Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Javascript is disabled in your browser. Please enable Javascript to view PeerJ. Differentially expressed serum proteins in children with or without asthma as determined using isobaric tags for relative and absolute quantitation proteomics All reviews of published 2023. Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the 2020. The first revision was submitted on August 1st, 2020 and was reviewed by 2 reviewers and the Academic Editor. A further revision was submitted on August 26th, 2020 and was reviewed by the Academic Editor. The 2020. Version 0. 3 (accepted) · Aug 26, 2020 · changes you have made in the manuscript have improved the manuscript. Congratulations! ! [# PeerJ - this decision was reviewed and approved by Vladimir Uversky, a PeerJ covering this Section #] 0. 3 (PDF) Download author's response letter - submitted Aug 26, 2020 Version 0. 2 · Aug 11, 2020 · Please address the comments of the reviewers and submit a revised manuscript. · Aug 8, 2020 Basic reporting No comment. Experimental design No comment. Validity of the findings No comment. Additional comments Asthma is one of the most common chronic noncommunicable diseases, which is a chronic inflammatory disease of the lower airway that is commonly encountered by the otolaryngologist. Asthma is a serious global health issue and asthma guidelines recommend a stepwise approach to management with goals to achieve control and minimize future risk. It is a good idea to investigate the protein composition and expression levels in serum samples obtain from children with or without asthma. In this manuscript, Dr. Fang and colleagues looked at the role of the differentially expressed proteins (DEPs) identified by using isobaric tags for relative and absolute quantitation (iTRAQ) combined with liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses in the pathogenesis of childhood asthma. The study provides the conclusion, which showed that numerous DEPs that may play important roles in the pathogenesis of childhood asthma. Those proteins may be novel biomarkers of childhood asthma and may provide new clues for the early clinical diagnosis and treatment of childhood asthma. After the modification, the data quality and language description are improved. [SEP] Justify:

Output: The text discusses a specific study related to differentially expressed serum proteins in children with asthma but does not mention or confirm the broader definition of proteomics as the study of the entire set of proteins expressed in a cell. Therefore, it does not support or contrast the claim, making it irrelevant.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: 7H2O, FeSO4. 7H2O, FeCl3, NaCl at concentration of 0. 1% (w/v)). Similarly the effect of surfactants was studied by supplementing the culture medium with Tween 80 and Tween 40 at concentration of 1. 5% (v/v). All media containing gelatinized starch sources were autoclaved at 121 °C for 20 min, while for the media containing raw starch flour, starch powder was sterilized by washing in ethanol and added to sterile nutrient broth. 3. 5. Partial enzyme purificationThe culture supernatant was supplemented with solid ammonium sulphate to 65% (w/v) final concentration, with mechanical stirring at 4°C. The suspension was retained for 1 h at 4 °C, and centrifuged at 8000 g for 30 min at the same temperature. The resultant supernatant was brought to 70 % w/v ammonium sulphate saturation at 4°C. 50-70% (w/v) ammonium sulphate precipitate was recovered, dissolved in 0. 1 M phosphate buffer and dialysed using Spectra/PorR, VWR 2003 dialysis membrane overnight against the same buffer at 4°C and used as partial purified enzyme solution. 3. 6. Effect of temperature and pH on activity and stabilityThe optimal temperature for amylase activity was determined by assaying activity between 30 and 100°C for 30 min in 50 mM phosphate buffer. Measurement of optimum pH for amylase activity was carried out under the assay conditions for pH range of 3. 0-10. 0, using 50mM of three buffer solutions: Tris-HCl (pH 3. 0), Na2HPO4-Citrate (pH 4. 0 – 6. 0), and Glycine-NaOH (pH 7. 0-10. 0). The temperature stability was determined by incubating the partial purified enzyme solution in water bath for temperature range of 30-100°C for 30, 60, 90, 120, 180 min and then cooled with tap water. The remaining α-amylase activity was measured and expressed as the percentage of the activity of untreated control taken as 100%. [SEP] Justify:

Output: The text discusses methods related to enzyme activity and purification, specifically an amylase enzyme, but does not mention lactic acid bacteria or their role in fermentation processes. Therefore, it is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Panspermia is a hypothesis about the transfer of life between planets. [SEP] Text: Therefore, scientists study bioforming: the seeding of a planet with life. Bioforming a planet There is an alternative method for altering a planet’s environment. suggest that bioforming provides a faster alternative for planet-wide alterations. Here, genetically engineered organisms can be introduced to an inhospitable planet. These cells could gradually modify the surface environment and atmosphere through processes such as excretion of gases or production of proteins whilst utilising whatever materials are available on the planet surface. Ultimately, they could create an environment more suitable for complex forms of life and habitable by humans. This seeding of a planet with life is known as directed panspermia. Nanocraft could travel at 20% the speed of light, making the journey to in just 20 years. Molecular biologists are already well versed in manipulating DNA in simple organisms such as bacteria and viruses. Using various techniques, scientists can find specific DNA code inside a cell and remove or alter it. This enables us to treat and prevent diseases, correct genetic defects and improve crop yields. Scientists are constantly learning more about the environmental conditions on exoplanets, and as telescope technologies improve, it will be possible to make accurate analyses of the atmospheric and surface conditions on distant bodies. Once we know more about a planet, propose that simple biological organisms already found on Earth could be tailored for survival in specific conditions using genetic engineering techniques. There have also been successful examples of completely synthetic DNA made from digitised genome sequences. Whilst scientists are within the earliest stages of synthetic biology and digitally designing a complete microbe, the research team suggest this method would ultimately be the most successful for the creation of the earliest colonisers. Using millions of computer simulations based on the known planetary conditions, scientists could create a synthetic microbial colonist that would be perfectly designed for the environment on an exoplanet. 2020, NASA’s discovered its first Earth-sized planet in the habitable zone. The find is called TOI 700 d. Dotted Yeti/Shutterstock. com Travelling across the stars As a species, we are only beginning to travel away from our home planet. We have successfully landed on the Moon, the closest planetary body to us, we are just beginning to explore Mars in detail using rovers, and probes have flown past all major planetary bodies. 1 and 2 probes, launched in the 1970s, are currently the only man-made objects to reach interstellar space outside of our solar system. [SEP] Justify:

Output: The text corroborates the claim by discussing 'directed panspermia' as a method of introducing life from one planet to another. It explains bioforming as the seeding of a planet with life, which aligns with the concept of panspermia being a hypothesis about life transfer between planets. Additionally, it describes how genetically engineered organisms may be introduced to inhospitable planets, further supporting the idea of life transfer.


Input: Task: contrast the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Numerous studies have successfully demonstrated the utility of high-resolution electrospray ionization liquid chromatography-tandem mass spectrometry (LC-ESI-MS/MS), which allows the highly sensitive identification of hundreds of distinct proteins in a given biomedical sample (Korte, Gaffney & Powell, 2012). Therefore, our current study incorporated LC-ESI-MS/MS label-free shotgun proteomic methodology with the aim of identifying significant changes in the expression levels of plasma proteins from SLE patients compared with healthy controls. The proteins identified as having altered expression levels may serve as potential candidate biomarkers for SLE disease assessment and monitoring of the disease progression. Materials and of SLE samples and healthy control samples A total of 19 SLE patients (female/male; 18/one; mean age 32. 1 ranging from 22 to 54 years) and the same age and gender-matched 12 healthy controls (female/male; nine/three; mean age 32. 9 ranging from 26 to 54 years of age) gave plasma samples that were obtained from the Hospital (CGH), Taipei, Taiwan. The disease assessment of the collected SLE samples was performed according to the classification criteria of the of Rheumatology (Tan et al. , 1982). () scoring method was used to determine the level of SLE disease activity (Bombardier et al. , 1992). Based on the disease activity index parameter results, all of the recruited SLE patients had active disease (more than eight) with high titers of anti-ds DNA antibodies, and the presence of proteinuria and low levels of complement. The demographic characteristics of patients and controls are presented in Table 1. Plasma was prepared from the whole blood samples, which were collected in heparin-containing tubes from both the SLE patients and the healthy controls. All of the patient samples were collected prior to the clinical treatment. The protein concentrations of the collected samples were determined by Bradford protein assay (Zor & Selinger, 1996) and the samples were stored at −80 °C until further analysis. This study obtained approval from the Board (IRB) (Approval code CT-09905) for at the Hospital (CGH), Taipei, Taiwan. Informed consent was provided by all blood donors. Table 1: General and demographic characteristics of the collected SLE patients and healthy controls plasma samples. [SEP] Justify:

Output: The text contrasts with the claim as it discusses a specific application of proteomics, focusing on the identification of proteins in plasma samples from SLE patients compared with healthy controls. It does not directly address the broader definition of proteomics as the study of the entire set of proteins in a cell.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: The first order inactivation rate constants, ki were calculated from the equation:lnA= lnA0−kit, where A0 is the initial value of amylase activity and A the value of amylase activity after a time t (min). For the determination of pH stability, the enzyme was incubated in a water bath at 60 °C at varying pH value for 30 min. The residual activity was detected under the same conditions and expressed as the percentage of the activity of untreated control taken as 100%. 3. 7. Effect of metal salts and chelating agentThe effect of metal salts and EDTA on amylase activity was determined by adding 0. 05 to 0. 1% (w/v) of metal salts (CaCl2. 2H2O, MgSO4. 7H2O, FeSO4. 7H2O, NaCl, FeCl3, CuSO4. 5H2O) and EDTA to the standard assay. The effect of metal salts and chelating agent on amylase activity were evaluated by pre-incubating the enzyme in the presence of effectors for 30 min at 60°C. The remaining amylase activity was determined and expressed as the percentage of the activity of untreated control taken as 100%. 3. 8. Analytical methodsCell growth was evaluated by reading the absorbance of culture medium at 600 nm using a Secoman spectrophotometer and numeration of total colony forming unit by 10-fold serial dilution of fermented broth and pour plating on MRS-starch agar (Rogosa and Sharpe medium in which glucose has been replaced by soluble starch (Prolabo-Merck Eurolab, France)). In order to evaluate the capacity of microorganism to acidify the culture medium, the pH of the fermented broth was measured using an electronic pH meter (S20, Japan) The amylolytic power of Lactic acid bacteria was determined using the method of wells by inoculation of 10 μl of microbial strain in 4 mm depth micro-wells on the surface of MRS-starch agar plate. The starch hydrolysis halo was revealed after 48 h of incubation using iodine solution. [SEP] Justify:

Output: The text is largely focused on the methods and experimental procedures related to enzyme activity and microbial growth assessment, specifically involving amylase and interactions with metal salts and chelating agents. While it mentions lactic acid bacteria in the context of determining their amylolytic power, it does not explicitly discuss their importance for fermentation processes. Thus, it does not provide direct relevance to the claim.


