Input: Claim: Pollution can be completely eliminated by using current technologies. [SEP] Text: Skip to main contentScientific AmericanSign inSeptember 1, 200511 min readEliminated? Market economics and globalization are lifting the bulk of humanity out of extreme poverty, but special measures are needed to help the poorest of the poorD. SachsAlmost everyone who ever lived was wretchedly poor. Famine, death from childbirth, infectious disease and countless other hazards were the norm for most of history. Humanity's sad plight started to change with the Industrial Revolution, beginning around 1750. New scientific insights and technological innovations enabled a growing proportion of the global population to break free of extreme poverty. Two and a half centuries later more than five billion of the world's 6. 5 billion people can reliably meet their basic living needs and thus can be said to have escaped from the precarious conditions that once governed everyday life. One out of six inhabitants of this planet, however, still struggles daily to meet some or all of such critical requirements as adequate nutrition, uncontaminated drinking water, safe shelter and sanitation as well as access to basic health care. These people get by on $1 a day or less and are overlooked by public services for health, education and infrastructure. Every day more than 20,000 die of dire poverty, for want of food, safe drinking water, medicine or other essential needs. For the first time in history, global economic prosperity, brought on by continuing scientific and technological progress and the self-reinforcing accumulation of wealth, has placed the world within reach of eliminating extreme poverty altogether. This prospect will seem fanciful to some, but the dramatic economic progress made by China, India and other low-income parts of Asia over the past 25 years demonstrates that it is realistic. Moreover, the predicted stabilization of the world's population toward the middle of this century will help by easing pressures on Earth's climate, ecosystems and natural resources--pressures that might otherwise undo economic gains. On supporting science journalismIf you're enjoying this 2000. A dedicated cadre of development agencies, international financial institutions, nongovernmental organizations and communities throughout the developing world already constitute a global network of expertise and goodwill to help achieve this objective. This past January my colleagues and I on the U. N. published a plan to halve the rate of extreme poverty by 2015 (compared with 1990) and to achieve other quantitative targets for reducing hunger, disease and environmental degradation.

Output: contrast


Input: Claim: Symbiotic relationships in microbiomes can influence health. [SEP] Text: Ο μεγάλος αριθμός νέων τάξων που περιγράφηκαν στην παρούσα διδακτορική διατριβή υπογραμμίζει την αναγκαιότητα για την εφαρμογή προσεγγίσεων που βασίζονται στην απομόνωση με σκοπό την αποκάλυψη της πραγματικής ποικιλότητας των συμβιωτικών κυανοβακτηρίων.

Output: pass


Input: Claim: Pollution can be completely eliminated by using current technologies. [SEP] Text: In my recent book, of Poverty, I argue that a large-scale and targeted public investment effort could in fact eliminate this problem by 2025, much as smallpox was eradicated globally. This hypothesis is controversial, so I am pleased to have the opportunity to clarify its main arguments and to respond to various concerns that have been raised about it. as UsualEconomists have learned a great deal during the past few years about how countries develop and what roadblocks can stand in their way. A new kind of development economics needs to emerge, one that is better grounded in science--a "clinical economics" akin to modern medicine. Today's medical professionals understand that disease results from a vast array of interacting factors and conditions: pathogens, nutrition, environment, aging, individual and population genetics, lifestyle. They also know that one key to proper treatment is the ability to make an individualized diagnosis of the source of illness. Likewise, development economists need better diagnostic skills to recognize that economic pathologies have a wide variety of causes, including many outside the traditional ken of economic practice. � [break]Public opinion in affluent countries often attributes extreme poverty to faults with the poor themselves--or at least with their governments. Race was once thought the deciding factor. Then it was culture: religious divisions and taboos, caste systems, a lack of entrepreneurship, gender inequities. Such theories have waned as societies of an ever widening range of religions and cultures have achieved relative prosperity. Moreover, certain supposedly immutable aspects of culture (such as fertility choices and gender and caste roles) in fact change, often dramatically, as societies become urban and develop economically. Most recently, commentators have zeroed in on "poor governance," often code words for corruption. They argue that extreme poverty persists because governments fail to open up their markets, provide public services and clamp down on bribe taking. It is said that if these regimes cleaned up their acts, they, too, would flourish. Development assistance efforts have become largely a series of good governance lectures. The availability of cross-country and time-series data now allows experts to make much more systematic analyses. Although debate continues, the weight of the evidence indicates that governance makes a difference but is not the sole determinant of economic growth. According to surveys conducted by Transparency International, business leaders actually perceive many fast-growing Asian countries to be more corrupt than some slow-growing African ones.

Output: contrast


Input: Claim: Symbiotic relationships in microbiomes can influence health. [SEP] Text: Τα στελέχη των συμβιωτικών κυανοβακτηρίων διερευνήθηκαν για τη δυνατότητα να παράγουν βιοδραστικές ενώσεις και πραγματοποιήθηκε εκτίμηση της βιοδραστικότητας των εκχυλισμάτων τους (αντιμικροβιακής και αντικαρκινικής). Στα στελέχη συμβιωτικών κυανοβακτηριών ανιχνεύτηκαν γονίδια που εμπλέκονται στη μη ριβοσωμική πολυκετιδική σύνθεση (PKS).

Output: pass


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: It is important to outline that the compounds produced by the cells, metabolizing the substrate, can modify the system, producing also compounds that can stimulate the growth of symbiotic species or inhibit the growth of antagonistic microorganisms. The conversion of carbohydrates to metabolites as acetic acid, lactic acid or CO2 implies the acidification of the system. The contemporary pH decrease and the presence of sugar (osmotic stress) stimulate the exopolysaccharides (EPSs) production. In fact, in sourdough EPSs can be involved in acid tolerance of sourdough LAB [98]. EPSs are long-chain polysaccharides consisting of branched, repeating units of sugars or sugar derivatives. These sugar units are mainly glucose, galactose and rhamnose, in different ratios [99]. The presence of EPSs in the system can create a novel stress to the cells. The inclusion of cells within biofilm can increase their resistance to unfavorable environmental factors such as extreme temperature, low pH and osmolarity, the changes in the texture can induce in LAB also specific stress responses. For example in yogurt production, the acidification by LAB implies proteins coagulation and thereby changes in the viscosity of the milk. In L. bulgaricus, during the acid adaptation present in the fermentation milk to obtain yogurt, some cellular changes were observed: the chaperones and ClpL were induced and ClpC was repressed [100]. Some genes involved in the biosynthesis of fatty acids were induced (fabH, accC, fabI), while the genes involved in the mevalonate pathway of isoprenoid synthesis (mvaC, mvaS) were repressed [101, 102]. The changes in Aw value are depending not only on EPSs production by LAB after the exposition to acidic and osmotic stress, but also on the ingredients composition and on the step of fermentation. Considering cheese, the Aw decreases during manufacture and ripening as a result of dehydration, salting, and production of water-soluble solutes from glycolysis, proteolysis, and lipolysis; the cheese Aw values range from 0. 70 for extra hard cheeses to 0. 99 for fresh, soft cheeses, such as cottage cheese, while semi-hard cheeses have Aw values of around 0. 90.

Output: corroborate


Input: Claim: Pollution can be completely eliminated by using current technologies. [SEP] Text: This capital flight includes not only financial capital but also the human variety, in the form of skilled workers--doctors, nurses, scientists and engineers, who frequently leave in search of improved economic opportunities abroad. The poorest countries are often, perversely, net exporters of capital. technology to overcome these handicaps and jump-start economic development exists. Malaria can be controlled using bed nets, indoor pesticide spraying and improved medicines. Drought-prone countries in Africa with nutrient-depleted soils can benefit enormously from drip irrigation and greater use of fertilizers. Landlocked countries can be connected by paved highway networks, airports and fiber-optic cables. All these projects cost money, of course. Many larger countries, such as China, have prosperous regions that can help support their own lagging areas. Coastal eastern China, for instance, is now financing massive public investments in western China. Most of today's successfully developing countries, especially smaller ones, received at least some backing from external donors at crucial times. The critical scientific innovations that formed the underpinnings of the were bankrolled by the Rockefeller Foundation, and the spread of these technologies in India and elsewhere in Asia was funded by the U. S. and other donor governments and international development institutions. � [break]We in the U. N. have listed the investments required to help today's impoverished regions cover basic needs in health, education, water, sanitation, food production, roads and other key areas. We have put an approximate price tag on that assistance and estimated how much could be financed by poor households themselves and by domestic institutions. The remaining cost is the "financing gap" that international donors need to make up. For tropical Africa, the total investment comes to $110 per person a year. To place this into context, the average income in this part of the world is $350 per annum, most or all of which is required just to stay alive. The full cost of the total investment is clearly beyond the funding reach of these countries. Of the $110, perhaps $40 could be financed domestically, so that $70 per capita would be required in the form of international aid. Adding it all up, the total requirement for assistance across the globe is around $160 billion a year, double the current rich-country aid budget of $80 billion. This figure amounts to approximately 0. 5 percent of the combined gross national product (GNP) of the affluent donor nations.

Output: contrast


Input: Claim: Symbiotic relationships in microbiomes can influence health. [SEP] Text: Στελέχη που ανήκουν στα γένη Leptothoe, Metis και Aegeococcus εμφάνισαν ενδιαφέρουσες βιοδραστικότητες (αντιμικροβιακές ή/και αντικαρκινικές).

Output: pass


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: However, the food system is usually a consortium of different microorganisms: for example in bakery products and in fermented sausages the fermentation is carried out both by yeasts and LAB; the formers can therefore consume the amount of oxygen present in the mix, allowing the growth of LAB. The same thing happens for fermented vegetables, where naturally occurring Gram negative bacteria and yeast rapidly remove the oxygen, promoting the rapid predominance of Lactobacilli. Some secondary metabolites such as bacteriocins can play a role in LAB performances and metabolism, affecting also the total population and ecology of fermented foods [107, 108]. Bacteriocins are antimicrobial peptides or proteins produced by bacteria that can be active on different microorganisms, depending on their structure. LAB belonging to the genera are known to produce bacteriocins with both narrow and broad inhibitory spectra [109]. The use of functional LAB starter cultures (eg. bacteriocinogenic starter cultures), well adapted to the environment and the process conditions applied, may contribute to the development of better controllable and more efficient production processes [110]. An example can be nisin, a peptide produced by L. lactis ssp. lactis, that has a narrow spectrum affecting primarily only Gram-positive bacteria and their spores, including lactic acid bacteria, Bacillus, Clostridium, Listeria, and Streptococcus. However some LAB such as Streptococcus thermophilus and L. plantarum are able to produce the enzyme nisinase, which neutralizes the antimicrobial activity of the peptide [111]. Therefore these LAB could be suitable for a co-fermentation with L. lactis. Another interesting case of bacteriocin production, as a consequence of oxidative stress and carbon dioxide exposure, has been reported [110]: oxidative stress and carbon dioxide are involved in the production of a specific bacteriocin, amylovorin L, by Lactobacillus amylovorus, able to inhibit other LAB species. During traditional sourdough fermentation, a decrease in redox potential of the rather firm mixture occurs. The oxygen initially present is consumed by Candida spp. or converted into hydrogen peroxide or water, thereby creating microaerophilic or anaerobic environment in which the growth of the desired LAB is favored.

