Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Evidence indicates that 11 related pathways, including arginine biosynthesis, extracellular-receptor interactions, and lysosome-related processes, are related to diabetic complications. Sumarriva et al. 33 analysed the plasma of patients with and without diabetic retinopathy using mass spectrometry. Arginine-related pathways were found to be dysregulated in patients with diabetic retinopathy. Furthermore, Peters et al. 34 demonstrated that arginine is the substrate of nitric oxide synthase and arginase. Increased arginase activity increases nitric oxide synthase pathway uncoupling, and ROS formation has been observed in diabetic rats. 34 In our study, KEGG enrichment analysis revealed between-group differences in arginine biosynthesis and metabolism, suggesting that the imbalance of arginine-related pathways may play a role in the pathogenesis of DK. Lysosomes perform biological functions such as membrane repair, secretion, energy metabolism, and signal transduction. 35 Zheng et al. 36 reported that hyperglycaemia and oxidative stress in patients with diabetes activated autophagy turnover of damaged cell components, thus maintaining cell homeostasis. However, in the long term, it increases the burden on the lysosomal system, leading to a decline in cell resistance to additional stress and eventually results in cell damage. 36 The ECM-receptor interaction is a microenvironmental pathway that maintains the structure and function of cells and tissues. 37 The ECM comprises a complex mixture of structural and functional macromolecules, including collagen, fibronectin, and laminin. 38 Matsumura et al. ,39 Priyadarsini et al. ,40 and Pouw41 et al. found that changes in the ECM caused diabetes-related corneal epithelial adhesion and abnormal wound healing. Therefore, DK may involve multiple signalling pathways. Among the top 50 interaction network maps screened in this study, we focused on VDAC3, a subtype of the VDAC on the outer membrane of mammalian mitochondria. 42,43 VDAC1 and VDAC2 have been previously described. 42 VDAC3 has been associated with ROS abundance in the oxidative environment and between mitochondrial membranes. 44,45 It is the preferred target of mitochondrial ROS generated by complex III; furthermore, a small amount of ROS can be oxidised in the mitochondrial double membrane space. [SEP] Justify:

Output: The text does not directly address or relate to the claim about proteomics. Instead, it discusses various biological pathways and mechanisms related to diabetic complications and cell biology without mentioning the study of proteins as a whole.


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 behavioral phenotype of Syt10Cre/Cre Bmal1fl/- mice was indistinguishable from the phenotype of Bmal1-/- mice, confirming the efficiency of SCN disruption. Furthermore the behavioral phenotype of Syt10Cre Bmal1fl mice was inversely correlated with the number of BMAL1 positive cells in the SCN. The Syt10Cre line will be a helpful tool to investigate the complexity of the mammalian circadian network. In the second part of this thesis Syt10Cre/Cre Bmal1fl/- mice are used to investigate the hierarchical structure of the mammalian circadian timing system. A major difference to the above-mentioned SCN ablation studies is that Syt10Cre/Cre Bmal1fl/- mice still show rhythmic wheel running behavior in LD conditions. We showed that this behavioral synchronization to the LD cycle is directly light- and not clock-driven. The disruption of the SCN clock on the molecular level was confirmed by in situ hybridization. Despite the absence of a functional SCN clock, corticosterone is rhythmic in Syt10Cre/Cre Bmal1fl/- mice in LD. However the amplitude of this rhythm is markedly reduced, indicating that although the SCN clock is dispensable for rhythmic release of corticosterone in LD, the amplitude of this rhythm is regulated by the SCN clock. Upon placing the mutant animals into DD, corticosterone rhythms dampen, indicating that in DD the SCN clock is essential for maintenance of corticosterone rhythmicity. Furthermore we analyze clock gene expression rhythms in peripheral tissues of Syt10Cre/Cre Bmal1fl/- mice in LD and DD. To our surprise, peripheral clocks continue to oscillate in Syt10Cre/Cre Bmal1fl/- mice in LD. This indicates that a functional clock in the SCN is not necessary for synchronized rhythmicity of peripheral clocks, but that light can directly synchronize peripheral clocks. Upon release into DD, however, clock gene rhythms in peripheral organs dampen. Thus in constant conditions the SCN clock is necessary to synchronize peripheral clocks. The third part of this thesis describes the first attempts towards the development of a combinatorial Cre system, which will allow very specific targeting of brain nuclei. The idea is based on complementation of two parts of the Cre enzyme, which individually are not active. If co-expressed in one cell, however, functional Cre is reconstituted. [SEP] Justify:

Output: The text corroborates the claim by detailing the role of the SCN in regulating circadian rhythms, particularly emphasizing that despite the absence of a functional SCN clock, the amplitude of corticosterone rhythms is affected by it, indicating its regulatory role. The mention of experiments involving Syt10Cre/Cre Bmal1fl/- mice supports the idea that the SCN is critical for maintaining proper circadian timing, especially when placed in constant conditions (DD), further underscoring the SCN's significance as the master clock.


Input: Task: contrast the claim using the given text. Claim: Only trees growing in tropical regions can be used for dendrochronological studies. [SEP] Text: This species is one of the few deciduous oak species thriving in the Mediterranean xerothermic conditions [8], [9], which makes it an interesting option for reforestation in Greece and other Mediterranean countries. Indeed, the anticipated climate change effects on the growth, productivity and present distribution of the Mediterranean vegetation [10], [11], renders necessary the quest of species that would easily adapt to the new conditions and the investigation of their behaviour. Based on a study about the impact of climate change in Greece [12], the expected temperature increase and precipitation decrease will result in the expansion of heat tolerant forest plant species by 2-4% and desertification by 1-2%, depending on the climate change scenario. Valonia oak with its ability to grow in xerothermic environments, even within phrygana [5], could be one of the recommended species for the future, being less flammable than xerothermic conifers and easily regenerating after a forest fire [4]. In this context, the exploration of valonia oak tree-ring width variability and its climate-growth relationships that can be examined through dendrochronological studies is essential for predicting its future growth trend. The long time series of tree-ring width measurements can substantially contribute to this study. Radial growth combines the effects of climate, site-specific factors, and natural and human disturbances [13], [14], [15]. There are many large deciduous oak trees throughout Greece and some are particularly close to historical sites. However, only few of the Greek deciduous oaks species have been used to construct tree-ring chronologies from samplings carried out on living trees [16] and mostly from wood of historical monuments [17], [18]. Concerning valonia oak, there have been few dendrochronological studies in Greece and the Mediterranean region [19], [20]. The objectives of this study were the construction of a local tree-ring width chronology of this species in and the investigation of tree-rings to climate relationships. trees were growing in Xeromero, a typical valonia oak forest of the Aetoloakarnania prefecture, (Figure 1). It is an old forest with rich fauna and flora [21] and old-age stands that have not been harvested for centuries. It is the largest forest of valonia oak in the Balkans and probably one of the largest within its distribution area in the Mediterranean basin. [SEP] Justify:

Output: The text contrasts the claim by providing evidence that deciduous oak species, such as the valonia oak, thrive in Mediterranean conditions and are subject to dendrochronological studies. It discusses various aspects of valonia oak growth, its adaptability to climate changes, and the exploration of its tree-ring width variability, indicating that non-tropical species can also be used for dendrochronological research.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: 44 The protruding cysteine on VDAC3 leads to conformational changes and ubiquitination of VDAC3. In the presence of increased ROS levels, damaged single VDAC3 or VDAC3-containing membrane plaques can bind to mitochondrial vesicles and target lysosomes. 44 When the ROS level reaches the maximum oxidation threshold, VDAC3 in the mitochondria is irreversibly oxidised and modified, eventually causing mitophagy and sending a single mitochondrial ROS load signal to other parts of the cell. 45 Therefore, VDAC3 is considered an oxidised sensor for reducing homeostasis and ROS. 45 In our study, patients with DK had significantly higher VDAC3 levels in the tear fluid than patients without DK. Therefore, we conclude that tear VDAC3 can be used as a DK biomarker. These findings revealed between-group differences in tear protein expression profiles. However, this study had limitations. The study relied solely on GO and KEGG enrichment analyses, protein interaction networks, and other bioinformatics methods to infer the potential pathways and biomarkers associated with DK. Further research should combine the findings of bioinformatics analyses with western blotting, enzyme-linked immunosorbent assays, and other antibody-based methods to confirm differences in protein expression between patients with and without DK. Moreover, the sample size of this study was relatively small, and all patients were of Chinese descent. Therefore, further large-scale studies including other ethnicities are warranted. In conclusion, significant differences were observed in tear protein expression profiles between patients with and without DK, suggesting the potential involvement of various signalling pathways in DK, including arginine-related pathways, ECM-receptor interactions, and lysosome-related processes. Furthermore, VDAC3 may be a potential biomarker for DK. Animal or cell experiments are warranted to clarify the role of relevant molecules and pathways in DK. Overall, our findings contribute to clinical ophthalmic practice by furthering our understanding of DK. of interest: None. Ethics approval and consent to participate: This study was approved by the Committee of Zhujiang Hospital, University (2022-KY-219-01). All participants have read and understood the study's nature, purpose, risks, and procedures and signed an informed consent form. Consent for publication: Not applicable. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the role of VDAC3 in disease mechanisms, particularly in diabetic keratopathy (DK), without addressing the broader scope of proteomics and its focus on studying the entire set of proteins 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: Der erste Teil dieser Arbeit beschreibt die Herstellung und Validierung eines neuen transgenen Mausmodels, in dem die zentrale zirkadiane Uhr ausgeschaltet wurde. Es ist allgemein anerkannt, dass das zirkadiane System von Säugern hierarchisch organisiert ist, mit einem zentralen Schrittmacher im (SCN) des Hypothalamus und untergeordneten peripheren Uhren. beruht auf SCN-Läsionsstudien, die zeigen, dass in Abwesenheit des SCN alle peripheren Uhren arrhythmisch werden. von Läsionen ist, dass gleichermaßen afferente und efferente Verbindungen durchtrennt werden. In dieser Arbeit wurde daher ein genetisches Modell genutzt. Eine SCN-Cre-Treiberlinie (Syt10Cre) wurde hergestellt, in der gezeigt werden konnte, dass Cre im Großteil der SCN-Zellen aktiv ist, nicht aber in peripheren Geweben mit Ausnahme des Testis. Zur funktionellen Charakterisierung wurde mittels der Syt10Cre-Linie das essentielle Uhrengen Bmal1 deletiert (Bmal1fl/fl). Die Laufradaktivität von Syt10Cre Bmal1fl-Mäusen wurde unter Licht-Dunkel (LD) Bedingungen und in konstanter Dunkelheit (DD) untersucht. Es konnte ein Dosis-abhängiger Phänotyp gefunden werden: je weniger Zellen im SCN noch BMAL1-Protein exprimierten, desto weniger rhythmisch war die Laufradaktivität. [SEP] Justify:

Output: The text corroborates the claim by stating that the circadian system in mammals is hierarchically organized, with the central pacemaker located in the SCN. It goes on to highlight that studies involving SCN lesions demonstrate that without the SCN, all peripheral clocks become arrhythmic, effectively supporting the role of the SCN as the master clock in regulating circadian rhythms.