Input: Task: corroborate the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: Molecules, morphometrics and new fossils provide an integrated view of the evolutionary history of Rhinopomatidae (Mammalia: Chiroptera) 1. We also report the first Neogene fossil record of Rhinopomatidae and discuss the history of this unique family of bats. Figure 1Extant geographic distributions of species of rhinopomatid bats. (after [9, 56]): gray grid – R. hardwickii lineage, dashed line – R. microphyllum, dotted line – R. muscatellum lineage, full line – R. macinnesi. Localities of the DNA samples used in the present paper (comp. Table 1): dots – R. hardwickii lineage, diamonds – R. microphyllum, squares – R. muscatellum lineage, asterisk – fossil Rhinopoma aff. Hardwickii. Type localities of individual named taxa: ar – arabium Thomas, 1913, as – asirensis Nader et Kock, 1982, co – cordofanicum Heuglin, 1877, cy – cystops Thomas, 1903, hd – hadithaensis Khajuria, 1988, hr – harrisoni Schlitter et DeBlase, 1974, hw – hardwickii Gray, 1831, ki – kinneari Wroughton, 1912, le – lepsianum Peters, 1859, ma – macinnesi Hayman, 1937, mi – microphyllum Brünnich, 1782, mu – muscatellum Thomas, 1903, pu – pusillum Thomas, 1920, se – sennaariense Kock, 1969, si – seianum Thomas, 1913, so – sondaicum et De Vree, 1994, su – sumatrae Thomas, 1903, tr – tropicalis Kock, 1969. Full size imageTable 1 Taxonomic structure of Rhinopomatidae: a tabular surveyFull size tableResultsMorphometryDespite using a considerably extended set of morphometrical characters and applying multivariate morphometric analyses (based on 252 specimens, including types of 7 taxa, see [16] for details) our results revealed the same pattern of variation as reported in detail by [9], and Benda et al. [16, 17]. Rhinopoma microphyllum, R. [SEP] Justify:

Output: The text corroborates the claim by discussing how both new fossils and other methodologies, such as morphometrics, contribute to an integrated view of the evolutionary history of the Rhinopomatidae family of bats. It specifically mentions the 'first Neogene fossil record of Rhinopomatidae,' underscoring that fossils indeed provide significant insights into the evolutionary history of this group.


Input: Task: pass the claim using the given text. Claim: Gene expression analysis helps understand cellular responses to stimuli. [SEP] Text:  491) 72, 67 Pro-LDBPK_181-100 2(510, 519) - LDBPK_180370 8(23, 33, 147, 634, 640, 767, 1126, 1191) 114, 127, 65 Pro-LDBPK_180-920 2(817, 999) 182 LDBPK_180360 2(1023, 1030) - Pro-LDBPK_180-810 3(230, 827, 1372) - LDBPK_180270 5(54, 310, 698, 892, 988) 194, 96 Pro-LDBPK_180-790 3(327, 651, 757) 106 LDBPK_181100 2(290, 811) - Pro-LDBPK_180-650 9(173, 502, 546, 660, 723, 785, 872, 1098, 1816) 44, 114, 63, 62, 87 LDBPK_181080 7(112, 452, 550, 887, 1403, 2345, 2400) 98, 55 Pro-LDBPK_180-580 3(141, 510, 626) 116 LDBPK_180920 8(223, 257, 308, 1088, 1246, 1282, 1389, 1790) 51, 158, 107 Pro-LDBPK_180-510 9(226, 422, 902, 918, 1106, 1175, 1473, 1586, 1929) 196, 188, 69, 113 LDBPK_180810 5(32, 202, 701, 730, 759) 170 Pro-LDBPK_170-660 1(149) - LDBPK_180790 5(193, 257, 304, 704, 1014) 64, 47 Pro-LDBPK_170-610 3(124, 192, 783) 68 LDBPK_180650 2(53, 403) - Pro-LDBPK_212-210 2(263, 427) 164 LDBPK_180580 2(15, 113) 98 LDBPK_180510 23(305, 554, 560, 631, 722, 1073, 1142, 1243, 1423, 1447, 1484, 15 [SEP] Justify:

Output: The text appears to be a dense list of identifiers and values related to gene expression data, but it does not provide any clear information or context directly supporting or contrasting the claim regarding gene expression analysis and its usefulness in understanding cellular responses to stimuli. Therefore, this text is deemed irrelevant to the claim.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: The amylolytic power was defined as the average diameter (mm) of hydrolysis halo provoked by a strain after its inoculation in micro-well on MRS-starch agar plate for 48 h incubation at optimum temperature of growth for three assaysThe activity of amylase both in crude and purified extracts was assayed by iodine method. In a typical run, 5 ml of 1% soluble starch solution and 2 ml of 0. 1M phosphate buffer (pH 6. 0) were mixed and maintained at a desired temperature for 10 min, then 0. 5 ml of appropriately diluted enzyme solution was added. After 30 min the enzyme reaction was stopped by rapidly adding 1ml of 1M HCl into the reaction mixture. For the determination of residual starch, 1 ml of the reaction mixture was added to 2. 4 ml of diluted iodine solution and its optical density was read at 620 nm using a spectrophotometer (Secoman). One unit of amylase activity (U) was defined as the amount of enzyme able to hydrolyse 1 g of soluble starch during 60 min under the experimental condition. The lactic acid was determined according to Kimberley and Taylor [51]. The nature of amylase (endo-acting or exo-acting) was determined according to Ceralpha method (Megazyme) which uses a blocked maltoheptaoside as substratre [57]. The affinity of the enzyme preparation from selected LAB toward raw cassava starch was studied by incubating 0. 2 g of raw cassava flour with 1ml of the enzyme solution at 60 ◦C for 15 min. After centrifugation, the α-amylase activity of the supernatant was measured and the adsorption percentage was calculated as follows: Adsorption (%)=A−BA×100, A is the original α-amylase activity and B is the α-amylase activity in the supernatant after adsorption on raw potato starch granules. For the determination of raw starch digestibility, raw cassava was used and the reaction mixture containing 100 U of α-amylase preparation from the selected LAB and 100 mg of raw cassava starch in a final volume of 10ml dispensed in 100ml Erlenmeyer flasks were incubated in alternative water bath shaker at 60◦C and 150 oscillations per min. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the amylolytic power of enzymes and their activities without mentioning the role of lactic acid bacteria in fermentation processes. It details experimental methods regarding amylase activity and starch digestibility but does not correlate with 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: 2, 3 and 4), and only 0. 5% genetic distance was found between (a) and (b), which are the most distant geographically. In contrast to the inner shallow cline of genetic variation, clade II is separated from the Iranian one (clade I) by a relatively deep genetic gap (8–9%). Deep divergence was also found within the R. muscatellum lineage. haplotypes (clade III) and the haplotypes identified in Iran (clade IV) differ by a genetic distance of about 8–9%. Although the two available specimens of R. microphyllum (clade V) represented very distant geographic regions (Levant vs. India) and the local forms have traditionally been considered to be distinct subspecies or even separate species (R. microphyllum and R. kinneari), their genetic distance was very small (0. 5%). Interestingly, reconstruction of the topology of deep branches within the family using outgroup rooting resulted in sister positions for R. microphyllum and R. muscatellum lineages (Figure 3). The molecular clock analysis provided the minimum estimate of radiation of the family, i. e. the separation of the R. hardwickii lineage, to be approximately 28. 1 Ma. The next step, the splitting of the R. microphyllum and R. muscatellum lineages, was dated minimally to about 20. 9 Ma. The split between clades I and II happened about 14. 1 Ma, and the split between clades III and IV about 10. 0 Ma. Fossil recordWe found a rich sample of fossil remains unquestionably belonging to Rhinopoma sp. in a lithified infilling of a limestone karst cavity in Elaiochoria (Chalkidiki, Greece). [SEP] Justify:

Output: The text corroborates the claim by mentioning the discovery of a rich sample of fossil remains belonging to Rhinopoma sp., which directly relates to understanding the evolutionary history of life. The context of the fossil findings in relation to genetic distances and lineages further supports the idea that fossils are crucial in studying evolutionary relationships.


