Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Javascript is disabled in your browser. Please enable Javascript to view PeerJ. Related research -290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology View 10. 7717/peerj. 3558 Published 2017-07-10 Accepted 2017-06-19 Received 2017-05-09 -assembled genomes, Mediterranean sea, Bacteria, Archaea, Tara oceans Copyright © 2017 Tully et al. is an open access 2017. 290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology. PeerJ 5:e3558 The authors have chosen to make the review history of this 7. 2 Tbp of metagenomic data from 243 ocean samples from throughout the global ocean, specifically targeting the smallest members of the ocean biosphere, the viruses, Bacteria and Archaea, and picoeukaryotes (Sunagawa et al. , 2015). Initial work on these fractions produced a large protein database, totaling >40 million nonredundant protein sequences and identified >35,000 microbial operational taxonomic units (OTUs) (Sunagawa et al. , 2015). Leveraging the publically available metagenomic sequences from the “girus” (giant virus; 0. 22–1. 6 µm), “bacteria” (0. 22–1. 6 µm), and “protist” (0. 8–5 µm) size fractions, we have performed a new joint assembly of these samples using current sequence assemblers (Megahit (Li et al. , 2016)) and methods (combining assemblies from multiple sites using Minimus2 (Treangen et al. , 2011)). These metagenomic assemblies were binned using BinSanity (Graham, Heidelberg & Tully, 2017) into 290 draft microbial genomes with an estimated completeness ranging from 50–100%. Environmentally derived genomes are imperative for a number of downstream applications, including comparative genomics, metatranscriptomics, and metaproteomics. This series of genomic data can allow for the recruitment of environmental “-omic” data and provide linkages between functions and phylogenies.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Peña et al. 2021). Therefore, acidification is also likely to cause shifts in community composition of CCA on reefs. CCA play a number of vitally important roles for corals. CCA cement and stabilise the reef substratum (Guinotte and Fabry 2008) which provides stable and suitable habitat for juvenile corals to settle on. However, reef pavement (solid carbonate substratum covered with CCA, turf algae and other sessile invertebrates), has been found to have dissolution rates 86% higher in acidified compared to ambient conditions. Similarly, reefs with low cementation rates under natural acidification suffered an almost complete loss of reef framework following a disturbance, with very low rates of coral recovery (Manzello et al. 2008). Furthermore, like corals, CCA are likely susceptible to increased bioerosion under OA. In addition to reduced abundance, this may contribute to a decrease in reef cementation in the future, reducing the available substrate for settlement of coral recruits. CCA are often used as a suitable settlement substrate, with declines in CCA abundance therefore reducing available settlement space. For example, during an in situ experiment at naturally acidified reefs in Guinea, 81% of coral recruits settled on CCA, despite it only accounting for 12% of substrate (Fabricius et al. 2017). This will therefore compound the effects of reduced reef cementation, further reducing the availability of suitable space for larval settlement. Finally, CCA act as an important settlement cue for coral larvae (Heyward and Negri 1999) and increased pCO2 can disrupt the response of corals to CCA (Table 1). For example, when CCA were pre-exposed to high pCO2, larval settlement declined between 54 to 87% (Doropoulos and Diaz-Pulido 2013; Webster et al. 2013). In addition, a loss of affinity has been shown between coral larvae and the most favourable CCA species (Titanoderma sp. ) which may further reduce settlement (Doropoulos et al. 2012). To exacerbate this effect, CCA species are differentially affected by increased pCO2 (see review: Hofmann and Bischof 2014) resulting in altered community compositions, with preferred settlement species such as Titanoderma sp. thought to be less tolerant of acidified conditions (Fabricius et al. 2015).

Output: corroborate


Input: Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: Research output: Book/Report › Report › Professional TY - BOOKT1 - Biodegradability of biodegradable mulch filmT2 - A review of the scientific literature on the biodegradability of materials used for biodegradable mulch filmAU - van der Zee, MaartenN1 - Project number 6229110400PY - 2021Y1 - 2021N2 - This report presents the findings of a desk study, commissioned by NRK-V and executed independently by WFBR. The objective of the desk study is to provide insight in the information available in the public and scientific literature regarding the biodegradability of biodegradable mulch film for use in agriculture and horticulture. Biodegradability of plastic describes the potential to undergo biodegradation in a suitable environment. Biodegradation does not only depend on the chemistry of the polymer, but also on the presence and activity of the biological systems involved in the process. This means that biodegradability in soil can be different from biodegradability in industrial composting conditions. The biodegradation of plastic is defined as its complete microbial utilization, resulting in its conversion to CO2, (and/or CH4), water and biomass by the metabolic activity of microorganisms. Not all materials labelled ‘biodegradable’, ‘oxo-(bio)degradable’ or ‘compostable’ will actually biodegrade at sufficient rate at ambient temperatures in soil to prevent accumulation of plastic (residues) in the field. Typically, mulch films are produced by combining polymeric feedstocks with other components (via master batches), such as processing aids, plasticizers and colorants, which are then further processed through extrusion into film. Regarding biodegradability and environmental fate it is important to consider not only the polymeric constituents, but all components that are used to produce the mulch film. In this report the biodegradability is discussed of the main polymeric constituents commonly employed for biodegradable mulch film. These include (thermoplastic) starch and several polyesters, including poly(butylene adipate-co-terephthalate) (PBAT), poly(butylene succinate) (PBS), poly(lactic acid) (PLA) and poly(hydroxy alkanoate) (PHA).