Input: Task: contrast the claim using the given text. Claim: Only trees growing in tropical regions can be used for dendrochronological studies. [SEP] Text: This forest had particular value in the past due to the superior quality of the acorns produced, compared to others from similar Greek forests in terms of tannin content and its grazing-pasture use and value [22]. Within this area, valonia oak usually forms stands of open canopy, growing on shallow calcareous soils at an altitude ranging from 0 to 580 m a. s. l. Based on the Station, located 20 kilometres from the sampling site, for the period of 1956-2012 (Meteorological Service), the mean annual precipitation in the region is 938. 5 mm and the mean annual temperature is 16. 8oC. The drought period, based on the ombrothermic diagram [23], lasts for 3. 5 months from late May to early September. 1. (a) Map of the Xeromero forest, (b) satellite image of sampling site (www. ktimatologio. gr) and (c) the ombrothermic diagram of the nearest meteorological station of Agrinio (24 m a. s. l. ) for the period from 1956 to 2012. Forty trees were sampled based on dendrochronological criteria [13], [15], from an area of approximately 5 ha representative of the valonia oak stands characteristics and with homogeneous topography (Figure 1). The sampling included cross sections that were taken at breast height (1. 3 m) from 20 trees during previous loggings and 20 tree cores that were extracted, also at breast height, from the remaining ones. Tree diameters at breast height ranged from 27. 7 to 98. 1 cm. It should be noted that trees of diameter at breast height over 25 cm were not easy to be found in the area. The tree-ring cores were extracted using Pressler’s increment borers of 40 and 60 cm long, with special care to avoid ramifications and irregular wood structure, as much as possible. The trees cross-sections and cores were dried, planed and sanded with progressively finer grades of sandpaper (80, 100, 200, 400 and 600 grit) until the tree-rings were distinguishable under a stereomicroscope. Radial increments and selected radial directions of cross sections were measured to the nearest 0. [SEP] Justify:

Output: The text contrasts the claim by discussing the use of valonia oak trees, which are not tropical but rather Mediterranean, for dendrochronological studies. It details the sampling of these trees in Xeromero forest, highlighting their growth conditions and characteristics, thereby providing evidence that trees outside tropical regions can also be used for this type of scientific examination.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Funding: This study was supported by the Science and (Grant number 202002020046) and Foundation (Grant number 2022A1515012346). Authors' contributions: Concept and design were by XL, ZC, and YZ; Data collection was by ZC, YL, and LL; Administrative, technical or logistic support was provided by YZ; Analysis and interpretation were by ZC, YZ, and JL; Drafting the manuscript was by ZC, JL, and YL; Critical revision of the manuscript was by XL, and YZ; Final approval of the manuscript was by and LL; All authors reviewed the manuscript and agreed to be accountable for all aspects of the work. All authors read and approved the final manuscript. Acknowledgements: None. Availability of data and materials: The relevant data in this 199. Ljubimov AV. Diabetic complications in the cornea. Vision Res. 2017;139:138–152. Ocular surface diabetic disease: a neurogenic condition? Ocul Surf. 2021;19:218–223. IDF diabetes atlas: global, regional and country-level diabetes prevalence estimates for 2021 and projections for 2045. Clin Pract. 2022;183:109119. & Flaxel CJ. Diabetic eye disease: a review of screening and management recommendations. Ophthalmol. 2021;49:128–145. Group of Society. Chinese multidisciplinary expert consensus on preventing and treating diabetic eye disease. 2021 ed. Diabetes Mellitus. 2021;13:1026–1042. & Willcox M. The impact of diabetes on corneal nerve morphology and ocular surface integrity. Ocul Surf. 2018;16:45–57. & Tong L. A systematic review on the impact of diabetes mellitus on the ocular surface. Nutr Diabetes. 2017;7:e251. & Liu YC. Diabetic corneal neuropathy. J Clin Med. 2020;9:3956. Zhu L, & Robertson DM. The impact of hyperglycemia on the corneal epithelium: molecular mechanisms and insight. Ocul Surf. 2019;17:644–654. & Robertson DM. Chronic hyperglycemia compromises mitochondrial function in corneal epithelial cells: implications for the diabetic cornea. Cells. 2022;11:2567. [SEP] Justify:

Output: The text is irrelevant to the claim about proteomics. It primarily discusses funding, authors' contributions, and various studies related to diabetes and ocular surface implications. There is no mention of proteomics or its focus on proteins expressed in cells.


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: Entlässt man diese Tiere in konstante Dunkelheit schwächt sich der Glukokortikoidrhythmus immer weiter ab, was darauf hinweist, dass in konstanter Dunkelheit die Uhr im SCN notwendig ist, um einen Glukokortikoidrhythmus aufrechtzuerhalten. wurden unter LD-in peripheren Organen von Syt10Cre/Cre Bmal1fl/- Mäusen gemessen. Überraschend war, dass periphere Uhren in Syt10Cre/Cre Bmal1fl/- Mäusen in LD rhythmisch waren, was darauf hindeutet, dass der SCN als Gewebe zwar notwendig ist um periphere Uhren zu synchronisieren, die SCN-Uhr per se aber nicht. Sobald die Tiere in konstante Dunkelheit entlassen wurden, konnte eine deutliche Dämpfung der Rhythmen in peripheren Uhren gemessen werden. waren sogar komplett arrhythmisch exprimiert, was die hierarchische Struktur des zirkadianen Systems unter konstanten Bedingungen bestätigt. Im dritten Teil dieser Arbeit werden die ersten Schritte zur Entwicklung eines kombinatorischen Cre-Systems beschrieben. Dieses kombinatorische Cre-System soll sehr spezifische genetische Manipulationen im Mausmodell ermöglichen. basiert auf der Komplementierung zweier Cre-Teilproteine, die einzeln nicht aktiv sind. Sind sie aber in einer Zelle co-exprimiert, wird funktionelles Cre-Protein wiederhergestellt. [SEP] Justify:

Output: The text corroborates the claim by providing evidence that the SCN is necessary to maintain a glucocorticoid rhythm in constant darkness, demonstrating its role as an essential regulator in the circadian system. It indicates that peripheral clocks depend on the SCN for synchronization, reinforcing the idea that the SCN functions as the master clock for circadian rhythms.


Input: Task: contrast the claim using the given text. Claim: Only trees growing in tropical regions can be used for dendrochronological studies. [SEP] Text: This period of 14 months was chosen taking into account that tree growth in the southern most Mediterranean regions may continue until November or even until the beginning of winter. As for scPDSI, according to Wells et al. [33], this index is calculated from precipitation and temperature data as well as from the available local soil water content and it varies from -4 (extreme drought) to +4 (extremely wet). The climatic data were obtained from the [34], [35] due to the incomplete data from the local meteorological stations in the proximity of the study area. We used monthly precipitation and mean temperature data of the CRU TS3. 22 [36] and monthly UCAR scPDSI drought indices [37]. The closest grid point to the site studied was selected from each gridded data category. The results of the climate-growth relationships are presented as a ratio between the regression coefficient of each monthly climatic parameter and the associated standard deviation (mean of 50 simulations) [30]. -Dating and Tree-From the cross-dating procedure it derives that, due to the wood structure of valonia oak trees (in many cases tree-rings are very thin and not distinguishable, there is presence of discoloration and wood abnormal structure), cross-dating in the middle and old-age group is difficult (Figure 2). The difficulty degree increased with narrow tree-rings. For this reason, cross-dating was possible for 19 out of the 20 cross sections (rate 95%) and 11 out of the 20 cores (rate 55%). 2. Cross section of a valonia oak tree from the study area. Based on the total cross-dated elementary series, master chronology length was 365 years, mean tree-ring width was 0. 89 mm, standard deviation 0. 31 mm, mean sensitivity 0. 21 and the first-order autocorrelation 0. 67 (Table 1). The above mentioned statistics do not differ substantially if calculated separately for each tree age class of 100 years. Tree-ring width in the three age classes tested ranged from 0. 86 to 0. 90 mm (std 0. 28 mm), mean sensitivity from 0. 19 to 0. 21 and first-order autocorrelation from 0. 60 to 0. 67 (Table 1). The EPS value for the common period of the series (1815-2010) was 0. 68 and exceeded the threshold value of 0. [SEP] Justify:

Output: The text contrasts the claim by providing information about dendrochronological studies on valonia oak trees, which are not tropical trees, suggesting that tree species from various regions can be used for such studies. The mention of Mediterranean regions indicates that dendrochronological methods can be applied beyond tropical areas.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: & Bennett DLH. New horizons in diabetic neuropathy: mechanisms, bioenergetics, and pain. Neuron. 2017;93:1296–1313. & Kwok JSWJ. Diabetic corneal neuropathy: pathogenic mechanisms and therapeutic strategies. Front Pharmacol. 2022;13:816062. & Xie L. Mechanistic investigations of diabetic ocular surface diseases. (Lausanne). 2022;13:1079541. & Grandori R. Mass spectrometry-based tear proteomics for noninvasive biomarker discovery. Rev. 2022;41:842–860. & Shippy SA. Tear analysis as the next routine body fluid test. Eye (Lond). 2020;34:1731–1733. Pensyl CD & Dillehay SM. The repeatability of tear mucus ferning grading. Sci. 1998;75:600–604. Doughty MJ. Goblet cells of the normal human bulbar conjunctiva and their assessment by impression cytology sampling. Ocul Surf. 2012;10:149–169. Nättinen J, Jylhä A, Aapola U, Mäkinen P, Beuerman R, Pietilä J et al. Age-associated changes in human tear proteome. Clin Proteomics. 2019;16:11. Bencúrová DM, Mandíková Š & Daňková P. Age and sex-specific differences in interleukin 4, interferon gamma, macrophage migration inhibitory factor, and vascular endothelial growth factor levels in the tears of healthy subjects. Ophthalmol. 2022;32:1900–1906. The effects of diabetic duration on lacrimal functional unit in patients with type II diabetes. J Ophthalmol. 2019;2019:8127515. Ozaki K, & Matsuura T. Extended duration of hyperglycemia result in human-like corneal nerve lesions in mice with alloxan- and streptozotocin-induced type 1 diabetes. Vis Sci. 2018;59:5868–5875. Association between tear and blood glucose concentrations: random intercept model adjusted with confounders in tear samples negative for occult blood. J Diabetes Investig. [SEP] Justify:

