Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: 0 1812702. 1 ± 203016. 6 3. 8 3. 90 ± 0. 25 1. 33 ± 0. 1 2. 93 + Negative regulation of complement activation 0. 0003 _HUMAN 526 81 15. 9 100 141897. 8 ± 32858. 1 206974. 9 ± 13351. 4 0. 6 1. 10 ± 0. 4 6. 22 ± 0. 3 0. 1 − Transporting thyroxine and retinol 0. 03 Glycoproteins Alpha-1-acid glycoprotein 1 ORM1 A1AG_HUMAN 210 79 23. 51 23. 9 181401. 5 ± 70555. 5 63420. 2 ± 556. 6 2. 9 2. 27 ± 0. 44 0. 950 ± 0. 03 2. 3 + Acute phase, inflammatory response 0. 04 Alpha-1-acid glycoprotein 2 ORM2 A1AG2_HUMAN 140 75 23. 60 13 145187. 4 ± 48088. 9 64026. 6 ± 3758. 3 2. 3 1. 95 ± 0. 39 0. 967 ± 0. 03 2. 03 + Acute phase response, inflammatory response 0. 04 Alpha-1-B glycoprotein A1BG A1BG_HUMAN 160 56 54. 2 18 74140. 823134 ± 0. 7 31670. 2 ± 4148. 3 2. 34 1. 18 ± 0. 1 0. 47 ± 0. 04 2. 5 + Platelet degranulation 0. 03 Antiproteases Alpha-1-antitrypsin 1 A1AT_HUMAN 96 35 46. 7 30. 1 265406. 2 ± 49373. 2 83843. 4 ± 8059. 6 3. 2 21. 41 ± 0. 72 5. 85 ± 0. 17 3. 65 + Acute phase, inflammatory response 0. 02 Alpha-1-antichymotrypsin 3 AACT_HUMAN 82 11 47. 6 30. 1 38590. 6 ± 17174. 4 16122. 3 ± 1641. 8 2. 9 0. 71 ± 0. 2 0. 57 ± 0. 3 1. 24 + Acute phase, inflammatory response 0. 04 Binding proteins _HUMAN 72 7 51. [SEP] Justify:

Output: The text is irrelevant to the claim about proteomics because it consists of numerical data and descriptions of proteins and their functions without any contextual explanation related to the field of proteomics or its definition.


Input: Task: corroborate the claim using the given text. Claim: The suprachiasmatic nucleus (SCN) in the brain is the master clock regulating circadian rhythms. [SEP] Text: Melatonin can reset the circadian clock only at temporally distinct times, dusk and dawn. When melatonin is administered at dusk, it phase advances the firing rate of SCN neurons in rat and mouse [5, 9]. McArthur et al. also described a behavioral activity phase advance in response to melatonin between circadian time (CT) 23 and 01 (dawn) [12]. Melatonin is believed to exert these effects via two specific, high affinity, guanine nucleotide binding protein (G protein) coupled receptors (GPCR) in the SCN, MT1 and MT2 [21]. MT1 mRNA is expressed in the SCN, however the expression of MT2 receptor mRNA has been more difficult to evaluate [15, 18, 23, 26]. There is evidence that there is a circadian rhythm of the expression of the MT1 receptor mRNA as well as of melatonin binding in the rat brain. Melatonin receptor MT1 mRNA expression exhibited a distinct circadian rhythm peaking during subjective night [10]. However, another study found that MT1 mRNA peaked 3 hours ahead of melatonin binding [10, 15]. This result however has been controversial, as in another study there was no statistically significant variation in mRNA levels across the circadian cycle [26]. Poirel et al. were not able to detect any expression of MT2 receptors mRNA in SCN [18]. Using binding studies, MT2 receptors in the SCN are expressed in very low levels [3, 9]. The above-mentioned studies used methods such as RT-PCR or in situ hybridization (ISH) as well as receptor binding to infer the presence of both MT1 and MT2 receptors in the SCN tissue. A circadian rhythm of receptor protein synthesis and localization has not been demonstrated due to the lack of specific antibodies for MT1 and MT2 receptors. Such a rhythm would explain the temporal gating of melatonin efficacy in modulating behavioral rhythm and electrophysiology. Therefore, this study describes the use of immunohistochemistry in the study of the circadian distribution of melatonin receptors MT1 and MT2 in the SCN. 2. Experimental procedure 2. 1. Animals and tissue preparation rats (Charles River, Wilmington, MD), 4–6 weeks old, were entrained for at least 2 weeks to a 12/12 LD cycle prior to the experiments. [SEP] Justify:

Output: The text corroborates the claim by detailing the role of melatonin and its receptors in the SCN, which is critical for regulating circadian rhythms. It specifically mentions how melatonin can phase advance the firing rate of SCN neurons and discusses the expression of melatonin receptors MT1 and MT2 within the SCN, further supporting the idea that the SCN acts as a master clock in managing circadian rhythms.


Input: Task: contrast the claim using the given text. Claim: All mollusks live in saltwater environments and cannot survive in freshwater. [SEP] Text: Although energetically less efficient than end-products, utilisation of sulfur and nitrogen cycle intermediates might allow the development of microorganisms over a broader spectrum of environmental gradients, supporting a wide distribution of the hydrocarbon short cycle in aquatic environments, as observed in this study. ConclusionsOur analysis of hydrocarbon cycling genes and populations of a petroleum-free model ecosystem that is physically, chemically and microbiologically relevant to many aquatic biomes revealed that the hydrocarbon short cycle is not limited to marine waters and likely occurs under a broad range of salinity and oxygen concentrations, from oxic freshwaters to anoxic marine waters (Fig. 5). Entangled with sulfur and nitrogen cycles, the hydrocarbon short cycle involved diverse microorganisms, including lineages that are common and often predominate in freshwater and marine ecosystems. were found as major drivers of the hydrocarbon production in the euphotic zone, our results also pointed out that widely distributed lineages of the Flavobacteriaceae, PVC, Nitrospina and Deltaproteobacteria phyla could contribute to the hydrocarbon biogenic production (Fig. 5). Analysis of hydrocarbon degradation genes highlighted that the degradation of bacterial alkanes involved a large diversity of microbial lineages that differ from petroleum hydrocarbon degrading species. Since the efficiency and rapidity of the microbial response to oil inputs could be linked to the history of contamination 42, a major consequence of this decoupling is that hydrocarbons produced by bacteria might have little or no priming effect on attenuating oil spills. The ability of these microorganisms to degrade petroleum hydrocarbons should be investigated to test this hypothesis. However, particular attention must be paid to pristine environments, such as High-Arctic ecosystems that are increasingly threatened by oil exploitation and shipping, to prevent any oil contamination that might remain undegraded by the native microbial population. description, sample collection and nucleic acid extraction High-(Ellesmere Island, 82° 59. 667’ N, 75° 26. 602’ W) is a permanently ice-covered, highly stratified meromictic saline lake with an oxygenated freshwater layer (14. 1 mg/L of oxygen; salinity < 0. [SEP] Justify:

Output: The text contrasts the claim by indicating that a significant number of microorganisms thrive in both freshwater and marine environments, suggesting that not all aquatic life is restricted to saltwater. The description of a freshwater layer in a saline lake implies that some aquatic organisms can survive in freshwater, countering the notion that mollusks exclusively inhabit saltwater environments.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: 67 22. 9 29538. 1 ± 8529. 0 124043. 9 ± 9040. 8 0. 2 1. 0 ± 0. 01 1. 7 ± 0. 1 0. 5 − Heme binding, transporter metabolism 0. 001 Hemoglobin beta subunit _HUMAN 81 9 16 42. 9 221930. 6 ± 78425. 9 83935. 03 ± 16376. 4 2. 64 3. 27 ± 0. 2 0. 90 ± 0. 01 3. 63 + Heme binding, oxygen binding 0. 04 _HUMAN 176 26 45. 2 30. 5 276225. 3 ± 89525 121576. 9 ± 19207 2. 27 5. 10 ± 0. 2 1. 09 ± 0. 01 2. 6 + Hemoglobin binding 0. 04 DOI: 10. 7717/peerj. 4730/table-3 Notes: The protein abundance differences among two groups were quantified using students t-test. a Uniprot data entry. b Mascot protein score revealed by MudPIT scoring. The integrated levels of expression. All the identified matches are significant with a significance level of 99% (p < 0. 01) were considered a positive match when there are at least two unique peptides corresponding to the significance threshold with an ion score of 70. c Number of matched peptides used to identify the protein. At least one matching peptide for each identified protein must fulfill the significance criteria (p < 0. 01) and also be unique. d Molecular weight in kDa. e Number of peptides matched with a threshold significance value of p < 0. 05. f The matched peptide features (area under the curve) intensity of the patients compared to the controls. g The statistical significance value after protein quantification data analysis. Protein profile of the differentially expressed proteins Based on the bioinformatics analysis, the identified differentially expressed proteins were found to be immunoglobulins, acute phase reactants, glycoproteins, transporters, antiproteases, and binding proteins. Mounting evidence reveals that most of the identified proteins play crucial roles in immune system regulation, inflammation, and acute inflammatory responses. SLE patients were found to have a 2. 8- to more than 3. 5-fold increase in expression of several immunoglobulin heavy and light chains (p < 0. [SEP] Justify:

Output: The text does not directly support or contradict the claim about proteomics. Instead, it discusses protein abundance differences and various proteins found in a specific study, focusing on their roles and significances in relation to other conditions like SLE. There is no mention of the scope of proteomics as studying the entire set of proteins expressed in a cell.


Input: Task: corroborate the claim using the given text. Claim: The suprachiasmatic nucleus (SCN) in the brain is the master clock regulating circadian rhythms. [SEP] Text: In the hippocampus labeling was found in CA1, CA2, and CA3 regions mainly around cell bodies (Fig. 2A and 2C). Label was also found in the cortex in the neurons of the deep layers and appeared to be restricted to the somas of the neurons and not the processes (Fig. 2B and 2D). We did not observe circadian changes in the pattern of MT1 receptor expression. Fig. 2 MT1 receptors localization in the cortex and the hippocampus. A) low and C) high magnification pictures showing label of hippocampal neurons with anti-MT1 antibody. Scale bars are 80 and 20 µm respectively. B) and D) show labeling with anti-MT1 antibody in cortical neurons in low and high magnification respectively. Scale bars are 80 and 20 µm respectively. When the pattern of labeling for MT1 receptors within the SCN was examined across the circadian cycle, MT1 receptors were detected within the SCN particularly at dusk (ZT 11–13) (Fig. 3). Labeling was dense and had a diffuse pattern at that circadian time. In addition, labeling extended into the optic chiasm representing probably labeling of neuronal dendrites. There was no difference in distribution of the labeling within each SCN. During the other three circadian times: ZT 23–01 (dawn), ZT 5–7 (mid-day), and ZT 17–19 (midnight), labeling was also observed, but it was less pronounced when compared to the dusk period. Also the pattern of labeling was more discrete, probably labeling only somas of SCN neurons. Fig. 3 MT1 receptors localization in rat SCN across the circadian cycle. Labeling with MT1 antibody in the SCN is shown at A) midday ZT 5–7, B) dusk ZT 11–13, C) midnight ZT 23–01, and D) dawn ZT 17–19, respectively. 3V indicates the third ventricle, OC is the optic chiasm. Scale bar in each picture is 80 µm. Our attempt of quantification confirmed that there was a significant variation in MT1 receptor density in the SCN across the circadian cycle, compared to non-SCN areas. One-way ANOVA indicated a significant daily variation in the density of label for MT1 in the SCN (p<0. 001). [SEP] Justify:

Output: The text corroborates the claim by providing evidence that MT1 receptors within the SCN vary across the circadian cycle, particularly showing significant variation at dusk (ZT 11–13). This suggests that the SCN plays a critical role in regulating circadian rhythms since the density of labeling for MT1 receptors was confirmed to vary across different circadian times, supporting its designation as the 'master clock.'


