Input: Task: pass the claim using the given text. Claim: The search for extraterrestrial life involves studying extremophiles on Earth. [SEP] Text: Bennett offers a host of lessons here not only about global warming and environmental degradation, but our place in the universe as well. ---by planet, moon by moon, [Beyond UFOs] explores the possibility of life elsewhere in this solar system. It then speculates about other solar systems in our galaxy where, according to the prevailing scientific view, simple life almost surely exists and intelligent life is plausible. For the most part, Bennett's search for extraterrestrial life adds up to a very satisfying package. . . . At its core, this book delivers a combination that is hard to beat: solid yet highly speculative science plus accessible prose that add up to an out-of-this-world reading experience. ---Fred Bortz, Seattle TimesIn cogent and entertaining language, astrophysicist and popular writer Bennett explains that the determining factor in whether we can locate intelligent life elsewhere in the universe is whether such a civilization--and our own--can continue long enough to develop the highly sophisticated technology needed for interstellar travel. . . Bennett does a wonderful job of explaining the conditions necessary for simple life, how we might discern its existence and where we should be looking. He then does the same thing for intelligent life. While he is fair to those who believe life is incredibly rare, he makes a compelling case that life is likely to be abundant. "Precise, accurate, lucid, and engaging. This is popular-science writing at its best. I enjoyed reading this book. "—"This is a fascinating book about the living universe, well-written and timely. "—David Morrison, coauthor of System and Voyages to the PlanetsThis is a highly readable and enjoyable book that centers on astrobiology--a discipline that melds astronomy, biology, geology--and a little bit of luck--to explore the prospect of life on other worlds. . . . Bennett is an excellent writer, taking the reader on an exploration quest to find alien life, and how difficult solar system sleuthing can be, such as on Mars, Jupiter's Europa, or on Saturn's Titan. You'll also find an excellent treatment on current activities surrounding the on-going search for extraterrestrial intelligence. Winner of the 2010 US Review of Books's in Culture"With the possible exception of the God question, I can think of no subject that has inspired such wide-eyed wonder and speculation as the matter of whether or not we are alone in the cosmos. [SEP] Justify:

Output: The text does not directly address the claim regarding studying extremophiles on Earth in the search for extraterrestrial life. Instead, it focuses on the broader themes of the potential for life on other planets, the factors that contribute to discovering such life, and the exploration of astrobiology without mentioning extremophiles. Therefore, it does not corroborate or contrast the claim.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: The ATP measurements were made at 24h, where OD of the mutant is decreasing (thus less ATP would be expected). Same issue with NAD/NADH measurement. Figure 4C – Lines are undefined in the figure legend. Also, growth should be plotted on a semi-log scale, see: Figure 5 – based on the growth curve shown in Figure 4, the OC culture lags behind and does not reach maximum OD until day 5. What do these measurements look like at day 5 (or 6)? It seems likely that the authors are drawing conclusions from cells in two different states (stationary phase vs exponential phase) rather than focusing on the finding that having an external electron acceptor appears to accelerate the metabolism of cells. Line 465 – Description of the experiment setup in 2B does not include addition of flavins for the iron reduction assay, so it is unclear why the authors claim that both flavins and quinones are necessary for EET in diverse LAB species. Line 473 – Iron and electrode reduction is dependent on addition of DHNA. Are these cells likely to ever encounter 20 ug/mL DHNA in the environment? Is the EET activity observed relevant to normal physiology for these organisms, or a lab artifact caused by providing a non-native electron carrier? The argument beginning on line 491 underscores the artificial nature to me. Line 559 – none of the 412. doi: 10. 1111/mmi. 12566. Emde R, Schink B. Formation by Propionibacterium freudenreichii subsp. freudenreichii in a Three-Culture System. Microbiol. 1990 Sep;56(9):2771-6. doi: 10. 1128/aem. 56. 9. 2771-2776. 1990. And other 865. doi: 10. 1016/j. tibtech. 2016. 04. 009. . Anodic electro-fermentation: Empowering anaerobic production processes via anodic respiration. Biotechnol Adv. 2021 May-Jun;48:107728. doi: 10. 1016/j. biotechadv. 2021. 107728. 1A to Figure 3A, the extent of Fe3+ reduction seems quite different. Were the conditions the same for these two experiments? If so, an explanation should be added to the text. [SEP] Justify:

Output: The text does not address the importance of lactic acid bacteria for fermentation processes. Instead, it focuses on specific measurement issues and experimental observations related to a study, without mentioning lactic acid bacteria or their role in fermentation.


Input: Task: corroborate the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: Prototheria and Metatheria species contain only one FIB protein each, but the Xenarthra species D. novemcinctus (basal Eutheria species) has two FIB sequences. The Afrotheria, Laurasiatheria, and Euarchontoglires maintain a very marked pattern of two FIB Proteins each (Fig 2E). Phylogenomic microsynteny-network approach to elucidate the evolutionary history of FIB proteins in higher eukaryotes For all detected orthologous and paralogous FIBs sequences, we identified all syntenic FIB genes by pairwise inter- and intra-species microsynteny block detection. To decipher the evolutionary history of FIB genes in major eukaryotic lineages, we implemented a microsynteny-network approach coupled to phylogenetic profiling (“phylogenomic synteny profiling” as described by [34]) on fungi, plants, and animals. In these networks, nodes represent genes and edges represent a syntenic relationship between them. As reported by [34], some clades (such as primates and Brassicaceae) were overrepresented due to research sampling biases. Fig 3 depicts the general topology of the clustered microsynteny networks for fungi, plants, and animals. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFig 3. Microsynteny networks of FIB genes of the three major Eukaryotic taxa. a) Microsynteny networks of FIB genes in Fungi. Nine microsynteny communities from three different phyla (Mucoromycota, Basidiomycota, and Ascomycota). b) Microsynteny networks of FIB genes in plants formed six synteny clusters: a synteny supercluster for all angiosperms (purple nodes), and five small synteny clusters for specific clade such as Rosids (green nodes), Fabaceae (blue nodes), (orange nodes), Oryza-specific cluster (red nodes), and a small Fabaceae group (pink nodes) that poorly linked to the Angiosperm supercluster (one link). c) Microsynteny networks of FIB genes in animals. [SEP] Justify:

Output: The text corroborates the claim by discussing a phylogenomic microsynteny-network approach to elucidate the evolutionary history of FIB proteins in higher eukaryotes. This approach includes studying major eukaryotic lineages, which implies that understanding such genetic relationships aids in deciphering the evolutionary history of life, thereby supporting the claim that fossils, which inform us about evolutionary relationships, provide significant insights into the evolutionary history of life.


Input: Task: pass the claim using the given text. Claim: The search for extraterrestrial life involves studying extremophiles on Earth. [SEP] Text: You’ll be pleased to know that I’m absolutely not going to go down that road. However, I am going to briefly consider each of the three components of RIM. Since these three things are crucial in allowing us to distinguish life forms from inert entities – potentially throughout the universe – it simply won’t work if we’re fuzzy about their meanings. This point was brought home to me when I was reading the Introduction to astrobiology written by the planetary scientist David C. Catling in 2013. With regard to metabolism, Catling says the following: ‘All life metabolizes but so does my car. ’ I don’t agree with him, but I see what he means. The burning of a fuel such as petrol powers a car in much the same way as the burning of a fuel such as glucose powers a living organism. is right to see a parallel. But he’s wrong – in my view – to equate automotive and biological ‘metabolism’. I have an instinctive feeling that the two are different in some fundamental way, and perhaps you do too. But what is it? Of course, the fuels are different, but that’s not the best approach to this issue, because we can’t guarantee that the fuel of alien life is glucose. Here’s a better approach. A life form metabolizes right from the start; a car doesn’t. An organism is not simply a collection of cells, membranes, vesicles, filaments, and so on, that is inert until some point in its life when it gets fired up with an infusion of glucose or some other fuel. In contrast, a car is an object of precisely this latter sort. It’s a collection of metal and plastic parts that gets built in stages and hasn’t a whiff of ‘metabolism’ until after it’s complete – or has reached its ‘adult’ stage, to stretch the use of that term – and someone turns on the ignition. So, to be a life form from a metabolic perspective you need to be metabolizing right from the start. Even the very first cell of a new human or other animal – the zygote – metabolizes. An organism is an intrinsically metabolizing thing. Its default state is to metabolize. [SEP] Justify:

Output: The text does not engage with the claim regarding the search for extraterrestrial life and its relation to extremophiles on Earth. Instead, it discusses concepts of metabolism and life forms, particularly contrasting the metabolic processes of living organisms with automotive systems. Therefore, it is irrelevant to the claim.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: Lines 104-106: Can DHNA itself be used as an electron shuttle? This should be addressed. Line 137: Where the authors compare current density capacity for L. plantarum to that of S. oneidensis--are the quoted values for S. oneidensis using (an) endogenously produced shuttle(s), or are they for S. oneidensis + (an) added shuttle(s)? This should be clarified, because L. plantarum has no current density capacity without added DHNA. Line 139: "current production was not dependent on the carbon source or growth medium, and current increased after supplementation of riboflavin in the growth medium". Both of these claims are hard to evaluate because the plots in figure 1 and figure1-—figure supplement 2 are shown for different lengths of time, different carbon sources (electron donors), and different media. To make it easier for the reader to compare, it would help to have the name of the medium as a title for each current density plot. To judge whether riboflavin truly increases current, we should compare figure 1c to figure 1-—figure supplement 2D. In figure 1c, with no riboflavin added, current increases to ~120 uA/cm2 at around 1 day. In the supplemental figure, this increase is not seen until after riboflavin is added. Without a control, it is hard to know whether this increase was dependent on the riboflavin addition. Line 154: Please define homofermentative. Line 160: "the percentage of" should be removed figure 2-—figure supplement 2C: I am confused about how this experiment controls for the possibility that reduction of soluble iron (i. e. , the ferric ammonium citrate ), which wouldn't necessarily require EET, contributes to the higher levels of ferrous iron observed when DHNA and ferric ammonium citrate are both added. Maybe a control with no ferrihydrite added would tell us whether ferric ammonium citrate is being reduced. Line 194: more background should be provided for the FLEET-inducing conditions Lines 304-309: More background information is needed to understand the motivation behind these experiments. Were oxygen and nitrate available as electron acceptors? [SEP] Justify:

Output: The text does not address the claim regarding the importance of lactic acid bacteria in fermentation processes. Instead, it discusses various experimental details and critiques regarding current density and electron shuttles in relation to specific strains, such as L. plantarum and S. oneidensis. Since it does not provide any information supporting or refuting the claim about lactic acid bacteria, it is deemed irrelevant.


