhibit reduced growth in near-future OA conditions (Ries et al. 2009; Albright et al. 2012; Stumpp et al. 2012b).

Output: corroborate


Input: Claim: Composting food waste has no environmental impact. [SEP] Text: This high degradation can also be associated with the addition of PR in both treatments that provide nutrients and energy for microorganisms, accelerating transformation processes [5]. The addition of PR increased the quantity of inorganic material in both end-products, associated to phosphorous mineralization, and thus, intervene in the reported ash content in both treatments in contrast with our previous studies where this amendment material was not introduced [1]. (CEC) is used to evaluate the humification degree and nutrient retention capacity of compost. In both treatments, CEC was higher compared to the standard of NTC 5167 for soil improvers [26]. Despite the fact, there was not statistical significant differences, there were higher values in TA compared to TB possibly due to an increase in the humification processes in GW during the cooling and maturation phases, evidenced in a lower OC content at the end of the process. The results show that in both treatments, the end-products are able to improve the water and nutrient retention capacity of soils [4, 5]. The water retention capacity for a mature product must be higher to 100% [26] or 75% wet weight [50]. This parameter allows stablishing the product capacity to retain moisture, which is fundamental during the use of the product for agricultural purposes. The treatments had higher values compared to those established by the literature without statistical significant differences comparing TA and TB. The high water retention capacity in these products is connected to their low density (i. e. density was 0. 50 g cm− 3 for TA and 0. 46 g cm− 3 for TB) and high porosity of materials such as GW, and to the processes of transformation and mineralization of organic matter. Finally, the phosphorous content in TA and TB was higher to the standard from the NTC 5167 for soil improvers [26]. According to Khan and Joergensen [51], the solubilization of PR could increase microbial biomass to release inorganic phosphorous. The high porosity of PR could also provide and habitat to the high microbial biomass [9, 52]. P is a central component of the energy-carrying molecule (adenosine triphosphate, ATP) in all cells; increased P availability resulting from PR addition may increase the formation of ATP during microbial activity and reproduction, and therefore enhance the decomposition of organic waste [5, 53].

Output: contrast


Input: Claim: Proteins can fold into their functional forms due to specific sequences of amino acids. [SEP] Text: 200702009(1F9, rat monoclonal)1:50 (IF)AntibodyGoat anti-DLL4R and D SystemsCat. #AF1389 RRID:AB_3547701:50 (IF)AntibodyMouse anti- panCadherinSigma-AldrichCat. #C1821 RRID:AB_4768261:250 (IF)AntibodyDonkey anti- mouse Alexa 555InvitrogenCat. #A-31570 RRID:AB_25361801:100 (IF)AntibodyDonkey anti-goat Alexa 488InvitrogenCat. #A-11055 RRID:AB_25341021:100 (IF)AntibodyDonkey anti-rat Alexa 488InvitrogenCat. #A-21208 RRID:AB_25357941:100 (IF)AntibodyAnti-FLAG- Peroxidase (HRP)Sigma-Aldrich(M2 mouse, monoclonal purified) Cat. #A8592 RRID:AB_4397021:10 000 (WB)AntibodyMouse anti-β-TubulinSigma-AldrichCat. #T7816 RRID:AB_2617701:500 000; 1:1 000 000 (WB)AntibodyAnti-mouse HRPAmershamCat. #NA931 RRID:AB_7722101:10 000 (WB)AntibodyMHC (Chain)Sigma-AldrichCat. #M4276 RRID:AB_4771901:250 (IHC)AntibodyAnti-DIG AP fab fragmentRocheCat. #10932741: 5 000 (ISH)AntibodyAnti-mouse biotinylated (BA9200/goat)Vector LaboratoriesCat. #BA-9200 RRID:AB_23361711:200 (IHC)Commercial assay or kit5X ReagentPromegaCat. #E1531Commercial assay or kit ReagentPromegaCat. #E1483Commercial assay or kit. #18090050Commercial assay or kitExpand High-Fidelity PCR systemRocheCat. #04743733001Commercial assay or kitTri-ReagentSigma-AldrichCat.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: In the present experiment, the relatively mild change in pCO2/pH alone did not result in significantly reduced growth. A pCO2 change of similar magnitude applied in Shirayama and Thornton (2005) only resulted in differences in size after longer (>12 weeks) experimental periods. In our study, the largest reduction was seen when temperature was elevated and pH decreased/pCO2 increased. As for most poikilothermic invertebrates, echinoid metabolism follows the Q10 rule and increases with temperature increase (Ulbricht and Pritchard 1972). This was also observed here for respiration and ammonium excretion, although the increase in respiration was subtle and not significant. For both parameters, the highest metabolic rate was observed in the high temperature/high pCO2 treatment. Responses of echinoderm respiration to pH changes vary widely and often deviate from the assumption that low pH/hypercapnia induces metabolic depression in marine invertebrates (Pörtner et al. 2004; Pörtner 2008). In a previous study, we showed that respiration in Echinometra sp. A can be subtly reduced under intermediate pCO2 conditions (785–1,261), but were at the same level as the control at 1,786 μATM CO2 (Uthicke et al. 2013). A similar pattern was also observed for temperate ophiuroids and asteroids (Christensen et al. 2011; McElroy et al. 2012). Two boreal-temperate ophiuroid species exhibited increased metabolic rates with decreasing pH (Wood et al. 2008, 2011). In the present study, pH had a slightly enhancing effect on respiration, but this was more distinct under elevated temperatures. Ammonium excretion rates in tropical holothurians in summer were also higher than those at colder temperatures (Uthicke 2001). A previous study on a temperate echinoid species detected clearly higher ammonium excretion rates under elevated pCO2, but only under treatment conditions much higher than used here (~2,800 uATM; Stumpp et al. 2012b). The latter study also observed reduced O:N ratios, which was interpreted as higher protein catabolism as an additional mechanism for removing protons. Reduced O:N ratios are generally interpreted as a shift in substrate for oxidative metabolism, e. g.

Output: corroborate


Input: Claim: Composting food waste has no environmental impact. [SEP] Text: Therefore, an increase on the microbial biomass during composting could contribute with an increase in the organic content of C and P in the end-product, as evidenced in the results from both products. Despite the fact, there were not statistical significant differences between the treatments, there were smaller values of P in TB, which can be associated to a more intense activity of organic matter degradation during the first two phases of the process in the traditional composting. 4. conclusions of this work are: Traditional composting had higher biodegradation rates during the mesophilic and thermophilic active composting phases than the Composting (i. e. higher temperatures reached for longer periods and a higher reduction of volatile solids). However, during the cooling and maturation phases, both treatments showed similar process conditions as these were judged by the temperature, volatile solids, pH, and electrical conductivity. The twelve parameters measured here (moisture, pH, electric conductivity, total organic carbon, total nitrogen, C/N ratio, cation exchange capacity, water retention capacity, density, ash, total phosphorous, and lignin) on the end-products resulting from both the two-stage composting and traditional composting did not statistically differ. Both end-products could be used as soil improvers. Two-stage composting of green waste, food waste, phosphoric rock and sawdust at the end of the process did not influence of the processing time, degradation rate or end-product quality compared with traditional composting. Additional complementary strategies must be evaluated to improved GW composting. DeclarationsAvailability of data and materials All data generated or analyzed during this study are within the submitted manuscript. Competing interests The authors declare they have no competing interests. project was financed by the de Santander (Colombia) through project 2354 of 2017 Authors' contributions All authors read and approved the final manuscript. authors wish to thank the de Santander for the support to carry out this work. Authors' information (optional) None. 74. . Evaluation of thermophilic fungal consortium for organic municipal solid waste composting. Bioresour Technol. 2014;168:214–21. Application of seasonal freeze-thaw to pretreat raw material for accelerating green waste composting. J Environ Manag. 2019;239:96–102. Zhang L, Sun X.

Output: contrast


Input: Claim: Proteins can fold into their functional forms due to specific sequences of amino acids. [SEP] Text: #T9424Chemical compound, drugSulfo-NHS-LC-BiotinThermoCat. #21335Chemical compound, drug. #29200Chemical compound, drugc-free CocktailRocheCat. #04693159001Chemical compound, drugBM-Purple AP substrate RocheSigma-AldrichCat. #11442074001Chemical compound, drugG418BiochromCat. #291–25125 μg/mlChemical compound, drugHATGibcoCat. #31062–0371:300Chemical compound, drugHTGibcoCat. #110670301:100Chemical compound, drugTunicamycinSigma-AldrichCat. #T77651 μg/mlChemical compound, drugAlcian blueSigma-AldrichCat. #A52685% working solutionChemical compound, drugAlizarin redSigma-AldrichCat. #A55335% working solutionsubstrateAdvanstaCat. #12042-D20as recommended by the manufacturer.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: After an exposure of 9 months, individuals of Hemicentrotus pulcherrimus exposed to elevated pCO2 delayed spawning and gonad development by 1 month (Kurihara et al. 2013). Histological examination indicated that the gonads of most of the Echinometra sp. A held under conditions other than the control had fewer mature gametes. For the females, gonad condition indicated degeneration/resorption of the eggs or differential gamete release in high temperature and low pH treatments. For the males, decline in gonad condition was seen in the low pH treatments, and a synergistic effect of the stressors pH and temperature was suggested. It seems that both females and males may have released gametes over the incubation period. Spawning, however, was not observed and may have occurred at night. The urchins from the control tanks are likely to have continued to recruit gametes to the lumen (supported by the feeding regime) in continual gamete development as occurs over the long approximately 5- to 6-month spawning period of this urchin on the GBR (M Byrne pers. obs. ). In contrast, gonads of urchins in treatments with elevated temperature and/or elevated pCO2 were unable to generate new cohorts of gametes. The response of the gonads to high temperature/low pH conditions may have been an acute disturbance response rather than a response on gonad development. However, given the difference observed between the treatments, gonad condition is also an indicator of stress on the metabolism of the urchins. The differences in the response of gonad development in experimental treatments, based on data from weight and histological condition, show that the use of a gonad index can only provide a proxy of organism response, as shown in other studies of sea urchin reproduction (Byrne 1990; Byrne et al. 1998). In order to determine the reproductive response of sea urchins and other organisms to ocean change conditions, it will be important to maintain the brood stock in experimental conditions from the outset of gonad development cycle or conduct studies in organisms under naturally elevated pCO2 such as those on vent systems (Hall-Spencer et al. 2008; Fabricius et al. 2011).