Input: Task: contrast the claim using the given text. Claim: Machine learning is increasingly used in predicting protein structures. [SEP] Text: The fact that the dataset was homogeneous (residents of Spain, all of whom were employed) constitutes a limitation of the research. Therefore, it is recommended that a future study be conducted that examines the prediction and importance of criteria and other indices for the prediction of metabolic syndrome in other populations based on additional datasets. The results of the study can be used with clinical informatics considerations, to assist in making monitoring and treatment decisions for patients through digital health systems. interventions can be beneficial for improving systolic blood pressure and anthropometric outcomes like waist circumference. 32 Automatized follow-up and alert systems provide support for the control and reduction of diseases associated with high blood pressure. Integration of new physiological variables for monitoring is feasible, and will broaden the scope for the early detection of chronic diseases including those associated with the metabolic syndrome, which could result in a reduction in their frequency. 33 The use of E-Health apps in most cases is voluntary, but persistence to goals can set the stage for long-term use, thereby promoting more favorable health outcomes. 34 The use of digital health-based lifestyle interventions may increase engagement and persistence in self-healthcare,35 which is essential in the case of the syndrome. ConclusionsIn this study, methods for predicting the syndrome through machine learning were examined. The study, using data drawn from a Spanish sample, examined the optimal number of indices needed to make a reliable prediction of the syndrome, whether each of the five indices for predicting the syndrome are equally important, and if not, what is the order of their importance, whether a reliable prediction can be made using calculated blood pressure indices – estimated mean arterial pressure and pulse pressure – instead of blood pressure indices, and the effect of gender on the indices’ importance and the prediction. According to the definition, at least three criteria are to be selected, with the assumption that all five indices for determination of the syndrome are of equal importance. In this study we show that this may not be the case. Moreover, the indices importance and their prediction quality included indices and other personal information, health habits, anthropometric measurements and blood measurements vary according to gender. Optimal results are obtained by using all five indices for prediction, and even when using just four instead of three indices, good prediction can be attained. [SEP] Justify:

Output: The text contrasts the claim by discussing the use of machine learning in predicting metabolic syndrome rather than protein structures. It does not provide evidence or examples related to predicting protein structures, indicating a different application of machine learning.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: On the other hand the maximum value of lactic acid was produced at the same temperature. Many other investigators reported that maximum amylase production occurred at the optimum growth temperature [56, 53]. These results are contrary to the findings of Chandra et al. [57] who studied the growth and amylase production of Bacillus licheniformis CUM 305. They have observed that this microorganism grew very well at 30°C, but did not produce α-amylase at that temperature. In addition, Saito and Yamamoto [58] found α-amylase production at 50°C and cell growth at a temperature lower than 45°C for another strain of B. licheniformis. The amylase and lactic acid production by L. fermentum 04BBA19 was influenced significantly by initial pH of culture broth (Fig. 3b). Maximum amylase and lactic acid production was achieved for pH range of 4. 0-6. 5. These results could be explained by the fact that pH generally act by inducing morphological change in microorganism which facilitate enzyme production [59]. 4. 3. Optimisation of amylase and lactic acid productionAmylase production is known to be induced by a variety of carbohydrate, nitrogen compounds and minerals [60, 61]. In order to achieve high enzyme yield, efforts are made to develop a suitable medium for proper growth and maximum secretion of enzyme, using an adequate combination of carbohydrates, nitrogen and minerals [53, 62]. Figure 3. a) Effect of temperature on microbial growth (○), α-amylase (●) and lactic acid () production. (b) Effect of initial pH of culture broth on α-amylase (●) and lactic acid () production. The data shown are averages of triplicate assays within 10% of the mean value. From the use of different carbohydrate sources in the present study, soluble starch proved to be the best inducer of amylase production (Table 1). In the presence of soluble starch at concentration of 1% (w/v), the enzyme yield reached 107. 0±1. 2 U/ml after 48 hours of fermentation, while in the presence of raw cassava starch at the same concentration, the enzyme yield was 67. 1±0. 5 U/ml. These results are in agreement with the reports of Cherry et al. [SEP] Justify:

Output: The text does not directly address the significance of lactic acid bacteria in fermentation processes. Instead, it details various studies related to the production of α-amylase and lactic acid by different microorganisms under varying conditions such as temperature and pH. While lactic acid is mentioned, the focus is more on amylase production and the conditions affecting these processes rather than establishing the importance of lactic acid bacteria specifically.


Input: Task: corroborate the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: The fauna indicates an early Turolian age, (MN 10–11), some 8–10 Ma. The analysis of the record [see Additional files 2 and 3] shows that: (i) the fossil material contains the all the morphological features that clearly distinguish Rhinopomatidae from other chiropteran families and, moreover, it falls within the variation of the Recent forms of the genus; (ii) the morphology corresponds to the hardwickii in the fine details of the dentition, in the shape of the distal epiphysis of the humerus, and in the shape of the proximal epiphysis of the radius; and (iii) the fossil material shows relatively large size variation and seems to exceed the range of variation in the Recent R. hardwickii, both in mean values and in the highest values (comp. Figure 2). DiscussionEven with the present analysis, the family Rhinopomatidae remains an enigmatic group whose history, taxonomic content, patterns of variation and phylogenetic relationships are far of being properly comprehended. Nevertheless, the data summarized here substantially improve the scarce information on these subjects. We will discuss them in regard to (a) composition of the group, (b) possible phylogeographic patterns and (c) evolutionary history. Composition of RhinopomatidaeThe analysis of the family Rhinopomatidae by [9] demonstrated that the genus consists of four species that differ in the shape of the palatal incision, the rostral ridges, the narial swellings, in the relative length of the tail, and in overall body size. The most distinctive in all these characters was R. microphyllum, whereas the differences between the remaining forms were less pronounced, exhibiting a broad measure of overlap in most metrical characters. Our analysis (n = 252) provided the same picture (Figure 2). All of these data suggest that the major phenotypic divergence within the genus is that between R. microphyllum (including R. m. kinneari, R. m. sumatrae and R. m. asirensis) and the remaining forms, which thought to be closely related to a medium-sized species, R. hardwickii (Figure 2c), see [18]. [SEP] Justify:

Output: The text corroborates the claim by presenting a detailed analysis of fossil material related to the family Rhinopomatidae, which includes morphological comparisons to recent forms. It discusses how the morphological features help to distinguish this group from other families and suggests that such fossil analysis substantially improves our understanding of their evolutionary history. This aligns with the claim that fossils provide insights into the evolutionary history of life by highlighting the importance of fossil data in understanding morphological variations and phylogenetic relationships.


Input: Task: contrast the claim using the given text. Claim: Coral reefs support a diverse range of marine species. [SEP] Text: However, the ecological context and the hypotheses to elucidate an overall pattern beyond what previous studies have found are not clearly stated. In addition, the network analysis presentation disregards the hosts' functional traits and lacks ecological relevance. The assigned morphological characteristics of the species are not specified and could be biased. The PCO is not discriminated by functional traits (or factors), so observing grouping by sponge functional patterns is impossible. Overall, the discussion of the manuscript lacks the ecological context and background on sponge morphology (incorrect assignments for many species), sponge-host interactions and fails to support the conclusions. The discussion travels too far from the data. It does not focus on what the data prove or demonstrate how the obtained results expand previous knowledge or support and challenge previous paradigms. In addition, the manuscript's English language and writing style needs improvement. Experimental design The experimental design (how many studies and from which locations were finally used for this specific metanalysis? ) is not specified. How many records of host species were assessed per location? What is the bias in terms of replication? Please include this information in the methods. Also, the tables in the with associated fauna and records should be merged, and a column with the location for each study should be included. Validity of the findings PCO figure should be discriminated by functional traits (i. e. , morphology). The network, patterns, and major contributors to the network structure are poorly explained. Overall, the results do not clarify how host-guest interactions vary based on functional groups; what are the major patterns? And how it varies across species. Figure 1. This figure refers to all the records obtained by the network and is not specific to the records used in this study after filtration. I suggest correcting this figure and including only the records used in this study after the data was filtrated (many records come from the same authors, so that you could add numbers or color-code per author). Also, adding the replicates (n= the number of host-species interactions) per location can help to understand the contribution of the studies and the number of records per location. Figure 2- This figure, as it is, lacks the most relevant information related to the functional characteristics of sponges. To explicitly show the functional characteristics of sponges and how they connect to specific hosts, sponges should be divided by functional characteristics such as 1. generalists and specialists, 2. [SEP] Justify:

Output: The text contrasts the claim by indicating that the manuscript lacks ecological context and fails to support its conclusions, particularly regarding the interactions and morphology of marine species, which are essential for demonstrating the diversity of marine life supported by coral reefs. It mentions that host-guest interactions are not clarified based on functional groups and critiques the experimental design, suggesting that it does not adequately assess the diversity or characteristics relevant to marine species associated with coral reefs.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: 7±0. 5bBeef extract92. 4±0. 5c7. 3±0. 2bPeptone88. 3±1. 7d7. 1±0. 3bTryptone75. 3±0. 5e6. 5±0. 5bSoya bean meal397. 3±0. 4a29. 2±0. 4aAmmonium sulphate95. 4±1. 5c7. 2. ±0. 8bUrea76. 3±0. 3e5. 3±0. 6cMinerals (0. 1% w/v)CaCl2. 2H2O 412. 1±0. 6a33. 2±0. 1aMgSO4. 7H2O315. 1±0. 4b31. 2±0. 5aFeSO4. 7H2O237. 3±0. 7c20. 2±0. 4bNaCl315. 2±0. 9b22. 1±0. 6bCuSO4. 5H2O12. 2±0. 6e3. 2±0. 3dSurfactants (1. 5% w/v)Tween-40209. 5±0. 1b27. 3±0. 4bTween-80215. 1±0. 3a35. 2±0. 3aGelatinized starchy sources (1 %w/v)Corn flour303. 5±0. 2a36. 3±0. 6aCassava flour182. 3±0. 4c24. 2±0. 8dSorghum flour305. 8±0. 7a35. 2±0. 1aRice flour187. 3±0. 8c30. 1±0. 5bTapioca flour237. 4±0. 6b27. 2±0. 7cRaw starchy sourcesCassava starch67. 1±0. 5c21. 3±0. 4aPotato starch87. 2±0. 5a23. 4±0. 1aCocoyam starch78. 6±0. 2b22. 7±0. 4aMediaBasal medium107. 5±0. 38. 7±0. [SEP] Justify:

Output: The text does not address or relate to the importance of lactic acid bacteria in fermentation processes. Instead, it consists of numerical data regarding various nutrients and their concentrations, which are not conducive to evaluating the claim about lactic acid bacteria.