Input: Task: corroborate the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: retrieved and grouped FIBs from each Mammalia synteny community (Fig 7B) and replotted the number of exons per syntenic cluster. Surprisingly, the number of exons is specific to the syntenic community: 82% of FIB genes from the mammals syntenic cluster A contained 9 exons while among the FIB-like genes from mammal cluster B, 56% of genes contained a unique exon and 35% contained 2 exons (summing a 91% of FIBs with one or two exons; Fig 7C). Both microsynteny communities in mammals possess distinctive genomic features that were dependent on their origin. When plotting the syntenic clusters (S. Cluster) on the ML tree (Fig 7D), we found that FIB cluster (S. Cluster A) remains syntenic to Monodelphis domestica, a species from the Metatheria clade (S15 Fig). This syntenic link shows evidence that the FIB cluster comes from the Theria clade (e. g. , marsupials), and also shows evidence for a duplication event before the Eutheria split (e. g. , ruminants, felines, rodents, primates). Therefore, the FIB group remains syntenic to Theria species, unlike the FIB-like group. This finding is in accordance with the number of shared exons between Theria species and members of the mammal cluster A (the group of FIB syntelogs). Furthermore, the FIB-like S. (clade) had no syntenic relationship to any Theria species. The branches of both clades of mammals (and B) presented bootstrap values above 70 percent (S15A and S15B Fig). To better understand the evolutionary divergence of these syntenic communities, we determined the rate of synonymous substitutions (Ks), along with coding sequences (codon alignment strategy) by pairwise comparison of each group of syntelogs (Fig 7E). The distribution of synonymous substitutions among FIB and FIB-like proteins have a different rate of divergence (Ks) according to their genomic context. FIB proteins (S. Cluster A) contained a mean Ks value of 0. 52 (Fst_Qu = 0. 4 & Trd_Qu = 0. 59) compared to FIB-like group (S. [SEP] Justify:

Output: The text corroborates the claim by providing evidence of syntenic relationships between different clades of mammals and their genomic features. It discusses findings such as the syntenic link between the FIB cluster and Monodelphis domestica, which indicates a connection to the Metatheria clade and supports evolutionary relationships. This illustrates how genomic data derived from fossils can shed light on the evolutionary history of life, particularly in terms of divergence and shared traits among species.


Input: Task: contrast the claim using the given text. Claim: The search for extraterrestrial life involves studying extremophiles on Earth. [SEP] Text: In contrast, searching for the technosignatures of intelligent civilizations is centred on longer wavelengths – those of the radio range. I’m going to use radio as a pragmatic way of defining intelligence from a SETI perspective. But let’s first look at the span of intelligences among animals on Earth from a different perspective. Intelligence is a continuous variable, not a binary one. Life forms here, and probably elsewhere too, show a wide range of behaviours that can be interpreted as indicating a wide range of intelligence underlying them. The construction of a scale for the measurement of intelligence is notoriously difficult, even within the confines of a particular species – humans. How intelligent someone is cannot be completely captured on a single scale; intelligence is a multidimensional property. Paradoxically, though, in a multi-species context the job actually gets easier rather than harder. The reason for this is that the differences we’re dealing with are much greater. A scale for intelligence in the context of life on Earth starts from zero and extends indefinitely upwards. Organisms that lack nervous systems are deemed to have no intelligence. These include all microbes and plants, as well as the most primitive of animals – sponges and a little-known group called placozoans (which translates as ‘flat animals’). Slightly more advanced animals such as jellyfish have diffuse nervous systems but lack brains, and don’t really exhibit any behaviour that merits the description intelligent. There are many animals that have small brains, including insects and arachnids. These typically have rather fixed, instinctive behaviour patterns, but some seem more intelligent than others. Jumping spiders – for example those of the genus Portia – have been put forward as the most intelligent arthropods, owing to their complex patterns of hunting behaviour. The most intelligent invertebrates of all are octopuses; there’s a great book about octopus intelligence by Peter Godfrey-Smith, called Other Minds. Many studies on these wonderful creatures, both in the lab and in the field, have illustrated complex behaviours that are clearly learned rather than instinctive. Octopuses exceed many vertebrates in intelligence. However, some groups of birds seem to be particularly intelligent – notably crows and parrots. And many mammalian groups show high intelligence, especially cetaceans (dolphins and whales) and primates. [SEP] Justify:

Output: The text contrasts the claim by shifting focus from extremophiles on Earth to the search for technosignatures of intelligent civilizations, particularly through radio waves. The discussion on intelligence in various life forms on Earth does not directly support the study of extremophiles in the context of extraterrestrial life, indicating a difference in perspective.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: We revised claims to more precisely reflect our findings and, for other claims, provided additional experimental data to further support them as follows: (1) We provide new data on formate and pyruvate and the implications of those data on yield of ATP and fermentation products (discussed in our response to point 1 above). (2) We provide new evidence that L. plantarum performs EET with physiologically-relevant (low) concentrations of DHNA (concern raised by Reviewers #2 and #3). DHNA is present at a range of concentrations (0. 09-0. 5 ug/mL) in foods and other environments inhabited by L. plantarum. Our new data (Figure 1—figure supplement 3) shows that L. plantarum supplied with 0. 010 ug/mL DHNA, which is on the lower end of this range, still produces significant current and iron reduction. Additionally, we now show that this DHNA-dependent EET causes a significant decrease in pH (Figure 1—figure supplement 3), indicating EET affects the physiology of L. plantarum. Lastly, while these data indicate that physiologically relevant levels of DHNA have physiological effects on L. plantarum in laboratory culture media, we also qualify our conclusions to explain that the extent and physiological impact of EET will depend on the environmental and nutritional conditions of the niche L. plantarum is inhabiting (lines 153-162). (3) More background information is provided on the rationale and need for measuring oxidation-reduction potential (ORP) (concern raised by Reviewers #1 and 2) (lines 213-217). Appropriate statistical tests are also now applied to the ORP data. Lastly, new data are included (Figure 3B and Figure 3—figure supplement 1) showing that DHNA supplementation is required for robust ORP reduction by wild-type L. plantarum, further linking EET activity to its ability to modulate extracellular ORP during fermentation. (4) Reviewer #3 suggested that the claim that EET proceeds independently of respiration may be overstated. We now explain our current understanding and the limits on that understanding. Our results show EET proceeds via a respiratory protein, but ATP generation during EET is mainly produced by substrate-level phosphorylation, not oxidative phosphorylation. [SEP] Justify:

Output: The text does not specifically address the role of lactic acid bacteria in fermentation processes. Instead, it discusses various experimental findings related to L. plantarum, including its physiological effects and biochemical processes involving DHNA and oxidation-reduction potential (ORP). While it may imply some relevance through the mention of L. plantarum, it does not directly support or contradict the claim regarding the importance of lactic acid bacteria in fermentation.


Input: Task: corroborate the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: Plant FIBs: A conserved genomic context on a very shifting genomic history We observed a single large microsynteny cluster in plants that implies a local genomic region that is less accessible to genomic alterations leading to a higher degree of conservation on these portions of genomic DNA. We detected a conserved genomic context of FIB across plants, even between monocots and eudicots. This conservation was surprising, as plants have undergone several rounds of ancient paleopolyploidization events (ζ, ε, γ, τ, σ, ρ WGD; [47, 61, 62] and several lineage-specific WGD (At-α, At-β, Br-α, Musa-α, Musa-β, among others; [63, 64]. The duplication events resulted in highly fractionated and reshuffled genomes that can lead to several clade-specific syntenic communities. However, this was not the case for FIBs. Recently, [34] carried out a broad microsynteny comparative analysis of all coding genes across 107 plant genomes and found conservation in only 8. 7% of all syntenic clusters between monocots and eudicots. The FIB family is within this small percentage of syntenic clusters. Our analysis shows a considerable increase in gene content in taxa that underwent recent specific WGDs as the case of Brassicaceae family, and specifically the Brassica genus. Recent work in Glucosinolates (GS) found that gene family expansion has taken place due to the retention of duplicated genes, and most of them (≥70%) are actively expressed in globally or in specific tissues, with different expression patterns [65]. Variation in gene copy numbers, retention of duplicated copies, and posterior sub- neofunctionalization play an essential role in the environmental adaptation and can lead to beneficial or necessary functions as occurs in the salt-tolerant species E. salsugineum [66]. These results highlight the key role of WGD on gene family expansion and gene functional diversification among plant families. A clear example of results from WGD/WGT is the Brassicaceae genomes; this clade has a mix of duplicated and triplicated regions that occurred after the eudicot paleohexaploidization event (At-γ). These events have played a significant role in Brassicaceae evolution [67, 68]. [SEP] Justify:

Output: The text corroborates the claim by discussing the evolutionary history and genomic conservation in plants, particularly via the context of whole-genome duplications (WGDs). It highlights how these genomic changes contribute to the evolutionary process, detailing the conservation of FIBs and their role in the adaptation and evolution of specific plant families like Brassicaceae. This indicates that such genetic and evolutionary insights derived from studying plant genomes align with the broader implications of fossils in understanding the evolutionary history of life.


Input: Task: contrast the claim using the given text. Claim: All mushrooms have medicinal properties. [SEP] Text: Acasa > Reviste de specialitate > Farmacist. ro > Ciuperci medicinale cu proprietăţi imunostimulatoare şi antitumorale (II) NUTRIŢIE Ciuperci medicinale cu proprietăţi imunostimulatoare şi antitumorale (II) Medicinal mushrooms with immunostimulating and antitumor properties (II) Gabriela Vlăsceanu First published: 20 septembrie 2024 Editorial Group: : 10. 26416/Farm. 218. 3. 2024. 10048 have been an integral part of diet and medicinal practices since ancient times. In ancient Chinese culture, they were valued for both their nutritional properties and medicinal benefits. The first book on remedies belonging to the Chinese civilization mentions the therapeutic effects of various species of mushrooms. In the last three decades, researchers from all over the world, especially from countries such as Japan, China, Korea, the USA and Canada, have conducted numerous studies that have confirmed the beneficial effects of mushrooms on human health. These studies have highlighted their immunological, antioxidant, anti-tumor, and anti-inflammatory properties. The discovery of penicillin in 1928, derived from the mold Penicillium notatum (a lower fungus), was a watershed moment in medical history, revolutionizing the treatment of bacterial infections and saving millions of lives. This discovery also opened doors for the synthesis of other exceptional drugs. Over the past three decades, interest in medicinal mushrooms and their therapeutic properties has grown significantly. These mushrooms have been studied for their potential in treating immunological conditions and cancer. Thus, medicinal mushrooms have become the subject of intensive research in the field of complementary medicine. Keywords medicinal, immune-stimulating, anti-tumor mushrooms au fost parte integrantă a dietei şi a practicilor medicinale încă din cele mai vechi timpuri. În cultura chineză antică, acestea erau valorificate atât pentru proprietăţile lor nutritive, cât şi pentru beneficiile medicinale. [SEP] Justify:

Output: The text contrasts the claim by discussing the medicinal properties of specific medicinal mushrooms, rather than implying that all mushrooms possess these properties. It highlights beneficial effects and therapeutic uses of certain species, indicating that while some mushrooms may have medicinal benefits, it does not support the blanket statement that all mushrooms have such properties.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: We also acknowledge that EET could involve other as-yet unidentified respiratory components (lines 478-485 and 504-5) and that we cannot exclude ATP generation by oxidative phosphorylation (lines 482-485). Reviewer #1 (Recommendations for the authors): 1) The only weakness: The methods and results of metabolite analyses are not sufficiently described. This requires explanation if conclusions are to be made about yield, fermentation, and physiology. The paper provides strong evidence that electron diversion to external acceptors is an electron sink. However, while quantitative conclusions are made about fermentation, only ~30% of the mannitol can be accounted for in the EET condition that is the focus of this paper. Put another way, the paper is about where electrons go, but the majority of the electrons are missing. Clarify if this strain can excrete products such as sugar polymers, sugars, pyruvate, formate, glycerol, acetoin, or butanediol. State if standards for these were included in the product analysis (an RI detector can pick up nearly all of these). Explain why formate isn't present (was it not measured? ), as this would allow determination of flux through PFL vs. a pyruvate excretion, a carbon sink of acetoin, or butanediol. Could missing carbon be due to excretion of a partially oxidized sugar like fructose (which would also show up on an RI detector), or accumulation of storage polysaccharide? We thank the Reviewer for the Reviewer’s strong endorsement of our manuscript and clear recommendations for improvements. In the revised manuscript, we provide additional data showing where ~80% of the carbon goes under EET conditions (1) and where the majority of the carbon goes under open circuit conditions. With this more complete information, our balances account for between 77-96% of the electrons (see Supplement file 1). These new data more completely support our conclusion that EET increases fermentation product yield, metabolic flux, and environmental acidification. A) Address these questions in the section around line 299; where fermentation products are mentioned as being present or absent. What was looked for, but not found (lactate yes, succinate no), vs which were not looked for, (pyruvate? Formate? Acetoin, etc). This makes it clear that carbon is not missing, just that the methods were unable to detect it. [SEP] Justify:

Output: The text does not address the importance of lactic acid bacteria in fermentation processes. Instead, it discusses various aspects of electron transfer and carbon tracking during fermentation without mentioning lactic acid bacteria specifically. Therefore, it does not corroborate or contrast the claim, leading to the conclusion that it is irrelevant.


Input: Task: corroborate the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: These phylogenies additionally suggest that Grauer’s gorilla share a common ancestor with Virunga mountain gorillas that post-dates the split between the Virunga and Bwindi populations. Grauer’s gorillas thus appear more divergent to both the Bwindi and Virunga in the full SNP dataset due to the presence of alleles that introgressed from the genetically divergent gorilla. Although our methods are not suitable to formally test for gene flow between Bwindi and Virunga mountain gorilla populations, the mitochondrial phylogeny indicates that their sister relationship was likely reinforced by gene flow that postdates the separation between Virunga and Grauer’s gorillas. Comparative gorilla genetic diversityAfter variant calling and filtering across all genomes, we identified more than 22 million single nucleotide polymorphisms (SNPs) across all individuals included in the dataset, with 15. 2 million SNPs at frequency > 5%. Of these variants, 35% were found in both gorilla species, 51% were found only in western gorillas and 14. 3% of variants were unique to eastern gorillas. Similar patterns of diversity, with more diversity in western compared to the eastern species, were found for indels. Among indels, 59. 0% were unique to western gorillas and only 13. 9% were unique to eastern gorillas. We estimated conservation-relevant genomic parameters by measuring genome-wide autosomal heterozygosity and the number and length of long runs of homozygosity in each gorilla genome. Eastern gorilla heterozygosity ranged between 0. 55–0. 80 per thousand base pairs (kb), which is threefold lower than the 1. 4–2. 0 per kb observed in the western lowland gorillas (Fig. 5). The difference is driven by the large fraction of the eastern gorilla genomes, between 35 and 50%, in long runs (> 100 kb) of complete homozygosity, whereas this fraction is below 10% in most western lowland gorilla genomes (Fig. 5). Long runs of homozygosity are a measure of the relatedness between mating pairs in past generations, and thus roughly reflect recent effective population size. Among eastern gorillas, the Grauer’s gorillas showed the highest genome fraction in runs of homozygosity, despite being the largest extant eastern gorilla population. [SEP] Justify:

Output: The text corroborates the claim by discussing the genetic diversity and evolutionary relationships among gorilla populations, which are relevant to understanding evolutionary history. Phrases like 'suggest that Grauer’s gorilla share a common ancestor with Virunga mountain gorillas' indicate that genetic analysis gives insights into their evolutionary past, aligning well with the notion that fossils, as physical remnants of life, serve to illuminate evolutionary history.


Input: Task: contrast the claim using the given text. Claim: All mushrooms have medicinal properties. [SEP] Text: De fapt, în prima carte despre remedii aparţinând civilizaţiei chineze, se menţionează efectele terapeutice ale diferitelor specii de ciuperci. În ultimele trei decenii, cercetătorii din întreaga lume, cu precădere din ţări precum şi Canada, au realizat numeroase studii care au confirmat efectele benefice ale ciupercilor asupra sănătăţii umane. Aceste studii au evidenţiat proprietăţile lor imunologice, antioxidante, antitumorale şi antiinflamatorii. Descoperirea penicilinei în 1928, derivată din mucegaiul Penicillium notatum (o ciupercă inferioară), a fost un moment de cotitură în istoria medicală, revoluţionând tratamentul infecţiilor bacteriene şi salvând milioane de vieţi. Această descoperire a deschis, de asemenea, uşi pentru sinteza altor medicamente de excepţie. În ultimele trei decenii, interesul pentru ciupercile medicinale şi proprietăţile lor terapeutice a crescut semnificativ. Aceste ciuperci au fost studiate pentru potenţialul lor în tratarea afecţiunilor imunologice şi a cancerului. Astfel, ciupercile medicinale au devenit subiect de cercetare intensivă în domeniul medicinei complementare. [SEP] Justify:

Output: The text contrasts the claim by discussing the medicinal properties of various species of mushrooms, yet it does not support the assertion that all mushrooms possess such properties. It highlights research on specific types of mushrooms and their beneficial effects, suggesting that while some mushrooms have recognized medicinal benefits, this does not extend to all species.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: We agree with the Reviewer on this recommendation to provide more clarity on the methods and results of the metabolite analyses. As a result, we have included additional information in the Materials and Methods (lines 712-720) and in the Results (lines 323-325 and 328-335). As described in detail below, we can account for ~80% of the carbon and electrons under EET conditions, which captures a majority of both the carbon and electron flow. With our HPLC methods, we were able to detect the following compounds using standards: acetate, formate, pyruvate, malate, lactate, succinate, oxalacetate, fumarate, ethanol, acetoin, butanediol, mannitol, glucose and fructose (now indicated on lines 712-720 in Materials and Methods). Despite being extensively studied, L. plantarum have not been reported to make storage polysaccharides, and thus it is very unlikely that storage polysaccharides could account for the remaining missing carbon. We detected large and significant changes in the concentration of main fermentation end-products, acetate, lactate and ethanol (Figure 5). We detected significant, but small changes, in pyruvate and formate production (now shown in Figure 5—figure supplement 2). We did not detect fructose, malate, glucose, oxaloacetate, fumarate, acetoin or 2,3-butanediol in the samples. We have included this new information in the revised Results section (lines 333-334). We also now include carbon in biomass as part of the carbon recovery in an updated Table 1 and updated Table S1. (We also revised other portions of Table S1 to correct a prior error. ) Taken together, these updated measurements increase the carbon recovery observed under both EET and OC conditions. Under EET conditions, ~80% of the carbon is recovered in fermentation products, while under OC conditions, we can account for ~55% of the carbon. We did not measure CO2 production because our bioelectrochemical reactors are not gas tight. Thus, we suggest the missing carbon is likely due to CO2 production, but we cannot rule out production of other unidentified metabolites. [SEP] Justify:

Output: The text does not provide direct information regarding the importance of lactic acid bacteria in fermentation processes, as it primarily focuses on the methods, results, and findings related to various metabolites without making connections to the specific role of lactic acid bacteria in fermentation. Therefore, it is categorized as irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: In the comparison between Grauer’s and mountain gorillas, we uncovered genes involved in skeletal and cardiac muscle strength, brain and neurological functions, diet, and digestion (Fig. 6, Table S10). The two eastern subspecies differ from each other in social organization, markedly in the proportion of multi-male groups [70] and several of the detected genes are proposed to be involved in social behavior and aggression, suggesting that behavioral functions might be under selection. Grauer’s gorillas occupy lower altitudes than mountain gorillas and the diets between the two subspecies differ, specifically in the proportion of consumed fruits and the diversity of dietary items [33, 57]. Genes under selection in mountain gorillas are involved in sweet taste signaling, lipid catabolic processes, and regulation of insulin secretion. We caution, however, that due to the levels of inbreeding in eastern gorillas, the used selection statistics can be biased [34]. Additionally, the low population size of the eastern gorillas results in a high amount of drift, which may create patterns that could be wrongly interpreted as signals of selection [44]. Finally, the comparison between Bwindi and Virunga mountain gorilla populations uncovered unique protein sequences in Bwindi, which play an important role in cholesterol homeostasis and mediate platelet aggregation (Fig. 6), which is involved in high altitude adaptation. Protein sequences unique to Virunga were involved in cytokine and environmental stress response and craniofacial morphology. DiscussionDespite decades of genetic studies on gorillas, much of their evolutionary history remains a mystery. We detected multiple signals indicative of introgression between gorilla subspecies, which together with recently reported admixture from a possible unsampled “ghost” population [60] show that gene flow was likely common throughout gorilla evolution. The inclusion of whole genome data from Bwindi mountain gorillas allowed us to uncover novel aspects of the gorilla evolutionary history. We detected a strong genetic similarity between Virunga mountain gorillas and Grauer’s gorillas to the exclusion of the Bwindi mountain gorilla population, and obtained indications of gene flow between and Grauer’s gorillas, likely to the exclusion of all mountain gorilla populations. The here reported evolutionary relationships among eastern gorillas are in disagreement with previous studies [72, 90] and the inferred Cross River—Grauer’s gorilla gene flow appears contrary to expectations based on present-day geographic distributions. [SEP] Justify:

Output: The text provides insights into the evolutionary history of gorillas, specifically discussing genetic studies and evolutionary relationships among different gorilla subspecies. It mentions the detection of multiple signals indicative of introgression and gene flow throughout gorilla evolution, as well as the discovery of novel aspects related to their evolutionary history. Although the text primarily focuses on genetic data rather than fossils specifically, it supports the claim by demonstrating how such studies contribute to our understanding of evolutionary history.


Input: Task: contrast the claim using the given text. Claim: All mushrooms have medicinal properties. [SEP] Text: Cuvinte cheie ciuperci medicinale imunostimulatoare antitumorale În anii 1980, cercetătorii de la au făcut o descoperire semnificativă referitoare la proprietăţile imunostimulatoare ale componentelor polizaharidice din ciupercile medicinale. Aceste componente au fost identificate ca având potenţial antitumoral şi au fost clasificate drept astfel de substanţe de către US Institute. Pe lângă efectele antitumorale, ciupercile medicinale au fost recunoscute şi pentru alte proprietăţi farmacologice valoroase. Printre acestea se numără proprietăţile antimicrobiene, antiinflamatorii, antiaterogenice şi hepatoprotectoare. În zilele noastre există o tendinţă crescândă de a căuta soluţii terapeutice în medicina alternativă şi tradiţională, bazată pe experienţe vechi, de milenii. Investigaţiile moderne asupra proprietăţilor medicinale ale ciupercilor au început la sfârşitul anilor 1960, când au fost demarate cercetări privind mecanismele de acţiune prin care diferitele specii de ciuperci îşi exercită efectele benefice. Asemenea altor forme de medicină alternativă, cum ar fi ceaiurile medicinale, ciupercile medicinale câştigă tot mai multă acceptare şi popularitate în lumea contemporană. [SEP] Justify:

Output: The text contrasts the claim by discussing the medicinal properties of specific medicinal mushrooms while not asserting that all mushrooms possess such properties. It mentions significant findings related to immunostimulatory components from medicinal mushrooms but does not generalize this to all species of mushrooms, suggesting that the claim is too broad.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: 604-610. 1980. We thank the Reviewer for these insights. We removed the energy-spilling reference from the manuscript. Since our data shows that final biomass is not affected by EET whereas energy conservation is, it seems likely that growth is not strongly coupled to energy conservation under EET conditions. We strongly agree with the Reviewer’s suggestion that the low pH under EET conditions may uncouple ATP generation and growth. We also hypothesize that this ATP produced from substrate-level phosphorylation might be used to create proton motive force to maintain intracellular pH and biosynthetic functions. We have included this hypothesis in the main manuscript (lines 406-409). 7) The value for Geobacter ATP/substrate yield in Table S2 seemed very high. Mahadevan says Geobacter produces 0. 5 mol ATP/mol acetate when using extracellular acceptors (3x higher when using internal acceptors like fumarate). understand the adjustment for 6-carbon compounds, would this make the value for Geobacter using EET to be 1. 5 mol ATP/mol 6-C substrate? We thank the Reviewer for this correction. We incorrectly provided the thermodynamic boundary for the ATP/substrate yield from the referenced study. We now provide the value of 1. 5 mol ATP/mol 6 carbon substrate (0. 5 mol ATP/mol acetate) (Mahadevan et al. , 2006 – Microbiol) in 2. Reviewer #2 (Recommendations for the authors): Line 21 – acronyms like this make our field more challenging to understand and are unnecessary. Does the work presented actually support 'energy conservation'? Growth seems to occur after EET activity takes place rather than with it as discussed below. We agree with the Reviewer that a broad scientific audience will find the FLEET acronym confusing and have eliminated it from the manuscript. also questions whether our findings indicate that EET supports energy conservation in L. plantarum. In biochemistry, energy conservation is defined as the conversion of light or chemical energy into cellular energy in the form of ATP by an organism (Russell and Cook 1995 – Microbiol Rev). In rapidly dividing cells, energy conservation, a catabolic process, is associated with growth, an anabolic process. [SEP] Justify:

Output: The text does not relate to the claim regarding the importance of lactic acid bacteria in fermentation processes. Instead, it focuses on energy conservation, ATP generation, and metabolic processes involving Geobacter and EET (electricity-generating microorganisms) without mentioning lactic acid bacteria or fermentation. Therefore, it is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Mass extinctions have shaped the diversity of species on Earth. [SEP] Text: A new high-resolution chronology for the late Maastrichtian warming event: establishing robust temporal links with the onset of Deccan volcanism. Geology 46:147–50 [2007. The stability of the stratospheric ozone layer during the end-Permian eruption of the Siberian Traps. Philos. Trans. R. Soc. A 365:1843–66 [2012. Magnitude and consequences of volatile release from the Siberian Traps. Earth Planet. Sci. Lett. 317–318:363–73 [2014. Sulfur isotopic evidence for sources of volatiles in magmas. Earth Planet. Sci. Lett. 394:58–69 [2017. Volatiles and the tempo of flood basalt magmatism. Earth Planet. Sci. Lett. 458:130–40 [2011. Significant increases in global weathering during Events 1a and 2 indicated by calcium isotopes. Earth Planet. Sci. Lett. 309:77–88 [2010. Pyrite framboid study of marine Permian–Triassic boundary sections: a complex anoxic event and its relationship to contemporaneous mass extinction. Geol. Soc. Am. Bull. 122:1265–79 [2014. Large igneous provinces and mass extinctions: an update. Volcanism, Impacts, and Mass Extinctions: Causes and 29–55 Geol. Soc. Am. Spec. Pap. 505 Boulder, CO: Geol. Soc. Am. [2012. Osmium-isotope evidence for volcanism, weathering, and ocean mixing during the early Aptian OAE 1a. Geology 40:583–86 [2015. Calcium isotope evidence for dramatic increase of continental weathering during the Toarcian oceanic anoxic event (Early Jurassic). Earth Planet. Sci. Lett. 411:164–76 [2011. Rapid expansion of oceanic anoxia immediately before the end-Permian mass extinction. PNAS 108:17631–34 [2017. Initial pulse of sills as the trigger of the end-Permian mass extinction. Nat. Commun. 8:164 [2017. Hydrological and associated biogeochemical consequences of rapid global warming during the Paleocene-Maximum. Glob. Planet. Change 157:114–38 [2011. [SEP] Justify:

Output: The text discusses multiple studies and geological events that relate to mass extinctions, such as the end-Permian mass extinction and its triggers, notably the Siberian Traps volcanism. This context supports the claim that mass extinctions have influenced the diversity of species, as these geological events are considered pivotal in shaping evolutionary outcomes and species diversity on Earth.


Input: Task: contrast the claim using the given text. Claim: All mushrooms have medicinal properties. [SEP] Text: Acestea sunt văzute ca o sursă naturală şi holistică de tratament şi prevenire a diverselor afecţiuni şi sunt subiectul unor cercetări ample care îşi propun să înţeleagă mai bine potenţialul lor terapeutic(1). Figura 1. Nouă specii de ciuperci terapeutice(1) Conceptul de utilizare a ciupercilor imunomodulatoare în tratamentul cancerului, în special în ceea ce priveşte potenţialul lor antiangiogenetic, a fost studiat şi este un subiect de interes în cercetarea medicală. Angiogeneza este procesul prin care noi vase de sânge sunt formate din vasele de sânge existente şi este un aspect crucial în dezvoltarea şi creşterea tumorilor. Blocarea acestui proces (antiangiogeneză) poate încetini sau opri creşterea şi metastazarea tumorilor. Există cercetări care sugerează că anumiţi compuşi găsiţi în ciupercile medicinale ar putea avea proprietăţi antiangiogenetice şi imunomodulatoare, care ar putea contribui la inhibarea creşterii tumorilor şi la stimularea răspunsului imun împotriva cancerului. [SEP] Justify:

Output: The text contrasts the claim by discussing specific therapeutic properties of certain medicinal mushrooms, indicating that not all mushrooms may possess such qualities. It emphasizes the potential of certain compounds in therapeutic mushrooms against cancer, suggesting that while some mushrooms may be beneficial, it does not imply that all mushrooms share medicinal properties.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: However, catabolism need not be coupled with anabolism, and energy conservation can still occur in cells that are not rapidly dividing, e. g. in resting cell suspensions (Russell and Cook 1995 – Microbiol Rev). In L. plantarum, EET increases the rate at which chemical energy (in mannitol) is converted to cellular energy (in ATP) per cell by ~1. 75-fold (Figure 5C), indicating that EET increases the rate of energy conversation per cell. EET increases the amount of cellular energy obtained per chemical energy (Ymannitol) (Table 1) by ~1. 75-fold, indicating that EET is also a more efficient energy conservation strategy in L. plantarum. To understand how the anabolic process of energy conservation is coupled to the catabolic process of growth, we can compare changes in ATP to changes in biomass. At the start of EET, increased ATP levels are accompanied by a significant shortening of lag phase (Figures 1C, 4C). Since lag phase is the period microorganisms use to accumulate ATP for exponential growth, this shortened period suggests catabolic and anabolic processes are well coupled at this stage. However, by stationary phase, the biomass yield (Table 1) decreased under EET conditions, suggesting a much poorer coupling of catabolic and anabolic processes. Line 27 – 'fermentation yield' referring to biomass yield or fermentation product yield? The text was revised to clarity that ‘fermentation product yield’ is being discussed here. Line 29, Line 45, Line 75, Line 86, Line 479 – blending fermentation and respiration has been known for over a decade in Shewanella (see Hunt et al. , 2010, JBact). The description on Line 517 regarding the major finding from this reference is incorrect. PMF is not used by S. oneidensis anaerobically to generate ATP as demonstrated by the robust anaerobic growth of an ATP synthase mutant. First, our work was very much inspired by the observations in S. oneidensis and other work, so we apologize for the inadvertent omission of the Hunt et al. J. Bacteriology 2010 reference in the introduction and mis-stating of the ATP synthesis result. In the revised manuscript, we removed the reference to S. [SEP] Justify:

Output: The text does not directly address the role of lactic acid bacteria in fermentation processes. Instead, it discusses energy conservation mechanisms in certain bacteria, specifically L. plantarum, without providing evidence or relevance to the claim regarding lactic acid bacteria and fermentation.


Input: Task: corroborate the claim using the given text. Claim: Mass extinctions have shaped the diversity of species on Earth. [SEP] Text: Environmental determinants and ecologic selectivity of benthic faunas from nearshore to bathyal zones in the end-Permian mass extinction: brachiopod evidence from South China. Palaeogeogr. Palaeoclimatol. Palaeoecol. 308:84–97 [2015. Oxygen limitations on marine animal distributions and the collapse of epibenthic community structure during shoaling hypoxia. Glob. Change Biol. 21:2989–3004 [2017. Organism activity levels predict marine invertebrate survival during ancient global change extinctions. Glob. Change Biol. 23:1477–85 [2011. Acidification, anoxia, and extinction: a multiple logistic regression analysis of extinction selectivity during the Middle and Late Permian. Geology 39:1059–62 [2004. Why does metabolism scale with temperature. ? Funct. Ecol. 18:243–51 [2015. Ocean acidification and the Permo-Triassic mass extinction. Science 348:229–32 [2018. Uranium isotope evidence for two episodes of deoxygenation during Event 2. PNAS 115:2918–23 [1994. Large igneous provinces: crustal structure, dimensions, and external consequences. Rev. Geophys. 32:1–36 [2014. Euechinoidea and Cidaroidea respond differently to ocean acidification. Comp. Biochem. Physiol. A 174:45–55 [2013. Buffer capacity of the coelomic fluid in echinoderms. Comp. Biochem. Physiol. A 166:199–206 [1920. The alkali reserve of marine fish and invertebrates: the excretion of carbon dioxide. J. Biol. Chem. 44:329–44 [2018. Similar controls on calcification under ocean acidification across unrelated coral reef taxa. Glob. Change Biol. 24:4857–68 [2015. Investigating the paleoecological consequences of supercontinent breakup: Sponges clean up in the Early Jurassic. Sediment. Record 13:24–10 [2003. On the ages of flood basalt events. C. R. Geosci. 335:113–40 [2016. [SEP] Justify:

Output: The text discusses various studies that examine the environmental determinants and ecological effects of mass extinctions, particularly focusing on the end-Permian mass extinction and its consequences on marine faunas. This directly supports the claim by indicating that mass extinctions are crucial events that influence the diversity of species, as noted in the phrase 'the collapse of epibenthic community structure during shoaling hypoxia' and other references to extinction selectivity and ocean acidification impacting marine biodiversity.


Input: Task: contrast the claim using the given text. Claim: All mushrooms have medicinal properties. [SEP] Text: Tabelul 1 Ciupercile medicinale, sursă de compuşi naturali cu efect anticancer(2) Cu toate acestea, este important să subliniem că, deşi există anumite dovezi şi studii care susţin aceste afirmaţii, utilizarea ciupercilor medicinale în tratamentul cancerului nu este încă parte a protocoalelor standard de tratament. Sunt necesare mai multe cercetări pentru a înţelege pe deplin potenţialul şi eficacitatea lor, precum şi pentru a stabili dozele şi modalităţile de administrare corecte. Potenţialul ciupercilor medicinale în tratarea unor afecţiuni precum cancerul, hepatitele, bolile autoimune şi altele a fost într-adevăr cercetat şi este subiectul unor studii în curs. Diverse specii de ciuperci au fost testate pentru potenţialul lor anticancerigen, în studii realizate de al Universităţii din Tokyo şi din Tokyo. Se pare că unele specii de ciuperci au arătat un grad semnificativ de eficacitate în inhibarea creşterii tumorilor în teste de laborator, la dozele specificate. Totuşi, este important să subliniem că rezultatele studiilor de laborator trebuie interpretate cu precauţie. [SEP] Justify:

Output: The text contrasts the claim by highlighting that, while there is evidence supporting the medicinal properties of certain mushrooms, the use of medicinal mushrooms in standard cancer treatment protocols is not yet established. It stresses the need for further research to fully understand their potential and effectiveness, indicating that not all mushrooms are recognized as having medicinal properties.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: oneidensis as a well understood respiratory microorganism (line 45), have replaced reference 14 with the Hunt et al. J. Bacteriology 2010 (our original intention) (line 80), removed the word recent when describing these findings (line 85), and revised the discussion to correctly describe that fumarate reduction supports the creation of ATP via substrate level phosphorylation, not PMF in S. oneidensis (line 523). Second, we do not claim that our work is the first observation of a hybrid metabolism that blends fermentation and respiration. Rather, this work quantitatively elucidates a different blending of fermentation and respiration that both contrasts with and expands upon previous work. As a counterpoint to the prior observation that substrate-level phosphorylation is the major energy conservation strategy during anaerobic fumarate reduction in a non-fermentative organism (S. oneidensis), our work demonstrates that a blending of fermentation and respiration occurs during reduction of solid electron acceptors in a primarily fermentative organism (L. plantarum) (lines 28-30, 525-527). Going beyond prior qualitative observations, we show that this hybrid metabolism leads to ~1. 75x-more efficient and ~1. 75x-faster energy conservation (Ymannitol, mannitol flux), but an overall ~1. 5-fold weaker coupling between anabolism and catabolism (lower biomass yield). Additionally, we discover that this hybrid metabolism substantially affects the intracellular redox state and show redox change arises from a ~2:1 use of endogenous to extracellular electron acceptors. This fuller discussion is included in the manuscript (lines 525-535). Line 61 – implied here is that LAB are auxotrophic for heme and menaquinone, but should be explicitly stated. The text was revised to incorporate the Reviewer’s suggestion (lines 66-68). Page 8 (top) – the comparison to other organisms is not particularly helpful unless current per unit cell or unit biomass is quantified, nor does it seem particularly relevant to the overall theme of this manuscript. We agree with the Reviewer that current should be normalized per unit biomass, and we believe that this normalized value provides context for how significant EET is as a metabolic activity. In the revised manuscript, we normalize the current from L. [SEP] Justify:

Output: The text does not directly address the claim about lactic acid bacteria being important for fermentation processes. Instead, it discusses a hybrid metabolism in different bacterial organisms, specifically focusing on S. oneidensis and L. plantarum, and the metabolic processes involved without directly linking to the significance of lactic acid bacteria in fermentation.


Input: Task: corroborate the claim using the given text. Claim: Mass extinctions have shaped the diversity of species on Earth. [SEP] Text: Extinction of fish-shaped marine reptiles associated with reduced evolutionary rates and global environmental volatility. Nat. Commun. 7:10825 [2014. Ichthyosaurs from the indicate a severe turnover across the Triassic–Jurassic boundary. Naturwissenschaften 101:1027–40 [2007. Tropical warming and intermittent cooling during the Cenomanian/Turonian oceanic anoxic event 2: sea surface temperature records from the equatorial Atlantic. Paleoceanography 22:PA1219 [2013. Surviving rapid climate change in the deep sea during the Paleogene hyperthermals. PNAS 110:9273–76 [2017. Extreme warmth and heat-stressed plankton in the tropics during the Paleocene-Maximum. Sci. Adv. 3:e1600891 [2016. Ocean warming, not acidification, controlled coccolithophore response during past greenhouse climate change. Geology 44:59–62 [2006. Nannoplankton extinction and origination across the Paleocene-Maximum. Science 314:1770–73 [2010. A framework for community interactions under climate change. Trends Ecol. Evol. 25:325–31 [2017. Isotopic signatures of mercury contamination in latest Permian oceans. Geology 45:55–58 [2005. Photic zone euxinia during the Permian-Triassic superanoxic event. Science 307:706–9 [2015. Plasticity in thermal tolerance has limited potential to buffer ectotherms from global warming. Proc. R. Soc. B 282:20150401 [2017. Very large release of mostly volcanic carbon during the Palaeocene–Maximum. Nature 548:573–77 [1999. The early Toarcian (Early Jurassic) and the Cenomanian–Turonian (Late Cretaceous) mass extinctions: similarities and contrasts. Palaeogeogr. Palaeoclimatol. Palaeoecol. 154:39–66 [2008. Catastrophic ocean acidification at the Triassic-Jurassic boundary. Neues Jahrb. Geol. Paläontol. 249:119–27 [2012. Conditions of Mytilus edulis extracellular body fluids and shell composition in a pH-treatment experiment: acid-base status, trace elements and δ11B. [SEP] Justify:

Output: The text corroborates the claim by discussing several mass extinctions and their consequences such as the extinction of marine reptiles, which points towards major ecological turnovers and evolutionary impacts during events like the Triassic–Jurassic boundary and the Cenomanian/Turonian oceanic anoxic event. This indicates that mass extinctions, mentioned in various studies, have indeed played a significant role in shaping the diversity of species.


Input: Task: contrast the claim using the given text. Claim: All mushrooms have medicinal properties. [SEP] Text: Este necesar să se efectueze cercetări suplimentare, inclusiv studii clinice la oameni, pentru a confirma eficacitatea şi siguranţa ciupercilor ca tratament pentru cancer(2). De exemplu, AHCC (Correlated Compound) este un supliment care a captat atenţia cercetătorilor şi profesioniştilor din domeniul sănătăţii datorită potenţialului său în susţinerea sistemului imunitar şi a sănătăţii generale. Figura 2. AHCC – amestec organic din opt ciuperci care susţin imunitatea(3) Figura 3. Proprietăţile anticanceroase ale Fomitopsis pinicola(15) Figura 4. Proprietăţile anticanceroase ale Hericium erinaceus(15) Figura 5. Proprietăţile anticanceroase ale Inonotus obliquus(15) Figura 6. Proprietăţile anticanceroase ale Trametes versicolor(15) AHCC este un extract obţinut din miceliul mai multor subspecii de ciuperci medicinale hibridizate, fiind recunoscut pentru proprietăţile sale antiinflamatoare, imunomodulatoare şi antioxidante. Este bogat în alfa- şi beta-glucani, compuşi care au fost asociaţi cu îmbunătăţirea funcţiei imune. [SEP] Justify:

Output: The text contrasts the claim by indicating that further research is necessary to confirm the effectiveness and safety of mushrooms as treatments, suggesting that not all mushrooms may have medicinal properties. It notes that while certain compounds derived from mushrooms show potential, such as AHCC and others, it does not state that all mushrooms possess these medicinal benefits.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: This important facet of the experiment is now described in the manuscript (lines 219-223). Figure 3D – did the authors include a strain that lacked the cluster? No, we did not probe a strain that lacked the FLEET locus because this experiment was designed to probe the importance of specifically PplA for current production. Rather, we investigated strains lacking the FLEET locus using our Fe3+ reduction assay since this experiment allows testing a larger variety of species at the same time. We believe that the Reviewer’s suggestion would be a useful expansion of our experiment and will include this in our future studies. Line 252 – unclear to me how ICP-MS can distinguish between iron inside a cell and associated with the cell surface. We appreciate the Reviewer’s question here. While ICP-MS cannot spatially resolve iron that is intracellular vs. extracellular, we removed surface-associated metals by washing the cells twice in PBS before performing ICP-MS. This washing procedure has been shown in other bacteria to remove loosely bound metals (see Kumar et al. , 2020 – Nat. Sci. Reports and Arauz et al. , 2008 – J. Haz. Materials). An ICP-MS section was added to the Materials and methods (lines 811-821) to clarify these points. Line 256 – have other metals been tested? Frequently manganese substitutes for iron in enzymes from non-iron dependent bacteria. Manganese oxide is also a known substrate for EET in Geobacter and Shewanella and could be nutritionally significant to LAB. For simplicity, we focused on intracellular iron concentrations within the paper, but indeed ICP-MS was also able to detect other metals in L. plantarum cells. We now include the other findings from the ICP-MS analyses in Figure 4—figure supplements 1 and 2. Although quantities of barium and calcium were significantly lower and higher in the ndh2 mutant compared to the wild-type strain, respectively, these differences were not observed for wild-type L. plantarum when grown in EET-simulating culture medium (mMRS with DHNA and iron supplementation) compared to the mMRS control medium. In addition, these two metals are not expected to be redox-active metals for EET. [SEP] Justify:

Output: The text does not address or provide any information specifically regarding the role of lactic acid bacteria in fermentation processes. Instead, it primarily discusses experimental details related to iron and metal analyses in bacterial strains, which is irrelevant to the claim about the importance of lactic acid bacteria in fermentation.


