Input: Task: contrast the claim using the given text. Claim: The upfront cost of sustainable architecture is always lower than traditional methods. [SEP] Text: The house spatial organization and its elements; the courtyard, Mashrabeiyah, wind catchers, and the use of low-technology in house construction system as thick bearing walls provide energy efficiency and good indoor environment quality. Moreover, the Mashrabeiyah works as a curtain to provide both privacy for house residents and cross ventilation to the indoor environment, and the use of natural building material with zero-carbon emission. In the future, apply the low-technology used in hose construction systems in the form of advanced technology. 2021. [2] Guide. (2020). accessed on Oct. 14, 2020. [3] Mahgoub, M. H. (2013). Urban morphology impact microclimate of the Fatimid city, Cairo, Egypt. on "Changing Cities": Spatial, morphological, formal & socio-economic dimensions Skiathos Island, Greece. accessed on Oct. 14, 2020. [4]. (2020). Educational, Scientific, and Cultural Organization. for Historic Cairo. accessed on Oct. 14, 2020. [5] Ibrahim, A. M. (1990). Architectural design and urban planning foundations – Cairo as a state research. of Planning and (CAPS), Cairo, Egypt. www. noor-book. com/book/review/330648. [6] Lamei, S. M. (1984). Heritage in Egypt. Dar Al-Nahda Al-Arabia, Beirut, Lebanon. (In Arabic). www. ciah. biz/content/prof-lamei-publications. [7] Abdelkader, R. , Park, J. H. (2020). Spatial principal of traditional Cairene courtyard houses in Cairo. Journal of 17(2): 245-252. htpps:// [8] Ragheb, R. A. , Naguib, I. M. (2018). Reinvestment of the urban context in Historic cities: The case study of. 2018: 20th Int. Conf. on and Assessment. Vienna, Austria. www. researchgate. net/publication/330831919_Reinvestment_of_the_Urban_Context_in_Historic_Cities_The_Case_Study_of_El_Sheikh_Kandil_Street_Rosetta_Egypt, accessed on Sep. 12, 2021. [SEP] Justify:

Output: The text contrasts the claim by discussing elements of sustainable architecture such as energy efficiency, use of low-technology, and natural building materials with zero-carbon emissions without mentioning upfront costs. It implies that these elements may not necessarily correlate with lower upfront costs compared to traditional methods, suggesting that the cost comparison is more complex than the claim states.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Contig grouping No. of contigs N50a Total sequence (bp) Megahit assemblies 200–499 bp 24,999,285 n. d. 9,293,098,676 Megahit assemblies 500–1,999 bp 16,103,221 n. d. 13,382,057,993 Megahit assemblies ≥2 kb 1,517,360 4,658 6,691,877,664 Megahit assemblies ≥2 kb (post-CD-HIT-EST) 1,126,975 4,520 4,894,479,496 Minimus2 contigs 158,414 15,394 1,727,079,865 Minimus2 + unincorporated Megahit contigs ≥2 kb (data-rich-contigs) 660,937 5,466 3,612,405,904 Minimus2 + unincorporated Megahit contigs ≥7. 5 kb (binned-contigs) 95,506 20,556 1,725,063,313 DOI: 10. 7717/peerj. 3558/table-2 Notes: aN50—length of DNA sequence above which 50% of the total is contained. Unsupervised binning was performed using both transformed and raw coverage values for a subset of 95,506 contigs from the data-rich-contigs that were ≥7. 5 kb (referred to further as binned-contigs). Binning using the transformed coverage data generated 237 putative draft genomes containing 15,032 contigs (1). Contigs not in putative genomes were re-binned based on raw coverage values, generating 53 additional putative draft genomes encompassing 3,348 contigs. In total, 290 putative draft genomes were generated with 50–100% completion (mean: 69%) with a mean length and number of putative CDS of 1. 7Mbp and 1,699, respectively (1). In analyzing the quality of generated draft genomes, 31 of the genomes had a contamination value >10%, but had a cumulative redundancy value <10%, while an additional 12 genomes had a cumulative redundancy value >10% (genomes highlighted in 1). For instances where the predicted strain heterogeneity is high and sharply reduces the calculated cumulative redundancy value (e. g. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses various statistics and details regarding contigs and draft genomes without mentioning X-ray crystallography or its application in determining protein structures.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Overall, whereas all of the temperate/sub-tropical coral communities showed a complete loss of corals between control and seep sites, only two of the seven warm water coral reefs showed a significant loss of coral cover across a similar pCO2 gradient (Inoue et al. 2013; Enochs et al. 2015b; Fig. 3). Therefore, the high light levels available in warm tropical waters, and the increases in metabolic rates that accompany moderate increases in water temperature, could allow certain species of corals (e. g. Porites) to maintain growth rates on tropical reefs despite changes in pCO2. In contrast, increasing pCO2 has major effects on coral growth under more marginal conditions. Fig. 3The percentage cover of hard corals (top) and soft corals (bottom) along a pCO2 gradient at eight of the ten naturally acidified sites reviewed here. Coral cover data are not shown for two sites because of lack of stated pCO2 values (Mesoamerica, site 4) and coral cover (Ishia, site 10); however, both studies note significant to total loss of coral cover. Abundances for Iwotorishima (Japan) are approximate, based on broad percentage categories. Site numbers in legend correspond to Fig. 2Full size imageTable 2 A summary of the physical site characteristics of the naturally acidified sites in this review ‘*’ = data extracted from a figure in source publication, ‘−’ = no data availableFull size tableDifferences in local species composition may also influence the impact of pCO2 on abundance. Among-species variation in sensitivity to acidification has been widely discussed (e. g. McCulloch et al. 2012; Agostini et al. 2021) with the premise that declines in abundance are driven in part by declines in less tolerant, ‘loser’ species. However, ‘winners’ and ‘losers’ are not consistent between sites. For example the abundance of Acropora spp. declined at many of the acidified sites (e. g. Palau) but increased ~ 65% under high pCO2 at the Indonesia seep site (Barkley et al. 2015; Januar et al. 2016). [SEP] Justify:

Output: The text corroborates the claim by detailing the effects of ocean acidification (pCO2) on temperate/sub-tropical and warm water coral communities. It states that increasing pCO2 has major effects on coral growth, particularly in marginal conditions, reinforcing the impact of ocean acidification. Additionally, it highlights how species like Acropora spp. face declines in abundance at acidified sites, thereby linking the phenomenon of ocean acidification to the health and changes in coral reefs.


Input: Task: contrast the claim using the given text. Claim: The upfront cost of sustainable architecture is always lower than traditional methods. [SEP] Text: Moreover, in most of the city's houses, there is a water well, a backyard "Bustan" for agricultural vegetables, and in villages, a water basin to collect rainwater from re-using it in agriculture. Furthermore, the sewerage system and its waste as a fuel for public baths preserve the environment from pollution. Furthermore, the houses in Sana'a contain water well, while in rural areas, it contains a basin to collect rainwater and use it in agriculture [18]. Also, use the sewerage waste as fuel for public baths and natural fertilizers. The house architecture elements, building material, and openings significantly impact energy saving and efficiency [19]. It was evident from studying that local context and indigenous traditional knowledge have influenced traditional Yemeni architecture [20, 21]. 7. Applications in the 7. 1 European influence on Arab regional architecture architecture influenced the Arab region's architecture during the twentieth and the beginning of the twenty-first centuries through the application of the International style of the glass skyscrapers (Figure 16) Dubai tower, which led the Arab cities to lose their identity, many Arab architects’ moved toward new modern approaches that integrated the building and environment towards sustainability. 16. jpg Figure 16. center and skyscrapers [22] 7. 2 Application of traditional architectural elements and techniques 7. 2. 1 's in Cairo which designed by the Egyptian architect Abd Al-and opened in 2018. The university buildings contain much traditional Islamic architecture; stone walls provide temperature insulation, Mashrabiyah for privacy and cross ventilation, and courtyards provide social interaction and shade (Figure 17) [23]. 7. 2. 2 Qatar University, 1973 the university was established following the planning and design of traditional Islamic architecture buildings, which contain internal courtyards and wind catchers (Malkaf), (Figure 18 a, b) that provide continuous ventilation and ventilation. Techniques [24]. 17. jpg Figure 17. [23] 18. 1. jpg (a) 18. 2. jpg (b) Figure 18. The wind catchers (Malkaf) and courts, Campus, Doha [25] 8. is concluded from the previous study that the traditional house architecture in Yemen and other Arab regions has been influenced by the Islamic context, cultural and natural environment also, while international architecture schools have influenced the contemporary architecture in the Arab region in both Europe and the United States, the International style and skyscrapers glass boxes. [SEP] Justify:

Output: The text contrasts the claim by discussing traditional architectural methods which are influenced by local context and traditional knowledge in Yemen and other Arab regions. It highlights that while sustainable architecture techniques, such as water collection and use of natural materials, are being integrated, it does not assert that the upfront costs of these sustainable practices are lower than conventional methods. Instead, it emphasizes the influence of both traditional and contemporary designs without making a direct comparison of costs.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: , TMED1), downstream analysis of these genomes may offer opportunities to examine within strain variation, if the gene content varies between contigs, or identify duplicate contigs that can be removed to rectify contamination issues. For instances where cumulative redundancy values remain high (e. g. , TMED20 or TMED106), downstream analysis utilizing composition signatures, for example within Anvi’o (Eren et al. , 2015), should be able to identify problematic contigs and reduce the overall contamination reported for the genome. All other contigs were grouped into bins with at least five contigs, but with estimated completion of 0–50% (2,786 low completion bins; 74,358 contigs; 2) or did not bin (2,732 contigs). Nearly a quarter of the 2,786 low completion bins (24. 7%) have an estimated completion of 0%. These bins may be good candidates for exploring small double-stranded viral genomes or episomal genetic elements. Taxonomy, phylogeny, & potential organisms of interest The 290 putative draft genomes had a taxonomy assigned to it via CheckM during the pplacer step. All of the genomes, except for 20, had an assignment to at least the Phylum level, and 83% of the genomes had an assignment to at least the Class level (1). Phylogenetic information was determined for as many genomes as possible. Genomes were assessed for the presence of full-length 16S rRNA genes. In total, 37 16S rRNA genes were detected in 35 genomes. 16S rRNA genes can prove to be problematic during the assembly steps due to the high level of conservation that can break contigs (Miller, Koren & Sutton, 2010) (Fig. 3). The conserved regions of the 16S rRNA, depending on the situation, can over- or under-recruit reads, resulting in coverage variations that can misplace contigs into the incorrect genome. As such, most of the 16S rRNA phylogenetic placements support the taxonomic assignments, while eight of the assignments were contradictory in nature (denoted in 1). An example of this nonconformity of 16S rRNA assignment would be TMED32. 32 is assigned to the via CheckM and the ribosomal marker tree and contains three 16S rRNA sequences. [SEP] Justify:

Output: The text discusses genomic analysis, contamination issues, and phylogenetic assignments related to 16S rRNA genes, which are unrelated to the claim about X-ray crystallography and protein structures. There is no mention of X-ray crystallography or its applications in the text, making it irrelevant.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Despite the suggested resilience of soft corals to acidification, of the four sites that reported soft coral abundance, only two noted a significant increase in at seep sites with intermediate pCO2 conditions compared to the control sites. Furthermore, at these locations, soft coral cover subsequently declined at the highest pCO2 conditions surveyed (Fig. 3, Table 2). Changes in species diversity, richness, and community composition with increasing pCO2 Coral species richness at the ten acidified sites reviewed here consistently declined with increased pCO2, likely driven by the loss of vulnerable species. Species richness has been reported (or can be inferred) at eight of the ten high pCO2 sites (Table 2), of which seven showed large declines in species richness, from − 31% to − 100%. The remaining site, Palau, had a 50% increase in species richness and a 10% increase in diversity (Shannon diversity index) between the least and most acidic site (Shamberger et al. 2014; Table 2). While this site provides optimistic evidence on the effect of acidification, there are a number of potential reasons for an increase in species richness. For example, the retention of pCO2 adapted larvae within the semi-enclosed lagoon, the duration and source of acidic exposure (hydrographic processes; Golbuu et al. 2016) which result in alterations to other water chemistry parameters such as low total alkalinity, and habitat differences between the control (outer reef) and acidified (lagoonal) sites reflecting differences in community composition. A shift in coral community composition has been observed at every naturally acidified site studied to date compared to the control sites. This includes a shift from hard to soft coral (Iwotorishima, Japan), hard coral to macroalgae with corals still present (CNMI) or with corals absent (Shikine, Japan; Ishia, Italy), reduced richness of hard coral (PNG, Indonesia, Mesoamerica and ETP), and increased species richness of hard coral but a shift in dominant species (Palau; Table 2). This variety again shows the complexity of predicting the effect of acidification on coral communities but suggests that reefs are unlikely to retain their current composition in the future. Evidence of indirect effects at naturally acidified locationsBy reviewing studies of coral diversity and abundance at naturally acidified locations (Table 2), we identify some common indirect effects of OA that structure coral communities. [SEP] Justify:

Output: The text supports the claim by providing detailed evidence of how coral reefs are impacted by ocean acidification. It discusses declines in soft coral cover and species richness at high pCO2 conditions, as well as shifts in coral community composition due to acidification. The mention of consistent declines in coral species richness at acidified sites, alongside the complexity of the predicted effects of acidification on coral communities, corroborates the assertion that coral reefs are significantly affected by ocean acidification.


Input: Task: contrast the claim using the given text. Claim: Overfishing has led to declining fish populations in many regions. [SEP] Text: 0001[overfishing;factory processing ships;groundfish;Takiji Kobayashi]War II finally over, Japan, the Soviet Union, and the took three very different approaches to their fishing industry. Fishing was vital for Japan, a key to its economic recovery, and the government bet heavily on rebuilding the Japanese fishing fleet that had been the world's largest during the 1930s. embarked on building what would become the world’s largest fishing fleet, operating on every ocean and challenging American post-war ocean supremacy. Fishing was never a vital industry in the United States, and fishermen faced declining catches on both the East and West coasts. The story begins with Truman visiting Seattle in 1945, and the announcement of the world’s largest fishing project, the 423-foot Pacific Explorer. Americans were set to claim the high-seas tuna fishery started by the Japanese in the Mandated Islands, and the king crab and bottomfish fisheries they had exploited in Alaskan waters. With all three nations embarking on an expansion of fishing, at different scales, the stage is set for the collapse of fish stocks, international disputes, and a war over who will be the leading fishing nation in the Pacific. This 2. Islands and WarDOI: 10. 7208/chicago/9780226443409. 003. 0002[nuclear testing;territorial clamis;geography;for the Exploration of the Seas;ICES]War transforms the fate of many countries. Some countries thrive under their new geographical importance, others do not. Iceland was transformed by the war. It went from an almost feudal economy, struggling to sell salted and dried fish in southern Europe, to a strategically important nation, with new demands for its fish and its labor. Other places were not so lucky. The Marshall, Mariana, and in the equatorial Pacific were successively invaded by German, Japanese, and American colonizers. Their geographic isolation made them attractive for nuclear testing. had begun a fishery for tuna in the islands in the 1920s and now Americans wanted a line of fishing boat to add to their claims of the high-seas tuna stocks. But at home in the United States, while fishing was considered a vital industry during the war, the post-war fisheries were generally small and owner-financed, with limited technology, range, and capacity. [SEP] Justify:

Output: The text contrasts the claim by discussing the expansion of fishing fleets and practices after World War II, indicating that as nations like Japan and the United States expanded their fishing efforts, the stage was set for the collapse of fish stocks. This implies that overfishing contributed to declining fish populations, as noted in the phrase 'the stage is set for the collapse of fish stocks,' suggesting that intensified fishing activities could lead to declines in those populations.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: One of the 16S rRNA sequences is conformational, with placement in the Family Flammeovirgaceae, while the remaining two 16S rRNA are assigned to the Mitochondria. For future research purposes, contigs with contradictory 16S rRNA or incongruent phylogenetic/taxonomic signatures should be removed. Downstream analysis should allow for the determination of the most parsimonious result in any draft genome with contradictory phylogenetic assignments. Beyond the 16S rRNA gene, genomes were searched for 16 conserved, syntenic ribosomal markers. Sufficient markers (≥8) were identified in 210 of the genomes (72%) and placed on a tree with 6,080 reference sequences and used to assign a putative phylogeny (1). Phylogenies were then assigned to the lowest taxonomic level that could be confidently determined (Fig. 4). These putative results reveal a number of genomes were generated that represent multiple clades for which environmental genomic information remains limited, including: Planctomycetes, Verrucomicrobia, Cyanobacteria, and uncultured groups within the Alpha- and Gammaproteobacteria. Relative abundance A length-normalized relative abundance value was determined for each genome in each sample based on the number of reads recruited to the data-rich-contigs. The relative abundance for the individual genomes was determined based on this portion of the dataset (3). In general, the genomes had low relative abundance (maximum relative abundance = 1. 9% for TMED155 a putative Cyanobacteria at site TARA023 from the protistan size fraction sampled at the surface; 1). The draft genomes accounted for 1. 57–25. 16% of the approximate microbial community as determined by the data-rich-contigs (mean = 13. 69%), with the ten most abundant genomes in a sample representing 0. 61–10. 31% (Table 1). The goal of this project was to provided preliminary putative genomes from the microbial metagenomic datasets. The 290 putative draft genomes and 2,786 low completion bins were created using the 20 samples and six stations from the Mediterranean Sea. [SEP] Justify:

Output: The text does not directly address the claim regarding X-ray crystallography and its application in determining the 3D structures of proteins. Instead, it discusses 16S rRNA sequencing, genomic data, and phylogenetic assignments without any mention of X-ray crystallography.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: The majority of sites (6 of 10) report an increase in macroalgal abundance as pCO2 increases. These studies support interpretation of an increase in competitive dominance by algae, and overgrowth of corals (Enochs et al. 2015b; Glynn et al. 2018) and of CCA (Kroeker et al. 2013; Crook et al. 2016; Table 3) under OA, which in some cases resulted in a complete phase shift to macroalgal abundance (Enochs et al. 2015b). In addition to changes in macroalgae, CCA consistently declines in abundance and diversity as pCO2 increases (Table 3). Evidence from the PNG vents indicates that these declines in CCA abundance were the strongest predictor of recruit density (Fabricius et al. 2017) suggesting a reduction in CCA may have major implications for the long-term persistence of corals at this site. Effects on recruitment have yet to be investigated at any other site. However, acidification also appears to reduce reef cementation in the ETP (Manzello et al. 2008) and at the Shikine vent in Japan where the thick carbonate crusts formed in part by CCA were notably thinner (Peña et al. 2021). This indicates a potential reduction in substrate stability in the future, with further implications for additional declines in recruitment. Table 3 Evidence of indirect effects of acidification on corals and coral communities from the naturally acidified sites considered by this reviewFull size tableBioerosion tends to be higher at the acidified sites compared to nearby control sites (Table 3). This is due to an increase in either the abundance of bioeroders (Fabricius et al. 2011) or their bioerosive capacity (Enochs et al. 2016a) and potentially exacerbated by decreased coral skeletal density (Manzello et al. 2014; Barkley et al. 2015). The extent of this bioerosion is variable but in the site where corals appear to fare best under acidification (Palau), bioerosion was still 11-fold higher than the control reefs (Barkley et al. 2015). Furthermore, at a reef with lower coral cover in the ETP, bioerosion resulted in the complete loss of the reef framework following a major coral mortality event and prevented recovery back to reef status (Manzello et al. 2014). [SEP] Justify:

Output: The text corroborates the claim by providing multiple lines of evidence indicating how ocean acidification affects coral reefs. Various studies are referenced that show a decline in coral-associated organisms (like CCA) and greater abundance of macroalgae as pCO2 increases, indicating competitive pressures on corals. Moreover, it states that acidification leads to reduced reef cementation and increased bioerosion, which further implicates negative effects on coral health and stability, supporting the claim that coral reefs are indeed affected by these environmental changes.


Input: Task: contrast the claim using the given text. Claim: Overfishing has led to declining fish populations in many regions. [SEP] Text: and the were rapidly industrializing, American were just starting to build larger boats to fish in deeper water. This 3. and FishingDOI: 10. 7208/chicago/9780226443409. 003. 0003[Fishery Investigations;Investigations;fish sticks;freezer ships;POFI;CalCOFI]II brought prosperity to Iceland and its fishermen. The war, including American military spending, helped modernize the country. But when the war ended, Iceland wanted the Americans to leave; the Americans saw their military bases as being more strategically important than ever and lobbied to stay. In an attempt to woo the Icelanders, the American embassy tried to find ways to sell Icelandic fish. Imported fish, from Japan and Iceland, was hurting American fishermen. As the war ended,the American government moved ahead with research on fish stocks, creating the (POFI) and CalCOFI, later named the Investigations. Meanwhile, the fishing industry was investing in freezer ships, hoping for a future transferring frozen salmon and tuna back to the mainland US to can. But other nations were building factory ships that caught and processed fish at sea. The only similar American venture, the Pacific Explorer, was not equipped to process at sea, and its fishing effectiveness was hampered by political interference by other American fishing boats. The ship made two voyages before being sold for scrap. This 4. TariffsDOI: 10. 7208/chicago/9780226443409. 003. 0004[tariffs;free trade;Allied Powers;of Japan;American Samoa;tuna canneries]The US moved swiftly after II to reduce tariffs for its trading partners, causing widespread dislocation in many domestic industries. Fishing was one of the first to feel the impact of low tariffs, with fishermen facing imports from Canada, as well as from the new trading partner, Iceland. As the strove to rebuild the Japanese economy, it increased imports to canned and frozen tuna to the U. S. The domestic fishing industry would spend the next decade seeking protection from Congress from low tariffs, but the Departments of State and Defense objecting, saying tariffs could not be increased on either nation. Meanwhile, in American Samoa, the administration looked for a partner to operate the fish plant built by the Navy during the war. Company in signed a five-year lease and rebuilt the plant, which was supplied by Japanese tuna boats. [SEP] Justify:

Output: The text contrasts with the claim by highlighting the development of industrial fishing techniques and competition from imports after World War II. It discusses the modernization of fishing boats and the problems faced by American fishermen due to imports from countries like Japan and Iceland. This indicates a shift in fishing practices and markets that diverges from the context of overfishing leading to declines in fish populations, thereby suggesting that external factors such as tariffs and international competition are significant in this scenario.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Initial assessment of the phylogeny of these metagenomic-assembled genomes based on concatenated ribosomal markers indicates several new genomes from environmentally relevant organisms, including approximately 10 new Cyanobacteria genomes within the genera Prochlorococcus and Synechococcus and 22 new SAR11 genomes. Additionally, there are putative genomes from the marine Euryarchaeota (n = 13), Verrucomicrobia (n = 15), and Planctomycetes (n = 7). Additionally, the low completion bins may house distinct viral genomes. Of particular interest may be the 40 bins with 0% completion (based on single-copy marker genes), but that contain >500 kb of genetic material (including 3 bins with >1 Mb). These large bins lacking markers may be good candidates for research in to the marine “giant viruses” and episomal DNA sources (plasmids, etc. ). It should be noted, researchers using this dataset should be aware that all of the genomes generated from these samples should be used as a resource with some skepticism towards the results being an absolute. Like all results for metagenome-assembled genomes, these genomes represent a best-guess approximation of a taxon from the environment (Sharon & Banfield, 2013). Researchers are encouraged to confirm all claims through various genomic analyses and accuracy may require the removal of conflicting sequences. Statistics, taxonomic and phylogenetic assignments for the putative high-quality genomes DOI: 10. 7717/peerj. 3558/supp-1 and CheckM taxonomy for low completion bins DOI: 10. 7717/peerj. 3558/supp-2 abundance values determined for each genome based the length-normalized fraction of reads recruited to the genome relative to reads recruited for the data-rich-contigs DOI: 10. 7717/peerj. 3558/supp-3 Download SINA alignment of 16S rRNA sequences from the 37 draft genomes and 406 reference sequences DOI: 10. 7717/peerj. 3558/supp-4 file of the 16S rRNA tree used to generated Fig. 3. Contains Shimodaira-Hasegawa local support values DOI: 10. 7717/peerj. 3558/supp-5 about the 6,080 reference genomes used to generate the 16 ribosomal marker protein tree DOI: 10. 7717/peerj. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses metagenomic-assembled genomes, their phylogenetic assessment, and various genomic analyses, without mentioning X-ray crystallography or its application in determining the 3D structures of proteins.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Consequently, indirect effects of bioerosion on the integrity of coral skeletons and the reef substratum are a significant factor for long term persistence of reefs under acidification. Linked to changes in coral cover and bioerosion, almost every site (8 of 10) exhibited a decrease in structural complexity with acidification (Table 3). These changes have indirect effects on other organisms, for example, changes in abundance within the fish community from PNG were likely driven by changes in structure and habitat provision (Munday et al. 2014). However, the implications of such changes for corals have not been investigated. Without knowing whether the interactions with corals and fish and/or invertebrates had positive, negative or neutral effects on corals, it is hard to extrapolate what the impact of these changes might be. However, we stress that as the structural complexity of the reef plays a key role in ecosystem functions and processes, the indirect effects of loss of structural complexity on corals, and many other reef organisms, may be important. Finally, the among-site differences in responses to changing pCO2 highlight that there are many potential internal and external factors that moderate indirect effects and therefore may shape how coral communities respond to OA. For example, the indirect effects reported here for PNG and CNMI are similar (increased macroalgal abundance, decreased CCA, increased bioerosion and a decrease in structural complexity) yet in PNG coral cover is maintained and in CNMI coral cover decreases (Table 2). This difference may result from both direct physiological effects (calcification declined at CNMI but not at PNG) and indirect effects (in PNG there was evidence of an increase in herbivorous urchin (Fabricius et al. 2014), while in the CNMI, the herbivores avoided predating the dominant algal species (Enochs et al. 2015b)). As highly complex environments, the number of potential external factors which may result in indirect effects is significant. For example, reefs are increasingly exposed to other anthropogenic stressors like rising water temperatures and decreasing water quality such as increased turbidity, pollution and/or eutrophication. Similarly, internal factors from within the coral holobiont, such as changes in both the microbial communities and zooxanthellae populations resulting from OA (Mason 2018; Biagi et al. 2020), may also act as a source of indirect effects on corals and coral communities. [SEP] Justify:

Output: The text corroborates the claim by detailing how ocean acidification leads to indirect effects on coral reefs, specifically the integrity of coral skeletons and the structural complexity of reefs. It mentions that changes in coral cover and bioerosion have been observed in numerous sites, indicating that acidification negatively impacts coral ecosystems. It also discusses how these changes affect other reef organisms and highlights the importance of structural complexity in the ecosystem's functioning, which further supports the claim that coral reefs are affected by rising ocean acidity and associated warming.


Input: Task: contrast the claim using the given text. Claim: Overfishing has led to declining fish populations in many regions. [SEP] Text: Tuna canned in could enter the US with no duty, adding to the financial troubles of the tuna fleet. The cannery in Samoa, and the Japanese boats that delivered tuna to it were important steps in the post-war globalization of fishing. This 5. IndustrializationDOI: 10. 7208/chicago/9780226443409. 003. 0005[Fairtry;motherships;pulse fishing;fish sticks;tariffs;free trade]The first factory processing ship, the Fairtry, launched in Scotland in 1954, changing fishing forever. immediately ordered two dozen and embarked on a series of five-year plans designed to greatly increase their fish and whale harvests. As new ships came on line, the Soviets developed a fishing system, with exploratory vessels transmitting data to motherships that coordinated the catcher fleet. They pulse fished, which means they took everything in their nets before catches dropped and they moved on. The fisheries were effective but inefficient, often wasting the catch, and there was a lack of shore side support facilities to distribute the catch. In the US, processors developed the fish stick and demand for the frozen, bread-covered sticks grew briskly. While federal fishery officials tried to create markets for American fish, the problem was not lack of markets, but that markets were undermined by cheaper imports from Canada, Iceland, and Japan. Fishermen continued to fight for tariff relief and to be blocked the Departments of State and Defense. This 6. TreatiesDOI: 10. 7208/chicago/9780226443409. 003. 0006[Sebastes alutus;industrial fishing;freedom of the seas]The post-war Japanese government had few options for expansion, other than its fishing fleet. They built two fleets, one for the northern seas, to catch salmon and king crab, and a second to go south in search of tuna. There were Japanese boats off Argentina and Brazil in 1955. They also had big factory processing boats operating around Australia and New Zealand, in the Indian Ocean, off northwest Africa, in Newfoundland and in Antarctica. The first fleet of Soviet vessels in the Pacific arrived in the international waters off Alaska in 1959, moving steadily from species to species, and from Alaska to British Columbia, Washington, Oregon and California. fishery decimated the region’s largest rockfish population, Sebastes alutus. [SEP] Justify:

Output: The text contrasts the claim by providing specific examples of overfishing's impact on fish populations. It mentions that the fishery 'decimated the region’s largest rockfish population, Sebastes alutus.' This directly supports the idea that overfishing has led to declining fish populations, contradicting any assertion that may suggest overfishing does not contribute to these declines.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: 3558/supp-6 alignment file of 16 ribosomal marker proteins used to determine phylogeny for the draft genomes utilizing 6,080 reference genomes DOI: 10. 7717/peerj. 3558/supp-7 file of concatenated 16 ribosomal marker proteins, including FastTree determined local support values using the Shimodaira-Hasegawa test for draft and reference genomes DOI: 10. 7717/peerj. 3558/supp-8 We are indebted to the project and team for their commitment to open-access data that allows data aficionados to indulge in the data and attempt to add to the body of science contained within. This is C-DEBI Contribution 333. authors declare there are no competing interests. Benjamin J. Tully conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper. reviewed drafts of the paper, provided origins of assembly workflow. Elaina D. Graham performed the experiments, reviewed drafts of the paper. John F. Heidelberg contributed reagents/materials/analysis tools, reviewed drafts of the paper. The following information was supplied regarding data availability: This project has been deposited at DDBJ/ENA/GenBank under the BioProject accession no. PRJNA385857 and drafts of genomes are available with accession no. NHBG00000000– NHMJ00000000. All contigs generated using Megahit from each sample are available through iMicrobe ( TARA Oceans has deposited the reads in the (SRA) with accessions ERS488346, ERS488330, ERS477998, ERS477979, ERS488509, ERS488486, ERS478040, ERS477953, ERS477931, ERS488147, ERS488119, and ERS478017. Additional files have been provided and are available through FigShare, such as: all contigs from Minimus2 + Megahit output used for binning and community assessment; contig read counts per sample; the putative genome contigs and Prodigal-predicted nucleotide and protein putative files; the ribosomal marker HMM profiles; reference genome markers; draft genome markers; low completion bins, and contigs without a bin. [SEP] Justify:

Output: The text does not address or provide information about X-ray crystallography or its use in determining the 3D structures of proteins. Instead, it discusses alignment files of ribosomal marker proteins and associated data availability, which is unrelated to the claim itself.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: In conjunction with OA, these other factors may ultimately exacerbate the extent to which indirect effects affect corals and coral communities, either through compounding the effects highlighted here, or through additional indirect effects not yet considered. Clearly, potential feedbacks between changes in the physical environment as well as the diversity, abundance and behaviours of species in different coral reef trophic groups will shape coral reef futures. The future of indirect effects researchIn this review we have identified a range of indirect effects which have the potential to have significant impacts on coral and coral communities. Consequently, single-species studies that assess the effects of OA on coral physiology potentially underestimate the effects of OA on coral communities and limit our ability to extrapolate findings to an ecosystem scale. We therefore recommend that the indirect effects of acidification be more widely considered in acidification research. Indirect effects research can be done using a number of research methods. Small-scale, short-term experiments are the basis of much ocean acidification research and an effective method to establish the impact on simple or paired interactions. Larger-scale, long-term aquaria or mesocosm experiments allow us to potentially include more ecosystem functions/processes such as competition and bioerosion. However, these experimental set-ups are limited in ecological complexity and therefore need to target specific species, interactions or processes. In-situ manipulations are becoming more feasible through the use of FOCE (Carbon Enrichment; Stark et al. 2019) and SCoRE-FOCE (; Srednick et al. 2020) experimental flumes. In-situ flumes use natural communities and therefore have greater ecological complexity; however, they may be unable to account for interactions with more mobile taxa such as fish and can be challenging/expensive to run over ecologically meaningful timescales. FOCE experiments may therefore be most useful for research on benthic indirect effects such as bioerosion. At present, studies using naturally acidified sites remain the only method where it is possible to consider large-scale community and ecosystem level effects, including multi-species interactions and effects on food-webs, using corals which have experienced lifetime exposure to acidification. However, these sites are not perfect analogues of future acidified conditions. [SEP] Justify:

Output: The text corroborates the claim by discussing the indirect effects of ocean acidification (OA) on corals and coral communities. It highlights that factors such as changes in the physical environment and species interactions will shape the futures of coral reefs, indicating that ocean acidification significantly impacts coral ecosystems. The text also emphasizes the importance of considering indirect effects of acidification in research, supporting the idea that coral reefs are indeed affected by these environmental changes.


Input: Task: contrast the claim using the given text. Claim: Overfishing has led to declining fish populations in many regions. [SEP] Text: New synthetic nets were being introduced, much lighter than the old cotton nets and requiring much smaller crews. A decade later, superfast refrigeration allowed tuna to be caught anywhere in the world and transported to a cannery where the labor was cheapest. The focus of fisheries science has shifted over the decades, from a focus on identification and classification of fish, to mathematical models, a trend solidified with the introduction of computers that made it possible to analyze increasing amounts of data. These fish population demographics studies, used to develop fishing equations for predicting stock abundance, became the mainstay of American fisheries biology. This 10. 7208/chicago/9780226443409. 003. 0009[fish processing;Science;re-building plans]The post-war agreements between the US with Iceland and Japan helped cement the foreign policy goals of strengthening the economies in both countries, but there was a heavy price to pay for the fish stocks involved. built the world’s largest fishing fleet, and it operated with ruthless efficiency, until the stocks faltered and nations implemented expanded territorial zones. Low wages at fish plants in American Samoa, combined with the development of high-seas freezing, contributed to the establishment of fish processing in low wage countries such as Thailand. Fishing developed with the understanding that the removal of old fish freed up food for younger fish to grow more quickly, an essentially economic understanding of ocean systems that was challenged by new data showing the importance of old fish in reproduction. While the story of the development of fishing during the post-war years was straight forward, the new understanding of fish and fish populations is much more challenging, as scientists seek to rebuild fish populations. Especially important are told fish, that produce more viable progeny in a warmer and more acidic ocean. This 2017. Page maintained by BiblioVault. [SEP] Justify:

Output: The text contrasts the claim by illustrating how the development of fishing practices and technology has led to significant impacts on fish populations. It describes the growth of the world's largest fishing fleet and points to the problems that arose when stocks began to falter due to overfishing, indicating a direct connection between those practices and the decline of fish populations. Furthermore, it highlights a shift in understanding regarding the balance of fish populations and the importance of preserving older fish for reproduction, suggesting that prior economic practices may have contributed negatively to fish demographics.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Tully, Benjamin; Sachdeva, Rohan; Graham, Elaina; Heidelberg, John (2017): 290 Genomes from the Mediterranean Sea: Supplemental Data. figshare. was provided by the Center for (C-DEBI) to BJT and JFH (OCE-0939654). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972-1973 üller. 2004. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. 14:1147-1159 Edgar RC. 2004. : multiple sequence alignment with high accuracy and high throughput. Research 32:1792-1797 Eren AM, Esen Ö. 2015. Anvio: an advanced analysis and visualization platform for omics data. PeerJ 3:e1319. 2008. The microbial engines that drive earth’s biogeochemical cycles. Science 320:1034-1039. 2011. HMMER web server: interactive sequence similarity searching. Research 39:W29-W37. 2012. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28:3150-3152. 2017. BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation. PeerJ 5:e3035-19 Huang X, Madan A. 1999. CAP3: a DNA sequence assembly program. 9:868-877. 2016. A new view of the tree of life. 1(5):16048 --. 2011. A holistic approach to marine eco-systems biology. PLOS Biology 9:e1001177–5 -. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647-1649 Lagesen K, Hallin P, Rødland EA, Staerfeldt H-. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Research 35:3100-3108 Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. [SEP] Justify:

Output: The text provided does not relate to the claim in any manner. It contains citations and references to various studies and bioinformatics tools but does not discuss X-ray crystallography or the determination of 3D structures of proteins.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: For example, these sites often have connectivity to ambient reefs which allows new recruits to arrive from ambient reefs and movement of mobile organisms in and out of the acidified area (Munday et al. 2014). Physically these sites may also differ from future acidified reefs. For example, the source of acidity may also result in other changes to the water chemistry such as elevated levels of DIC (dissolved inorganic carbon; Crook et al. 2012) or other volcanic gases or elements (see review; Gonzalez-Delgado and Hernández 2018). Nevertheless, these sites are useful proxies to identify indirect effects of potential concern. We suggest that a combination of all research methods will allow us the greatest progression in our understanding of the indirect effects of acidification on corals. Here we focused specifically on how indirect effects affect corals and coral communities but our review of the literature illuminates many other potential indirect effects via other taxa, and potentially complex feedbacks among taxa in different trophic groups. For example the increased competitive success of fleshy algae over CCA (Crook et al. 2016) which may or may not be mediated by herbivory. Interactions such as these equally have the potential to affect structure and function of our future coral reefs and also need to be investigated. Understanding ecosystem trajectories is particularly challenging when ecosystem functioning could change via a cascade of altered interactions, such as what might occur in response to an ecological tipping point or within a trophic chain (e. g. Ferreira et al. 2021). Clearly, however, the ecological impact of these indirect effects can be significant (Mumby 2017), and therefore identifying and understanding them is vitally important in our ability to scale up direct physiological effects of OA to an ecosystem level. Future directions and knowledge gapsOur review highlights multiple pathways of indirect effects of OA that have the potential to exacerbate the impact of the direct physiological effects on coral colonies (i. e. lower calcification, slower growth, decreased recruitment) and communities (reduced hard coral abundance and species richness). These direct effects, alone, can have flow-on effects to reef ecosystem services like food provisioning and coastal protection. [SEP] Justify:

Output: The text corroborates the claim by discussing the indirect effects of ocean acidification (OA) on corals and coral communities. It highlights how these direct physiological effects, such as lower calcification and reduced growth rates, impact coral reefs and their ecosystems. The mention of potential changes in competitive dynamics, such as the success of fleshy algae over coral, indicates the impacts of OA on coral reef structure and function. Overall, the text emphasizes the ecological significance of these effects, supporting the claim that coral reefs are affected by ocean acidification.


Input: Task: contrast the claim using the given text. Claim: Overfishing has led to declining fish populations in many regions. [SEP] Text: (2001) correlated the catch correction factor with natural mortality across 15 sardine and anchovy stocks and found a strong negative correlation (1. 05 – 0. 353M; R2 = 0. 78). This regression pattern implies that the catch contribution to SP should be upward for stocks with low natural mortality (where growth outweighs predation) and downward for stocks with high natural mortality. Pending a study that expands the relationship to all categories of fishes, we do not compensate here for mortality replacement given that the vast majority of the stocks we are examining have low natural mortality rates and hence will have compensation factors close to unity. We also note that the compensation factor has no implications for whether the SP–B relationship displays nonstationarity, a major topic in the present study. Instead of doing away with SP analysis in favor of more complex modeling, we suggest that SP vs. B plots should be one of the basic pieces of information presented in all stock assessments, further strengthening the call of Hilborn (2001) and Jacobson et al. (2001). We see this as every bit as important as the assessment information typically presented, e. g. , in the form of tables of catch over time, diagnostic fits of assessment models to abundance index data, or plots of fits to size–age data. We make this suggestion for five reasons: (i) The SP vs. B plots provide an overall summary of stock performance and include effects not necessarily included in stock assessment models when the Bt values are obtained independently of the assessment model results, e. g. , are based directly on survey estimates. (ii) The plots provide a direct check on whether predictions of changes in biomass (Bt+1 – Bt) can be made reliably just based on catch and Bt or relative Bt information, in particular whether similar B levels have exhibited similar SP at different historical times, i. e. , whether there has been nonstationarity in production processes. (iii) The plots are a diagnostic for whether stocks have exhibited strong compensatory response, i. e. , increase in SP/B at low stock sizes. Stocks that have not exhibited such responses have very likely been overfished over the whole period of historical record, e. g. , 2J3KL and Kattegat cod stocks. Stock size reference points, e. g. [SEP] Justify:

Output: The text contrasts the claim by discussing the concept of fish stocks and their natural mortality rates, emphasizing that certain stocks have likely been overfished historically. It mentions that stocks like 2J3KL and Kattegat cod have very likely been overfished throughout the historical record, which supports the idea that overfishing contributes to declining populations. The emphasis on compensation factors and stock performance also implies the repercussions of overfishing on fish populations.


Input: Task: pass the claim using the given text. Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: 9:357-359 Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. and Evolution 25:1307-1320 -M, Leung C-M, Ting H--W. 2016. v1. 0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102:3-11. 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923-930. 1995. An estimate of global primary production in the ocean from satellite radiometer data. Journal of 17:1245-1271 örster önig A, Liss T, Lüssmann -H. 2004. ARB: a software environment for sequence data. Research 32:1363-1371. 2010. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11:538. 2010. Assembly algorithms for next-generation sequencing data. Genomics 95:315-327. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. 25:1043-1055. 2010. FastTree 2—approximately maximum-likelihood trees for large alignments. 5:e9490 Pruesse E, Peplies J, Glöckner FO. 2012. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823-1829 Sharon I, Banfield JF. 2013. Microbiology. Genomes from metagenomics. Science 342:1057-1058 Shimodaira H, Hasegawa M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. and Evolution 16:1114-1116 -’--Llonch M, Sarmento H, Vieira--. 2015. Ocean plankton. Structure and function of the global ocean microbiome. Science 348:1261359. 2011. Next generation sequence assembly with AMOS. in Bioinformatics 11. 8. 1998. Prokaryotes: the unseen majority. Proceedings of the of Sciences of the of America 95:6578-6583 Yang Z. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses various research articles and topics related to bioinformatics and microbial genomes without mentioning X-ray crystallography or its application in determining protein structures.


Input: Task: corroborate the claim using the given text. Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Based on our synthesis of the literature, we propose that the indirect effects of greatest concern are that a decline in CCA, and the settlement cues and habitat they provide, is likely to drive a reduction in recruitment of corals and impede population replenishment after disturbances. We suggest that manipulative field experiments, such as controlled seeding of coral larvae at naturally acidified locations and monitoring of settlement success and post-settlement survival compared with nearby control locations, are needed to resolve existing data gaps. Moreover, declining CCA will lead to diminished levels of reef cementation which can cause coral mortality due to substratum instability (Madin et al. 2012). Detailed monitoring of coral survival after storms at naturally acidified locations compared with nearby control sites, accompanied by measurement of CCA abundance and substratum strength, will provide new insights about how CCA loss affects coral survival. In addition to changes in CCA, increased bioerosion is likely to compound effects of decreased calcification and increase dissolution, to shift corals from net skeleton accretion towards net skeleton loss. While as yet there is limited evidence of a significant direct effect on coral abundance and diversity resulting from reduced structural complexity, a recent study indicates that coral biodiversity is highest at intermediate roughness (rugosity) of reef substrata (Torres-Pulliza et al. 2020). Field-based observations of the magnitude of bioerosion, and the diversity and abundance of bioeroding taxa, are required to link changes in bioerosion to differences in structural complexity on reefs, and to link these changes to coral diversity. A loss of structural complexity on reefs due to OA (via decreased cementation and increased erosion) is also likely to result in changes to reef functions more broadly. More complex reefs support higher diversity and abundance of fishes and therefore OA could affect the critical reef ecosystem services of food provision. Our review highlights the need to extend from single species studies, to studies that explicitly characterise how species interactions change, and how trophic linkages are altered, as pCO2 increases. [SEP] Justify:

Output: The text corroborates the claim by discussing how ocean acidification (OA) impacts coral reefs via indirect effects such as a decline in Crustose Coralline Algae (CCA), leading to reduced recruitment of corals and impaired population replenishment. It emphasizes that diminished levels of CCA will lead to increased substratum instability, potentially causing coral mortality. Additionally, it highlights changes in bioerosion and decreased calcification, which are likely effects of increasing ocean acidification, supporting the notion that coral reefs are affected by these environmental changes.


Input: Task: contrast the claim using the given text. Claim: Coral reefs are highly sensitive to changes in water temperature and acidity. [SEP] Text: There were sufficient data to consider the relationships between median spawning month of two species, Acanthopagrus australis (four records) and Pagrus auratus (six records), and SST and photoperiod at a smaller spatial scale, although the data sets were too small for statistical analysis. ResultsWhen data for all species are viewed at a family level, deviations in median spawning month from month of minimum SST are distributed fairly evenly before and after the month of minimum SST (Fig. 2). For both the Northern (Fig. 2a) and (Fig. 2b) [and consequently for the combined data set (Fig. 2c)] there is a clear decrease in the deviation of median spawning month away from the month of minimum SST, as mean annual SST increases. At mean annual SSTs of about 20°C and below, the deviation in median spawning month of sparids away from the month of minimum SST varies greatly, with deviations up to 6 months. In contrast, for mean annual SSTs of 21°C and above, the maximum deviation from the month of minimum SST is 3. 5 months, with only 3 deviations greater than 2. 25 months from a total of 41 data points (Fig. 2c). The reduction in deviation is significant. Quantile regression analysis (Scharf et al. 1998) indicated significant reductions in both the upper (80% quantile: y = 9. 8 − 0. 30x, P < 0. 002, n = 88) and lower (20% quantile: y = −8. 0 + 2. 50x, P = 0. 022, n = 88) boundaries of the data with increasing SST (Fig. 2c). Furthermore, the mean of the absolute value of deviation in spawning month decreased significantly with increasing SST (Table 2; Fig. 3a), reflecting the reduction in deviation with increasing minimum SST. This relationship was strong, as indicated by the high r 2 (0. 7677) and large F-value (307. 43). Fig. 2Deviation in sparid mean spawning month away from the month of minimum sea surface temperature (SST). Solid lines on part c represent 80 and 20% quantile regressions describing upper and lower boundaries of the data cloud for SST < 21°C. [SEP] Justify:

Output: The text contrasts with the claim by discussing the spawning month deviations of specific fish species as related to sea surface temperature (SST), suggesting a stability in the timing of spawning relative to increasing SST. It implies that while there are fluctuations at lower SSTs, the deviations in spawning month become less variable with warmer SSTs. This could suggest that certain marine organisms, potentially including those associated with coral reefs, might be less sensitive to temperature changes in terms of spawning timing than one might presume from the claim about coral reefs being highly sensitive overall.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: Biosynthesis of fragrance 2-phenylethanol from sugars by Pseudomonas putida access Published: 02 April 2024 Biosynthesis of fragrance 2-phenylethanol from sugars by Pseudomonas putida Patricia Godoy1, Zulema Udaondo2, Estrella Duque1 & …Juan L. Ramos1 Show authors Biotechnology for Biofuels and Bioproducts 2. The two strains without the pPE-1 plasmid did not produce 2-PE as expected (not shown). We found that the P. putida CM12-5 (pPE-1) and P. putida CM12-5Δgcd (xylABE) (pPE-1) produced about 50 ppm 2-PE when glucose was the growth substrate (Fig. 2). However, with xylose, negligible 2-PE accumulated, i. e. , less than 3 ppm was detected in the culture medium (not shown). When glucose and xylose were present simultaneously, a production level of 2-PE similar to that obtained with glucose alone was achieved (Fig. 2). These strains accumulated low amounts of phenylalanine in the culture medium (< 3 ppm) under all growth conditions (not shown), which suggests that almost all phenylalanine produced intracellularly was channeled towards 2-PE production. Fig. 2Production of 2-PE in the presence of glucose (open bars) or mixture of glucose:xylose (closed bars) as the C source. P. putida CM12-5 (pPE-1) and CM12-5Δgcd (xylABE) (pPE-1) cells were grown overnight with glucose as the C source. The cultures were then washed and diluted to DO660 of 0. 1 diluted in fresh medium with glucose (0. 5% w/v) or glucose:xylose (0. 375% w/v:0. 125% w/v) as the C source, and 2-PE production was measured after 24 h incubation. [SEP] Justify:

Output: The text does not address the claim regarding bioengineered yeast producing biofuels; instead, it discusses the biosynthesis of 2-phenylethanol (2-PE) from sugars by Pseudomonas putida, which is a different organism and context. Therefore, it is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Machine learning models are used in many areas, including healthcare and finance. [SEP] Text: Voice of the Publisher > Vol. 9 No. 4, December 2023 Importance of Models in Detection (). DOI: 10. 4236/vp. 2023. 94017 132 Downloads 704 Views 215. doi: 10. 4236/vp. 2023. 94017. 1. healthcare industry is open to the most significant industries in the society. It is an organization that plays a pivotal role in society, aiming to provide quality medical services. However, despite the benefits, the industry is also raided by numerous challenges. Healthcare fraud has been a significant challenge that has to be addressed. There are numerous fraudulent activities within healthcare Fernando, Gammulle, Denman, Sridharan, & Fookes (2021). These problems present financial implications, and they also jeopardize the well-being of patients. Consequently, they also erode the trust within the system. Many research works have stated that fraudulent activities in the healthcare sector costs billions of dollars annually and are a persistent concern for healthcare providers, according to Johnson & Activities (2019). In this era of data-driven decision-making and technological advancements, healthcare fraud detection has gained prominence. According to ( Springer (n. d. ) of and Analytics), the growing interest in statistical methods for data science spans across various disciplines, including statisticians, computer scientists, computational mathematicians, and physicists, emphasizing the importance of interdisciplinary collaboration. Many cybersecurity crimes are also on the rise. There have been traditional rule-based approaches that have proven inadequate in identifying sophisticated and evolving fraud schemes, according to the work of Nassif, Talib, Nasir, & Dakalbab (2021). Nonetheless, the healthcare industry is increasingly turning to advanced technologies, particularly machine learning, and they are supposed to enhance its fraud detection capabilities. Machine learning models offer improvement when it comes to the accuracy and efficiency of fraud detection in healthcare. The models can analyze vast volumes of structured and unstructured data. They have also been known to identify patterns and anomalies that are often elusive to human reviewers. According to Dissanayake, Fernando, Denman, Sridharan, Ghaemmaghami, & Fookes (2020) machine learning enables continuous learning from new data, and it allows the process of fraud detection systems in relation to threats. 2. Materials and success of machine learning-based healthcare fraud detection relies heavily on the availability and preprocessing of relevant data. [SEP] Justify:

Output: The text corroborates the claim by detailing how the healthcare industry is increasingly adopting machine learning technologies, particularly for fraud detection. It states that machine learning models improve the accuracy and efficiency of fraud detection, which connects directly to their application in healthcare. The mention of machine learning's ability to analyze large data sets and identify patterns supports the idea that these models are highly relevant in this field.


Input: Task: contrast the claim using the given text. Claim: Coral reefs are highly sensitive to changes in water temperature and acidity. [SEP] Text: 1997, 1998a, b, 1999, 2000, 2001, 2002a, b). In these areas, the spawning season of P. auratus deviates little from the month of minimum SST. Thus, by utilising winter spawning, tropical sparids can spawn over similar temperature ranges to more temperate species and/or populations, albeit at the cost of a shortened reproductive period. Tropical sparids such as A. berda and A. australis occur in the same locations (estuaries) throughout the year (Sheaves 1992, 1993, 1998), thus the temperature ranges experienced at these locations remain within adult tolerance levels. Despite this, both species spawn in winter, and in increasingly warmer waters the timing of spawning of A. australis moves progressively closer to the month of minimum SST. This, together with the family-wide relationship between SST and spawning season, suggests that thermal requirements for gamete development, or gamete, egg or larval survival, rather than thermal requirements of adults, may play an important part in determining the warm water limits of distribution of these species in particular, and sparids in general. If adults possess the physiological ability to withstand high temperatures but gametes, larvae, etc. , do not, targeting spawning at times of minimum water temperatures is an obvious tactic to allow a species to maximise penetration into warmer waters. In essence, tropical sparids may be members of a temperate group, limited in distribution by the temperature tolerances of gametes, eggs or larvae, but maximising their penetration into conditions at the upper limits of their thermal tolerance by targeting spawning to times of low water temperature. Although direct cueing of the timing of reproduction on water temperature to allow the production of gametes, eggs, larvae or juveniles when physical conditions are appropriate is an intriguing and plausible reason for the winter spawning of warmer water sparids, it is not the only possible explanation. Rather than a direct cue to accommodate the physiological needs of early stages, water temperature has often been suggested as a proximate cue that initiates gonad maturation and spawning, so that larvae are produced at times when their planktonic prey are abundant (Bye 1984). For example, the timing of spawning of the osmerid, Mallotus villosus, is related to warming sea temperatures that lead to production of larvae when conditions are optimal for zooplankton (Carscadden et al. [SEP] Justify:

Output: The text contrasts the claim by discussing how tropical sparids, despite potentially facing warmer waters, use spawning strategies that allow them to maximize reproduction and distribution in these conditions. It suggests that the adults can tolerate higher temperatures, but implies that the temperature sensitivity may actually lie in the gametes and larvae rather than the adult fish. This argument indicates a complex relationship with temperature rather than simple sensitivity, therefore providing information that may directly rebut the claim's assertion about coral reefs.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: The figure shows the average of three independent assaysFull size imageSince xylose is metabolized through the pentose phosphate pathway (PPP), it is likely that phosphoenolpyruvate (PEP) levels in CM12-5Δgcd (xylABE) are limiting the operation of the shikimate pathway (Fig. 1), which is critical for production of l-phenylalanine and its subsequent channeling towards 2-PE. Effect of the addition of the Ehrlich pathway and shikimate pathway intermediates on 2-PE productionTo determine if the limiting factor in the process was related to the production of the primary substrate, l-phenylalanine (l-Phe), or pathway intermediates, i. e. , phenyl acetaldehyde (PA) and phenylpyruvate (PP), we carried out resting cells assays in which 1 mM l-Phe (165 ppm), 1 mM PA (120 ppm) or 1 mM PP (186 ppm) were added to cultures of CM12-5 (pPE-1) and CM12-5Δgcd (xylABE) (pPE-1), in a medium with glucose or with xylose as the C source. Figure 3 shows that, regardless of the C source used (glucose or xylose), 2-PE production reached concentrations of about 100–120 ppm 2-PE in both strains, increases that represent production about 200% higher than those obtained in the absence of Ehrlich pathway intermediates. Therefore, the transformation of l-Phe into 2-PE through the Ehrlich pathway was not compromised. This suggests that the initial amount of l-Phe in the cells is the main limiting factor in the production of 2-PE. Fig. 3Production of 2-PE by resting cells in the presence of Ehrlich pathway intermediates: l-phenylalanine (l-Phe), phenylacetaldehyde (PA) or phenylpyruvate (PP). CM12-5 (pPE-1) (blue bars) and CM12-5Δgcd (xylABE) (pPE-1) (red bars) cells were grown in the presence of glucose as the C source until reaching a DO660 of 1, the cultures were then washed and concentrated in 1xM9 + 0. [SEP] Justify:

Output: The text does not address the claim about bioengineered yeast producing biofuels from sugars. Instead, it discusses the production of 2-PE (2-Phenylethanol) related to nitrogen and carbon sources, particularly focusing on the shikimate pathway and different precursor compounds. There is no mention of biofuels or the capability of yeast to convert sugars into biofuels.


Input: Task: corroborate the claim using the given text. Claim: Machine learning models are used in many areas, including healthcare and finance. [SEP] Text: Adhering to ethical practices, the researcher made sure that our research met data privacy regulations. The study had a focus on safeguarding sensitive patient information and complying with relevant legal and ethical standards. Ethics also concerns the security and privacy of the information. 3. results section of this research presents the results of the machine learning-based healthcare fraud detection experiments. The performances are based on various algorithms and provide insights into the effectiveness of machine learning models in addressing healthcare fraud. 3. 1. The research evaluated the performance of four machine learning algorithms: (XGBoost), and (CNN and RNN). Below is a summary of the key performance metrics of these models. The precision of a model assesses its proficiency in accurately classifying fraud cases, while recall quantifies the degree to which it can successfully identify every confirmed case of fraud. The F1-score is a performance measurement that considers both precision and recall. metric showcases the level of distinction a model can achieve between fraudulent and non-fraudulent transactions. The data from Table 1 shows that the machine-learning methods beat as a benchmark. The ensemble methods, and XGBoost, are shown to have high precision and recall, suggesting their ability to identify a significant number of fraud cases while minimizing false alarms. By focusing on CNNs and RNNs, deep learning reaches significant precision and recall scores of over 95%. 3. 2. To gain insights into the factors contributing to fraud detection, we analyzed feature importance scores for the and XGBoost models. Figure 1 illustrates the top ten most important features identified by both models. Table 1. Model performance metrics. Source: Srivastava (2023) Link ( Ariwala, 2023 ) Link, (Updated on Apr 05/2023). Figure 1. Illustrates the top ten most important features identified by both models. 3. 3. With a sensitivity analysis, we calculated model robustness by introducing synthetic variations in the dataset. Our models consistently displayed performance stability across different variations, suggesting their adaptability to rapidly changing fraud patterns. As stats in Figure 1, Machines are much better than humans at processing large datasets. They are able to detect and recognize thousands of patterns on a user’s purchasing journey instead of the few captured by creating rules. 3. 4. Real-Deployed within a healthcare provider’s fraud detection system in real-world applications, our best-performing model is the CNN. [SEP] Justify:

Output: The text corroborates the claim by detailing the use of machine learning models specifically in healthcare, as it discusses a research study focused on fraud detection within healthcare systems. The mention of various machine learning algorithms such as XGBoost, CNN, and RNN and their effectiveness in processing large datasets and detecting patterns aligns with the broader application of machine learning in different sectors, including healthcare.


Input: Task: contrast the claim using the given text. Claim: All coral reefs can be fully restored through artificial means. [SEP] Text: IntroductionCoral populations worldwide are sensitive to a range of biotic and abiotic pressures (Riegl 2020), many of which will be exacerbated by future climatic change and human exploitation (Wolff et al. 2018; Riegl and Glynn 2020). Subsequently, the future status of coral reef ecosystems relies on the resilience of coral populations, specifically their capacity to endure, and recover from, increasingly frequent disturbance events (Holling 1973). Accordingly, a resilience-orientated focus is becoming commonplace in reef management (Mcleod et al. 2019, 2021), necessitating an ability to predict the responses of coral populations to varying biotic and abiotic regimes (Lam et al. 2020). Yet, a limited understanding for the dynamics underpinning coral population performance and resilience still hinders our capacity to recognise and manage the climate induced reassembly and/or collapse of coral reef ecosystems (Bellwood et al. 2004; Edmunds and Riegl 2020). Although limited, the application of demographic theory within coral research is not a novel concept (Edmunds et al. 2014). Structured population models offer insight into how the state of individuals (typically their size, age, or developmental stage; Caswell 2001) arbitrates their survival and reproduction and how these fitness components in turn shape the overall responses of populations to local biotic and abiotic conditions (Box 1; Benton et al. 2006). Understanding how patterns in the survival, progression (i. e. growth), retrogression (i. e. negative growth, shrinkage; Salguero-Gómez and Casper 2010), and reproduction of individual colonies, influence population-level characteristics will improve effective management (Riegl et al. 2018; Brito-Millán et al. 2019a; Madin et al. 2020; Pisapia et al. 2020). Appropriately, state-structured demographic approaches are being increasingly utilised to quantify the mechanisms supporting or preventing the persistence and revival of disturbed coral communities (e. g. Kayal et al. 2018; Cant et al. 2021c). Accordingly, there is a growing appreciation for how the size structure of coral populations influences their dynamics and endurance (Bak and Meesters 1998, 1999; Anderson and Pratchett 2014; Dietzel et al. 2020; Lachs et al. [SEP] Justify:

Output: The text contrasts the claim by highlighting the complexities and challenges associated with restoring coral reefs. It discusses various pressures on coral populations, such as climate change and human exploitation, which hinder their capacity to recover. Furthermore, it emphasizes the need for a better understanding of coral dynamics and population resilience, indicating that restoration efforts may not fully succeed due to limited knowledge and ongoing environmental threats.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: 5% (w/v) glucose or xylose to reach a DO660 of about 10, and the effect of 1 mM l-Phe PA or PP supplements on 2-PE production was measured after 24 h of incubation. The figure shows the average values of three independent assaysFull size imageOn the other hand, l-phenylalanine in P. putida is made through the shikimate pathway, in which shikimate and chorismate are intermediates (Fig. 1), and hence we tested whether the addition of 1 mM shikimate (174 ppm) or 1 mM chorismate (226 ppm) would also lead to an increase in 2-PE production. Supplementation with chorismate to CM12-5 (pPE-1) and CM12-5Δgcd (xylABE) (pPE-1) growing with glucose or xylose (Table 1) led to production levels of about 1 ppm 105 ppm 2-PE (Table 1), a value similar to that reached when Ehrlich pathway intermediates were added. However, this was not the case with shikimate, as it was only partially consumed by the cells, and also because it was biotransformed in side dead-end products (3-hydroxyshikimic acid, quinate and acetate) both with glucose or xylose as the C source (data not shown). This implies that an appropriate channeling of shikimate to chorismate is a critical issue in the synthesis of 2-PE by this host platform. Hence, our data support the hypothesis that the intracellular levels of l-Phe maybe the limiting step in the biosynthesis of 2-PE. Moreover, this was particularly noticeable, when xylose was used as the sole C source, since with this C-source a clear limitation of the available intermediates for the synthesis of l-Phe was identified. Table 1 Effect of shikimate pathway intermediates chorismic acid (CA) and shikimic acid (SA) on the synthesis of 2-PE in P. putida CM12-5 (pPE-1) and CM12-5Δgcd (xylABE) (pPE-1) strainsFull size tableIncreasing phenylalanine production and 2-PE levels in P. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses specific biochemical processes and experimentation involving the production of 2-PE in Pseudomonas putida, rather than addressing bioengineered yeast or their ability to produce biofuels from sugars. There is no mention of yeast or biofuel production within the provided content.


Input: Task: corroborate the claim using the given text. Claim: Machine learning models are used in many areas, including healthcare and finance. [SEP] Text: Over six months, it detected 92% of fraudulent claims with a low false-positive rate, significantly reducing financial losses. 4. this section, the researcher interprets the results presented in the previous section and discusses their implications for healthcare fraud detection. It is, therefore, important to address the broader context of machine learning adoption in the healthcare industry. 4. 1. our study, machine learning models, particularly ensemble methods and deep learning models, significantly outperformed the baseline model in detecting healthcare fraud. Precision and recall scores that are high demonstrate the effectiveness of these models in recognizing fraudulent activities ( Chalapathy & Chawla, 2019 ). In healthcare fraud detection, high precision values are crucial for minimizing false positives and reducing the burden on investigators ( Naidoo & Marivate, 2020 ). High recall values reflect the models’ ability to capture a significant amount of actual fraud cases, contributing to fraud prevention and financial savings. The implications of these outcomes showcase how machine learning can reshape fraud detection within healthcare settings. 4. 2. importance scores from the analysis showed that claim type, diagnosis codes, and provider specialty significantly impact fraud detection. The importance of these features is emphasized when developing fraud detection algorithms and implementing fraud prevention strategies Dissanayake, Fernando, Denman, Sridharan, Ghaemmaghami, & Fookes (2020). Healthcare organizations can reinforce their fraud detection systems by paying attention to specific features. 4. 3. analysis in our research showed how machine learning models are flexible enough to handle varying fraud patterns. With healthcare fraud schemes changing and adapting, an important characteristic is having the ability to evolve as well Nassif, Talib, Nasir, & Dakalbab (2021). The progressively learning abilities of machine learning models make them well-suited for identifying and preventing healthcare fraud. 4. 4. Real-practical use of our best-performing model, the CNN, was showcased when paired with a real-world healthcare provider’s fraud detection system as part of our research. The model performed exceptionally well in identifying fraudulent claims while keeping false positives to a minimum, leading to major savings in financial losses ( Nassif et al. , 2021 ). The successful real-world integration of machine learning into healthcare fraud prevention has shown tangible benefits. 4. 5. [SEP] Justify:

Output: The text corroborates the claim by providing evidence of the application of machine learning models in healthcare fraud detection, detailing their effectiveness in identifying fraudulent claims and reducing financial losses. It highlights the successful integration of these models in real-world healthcare settings, pointing to their significant role in financial savings and fraud prevention.


Input: Task: contrast the claim using the given text. Claim: All coral reefs can be fully restored through artificial means. [SEP] Text: 2021), with recent appeals for efforts to be concentrated towards gauging the resilience of coral communities (Pisapia et al. 2020). However, we argue here that the contemporary application of state-structured demographic tools in evaluating the viability of coral populations, and their communities, does not reflect our need to anticipate their resilience. Box 1 Scaling from individuals to communitiesFull size tableFig. 1Records of survival, size, and reproductive output, collected from tagged coral colonies over time, can enhance our understanding of population trajectories and, when collected across multiple populations, can be used to predict community reassembly under future climate scenarios. Here, subscript notation is used to reflect how the changing state of individuals corresponds with changes in individual-level characteristics. In this schematic the state of individuals refers to colony size and thus the growth (g) of individuals between size x and y is expressed as gyxFull size imagePrevailing knowledge of coral population dynamics centres around long-term (i. e. asymptotic) population characteristics (Box 2), with measures of long-term population growth rate (λ) often used for projecting the viability of coral assemblages (e. g. Foster and Foster 2013, 2018; Edmunds 2015, 2020; Riegl et al. 2017; Kodera et al. 2020; Cant et al. 2021c; Shlesinger and van Woesik 2021). Indeed, the same is true across ecological theory, with our understanding of population dynamics focused on asymptotic population characteristics (Morozov et al. 2020). Quantifying the asymptotic characteristics of various populations presents a valuable comparative tool for exploring abiotic tolerances (Beissinger and Westphal 1998). Yet, for populations to realise their asymptotic potential, they require the persistence of stable conditions over extended timescales (Caswell 2001). In reality, though, seasonality exposes populations to periodic abiotic shifts, whilst predation, human exploitation, or storm and fire events generate recurrent and instantaneous disturbances. These short-term abiotic and biotic disturbances ensure that natural environments rarely exist at a stable equilibrium (Williams et al. 2011; Hastings et al. 2018). Consequently, evaluating the resilience and viability of populations requires an understanding for how the dynamics of populations manifest across timescales more representative of the disturbance cycles to which they are exposed (Hastings 2010). [SEP] Justify:

Output: The text contrasts the claim by suggesting that the resilience and viability of coral populations are influenced by disturbances and that natural environments do not typically exist at a stable equilibrium. It discusses the need for stable conditions over extended timescales for populations to reach their potential, implying that full restoration through artificial means may not account for the complexities of these natural disturbances and population dynamics.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: putida It has been described that l-Phe exerts feedback inhibition of its own synthesis through interaction of the amino acid with the R-domain of chorismate mutase/prephenate dehydratase, PheA, a bifunctional enzyme in the shikimate pathway for the synthesis of aromatic amino acids [34]. Molina-Santiago et al. [24] constructed PheAfbr, a PheA mutant variant in which the R-domain of PheA was deleted and the allosteric sensitivity to phenylalanine was eliminated. This PheAfbr mutant variant was expressed in plasmid pPHE1. This study confirmed that CM12-5 (pPHE1) accumulated higher titers of L-phenylalanine in the culture medium i. e. , up to 350 ± 10 mg L−1 versus around 300 ± 5 mg L−1 for CM12-5 (Fig. 4A). Then, CM12-5 (pPHE1) was transformed with pPE-1 and 2-PE measured in the medium. It was found that 2-PE increased from about 50–60 ppm to near 95 ± 5 ppm (Fig. 4B), production levels similar to those achieved with exogenous supplementation of l-Phe in resting cell assays. This confirmed that the limitation in the production of l-Phe is an obvious step in the production of 2-PE. Fig. 4l-Phe production and 2-PE production from 1. 5% (w/v) glucose of Pseudomonas putida CM12-5 derivative strains without and with the pPE-1 plasmid. Cells were grown overnight with glucose as the C source, then the cultures were diluted to DO660 of 0. 1 in fresh medium with 1. 5% (w/v) glucose, and l-Phe production (panel A) or 2-PE (panel B) was measured after 24 h incubation. The figure shows the average values of three independent assaysFull size imageThereafter, it was decided to search for clones that can produce more l-Phe than the CM12-5 and CM12-5 (pPHE1) strains. To this end, the P. [SEP] Justify:

Output: The text does not provide any information about bioengineered yeast or its ability to produce biofuels from sugars. Instead, it discusses the feedback inhibition in the synthesis of L-phenylalanine via Pseudomonas putida, which is unrelated to the claim regarding biofuels and yeast.


Input: Task: corroborate the claim using the given text. Claim: Machine learning models are used in many areas, including healthcare and finance. [SEP] Text: Data Privacy—Machine learning models have shown great promise in identifying healthcare fraud, yet there are still critical ethical and data privacy considerations that must be addressed ( Johnson & Khoshgoftaar, 2019 ). Regulatory standards and protection are crucial when handling patient data in healthcare organizations. Transparency and accountability in the use of machine learning models are essential for preserving public trust. 4. 6. Healthcare fraud detection offers opportunities for future machine learning research, especially in advanced techniques such as anomaly detection and reinforcement learning. Data scientists, healthcare professionals, and policymakers can work together interdisciplinary to develop fraud prevention strategies that combine technological solutions with regulatory measures Fernando, Gammulle, Denman, Sridharan, & Fookes (2021). The research emphasizes the vital part played by machine learning models in healthcare fraud detection. Healthcare organizations looking to address fraud, protect patient data, and uphold the integrity of the healthcare system find promising solutions in these models’ remarkable performance, adaptability, and real-world effectiveness. 5. this research, the report has explored the significance of machine learning models in healthcare fraud detection and their potential to revolutionize fraud prevention in the healthcare sector. 5. 1. have shown that machine learning models, specifically ensembles like and XGBoost, along with deep learning models such as CNNs and RNNs, significantly improve healthcare fraud detection effectiveness. By outperforming conventional approaches and achieving both high precision and recall scores, these models reliably identified fraudulent behaviour with low incidence of false positives. 5. 2. critical role of specific features, such as claim type, diagnosis codes, and provider specialty, in detecting healthcare fraud is highlighted by our analysis. Healthcare organizations looking to prevent fraud should prioritize these features, leading to more accurate fraud detection systems. 5. 3. learning models demonstrate robustness and adaptability to fraud pattern variations. Ongoing adaptation via new data lets them actively combat healthcare fraud effectively. The adaptability of these models keeps them effective despite shifting fraud strategies. 5. 4. Real-best-performing model, the CNN, deployed successfully in a healthcare provider’s fraud detection system, is an example of machine learning’s practical application in the real world. The effectiveness of this model is exemplified by its ability to lower financial losses while keeping the false-positive rate low for healthcare organizations. Conflicts of author declares no conflicts of interest regarding the publication of this paper. 0924. [SEP] Justify:

Output: The text corroborates the claim by discussing the application of machine learning models specifically in healthcare, particularly in identifying healthcare fraud. It highlights the promise and effectiveness of these models in a specific area, which is a part of the broader context of their use in various sectors, including finance. The text illustrates the models' adaptability and significance in detecting patterns in healthcare fraud, thus supporting the claim about their use in multiple fields.


Input: Task: contrast the claim using the given text. Claim: All coral reefs can be fully restored through artificial means. [SEP] Text: Anticipating the future condition and endurance of populations thus requires an awareness for their transient characteristics (Ezard et al. 2010). Transient shifts in the state structure of populations can elevate (amplification) or diminish (attenuation) their growth rates relative to asymptotic projections (Townley et al. 2007). Equally, for populations existing in a transient state, there is a natural tendency for their state structure to converge towards a stable distribution (Caswell 2001). Intuitively, with population resilience comprised of the attributes of resistance (the ability to withstand disturbances), compensation (the ability to benefit from disturbances) and recovery (the speed and ability to reattain stationary equilibria), the transient dynamics of populations therefore represent quantifiable measures of these features of resilience (Box 3; Hodgson et al. 2015; Capdevila et al. 2020). Box 3 Measuring transient population characteristicsFull size tableFig. 4Various measures exist for quantifying transient population characteristics. Disturbances (*) disrupt the structural composition of populations forcing them into a transient phases during which their trajectories will deviate from asymptotic expectations (λ, dashed line). The response of a population during this transient phase is contingent on their capacity for amplification (increases in population growth) and attenuation (declines in population growth). Using the measures of reactivity and maximal amplification (describing the initial, and maximum, increase in population growth rate during transient conditions) ecologists can quantify the relative amplification potential of natural populations. Alternatively, the measures of first-step attenuation and maximal attenuation can be used to describe the initial, and maximum decline in population growth rate during transient conditions. Meanwhile, damping ratio estimates describe the time required for a perturbed population to reobtain a stable equilibrium. Accordingly, by revealing the capacity for populations to grow (compensation), avoid declines (resistance), and/or recover following a disturbance event, these transient metrics present ecologists with measures of population resilienceFull size imageTransient dynamics and the resilience of coral communitiesTransient demographic approaches present an effective tool for explicitly evaluating the resilience of natural populations (Capdevila et al. 2020). Indeed, such approaches have proven instrumental in our understanding of the establishment of populations within new and variable environments (Iles et al. 2016; McDonald et al. 2016, 2017; Jelbert et al. 2019). [SEP] Justify:

Output: The text contrasts the claim by detailing the transient characteristics and resilience of coral populations. It emphasizes that populations exist in a transient state that influences their growth rates and recovery processes. This suggests that while restoration efforts may exist, full restoration is complicated by the inherent dynamics and resilience characteristics of coral populations, which may not align with the idea of complete restoration through artificial means.


Input: Task: pass the claim using the given text. Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: putida CM12-5 and CM12-5 (pPHE1) strains were subjected to random mutagenesis with EMS and selection of clones resistant to high concentrations (> 3 mg mL−1) of the l-phenylalanine analogue p-fluoro-phenylalanine (FPA), the mutagenesis was carried out as described in Materials and Methods. One clone of each strain (named PG1E and PG2E), which were able to accumulate about 300 and 450 ppm L-Phe, respectively, when grown with 1. 5% (w/v) glucose (Fig. 4A) were kept. These overproducer strains were subsequently transformed with pPE-1 plasmid and 2-PE accumulation determined. With P. putida PG1E, around 100 ppm 2-PE accumulated and the highest levels of 2-PE were reached with PG2E that accumulated at close to 120 ppm (Fig. 4B). As the highest l-Phe and 2-PE productions were achieved with PG2E strain, it was decided to sequence its genome to determine which genomic changes were responsible for l-Phe overproduction. When comparing the genome of this l-Phe overproducer derivative PG2E with DOT-T1E genome, we found that, apart from the five mutations involved in l-Phe degradation pathways generated by direct mutagenesis and described in Molina-Santiago et al. [24], up to 400 SNP (see Additional file 2: Table S1) were found. To refine the study, the SNP in the genes that encode proteins related to l-Phe metabolism (Additional file 4: Table S3) were analyzed. A H431P change in shikimate dehydrogenase (QuiA) that may prevent the misrouting of shikimate to 3-hydroxyskimate was identified; together with a set of mutations in genes encoding enzymes of the phenylacetic acid (PAA) degradation pathway. As suggested by L324P in PaaH_2, Y154C in PaaK, V154A and F284L in PaaA (Additional file 3: Table S2). Indeed, due to the mutations in the paa genes, the PG2E strain lost the ability to metabolize PAA (see Additional file 1: Fig. S1). [SEP] Justify:

Output: The text describes the random mutagenesis of P. putida strains and their ability to produce l-phenylalanine and 2-phenylethanol, but it does not explicitly mention bioengineering yeast or the production of biofuels from sugars. Therefore, it is deemed irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Machine learning models are used in many areas, including healthcare and finance. [SEP] Text: [2] Ariwala, P. (2021). A for with Machine Learning. Maruti Techlabs. [3] Chalapathy, R. , & Chawla, S. (2019). for Anomaly Detection: A Survey. [4] Dissanayake, T. , Fernando, T. , Denman, S. , Sridharan, S. , Ghaemmaghami, H. , & Fookes, C. (2020). for Detection without Segmentation. IEEE Journal of Biomedical and Health Informatics, 25, 2162-2171. [5] Fernando, T. , Gammulle, H. , Denman, S. , Sridharan, S. , & Fookes, C. (2021). for Detection—A Survey. ACM (CSUR), 54, 1-37. [6] Johnson, J. M. , & Khoshgoftaar, T. M. (2019). . Journal of Big Data, 6, 63. [7] Naidoo, K. , & Marivate, V. (2020). Detection of. Design, Implementation and Use of Information and (10. 1007/978-3-030-44999-5_35 [8]. , & Dakalbab, F. M. (2021). for Anomaly Detection: A Systematic Review. IEEE Access, 9, 78658-78700. [9] Springer (n. d. ). of and Analytics. [10] Srivastava, T. (2023). 12 for Know (Updated 2023). Analytics Vidhya. [11] Tallón-Ballesteros, A. , & Chen, C. (2020). Explainable AI: Value to -Based Systems. , 332, 152. [SEP] Justify:

Output: The text references various studies and surveys that discuss applications of machine learning models in areas such as healthcare, specifically in anomaly detection. This supports the claim that machine learning is utilized in healthcare and potentially finance, as the references indicate a broad relevance of machine learning in various sectors.