Output: corroborate


Input: Claim: Composting food waste has no environmental impact. [SEP] Text: Influence of bulking agents on physical, chemical, and microbiological properties during the two-stage composting of green waste. Waste Manag. 2016;48:115–26. Zhang L, Sun X. Addition of fish pond sediment and rock phosphate enhances the composting of green waste. Bioresour Technol. 2017;233:116–26. Zhang L, Sun X. Improving green waste composting by addition of sugarcane bagasse and exhausted grape marc. Bioresour Technol. 2016;218:335–43. Reyes-Torres M, Oviedo-Ocaña ánchez A. A systematic review on the composting of green waste: feedstock quality and optimization strategies. Waste Manag. 2018;77:486–99. . Chemical, microbial and physical properties of manufactured soils produced by co-composting municipal green waste with coal fly ash. Bioresour Technol. 2009;100:5203–09. . Phosphorus availability from rock phosphate: combined effect of green waste composting and sulfur addition. J Environ Manag. 2016;182:557–63. . Effects of brown sugar and calcium superphosphate on the secondary fermentation of green waste. Bioresour Technol. 2013;131:68–75. Additives aided composting of green waste: effects on organic matter degradation, compost maturity, and quality of the finished compost. Bioresour Technol. 2012;114:382–88. Zhang L, Sun X. Changes in physical, chemical, and microbiological properties during the two-stage co-composting of green waste with spent mushroom compost and biochar. Bioresour Technol. 2014;171:274–84. Arias O, Viña S, Uzal M, Soto M. Composting of pig manure and forest green waste amended with industrial sludge. Environ. 2017;586:1228–36. Zhang L, Sun X. Using cow dung and spent coffee grounds to enhance the two-stage co-composting of green waste. Bioresour Technol. 2017;245:152–61. Himanen M, Hänninen K. Effect of commercial mineral-based additives on composting and compost quality. Waste Manag. 2009;29:2265–73.

Output: contrast


Input: Claim: Proteins can fold into their functional forms due to specific sequences of amino acids. [SEP] Text: #RPN2106as recommended by the manufacturerSequence-based reagentDLL1 wt ForotherNA5‘--3’Sequence-based reagentDLL1 wt RevotherNA5‘--3’Sequence-based reagentDll1lacZ ForotherNA5‘--3’Sequence-based reagentDll1lacZ RevotherNA5‘--3’Sequence-based reagentDll1Dll1ki ForotherNA5‘--3’Sequence-based reagentDll1Dll1ki RevotherNA5‘--3’ Sequence-based reagentDll1Dll4ki ForotherNA5‘--3’Sequence-based reagentDll1Dll4ki RevotherNA5‘--3’Sequence-based reagentDll1loxP ForotherNA5‘--3’Sequence-based reagentDll1loxP RevotherNA5‘--3’Sequence-based reagentT(s):Cre ForotherNA5‘--3’Sequence-based reagentT(s):Cre RevotherNA5‘--3’Sequence-based reagentZP3:Cre ForotherNA5‘--3’Sequence-based reagentZP3:Cre RevotherNA5‘--3’Sequence-based reagentHprt-CAGD1ECD_ D4ICD + neo Forthis paperNA5‘--3’Sequence-based reagentHprt-CAGD1ECD_ D4ICD + neo Revthis paperNA5‘--3’Sequence-based reagentHprt-CAGD4ECD_ D1ICD + neo Forthis paperNA5‘--3’Sequence-based reagentHprt-CAGD4ECD_ D1ICD + neo Revthis paperNA5‘--3’Sequence-based reagentHprtD1ECD_D4ICDrec and HprtD4ECD_D1IC(activated allele)this paperNA5‘--3’Sequence-based reagentHprtD

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: The boreal-temperate echinoid Strongylocentrotus droebachiensis exhibited reduced gonadal growth in treatments with >1,000 µATM pCO2 compared to controls (Stumpp et al. 2012b). Several studies examined gonad development in echinoids under different temperatures from an aquaculture perspective. For instance, gonads of the S. droebachiensis showed little differences in development in two treatments differing by 9 °C temperature (Garrido and Barber 2001). In contrast, gonadal growth in the temperate species Paracentrotus lividus was reduced when temperature exceeded 22 °C (ambient = up to 24 °C in summer; Shpigel et al. 2004). In the latter studies and for the data presented here, it is possible that higher energy demand through faster metabolism at higher temperatures reduced energy availability for gonad development. These responses may also reflect the general trend in ectotherms ascribed to the temperature size rule, with facilitation of growth by moderate warming up to thermal limits where growth decreases (Sheridan and Bickford 2011). Coelomic fluidAmongst echinoderms, echinoids have the highest buffer capacity of the coelomic fluid to ambient pCO2 increase (Collard et al. 2013). The intestine of these animals can act as a barrier for bicarbonate ions and is selective for ion diffusion (Holtmann et al. 2013). Coelomic fluid pH in the tropical species investigated here was at similar low levels as reported for temperate echinoids (Miles et al. 2007; Spicer et al. 2011); more extreme values (down to ~pH 7. 2) were observed during emersion (Burnett et al. 2002). Coelomic fluid pH of S. droebachiensis decreased significantly (acidosis) after 4 d of exposure to moderately and highly elevated (>1,400 μATM) pCO2, but values recovered after a longer exposure, possibly due to carbonate dissolution of the test (Spicer et al. 2011). Similarly, pH in the coelomic fluid dropped sharply in Psammechinus miliaris after short-term (days) exposure and recovered slightly after longer exposure periods (Miles et al. 2007).

Output: corroborate


Input: Claim: Composting food waste has no environmental impact. [SEP] Text: Hernández-Gómez A, Calderón A, Medina C, Sanchez-Torres V, Oviedo-Ocaña E R. Implementation of strategies to optimize the co-composting of green waste and food waste in developing countries. A case study: Colombia. Pollut Res. 2020;1–7. ’. Feedstock mixture composition as key factor for C/P ratio and phosphorus availability in composts: role of biodegradation potential, biochar amendment and calcium content. Valorization. 2017;8:2553–67. . Co-composting of green waste and food waste at low C/N ratio. Waste Manag. 2010;30:602–09. . Sustainable recycling of municipal solid waste in developing countries. Waste Manag. 2009;29:915–23. . Chemical and physical properties of pruning waste compost and their seasonal variability. Bioresour Technol. 2006; 97: 2071–76. . Compost quality attributes, measurements, and variability. In: editors. in Systems. Boca Raton: Lewis Publishers; 2001. p. 95–120. Effects of inoculation with Phanerochaete chrysosporium at various time points on enzyme activities during agricultural waste composting. Bioresour Technol. 2010;101:222–27. Dulac N. The organic waste flow in integrated sustainable waste management. In: Scheinberg A, editor. Tools for Decision-Makers-Experiences from the (1995–2001). Nieuwehaven: WASTE; 2001. . A standardized Dewar test for evaluation of compost self-heating. BioCycle 1995;36:1–16. . Phytotoxicity indices of organic residues during composting. Vegetal 2007;7:28–37 [in Spanish]. . Norma Técnica Colombiana NTC 5167. Productos para la industria agrícola. Productos orgánicos usados como abonos o fertilizantes y enmiendas de suelo. Bogotá: de Normas Técnicas y Certificación; 2004. . Methods for Dietary Fiber, Fiber, and in Relation to Animal Nutrition. J Dairy Sci. 1991;74:3583–97. . Technologies.