Input: Task: corroborate the claim using the given text. Claim: Mass extinctions have shaped the diversity of species on Earth. [SEP] Text: Palaeotethys seawater temperature rise and an intensified hydrological cycle following the end-Permian mass extinction. 26:675–83 [2017. carbonate carbon isotope variability traces heterogeneous organic carbon accumulation and authigenic carbonate formation. Clim. Past 13:1635–59 [2015. U-Pb geochronology of the and relation to the end-Cretaceous mass extinction. Science 347:182–84 [2010. asteroid impact and mass extinction at the Cretaceous-Paleogene boundary. Science 327:1214–18 [2011. Critical oxygen levels and metabolic suppression in oceanic oxygen minimum zones. J. Exp. Biol. 214:326–36 [2014. Emplacement characteristics, time scales, and volcanic gas release rates of continental flood basalt eruptions on Earth. Volcanism, Impacts, and Mass Extinctions: Causes and 319–37 Geol. Soc. Am. Spec. Pap. 505 Boulder, CO: Geol. Soc. Am. [2005. Gas fluxes from flood basalt eruptions. Elements 1:283–87 [2016. Eighty-five million years of gyre ecosystem structure: long-term stability marked by punctuated change. Proc. R. Soc. B 283:20160189 [2018. Global perturbation of the marine calcium cycle during the Permian-Triassic transition. GSA Bull 130:1323–38 [2014. Warming, euxinia and sea level rise during the Paleocene–Maximum on the Plain: implications for ocean oxygenation and nutrient cycling. Clim. Past 10:1421–39 [2013. Energy-limited tolerance to stress as a conceptual framework to integrate the effects of multiple stressors. Integr. Comp. Biol. 53:597–608 [2008. Interactive effects of metal pollution and temperature on metabolism in aquatic ectotherms: implications of global climate change. Clim. Res. 37:181–201 [2015. Anoxia/high temperature double whammy during the Permian-Triassic marine crisis and its aftermath. Sci. Rep. 4:4132 [2017. Energetic costs of calcification under ocean acidification. Glob. Biogeochem. Cycles 31:866–77 [2012. [SEP] Justify:

Output: The text corroborates the claim by referencing several mass extinctions, such as the end-Permian and end-Cretaceous mass extinctions, which imply significant ecological changes that impacted species diversity. These events are critical in understanding how mass extinctions have influenced the diversification and evolutionary trajectories of life on Earth.


Input: Task: contrast the claim using the given text. Claim: All mushrooms have medicinal properties. [SEP] Text: De-a lungul anilor, AHCC a fost supus unui număr semnificativ de cercetări clinice şi preclinice, iar rezultatele iniţiale sunt promiţătoare în ceea ce priveşte beneficiile sale potenţiale pentru sănătatea umană. S-a constatat că AHCC poate avea efecte benefice într-o varietate de condiţii, inclusiv în sprijinirea sistemului imunitar în faţa infecţiilor, în gestionarea inflamaţiei şi în susţinerea sănătăţii generale. De asemenea, este demn de remarcat faptul că AHCC este utilizat în spitale şi a fost subiectul unor evenimente ştiinţifice prestigioase, cum ar fi Simpozionul Asociaţiei pentru Cercetarea AHCC, ceea ce subliniază interesul şi relevanţa sa în comunitatea medicală. Studiile efectuate pe animale şi la oameni sugerează că AHCC poate creşte activitatea celulelor NK (celulele natural killer) şi a macrofagelor, sporeşte producţia de citokine şi poate reduce efectele secundare ale chimioterapiei, precum şi metastaza cancerului de sân la şoareci. [SEP] Justify:

Output: The text contrasts the claim by discussing the specific medicinal properties of AHCC, which is derived from mushrooms, but does not provide evidence that all mushrooms have medicinal properties. Instead, it suggests that while AHCC shows promise in certain health conditions, this does not imply that every type of mushroom possesses medicinal benefits.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: Line 262 – does this mean a large amount of the cells that grew are now dead? makes an interesting observation. Indeed, the combination of a 4-fold increase in dry weight and only 2-fold increase in viable cells may indicate that a fraction of the biomass was dead or not metabolically active enough to form a colony at the time point sampled. In support of this idea, our measurements of cell density by OD600 suggest that cells reach stationary phase shortly after reaching maximum current density. Additionally, shortly after maximum current density (after day 2, Figure 3C), the rates of mannitol consumption, lactate production, and ethanol production decrease (Figure 4). Thus, we hypothesize that at the point of maximum current density, when dry weight and CFU measurements were taken, the cells are entering stationary phase and a fraction of them are metabolically inactive or dead. In the revised manuscript, we point out that this discrepancy could be due to the increased acid stress on L. plantarum resulting from EET condition (lines 337-340). Figure 4 (and Figure 1) – I don't understand why maximum current output is completely decoupled from when biomass spikes. At 24h (maximum current), basically no growth has occurred. At 2 days and 5 days, when biomass is the greatest (in the WT culture), very little current is produced. This seems like direct evidence that EET is not coupled with metabolism in these bacteria. The ATP measurements were made at 24h, where OD of the mutant is decreasing (thus less ATP would be expected). Same issue with NAD/NADH measurement. We apologize for introducing confusion here, which stemmed from a lack of clarity about which current density and biochemical measurements were from different experiments. We have clarified in the that the same set of experiments yielded the current density plots in Figure 3 and the metabolite and pH measurements shown in Figure 5. We have also clarified that another set of experiments were used to generate the current density shown in Figure 1C and the ATP and NAD/NADH ratios shown in Figure 4. Comparison of the data shown in Figure 1C and 4C show maximum current is closely followed by maximum OD. After one day, the current density has reached its maximum, but no significant increase in planktonic biomass was observed. [SEP] Justify:

Output: The text does not address the importance of lactic acid bacteria in fermentation processes directly. Instead, it discusses experimental observations related to cell growth, metabolic activity, and measurements of current density in the context of L. plantarum. It raises questions about the relationship between maximum current output and biomass, as well as the metabolic state of the bacteria, but does not explicitly support or refute the claim regarding the importance of lactic acid bacteria in fermentation.


Input: Task: corroborate the claim using the given text. Claim: Mass extinctions have shaped the diversity of species on Earth. [SEP] Text: Rapid acidification of the ocean during the Paleocene-Eocene thermal maximum. Science 308:1611–15 [2003. A transient rise in tropical sea surface temperature during the Paleocene-Maximum. Science 302:1551–54 [10. 1146/annurev-earth-053018-060136 of Earth and 47, 275 (2019);content/journals/10. 1146/annurev-earth-053018-060136content/journals/10. 1146/annurev-earth-053018-060136 Data & Media loading. . . 10. 1146/annurev-earth-053018-060136 dcterms_title,dcterms_subject,pub_keyword -contentType:Journal -contentType:Contributor -contentType:Concept -contentType:Institution 4 4 2003. Selective extinction among bivalves: a consequence of anoxia. Geology 31:1077–80 [1987. Why the rhynchonellid brachiopods survived and the spiriferids did not: a suggestion. Palaeontology 30:853–57 [2011. Terrestrial–marine teleconnections in the collapse and rebuilding of marine ecosystems. Palaeogeogr. Palaeoclimatol. Palaeoecol. 308:1–11 [1980. Extraterrestrial cause for the Cretaceous-Tertiary extinction. Science 208:1095–108 [2017. Mass extinction in tetraodontiform fishes linked to the Palaeocene–Eocene thermal maximum. Proc. R. Soc. B 284:20171771 [2014. Extreme warming of tropical waters during the Paleocene–Maximum. Geology 42:739–42 [2012. Carbon cycle dynamics following the end-Triassic mass extinction: constraints from paired δ13Ccarb and δ13Corg records. Geochem. Geophys. Geosystems 13:Q09008 [2002. Anatomical and ecological constraints on Phanerozoic animal diversity in the marine realm. PNAS 99:6854–59 [2010. Carbon sequestration activated by a volcanic CO2 pulse during Event 2. Nat. Geosci. 3:205–8 [2018. [SEP] Justify:

Output: The text describes various events related to mass extinctions and their consequences on different species and ecosystems, which supports the claim that mass extinctions have played a significant role in shaping species diversity. For example, it mentions 'selective extinction among bivalves' and the impact of 'anoxia,' indicating how mass extinctions have affected specific groups and overall biodiversity.


Input: Task: contrast the claim using the given text. Claim: All mushrooms have medicinal properties. [SEP] Text: Studiile clinice efectuate la pacienţi cu cancer hepatic avansat au arătat că AHCC poate îmbunătăţi prognosticul şi supravieţuirea, în comparaţie cu grupurile de control. Totuşi, este important să reţinem că rezultatele acestor studii sunt preliminare şi sunt necesare cercetări suplimentare pentru a confirma eficacitatea şi siguranţa AHCC în diverse condiţii patologice, iar dozele recomandate în literatura de specialitate nu sunt direct aplicabile în practica clinică şi ar trebui ajustate în funcţie de fiecare pacient, sub supravegherea unei echipe medicale(2-14). Din medicina populară asiatică şi din Extremul Orient, de exemplu, au fost studiate patru ciuperci comune pentru a se demonstra natura lor chimică complexă şi potenţialul lor anticancerigen. Prezentăm efectele diferitelor derivate ale ciupercilor, iar mecanismele lor sunt descrise pe diverse modele. Pictogramele (şoarece, macrofage, om) indică rezultatele obţinute pe modele animale, celule, respectiv la subiecţi umani(15). Studiile privind potenţialul anticancerigen al ciupercilor medicinale indică faptul că acestea pot fi eficiente în inhibarea proceselor specifice cancerului şi în activarea apoptozei celulelor tumorale. [SEP] Justify:

Output: The text contrasts the claim by discussing studies that specifically investigate certain medicinal mushrooms in the context of advanced liver cancer treatment. It highlights that while some mushrooms may have anticancer properties, it does not imply that all mushrooms possess medicinal properties. Furthermore, it mentions the need for additional research to confirm the efficacy and safety of the mentioned mushrooms, indicating that not all mushrooms may have medicinal benefits.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: Between day one and day two, lower but significant current is produced, the cell density reaches ~90% of its maximum, and the consumption of mannitol and production of lactate also increases dramatically. Overall, these observations show that current production is followed by increases in growth and metabolic flux. We hypothesize that the delay observed between current production and the boost in growth and metabolites could be the time cells need to accumulate ATP and compounds needed to enter exponential growth (now included on lines 274-278). In future experiments, we seek to more precisely relate current produced and growth by continuously monitoring of L. plantarum cell density under EET conditions. Figure 4C – Lines are undefined in the figure legend. Also, growth should be plotted on a semi-log scale, see: We have addressed the reviewer recommendation and edited Figure 4C accordingly. Figure 5 – based on the growth curve shown in Figure 4, the OC culture lags behind and does not reach maximum OD until day 5. What do these measurements look like at day 5 (or 6)? It seems likely that the authors are drawing conclusions from cells in two different states (stationary phase vs exponential phase) rather than focusing on the finding that having an external electron acceptor appears to accelerate the metabolism of cells. is correct that at the time of ATP and NAD/NADH measurements, the cells performing EET and cells under OC were at different growth stages. 4, we probed how EET in L. plantarum affected growth, ATP and intracellular redox state. To show this connection, we chose to measure ATP and NAD+/NADH when EET rate is maximum (maximum current density). These measurements show that energy metabolism is greatly accelerated and changed by EET: cells exhibit higher viability, biomass and ATP accumulation and maintain a higher NAD+/NADH ratio. We agree that performing those measurements at other time points would provide a more dynamic picture of the relationship between EET, energy conservation and redox balancing. Our laboratories will address these questions in future studies. Line 465 – Description of the experiment setup in 2B does not include addition of flavins for the iron reduction assay, so it is unclear why the authors claim that both flavins and quinones are necessary for EET in diverse LAB species. [SEP] Justify:

Output: The text does not provide any direct information regarding the importance of lactic acid bacteria in fermentation processes. Instead, it discusses various experimental observations related to current production, growth rates, and metabolic changes in L. plantarum without explicitly mentioning fermentation or its significance. Therefore, the text is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Mass extinctions have shaped the diversity of species on Earth. [SEP] Text: A new high-resolution chronology for the late Maastrichtian warming event: establishing robust temporal links with the onset of Deccan volcanism. Geology 46:147–50 [2007. The stability of the stratospheric ozone layer during the end-Permian eruption of the Siberian Traps. Philos. Trans. R. Soc. A 365:1843–66 [2012. Magnitude and consequences of volatile release from the Siberian Traps. Earth Planet. Sci. Lett. 317–318:363–73 [2014. Sulfur isotopic evidence for sources of volatiles in magmas. Earth Planet. Sci. Lett. 394:58–69 [2017. Volatiles and the tempo of flood basalt magmatism. Earth Planet. Sci. Lett. 458:130–40 [2011. Significant increases in global weathering during Events 1a and 2 indicated by calcium isotopes. Earth Planet. Sci. Lett. 309:77–88 [2010. Pyrite framboid study of marine Permian–Triassic boundary sections: a complex anoxic event and its relationship to contemporaneous mass extinction. Geol. Soc. Am. Bull. 122:1265–79 [2014. Large igneous provinces and mass extinctions: an update. Volcanism, Impacts, and Mass Extinctions: Causes and 29–55 Geol. Soc. Am. Spec. Pap. 505 Boulder, CO: Geol. Soc. Am. [2012. Osmium-isotope evidence for volcanism, weathering, and ocean mixing during the early Aptian OAE 1a. Geology 40:583–86 [2015. Calcium isotope evidence for dramatic increase of continental weathering during the Toarcian oceanic anoxic event (Early Jurassic). Earth Planet. Sci. Lett. 411:164–76 [2011. Rapid expansion of oceanic anoxia immediately before the end-Permian mass extinction. PNAS 108:17631–34 [2017. Initial pulse of sills as the trigger of the end-Permian mass extinction. Nat. Commun. 8:164 [2017. Hydrological and associated biogeochemical consequences of rapid global warming during the Paleocene-Maximum. Glob. Planet. Change 157:114–38 [2011. [SEP] Justify:

Output: The text includes references to significant geological events, including mass extinctions and their associated environmental consequences. It discusses the end-Permian mass extinction, which suggests a link between cataclysmic geological activity and biodiversity changes. This supports the claim that mass extinctions have impacted the diversity of species on Earth.


Input: Task: contrast the claim using the given text. Claim: All mushrooms have medicinal properties. [SEP] Text: De asemenea, ele pot avea acţiuni indirecte, cum ar fi imunomodularea, care pare să fie comună pentru multe specii de ciuperci medicinale. Această imunomodulare poate contribui semnificativ la potenţialul terapeutic al acestor ciuperci. Extrasele de ciuperci, care sunt testate împotriva diverselor tipuri de cancer în diferite modele experimentale, prezintă activităţi imunostimulatoare şi pot avea, de asemenea, proprietăţi antioxidante, antibacteriene şi antiinflamatorii. Aceste activităţi multiple pot fi utile în prevenirea cancerului şi în reducerea riscului de apariţie a bolilor tumorale. Ciupercile medicinale trec printr-o serie de etape în dezvoltarea medicamentelor, inclusiv extracţia, fracţionarea şi purificarea compuşilor activi. Aceşti compuşi sunt apoi testaţi împotriva modelelor de cancer în studii preclinice, animale şi clinice. În paralel, se studiază mecanismele de acţiune ale acestor compuşi şi ţintele lor moleculare, pentru a înţelege mai bine modul în care aceste ciuperci pot fi utilizate în terapia cancerului. [SEP] Justify:

Output: The text contrasts the claim by discussing the specific medicinal properties of certain mushrooms, particularly medicinal mushrooms, which have immune-modulating effects and other therapeutic benefits. It implies that not all mushrooms have these properties, as it focuses on species classified explicitly as 'medicinal mushrooms,' thus suggesting that the claim lacks universality.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: We included both flavins and quinones in this statement because we show that flavins are required for EET in Figure 1—figure supplement 1D and Figure 1—figure supplement 2D. Flavins are required as cofactors for Ndh2 (as FAD – see Heikal et al. , 2014 – Mol Micro) and PplA (as FMN – see Light et al. , 2018 – Nature). L. plantarum and several other LAB which we found to be EET-active are auxotrophic for riboflavin (Burgess et al. , 2004 – Microbio) so riboflavin was already supplemented in the growth medium as the vitamin itself (in CDM) or within yeast extract (in MRS). In the iron reduction assay, cells are metabolically active, but not growing, and would have sufficient holo-Ndh2 and holo-PplA carried over from their growth medium to perform EET. This is supported by new data in Figure 1figure supplement 1E where additional riboflavin supplementation into mMRS did not increase subsequent iron reduction. As such, we decided to not include riboflavin in the iron reduction assay used for Figure 2B. Line 473 – Iron and electrode reduction is dependent on addition of DHNA. Are these cells likely to ever encounter 20 ug/mL DHNA in the environment? Is the EET activity observed relevant to normal physiology for these organisms, or a lab artifact caused by providing a non-native electron carrier? The argument beginning on line 491 underscores the artificial nature to me. is correct in stating that it is unlikely for L. plantarum to encounter 20 µg/mL DHNA in its native environment. DHNA is found in concentrations of 0. 089-0. 44 μg/mL in commercial fermented beverages, and under laboratory conditions, microbes can synthesize and secrete DHNA leading to concentrations of 0. 37-48 μg/mL (lines 153-156). To test if EET in L. plantarum is relevant under these physiological concentrations, we probed whether L. plantarum can perform EET with a sub-physiological DHNA concentration of 0. 01 μg/mL. Indeed, L. plantarum produced significant current density and a significant decrease in pH (new Figure 1—figure supplement 3). [SEP] Justify:

Output: The text is irrelevant to the claim as it does not discuss the role of lactic acid bacteria (LAB) in fermentation processes. Instead, it focuses on other biochemical aspects related to EET and the specific conditions under which L. plantarum operates, without providing information on the importance of LAB in fermentation.


Input: Task: corroborate the claim using the given text. Claim: Mass extinctions have shaped the diversity of species on Earth. [SEP] Text: Environmental determinants and ecologic selectivity of benthic faunas from nearshore to bathyal zones in the end-Permian mass extinction: brachiopod evidence from South China. Palaeogeogr. Palaeoclimatol. Palaeoecol. 308:84–97 [2015. Oxygen limitations on marine animal distributions and the collapse of epibenthic community structure during shoaling hypoxia. Glob. Change Biol. 21:2989–3004 [2017. Organism activity levels predict marine invertebrate survival during ancient global change extinctions. Glob. Change Biol. 23:1477–85 [2011. Acidification, anoxia, and extinction: a multiple logistic regression analysis of extinction selectivity during the Middle and Late Permian. Geology 39:1059–62 [2004. Why does metabolism scale with temperature. ? Funct. Ecol. 18:243–51 [2015. Ocean acidification and the Permo-Triassic mass extinction. Science 348:229–32 [2018. Uranium isotope evidence for two episodes of deoxygenation during Event 2. PNAS 115:2918–23 [1994. Large igneous provinces: crustal structure, dimensions, and external consequences. Rev. Geophys. 32:1–36 [2014. Euechinoidea and Cidaroidea respond differently to ocean acidification. Comp. Biochem. Physiol. A 174:45–55 [2013. Buffer capacity of the coelomic fluid in echinoderms. Comp. Biochem. Physiol. A 166:199–206 [1920. The alkali reserve of marine fish and invertebrates: the excretion of carbon dioxide. J. Biol. Chem. 44:329–44 [2018. Similar controls on calcification under ocean acidification across unrelated coral reef taxa. Glob. Change Biol. 24:4857–68 [2015. Investigating the paleoecological consequences of supercontinent breakup: Sponges clean up in the Early Jurassic. Sediment. Record 13:24–10 [2003. On the ages of flood basalt events. C. R. Geosci. 335:113–40 [2016. [SEP] Justify:

Output: The text provides various studies and evidence connected to different mass extinction events and their ecological consequences, supporting the claim that mass extinctions have impacted species diversity. For example, the mention of 'environmental determinants and ecologic selectivity of benthic faunas from nearshore to bathyal zones in the end-Permian mass extinction' suggests a direct relationship between mass extinction events and changes in species diversity, thus corroborating the claim.