Input: Task: contrast the claim using the given text. Claim: All mollusks live in saltwater environments and cannot survive in freshwater. [SEP] Text: 7 ppt) located under the ice down to 12m depth, a chemo- and halocline located below the freshwater down to 24m and an anoxic marine-derived saline (oxygen below detection limit of the profiler; salinity > 30 ppt) and sulfate (~ 20 mM) and sulfide (~ 0. 3 mM) rich waters below 24 m. Light penetrates through the ice to the water column beneath, with an oxygen-containing euphotic zone that extends to 22 m. Water samples were collected in summer 2017 from three separate 24 cm-diameter holes drilled in the center of through the 0. 6 m thick ice cover. The sampling strategy and experimental procedures used in this study were previously detailed 20. Briefly, one litter of water was collected at eight different depths (2m, 6m, 14m, 22m, 34m, 40m, 55m and 65m) in the three holes, spanning the oxygen, salinity and temperature gradients of the lake water column. Triplicate water samples were filtered through separate 0. 22 µm pore size Sterivex filters™ (Merck Milipore) and then stored below − 50ºC until nucleic acid extraction. Nucleic acids were extracted using the DNA/RNA with modifications 43. Metagenomic library preparation, sequencing and analysis. One metagenomic library per sampled depth was prepared using XT kit and each library were sequenced in two Illumina MiSeq (2*300 bp) runs and one Illumina NexSeq run (2*150 bp) at the Institut de et des Systèmes (IBIS) sequencing platform (Université Laval, Canada) and at the CGEB – Resource (Dalhousie University, Canada) respectively. Datasets were quality filtered using Trimmomatic v. 0. 39 44. Reads of ribosomal small subunit were extracted from metagenomic reads using Infernal v. 1. 1. 4 45, and taxonomic affiliation of the extracted 16S rRNA reads longer than 100 bp were determined using BLAST against Silva database release 138 as reference 46. Since metagenomic 16S rRNA reads spanned various regions of the 16S rRNA gene, taxonomic assignments were limited to the genus level. [SEP] Justify:

Output: The text does not specifically mention mollusks or their habitats, but it describes a freshwater environment that includes various water quality parameters such as salinity and depth. This suggests the presence of a freshwater ecosystem, which is indicative that some organisms, potentially including certain species of mollusks, can survive in freshwater conditions. Therefore, it contrasts with the claim that all mollusks cannot survive in freshwater.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: 01), a 2. 6- to 3. 5-fold increase in expression of acute phase proteins (APPs) (alpha-2 macroglobulin (A2M), serotransferrin (TF/TRFE), ceruloplasmin (CP), clusterin (CLU), serum albumin (ALB), and transthyretin (TTR)) (p < 0. 01), a 2. 7- to 4. 0-fold increase in expression of various glycoproteins, including alpha-1-acid glycoprotein (ORM1/A1AG1), alpha-1-acid glycoprotein 2 (ORM2/A1AG2), and alpha-1-B glycoprotein (A1BG) (p < 0. 04), a 3. 2-fold increase in expression of alpha-1-antichymotrypsin (A1ACT/3) (p < 0. 01), alpha-1-antitrypsin (A1AT/1) and a 1. 4- to seven-fold increase in expression of hemoglobin subunit alpha-1 (HBA1), hemoglobin subunit beta (HBB), and haptoglobin (HP/HPT) (p < 0. 01). By way of contrast, the expression of clusterin (CLU), apolipoprotein A-1 (APOA1), apolipoprotein A-2 (APOA2), and transthyretin (TTHY/TTR) were significantly decreased in SLE patients by 0. 2- to 0. 4-fold (p < 0. 01). Functional annotation of the identified proteins To gain valuable insight of the identified differentially expressed proteins from our analysis the international standardized gene function classification system of GO and the DAVID database were employed. When analyzed for CC analysis by GO annotations, most of the identified differentially expressed proteins were found in the extracellular space (46%), while others are macromolecular in nature (27%) and yet others were found to be part of membrane complexes (27%) (Fig. 3A). As shown in Fig. 3B, the BP evaluations of the GO annotations revealed that the identified proteins are largely involved in biological regulation (15. 5%), complement activation (9. 5%), negative regulation of the immune response (12. [SEP] Justify:

Output: The text does not directly address the core concept of proteomics as it focuses on specific proteins and their expression levels in certain contexts, without explaining the overall study of all proteins expressed in a cell. Therefore, it is irrelevant to the claim.


Input: Task: pass the claim using the given text. Claim: The suprachiasmatic nucleus (SCN) in the brain is the master clock regulating circadian rhythms. [SEP] Text: Average MT1 receptor density in the SCN was significantly increased (indicated by low pixel values) at dusk compared to dawn (p < 0. 05) and mid-night (p < 0. 01) (Fig. 4). The average density of MT1 receptor label was higher at dusk than at midday; however this increase was statistically insignificant. On the other hand, MT1 receptor density compared to dawn and both midday and midnight was statistically insignificant, although the label was greater at dawn compared to these two circadian times. Fig. 4 Circadian rhythm of MT1 receptors density in the SCN. Normalized pixel density is plotted at different CTs. * and ** indicates that p value is less than 0. 5 and less than 0. 01 respectively, ns statistically insignificant. At midday (ZT 5–7) and dusk (ZT 11–13), label for MT1 extended into the optic chiasm apparently in dendritic processes. This identification was confirmed using antibody against MAP2 the dendrite marker [8]. This label probably originated from previously unobserved cell bodies in the optic chiasm that send dendritic processes into the SCN (Fig. 5). Fig. 5 MAP2 staining in the SCN and optic chiasm. A) Labeling of the dendrites within the SCN is shown with red color. The arrow points to a neuron within the optic chiasm. B) An overlay of both DAPI labeling the nuclei (blue) and MAP2 labeling the dendrites (Red). C) Same as in B but in a different section; notice a more distant neuron within the SCN (arrows). 3V indicates the third ventricle. OC is the optic chiasm. Scale bar is 20 µm. No clear labeling for MT2 receptors was observed in the SCN at the same antibody concentration that was used for MT1 was detected at (1:500). When the concentration of the antibody was increased to 1:100, only minimal labeling was detected in the SCN (Fig. 6). On the other hand, at 1:100 concentration clear MT2 labeling was detected in the paraventricular nucleus (Fig. 7) as well as in the retina (data not shown). Fig. 6 MT2 receptors immunostaining in the SCN. 3V indicates the third ventricle, OC is the optic chiasm. Scale bar is 80 µm. Fig. [SEP] Justify:

Output: The text does not directly corroborate or contrast the claim about the SCN being the master clock regulating circadian rhythms. Instead, it discusses the density of MT1 and MT2 receptors in the SCN and their behavior during different circadian times. While it provides some information related to the SCN's functions, it does not explicitly support or refute the claim that the SCN regulates circadian rhythms.


Input: Task: contrast the claim using the given text. Claim: All mollusks live in saltwater environments and cannot survive in freshwater. [SEP] Text: Skip to main content in a journal Publish with us Track your research and Ecology of Bulgaria 85. 5%). Typical for the is the zone composed ofMytilus galloprovincialis (down to 70 m) andModiolula phaseolina (70–140 m). The freshwater mollusks are represented by two classes: Gastropoda (71 species) and Bivalvia (24 species). The highest diversity of freshwater mollusks (77 species, or 80. 1%) is found in the lowlands (below 200 m above sea level). The freshwater mollusks are divided into 22 zoogeographical categories; they include 20 endemic species (21. 1%); 11 freshwater species are considered relicts (preglacial, glacial, or Caspian). The terrestrial mollusks are represented by two subclasses of Gastropoda. The highest diversity of terrestrial mollusks (181 species, or 76. 0%) is found in the hills and mountains. The terrestrial mollusks are divided into 36 zoogeographical categories; they include 68 endemic species (28. 5%), 21 preglacial relicts (8. 8%), and one glacial relict. In Bulgaria, 206 mollusk species (42. 3%) are considered important for conservation This is a preview of subscription content, log in via an institution to check access. Access this 34. 9910 units per month Download 29. 95 Price excludes VAT (USA) Available as PDF Read on any device Instant download Own it forever Buy 259. 00 Price excludes VAT (USA) Available as PDF Read on any device Instant download Own it forever Buy e329. 99 Price excludes VAT (USA) Compact, lightweight edition Dispatched in 3 to 5 business days Free shipping worldwide - see info 329. 99 Price excludes VAT (USA) Durable hardcover edition Dispatched in 3 to 5 business days Free shipping worldwide - see info calculation will be finalised at checkout Purchases are for personal use only Institutional subscriptions to display preview. Download preview PDF. Unable to display preview. Download preview PDF. Similar content being viewed by others of the Circumpolar Arctic: a review on their taxonomy, diversity and biogeography 1991. Compendium of Seashells. CharlesLetts & Co. , London. 1956. [Hydrologische und hydrobiologischeUntersuchungen über den Rabischa-See]. [SEP] Justify:

Output: The text contrasts the claim by stating that there are freshwater mollusks, specifically mentioning 71 species of Gastropoda and 24 species of Bivalvia found in freshwater environments. It highlights the biodiversity of freshwater mollusks and indicates that they thrive in lowland areas, contradicting the assertion that all mollusks are limited to saltwater habitats.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: 1%), multicellular organismal processes (14%), immune system processes (8. 6%), metabolic processes (12. 1%), the acute inflammatory response (10. 3%), and localization (14. 7%). On the other hand, when analyzed in terms of MF, the identified proteins were mostly involved in binding (41. 2%), catalytic activity (38. 2%), receptor activity (14. 7%), transporter activity (14. 7%), and serine peptidase activity (7. 2%) (Fig. 3C; Tables S3 and S4). Therefore, based on the functional analysis, the identified proteins seem to primarily play important roles in immune system regulation (p = 0. 001), in complement system activation (p = 0. 01), in the innate and adaptive immune system responses (p = 0. 003) and, potentially, in the acute inflammatory response (p = 0. 002). Figure 3: Gene ontology (GO) enrichment analysis of the differentially expressed proteins. (A) Cellular component analysis of the identified proteins. (B) Biological function. (C) Molecular function of the identified proteins. The pie charts were generated using Panther version 11. 0 released 2016-07-15. Download full-size image DOI: 10. 7717/peerj. 4730/fig-3 According to KEGG pathway annotation, the identified protein cohort was classified into more than 25 pathways (Tables S5 and S6) with the top 18 of them being shown in Fig. 4. Among 19 identified differentially expressed proteins, nine proteins (A2M, A1AT, A1105, KV315, IGG4, 1, TF) were involved in complement and coagulation pathway, 12 proteins (A1AT, A11, 315, 105, A21AG2) were involved in homeostasis and immune system processes (p = 8. 8 × 10−8). In addition to the above findings, the majority of them were involved in a number of potentially interesting pathways such as scavenging heme from plasma, platelet activation, acute-phase responses, degranulation, signaling, aggregation, and the creation of C4 and C2 activators, etc. These pathways are highly relevant to the present study since SLE is an autoimmune disease caused by abnormalities that affect the immune system and in turn cause an acute inflammatory response. [SEP] Justify:

Output: The text does not address or support the claim about proteomics studying the entire set of proteins expressed in a cell. Instead, it focuses on specific protein functions and pathways related to immune system processes and inflammation, which is not directly related to the overarching definition of proteomics.


Input: Task: corroborate the claim using the given text. Claim: The suprachiasmatic nucleus (SCN) in the brain is the master clock regulating circadian rhythms. [SEP] Text: 7 MT2 receptor immunolabeling in the paraventricular nucleus. 3V is the third ventricle. Scale bar is 80 µm. 4. results of this study show that the localization and distribution of melatonin receptors MT1 is regulated in a circadian mode in rat SCN. The highest observed receptor density was detected at dusk (ZT 11–13), which is the observed window of time for melatonin actions in SCN [5, 9, 12]. MT1 receptor density was elevated at dusk compared to that at dawn (ZT 23–01) and midnight (ZT17–19). Our attempt to quantify these changes showed that there was no statistically significant difference between MT1 receptor density at dusk and mid-day. These data suggest that the synthesis of melatonin receptors MT1 undergoes cyclic changes throughout the circadian cycle. Darkness signals conveyed to the SCN via the retinohypothalamic tract (RHT) result in MT1 receptor being synthesized and shuttled to the dendritic membrane, while during the day the receptors are degraded. This cyclic pattern of melatonin receptors expression and degradation fits perfectly with the observations that melatonin was most effective in influencing SCN function only at specific windows of time [5]. These data also agree with mRNA expression data that found a rhythm of expression similar to our model in rat SCN [15, 18] as well as with data from binding studies [10]. et al. [26] did not find a statistically significant variation in MT1 mRNA receptor expression across the circadian cycle, they still found a pattern of variation in its expression similar to the model proposed here. However, and since this is a novel approach to define daily changes in melatonin receptor expression, further studies are needed to confirm these results using more advanced methods of quantification. There were no apparent daily changes in MT1 labeling in the cortex and the hippocampus, but we did not test a number of rat brains large enough for statistical analysis to confirm this result. The similar labeling pattern of MT1 and MAP2 suggests that MT1 receptor is mainly present in the dendrites and somas of SCN neurons. Moreover, labeling extended to what appears to be neurons within the optic chiasm (Fig. 3 and 5), which suggests the possibility of a population of SCN neurons within the optic chiasm that have a role in melatonin regulation of the circadian pacemaker. [SEP] Justify:

Output: The text corroborates the claim by discussing the role of melatonin receptors MT1 in the SCN, indicating that their localization and cycling is regulated in a circadian manner within the SCN. It highlights how darkness signals prompt synthesis and insertion of MT1 receptors into the SCN neurons, which aligns with the function of the SCN as the master clock of circadian rhythms. The cyclic pattern of receptor expression and the influence of melatonin on SCN function at specific times further supports the role of SCN in regulating circadian rhythms.


Input: Task: contrast the claim using the given text. Claim: All mollusks live in saltwater environments and cannot survive in freshwater. [SEP] Text: Godishnik na Sofiiskiyauniversitet. Biologo-geologo-geografski fakultet (Annuaire del’Université de Sofia, Faculté de Biologie, Géologieet Géographie) 49( 1– Biology): 1–30 (in Bulgarian). 1959. aus den unterirdischenGewässern Bulgariens. Archiv für Molluskenkundev 88( 1/3): 51–54. 1972. aus HöhlengewässernBulgariens. Archiv für Molluskenkunde 102( 1/3): 107–112. 1976. [Revision der Fam. Pisididae Gray, 1857(Bivalvia– Mollusca) in Bulgarien]. Godishnik na Sofiiskiyauniversitet ‘‘Kliment Ohridski’’. Biologicheski fakultet (Annuairede l’Université de Sofia ‘‘Kliment Ohridski’’, Faculté deBiologie) 69( 1– Zoology): 109–119 (in Bulgarian). 1983. [Ferrissia wautieri (Mirolli)(Gastropoda, Ancylidae)– a new representative of the Bulgarianfreshwater fauna]. Acta zoologica bulgarica 21: 95–97 (inBulgarian). 63. 64. 4. Pensoft & BackhuysPublishers BV, Sofia & Leiden. 138. 1994. [Littoriniformes,Rissoiformes]. Ukrainy. Tom 29. Mollyuski. Vypusk 1,kniga 2. [Fauna of Ukraine. Vol. 29. Mollusks. No. 4, 2]. Naukovadumka [Scientific Thought], Kiev (in Russian). 1990. Zoogeography of Fresh Waters. 1. and Dispersal of Freshwater Animals. Aula-Verlag, Wiesbaden. 1972. Essai sur la faune cavernicole de Bulgarie. III. Résultats des recherches biospéologiques de 1966 á1970. [SEP] Justify:

Output: The text contrasts the claim by providing references to multiple sources discussing freshwater mollusks, such as 'Ferrissia wautieri (Gastropoda, Ancylidae)– a new representative of the Bulgarian freshwater fauna'. This indicates that some mollusks do indeed inhabit freshwater environments, directly opposing the claim that all mollusks are limited to saltwater.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Based on the KEGG pathway analysis most of the identified proteins particularly (A2M, A1AT, A1105, KV315, IGG4, 1, and TF) significantly involved in complement coagulation cascades, regulation of innate and adaptive immune systems, inflammatory responses, platelet activation, and transportation of small molecules. A set of nine APPs were up-regulated (A2M, A1AG, ORM1, A1AT, A1) and two were down-regulated (APOA1, APOA2) in our analysis. These proteins were predominantly responsible for acute phase reactions including inflammation and dysregulation of the immune system (Simon, 2013). In addition to this, APPs also play active roles in various physiological and pathological activities related to disease exacerbation (Simon, 2013). It seems likely that the identified some of the identified APPs (A2M, A1AT, and A1ACT) play an important role in the complement and coagulation cascades which is an important pathway that plays a crucial role in SLE pathogenesis. Therefore, these proteins may be able to help our understanding of the mechanisms of immune reactions and inflammatory responses involved in SLE. Alpha-2 macroglobulin protein has been previously found to be involved in a number of different diseases, including nephrotic syndrome, diabetes, and liver cirrhosis (der Velden et al. , 1998). This is the first time we are reporting the higher abundance of A2M were identified in SLE patients compared to healthy individuals. In addition to these, several immunoglobulins heavy, and light chains were also found to be up-regulated in this study, and these changes illustrate that there is an imbalance in the immune system and homeostasis during SLE. APOB have been shown to play a significant role in immune system regulation and inflammation. It was previously identified in the lupus patients with cardiovascular diseases and myocardial infarction, along with changes in low and high-density lipoproteins () (Bots et al. , 2016; Smržová et al. , 2014). Our study also identified consistently up-regulated APOB expressions in SLE. We believe that this is the first report that shows increased expressions of APOB protein in SLE patients without any cardiac complications. [SEP] Justify:

Output: The text does not address the claim regarding proteomics studying the entire set of proteins expressed in a cell. Instead, it focuses on specific proteins related to certain pathways and conditions, particularly in the context of systemic lupus erythematosus (SLE) and immune responses. Therefore, it is considered irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: The suprachiasmatic nucleus (SCN) in the brain is the master clock regulating circadian rhythms. [SEP] Text: Molecular dissection of two distinct actions of melatonin on the suprachiasmatic circadian clock Neuron 19: 91–102, DOI: Masana, M. I. , Benloucif, S. and Dubocovich, M. L. (2000). Circadian rhythm of mt1 melatonin receptor expression in the suprachiasmatic nucleus of the C3H/HeN mouse J 28: 185–92, DOI: McArthur, A. J. , Gillette, M. U. and Prosser, R. A. (1991). Melatonin directly resets the rat suprachiasmatic circadian clock in vitro 565: 158–61, DOI: McArthur, A. J. , Hunt, A. E. and Gillette, M. U. (1997). Melatonin action and signal transduction in the rat suprachiasmatic circadian clock: activation of protein kinase C at dusk and dawn Endocrinology 138: 627–34. Milton, S. J. (1999). in the Biological and Health Sciences. third edn. USA: WCB/McGraw-Hill. Monti, J. M. and Cardinali, D. P. (2000). A critical assessment of the melatonin effect on sleep in humans Recept 9: 328–39, DOI: Neu, J. M. and Niles, L. P. (1997). A marked diurnal rhythm of melatonin ML1A receptor mRNA expression in the suprachiasmatic nucleus Res 49: 303–6, DOI: Nonno, R. , Pannacci, M. , Lucini, V. , Angeloni, D. , Fraschini, F. and Stankov, B. M. (1999). Ligand efficacy and potency at recombinant human MT2 melatonin receptors: evidence for agonist activity of some mt1-antagonists Pharmacol 127: 1288–94, DOI: Pitrosky, B. , Kirsch, R. , Malan, A. , Mocaer, E. and Pevet, P. (1999). Organization of rat circadian rhythms during daily infusion of melatonin or S20098, a melatonin agonist Physiol 277: R812–28. Poirel, V. J. [SEP] Justify:

Output: The text provides information on various studies related to melatonin's effects on the suprachiasmatic nucleus (SCN), which is recognized as a significant regulator of circadian rhythms. The mention of the SCN in the context of melatonin's actions supports the claim that it functions as the master clock for circadian regulation.


Input: Task: contrast the claim using the given text. Claim: All mollusks live in saltwater environments and cannot survive in freshwater. [SEP] Text: Archiv für Molluskenkunde 99( 1/2): 35–40. 1998. Annotated check-list of the Bulgarian terrestrialsnails (Mollusca, Gastropoda). Linzer biologische Beiträge 30( 2): 745–765. 1998. Species composition of theterrestrial snails (Mollusca, Gastropoda) from coniferous andalpine areas of the Mountains, Bulgaria. Historianaturalis bulgarica 9: 19–26. 2000. Species composition and origins ofthe terrestrial gastropod fauna of Sofia City, Bulgaria. Ruthenica 10( 2): 121–131. 522. 536. 1947. [Synopsis and distribution of freshwaterMollusca in Bulgaria]. Godishnik na Sofiiskiya universitet. Fiziko-matematicheski fakultet (Annuaire de l’Université deSofia. Faculté physico-mathématique) 43( 3): 33–54 (inBulgarian). 1990. Donau vom Schwarzwald bis zum Schwarzen Meer. Akaprint, Budapest. 1982. [On principles of regionalization andunification of terminology in marine biogeography]. In Kusakin,O. G. (ed), Morskaya biogeografiya, predmet, metody, printsipyrayonirovaniya [Marine Biogeography, Its Subject, Methods, andPrinciples of Regionalization]. Nauka [Science], Moscow: 94–98 (in Russian). 1966. [Ponto–Caspiangastropod molluscs in the Azov–basin]. Zoologicheskiizhurnal 45( 3): 352–362 (in Russian). 1968. [Zoogeographicalcharacteristics of the gastropod mollusks of Black and Azov Seas]. issledovaniya Chernogo morya i ego promyslovykhresursov [of the Resources]. Nauka [Science], Moscow: 70–83 (in Russian). 1972. [Class Gastropoda]. In Opredelitel’ fauny Chernogo iAzovskogo morey [to theFauna of Black and Azov Seas]. 3. [SEP] Justify:

Output: The text lists various studies and academic articles related to freshwater mollusks, specifically mentioning species composition and distribution of terrestrial and freshwater mollusks in Bulgaria. This directly contrasts with the claim, which asserts that all mollusks cannot survive in freshwater environments, indicating that at least some mollusks do inhabit these freshwater ecosystems.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: It has been shown to be responsible for transporting hemoglobin, inhibiting iron loss and preventing kidney damage when hemolysis is occurring (Galicia & Ceuppens, 2011). Another study found higher expression of HP in SLE patients may contribute to hypergammaglobulinemia, systemic vasculitis and cardiovascular disorders (Pavón et al. , 2006). Therefore, the observed HP changes from this study is consistent with the findings of the previous study and suggests that the increased HP expressions may cause severe clinical manifestations in SLE. Two hemoglobin scavenger proteins such as HBB and HPX showed differential regulations from our findings were implicated with HDL and influence the inflammatory properties of HDL and scavenging of oxygen binding and transport from the lungs to the peripheral tissues and also involved in a number of inflammatory diseases (Newkirk et al. , 1999). In addition, the depletion of HPX levels implicated in a number of inflammatory diseases such as septic shock and experimental autoimmune encephalomyelitis (Mehta & Reddy, 2015). The primary function of HPX is heme scavenging and it protects against oxidative stress and related inflammatory diseases. Moreover, the precise role of these proteins in SLE is not recognized yet, and to the best of our knowledge this is first plasma proteomic study reporting the down-regulated expressions of HPX and up-regulated HBB in lupus patients. The two more down-regulated proteins from our analysis areTTHY which are also potentially associated with SLE pathogenesis. These play crucial roles in immune system dysregulation and are associated with alterations in inflammatory reactions. CLU is a glycoprotein with ubiquitous tissue distribution that has been reported to be implicated in several physiological processes. Earlier evidence has shown that lower levels of CLU/apoJ are associated with some feature of SLE such as a diminished control of antibody-mediated inflammation at the sites of apoptosis where auto-antigens are exposed (Andrade, Casciola-Rosen & Rosen, 2000). Moreover, CLU may have a protective role against SLE disease activity because disturbances in apoptosis and complement function seem to play essential roles in SLE pathogenesis (Burger & Dayer, 2002). The down-regulated expression level of CLU in SLE patients identified by our analysis might be associated with the fact that the patients studied had active disease. [SEP] Justify:

Output: The text does not directly address the claim about proteomics studying the entire set of proteins expressed in a cell. Instead, it details findings related to specific proteins and their roles in various diseases, particularly systemic lupus erythematosus. The claims about HP, HBB, HPX, and CLU do not provide a broader definition or scope of proteomics itself, making it irrelevant to the specific claim about the field.


Input: Task: corroborate the claim using the given text. Claim: The suprachiasmatic nucleus (SCN) in the brain is the master clock regulating circadian rhythms. [SEP] Text: blot analysis of isolated SCN from individual animals, we quantified BMAL1 expression (as a percentage of α-Tubulin expression) over a 24-h period in isolated SCN after GSK3-KI or WT control mice were housed in DD for at least 2 weeks. Cosinor nonlinear regression revealed a significant BMAL1 expression rhythm in WT mice (n = 27/time course; cosinor nonlinear regression analysis; p < 0. 05 for SCN) with peak BMAL1 expression in the subjective night (mesor, 0. 82 ± 0. 08; amplitude, –0. 30 ± 0. 11; phase, 14. 85 ± 10. 61; Figure 2). In GSK3-KI mice, however, BMAL1 expression did not exhibit a significant 24-h rhythm (n = 25/time course; as determined by cosinor nonlinear regression analysis, p = 0. 91; Figure 2). There were no significant differences in α-tubulin expression levels with respect to time or genotype (p > 0. 05). These results indicate that constitutive GSK3 activation disrupts circadian expression of BMAL1 in the central pacemaker. Based on phosphorylation status, we predict that GSK3β activity is highest in WT SCN neurons at approximately CT16, when BMAL1 protein levels peak. GSK3α activity likely peaks around CT9, a time at which BMAL1 protein levels are increasing. These observations are consistent with the conceptual model that GSK3-mediated phosphorylation is an early event, which primes BMAL1 for subsequent degradation via ubiquitin/proteosomal degradation (Figure 2; Sahar et al. , 2010). The possibility also remains that chronic GSK3 activation influences BMAL1 protein levels indirectly, through phosphorylation of other clock components (e. g. , REV-ERBα, which in turn represses Bmal1 transcription). Figure 2. Rhythmic BMAL1 expression in mice with chronic GSK3 activation. (A) blots of BMAL1 reblotted for α-tubulin. [SEP] Justify:

Output: The text corroborates the claim by discussing the role of BMAL1 expression within the SCN, a central pacemaker for circadian rhythms. It details how a rhythmic expression of BMAL1 and its regulation by GSK3 activity supports the SCN's function in regulating circadian rhythms, which is consistent with the claim that the SCN serves as the master clock.


Input: Task: contrast the claim using the given text. Claim: All mollusks live in saltwater environments and cannot survive in freshwater. [SEP] Text: Nauchni trudove na Plovdivskiya universitet ‘‘PaisiiHilendarski’’ (Travaux scientifiques de l’Université dePlovdiv ‘‘Paisii Hilendarski’’), Animalia, 37( 6): 35–38 (inBulgarian). 2002. [Species composition and zoogeographicalcharacterization of the terrestrial shell malacofauna (Mollusca,Gastropoda) in the Dobrostanski ridge of the withecological notes]. Historia naturalis bulgarica 14: 89–102 (inBulgarian). 2002. [Species composition, habitatdistribution, zoogeographical structure and origin of themalacofauna in town (Bulgaria)]. Nauchni trudove naPlovdivskiya universitet ‘‘Paisii Hilendarski’’ (Travauxscientifiques de l’Université de Plovdiv ‘‘PaisiiHilendarski’’), Animalia, 38( 6): 5–16 (in Bulgarian). 1906. Notes sur les Bivalves d’eau douce deBulgarie. Godishnik na Sofiiskiya universitet. Fiziko-matematicheski fakultet (Annuaire de l’Université deSofia. Faculté physico-mathématique) 2: 61–67. 1908. [Sur les Helicides de la Bulgarie]. universitet. Fiziko-matematicheski fakultet(Annuaire de l’Université de Sofia. Facultéphysico-mathématique) 3/4: 1–21 (in Bulgarian). 1964. [The lakes of Bulgaria]. Izvestiya na Instituta pohidrologiya i meteorologiya [Proceedings of the Institute ofHydrology and Meteorology] 16: 1–243 (in Bulgarian). 95. 82. 1957. Die Land- undSüsswasser-Mollusken der nördlichen Balkanhalbinsel. [SEP] Justify:

Output: The text contrasts the claim by mentioning the composition of terrestrial and freshwater mollusks in Bulgaria, indicating that at least some mollusk species can be found in freshwater environments, thereby refuting the claim that all mollusks can only live in saltwater.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Therefore, the above findings on CLU expression levels among SLE patients suggest that this protein is likely to be an important biomarker with respect to SLE disease activity. Another down-regulated protein identified is TTR, which is a serum and cerebrospinal fluid transporter of the thyroid hormone thyroxine (T4), and of retinol (Zheng et al. , 2001). Earlier proteomic observations by Rana et al. showed the increased expression of TTR in serum obtained from pediatric SLE patients compared to controls (Rana et al. , 2012). In our proteomic study, we have identified TTR reduced expressions in adult SLE patients. the above as a whole, we have demonstrated that the identification of a single protein that possesses exclusive characteristics of an SLE marker is indeed very challenging. The identification of differential expressions of proteins in the plasma between SLE patients and controls will help to develop novel approaches for the early disease detection, prevention, and the treatment of SLE. Our findings have revealed that a number of proteins show changes in expression associated with the presence of SLE. Moreover, some of the identified proteins and their expressions from this study support the findings of previous studies. Additionally, our findings may play a significant role in inflammation, acute phase responses, disease activity and immune dysregulation when SLE is present. Nevertheless, these interesting findings would require subsequent investigation to validate and confirm. Finally, LC-MS/MS combination with label-free quantification is clearly an excellent technique for the profiling of differentially regulated proteins in the disease samples. A complete list of identified proteins in the plasma samples of SLE Patients during triplicate analysis. DOI: 10. 7717/peerj. 4730/supp-1 complete list of differentially expressed significant proteins identified in the SLE Patients samples compared to healthy controls. DOI: 10. 7717/peerj. 4730/supp-2 ontology biological process (BP) data for all the identified proteins from SLE patients. DOI: 10. 7717/peerj. 4730/supp-3 ontology molecular function (MF) data for all the identified proteins from SLE patients. DOI: 10. 7717/peerj. 4730/supp-4 and pathway analysis data of the identified proteins from SLE patients. DOI: 10. 7717/peerj. [SEP] Justify:

Output: The text discusses the findings related to specific proteins in the context of SLE (Systemic Lupus Erythematosus) but does not address the broader topic of proteomics or the study of the entire set of proteins expressed in a cell. Therefore, it does not relate to the claim and is considered irrelevant.


Input: Task: corroborate the claim using the given text. Claim: The suprachiasmatic nucleus (SCN) in the brain is the master clock regulating circadian rhythms. [SEP] Text: Application of this small-molecule GSK3 inhibitor nearly doubled the amplitude of the chi-squared periodogram analysis and significantly shortened the period length of SCN explant PER2::LUC rhythms (n = 9/group; t tests, p < 0. 05; Figure 3A,B), suggesting that chronic GSK3 inhibition enhances the amplitude and speeds up the periodicity of the molecular clock. These results are consistent with previous in vitro studies that show that molecular clock amplitude is enhanced and period is shortened by pharmacological GSK3 inhibition in fibroblasts and mammalian cell lines (Hirota et al. , 2008; Vougogiannopoulou et al. , 2008; Li et al. , 2012). On the other hand, molecular clock amplitude is reduced by GSK3 overexpression (Sahar et al. , 2010; Li et al. , 2012). Although it is well documented that the GSK3 inhibitor lithium lengthens the period of circadian rhythms (Mason and Biello, 1992; Abe et al. , 2000; Hirota et al. , 2008; Mohawk et al. , 2009; Osland et al. , 2011), our results with a more selective GSK3 inhibitor raise the possibility that lithium-induced effects may be due to nonspecific targets, perhaps via inositol phosphatase inhibition (Quiroz et al. , 2004). Figure 3. GSK3 inhibition modulates the molecular clock. (A) Representative bioluminescent traces from PER2::LUC organotypic SCN cultures treated with vehicle (black) or CHIR-99021 (20 µM; gray). (B) Bar graph (mean ± SEM) of amplitude (left; t(16) = 2. 68; *p < 0. 05) and period length (right; t(16) = −3. 83, *p < 0. 05). The present study shows that both GSK3 isoforms are rhythmically inactivated in the SCN in constant conditions, consistent with previous evidence in LD (Iwahana et al. , 2004; Iitaka et al. , 2005). These results support the model that GSK3 activity is clock controlled (Durgan and Young, 2010), potentially regulated by rhythmic phosphorylation of AKT (Panda et al. [SEP] Justify:

Output: The text corroborates the claim as it discusses the regulation of circadian rhythms in the SCN and mentions results indicating that GSK3 activity is rhythmically inactivated in the SCN, supporting the understanding of the SCN as a central regulator of circadian rhythms. It also refers to previous evidence related to the molecular clock functions in the SCN, aligning with the idea that the SCN acts as the master clock.


Input: Task: contrast the claim using the given text. Claim: All mollusks live in saltwater environments and cannot survive in freshwater. [SEP] Text: [On the alimentary zoobenthos dynamicsin during the 1967–1974 period]. Izvestiya. Institut po ribni resursi– Varna (Proceedings. Institute of Fisheries– Varna) 14: 43–56 (in Bulgarian). 1960. [Zoobenthosdistribution in the Sea area]. Trudove naTsentralniya nauchnoizsledovatelski institut po ribovadstvo iribolov– Varna (Arbeiten des Zentralen Forschungsinstitutesfür Fischzucht und (Bulgarien)) 3: 117–166 (inBulgarian). 1966. [Distribution of thezoobenthos in the sand biocoenosis of the Seacoast]. Izvestiya na Nauchnoizsledovatelskiya institut za ribnostopanstvo i okeanografiya– Varna (Proceedings of the ResearchInstitute of Fisheries and Oceanography–Varna) 7: 69–95 (inBulgarian). 1967. [Dynamics of thezoobenthos in the lakes along the Sea coast in the1964–1966 period]. Izvestiya na Nauchnoizsledovatelskiya institutza ribno stopanstvo i okeanografiya– Varna (Proceedings of theof Fisheries and Oceanography– Varna) 8: 177–194 (in Bulgarian). 1984. [A new mollusk speciesfor the Black Sea,Cunearca cornea (Reeve)]. Priroda[Nature] (Sofia) 33( 5): 63–64 (in Bulgarian). 1983. Die LandschneckenNord- und Mitteleuropas. Parey, Hamburg & Berlin. 1939. Systematische, anatomische, ökologische undtiergeographische Studien an südosteuropäischen Heliciden(Moll. Pulm. ). Archiv für Naturgeschichte N. F. 8( 3/4): 327–517. 1941. Nachträge zur südosteuropäischenHelicidenfauna (Moll. Pulm. ). I. [SEP] Justify:

Output: The text discusses various studies related to zoobenthos, which include aquatic organisms such as mollusks. The mention of zoobenthos in various coastal and lacustrine environments suggests that mollusks may inhabit both saltwater and possibly freshwater ecosystems. Therefore, it contrasts with the claim that all mollusks exclusively live in saltwater and cannot survive in freshwater.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: 4730/supp-5 and pathway analysis data of the identified proteins from SLE patients. DOI: 10. 7717/peerj. 4730/supp-6 representative LC-MS/MS proteomic analysis report of SLE patient’s complete list of identified proteins compared to healthy controls. Out of 19 SLE patients triplicate analysis, we have uploaded one SLE patient raw data LC-MS/MS as a reference. DOI: 10. 7717/peerj. 4730/supp-7 lupus erythematosus LN Lupus nephritis LC-ESI-MS/MS Liquid chromatography electrospray ionization tandem mass spectrometry EmPAI Exponentially modified protein abundance index BPC Base peak chromatogram XIion chromatograms AUC Area under the curve A2M Alpha 2 macroglobulin TTR//-100 GO Gene ontology KEGG Kyoto encyclopedia of genes and genomics and for the Retrieval of Interacting Genes/Proteins, Version 9. 1 PPI Protein–protein interaction networks APphase proteins CC Cellular components MF Molecular function BP Biological process would like to thank Hospital (CGH) for providing the SLE and healthy plasma samples for our proteomic analysis. authors declare that they have no competing interests. conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, approved the final draft. Shih-authored or reviewed drafts of the paper, approved the final draft, samples provider. Wei-contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft. Shir-conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft. The following information was supplied relating to ethical approvals (i. e. , approving body and any reference numbers): This study was approved by the Board (IRB) for at Hospital, Taiwan (IRB project identification code: CT-099005). [SEP] Justify:

Output: The text does not directly address the claim regarding proteomics studying the entire set of proteins expressed in a cell. Instead, it discusses the identification of proteins from SLE patients and provides technical details related to proteomic analysis without confirming or denying the broad definition of proteomics.


Input: Task: corroborate the claim using the given text. Claim: The suprachiasmatic nucleus (SCN) in the brain is the master clock regulating circadian rhythms. [SEP] Text: Journal of Circadian RhythmsStart SubmissionBecome a ReviewerReading: Neurotransmitters of the suprachiasmatic nucleiDownloadXML (US English)PDF (US English)Alt. DisplayShareShareReviewNeurotransmitters of the suprachiasmatic nucleihas been extensive research in the recent past looking into the molecular basis and mechanisms of the biological clock, situated in the suprachiasmatic nuclei (SCN) of the anterior hypothalamus. Neurotransmitters are a very important component of SCN function. Thorough knowledge of neurotransmitters is not only essential for the understanding of the clock but also for the successful manipulation of the clock with experimental chemicals and therapeutical drugs. This 10. 1186/1740-3391-4-2Submitted on Dec 6, 2005Accepted on Feb 16, 2006Published on Feb 16, 20064. 0 advances have been made in the study of mechanisms of the circadian clock in the past decade. Since the identification of a master circadian clock in the suprachiasmatic nuclei (SCN) of the anterior hypothalamus of mammals, researchers sought to identify the nature of the clock and characterize its components. The SCN, acting as circadian pacemakers, have the function of orchestrating the timing in physiology and behaviour. They control circadian rhythms in other parts of the brain, such as the cerebral cortex, in the pineal gland, and in peripheral tissues such as liver, kidney and heart [1]. The circadian clock not only can generate its own rhythms but can also be entrained by the environmental light-dark (LD) cycle. Multiple single cell circadian oscillators that are present in the clock can, when synchronized, generate coordinated circadian outputs which ultimately regulate the overt rhythms. Studies pertaining to the molecular mechanisms of the clock have yielded valuable results with the identification of a protein responsible for the setting of the length of periods of activity and inactivity within cells. Many years of research by a dedicated team of scientists culminated in the discovery of this protein [2]. It is believed that the identification of this protein will have far reaching implications not only in the understanding of the working of the clock but also in clinical applications, such as the treatment of jet lag and the design of optimal times for the administration of anti-cancer drugs. [SEP] Justify:

Output: The text corroborates the claim by stating that the suprachiasmatic nucleus (SCN) is identified as the master circadian clock in the anterior hypothalamus of mammals. It discusses how the SCN functions as a circadian pacemaker that orchestrates timing in physiology and behavior, thus supporting the assertion that the SCN regulates circadian rhythms.


Input: Task: contrast the claim using the given text. Claim: All mollusks live in saltwater environments and cannot survive in freshwater. [SEP] Text: Izvestiya na Zoologicheskiya institut s muzei(Bulletin de l’Institut de zoologie et musée) 15: 203–214 (inBulgarian). 1968. der Arioniden in Bulgarien. Malakologische Abhandlungen. für TierkundeDresden 2( 17): 235–241. 1970. im westlichen Teil desBalkan-Gebirges (Bulgarien). Malakologische Abhandlungen. für 3( 7): 71–79. 1972. [Nacktschnecken (Familien Arionidae,Limacidae und Milacidae) aus dem Vitoscha-Gebirge]. Izvestiya naZoologicheskiya institut s muzei (Bulletin de l’Institut dezoologie et musée) 35: 139–154 (in Bulgarian). 2001. Recherches hydrobiologiques des zoneshumides de la côte bulgare de la Mer Noire. I. Le lac de Vaja. Rivista di Idrobiologia 40( 2/3): 321–334. 1925. K problému marinniho plistocenu u Varny. Věstnìk Stàtnìho geologického ùstavuČeskoslovenské republiky 1: 1–6. 1940. zur Kenntnis derMollusken-Fauna von Bulgarien. Archiv für Molluskenkunde 72: 85–88. 1941. Posttertiaria nonmarina mollusca bulgarica. Věstnìk Kràlovské České SpolečnostiNauk, Třìda matematicko-přìrodov룥ckà(Prague):1–39. 1947. [The freshwater molluscs of the lakes of Varnaand of Gebedže]. [SEP] Justify:

Output: The text contrasts the claim by mentioning 'the freshwater molluscs of the lakes of Varna and of Gebedže,' indicating that there are indeed mollusks that inhabit freshwater environments, directly opposing the assertion that all mollusks cannot survive in freshwater.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: The following information was supplied regarding data availability: Madda, Rashmi; Lin, Shih-Chang; Sun, Wei-Hsin; Huang, Shir-Ly (2018): Plasma proteomic analysis of systemic lupus erythematosus patients using liquid chromatography/tandem mass spectrometry with label-free quantification. figshare. Fileset. work was supported by grants from the University and CGH collaborative project. The grant registration numbers are 104G909-4, 10310061-4, 10210061-3, 105-G1-3-2, 106-G1-3-2 and MOST 106-2320-B-008-004-MY3. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 2001. Anti-apolipoprotein A-I autoantibody: characterization of monoclonal autoantibodies from patients with systemic lupus erythematosus. Rheumatology 28:990-995. 2017. Urinary haptoglobin, alpha-1 anti-chymotrypsin and retinol binding protein identified by proteomics as potential biomarkers for lupus nephritis. Clinical & 188(2):254-262. 2003. An approach to remove albumin for the proteomic analysis of low abundance biomarkers in human serum. Proteomics 3(10):1980-1987. 2015. Proteomic analysis of Class IV lupus nephritis. Transplantation 30(1):62-70 Almoallim H, Al-. 2012. Anti-tumor necrosis factor-α induced systemic lupus erythematosus. Journal 6(1):315-319. 2002. The human plasma proteome: history, character, and diagnostic prospects. Molecular & 1(11):845-867 Andrade F, Casciola-Rosen L, Rosen A. 2000. Apoptosis in systemic lupus erythematosus. Clinical implications. Clinics of 26(2):215-227. 2004. Apolipoprotein A-I infiltration in rheumatoid arthritis synovial tissue: a control mechanism of cytokine production. & Therapy 6(6):R563-R566. 1992. [SEP] Justify:

Output: The text does not directly address the claim regarding proteomics and instead provides various references related to plasma proteomic analysis and systemic lupus erythematosus. While it mentions proteomics, it does not clarify the scope of proteomics studies as related to the entire set of proteins expressed in a cell, making it irrelevant to the specific claim.


Input: Task: corroborate the claim using the given text. Claim: The suprachiasmatic nucleus (SCN) in the brain is the master clock regulating circadian rhythms. [SEP] Text: The master clock, as it is often called, is reset by light or photic stimuli [3] as well as by arousal-inducing or non-photic stimuli [4]. Whether the input is photic or non-photic, it reaches the clock through neurotransmitters in nerve terminals. Neurotransmitters are released at the inputs for entrainment, in the clock itself for integration and consolidated output, and in efferent projections for the control of overt rhythms. Several reviews on the neurotransmitters of the SCN have been previously published [5 - 10]. The present review concentrates on studies conducted in the last decade and gives particular attention to neurotransmitters whose involvement in the circadian clock have not been traditionally recognized. About neurotransmitters in general Studies have indicated the presence of a large number of neurotransmitters in the SCN [11 - 15]. However, information about their role individually as well as in combination in the functioning of the clock has been slow to come. It is observed that the presence of neurotransmitters in the afferent and efferent projections of the SCN is equally important for the entrainment of the clock and for the control of overt rhythms. Thus, we have neurotransmitters released at the inputs for entrainment, in the clock itself for the integration and consolidated output, and in the efferent projections for the control of overt rhythms. There have been attempts to categorize the putative neurotransmitters of the SCN on the basis of their origin and function [16] and there have been reports indicating subdivisions of the SCN with relation to neurotransmitter function [17]. Further, it has been reported [18] that the human SCN also have well defined subdivisions with chemically defined neuronal groups comparable to the well defined subdivisions reported in the case of experimental animals, mainly rodents. There are many excellent reviews [19 - 22] highlighting various aspects of the neurotransmitters. From a functional point of view, two important aspects emerge. One is the fact that one particular neurotransmitter may have more than one function and thereby make the prediction of the function more difficult and complex. Another aspect is that the neurotransmitter input from various pathways and their influence may vary (1) by itself and (2) by way of modification of SCN function. [SEP] Justify:

Output: The text corroborates the claim by discussing the functions of the suprachiasmatic nucleus (SCN) as the master clock, specifically mentioning how it acts through neurotransmitters to regulate circadian rhythms. The phrases 'the master clock' and 'entrainment of the clock' support the idea that the SCN is central to circadian regulation, reinforcing the claim that it is indeed the master clock.


Input: Task: pass the claim using the given text. Claim: Octopuses and snails are biologically identical, differing only in size. [SEP] Text: find support for two ways that cells segregate mitochondria as they multiply, and show that the decrease in the number of mitochondrial DNA molecules during bottlenecking is flexible. This reconciles a debate amongst previous studies. These findings are confirmed using new experimental data from mice, which are genetically distinct from existing studies, illustrating the generality of the model's findings. Furthermore, an analytic mathematical description that describes in detail how bottlenecking might work is produced. Finally, Johnston et al. provide examples using this new theoretical model to suggest therapeutic strategies for diseases caused by mitochondrial DNA mutations. Future work will need to test these suggestions, and link mathematical understanding of mitochondria with healthcare data. are vital energy-producing organelles within eukaryotic cells, possessing genomes (mitochondrial DNA, mtDNA) that replicate, degrade and develop mutations (Rand, 2001; Wallace and Chalkia, 2013). MtDNA mutations have been implicated in numerous pathologies including fatal inherited diseases and ageing (Lightowlers et al. , 1997; Wallace, 1999; Poulton et al. , 2009; Wallace and Chalkia, 2013). Combatting the buildup of mtDNA mutations is of paramount importance in ensuring an organism's survival. Substantial recent medical, experimental, and media attention has focused on methods to remove (Bacman et al. , 2013) or prevent the inheritance of (Bredenoord et al. , 2008; Poulton et al. , 2009; Craven et al. , 2010; Poulton et al. , 2010; Burgstaller et al. , 2015) mutated mtDNA in humans. One means by which organisms may ameliorate the mtDNA damage that builds up through a lifetime is through a developmental process known as bottlenecking. Immediately after fertilisation, a single oocyte (which may contain >105 individual mtDNAs) may have a nonzero mtDNA mutant load or heteroplasmy (the proportion of mutant mtDNA in the cell). As the number of cells in the developing organism increases, the intercellular population then acquires an associated heteroplasmy variance, that is, the variance in mutant load across the population of cells (Figure 1A), allowing removal of cells with high heteroplasmy and retention of cells with low heteroplasmy. Intense and sustained debate exists as to the mechanism by which this increase of heteroplasmy variance occurs. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses mitochondrial DNA, bottlenecking in cell division, and related medical implications without mentioning octopuses, snails, or any comparison between their biological identities. Thus, it does not provide any supporting or contrasting information regarding the claim.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Derivation of the. A disease activity index for lupus patients. Arthritis & Rheumatism 35(6):630-640 Bots SH, Van der de. 2016. The influence of baseline risk on the relation between HbA1c and risk for new cardiovascular events and mortality in patients with type 2 diabetes and symptomatic cardiovascular disease. 15(1):101. 2012. Association of noninvasively measured renal protein biomarkers with histologic features of lupus nephritis. Arthritis & Rheumatism 64(8):2687-2697 Burger D, Dayer JM. 2002. High-density lipoprotein-associated apolipoprotein A-I: the missing link between infection and chronic inflammation. 1(1–2):111-117 Crispín JC, Liossis S-NC, Kis--T, Tsokos GC. 2010. Pathogenesis of human systemic lupus erythematosus: recent advances. Trends in 16(2):47-57 MGM, de Sain-van. 1998. Plasma α2 macroglobulin is increased in nephrotic patients as a result of increased synthesis alone. 54(2):530-535 Galicia G, Ceuppens JL. 2011. Haptoglobin function and regulation in autoimmune diseases. In: Francisco Veas, ed. Proteins—Regulation and Functions of Proteins, Prof. London: InTech. . 2006. Human body fluid proteome analysis. Proteomics 6(23):6326-6353. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. 4(1):44-57. 2005. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Molecular & 4(9):1265-1272. 2015. Biomarkers identified from serum proteomic analysis for the differential diagnosis of systemic lupus erythematosus. Lupus 24(6):582-587. 2012. Contribution of mass spectrometry-based proteomics to defining cellular mechanisms and diagnostic markers for systemic lupus erythematosus. & Therapy 14:204-214. 2014. Systemic lupus erythematosus. [SEP] Justify:

Output: The text does not directly address or discuss the claim regarding proteomics and its focus on the entire set of proteins expressed in a cell. Instead, it provides references to various studies and topics related to lupus and other diseases, none of which specifically clarify or confirm the nature of proteomics as defined in the claim.


Input: Task: corroborate the claim using the given text. Claim: The suprachiasmatic nucleus (SCN) in the brain is the master clock regulating circadian rhythms. [SEP] Text: Neurotransmitters like acetylcholine, glutamate, neuropeptide Y (NPY), serotonin, vasoactive intestinal peptide (VIP), peptide histidine isoleucine (PHI), and arginine vasopressin (AVP) have been implicated in the functioning of the SCN. Glutamate and pituitary adenylate cyclase-activating polypeptide (PACAP) are indicated as principal neurotransmitters of the retinohypothalamic tract (RHT), although excitatory amino acids like L-aspartate and N-acetyl-aspartylglutamate may also function as neurotransmitters in RHT. also might be a candidate as a neurotransmitter in RHT. Functional studies over the years have given evidence that PACAP alone or in concert with glutamate may be responsible for the light signalling to the clock. The role of AVP in circadian time keeping has been well established. Its role in the control of circadian rhythm of food and water intake has been reported and well documented. Another intrinsic neuropeptide, VIP, acting through VPAC2 receptor (a type of receptor for VIP), participates in both resetting to light and maintenance of ongoing rhythmicity of the SCN. NPY and GABA seem to be the neurotransmitters in the projection from the intergeniculate leaflet to the SCN. Raphe nuclei projections to the SCN contain serotonin. AVP and prokineticin 2 are seen in the outputs from the SCN. The neurotransmitter-dependent molecular basis of the working of the clock is yet to be understood completely. The specific roles of the various neurotransmitters may be based on the response of the neurons of the SCN on application of a neurotransmitter, capacity to phase shift a particular rhythm on application of neurotransmitter, effect of lesions on the entrained and free running rhythms, and disruptions seen in the rhythms after blockade by the antagonist/inhibitors. Possible targets for some of the neurotransmitters are the clock genes per1 and per2, which are induced in the SCN by light or by neurotransmitters, at night. Evidence indicating co-localization of some of the neurotransmitters in the SCN has further complicated the investigations into the role of neurotransmitters in the working of the clock. [SEP] Justify:

Output: The text corroborates the claim by detailing the role of neurotransmitters in the functioning of the suprachiasmatic nucleus (SCN), which is suggested as essential in regulating circadian rhythms. It emphasizes that various neurotransmitters (like AVP and VIP) are implicated in maintaining and resetting the rhythmicity of the SCN, thereby supporting the role of the SCN as the master clock of circadian rhythms.


Input: Task: pass the claim using the given text. Claim: Octopuses and snails are biologically identical, differing only in size. [SEP] Text: Several experimental results in mice suggest that, during development, the copy number of mtDNA per cell in the germ cell line drops dramatically to ∼102, reducing the effective population size of mitochondrial genomes (Cree et al. , 2008; Wai et al. , 2008). One postulated bottlenecking mechanism is that this low population size accelerates genetic drift and so increases the cell-to-cell heteroplasmy variance (Bergstrom and Pritchard, 1998; Aiken et al. , 2008; Cree et al. , 2008; Wonnapinij et al. , 2010), which was first observed to generally increase from primordial germ cells through primary oocytes to mature oocytes (Jenuth et al. , 1996). However, independent experimental evidence (Wai et al. , 2008) suggests that heteroplasmy variance increases negligibly during this copy number reduction, though this interpretation has been debated (Samuels et al. , 2010). Wai et al. (2008) shows heteroplasmy variance rising during folliculogenesis, after the mtDNA copy number minimum has been passed. In yet another picture, supported by conflicting experimental results (Cao et al. , 2007, 2009), heteroplasmy variance increases with a less pronounced decrease in mtDNA copy number (a minimum copy number >103 in mice), solely through random effects associated with partitioning at cell divisions. Clearly a consensus on this important mechanism is yet to be reached. Figure 1 Download asset Open asset The mitochondrial bottleneck, and elements of a general model for bottlenecking mechanisms. (A) The mitochondrial DNA (mtDNA) bottleneck acts to produce a population of oocytes with varying heteroplasmies from a single initial oocyte with a specific heteroplasmy value. During development, mtDNA copy number per cell decreases (by a debated amount, which we address; see Main text) then recovers, suggesting a ‘bottleneck’ of cellular mtDNA populations. (B) Cellular mtDNA populations during the bottleneck are modelled as containing wildtype and mutant mtDNAs. MtDNAs can replicate and degrade within a cell cycle, with rates λ and ν respectively. (C) At cell divisions, the mtDNA population is partitioned between two daughter cells either deterministically, binomially, or through the binomial partitioning of mtDNA clusters. [SEP] Justify:

Output: The text is irrelevant to the claim about octopuses and snails being biologically identical, as it discusses findings related to mitochondrial DNA (mtDNA) bottleneck mechanisms in mice and does not mention octopuses or snails at all. Thus, it does not corroborate or contrast with the claim.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Lancet 384(9957):1878-1888. 2010. Urinary monocyte chemoattractant protein-1 correlates with disease activity in lupus nephritis. 25(11):2283-2288. 2015. Role of hemoglobin/heme scavenger protein hemopexin in atherosclerosis and inflammatory diseases. in Lipidology 26(5):384-387. 1999. Systemic lupus erythematosus, a disease associated with low levels of clusterin/apoJ, an anti-inflammatory protein. Journal of Rheumatology 26:597-603 Pavón EJ, Muñoz án -Rubio J-L, Sola R, Navarro-Pelayo F, Raya-Alvarez E, Ortego-. 2006. Proteomic analysis of plasma from patients with systemic lupus erythematosus: Increased presence of haptoglobin α2 polypeptide chains over the α1 isoforms. Proteomics 6(S1):S282-S292 Pisetsky DS. 1997. Systemic lupus erythematosus. A. Epidemiology, pathology and pathogenesis. In: Klippel JH, ed. Primer on the (11th edition). Georgia: Arthritis Foundation. 246-251. 2012. A comparative proteomic study of sera in paediatric systemic lupus erythematosus patients and in healthy controls usin and LC MS Apolot study. 10:24. 2006. Exploring human plasma proteome strategies: High efficiency in-solution digestion protocol for multi-dimensional protein identification technology. Journal of 1111(2):175-191. 2007. Lipocalin-2, TWEAK, and other cytokines as urinary biomarkers for lupus nephritis. Annals of the Academy of Sciences 1109(1):265-274 Simon JD. 2013. Inflammation and acute phase proteins in hemostasis. In: Janciauskiene S, ed. Proteins. London: InTech. [SEP] Justify:

Output: The text is primarily a list of references and articles related to various studies on diseases such as systemic lupus erythematosus, mentioning specific proteins and their associations with conditions. While it references research involving proteomics, it does not directly affirm or explain the claim that proteomics studies the entire set of proteins expressed in a cell; thus, it is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: The suprachiasmatic nucleus (SCN) in the brain is the master clock regulating circadian rhythms. [SEP] Text: It is likely that the functioning of the clock may depend on the presence of a particular neurotransmitter on a mechanism in which co-localized neurotransmitters interact in a functionally significant manner. With more information available on the role of neurotransmitters in the working of the clock, which is involved in so many functions of the body, better opportunity for neurotransmitter-based manipulation of the clock has also been reported. Problems of shift-work insomnia and ill effects of jet lag are among the clock-related functions for which much attention has been given in recent years. Melatonin has been in use with some success in reducing the above effects. However, search for other chronobiotic agents is continuing and it is likely that there may be some new dimensions given to the problem and its solution in future. A report of a close relationship between circadian clock and cell proliferation makes things even more interesting. Investigations into the role of neurotransmitters in the SCN as well as in the afferent and efferent inputs have come a long way with the advent of newer techniques of positron emission transaxial tomography (PET) scan and polymerase chain reaction (PCR). In both plants and animals, circannual rhythms are widely distributed. Endogenous circannual rhythms form the basis for many seasonal rhythms. A number of neuroendocrine mechanisms have been implicated in the regulation of seasonal changes in the physiology and behaviour of animals. Some of these neuroendocrine pathways are necessary for the regulation of particular overt seasonal responses, though they may not be directly linked to the circadian time-keeping system. Photoperiodic input and circannual function may have profound influence on many of the functions of body. Naturally, neurotransmitters are involved not only in circadian function but also in seasonal processes. It has been postulated that heterogeneity of the clocks which are seen within the SCN may be one of the factors that form the basis of seasonal adaptations [23]. A typical example of the close linkage between seasonal rhythms and affective disorders can be seen in a seasonal form of mood disorder, seasonal affective disorder (SAD). Treatment for SAD based on circadian principles includes not only light therapy but also the use of certain drugs, again based on circadian principles involving neurotransmitters. The SCN has been subdivided into a dorsomedial shell and a ventrolateral core. [SEP] Justify:

Output: The text corroborates the claim by discussing the role of the suprachiasmatic nucleus (SCN) in various circadian and circannual functions, indicating that the SCN is involved in the regulation of the body's clock mechanisms. Additionally, it highlights the relationship between neurotransmitters and the functioning of the clock, comprehensively illustrating how the SCN plays a critical role in regulating circadian rhythms and other related functions.


Input: Task: pass the claim using the given text. Claim: Octopuses and snails are biologically identical, differing only in size. [SEP] Text: In our case, this goodness-of-fit is computed using a comparison of squared residuals associated with the trajectories of mean mtDNA copy number and normalised heteroplasmy variance (see ‘Materials and methods’ and 0. 006; optimal fits to data generally show 0. 005 < α < 0. 01), and the proportions of loci visible in Wai et al. (2008) are substantially higher than this required 1% value. We show in 40. * denotes measurements in mature oocytes, modelled as 100 dpc (see ‘Materials and methods’). Note: the range in (B) does not correspond to a credibility interval on individual measurements, but rather on an expected underlying (population) variance, from which individual variance measurements are sampled. We thus expect to see, for example, several measurements lower than this range due to sampling limitations (see text). (C) Posterior distributions on mtDNA turnover ν with time. (D) Posterior distribution on min E(m), the minimum mtDNA copy number reached during development. (E) Posterior distribution on σ=∑i=36τ′iνi, a measure of the total amount of mtDNA turnover. Figure 3D shows posterior distributions on the copy number minimum and total turnover (see ‘Materials and methods’) resulting from this process; posteriors on all other parameters are shown in 1. Substantial flexibility exists in the magnitude of the copy number minimum, illustrating that observed heteroplasmy variance can result from a range of bottleneck sizes from ∼200 to >103; going some way towards reconciling the conflict between Cao et al. (2007) and Cao et al. (2009) and Cree et al. (2008) and Wai et al. (2008). The total amount of mtDNA turnover (presented as σ=∑i=36νiτ′i, the product of turnover rate and the time for which this rate applies, summed over quiescent dynamic phases; for example, a turnover rate of 0. 1 hr−1 for 30 days yields σ = 0. 1 × 24 × 30 = 72) is constrained more than the specific trajectory of mtDNA turnover rates, showing that a variety of time behaviours of turnover are capable of producing the observed heteroplasmy behaviour. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses mitochondrial DNA turnover and associated calculations without any mention of octopuses, snails, or biological identities. There are no comparisons or contrasts made regarding their biological characteristics.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Javascript is disabled in your browser. Please enable Javascript to view PeerJ. Serum proteins differentially expressed in early- and late-onset preeclampsia assessed using iTRAQ proteomics and bioinformatics analyses All reviews of published 2023. Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the 2020. The first revision was submitted on March 17th, 2020 and was reviewed by 2 reviewers and the Academic Editor. A further revision was submitted on May 14th, 2020 and was reviewed by the Academic Editor. The 2020. Version 0. 3 (accepted) · Jul 28, 2020 · would like to start this letter with an apology for the delay in my decision. I'm sure you understand that everybody's lives have been disrupted by the pandemic, which has both taken us away from our offices and changed the timing and length of our (remote) meetings. I really wanted to read the manuscript very carefully and assess whether you had revised the manuscript in line with the reviewer's comments. After a careful reading I have reached the conclusion that you have done so; therefore, I feel this version is now acceptable. Please accept my apologies. I hope that things are going well for you during these trying times. [# PeerJ - this decision was reviewed and approved by Paula Soares, a PeerJ covering this Section #] 0. 3 (PDF) Download author's response letter - submitted May 14, 2020 Version 0. 2 Walter de Azevedo Jr. · Apr 8, 2020 · Two reviewers evaluated the revised version of this manuscript. Both reviewers asked for additional corrections. In my view, this manuscript needs a minor revision. [# PeerJ Staff Note: The review process has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at editorial. support@peerj. com for pricing (be sure to provide your manuscript number and title) #] Reviewer 1 · Mar 24, 2020 Basic reporting See attachment Experimental design See attachment Validity of the findings See attachment Additional comments See attachment Annotated reviews are not available for download in order to protect the identity of reviewers who chose to remain anonymous. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses issues related to the peer review process, reviewer comments, and publication details, without providing any information about proteomics or protein studies.


Input: Task: corroborate the claim using the given text. Claim: The suprachiasmatic nucleus (SCN) in the brain is the master clock regulating circadian rhythms. [SEP] Text: This is based on retinal innervation patterns as well as the observation that these regions are defined by phenotypically distinct cell types [24]. Each nucleus contains about 10,000 neurons, thereby making 20,000 neurons in total. These neurons are characterized by small size and high density [25]. Isolated individual neurons are reported to produce circadian oscillations with periods ranging from 20–28 h [26,27]. Circadian oscillations are generated in the individual neurons of the SCN by a molecular regulatory network. Though individual cells oscillate with periods ranging from 20–28 h, at the tissue level SCN neurons display synchrony indicative of a robust inter-cellular coupling, and neurotransmitters appear to have an important role in the inter-cellular coupling. Gondze and co-workers [28] have introduced a molecular model for the regulatory network underlying the circadian oscillators in the SCN and stated that effective synchronization is achieved when the average neurotransmitter concentration damps the individual oscillators. Cells are effectively synchronized due to global neurotransmitter oscillation. Neither spiking in the neurons of the SCN nor chemically mediated transmission is needed for the pacemaking activity seen in individual cells. However, synchronization of circadian rhythmicity across neurons in the SCN does require neurotransmitters [25,29] and development of action potentials [30]. Before attempting a discussion of the neurotransmitters, it is necessary to identify the afferent projections to the SCN, and neurotransmitters present in it, neurotransmitters intrinsic to the SCN, and efferent projection with its neurotransmitters. The SCN is composed of different neuronal elements, each having its own specific function. Intensive interconnection and interaction among the heterogeneous neuronal elements is responsible for the functional output of the SCN. Different neurons of the SCN contain different neuropeptides, with several neurons having co-localization of neurotransmitters. Thus, we have, for example, gamma amino butyric acid (GABA) and glutamate, GABA and and corticotrophin releasing hormone (CRH), AVP and its carrier protein neurophysin, VIP and peptide histidine isoleucine (PHI), and VIP and somatostatin (SS). Co-localization of different neuropeptides is seen not only in rat SCN but also in human SCN [31 - 33]. [SEP] Justify:

Output: The text corroborates the claim by detailing the SCN's role in generating circadian oscillations and how individual neurons within the SCN display synchrony that indicates their involvement in regulating circadian rhythms. It explains that a molecular regulatory network within the SCN is responsible for these oscillations and emphasizes the importance of neurotransmitters in achieving synchronization among the SCN neurons, ultimately supporting the idea that the SCN functions as the master clock.


Input: Task: pass the claim using the given text. Claim: Octopuses and snails are biologically identical, differing only in size. [SEP] Text: Following this recursion for n phases of bottlenecking and simplifying the resultant multi-layer fraction gives rise to the solution (54) goverall=h0=A′z+B′C′z+D′, where (55) [A′B′C′D′]=∏i=1n[AiBiCiDi], from which Goverall=goverallm0 follows straightforwardly. The following results will be of assistance: (56) E(m)=ddz(A′z+B′C′z+D′)m0|z=1=m0(A′D′−B′C′)(A′+B′C′+D′)m0−1(C′+D′)2, (57) d2dz2(A′z+B′C′z+D′)m0|z=1=m0(B′C′−A′D′)(A′+B′C′+D′)m0(B′C′(m0+1)+A′(2C′+D′(1−m0)))(A′+B′)2(C′+D′)2, (58) =−(A′+B′C′+D′)(A′+B′)2(B′C′(m0+1)+A′(2C′+D′(1−m0)))E(m). [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses a mathematical solution involving recursion and does not mention any biological aspects of octopuses or snails. There is no information supporting or contrasting the claim regarding their biological identity.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Cite this review as (2020) #1 of "Serum proteins differentially expressed in early- and late-onset preeclampsia assessed using iTRAQ proteomics and bioinformatics analyses (v0. 2)". PeerJ Reviewer 2 · Apr 1, 2020 Basic reporting Please see my first report Experimental design Please see my first report Validity of the findings Please see my first report Additional comments The authors have made an effort to introduce the changes and modifications suggested in the previous version. As a consequence, I understand that the overall quality of the manuscript has improved substantially and that now it can be considered acceptable for publication. I would just like to suggest a few minor changes to the text that are detailed below. Line 33: What is exactly the meaning of the expression “an absolute log10 fold change (i. e. , >1. 2 difference)”? It seems confusing to me. Could it be expressed more clearly? Line 48: instead of “The downregulated” Line 83: What does it mean R 2007? Line 127: The expression “All the remaining samples were used” is unclear Line 128: Use "After labeling with iTRAQ" instead of "After labeling". In addition it should be specified the iTRAQ version (4plex? 8plex? ) across the manuscript. Line 134-135: methyl cyanide is correct but very few people use it. It is much popular to use acetonitrile. Line 155: please specify the reference of the kit used Line 156: use "manufacturer instructions" instead of "kit instructions" Line 197: It is more appropriate to use "interact" instead of writing "coordinate with one another" Line 231: the expression "we used ELISA to identify again" is grammatically wrong, but it is also meaningless. Please correct. Line 255: Use "previous evidence" instead of "much evidence" Line 278: Factor VII instead of factor VI? Line 284:" consumes" is inappropriate in this context, please use a more adequate expression. [SEP] Justify:

Output: The text does not address the claim regarding proteomics specifically studying the entire set of proteins expressed in a cell. Instead, it provides a series of comments and suggestions on a manuscript related to serum proteins and the iTRAQ proteomics technique, but does not clarify or support the claim itself.


Input: Task: corroborate the claim using the given text. Claim: The suprachiasmatic nucleus (SCN) in the brain is the master clock regulating circadian rhythms. [SEP] Text: The combination of a variety of peptides with or without amino acid neurotransmitters within a single nucleus gives the SCN a variety of signalling properties as well. A set of SCN neurons and their neurotransmitters has the function of conveying the daily light-dark signal to hypothalamic target structures [34 - 36]. Three major incoming pathways have been identified for the SCN. These have been defined as the retinohypothalamic tract (RHT), geniculohypothalamic tract (GHT), and the projection from the raphe nuclei (Figure 1). Photic information is relayed directly from the retina to the SCN by way of the monosynaptic retinohypothalamic tract [37,38]. It is seen that transection of all visual pathways leaving the optic chiasm makes animals blind with no visual reflexes but with perfect normal entrainment of circadian rhythms. This has indicated that RHT is sufficient for entrainment. Also it has been demonstrated that sectioning of RHT abolishes entrainment without affecting visual functions [39]. Although the exact mechanism by which a monophasic stimulus, light, produces either no response or a biphasic response in SCN neurons is unclear at present, Myers and co-workers [40] provided a potential molecular explanation for the phenomenon. Using electron microscopy and immunohistochemistry, they identified the excitatory amino acid glutamate and pituitary adenylate cyclase-activating polypeptide (PACAP) as the main neurotransmitters of the RHT [41 - 43]. Although substance P (SP) was thought of as a neurotransmitter of the RHT, there is now substantial evidence against this possibility [44 - 46]. Figure 1 Afferent inputs and efferent pathways of the SCN. RHT: Retinohypothalamic tract, GHT: Geniculohypothalamic tract, OC: Optic chiasm, 3V: Third ventricle, IGL: Intergeniculate leaflet, DM: : : : Gamma amino butyric acid, PACAP: Pituitary adenylate cyclase-activating polypeptide. Retinohypothalamic tract (RHT) and its neurotransmitters The principal neurotransmitters involved in conveying photic information to the SCN have been identified as glutamate and PACAP. [SEP] Justify:

Output: The text corroborates the claim by discussing various aspects of the suprachiasmatic nucleus (SCN) and its role in conveying daily light-dark signals, which are crucial for circadian rhythm regulation. It explains that the retinohypothalamic tract (RHT) transmits photic information directly to the SCN, supporting the notion that the SCN serves as a master clock in this context.


Input: Task: contrast the claim using the given text. Claim: Octopuses and snails are biologically identical, differing only in size. [SEP] Text: The findings will add another piece to the puzzle of how the brain and nervous has evolved to control the behaviour of these remarkably sophisticated animals. Russell WyethAssociate ProfessorSt. UniversityWillem has conceived an exciting project on the edges of what we know about octopus sensory experience - despite the interest in how octopuses perceive the world, little work has ever been done on how their behavior is tied to the chemical sensory ability. Willem is getting excellent behavioral data and needs the ability to visualize the plumes in the water that the octopuses is tracking. Funds for the laser will allow him to fill in that side of the experimental design, and complete a fascinating study. David ScheelProfessor of think the information discovered from this project will add a very interesting 2017. His primary advisor is Dr. at University who has been studying octopus ecology for more than two decades. For his Willem is investigating octopus odor tracking at the Laboratories. Venkatesh GopalDr. Gopal has extensive experience—including postdoctoral research at of Technology (MIT) and Northwestern University—in classical and quantum optics, quantum information processing, and neuroscience. His current research interests lie in understanding how biological systems process sensory information, with an emphasis on how possibly “optimal” movement strategies emerge to gather information efficiently. Lab Notes6 PostedIn case anyone needed some cool octopus photosApril 17, 202144326Hey everyone! I hope you all are having a fantastic. . . December 30, 202044319New favorite clip! An octopus appears to be tricked by. . . December 18, 202087320The octopus Slaanesh foraging in the dark finds a piece of shrimp from one of three possible locations on the first try. In the flume tank water moves from right to left, the space is in a black out tent and illuminated by near-infrared lamps invisible to the eye but not cameras. Example of what can be tracked by a custom trained markerless pose estimator DeepLabCut model. In the top left you can see the convex hull of the points predicted by the model. Top middle is the convex hull rotated into the reference frame of the octopus. Top right shows a plot of the center of mass velocity on top and the area of the convex hull of the four quadrats around the octopus, forward left, forward right, back left, back right. [SEP] Justify:

Output: The text contrasts the claim by discussing the complexity of octopuses as sophisticated animals with intricate behaviors and sensory experiences, indicating that they possess unique biological traits. It emphasizes ongoing research into octopus behavior, sensory processing, and ecological studies, suggesting significant biological differences from snails, which are not mentioned in the text. This implies that octopuses are not identical to snails in terms of biological structure or function.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Line 291: Use "support" instead of "add to" Line 339: please use "previous studies have shown that" instead of "a study shows that" Line 340: please use "which is involved" instead of "which involved" line 342: please use "were similar" instead of "was similar" Cite this review as (2020) #2 of "Serum proteins differentially expressed in early- and late-onset preeclampsia assessed using iTRAQ proteomics and bioinformatics analyses (v0. 2)". PeerJ 0. 2 (PDF) Download author's response letter - submitted Mar 17, 2020 Version 0. 1 (original submission) Walter de Azevedo Jr. · Jan 13, 2020 · Three specialists in the field evaluated your manuscripts. Two of them recommend major revisions. I agree with them - please respond to all the comments. [# PeerJ Staff Note: Please ensure that all review comments are addressed in an appropriate rebuttal letter, and please ensure that any edits or clarifications mentioned in the rebuttal letter are also inserted into the revised manuscript (where appropriate). Direction on how to prepare a rebuttal letter can be found at: #] Reviewer 1 · Dec 10, 2019 Basic reporting No comment. Experimental design The use of small sample (4 per sub-group) size should be justified. Validity of the findings 1. Were the top three differentially expressed proteins equal in all the samples of the sub-groups? 2. LRP1, APOC1, and APOL3 were linked to which gestational sub-group? 3. Whether the differentially expressed proteins are placenta-specific needs be clarified. If not, how do you justify them as a biomarker? 4. Power analysis should be carried out to determine the acceptability of the findings. Cite this review as (2020) #1 of "Serum proteins differentially expressed in early- and late-onset preeclampsia assessed using iTRAQ proteomics and bioinformatics analyses (v0. 1)". PeerJ Reviewer 2 · Dec 16, 2019 Basic reporting In this manuscript, the authors analyze a set of serum samples obtained either from control individuals or patients diagnosed with early and late preeclampsia. [SEP] Justify:

Output: The text does not address the claim regarding proteomics or its study of proteins. Instead, it focuses on manuscript review comments, revisions needed for publication, and specific queries related to a research study, without providing any information about what proteomics entails or its scope.