Output: corroborate


Input: Claim: All languages are equally complex and structured. [SEP] Text: AbstractThe simple answer to both questions in the title of this paper: No. We concentrate on three key aspects of the banking system's difficulties during the 2001–02 crisis. Two are related to bank behavior (increasing dollarization of the balance sheet and expanding exposure to the government), and the other is related to the degree by which banks were hurt by depositor p2001. We find that there was substantial cross-bank variation, that is, not all banks behaved equally nor were hurt equally by the macroeconomic shocks they faced during the run-up to the crisis. Furthermore, using panel data estimation, we find that depositors were able to distinguish high-risk from low-risk banks, and that individual bank's exposure to currency and government default risk depended on fundamentals and other bank-specific characteristics. Finally, our results have implications for the existence of market discipline in periods of stress, and for banking regulation, which may have led banks to underestimate some of the risks they incurred. This is a preview of subscription content, log in via an institution to check access. Access this 34. 9910 units per month Download 39. 95 Price excludes VAT (USA) Tax calculation will be finalised during checkout. Instant access to the full 6. 7 percent. Argentina is less open than most countries. During 1990–95, total trade represented 16 percent of GDP, whereas it was 37 percent in Mexico and 46 percent in Chile. Moreover, as pointed out by the Office of the IMF (2004), the differences in Argentina's degree of openness in relation to other hard peg economies are even more pronounced; for a sample of eight hard peg economies throughout the world, total trade averaged 96 percent of GDP. Analysts as well as the government agreed that the exchange rate was overvalued, although there was no consensus on the degree of overvaluation. As the study by the Office (2004) reports, by spring of 2000 overvaluation was estimated at 7 percent by Goldman Sachs, 13 percent by JP Morgan, and 17 percent by Deutsche Bank. Ex post, Perry and Servén (2002) estimated the Argentine peso to be overvalued by 55 percent by 2001. In particular, de la Torre, Levy-Yeyati, and Schmukler (2003); della Paolera and Taylor (2003); and Levy-Yeyati, Martínez Pería, and Schmukler (2004).

Output: contrast


Input: Claim: Symbiotic relationships in microbiomes can influence health. [SEP] Text: Με σκοπό να κατανοήσουμε καλύτερα τη βιολογία των συμβιωτικών με σπόγγους κυανοβακτηρίων, αλληλουχήθηκαν τα γονιδιώματα των στελεχών που παρουσίασαν το μεγαλύτερο μεταβολικό δυναμικό και ανήκουν στο γένος Leptothoe (Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115), και πραγματοποιήθηκε συγκριτική γονιδιωματική ανάλυση με άλλα στελέχη του ίδιου γένους (είτε συμβιωτικά με άλλους οργανισμούς, είτε μη συμβιωτικά).

Output: pass


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: While in a large-scale sourdough type II fermentation currently the use of dough mixture with high dough yield is exploited. This sourdough has to be stirred to liberate part of the carbon dioxide produced to prevent running over. During mixing, oxygen is incorporated into the dough. Also, the development of yeast and hence the production of carbon dioxide is favored in continuously stirred sough mixtures with high water content. Elevation of the airflow rates leading to oxidative stress conditions resulted in an enhanced specific amylovorin L production. Growth in the presence of carbon dioxide also increased the specific bacteriocin production. Mild aeration or a controlled supply of oxygen as well as growth in an environment containing high amounts of carbon dioxide might thus contribute to the competitiveness of L. amylovorus DCE471 in a sourdough ecosystem [110]. The production of plantaricin A by L. plantarum was also demonstrated in relation to a quorum sensing mechanism [79]. Another example of the influence of the process on LAB metabolism has been widely described [112]. monitored the evolution of the gene expression of L. plantarum IMDO 130201 during a sourdough process. In particular, the genes and the metabolites related to acidic stress were analyzed. It is interesting to highlight that during the pH decrease (production of lactic acid by L. plantarum) the genes coding for plantaricin production had higher levels of expression at low pH values, indicating that the bacteriocin production was activated under acid stress conditions by L. plantarum IMDO 130201 strain. The presence of the pheromone plantaricin A (PlnA) in a system inoculated with L. plantarum DC400 was also reported [79]. Biosynthesis of PlnA was variously stimulated depending on the microbial partner. In fact, L. sanfranciscensis DPPMA174 induced the highest synthesis of PlnA, which, in turn, determined lethal conditions for it. The proteome of L. sanfranciscensis DPPMA174 responded to the presence of PlnA. The up-regulation of 31 proteins related to stress response, amino acid metabolism, energy metabolism, membrane transport, nucleotide metabolism, regulation of transcription and cell redox homeostasis was found.

Output: corroborate


Input: Claim: Language can be perfectly translated without loss of meaning. [SEP] Text: The performance succeeded but they found the distance between the reality of colonized Joseon and the situation in the translated dramasin 1924 when they got into action as the professional theatrical company, Towolhoe's performance of translated drama had two characteristics one is that they concentrated their efforts on ‘the creative adaptation’ and the other is that they kept performing a enlightened work and an entertaining work together continuously on the same day. Towol hoe's ‘the creative adaptation’ is the way that the foreign original dramas were utilized in terms of the subject matters. Because according to the situation of colonized Joseon considerable parts were changed, there were much difference between the works performed and the original works. But the fundamental limits which translated dramas had, that is, alienation from the reality of colonized country were much solved and heightened the effect of performance. The reason they took the way of performing a enlightened work and an entertaining work together was that they responded the social request which thought much of the social role of drama. was the professional theatrical company, they could perform the works which passed through Japanese censorship. Despite their effort, they could not but perform only such works as Irish dramas and Yamamoto Yujo's Kill the Baby which adapted in Japan since the works beyond couldn't pass the censorship. As the result, entertaining works became relatively outstanding in the perfor mance of translated dramas. In the entertaining translated dramas, songs and dance were made active use of and the original works were often adapted according to the popular songs. Ariranggogae, the creative work performed on the November in 1929 was the summit in which the experience of Towolhoe's performance of translated dramas was all dissolved. This work began from the folk song Arirang which was prevalent throughout the country after the movie Arirang. This work passed the censorship, representing loving people's separation in the foreg round and connected with the phenomenon of abandoning farming those days. The reason why this work which didn't have anything new in contents succeeded was that Towolhoe had much experience in performance. Espe cially Arirang which Seok Kumseong, the actor sang maximized the drama tic effect in the performance. It was evaluated that Towolhoe's performance of translated dramas had a great contribution to forming and settling the modern drama of colonized Joseon.

Output: contrast


Input: Claim: Symbiotic relationships in microbiomes can influence health. [SEP] Text: Στα γονιδιώματα των συμβιωτικών με σπόγγους κυανοβακτηρίων παρατηρήθηκαν χαρακτήρες που σηματοδοτούν έναν συμβιωτικό τρόπο διαβίωσης, όπως η μείωση του μεγέθους του γονιδιώματος, αλλά και η παρουσία πρωτεϊνών που ομοιάζουν με αυτές των ευκαρυωτών.

Output: pass


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: In fact, probiotic lactobacilli encounter various environmental conditions upon ingestion by the host and during transit in the gastro intestinal tract (GIT). They need to survive to: 1) the harsh conditions of the stomach secretion generating a fasting pH of 1. 5, increasing to pH 3 to 5 during food intake; 2) the bile excreted by liver in small intestine represents another challenge for bacteria entering the GIT. Bile salts also seem to induce an intracellular acidification so that many resistance mechanisms are common for bile and acid stress. Indeed, the protonated form of Figure 3. Sourdough fermentation dynamics. Case of possible parallel phenomena interesting acid and osmotic stress. bile salts is thought to exhibit toxicity through intracellular acidification in a manner similar to those of organic acids like the lactic acid produced by the lactobacilli themselves. For a detailed overview of acid, bile, and other stress resistance mechanisms of lactobacilli, the reader is referred to more extensive review [113]. 3) In analogy to the stresses encountered by intestinal pathogens, they also encounter oxidative and osmotic stress in GI tract. 4) Interactions with other microbes and 5) Interactions with cells of the host immune system and the various antimicrobial products that they produce can also impose a serious threat for the probiotic microbes. Analogously to what described in food LAB, the phenomenon of cross-adaptation is often observed, i. e. , that adaptation to one stress condition also protects against another stress factor, implying some common mechanisms. In this respect, also for probiotic LAB non-actively-growing stationary-phase cells are generally more resistant to various stressors than early-log-phase cells. 5. 1. Maintaining integrity of the cell envelopeThe different macromolecules constituting the cell membranes and cell walls of lactobacilli have been shown to contribute to maintaining cell integrity during stress to various degrees. For example, low pH caused a shift in the fatty acid composition of the cell membrane of an oral strain of L. casei. Similarly, bile salts have been shown to induce changes in the lipid cell membrane of Lactobacillus reuteri CRL1098. The role of EPS in acid and bile resistance is less clear. However, EPS production has not been studied in detail after exposure to bile.

Output: corroborate


Input: Claim: Language can be perfectly translated without loss of meaning. [SEP] Text: Despite their effort, they could not but perform only such works as Irish dramas and Yamamoto Yujo's Kill the Baby which adapted in Japan since the works beyond couldn't pass the censorship. As the result, entertaining works became relatively outstanding in the perfor mance of translated dramas. In the entertaining translated dramas, songs and dance were made active use of and the original works were often adapted according to the popular songs. Ariranggogae, the creative work performed on the November in 1929 was the summit in which the experience of Towolhoe's performance of translated dramas was all dissolved. This work began from the folk song Arirang which was prevalent throughout the country after the movie Arirang. This work passed the censorship, representing loving people's separation in the foreg round and connected with the phenomenon of abandoning farming those days. The reason why this work which didn't have anything new in contents succeeded was that Towolhoe had much experience in performance. Espe cially Arirang which Seok Kumseong, the actor sang maximized the drama tic effect in the performance. It was evaluated that Towolhoe's performance of translated dramas had a great contribution to forming and settling the modern drama of colonized Joseon. It may fairly be said that the aim which its modern drama headed forward could be seen for the first time thanks to Towolhoe. KW - 토월회, 번역극, 창작적 번안, 식민지조선의 근대극, <아리랑고개> DO - 10. 17291/kolali. 2014. . 168. 012 UR - ER - 김재석 (2014). 토월회의 번역극 공연인식과 그 의미. 국어국문학, 168, 297 - 335. 김재석.