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: This method was initially performed on the seven sites from the containing microbial metagenomic samples (TARA007, −009, −018, −023, −025 and −030), but will continue through the various Longhurst provinces (Longhurst et al. , 1995) sampled during the project (Fig. 1). All of the assembly data is publically available, including the initial Megahit assemblies for each site from the various size fractions and depths along with the recovered putative (minimal quality control) genomes. Figure 1: Map illustrating the locations and size fractions sampled for the datasets. Girus, ‘giant virus’ size fraction (0. 22–1. 6 µm). Bact, ‘bacteria’ size fraction (0. 22–1. 6 µm). Prot, ‘protist’ size fraction (0. 8–5. 0 µm). The map in Fig. 1 was modified under a CC BY-SA 3. 0 license from ‘of ’ by historicair ( Download full-size image DOI: 10. 7717/peerj. 3558/fig-1 Figure 2: Workflow used to process metagenomic datasets. Download full-size image DOI: 10. 7717/peerj. 3558/fig-2 Materials and generalized version of the following workflow is presented in Fig. 2. Sequence retrieval and assembly All sequences for the reverse and forward reads from each sampled site and depth within the were accessed from Biology Laboratory-Institute (EMBL-EBI) utilizing their FTP service (Table 1). Paired-end reads from different filter sizes from each site and depth (e. g. , TARA0007, girus filter fraction, sampled at the deep chlorophyll maximum) were assembled using Megahit (Li et al. , 2016) (v1. 0. 3; parameters: -preset, meta-sensitive). To keep consistent with TARA sample nomenclature, “bacteria” or “BACT” will be used to encompass the size fraction 0. 22–1. 6 µm. Megahit assemblies ≥2 kb in length from all samples were pooled and combined based on ≥99% semi-global identity using CD-HIT-EST (Fu et al. , 2012) (v4. 6; -c 0.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: These effects suggest loss of CCA, or changes to the community composition of CCA, is a major pathway of indirect effects of OA on coral communities. Habitat provisionCorals are ecosystem engineers that build three-dimensional structures that provide habitat, shelter and food for many other reef organisms. This structural complexity they create affects species richness and abundance of many reef organisms, and is a driver of reef ecosystem functioning (Graham and Nash 2013). Consequently, degradation of structural complexity from acidification (Fabricius et al. 2011; Manzello et al. 2014; Enochs et al. 2015b) can have significant implications for a wide variety of taxa and the functioning of acidified reefs. Here we consider the interactions between corals with fish, invertebrates and zooplankton. Under ambient conditions, fish–coral interactions are often mutually beneficial. For example, associations with fish have been shown to benefit corals through enhanced colony growth (Chase et al. 2014) and photosynthesis (Garcia-Herrera et al. 2017), reduced sedimentation and sediment-induced partial mortality (Chase et al. 2018), and protection from predation (Chase et al. 2014). Furthermore, provision of habitat and shelter for herbivorous fish also benefit corals through maintenance of algal populations. For instance, herbivory pressure was > 7 times higher in high-complexity areas compared to low-complexity areas (Santano et al. 2021). Moreover, declines in structural complexity at naturally acidified sites can drive a shift in fish community composition (Cattano et al. 2020), and altered abundances of some fish species at acidified compared with ambient areas (Munday et al. 2014). To the best of our knowledge, the effect of ocean acidification on interactions between corals and fish have not yet been investigated, and therefore, how changes in fish abundance or community composition indirectly affect corals ability to persist under acidified conditions remains unknown. Many invertebrates use coral for habitat, with almost 1,000 known coral–invertebrate associations (Stella et al. 2011), although this number is likely to have increased over the last decade. This includes species which live in the branches and crevices coral provide, and boring organisms who reside within the coral tissue/skeleton (Stella et al. 2011).

Output: corroborate


Input: Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: It is important to realize that general statements regarding the biodegradability of these polymers are not possible, because variations of comonomer composition, molar mass, etc. within a polymer family, can have substantial effects on physical properties and biodegradation behaviour. Polymer grades that have passed the biodegradability requirements as stipulated in EN 17033 are likely to actually biodegrade to CO2 and water (and biomass) at sufficient rate when applied in agri- or horticulture in the Netherlands. Certification according to ‘DIN geprüft Biodegradable in soil’, ‘’, ‘OK compost HOME’ and ‘DIN Geprüft Home compostable’ is considered a reliable confirmation that fulfilment of the biodegradability requirements of EN 17033 has been demonstrated. AB - This report presents the findings of a desk study, commissioned by NRK-V and executed independently by WFBR. The objective of the desk study is to provide insight in the information available in the public and scientific literature regarding the biodegradability of biodegradable mulch film for use in agriculture and horticulture. Biodegradability of plastic describes the potential to undergo biodegradation in a suitable environment. Biodegradation does not only depend on the chemistry of the polymer, but also on the presence and activity of the biological systems involved in the process. This means that biodegradability in soil can be different from biodegradability in industrial composting conditions. The biodegradation of plastic is defined as its complete microbial utilization, resulting in its conversion to CO2, (and/or CH4), water and biomass by the metabolic activity of microorganisms. Not all materials labelled ‘biodegradable’, ‘oxo-(bio)degradable’ or ‘compostable’ will actually biodegrade at sufficient rate at ambient temperatures in soil to prevent accumulation of plastic (residues) in the field. Typically, mulch films are produced by combining polymeric feedstocks with other components (via master batches), such as processing aids, plasticizers and colorants, which are then further processed through extrusion into film. Regarding biodegradability and environmental fate it is important to consider not only the polymeric constituents, but all components that are used to produce the mulch film.

