Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: , 2000; Weinberg, 1997). To test whether EET allowed increased iron acquisition by L. plantarum, we measured intracellular iron by Plasma-(ICP-MS). There was no significant difference in intracellular iron concentrations between L. plantarum growth in mMRS supplemented with DHNA and iron compared to growth in mMRS alone (Figure 4—figure supplement 1). Moreover, deletion of ndh2 did not significantly change the amount of intracellular iron (Figure 4—figure supplement 1). ICP-MS showed that other redox-active metals used for EET, such as manganese and copper (Kouzuma et al. , 2012; Fan et al. , 2018) were also not affected (Figure 4—figure supplements 1 and 2). In contrast to studies in E. faecalis in which iron supplementation leads to intracellular accumulation of this metal (Keogh et al. , 2018), these data show that L. plantarum does not use EET to increase its acquisition of iron or other redox-active metals, suggesting EET may instead play a role in energy conservation. We next sought to understand if EET impacts energy conservation in L. plantarum by comparing its growth and ATP levels in the presence of a polarized anode. The highest current density (i. e. greatest EET activity) produced by L. plantarum in mannitol CDM typically occurred within 24 hr after inoculation into the bioreactor (Figure 1C). At this point, there was an approximately 4-fold higher dry cell weight and 2-fold higher numbers of viable cells compared to L. plantarum incubated in open circuit (OC) conditions (Figure 4A–B) Current density declined from its maximum value when L. plantarum cells performing EET were in exponential growth (Figures 1C and 4C). By comparison, growth was not observed until two days later under OC conditions (Figure 4C). During peak current production, intracellular ATP levels were significantly higher (4. 5-fold) under EET compared to OC conditions (Figure 4D and Table 1). These results strongly suggest faster ATP accumulation under EET conditions allowed L. plantarum to exit lag phase more rapidly. ATP levels were also greater in L.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: At present, it is difficult to reconcile any scenario for the evolution of Venus as a planet that may still be habitable for even the most extreme and adaptive of Earth-like life. Still, Venus presents an excellent laboratory for better understanding atmospheric evolution and surface–atmosphere interactions under more extreme conditions than those on Earth. was ever habitable, similar processes could be operating on exoplanets under similar conditions, and studying Earth's nearest neighbor can provide insights into the habitability of such exoplanets. See 9. 3. 1. 3 for considerations regarding life as we don't know it on Venus. 7. 2. 3. EuropaJupiter's moon Europa (Fig. 7. 5) is an especially attractive target in the study of habitability. Evidence supports the presence of an ocean over 100 km deep with an overlying ice shell over 20 km thick. The large orbital eccentricity of Europa, maintained by orbital resonances with Io and Ganymede, causes extensive tidal heating that helps maintain a liquid ocean (Tobie et al. , 2003). Silicate rock in contact with the europan ocean is likely to provide a source of chemical energy for life. Chemical reactions and leaching interactions between Europa's ocean and mantle may have altered the composition and oxidation state of the ocean, which have important consequences for habitability and possible origins of life. FIG. 7. 5. The surface of Europa, as imaged by the Galileo spacecraft. Cycloid ridges and chaos terrains imply recent geologic activity that helps us understand the potential habitability of this intriguing world. Credit: NASA/JPL-Caltech/SETI Institute. 7. 2. 3. 1. Evidence for an oceanThe strongest evidence for a subsurface europan ocean comes from magnetic sounding (Khurana et al. , 2009), with additional support provided by geological features (e. g. , Figueredo and Greeley, 2004). Jupiter applies an oscillating magnetic field to Europa. An induced magnetic field that oscillates along with Jupiter's rotation has been observed from Galileo magnetometer measurements near Europa (Kivelson et al. , 2000), and the best explanation of these measurements is a liquid water ocean with a salinity roughly comparable to oceans on Earth (Hand and Chyba, 2007). Other materials cannot explain the induced field observed near Europa. A more detailed discussion is found in the supplementary material. 7. 2. 3. 2.

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: , 2023; Heo and Feig, 2022; Lee et al. , 2022; Lee et al. , 2023; Liang et al. , 2022; Qiao et al. , 2022; Scardino et al. , 2023; Wong et al. , 2022). Our study stands apart in two regards. First, we use structural models generated without any use of known structures of the target protein. For machine-learning methods, this requires ensuring that no structure of the target protein was used to train the method. Second, we perform a systematic comparison that takes into account the variation between experimentally determined structures of the same protein when bound to different ligands. Our results reveal both strengths and weaknesses of AF2 models. The structural accuracy of ligand-binding pockets in AF2 models is usually substantially higher than that of traditional homology models. Indeed, the typical difference between corresponding binding pockets in an AF2 model and in an experimentally determined structure is only slightly larger than the typical difference between two experimentally determined structures of the same protein with different ligands bound. Surprisingly, however, ligand-binding poses predicted given AF2 models are not significantly more accurate than those predicted given traditional models and are much less accurate than those predicted by docking computationally to experimentally determined protein structures. Our results provide guidelines as to how AF2 models should—and should not—be used for effective ligand-binding prediction. Our findings also suggest opportunities for improving structure prediction methods to maximize their impact on drug discovery. of proteins and models to ensure a fair comparison Evaluating the accuracy of predicted ligand-binding poses requires that we examine protein–ligand complexes whose structures have been determined experimentally. We wish to ensure, however, that the predicted structures of a given protein are not informed by experimentally determined structures of that same protein. AF2 and other recent neural-network-based protein structure prediction methods use experimentally determined protein structures in two ways: first, to train the neural network and second, as templates for prediction of individual protein structures (Baek et al. , 2021; Jumper et al. , 2021). The AF2 neural network was trained on structures in the Bank (PDB) (Berman et al. , 2000) as of April 30, 2018 so we evaluated structural models of proteins for which no experimentally determined structure was available as of that date.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: plantarum when in the presence of both mannitol and DHNA, compared to either mannitol or DHNA separately (Figure 4D). Thus, EET allows L. plantarum to initiate growth and accumulate ATP more rapidly, indicating that EET significantly increases energy conservation in L. plantarum. Figure 4 with 3 supplements see all Download asset Open asset Growth, ATP, and redox balance of L. plantarum changes when an anode is provided as an extracellular electron acceptor. These measurements and the current density plot shown in Figure 1C are from the same experiment. (A) Viable cells and (B) dry weight at the point of maximum current density under current circulating conditions (EET) and at open circuit conditions (OC) at the same time point. (C) Change in cell numbers measured by OD600 over time in the bioreactors under EET (continuous line) and OC conditions (dotted lines). (D) ATP production per OD600 unit and (E) NAD+/NADH ratios at the point of maximum current density. The bioreactors were shaken vigorously to dislodge cells before sampling. The avg ± stdev of three biological replicates is shown. Significant differences were determined by one-way ANOVA with (A and B) Dunn-Sidak post-hoc test (n = 3) and (D and E) Dunnett’s post-hoc test (n = 3), * p < 0. 05; ** p < 0. 01; *** p < 0. 001; **** p < 0. 0001. See also Figure 1 panel C and Figure 4—figure supplement 3 and related data in Figure 4—source data 1. Figure 4—source data 1 Raw data of Figure 4A–D. Download elife-70684-fig4-data1-v2. xlsx Table 1 Bioenergetic balances suggest energy conservation under EET conditions occurs via substrate-level phosphorylation. The reactors contained 20 µg/mL of DHNA and mannitol as the electron donor. Balances were calculated with data obtained by day four from Figure 5. See also Supplementary file 1. SLP stands for substrate-level phosphorylation. Yfermentation refers to the total fermentation products obtained (see Supplementary file 1) per mol of sugar consumed.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: Surface conditionsEuropa rests deep within the extensive magnetosphere of Jupiter. The strong jovian magnetic field traps charged p0. 01 nbar; Kliore et al. , 1997), so these p7. 5) is covered in tectonic features reminiscent of subduction faults and fractures common on Earth (Leonard et al. , 2018). There is some evidence of subduction (Kattenhorn and Prockter, 2014), although features may be created by interaction between the conductive and convective ice layers, mediated by tidal forces (Barr and Hammond, 2015). Some evidence suggests that plumes may be erupting from the surface of Europa. Observations with the Telescope (Roth et al. , 2014b) and in situ measurements from Galileo (Jia et al. , 2018; Arnold et al. , 2019) each show some indications of water vapor lofted to high altitudes. Later observations with Hubble have seen no further evidence of plumes, suggesting that europan plumes can only be intermittent, if they are indeed present (Roth et al. , 2014a). Further studies have had difficulty corroborating these observations—there does not appear to be any thermal anomalies on the surface that would be expected where the plumes erupt (Rathbun and Spencer, 2020), a stark contrast with the plumes of Enceladus (Porco et al. , 2014). does have plumes, they are likely to contain material not from the ocean but from shallower melt or brine pockets within the ice shell, as fractures are unlikely to reach directly from the ocean to the surface (Rudolph and Manga, 2009; Howell and Pappalardo, 2019). 7. 2. 3. 3. Ocean habitabilityEuropa seems to have many of the conditions required to support habitable environments. Hydrothermal vents likely exist in the subsurface ocean of Europa, providing a possible energy source for metabolism (Lowell and DuBose, 2005; Vance and Melwani Daswani, 2020). If there is a transport mechanism through the ice shell (e. g. , Kalousová et al. , 2014), introduction of oxidized surface materials may provide rich sources of chemical energy for the likely reduced ocean (Fig. 7. 6; Vance et al. , 2019; Hand et al. , 2020).