Input: Task: contrast the claim using the given text. Claim: All mushrooms have medicinal properties. [SEP] Text: În ciuda progreselor înregistrate în domeniul cercetării asupra ciupercilor medicinale, există încă multe aspecte care trebuie investigate mai detaliat, cum ar fi identificarea exactă a compuşilor activi şi înţelegerea mecanismelor lor de acţiune la nivel molecular. Cu toate acestea, cercetările continue în acest domeniu ar putea aduce noi perspective şi tratamente inovatoare pentru cancer, în special prin explorarea sinergiei dintre diferitele componente ale ciupercilor medicinale. Am arătat astfel că unele aspecte ale fungoterapiei tumorilor sunt studiate relativ bine, în timp ce altele încă aşteaptă să fie dezvăluite pe deplin (identificarea tipurilor de cancer care sunt susceptibile la tratamentele fungice). În final, subliniem că ciupercile medicinale au fost studiate intens pentru a se explica natura lor chimică şi mecanismele de acţiune ale capacităţii lor biomedicale. Tratamentul adecvat al cancerului, nedăunător pentru ţesuturile sănătoase, a devenit un obiectiv în ultimele decenii, iar compuşii de origine fungică oferă un rezervor vast de potenţiale medicamente inovatoare. Autor pentru corespondenţă: Conf. dr. farm. pr. Gabriela Vlăsceanu E-mail: ga. vlasceanu@yahoo. com : niciunul declarat. : niciunul declarat. [SEP] Justify:

Output: The text contrasts the claim by indicating that despite advances in research on medicinal mushrooms, there are still many aspects that need further investigation, particularly in identifying specific active compounds and understanding their molecular mechanisms. It emphasizes that while some mushrooms have been studied for their potential medicinal effects, not all mushrooms are confirmed to have such properties, suggesting that not all mushrooms can be deemed medicinal without further evidence.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: Far from being artificial, these results show that the concentrations of DHNA in environments known to support L. plantarum growth have significant effects on its physiology and mechanisms to outcompete neighboring organisms. Line 559 – none of the 5. 5±2. 7-14. 54±0. 29 μg/g were quantified in distal colonic contents (Conley and Stein, 1992 – of Gastroenterol), and of 25. 3-34. 4 nmol/g were quantified from fecal samples (Karl et al. , 2017 – Clin Nut). Although we mainly focused on DHNA in this manuscript, it is reasonable to anticipate that L. plantarum can perform EET in the GI tract by responding to different forms of quinones due to their shared molecular structures. We will consider testing this hypothesis in our future studies. Line 637 – is ferrozine toxic to these cells? While not included in the data for this manuscript, we found that ferrozine does not inhibit L. plantarum growth. Therefore, there is no evidence that ferrozine is toxic to L. plantarum, nor do we expect that compound to impact the ferrihydrite reduction assay, which takes place over three hours and requires metabolically active, but not actively growing cells. Line 646 – Were these mutants complemented? Efforts for mutant complementation were made, but restoration of EET activity was variable, potentially because critical epigenetic regulatory conditions were not provided or because of the challenges of over-expression of membrane-bound proteins (Kang and Tullman-Ercek, 2018 – Methods). We are currently in the process of mutating all genes in the L. plantarum EET pathway and are including complementation analysis in order to identify the effects of gene proximity and synteny on EET activity. Line 653 – the suicide vector should be identified and referenced here. The text has been revised to specify the suicide vector along with a citation. General comments: Unclear why Figure 1C shows twice as much current twice as fast as Figure 3C in what appears to be identical conditions? We observe somewhat variable current production depending on the exact conditions used for inoculation of bioreactors. Although we maintained identical culturing conditions for L. plantarum before introducing the cells into bioelectrochemical reactors, the inoculum did show mild growth differences. [SEP] Justify:

Output: The text is irrelevant to the claim because it discusses the physiological effects of L. plantarum and various experimental observations, but it does not address the importance of lactic acid bacteria in fermentation processes specifically.


Input: Task: corroborate the claim using the given text. Claim: Mass extinctions have shaped the diversity of species on Earth. [SEP] Text: Extinction of fish-shaped marine reptiles associated with reduced evolutionary rates and global environmental volatility. Nat. Commun. 7:10825 [2014. Ichthyosaurs from the indicate a severe turnover across the Triassic–Jurassic boundary. Naturwissenschaften 101:1027–40 [2007. Tropical warming and intermittent cooling during the Cenomanian/Turonian oceanic anoxic event 2: sea surface temperature records from the equatorial Atlantic. Paleoceanography 22:PA1219 [2013. Surviving rapid climate change in the deep sea during the Paleogene hyperthermals. PNAS 110:9273–76 [2017. Extreme warmth and heat-stressed plankton in the tropics during the Paleocene-Maximum. Sci. Adv. 3:e1600891 [2016. Ocean warming, not acidification, controlled coccolithophore response during past greenhouse climate change. Geology 44:59–62 [2006. Nannoplankton extinction and origination across the Paleocene-Maximum. Science 314:1770–73 [2010. A framework for community interactions under climate change. Trends Ecol. Evol. 25:325–31 [2017. Isotopic signatures of mercury contamination in latest Permian oceans. Geology 45:55–58 [2005. Photic zone euxinia during the Permian-Triassic superanoxic event. Science 307:706–9 [2015. Plasticity in thermal tolerance has limited potential to buffer ectotherms from global warming. Proc. R. Soc. B 282:20150401 [2017. Very large release of mostly volcanic carbon during the Palaeocene–Maximum. Nature 548:573–77 [1999. The early Toarcian (Early Jurassic) and the Cenomanian–Turonian (Late Cretaceous) mass extinctions: similarities and contrasts. Palaeogeogr. Palaeoclimatol. Palaeoecol. 154:39–66 [2008. Catastrophic ocean acidification at the Triassic-Jurassic boundary. Neues Jahrb. Geol. Paläontol. 249:119–27 [2012. Conditions of Mytilus edulis extracellular body fluids and shell composition in a pH-treatment experiment: acid-base status, trace elements and δ11B. [SEP] Justify:

Output: The text corroborates the claim by discussing various mass extinctions, such as the extinction of fish-shaped marine reptiles and significant environmental events, which indicate a severe turnover of species. These mass extinctions are associated with reductions in evolutionary rates and global environmental volatility, suggesting their pivotal role in shaping the diversity of species on Earth.


Input: Task: contrast the claim using the given text. Claim: All mushrooms have medicinal properties. [SEP] Text: 1999;20(3):145-152. Department of Biochemistry, School of Medicine. AHCC on immobilization stress in the rat: beneficial effects of active hexose correlated compound. of Medical Sciences. 2001;28(1):559-565. . Amelioration by active hexose correlated compound of endocrine disturbances induced by oxidative stress in the rat. Endocr Regul. 2004 Mar;38(1):7-13. . Suppressive effects of on the increased activity of hepatic and renal ornithine decarboxylase induced by oxidative stress. Life Sci. 2003 Dec 19;74(5):593-602. doi: 10. 1016/j. lfs. 2003. 06. 038. Wang S. Preventive effects of active hexose correlated compound (AHCC) on oxidative stress induced by ferric nitrilotriacetate in the rat. of Medical Sciences. 2001;28(2-3):745-752. Daddaoua A, Martínez-Plata E, López-ález árez MD, de Medina FS, Martínez-Augustin O. Active hexose correlated compound acts as a prebiotic and is antiinflammatory in rats with hapten-induced colitis. J Nutr. 2007 May;137(5):1222-82. . Medicinal mushrooms as an attractive new source of natural compounds for future cancer therapy. Oncotarget. 2018 Jun 26;9(49):29259-29274. Articole din ediţiile anterioare NUTRIŢIE | Ediţia 2 217 2024 Ciupercile medicinale şi sistemul imunitar (I) Gabriela Vlăsceanu Ciupercile au fost utilizate de-a lungul istoriei pentru proprietăţile lor medicinale. [SEP] Justify:

Output: The text provides a broad overview of various studies that focus on the medicinal properties of specific compounds derived from mushrooms, particularly the active hexose correlated compound (AHCC), but does not support the claim that 'All mushrooms have medicinal properties.' Instead, it suggests that only certain mushrooms or compounds within mushrooms have recognized beneficial effects, thus contrasting the claim.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: This can cause significant differences in the electrochemical output (current density). Thus, we suggest the differences in the current density production by the wild-type strain between Figure 1C and Figure 3C result from possible differences on the initial number and activity of cells. Future work will seek to uncover how initial conditions affect EET in L. plantarum. Reviewer #3 (Recommendations for the authors): Figure 1A – though the tubes are aligned with the plot below, it may be helpful for some readers to have labels on this image to clarify the conditions of each. Numbered labels are now provided in Figure 1A to connect the image and the graph. Figure 1C – for the top line, the "+DHNA+mannitol" label should be on one line Figure 1C has been revised to include this suggestion. Figure 4A – labeling should be more consistent ("anodic" vs. "EET") We have revised the Figure accordingly and replaced anodic with EET. Figure 4A – "log" should be removed from the y-axis label We thank the reviewer for noticing this. We have corrected this typo. Figure 4C – points on this plot should be connected with straight lines We have addressed this suggestion accordingly, and we have also plotted Figure 4C in a semi-logarithmic scale following another reviewer’s suggestion. Figure 5D – axis label is cut off We thank the reviewer for noticing this and we have corrected this typo. Figure 5G – FLEET should not be mentioned in the model at all. Instead, Ndh2 should be labeled We have edited the Figure following the recommendations of the reviewer. Figure 6A – Label differences between the two kale juice bottles We apologize for omitting some of the details of the juice preparation in that plot. We have indicated the differences between the two juices in Figure 6D by adding details on the preparation steps. Authors should also provide more information for the definitions of YATP and the values in Table 1 We have provided the definition of each yield at the bottom of Table 1. Line 137: Where the authors compare current density capacity for L. plantarum to that of S. oneidensis—are the quoted values for S. oneidensis using (an) endogenously produced shuttle(s), or are they for S. oneidensis + (an) added shuttle(s)? This should be clarified, because L. [SEP] Justify:

Output: The text does not address the claim regarding the importance of lactic acid bacteria in fermentation processes. Instead, it discusses specific figures and suggestions for figures related to a study on current density and electrochemical outputs in strains, focusing on revisions and clarifications from a reviewer. As such, it does not provide any relevant information regarding the role of lactic acid bacteria in fermentation.