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: 99) in order to reduce the number of redundant contigs for the downstream assembly step. The reduced set of contiguous DNA fragments (contigs) was then cross-assembled based on a minimum of 100 bp overlaps with 95% nucleotide identity using Minimus2 (Treangen et al. , 2011) (AMOS v3. 1. 0; parameters: -= 100 MINID = 95). This assembly method is available on Protocols. io at Table 1: Statistics for Megahit contigs, recruitment to data-rich-contigs, and relative abundance of draft genome results for each sample. TARA sample site Size fraction (Girus, Bacteria, or Protist) Depth (Surface or DCMa) No. of reads No. of initial Megahit assembly N50c (bp; initial Megahit assembly) Longest initial Megahit assembly (bp) Recruitment (% data-rich-contigs) Relative abundancec of draft genomes (%) Relative abundancec of ten most abundant genomes (% ) TARA007 Girus DCM 178,519,830 1,318,470 828 220,754 72. 84 14. 64 6. 35 TARA007 221,166,612 1,308,847 861 211,946 81. 74 14. 83 6. 12 TARA007 Protist DCM 744,458,992 4,667,618 654 188,635 19. 45 8. 60 3. 18 TARA007 265,432,098 2,590,120 564 18,444 25. 58 1. 57 0. 61 TARA009 Girus DCM 416,553,274 2,796,841 831 1,643,839 69. 48 14. 16 6. 32 TARA009 489,617,426 1,787,467 929 1,142,851 68. 85 12. 29 4. 76 TARA009 Protist DCM 329,036,110 1,938,636 613 95,724 22. 07 13. 35 4. 20 TARA009 370,813,078 1,700,350 588 292,050 22. 53 15. 97 6. 17 TARA018 Bacteria DCM 408,021,182 2,520,645 840 1,573,060 76. 22 11. 49 3.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Overall, invertebrate communities appear to be negatively affected by acidification and the associated loss in structural complexity (Fabricius et al. 2014). The implications of changes in invertebrate communities or coral–invert interactions depend on the interacting taxa. For example, populations of the herbivorous urchin Diadema savignyi, increased dramatically at the acidified site in Guinea (PNG; Fabricius et al. 2014) which could benefit corals through increased herbivory. In contrast, increased abundance of vermitid gastropods which bore into large Porites colonies (Fabricius et al. 2014), may negatively affect corals through weakening their structure. Finally, the mutualistic relationship between the coral host (Pocillopora verrucosa), and two ectosymbionts Trapezia spp. crabs and Alpheus, spp. shrimp reduced the impact of acidification on calcification in the host coral (Doo et al. 2018; Table 1). However, it is not clear whether this is because the ectosymbionts reduced the sensitivity of the coral to acidification or provided a resource or service that prevented the reduction in calcification seen in the corals without ectosymbionts. Due to high diversity of coral-associated invertebrates and the range of responses in interactions to acidification, it is hard to predict the potential changes in interactions and what the outcomes of those may be for corals. Furthermore, additional changes in the physical (water flow and temperature) and chemical (e. g. dissolved nutrients and oxygen) conditions of the ocean as a result of acidification and climate change could further exacerbate changes in interactions between the organisms involved in these symbioses. Demersal zooplankton use coral to shelter from predation during the day (Alldredge and King 1977). Similarly to fish, declines in structural complexity under acidified conditions have also been shown to result in reduced biomass and abundance of zooplankton (Smith et al. 2016; Allen et al. 2017). However, zooplankton are an important heterotrophic food source for corals (Houlbrèque and Ferrier‐Pagès 2009) and declines in their abundance has the potential to impact corals, through altered availability of food.

Output: corroborate


Input: Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: of Materials > Vol. 12 No. 3, July 2022 Lactic Acid-Material for Melt Adhesive: Review () Ravindra V. . DOI: 10. 4236/ojopm. 2022. 123003 307 Downloads 1,507 Views 45. doi: 10. 4236/ojopm. 2022. 123003. 1. Introduction Bio-based and Bio-degradable materials Recently, to reduce their dependency on hydrocarbon materials, focus has been concentrated to making these adhesive recipes completely bio-based, sustainable and biodegradable. To reach this, research and developments are targeting on the uses of starch, lignin, tannin, soy protein, polylactides and vegetable oils based fatty acid as a partial/fully replacement to the hydrocarbon-based polymers [1]. Figure 1 is showing the classification of bio-degradable, renewable, non-biodegradable and petrochemical raw materials. Definitions: Bio-based materials: Fully or partially obtained from biomass e. g. , plants; Bio-degradable materials: The breakdown of organic matter into carbon dioxide, water and biomass by the action of microorganisms such as bacteria or fungus. Currently, Hot melt adhesives (HMAs) are based on petroleum-based materials and those are not biodegradable. To reduce the dependency on the petroleum sources and achieve biodegradability, bio-based raw material can be used in HMAs. Here, we review the uses of PLA in the hot melt adhesive segment. 2. Hot melt melt adhesives (HMAs) are one of the most growing sectors within the adhesive industry [2] [3]. HMAs can be useful for high-speed manufacturing and applications that require bonding versatility, large gap filling, and minimal shrinkage. HMAs do not require a carrier fluid such as an organic solvent or water, which eliminates the need for drying the liquid adhesive layer once it is applied to a substrate. Elimination of the drying step reduces solvent usage, increases production line speeds, and lowers transportation costs [4] [5]. HMA is a thermoplastic material which is solid at room temperature and is applied on the adherend in its molten state. The adhesive bond is formed after Figure 1. Bio-based and biodegradable materials. HMA is cooled. Therefore, HMAs provide several advantages e. g.

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: 18 TARA018 414,976,308 2,604,031 816 2,086,508 75. 80 11. 03 3. 02 TARA023 Bacteria DCM 147,400,552 1,273,576 830 213,456 76. 08 13. 29 4. 09 TARA023 149,566,010 1,237,617 825 134,179 75. 98 13. 82 4. 01 TARA023 Protist DCM 508,610,652 2,707,801 734 336,689 28. 23 25. 07 7. 83 TARA023 397,044,232 2,246,571 593 397,140 23. 00 25. 16 10. 31 TARA025 Bacteria DCM 386,627,816 2,516,865 806 388,546 69. 77 14. 55 5. 35 TARA025 457,560,422 2,326,838 857 330,773 75. 57 10. 99 3. 18 TARA030 Bacteria DCM 346,837,034 1,968,945 1,097 508,775 80. 16 10. 31 2. 57 TARA030 478,785,582 1,639,697 1,194 204,976 77. 70 7. 26 2. 64 TARA030 Protist DCM 426,896,616 1,620,343 616 478,892 15. 12 17. 83 5. 13 TARA030 430,029,974 1,838,588 628 287,782 22. 36 17. 60 6. 73 DOI: 10. 7717/peerj. 3558/table-1 Notes: aDCM—deep chlorophyll maximum. bN50—length of DNA sequence above which 50% of the total is contained. cRelative abundance—determined using the reads recruited data-rich-contigs. Metagenome-assembled genomes Due to memory limitations during the binning step, contigs ≥7. 5 kb in length generated during the two-step assembly process (includes Minimus2 contigs and unincorporated Megahit contigs) were used to recruit sequence reads from each of the Tara samples using Bowtie2 (Langmead & Salzberg, 2012) (v4. 1. 2; default parameters).