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: , 2021), we find that the global structural accuracy of the AF2 models is substantially better than that of the traditional template-based models. In particular, when computing RMSDs based on all non-hydrogen atoms in each protein, we find a median RMSD of 2. 9 Å between AF2 models and corresponding experimentally determined structures, compared to a median RMSD of 4. 3 Å for traditional models (Figure 1—figure supplement 1). Next, we turn our attention to the orthosteric binding pocket of each protein—that is, the region where native ligands and most other ligands, including those in our dataset, bind. AF2 was trained to optimize global structural accuracy, with an emphasis on correctly predicting the structure of the protein backbone. The accuracy of binding pocket prediction, on the other hand depends heavily on side-chain conformations in this local region. Nevertheless, we find that AF2 predictions of binding pocket structures are typically very accurate. In fact, the binding pocket RMSD between an AF2 model and an experimentally determined structure is typically nearly as low as the RMSD between two experimentally determined structures of the same protein with different ligands bound (Figure 1). In contrast, binding pockets in the traditional template-based models are much less accurate, with a median RMSD of 3. 3 Å for traditional models vs. 1. 3 Å for AF2 models. We note that the binding pockets of a few AF2 models are highly inaccurate (approximately 5 Å RMSD), as is the case for several of the traditional models. Figure 1 with 2 supplements see all Download asset Open asset Structural accuracy of modeled binding pockets. Binding pockets are defined to include all amino acid residues with any atom within 5 Å of the ligand in an experimentally determined structure. We compute all-atom binding pocket root mean squared deviations (RMSDs) between each modeled structure and all experimentally determined structures of the same protein. For comparison, we also compute binding pocket RMSDs between all pairs of experimentally determined structures of the same protein with different ligands bound. The middle line of each box in the plot is the median RMSD, with the box extending from the first to the third quartile and defining the ‘interquartile range’.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: Ymannitol is the ATP produced from the total fermentation products per mol of sugar consumed, and YATP is the dry weight measured per mol of ATP produced from fermentation products. NADH consumed*Calculated ATP†(from metabolites)Biomass yield-dw/mol-mannitolmmol product/mmol-mannitolmol ATP/mol mannitolg dw/mol 6. 44 ± 0. 48 via anode16. 69 ± 2. 72 via SLP16. 6 ± 1. 54. 85 ± 0. 331. 53 ± 0. 131. 59 ± 0. 133. 09 ± 0. 36OC5. 51 ± 0. 97 via SLP5. 7 ± 0. 67. 21 ± 1. 410. 87 ± 0. 090. 89 ± 0. 098. 06 ± 0. 86 * Calculated based on production of 3 mol of NADH produced per mol of mannitol, 1 mol of NAD+ per lactate, 2 mol of NAD+ per ethanol, 2 mol of NAD+ mol per succinate produced and 0. 5 mmol of NAD+ per mol of electrons harvested on the anode. † Calculated based on production of 1 mol of ATP per lactate, 2 mol per acetate, 1 mol per ethanol, and 3 mol per succinate produced. Because fermentation, anaerobic respiration, and aerobic respiration are each associated with a different NAD+/NADH ratio, energy conservation is linked to intracellular redox homeostasis (Holm et al. , 2010). Therefore, we probed redox homeostasis in L. plantarum under EET conditions by measuring intracellular NAD+/NADH at the point of maximum current density (Figure 4E). L. plantarum showed an 8-fold higher NAD+/NADH ratio under EET conditions compared to OC (Figure 4E). This result was not limited to the presence of a polarized anode as L. plantarum also contained a significantly higher NAD+/NADH ratio when Fe3+ was available as a terminal electron acceptor (Figure 4—figure supplement 3). These NAD+/NADH ratios are more similar to those found for in E. coli performing aerobic respiration (de Graef et al. , 1999) or G.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: Pockets of concentrated brine may also become trapped in the ice shell, thereby providing environments suitable for psychrophilic (6. 3. 1. 1) and halophilic (6. 3. 3. 1) organisms (Boetius et al. , 2015; Cooper et al. , 2019). Considerations for life as we don't know it on Europa are discussed in 9. 3. 2. 2. FIG. 7. 6. Sources of biologically important molecules that could potentially sustain life in Europa's ocean. The high-radiation environment at the surface acts as a source of oxidants, and water–rock reactions at the seafloor may act as a source of reductants. If there is some process that cycles crustal material between the surface and the ice–ocean interface, similar to plate tectonics on Earth, this interface likely represents a habitable environment. Europa's ice shell is expected to be quite thick (over 20 km), which may preclude such cycling. Subduction on Europa likely cannot cycle surface material directly into the ocean (Howell and Pappalardo, 2019). This has important consequences for studies of the habitability of the europan ocean that rely on transport of oxidants from the surface into the ocean (e. g. , Hand et al. , 2009; Vance et al. , 2016). There is mounting evidence that the europan ice shell is in the process of thickening and cooling (Leonard et al. , 2018; and McNamara, 2019; Howell and Pappalardo, 2019). The thickness and properties of the ice shell also dictate how energy from tidal interactions will be distributed (Matsuyama et al. , 2018), so a thorough understanding of the dynamics of the europan ice shell is critical to understanding the habitability of the ocean. The location of Europa in the and its bulk density suggest that it is likely constructed of rock, ice, and metals sourced from CI chondrite material (Sohl et al. , 2002), although there may be an additional cometary component (Néri et al. , 2020). Laboratory analog research on leaching of salts from chondritic material suggests MgSO4 may be a primary salt in the europan ocean (Kargel et al. , 2000). This is supported by putative detection of MgSO4 spectral features on the surface (McCord et al.

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: Whiskers extend to last data points that are within 150% of the interquartile range, and outlier data points beyond those are shown individually. The plotted data is based on 150 RMSD values (comparisons) for experimentally determined structures with different ligands bound, 52 for AlphaFold 2 models, and 78 for traditional models. Binding pose prediction using AF2 models or traditional models yields similar accuracy Next, we assess the accuracy of ligand-binding poses predicted by computational docking to AF2 models and traditional template-based models. For each ligand we consider, the binding pose to a target protein is known based on an experimentally determined structure of the ligand bound to the protein, which we call the reference structure. Using industry-standard software, we docked each ligand to both AF2 and GPCRdb models of the protein. A predicted pose is considered correct if its RMSD from the experimentally determined pose is ≤2. 0 Å (Figure 2), a widely used criterion for correct pose prediction (Erickson et al. , 2004; Gohlke et al. , 2000; Paggi et al. , 2021). Figure 2 with 2 supplements see all Download asset Open asset Accuracy of ligand-binding poses predicted by computational docking to AlphaFold 2 models, traditional template-based models, or protein structures determined experimentally in complex with a ligand different from the one being docked. We plot the fraction of docked ligands whose pose is predicted correctly (see Methods). Error bars are 90% confidence intervals calculated via bootstrapping. *** for p-values <0. 001, ns for p-values >0. 05. 40 - 54 ligands were evaluated for each set of structures or models. For comparison, we also dock each ligand to structures of the same protein determined experimentally with other ligands bound (cross-docking). Note that when calculating pose prediction accuracy (Figure 2), we exclude cases where the ligand is docked back to the reference structure; such ‘self-docking’ yields much higher accuracy (Figure 2—figure supplement 1) but is of little practical utility, because in practice one wishes to predict binding poses that have not already been determined experimentally.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: sulfurreducens performing anaerobic respiration than in LAB performing fermentation (Guo et al. , 2017). Taken together, our data indicate that EET is involved in energy conservation, and the intracellular redox balance during EET mimics a respiratory rather than a fermentative process. EET increases fermentative metabolism through substrate-level phosphorylation and reduction in extracellular pH Metal-reducing bacteria use EET in anaerobic respiration (Richter et al. , 2012; Shi et al. , 2007). Ndh2 is considered an anaerobic respiratory protein, and L. plantarum can perform anaerobic respiration with exogenous menaquinone and heme using an electron transport chain (Brooijmans et al. , 2009b). This led us to hypothesize that those electron transport proteins could also be involved for EET to conserve energy as part of anaerobic respiration. To test this hypothesis, we examined whether any of the known electron transfer proteins needed for PMF generation in aerobic and anaerobic respiration are required for L. plantarum EET. Neither the addition of heme to restore bd-type cytochrome (cydABCD) used in aerobic respiration, nor deletion of the respiratory nitrate reductase (ΔnarGHJI) significantly altered current production (Figure 5—figure supplement 1A-B). Because Ndh2 is a type-dehydrogenase which does not contribute to a proton gradient (Lin et al. , 2008; Nakatani et al. , 2020), these observations show that while EET does involve a respiratory protein, it does not involve any of the known PMF-generating electron transfer proteins in L. plantarum. Respiration is also associated with the tricarboxylic acid (TCA) cycle. L. plantarum, like other LAB, does not possess an oxidative branch of the TCA cycle and only contains a reductive branch (Tsuji et al. , 2013). To probe whether the reductive branch was active during EET, we also examined production of succinate, the terminal end-product of the reductive branch. EET did not increase the succinate concentration (Figure 5—figure supplement 2).

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: , 1998; Fox-Powell et al. , 2019), although other materials may explain the observed spectra (Hibbitts et al. , 2019), such as NaCl that may come from the subsurface (Trumbo et al. , 2019). Some studies (e. g. , Brown and Hand, 2013) suggest that surface S and O may be implanted exogenously from volcanic activity on Io, and their presence on the surface does not preclude an ocean dominated by chlorides such as NaCl. 7. 2. 3. 4. Upcoming explorationAn overview of the upcoming and JUICE missions is included in the supplementary material. 7. 2. 4. EnceladusEnceladus is a small (504 km diameter), icy moon of Saturn. Despite its small size, Enceladus has received abundant scientific attention, including measurements from the and Cassini missions. This moon is of particular astrobiological interest, as there is strong evidence of a global ocean below its icy surface that is in contact with a rocky core. The existence of a subsurface ocean on Enceladus is supported by several lines of evidence. Images taken by Cassini show a physical libration (wobble) of the icy crust that is too large for an icy shell anchored to the silicate core of the moon but is consistent with a subsurface liquid ocean (Thomas et al. , 2016). Gravity and shape data of the moon indicate the icy crust may be tens of kilometers thick on average but less than 11 km thick at the southern pole, with a liquid ocean beneath (Beuthe et al. , 2016; Čadek et al. , 2016). Numerous persistent jets of water vapor and small icy p7. 7; e. g. , Porco et al. , 2006; Waite et al. , 2006; Postberg et al. , 2009, 2011). FIG. 7. 7. The south polar plumes of Enceladus, lit by the Sun from behind the camera of the Cassini spacecraft. Ice grains from subsurface reservoirs of liquid water are ejected into space and reflect the sunlight. Credit: NASA/JPL-Caltech/SSI.