Output: contrast


Input: Claim: Symbiotic relationships in microbiomes can influence health. [SEP] Text: Μέσω αναλύσεων εξόρυξης γονιδιώματος (genome mining) εντοπίστηκε στα γονιδιώματα του γένους Leptothoe μεγάλος αριθμός συστοιχιών γονιδίων που εμπλέκονται στη βιοσύνθεση ενώσεων (περισσότερες από 100 συστοιχίες). Συμπερασματικά, υπογραμμίζεται το μεταβολικό δυναμικό των στελεχών του γένους και η ανάγκη για περαιτέρω διερεύνηση με σκοπό την ανακάλυψη νέων ενώσεων με φαρμακευτικό ενδιαφέρον.

Output: pass


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: University of Teramo, Teramo, Italy. 9. . . E2006TwoHfuranones as possible signaling molecules in Lactobacillus helveticus. Appl. Environ. Microbiol. 7260536061 10. . SGuerzoniM. E2007New signaling molecules in some Gram-positive and Gram-negative bacteria. Int. J. Food Microbiol. 1202533 11. . E2007Potential of high-pressure homogenization in the control and enhancement of proteolytic and fermentative activities of some Lactobacillus species. Food Chem. 102542550 12. GuerzoniM. 2007Generation of aroma compounds in sourdough: effects of stress exposure and lactobacilli-yeasts interactions. Food Microbiol. 24139148 13. . . E2008Influence of starch addition and dough microstructure on fermentation aroma production by yeasts and lactobacilli. Food Chem. 10812171225 14. MontanariCSado-kamdemS. LSerrazanettiD. IEtoaF. XGuerzoniM. E2010Synthesis of cyclopropane fatty acids in Lactobacillus helveticus and Lactobacillus sanfranciscensis and their cellular fatty acids changes following short term acid and cold stresses. Food Microbiol. 27493502 15. SerrazanettiD. INdagijimanaMSadoS. LCorsettiAVogelR. FEhrmannMGuerzoniM. E2011Acid stress-mediated metabolic shift in Lactobacillus sanfranciscensis LSCE1. Appl. Environ. Microbiol. 7726562666 16. KlaenhammerT. RBarrangouRBuckB. LAzcarate-perilM. AAltermannE2005Genomic features of lactic acid bacteria effecting bioprocessing and health. FEMS Microbiol. Rev. 29393409 17. van de (2002Stress responses in lactic acid bacteria. Antonie Leeuwenhoek. 82187216 18. Hörmann. F2006Comparative proteome approach to characterize the high-pressure stress response of Lactobacillus sanfranciscensis DSM 20451T.

Output: corroborate


Input: Claim: Languages evolve in a predictable and uniform manner. [SEP] Text: From the decomposition of trait responses, α-farnesene would be the most likely candidate for a trait under direct hoverfly selection. Other traits also had observed and direct responses aligned but their predictions were not significantly different from zero (benzaldehyde, 2-amino benzaldehyde, phenylacetaldehyde, phenylethyl alcohol, 1-butene-4-isothiocyanate) or did not include the observed change within their HPD (plant height, indole) (Table S6). The VOC indirect response components were all positive and not significantly different from zero (although not for α-farnesene). All morphological traits’ indirect responses were positive and significant (Fig. 2b; Table S6). Effects of genetic covariance on predicting evolutionary trajectoriesWe measured the overall constraining effect of genetic co-variation on the response to selection by comparing the angle θ between the selection response vector (△z) and the first PC of G (PC1, or gmax, see methods) with the angle γ between △z and the selection gradient (β). In the tall and short artificial selection experiments, the trait responses were strongly aligned with gmax, with θ angle of 8. 9 degree (95% HPD: 5. 5, 13. 7) and 20. 1 degree (95% HPD: 17. 5, 23. 5), respectively. Given the close association of gmax with the first trait axis (height) (Fig. 3c) and thus with the selection gradients under artificial selection, the angle γ between △z and β is 6. 8 and 16. 7 degree in tall and short, respectively. In contrast, under pollinator selection, △z is more aligned with gmax than β, with θ of 50. 6 degree (95% HPD: 44. 7, 55. 0) and 54. 3 degree (95% HPD: 52. 0, 57. 0), when compared to γ, equal to 62. 96 and 83. 2 degree for bumblebee and hoverfly treatments, respectively. Fig. 3Comparison of the size and orientation of the major and five first eigenvectors (PCs) of the G-matrices in the artificial selection experiment.

Output: pass


Input: Claim: Symbiotic relationships in microbiomes can influence health. [SEP] Text: In addition, this approach revealed that the photosynthetic communities of sponges are also consisted of eukaryotes; five strains of photosynthetic eukaryotes belonging to four different phyla (Bacillariophyta, Cercozoa, Rhodophyta, and Chlorophyta) were isolated and characterised. Aiming to further characterise the sponge-associated cyanobacterial strains, an extensive polyphasic approach (i. e. , a combination of molecular, morphological and ecological data) was performed. This approach resulted in the description of six new genera (Leptothoe, Rhodoploca, Cymatolege, Metis, Aegeococcus, and Thalassoporum) and ten new species (Le. sithoniana, Le. spongobia, Le. kymatousa, R. sivoneniae, C. spiroidea, C. isodiametrica, M. fasciculata, A. anagnostidisii, A. thuretii, T. komarekii) inside Synechococcales, and a new pleurocapsalean species (Xenococcus spongiosum). The considerable number of novel taxa characterised in this study highlighted the great cyanobacterial diversity living in association with the sponges, and emphasise the importance of employing polyphasic culture-dependent approaches in order to reveal the true sponge-associated cyanobacterial diversity. Further, the potential of sponge‐associated cyanobacteria strains for the production of bioactive compounds and the biological activity of their extracts were assessed. Genes encoding for non‐ribosomal polyketide synthases (PKSs) were detected in all strains, while strains belonging to Leptothoe, Metis, and Aegeococcus were found to have bioactivities (antimicrobial and/or cytotoxic). In order to better understand the biology of sponge-associated cyanobacteria, two draft genomes of the promising sponge-associated strains belonging to Leptothoe (Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115) were sequenced, and a comparative genomic analysis of host-associated and free-living members of this genus was performed.

Output: pass


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: I2001Oxidative stress and mechanisms of protection against it in bacteria. Biochem. Moscow. 6647648960. . P1998Oxygendependent regulation of the expression of the catalase gene katA of Lactobacillus sakei LTH677. Appl. Environ. Microbiol. 641359136561. . 2003Oxidative stress in Lactococcus lactis. Genet. Mol. Res. 2:348-359. 62. Bruno-bárcenaJ. MAndrusJ. MLibbyS. LKlaenhammerT. RHassanH. M2004Expression of a heterologous manganese superoxide dismutase gene in intestinal lactobacilli provides protection against hydrogen peroxide toxicity. Appl. Environ. Microbiol. 704702471063. JänschAKorakliMVogelR. FGanzleM. G2007Glutathione reductase from Lactobacillus sanfranciscensis DSM20451T: contribution to oxygen tolerance and thiol exchange reactions in wheat sourdoughs. Appl. Environ. Microbiol. 734469447664. . DMaguinE2000Acid- and multistress-resistant mutants of Lactococcus lactis: identification of intracellular stress signals. Mol. Microbiol. 3551752865. CotterP. DHillC2003Surviving the acid test: responses of Gram-positive bacteria to low pH. Microbiol. Mol. Biol. Rev. 6742945366. PieterseBLeerR. JSchuren FHJ, van der Werf MJ (2005Unravelling the multiple effects of lactic acid stress on Lactobacillus plantarum by transcription profiling. Microbiol. 1513881389467. PiuriMSanchez-rivasCRuzalS. M2005Cell wall modifications during osmotic stress in Lactobacillus casei. J. Appl. Microbiol. 98849568. PiuriMSanchez-rivasCRuzalS. M2003Adaptation to high salt in Lactobacillus: role of peptides and proteolytic enzymes. J. Appl. Microbiol.

Output: corroborate


Input: Claim: Languages evolve in a predictable and uniform manner. [SEP] Text: The relevance of predictions of evolutionary constraints depends on the constancy of patterns of genetic variance-covariance over time. Our study shows that constancy cannot be assured when selection strongly reduces the genetic variance of a trait, as during artificial selection for taller plants (see also [46, 53, 54]). Yet, using Gcontrol as an estimate of the ancestral G-matrix allowed us to make correct evolutionary predictions of the direction of selection responses in most cases. Had we used Gtall in the tall selection experiment, we would have badly underestimated the selection response of plant height and floral scents (results not shown). This illustrates two important points concerning the evolutionary significance of the structure of the G-matrix. First, changes in G can happen quickly, over just a few generations, and we have illustrated a rapid change in trait variance caused by selection. Second, despite those changes, estimation of G is still useful to make predictions of future trait changes over few generations. This can be useful to predict evolution and adaptation under rapid environmental changes, for instance, because the state of the G-matrix before a change in selection pressures will strongly influence the resulting evolutionary trajectory of a population, as we have shown here. The evolutionary significance of the structure of the G-matrix is still debated, especially regarding the interpretation of the constraining effects of the main eigenvectors of G (especially gmax). The debate, however, mostly crystallized on inferences of past evolutionary constraints from contemporary estimates of trait variance-covariance patterns. The retrospective use of G is questionable knowing how evolutionarily labile are patterns of variance-covariance, an important caveat already emphasized by Turelli [55]. Indeed, many processes may affect the evolution of trait variance and covariances because they depend on variation in allele frequencies in a population. As such, genetic drift [56] and fluctuating selection [57], have been shown to reduce the stability of the G-matrix, while migration [58], correlational selection [56], and mutation [56, 59] can improve its stability (reviewed in [60]). Those changes thus make retrospective use of G at the least dangerous, unless its long-term stability can be determined. Prospective use of G is potentially less sensitive to such variations when predicting short term selection responses.