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: The extent of this impact is likely to be species specific, depending on the reliance of each species on heterotrophic food sources. Moreover, some species are capable of mitigating the effects of acidification by increasing heterotrophic energy contributions (Towle et al. 2015). A decline in zooplankton may therefore reduce the resilience of some corals to acidification. Overall, we suggest that the changes in habitat interactions reviewed here are likely to have only sub-lethal consequences for corals. However, they highlight the possibility of multiple small shifts in the functioning of coral reef ecosystems to accumulate, which may ultimately contribute to a shift in communities greater than that expected from the physiological stressors. This may be particularly be the case where changes affect mutually beneficial relationships, creating the possibility of a negative feedback loop. In this case, fewer beneficial habitat associations reduce physiological coral health and/or survival, which further affects habitat associations. Such effects are extremely hard to predict and with the current paucity of data on the indirect effects on corals of changes to habitat associations, this remains a significant knowledge gap. BioerosionBioeroders are a diverse range of organisms including bacteria, algae, sponges, molluscs and fish, which cause erosion through grazing of, attachment to, or embedding in, the coral skeleton (Wisshak et al. 2012; Glynn and Manzello 2015; Schönberg et al. 2017). There is significant evidence from naturally acidified reefs that bioeroder abundance increases under high pCO2 (Crook et al. 2013; Enochs et al. 2016b) (Table 1). This may be the result of reduced competition for space between settling bioeroders such as sponges (Schönberg and Ortiz 2008) or an increase in dead coral habitat which supports a high number of invertebrates (Tribollet and Golubic 2011; Valentino 2014). Increased bioeroder abundance may have additional indirect effects on coral populations by reducing the available space for settlement. However, increased bioeroder abundance is not found for all bioeroding species (e. g. grazers; Schönberg et al. 2017) or where other factors like habitat are limiting (Valentino 2014). The bioerosive capacity of many species is increased under high pCO2 (Table 1).

Output: corroborate


Input: Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: , rapid setting times and elimination of volatile organic compounds [6] [7] [8]. Main application area of the HMAs is in packaging [9]. HMAs are often used to bond two substrates together so as to maintain the two substrates in a fixed relation to each other HMAs compositions have historically been based on petroleum-derived polymers, and these compositions are further tackifier, plasticized, and reinforced with a variety of resins, oils and waxes that can be derived from both petroleum and naturally occurring feedstocks such as wood, gum and tall oil rosin, and terpenes. Useful fillers and/or rheology modifiers are chalk, barite, quartz, gypsum, calcium oxide, magnesium oxide, silica [10] [11]. 3. offer advantages over their contemporary water-based and solvent-based adhesives like low volatile organic compounds (VOCs), 100% solid, fast drying, setting etc. The HMAs are designed to be applied in consumer goods, packaging, construction, transportation, electronics, healthcare, and for other applications like bookbinding, furniture etc. [12] [13]. These are generally available as granules, powder, slats, blocks, foils, ribbons etc. It is then applied by bringing it between two substrates. Once cooled, it will set and solidify. The solidification mechanism depends on open time and set time. Open time denotes the time during which sufficient tack is retained on the surface on the other hand, set time is referred as the time for developing acceptable bond strength at 20˚C. As the HMAs need heating, special applicators are needed for its application. Special glue gun that can be loaded with the solid adhesive sticks or rods which are fed and heated in the gun nozzle producing liquid adhesive. HMAs are solid materials at low temperatures (typically < 80˚C) and can melt to liquid or viscous-flow state at elevated temperatures, in which form they are applied on the surface of substrates [14] - [19]. Currently, almost all the base polymers for HMAs on the market are primarily derived from petroleum resources, such as ethylene vinyl acetate, block copolymers of styrene and butadiene or isoprene, polyesters, polyamides, polyurethanes and polyolefin’s [20] [21] [22] [23]. 4.