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: Strikingly, binding pose prediction accuracy was similar when using AF2 models or traditional template-based models, despite the fact that binding pocket structures were substantially more accurate in AF2 models. Although the fraction of ligands docked correctly was slightly higher when using AF2 models (15%) than when using traditional models (9%), this difference was not statistically significant (p > 0. 5). On the other hand, binding pose prediction accuracy was far higher when docking to experimentally determined protein structures (44%), even though these structures were determined in complex with ligands different from those being docked. The docked poses analyzed above were determined with the widely used commercial docking software package Glide, run in SP mode (for ‘standard precision’) (Friesner et al. , 2004). To verify the robustness of our results, we repeated all docking experiments using a completely different docking software package—Rosetta docking (Park et al. , 2021)—as well as with Glide run in XP mode (for ‘extra precision’) (Friesner et al. , 2006). In both cases, we again found that, when used for ligand-binding pose prediction, AF2 models substantially underperformed experimentally determined structures and did not significantly outperform traditional models (Figure 2—figure supplement 2). In fact, the difference in binding pose prediction accuracy between AF2 models and traditional models was even smaller when using Rosetta docking or Glide XP than when using Glide SP. Closer look at discrepancy between structural accuracy and pose prediction accuracy The results of the previous two sections contrast sharply with one another. AF2 models nearly match experimentally determined structures—and are much better than traditional template-based models—in binding pocket accuracy, as measured by a standard structural metric. Yet AF2 models fare much worse than experimentally determined structures—do not significantly outperform traditional models—when used to predict ligand-binding poses. Figures 3 and 4 provide illustrative examples. Figure 3 with 1 supplement see all Download asset Open asset An example in which docking to an AlphaFold 2 (AF2) model yields poor results even though the model’s binding pocket has high structural accuracy.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: , 2018Rifampicin-resistant mutant of NCIMB8826Strain information listed in Supplementary file 3Strain, strain background (Lactiplantibacillus plantarum)MLES100This studyDeletion mutant of NCIMB8826 lacking ndh2Plasmid information listed in Supplementary file 3Strain, strain background (Lactiplantibacillus plantarum)MLES101This studyDeletion mutant of NCIMB8826 lacking pplAPlasmid information listed in Supplementary file 3Strain, strain background (Lactiplantibacillus plantarum)MLEY100This studyDeletion mutant of NCIMB8826 lacking narGHIJPlasmid information listed in Supplementary file 3Strain, strain background (Lactiplantibacillus plantarum)B1. 3Yin et al. , 2018 Strain information listed in Supplementary file 3Strain, strain background (Lactiplantibacillus plantarum)AJJ11Yu et al. , 2021 Strain information listed in Supplementary file 3Strain, strain background (Lactiplantibacillus plantarum)8. 1Yu et al. , 2021 Strain information listed in Supplementary file 3Strain, strain background (Lactiplantibacillus plantarum)ATCC 202195Wright et al. , 2020 Strain information listed in Supplementary file 3Strain, strain background (Lactiplantibacillus plantarum)NCIMB700965Heeney and Marco, 2019 Strain information listed in Supplementary file 3Strain, strain background (Lactiplantibacillus pentosus)BGM48Golomb et al. , 2013 Strain information listed in Supplementary file 3Strain, strain background (Lactiplantibacillus casei)BL23Mazé et al. , 2010 Strain information listed in Supplementary file 3Strain, strain background (Levilactobacillus brevis)ATCC 367Makarova et al. , 2006 Strain information listed in Supplementary file 3Strain, strain background (Lactococcus lactis)KF147Siezen et al. , 2010b Strain information listed in Supplementary file 3Strain, strain background (Lactococcus lactis)IL1403Bolotin et al.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: The composition of these plumes was sampled directly by the Cassini spacecraft with multiple plume fly-throughs, in addition to in situ samples and measurements of the E-ring of Saturn, which is sourced from the plumes of Enceladus (Spahn et al. , 2006). A variety of grains were observed in the plumes, with compositions ranging from salt-rich (Postberg et al. , 2009; Khawaja et al. , 2019) to water-dominated (Waite et al. , 2006; Teolis et al. , 2010), to grains rich in organic molecules or silicates (Postberg et al. , 2008, 2018). In addition to the grain composition, Cassini instruments measured the plume gas composition and found it to be predominantly H2O, along with significant CO2, CH4, NH3, and H2 (Waite et al. , 2006, 2017). These measurements indicate the icy plumes are likely sourced from a subsurface liquid ocean in contact with a silicate core. Alternative explanations for the source of the plumes, discussed in the supplementary material, have been considered, but none are consistent with observations. To remain consistent with observed salt and NH3 measurements, the temperature of the subsurface ocean may be above −1°C on average (Glein et al. , 2018). Similarly, from constraints of CO2 in the plume, NaCl and bicarbonate p7. 1. 1. 1 in the supplementary material). A source of chemical energy may be available in the form of H2 and CH4 generated from serpentinization of the silicate core and radiolysis of water in the seafloor pore space (Bouquet et al. , 2017). The combination of all these factors indicates that the enceladean ocean may be habitable to life as we know it. It is unknown if the conditions for the origin of life, either at present or in the past, have been met on Enceladus. Even if the conditions for life and abiogenesis are present in the enceladean ocean, the moon may be too young to have formed a biosphere. Models and measurements of saturnian moons and rings indicate they may be only a few hundred million years old or less (Ćuk et al. , 2016; Iess et al. , 2019), although this proposal is debated (Crida et al.

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: We predict the binding pose of the drug aprepitant to its target, the neurokinin-1 receptor (NK1R) given either the AF2 model (orange) of NK1R or the experimentally determined structure (blue, PDB entry 6E59) of NK1R bound to a different ligand, L760735. (A, B) The binding pocket of the AF2 model is more similar (lower root mean squared deviation [RMSD]) than the binding pocket of the L760735-bound structure to the binding pocket of the aprepitant-bound structure (the ‘reference structure’, white, PDB entry 6J20). Amino acid residues whose positions differ most from the reference structure are shown in sticks (see Methods). (C, D) The aprepitant binding pose predicted by docking is much less accurate (higher RMSD) when using the AF2 model than when using the L760735-bound structure. Ligand L76035 shares a scaffold with aprepitant; for completeness, we include another example with highly dissimilar ligands in Figure 3—figure supplement 1. We note that the experimentally determined L760735-bound structure is a low-resolution structure with suboptimal goodness of fit to experimental data; despite this, docking aprepipant to this structure yields an accurate pose. Figure 4 Download asset Open asset An example in which docking to a traditional template-based model yields better results than docking to an AlphaFold 2 (AF2) model, even though the AF2 model’s binding pocket has higher structural accuracy. We predict the binding pose of the psychedelic LSD to its primary target, the serotonin 2A receptor (5HT2A) given either the AF2 model (orange) or a traditional model (green) of 5HT2A. (A, B) The binding pocket of the AF2 model is more similar (lower root mean squared deviation [RMSD]) than that of the traditional model to the binding pocket of the experimentally determined LSD-bound structure (the ‘reference structure’, white, PDB entry 6WGT). Amino acid residues that differ most from the reference structure are shown in sticks.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: , 2001 Strain information listed in Supplementary file 3Strain, strain background (Lactiplantibacillus Rhamnosus)GGKankainen et al. , 2009 Strain information listed in Supplementary file 3Strain, strain background (Lactiplantibacillus murinus)ASF361Wannemuehler et al. , 2014 Strain information listed in Supplementary file 3Strain, strain background (Enterococcus faecalis)ATCC 29212Minogue et al. , 2014 Strain information listed in Supplementary file 3Strain, strain background (Enterococcus faecalis)ATCC 8459Kopit et al. , 2014 Strain information listed in Supplementary file 3Strain, strain background (Pediococcus pentosaceus)ATCC 25745Makarova et al. , 2006 Strain information listed in Supplementary file 3Strain, strain background (Streptococcus agalactiae)ATCC 27956McDonald and McDonald, 1976 Strain information listed in Supplementary file 3Strain, strain background(Escherichia coli)DH5αTaylor et al. , 1993fhuA2 lac(del)U169 phoA glnV44 Φ80’ lacZ(del) M15 gyrA96 recA1 relA1 endA1 thi−one hsdR17, amplification of cloning vector Strains and culture conditions Request a detailed protocol All strains and plasmids used in this study are listed in Supplementary file 3. Standard laboratory culture medium was used for routine growth of bacteria as follows: Lactiplantibacillus spp. , Lacticaseibacillus spp. , Levilactobacillus brevis, Ligilactobacillus murinus, and Pediococcus pentosaceus, MRS (); Lactococcus lactis and Streptococcus agalactiae, M17 (BD) with 2% w/v glucose; Enterococcus faecalis, and Enterococcus faecium, BHI (BD); and Escherichia coli, LB (). Bacterial strains were incubated without shaking except for E. coli (250 RPM) and at either 30 or 37 °C. Where indicated, strains were grown in filter-sterilized MRS (De MAN et al.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: , 2019; Neveu and Rhoden, 2019). is old, its porous interior may have already been completely serpentinized, halting the production of chemical energy sources (Zandanel et al. , 2021). Future missions to this icy moon are necessary to confidently detect life in the subsurface ocean, should it exist. For a more in-depth consideration of Enceladus and its astrobiological relevance, see the recent review by Cable et al. (2020). Considerations for the possibility of life as we don't know it on Enceladus are discussed in 9. 3. 2. 3. 7. 2. 4. 1. Comparison between Enceladus and EuropaEnceladus and Europa share a number of key similarities and differences worthy of note. Both are icy moons known to harbor subsurface liquid water oceans that may be abodes for life. (Anderson et al. , 1998) and Enceladus (Neumann and Kruse, 2019) are likely differentiated. Europa's bulk density and axial moment of inertia imply that it is mostly silicate rock, with a possible iron core and a water + ice layer with a thickness close to just 10% of the body radius (7. 2. 3. 2). Enceladus, in contrast, likely has a porous core of silicates and a water + ice layer with a thickness of up to about 25% of the body radius. Cassini sampling of the plumes of Enceladus implies a high ocean pH as described above. A variety of ocean compositions and pH values have been postulated for Europa's ocean (Zolotov and Kargel, 2009), but there is insufficient evidence to constrain it as yet. Europa's surface is more heavily irradiated than that of Enceladus, thus causing increased oxidation of surface materials from O liberated by photolysis of H2O (Parkinson et al. , 2008; Hand et al. , 2009). Like that of Enceladus, Europa's surface is mostly water ice (Carlson et al. , 2009), but Europa has a large amount of darker material on its surface as well, likely sourced from volcanoes on Io or other endogenous sources (Hand and Carlson, 2015; Hibbitts et al. , 2019).