Output: contrast


Input: Claim: Symbiotic relationships in microbiomes can influence health. [SEP] Text: 12681/eadd/48973 Διεύθυνση Handle ND48973 Εναλλακτικός τίτλοςSponges and cyanobacteria symbiotic relationships in the Sea ΣυγγραφέαςΚωνσταντίνου, Δέσποινα (Πατρώνυμο: Ιωάννης) Ημερομηνία2021 ΊδρυμαΑριστοτέλειο Πανεπιστήμιο Θεσσαλονίκης (ΑΠΘ). Σχολή Θετικών Επιστημών. Τμήμα Βιολογίας. Τομέας Βοτανικής.

Output: pass


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: SchneiderM1988Zur mikrobiologie von sauerkraut bei der vergärung in verkaufsfertige kleinbehältern. University, Stuttgart. 90. PedersonC. SAlburyM. N1969The sauerkraut fermentation. 824, Geneva, New York. 91. Ruiz-barbaJ. LGarrido-fernandezAJiménez-diazR1991Bactericidal action of oleuropein extracted from green olives against Lactobacillus plantarum. Let. Appl. Microbiol. 12656892. 1994Hydrolysis of oleuropein by Lactobacillus plantarum strains associated with olive fermentation. Appl. Environ. Microbiol. 6041424147 93. . . LRizzelloC. GViscontiA2005Study of Adhesion and Survival of Lactobacilli and Bifidobacteria on with the Aim of Formulating a Food. Appl. Environ. Microbiol. 714233424094. Ruiz-barbaJ. LJiménez-diazR1995Availability of essential B-group vitamins to Lactobacillus plantarum in green olive fermentation brines. Appl. Environ. Microbiol. 611294129795. OSullivanECondonS (1997Intracellular pH is a major factor in the induction of tolerance to acid and other stresses in Lactococcus lactis. Appl. Environ. Microbiol. 634210421596. SandersJ. WVenemaGKokJ1999Environmental stress responses in Lactococcus lactis. FEMS Microbiol. Rev. 2348350197. GuerzoniM. EGianottiASerrazanettiD. I2011Fermentation as a tool to improve healthy properties of bread”. In V. R. Preedy, R. R. Watson, & V. B. Patel, (Eds. ), Flour and breads and their fortification in health and disease prevention (385393London, Burlington, San Diego: Academic Press, Elsevier. 98. GänzleM.

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: Peer review processEditorsReviewer #1Reviewer #2Author ResponsePeer review processNot revised: Preprint includes the authors’ original preprint (without revision), an eLife assessment, public reviews, and a provisional response from the authors. Read more about eLife’s peer review process. of of AmericaReviewer #1 (Public Review): The authors assess the accuracy of AlphaFold2 (AF2) structures for small molecule ligand pose prediction versus the accuracy with traditional template-based homology models and experimental crystal structures (with a different ligand). They take a careful, rigorous approach leveraging the wealth of structural data around the GPCR protein family and using state-of-the-art docking methods. They find that binding sites are significantly more accurately modeled by AF2 compared to traditional template-based approaches, but this does not translate to greater accuracy in small-molecule docking pose prediction. The important findings around this conclusion have broad implications for the use of AF2 models in ligand binding pose prediction for proteins and drug design. Strengths: The strength of the work is the rigor and careful, thoughtful comparison that cleverly leverages the cut-off date of April 30th, 2018 used in the training of AF2. While the authors list their limited number of docking methods as a caveat, the fact that they use three state-of-the-art ligand docking methods is a strength of the work; many studies use just one. The rigorous analysis of the binding site RMSD and docked ligand pose RMSD is novel to my knowledge and is particularly insightful. Weaknesses: The authors are rigorous in their approach by using state-of-the-art workflows that are high-throughput in nature. However, human expert-refined models and expert selection from multiple models could improve the results of ligand pose prediction when using protein models. The authors alluded to this for traditional models but this can also be true when starting from AF2 models. This is difficult to test systematically and rigorously, however. One possible experiment is to explore whether using multiple AF2 models (there are five by default) would have an effect on pose accuracy, perhaps for selected examples such as NK1R, 5HT2A, and DRD1 to help build out the discussion further.

Output: contrast


Input: Claim: Symbiotic relationships in microbiomes can influence health. [SEP] Text: Εργαστήριο Βοτανικής Εξεταστική επιτροπήΓκέλης ΣπυρίδωνΒοουλτσιάδου ΕλένηFewer DavidΑμπατζόπουλος ΘεόδωροςΚωνσταντινίδης ΘεοφάνηςΠαντερής ΕμμανουήλΚαππάς Ηλίας Επιστημονικό πεδίοΦυσικές Επιστήμες ➨ Βιολογία ➨ Θαλάσσια βιολογία και Βιολογία γλυκών υδάτων Λέξεις-κλειδιάΣπόγγοι; Συμβιωτικά στελέχη κυανοβακτηρίων; Νέα γένη; Νέα είδη; Μεταβολικό δυναμικό; Συγκριτική γονιδιωματική ΧώραΕλλάδα ΓλώσσαΑγγλικά Άλλα στοιχεί

Output: pass


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: GSchwabC2009Ecology of exopolysaccharide formation by lactic acid bacteria: sucrose utilisation, stress tolerance, and biofilm formation. In: Ulrich, M. (Ed. ), Bacterial Polysaccharides- and Trends. Horizon Press. 99. WelmanA. DMaddoxI. S2003Exopolysaccharides from lactic acid bacteria: perspectives and challenges. Trends Biotechnol. 21269274 100. LimE. MEhrlichS. DMaguinE2000Identification of stress-inducible proteins in Lactobacillus delbrueckii subsp. bulgaricus. Electrophoresis. 2125572561101. 2007Acidification improves cryotolerance of Lactobacillus delbrueckii subsp. bulgaricus CFL1. J. Biotechnol. 128659667102. 2008Acid adaptation of Lactobacillus delbrueckii subsp. bulgaricus induces physiological responses at membrane and cytosolic levels that improves cryotolerance. J. Appl. Microbiol. 10510711080103. LiuS. QAsmundsonR. VGopalP. KHollandRCrowV. L1998Influence of Activity on by Lactococcus lactis subsp. cremoris at Different pH Values. Appl. Environ. Microbiol. 6421112116 104. . 1996The lactic acid stress response of Lactococcus lactis subsp. lactis. Curr. Microbiol. 33194199105. BroadbentJ. RLinC1999Effect of heat shock or cold shock treatment on the resistance of Lactococcus lactis to freezing and lyophilization. Cryobiology. 3988102 106. BehrJGänzleM. GVogelR. F2006Characterization of a highly hop-resistant Lactobacillus brevis strain lacking hop transport. Appl. Environ. Microbiol. 72648392107. 1993Detection and characterization of a bacteriocin produced by Lactobacillus plantarum C19. Can. J. Microbiol. 3911731179108. Jiménez-diazRRios-sanchezR.

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: Another possible weakness is that the authors focus only on GPCRs for reasons they state but make a good argument as to why the conclusions are likely to extend to other protein classes. Context: One of the most common and impactful uses of protein structures is in small molecule therapeutic chemical tool design. When no experimental structure is available, models are frequently used and such models include traditional template-based homology models and, more recently, AF2 models. AF2 is widely recognized as an inflection point in protein structure prediction due to the unprecedented accuracy of the protein structure models produced automatically. However, understanding whether this unprecedented accuracy translates to better small molecule ligand pose prediction has been an open question, and this study directly addresses the question in a systematic, rigorous approach. #2 (Public Review): While the question of 'are AlphaFold-predicted structures useful for drug design' has largely seen comparisons of AF versus experimental protein structures, this paper takes a less explored (but perhaps more practically important) angle of 'are AlphaFold-predicted structures any better than the previous generation of homology modeling tools' to the protein-ligand (rigid) docking problem. The conclusions of this work will be of largest interest to the audience less familiar with the precision required for successful rigid docking, while the expert crowd might find them obvious, yet a good summary of results previously shown in the literature. Further work, understanding the structural objectives/metrics that should be placed on future AlphaFold-like models for better pose prediction performance, would greatly expand the practicality of the observations made here. The main conclusion of the paper, that structural accuracy (expressed as RMSD) of the protein model is not a good predictor of the accuracy the model will show in rigid docking protein-ligand pose prediction, is a good reminder of the well-appreciated need for high-quality side chain placements in docking. The expected phenomenon of AlphaFold predicting 'more apo-like structures' is often discussed in the field, and readers should be cautious about drawing conclusions from the rigid (rather than flexible, as in some previous works) docking done here. The authors have very clearly communicated that the use of AlphaFold-generated structures in traditional docking might not be a good idea, and motivated that the time of a molecular designer might be better spent preparing a high-quality homology model.

Output: contrast


Input: Claim: Symbiotic relationships in microbiomes can influence health. [SEP] Text: αxvi, 206 σ.

Output: pass


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: MDesmazeaudMRuiz-barbaJ. LPiardJ. C1993PlantaricinSand T, two new bacteriocins produced by Lactobacillus plantarum LPCO10 isolated from a green olive fermentation. Appl. Environ. Microbiol. 5914161424109. KlaenhammerT. R1988Bacteriocins of lactic acid bacteria. Biochim. 70337349110. NeysensPDe VuystL2005Carbon dioxide stimulates the production of amylovorin L by Lactobacillus amylovorus DCE 471, while enhanced aeration causes biphasic kinetics of growth and bacteriocin production. Int. J. Food Microbiol. 105191202111. DavidsonP. MHarrisonM. A2002to Stresses by Food Preservatives, in Adaptation and Food Safety. Ed. A. E. Yousef and V. K Juneja. CRC Press112. 2011Adaptation of Lactobacillus plantarum IMDO 130201, a Isolate, to Growth in at Different pH Values through Expression. Appl. Environ. Microbiol. 7734063412 113. (2008Genes and Molecules of Probiotic Action. Microbiol. Mol. Biol. R. 72728764 114. JobinM. 1999Expression of the Oenococcus oeni trxA gene is induced by hydrogen peroxide and heat shock. Microbiol. 14512451251115. CapozziVArenaM. 2011The hsp 16 Gene of the acidophilus Regulated by Salt, as Revealed by (qRT-PCR) Analysis. Int. J. Mol. Sci. 1253905405116. PieterseB2006Transcriptome analysis of the lactic acid and NaCl-stress response of Lactobacillus plantarum Ph. D. thesis. Wageningen University, Wageningen, The Netherlands117. . DVolkerUHeckerM2001of the Response of Bacillus subtilis. J. Bacteriol. 18356175631118. WangJ. CZhangW. YZhongZWeiA. BBaoQ. HZhangYSunT.