Output: contrast


Input: Claim: Proteins can fold into their functional forms due to specific sequences of amino acids. [SEP] Text: 1ECD_D4ICDrec and HprtD4ECD_D1IC(activated allele)this paperNA5‘--3’Sequence-based reagentDll1D1N-E3_D4ki Forthis paperNA5‘--3’Sequence-based reagentDll1D1N-E3_D4ki Revthis paperNA5‘--3’Sequence-based reagentDll1D1N-E3_D4ki Forthis paperNA5‘--3’Sequence-based reagentDll1D1N-E3_D4ki Revthis paperNA5‘--3’Sequence-based reagent Y-Chromosome ForotherNA5‘--3’Sequence-based reagentY-Chromosome RevotherNA5‘--3’Sequence-based reagentmNotch1 ForotherNA5‘--3’Sequence-based reagentmNotch1 RevotherNA5‘--3’Sequence-based reagenthNOTCH1 ForPMID: 22002304; DOI: 10.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Decreased external pH also reduced coelomic fluid pH significantly in Paracentrotus lividus after a 19-d exposure (Catarino et al. 2012). All of the above studies were conducted under distinctly higher pCO2 increase than in the present study. This and the fact that our experiment also constitutes a longer term exposure (77 d) may explain why no significant decrease in pH of the coelomic fluid was observed in Echinometra sp. A. Miles et al. (2007) described increases in magnesium in the coelomic fluid under increased pCO2 and interpreted this finding as indication for Mg calcite dissolution. Also calcium concentrations in the coelomic fluid can increase with increased pCO2 (Spicer et al. 2011). Magnesium and calcium in the coelomic fluid of Paracentrotus lividus also did not change with external pH, but were altered by temperature (Catarino et al. 2012). In our study, both magnesium and calcium showed no significant differences between treatments, but values of both elements were significantly lower than in the surrounding sea water. This is an indicator that calcification still occurs under mild ocean acidification as mimicked in our experiments. The fact that urchins in all treatments still achieved positive growth supports this interpretation. Sodium and potassium in S. droebachiensis remained unaffected by increased pCO2 (Spicer et al. 2011), but no comparison was given to the external medium. In the present study, sodium was not affected by treatment, but was also lower than in the aquarium water. It is unclear what caused the apparently erratic pattern in potassium values in the coelomic fluid, with values similar to the external medium in two treatments, and more variation and slightly elevated values in the remaining two (28/7. 9 and 31/8. 1). In summary, we detected evidence that interactive effects of likely near-future conditions of elevated SST and elevated pCO2/reduced pH will change the metabolism and have significant negative effects on growth of Echinometra sp A. However, effects were subtle, and ultimately most animals were still able to calcify and grow under those conditions. Densities of adult coral reef echinoids including Echinometra spp. can be equally high or above those of control areas at sites with elevated pCO2 (Fabricius et al.

Output: corroborate


Input: Claim: Composting food waste has no environmental impact. [SEP] Text: Singapore: Journal of Composting and Organics Recycling; 2005. . Maturation of green waste compost as affected by inoculation with the white-rot fungi Trametes versicolor and Phanerochaete chrysosporium. Environ Technol. 2017;38:872–79. Haug RT. The practical handbook of compost engineering. Boca Raton: CRC Press; 1993. Böhm R. Pathogenic Agents. In: Diaz LF, de Bertoli M, Bidlingmaier W, editors. and Technology. The Netherlans: Series; 2007. . Effect of microbial inoculation on physicochemical properties and bacterial community structure of citrus peel composting. Bioresour Technol. 2019;291:121843. Zhang L, Sun X. Addition of seaweed and bentonite accelerates the two-stage composting of green waste. Bioresour Technol. 2017;243:154–62. Sundberg C, Smårs S, Jönsson H. Low pH as an inhibiting factor in the transition from mesophilic to thermophilic phase in composting. Bioresour Technol. 2004;95:145–50. de. The biology of composting: A review. Res. 1983;1:157–76. Zhang L, Sun X. Effects of earthworm casts and zeolite on the two-stage composting of green waste. Waste Manag. 2015;39:119–29. . A review of the use of composted municipal solid waste in agriculture. Environ. 2008;123:1–14. Tiquia SM. Reduction of compost phytotoxicity during the process of decomposition. Chemosphere. 2010;79:506–12. . Biodegradable municipal waste composts: analysis and application to agriculture. Trust & Defra; 2005. Seed germination test for toxicity evaluation of compost: Its roles, problems and prospects. Waste Manag. 2018;71:109–14. Effect of inoculating white-rot fungus during different phases on the compost maturity of agricultural wastes. Process Biochem. 2009;44(4):396–400. Tiquia S. Microbiological parameters as indicators of compost maturity. J Appl Microbiol. 2005;99:816–828. .

Output: contrast


Input: Claim: Proteins can fold into their functional forms due to specific sequences of amino acids. [SEP] Text: 1038/onc. 2011. 467NA5‘--3’Sequence-based reagenthNOTCH1 RevPMID: 22002304; DOI: 10. 1038/onc. 2011. 467NA5‘--3’Sequence-based reagenthNOTCH2 Forthis paperNA5‘--3’ Sequence-based reagenthNOTCH2 Revthis paperNA5‘--3’Sequence-based reagenthNOTCH3 ForPMID: 16327489; PMCID: PMC1409885NA5‘--3’Sequence-based reagenthNOTCH3 RevPMID: 16327489; PMCID: PMC1409885NA5‘--3’Sequence-based reagenth: 22002304; DOI: 10. 1038/onc. 2011. 467NA5‘--3’Sequence-based reagenth: 22002304; DOI: 10. 1038/onc. 2011.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: IntroductionCoral reef ecosystem degradation due to climate change impacts can alter reef community structure, potentially causing phase shifts toward macroalgal-dominated reefs (Graham et al. 2015). As a result, coral cover continues to decline in most reef ecosystems worldwide, resulting from the combination of local and global disturbances (Sully et al. 2022). Local disturbances on coral reefs include point source pollution, sedimentation, eutrophication, extreme weather events (Fabricius et al. 2008), and predator outbreaks (Ban et al. 2014). Global stressors include warming seawater temperatures due to elevated atmospheric CO2 that ultimately lead to higher disease prevalence and weakened coral immunity responses, as well as causing global bleaching events (Ban et al. 2014). However, the potential for local and global stressors to interact is particularly alarming due to the likelihood that compounding effects could exacerbate the deterioration of coral reef structural integrity (Tebbett et al. 2023). Evidence shows decadal scale recovery stimulated through coral larval recruitment is possible (Gilmour et al. 2013). However, repeated disturbances across a short temporal scale impede recovery trajectories (Hughes et al. 2018). Fleshy macroalgae, in particular, outcompete slower-growing corals for resources (e. g. , nutrients, light, and space) by rapid colonization of bare substrata post-disturbance events (McManus and Polsenberg 2004). Elevated pCO2 from anthropogenic sources are generally associated with increased growth rates in fleshy macroalgal species (Johnson et al. 2014). Algae tend to benefit from increased CO2 and associated OA conditions, while flexible HCO3− users are less affected by fluctuations in chemical conditions (Ho et al. 2020). From a larger ecological perspective, understanding of the effects of OA on reefs that have shifted to dominance by macroalgae is still limited. Specifically, there is a need to explore how species interactions might influence coral growth rates, which could be altered by the presence of fleshy macroalgae. Some evidence indicates that photosynthesizing organisms have the ability to buffer against impacts of OA by elevating localized pH in the microenvironment (Bergstrom et al. 2019; Doo et al. 2020). However, relatively little is known about the impacts of coral–macroalgal interactions on coral growth under projected OA.

Output: corroborate


Input: Claim: Composting food waste has no environmental impact. [SEP] Text: The influence of municipal solid waste compost on yield, soil phosphorus availability and uptake by two vegetable crops grown in a Pugwash sandy loam soil in Nova Scotia. Environ. 2005;106:57–67. Nutrient transformations during composting of pig manure with bentonite. Bioresour Technol. 2012;121:362–68. . Coal fly ash and lime addition enhances the rate and efficiency of decomposition of food waste during composting. Bioresour Technol. 2009;100:3324–31. . LCA Report: of Management in Arhus Kommune. Copenhagen: of Denmark; 2009. . Co-Waste, Plant Residues, and Rock Phosphate: and Evaluation of Compost Maturity. Anal. 2018;49:751–62. Impact of fly ash and phosphatic rock on metal stabilization and bioavailability during sewage sludge vermicomposting. Bioresour Technol. 2013;136:281–87. . Composting of selected organic wastes from peri-urban areas of Harare, Zimbabwe. . 2013;2:14. . Co-composting of vegetable wastes and carton: Effect of carton composition and parameter variations. Bioresour Technol. 2017;227:171–78. . Changes in microbial biomass and P fractions in biogenic household waste compost amended with inorganic P fertilizers. Bioresour Technol. 2009;100:303–09. . Response of fed dung composted with rock phosphate on yield and phosphorus and nitrogen uptake of maize crop. Biotechnol. 2011;10:12595–601. Billah M, Bano A. Role of plant growth promoting rhizobacteria in modulating the efficiency of poultry litter composting with rock phosphate and its effect on growth and yield of wheat. Res. 2015;33:63–72. :PostedVersion 1posted You are reading this latest preprint versionlets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing.