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: (C, D) The LSD-binding pose predicted by docking is less accurate (higher RMSD) when using the AF2 model than when using the traditional model. To further quantify these results, we compare pose prediction accuracy for structures and models with similar binding pocket accuracy. In particular, we calculate pose prediction accuracy as a function of binding pocket accuracy (RMSD) for both experimentally determined structures and models. As expected, we find that average pose prediction accuracy increases as binding pocket accuracy increases (i. e. , RMSD to reference structure decreases). This trend holds for experimentally determined structures, AF2 models, and traditional template-based models (Figure 5 and Figure 5—figure supplement 1). Yet for the same binding pocket accuracy (RMSD from the reference structure), AF2 models yield lower average pose prediction accuracy than experimentally determined structures (Figure 3). In contrast, in cases where traditional models and experimentally determined structures have similar binding pocket accuracies, they yield similar pose prediction accuracies (Figure 5—figure supplement 1). Figure 5 with 1 supplement see all Download asset Open asset Pose prediction accuracy as a function of binding pocket structural accuracy when docking to AlphaFold 2 (AF2) models or experimentally determined structures. Docking to an experimentally determined structure generally leads to more accurate pose prediction than docking to an AF2 model with the same binding pocket root mean squared deviation (RMSD). The difference between the two curves is statistically significant for all binding pocket RMSD values below 1. 1 Å (see Methods). 5—figure supplement 1 for additional data, including results for traditional models and for various docking methods. We also considered the possibility that the improved performance of experimentally determined structures relative to AF2 models might be because, in some cases, the structure used for docking was determined with a bound ligand similar (though not identical) to the ligand being docked. Eliminating such cases from consideration does lead to decreases in both aggregate binding pocket accuracy and pose prediction accuracy of experimentally determined structures, but experimentally determined structures continue to yield significantly more accurate pose predictions than AF2 models (p < 0. 01) (Figure 1—figure supplement 1 and Figure 2—figure supplements 1 and 2). recent papers have concluded that AF2 models fall short of experimentally determined structures when used for ligand docking (Díaz-Rovira et al. , 2023; He et al.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: , 1960) lacking beef extract with either 110 mM glucose [gMRS] or 110 mM mannitol [mMRS], or a chemically defined minimal medium (Supplementary file 4) with 125 mM glucose [gCDM] or 125 mM mannitol [mCDM] for 18 hr (Aumiller et al. , 2021). Riboflavin (1 mg/L) was routinely added to the CDM. When indicated, culture medium was supplemented with 20 μg/mL of the quinone 1,4-dihydroxy-2-naphthoic acid (DHNA) (), 1. 25 mM ferric ammonium citrate (C6H8FeNO7) (1. 25 mM) (), riboflavin (Sigma-Aldrich, St. ), or 5 μg/mL erythromycin (VWR). DNA sequence analysis Request a detailed protocol gene locus of L. plantarum NCIMB8826 was identified using NCBI basic local alignment search tool (BLAST) (McGinnis and Madden, 2004) using the L. monocytogenes 10403genes (lmo2634 to lmo2641) as a reference. L. plantarum genes were annotated based on predicted functions within the FLEET pathwa (Light et al. , 2018). FLEET locus genes were identified in other LAB by examining 1,788 complete Lactobacillales genomes available at NCBI (downloaded 02/25/2021). A local BLAST (ver 2. 10. 1) database containing these genomes was queried using tBLASTx with NCIMB8826 FLEET genes a reference. A gene was considered to be present in the Lactobacillales strain genome if the Bit-score was >50 and the E-value was <10–3 (Pearson, 2013). Heatmaps showing the percentage of strains in Lactobacillales genera and the Lactobacillus-genus complex (Zheng et al. , 2020) identified to contain individual FLEET genes were visualized using the R-studio package ggplot2 (Wickham, 2011) with clustering done through UPGMA. loci of L. plantarum strain 8.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: In contrast, Enceladus has a very bright surface consistent with pure ice plus a small amount of NH3 and tholins in a global coating spread by the action of plumes (Hendrix et al. , 2010). Many lines of evidence have confirmed the presence of plumes at Enceladus, including direct images (Fig. 7. 7), but only intermittent plume activity is expected on Europa as described above. Alternative explanations may account for existing observations instead of plumes (Roth, 2021; Styczinski and Harnett, 2021). Europa is much larger than Enceladus (radii approximately 1560 km and 252 km, respectively), with a higher surface gravity. The ice shell of Enceladus may be as thin as a few kilometers at the south pole (Hemingway and Mittal, 2019), while Europa's stronger gravity likely prevents any conduit from reaching all the way from the ocean to the surface (Rudolph and Manga, 2009). and Enceladus are both thought to have liquid water oceans in contact with silicate rock, they are both promising candidates in the search for life elsewhere. Each may be habitable. What we learn about one moon can sometimes help us understand the other, but we must always keep in mind that Europa is not Enceladus, and vice versa, and exercise caution in studying these bodies. 7. 2. 5. TitanTitan is the largest moon of Saturn, with a radius of 2575 km (50% larger than Earth's moon), and it is the only moon in the with a significant atmosphere. Due to its thick atmosphere (1. 5 bar surface pressure) and accompanying haze p7. 8 shows an image of Titan in front of Saturn, taken by Cassini. FIG. 7. 8. Titan in front of its parent planet Saturn, a natural-color image taken by the Cassini spacecraft. The hazy appearance is the result of the organic-rich haze p7. 9; Hörst et al. , 2012). These organic molecules would fall to the surface, forming the observed dunes, lakes, and seas. mission, scheduled to launch in June 2027, will explore the surface of Titan to characterize the environment and search for signs of life. FIG. 7. 9. Photochemistry in Titan's atmosphere. Energetic photons and charged p7. 1. 5. 4 in the supplementary material).

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: , 2023; Heo and Feig, 2022; Scardino et al. , 2023). Our results agree with this conclusion but go beyond it in several ways. We compare AF2 models and traditional template-based models, rigorously ensuring that none of these models was informed by experimentally determined structures of the protein being modeled. We find that, in terms of structural accuracy of the binding pocket, AF2 models are much better than traditional models; indeed, the RMSD between an AF2 model and an experimentally determined structure is typically comparable to the RMSD between two structures determined experimentally with different ligands bound. Yet, when used for docking, AF2 models yield pose prediction accuracy similar to that of traditional models and much worse than that of experimentally determined structures. A few caveats are in order. First, building a traditional template-based model is not always possible. We only considered template-based models in cases where a structure was available for another protein with at least 40% sequence identity. However, 80% of human drug targets have at least 50% sequence identity to a protein whose structure was known in 2017 (Somody et al. , 2017), and that number is even higher today. In addition, we note that the traditional models we used were generated relatively quickly by an academic group along with models for hundreds of other proteins. An expert working on a drug discovery project could frequently build a better template-based model—for example, by examining the predictive utility of several models (Carlsson et al. , 2011; Haddad et al. , 2020). Second, our study examined only GPCRs. The results might in principle be different for other classes of drug targets. However, GPCRs have very diverse binding pockets, which have evolved to binding an extremely broad range of ligands, ranging from very small molecules to peptides and proteins, with high specificity (Venkatakrishnan et al. , 2013). Our conclusions thus likely apply to many non-GPCR drug targets—and GPCR targets alone account for roughly half of drug discovery projects. We also note that, for GPCRs specifically, one can often improve docking performance by using a model or an experimentally determined structure in the activation state to which a given ligand preferentially binds (Heo and Feig, 2022; Lee et al. , 2022).

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: 1 and NCIMB700965 were aligned to the NCIMB8826 genome in Meg(). Insoluble iron reduction assays Request a detailed protocol Cells were collected by centrifugation at 10,000 g for 3 min, washed twice in phosphate-buffered saline (PBS), pH 7. 2 ( and adjusted to an optical density (OD) at 600 nm (OD600nm) of 2 in the presence of 2. 2 mM ferrihydrite (Schwertmann and Fischer, 1973; Stookey, 2002) and 2 mM ferrozine (Sigma-Aldrich). Where indicated, 55 mM glucose or mannitol, 20 μg/mL DHNA, and riboflavin were added. After 3 hr incubation at 30 °C, the cells were collected by centrifugation at 10,000 g for 5 min and the absorbance of the supernatant was measured at 562 nm with a Synergy 2 spectrophotometer (). Quantities of ferrihydrite reduced were determined using a standard curve containing a 2-fold range of FeSO4 (Sigma-Aldrich) (0. 25 mM to 0. 016 mM) and 2 mM ferrozine. The FeSO4 was dissolved in 10 mM cysteine-HCl () to prevent environmental re-oxidation of Fe2+ to Fe3+ in the standard curve. For testing iron reduction activity of cells with a DHNA concentration of 0. 01 μg/mL in the medium, iron(III) oxide nanop5. Splicing-by-overlap extension (SOEing) PCR was used to combine PCR products as previously described (Heckman and Pease, 2007). PCR products were digested with restriction enzymes or SalI () for plasmid ligation and transformation into E. coli DH5α. The resulting plasmids were then introduced to L. plantarum NCIMB8826 by electroporation. Erythromycin-resistant mutants were selected and confirmed for plasmid integration by PCR (see Supplementary file 5 for primer sequences). Subsequently, deletion mutants were identified by a loss of resistance to erythromycin, PCR (see Supplementary file 5 for primer sequences) confirmation, and DNA sequencing ( Bioelectrochemical reactors (BES) construction, operation, and electrochemical techniques Request a detailed protocol L.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: See the review by Lunine et al. (2020) for further discussion of the astrobiological relevance of Titan. See 9. 3. 2. 1 for a discussion of such life as we don't know it on Titan. 7. 2. 6. Ganymede and CallistoJupiter's two largest moons, Ganymede and Callisto, share many characteristics and are both of astrobiological interest. Ganymede is widely believed to possess a subsurface ocean. Callisto may also possess an ocean. Each moon is larger than Earth's moon and has a low density, consistent with large quantities of water + ice in their makeup (Schubert et al. , 2004). Unlike Ganymede, Callisto is likely not fully differentiated (Anderson et al. , 2001), but dominant ice at the surface suggests that it has differentiated enough to form an ocean that may persist today. Three characteristics common to both moons are influential to considerations of their possible habitability: their ancient surfaces, presence of magnetic induction signals, and high-pressure ices deep in their interiors. The surfaces of Ganymede and Callisto are extensively cratered, to the point of saturation in many areas (Pappalardo et al. , 2004). A wide variety of organic molecules have been identified on the surfaces of both moons (McCord et al. , 1997). These molecules may have been emplaced by exogenous sources, such as impacts, or endogenous sources, such as tectonic activity. However, both moons have very old surfaces. Callisto exhibits no apparent endogenic activity, suggesting a surface age over 4 billion years everywhere. Ganymede's surface age is probably at least 1 billion years everywhere, with some regions as much as 4 billion years old (Showman and Malhotra, 1999). Although the younger terrain on Ganymede may have been resurfaced at some point in that moon's history, it must have taken place very long ago (Showman et al. , 2004). Therefore, cycling of material between the surfaces and possible oceans of these bodies likely does not happen, and surface composition may not be informative of ocean composition. Ganymede has an intrinsic magnetic field that creates a mini-magnetosphere, largely shielding its surface from Jupiter's intense radiation belts (Kivelson et al. , 1997).