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: The visual presentation of the conclusions is very clear but might leave the reader wanting a more in-depth discussion of which structural elements of the AF models lead to bad docking outcomes. For example, Fig. 3 presents an example of a very accurate AlphaFold prediction leading to the ligand being docked completely outside of the binding pocket. Close inspection of the Figure suggests a clash of the ligand with the slightly displaced tryptophan residue in the AF model that might be to blame, as can be confirmed by comparison of the model and PDB structure by the reader themselves but has not been discussed by the authors. Only a few examples of the systems used are shown even visually, leaving the reader unable to study more interesting cases in depth without re-doing the work themselves. The authors acknowledged that several recent studies exist in this space. They point out two advancements made in their work, worthy of further review. Similarly, it's important to evaluate the novelty of this work's claims vs previously available results, and the diversity of information made available to the reader. "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. " This is done by limiting the scope of the work to GPCRs whose structures became available only after the training date of AlphaFold (April 30, 2018), as well as not using templates available after that date during prediction. The use of a time limit seems less preferable than the approach taken in Ref. 1 of discarding templates above a sequence identity cutoff. On the other hand, the 'ablation test' performed in Ref. 2 showed no loss in accuracy when no templates were used at all. Authors should discuss in more detail whether these modeling choices could change anything in their conclusions and why they made their choices compared to those in previous work. "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. " Cross-docking is indeed a more appropriate comparison than self-docking (as done in previous works), and the observation that the accuracy of AF models is similar to that between different holo structures of the same protein is interesting.

Output: contrast


Input: Claim: Symbiotic relationships in microbiomes can influence health. [SEP] Text: , εικ. , πιν. , χαρτ. , σχημ. , γραφ. Ειδικοί όροι χρήσης/διάθεσηςΤο έργο παρέχεται υπό τους όρους της δημόσιας άδειας του νομικού προσώπου Corporation:Αναφορά Δημιουργού 3.

Output: pass


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: . P2012Transcriptome analysis of probiotic Lactobacillus casei during fermentation in soymilk. J. Ind. Microbiol. Biotech. 39191206119. AnandanS2006Genomic and for Stress Responses. In: Advances in Safety. V. Juneja, J. P. Cherry and M. H Tunick eds. ACS Books. 120. (2005Differential proteomic analysis in the study of prokaryotes stress resistance. Ann. Ist. Super. Sanità. 41459468121. NezhadM. HKnightMBritzM. L2012Evidence of changes in cell surface proteins during growth of Lactobacillus casei under acidic conditions. Food. Sci. Biotech. 21253260122. . FLeroiFTresseO2010Adaptation to Cold and of the Lactococcus piscium -4031. Appl. Environ. Microbiol. 7680118018123. JardinJMollé2012Quantitative proteomic analysis of bacterial enzymes released in cheese during ripening. Int. J. Food Micro. 1551928124. (2004Survey of bacterial proteins released in cheese: a proteomic approach. Int. J. Food Microbiol. 94185201125. GüellMYusELluch-senarMSerranoL2011Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat. Rev. Microbiol. 9658669126. 2012Lactobacillus casei combats acid stress by maintaining cell membrane functionality. J. Ind. Microbiol. Biotechnol. Accepted127. CodaRRizzelloC. GPintoDGobbettiM2012during of Cereal Flours, Appl. Environ. Microbiol. 7810871096128. (1998of Lactobacillus plantarum to Salt and Nonelectrolyte Stress. J. Bacteriol. 18047184723129. MehmetiIFaergestadE. . FHoloH2012Growth Rate-in Enterococcus faecalis: Effects on the Transcriptome and Proteome, and of Lactate Dehydrogenase. Appl. Environ. Microbiol. 78170176130.

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: Previous literature on cross-docking should however be discussed, and the well-known conclusions from it that small variations in side-chain positions, in otherwise highly similar structures, can lead to large changes in docked poses. It is important to realize that AlphaFold models are 'just another structure' - if previous literature is sufficient to show the sensitivity of rigid docking, doing it again on AF structures does not add to our understanding. Further, Ref. 3 might have already addressed the question of correlation between binding site RMSD and docking pose prediction accuracy - see e. g. 3 there (also Figure S15 in Ref. 2). Further, the authors should discuss the commonly brought up problem of AlphaFold generating 'more apo-like structures' - are the models used here actually 'holo-like' because of the low RMSDs? (what RMSD differences are to be expected between apo and holo structures of these systems? ) How are the volumes of the pockets affected? The position on this problem taken by previous works is worth mentioning - "much higher rmsd values are found when using the AF2 models (. . . ), which reflect the difficulties in performing docking into apo-like structures" in Ref. 1 and "computational model structures were predicted without consideration of binding ligands and resulted in apo structures" in Ref. 2. Because of this 'apo problem', Ref. 2 assumed that rigid docking (as done here) would not succeed and used flexible docking where "two sidechains at the binding site were set to be flexible". In fact, the reader of this new paper will be left to wonder if it is not simply presenting a subset of the results already seen in Ref. 2, where "the success ratios dropped significantly for them because misoriented sidechains prevented a ligand from docking (Figure S14)". While this conclusion is not made as clear in Ref. 2 as it is here, a comparison of Figures 4 and S14 there will lead the reader to the same conclusion, and more -- that flexible docking meaningfully improves the performance of AF models, and more so than homology models. Finally, certain data analyses present in previous works but not here should be necessary to make this work more informative to the readers: a) Consideration of multiple top poses, e. g. , in Ref.

Output: contrast


Input: Claim: Symbiotic relationships in microbiomes can influence health. [SEP] Text: 0 (CC-BY) Στατιστικά χρήσης ΠΡΟΒΟΛΕΣ Αφορά στις μοναδικές επισκέψεις της διδακτορικής διατριβής για την χρονική περίοδο 07/2018 - 07/2023. Πηγή: Google Analytics. ΞΕΦΥΛΛΙΣΜΑΤΑ Αφορά στο άνοιγμα του online αναγνώστη για την χρονική περίοδο 07/2018 - 07/2023. Πηγή: Google Analytics. ΜΕΤΑΦΟΡΤΩΣΕΙΣ Αφορά στο σύνολο των μεταφορτώσων του αρχείου της διδακτορικής διατριβής. Πηγή: Εθνικό Αρχείο Διδακτορικών Διατριβών.

Output: pass


Input: Claim: Europa’s subsurface ocean may harbor conditions suitable for life. [SEP] Text: 2632-3338/5/2/56 present best-fit values of porosity—and the corresponding effective thermal inertiae—determined from three different depths in Europa's near-subsurface (∼1–20 cm). The porosity of the upper ∼20 cm of Europa's subsurface varies between 75% and 50% (Γeff ≈ 50–140 J m−2 K−1 s−1/2) on the leading hemisphere and 50%–40% (Γeff ≈ 140–180 J m−2 K−1 s−1/2) on the trailing hemisphere. Residual maps produced by comparison with these models reveal thermally anomalous features that cannot be reproduced by globally homogeneous porosity models. These regions are compared to Europa's surface terrain and known compositional variations. We find that some instances of warm thermal anomalies are co-located with known geographical or compositional features on both the leading and trailing hemisphere; cool temperature anomalies are well correlated with surfaces previously observed to contain pure, crystalline water ice and the expansive rays of Pwyll crater. Anomalous regions correspond to locations with subsurface properties different from those of our best-fit models, such as potentially elevated thermal inertia, decreased emissivity, or more porous regolith. We also find that ALMA observations at ∼3 mm sound below the thermal skin depth of Europa (∼10–15 cm) for a range of porosity values, and thus do not exhibit features indicative of diurnal variability or residuals similar to other frequency bands. Future observations of Europa at higher angular resolution may reveal additional locations of variable subsurface thermophysical properties, while those at other wavelengths will inform our understanding of the regolith compaction length and the effects of external processes on the shallow subsurface. Export citation and abstract 4. 0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. 1. IntroductionThe surface of Europa, the smallest of the Galilean Satellites, is notable for its varied terrain units and hemispheric asymmetries—particularly when compared to its sister moons that are resurfaced by active volcanoes (Io), heavily cratered and relatively dark (Callisto), or somewhat intermediary (Ganymede) (see the reviews in Greeley et al.

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: 2, Figures 4 and S14 mentioned before, comparison of success rates in top 1 and top 3 docked poses add much context. b) Notes on the structural features preventing successful docking, see e. g. , in Ref. 1, Table 2 or in Ref. 4, Tables 2 and 4. This work has the potential to become an important piece of the puzzle, if deeper insights into the reasons for AF model failures are drawn by the authors. These could include a discussion of the problematic structural elements (clashes of side chain with ligands, missing interactions/waters, etc. ), potential solutions with some preliminary data (flexible docking, softening interactions, etc. ), or proposals for metrics better than RMSD to score the soundness of pockets generated by AF for docking. 1. Díaz-Rovira, A. M. , Martín, H. , Beuming, T. , Díaz, L. , Guallar, V. , & Ray, S. S. (2023). for Virtual Screening? Application of to AlphaFold2 Predicted Structures. Journal of and Modeling, 63(6), 1668-1674. 2. Heo, L. , & Feig, M. (2022). Multi-state modeling of G-protein coupled receptors at experimental accuracy. Proteins: Structure, Function, and Bioinformatics, 90(11), 1873-1885. 3. Beuming, T. , & Sherman, W. (2012). Current assessment of docking into GPCR crystal structures and homology models: Successes, challenges, and guidelines. Journal of and Modeling, 52(12), 3263-3277. 4. Scardino, V. , Di Filippo, J. I. , & Cavasotto, C. (2022). How good are AlphaFold models for docking-based virtual screening? [Preprint]. Chemistry. thank the reviewers and editor for their careful evaluation of our manuscript, and we appreciate their favorable assessment of our work. Below, we clarify a few points concerning the relationship between our study and previous studies evaluating ligand docking to protein models. As reviewer 2 correctly notes, several previous assessments of AF2 models have simply excluded templates above a sequence identity cutoff when using AF2 to predict structures.