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Read counts for each contig were determined using featureCounts (Liao, Smyth & Shi, 2014) (v1. 5. 0; default parameters). Coverage was determined for all contigs by dividing the number of recruited reads by the length of the contig (reads/bp). Due to the low coverage nature of the samples, in order to effectively delineate between contig coverage patterns, the coverage values were transformed by multiplying by five (determined through manual tuning). Transformed coverage values were then utilized to cluster contigs into bins utilizing BinSanity (Graham, Heidelberg & Tully, 2017) based on a preference value of −3 to be run for a maximum of 4,000 iterations with completion if convergence is achieved for 400 consecutive iterations and a damping value of 0. 9 (parameters: -p -3, -m 4,000, -v 400, -d 0. 9). Bins were assessed for the presence of putative microbial genomes using the lineage workflow in CheckM (Parks et al. , 2015) (v1. 0. 3; parameters: lineage_wf). Bins were split in to three categories: (1) putative draft genomes (≥50% complete and ≤10% cumulative redundancy (% contamination—(% contamination × % strain heterogeneity ÷ 100))); (2) draft genomes with high contamination (≥50% complete and ≥10% cumulative redundancy); and (3) low completion bins (<50% complete). The high contamination bins containing approximately two genomes, three genomes, or ≥4 genomes used BinSanity (Binsanity; -m 2000, -v 200, -d 0. 9) with variable preference values (-p) of −1,000, −500, and −100, respectively. The resulting bins were added to one of the three categories: putative draft genomes, high contamination bins, and low completion bins. The high contamination bins were processed for a third time with the Binsanity-refine utilizing a preference of −100 (-p −100). These bins were given final assignments as either putative draft genomes or low completion bins. Any contigs not assigned to putative draft genomes were assessed using BinSanity using raw coverage values.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Chemical bioerosion is less physiologically costly under high pCO2 (Wisshak et al. 2012) which may increase the bioerosive capacity of boring species. For example, it is estimated that rates of chemical bioerosion by an excavating sponge (Cliona caribbaea) could double by the end of the century (Webb et al. 2017). In addition, taxa using mechanical bioerosion may have increased bioerosive capacity where coral skeletons are weaker, less dense/more porous. While corals with lower density were more likely to have evidence of bioerosion than high density corals (Barkley et al. 2015), this correlation has not been explicitly tested under acidification. Furthermore, under ambient conditions, skeletal density does not always result in increased bioerosion. For example, the highest rates of bioerosion were found in the coral genus with the highest skeletal density (Pavona; Cosain-Díaz et al. 2021). These contrasting findings may be explained in part by variable rates of bioerosion between morphologies, with the most dense coral also being the morphology with the highest rates of bioerosion (massive; Cosain-Díaz et al. 2021). However, where density does affect bioerosive capacity, we are likely to underestimate the net effect of OA on coral growth by considering the direct effects in isolation. Finally, bioeroders may have increased biomass and faster growth (Fang et al. 2013; Uthicke et al. 2016), ultimately allowing an individual to have a greater rate of bioerosion or lifetime erosive capacity. The combination of increased bioeroder abundance and bioerosion capacity is expected to result in a large increase in total bioerosion under high pCO2. By the end of this century, these increases in bioerosion from sponges alone are estimated to be 7% under RCP 4. 5, 16% under RCP6 and 31% under RCP8. 5 compared to ambient conditions (393 µatm; Wisshak et al. 2012; IPCC 2014). Similarly, total volume removed by bioerosion under Ω aragonite saturation < 2 (comparable to RCP8. 5) may increase up to 78% compared to ambient aragonite (Ω aragonite > 3. 5; Crook et al. 2013).

Output: corroborate


Input: Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: Need of Renewable and Bio-in Adhesive “Renewable resource” is used herein to refer to a resource that is produced by a natural process at a rate comparable to its rate of consumption. “Bio-based” is used herein to refer to a component of the hot melt adhesive that is produced or is derived from at least 50% by weight of a renewable resource. Bio-based materials are not necessarily compostable [24]. Packaging materials contain small amount of adhesives but that can nevertheless have a significant effect on the repulpability of the package. Recycled paper from packaging material waste is used in combination with virgin fibers in the paper making process and traditional hot melt adhesives are likely to contaminate the paper made in this way. It is therefore desirable that the adhesives used in packages would degrade in the recycling process. Other issues related to adhesives and packaging materials are the increasing demands on compostability and the use of materials from renewable resources. In compost environments it is important that the major part of packaging material is degradable in a certain time, which also includes the adhesives used. Biodegradable hot melt adhesives prepared from renewable raw materials have a potential for use in packaging applications [25]. Renewability of the adhesive raw materials can be considered to be an asset compared to petroleum derived polymers due to increased environmental awareness [26] [27] [28] [29]. 5. Polylactic Acid-acid (PLA) has been a subject for numerous studies during the past decades and several attempts have been made in order to commercialise this polymer on industrial scale. Lactic acid is the simplest molecule showing optical activity. The l-stereo form is the most commonly occurring one in nature, while the d-form can be produced either by biological or chemical methods. Lactic acid-based polymers are interesting because the starting chemical, lactic acid, can be obtained from renewable sources by fermentation. PLA is also compostable which means that a CO2—neutral life cycle can be established for the material [30]. PLA homopolymer has a glass transition temperature in the range 55˚C - 60˚C and a melting temperature of about 170 ˚C [31].

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Two additional rounds of refinement were performed with the first round of refinement using preference values based on the estimated number of contaminating genomes (as above) and the second round using a set preference of −10 (-p −10). Following this binning phase, contigs were assigned to draft genome bins (e. g. , genome 1, referred to as TMED1, etc. ), low completion bins with at least five contigs (0–50% complete; TMEDlc1, etc. lc, low completion), or were not placed in a bin (S1 and S2). Taxonomic and phylogenetic assignment of draft genomes The bins representing the draft genomes were assessed for taxonomy and phylogeny using multiple methods to provide a quick reference for selecting genomes of interest. Taxonomy was assigned using the putative placement provided via CheckM during the pplacer (Matsen, Kodner & Armbrust, 2010) step of the analysis to the lowest taxonomic placement (parameters: tree_qa -o 2). This step was also performed for all low completion bins. Figure 3: FastTree approximate maximum-likelihood phylogenetic tree constructed with 37 and 406 16S rRNA genes from putative draft genomes and 4. Phylogenetic tree with Shimodaira–Hasegawa local support values as available in Newick format in 5. Download full-size image DOI: 10. 7717/peerj. 3558/fig-3 Two separate attempts were made to assign the draft genomes a phylogenetic assignment. Draft genomes were searched for the presence of the full-length 16S rRNA gene sequence using RNAmmer (Lagesen et al. , 2007) (v1. 2; parameters: -S bac -m ssu). All full-length sequences were aligned to the reference database (Ref123) using the SINA web portal aligner (Pruesse, Peplies & Glöckner, 2012) ( These alignments were loaded in to ARB (Ludwig et al. , 2004) (v6. 0. 3), manually assessed, and added to the non-redundant 16S rRNA gene database (SSURef123 NR99) using ARB Parsimony (Quick) tool (parameters: default). A selection of the nearest neighbors to the Tara genome sequences were selected and used to construct a 16S rRNA phylogenetic tree.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Such increases in bioerosion rates have been shown to result in significant declines in net calcification (Stubler et al. 2014) and even a switch from net calcification to net dissolution (Enochs et al. 2016a). Therefore, in conjunction with the predicted changes in net accretion, bioerosion could be a significant contributor to coral cover declines in the future. Coral diseaseCoral disease results from interactions between the host corals and the pathogen causing the disease. Worldwide, the prevalence of coral diseases has increased in recent decades due to a number of factors, such as rising water temperatures (Tracy et al. 2020), and decreasing water quality including nutrient enrichment (Vega-Thurber et al. 2014), plastic pollution (Lamb et al. 2018) and metal pollution (Tracy et al. 2020). However, the effect of acidification on coral diseases is largely unknown and remains a significant knowledge gap (et al. 2020). To date, only one study has empirically shown an impact of acidification on disease dynamics, which found that low pH (7. 7) decreased the progression of black bank disease on Orbicella faveolata under experimental conditions (Muller et al. 2017). This suggests that future acidified conditions may be less favourable to black band disease and result in decreased prevalence and/or progression. However, coral diseases are caused by a range of pathogens including marine and terrestrial bacteria, cyanobacteria and viruses (Sokolow 2009; et al. 2020), meaning the results from Muller et al. (2017) cannot easily be extrapolated to diseases caused by other pathogens. Despite limited information on coral disease under acidification, there are some indications that pathogen abundance and virulence, and coral susceptibility may change (Table 1). Increased abundances of disease-associated bacteria within the coral microbiome have been found experimentally (Meron et al. 2011; Grottoli et al. 2018; Table 1; et al. 2020), and at the seep site in PNG (Morrow et al. 2015), however, this did not result in an increase in infections. Furthermore, microbial pathogens were absent entirely at the seep site in Ishia, Italy (Meron et al. 2012). In addition, there is some evidence that pathogen virulence may be affected by acidification, potentially due to pathogen pH tolerance limits.