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: In this study, we did not limit the ligands docked to each structure or model to those that preferentially bind one specific activation state. We made this choice for several reasons: many other classes of drug targets do not have well-defined activation states; in practical applications, the preferred activation state for a given ligand may not be known when one docks it; and AF2 does not produce models in specific activation states by default. Third, we have not examined performance of the full range of available computational docking methods (Pagadala et al. , 2017). Our results are, however, consistent across the three docking methods we examined: and Rosetta docking. In each case, AF2 models yield docking accuracy similar to that of traditional models and substantially worse than that of experimentally determined structures. Our results have important implications for practitioners of structure-based drug discovery. Our findings suggest that, despite dramatic recent improvements in protein structure prediction, structural models (in particular, AF2 models) yield substantially poorer accuracy than experimentally determined structures in prediction of ligand-binding modes. Moreover, when a reasonable structural template is available—as is typically the case—AF2 models should not be expected to yield significantly better pose prediction accuracy than traditional models. Indeed, with sufficient effort, an expert may well be able to build a traditional template-based model that yields better performance than an AF2 model. Despite these findings, we believe that AF2 and other recently developed protein structure prediction methods will prove valuable in certain structure-based drug discovery efforts. Up-to-date AF2 models for any human protein are readily available for download (Tunyasuvunakool et al. , 2021; Varadi et al. , 2022). In contrast, expertise is required to build a decent template-based model, and up-to-date, downloadable repositories of such models are not available for all drug targets. Also, in the relatively rare cases when no structural template is available for a drug target, approaches like AF2 may be the only realistic option short of solving a structure experimentally. Our results also point to opportunities for developing improved computational modeling methods. Existing deep-learning methods for protein structure prediction were developed with the aim of maximizing structural accuracy for models. We find that the RMSD of a model—a classic structural accuracy metric—is not a good predictor of the accuracy that model yields for pose prediction.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: plantarum NCIMB8826 strains were grown overnight (approximately 16–18 hr) from glycerol stocks in MRS. Cells were harvested by centrifugation (5200 g, 12 min, 4 °C) and washed twice in PBS. When L. plantarum wild-type EET activity versus the Δndh2 (MLES100) and ΔpplA (MLES101) deletion mutants was compared, cells were grown as described and the number of cells was normalized across the three strains prior to inoculation in the BES. The bioreactors consisted of double-chamber electrochemical cells (Adams & Chittenden, Berkeley, CA) (Figure 1B) with a cation exchange membrane (CMI-7000, Membranes International, Ringwood, NJ) that separated them. A three-electrode configuration was used consisting of an Ag/AgCl sat KCl reference electrode (), a titanium wire counter electrode, and a 6. 35-mm-thick graphite felt working electrode (anode) of 4 × 4 cm () with a piece of Ti wire threaded from bottom to top as a current collector and connection to the potentiostat. We used a Bio-Instruments (TN, USA) potentiostat model VSP-300 for performing the electrochemical measurements (chronoamperometry). The bioreactors were sterilized by filling them with ddH2O and autoclaving at 121 °C for 30 min. The water was then removed and replaced with 150 mL of filter sterilized mMRS or mCDM media for the working electrode chamber, and 150 mL of M9 medium (6. 78 g/L Na₂HPO₄, 3 g/L KH2PO4, 0. 5 g/L NaCl, 1 g/L NH4Cl) (BD) for the counter electrode chamber. Both media of the working electrode chamber were supplemented with 20 μg/mL DHNA or 0. 01 μg/mL diluted 1:1 in DMSO:ddH2O where appropriate. To test the role of bd-cytochrome, heme was added in a final concentration of 10 μg/mL (diluted 1:1 in DMSO: ddH2O).

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: Galileo measurements (Kivelson et al. , 2002) and UV images of Ganymede's auroras (Saur et al. , 2015) are consistent with the presence of an ocean, but definitive proof of a subsurface ocean is lacking. Callisto shows no intrinsic magnetic field, but instead it shows a relatively strong induced magnetic field (Zimmer et al. , 2000). Initially, this condition was attributed to a subsurface ocean, but research examining the plasma environment has suggested that induction purely in Callisto's ionosphere may be able to account for the entire observed field (Hartkorn and Saur, 2017; Liuzzo et al. , 2017). Water−rock interactions are likely critical to the possible habitability of Ganymede and Callisto. However, these moons are so large and the pressures at depths consistent with their likely oceans are so great that exotic phases of water are formed, known as high-pressure ices (Journaux et al. , 2020). Layers of ice below the oceans could be detrimental to both origin-of-life scenarios and ongoing habitability, as they may stifle chemical interaction at the water−rock interface. However, the properties of high-pressure ices, especially for relevant ocean compositions, are not understood well enough to rule out complex dynamics such as upward “snow” in the presence of high salinity (Vance et al. , 2014). Convection in the high-pressure ices may also facilitate contact between the ocean and silicates (Kalousová et al. , 2018). Heat escaping from the interior may drive the formation of dense brine layers that underlie the high-pressure ices and sustain water−rock contact (Vance et al. , 2018), potentially providing abodes for life. Although the structures of both Ganymede and Callisto present challenges to conceiving of them as habitable worlds, each may yet contain a subsurface ocean with the ingredients needed to sustain life. If the interiors of these icy ocean worlds support life, life may be quite common indeed. 7. 2. 7. Other icy worlds7. 2. 7. 1. CeresCeres is the only extant dwarf planet in the asteroid belt, making it the closest dwarf planet to the Sun.

Output: corroborate


Input: Claim: Taxation is always harmful to economic growth. [SEP] Text: AbstractWe investigate theoretically and empirically the relationship between capital taxation and economic growth. Using a long cross-country panel data set going back to 1965 and employing a variety of econometric techniques, we document that greater reliance on capital taxation, measured in different ways, is not negatively associated with growth rates. Exploring potential heterogeneity in this relationship across countries, we find that capital taxation and growth rates tend to be positively related for developed countries, but for developing countries the relationship is in most cases statistically insignificant. To rationalize these empirical findings we propose a multi-country innovation-based growth model where innovations spill over from leading to lagging economies. In the context of this model we demonstrate that positive rates of capital taxation can increase the long-run growth rate in leading economies where the engine of growth is domestic innovation activity. However, this is not the case in lagging economies where growth is driven by imitation of existing innovations from the technology frontier. Similar content being viewed by others Capital taxation, investment, growth, and welfare 2014. This is particularly important, as it allows us to exploit changes in tax policies over time. The data also extend beyond current OECD members to cover several developing countries from Asia, Africa and Latin America. Combining these data with standard national accounts data from the Table, we assess whether and to what extent greater reliance on capital taxation is harmful for economic growth. We perform this assessment using a variety of econometric techniques. These include the standard fixed-effect panel regressions, as well as the panel error-correction techniques developed by Pesaran et al. (1999). The latter allow us to exploit the annual frequency of our data and separate the short-run from the long-run impact of capital taxation. To eliminate potential endogeneity concerns, due to feedback from economic growth on the tax structure as well as due to possible omitted variables, we also document estimation results using the difference and the system generalized methods of moment (GMM) estimators proposed by Arellano and Bond (1991) and Blundell and Bond (1998), respectively. The results that we obtain do not support the standard theory prescriptions. We find that shifts in the tax burden toward capital, conditional on the overall level of taxation, do not systematically reduce rates of economic growth. In many specifications, the association between capital taxation and growth rates is in fact positive and in the remaining ones it is not statistically different from zero.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: The medium in the working electrode chamber was continuously mixed with a magnetic stir bar and N2 gas was purged to maintain anaerobic conditions for the course of the experiment. The applied potential to the working electrode was of +0. 2 V versus Ag/AgCl (sat. KCl) (). Reactors run under OC conditions were similarly assembled but kept at open circuit and used as control for non-current circulating conditions. Once the current stabilized, the electrochemical cells were inoculated to a final OD600 of 0. 12–0. 15 with the cell suspensions prepared in PBS. Current densities are reported as a function of the geometric surface area of the electrode (16 cm2). The bioreactors were sampled by taking samples under sterilized conditions at different time points for subsequent analysis. The samples for organic acids analyses were centrifuged (15,228 g, 7 min) and the supernatant was separated for High-Chromatography (HPLC) assessments. Samples for ATP and NAD+/NADH analyses were flash frozen in a dry ice/ethanol bath. Metabolite analysis Request a detailed protocol Organic acids, ethanol, and sugar concentrations were measured by HPLC (Agilent, 1260 Infinity), using a standard analytical system (Shimadzu, Kyoto, Japan) equipped with an column (Bio-Rad, HPX-87H 300 × 7. 8 mm) heated at 60 °C. The eluent was 5 mM of sulfuric acid, used at a flow rate of 0. 6 mL min–1. We used a refractive index detector 1260. A five-point calibration curve based on peak area was generated and used to calculate concentrations in the unknown samples. The following standards were included in the HPLC measurements: acetate, formate, pyruvate, malate, lactate, succinate, oxalacetate, fumarate, ethanol, acetoin, butanediol, mannitol, and glucose. No gaseous products were measured. BES biomass growth determination Request a detailed protocol Bioreactors were shaken to remove the cells attached to the working electrode and afterwards sampled to measure viable cells (colony forming units [CFUs]) and total biomass (dry weight). Samples for CFU enumeration were collected under sterile conditions at the time of inoculation and at the time of approximately maximum current density.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: It has astrobiological significance due to the potential presence of past and/or presently habitable conditions (Castillo-Rogez et al. , 2020). Results from the Dawn mission to Ceres (2015 − 2018) demonstrated that this water-rich body has experienced a dynamic history of water–rock interactions, which likely are still occurring today. The spectral identification of phyllosilicates and carbonates on Ceres demonstrates that primary volcanic minerals were aqueously altered (Milliken and Rivkin, 2009; et al. , 2016; Carrozzo et al. , 2018). Small deposits of organic molecules have also been identified on the surface of Ceres (et al. , 2017). There is evidence that Ceres may currently have liquid water in the subsurface. Occator crater on Ceres contains evidence for recent—perhaps ongoing—surface brine emplacement, spurred by its parent impact event (et al. , 2020; Raymond et al. , 2020). Evidence for the presence of a subsurface brine pocket beneath Occator crater comes from gravity anomaly mapping (Raymond et al. , 2020), spectral identification of hydrated sodium chloride on the dome (et al. , 2020), and surface morphological expressions of recent aqueous activity (Nathues et al. , 2020; Schenk et al. , 2020; Schmidt et al. , 2020; Scully et al. , 2020), all acquired during Mission 2. Brine reservoirs can be preserved on this relatively small, heat-deprived body if ∼35% or more of the crust is composed of methane clathrate hydrate, which is a strongly thermally insulating material (Castillo-Rogez et al. , 2019). Prospects for a habitable environment in the subsurface of Ceres are certainly higher than in any other object in the asteroid belt, and clear evidence for past water–rock interactions also indicates that Ceres could have previously been habitable. 7. 2. 7. 2. The moons of UranusUranus has five large moons. From nearest to farthest from the planet, they are Miranda, Ariel, Umbriel, Titania, and Oberon, all of which orbit near the rotational equator of Uranus. They are likely natural satellites, formed from the same planetary nebula as the planet.

Output: corroborate


Input: Claim: Taxation is always harmful to economic growth. [SEP] Text: We then explore whether the estimated effect is potentially heterogeneous across countries. Separating the countries based on their level of development, we provide evidence that the association between capital taxation and growth tends to be more positive in high-income countries in our sample and less positive or even negative in low-income countries. We further document that these empirical findings are robust to the specific measure of capital taxation that we employ, to the exact way we distinguish between high- and low-income countries and to the inclusion of other variables that influence the relationship between capital taxation and economic growth as controls. To rationalize our empirical findings, we propose a variant of the multi-country innovation-based growth model of Aghion and Howitt (1992). The model allows for capital accumulation so that we can analyze the link between capital taxation and innovation, which is the main engine of growth in the model. It also incorporates technology transfer, as in Aghion et al. (2005) and Acemoglu et al. (2006), with innovations produced in leading economies spilling over to lagging economies. In the model, there are two channels through which capital taxation can influence economic growth. The first is by shifting the tax burden away from labor taxation, which reduces the market size for new innovations and has an adverse effect on domestic rates of innovation. The second one is by financing productive government spending, which raises the productivity of innovating firms. Using this model, we study the effects of capital taxation on the long-run equilibrium level and the growth rate of output for different economies which vary in their proximity to the technology frontier. As our analysis demonstrates, starting from a benchmark equilibrium with zero capital taxation, a shift to positive capital taxation can increase the long-run growth rate, either when this comes with a corresponding reduction in labor taxation or when the additional tax revenue is used to finance productive government spending. These effects, however, apply only in the case of leading economies which actively engage in innovation. This is because in leading economies lower labor taxation and more productive government spending increase the rate of long-run growth by stimulating innovation. In the case of lagging economies, there is no innovation taking place domestically and economic growth is driven by the imitation of existing innovations developed in leading economies. Thus, any change in capital taxation does not alter the ability of the country to tap on the existing global stock of innovations or the long-run rate of economic growth, which is effectively exogenous.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: Samples were serially diluted (1:1000 to 1:1000000) in sterile PBS and plated on MRS for CFUs enumeration after overnight incubation at 30 °C. Dry weight was determined using a 25 mL sample collected at approximately maximum current density. Cells were harvested by centrifugation (5250 g, 12 min, 4 °C) and washed twice in 50 mL ddH2O. Afterwards cells were resuspended in 1 mL of ddH2O and transferred to microfuge tubes (previously weighted). Cells were harvested by centrifugation (5250 g, 12 min, 4 °C), and the tubes were then transferred to an evaporator to remove humidity. The microfuge tubes were then cooled in a desiccator for 30 min and the weight of each tube was measured to determine cell weight. The difference between the weight of each tube with the pellet and before containing it allowed us to determine the dry weight/mL. RNA-seq library construction and transcriptome analysis Request a detailed protocol L. plantarum NCIMB8826 was grown in triplicate to exponential phase (OD600 1. 0) at 37 °C in mMRS with or without the supplementation of 20 μg/mL DHNA and 1. 25 mM ferric ammonium citrate. Cells were collected by centrifugation at 10,000 g for 3 min at 4 °C, flash frozen in liquid N2 and stored at –80 °C prior to RNA extraction as previously described (Golomb et al. , 2016). Briefly, frozen cell pellets were resuspended in cold acidic phenol:chloroform:isoamyl alcohol (pH 4. 5) [125:24:1] () before transferring to 2 mL screw cap tubes containing buffer (200 mM NaCl, 20 mM EDTA), 20% SDS, and 300 mg 0. 1 mm zirconia/silica beads. RNA was extracted by mechanical lysis with an MP Fastprep bead beater () at 6. 5 m/s for 1 min. The tubes were centrifuged at 20,000 g at 4 °C for 3 min and the upper aqueous phase was transferred to a new tube.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: Uranus orbits the Sun at a distance of nearly 20 AU, so this frigid system receives nearly 400 times less insolation than Earth. However, evidence for an ocean in Pluto's subsurface (7. 2. 7. 4) suggests that the habitability of one or more uranian moons is plausible. All we know of the Uranus system comes from measurements by the Voyager 2 mission and remote observations from Earth, and these are not sufficient to determine the presence or absence of subsurface oceans. The large, natural moons of Uranus appear to have engaged in orbital resonances that resulted in their current orbital arrangement (Ćuk et al. , 2020). Extensive faulting on the surface of Miranda suggests past heating events akin to present-day heating of Europa (Beddingfield et al. , 2015). Evidence for relict tidal heating is also seen in Miranda's 1-billion-year-old coronae features (Plescia, 1988; Beddingfield and Cartwright, 2020). Ammonia detected on the surface of Ariel is indicative of recent geological activity because this species is expected to be destroyed on short timescales (Cartwright et al. , 2020). Even a small amount of ammonia mixed into their oceans may allow Titania and Oberon to retain liquid layers up to the present (Hussmann et al. , 2006). Models assuming simple primordial compositions of silicates and water predict that an ocean in Miranda would have frozen out by the present era (Hussmann et al. , 2006). However, the presence of volatile clathrates or other insulating materials could support the persistence of liquids by providing thermal insulation and adding rigidity to the ice, both of which inhibit solid-state convection and therefore heat loss (Croft, 1987; Castillo-Rogez et al. , 2019; Kamata et al. , 2019). Evidence indicates that Saturn's moon Titan and the dwarf planets Ceres and Pluto each have methane clathrates that are expected to impede solid-state convection in ice, leading to inefficient cooling that slows the freeze-out of subsurface oceans. The presence of ammonia on the surface of Ariel suggests a similar role for volatiles that may aid in retaining heat (Cartwright et al. , 2020). Uranus applies strong magnetic oscillations to its inner moons (Arridge and Eggington, 2021; Weiss et al. , 2021).