Output: contrast


Input: Claim: Symbiotic relationships in microbiomes can influence health. [SEP] Text: ΧΡΗΣΤΕΣ Αφορά στους συνδεδεμένους στο σύστημα χρήστες οι οποίοι έχουν αλληλεπιδράσει με τη διδακτορική διατριβή. Ως επί το πλείστον, αφορά τις μεταφορτώσεις. Πηγή: Εθνικό Αρχείο Διδακτορικών Διατριβών. "Συμβιωτικές σχέσεις σπόγγων και κυανοβακτηρίων στο Βόρειο Αιγαίο" Πληκτρολογήστε το κείμενο της εικόνας!

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: How life began on Earth is unknown, yet the conditions relevant to possible origins are critical to understanding where habitable environments may be found. Our understanding of what constitutes a habitable environment on Earth has also changed over time and with better understanding of extremophiles. Based on modern ideas about life and habitability on Earth, in this 7. 1. FIG. 7. 1. Overview of the many interrelated factors and processes that affect considerations of habitability. Many factors may be grouped into multiple categories. CMEs = coronal mass ejections. Potentially habitable regions can be predicted based on the availability of basic requirements, such as the essential “” elements (2. 2. 2), mild temperatures and pressures, and limited ionizing radiation. In practice, it is much simpler to determine which environments are not habitable, because an environment outside the livable range of even one essential characteristic renders the system uninhabitable. For example, the surface of Venus is much hotter than known life can tolerate and nearly devoid of water (Taylor et al. , 2018). All life on Earth requires liquid water to grow and reproduce (2. 2. 2. 1). Therefore, it is reasonable to conclude that the hot and dry surface of Venus cannot currently support life as we know it. Conversely, it is difficult to verify whether an environment contains all life-essential ingredients. There are many potentially habitable environments in the (and beyond) that may have the requirements for life to survive, either now or in the past. Potentially habitable environments are discussed in more detail in 7. 2. It is important to note that discussion of habitability does not mean that the environment may support humans or other familiar forms of complex life. Most potentially habitable environments on other astronomical bodies are similar to environments that we would consider extreme on Earth (such extreme Earth environments are discussed in 6. 3). Extremophiles live at the boundaries of where known life can exist, and they are all microscopic (Pikuta et al. , 2007). For the majority of Earth's history, the only life-forms were single-celled organisms (see 5. 4. 2). This suggests that if we were able to take a snapshot of extant life in a habitable environment at some random point in the life-filled history of a planetary object, the observed life would most likely be microbial.

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: Such AF2 predictions are still informed by all structures in the PDB before April 30, 2018, because these structures were used to train AF2—that is, to determine the tens of millions of parameters (“weights”) in the AF2 neural network. Machine learning methods nearly always perform better when evaluated on the data used to train them than when evaluated on other data. For this reason, we consider AF2 models only for proteins whose structures were not used to train AF2—that is, for proteins whose structures were not available in the PDB before April 30, 2018. Previous papers (including Beuming and Sherman, 2012, have shown a clear correlation between the binding pocket RMSD of a protein model and pose prediction accuracy based on that model. Our main findings are unexpected in light of these previous reports: we find that AF2 models yield pose prediction accuracy similar to that of traditional homology models despite having much better binding pocket RMSDs, and that AF2 models yield substantially worse pose prediction accuracy than experimentally determined structures with different ligands bound despite having similar binding pocket RMSDs. Reviewer 2 also correctly notes that previous papers have described AF2 models as “apo models,” because these models do not include coordinates for bound ligands. As noted by the AF2 developers (e. g. , however, AF2 is designed to predict coordinates of protein atoms as they might appear in the PDB, and AF2 models are thus frequently consistent with structures in the presence of ligands even though those ligands are not included in the models. GPCR structures in the PDB, including those used to train AF2, nearly always contain a ligand in the orthosteric binding pocket. An AF2 model of a GPCR should thus not be viewed as an attempt to predict the GPCR’s structure in the unliganded (apo) state. Finally, we did not apply flexible docking in this study because previous work has found that standard flexible docking protocols typically improve pose prediction performance only when given prior information on which amino acid residues to treat as flexible. For example, previous studies that performed successful flexible docking to AF2 models generally used prior knowledge of the ligand’s experimentally determined binding pose to identify the residues to treat as flexible.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: Figure 1 with 3 supplements see all Download asset Open asset L. plantarum can reduce both Fe3+ and an anode through EET. (A) Reduction of Fe3+ (ferrihydrite) to Fe2+ by L. plantarum NCIMB8826 after growth in mMRS. The assays were performed in PBS supplemented with 20 µg/mL DHNA and/or 55 mM mannitol. Fe2+ was detected colorimetrically using 2 mM ferrozine. For L. plantarum inactivation, cells were incubated at 85℃ in PBS for 30 min prior to the assay. Significant differences were determined by one-way ANOVA with Tukey’s post-hoc test (n = 3), *** p < 0. 001. (B) Two-chambered electrochemical cell setup for measuring current generated by L. plantarum. (C) Current density production over time by L. plantarum in CDM supplemented with 20 µg/mL DHNA and/or 110 mM mannitol. The anode was polarized at +0. 2VAg/AgCl. The avg ± stdev of three biological replicates is shown. See also Figure 1—figure supplement 1 and Figure 1—figure supplement 2 and related data in Figure 1—source data 1. Figure 1—source data 1 Raw data of Figure 1A and B. Download elife-70684-fig1-data1-v2. xlsx Next, we investigated whether the ability of L. plantarum to reduce insoluble iron was altered by growth media. L. plantarum was able to reduce iron after growth in either complete (MRS) medium or chemically defined medium (CDM) (Figure 1—figure supplement 1B). Iron reduction was greater when mannitol, a sugar alcohol, rather than glucose, was provided as the sole carbon source in MRS (Figure 1—figure supplement 1B). However, reduction was highest when L. plantarum was incubated in mannitol-containing MRS (mMRS) with both DHNA and ferric ammonium citrate present (Figure 1—figure supplement 1D). The addition of riboflavin to the growth medium did not further increase iron reduction by L.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: It is possible that environments that have been habitable for far longer than Earth may never develop complex life with multicellular organisms. We cannot know with certainty, as we are still uncovering how life transitioned from entirely unicellular and microscopic to complex, multicellular life on Earth (see 5. 4. 3). Discussion of the many factors affecting planetary habitability is expanded in the supplementary material. 7. 2. Considerations for Habitable EnvironmentsThus far, the only known habitable environments are found on Earth. However, there are a number of potentially habitable environments scattered throughout the Solar System, many of which currently or in the past could resemble extreme environments on Earth (see 6. 3). The rocky planets Mars and Venus are especially compelling targets for understanding habitability due to their similarity in size and location to Earth. There are several examples within the of uninhabitable planets with potentially habitable moons. The study of extrasolar planets and their parent stars also informs us about the formation and evolution of potentially habitable worlds. The similarity of planetary processes among diverse star systems suggests that moons orbiting exoplanets (i. e. , exomoons; Teachey and Kipping, 2018) are also worthy of consideration as potentially habitable environments, although no such bodies have been observed to date. This section covers the state of our current understanding of the potential habitability of extraterrestrial environments in the and beyond. Several key bodies are the subjects of spacecraft missions in progress or in development: Mars (7. 2. 1), Venus (7. 2. 2), Europa (7. 2. 3), Titan (7. 2. 5), Ganymede (7. 2. 6), and exoplanets (7. 2. 10). These bodies are focal points of research activity and funding opportunities. We cover numerous other bodies because they have significance to the field of astrobiology even if they are not thought to be habitable. 7. 2. 1. MarsSystem bodies, Mars has received by far the most attention in the search for life beyond Earth. Exploration of Mars by multiple orbital and landed spacecraft has characterized global trends in the evolution of climate, aqueous activity, and geochemistry. Scientific consensus has tended toward less habitable surface conditions as the evolution of Mars progressed. In-depth exploration of Meridiani Planum, Gusev crater, and Gale crater by the rovers Opportunity (Arvidson et al.

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: Skip to Content eLife home page your research Search by keyword or author Reset form my search to Research 10. 7554/eLife. 89386. 2 Open access Copyright information Version of RecordDecember 22, 2023 Read the peer reviews Reviewed preprintAugust 8, 2023 Open annotations (there are currently 0 annotations on this page). 7,382 views 560 downloads 44 9386. Copy to clipboard Download BibTeX Download. RIS Full text Figures and data Peer review Side by side Peer review process #1 (Public Review): Reviewer #2 (Public Review): Author response Peer review process Version of Record: This is the final version of the 2. While the authors list their limited number of docking methods as a caveat, the fact that they use three state-of-the-art ligand docking methods is a strength of the work; many studies use just one. The rigorous analysis of the binding site RMSD and docked ligand pose RMSD is novel to my knowledge and is particularly insightful. Weaknesses: The authors are rigorous in their approach by using state-of-the-art workflows that are high-throughput in nature. However, human expert-refined models and expert selection from multiple models could improve the results of ligand pose prediction when using protein models. The authors alluded to this for traditional models but this can also be true when starting from AF2 models. This is difficult to test systematically and rigorously, however. One possible experiment is to explore whether using multiple AF2 models (there are five by default) would have an effect on pose accuracy, perhaps for selected examples such as NK1R, 5HT2A, and DRD1 to help build out the discussion further. Another possible weakness is that the authors focus only on GPCRs for reasons they state but make a good argument as to why the conclusions are likely to extend to other protein classes. Context: One of the most common and impactful uses of protein structures is in small molecule therapeutic chemical tool design. When no experimental structure is available, models are frequently used and such models include traditional template-based homology models and, more recently, AF2 models. AF2 is widely recognized as an inflection point in protein structure prediction due to the unprecedented accuracy of the protein structure models produced automatically.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: plantarum (Figure 1—figure supplement 1E), potentially because riboflavin is already present in high quantities in MRS, a medium containing yeast extract (Tomé, 2021). Thus, L. plantarum was grown in mMRS supplemented with DHNA and iron before ferrihydrite reduction assays in all subsequent experiments. L. plantarum EET activity was confirmed in a bioelectrochemical reactor by quantifying electron output as current (Figure 1B). L. plantarum reduced a carbon electrode (anode) polarized to +200 mVAg/AgCl in the presence of both DHNA and an electron donor (mannitol) (Figure 1C). No current was observed in the absence of L. plantarum (Figure 1—figure supplement 2A), indicating that current production stems from a biological process. L. plantarum produced a maximum current of 129 ± 19 µA/cm2 in mCDM (Figure 1C) and 225 ± 9 µA/cm2 in mMRS (Figure 1—figure supplement 2B). Under EET conditions in mCDM, the L. plantarum biomass was 2. 7 mg (dry cell mass). Assuming 50% of the dry cell mass was protein, the specific electron transfer rate was 57 µmol electrons/mg- protein/hr and the current production was 1. 5 mA/mg-protein. This value is lower than that reported for Geobacter sulfurrenducens (4–8 mA/mg-protein) (Marsili et al. , 2010; Rose and Regan, 2015), the model species for direct EET, and higher than that of Shewanella oneidensis (0. 67 mA/mg-protein) (Marsili et al. , 2008), the model species for mediated EET. It should be noted that these species, unlike L. plantarum, can synthesize riboflavin and quinones and do not require the addition of either for EET activity. Similar to our iron reduction experiments, EET to an anode occurred with different electron donors and growth media (Figure 1—figure supplement 2B-C), and current increased after supplementation of riboflavin when it was omitted from the growth medium (Figure 1—figure supplement 2D). Because of these differences, CDM was amended with mannitol and riboflavin in subsequent experiments.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: , 2014), Spirit (Ruff et al. , 2020), and Curiosity (Grotzinger et al. , 2014), respectively, has revealed regional and temporal variability in the potential habitability of the martian surface and near subsurface. Mars, like Earth, has hosted a wide diversity of environments that offer clues to understanding the habitability of Mars now or in the past. 7. 2. 1. 1. Global trends in climate and aqueous activityWhile volcanically generated basalt is the predominant type of rock on the martian surface, there is also evidence for the presence of liquid water throughout most of its history, with decreasing frequency through time (Kite, 2019). Because the presence of surface liquid water is critical for the habitability of a planetary surface, the climate has largely dictated the long-term surface habitability of Mars. The subsurface habitability of Mars is also dictated by climate, which impacts the crustal depths at which ice versus liquid water is stable, as well as the geochemical characteristics of any subsurface liquid water (7. 1. 3 in the supplementary material). The climate of ancient Mars and the geochemical characteristics of surface and subsurface water can be determined by studying the geologic record of Mars. The history of Mars is broken into three major eras (Fig. 7. 2): Noachian (4. 1–3. 7 Ga), Hesperian (3. 7–3. 1 Ga), and Amazonian (3. 1 Ga–present), each with different predominant conditions. During the Noachian, significant alteration of primary volcanic deposits formed clay and carbonate minerals on the surface and subsurface of Mars, which required the presence of liquid water (Bibring et al. , 2006). Transient warming episodes are thought to have occurred during the Hesperian, but with a lower frequency compared to the Noachian (Kite, 2019). Under such “warm and wet” periods, fluvial activity (e. g. , erosion by rivers) occurred during the Noachian and was particularly heightened during the Noachian–Hesperian transition (based on the relatively large number of fluvial channels visible in Noachian terrains from orbit; Fassett and Head, 2008).