Input: Task: corroborate the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: This split is supported by morphometric differences (Fig. 2). Recent allopatry is more obvious in this case because clades III and IV are geographically isolated by the Arabian Desert. However, geographic positioning of major genetic breaks in R. hardwickii and R. muscatellum lineages coincides with this division (Fig. 4). With respect to the genetic species concept, it is reasonable to consider species status also for clades III and IV [for taxonomic rearrangements in the R. muscatellum lineage, see Additional file 1]. (iv) Considering the relatively deep genetic divergences within the morphospecies R. hardwickii and R. muscatellum (in the sense of [9]), the surprisingly low degree of geographic divergence of mtDNA in R. microphyllum calls for a comment. At least two qualities of this species are worth discussing in this connection: (i) its larger body size, and (ii) the well-pronounced seasonality of its life cycle and reproduction, including regular seasonal movements [e. g. [27]]. Both of these factors may contribute to increases in vagility and the rate of gene flow. (v) The sister status of the R. microphyllum and R. muscatellum phylogroups contradicts traditional arrangements of the family where R. hardwickii and R. muscatellum are considered as the most closely related taxa based on similarities in narial morphology and body size (Figure 2c) [18, 28]. The morphological polymorphism in genetically uniform populations of R. cystops (clade II) and R. microphyllum (clade I) does, however, indicate that the body size can undergo rapid rearrangement regardless whether in reaction to environmental conditions or as a character displacement due to interspecific interactions. Worth mentioning in this context is the large body size of the fossil Rhinopoma aff. R. hardwickii, which clearly exceeds the limits of the Recent R. hardwickii to which the fossil form is linked by its morphological characters. All these cases suggest that body size, traditionally applied as a significant character in taxonomy of the genus (because of considerable uniformity in other morphological characters) is controlled by ecological factors rather than by a strict taxon-specific developmental constraint. [SEP] Justify:

Output: The text corroborates the claim by discussing the morphological traits and evolutionary relationships among various species, including reference to the fossil Rhinopoma aff. R. hardwickii. This fossil is linked to recent species by its morphological characters, indicating that fossils can inform us about the evolutionary history and morphological development of life forms. The mention of the fossil's larger body size in comparison to its modern counterpart supports the idea that fossils provide insights into evolutionary changes over time.


Input: Task: pass the claim using the given text. Claim: Phytoplankton produce a significant portion of Earth's oxygen. [SEP] Text: But lab work shows that in gas-phase chemistry, other factors produce isotope variation. It turns out that sulfate, which forms when sulfur is oxidized, is a very complicated molecule in gas-phase reactions. In particular, reaction products that include the 33S isotope are anomalously large compared with those that contain 34S or 32S. Such anomalies are called mass-independent fractionation. On Mars, UV light photolyzes sulfate and leads to fractionation. Laboratory experiments revealed that sulfur isotopes in Martian rocks show a mass-independent distribution. If there were no oxygen in Earth's atmosphere, UV light would get through as well, and similar anomalies would appear in the sulfur isotope record. “We know that sulfur in today's atmosphere gets oxidized by peroxide in ozone,” explains Thiemens. Farquhar did indeed see this isotope variation in 2. 45 billion-year-old Earth rocks. “We realized that this variation existed and the only mechanism we knew of that could produce it was related to gas-phase reactions,” he says. All that remained was to figure out the atmospheric conditions. “The sulfur allows you to see at most how much oxygen there was at the time,” says Thiemens. During the period prior to 2. 45 billion years ago, the photolytic effect can be seen. Then, when there was sufficient oxygen in the atmosphere, normal mass-dependent chemistry appears in the isotope record. Models suggested that this oxygen threshold is about 10 ppm. “We have been able to show fine-scale differences between the [sulfur isotopes] that show up. They fall into bins in different places in Earth's early record, and might give insight to what's happening in the atmosphere and oceans at any given times,” summarizes Farquhar. The sulfur isotope study provided one of the first continuous records that could be used to demonstrate a long-advocated change in oxygen levels. Other studies have used metals to study reactions that might be related to air oxidation states and redox reactions that occur in oceans and during weathering. Earlier or later? “There are polarized views in the geochemical and early Earth community about when oxygenic photosynthesis evolved,” says of the University of British Columbia. One camp insists that oxygen appeared in the atmosphere 2. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses gas-phase chemistry, isotope variation in sulfur, and historical atmospheric conditions, without mentioning phytoplankton or their role in oxygen production. Therefore, it does not corroborate or contrast the claim about phytoplankton's contribution to Earth's oxygen.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: In this respect, this amylase could be used in starch hydrolysis, brewing and baking. Figure 5. a) Effect of temperature on activity (○) and stability (■) of α-amylase from L. fermentum 04BBA19. (b) Effect of pH on activity (╳) and stability (■) of α-amylase from L. fermentum 04BBA19. The data shown are averages of triplicate assays within 10% of the mean value. The metal salts generally act on activity of enzyme through their ions. The enzyme activity was highly improved by Ca2+, while Fe2+, Fe3+, Na+ and Mg2+ had less significant effect. On the contrary Cu2+ and EDTA acted as inhibitors (Fig. 7). The behaviour of the enzyme towards metal ions, particularly calcium, indicates its metalloenzyme nature, which is confirmed by the action of EDTA. Figure 6. Thermostability pattern of α-amylase from L. fermentum 04BBA19, at 80, 90, 100°C without CaCl2. 2H2O (●) and with 0. 1% (w/v) CaCl2. 2H2O (□). The enzyme was pre-incubated at optimum pH, for 30, 60, 90, 120 and 180 min at temperatures (80, 90 and 100°C). The remaining activity was determined incubating the enzyme at optimum temperature, 60°C for 30 min. The data shown are averages of triplicate assays with SD within 10% of mean value. Temperatures80 °C90°C100°CCaCl2. 2H2O (% w/v)ki (10-3. min-1)T (min)ki (10-3. min-1)T (min)ki. (10-3. min-1)T (min)03. 4204. 05. 6123. 87. 987. 70. 11. 9364. 82. 6266. 63. 8182. 4Table 3. Inactivation rate constant (ki) and half-live (T) of amylase from L. fermentum 04BBA19 at 80, 90 and 100°C in the absence and the presence of 0. 1% (w/v) CaCl2. [SEP] Justify:

Output: The text provided discusses the activity and stability of α-amylase from the bacterium L. fermentum, focusing on its interactions with metal ions and temperature conditions. However, it does not mention the role of lactic acid bacteria in fermentation processes or provide any evidence supporting their importance in this context. Therefore, the text is 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 that respect it is similar to Megadermatidae (4 genera, 5 species) and Craseonycteridae (1 genus, 1 species), which are the sister clades of Rhinopomatidae according to the recent molecular data [3]. The present paper dates the beginning of radiation of extant clades of Rhinopomatidae (i. e. the separation of the R. hardwickii clade), to about 29 Ma in the Oligocene. Nevertheless, the datum is apparently not relevant for the beginning of the family which arose with the earliest divergence of Rhinolophoidea, which molecular clock studies place at 50–55 My [3, 7]in the Early Eocene. In contrast to other groups of Rhinolophoidea, whose early divergence is well represented in the fossil record, no such information is available for Rhinopomatidae and Craseonycteridae. In contrast to Creaseonycteriae, Rhinopomatidae occupies quite a large range comparable to that of other rhinolophoid families. At least for that reason, the absence of fossil record is unusual and calls for comment, at least as a background story to the discussion on meaning of the first Neogene record of the family reported in this paper. Despite the fact that the fossil record of bats is sometimes regarded as being quite a poor [3], it is actually rich enough to enable discussions on major differences in phylogeny and early paleobiogeography of particular chiropteran clades at least in Europe and northern Africa. The remains of bats, including rich and taxonomically diversified assemblages, have been found in more than 130 European and sites of the Late Eocene, Oligocene and age [29–31] and current views on the structure of chiropteran fauna and the history of particular clades during that period [32] can be considered relevant and reliable. Among Rhinolophoidea, Hipposideridae and Rhinolophidae are particularly rich in their fossil record and, with a number of divergent clades, they have predominated the fossil assemblages in Europe, Africa, and even Australia since the [32–34]. In contrast, no relevant fossil record is available for Craseonycteridae or (until this paper) for Rhinopomatidae. [SEP] Justify:

Output: The text supports the claim as it discusses the fossil record of various bat families, particularly focusing on Rhinolophoidea, and illustrates how these fossils contribute to understanding the phylogeny and evolutionary history of these clades. The mention that certain families have a rich fossil record, enabling discussions on phylogeny and paleobiogeography, aligns directly with the claim that fossils provide insights into the evolutionary history of life.


Input: Task: contrast the claim using the given text. Claim: Phytoplankton produce a significant portion of Earth's oxygen. [SEP] Text: ” Additionally, independent genomic analyses help to constrain the evolution of different genes involved directly in oxygenic photosynthesis, as well as of other cyanobacteria elements; these analyses will move us closer to an overall timing constraint. The next big thingA billion years of anoxic oceans followed the Event. Geochemical evidence points to the general oxygenation of the oceans around 635 million years ago, likely requiring a minimum of 10% present atmospheric levels. Whether through cause or effect, the ecosystem began to diversify at around the same time. “Right now, we lack solid constraints on the baseline of atmospheric oxygen leading up to the second rise,” says of Yale University. “That makes it difficult to understand the potential consequence, but also what geochemical change would have induced fundamental changes in oxygen levels. ”But the “boring billion” years between the two major oxygen rises brought with them dropping oxygen levels and constrained evolutionary activity. University of Tasmania geologist analyzed ancient seafloor muds to track trace elements absorbed from the seawater over time in pyrite iron sulfate, a unique mineral that forms in the muds. “Some trace elements are more soluble in the ocean when oxygen increases,” explains Large. “Thus we can use the trends in trace elements in pyrite to predict periods when atmosphere oxygen rose and fell. ” A laser analysis that detects lower levels than was previously possible showed that many nutrient trace elements decrease in the ocean from 1800 to 800 million years ago. Trace elements and oxygen likely declined because tectonics were stable and little erosion occurred on the continents. The lack of nutrients meant a drop in bacteria, leading to less oxygen being liberated to the atmosphere. Ultimately, however, a better global database of samples and laser geochemistry is needed to produce more robust curves for trace elements and oxygen. “We speculate that the increased trace elements [at 750 million years ago] led to a rapid increase in bacteria and plankton in the oceans, which in turn released oxygen to the atmosphere and sped up oxidative erosion of the continents,” says Large. The increased ocean productivity led to increased carbon burial on the sea floor, which drew trace elements and sulfur to the muds as sedimentary pyrites. That burial process increased atmospheric oxygen even more, and the Cambrian explosion of life was primed. Noah's arkThere were definitely no animals before the 2. [SEP] Justify:

Output: The text contrasts the claim by discussing various geological and geochemical processes related to the oxygenation of the oceans, including the role of bacteria and plankton. It suggests that there have been periods with dropping oxygen levels due to a lack of nutrients, leading to less oxygen being liberated—not supporting the idea that phytoplankton consistently produce a significant portion of Earth's oxygen. Furthermore, the mention of 'increased bacteria and plankton' signifies sporadic increases rather than a consistent contribution.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: Advertisement AcknowledgementWe gratefully acknowledge the assistance of the Ministry of and Brewing society “Société Anonyme des Brasseries du Cameroun” (SABC) who supported this work through Research-Programme. 1. ReddyG. AltafM. NaveeanaB. J. VentkateshwarM. VijayKumar. E. 2008Amylolytic bacterial fermentation. A review. 2622342. AxelssonL. 2004Lactic acid bacteria: classification and physiology. In: Salminen S, von Wright A, Ouwehand A, editors. Lactic acid bacteria: microbiological and functional aspects. 3rd rev. and exp. ed. New York: Marcel Dekker, Inc. ; 2004. 1663. AsoodehA. ChamaniJ. LagzianaM. 2010A novel thermostable, acidophilic α-amylase from a new thermophilic “Bacillus sp. Ferdowsicous” isolated from Ferdows hot mineral spring in Iran: Purification and biochemical characterization. Inter. J. Biol. Macromol. 462892974. SaxenaR. K. DuttK. ArgawalL. NayyarP. 2007A highly thermostable and alkaline amylase from a Bacillus sp PN5. Biores. Technol. 982602655. 2003Developments in industrially important thermostable enzymes: a review. Biores. Technol. 8917346. . 2006Metabolic engineering approaches for lactic acid production. Process Biochem. 4199110007. NguyenT. T. LoiseauG. Icard-VernièreC. RochetteI. TrècheS. GuyotJ. P. 2007Effect of fermentation by amylolytic lactic acid bacteria in process combinations, on characteristics of rice/soybean slurries: A new method for preparing high energy density complementary foods for young children. Food Chem. 1006236318. Songré-OuattaraL. T. Mouquet-RivierC. Icard-VernièreC. HumblotC. DiawaraB. GuyotJ. P. [SEP] Justify:

Output: The text is largely a compilation of references and acknowledgments related to various studies and publications, but it does not provide specific information regarding the role or importance of lactic acid bacteria in fermentation processes. Therefore, it is 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: The situation with Megadermatidae is more intricate. The first evidence of appearance of true Megaderma in Europe comes from the (MP25 Carrascosa del Campo, Spain [35]; MP29 Saint-Victor-la-Coste, France [36]; MP 29 Herrlingen 9, Germany [37]) and a number of further records are of Miocene and Pliocene age [37]. In contrast to hipposiderids or nycterids, the family is absent from sites (including Fayum or Taquah in Oman [30, 38] but appears in the of Thailand and even in Australia [39]. Eocene to genus Necromantis, often regarded as a megadermatid [31], differs from true megadermatids in several characters (including basisphenoidal pits, a key character of emballonurids, which is invariably absent in rhinolophoids) and most probably does not belong to that stock. The absence of Rhinopomatidae and the late first appearance datum of Megadermatids in the fossil record contrasts with the fact that other groups such as Emballonuridae, Hipposideridae, Rhinolophidae, Molossidae, and Vespertilionidae s. l. are constant components of the western Palaearctic and African fossil record since the late Eocene [31, 29, 40]. All had already produced a number of subclades during the Oligocene and [32, 37, 41]. The absence of any rhinopomatids in the fossil record is surprising because these bats differ from all others in a number of conspicuous dental and skeletal specificities by which they are easily distinguishable, even based on a single fragmentary tooth. Moreover, rhinopomatids are cave-dwellers, which predisposes them to be particularly common in the fossil record. Under such conditions their absence in fossil record can be interpreted as a real fact which most probably reflects actual absence of the group in the western Palaearctics prior to the Miocene. [SEP] Justify:

Output: The text corroborates the claim by discussing the fossil record of Megadermatidae, noting the intricacies of its evolutionary history and providing specific examples of fossil findings in different geographical locations. It also emphasizes the absence of certain groups in the fossil record and how this absence can indicate actual historical distribution, thus offering insights into the evolutionary pathways of life.


Input: Task: pass the claim using the given text. Claim: Deep-sea hydrothermal vents host unique ecosystems reliant on chemosynthesis. [SEP] Text: Products were purified using Millipore-Sigma (St. ) 03010 with a vacuum manifold and quantified using Scientific () QuantIT PicoGreen ds11496 on the BioRad CFX96 Touch Real-. Barcoded samples were combined in equimolar amounts into a single tube and purified with 28104 before submission to Laragen () for 2 × 250 bp paired end analysis on the Illumina MiSeq platform with PhiX addition of 15–20%. MiSeq 16S rRNA sequence data was processed in Ecology (v1. 8. 0). Raw sequence pairs were joined and quality-trimmed using the default parameters in QIIME. Sequences were clustered into de novo operational taxonomic units (OTUs) with 99% similarity using open reference clustering protocol, and then, the most abundant sequence was chosen as representative for each de novo OTU. Taxonomic identification for each representative sequence was assigned using the Silva-119 database, clustered at 99% similarity. A threshold filter was used to remove any OTU that occurred below 0. 01% in the combined samples dataset. Analyses are based on Bray-Curtis distances of fourth-root transformed data, which minimizes errors in the ordination due to PCR bias, while not sacrificing genuine differences between samples. Quantification and statistical analyses are described in the “Results” sections and figure legends. Comparisons were performed using ANOVA and statistical significance was declared at p < 0. 05. Statistical analyses of beta diversity (e. g. , ) were performed with Primer E. The raw Illumina 16S rRNA barcode sequences and metadata collected in this study are available from the (BioProject # PRJNA671766). The processed sequence data, as well as representative sequences, are available on the ( along with representative SUP05 OTUs in 6: DataFile S1). Molecular analysis of the anemone host Ostiactis pearseae Phylogenetic relationships were determined via sequencing of three mitochondrial markers, the 12S rRNA, 16S rRNA, and cytochrome oxidase III genes, and the partial nuclear 18S rRNA gene. An 862-bp product of the 12S rRNA gene was amplified via primers ANTMT12SF (5′--3′) and ANTMT12SR (5′--3′) according to [71]. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses specific molecular and statistical analysis methods regarding sequence data without mentioning deep-sea hydrothermal vents, ecosystems, or chemosynthesis. Therefore, it does not provide any corroborative or contrasting evidence related to the claim.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: 1997Lactic acid fermentation in a recycle batch reactor using immobilized Lactobacillus casei. 558435347. TatsinkouF. B. TaveaF. JiwouaC. NdjouenkeuR. 2009Screening of thermostable amylase producing bacteria and yeasts strains from some cameroonian soils. Afr. J. Microbiol. Res. 3950451448. TatsinkouF. B. TaveaF. JiwouaC. NdjouenkeuR. 2011Simultaneous production of raw starch degrading highly thermostable a-amylase and lactic acid by Lactobacillus fermentum 04BBA19. Afr. J. Biotechol. 10346564657449. SchillingerU. LuKe. F. K. 1987Identification of lactobacilli from meat and meat products. 419920850. DykesG. A. BritzT. J. vonHoly. A. 1994Numerical taxonomy and identification of lactic acid bacteria from spoiled, vacuum packaged Vienna sausages. Journal of 7624625251. KimberleyA. C. TaylorC. 1996A simple colorimetric assay for muramic acid and lactic acid. Appl. Biochem. Biotechnol. 56495852. Miller GL1959Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal. Chem. 3142642953. GoyalN. GuptaJ. K. SoniS. K. 2005A novel raw starch digesting thermostable α-amylase from Bacillus sp. I-3 and its use in the direct hydrolysis of raw potato starch. Enzyme and Microb. Technol. 3772373454. LiuD. X. XuY. 2008A novel raw starch digesting α-amylase from a newly isolated Bacillus sp YX-1: purification and characterization. Biores. Technol. 994315432055. HillerP. WaseD. EmeryA. N. 1996Production of α-amylase by Bacillus amyloliquefaciens in batch and continuous culture using a defined synthetic medium. Biotechnol. Lett. 1879579956. [SEP] Justify:

Output: The text does not directly address the claim regarding the importance of lactic acid bacteria in fermentation processes. Instead, it provides a collection of references and titles of studies related to lactic acid fermentation and various strains of bacteria, without explicitly discussing their significance in fermentation.


Input: Task: corroborate the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: Cricetidae) and a considerable contribution of non-mammalian taxa from the Indian and Indomalaysian provinces such as Gavialosuchus, Tomistoma, and Varanidae. The spread of these taxa into Europe has been dated to ca. 18 Ma [46]. Recent paleogeographic analyses [47, 48] supplement the picture with further data that show continuity between the Mediterranean-Iranian and the eastern Indian-east African marine provinces until the final disappearance of the seaway in the Early Miocene. In case of Rhinopomatidae, no such evidence is available. Miocene fossil record reported in this paper is apparently not related to the early history of the clade. Nevertheless, the results of molecular studies provide valuable information. The first dated split within the family (R. hardwickii s. l. vs. R. microphyllum-muscatellum: 28. 1 Ma) shows no phylogeographic signal – both clades are broadly sympatric. Nevertheless, the next cladogenetic events (R. microphyllum vs. R. muscatellum: 20. 9 Ma) have clear phylogeographic correlates. In the later events, the phylogeographic signals are even more pronounced: clades I vs. II (14. 1 Ma): Iran vs. Levant to Africa, and clades IV and III (10 Ma): Iran vs. Yemen. According to traditional biogeography [49, 50], the region with the largest concentration of taxonomic diversity is the most likely candidate for being the source area of the group in question. In the case of rhinopomatids, the present results would suggest Iran to be such a candidate. At the very least, these results suggest that Iran was an area of paleoendemism that played host for the ancestral clades more than 11 Ma ago. Nevertheless, the terrestrial conditions appeared in the respective region first at the time of Oligocene/Miocene transition [51] and thus the source area of the clades that colonized at in that time was apparently situated in other regions. [SEP] Justify:

Output: The text corroborates the claim by discussing various taxa from the Miocene fossil record and how molecular studies provide insights into their evolutionary history. It emphasizes that the fossil evidence, combined with paleogeographic analyses, enriches our understanding of the continuity and development of different clades and their geographic distribution over time, which directly relates to the evolutionary history of these life forms.


Input: Task: pass the claim using the given text. Claim: Sea turtles navigate using the Earth’s magnetic field. [SEP] Text: For the readers’ convenience, all the calculations are presented in the compact Table 2. The table shows that the thermocurrents Ilow are all-sufficient, they are able not only generate the main dipole field of Earth В T T l o w but to maintain it for a long time at 3. 64 × 10−5 T level. This value is calculated for the points of Earth on its equator and, as seen, it is close to the real and modern intensity of the EMF. At the same time, the heat, produced by the thermocurrents Ilow, is only Q b c = 2. 25 × 10 14 J per year (2. 25 × 1021 erg per year) and is comparable to the heat of the thermocurrents Itop. The Earth’s magnetic moment was also calculated as M = 4 π R G 2 I l o w. At the current Ilow of 3. 52 × 109 А and spherical surface with the solid core’s radius of RG = 1400 km (see in Table 2) it is 8. 67 × 1022 Table 2. Calculation of electrical and magnetic parameters of Earth’s metal core. А・m2, which is close to the known value М = 8. 2 × 10 22 А ⋅ m 2. Let us briefly note, that a toroidal magnetic field forms within the metal core. The field’s field lines are spherical circles that do not leave the conducting core (Figure 1(a) and Figure 1(b)). The centrifugal force F C f and the thermo e. m. f. ЕТ have been generating a through channel with electron deficit for 3. 5 billion years in the toroidal field in the core center. The channel is the entrance/exit for the poloidal magnetic field which is self-generating in the conductive medium. The field is definitely dipole and it has local poles with diameter to 500 km for entrance/exit of the field lines bundles of the poloidal field with tilt of 900 - 890. There is a confirmation for it [39]. 4. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the Earth's magnetic field and its calculations but does not mention sea turtles or their navigation methods. Therefore, it does not corroborate or contrast the claim about sea turtles.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: BurhanA. NisaU. GökhanC. ÔmerC. AshabilOsman. G. 2003Enzymatic properties of a novel thermostable, thermophilic, alkaline amylase and chelator resistant amylase from an alkaliphilic Bacillus sp isolate ANT-6. Process Biochem. 381397140357. ChandraA. K. MeddaS. BhadraA. K. 1980Production of extracellular thermostable α-amylase by Bacillus licheniformis. J. Ferment. Technol. 5811058. SaitoN. YamamotoK. 1975Regulatory factors affecting α-amylase production in Bacillus licheniformis. J. Bacteriol. 12184885659. GuptaR. GigrasP. MohapatraH. GoswamiV. K. ChauhanB. 2003Microbial α-amylases: a biotechnological perspective. Process Biochem. 381599161660. MuralikrishnaG. NirmalaM. 2005Cereal α-amylase-an overview. Carbohydrate polymer 6019317361. GangadharanD. SivaramakrishnaK. . 2008Response surface methodology for the optimisation of alpha amylase production by Bacillus amyloliquefaciens. Biores. Technol. 994597460262. SodhiH. K. SharmaK. GuptaJ. K. SoniS. K. 2005Production of a thermostable-amylase from Bacillus sp PS-7 by solid state fermentation and its synergistic use in the hydrolysis of malt starch for alcohol production. Process Biochem. 4052553463. CherryH. M. HussainT. AnwarM. N. 2004Extracellular glucoamylase from isolate of Aspergillus fumigates. Pak. J. Biol. Sci. 7111988199264. 2000Culture conditions for the production of thermostable amylase by Bacillus sp. Brazilian J. Microbiol. 3129830265. HalsetineC. RolfsmeierM. BlumP. [SEP] Justify:

Output: The text is irrelevant to the claim about lactic acid bacteria's importance in fermentation processes. Instead, it discusses various studies and enzymatic properties related to α-amylases produced by Bacillus species and other microbial processes. There is no mention of 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: Skip to content Menu AGU. org to by AGU for dropdown menu Space & & & & dropdown menu ’ Highlights Editors’ Eos en Español Eos 简体中文版 to for: inClues to Tibetan Plateau’s bones of ancient rhinos, elephants, and fish constrain when the rose high enough to prevent migration, a move that forced animals to adapt to high-altitude conditions. by Kimberly M. S. Cartier 12 December 201726 January 2023 Share this:Click to print (Opens in new window)Click to email a link to a friend (Opens in new window)Click to share on Twitter (Opens in new window)Click to share on Facebook (Opens in new window)Click to share on LinkedIn (Opens in new window) A fossil skeleton of a woolly rhinoceros (Coelodonta antiquitatis), an extinct species that once roamed the Eurasian continent. Fossils of this species’s Tibetan cousins (Coelodonta thibetana) are now helping scientists reconstruct the elevation history of the Tibetan Plateau. Credit: -SA 4. 0 Called the Rooftop of the World, the perches high above the surrounding terrain, surpassed only by the Himalayan mountains that mark its southern border. But when and how the plateau reached its high elevation has remained unclear. For one scientist and his team, tracing the evolution of the now has a much-needed clue: vertebrate fossils—woolly rhinos, shovel-tusked elephants, and climbing perch, to be precise. “Vertebrates are very sensitive to climatic and environmental changes. ” “Most modern vertebrate fauna of the have long histories living in this plateau,” said Deng Tao, deputy director of the of of and Paleoanthropology in Beijing and lead scientist on the study. What’s more, “vertebrates are very sensitive to climatic and environmental changes,” he said. Could the story of the plateau’s evolution lie in their bones? Deng’s answer is yes. After examining fossils of animals that lived and died on the plateau over the past 34 million years, he and his team could trace when the plateau’s elevation was low enough to allow animals to migrate across it. This newsletter rocks. [SEP] Justify:

Output: The text corroborates the claim by discussing how vertebrate fossils, including those of woolly rhinos and ancient elephants, are used by scientists to trace the elevation history of the Tibetan Plateau, which is an example of evolutionary history. The mention of fossils being sensitive to climatic and environmental changes further supports the idea that fossils can provide significant insights into the evolution of life.


Input: Task: contrast the claim using the given text. Claim: Cave paintings offer a glimpse into prehistoric human expression. [SEP] Text: 2000); and Foissac Cave, France (García and Duday 1983), dated in the Middle Palaeolithic, Upper Palaeolithic, Mesolithic and Chalcolithic, respectively, are not associated with symbolic elements. was quarried for clay in the Chalcolithic. The deep zone of (United States) was also used for mining activities (Kennedy and Watson 1997; Willey et al. 2009). However, the prehistoric traces in (Tennessee, USA) are more interesting for our case study. Watson et al. (2005) documented a single visit by a group of nine individuals about 4500 BP. The cave was never used for any specific purpose, so the tracks represent an isolated event. The footprint site in Sala and Galerías de las Huellas similarly represents a single event, a simple exploration, but its surroundings, Laberinto Otilio, and Galería del Cacique, were explored earlier several times. They are in the eastern part of Palomera Cave, where different types of evidence and human activities have been identified over a distance of more than a kilometre in length. They show that during prehistory, the inhabitants of this karst transited and explored the cave until they met the sediment plug in the San Bernabé cirque, leaving marks in the underground landscape, small hearths, torches, stones or rock art, graves, etc. This indicates that the exploration of the interior of this cave system was an activity that was carried out with certain normality. This exploration must have represented an initial contact of the underground world that they wanted to conquer and then select at a later time the different symbolic places that have contributed to the singularity of this site, which has been designated as Heritage since 1972. ConclusionThe human footprint site of Sala and Galerías de las Huellas is one of the most important sites in the Ojo Guareña Cave system, located about 1200 m from Palomera Cave. It is dated in about 4600–4200 calBP, a range that suggests a use of the dark area of the cave in the Chalcolithic, although intensive human traffic in the immediate environment (Laberinto Otilio-Sala Negra-Sala del Cacique) is documented during the Upper Palaeolithic, Mesolithic and Neolithic. [SEP] Justify:

Output: The text contrasts the claim by mentioning that certain prehistoric caves, such as Foissac Cave, are 'not associated with symbolic elements.' This indicates that not all cave sites are linked to symbolic human expression, and it suggests that while some caves may contain intriguing findings, they do not necessarily support the idea that all cave art or markings represent a glimpse into human expression.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: 1996The glucose effect and regulation of α-amylase synthesis in the hyperthermophilic archeon Sulfolobus solfataricus. J. Bacteriol. 17894595066. GaoL. YangH. WangX. HuangZ. IshiiM. IgarashiY. CuiZ. 2008Raw straw fermentation using lactic acid bacteria. Biores. Technol. 992742274867. MSTanyildiziOzer. D. EbiolM. 2005Optimisation of α-amylase production by Bacillus sp using response surface methodology. Processs Biochem. 402291229668. WuW. X. MabinadjiJ. TatsinkouF. B. 1999Effect of culture conditions on the production of an extracellular thermostable alpha-amylase from an isolate of Bacillus sp. J. Sci 2540440869. ReddyP. R. ReddyG. SeenayyaG. 1999Enhance production of thermostable β-amylase and pullulanase in the presence of surfactant by Clostridium thermosulfurogenes SV2. Process Biochem. 34879270. AguilarG. Morlon-GuyotJ. Trejo-AguilarB. GuyotJ. P. 2000Purification and Characterization of an extracellular alpha-amylase produced by Lactobacillus manihotivorans LMG 18010T, an amylolytic lactic bacterium. Enzyme Microb. Technol. 2740641371. UnderkofferL. 1976Microbial enzyme B. Litsky W. (Eds). Industrial Microbiology. Mc Graw-Hill, New York. 72. 1992Purification and characterisation of a thermostable alpha amylase from Bacillus licheniformis. J. of Bacteriol. 2827728973. VihinenM. MantsalaP. 1990Characterization of a thermostable Bacillus stearothermophilus alpha-amylase. Biotechnol. Appl. Biochem. 1242743574. CanganellaF. AndradeC. AntranikianG. [SEP] Justify:

Output: The text discusses various studies and publications related to the production of enzymes, particularly alpha-amylase, by different microorganisms, including lactic acid bacteria. However, it does not explicitly mention the importance of lactic acid bacteria specifically to fermentation processes. As a result, the text is largely irrelevant to the claim, thus classified as 'pass'.


Input: Task: corroborate the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: Get the most fascinating science news stories of the week in your inbox every Friday. Sign up now “The uplift of the was an important factor of global climate change during the late Cenozoic [era],” Deng said, “and it strongly influenced the development of the Asian monsoon system. ” Pinpointing the timing and speed of the plateau’s uplift will help scientists better understand the geophysical processes that shaped southern Asia’s landscape and the forces that influenced the paleoclimate in the region. Their study, which Deng will present Thursday, 14 December, at the 2017 Meeting in New Orleans, La. , suggests that the region hit its last growth spurt approximately 20 million years ago. This early uplift time frame agrees well with most isotopic records. Fossils as a Window into Plateau, the youngest and highest in the world, rises approximately 5,000 meters above sea level, nearly one third of the way to the tropopause. Its height and location shape atmospheric flow and climate in the region. At present, the supports a diverse range of ecosystems, including deserts, forests, and tundra, all adapted to its high-altitude environment. Modern topographical map of the and the surrounding region showing areas of low (green) to high (red and white) elevation. Credit: Darekk2, GLOBE, and ETOPO1, CC BY-SA 4. 0 In the same way, past fauna would have reflected past environments, the researchers figured. To test this, Deng and his team examined newly excavated as well as archived fossils of ancient fish and mammals from the plateau that date to the late Oligocene (34–23 million years ago (Ma)) through the mid-Miocene (23–5. 3 Ma) and Pliocene (5. 3–2. 6 Ma) epochs. They analyzed fossils of rodents, fish, Tibetan woolly rhinoceroses, shovel-tusked elephants, and ancestral relatives of arctic foxes, snow leopards, and bighorn sheep. Although previously published results by the team parse out analyses of separate species, the results on display at the 2017 aggregate these studies, other research, and new fossil analysis into one comprehensive view. And what they found painted a clear picture. [SEP] Justify:

Output: The text corroborates the claim by discussing the examination of fossils from the plateau, which are analyzed to reflect past environments and provide insights into the evolutionary history of various species, including ancient fish and mammals. It emphasizes the significance of fossil analysis in revealing a comprehensive view of historical fauna, aligning with the claim that fossils can illuminate evolutionary history.


Input: Task: contrast the claim using the given text. Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: In the same study, BED subjects had lower medial orbitofrontal cortex and ventral striatal volumes relative to non-BED obese subjects—a group difference that was lost with the inclusion of the Two-step task outcome as a covariate of no interest, suggesting that these neural regions may mediate the impairment in goal-directed behaviors. More crucially, the same study analyzed perseverative behaviors, showing that BED subjects were markedly more likely to choose the same stimulus irrespective of the outcome. Overall, these findings suggest a shift toward behavioral inflexibility, or choosing the same stimuli whether they have (habit formation) or have not (perseveration) been previously reinforced, rather than being guided by goals and changing outcomes. recent study focused on the construct of exploration, in which subjects either favored restricted exploitative choices in which the action-outcome contingencies were known or explored the environment in which the contingencies were unknown. Reference Frank, Doll, Oas-Terpstra and Moreno 39 Thus, exploration occurred as a function of tolerance of uncertainty. In the task, subjects chose the time in which to stop a clock, which then resulted in either random wins or losses. The tendency to stay and exploit the same time choice or explore alternate times was assessed. The study showed a reduction in exploratory behaviors in alcohol use disorders across both gain and loss valences. and Voon 40 In this same study, although neither obese BED nor obese non-BED subjects scored differently from healthy volunteers when compared to each other, BED were more exploratory in the loss domain compared to non-BED subjects. These findings suggest that BED subjects were less avoidant of uncertainty and more exploratory in the context of losses compared to obese non-BED subjects. Summary of compulsivity studies Thus, BED appears to be impaired across multiple domains of compulsivity. BED subjects have greater impairments in set shifting compared to non-BED obese controls, particularly with low BMI with similar impairments across both groups with higher BMIs. BED is also impaired in habit formation and perseveration. In contrast, compared to obese subjects without is associated with greater exploratory tendencies, particularly in a loss context, which may be related to greater tolerance of uncertain losses rather than specifically to enhanced exploratory tendencies. Attentional and to Attentional bias provides a measure of the motivational salience of a stimulus. [SEP] Justify:

Output: The text contrasts the claim by discussing various cognitive and behavioral findings related to binge eating disorder (BED) subjects, including their behavioral inflexibility in decision-making. It states that BED subjects are more likely to choose the same stimulus regardless of the outcome, which signifies a lack of adaptability and consideration in decision-making. This indicates that cognitive biases might be present but are shown as impediments to effective decision-making rather than support for the idea that cognitive biases can significantly enhance decision-making.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: 1994Characterization of amylolytic and pullulytic enzymes from thermophilic archea and from a new Ferividobacterium species. Appl. Microb. Biotechnol. 4223924575. KwakY. AkebaT. KudoT. 1998Purification and characterization of enzyme from hyperthermophilic archeon Thermococcus profundus, which hydrolyses both α-1-4 and α-1-6 glucosidic linkages. J. Ferment. Bioeng, 8636336776. PrakashB. VidyagarM. MSMadhukumarMuralikrishna. G. SreeramuluK. 2009Production, purification and characterization of two extrememely halotolerant thermostable, and alkaline stable α- amylases from Chromohalobacter sp TVSP 101. Process Biochem. 4421021577. BayramogluG. YilmazM. AricaY. 2003Immobilization of a thermostable a-amylase onto reactive membranes: kinetics characterization and application to continuous starch hydrolysis. Food chem. 57839078. LeeHs. SeG. CarterS. 2001Amylolytic cultures of Lactobacillus acidophilus: potential probiotics to improve dietary starch utilization. J food Sci. 66:2. 79. OhkouchiY. InoueY. 2006Direct production of L(+)-lactic acid from starch and food wastes using Lactobacillus manihotivorans LMG18011. Bioresour. Technol 9715546280. MetteHedegaard. ThomsenGuyot. J. P. KielP. Batch fermentations on synthetic mixed sugar and starch medium with amylolytic lactic acid bacteria. Biotechnol 200774540681. KrishnanS. BhattacharyaS. KaranthN. G. 1998Media optimization for production of lactic acid by Lactobacillus plantarum NCIM 2084 using response surface methodology. 121052182. JunyaNarita. NakaharaS. FukudaH. KondoA. 2004Efficient production of L-(+)-lactic acid from raw starch by Streptococcus bovis 148. [SEP] Justify:

Output: The text is irrelevant to the claim as it primarily lists various studies and publications related to the characterization of enzymes, probiotics, and lactic acid production but does not directly address the importance of lactic acid bacteria in fermentation processes. While it mentions Lactobacillus and its application in certain processes, it lacks a clear statement or evidence linking the bacteria specifically to their importance for fermentation.


Input: Task: corroborate the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: During the late Oligocene, large mammals like the Tibetan woolly rhinoceros and shovel-tusked elephant roamed from northwestern China to the Indian subcontinent, Deng explained. The distribution of their fossils north and south of Tibet during the Oligocene indicates that the plateau’s elevation was low enough to allow migration across the continent. In addition, the team found fossils suggesting that lowland species like the ancestors of climbing perch likewise made their homes in Tibet during the late Oligocene. fossil of Eoanabas thibetana, an ancestor of the modern-day climbing perch, collected in central Tibet and used to constrain the latest period of a low-elevation Tibet. Credit: Wu et al. , 2017, CC BY 4. 0 Adapt or Perish in High-By the early Miocene, however, fossil records suggest that the plateau was elevated enough that large mammals who lived just north of Tibet had to curtail their southward migration, Deng explained. For example, although paleontologists have found shovel-tusked elephant fossils from the mid-Miocene northward of the plateau, none exist within or south of the plateau during that epoch. (top) Skull and (bottom) mandible fossils from a Tibetan woolly rhinoceros (Coelodonta thibetana), a cold-adapted mammal from the Pliocene. These fossils were discovered in the in the Tibetan Plateau. Credit: Deng and Ding, 2015, Vertebrates that were trapped on the now-elevated either evolved to survive in a high-altitude cryosphere or died out. Lowland-adapted species of fish and rodents perished, and their fossils disappeared. For vertebrates that survived, including the ancestral forms of the woolly rhinoceros, snow leopard, arctic fox, and bighorn sheep, their Pliocene fossils show that the animals had long since adapted to freezing temperatures at high elevations, Deng said. The plateau must have uplifted a few million years prior to the most recent ice age at the end of the Pliocene, the researchers argue, for the animals to have been well adapted to the cold by then. [SEP] Justify:

Output: The text corroborates the claim by discussing how the distribution of fossil remains from large mammals like the Tibetan woolly rhinoceros and shovel-tusked elephant provides insights into their migration patterns and adaptations over time in response to environmental changes. It illustrates how the fossil records inform us about evolutionary adaptations, such as the survival of certain vertebrates adapted to high-altitude habitats, thereby supporting the claim regarding the significance of fossils in understanding evolutionary history.


Input: Task: contrast the claim using the given text. Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: The capacity to inhibit motor responses appears to be impaired to a greater extent in BED compared to non-BED obese controls, only in the context of a motivationally salient food cues. BED subjects exhibit enhanced behavioral inflexibility across multiple domains, with impairments in set shifting, habit formation, and perseveration. The presence of food cues was associated with enhanced motivation and impaired self-regulation with multiple attentional and early and late inhibitory impairments in BED, including enhanced ERP responses, longer gaze duration, difficulties with saccade away from the cue, and motor response inhibition both with action restraint and cancellation. Thus, food cues appear to impair self-control particularly in BED, possibly through attentional mechanisms, working memory, or cognitive load. An investigational specific mu-receptor opioid antagonist has been shown to influence late inhibitory processes and motivational responses to food cues, with a mixed influence on subjective hedonic ratings suggesting a potential mechanistic role for the mu-opioid receptor in mediating these processes. However, the role of mu-opioid receptor antagonists is not clear as randomized controlled trials report a mixed effect on binge eating. Thus, rather than flexible responding guided by changing environmental outcomes, binge eating is characterized by enhanced attention and memory biases and impaired self-regulation in the context food cues, along with impulsive choices and difficulties across multiple domains of behavioral inflexibility. These findings suggest critical cognitive domains that may guide therapeutic interventions. Voon does not have anything to disclose. 1. . The prevalence and correlates of eating disorders in the Survey Replication. Biol Psychiatry. 2007; 61(3): 348–358. 2. The prevalence and correlates of binge eating disorder in the. Biol Psychiatry. 2013; 73(9): 904–914. 3. Innovative solutions to novel drug development in mental health. Rev. 2013; 37(10 Pt 1): 2438–2444. 4. Research domain criteria (RDoC): toward a new classification framework for research on mental disorders. Psychiatry. 2010; 167(7): 748–751. 5. . Binge eating disorder and food addiction. Abuse Rev. 2011; 4(3): 201–207. 6. “Eating addiction”, rather than “food addiction”, better captures addictive-like eating behavior. Rev. 2014; 47: 295–306. CrossRef7. [SEP] Justify:

Output: The text contrasts the claim by discussing how binge eating disorder (BED) influences decision-making through impaired self-regulation and enhanced attention biases specifically in the context of food cues. It highlights issues such as behavioral inflexibility and impulsive choices, which indicate that BED subjects make decisions in an impaired manner due to cognitive biases associated with food cues. Instead of illustrating how cognitive biases can influence decision-making positively or in a general sense, the text points out the negative impact of those biases on behavior, especially in the context of binge eating.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: A mol of pyruvate could be excreted as succinate due to TCA cycle oxidation (indicating respiration), manifesting as excess electrons relative to the amount of succinate produced (as additional pyruvate would have to be used to make OAA). Conversely, succinate could be due to electron disposal via a reductive pathway (indicating fermentation). Lacking good carbon or electron recovery, neither can be ruled out, though the non-respiratory reductive pathway is most logical. 6) Table 1/line 403-: The low YATP in cells using EET is a possible 'different energy conversion strategy'. (Side note- an energy spilling/Russell mechanism would be an 'ATP-dissipating', not -accumulating). I'd suggest uncoupling of acid production from growth by low pH seems likely. In most strains, simple glycolytic pathway functions at low external pH, but complex protein synthesis and replication processes become inhibited, ATP from substrate turnover is needed to maintain pmf and internal pH, and high internal organic acids become toxic. Citable yield/pH data can be hard to locate as it comes from the 80's in the age of calling every lactic acid bacterium a Streptococcus, but since the non-EET cultures at neutral pH got close to the Bauchop and Elsden YATP, and EET cultures at pH 4 were a fraction of this, these data look like common behaviour of many lactic acid bacteria. In future comparisons, pH control could help estimate energy yields from EET. The first paper I found in a quick search to illustrate pH effects was: Russell and Dombrowski, DOI: 10. 1128/aem. 39. 3. 604-610. 1980. 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? Reviewer #2 (Recommendations for the authors): Line 21 – acronyms like this make our field more challenging to understand and are unnecessary. [SEP] Justify:

Output: The text does not specifically address the importance of lactic acid bacteria for fermentation processes. Instead, it discusses various metabolic pathways involving pyruvate and succinate, and the context around energy production and pH effects in bacterial cultures. While it mentions lactic acid bacteria in relation to energy yields and pH, it does not define their importance in fermentation processes, making the text largely 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: That uplift timing supports that theory the Tibetan Plateau’s rise to the top resulted from the collision of the Indian and Eurasian continental plates that occurred 40–50 Ma. The evolutionary history suggested by this timing also agrees with the past environmental conditions suggested by isotope ratios of oxygen, hydrogen, and calcium found in carbonate rocks that surround the fossils. and his team, the geographic locations of the fossil deposits and their stratigraphic origins tell a single story: a low-elevation Tibet in the late Oligocene, a constant uplift in the early Miocene, and a modern-elevation by the middle to late Miocene. “Fossils are really valuable and probably an underused source of insights. ” “Fossils are really valuable and probably an underused source of insights,” said about resolving the controversy surrounding the timing of the uplift. Freeman is an isotope biogeochemist and a professor of geosciences at University in University Park. “Although their record can be discontinuous, they would be excellent for marking changes on broad time and spatial scales. ” She added that she “certainly welcome[s] this additional perspective on a tricky problem. ” However, not all paleoelevation proxies agree with the early Miocene rise suggested by fossils and stable isotope measurements. For example, isotope studies of tooth enamel found in fossils from the high Himalayas dating to the late Miocene show signatures consistent with the animals chewing C4 grasses, plants species that thrive in warmer conditions. Those results indicate that Tibetan climate in the late Miocene might have been much warmer, suggesting that elevations were likely much lower than they are today and contradicting the recent fossil-based analysis. How do you resolve this discrepancy? “We want to find more fossil records from Cenozoic basins in the Tibetan Plateau,” Deng said. More fossils, the team thinks, will clear up the fuzzier details of the plateau’s past. —Kimberly M. S. Cartier (@AstroKimCartier), Citation: Cartier, K. M. S. (2017), Fossils provide new clues to Tibetan Plateau’s evolution, Eos, 98, Published on 12 December 2017. Text © 2017. The authors. CC BY-NC-ND 3. [SEP] Justify:

Output: The text corroborates the claim by stating that 'fossils are really valuable and probably an underused source of insights.' It discusses how fossil deposits and their origins can reflect a detailed evolutionary history of the Tibetan Plateau, indicating that fossils yield important information about past environmental conditions and uplift events which are key to understanding evolutionary processes.


Input: Task: contrast the claim using the given text. Claim: The dual-process theory explains intuitive vs. analytical thinking. [SEP] Text: In contrast, studies in which analytical thinking was found to be superior (e. g. , MacGregor et al. , 1988; Tversky & Kahneman, 1974) used abstract deliberative tasks that involved numerical stimuli and presented an objective criterion as well as logical rules. To conclude, we propose that the debate as to whether decision quality is best when using intuitive or analytical thinking might be clarified once each thinking mode is examined within a task that favors such thinking. [SEP] Justify:

Output: The text contrasts the claim by discussing how analytical thinking can be superior in specific tasks that require abstract deliberation, while suggesting that understanding the dual-process theory's implications on decision quality could benefit from examining tasks that favor either intuitive or analytical thinking. This indicates a debate regarding the effectiveness of each thinking mode rather than a straightforward endorsement of dual-process theory.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: Does the work presented actually support 'energy conservation'? Growth seems to occur after EET activity takes place rather than with it as discussed below. Line 27 – 'fermentation yield' referring to biomass yield or fermentation product yield? 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. Line 61 – implied here is that LAB are auxotrophic for heme and menaquinone, but should be explicitly stated. 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. Line 152 – predicted to encode Line 182 – predicted to encode Line 183 – under the condition tested. Line 200 – isn't this already known from the Listeria work? Line 206 – unclear what 'extracellular redox potential' is, unclear to me if any differences are significant in Figure 3B. I guess this is a measurement of Fe(II) Fe(III) in the medium? Figure 3D – did the authors include a strain that lacked the cluster? Line 252 – unclear to me how ICP-MS can distinguish between iron inside a cell and associated with the cell surface. 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. Line 262 – does this mean a large amount of the cells that grew are now dead? 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. [SEP] Justify:

Output: The text does not directly address the claim about the importance of lactic acid bacteria (LAB) in fermentation processes. Instead, it critiques various lines and findings related to microbial growth and energy conservation without providing specific information about lactic acid bacteria or their role in fermentation. Because the focus is on other aspects of microbial metabolism and growth, the relevance to the claim is minimal.


Input: Task: corroborate the claim using the given text. Claim: Fossils provide insights into the evolutionary history of life. [SEP] Text: A phylogenomic and microsynteny analysis on 60 plant genomes generated clues about how evolutionary processes (genome diversification) leads to differential biochemical properties, distinctive gene expression patterns, and specific-gene expansion [32], shedding light on the contribution of evolutionary mechanisms to plant adaptations in restrictive environments. Phylogeny and a microsynteny network approach on 171 fully sequenced genomes from the Tree of Life unravelled the evolutionary history of TMBIM protein family. Synteny revealed that some groups of genes from monocots transposed to another genomic context during evolution; specific patterns of gene duplication in angiosperms were also observed [33]. Recently, [34] an in-depth network-based phylogenomic synteny analysis on 87 mammalians and 107 angiosperm genomes identified long-term conservation and several lineage-specific patterns of evolution related to the genomic context of genes. Interestingly, several “rebel-genes” that transpose to another genomic context in mammalian genomes and conserved single-copy genes in angiosperms were detected. We provide a phylogenetic overview of FIB proteins across the Tree of Life by using 1049 available complete sequenced genomes spanning viruses, Bacteria, Archaea, protists, fungi, plants, and animals. Additionally, we applied a novel microsynteny network approach on fungi, plants, and animals to unravel the evolution of genome structure and its consequences on FIB dynamics. Our goal is to identify patterns of genome evolution to provide insights into how genome dynamics may have contributed to trait evolution. Our evolutionary analyses provide the first comprehensive survey of FIB proteins over four billion years of evolutionary history. fibrillarin family through the tree of life: General trends We performed a homology search for FIB proteins across 1049 completely genome-sequenced organisms from the three domains of life (Bacteria, Archaea, and Eukarya) and viruses (For discussion about the fourth domain please see [35]). [SEP] Justify:

Output: The text corroborates the claim by discussing various analyses that contribute to understanding evolutionary processes and history across different organisms. It emphasizes the importance of phylogenomic analyses and gene dynamics in revealing insights into the evolutionary history of protein families, ultimately supporting the idea that such studies—similar to fossil analysis—provide valuable insights into the evolution of life.