Output: corroborate


Input: Claim: Taxation is always harmful to economic growth. [SEP] Text: The remainder of this paper is organized as follows. Section 2 provides a brief summary of the theoretical and empirical literature investigating the relationship between capital taxation and economic growth. Section 3 discusses our data set as well as our empirical strategy. Section 4 reports our regression results. Section 5 presents our theoretical model, while Sect. 6 describes the equilibrium of the model. Lastly, Sect. 7 offers some concluding remarks and discusses some policy implications. 2 Literature reviewMost of the literature on capital taxation and economic growth originates from the seminal theoretical contributions of Judd (1985) and Chamley (1986). Within the framework of the standard optimal growth model of Ramsey (1928), Cass (1965) and Koopmans (1965), both authors demonstrate that the taxation of capital has strong negative effects on capital accumulation and ultimately leads to a lower level of capital and output. This implies that in equilibrium capital should be taxed at a zero rate, a conclusion that, although striking, is general and robust to different specifications. As shown by Atkeson et al. (1999), the Chamley–Judd result will naturally emerge in any model where taxes are restricted to be linear and the government is assumed to be benevolent and unable to commit to future taxes. Footnote 2These results also extend to several endogenous growth models, as exemplified by Jones et al. (1993), Milesi-Ferretti and Roubini (1998) and Aghion et al. (2013). Within this class of models, though, there are setups in which the optimal tax rate on capital may differ from zero. et al. (1993) demonstrate, capital taxation may be growth enhancing if the resulting revenue is used to fund productive government spending. Similarly, Aghion et al. (2013) show that in an innovation-based growth model, taxing capital can increase growth rates by allowing the government to limit the adverse effect of high labor taxation. Innovation-based growth models also imply that different forms of capital taxation can have different effects on growth. Peretto (2003), for example, highlights that corporate income taxation can be growth enhancing while asset income taxation is growth retarding. Similarly, Peretto (2007), Abel (2007) and Anagnostopoulos et al. (2012) show that the taxation of dividends and retained earnings do not have the same effects on growth and that shifting the corporate tax burden from the latter to the former can boost growth rates.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: The aqueous phase was extracted twice with chloroform:isoamyl alcohol [24:1] (), The aqueous phase was then transferred to a new tube for RNA ethanol precipitation (Green and Sambrook, 2020). RNA was then quantified on a Nanodrop 2000c (ThermoFisher), followed by double DNAse digestion with the Turbo DNA-free Kit (Invitrogen) according to the manufacturer’s protocols. The quality of the remaining RNA was checked using a Bioanalyzer RNA 6000 () (all RIN values > 9) and then quantified with the Qubit 2. 0 (). For reverse-transcription PCR (RT-PCR), 800 ng RNA was converted to cDNA with the c() according to the manufacturer’s protocols. Quantitative RT-PCR was performed on a 7,500 Fast Real-Time PCR System (Applied Biosystems) using the (ThermoFisher) and RT-PCR primers listed in Supplementary file 5. The 2-ΔΔCt method was used for relative transcript quantification using rpoB as a control (Livak and Schmittgen, 2001). For sequencing, ribosomal-RNA (rRNA) was depleted from 4 μg RNA using the RiboKit v2 with specific probes for prokaryotic rRNA (ThermoFisher) following the manufacturer’s instructions. RNA was then fragmented to approximately 200 bp, converted to cDNA, and barcoded using the NEBnext Ultra-directional RNA for Illumina () with NEOligos for Illumina (1) (Biolabs) following the manufacturer’s protocols. cDNA libraries containing pooled barcoded samples was run across two lanes of a HiSeq400 () on two separate runs for 150 bp paired-end reads ( An average of 36,468,428 raw paired-end reads per sample was collected (Supplementary file 6). The DNA sequences were quality filtered for each of the 12 samples by first visualizing with FastQC (ver. 0. 11. 8) (Andrews, 2010) to check for appropriate trimming lengths, followed by quality filtering with Trimmomatic (ver. 0. 39) (Bolger et al. , 2014). Remaining reads then were aligned to the NCIMB8826 chromosome and plasmids using Bowtie2 (ver. 2.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: If oceans persist within the moons Miranda, Ariel, or Umbriel, future missions may be able to use magnetic signals to detect or even characterize these oceans (Cochrane et al. , 2021). The larger, outer moons Titania and Oberon are subjected to weaker magnetic oscillations and spend significant portions of their orbits outside the uranian magnetosphere (Paty et al. , 2020). Magnetic signals are not expected to be as useful for probing for oceans at the outer moons. The potential for subsurface oceans in these moons suggests that habitability in planetary systems may extend far beyond the habitable zone. However, a more complete understanding of the prospects for life on these bodies awaits future exploration. 7. 2. 7. 3. TritonTriton is the largest moon of Neptune and bears a number of intriguing characteristics relating to habitability. Neptune is the farthest planet from the Sun, so Triton receives little warming in the form of sunlight. However, imagery from the Voyager 2 mission shows a mysterious “cantaloupe terrain” that implies a possibly very young surface (Schenk and Zahnle, 2007). Dark streaks scattered across the south polar region have been identified as plumes of material erupting from the surface (see Fig. 7. S6; Soderblom et al. , 1990). The source of the heating causing the geologic activity is not known, but surface features show evidence of active and extensive resurfacing (Stern and McKinnon, 2000) that may be the result of substantial warming that could sustain an ocean. Triton orbits in a retrograde direction, unlike other large moons. The unusual orbital configuration of Triton and the arrangement of other satellites of Neptune indicates that Triton likely formed in the Kuiper Belt, similar to Pluto, and was subsequently captured by Neptune (e. g. , Agnor and Hamilton, 2006). If the orbit of Triton was highly elliptical upon capture, then tidal heating from circularization over time, along with radiogenic heating, could have sustained a liquid, subsurface ocean (Martin-Herrero et al. , 2018). Such an ocean could be only a few tens of kilometers below the icy surface (Ruiz, 2003) and, similar to Enceladus (7. 2.

Output: corroborate


Input: Claim: Taxation is always harmful to economic growth. [SEP] Text: Optimal rates of capital taxation are also shown to be positive in various models with heterogeneous agents. Aiyagari (1995), for example, demonstrates that this is the case in the presence of incomplete insurance markets and borrowing constraints. Saez (2013) and Golosov et al. (2013) provide a similar result in an environment of income inequality due to unobserved heterogeneity across agents. In an overlapping generations model, Conesa et al. (2009) and Jacobs and Bovenberg (2009) show that positive capital taxation is warranted as it allows the government to reduce distortionary labor taxation which harms younger generations and hampers human capital accumulation. Finally, Cozzi (2004), Gordon and Li (2009) and Acemoglu et al. (2011) provide examples of how capital taxation can be growth enhancing by easing various political constraints of the government. Footnote 3In parallel with the development of this extensive theoretical literature, a related literature has emerged investigating empirically the relationship between capital taxation and economic growth. An important challenge in these empirical studies is measuring capital taxation, as pinning down this form of taxation is not as straightforward in practice as it is in theory. Most of the existing studies have focused on the impact of corporate taxation, which constitutes one clear form of capital taxation. Following this approach, Lee and Gordon (2005) find that statutory corporate tax rates are negatively correlated with growth rates across countries, whereas Arnold et al. (2011) find the same result for the ratio of corporate to total taxation. Similarly, Djankov et al. (2010) show that high effective corporate tax rates have also a negative impact on investment, foreign direct investment, and entrepreneurial activity. These findings appear in line with the theoretical conclusions of Chamley and Judd. Employing broader measures of capital taxation, however, leads to less clear-cut results. For example, in a cross-country panel, Mendoza et al. (1997) estimate the impact on growth of effective tax rates on capital income stemming from dividends, royalties, interest, rents and property and find that it is not statistically different from zero. Easterly and Rebelo (1993) obtain similar results in the context of simple cross-sectional regressions. More recent studies by Widmalm (2001), Angelopoulos et al. (2007) and Arachi et al. (2015) investigating the impact of different capital tax instruments on growth rates also find the relationship to be weak and non-robust.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: 3. 5) in the [-sensitive] mode (Langmead and Salzberg, 2012). The resulting ‘. sam’ files containing aligned reads from Bowtie2 were converted to ‘. bam’ files with Samtools (ver 1. 9) (Li et al. , 2009) before counting aligned reads with FeatureCounts in the [-- stranded = reverse] mode (ver. 1. 6. 4) (Liao et al. , 2014). Reads aligning to noncoding sequences (e. g. rRNA, tRNA, trRNA, etc. ) were excluded for subsequent analyses. Differential gene expression based on culture condition was determined with DESeq2 (Love et al. , 2014) using the Wald test in the R-studio shiny app DEBrowser (ver 1. 14. 2) (Kucukural et al. , 2019). Differential expression was considered significant with a False-discovery-rate (FDR)-adjusted p-value < 0. 05 and a Log2 (fold-change) >0. 5. Clusters of (COGs) were assigned to genes based on matches from the eggNOG (ver. 5. 0) database (Huerta-Cepas et al. , 2019). Redox probe assays Request a detailed protocol Hamilton oxidation-reduction potential (ORP) probes () were inserted into air-tight Pyrex () bottles containing mMRS supplemented with 20 μg/mL DHNA and/or 1. 25 mM ferric ammonium citrate and incubated in a water bath at 37 °C. A custom cap for the Pyrex bottles was 3D printed with polylactic acid filament (2. 85 mm diameter) such that the ORP probe threads into the cap and an o-ring seal can be used to provide an air-tight seal between the probe and the cap. The ORP was allowed to equilibrate over 40 min before L. plantarum NCIMB8826, Δndh2 (MLES100), or ΔpplA (MLES101) were inoculated at an OD600 of 0. 10. Two uninoculated controls were used to measure baseline ORP over time. The ORP data was collected via Modbus TCP/IP protocol () into a database () and analyzed in (). pH was measured using a SevenEasy pH meter ().

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: 4), could be the source of the plumes observed by Voyager 2 coming from Triton, although these could also be the result of rapid vaporization of subsurface ices (Smith et al. , 1989). Few constraints exist for the composition and structure of both the surface and subsurface on Triton. Thus, future missions capable of measuring the plumes and the bulk composition of Triton are necessary to constrain the presence of a subsurface ocean and potential habitability. 7. 2. 7. 4. Pluto2015, NASA's spacecraft flew past Pluto (Stern et al. , 2015) and showed it to be an icy body with a geologically active surface. The surface age is possibly less than 10 million years in places (Grundy et al. , 2016; Moore et al. , 2016), with CH4, N2, and even haze p7. 2. 8. Mercury and the Moonnor the Moon are expected to be habitable today, although there is evidence that both bodies contain ice in some locations on their surfaces. Discussion of the habitability characteristics (e. g. , the presence of water) for these bodies is expanded in the supplementary material. 7. 2. 9. Giant planetsGiant planets are typically not thought to be habitable, mainly due to strong winds that cycle material between very high and very low pressures and temperatures relative to those found at Earth's surface (Ingersoll et al. , 2000). Discussion of habitability for giant planets is expanded in the supplementary material. 7. 2. 10. Habitability of exoplanetsCharacterization of exoplanets is an important frontier in the search for life beyond Earth. Over the past two decades, thousands of confirmed and candidate exoplanets have been detected, mostly from dimming of the parent star when the planet passes between Earth and the star, called a transit (see 8. 4. 1). Transits yield an estimate of the size and orbital period, and complementary techniques can give an estimate of the mass of a planet. Of the planets that are detected, multiple factors narrow the list of candidates that may have habitable conditions, such as the planet's size and composition. These factors can be combined to yield a single metric for the prevalence of habitable planets or Earth-like exoplanets, often referred to as ηEarth; these factors are described in more detail in 8. 4. 2.

Output: corroborate


Input: Claim: Taxation is always harmful to economic growth. [SEP] Text: If taxation is generally harmful for growth, an increase in capital taxation not matched by a corresponding reduction in some other tax would always be expected to be harmful for growth as well. By keeping the total level of taxation fixed, the specific impact of an increase in the extent of capital taxation can be assessed. A higher share of capital taxation in total taxation or a higher average or marginal rate of capital taxation would thus imply that a country has shifted the burden of taxation more toward capital relative to other forms of taxation. 3. 2 DataTo estimate the above specification, we use tax data provided by the OECD. Specifically, from the database we obtain information on total tax revenue as well as the amounts of tax revenue coming from different forms of taxation. The data cover the years since 1965, although for several countries data are only available for a subset of this time period. In total, we have tax data for 77 countries, which include all current OECD members, as well as several Asian, African and countries. We combine these tax data with national account information for these 77 countries provided by the Table, version 9. 0 to construct an unbalanced annual panel data set covering the years from 1965 to 2014. A list of the countries included in our data set is provided in “Section A” of 4. 1 Baseline resultsHaving discussed the nature of the data and our empirical strategy, we now turn to the presentation of our estimation results. Table 1 displays the results from the estimation of our main regression specification (1) by means of ordinary least squares. The first column of this table shows the estimation results for a specification that does not include any capital taxation measure. The results suggest that our dynamic-panel specification fits the data very well with a within R-squared that exceeds 0. 9. The estimated coefficients have the expected signs and are statistically significant at conventional levels, with the exception of population growth. The coefficient on the lagged value of output per capita is positive and less than one, signifying the presence of conditional convergence (Islam 1995). The coefficient on the investment share is positive suggesting a strong effect of investment spending on growth. This also holds for the growth rate of human capital. Finally, the coefficient of the total taxation share is negative underscoring primarily the adverse effect that tax distortions have on growth rates (Kneller et al. 1999).