Output: The text is irrelevant to the claim as it primarily discusses various studies and articles related to diabetic neuropathy and tear proteomics without directly addressing the broader definition or scope of proteomics itself. The lack of focus on the definition or concept of proteomics means it does not support or contradict 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: Journal of Circadian RhythmsStart SubmissionBecome a ReviewerReading: Overexpression of Prokineticin 2 in Leads to Rhythms in the (US English)XML (US English)Alt. DisplayShareShareResearch 2. In the current study, transgenic mice with the overexpression of PK2 have been generated. These transgenic mice displayed reduced oscillation of the PK2 expression in the SCN and decreased amplitude of circadian locomotor rhythm, supporting the important signaling role of PK2 in the regulation of circadian rhythms. Altered molecular rhythms were also observed in the SCN in the transgenic mice, indicating that PK2 signaling also regulates the operation of core clockwork. This conclusion is consistent with recent reports showing the likely signaling role of PK2 from the intrinsically photosensitive retinal ganglion cells to SCN neurons. Thus, PK2 signaling plays roles in both the input and the output pathways of the SCN circadian clock. Keywords:prokineticin 2suprachiasmaticcircadian clockintrinsically photosensitive retinal ganglion cellsoverexpressionoutputtransgenic miceYear: 2018Page/10. 5334/jcr. 170Submitted on Aug 15, 2018Accepted on Sep 29, 2018Published on Nov 6, 20184. 0 rhythms are the ~24-hour oscillations of the physiological and behavioral processes that are controlled by internal clocks. In mammals, the master pacemaker driving circadian rhythms resides in the suprachiasmatic nuclei (SCN) of the anterior hypothalamus. A clear view of molecular clock mechanisms within the SCN has emerged. The core molecular clockwork consists of autoregulatory transcriptional and translational feedback loops that have both positive and negative elements [27, 33]. In contrast, much less is known about the output mechanism by which the SCN circadian pacemaker sends timing information for eventual control of physiological and behavioral rhythms [9, 14, 15, 19, 21, 23, 27, 33]. Control of gene transcription is the key to the mechanisms of SCN output. Systematic gene expression profiling has identified 101–337 cycling transcripts in the SCN [24, 30], dependent on slightly different criteria and filtering methods used. However, the so-called first-order clock-controlled genes (CCGs), i. e. [SEP] Justify:

Output: The text corroborates the claim by explicitly stating that 'the master pacemaker driving circadian rhythms resides in the suprachiasmatic nuclei (SCN) of the anterior hypothalamus.' This supports the notion that the SCN functions as a master clock in regulating circadian rhythms.


Input: Task: contrast the claim using the given text. Claim: Only trees growing in tropical regions can be used for dendrochronological studies. [SEP] Text: 85 [29] in the year 1981. TABLE 1. Descriptive statistics of valonia oak tree-ring width raw data, for all trees and for the three age classes. From the graphical representation of the tree-ring raw mean chronologies and the 20 years mean moving average for each age class (Figure 3), an intense appearance of low frequency variation has been observed throughout the period without noticing any periodicity. The examination of the tree-rings growth trend indicated a growth reduction from the beginning of the chronologies until the period of 1880-1900. Then, an increase trend was observed which was, however, halted in the period of 1990-2000 with a tendency to revert afterwards. Focusing on the master residual chronology (Figure 4), it shows a more intense inter-annual variation in the period of 1650-1745 compared to the following period with the exception of the years 1990 and 2000 when particularly narrow tree rings were observed. Characteristic narrow tree-rings were also observed in the years 1661 and 1715, with particularly wide rings appearing in the years 1660, 1687 and 1718. Many of these years were used in cross-dating as pointer years. 3. Tree-ring width mean chronologies for three age classes; the bold line superimposed indicates the mean moving average of 20 years and the dashed line shows the number of samples used in each chronology. 4. Master residual chronology of tree-ring widths (TRW); the dashed line shows the number of samples used in the chronology. Tree-Rings to Statistically significant (p<0. 05) positive correlations were calculated between tree-ring width and January and March precipitation (Figure 5). No significant correlations were found between tree-ring widths and mean temperature of any month. Regarding the scPDSI drought index, a positive significant correlation (p<0. 05) appeared in June and July (Figure 6). 5. Tree-ring to climate relationships calculated between master residual chronology and 28 climatic parameters (monthly precipitation and mean monthly temperature) for the period of 1981-2013. Dashed horizontal lines indicate 95% significance level, R=r/s, r= mean regression coefficient, s= mean standard deviation (for 50 simulations). 6. Tree-ring to climate relationships calculated between master residual chronology and 14 climatic indices (monthly scPDSI) for the period of 1981-2013. [SEP] Justify:

Output: The text contrasts the claim by providing data on tree-ring studies conducted on valonia oak trees without indicating any restriction to tropical regions. It discusses tree-ring width and growth trends, as well as correlations with climate parameters, which implies that dendrochronological studies can be performed on trees outside tropical areas.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: 2021;12:266–276. Soria J, Acera A, Merayo-LLoves J, Durán JA, González N, et al. Tear proteome analysis in ocular surface diseases using label-free LC-MS/MS and multiplexed-microarray biomarker validation. Sci Rep. 2017;7:17478. & Chen H. Detection of tear components using matrix-assisted laser desorption ionization/time-of-flight mass spectrometry for rapid dry eye diagnosis. J Proteome Res. 2020;19:3644–3651. & Grus FH. Alterations in the tear proteome of dry eye patients–a matter of the clinical phenotype. Vis Sci. 2013;54:2385–2392. Ciliary neurotrophic factor promotes the activation of corneal epithelial stem/progenitor cells and accelerates corneal epithelial wound healing. Stem Cells. 2015;33:1566–1576. & Yang L. The proinflammatory cytokines IL-1β and TNF-α modulate corneal epithelial wound healing through p16Ink4a suppressing STAT3 activity. J Cell Physiol. 2020;235:10081–10093. Inhibition of soluble epoxide hydrolase 2 ameliorates diabetic keratopathy and impaired wound healing in mouse corneas. Diabetes. 2018;67:1162–1172. Cytoprotective effect of lacritin on human corneal epithelial cells exposed to benzalkonium chloride in vitro. Res. 2014;39:604–610. Ontology KnowledgeBase in 2023. Genetics. 2023;224:iyad031. Prediction and analysis of retinoblastoma related genes through gene ontology and KEGG. BioInt. 2013;2013:304029. Arginine and carnitine metabolites are altered in diabetic retinopathy. Vis Sci. 2019;60:3119–3126. Plasma arginine and citrulline are elevated in diabetic retinopathy. Ophthalmol. 2022;235:154–162. Relationship between lysosomal dyshomeostasis and progression of diabetic kidney disease. Dis. 2021;12:958. [SEP] Justify:

Output: The text provided discusses various studies related to tear proteome analysis and the effects of different factors on corneal epithelial cells, but it does not explicitly address or define proteomics or its scope. Therefore, it is irrelevant to the claim regarding the study of 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: , CCGs that contain E-box enhancers are very rare [24, 27, 30]. In fact, only nine genes harboring one or more E-box enhancers that are conserved in both human and mouse genomes were identified in these cycling genes [24], illustrating the rarity and also the importance of these first-order CCGs. It is likely that the oscillation of the majority of cycling genes in the SCN is secondary to the oscillation of these first-order CCGs. In mammals, lesion and transplant studies have indicated that signals that mediate the SCN output appear to be secreted molecules [28, 29]. Thus, CCGs in the SCN that encode secreted molecules could be crucial signaling molecules for transmitting timing information out of the SCN. Two secreted molecules, prokineticin 2 (PK2) and vasopressin (AVP), that are encoded by respective CCGs, have been indicated as candidate SCN output molecules [4, 12]. AVP is the first CCG identified that regulates circadian rhythm of endocrine and locomotor activities [12, 13, 14]. Molecular studies have revealed that the transcription of the AVP precursor gene in the SCN is rhythmically regulated by the interaction of core molecular oscillators with E-box enhancers [12]. AVP-deficient Brattleboro rats display attenuated rhythms in a variety of circadian parameters, including body temperature, hormone synthesis, SCN neural firing and sleep-wakefulness [8, 11, 13, 34]. Recent study has indicated that AVP receptors V1a and V1b are critical for mediating AVP in the generation of overt circadian rhythms [18, 35]. In vitro and in vivo studies have revealed that PK2 is also a first-order CCG in the SCN, as its mRNA levels are regulated by CLOCK and BMAL1 acting on E-box enhancers in the gene’s promoter [4]. PK2 mRNA exhibits over 50-fold of diurnal oscillation, peaking in the SCN during the middle day and being essentially absent during night [4, 5]. This pattern of high amplitude oscillation is altered by light exposure, the main input for entraining and resetting of the SCN clock. [SEP] Justify:

Output: The text corroborates the claim by discussing the role of the suprachiasmatic nucleus (SCN) in regulating circadian rhythms, specifically noting that molecules encoded by cycling genes in the SCN, such as prokineticin 2 (PK2) and vasopressin (AVP), are crucial for transmitting timing information and influencing circadian parameters. For instance, it mentions how AVP is identified as a key component that regulates the circadian rhythm of various activities. Additionally, the text discusses how molecular studies show rhythmic regulation of genes in the SCN, which is central to the function of the SCN as the master clock.


Input: Task: contrast the claim using the given text. Claim: Only trees growing in tropical regions can be used for dendrochronological studies. [SEP] Text: Dashed horizontal lines indicate 95% significance level, R=r/s, r= mean regression coefficient, s= mean standard deviation (for 50 simulations). dendochronological study of valonia oak trees created a new master chronology for the time period of 1650-2014 that may contribute to the densification of the dendrochronological network in South-[18], [38], [39], [40], [41]. It may be used in comparison with new chronologies of the species but also with other oak species. Furthermore, it may contribute to climate reconstruction studies that have been the subject of several researches in the eastern Mediterranean region who used long tree-ring time-series [42], [43], [44], [45], [46], [47], [48]. At this stage, due to low EPS value found before 1981, the constructed chronology needs to be upgraded with more elementary chronologies from new cores or cross sections. Regarding the ages of valonia oak trees it appears that the observed forest is composed of uneven-aged stands, although they seemingly resemble to be even-aged. This impression is given because of the single-layer structure of the forest, the open canopy cover and the lack of lower diameter class trees. The presence of old-age trees in the study site and the region in general [20] indicates that these stands have evolved after the French-Hellenic exploitation of forests in the 17th century [6], a period during which many large-diameter trees were harvested to produce shipbuilding timber. After this period, according to data from the local Forest Service, there has not been any systematic logging and the stands were only used for the production of acorn cups for tannin production collected mainly from large, sparsely scattered trees. These old-age trees are nowadays reserved mainly for ecological purposes. The small tree-ring widths, on average did not exceed 1 mm (Table 1) and did not show any significant decreasing trend with age, is a species-specific characteristic which is slow-growing and usually developing on shallow, degraded calcareous soils. Mean sensitivity (mean value 0. 21) is relatively high compared to the Greek coniferous species [49] and is almost proportional to the values of Aleppo pine in the sub-humid bioclimate type [50], whereas it is higher than the mean sensitivity of other deciduous Greek oak species [16]. [SEP] Justify:

Output: The text contrasts the claim by discussing a dendrochronological study of valonia oak trees, which are typically found in temperate and Mediterranean regions, specifically addressing their contribution to dendrochronological networks and climate reconstruction studies. This implies that trees from other regions, not just tropical ones, can be utilized for such studies.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Lysosomal dysfunction-induced autophagic stress in diabetic kidney disease. J Med. 2020;24:8276–8290. & Järveläinen H. Extracellular matrix-cell interactions: focus on therapeutic applications. Cell Signal. 2020;66:109487. Low molecular weight fucoidan alleviates diabetic nephropathy by binding fibronectin and inhibiting ECM-receptor interaction in human renal mesangial cells. Biol Macromol. 2020;150:304–314. Changes in matrix metalloproteinases in diabetes patients’ tears after vitrectomy and the relationship with corneal epithelial disorder. Vis Sci. 2015;56:3559–3564. - Complete metabolome and lipidome analysis reveals novel biomarkers in the human diabetic corneal stroma. Res. 2016;153:90–100. Cell-matrix interactions in the eye: from cornea to choroid. Cells. 2021;10:687. Queralt-Martín A lower affinity to cytosolic proteins reveals VDAC3 isoform-specific role in mitochondrial biology. J Gen Physiol. 2020;152:e201912501. & Checchetto V. Voltage-dependent anion selective channel 3: unraveling structural and functional features of the least known porin isoform. Front Physiol. 2021;12:784867. Reina S, Guarino F, Magrì A & V. VDAC3 as a potential marker of mitochondrial status is involved in cancer and pathology. Front Oncol. 2016;6:264. ì A, & V. Voltage dependent anion channel 3 (VDAC3) protects mitochondria from oxidative stress. Redox Biol. 2022;51:102264. Additional DeclarationsThere is conflict of interestSupplementary FilesSummaryBox. [SEP] Justify:

Output: The text does not address or relate to the claim about proteomics specifically studying the entire set of proteins expressed in a cell. Instead, it presents various studies and findings related to diabetic kidney disease, cellular interactions, and mitochondrial biology without mentioning proteomics, making it 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: The molecular rhythm of PK2 responds asymmetrically to the shifts of light/dark cycles, showing faster adaption to delay than advance of light/dark cycles, consistent with rate of circadian behavioral adaptation [5, 36]. Exogenous application of PK2 altered locomotor activity and feeding pattern [4], consistent with PK2 functioning as day time signal. Importantly, PKR2 is densely expressed in essentially all the known primary SCN targets, including the dorsomedial hypothalamic nuclei, paraventricular nuclei of hypothalamus, lateral septum, paraventricular thalamic nuclei and the bed nucleus of the stria terminalis [2, 4, 6, 16, 31, 32]. Studies using a bacterial artificial chromosome (BAC) transgenic mouse line, in which the enhanced green fluorescence protein (EGFP) reporter gene expression was driven by the PK2 promoter, indicates a circadian oscillation of the number of EGFP-positive neurons in the SCN [38]. The data from this strain of transgenic mice also revealed that EGFP-expressing neurons in the SCN projected to many known SCN target areas, including the ventral lateral septum, medial preoptic area, subparaventricular zone, paraventricular nucleus, dorsomedial hypothalamic nucleus, lateral hypothalamic area and paraventricular thalamic nucleus [38], where the receptor for PK2 (PKR2) is expressed [4, 6]. At cellular level, PK2 was shown to regulate the excitability of PKR2-positive neurons, such as the neurons of a primary SCN target, the paraventricular hypothalamic nucleus [37] or the SCN neurons themselves [3, 26]. PK2-deficient mice displayed remarkably reduced amplitudes in the oscillation of a variety of circadian parameters, including locomotor activity, sleep–wake cycle, body temperature, circulating glucocorticoid and glucose levels, as well as the expression of peripheral clock genes [10, 17]. Deficiency in the PKR2 led to almost identical defects in circadian rhythms as that of PK2-deficiency [25]. In the current study, we provide further supporting genetic evidence for the signaling role of PK2 in the regulation of circadian rhythms by overexpressing PK2 in the transgenic mice. [SEP] Justify:

Output: The text corroborates the claim by providing evidence of how PK2, a signaling molecule, is involved in the regulation of circadian rhythms and is expressed in the SCN, which is known to function as the master clock in the brain. It highlights that PK2 and its receptor PKR2 play significant roles in the modulation of circadian behaviors and rhythms, supporting the claim that the SCN regulates these physiological processes.


Input: Task: contrast the claim using the given text. Claim: Only trees growing in tropical regions can be used for dendrochronological studies. [SEP] Text: The relatively high mean sensitivity values found suggest a significant climatic signal, as reflected by valonia oak tree-rings, and are indicative of the appropriateness of the species to be used in dendrochronological studies. The high first-order autocorrelation indicates a low frequency variation in the tree-ring chronologies, revealing the residual action of certain site factors during the formation of successive tree-rings [13]. This variation can be interpreted mainly by the effects of anthropogenic factors that have affected those forests in the past, such as pruning for higher acorn production and grazing, and the influence of different environmental factors such as climate. The analysis of the low and high frequency variation in the chronologies, in relation to other research or historical data, enhances the hypothesis of climate effect. For example, the last decade of the 20th century is a period of a decreasing tendency in tree-ring width, noted and characterized as dry and warm for Greece and [51], [52]. Furthermore, the year 1715, with the distinctive narrow tree-rings, was marked with long dry periods and was characterised as a year of great famine, especially for the central and southern Greece [53]. Concerning tree-rings to climate relationships, January precipitation that precedes the tree-ring formation phase as well as March precipitation coinciding with the commencement of tree-ring growth, play a prevailing role in valonia oak tree-ring growth. The positive effect of winter precipitation could be attributed to water available in the soil for use during the tree-growing season. Moreover, spring precipitation could attribute to the increased water demands for various physiological processes such as the intense cambium reactivation and growth release after winter dormancy. For the same species in Jordan, Touchan and Hughes [19] showed a relatively high positive correlation between October and May precipitations. The positive correlation of tree-ring widths with June and July scPDSI drought index explains the positive effect of drought reduction during the tree-ring growth period. Climate to growth relationships calculated signify, in a way, the xerothermic character of valonia oak. The adaptability of the species to grow in xerothermic environments confirms the results of the previous research on its ecophysiological response to summer drought [54]. [SEP] Justify:

Output: The text contrasts the claim by discussing the suitability of the valonia oak, which is not a tropical tree, for dendrochronological studies. It highlights how the tree-rings of valonia oak reflect significant climatic signals and adaptability to xerothermic environments, indicating that trees from non-tropical regions also provide valuable data for these studies.


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. Related research -proteomic analysis of systemic lupus erythematosus patients using liquid chromatography/tandem mass spectrometry with label-free quantification View 10. 7717/peerj. 4730 Published 2018-05-08 Accepted 2018-04-18 Received 2018-01-04 -MS/MS, Biomarkers, Label-free quantification, Proteomic analysis, Plasma, Proteomics, Protein profiling Copyright © 2018 Madda et al. is an open access 2018. Plasma proteomic analysis of systemic lupus erythematosus patients using liquid chromatography/tandem mass spectrometry with label-free quantification. PeerJ 6:e4730 The authors have chosen to make the review history of this 1. 5- to three-fold up-regulation and five had <0. 2- to 0. 6-fold down-regulation. Gene ontology and DAVID (Visualization, and Integrated Discovery) functional enrichment analysis revealed that these proteins are involved in several important biological processes including acute phase inflammatory responses, complement activation, hemostasis, and immune system regulation. study identified a group of differentially expressed proteins in the plasma of SLE patients that are involved in the imbalance of the immune system and inflammatory responses. Therefore, these findings may have the potential to be used as prognostic/diagnostic markers for SLE disease assessment or disease monitoring. lupus erythematosus (SLE) is a chronic autoimmune disease involving multiple organs that are characterized by excessive production of antinuclear antibodies (Crispín et al. , 2010). The particular reasons behind the cause of SLE have not been recognized yet, but numerous factors have been shown to be related to the development of SLE, including genetic factors, environmental triggers, hormonal imbalance, and life cycle changes (Lisnevskaia, Murphy & Isenberg, 2014). One of the most important mechanisms involved in the development of SLE is alteration to immune reactions; this involves auto-antibodies that target the patient’s own tissues and subsequently lead to inflammation (Pisetsky, 1997). [SEP] Justify:

Output: The text provided does not directly address the claim about proteomics and its focus on the entire set of proteins expressed in a cell. Instead, it discusses a specific study related to proteomic analysis in systemic lupus erythematosus (SLE) patients without clarifying the general principles of proteomics itself. Therefore, this text 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: Figure 3 Reduced circadian locomotor rhythmicity in the PKR2-PK2 transgenic mice. The actograms of spontaneous locomotor activities of the PKR2-PK2 transgenic mice and control mice under LD and DD (shadowed) are doubly plotted. Under DD, the transgenic mice displays reduced locomotor rhythmicity. Locomotor rhythm displayed bimodal phenotype, particularly for the mouse line TG14. Figure 4 Quantitative analysis of locomotor rhythmicity of the PKR2-PK2 transgenic mice. FFT value, an index for the amplitude of the locomotor circadian rhythmicity was plotted. Both the TG10 and TG14 mice displayed significantly reduced amplitude of circadian rhythmicity. * p < 0. 05, ** p < 0. 01. Altered circadian gene expression in the SCN of the PKR2-PK2 transgenic mice We then examined the effects of PK2 overexpression on the rhythm of the SCN circadian genes by in situ hybridization (Figure 5). In the SCN of the PKR2-PK2 transgenic mice, the mRNA expression of Bmal1, one of the key core components of the circadian clock, was significantly altered, compared to control mice. The changes in the expression of Cry2, Per1 and Per2 in the SCN of the PKR2-PK2 transgenic mice were also significant, although less remarkable than that of Bmal1 (Figure 5). Subtle alteration of clockwork expression in the SCN and elongated behavioral period had actually previously been noted in PK2-deficient mice [17]. Taken together, these data suggest that PK2 signaling may feedback to affect the expression of the core oscillator genes in the SCN. Figure 5 Altered molecular rhythmicity in the SCN of the PKR2-PK2 transgenic mice. The transgenic mice (open square) and wild-type controls (filled squares) were sampled every 3 hr and in situ hybridizations on coronal brain sections were performed to quantify the expression of five core oscillator genes. Each data represents mean ± SEM of three mice. * p < 0. 05. [SEP] Justify:

Output: The text corroborates the claim by detailing how the SCN in the PKR2-PK2 transgenic mice shows significant alterations in the expression of core components of the circadian clock, such as Bmal1, Cry2, Per1, and Per2. This suggests a functional role for the SCN in regulating circadian rhythms, aligning with the idea of the SCN as the master clock.


