Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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].

Output: contrast


Input: 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).

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: 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).

Output: pass


Input: 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].

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: 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).

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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].

Output: corroborate


Input: 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.

Output: contrast


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

Output: pass


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

Output: corroborate


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

Output: contrast


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

Output: pass


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

Output: corroborate


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

Output: contrast


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

Output: pass


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

Output: pass


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

Output: contrast


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

Output: pass


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

Output: corroborate


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

Output: contrast


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

Output: pass


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

Output: corroborate


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

Output: contrast


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

Output: pass


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

Output: corroborate


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

Output: contrast


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

Output: pass


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

Output: corroborate


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

Output: contrast


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

Output: pass


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

Output: corroborate


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

Output: contrast


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

Output: pass