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: However, understanding whether this unprecedented accuracy translates to better small molecule ligand pose prediction has been an open question, and this study directly addresses the question in a systematic, rigorous approach. Reviewer #2 (Public Review): While the question of 'are AlphaFold-predicted structures useful for drug design' has largely seen comparisons of AF versus experimental protein structures, this paper takes a less explored (but perhaps more practically important) angle of 'are AlphaFold-predicted structures any better than the previous generation of homology modeling tools' to the protein-ligand (rigid) docking problem. The conclusions of this work will be of largest interest to the audience less familiar with the precision required for successful rigid docking, while the expert crowd might find them obvious, yet a good summary of results previously shown in the literature. Further work, understanding the structural objectives/metrics that should be placed on future AlphaFold-like models for better pose prediction performance, would greatly expand the practicality of the observations made here. The main conclusion of the paper, that structural accuracy (expressed as RMSD) of the protein model is not a good predictor of the accuracy the model will show in rigid docking protein-ligand pose prediction, is a good reminder of the well-appreciated need for high-quality side chain placements in docking. The expected phenomenon of AlphaFold predicting 'more apo-like structures' is often discussed in the field, and readers should be cautious about drawing conclusions from the rigid (rather than flexible, as in some previous works) docking done here. The authors have very clearly communicated that the use of AlphaFold-generated structures in traditional docking might not be a good idea, and motivated that the time of a molecular designer might be better spent preparing a high-quality homology model. The visual presentation of the conclusions is very clear but might leave the reader wanting a more in-depth discussion of which structural elements of the AF models lead to bad docking outcomes. For example, Fig. 3 presents an example of a very accurate AlphaFold prediction leading to the ligand being docked completely outside of the binding pocket. Close inspection of the Figure suggests a clash of the ligand with the slightly displaced tryptophan residue in the AF model that might be to blame, as can be confirmed by comparison of the model and PDB structure by the reader themselves but has not been discussed by the authors.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: plantarum, Lactiplantibacillus pentosus, Lacticaseibacillus rhamnosus, Lacticaseibacillus casei, Enterococcus faecium, and Enterococcus faecalis are capable of Fe3+ reduction (Figure 2B). The genomes of those species also contain a complete FLEET locus (Figure 2A and Figure 2—figure supplement 1). Conversely, strains of Lactococcus lactis, Ligilactobacillus murinus, Levilactobacillus brevis, Pediococcus pentosaceus, and Streptococcus agalactiae showed little to no iron reduction activity (Figure 2B). The presence of FLEET-associated genes varied between those species, but only strains of species found to contain both ndh2, a predicted membrane-bound, type-dehydrogenase, and pplA were able to reduce iron under the conditions tested. L. plantarum NCIMB8826 exhibited the highest EET activity resulting in at least 2. 5-fold greater Fe3+ reduction than the other L. plantarum strains (Figure 2B). Remarkably, however, the L. plantarum NCIMB8826 genome and the genomes of 138 other L. plantarum strains queried all harbored a complete FLEET locus including ndh2 and pplA (Figure 2—figure supplement 1 and Figure 2—figure supplement 2A). Among those strains tested for the capacity to reduce Fe3+, L. plantarum NCIMB700965 and 8. 1 could not reduce Fe3+ but possessed all genes in the FLEET pathway. Closer examination of both strains by aligning their FLEET loci with NCIMB8826 revealed unique IS30-family transposons in the intergenic promoter regions spanning ndh2 and pplA (Figure 2—figure supplement 2A). These genes were minimally expressed in L. plantarum NCIMB700965 and 8. 1 in comparison to NCIMB8826 (Figure 2—figure supplement 2B). ndh2 and pplA were also the only two genes in the FLEET gene locus that were induced when L.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: While lakes and other potentially habitable surface environments may have existed early in Mars' history, during the Noachian era these climate-driven habitable environments would likely not be long-lived. Thus, any inhabiting life-forms would require refugia (see 7. 1. 5 in the supplementary material) to survive after transient, reducing greenhouse events had passed. Study of the martian climate has suggested a dramatic loss of atmospheric gases over time, but the causes of this loss are not well understood (Jakosky, 2021). Loss of an atmosphere impacts habitability at the surface because the stability of liquids like water is reduced there. The main proposed mechanisms that may account for atmospheric loss on Mars are solar wind stripping due to lack of a protective magnetic field and impact erosion. These mechanisms are discussed in more detail in the supplementary material. Some researchers have hypothesized that Mars may have had an ocean-sized body of water in its low-lying northern hemisphere (e. g. , Citron et al. , 2018), but this theory has substantial challenges. Most terrain north of 30°N on Mars is part of the northern lowlands, which is ∼1–3 km lower in elevation than the more ancient southern highlands. Some have interpreted shoreline features to exist along the rim of this basin. Near this area, there is strong evidence for inland-sea-sized bodies of water on Mars (105 to 107 km3 water, between the volumes of Earth's and double the Mediterranean Sea), including the Eridania sea and seas within Valles Marineris. There is some evidence for submarine hydrothermal activity in the geologic record of Eridania basin, similar to subseafloor hydrothermal processes that supply energy for chemotrophic communities in Earth's oceans. Water drained into the northern lowlands of Mars from an inland sea in the Eridania basin in the late Noachian and from seas in in the late Hesperian or early Amazonian. Water from both of these drainage events would have pooled in the northern lowlands, and some researchers have proposed that a long-lived northern ocean existed in this topographic low. However, geologic interpretations for the existence of this northern ocean are contested (e. g. , Salvatore and Christensen, 2014; Grant and Wilson, 2017), and the hypothesis of a long-lived northern ocean on Mars remains a matter of some debate. 7. 2. 1. 2.

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: Only a few examples of the systems used are shown even visually, leaving the reader unable to study more interesting cases in depth without re-doing the work themselves. The authors acknowledged that several recent studies exist in this space. They point out two advancements made in their work, worthy of further review. Similarly, it's important to evaluate the novelty of this work's claims vs previously available results, and the diversity of information made available to the reader. "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. " This is done by limiting the scope of the work to GPCRs whose structures became available only after the training date of AlphaFold (April 30, 2018), as well as not using templates available after that date during prediction. The use of a time limit seems less preferable than the approach taken in Ref. 1 of discarding templates above a sequence identity cutoff. On the other hand, the 'ablation test' performed in Ref. 2 showed no loss in accuracy when no templates were used at all. Authors should discuss in more detail whether these modeling choices could change anything in their conclusions and why they made their choices compared to those in previous work. "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. " Cross-docking is indeed a more appropriate comparison than self-docking (as done in previous works), and the observation that the accuracy of AF models is similar to that between different holo structures of the same protein is interesting. Previous literature on cross-docking should however be discussed, and the well-known conclusions from it that small variations in side-chain positions, in otherwise highly similar structures, can lead to large changes in docked poses. It is important to realize that AlphaFold models are 'just another structure' - if previous literature is sufficient to show the sensitivity of rigid docking, doing it again on AF structures does not add to our understanding. Further, Ref. 3 might have already addressed the question of correlation between binding site RMSD and docking pose prediction accuracy - see e. g. 3 there (also Figure S15 in Ref. 2).