Output: corroborate


Input: Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: In other embodiments, the PLA polymer is a crystalline homopolymer including (L-lactide) monomeric units. The major component of the HMA composition, which is present in an amount of about 60 wt% to about 99 wt% of the composition, includes a homo- or copolymer of poly (lactic acid), referred to herein generally as PLA. [33] 6. in acid (PLA) can be used for packaging materials, especially adhesives owing to its good processability and the excellent mechanical properties of its molded products. Therefore, the use of these materials as a substitute for non-biodegradable synthetic polymers can be considered to be environmentally beneficial. In one such study, copolymers with PLA: polycaprolactam (PCL) molar ratios 81:19 were tested for open time, adhesion, setting time, hot tack development, viscosity and weight loss of adhesives. To limit the unwanted thermal degradation, acetic anhydride is used as a stabilizer. This copolymer-based HMAs is used in industrial glue lamination process. The measured properties were evaluated against commercial ethylene-vinyl acetate HMAs [5]. The unique characteristics of PLLA/are its excellent hot tack and a combination of long open time with moderate setting time. The same copolymer in the same molar ratio can also be used as biodegradable HMA for food packaging applications [34] - [42]. HMA includes: a lactic acid and caprolactone copolymer resin, a crystalline lactic acid oligomer wax, and said amorphous lactic acid oligomer tackifier, characterized in that the amorphous lactic acid oligomer tackifier includes an amorphous polymerisation product of 1) lactic acid monomer and 2) a multifunctional polymerization initiator containing three or more hydroxy and/or amino groups [43] The poor stability of lactic acid based polymers have been demonstrated in several publications and different approaches have been reported to be efficient in the improving the stability on of PLA. This PLA/PCL copolymer was stabilized by end-capping of the hydroxyl groups with acetic anhydride or by treating the polymer with peroxide.

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Genome-identified 16S rRNA sequences and SILVA reference sequences were aligned using the SINA web portal aligner (4). An approximately-maximum-likelihood tree with Shimodaira–Hasegawa local support values (Shimodaira & Hasegawa, 1999) was constructed using FastTree (Price, Dehal & Arkin, 2010) using the generalized time reversible and discrete gamma models (Yang) (v2. 1. 3; parameters: -nt -gtr -gamma; Fig. 3; 5). Draft genomes were assessed for the presence of the 16 ribosomal markers genes used in Hug et al. (2016). Putative CDSs were determined using Prodigal (v2. 6. 3; parameters: -m -p meta) and were searched using HMMs for each marker using HMMER (Finn, Clements & Eddy, 2011) with matches based on an e-value cutoff of 1 × 10−3 (v3. 1b2; parameters: hmmsearch -E 1E −10). If a genome had multiple copies of any single marker gene, neither was considered, and only genomes with ≥8 markers were used to construct a phylogenetic tree. Markers identified from the draft genomes were combined with markers from 6,080 reference genomes accessed from (6) that represent the major bacterial phylogenetic groups. Each marker gene was aligned using (Edgar, 2004) (parameters: -maxiters 8) and automatically trimmed using trimAL (Capella-Gutiérrez, Silla-Martínez & Gabaldón, 2009) (v1. 2rev59; parameters: -automated1). Automated trimming results were manually curated in Geneious (Kearse et al. , 2012) (7). Final alignments were concatenated and used to construct an approximately-maximum-likelihood tree using the LG (Le & Gascuel, 2008) and Gamma models with Shimodaira–Hasegawa local support values with FastTree (v2. 1. 10; parameters: -lg -gamma; Fig. 4; 8). A separate tree was constructed using the same concatenated alignments and tree-building parameters for the 210 draft genomes, without the reference genomes (Fig. 4).