Input: Task: contrast the claim using the given text. Claim: Only trees growing in tropical regions can be used for dendrochronological studies. [SEP] Text: According to personal observations in south Greece, valonia oak in periods of very intense summer drought sheds its leaves and re-sprouts smaller new ones, in late summer or early autumn along with the first rains after drought. oak in is of particular dendrochronological-dendroclimatological interest due to the old age of the trees, but also due to its response to climate variations. Tree-ring widths to climate relationships analysed in this research help us to adequately decode the role of climate on the inter-annual growth variability of the species. Winter precipitation and drought during the summer period play a major role in the radial growth of valonia oak. The study of these relationships combined with the scenarios of climate change can be a guide for predicting valonia oak forests future growth, but also for the usability of the species in reforestation practices in the Mediterranean area. Nevertheless, this study contributes to the dendrochronological research and, generally, to the knowledge of the species autoecology. research has been co-financed by the (Fund – ESF) and Greek national funds through the “Education and Lifelong Learning” of the (NSRF) - Program:. Investing in knowledge society through the 380360. 70. DOI: 1993 Flora Europaea. Vol. 1, 581 p 2001 Establishment of Quercus ithaburensis Decaisne ssp. macrolepis (Kotschy) Hedge & Yaltirik) in competence with understory vegetation in sylvopastoral systems. PhD thesis, of Thessaloniki, Faculty of Forestry and Natural Environment, Thessaloniki, Greece, 143 p (in Greek) 2008 Distribution and phytogeographical analysis of Quercus ithaburensis macrolepis in Greece. 34: 73-82 2002 Valonia oak forests (17th-19th century): economical perspectives. In: (eds) Valonia oak forests: the past, the present, and the future. Giahoudis Publishing, Thessaloniki, Greece, pp 67-96 (in Greek) 2015 The contribution of valonia oak silvopastoral systems in to local development and the environment. [SEP] Justify:

Output: The text contrasts the claim by discussing the significance of valonia oak, which grows in a Mediterranean region—specifically, south Greece—for dendrochronological studies. It highlights that the valonia oak's age and response to climate variations make it important for dendrochronological and dendroclimatological research, thereby suggesting that species outside tropical regions can also be utilized for such studies.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: SLE patients Healthy individuals Number of samples 19 12 Female: male (% female) 18:1 (94. 7%) 9:3 (75%) Age (years) 32. 1±1. 5a 32. 9±2. 1a score (average) 8. 47 ± 2. 8a N/A Anti-ds DNA antibodies <30 (n = 19) 2 (10. 52%) N/A 30 to <60 (n = 19) 2 (10. 52%) N/A 60–200 (n = 19) 7 (36. 8%) N/A >200 (n = 19) 8 (42. 1%) N/A Anti-nuclear antibodies (ANA) ≥1:640 N/A DOI: 10. 7717/peerj. 4730/table-1 Notes: N/A, not applicable. a Data are represented as mean ± standard deviation. Depletion of high abundance serum albumin protein In order to identify the various low and high abundance proteins by mass-based proteomic analysis, highly abundant serum albumin was depleted from the SLE and control samples by using a dye-based proteo-prep blue albumin removal kit (). Using the manufacturer’s protocol, spin columns were suspended with slurry and centrifuged at 8,000 × g for 10 s. Next, 0. 1 ml of serum samples were added to the spin columns and the columns were incubated for 10 min. Subsequently, the samples were centrifuged at 8,000 × g for 60 s; this was repeated twice to remove further serum albumin (Ahmed et al. , 2003). The protein concentrations of the depleted serum samples were determined by Bradford assay and the samples were stored at −80 °C until further analysis. Protein precipitation and in-solution digestion The depleted SLE and healthy plasma samples were precipitated using 100% ice-cold acetone and then kept overnight at −20 °C. Then the samples were centrifuged at 14,000 × g for 10 min, and the pellets were dissolved in 100 μl of 25 mM NH4HCO3 and 6. 5 M urea (0. 1–1 μg/μl); this was followed by an in-solution digestion procedure used in previous studies (Ru et al. , 2006). [SEP] Justify:

Output: The text does not address or provide information relevant to the claim about proteomics studying the entire set of proteins expressed in a cell. Instead, it discusses a specific experimental procedure for analyzing proteins in samples from SLE patients and healthy individuals, which is more focused on methodology rather than the definition or scope of proteomics as a 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: overexpression of PK2 leads to reduced oscillation of PK2 mRNA levels in the SCN and decreased amplitude of behavioral rhythm In this study, we demonstrated that overexpression of PK2 in transgenic mice under the control of its receptor (PKR2) led to reduced oscillation of PK2 mRNA in the SCN and decreased amplitude of circadian locomotor rhythms. The oscillation of PK2 mRNA in the SCN was reduced, primarily due to the increase PK2 expression in the SCN during the dark phase (Figures 1 and 2). The reduction of circadian locomotor rhythm was observed in two lines of independent transgenic mice (Figures 3 and 4). These observations were consistent with the signaling role of PK2 as an output signaling molecule of the SCN circadian clock. PK2 has been postulated as an SCN output molecule based on several previous findings [4, 5, 17, 25, 38]. Particularly, results from knockout mice that lack functional PK2 or its receptor (PKR2) have strongly supported the essential role of PK2 signaling for the maintenance of robust circadian rhythms. In the absence of PK2 signaling, the amplitudes of circadian locomotor parameters were remarkably reduced, with rhythmicity amplitude of wheel-running activity of PK2-deficient mice less than 20% of wild type mice [17, 25]. Rhythmicity of other circadian parameters, including sleep–wake cycle, body temperature, circulating glucocorticoid and glucose levels, as well as the expression of peripheral clock genes, was also significantly reduced [17, 25]. The current overexpression studies in the transgenic mice have provided corroborative evidence for a signaling role of PK2 in the control of circadian rhythms. Perturbation of PK2 signaling and molecular rhythms in the SCN The altered molecular rhythms in the SCN of the PKR2-PK2 transgenic mice indicate that PK2 also appears to regulate the molecular rhythmicity of core clockwork, particularly the amplitude of Bmal 1 (Figure 5). PK2 has been primarily considered as an output signaling molecules of the SCN [4, 5, 17, 25]. However, the receptor for PK2, PKR2, is highly expressed in the SCN [4, 6], and SCN neurons are known to form local circuits within the SCN, sending collateral projections within the SCN [1, 2, 7]. [SEP] Justify:

Output: The text corroborates the claim by providing detailed insights into the role of PK2 as an output signaling molecule of the SCN circadian clock. It describes how PK2 influences the oscillation of mRNA levels in the SCN and behavioral rhythms, which supports the SCN's function as a master regulator of circadian rhythms. It further mentions that knockout mice lacking functional PK2 or its receptor exhibit significantly reduced rhythmicity, highlighting the essential role of the SCN in controlling circadian rhythms.


Input: Task: contrast the claim using the given text. Claim: Only trees growing in tropical regions can be used for dendrochronological studies. [SEP] Text: In: Lekkas TD (ed) Proceedings of the 14th on and Technology, CEST-2015_00100, Rhodes, Greece, 3-5 September 2015 QUÉ1980 Les forêts feuillues du pourtour méditerranéen. Constitution, écologie, situation actuelle, perspective. Revue Forestière Française 32 (3): 253-268 2002 The position of valonia oak in the Mediterranean ecosystems. In: (eds) Valonia oak forests: the past, the present, and the future. Giahoudis Publishing, Thessaloniki Greece, pp 13-23 (in Greek) 2007 Climate change effects on Mediterranean forest and preventive measures. 33 (1): 29-40. DOI: IPCC 2007 Climate change 2007: the physical science basis. In: (eds) Contribution of I to the Fourth Assessment. Report of the on Climate Change. /996 p 2011 The environmental, economic and social impacts of climate change in Greece, Impacts Study. of Works, Athens, Greece, 470 p 1976 Tree-rings and climate. Academic Press, London, UK, 567 p 1989 Dendroecology: a tool for evaluating variations in past and present forest environments. Res 19: 111-189. DOI: 1996 and Environment: Dendroecology. Birmensdorf, Institute for Forest, Snow and Landscape Research. Haupt, Berne, Stuttgart, Vienna, 609 p NOAA 2015 International Tree-Bank. url: (15 December 2015) 1983 Dendrochronological investigations in the Aegean and Neighboring regions 1977-1982. J 10 (4): 411-420. DOI: 1987 Dendrochronological investigations in the Aegean and Neighboring regions 1983-1986. J 14 (4): 385-398. DOI: ΜΚ 1999 Dendrochronology in Jordan. J 42 (4): 291-303. DOI: 2013 Dating and tree-rings analysis of valonia oak aged trees from the Xeromero forest of Aetoloakarnania prefecture In: Association, Protection and management of Greek forests in a period of financial crisis and the challenge of natural silviculture. [SEP] Justify:

Output: The text contrasts the claim by discussing dendrochronological investigations and studies conducted in various regions such as the Mediterranean and Jordan, which implies that trees in non-tropical regions are also applicable for dendrochronological studies.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: Next, the protein samples were reduced with 100 mM DTT at 37 °C for 30–40 min and alkylated with 200 mM IAA in the dark at room temperature for 25–35 min. After this, the protein samples were digested with sequencing grade trypsin () using a 50:1 ratio at 37 °C. The reaction was quenched by adding 2 μl of 50% formic acid (FA), the mixture vortexed and then centrifuged in order to collect the peptides. Finally, the solution was lyophilized and desalted using a C18 zip-tip procedure. Nano UPLC and mass spectrometry conditions ESI interface Q-TOF MS/MS was carried out at a resolution of about 10,000 full-width half maximum performance. In order to calibrate the instrument, an external standard of lock mass BSA was continuously infused at a constant flow rate of 0. 25 μl/min using the Nano-auxiliary pump at an interval of 20 s (lock spray frequency). The precursor mass error was less than 2 ppm and for accuracy, the lock mass data were averaged. The acquired peptide spectra were eluted using the positive V mode with a scan mass range of 50–2,000 m/z and a scan time of 1 s. After reconstituting in 3% ACN and 0. 1% FA, the digested 400 ng peptides were injected into an online nano-coupled Q-TOF, Synapt-HDMS mass spectrometer (). The peptides were separated using a C18 reverse phase column (1. 7 μm × 75 μm × 250 mm) (). The binary solvent system used consisted of 99. 9% water and 0. 1% FA (mobile phase A) and 99. 9% ACN and 0. 1% FA (mobile phase B). The peptides were initially pre-concentrated and desalted online at a flow rate of 5 μl/min using a 5 μm symmetry C18 trapping column (internal diameter 180 mm, length 20 mm) () with 0. 1% FA. After injection, the peptides were eluted into the Nano-LockSpray ion source at a flow rate of 300 n/l and a gradient of 2–40% for 120 min. Then the column was washed and equilibrated. [SEP] Justify:

Output: The text describes a detailed method for preparing protein samples and using mass spectrometry for analysis. However, it does not explicitly mention the concept of proteomics or the study of the entire set of proteins expressed in a cell. Therefore, the text 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: Therefore, in addition to affecting SCN target neurons such as the paraventricular nucleus of thalamus [37], PK2 signaling functions upstream of the SCN, as supported by recent report showing the expression of PK2 in the intrinsically photosensitive retinal ganglion cells that project to SCN neurons [39]. Careful analysis of PK2-deficient mice indicated the free-running periods of residual circadian rhythms in the absence of PK2 signal is slightly lengthened [17]. Subtle alteration in the expression of one clockwork gene was indeed observed in the SCN of PK2-deficient mice [17]. A recent study with mice that have Bmal1 deletion specific to AVP-positive subpopulations of the SCN neurons showed altered circadian expression of genes in the SCN [22], including reduced PK2 expression rhythm. As the PK2 rhythm in the SCN is also reduced in V1a-null mice [18], the two SCN output molecules, PK2 and AVP, may have a similar effect in modulating the molecular rhythm in the SCN. Taken together, these results appear to support the inference that PK2 signaling plays a role in both the input and output of the SCN clock. research is supported in part by grants from NIH (MH67753 and DK91916). The authors have no competing interests to declare. 55. DOI: Buijs, RM. The anatomical basis for the expression of circadian rhythms: the efferent projections of the suprachiasmatic nucleus. Res. 1996; 111: 229–40. DOI: and Zhou, QY. of TRPV2 in the is Regulated by Prokineticin 2 Signaling. Journal of Circadian Rhythms. 2015; 13: 2. DOI: and Zhou, QY. Prokineticin 2 transmits the behavioural circadian rhythm of the suprachiasmatic nucleus. Nature. 2002; 417: 405–10. DOI: and Zhou, QY. Regulation of prokineticin 2 expression by light and the circadian clock. BMC Neurosci. 2005; 6: 17. DOI: and Zhou, QY. Expression of prokineticins and their receptors in the adult mouse brain. J Comp Neurol. 2006; 498: 796–809. DOI: Colwell, CS. [SEP] Justify:

Output: The text corroborates the claim by detailing the role of the SCN in regulating circadian rhythms, particularly through the influence of PK2 signaling on SCN neurons. It discusses various studies indicating how alterations in signaling related to the SCN affect circadian rhythms, further supporting the assertion that the SCN serves as the master clock. The presence of genes' expression rhythm being altered in the SCN and the implications of PK2's role in SCN functioning reinforce the overall claim regarding the SCN's regulatory functions.


Input: Task: contrast the claim using the given text. Claim: Only trees growing in tropical regions can be used for dendrochronological studies. [SEP] Text: 1901- Dec. 2013). 24 September 2014. DOI: A global data set of for 1870-2002: Relationship with soil moisture and effects of surface warming. J Hydrometeorol 5 (6): 1117-1130 DOI: 2009 A 924-year regional oak tree-ring chronology for North-Central Turkey. In: (eds) Tree-Rings, Kings and Archaeology and Environment: in Honor of Kuniholm. Oxbow Books, Oxford, UK, pp 71-80 2014 Spatial patterns of climate influence on tree growth. 24 (4): 381-392. DOI: WAŻÖÜ, Ü 2015 Bridging the gaps in tree-ring records: creating a high-resolution dendrochronological network for south eastern Europe. Tree-ring Res 70 (3): 39-50. DOI: 2009 Is there a separate tree-ring pattern for Mediterranean oak? In: Manning S, Bruce MJ (eds) Tree-rings, kings, and old world archaeology and environment. Oxbow Books, Oxford, UK, pp 41-50 2001 Aegean tree-ring signature years explained. Tree-57 (1): 67-73 2005 A Reconstruction (1689-1994 AD) of April-August precipitation in the southern part of Central Turkey. Climatol 25 (4): 537-548. DOI: Ü, D'Ö2008 Tree-ring reconstructions of precipitation and streamflow for north-western Turkey. Climatol 28 (2): 173-183. DOI: 2005 Reconstruction of spring/summer precipitation for the eastern Mediterranean from tree-ring widths and its connection to large-scale atmospheric circulation. 25 (1): 75-98. DOI: 2007 May-June precipitation reconstruction of southwestern Anatolia, Turkey, during the last 900 years from tree rings. 68 (2):196-202. DOI: 2007 A regional high-frequency reconstruction of May–June precipitation in the north Aegean from oak tree-rings, AD 1089-1989. Climatol 27 (8): 1075-1089. DOI: 2013 A 250-year annual precipitation reconstruction and drought assessment for Cyprus from Pinus brutia tree-rings. Climatol 34 (8): 2702-2714. [SEP] Justify:

Output: The text contrasts the claim by providing examples of dendrochronological studies conducted on trees in non-tropical regions, specifically mentioning a '924-year regional oak tree-ring chronology for North-Central Turkey' and further reconstructions of precipitation linked to various tree species, including oaks and pines, in Mediterranean climates. This indicates that trees outside of tropical regions are also significant for dendrochronological research.


Input: Task: pass the claim using the given text. Claim: Proteomics studies the entire set of proteins expressed in a cell. [SEP] Text: The digested plasma samples were run in triplicate and the data were analyzed by ProteinServer 4. 2 software (PLGS; ) (Aggarwal et al. , 2017). Each sample was injected three times to obtain technical triplicates. Label-free quantification To quantify the proteins from the LC-MS/MS, a label-free quantification analysis was performed using 8. 0 (Inc. , ) (Zhang et al. , 2012). Independent samples from each triplicate analysis were studied and compared between patients and the controls. Total raw data files were imported and processed using the Peaks software program for the interpretation of spectra and the retention time was set from 600 to 10,500 s. An in-house constructed Uniprot’s reference database of Homo sapiens (release 03_2014) contained 20,272 entries was added and combined with a decoy database (the sequences were reversed). For label-free quantification the following parameters were specified: enzymatic digestion by trypsin, with two missed cleavages; precursor mass tolerance was 10 ppm; fragment mass tolerance: 0. 7 Da, minimum charge: 2, maximum charge: 3. The specified fixed and variable modification consisted of carbamidomethylation (Cys), oxidation (M), and deamidated (N and Q). To determine the false-positive identification rate, the estimated spectra was used against decoy database. A false discovery rate (FDR) of ≤1%, with a peptide score of −10 log p ≥ 20 was considered adequate for confident protein identification. To determine the relative protein and peptide abundance in the tested samples, peptide feature based quantification was performed. The signal intensity of a peptide is directly proportional to the abundance of the peptide in the sample, therefore, the confidently identified peptide features were matched and the peptide intensity differences between two samples were able to be estimated. Likewise, the area under the curve of the extracted ion chromatograms (XICs) was measured and compared between two analyzed runs. To get the summed cumulative peak area of the protein, only unique peptides that are assigned to particular proteins were selected. The FDR was calculated based on the target/decoy database, and the peptides with an FDR of ≤1% were chosen as true positive hits (considering the risk of having one false positive in 20 observations). [SEP] Justify:

Output: The text provides a detailed description of a method used for protein quantification in samples but does not directly address or support the claim regarding the overall focus of proteomics on studying the entire set of proteins expressed in a cell. The methodologies described are relevant to proteomics but do not explicitly corroborate the claim that proteomics encompasses the entire set of proteins.


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: Linking neural activity and molecular oscillations in the SCN. Neurosci. 2011; 12: 553–69. DOI: Danguir, J. Sleep deficits in rats with hereditary diabetes insipidus. Nature. 1983; 304: 163–4. DOI: Hastings, MH, Brancaccio, M and Maywood, ES. Circadian pacemaking in cells and circuits of the suprachiasmatic nucleus. J Neuroendocrinol. 2014; 26: 2–10. DOI: and Zhou, QY. Altered circadian and homeostatic sleep regulation in prokineticin 2-deficient mice. Sleep. 2007; 30: 247–56. and Mihai, R. Vasopressin neurotransmission and the control of circadian rhythms in the suprachiasmatic nucleus. Res. 1998; 119: 351–64. DOI: de Vries, GJ and Reppert, SM. A molecular mechanism regulating rhythmic output from the suprachiasmatic circadian clock. Cell. 1999; 96: 57–68. DOI: Kalsbeek, A, van Heerikhuize, JJ, Wortel, J and Buijs, RM. A diurnal rhythm of stimulatory input to the hypothalamo-pituitary-adrenal system as revealed by timed intrahypothalamic administration of the vasopressin V1 antagonist. J Neurosci. 1996; 16: 5555–65. DOI: -and Buijs, RM. SCN outputs and the hypothalamic balance of life. J Biol Rhythms. 2006; 21: 458–69. DOI: Kuhlman, SJ and McMahon, DG. Encoding the ins and outs of circadian pacemaking. J Biol Rhythms. 2006; 21: 470–81. DOI: Leak, RK and Moore, RY. Topographic organization of suprachiasmatic nucleus projection neurons. J Comp Neurol. 2001; 433: 312–34. DOI: and Zhou, QY. Attenuated circadian rhythms in mice lacking the prokineticin 2 gene. J Neurosci. 2006; 26: 11615–23. DOI: and Zhou, QY. [SEP] Justify:

Output: The text corroborates the claim by referencing multiple studies that discuss the role of the suprachiasmatic nucleus (SCN) in regulating circadian rhythms. It mentions specific research on neural activity and molecular oscillations within the SCN, reinforcing the concept that the SCN acts as a master clock for biological rhythms.


Input: Task: contrast the claim using the given text. Claim: All mollusks live in saltwater environments and cannot survive in freshwater. [SEP] Text: 1 This guide describes procedures for obtaining laboratory data concerning bioconcentration of a test material added to dilution water—but not to food—by freshwater and saltwater fishes and saltwater bivalve mollusks using the flow-through technique. These procedures also should be useful for conducting bioconcentration tests with other aquatic species, although modifications might be necessary. 1. 2 Other modifications of these procedures might be justified by special needs or circumstances. Although using appropriate procedures is more important than following prescribed procedures, the results of tests conducted using unusual procedures are not likely to be comparable to those of many other tests. The comparison of results obtained using modified and unmodified versions of these procedures might provide useful information concerning new concepts and procedures for conducting bioconcentration tests. 1. 3 These procedures are applicable to all chemicals that can be measured accurately at the necessary concentrations in water and in appropriate tissues. Bioconcentration tests are usually conducted on individual chemicals but can be conducted on mixtures if appropriate measurements can be made. Some techniques described in this guide were developed for tests on non-ionizable organic chemicals (see 11. 1. 2. 1) and might not apply to ionizable or inorganic chemicals. 1. 4 Results of bioconcentration tests should usually be reported in terms of apparent steady-state and projected steady-state bioconcentration factors (BCFs) and uptake and depuration rate constants. Results should be reported in terms of whole body for fishes and in terms of total soft tissue for bivalve mollusks. For fishes and scallops consumed by humans, some results should also be reported in terms of the edible portion, especially if ingestion of the test material by humans is a major concern. For tests on organic and organometallic chemicals, the percent lipids of the tissue should be reported. 1. 5 This guide is arranged as follows: Documents 2 Terminology 3 Summary of Guide 4 Significance and Use 5 7 Apparatus 6 Facilities 6. 1 6. 2 6. 3 6. 4 Cleaning 6. 4. 4 Acceptability 6. 5 8 Requirements 8. 1 Source 8. 2 Treatment 8. 3 Characterization 8. 4 9 General 9. 1 9. 2 9. 3 Test Concentration(s) 9. 4 10 Species 10. 1 Size 10. 2 Source 10. 3 Care and Handling 10. 4 Feeding 10. 5 10. 6 Holding 10. [SEP] Justify:

Output: The text contrasts the claim by discussing 'saltwater bivalve mollusks' and their role in bioconcentration tests, implying that at least some mollusks can live and be tested in both freshwater and saltwater environments. The description indicates procedures for testing that involve both types of environments, suggesting that not all mollusks are restricted 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: Protein identification For the identification of proteins, the UniProtKB database (UniProt release 2015-10) and for Biotechnology non-redundant (NCBInr) was used for the database search using the Mascot software (version 2. 2, search engine. The following parameters were specified for searching altered proteins: enzymatic digestion by trypsin with two missed cleavages, followed by carbamidomethyl as fixed and oxidation (M) as variable modifications. The peptide mass tolerance was set at 50 ppm and the MS/MS tolerance was set at 0. 1 Da with an FDR of ≤ 1%. Proteins identified in all three technical replicates or in at least two of the three analyses were considered to be identified and their theoretical molecular mass (MW) and isoelectric point (pI) were determined using Mascot database. Bioinformatics analysis To interpret the biological processes (BPs), molecular functions (MFs), and cellular components (CCs) of the identified proteins, the international standardized gene function classification system of gene ontology (GO) ( and the DAVID ( (Visualization, and Integrated Discovery) database with for functional analysis were used (Huang, Sherman & Lempicki, 2009). For the protein–protein interaction (PPI) networks among these proteins, the (for the Retrieval of Interacting Genes/Proteins, Version 9. 1) database at the website: with default parameters were used. Statistical analysis The LC-ESI-MS/MS data was measured using peptide feature based and spectral counting based quantification in order to identify the differences in protein expression levels. Data are expressed as the mean ± standard deviation and differences were determined using two independent sample t-test and a paired t-test were used to determine the differentially regulated proteins between SLE and healthy controls. Statistical analysis were performed using the SPSS statistical package (SPSS16; SPSS Ltd. , Working, and Surrey, UK) for Windows. A probability value of less than 0. 05 with 95% confidence limit was considered as statistically significant and of p-values <0. 01 were considered as highly significant. for novel protein biomarkers from human biological fluids is able to provide essential clinical information and such information needs to be revealed via a range of proteomic strategies. [SEP] Justify:

Output: The text does not provide relevant information about the definition of proteomics or its focus on the entire set of proteins expressed in a cell. Instead, it details a specific methodology for protein identification and analysis without directly addressing the claim about what proteomics 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: Vasopressin receptor V1a regulates circadian rhythms of locomotor activity and expression of clock-controlled genes in the suprachiasmatic nuclei. . 2009; 296: R824–30. DOI: and Zhou, QY. The circadian output signals from the suprachiasmatic nuclei. Res. 2012; 199: 119–27. DOI: and Zhou, QY. Identification and molecular characterization of two closely related G protein-coupled receptors activated by prokineticins/endocrine gland vascular endothelial growth factor. J Biol Chem. 2002; 277: 19276–80. DOI: Loh, DH, Kudo, T and Colwell, CS. Short circuiting the circadian system with a new generation of precision tools. Neuron. 2015; 85: 895–8. DOI: and Sakurai, T. in AVP Neurons of the SCN for. Neuron. 2015; 85: 1103–16. DOI: Mistlberger, RE. Circadian regulation of sleep in mammals: role of the suprachiasmatic nucleus. Rev. 2005; 49: 429–54. DOI: and Hogenesch, JB. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell. 2002; 109: 307–20. DOI: and Maywood, ES. Prokineticin receptor 2 (Prokr2) is essential for the regulation of circadian behavior by the suprachiasmatic nuclei. . 2007; 104: 648–53. DOI: ’and Hu, WP. Prokineticin 2 regulates the electrical activity of rat suprachiasmatic nuclei neurons. PLoS One. 2011; 6: e20263. DOI: Reppert, SM and Weaver, DR. Coordination of circadian timing in mammals. Nature. 2002; 418: 935–41. DOI: Saper, CB, Cano, G and Scammell, TE. Homeostatic, circadian, and emotional regulation of sleep. J Comp Neurol. 2005; 493: 92–8. DOI: and Lehman, MN. A secreted coupling signal from the transplanted suprachiasmatic nucleus controlling circadian locomotor rhythms. Nature. [SEP] Justify:

Output: The text corroborates the claim by discussing the role of the suprachiasmatic nucleus (SCN) in regulating circadian rhythms, specifically mentioning the involvement of vasopressin receptors and other molecular mechanisms associated with circadian control within the SCN. This supports the designation of the SCN as the master clock in 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: Some cultivated oil degrading aerobic microorganisms such as Alcanivorax have been found to degrade pentadecane 15 and to bloom following cyanobacterial pentadecane amendments in seawater incubations 12. However, there is a gap in knowledge of in situ diversity of bacterial hydrocarbon degraders in the absence of petroleum (thermogenic) hydrocarbons that confound interpretations. Similarly, the contribution of non-phototrophic microorganisms to hydrocarbon production in marine waters has been little explored, yet the aphotic zone represents 90% of the ocean volume and non-cyanobacterial alkane production pathways have been identified 16,17. In addition, the distribution of this cryptic hydrocarbon cycle along oxygen, salinity and light gradients of aquatic ecosystems has not been addressed to date, notably under freshwater conditions where Cyanobacteria also flourish. The polar regions host numerous marine-derived lakes that formed following the isostatic rebound of the continents triggered by the melting of the ice sheets. Physically isolated from the ocean, freshwater from melting snow and ice accumulates over the trapped marine water. Due to the strong density and temperature differences between these waters, these lakes are highly stratified, with a mixolimnion consisting of the oxic surface freshwater layer immediately beneath the ice, and an anoxic (oxygen below detection; < 1 µM) marine monimolimnion at the bottom. The chemocline at the interface between these layers is the zone of highest chemical reactivity, associated with elevated microbial activities 18,19. is one such lake at the extreme north of the Arctic, and is a remote pristine ecosystem and natural laboratory to investigate microbial community assemblages and metabolism. The microbiome of the has been previously investigated 20–22, revealing a marked stratification of stable and active microorganisms and associated metabolic potentials following the salinity, light and redox gradients of the water column (Fig. 1). has physical, chemical and microbiological similarities with freshwater-, marine-, hadal- and deep-sea-like environments, and therefore offered an outstanding opportunity to investigate the hydrocarbon short cycle over a broad range of environmental conditions that are relevant to marine and freshwater ecosystems, and without interference from anthropogenic contaminants and natural seepage. [SEP] Justify:

Output: The text contrasts the claim by discussing the existence of aquatic ecosystems that encompass both freshwater and marine environments. It highlights the presence of numerous marine-derived lakes in polar regions that host unique microbial communities, suggesting that not all organisms require exclusively saltwater to survive. The mention of lakes being physically isolated from the ocean yet containing marine characteristics challenges the assertion that all mollusks, or aquatic organisms, can only thrive 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: 25 P18 173,378 36,186 0. 43 1. 26 P19 165,812 45,981 0. 42 1. 33 Overall 3,045,885 712,707 8. 25 24. 62 Healthy controls Total spectra Distict peptides FDR spectra FDR distinct peptide (%) H1 138,215 48,118 0. 31 1. 24 H2 196,228 56,286 0. 43 1. 23 H3 195,912 65,181 0. 47 1. 31 H4 177,050 47,143 0. 44 1. 34 H5 199,295 57,928 0. 38 1. 39 H6 189,378 39,196 0. 41 1. 22 H7 165,912 41,991 0. 41 1. 24 H8 177,550 39,823 0. 38 1. 24 H9 159,295 39,938 0. 41 1. 27 H10 193,378 39,186 0. 44 1. 28 H11 181,702 38,981 0. 45 1. 44 H12 152,080 38,643 0. 41 1. 33 Overall 2,125,995 552,414 4. 94 15. 53 DOI: 10. 7717/peerj. 4730/table-2 Note: * Total spectra observed for protein groups. A total of 122 proteins (homologs/same name proteins were eliminated) from the SLE patients were identified (Tables S1 and S7), and 143 proteins were identified from the healthy controls with the molecular masses ranging from 9 to 550 kDa and isoelectric point ranging from 3. 4 to 9. 0. Out of the 122 proteins, 19 were found to have significant changes in their expression levels, including 14 up-regulated and five down-regulated; all of these fulfilled the appropriate statistical criteria (either p < 0. 01 or p < 0. 05). A comparative LC-MS/MS base peak intensity (BPI) chromatograms of SLE and healthy controls were shown in Fig. 1. The BPI chromatograms show the number of marked variations in the patient group than in the control group. All of the proteins were identified by the presence of more than two and up to ten unique peptides with a protein score of >70, and a significance score of <20. [SEP] Justify:

Output: The text does not address the claim directly; instead, it presents specific numerical data regarding protein expression levels in patients and controls without explaining the broader context of proteomics. Therefore, it is irrelevant to the claim about proteomics studying the entire set of proteins.


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: Our finding that DCX is also expressed in neurons of the adult SCN is therefore a significant addition to our understanding of the adult roles of DCX. Furthermore, our findings add a potentially important new avenue of research into the molecular and functional organization of the SCN. The mammalian SCN is a discrete and yet complex neuronal cell group that has been extensively characterized in recent years. This hypothalamic nucleus is the subject of intense study because it forms the brain's 'master' circadian clock, coordinating daily rhythms of central and peripheral physiology, rhythms that impact upon health and disease [10, 16]. Molecular circadian clocks are not an exclusive property of SCN cells [16] but the intrinsic organization and extrinsic connections of the SCN provide it with a unique and central position in circadian control. The SCN contains many different neurotransmitters and neuropeptides [9, 17], neurochemical components that subserve both inputs to the SCN [9, 18] and also outputs that effect control over autonomic physiology [19]. Our finding that the SCN is, with respect to other hypothalamic and thalamic nuclei, an exclusive locus of adult DCX expression suggests that DCX is somewhat uniquely required in these SCN cells, and may therefore confer a specific property required for circadian function. Suprachiasmatic nucleus – a brain region of low NeuN expressionA second novel and interesting finding of the present study is that the SCN is a region of low NeuN expression. This finding would appear to be in accord with high DCX expression because down-regulation of DCX in differentiating neurons coincides with up-regulation of the mature neuronal marker protein NeuN [15]. However, we have found an apparently paradoxical inverse correlation in that NeuN is undetectable only in dorsal SCN neurons, whereas DCX is restricted to ventral SCN neurons, and is generally co-localized with NeuN. The functional significance of reduced NeuN expression in the SCN is unclear because although a limited number of other neurons including cerebellar Purkinje cells, and retinal phoreceptors do not express NeuN [14], the physiological role of this protein remains undefined. However, our finding defines an additional unusual property of SCN cells, in this case dorsal SCN neurons, that may relate to circadian function. [SEP] Justify:

Output: The text corroborates the claim by confirming that the SCN is referred to as the brain's 'master' circadian clock, which coordinates daily rhythms of physiology, thereby regulating circadian rhythms. It emphasizes the significance of the SCN in controlling these rhythms, which is integral to the claim being analyzed.


Input: Task: contrast the claim using the given text. Claim: All mollusks live in saltwater environments and cannot survive in freshwater. [SEP] Text: By contrast, genes coding for enzymes involved in the oxidation of sulfide (SQR) and thiosulfate (doxD, tsdA) and sulfate reduction (aprAB, dsrAB) were the most detected in hydrocarbon degraders. Potential sulfide oxidizers included members of the Marinimicrobia, Bacteroidales and Alphaproteobacteria lineages, whereas thiosulfate oxidizers were related to other Bacteroidetes lineages (Flavobacteriales including Scheiferiaceae, Cytophagales and Cryomorphaceae). Sulfate reduction pathway genes were identified in Desulfatiglandales, Syntrophales, and Abyssubacteria. In addition, dissimilatory nitrate reductase and sulfur oxidation genes were also identified in the highly dominant Nanopelagicales MAG with hydrocarbon degradation genes, whereas in the highly dominant Marinimicrobia MAGs sulfur oxidation genes were identified along nitrous-oxide reductase genes (Supplementary Fig. 1). hydrocarbon short cycle The upper water layer (0–12 m) of meromictic is derived from the snow and ice melt, leading to a freshwater stable environment (salinity < 0. 7 ppt) 23. This was consistent with, the microbial community composition being dominated by freshwater taxa, including Flavobacteriales (Bacteroidia), Burkholderiales (Betaproteobacteria), Nanopelagicales (ex Actinobacteria acl) and Cyanobacteria (Fig. 1), which are frequent major lineages in cold lakes and rivers 24,25. These lineages were previously detected using 16S rRNA sequencing, supporting an active metabolism at these depths 20. Cyanobacteria have been also detected in the anoxic dark waters, as in other polar meromictic lakes 26 and are a major constituent of the phototrophic plankton of 27. Multiple genes of long-chain fatty aldehyde decarbonylase (FAD) and aldehyde deformylating oxygenase (ADO), both producing C16-C18 alkanes 11, were identified in the 2m and 6m metagenomes, suggesting a strong potential for bacterial long-chain alkane production in the upper freshwater layer of the lake. [SEP] Justify:

Output: The text contrasts the claim by providing evidence that certain microbial communities and organisms, including those found in freshwater environments, can thrive in conditions that contradict the claim regarding mollusks. It mentions that the upper water layer of meromictic environments is derived from snow and ice melt, leading to a freshwater stable environment, which supports the presence and dominance of microbial taxa common in freshwater systems. This implies that certain life forms, potentially including organisms similar to mollusks, can adapt and live in freshwater, countering the assertion that all mollusks can only be found in 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: 72 ± 0. 1 0. 29 ± 0. 03 2. 47 + Immune response and regulation 0. 02 Ig kappa variable chain 105 IGKV1 KV105_HUMAN 132 11 12. 8 28. 9 86556. 5 ± 32535. 1 8556. 5 ± 5003. 5 10. 1 4. 51 ± 0. 23 0. 27 ± 0. 02 16. 7 + Immune response and regulation 0. 01 Acute phase proteins _HUMAN 2792 37 77 80. 8 313293. 8 ± 44564. 8 134161 ± 24375 2. 3 3. 28 ± 0. 1 1. 19 ± 0. 03 2. 2 + Iron transport 0. 004 _HUMAN 1093 26 122. 4 45. 2 16466. 94 ± 48797. 0 45533. 827 ± 6382. 4 3. 6 0. 37 ± 0. 03 0. 16 ± 0. 03 2. 3 + Iron transport 0. 01 _HUMAN 345 13 515 35. 8 31774. 2 ± 14099. 0 8020. 16 ± 931. 8 4 0. 26 ± 0. 05 0. 11 ± 0. 01 2. 4 + Lipid metabolism 0. 04 _HUMAN 189 12 52. 4 12 30586. 1 ± 12888. 3 8213311212. 8 ± 0. 3 0. 4 1. 15 ± 0. 06 1. 74 ± 0. 21 0. 6 − Innate immune response 0. 006 Apolipoprotein A1 APOA1 APOA1_HUMAN 161 10 30. 77 16 59486. 2 ± 15316. 8 122721. 61 ± 17765. 9 0. 5 39. 45 ± 6. 10 142. 53 ± 8. 2 0. 2 − Lipid transport 0. 009 Apolipoprotein A2 APOA2 APOA2_HUMAN 56 2 11. 75 53. 33 41611. 2 ± 13333. 1 67031. 6 ± 7289. 8 0. 6 43. 21 ± 5. 1 213. 42 ± 9. 12 0. 2 − Lipid transport 0. 04 Alpha-2-macroglobulin A2M A2MG_HUMAN 1290 77 163. 2 47. 8 6870155. 6 ± 1014642. [SEP] Justify:

Output: The text does not address the claim regarding proteomics, as it consists mainly of numerical data, specific variables, and references to proteins without context or explanation related to the study of all 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: Journal of Circadian RhythmsStart SubmissionBecome a ReviewerReading: of Melatonin MT1 and MT2 in the (US English)PDF (US English)Alt. DisplayShareShareResearch 2. The hypothesis that the density of these receptors varies across the circadian cycle was tested. Using immunohistochemistry with receptor-specific antibodies, the localization and distribution of melatonin receptors MT1 and MT2 was studied in the SCN at different circadian times (CT): CT 11–13 (dusk), 23-01 (dawn), 5-7 (mid-day), and 17-19 (midnight). Our results show that MT1 receptor density significantly increased at dusk relative to dawn and midnight (p<0. 01 and p<0. 001 respectively). Although MT1 receptors were wide spread in the SCN and parts of the optic chiasm at dusk, it was restricted to the SCN during mid-day period. MT2 receptors were not detected in the SCN. In conclusion, melatonin receptor MT1 density and distribution varies with circadian time. This creates a time window at which melatonin exerts its circadian phase shifts on the SCN. This also suggests that melatonin regulates SCN function via MT1 receptors with a minimal role for MT2. Keywords:melatonin receptorsSCNcircadian rhythmYear: 2015Page/10. 5334/jcr. abPublished on Mar 10, 20154. 0 1. Introduction Melatonin, “the chemical expression of darkness” [20], is a neuroendocrine hormone synthesized and secreted by the pineal gland [4, 25]. There is a circadian rhythm in melatonin synthesis and secretion that peaks at night and troughs during the day [20]. The circadian rhythm of melatonin synthesis is driven by the intrinsic circadian activity of the suprachiasmatic nucleus (SCN). This small paired nucleus in the anterior hypothalamus is entrained to a 24-hour period by the light/dark cycle (LD) [14]. The SCN is strategically positioned to receive visual input for LD entrainment through the retino-hypothalamic tracts [22]. On the other hand, melatonin feeds back on the SCN to regulate its function by modulation of SCN electrical activity [11, 12], resetting the clock [5, 6] and synchronizing locomotor activity [17, 19, 24]. [SEP] Justify:

Output: The text corroborates the claim by explaining that the suprachiasmatic nucleus (SCN) is responsible for driving the circadian rhythm of melatonin synthesis, thus acting as a master clock. It mentions that the SCN is entrained to a 24-hour cycle by the light/dark cycle and describes how melatonin feedback regulates the function of the SCN, affirming its critical role in 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: Based on the taxonomic affiliation of the contigs and MAGs with those genes, lacustrine Flavobacteriaceae and Cyanobacteria populations were likely the main hydrocarbon producers in this freshwater habitat. This indicates a new ecological role for Flavobacteriaceae members in these ecosystems, and suggests that the potential for hydrocarbon production in Cyanobacteria is not limited to marine species, providing field confirmation of results based on Cyanobacteria culture studies 28. Consistent with the bacterial production of long chain alkanes, genes coding for C15-C36 alkane monooxygenase (LadA), conferring the ability to degrade long-chain alkanes were also detected at 2m and 6m. The identification of these genes in two MAGs affiliated to Actinomycetales and Alpinimonas (Microbacteriaceae) that were recovered at 2m, suggests that long chain alkanes produced by the Flavobacteriaceae and Cyanobacteria could be readily degraded by members of the Actinobacteria phylum (Fig. 5). Likewise, numerous genes coding for alkane monooxygenase (alkB), and in lesser proportion cytochrome P450 alkane hydroxylase (CYP153), were also detected in the freshwater layer. Identified in MAGs affiliated to Burkholderiales, Sediminibacterium, Alphaproteobacteria and Nanopelagicales, these genes code for enzymes that confer the ability to degrade a large variety of (C5-C16) alkanes and alkenes that fall within the range of fatty aldehyde decarbonylase and aldehyde deformylating oxygenase products. By contrast, genes encoding for shorter hydrocarbon (methane, butane, propane) oxidation and aromatic hydrocarbon degradation were either not or little detected, suggesting that the hydrocarbon catabolism is centered on bacterial long-chain alkanes. Together these results indicate that long-chain hydrocarbon cycling, suspected to occur in oceans, also occurs in the upper low-conductivity layer of Lake A, extending the potential niche for this cycle to freshwaters. [SEP] Justify:

Output: The text contrasts the claim by discussing ecological roles and processes that occur specifically in freshwater habitats, indicating that certain life forms, including bacteria and their roles in hydrocarbon production, can thrive in freshwater environments. This suggests that the assertion that all mollusks are saltwater-dependent is not universally applicable, as it ignores the existence and ecological significance of organisms in freshwater environments.