Output: contrast


Input: Claim: Proteins can fold into their functional forms due to specific sequences of amino acids. [SEP] Text: 467NA5‘--3’Sequence-based reagentForward primer - correct integration into Hprt locusotherNA5’--3’Sequence-based reagentReverse primer - correct integration into Hprt locusotherNA5’--3’Sequence-based reagentForward primer - correct integration into Dll1 locusotherNA5‘--3’Sequence-based reagentReverse primer - correct integration into Dll1 locusotherNA5‘--3’Sequence-based reagentguideA-Forthis work, according to reagentguideB-Revthis work, according to DNA reagentUncx-probe (plasmid)DOI 10. 1007/ s004270050120Recombinant DNA reagentpLexM (plasmid)DOI 10. 1074/ jbc. M113. 454850Recombinant DNA reagentCas9 D10A nickase (plasmid)DOI 10. 1126/ science. 1231143Addgene #42335Recombinant DNA reagentDll1 5' SB probePMID: 26801181; PMCID: PMC4788113; DOI: 10. 1534/genetics. 115. 1845155’ probe: a 316 bp BamHI/AvaII fragment 3. 8 kb upstream of Dll1 exon 1 Recombinant DNA reagentDll1 3' SB probePMID: 26801181; PMCID: PMC4788113; DOI: 10. 1534/genetics. 115. 1845153’ probe: a 528 bp PCR fragment in Dll1 intron five obtained with primersalgorithmImageJ; :SCR_003070algorithm:SCR_002798Software, algorithm1000RRID:SCR_014215 Additional files Supplementary file 1 Relative cell surface expression levels of the ligand proteins used co-culture studies. Levels of one representative clone for each ligand protein were determined by cell surface biotinylation and quantitative analysis of Western blots after immunoprecipitation. Values for DLL1 and DLL4 see Figure 4—source data 3.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Sea presents a unique opportunity to understand future global change impacts on reefs as daily sea surface temperatures can exceed 31 °C in the Central region and 33 °C in the South during the summer (Chaidez et al. 2017). In addition to disturbance events due to climate change and industry (e. g. , Carvalho et al. 2019), extreme temperatures also cause disturbances such as coral bleaching which occur in the region (Eladawy et al. 2022). These disturbances can lead to a decline in coral cover and an increase in macroalgal cover, resulting in more coral–macroalgal interactions. Increased competition and greater potential for macroalgal phase shifts are potential outcomes as OA intensifies. Therefore, we exposed common reef-building Acropora spp. from the Sea to varying densities of Sargassum spp. and two pCO2 (475 and 1050 µatm) treatments. We simulated macroalgal-dominated reefs and future OA conditions, respectively, to quantify the potential physiological impact of macroalgae on coral calcification rates in the near future. Results from this study offer insight into how varying densities of macroalgae may interact with projected global climate change stressors (i. e. , OA) to modulate calcification rates of common reef-building corals. MethodsColony collection and treatments2022, fragments (3–5 cm) of Acropora spp. (composed of species millepora, hemprichii) were collected from in (22. 296863°N, 38. 964912°E). A maximum of 10 nubbins were collected from each coral colony, with colonies at a minimum of 10 m apart to ensure different genotypes (Baums et al. 2006). Sargassum sp. (cf. vulgare; herein referred to as Sargassum) were collected from the (22. 343043°N, 39. 084190°E) three weeks prior to the start of the experiment. Nubbins were glued (Glue) onto 5 × 5 cm white acrylic tiles and acclimated for 70 days in ambient (hereafter defined as the present day ocean conditions; i. e. , no CO2 enhancement) flow-through conditions prior to the experiment. This experiment was conducted in the indoor temperature-controlled SeaLabs aquaria space.

Output: corroborate


Input: Claim: Food waste reduction alone can solve global hunger issues. [SEP] Text: Loading metrics : Solve the : Solve the x Published: November 25, 2008 235. November 25, 2008Copyright: © 2008. This is an open-access 2. 2 million deaths in children under five years annually [2]. Those malnourished children who do survive are at heightened risk of long-term health, educational, and economic impairment [3]. Hunger is now arguably “the gravest single threat to the world's public health” [1]. There was therefore a tremendous sense of urgency among participants of the recent two-day international meeting in City on preventing and treating childhood malnutrition, organized by Columbia University's Institute of and the humanitarian organization Médecins sans Frontières (MSF). Christophe Fournier, President of MSF's International Council, called childhood malnutrition an “invisible crisis” and asked: “Why are we witnessing countless deaths from a preventable cause? ” There is no simple answer. 's framework on the determinants of nutritional status includes a complicated array of interconnected “basic determinants”—ecological, economic, and sociopolitical [4]. These basic determinants in turn give rise to three specific “underlying determinants”: the quality of health care services, caregiver resources such as maternal knowledge about child care, and food security (defined as secure access for all people at all times to sufficient quality and quantity of food in order to lead a healthy and active life [5]). An important challenge in preventing malnutrition is determining which of these three basic determinants should be the priority target. This is a highly contentious issue within the child nutrition community, and there does not seem to be a consensus. Some nutrition experts and health agencies, for example, believe that the focus should be on boosting caregiver resources—particularly educating mothers to feed their children the right foods [6,7]. Bank argues that most serious malnutrition is caused by bad sanitation and disease, leading to diarrhea, especially among young children, and that “women's status and women's education play big parts in improving nutrition” [7]. The child hunger crisis includes a knowledge crisis. In contrast, the meeting focused on only one of the three determinants—food insecurity, particularly in crisis regions where many humanitarian agencies work. Several speakers at the meeting argued that the world's poor lack access to food and that improving health services or educating mothers alone will not be enough to address the malnutrition crisis.

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: disordered regions make up a large part of the proteome, but the sequence-to-function relationship in these regions is poorly understood, in part because the primary amino acid sequences of these regions are poorly conserved in alignments. Here we use an evolutionary approach to detect molecular features that are preserved in the amino acid sequences of orthologous intrinsically disordered regions. We find that most disordered regions contain multiple molecular features that are preserved, and we define these as ‘evolutionary signatures’ of disordered regions. We demonstrate that intrinsically disordered regions with similar evolutionary signatures can rescue function in vivo, and that groups of intrinsically disordered regions with similar evolutionary signatures are strongly enriched for functional annotations and phenotypes. We propose that evolutionary signatures can be used to predict function for many disordered regions from their amino acid sequences. disordered protein regions are associated with a large array of functions (reviewed in Forman-Kay and Mittag, 2013), including cell signaling (Iakoucheva et al. , 2004; Tompa, 2014; Wright and Dyson, 2015), mediation of protein-protein interactions (Borgia et al. , 2018; Tang et al. , 2012; Tompa et al. , 2015), and the formation of membraneless organelles through phase separation (Banani et al. , 2017; Franzmann et al. , 2018; Nott et al. , 2015; Patel et al. , 2015; Riback et al. , 2017). These regions are widespread in eukaryotic proteomes (Peng et al. , 2013; Ward et al. , 2004), but do not fold into stable secondary or tertiary structures, and do not typically perform enzymatic functions (Uversky, 2011). Although intrinsically disordered regions can readily be identified based on their primary amino acid sequence (Dosztányi et al. , 2005; Uversky, 2002), it remains a challenge to associate these regions with specific biological and biochemical functions based on their amino acid sequences, limiting systematic functional analysis. In stark contrast, for folded regions, protein function can often be predicted with high specificity based on the presence of conserved protein domains (El-Gebali et al. , 2019) or enzymatic active sites (Ondrechen et al. , 2001).

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: In the elevated CO2 sump, an Aquacontroller system was used to control the remaining nine tanks (three NA, three LA, three HA treatments) by a solenoid that supplied pure CO2 gas to the sump. In this high CO2 treatment, the treatment was targeted at ~ 0. 3 pH units below the ambient (7. 70 pH target) sump, correspondent to a target pCO2 level of ~ 1000 µatm which is a value predicted to occur under the RCP 8. 5 “business-as-usual” scenario. Seawater pH, salinity, temperature, and dissolved oxygen were measured every day using a calibrated probe (Table S1). Total alkalinity samples were collected ~ 2 times a week and the accuracy/precision was evaluated using certified reference materials (CRMs; Batch #172 from A. Dickson Laboratory). Calcification measurementsThe effects of algal density on coral calcification were determined by changes in buoyant weight over the 34-day experiment. The change in buoyant weight, which represents changes in skeletal weight, was then converted to dry mass of CaCO3 using the density of aragonite (2. 93 g cm−3), and the density of seawater (1989). Surface area inferenceSurface area of all coral nubbins was determined by applying a constant generated from a subset of 20 acroporid corals that were buoyant weighed. Surface area was calculated by structure-from-motion and planar photographs (minimum 100 photographs per nubbin), following established methods outlined in (Lange and Perry 2020). Photographs were aligned in Agisoft Metashape, and a mesh was generated. Surface area of corals was then calculated with CloudCompare using generated mesh. Nubbin dry weight was modeled as a function of the calculated surface area (Fig. S1). A scaling factor was generated from the linear model and then applied to the entire data set to extrapolate surface area from dry weights (see Online Resource). Statistical analysisThe effects of pCO2 and algal density on calcification rates of Acropora spp. were analyzed with a blocked two-way ANOVA design. Assumptions for ANOVA were tested and met for homogeneity of variance through the Bartlett test and visual inspection of residual plots for normality.