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: Cells were collected at either 24 hr or at the greatest ORP difference between the wild-type and mutant strains (ΔmVmax) by centrifugation at 10,000 g for 3 min and used for ferrihydrite reduction analyses. ATP and NAD+/NADH quantification Request a detailed protocol Frozen cell pellets were suspended in PBS and lysed by mechanical agitation in a FastPrep 24 (MP Biomedicals) at 6. 5 m/s for 1 min. The cell lysates were then centrifuged at 20,000 g for 3 min at 4 °C. ATP and NAD+ and NADH in the supernatants were then quantified with the (ThermoFisher) and the Promega NAD/NADH-(), respectively according to the manufacturers’ instructions. Inductively coupled plasma-mass spectrometry (ICP-MS) Request a detailed protocol L. plantarum was inoculated in mMRS with or without 20 μg/mL DHNA and 1. 25 mM ferric ammonium citrate at an OD600 of 0. 10 for 3. 5 hr. Cells were then collected by centrifugation at 10,000 x g for 3 min and washed twice in PBS to remove cell-surface-associated metals. Viable cell numbers were enumerated by plating serial dilutions on MRS laboratory culture medium and the resulting cell materials were digested by incubating at 95 °C for 45 min in a 60% concentrated trace metal grade HNO3, allowed to cool, then diluted with MilliQ water to a final concentration of 6% HNO3. The contents were quantified with internal standards with an Agilent 7,500Ce ICP-MS () for simultaneous determination of select metals () at the UC Center for Spectrometry ( Kale juice fermentation assay Request a detailed protocol Green organic kale purchased from a market (Whole Foods) was washed with tap water and air dried for 1 hr as previously recommended (Kim, 2017). A total of 385 g of the leaves and stems were shredded with an electric food processor in 1 L ddH20. The kale juice was then diluted with 0. 35 L ddH2O and autoclaved (121 °C, 15 min). The juice was then centrifuged under sterile conditions at 8000 rpm for 20 min and the supernatant was collected.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: The distribution of observed planets is bimodal, with most planets categorized either as rocky or gaseous (see Fig. 3. 6). The density of smaller, rocky planets seems to be approximately fixed, consistent with a relatively fixed ratio of iron and silicates (Dressing et al. , 2015). Gaseous planets are very likely not habitable (7. 2. 9), but smaller gaseous planets may follow common pathways as they evolve that may cause them to become habitable as they lose their gas envelope (Dorn et al. , 2019; Rogers and Owen, 2021). This is supported by the consistent density of rocky planets, many of which may be evaporated cores of sub-Neptunes (Luger et al. , 2015). Sub-Neptunes are medium-sized planets with a radius between 1. 7 and 4 times that of Earth, and their greater volatile inventory suggests that they may be a common source of potentially habitable water worlds. The prevalence of ice as a planetary building block implies that water-rich super-Earths (planets of 1 to about 1. 7 Earth radii) may be abundant (Raymond et al. , 2004; Zeng et al. , 2019). While numerous planets have been detected in stellar habitable zones (see 7. 1. 4. 1 in the supplementary material), no planet has been confirmed as inhabited or even habitable. This inability to constrain exoplanet habitability arises because current telescopes are unable to characterize the atmospheres and surfaces of small, rocky planets, which are necessary observations to constrain surface habitability. Detecting signs of habitability and possibly life on exoplanets will likely require the use of telescopes currently under construction, such as ground-based extremely large telescopes (ELTs) or future space-based telescopes such as NASA's Observatory, which is based on the Observatory (HabEx) and Large UV/Optical/IR Surveyor () space telescope mission concepts. See 8. 4 for additional details on the detection and characterization of habitable and potentially inhabited exoplanets. There are already many planetary system candidates for future telescopes to target in the search for habitability and life beyond Earth. In particular, the red dwarf star systems (Anglada-Escudé et al. , 2016) and -1 (Gillon et al. , 2017) provide promising exoplanets for studying planetary habitability.

Output: corroborate


Input: Claim: Taxation is always harmful to economic growth. [SEP] Text: Footnote 4Table 1 Estimation results with different capital taxation measuresFull size tableAdding in column (2) the GDP share of corporate taxation instead of the GDP share of total taxation we now observe an interesting pattern. While its inclusion hardly affects the estimated coefficients of the other variables, the coefficient estimate of the corporate tax share is positive and statistically significant at the 1% level. This implies that conditional on the values of the standard growth determinants, a shift in the tax structure toward greater capital taxation is not harmful but beneficial for economic growth. In column (3) we include in the specification our first main measure of capital taxation, the ratio of corporate taxation in total taxation, controlling this time for the share of total taxation in GDP. This way we can better disentangle the effect of capital taxation on growth from that of total taxation. As discussed in the previous section, in this case the coefficient estimate on the corporate tax ratio reflects the effect of an increase in corporate taxation that does not increase the total tax share. This would correspond to an increase in corporate taxation that would be revenue neutral and which would be achieved by a simultaneous reduction in other forms of taxation. Such an increase would reflect a policy shift by the government toward a greater reliance on corporate taxation as a source of revenue. Here we again observe a positive and highly significant coefficient estimate. In columns (4) and (5) of Table 1, we estimate the same specification using instead our other two main measures of capital taxation, the broad tax ratio and the effective tax rate. In both cases, we see a qualitatively similar pattern. The coefficient estimates for these two capital measures are positive as well, although in column (4) the estimate that we obtain is below conventional levels of statistical significance. Yet, in neither case we see increases in capital taxation in the form of a higher tax ratio or a higher effective rate to be strongly negatively associated with economic growth. In the final two columns of the table, we estimate our main regression specification employing as a measure of capital taxation first the top marginal rate and then the effective marginal rate of corporate income taxation in each country. In both cases, the estimation is based on a smaller sample of countries due to data availability. Nevertheless, using also these variables, we do not see a negative association with growth rates. In column (6) the coefficient estimate that we obtain is positive but statistically insignificant. In column (7) the obtained coefficient is positive and statistically significant.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: A rifampicin-resistant variant of L. plantarum NCIMB8826-R (Tachon et al. , 2014) (grown for 19 hr in MRS medium at 37 °C, 50 μg Rif/mL) was inoculated to an estimated final OD of approximately 0. 05, and DHNA (20 μg/mL) was added where appropriate. Cells were collected and washed as previously described for the bioelectrochemical assays in mCDM. The anodic chambers of bioreactors assembled as previously described (anode of 4. 3*6 cm) were filled with 125 mL of the inoculated kale juice and incubated at 30 °C purged with N2. After 1 hr, the anodes were polarized to 0. 2 V versus Ag/AgCl (sat. KCl) (EET conditions) or kept at open circuit (OC, no EET). Viable cells were measured by plating 10-fold serial dilutions in MRS agar plates with 50 μg/mL of Rif. a detailed protocol The total electrons harvested on the anode were estimated by integrating the area (charge) under the chronoamperometric curve (current response (A) over time (s)), which was corrected by subtracting the current baseline obtained before L. plantarum was added to the system. This obtained charge was then converted to mol of electrons using the Faraday constant (96,485. 3 A*s/mol electrons). Data accession numbers Request a detailed protocol L. plantarum RNA-seq data are available in the (SRA) under BioProject accession no. PRJNA717240. A list of the completed Lactobacillales genomes used in the DNA sequence analysis is available in the repository at Add a comment + Open annotations. The current annotation count on this page is being calculated. Data availability L. plantarum RNA-seq data are available in the (SRA) under BioProject accession no. PRJNA717240. A list of the completed Lactobacillales genomes used in the DNA sequence analysis is available in the repository at All other data generated or analysed during this study are included in the manuscript and supporting files. The following data sets were generated (2021) 717240.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: hosts the closest potentially habitable exoplanet to Earth, and -1 contains multiple rocky planets in its habitable zone. Other systems with rocky exoplanets in the habitable zone exist (Kane et al. , 2016), and future missions will likely be necessary to constrain the habitability of such worlds. A critical uncertainty that both and -1 share stems from the larger fraction of energy being emitted at the shortest wavelengths (including X-ray and ultraviolet radiation) compared to more massive stars like the Sun (e. g. , France et al. , 2016). Smaller stars are also more likely to intermittently flare, emitting tens to hundreds of times more energy than usual (e. g. , Davenport et al. , 2016). The amount and type of high-energy radiation received by a planet has implications for the origin of life (e. g. , Ranjan et al. , 2017). Additionally, high-energy radiation can drive the escape of a planet's atmosphere (see 3. 4. 1. 5). Given the higher fluxes received by potentially habitable planets orbiting smaller stars, those planets could lose tens of Earth oceans of water during their lifetimes (e. g. , Fujii et al. , 2017). This could limit the duration of habitable conditions on these planets or even allow initially gas-dominated planets to become habitable (e. g. , Luger et al. , 2015). Given the preponderance of known planets orbiting smaller stars (e. g. , Dressing and Charbonneau, 2015) like and -1, understanding how stellar high-energy radiation impacts planetary habitability will be the focus of future work in bounding exoplanet habitability. This is not the only outstanding stellar question, however, as these planets face an additional hurdle stemming from their M-class hosts. Small stars take a much longer time to settle onto the stellar main sequence, an observed relationship between stellar temperature and luminosity that most stars follow (e. g. , Babusiaux et al. , 2018). As a star contracts out of a protostellar nebula, it must shed gravitational energy until it begins fusing hydrogen into helium in the core (see 3. 1. 1. 3). For smaller stars, this transition can take tens of millions of years, during which time any rocky planets within the conventional habitable zone would lose substantial amounts of water (e. g.

Output: corroborate