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: For example, growth in the bacterium Aurantimonas coralicida, which causes white plague type II, was strongly affected by pH with a clear lower limit beyond which no growth occurred (Remily and Richardson 2006). Finally, corals have shown decreased immunity under acidification, which may result in an increase in susceptibility (see review: Traylor-Knowles and Connelly 2017). Regardless of this potential decrease in virulence, we note that reduced growth and calcification in corals may reduce the ability of corals to recover if infection does occur and this could heighten the impacts of diseases on coral populations. Additional research is required on the prevalence of disease at naturally acidified sites, as well as both pathogen abundance and virulence, as well as coral susceptibility and recovery, to understand the effect of acidification on coral–pathogen interactions. Coral communities under acidified conditionsUltimately, the coral communities we see in the future will be the result of the combined impacts of both the direct and the indirect effects on corals. With consistent variability in findings between species, location and experimental studies, as well as the paucity of data on many indirect effects, our ability to accurately scale up our current knowledge to an ecosystem scale is limited. However, globally, there are a number of locations with naturally low pH/high pCO2 conditions as a result of volcanic gas seeps, hydrographic processes and localised low pH submarine springs. The natural gradients of pCO2 around these sites reveal how the direct and indirect effects of OA that are reviewed above could manifest at an ecosystem level. We review the evidence of indirect effects and the result of both direct and indirect effects on ecosystem level metrics, at ten naturally acidified coral communities or coral reefs (Fig. 2, Table 3). Seven of these sites occur around volcanic vents, where gas containing a high percentage of CO2 seeps through the seafloor and acidifies the surrounding waters. Of these seven, three occur in tropical coral reef ecosystems, in (Indonesia), Dobu, Esa’Ala and Upa-Upasina (PNG), and Maug (Commonwealth of Islands [CNMI]), and one on a sub-tropical reef in Iwotorishima (Japan). The remaining three vents are in temperate rocky shore environments where corals occur, in Shikine (Japan), and Panarea and Ishia (both Italy).

Output: corroborate


Input: Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: It was noticed, that these chemically stabilized polymers performed better during processing and also retained their mechanical properties better than the un-stabilized copolymer. Especially the acetic anhydride treated polymer seemed to be an interesting alternative. The rapid degradation of these PLA/is probably related to low initial molecular weight and the presence of a high amount of monomer residues. The low Tg-values of the PLA/PCL polymers also increase the chain mobility resulting faster degradation [44]. Utilizing biodegradable and renewable raw materials is a demanding challenge for the packaging industry. Many packages are of single-type use, which means rapid growth of municipal wastes [45] [46] [47]. Based on the previous studies, lactic acid-based polymers were chosen as candidate of a new generation hot melt adhesive. These samples degraded rapidly in the hydrolytic and compost environments. Additionally, these lactic acid-based polymers showed interesting adhesive properties [48]. In the case of biodegradable hot melt adhesives, the materials need to be stable enough during storage, in the process and in the application, but after the package has fulfilled its purpose, it should preferably degrade rapidly [49]. It can in any case be concluded that blending starch with a lactic acid-based HM adhesive proved to be a promising alternative for tailoring the degradation properties of the material. Because of the current high price of lactic acid-based polymers compared to conventional HM formulations, using starch blends would also be economically beneficial [17] [39] [50] - [69]. Patent [70] discloses a hot melt adhesive comprising polylactic acid and a polyvinyl alcohol-based resin. In addition, patent [71] discloses a hot melt adhesive composition comprising a thermoplastic resin and a tackifier as main components, wherein either one or both of these components comprise a lactic acid copolymer resin derived from PLA or lactic acid and other hydroxycarboxylic acids. This composition exhibits good self-life, high content of bio-degradable components, recyclable components and (or) components obtained from renewable natural materials [72].

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: Figure 4: Cladogram of a FastTree approximate maximum-likelihood phylogenetic tree constructed using 16 syntenic, single-copy marker genes for 210 draft genomes. Support for internal nodes were determined based on the Shimodaira–Hasegawa test (white ≥0. 500, gray ≥0. 750, black ≥0. 950). Sequence alignment for the draft genomes and the reference genomes used for phylogenetic assignment is available in 7. Phylogenetic tree of the draft genomes and the reference genomes used for phylogenetic assignment is available in Newick format in 8. Download full-size image DOI: 10. 7717/peerj. 3558/fig-4 Relative abundance of draft genomes To set-up a baseline that could approximate the “microbial” community (Bacteria, Archaea and viruses) present in the various Tara metagenomes, which included filter sizes specifically targeting both protists and giruses, reads were recruited against all contigs generated from the Minimus2 and Megahit assemblies ≥2 kb using Bowtie2 (default parameters). The contigs <2 kb in length likely constitute low abundance bacteria and archaea, bacteria and archaea with high degrees of repeats resulting in poor assembly, fragmented picoeukaryotic genomes, and problematic read sequences (low quality, sequencing artefacts, etc. ) and were not included in further analysis. All relative abundance measures are relative to the number of reads recruited to the assemblies ≥2 kb. Read counts were determined using featureCounts (as above). Length-normalized relative abundance values were determined for each draft genome for each sample: R e a d s b p p e r g e n o m e ∑ R e a d s b p a l l g e n o m e s × ∑ R e c r u i t e d r e a d s t o g e n o m e s ∑ R e c r u i t e d r e a d s t o a l l c o n t i g s ≥ 2 kb × 100. The initial Megahit assembly was performed on the publicly available reads for Tara stations 007, 009, 018, 023, 025, 030. Starting with 147–744 million reads per sample, the Megahit assembly process generated 1. 2–4.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: Carbonate chemistry at vent sites is variable depending on the composition of the vent gases; however, pCO2 conditions close to the vent can be high and well in excess of what is predicted under end of century conditions, particularly in temperate regions (e. g. 5066 µatm in Ishia, Italy; Hall-Spencer et al. 2008). The remaining three sites occur as a result of three different processes. in Palau, acidification occurs in tropical lagoonal reefs where there is restricted circulation of water in semi-enclosed bays (Golbuu et al. 2016). Acidification here is less extreme (~ 600 µatm) than at some of the vent sites. Morelos (Mesoamerica) submarine springs (or ‘Ojos’) discharge low-pH, low aragonite saturation groundwater, through natural localised springs in close proximity to the tropical Reef. This results in high levels of acidity (pH 7. 05, pCO2 data is not stated) as well as reduced salinity and total alkalinity (Crook et al. 2012). Finally, seasonal upwelling results in mild acidification (588 µatm) at the southern-most reefs in the subtropical (Pacific [ETP]), as well as exposure to cool waters and elevated nutrient levels. Reefs further north are less affected by the upwelling and experience more ambient ocean conditions (Manzello et al. 2014). Fig. 2The location of the ten natural acidified sites with associated corals which are reviewed here, ordered by smallest to largest decrease in coral cover.