Output: corroborate


Input: Claim: Food waste reduction alone can solve global hunger issues. [SEP] Text: A study by Save the Children UK, for example, conducted in Bangladesh, Myanmar, Ethiopia, and Tanzania, found that between 15% (in Ethiopia) and 79% (in Bangladesh) of households were simply too poor to adequately feed their children a healthy diet [5]. A systematic review by Dewey and Adu-Afarwuah found that educating mothers alone has little effect on childhood growth, morbidity, or development in regions where household food insecurity is prevalent, unless mothers also have access to nutrient-rich foods [8]. The meeting did not discuss or examine long-term solutions to food insecurity. Such solutions would include an array of policies to stimulate local agricultural and economic development (particularly the economic and social empowerment of women, the primary caregivers in most households) so that communities become food-secure in a sustainable and independent way. Instead, the meeting explored how the international community can urgently deliver more food aid, of better quality, to prevent and treat malnutrition in the highest-burden areas. Such an emergency measure is clearly needed to bring down death rates as quickly as possible—but it is not a sufficient long-term approach to the global malnutrition crisis. In examining the role of food aid in preventing malnutrition, the meeting's focus was on improving access to nutrient-rich complementary (weaning) foods from the ages of six months to two years, a critical window for child growth. Standard cereal-based food aid, used in many maternal and child health programs, usually consists of corn or wheat soy blends, which are mixed with water and served as a gruel [9]. Are these vegan fortified blends adequate for preventing malnutrition? This is another contentious issue. Few studies have evaluated the effect of feeding these blends to children at risk of malnutrition, and their efficacy in large-scale nutrition programs is not well established [10–12]. One concern about these blends is that they contain “anti-nutrients” that may interfere with nutrient absorption and dietary fibers that can affect appetite [9]. Another concern, which MSF is heavily publicizing, is whether the lack of animal-source foods in these blends is contributing to nutritional deficiencies and growth retardation. To support this view, MSF points to a 1994 study showing nutritional deficiencies and growth retardation in Dutch children aged four to 18 months who had been fed a macrobiotic vegan diet [13].

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Analogous methods to assign function to intrinsically disordered regions based on evolutionary conservation (or other sequence properties) are of continuing research interest (reviewed in van der Lee et al. , 2014). We and others (Davey et al. , 2012; et al. , 2012) have shown that short segments of evolutionary conservation in otherwise rapidly evolving disordered regions point to key functional residues, often important for posttranslational modifications, or other transient protein interactions (Tompa et al. , 2014). However, these conserved segments make up a small fraction of disordered regions (5%), and the vast majority of disordered amino acids show little evidence for evolutionary constraint in alignments of primary amino acid sequences (Colak et al. , 2013). It is currently unclear how intrinsically disordered regions persist at high frequency in the proteome, given these apparently low levels of evolutionary constraint (Afanasyeva et al. , 2018; Brown et al. , 2010; Colak et al. , 2013; de la Chaux et al. , 2007; Khan et al. , 2015; Light et al. , 2013; Tóth-Petróczy and Tawfik, 2013). One hypothesis for the preponderance of disordered regions despite high amino acid sequence divergence, is that the ‘molecular features’ of disordered regions that are important for function (such as length [Schlessinger et al. , 2011], complexity [Alberti et al. , 2009; Halfmann, 2016; Kato et al. , 2012; Molliex et al. , 2015], amino acid composition [Moesa et al. , 2012], and net charge [Mao et al. , 2010; Strickfaden et al. , 2007; Zarin et al. , 2017]) do not lead to detectable similarity in primary amino acid sequence alignments. Indeed, recently, evidence that such molecular features can be under evolutionary constraint has been reported for some proteins (Daughdrill et al. , 2007; Lemas et al. , 2016; Zarin et al. , 2017). For example, we showed that signaling function of a disordered region in the Saccharomyces cerevisiae protein Ste50 appears to depend on its net charge, and we found evidence that this molecular feature is under evolutionary constraint, despite no detectable sequence similarity in alignments (Zarin et al. , 2017).

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: As such, macroalgae with CCMs are not expected to benefit as much from increased CO2 compared to those lacking CCMs (Kübler et al. 1999). The macroalgae used in this study are likely adapted to large natural fluxes in physicochemical conditions and presumably experienced optimal growth conditions in the tanks (continuous growth and no degradation of macroalgae was observed); thus, the addition of CO2 was not beneficial to growth rates. Additionally, corals in both high and low algal density treatments exhibited similar decreases in calcification, and these results could be because the chosen algal densities were not substantially different. Sea is characterized both by naturally high salinity (> 40. 0 ppt) and high variation in temperatures, and the conditions at the collection site may fluctuate by several degrees each day (Safaie et al. 2018). These regions of naturally elevated seawater temperatures are also potential locations for coral–algal phase shifts (turf and macroalgal) to occur due to increased bleaching events (McManus and Polsenberg 2004). Although the presence of macroalgae decreased coral calcification in our experiment regardless of algal density (Fong and Todd 2021), future research could provide valuable insights on these interactions by investigating potential tipping points where coral health is adversely affected by the proximity to macroalgae. This is particularly crucial as further ecological processes such as reduced herbivory can also contribute to macroalgal dominance (Bozec et al. 2019). As coral reef ecosystems are facing escalating threats associated with climate change, the ecological trajectories (e. g. , cover) of foundation species in degraded reefs is crucial to understand. In our study, potential compensatory mechanisms (e. g. , Leung et al. 2017) of Sargassum buffering of coral calcification rates in elevated pCO2 were not observed. Our results emphasize the need for a more holistic approach to understanding tipping points that encompasses biodiverse coral communities, and how changes in species interactions may be modulated in future multi-stressor environments.

Output: corroborate


Input: Claim: Food waste reduction alone can solve global hunger issues. [SEP] Text: But several child nutrition experts that we spoke to say that this Dutch study may not be applicable to the use of corn or wheat soy blends in child feeding programs—unlike macrobiotic diets, these food blends are fortified. Nevertheless, one of the key take-home messages from the Columbia meeting was that food supplements for complementary feeding should not only be energy dense, nutrient rich, and free of anti-nutrients, but they should also contain animal-source foods such as milk. MSF has recently adopted a policy of including at least some animal-source food in its nutrition programs. “We would not provide our own children only cereal porridge, why do we accept a double standard in food aid? ” said Tido von Schoen-Angerer, of MSF's Access to Campaign. MSF is now promoting a complementary food supplement that it believes has the right composition: ready-to-use supplementary food. This supplement is typically a peanut-based paste enriched with milk solids, vitamins, and nutrients—it has a long shelf life and, unlike cereal-based food aid, it does not need to be mixed with water [14]. The idea of using such ready-to-use supplements for preventing malnutrition comes from the success of ready-to-use therapeutic food in the community-based treatment of severe acute malnutrition, which is the most life-threatening of all types of malnutrition. Based on solid clinical trial evidence, this treatment approach has now been endorsed by the Organization, the and the UN Committee on Nutrition [15]. Could a ready-to-use supplement also prevent malnutrition in high-burden areas (the 25–30 countries where the vast majority of children under three years old are at risk)? Donor-supported food programs are not enough as a long-term strategy. Although the idea remains highly controversial, there is support for it from preliminary efficacy trials. For example, Patel and colleagues compared standard food aid (corn soy blend) with ready-to-use food as complementary feeding regimens in children at risk of malnutrition from seven centers in rural Malawi [16]. Children who received ready-to-use food had greater rates of weight gain than children who received corn soy blend.

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Here we sought to test whether evolutionary preservation of molecular features is a general property of highly diverged intrinsically disordered protein regions. To do so, we obtained a set of 82 sequence features reported in the literature to be important for disordered region function (Supplementary file 1 - Table S1). We computed these for S. cerevisiae intrinsically disordered regions and their orthologs, and compared them to simulations of molecular evolution where conserved segments (if any) are retained, but where there is no selection to retain molecular features (et al. , 2014; et al. , 2012). Deviations from the simulations indicate that the highly diverged intrinsically disordered regions are preserving molecular features during evolution through natural selection (Zarin et al. , 2017). We find that many intrinsically disordered regions show evidence for selection on multiple molecular features, which we refer to as an ‘evolutionary signature’. Remarkably, we show that intrinsically disordered regions with similar evolutionary signatures appear to rescue function, while regions with very different signatures cannot, strongly supporting the idea that the preserved molecular features are important for disordered region function. By clustering intrinsically disordered regions based on these evolutionary signatures, we obtain (to our knowledge) the first global view of the functional landscape of these enigmatic protein regions. We recover patterns of molecular features known to be associated with intrinsically disordered region functions such as subcellular organization and targeting signals. We also identify new patterns of molecular features not previously associated with functions of disordered regions such as DNA repair and ribosome biogenesis. Finally, we show that similarity of evolutionary signatures can generate hypotheses about the function of completely disordered proteins. Taken together, our results indicate that evolutionary constraint on molecular features in disordered regions is so widespread that sequence-based prediction of their functions should be possible based on molecular features. Results Proteome-wide evolutionary analysis reveals evolutionarily constrained sequence features are widespread in highly diverged intrinsically disordered regions We identified more than 5000 intrinsically disordered regions (IDRs) in the S. cerevisiae proteome and quantified their evolutionary divergence (see Materials and methods). As expected, we found that the IDRs evolve more rapidly than the regions that were not identified as disordered (Figure 1—figure supplement 1). We also confirmed that the vast majority of these IDRs are distinct from Pfam domains (Figure 1—figure supplement 2).

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: IntroductionCoral reefs are amongst the most diverse ecosystems and support the livelihoods of millions of people (Cinner 2014). Rising atmospheric CO2 is increasing the temperatures and decreasing the pH of most surface seawaters (IPCC 2014). Understanding how these changes affect the accretion of aragonite skeletons by the tropical corals that underpin reef structures is key to predicting the future of coral reefs. Coral calcification is usually reduced at lower seawater pH (Erez et al. 2011), but massive Porites spp. corals, important reef-building species in the Indo-Pacific (Veron 1993), appear to be relatively resilient to ocean acidification (Fabricius et al. 2011; Crook et al. 2012). In culture studies, the calcification and linear extension rates of this genus can be reduced at high seawater pCO2 (Cole et al. 2016), but this suppression can be mitigated by increases in seawater temperature below the temperature stress threshold (Anthony et al. 2008; Edmunds 2012; Cole et al. 2018). The response of calcification to temperature change is seawater pCO2 dependent (Anthony et al. 2008; Cole et al. 2018; Edmunds 2012). The precipitation rate of synthetic (inorganic) aragonites is positively correlated with temperature (Burton and Walter 1987). However, the coral calcification increase observed by Cole et al. (2018) at high pCO2 is much higher than that predicted from synthetic aragonites, while at low pCO2, the change in coral calcification rate is lower than that predicted from synthetic aragonites. Understanding how temperature and seawater pCO2 interact to drive these changes in coral calcification is a goal of the current study. The coral skeleton forms from calcifying media (ECM) which may be contained between the basal layer of the coral tissue, the calicoblastic epithelia, and the underlying coral skeleton (Allemand et al. 2011) or contained within vesicles in the coral tissue (Mass et al. 2017). This calcification media is semi-isolated from ambient seawater, and both the pH and dissolved inorganic carbon (DIC) of the media are significantly higher than in local seawater (Sevilgen et al. 2019), facilitating precipitation of the aragonite skeleton.

Output: corroborate


Input: Claim: Food waste reduction alone can solve global hunger issues. [SEP] Text: In another trial [17], 313 Ghanaian infants were randomized to one of three complementary food supplements from the age of six to 12 months: (1) a ready-to-use food called Nutributter (a peanut-based spread that includes milk powder); (2) a multiple micronutrient powder called Sprinkles (the efficacy of this powder in controlling childhood anemia has been previously presented in PLoS Medicine [18]); and (3) a crushable multiple micronutrient tablet called Nutritabs. group had greater length and weight gains than did the other two supplementation groups. But skeptics say that there is not yet enough scientific evidence to support scaling up of ready-to-use supplementary food as a preventive intervention. Enserink recently reported in his news feature in Science: “The issue has pitted those who want to see solid evidence before embarking on a major aid program against those—impatient with talk about P-values, cost-effectiveness, and sustainability—who want to act now” [14]. Steve Collins, one of the founders of Valid International, which works to improve the delivery of humanitarian assistance, said at the meeting that in the malnutrition crisis we face “a problem, an opportunity, and a threat. ” The problem is that malnutrition is the world's greatest cause of underdevelopment and poverty, its scale is huge, and it is inextricably linked with other global problems including the HIV pandemic, global warming, and the food and population crises. The opportunity is that the G8 has begun talking about nutrition [19], and community-based treatment of severe acute malnutrition with ready-to-use therapeutic food has created a “positive vibe” in the nutrition community [15]. But the threat is that there is a lack of clarity in discussions about childhood malnutrition, its prevention, and its treatment. This lack of clarity was on show at the meeting—in discussions about ready-to-use foods, for example, it was hard to tell whether speakers were talking about their role in prevention or in treatment, and it was hard to know which stage of malnutrition was being discussed. Different diets, said Collins, will be needed for different types of malnutrition, and a variety of food products need to be developed for targeted food assistance. With all these products there will be questions about their efficacy, delivery, cost, and sustainability.

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: These results are consistent with previous reports (Brown et al. , 2010; Colak et al. , 2013; de la Chaux et al. , 2007; Khan et al. , 2015; Light et al. , 2013; Tóth-Petróczy and Tawfik, 2013) that the primary amino acid sequence alignments of IDRs show high levels of divergence and it is not possible to annotate IDR functions using standard homology-based approaches. To test for selection on molecular features in these IDRs, we applied a method that we recently used to show evidence of selection on an IDR in the S. cerevisiae Ste50 protein (Zarin et al. , 2017). We obtained 82 molecular features that have been reported or hypothesized to be important for IDR function (Supplementary file 1 - Table S1) and tested whether these molecular features are under selection in the S. cerevisiae IDRs (see Materials and methods for details). Briefly, we compare the distribution of a given molecular feature in a set of orthologous IDRs to a null expectation, which is formed by simulating the evolution of each IDR. When the mean or variance of the molecular feature across the orthologous IDRs deviates from the distribution of means or variances in our null expectation, we predict that this feature is under selection, and thus could be important for the function of the IDR in question. For example, in the Ste50 IDR, as reported previously (Zarin et al. , 2017), we found that the variance of the net charge with phosphorylation of the IDR falls outside of our null expectation, while the mean falls within our null expectation (Figure 1A). Figure 1 with 2 supplements see all Download asset Open asset Proteome-wide evolutionary analysis reveals evolutionarily constrained sequence features are widespread in highly diverged intrinsically disordered regions. (A) Left: Mean versus log variance of the ‘net charge with phosphorylation’ molecular feature for the real Ste50 IDR (a. a. 152–250) ortholog set and simulated Ste50 orthologous IDR sets (N = 1000). Right: Example simulated Ste50 orthologous IDR sets (no. 663 and no. 56 out of 1000) and the real Ste50 IDR and its orthologs, colored according to percent identity in the primary amino acid sequence.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: The three predominant forms of dissolved inorganic carbon in seawater are CO2, bicarbonate (HCO3−) and carbonate (CO32−). Increasing seawater pH shifts the DIC equilibrium to reduce the proportion of CO2 and increase the proportion of CO32−. CO2 can readily diffuse across cell membranes so the pH increase facilitates the invasion of CO2 into the calcification site and acts as a DIC concentration mechanism (Erez 1978). This allows the [DIC], [HCO3−] and [CO32−] to increase above that of seawater providing the DIC required to build the skeleton (Allison et al. 2014). Here, we use skeletal δ11B to estimate the pH of the calcification media (pHECM) in a series of corals cultured over a range of seawater pCO2 (180, 260, 400 and 750 µatm) and at 25 and 28 °C (Cole et al. 2018). These pCO2 conditions reflect conditions in the Maximum, the pre-industrial (Gattuso and Lavigne 2009), the present day and a future scenario. B speciation in seawater is controlled by ambient pH, and there is a large B isotope fractionation between the predominate dissolved species with borate, B(OH)4−, depleted in 11B compared to boric acid, B(OH)3 (Kakihana et al. 1977). Assuming that B(OH)4− is predominantly incorporated into the lattice during aragonite precipitation (Sen et al. 1994; Noireaux et al. 2015; Balan et al. 2016), skeletal δ11B reflects pHECM. Reports of B(OH)3 in tropical (Klochko et al. 2009) and deep water corals (Rollion-Bard et al. 2011) may reflect a change in B coordination (from tetrahedral B4 to trigonal B3) after aragonite precipitation (Klochko et al. 2009; Noireaux et al. 2015; Balan et al. 2016) or the incorporation of B3 in coral centres of calcification (Rollion-Bard et al. 2011). In this study, we avoid the analysis of centres of calcification and we assume that coral skeletal boron is derived from dissolved B(OH)4−.

Output: corroborate


Input: Claim: Food waste reduction alone can solve global hunger issues. [SEP] Text: The unfortunate reality is that the child hunger crisis includes a knowledge crisis—we still have scientific gaps, for example, in our understanding of what would be the perfect complementary food supplement for food aid. “It is sobering to realize,” wrote Lutter and Dewey, “that far more is known about formulating optimal foods for domestic livestock than about complementary feeding of young children” [20]. And while developing better quality complementary food supplements clearly has an important role to play in addressing the malnutrition crisis and saving lives now, particularly in emergency situations, donor-supported food programs are not enough as a long-term strategy. Other proven malnutrition interventions must also be scaled up. For example, the Hunger and Undernutrition Initiative, a global partnership started by and the Programme, is calling for the global scale-up of a range of “practical measures” [21]. These include health, hygiene, and nutrition education and promotion, micronutrient supplementation, household water treatment, hand washing, deworming, and “situation-specific household food security interventions” [21]. National and international development strategies and policies, together with political will and financing, are also required [22]. It will cost about $US8 billion a year to assist 100 million families to protect their children from hunger and malnutrition [21]—and yet current donor spending on programs to reduce undernutrition is only about $US250–$US300 million annually [23]. We commend the humanitarian aid agencies such as MSF and for, as one child health expert told us, “shaking up the ossified systems of international food aid. ” Food aid alone, however, as Lautze and colleagues have noted, “cannot be sufficient for combating the multi-faceted nature of the current [malnutrition] emergency” [24]. The reactive approach to dealing with malnutrition, although appropriate in responding to humanitarian crises, risks creating long-term dependency on medicalized food aid. Addressing the role of food aid in long-term efforts will require answering some difficult questions, including which basic determinants of malnutrition should be the major focus and who should coordinate the global response to the malnutrition crisis. The dialogue must therefore extend beyond the immediate context of food delivery to the broader sociopolitical sphere, including the role of humanitarian agencies and nongovernmental organizations themselves. We will explore many of these concerns in an upcoming commissioned series in PLoS Medicine.

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: (B) Percentage of IDRs that are significantly deviating from simulations in mean, log variance, or both mean and log variance of each molecular feature. (C) Frequency [1 + log(frequency)] of number of significant molecular features per IDR for the real IDRs (yellow) versus the random expectation (blue) obtained from a set of simulated IDRs. We applied this analysis to 5149 IDRs (see Materials and methods) and computed the percentage of IDRs where the evolution of each molecular feature fell beyond our null expectation (empirical p<0. 01, Figure 1B). We find that charge properties such as net charge and acidic residue content are most likely to deviate from our null expectation (more than 50% of IDRs) (Figure 1B). This is in contrast to non-conserved motif density, which deviates from our null expectation in 21. 6% of IDRs at most (for CDK phosphorylation consensus sites). Other molecular features that frequently deviate from our null expectation are sequence complexity (43. 0%), asparagine residue content (43. 3%), and physicochemical features such as isoelectric point (53. 9%). We also found that the mean of each molecular feature deviates from our null expectation more often than the variance (Figure 1B). These results suggest that there are many more molecular features that are under selection in IDRs than is currently appreciated (Daughdrill et al. , 2007; Lemas et al. , 2016; Zarin et al. , 2017). Next, we quantified the number of molecular features that are significant per IDR, assigning significance to a molecular feature if either the mean, variance, or both mean and variance of the molecular feature deviated from our null expectation (empirical p<0. 01, Figure 1C). Surprisingly, many IDRs have many significant molecular features, with a median of 15 significant molecular features per IDR (compared to one significant feature expected by chance; see Materials and methods). Although many of our features are correlated (see Discussion), these results suggest that the deviation from our expectations of molecular feature evolution is not due to a few outlier IDRs, but rather that most IDRs tend to have multiple molecular features that are under selection.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: After import, corals were maintained at ambient seawater pCO2 conditions for 2 months, kept under varying CO2 for 1 month, while the seawater pCO2 was gradually adjusted to the treatment conditions and then acclimated at the final treatment pCO2 for 4 months at 28 °C. Colonies were then stained with S and cultured for a 5-week experimental period during which calcification, respiration and net and gross photosynthesis were measured on 3 or 4 occasions (Cole et al. 2018). At the end of this time, a small segment of each colony (including tissue and skeleton) was removed by rock saw and preserved for future analysis. This reduced the surface areas of each colony by ~ 25%. Seawater temperatures were then reduced to 25 °C over a period of 4 weeks and then acclimated at this temperature for another month during which time the sawn edges of the coral colonies were overgrown by coral tissue. Finally, corals were restained with S, physiological rates were measured over a 5-week period as before, and the corals were then sacrificed. Further details on the coral culturing methods are provided in the supplementary information. It is likely that the import procedures and sawing of colonies resulted in some stress to the corals at the start of this study, but it is unlikely that this impacts the data presented here. Corals were cultured for a total of 11 months during this experiment, displayed no evidence of bleaching and maintained photosynthesis, respiration and calcification rates comparable to those of massive Porites spp. in the field (see supplementary information). Seawater characterisationThe physical characteristics of the culture seawater are detailed in Cole et al. (2018) and are summarised in Table 1. Dissolved nutrients were measured in filtered samples from each reservoir using a flow cell spectrophotometer (Lachat 8000) at the of Marine Science, the UK. [NO3− + NO2−] and [PO4−] fell to low levels (0. 04 and 0. 00 µM, respectively) in the first week of the 5-week experimental period in the 400 μatm pCO2 treatment at 28 °C (Table 1) and the polyps of these corals appeared retracted.

Output: corroborate


Input: Claim: Food waste reduction alone can solve global hunger issues. [SEP] Text: Communities & à Čeština Deutsch Español Français Gàidhlig Italiano Latviešu Polski Português Português do (lat) Türkçe Tiếng Việt Қазақ বাংলা हिंदी Ελληνικά Српски Yкраї́нська Log InNote: CGIAR users should log in with their username and password. For example, if your email is j. smith@cgiar. org, you would use jsmith here. Log in New user? Click here to register. Have you forgotten your password? research centersInstitute (IFPRI)2015 Global hunger index: Armed conflict and the challenge of hunger 2015 Global hunger index: Armed conflict and the challenge of hungerFiles(8. 68 MB, pdf)(French) (10. 29 MB, pdf)(German) (6. 59 MB, pdf)(Italian) (10. 19 MB, pdf)(Korean) (21. 74 MB, pdf)Show moreAuthors von Grebmer, Klaus Bernstein, Jill de 2015-10Date OnlineLanguageen; fr; de; it; koitem page ShareCitationvon Grebmer, Klaus; Bernstein, Jill; de Waal, Alex; Prasai, Nilam; Yin, Sandra; Yohannes, Yisehac. 2015. 2015 Global hunger index: Armed conflict and the challenge of hunger. Bonn, Germany; Washington, D. C. and Dublin, Ireland: Welthungerhilfe; Institute (IFPRI) and Concern Worldwide. Permanent link to cite or share this item link to download this itemDOI developing world has made progress in reducing hunger since 2000. The 2015 Index (GHI) shows that the level of hunger in developing countries as a group has fallen by 27 percent. Yet the state of hunger in the world remains serious. This marks the tenth year that IFPRI has assessed global hunger using this multidimensional measure. This report’s GHI scores are based on a new, improved formula that replaces the child underweight indicator of previous years with child stunting and child wasting.

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Intrinsically disordered regions with similar molecular features can perform similar functions despite negligible similarity of primary amino acid sequences The analysis above indicates that highly diverged IDRs typically contain multiple molecular features that are under selection. To summarize the set of preserved molecular features in each IDR, we computed Z-scores comparing either the observed mean or variance of each molecular feature in the orthologous IDRs to our simulations (see Materials and methods). We call these summaries of evolution of molecular features (vectors of Z-scores) ‘evolutionary signatures’. If the features are important for function, IDRs with similar evolutionary signatures are predicted to perform (or at least be capable of performing) similar molecular functions. To test this hypothesis, we replaced the endogenous Ste50 IDR with several IDRs from functionally unrelated proteins: Pex5, a peroxisomal signal receptor (Erdmann and Blobel, 1996), Stp4, a predicted transcription factor (Abdel-Sater et al. , 2004), and Rad26, a DNA-dependent ATPase involved in Repair (Gregory and Sweder, 2001; Guzder et al. , 1996) (Figure 2A). Ste50 is an adaptor protein in the Glycerol (HOG) and mating pathways (Hao et al. , 2008; Jansen et al. , 2001; Tatebayashi et al. , 2007; Truckses et al. , 2006; Yamamoto et al. , 2010) whose IDR is important for basal mating pathway activity (as measured by expression of a reporter driven by the Fus1 promoter) (Hao et al. , 2008; Zarin et al. , 2017). The IDRs that we used to replace the Ste50 IDR all have negligible similarity when their primary amino acid sequences are aligned, but vary in the similarity of their evolutionary signatures (to the Ste50 IDR, Figure 2A). We found that the basal mating reporter expression in each strain corresponded to how similar the evolutionary signature of the replacing IDR was to that of the Ste50 IDR (all mutants significantly different from wildtype and each other, Wilcoxon test p<0. 05, Figure 2B). To further assay mating pathway activity, we exposed the wildtype and chimaeric strains with IDRs from Pex5, Stp4 and Rad26 to mating pheromone.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: 61‰ (Foster et al. 2010). B evaporates in the water phase during seawater evaporation (Gast and Thompson 1959) to form aquarium seasalt and is replaced by the addition of boric acid by the manufacturer. Other seawater parameters (total alkalinity, [Ca2+], [Mg2+]) were comparable to natural seawater (Table 1). All corals increased the pHECM above that of seawater at both temperatures (Table 1, Fig. 1). Significant variations in pHECM occur both between the same coral genotype in different seawater pCO2 treatments and between different coral genotypes within the same seawater pCO2 treatment (one-way 2). pHECM is significantly higher in all coral genotypes at seawater pCO2 180 µatm compared to 750 µatm at both 25 and 28 °C (with the exception of G4 at 25 °C, Table 2). Mean pHECM is significantly lower at 28 °C compared to 25 °C in corals cultured at 180 µatm (paired 2 tailed t test of all 4 coral genotypes, p = 0. 00053) but not in the same coral genotypes cultured at the two temperatures at 750 µatm (p = 0. 65). Minor changes in pHsw occur between 25 and 28 °C within some pCO2 treatments (Table 1). To account for this, we also tested if the proton concentration gradient between the seawater and the ECM (i. e. [H+]sw-[H+]ECM) varied between corals. Mean [H+]sw-[H+]ECM of all four coral genotypes is significantly lower at 28 °C compared to 25 °C in corals cultured at 180 µatm (paired 2 tailed t test, p = 0. 028) but again differences are not significant in the same coral genotypes cultured at 750 µatm (p = 0. 63). Fig. 1a pHECM (pH extracellular calcification media, total scale) and b the [H+] concentration gradient between seawater and the ECM in all corals. Error bars are calculated from 95% confidence limits of skeletal δ11B analyses at 25 and 28 °C. Genotype numbering (G4-G7) follows that used in Cole et al.

Output: corroborate


Input: Claim: Food waste reduction alone can solve global hunger issues. [SEP] Text: This change reflects the latest thinking on the most suitable indicators for child undernutrition, one of three dimensions of hunger reflected in the GHI formula. Across regions and countries, GHI scores vary considerably. Regionally, the highest GHI scores, and therefore the highest hunger levels, are still found in Africa south of the Sahara and South Asia. Despite achieving the largest absolute improvements since 2000, these two regions still suffer from serious levels of hunger. Levels of hunger are alarming or serious in 52 countries. Most of the eight countries with alarming GHI scores are in Africa south of the Sahara. While no countries are classified in the extremely alarming category this year, this high level of hunger could still exist. Due to insufficient data, 2015 GHI scores could not be calculated for places that recently suffered from high levels of hunger, including Burundi, Comoros, of the Congo, Eritrea, Somalia, South Sudan, and Sudan. Translations: von Grebmer, Klaus; Bernstein, Jill; de Waal, Alex; Prasai, Nilam; Yin, Sandra; Yohannes, Yisehac. 2015. 2015 Indice de la faim dans le monde: Conflict armés et le défi de la faim. Bonn, Germany; Washington, D. C. and Dublin, Ireland: Welthungerhilfe; Institute (IFPRI) and Concern Worldwide. L’Indice de la faim dans le monde 2015 (GHI) montre que le niveau de la faim dans les pays en développement pris dans leur ensemble s’améliore depuis l’an 2000, affichant une baisse de 27%. Cependant, l’état de la faim dans le monde demeure malgré tout « grave ». Pour l’IFPRI, cette année marque le dixième anniversaire de son travail d’analyse multidimensionnelle de la faim dans le monde.

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: We found that the two chimaeric strains that were more similar in their evolutionary signatures to the wildtype (Pex5 and Stp4) began the process of ‘shmooing’, or responding to pheromone, whereas the strain that had the IDR with the most different evolutionary signature (Rad 26) could not shmoo (Figure 2C; full micrographs in Figure 2—figure supplement 1). Although it is challenging to quantitate similarity between evolutionary signatures comprised of correlated features (see Discussion), our ability to use these signatures to predict which IDRs can rescue signaling function suggests that they may be associated with IDR function. Figure 2 with 1 supplement see all Download asset Open asset Intrinsically disordered regions with similar evolutionary signatures can rescue wildtype phenotypes, while those with different evolutionary signatures cannot. (A) Multiple sequence alignment of Ste50 IDR (a. a. 152–250), Pex5 IDR (a. a. 77–161), Stp4 (a. a. 144–256), and Rad26 IDR (a. a. 163–239) shows negligible similarity when their primary amino acid sequences are aligned, while evolutionary signatures show that the Pex5 and Stp4 IDRs are more similar to the Ste50 IDR than the Rad26 IDR. While the Ste50 IDR has five consensus phosphorylation sites that are implicated in its function (Hao et al. , 2008; Yamamoto et al. , 2010; Zarin et al. , 2017), the Pex5 IDR and Rad26 IDR have none, and the Stp4 IDR has 4. IDRs are presented in order of increasing Euclidian distance between their evolutionary signatures, though we do not recommend using this measure to quantitate similarity between evolutionary signatures independently (see Discussion). The Ste50 IDR is located between the Motif (SAM) and (RA) domains in the Ste50 protein. (B) Boxplots show distribution of values corresponding to basal Fus1pr-GFP activity in an S. cerevisiae strain with the wildtype Ste50 IDR compared to strains with the Pex5, Stp4, or Rad26 IDR swapped to replace the Ste50 IDR in the genome.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: (2018). Hatched bars indicate results at 28ºC, and unhatched bars are 25ºCFull size imageTable 2 Summary of significant differences (p ≤ 0. 05, one-way ANOVA followed by Tukey’s pairwise comparisons) in calcification fluid pH between individuals of the same coral genotype in different seawater pCO2 treatments and between individuals of different genotypes within the same seawater pCO2 treatmentFull size tableWe plot coral calcification rate as a function of the [H+]sw-[H+]ECM gradient between the calcifying media and the surrounding seawater (Fig. 2). Calcification rate and the [H+] gradient are significantly correlated at 25 °C in genotypes G3 and G6, but all other relationships are not significant (Table 3). This partly reflects the small numbers in the regression analysis (n = 3 or 4), but it is noteworthy that calcification rate and the [H+] gradient are inversely related in all corals at 25 °C but demonstrate much more mixed behaviour at 28 °C. Fig. 2Calcification rates as a function of the [H+]sw-[H+]ECM gradient at 25 °C and 28 °C. The two significant correlations (p ≤ 0. 05) are indicated by solid lines. Error bars indicate 95% confidence limits in pHECM and 1σ of calcification measurements. Genotype numbering (G4-G7) follows that used in Cole et al. (2018)Full size imageTable 3 Coefficients of determination (r2) between [H +]sw-[H +]ECM and coral calcification rates at each temperature for each coral genotype. Full size tableOnly one reservoir was used for each pCO2 treatment, and to estimate variations between replicate reservoirs, we compare the results from this study to those of a previous study using the same aquarium system and culturing corals at 180, 400 and 750 µatm seawater pCO2 at 25 °C (Allison et al. 2018). We observe no significant difference in the pHECM between groups of corals cultured under the same conditions in both studies (t test, p > 0. 05) indicating that variations between replicate reservoirs are insignificant.

Output: corroborate


Input: Claim: Food waste reduction alone can solve global hunger issues. [SEP] Text: I punteggi di GHI di questo rapporto si basano su una nuova formula, rivista, che sostituisce l’indicatore “insufficienza di peso infantile” degli anni scorsi con il deperimento e il ritardo della crescita infantili. Questo cambiamento riflette gli ultimi sviluppi teorici sugli indicatori più idonei della sottonutrizione infantile, una delle tre dimensioni della fame espresse dalla formula del GHI. I punteggi di GHI variano notevolmente da regione a regione, e da Paese a Paese. A livello regionale, i punteggi di GHI più alti, e quindi i livelli più alti di malnutrizione, si registrano nell’Africa a sud del Sahara e in Asia meridionale. Nonostante abbiano ottenuto i più ampi miglioramenti in termini assoluti rispetto al 2000, queste due regioni presentano ancora livelli di fame grave. von Grebmer, Klaus; Bernstein, Jill; de Waal, Alex; Prasai, Nilam; Yin, Sandra; Yohannes, Yisehac. 2015. 2015 Global hunger index: Armed conflict and the challenge of hunger [in Korean]. Bonn, Germany; Washington, D. C. and Dublin, Ireland: Welthungerhilfe; Institute (IFPRI) and Concern Worldwide. 2000년부터 개발도상국들의 기아 상황은 진전을 이루고 있습니다.

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Boxplot boxes represent the 25th-75th percentile of the data, the black line represents the median, and whiskers represent 1. 5*the interquartile range. Outliers fall outside the 1. 5*interquartile range, and are represented by unfilled circles. Distribution of GFP activity is based on quantification of GFP intensity in single cells pooled from four colonies (which we define as biological replicates) for each strain; sample sizes for each distribution are as follows: WT n = 588 cells, Pex5 IDR n = 196 cells, Stp4 IDR n = 228 cells, Rad26 IDR n = 271 cells. (C) Brightfield micrographs showing each strain from part B following exposure to pheromone. Shmooing cells are those which have elongated cell shape, representing mating projections. Proteome-wide view of evolutionary signatures in disordered regions reveals association with function To test the association of function with evolutionary signatures in highly diverged IDRs, we clustered and visualized the evolutionary signatures for 4646 IDRs in the proteome (see Materials and methods) (Figure 3). Remarkably, the evolutionary signatures reveal a global view of disordered region function. The IDRs fall into at least 23 clusters based on similarity of their evolutionary signatures (groups A through W, Figure 3) that are significantly associated with specific biological functions (enriched for (GO) term, phenotype, and/or literature annotations, Rate [FDR]=5%, Benjamini-Hochberg corrected) (Table 1; full table of enrichments in supplementary data; clustered IDRs and evolutionary signatures in supplementary data). Given that this level of specificity of biological information has not been previously associated with sequence properties of highly diverged IDRs, we performed a series of controls, ensuring that our clusters are not based on sequence similarity between IDRs, that our annotation enrichment results are not due to a mis-specification of the null hypothesis, and to confirm that these annotation enrichment results cannot be obtained simply based on amino acid frequencies of IDRs (Supplementary file 1 - Table S2; see Materials and methods). Figure 3 Download asset Open asset Clustering evolutionary signatures shows that IDRs in the proteome share evolutionary signatures, and that these clusters of IDRs are associated with specific biological functions.

Output: pass