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: The effects on ORP occurred in the absence of changes in growth rates, cell yields, and medium pH (Figure 3—figure supplement 1A-D). The ΔmVmax was reached during mid-exponential phase (approximately 5 hr) (Figure 3—figure supplement 1B), and at that time, wild-type L. plantarum cells but not the Δndh2 or ΔpplA strains were active in the ferrihydrite reduction assay (Figure 3—figure supplement 1E). This difference in ferrihydrite reduction activity similarly persisted in stationary phase cells (12 hr) (Figure 3—figure supplement 1F). These observations show that ndh2 and pplA contribute to the capacity of L. plantarum to reduce iron and have relevance to the ORP-dependent activities occurring during food fermentations (van Dijk et al. , 2000). Figure 3 with 2 supplements see all Download asset Open asset L. plantarum requires ndh2 and conditionally pplA for EET. (A) Reduction of Fe3+ (ferrihydrite) to Fe2+ with wild-type L. plantarum or EET deletion mutants in the presence of 20 μg/mL DHNA and 55 mM mannitol after growth in mMRS supplemented with 20 μg/mL DHNA and 1. 25 mM ferric ammonium citrate. Significant differences determined by one-way ANOVA with Dunnett’s post-hoc test, **** p < 0. 0001. (B) Redox potential of mMRS supplemented with 20 μg/mL DHNA and 1. 25 mM ferric ammonium citrate after inoculation with wild-type L. plantarum or EET deletion mutants. Significant ORP differences between the wild-type and mutant strains determined by two-way with Tukey’s post-hoc test, * p < 0. 05 (WT vs. Δndh2); # p < 0. 05 (WT vs. ΔpplA). (C) Current density generated by wild-type L. plantarum and deletion mutants in mCDM supplemented with 20 μg/mL DHNA. The avg ± stdev is shown. (D) Current density generated by L. plantarum and two L. lactis strains lacking pplA in mCDM. For L.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: Past transient habitable environmentsA variety of martian environments have been studied for their potential to have been habitable in the past. Top among these environments are transient impact-generated hydrothermal systems, long-lived volcanically driven hydrothermal systems, and lakes that have been temporarily stable at the surface. Discussion of these environments is expanded in the supplementary material. 7. 2. 1. 3. Proposed habitable environments for modern MarsThe current state of knowledge regarding possible habitable environments for extant life on Mars is summarized in Carrier et al. (2020) and 6. 2. 1. 1). As the surface of Mars continued to get colder, the cryosphere would extend deeper, and potentially habitable subsurface environments would retreat to greater depths (Grimm et al. , 2017). Thus, the subsurface of Mars could have remained consistently habitable throughout its history and may continue to host microbial life today (Michalski et al. , 2013; Tarnas et al. , 2018). Surface features known as recurring slope lineae (RSL; Fig. 7. 3) observed by the Orbiter were initially thought to present potentially habitable environments on Mars (McEwen et al. , 2011). RSL are downward-moving darkened areas of hillsides coincident and recurrent with increased temperatures. However, the presence of liquid water in RSL is contested, and evidence suggests that RSL can be explained without the presence of liquid water (Dundas et al. , 2017; Schmidt et al. , 2017). RSL remain under “special region” status in NASA's planetary protection policies due to their potential habitability (see 10. 3. 1). FIG. 7. 3. Recurring slope lineae (RSL) on the surface of Mars. North is roughly to the left in this image, and the Sun is shining from the bottom. More details regarding this HiRISE image are available at Credit: NASA/JPL/University of Arizona. Ultimately, Earth-like organisms would require drastic adaptation to survive in surface environments on Mars, or in near-surface ice, brine, hydrated salt, or cave environments connected to Mars' desiccating and low-pressure atmosphere (Carrier et al. , 2020). The deep subsurface of Mars has potential for hosting Earth-like organisms, but only where groundwater is present.

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: Further, the authors should discuss the commonly brought up problem of AlphaFold generating 'more apo-like structures' - are the models used here actually 'holo-like' because of the low RMSDs? (what RMSD differences are to be expected between apo and holo structures of these systems? ) How are the volumes of the pockets affected? The position on this problem taken by previous works is worth mentioning - "much higher rmsd values are found when using the AF2 models (. . . ), which reflect the difficulties in performing docking into apo-like structures" in Ref. 1 and "computational model structures were predicted without consideration of binding ligands and resulted in apo structures" in Ref. 2. Because of this 'apo problem', Ref. 2 assumed that rigid docking (as done here) would not succeed and used flexible docking where "two sidechains at the binding site were set to be flexible". In fact, the reader of this new paper will be left to wonder if it is not simply presenting a subset of the results already seen in Ref. 2, where "the success ratios dropped significantly for them because misoriented sidechains prevented a ligand from docking (Figure S14)". While this conclusion is not made as clear in Ref. 2 as it is here, a comparison of Figures 4 and S14 there will lead the reader to the same conclusion, and more -- that flexible docking meaningfully improves the performance of AF models, and more so than homology models. Finally, certain data analyses present in previous works but not here should be necessary to make this work more informative to the readers: a) Consideration of multiple top poses, e. g. , in Ref. 2, Figures 4 and S14 mentioned before, comparison of success rates in top 1 and top 3 docked poses add much context. b) Notes on the structural features preventing successful docking, see e. g. , in Ref. 1, Table 2 or in Ref. 4, Tables 2 and 4. This work has the potential to become an important piece of the puzzle, if deeper insights into the reasons for AF model failures are drawn by the authors. These could include a discussion of the problematic structural elements (clashes of side chain with ligands, missing interactions/waters, etc. ), potential solutions with some preliminary data (flexible docking, softening interactions, etc.

Output: contrast


Input: Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: plantarum, the mCDM was supplemented with 20 μg/mL DHNA. The data correspond to the average of two (D) or three (A to C) biological replicates per strain. See also Figure 3—figure supplement 1 and Figure 3—figure supplement 2 and related data in Figure 3—source data 1. Figure 3—source data 1 Raw data of Figure 3A–C. Download elife-70684-fig3-data1-v2. xlsx Use of an anode as an external electron acceptor instead of ferrihydrite showed a similar, but not identical genetic dependency. L. plantarum Δndh2 produced a significantly lower current density (Figure 3C) and a lower peak current (Figure 3—figure supplement 2A). Surprisingly, L. plantarum ΔpplA was able to produce the same amount of current as the wild-type strain, suggesting that the lipoprotein PplA is not essential and might not be involved in anode reduction through EET. This observation led us to investigate the anodic-EET ability of other LAB species lacking pplA like Lactococcus lactis (Figure 3D). DHNA was not provided to these strains because they can synthesize demethylmenaquinone and other quinones (Rezaïki et al. , 2008). Both L. lactis strain IL1403 and strain KF147 were capable of current generation, confirming that PplA is not essential for LAB to produce current. This is consistent with the finding that other extracellular reductases besides PplA are responsible for EET activity in Gram-positive bacteria (Light et al. , 2019). Taken together these results show that EET activity is dependent upon the presence of the putative FLEET locus, and specifically ndh2 and conditionally pplA. L. plantarum increases energy conservation and balances intracellular redox state when performing EET Building from studies in E. faecalis (Keogh et al. , 2018), it has been suggested that EET improves growth by either enabling iron to be acquired as a macronutrient or by enhancing respiration (Jeuken et al. , 2020). It is worth noting that several studies have shown that L. plantarum does not require iron to grow (Elli et al.

Output: pass


Input: Claim: Astrobiology explores the potential for life beyond Earth. [SEP] Text: Such a scenario would make venusian origins of life more difficult, although a cloud-based origin of life is conceivable (e. g. , Dobson et al. , 2000). If the atmosphere of Venus never cooled enough to condense water on its surface, it would likely have lost much of its primordial water rapidly, within 100 million years (Hamano et al. , 2013). cooled enough to condense liquid water on its surface, it is possible that life could have emerged under conditions similar to origins on Earth. Life exhibits an ability to adapt and expand to fill even extreme habitats (see 6. 3). Furthermore, a “faint young Sun” (4. 1. 4) likely resulted in lower equilibrium temperatures on the surface of early Venus. General circulation models incorporating atmospheric feedback show that if Venus has been rotating slowly (taking longer than 16 Earth days per revolution) for most of its history, its surface may have remained hospitable until as recently as 0. 715 Ga (Way et al. , 2016). Venus may have experienced chemical weathering and subsequent carbon burial that provided a negative climate feedback as the young Sun warmed, helping to maintain a habitable environment on the surface of Venus over geologic timescales (Zolotov, 2019). If the surface environment at Venus gradually warmed to evaporate an Earth-sized ocean of water, organisms in that ocean may have had time to adapt to changing conditions and inhabit the clouds (e. g. , Limaye et al. , 2018), although such a scenario faces significant challenges. Greaves et al. (2021) identified an absorption feature in observations of Venus that they attributed to phosphine (PH3) in the cloud deck, which they claimed as a potential biosignature. However, this interpretation is contested. See 8. 3. 1. 3 for more on the possibility of phosphine on Venus. The crust of Venus exhibits widespread consistency in its surface age, ranging from 0. 3 to 0. 7 Ga, as inferred from crater densities (Solomon et al. , 1999). The broad consistency of surface age implies that a major catastrophe triggered a global resurfacing event (Strom et al. , 1994). Possible explanations for such an event are described in the supplementary material.

Output: corroborate


Input: Claim: All economic models accurately predict real-world behavior. [SEP] Text: ), or proposals for metrics better than RMSD to score the soundness of pockets generated by AF for docking. 1. Díaz-Rovira, A. M. , Martín, H. , Beuming, T. , Díaz, L. , Guallar, V. , & Ray, S. S. (2023). for Virtual Screening? Application of to AlphaFold2 Predicted Structures. Journal of and Modeling, 63(6), 1668-1674. 2. Heo, L. , & Feig, M. (2022). Multi-state modeling of G-protein coupled receptors at experimental accuracy. Proteins: Structure, Function, and Bioinformatics, 90(11), 1873-1885. 3. Beuming, T. , & Sherman, W. (2012). Current assessment of docking into GPCR crystal structures and homology models: Successes, challenges, and guidelines. Journal of and Modeling, 52(12), 3263-3277. 4. Scardino, V. , Di Filippo, J. I. , & Cavasotto, C. (2022). How good are AlphaFold models for docking-based virtual screening? [Preprint]. Chemistry. Author response We thank the reviewers and editor for their careful evaluation of our manuscript, and we appreciate their favorable assessment of our work. Below, we clarify a few points concerning the relationship between our study and previous studies evaluating ligand docking to protein models. As reviewer 2 correctly notes, several previous assessments of AF2 models have simply excluded templates above a sequence identity cutoff when using AF2 to predict structures. Such AF2 predictions are still informed by all structures in the PDB before April 30, 2018, because these structures were used to train AF2—that is, to determine the tens of millions of parameters (“weights”) in the AF2 neural network. Machine learning methods nearly always perform better when evaluated on the data used to train them than when evaluated on other data. For this reason, we consider AF2 models only for proteins whose structures were not used to train AF2—that is, for proteins whose structures were not available in the PDB before April 30, 2018.

Output: contrast