Output: corroborate


Input: Claim: Every material used in sustainable architecture is biodegradable. [SEP] Text: , the foils used in packaging flowers or plants, but also carpet backings. Suitable substrates further include metal foils and wood [24]. The hot melt adhesive according to the present invention is widely utilized for paper processing, bookbinding, disposable products and the like, and is particularly effectively utilized for disposable products because of excellent adhesion in a wet state. The “disposable products” are not particularly limited as long as they are the so-called sanitary materials. Specific examples thereof include disposable diapers, sanitary napkins, pet sheets, hospital gowns, operation white coats, urine liners, puerperant shorts, breast milk pads and armpit sweat pads. The present invention can provide a hot melt adhesive and an absorbent 9. global energy issues and dependency on petroleum resource focus has been shifted towards developing sustainable hot melt adhesives (HMAs) which are cost effective and bio-degradable. HMAs contain base polymer, tackifier and wax as primary components. In terms of environmental problems, such as global climate issues due to an increase of carbon dioxide emission, attempts had been made to produce HMAs using non-petroleum-based and bio-degradable resins, such as polylactic acid (PLA)-based resins. PLA copolymer-based HM adhesive was used in industrial glue lamination process. The unique characteristics of PLLA/PCL HM adhesive are its excellent hot tack and a combination of long open time with moderate setting time. Polyamide adhesives based on bio-based dimerized fatty acids had been available for HM applications. Blending of starch with a lactic acid-based HM adhesive proved to be a promising alternative for tailoring the degradation properties of the material. Hence, HMAs based on polylactic acid will continue to have a huge potential and sustainable and bio-degradable applications in packaging, sanatory and diaper adhesive industries. A lot of research has already been done on modification of PLA through copolymerization. However, the challenge remains to produce the PLA-based HMAs with high performance properties like synthetic resin HMAs. Conflicts of authors declare no conflicts of interest regarding the publication of this paper. 65. [2] Viljanmaa, M. , S&#246dergård, A. , Mattila, R. and Törmälä, P.

Output: contrast


Input: Claim: X-ray crystallography can be used to determine the 3D structures of proteins. [SEP] Text: 6 million contigs with a mean N50 and longest contig of 785 bp and 537 kb, respectively (Table 1). In general, the contigs generated from the Tara samples targeting the protist size fraction (0. 8–5 µm) had a shorter N50 value than the bacteria size fractions (mean: 554 bp vs 892 bp, respectively). Contigs from the Megahit assembly process were pooled and separated by length. Of the 42. 6 million contigs generated during the first assembly, 1. 5 million were ≥2 kb in length (Table 2). Several attempts were made to assemble the shorter contigs, but publicly available overlap-consensus assemblers (Newbler (454 Life Sciences), cap3 (Huang & Madan, 1999), and MIRA (Chevreux et al. , 2004)) failed on multiple attempts. Processing the ≥2 kb contigs from all of the samples through CD-HIT-EST reduced the total to 1. 1 million contigs. This group of contigs was subjected to the secondary assembly through Minimus2, generating 158,414 new contigs (all ≥2 kb). The secondary contigs were combined with the Megahit contigs that were not assembled by Minimus2. This provided a contig dataset consisting of 660,937 contigs, all ≥2 kb in length (Table 2; further referred to as data-rich-contigs). set of data-rich-contigs was used to recruit the metagenomic reads from each sample using Bowtie2. The data-rich-contigs recruited 15–81% of the reads depending on the sample. In general, the protist size fraction recruited substantially fewer reads than the girus and bacteria size fractions (mean: 19. 8% vs 75. 0%, respectively) (Table 1). For the protist size fraction, the “missing” data for these recruitments likely results from the poor assembly of more complex and larger eukaryotic genomes. The fraction of the reads that do not recruit in the girus and bacterial size fraction samples could be accounted for by the large number of low quality assemblies (200–500 bp) and reads that could not be assembled due to low abundance or high complexity (Table 2). Table 2: Assembly statistics at various steps during processing.

Output: pass


Input: Claim: Coral reefs are affected by ocean acidification and warming. [SEP] Text: 1- Bays, Palau; 2- Indonesia; 3- Dobu, Esa’Ala and Upa-Upasina, Guinea (PNG); 4- Puerto Morelos, Mesoamerica; 5- Maug, Commonwealth of Islands (CNMI); 6- Iwotorishima, Japan; 7- Galapagos, Pacific (ETP); 8- Shikine, Japan; 9- Panarea, Italy; 10- Ishia, ItalyFull size imageA number of other acidified sites have also been described in the literature, however, they are excluded here because they also experience elevated temperatures and/or deoxygenation (Bouraké, New Caledonia; Mangrove lagoons, northern Reef; Bahia Concepcion, California), or because there are no ecological records of coral communities at those sites, (Ambitle Island, PNG; Mayreau Gardens, Caribbean) or where the pCO2 gradient occurs and dissipates daily (Moorea, French Polynesia). Changes in coral abundance (coral cover) with increasing pCO2 The effect of acidification on hard coral abundance, with the exception of Porites spp. , is largely negative (Fig. 3). Seven of the ten naturally high pCO2 sites showed reduced hard coral cover compared with adjacent control sites (Fig. 3, Table 2). Nevertheless, the effect is not always negative, and there is limited evidence of a physiological ‘tipping point’ or threshold response to increasing pCO2. While the three temperate/sub-tropical coral communities, as well as the CNMI and Mesoamerican coral reefs, showed rapid declines in coral cover at ~ 500 µatm pCO2, coral cover at similar concentrations increased significantly at Palau (~ 31%), was maintained at seep locations in Indonesia (~ 4% increase) and PNG (~ 2% increase) and shifted from hard to soft coral cover at Iwotorishima (Fig. 3, Table 2). This suggests that effects of pCO2 on coral abundance are likely to be influenced by other indirect effects and/or environmental factors, and also by the species composition of coral present at each site (see below).

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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).

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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).

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast