Input: Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: ”Minor concerns:Title: I am not sure the comma is needed between hyperarid and phosphateResponse: I removed the commaLine 210: picrust should be 2Response: corrected (L208). Line 214: I think this should be spelled out more completely. It just sends the reader to a reference. This is a specialized set of functional annotations. I think it would help the reader interpret Figure 6 and where the annotations are coming from. Response: I added a description of the referenced study and explained the source of the functional annotations (L213 – L218):“…The function categories were chosen based on Meier et al. (2021). In their study, Meier et al. collected biocrusts from the Negev and analyzed bacterial metagenomes in the biocrusts to evaluate the distribution of metabolic potential among bacterial populations. To compare functional potential between various bacterial phyla, they selected metabolic genes encoded in the metagenomic-assembled genomes and grouped them into 10 function categories. ” Citation: RC2: 'Comment on egusphere-2022-1510', #2, 04 Mar 2023 This study is interesting as it identifies which bacteria proliferate in biocrusts from natural and postmining areas and examines functional gene abundances unlike previous studies that have focused on characterizing the microbial community composition of natural and post-mining biocrusts. This, I consider the approach novel. Nonetheless, I have a few comments that should be addressed:AbstractL19-23. I recommend deleting this sentence because it refers to a previous study, and the abstract should focus on the objectives and results of the present study. Then, in the Introduction or the Discussion, it is fine if mention to previous results is done. M&ML103-105. It is not clear the predominant p109. Add a short description of the biocrust sampled (thickness, cover, composition, …. ). Were there differences in the biocrust from natural and post-mining sites? ResultsRegarding the results of the proliferated bacterial community composition, it would be nice to include a figure with the relative abundances of the different bacteria phylum for natural and post-mining biocrusts to make the results clearer. DiscussionL354-357. Can you remind here when was the sampled post-mining site restored? Was it at 2007?

Output: contrast


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: Effects of the mu-opioid receptor antagonist GSK1521498 on hedonic and consummatory eating behaviour: a proof of mechanism study in binge-eating obese subjects. Mol Psychiatry. 2013; 18(12): 1287–1293. 46. Neural and behavioral effects of a novel mu opioid receptor antagonist in binge-eating obese people. Biol Psychiatry. 2013; 73(9): 887–894. 47. Effects of mu opioid receptor antagonism on cognition in obese binge-eating individuals. Psychopharmacology (Berl). 2012; 224(4): 501–509. 48. . Acute effects of morphine on distinct forms of impulsive behavior in rats. Psychopharmacology (Berl). 2009; 205(3): 489–502. 49. Wiskerke, J, Schetters, D, van Es, IE, et al. mu-Opioid receptors in the nucleus accumbens shell region mediate the effects of amphetamine on inhibitory control but not impulsive choice. J Neurosci. 2011; 31(1): 262–272.

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: Indirect pathways of demethylation are associated with DNA repair [11–14]. Two main stages, PGCs and preimplantation embryos, are important in the regulation by methylation. 2. 1. Epigenetic modification of the zygote and the preimplantation embryosIn mammals (human, bovine, rat, pig and mouse), the zygote undergoes genome‐wide demethylation [15–17] with the exception of imprinted genes [18]. The male pronucleus of the zygote undergoes selective demethylation due to the loss of DNA replication leading to asymmetric methylated sister chromatids [15, 16, 19, 20]. These events start following the sperm decondensation in humans and in mouse with some variations [17, 21, 22]. The female pronucleus of the zygote remains highly methylated at this stage [17, 21, 22]. Demethylation of the maternal genome starts with the first cleavage divisions [19, 23, 24]. By the morula stage, the mouse preimplantation embryos become undermethylated. Polarisation and compaction of individual blastomeres start at around eight‐cell stage of the developing embryo. Many factors are involved in these processes including E‐cadherin (CDH1), partitioning defective homologue 3 (PARD3), PARD6B and protein kinase C zeta [25–27]. The blastocyst stage embryo has a fluid‐filled cavity and two cell populations consisting of inner cell mass (ICM) and trophectoderm (TE). All the blastomeres are believed to be totipotent in cleavage embryos until four‐ to eight‐cell stage since these cells form both the ICM and TE lineage [28]. ICM develops into epiblast, whereas TE forms the extraembryonic tissues such as placenta. ICM is composed of pluripotent cells that have the capacity to develop into any cell type of the foetus. Transcriptional and epigenetic events strictly regulate these differentiation events. A number of transcriptional factors play a crucial role in blastocyst formation. These include caudal type homeobox 2 (CDX2) for TE specification, octamer 3/4 (OCT4) and NANOG for the establishment of ICM pluripotency [29–31].

Output: corroborate


Input: Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: Response: I added a description of the biocrusts in Gov mining site (L106 – L109):“…Biocrusts were sampled either from the post-mining site or the adjacent natural area. The biocrusts in Gov are thin (between 1. 5 - 2. 5 mm deep), and smooth. The site is characterized by areas covered in biocrusts or desert pavement. In each sampling site, we sampled along a 100 m strip at approximately 10 m intervals (Fig. 1). ”ResultsRegarding the results of the proliferated bacterial community composition, it would be nice to include a figure with the relative abundances of the different bacteria phylum for natural and post-mining biocrusts to make the results clearer. Response: Added a bar plot of Phyla relative abundances to the PCoA ordination in figure 5 (labeled ‘a’ and ‘b’) and statistical data in the supplementary file (Table S4). DiscussionL354-357. Can you remind here when was the sampled post-mining site restored? Was it at 2007? I wonder if one reason for the lack of photosynthetic potential difference between post-mining and natural biocrusts is because the biocrust in the post-mining site has been already recovered. For example, soil colonization by cyanobacteria can be faster than thought. Response: I mentioned the restoration year in L375. I agree that it is likely that the biocrusts we sampled have a significant cyanobacterial community, however we hypothesize that the recovery of the biocrust differs even within the mining site, emphasizing the importance of microenvironments, where certain areas have more developed biocrusts and others have less developed biocrust even within the same post-mining plot. I referenced this in the discussion (L376 – L383): “…However, in the current study, we sampled post-mining biocrusts at a different location in the Gov mining site (~500 m away from the original plot) due to technical constraints. In the new location we found that the photosynthetic potential of the biocrust in the post-mining plots did not differ from the natural biocrust. These results highlight the importance of microenvironments in shaping the functionality of biocrusts (Garcia-Pichel and Belnap, 1996).

Output: contrast


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: Skip to main content Intended for healthcare professionals Search this journalSearch all journalsEnter search terms. . . Searchsearch Enter search terms. . . Searchsearch Search Access/ProfileAccessView access optionsView profileCreate profile Cart 0 by discipline Select discipline: All disciplines All disciplines Life & & Sciences & HumanitiesSelect subject: All subjects All subjects Cardiology & Medicine & Endocrinology & -legal & Orthopaedics & Medicine & & & & Methods & & & & & Criminology & Economics & & & Management & Marketing & & & & & & & & PlanningBrowse journals Sage publishes a diverse portfolio of fully journals in a variety of disciplines. you can explore our Disciplines Hubs, including: Journal portfolios in each of our subject areas. Links to Books and content from across Sage. for/ Reviewers SocietiesFrequently asked questions In this journal : 3. 1 5-Factor: 3. 3 email alertsYou are adding the following journal to your email alertsNew contentMakingCreate email alert Restricted accessReview 10. 1177/0272989X14547740ContentsAbstract2013. Predefined exclusion criteria were used to identify 213 studies. During data extraction, information was collected on type of bias or heuristic studied, respondent population, decision type, study type (actual or hypothetical), study method, and study conclusion. Results. Of the 213 studies analyzed, 164 (77%) were based on hypothetical vignettes, and 175 (82%) were conducted with representative populations. Nineteen types of cognitive biases and heuristics were found. Only 34% of studies (n = 73) investigated medical personnel, and 68% (n = 145) confirmed the presence of a bias or heuristic. Each methodological quality criterion was satisfied by more than 50% of the studies, except for sample size and validated instruments/questions. Limitations are that existing terms were used to inform search terms, and study inclusion criteria focused strictly on decision making. Conclusions. Most of the studies on biases and heuristics in medical decision making are based on hypothetical vignettes, raising concerns about applicability of these findings to actual decision making. Biases and heuristics have been underinvestigated in medical personnel compared with patients. Get full access to this 1. . Uncertainty: Heuristics and Biases. 1st ed. New York: Press; 1982. Crossref2. Kahneman D, Tversky A.

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: CDX2 is extensively expressed in eight‐ and 16‐cell stage and it is expressed only in TE cells of the blastocyst [32]. Although OCT4 and NANOG are also expressed broadly at eight‐ and 16‐cell stage embryos, they are only expressed in ICM in blastocysts [32]. A number of transcription factors are required for blastocyst formation. Embryos lacking CDX2 expression cannot form blastocoel cavity but they have the ability to implant [30]. Lack of OCT4 or NANOG expression causes failure of ICM and the development of these embryos is arrested at the blastocyst stage [31, 32]. TEAD4 is another transcription factor that has a role in blastocyst transition in which the lack of TEAD4 nuclear localisation impairs TE‐specific transcriptional programme in inner blastomeres [33]. Furthermore, the aberrant expression of TCFAP2C transcription factor also leads to embryonic arrest during morula to blastocyst transition [34] and Klf5 mouse‐mutant embryos arrest at the blastocyst stage [35]. The remethylation process starts shortly after implantation [16, 22, 23, 36]. This de novo methylation occurs asymmetrically, such that ICM is hypermethylated possibly due to the Dnmt3b methylase [37], whereas TE remains hypomethylated due to the active demethylation by enzyme catalysis and passive demethylation [11, 14, 22]. Alteration of the methylation profiles in embryos has been shown to cause alterations of ICM and TE differentiation. Variations of the H3 arginine 26 residue (H3R26me) were shown to lead to changes of TE and ICM differentiation of a blastomere [38]. X‐chromosome inactivation is an epigenetic phenomenon in which the activity of X chromosomes is strictly regulated to equalise X‐chromosome expression and gene dosage between males and females and relative to autosome chromosomes [39]. For correct development, X‐chromosome dosage compensation is crucial. The inactivation of X chromosome occurs in at least two phases: initiation and maintenance. X‐inactivation mouse model systems have shown that the inactivation of X chromosome takes place during early embryogenesis of the female embryo by undergoing transcriptional silencing of genes along the X chromosome [40].

Output: corroborate


Input: Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: The similarities in active communities and photosynthetic potential could be due to more developed biocrusts in the new sampling locations compared to the previous ones. ”L369-370. There is little discussion on the results of the Picrust analysis. It would be nice to compare the results of this study with other studies that have also examined functional genes in biocrusts to see if abundances of the functional genes at this site greatly differ from those of biocrusts of other regions. Response: I added a paragraph addressing the analysis with reference and comparison to a previous study that used to infer functional potential (L395 – L405):“…analysis revealed no significant differences in the abundances of genes within any of the function categories examined (Fig. 6). In contrast, a previous study conducted in the Highlands, examined active bacterial communities during a rain and subsequent drying (Baubin et al. , 2021). The results indicated an increase in genes related to photosynthesis, light, and sensing following the rain, while the other function categories did not vary significantly. We note that the identity and abundances of the functional genes in the dry biocrusts detected by Baubin et al. , (2021) and here (Fig. 6) are similar. Therefore, we propose that the similarity between the post-mining and natural biocrust communities (Fig. 5) reflect similar functional potential (Fig. 6). However, low abundance of active ASVs were used to infer the abundances of functional genes (Fig. 6), and large variance between samples in post-mining biocrusts could mask significant differences (Table S5). ”L379-381. It is hypothesized that the low bacterial growth in harsh environments like this one could be because biocrusts prioritize activation and preparation for desiccation over growth. However, this hypothesis cannot be fully demonstrated with the reported results. Could you add 401. Is there any practical experience of the application of cyanobacteria inoculation to restore this mining site in Israel? If so, it would be nice to add a few sentences regarding the potential of this technique to restore biocrust in the current mining site. Response: No, there have not been any active restoration measures in Zin mining sites and no previous scientific studies regarding the mining practices of ICL mining company.

Output: contrast


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: New York: HarperOne; 2012. 20. Chapman GB. Time discounting of health outcomes. In: eds. Time and Decision: Economic and on Intertemporal Choice. New York: Foundation; 2003. p 395–418. 21. Croskerry P. The importance of cognitive errors in diagnosis and strategies to minimize them. Acad Med. 2003;78(8):775–80. CrossrefPubMedWeb of Science22. Reporting guidelines for survey research: an analysis of published guidance and reporting practices. PLoS Med. 2011;8(8):e1001069. CrossrefWeb of Science23. . of Reporting (CORE) index identifies important deficiencies in observational study conference abstracts. J Clin Epidemiol. 2008;61(12):1241–9. Crossref24. Meyrick J. What is good qualitative research? A first step towards a comprehensive approach to judging rigour/quality. J Health Psychol. 2006;11(5):799–808. CrossrefPubMedWeb of Science25. . The influence of positive affect on clinical problem solving. Making. 1991;11(3):221–7. CrossrefPubMedWeb of Science26. Myers RE. Decision counseling in cancer prevention and control. Health Psychol. 2005;24(suppl 4):S71–7. CrossrefPubMedWeb of Science27. Sharman SJ. Current negative mood encourages changes in end-of-life treatment decisions and is associated with false memories. Cogn Emot. 2011;25(1):132–9. CrossrefPubMedWeb of Science28. . Affect, framing, and persuasion. J Market Res. 2003;40(1):54–64. CrossrefWeb of Science29. Action tendency emotions evoked by memorable breast cancer messages and their association with prevention and detection behaviors. Health Commun. 2010;25(8):737–46. CrossrefPubMedWeb of Science30. Fox CR, Tversky A. Ambiguity aversion and comparative ignorance. In: Kahneman D, Tversky A, eds. Choices, Values, and Frames. New York: 2000. p 528–42. Crossref31. . Attitudes of obstetricians and gynecologists toward hormone replacement therapy. Making. 1998;18(4):406–11. CrossrefPubMedWeb of Science32.

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: In human preimplantation embryos, it has been shown that the reduced expression of X chromosomes in females ensures the dosage compensation [41]. expression activates the X‐chromosome inactivation by engaging proteins functioning in chromatin remodelling [3, 42]. With the advanced technologies, including single‐cell RNA sequencing, it has emerged that lncand XIST are expressed on the active X chromosome in the early human preimplantation embryos [43]. Furthermore, the expression of these two RNAs has never been shown to overlap. Introducing XACT into heterologous systems caused the accumulation of Xist RNA in cis and therefore it may be involved in the control of XIST association to chromosome in cis and may temper its ability of silencing. It is also possible that XACT functions in balancing the X‐chromosome inactivation at the early stages of preimplantation embryo development [43, 44]. Recently, the dosage compensation was shown to be driven by a CAG promoter of a new Xist allele (Xist(CAG)) [45]. Furthermore, Xist(CAG) upregulation in preimplantation embryos showed variation depending on the parental origin and the paternal expression was suggested to be preferentially inactivated with the paternal Xist(CAG) transmission [45]. 2. 2. Epigenetic modification of the gametesIn germ cells, methylation is maintained in a sex‐specific manner. Methylation in PGCs diminishes as they migrate to the gonads. Studies suggest that in females, remethylation occurs after birth when the oocytes are in the process of development. When demethylation is completed, the PGCs either enter mitosis in males or arrest at meiosis in females [46]. Reprogramming of the methylation in the embryo is necessary for parent‐specific expression of genes [14]. Gene expression varies during preimplantation embryo development due to these reprogramming events and appropriate gene expression determines the survival of the embryo [6]. Recently, short noncoding RNAs, microRNAs (miRNAs) and long noncoding RNAs (lncRNA) have gained importance in their potential function to affect numerous pathways by targeting multiple genes [47, 48]. Advertisement 3.

Output: corroborate


Input: Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: I address the need for active restoration measures in Zin mining sites (including cyanobacteria inoculation) in L439 – L444:“…Our results further emphasize the need for active restoration measures in the Zin mines. Such measures include soil inoculation with local cyanobacterial propagules (Acea, 2003, Wang et al. , 2009, Zhao et al. , 2016, et al. , 2017) and increased hydration (Morillas & Gallardo, 2015, Zhang et al. , 2018), which were effective in enhancing biocrust establishment and recovery following disturbances (Antoninka et al. , 2020). ”Table 1. Values should also include the standard deviation. Response: I added SD values to the table (L254 – L254). Citation: Report abuse × Please provide a reason why you see this comment as being abusive. You might include your name and email but you can also stay anonymous. Please provide a reason why you see this comment as being abusive. Please confirm reCaptcha. Comment* Name: Email: discussion Status: closed Comment types: AC – author | RC – referee | CC – community | EC – editor | CEC – chief editor | : Report abuse RC1: 'Comment on egusphere-2022-1510', #1, 03 Feb 2023 The manuscript “Only a minority of bacteria grow after wetting in both natural and post-mining biocrusts in a hyperarid, phosphate mine” presents the results of a H2-18-O stable isotope probing assay of the growing community members in hyperarid biocrusts that have been disturbed, or not, by mining activities. Overall, the manuscript is well conceived, written, and presented. The conclusions are sound and justified. I do have a concern that the authors have missed a swath of the literature that reports the response of biocrusts to physical disturbances, such as chronic physical trampling. These data show that physical disturbances differ from other disturbances and may affect the recovery of the biocrust community. I think some of this literature should be discussed in the context of what these authors see, and how it may be unique in these hyperarid sites. Similarly, transcriptomic studies that show the genes that are expressed during a wetting pulse and have documented metabolic a physiological changes in the bacterial community in a wetting pulse.

Output: contrast


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: CrossrefWeb of Science45. Kahneman D, Tversky A. Introduction judgment under uncertainty: Heuristics and biases. In: eds. Judgment under Uncertainty: Heuristics and Biases. New York: Press; 1982. Crossref46. . Early adoption of BRCA1/2 testing: who and why. Genet Med. 2003;5(2):92–8. CrossrefPubMedWeb of Science47. Parental angst making and revisiting decisions about treatment of attention-deficit/hyperactivity disorder. Pediatrics. 2009;124(2):580–9. CrossrefPubMedWeb of Science48. . Barriers to physician adherence to nonsteroidal anti-inflammatory drug guidelines: a qualitative study. Ther. 2008;28(6):789–98. CrossrefPubMedWeb of Science49. -Degnan D, Normand S-LT, Soumerai SB. Impact of adverse events on prescribing warfarin in patients with atrial fibrillation: matched pair analysis. BMJ. 2006;332(7534):141–5. CrossrefPubMed50. Cioffi J. A study of the use of past experiences in clinical decision making in emergency situations. Nurs Stud. 2001;38(5):591–9. CrossrefPubMedWeb of Science51. . Can induced anxiety from a negative earlier experience influence vascular surgeons’ statistical decision-making? A randomized field experiment with an abdominal aortic aneurysm analog. J Surg. 2006;203(5):642–52. CrossrefPubMedWeb of Science52. -. Narratives that address affective forecasting errors reduce perceived barriers to colorectal cancer screening. Med. 2010;71(1):45–52. CrossrefPubMedWeb of Science53. . The cognitive structuring of patient delay in breast cancer. Med. 2006;63(12):3137–49. CrossrefPubMedWeb of Science54. . How underlying patient beliefs can affect physician-patient communication about prostate-specific antigen testing. Pract. 2002;5(3):120–9. PubMed55. -Tsao G. What do patients consider when making decisions about treatment for hepatitis C? Med. 2005;118(12):1387–91. CrossrefPubMedWeb of Science56. .

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: Gene expression and small noncoding RNAs: microare a large family of short noncoding RNAs between 17 and 25 nucleotides (nt) in length [49]. MiRNAs were first identified in Caenorhabditis elegans over two decades ago [50] and since then many have been identified in multiple organisms, such as worms, flies, fish, frogs, mammals and plants, by molecular cloning and bioinformatics [51]. Most miRNA sequences are conserved among a wide range of mammalians [52], though there are some that differ from each other only by a single nucleotide [53]. The conserved miRNA sequences among different species can be distinguished by the nomenclature such that when only the first three letters differ this indicates the same sequence in different species, that is, hsa‐miR‐145 in Homo sapiens and mmu‐miR‐145 in Mus musculus [54]. MiRNAs have been shown to be of great importance in a wide variety of biological processes involving cell cycle regulation, apoptosis, cell differentiation, imprinting, homeostasis and development, including limb development [55], morphogenesis of lung epithelial [56], embryonic angiogenesis [57], formation of hair follicle and proliferation of T‐cell [58, 59]. They play key roles in regulating transcriptional and post‐transcriptional gene silencing in many organisms by targeting mRNAs for translational inhibition, cleavage, degradation or destabilisation [53, 60–64]. Each miRNA has multiple mRNA targets that may regulate up to 30% protein‐coding genes and shape protein production from hundreds to thousands of genes [65–67]. MiRNAs recognise their targets through base pairing of the complementary sequence of their seed sequence (2–8 nt of miRNAs) within the open reading frame (ORF) and 3′untranslated region (UTR) of target mRNA [68]. Although the targets of miRNAs are not fully known, bioinformatics studies show a range of possible target genes [69]. The functional activities and the predicted/observed targets of miRNAs can be identified using miRNA databases. These databases can be accessed using the following URL: ( and MiRNA biogenesisMiRNA biogenesis involves multiple important steps.

Output: pass


Input: Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: These studies show where resources may be going to rather than growth, and should probably be at least mentioned in this text. Minor concerns:Title: I am not sure the comma is needed between hyperarid and phosphateLine 210: picrust should be 2Line 214: I think this should be spelled out more completely. It just sends the reader to a reference. This is a specialized set of functional annotations. I think it would help the reader interpret Figure 6 and where the annotations are coming from. Citation: AC1: 'Reply on RC1', Talia Gabay, 20 Mar 2023 The manuscript “Only a minority of bacteria grow after wetting in both natural and post-mining biocrusts in a hyperarid, phosphate mine” presents the results of a H2-18-O stable isotope probing assay of the growing community members in hyperarid biocrusts that have been disturbed, or not, by mining activities. Overall, the manuscript is well conceived, written, and presented. The conclusions are sound and justified. I do have a concern that the authors have missed a swath of the literature that reports the response of biocrusts to physical disturbances, such as chronic physical trampling. These data show that physical disturbances differ from other disturbances and may affect the recovery of the biocrust community. I think some of this literature should be discussed in the context of what these authors see, and how it may be unique in these hyperarid sites. Response: I added literature regarding physical trampling and how they might compare to the mining disturbance in the hyper-arid (L358 – L370):…” Previous studies examining the effect of a physical disturbance (repeated trampling) on biocrust communities, revealed a decrease in the amount of extractable DNA, lower chlorophyll a, and a decrease in biomass and cyanobacteria abundance (Kuske et al. , 2012; Steven et al. , 2015; Chung et al. , 2019). However, these studies investigated a localized disturbance compared to mining disturbance, where the biocrust is completely removed over large spatial scales. Moreover, the previous studies were conducted in environments that were less extreme than the hyper-arid Zin Valley.

Output: contrast


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: JAMA. 2010;304(11):1198–203. CrossrefPubMedWeb of Science68. . Stage of adoption of the human papillomavirus vaccine among college women. Prev Med. 2009;48(5):420–5. CrossrefPubMedWeb of Science69. Parental attitudes about influenza immunization and school-based immunization for school-aged children. Dis J. 2010;29(8):751–5. CrossrefPubMedWeb of Science70. . The simultaneous analysis of patient, physician and group practice influences on annual mammography performance. Med. 1996;43(3):315–24. CrossrefPubMedWeb of Science71. Influenza among healthy young children: changes in parental attitudes and predictors of immunization during the 2003 to 2004 influenza season. Pediatrics. 2006;117(2):e268–77. CrossrefPubMedWeb of Science72. Misperceptions about influenza vaccination among parents of healthy young children. (Phila). 2007;46(5):408–17. CrossrefPubMedWeb of Science73. . The importance of social norms for uptake of catch-up human papillomavirus vaccination in young women. Sex Health. 2011;8(3):330–7. CrossrefPubMedWeb of Science74. Duffett-. Cervical cancer screening practices among university women. J Neonatal Nurs. 2008;37(5):572–81. CrossrefPubMedWeb of Science75. Seasonal and 2009 H1N1 influenza vaccine uptake, predictors of vaccination, and self-reported barriers to vaccination among secondary school teachers and staff. Hum Vaccin. 2011;7(1):89–95. CrossrefPubMed76. Zikmund-. “I’ll do what they did”: social norm information and cancer treatment decisions. Couns. 2011;85(2):225–9. CrossrefPubMedWeb of Science77. Croskerry P. Achieving quality in clinical decision making: cognitive strategies and detection of bias. Med. 2002;9(11):1184–204. CrossrefPubMedWeb of Science78. Fagerlin A, Zikmund-. Cure me even if it kills me: p9. CrossrefPubMedWeb of Science79. . What makes a tumor diagnosis a call to action?

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: Furthermore, HPAT5 was shown to interact with let‐7 family of miRNAs [110]. Implantation of embryos involves complex mechanisms and many different genetic and physiological factors are involved during the process. Developing preimplantation embryo must have a good coordinated interaction with the maternal uterine endometrium. LncRNAs were shown to be differentially expressed in endometrial tissues obtained from pigs with pregnancy and non‐pregnancy with two lnc_01729386 and TCONS_01325501, with potential roles in implantation [111]. Advertisement 5. Gene expression and assisted reproductive technologiesworld, approximately 1% of children are born with assisted reproductive technology (ART) treatments. The infertile couples have the best possibility to conceive a child with these treatments. Although these techniques have been considered to be safe in terms of foetal and post‐natal development [112, 113], there is an increased risk for morbidities, especially imprinting disorders [114]. Furthermore, the global gene expression profiles vary due to in vitro culture of zygotes [115, 116] and in vitro fertilisation processes [117]. Following in vitro culture, apoptotic and morphogenetic pathways have shown to be altered [118]. Intra‐cytoplasmic sperm injection (ICSI), one of the widely used ART techniques, provides infertile couples with sperm motility problems a great chance to have a baby. ICSI is a unique process in which the sperm is injected into the ooplasm [119]. However, ICSI bypasses a number of physiological processes that would normally take place. These embryos derived from ICSI were shown to be cleaved at a slower rate. Furthermore, a reduced number of embryos become hatched with a fewer number of cells and the calcium oscillations are shorter with different patterns [120]. Mice embryos generated by ICSI were shown to be obese and have anomalies of the organs [121]. Advertisement 6. ConclusionNormal development of preimplantation embryos involves complex mechanisms. For a normal developing embryo, the expression of both maternal and paternal genes is required. Several factors are involved in the regulation of parental genes in preimplantation embryos. Epigenetic modifications are one of the most important factors that are involved in the regulation of gene expression during preimplantation embryos. Extensive research studies have been performed throughout the years to establish the methylation profiles of the mammalian gametes and embryos.

Output: corroborate


Input: Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: Therefore, we expected the damage to the biocrust in Zin post-mining sites to follow similar patterns but to be more conspicuous than the previously reported disturbed biocrusts (Kuske et al. , 2012; Steven et al. , 2015; Chung et al. , 2019). Our previous report (Gabay et al. , 2022) supported this notion; we demonstrated differences in bacterial communities in natural and post-mining biocrusts, expecting these differences to be reflected in the proliferating communities of these biocrusts. "Similarly, transcriptomic studies that show the genes that are expressed during a wetting pulse and have documented metabolic a physiological changes in the bacterial community in a wetting pulse. These studies show where resources may be going to rather than growth, and should probably be at least mentioned in this text. Response: I added previous studies that showed expression of nitrogen cycling genes and metabolite production following wetting (L417 – L425):…” One study examining microbial nitrogen transformations in biocrusts collected from biome in Namibia and showed that following wetting, nitrogen cycling genes are expressed in biocrust organisms (Maier et al. , 2022). another study examining biocrust samples taken from the in Utah demonstrated a pulse of metabolite release following controlled wetting (Swenson et al. , 2018). Based on these reports (Maier et al. , 2022; Swenson et al. , 2018) and due to the extreme conditions in (Levi et al. , 2021), we suggest that hyperarid biocrust communities prioritize functions such as metabolite production, nutrient cycling and preparation for desiccation over growth. ”Minor concerns:Title: I am not sure the comma is needed between hyperarid and phosphateResponse: I removed the commaLine 210: picrust should be 2Response: corrected (L208). Line 214: I think this should be spelled out more completely. It just sends the reader to a reference. This is a specialized set of functional annotations. I think it would help the reader interpret Figure 6 and where the annotations are coming from. Response: I added a description of the referenced study and explained the source of the functional annotations (L213 – L218):“…The function categories were chosen based on Meier et al. (2021). In their study, Meier et al.

Output: contrast


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: CrossrefPubMedWeb of Science91. . The influence of default options on the expression of end-of-life treatment p10. CrossrefPubMedWeb of Science92. . The veil of experience: do consumers prefer what they know best? Health Econ. 2000;9(3):267–70. CrossrefPubMedWeb of Science93. Baron J, Ritov I. Reference points and omission bias. Process. 1994;59(3):475–98. CrossrefWeb of Science94. . Violence risk assessment and risk communication: the effects of using actual cases, providing instruction, and employing probability versus frequency formats. Behav. 2000;24(3):271–96. CrossrefPubMedWeb of Science95. Timmermans DRM, Ockhuysen-Vermey CF, Henneman L. Presenting health risk information in different formats: the effect on participants’ cognitive and emotional evaluation and decisions. Couns. 2008;73(3):443–7. CrossrefPubMedWeb of Science96. Tversky A, Griffin D. Endowments and contrast in judgments of well-being. In: Kahneman D, Tversky A, eds. Choices, Values, and Frames. New York: 2000. p 709–25. Crossref97. . “I know just how you feel”: the validity of healthy women’s perceptions of breast-cancer patients receiving treatment. J Psychol. 2002;32(1):110–23. CrossrefWeb of Science98. . It must be awful for them: perspective and task context affects ratings for health conditions. Mak. 2006;1(2):146–52. Web of Science99. . Ignorance of hedonic adaptation to hemodialysis: a study using ecological momentary assessment. J Exp Psychol. 2005;134(1):3–9. Crossref100. Attitudes to chemotherapy: comparing views of patients with cancer with those of doctors, nurses, and general public. BMJ. 1990;300(6737):1458–60. CrossrefPubMed101. Slot KB, Berge E. Thrombolytic treatment for stroke: patient p22. CrossrefPubMedWeb of Science102. .

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: In the more recent years, the importance of noncoding RNAs in the regulation of genes has become clear. A handful of studies have been performed to analyse the expression of microRNAs, which have been shown to regulate mRNAs that encode up to 30% human protein‐coding genes. The expression of miRNAs has been observed in mouse, bovine and human gametes and embryos. Furthermore, in the last couple of years, expression of long noncoding RNAs and their roles in embryonic development and implantation have been investigated. The extensive research studies have provided crucial understanding of the development of preimplantation embryos and the regulation of gene expression, and with the advancing technologies more molecular studies will help to comprehend the mechanisms better. 1. Jaroudi, S. and SenGupta, S. , DNA repair in mammalian embryos. Mutat Res, 2007. 635(1): 77. 2. William, L. , Human Embryology. New York. Vol. 2nd edition. 1997. 3. Schultz, R. M. , The molecular foundations of the maternal to zygotic transition in the preimplantation embryo. Update, 2002. 8(4): 31. 4. Moore, K. , Persaud, T. V. N. , Human. 6th ed. Philadelphia:Saunders Company;1998. 5. Telford, N. A. , Watson, A. J. , and Schultz, G. A. , Transition from maternal to embryonic control in early mammalian development: a comparison of several species. Dev, 1990. 26(1): 100. 6. Bell, C. E. , Calder, M. D. , and Watson, A. J. , Genomic RNA profiling and the programme controlling preimplantation mammalian development. Reprod, 2008. 14(12): 701. 7. McClay, D. W. and Clarke, H. J. , Remodelling the paternal chromatin at fertilisation in mammals. Reproduction, 2003. 125(5): 33. 8. Tamaru, H. and Selker, E. U. , A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature, 2001. 414(6861): 83. 9. Jackson, J. P. , et al. , Control of methylation by the histone H3 methyltransferase.

Output: corroborate


Input: Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: collected biocrusts from the Negev and analyzed bacterial metagenomes in the biocrusts to evaluate the distribution of metabolic potential among bacterial populations. To compare functional potential between various bacterial phyla, they selected metabolic genes encoded in the metagenomic-assembled genomes and grouped them into 10 function categories. ” Citation: RC2: 'Comment on egusphere-2022-1510', #2, 04 Mar 2023 This study is interesting as it identifies which bacteria proliferate in biocrusts from natural and postmining areas and examines functional gene abundances unlike previous studies that have focused on characterizing the microbial community composition of natural and post-mining biocrusts. This, I consider the approach novel. Nonetheless, I have a few comments that should be addressed:AbstractL19-23. I recommend deleting this sentence because it refers to a previous study, and the abstract should focus on the objectives and results of the present study. Then, in the Introduction or the Discussion, it is fine if mention to previous results is done. M&ML103-105. It is not clear the predominant p109. Add a short description of the biocrust sampled (thickness, cover, composition, …. ). Were there differences in the biocrust from natural and post-mining sites? ResultsRegarding the results of the proliferated bacterial community composition, it would be nice to include a figure with the relative abundances of the different bacteria phylum for natural and post-mining biocrusts to make the results clearer. DiscussionL354-357. Can you remind here when was the sampled post-mining site restored? Was it at 2007? I wonder if one reason for the lack of photosynthetic potential difference between post-mining and natural biocrusts is because the biocrust in the post-mining site has been already recovered. For example, soil colonizacion by cyanobacteria can be faster than thought. L369-370. There is little discussion on the results of the Picrust analysis. It would be nice to compare the results of this study with other studies that have also examined functional genes in biocrusts to see if abundances of the functional genes at this site greatly differ from those of biocrusts of other regions. L379-381.

Output: contrast


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: Health Psychol. 2012;31(1):114–21. CrossrefPubMedWeb of Science149. . The impact of counseling with a practical statistical model on patients’ decision-making about treatment for epilepsy: findings from a pilot study. Epilepsy Res. 1993;16(3):207–14. CrossrefPubMedWeb of Science150. . Framing effects in younger and older adults. . 2005;60(4):P215–8. CrossrefPubMedWeb of Science151. Monitoring styles in women at risk for cervical cancer: implications for the framing of health-relevant messages. Med. 1999;21(1):27–34. CrossrefPubMedWeb of Science152. . Acceptability of the H1N1 vaccine among older adults: the interplay of message framing and perceived vaccine safety and efficacy. Health Commun. 2012;27(6):559–68. CrossrefPubMedWeb of Science153. O’Connor AM. Effects of framing and level of probability on patients’ p26. CrossrefPubMedWeb of Science154. Park S-Y. The effects of message framing and risk perceptions for HPV vaccine campaigns: focus on the role of regulatory fit. Q. 2012;29(4):283–302. CrossrefPubMed155. . Message framing and pap test utilization among women attending a community health clinic. J Health Psychol. 2005;10(1):65–77. CrossrefPubMedWeb of Science156. . Persuading physicians to test their patients’ level of kidney functioning: the effects of message frame and point of view. Health Commun. 2010;25(2):107–18. CrossrefPubMedWeb of Science157. The effects of message framing and ethnic targeting on mammography use among low-income women. Health Psychol. 2001;20(4):256–66. CrossrefPubMedWeb of Science158. . Need for cognition and choice framing effects. J Mak. 1996;9(4):283–90. CrossrefWeb of Science159. Van ‘t,. Self-efficacy moderates message-framing effects: the case of skin-cancer detection. Psychol Health. 2010;25(3):339–49. CrossrefPubMedWeb of Science160. Van ‘t. Preaching to the choir?

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: Nature, 2002. 416(6880): 60. 10. Fuks, F. , et al. , The methyl‐CpG‐binding protein MeCP2 links DNA methylation to histone methylation. J Biol Chem, 2003. 278(6): 40. 11. Morgan, H. D. , et al. , Epigenetic reprogramming in mammals. Genet, 2005. 14 1: pp. R47–58. 12. Zhu, B. , et al. , 5‐Methylcytosine DNA glycosylase activity is also present in the human MBD4 (G/T mismatch glycosylase) and in a related avian sequence. Res, 2000. 28(21): 65. 13. Hardeland, U. , et al. , The versatile thymine DNA‐glycosylase: a comparative characterization of the human, Drosophila and fission yeast orthologs. Res, 2003. 31(9): 71. 14. Dean, W. , Lucifero, D. , and Santos, F. , DNA methylation in mammalian development and disease. 2005. 75(2): 111. 15. Oswald, J. , et al. , Active demethylation of the paternal genome in the mouse zygote. Curr Biol, 2000. 10(8): 8. 16. Mayer, W. , et al. , Demethylation of the zygoticpaternal genome. Nature, 2000. 403. 2. 17. Beaujean, N. , et al. , Non‐conservation of mammalian preimplantation methylation dynamics. Curr Biol, 2004. 14(7): pp. R266–7. 18. Reik, W. , Dean, W. , and Walter, J. , Epigenetic reprogramming in mammalian development. Science, 2001. 293(1089): 93. 19. Rougier, N. , et al. , Chromosome methylation patterns during mammalian preimplantation development. Genes Dev, 1998. 12(14): 13. 20. Dean, W. , et al. , Conservation of methylation reprogramming in mammalian development: aberrant reprogramming in cloned embryos. 2001. 98(24): 8. 21. Santos, F. and Dean, W.

Output: corroborate


Input: Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: It is hypothesised that the low bacterial growth in harsh environments like this one could be because biocrusts prioritize activation and preparation for desiccation over growth. However, this hypothesis cannot be fully demonstrated with the reported results. Could you add 401. Is there any practical experience of the application of cyanobacteria inoculation to restore this mining site in Israel? If so, it would be nice to add a few sentences regarding the potential of this technique to restore biocrust in the current mining site. Table 1. Values should include also the standard deviation. Citation: AC2: 'Reply on RC2', Talia Gabay, 20 Mar 2023 This study is interesting as it identifies which bacteria proliferate in biocrusts from natural and postmining areas and examines functional gene abundances, unlike previous studies that have focused on characterizing the microbial community composition of natural and post-mining biocrusts. This, I consider the approach novel. Nonetheless, I have a few comments that should be addressed: AbstractL19-23. I recommend deleting this sentence because it refers to a previous study, and the abstract should focus on the objectives and results of the present study. Then, in the Introduction or the Discussion, it is fine if mention to previous results is done. Response: I removed the section from the abstract. M&ML103-105. It is not clear the predominant p109. Add a short description of the biocrust sampled (thickness, cover, composition, …. ). Were there differences in the biocrust from natural and post-mining sites? Response: I added a description of the biocrusts in Gov mining site (L106 – L109):“…Biocrusts were sampled either from the post-mining site or the adjacent natural area. The biocrusts in Gov are thin (between 1. 5 - 2. 5 mm deep), and smooth. The site is characterized by areas covered in biocrusts or desert pavement. In each sampling site, we sampled along a 100 m strip at approximately 10 m intervals (Fig. 1). ”ResultsRegarding the results of the proliferated bacterial community composition, it would be nice to include a figure with the relative abundances of the different bacteria phylum for natural and post-mining biocrusts to make the results clearer.

Output: contrast


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: The influence of personal relevance on the effects of gain- and loss-framed health-promoting messages. J Health Psychol. 2011;17(5):712–23. CrossrefPubMedWeb of Science161. . Decisional strategy determines whether frame influences treatment p94. CrossrefPubMedWeb of Science162. . Gain versus loss framing in adherence-promoting communication targeting patients with chronic diseases: the moderating effect of individual time perspective. Health Commun. 2012;27(1):75–85. CrossrefPubMedWeb of Science163. . Breast screening in response to gain, loss, and empowerment framed messages among diverse, low-income women. J Poor Underserved. 2007;18(3):550–66. CrossrefPubMedWeb of Science164. Fahy A, Desmond DM. Irish mothers’ intentions to have daughters receive the HPV vaccine. Med Sci. 2010;179(3):427–30. CrossrefPubMedWeb of Science165. Han K-H, Jo S. Does culture matter? A cross-national investigation of women’s responses to cancer prevention campaigns. Women Int. 2012;33(1):75–94. CrossrefPubMedWeb of Science166. Lauver D, Rubin M. Message framing, dispositional optimism, and follow-up for abnormal Papanicolaou tests. Health. 1990;13(3):199–207. CrossrefPubMedWeb of Science167. Llewellyn-. Cancer patients’ decision making and trial-entry p12. CrossrefPubMedWeb of Science168. . The effects of framing and action instructions on whether older adults obtain flu shots. Health Psychol. 2002;21(6):624–8. CrossrefPubMedWeb of Science169. O’. Framing effects on expectations, decisions, and side effects experienced: the case of influenza immunization. J Clin Epidemiol. 1996;49(11):1271–6. CrossrefPubMedWeb of Science170. . A randomized evaluation of loss and gain frames in an invitation to screening for type 2 diabetes: effects on attendance, anxiety and self-rated health. J Health Psychol. 2010;15(2):196–204. CrossrefPubMedWeb of Science171. .

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: , Epigenetic reprogramming during early development in mammals. Reproduction, 2004. 127(6): 51. 22. Santos, F. , et al. , Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev Biol, 2002. 241(1): 82. 23. Monk, M. , Boubelik, M. , and Lehnert, S. , Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development, 1987. 99(3): 82. 24. Howlett, S. K. and Reik, W. , Methylation levels of maternal and paternal genomes during preimplantation development. Development, 1991. 113(1): 27. 25. De Vries, W. N. , et al. , Maternal beta‐catenin and E‐cadherin in mouse development. Development, 2004. 131(18): 45. 26. VB, A. , Cell polarity regulator PARD6B is essential for trophectoderm formation in the preimplantation mouse embryo. Biol Reprod, 2010. 83(3): 58. 27. Ducibella, T. , et al. , Changes in cell surface and cortical cytoplasmic organization during early embryogenesis in the preimplantation mouse embryo. J Cell Biol. , 1977. 74(1): 67. 28. Kelly, S. J. , Studies of the developmental potential of 4‐ and 8‐cell stage mouse blastomeres. J Exp Zool. 1977. 200(3): 76. 29. Chambers, I. , et al. , Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell, 2003. 113(5): 55. 30. Strumpf, D. , et al. , Cdx2 is required for correct cell fate specification and differentiation of trophectoderm in the mouse blastocyst. Development, 2005. 132(9): 102. 31. Nichols, J. , et al. , Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell, 1998. 95(3): 91. 32. Dietrich, J. E. and Hiiragi, T.

Output: corroborate


Input: Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: Response: Added a bar plot of Phyla relative abundances to the PCoA ordination in figure 5 (labeled ‘a’ and ‘b’) and statistical data in the supplementary file (Table S4). DiscussionL354-357. Can you remind here when was the sampled post-mining site restored? Was it at 2007? I wonder if one reason for the lack of photosynthetic potential difference between post-mining and natural biocrusts is because the biocrust in the post-mining site has been already recovered. For example, soil colonization by cyanobacteria can be faster than thought. Response: I mentioned the restoration year in L375. I agree that it is likely that the biocrusts we sampled have a significant cyanobacterial community, however we hypothesize that the recovery of the biocrust differs even within the mining site, emphasizing the importance of microenvironments, where certain areas have more developed biocrusts and others have less developed biocrust even within the same post-mining plot. I referenced this in the discussion (L376 – L383): “…However, in the current study, we sampled post-mining biocrusts at a different location in the Gov mining site (~500 m away from the original plot) due to technical constraints. In the new location we found that the photosynthetic potential of the biocrust in the post-mining plots did not differ from the natural biocrust. These results highlight the importance of microenvironments in shaping the functionality of biocrusts (Garcia-Pichel and Belnap, 1996). The similarities in active communities and photosynthetic potential could be due to more developed biocrusts in the new sampling locations compared to the previous ones. ”L369-370. There is little discussion on the results of the Picrust analysis. It would be nice to compare the results of this study with other studies that have also examined functional genes in biocrusts to see if abundances of the functional genes at this site greatly differ from those of biocrusts of other regions. Response: I added a paragraph addressing the analysis with reference and comparison to a previous study that used to infer functional potential (L395 – L405):“…analysis revealed no significant differences in the abundances of genes within any of the function categories examined (Fig. 6).

Output: contrast


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: Age differences in treatment decision making for breast cancer in a sample of healthy women: the effects of body image and risk framing. Forum. 2005;32(4):799–806. CrossrefPubMedWeb of Science172. . What do I have to lose? Effects of a psycho-educational intervention on cancer patient preference for resuscitation. J Behav Med. 2007;30(6):533–44. CrossrefPubMedWeb of Science173. . Effects of outcome framing on treatment decisions in the real world: impact of framing on adjuvant breast cancer decisions. Making. 1989;9(4):262–71. CrossrefPubMedWeb of Science174. Van den. Elective single-embryo transfer: persuasive communication strategies can affect choice in a young British population. Online. 2011;23(7):838–50. CrossrefPubMedWeb of Science175. Welkenhuysen M, Evers-Kiebooms G, d’Ydewalle G. The language of uncertainty in genetic risk communication: framing and verbal versus numerical information. Couns. 2001;43(2):179–87. CrossrefPubMedWeb of Science176. Witting M, Boere-. Predicting participation in ultrasound hip screening from message framing. Health Commun. 2012;27(2):186–93. CrossrefPubMedWeb of Science177. . Framing of outcome and probability of recurrence: breast cancer patients’ choice of adjuvant chemotherapy (ACT) in hypothetical patient scenarios. Res Treat. 2000;60(1):9–14. CrossrefPubMedWeb of Science178. . Omission and commission in judgment and choice. J Psychol. 1991;27(1):76–105. CrossrefWeb of Science179. . Omission bias and decision making in pulmonary and critical care medicine. Chest. 2005;128(3):1497–505. CrossrefPubMedWeb of Science180. Omission bias and pertussis vaccination. Making. 1994;14(2):118–23. CrossrefPubMedWeb of Science181. Omission bias and vaccine rejection by parents of healthy children: implications for the influenza A/H1N1 vaccination programme. Vaccine. 2010;28(25):4181–5. CrossrefPubMedWeb of Science182. . How do physicians weigh iatrogenic complications?

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: , Stochastic patterning in the mouse pre‐implantation embryo. Development, 2007. 134(23): 31. 33. Home, P. , et al. , Altered subcellular localization of transcription factor TEAD4 regulates first mammalian cell lineage commitment. . , 2012. 109(19): 7. 34. Paul, S. and Knott, J. G. , Epigenetic control of cell fate in mouse blastocysts: the role of covalent histone modifications and chromatin remodeling. Dev. , 2014. 81(2): 82. 35. Lin, S. C. , et al. , Klf5 regulates lineage formation in the pre‐implantation mouse embryo. Development, 2010 137(23): 63. 36. Davis, T. L. , et al. , The H19 methylation imprint is erased and re‐established differentially on the parental alleles during male germ cell development. Genet, 2000. 9(19): 94. 37. Watanabe, D. , et al. , Stage‐ and cell‐specific expression of Dnmt3a and Dnmt3b during embryogenesis. Mech Dev, 2002. 118(1–2): 90. 38. Torres‐Padilla, M. E. , et al. , Histone arginine methylation regulates pluripotency in the early mouse embryo. Nature, 2007. 445(7124): 8. 39. Disteche, C. M. , Dosage compensation of the sex chromosomes and autosomes. Dev Biol, 2016. 56: 18. 40. Namekawa, S. H. , et al. , Two‐step imprinted X inactivation: repeat versus genic silencing in the mouse. Biol, 2010. 30(13): 205. 41. Petropoulos, S. , et al. , Single‐cell RNA‐Seq reveals lineage and X chromosome dynamics in human preimplantation embryos. Cell, 167(1): p. 285. 42. McHugh, C. A. , et al. , lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature, 2015. 521: 236. 43. Vallot, C. , et al. , XACT noncoding RNA competes with XIST in the control of X chromosome activity during human early development. Cell.

Output: corroborate


Input: Claim: Mosses can only grow on trees and are never found on rocks or soil. [SEP] Text: In contrast, a previous study conducted in the Highlands, examined active bacterial communities during a rain and subsequent drying (Baubin et al. , 2021). The results indicated an increase in genes related to photosynthesis, light, and sensing following the rain, while the other function categories did not vary significantly. We note that the identity and abundances of the functional genes in the dry biocrusts detected by Baubin et al. , (2021) and here (Fig. 6) are similar. Therefore, we propose that the similarity between the post-mining and natural biocrust communities (Fig. 5) reflect similar functional potential (Fig. 6). However, low abundance of active ASVs were used to infer the abundances of functional genes (Fig. 6), and large variance between samples in post-mining biocrusts could mask significant differences (Table S5). ”L379-381. It is hypothesized that the low bacterial growth in harsh environments like this one could be because biocrusts prioritize activation and preparation for desiccation over growth. However, this hypothesis cannot be fully demonstrated with the reported results. Could you add 401. Is there any practical experience of the application of cyanobacteria inoculation to restore this mining site in Israel? If so, it would be nice to add a few sentences regarding the potential of this technique to restore biocrust in the current mining site. Response: No, there have not been any active restoration measures in Zin mining sites and no previous scientific studies regarding the mining practices of ICL mining company. I address the need for active restoration measures in Zin mining sites (including cyanobacteria inoculation) in L439 – L444:“…Our results further emphasize the need for active restoration measures in the Zin mines. Such measures include soil inoculation with local cyanobacterial propagules (Acea, 2003, Wang et al. , 2009, Zhao et al. , 2016, et al. , 2017) and increased hydration (Morillas & Gallardo, 2015, Zhang et al. , 2018), which were effective in enhancing biocrust establishment and recovery following disturbances (Antoninka et al. , 2020). ”Table 1. Values should also include the standard deviation. Response: I added SD values to the table (L254 – L254).

Output: contrast


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: p 473–88. Crossref194. Berndsen M, van der Pligt J. Time is on my side: optimism in intertemporal choice. (Amst). 2001;108(2):173–86. CrossrefPubMedWeb of Science195. . Extent and determinants of error in doctors’ prognoses in terminally ill patients: prospective cohort study. BMJ. 2000;320(7233):469–72. CrossrefPubMed196. The distinct role of comparative risk perceptions in a breast cancer prevention program. Med. 2011;42(2):262–8. CrossrefPubMedWeb of Science197. -P. Prognosis or “curabo effect? ” Physician prediction and patient outcome of surgery for low back pain and sciatica. Spine. 2005;30(12):1448–53. CrossrefPubMedWeb of Science198. . Discrepancies between patient and physician estimates for the success of stem cell transplantation. JAMA. 2001;285(8):1034–8. CrossrefPubMedWeb of Science199. . Ego bias, reverse ego bias, and physicians’ prognostic. Med. 1991;19(12):1533–9. CrossrefPubMedWeb of Science200. Loewenstein G, Prelec D. P2000. p 565–96. Crossref201. . Order of information: impact on perceived level of functional independence. Health Care. 2005;18(4):1–12. CrossrefPubMed202. . Clinical reasoning about new symptoms despite preexisting disease: sources of error and order effects. Fam Med. 1995;27(5):314–20. PubMed203. . Clinical diagnosis and the order of information. Making. 1998;18(4):412–7. CrossrefPubMedWeb of Science204. . Order of information affects clinical judgment. J Mak. 1996;9(3):201–11. CrossrefWeb of Science205. . Primacy effects in clinical judgments of contingency. Making. 1988;8(3):216–22. CrossrefPubMedWeb of Science206. . How the manner of presentation of data influences older patients in determining their treatment p8. CrossrefPubMedWeb of Science207. ’N, Unwin A.

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: Javascript is disabled in your browser. Please enable Javascript to view PeerJ. Related research -of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors View 10. 7717/peerj. 10 Published 2013-02-12 Accepted 2012-12-31 Received 2012-11-13 regulatory networks, Statistical network inference, Gene expression data, Experimental design, Interventional data Copyright © 2013 Emmert-This is an open access 2013. Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors. PeerJ 1:e10 inference of gene regulatory networks gained within recent years a considerable interest in the biology and biomedical community. The purpose of this paper is to investigate the influence that environmental conditions can exhibit on the inference performance of network inference algorithms. Specifically, we study five network inference methods, Aracne, BC33NET and MRNET, and compare the results for three different conditions: (I) observational gene expression data: normal environmental condition, (II) interventional gene expression data: growth in rich media, (III) interventional gene expression data: normal environmental condition interrupted by a positive spike-in stimulation. Overall, we find that different statistical inference methods lead to comparable, but condition-specific results. Further, our results suggest that non-steady-state data enhance the inferability of regulatory networks. than ten years after the completion of the Project (Consortium, 2004; Lander et al. , 2001; Venter et al. , 2001) it is nowadays generally acknowledged that in order to obtain a functional understanding of organisms and the emergence of their phenotypes it is not sufficient to study sequence data alone. Instead, within recent years there are increasing attempts to infer genome-scale molecular interactions from high-throughput data to tackle this problem. Depending on the applied technology, this resulted in the construction of protein–protein interaction networks, metabolic networks or transcription regulatory networks (Blais & Dynlacht, 2005; Förster et al. , 2003; Lee et al. , 2002; Ma et al. , 2004; Palsson, 2006; Yu et al. , 2008). These networks can be considered as phenomenological networks because each interaction within these networks is based on the measurement of the corresponding biochemical binding between genes or gene products.

Output: corroborate


Input: Claim: Sign languages have their own unique grammatical structures, different from the spoken languages in the same region. [SEP] Text: 3 Syllable and Mora SJ has a cross-linguistically common canonical syllable structure (C)(G)V(C) where V may be a long vowel or a diphthong, as inka/ ‘mosquito’,kya. ku/ ‘guest’,kai. ko/ ‘silkworm’, etc. The same canonical syllable structure is observed across most Mainland dialects, although some dialects show conspicuous divergence from this, as in Shiiba (Shimoji and Hirosawa, this volume) where there is a double glide sequencewy/, which is phonetically realized as a non-syllabic (i. e. glide) version of the rounded front vowel [ʏ], as inwyaata/ [ʏaːta] ‘boiled’ orhwyaa/ [ʏ̥aː] ‘fly’. Ryukyuan languages often have a more complex syllable structure with an onset cluster CC and/or with a special pre-onset slot which is filled only by a laryngeal ˀ. In Miyako, for example, there is a wide range of consonants which may form an onset geminate CC with the first C being a moraic onset, as inffa/ [fːa] ‘child’,ssan/ [sːaŋ] ‘not know’,vva/ [ʋːa] ‘2sg’,mma/ [mːa] ‘mother’, etc. (see Wang, this volume). It is a controversial issue whether onset geminates can be moraic (cf. Hayes 1989), but the Ryukyuan data suggests that they may be moraic in some languages (and other languages such as Trukese, Topinzi 2008). Miyako further has a rich array of syllabic consonants, and some of them may even carry an onset, as inpztu/ [ps̩tu] ‘person’ (CC̩. CV), etc. The mora plays a central role in most Japonic languages in such a way that the length contrast between long and short vowels and between singleton and geminate consonants is phonemic.

Output: pass


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: The impact of information order on intentions to undergo predictive genetic testing: an experimental study. J Health Psychol. 2010;15(7):1082–92. CrossrefPubMedWeb of Science208. . Presenting risks and benefits to patients. J Med. 2002;17(8):612–7. CrossrefPubMedWeb of Science209. Einhorn HJ. Learning from experience and suboptimal rules in decision making. In: eds. Judgment under Uncertainty: Heuristics and Biases. New York: Press; 1982. p 268–86. Crossref210. . Risk as feelings in the effect of patient outcomes on physicians’ future treatment decisions: a randomized trial and manipulation validation. Med. 2012;75(2):367–76. CrossrefPubMedWeb of Science211. Mazzocco K, Cherubini P. The effect of outcome information on health professionals’ spontaneous learning. Med Educ. 2010;44(10):962–8. CrossrefPubMedWeb of Science212. . What influences participants’ treatment preference and can it influence outcome? Results from a primary care-based randomised trial for shoulder pain. Gen Pract. 2004;54(499):93–6. PubMedWeb of Science213. . Absolutely relative: how research results are summarized can affect treatment decisions. Med. 1992;92(2):121–4. CrossrefPubMedWeb of Science214. Bhandari M, Tornetta P. Communicating the risks of surgery to patients. Trauma. 2004;30(3). Crossref215. . Completeness of reporting trial results: effect on physicians’ willingness to prescribe. Lancet. 1994;343(8907):1209–11. CrossrefPubMedWeb of Science216. . Influence of method of reporting study results on decision of physicians to prescribe drugs to lower cholesterol concentration. BMJ. 1994;309(6957):761–4. CrossrefPubMed217. How should the impact of different presentations of treatment effects on patient choice be evaluated? A pilot randomized trial. PLoS One. 2008;3(11):e3693. CrossrefPubMedWeb of Science218. The effect of alternative summary statistics for communicating risk reduction on decisions about taking statins: a randomized trial. PLoS Med. 2009;6(8):e1000134.

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: In this paper, we study an aspect of the experimental design of gene expression data in the particular context of inferring gene regulatory networks from such data. Specifically, we investigate the influence of environmental conditions on the inference performance of five popular network estimation algorithms, namely, Aracne (Margolin et al. , 2006), BC3NET (de & Emmert-Streib, 2012), CLR (Faith et al. , 2007), C3NET (Altay & Emmert-Streib, 2011; Altay & Emmert-Streib, 2010) and MRNET (Meyer, Kontos & Bontempi, 2007; Meyer, Lafitte & Bontempi, 2008). The rational behind our study is the fact that the information stored in the DNA is not sufficient to explain the phenotypic characteristics of an organism. Instead, there are genotype-environment interactions that have an important influence on this (Falconer & Mackay, 1996; Lynch & Walsh, 1998). For similar reasons studying the expression of genes without considering the environmental conditions of the cells under investigation is fragmented. In order to study the influence of environmental conditions on the gene expression, and ultimately on the inference performance of network inference algorithms, we focus on two important, biologically relevant conditions. The first environmental condition we study corresponds to the placement of cells into a rich media. This leads to an increased proliferation of the cells due to the surplus of nutrition. The second environmental condition corresponds to a positive spike-in stimulation of cells as induced, e. g. , by the administration of drugs. Here by spike-in stimulation we mean that the influence of a drug starts abruptly and lasts only for a short period of time. In addition to these two environmental conditions, we contrast the inference performance for data generated under these two conditions with results for data that correspond to a normal condition, where we do not assume an environment influence. For conducting these investigations we simulate gene expression data because this allows us controlling the corresponding conditions and simultaneously guarantees the availability of sufficiently large sample sizes to enable robust statistical findings that can be utilized to advance the experimental design of future gene expression studies aiming to infer gene regulatory networks. Specifically, for our study we generate 6600 different data sets and infer a total of 33,000 different regulatory networks.

Output: corroborate


Input: Claim: Sign languages have their own unique grammatical structures, different from the spoken languages in the same region. [SEP] Text: In Kyoto, a lexeme is specified for tone and prominence (accent), with both having a contrastive function. In Kagoshima, a word is specified for tone only, and a post-lexical and non-contrastive rule determines which syllable/mora is accented to realize the lexically specified tone (Falling or Level). For example, in Kagoshima Japanese, the wordonago/ ‘woman’ has a Falling tone (/onago/[F]) while the wordotoko/ ‘man’ has a Level tone (/otoko/[Lv]). A post-lexical rule then determines where the fall occurs (penultimate syllable), with the output foronágo/[F] becoming [ònágò]. In the case of the level tone, the final syllable is assigned H by a post-lexical rule. type is especially common in Kyūshū and Ryukyuan languages (see Kato, Tamamoto, Carlino and Urabe, this volume). 5 A few Japonic languages have a characteristic typically associated with a stress language, i. e. a foot-based metrical structure. This is true, for example, the Aoya dialect of Tottori (Western Japanese, Matsumori 2012), the Maisaka dialect of Shizuoka (Eastern Japanese, Poppe 2016), the Nakijin dialect of (Lawrence 1990), the Nagahama dialect of Irabu (Miyako, Southern Ryukyuan), etc. However, such languages are much less well documented than tone-like pitch accent languages as noted above. 6 2. 2 section discusses the morphosyntactic features of Japonic. From a broad range of topics pertaining to morphosyntax, this section focuses on the number category, adjectival expressions and alignment systems, since these in particular exhibit a surprising amount of internal diversity, are well documented in our volume, and are worth the special attention of theoretical linguists and typologists. There are of course many more typologically interesting topics which are not covered in this section simply due to limitations of space, and the reader is referred to § 3 of the present 2. 2.

Output: pass


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: CrossrefPubMedWeb of Science230. Nexøe J, Gyrd-. Danish GPs’ perception of disease risk and benefit of prevention. Fam Pract. 2002;19(1):3–6. CrossrefPubMedWeb of Science231. Nexøe J, Oltarzewska AM, Sawicka-. Perception of risk information: similarities and differences between Danish and Polish general practitioners. Care. 2002;20(3):183–7. CrossrefPubMedWeb of Science232. Nikolajevic-’Connell DL, Robertson J. Effects of information framing on the intentions of family physicians to prescribe long-term hormone replacement therapy. J Med. 1999;14(10):591–8. CrossrefPubMedWeb of Science233. Perneger TV, Agoritsas T. Doctors and patients’ susceptibility to framing bias: a randomized trial. J Med. 2011;26(12):1411–7. CrossrefPubMedWeb of Science234. . Patients’ self-estimated likelihood of taking a statin as prescribed after different types of prognostic information. Atherosclerosis. 2010;212(2):586–8. CrossrefPubMedWeb of Science235. Sarfati D, Howden-. Does the frame affect the picture? A study into how attitudes to screening for cancer are affected by the way benefits are expressed. J Med Screen. 1998;5(3):137–40. CrossrefPubMedWeb of Science236. A randomized trial of decision-making in asymptomatic carotid stenosis. Neurology. 2012;78(5):315–21. CrossrefPubMedWeb of Science237. Sinsky CA, Foreman-Hoffman V, Cram P. The impact of expressions of treatment efficacy and out-of-pocket expenses on patient and physician interest in osteoporosis treatment: implications for pay-for-performance programs. J Med. 2008;23(2):164–8. CrossrefPubMedWeb of Science238. Straus SE. Individualizing treatment decisions: the likelihood of being helped or harmed. Prof. 2002;25(2):210–24. CrossrefPubMedWeb of Science239. .

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: Despite the well known fact that the environment has an influence on the expression of genes this aspect is not well studied in the literature of methods for the inference of gene regulatory networks. Instead, most studies are based on observational data only (Emmert-Streib et al. , 2012). Notable exceptions in this context are studies that addressed related but different questions, e. g. , investigating the appropriate level of description to simulate gene expression data, the influence of the number of time points, the number of categories and the interval length between samples (Chen, 1999; Smith, Jarvis & Hartemink, 2002; Yu et al. , 2004; Husmeier, 2003). However, these studies have been conducted for time series data. Instead, in this paper we are not using longitudinal data. This paper is organized as follows. In the next section, we describe all methods and evaluation measures we are using for our analysis. Further, we provide a detailed explanation of the data we are using and their generation. In the results section we present results for three different types of data: (I) observational gene expression data: normal environmental condition (II) interventional gene expression data: growth in rich media (III) interventional gene expression data: normal environmental condition interrupted by a brief, positive stimulation (spike-in stimulation). We study these data for five network inference methods (Aracne (Margolin et al. , 2006), BC3NET (de & Emmert-Streib, 2012), CLR (Faith et al. , 2007), C3NET (Altay & Emmert-Streib, 2011; Altay & Emmert-Streib, 2010) and MRNET (Meyer, Kontos & Bontempi, 2007; Meyer, Lafitte & Bontempi, 2008) and two different topologies of regulatory networks. This paper finishes with a discussion and conclusions. this section we describe our model, the method and the data we are using for our analysis. Generation of gene expression data In order to simulate gene expression data we are using netsim (Di Camillo, Toffolo & Cobelli, 2009). Netsim is a R package that combines a fuzzy logic with differential equations to enhance the simulation of transcription regulation processes.

Output: corroborate


Input: Claim: The majority of world languages are tonal, meaning that pitch or tone can change the meaning of a word. [SEP] Text: Подготовка к ЕГЭ и ОГЭ Подготовка к ЕГЭ и ОГЭ Подготовка к ЕГЭ и ОГЭ Подготовка к ЕГЭ и ОГЭ Подготовка к ЕГЭ и ОГЭ Подготовка к ЕГЭ и ОГЭ Подготовка к ЕГЭ и ОГЭ Подготовка к ЕГЭ и ОГЭ Подготовка к ЕГЭ и ОГЭ Подготовка к ЕГЭ и ОГЭ Подготовка к ЕГЭ и ОГЭ Подготовка к ЕГЭ и ОГЭ Приемная комиссия Институты, факультеты, филиалы Военный учебный центр Платное обучение Управление международного сотрудничества Новости Смотреть все н

Output: pass


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: CrossrefPubMedWeb of Science252. Chao L-. End-of-life medical treatment choices: do survival chances and out-of-pocket costs matter? Making. 2008;28(4):511–23. CrossrefPubMedWeb of Science253. . The effect of offering different numbers of colorectal cancer screening test options in a decision aid: a pilot randomized trial. . 2008;8:4. CrossrefPubMedWeb of Science254. Brody H. Medicine’s ethical responsibility for health care reform: the top five list. N Med. 2010;362(4):283–5. CrossrefPubMedWeb of Science255. Decisions Foundation. Preference-sensitive decisions. Available from: URL:. Anxiety, fear of cancer, and perceived risk of cancer following lung cancer screening. Making. 2008;28(6):917–25. CrossrefPubMedWeb of Science257. . Resisting good news: reactions to breast cancer risk communication. Health Commun. 2006;19(2):115–23. CrossrefPubMedWeb of Science258. The impact of genetic counseling on risk perception and mental health in women with a family history of breast cancer. Cancer. 1999;79(5–6):868–74. CrossrefPubMedWeb of Science259. . Risk perceptions: assessment and relationship to influenza vaccination. Health Psychol. 2007;26(2):146–51. CrossrefPubMedWeb of Science260. . Heuristics in medical and non-medical decision-making. Q J A. 1992;44(2):211–35. CrossrefPubMedWeb of Science261. . Sensitivity to disgust, stigma, and adjustment to life with a colostomy. J Res Pers. 2007;41(4):787–803. CrossrefPubMedWeb of Science262. Gigerenzer G. Gut Feelings: of the Unconscious. New York: Viking; 2007. 10. 11770272989x14547740_table_s1. pdf84. 25 KBds_10. 11770272989x14547740_table_s2. pdf85. 39 KBCite 2014. PubMed: 25145577AuthorsAffiliationsJ. S. Blumenthal-Barby, PhDView all 41. 50 Issue - $186.

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: Differential equations are used to describe the continuous dynamics of gene expression on a continuous time scale and gene-specific kinetic parameters are used to achieve realistic simulations that mimic the real dynamical behavior of gene expression. For our study we are generating gene expression data for three different conditions that correspond to two different types of data: observational gene expression data: normal environmental condition interventional gene expression data: growth in rich media interventional gene expression data: normal environmental condition interrupted by a positive spike-in stimulation That means, we are generating gene expression data that correspond to observational (I) and interventional data (II and III). However, we are not generating data by gene knockout or silencing (Eccleston & Eggleston, 2004; Meister & Tuschl, 2004). The reason for this is that an inclusion of such perturbation experiments would limit the scope of this paper. Specifically, for human subjects it is for ethical reasons not possible to conduct in vivo gene-knockout experiments. Hence, if we would include such studies we would need to exclude a discussion of gene expression data, e. g. , from clinical studies. On the other hand, the chosen interventional strategies for the generation of the data are equally applicable to model organisms as well as human subjects. This allows a general extrapolation of our results. The first type of data we are generating corresponds to cells in normal environmental conditions meaning that for these simulations we do not use an external stimulation of the gene expression. The second type of data can be seen as a media rich environment which has a favorable effect on the proliferation of cells. For this condition each gene receives an external positive stimulus facilitating its expression. For your simulations this is accomplished by using a constant stimulation of a fixed positive constant Ec. The third type of data corresponds to time dependent interventional data because we alter the environmental condition of the cells over time. This change of the environmental condition translates into a change of the dynamic of the gene expression in a time dependent manner. Specifically, we start simulating gene expression under the same conditions as in (I) but add at a certain time point, ts, a constant but random stimulation Es×r for each gene. is a constant factor and r is a random variable uniformly sampled from [0,1]. This stimulation lasts a short period of time Δt = 0. 2. After this period, the gene expression is again governed by the same conditions as in (I).

Output: corroborate


Input: Claim: There are only three main language families in the world: Indo-European, Sino-Tibetan, and Afro-Asiatic. [SEP] Text: Кычанов; их работы в основном базировались на источниках на пали, санскрите и китайском языках, и, таким образом, они выпадают из темы нашего исследования. Тем не менее их влияние на тибетологию также значительно, а деятельность М. И. Воробьевой-Десятовской, Л. С. Савицкого, Р. Н. Крапивиной, А. В. Зорина создала связующее звено между «старым» и «новым» тибетоведением России.

Output: pass


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: The model corresponds to a SIR (susceptible-infected-recovered/immune) compartmental model capturing the disease transmission process [30] augmented with a belief model (Fig 1). It enables individuals to be characterized by both their epidemiological status and their opinion. Specifically, individuals can belong to one of 4 epidemiological compartments: susceptible, infected, immune through vaccination and immune naturally. In each compartment, individuals can be characterized either as “pro-vaccines” (positive opinion) or “sceptical” (negative opinion). Across time, individuals can change compartments: for instance, susceptible individuals may become infected, or they may choose to vaccinate. The system of compartments and flows between them is defined by a system of ordinary differential equations (see section 2. iii) to examine numerical simulations at different values of the parameters. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFig 1. Structure of the behaviour-incidence model. The model is an augmentation of a classic SIR compartmental model [30]. Individuals are characterized by both their epidemiological status (S: susceptible; I: infected; Rv: recovered through vaccination; Rg: recovered naturally) and for each compartment, their opinion of vaccination (positive: subscript p; non-shaded colours; negative: subscript n; shaded colours). CV and CI are compartments that indicate the total recalled number of individuals having suffered negative side effects from vaccination and infection, respectively. β indicates the rate of infection transmission; Ω indicates the rate at which individuals change their opinion (from positive to negative Ω or from negative to positive Ω′); δ indicates the number of individuals suffering side effects from either vaccination δV and infection δI; θ indicates the rate at which individuals vaccinate. Each individual dies at the same rate d. rate at which individuals become vaccinated is a function of both the epidemiological costs associated with infection and vaccination and the distribution of opinions of vaccination in the population. First, costs are defined by the epidemiology with the number of infected individuals and vaccination coverage determining the number of people suffering negative side effects from infection and vaccination, respectively. Individuals are assumed to vaccinate more quickly when the infection cost is high and more slowly when the vaccination cost is high.

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: For the subnetwork of the transcriptional regulatory network of S. cerevisiae (Fig. 4B) we find a surprising result because these results are qualitatively similar to the results for the normal condition (shown in Fig. 2B). This means that the underlying topology of the regulatory network is capable of compensating the dynamical modifications, as induced by the spike-in stimulation. Further, this behavior is method-independent because for all five inference methods, we observe qualitatively similar results. this paper we investigated the influence that environmental conditions can have on the inference performance of network inference algorithms. Specifically, we studied and compared the results for three different conditions: (I) observational gene expression data: normal environmental condition, (II) interventional gene expression data: growth in rich media, (III) interventional gene expression data: normal environmental condition interrupted by a positive spike-in stimulation. We found that different statistical inference methods lead to comparable but condition-specific results. That means, qualitatively, the five network inference methods (Aracne (Margolin et al. , 2006), BC3NET (de & Emmert-Streib, 2012), CLR (Faith et al. , 2007), C3NET (Altay & Emmert-Streib, 2011; Altay & Emmert-Streib, 2010) and MRNET (Meyer, Kontos & Bontempi, 2007; Meyer, Lafitte & Bontempi, 2008)) we used for our study showed a similar behavior in their inference performance, for each condition. The only exception we found is for (III) interventional gene expression data (normal environmental condition interrupted by a positive spike-in stimulation) and Erdös–Réyni networks, because for this condition MRNET and Aracne assume a significantly larger variation in the estimated F-scores than the other three inference methods (see Fig. 4). However, even for this condition the observed median F-scores are for all five methods comparable. Overall, we can draw the following conclusions from our numerical results. (1) The problem to infer gene regulatory networks from expression data is very challenging and depends on (A) the time point when data are measured, (B) the kind of the external stimulation and (C) the interconnectedness of the genes respectively their molecular interactions.

Output: corroborate


Input: Claim: Sign languages have their own unique grammatical structures, different from the spoken languages in the same region. [SEP] Text: Notice that the mirror image situation of SJ is found with regard to boundary-tone assignment, whereby the final lowering L% lowers the pitch of the final mora. In this way, pitch accent is characterized by its culminative nature, i. e. the existence of one prominent mora/syllable within the word domain, a feature which makes the pitch-accent system look like a stress system. However, the pitch accent system of Japonic differs from a stress system in that in the former, a word may crucially lack a prominent mora, i. e. a word may be ‘unaccented’ in Japanese linguistics terms, as in SJsakana/ [sàkáná] (%LHH) ‘fish’ and in Nambunazugi/ [nànzɯ̀ɡí] (LLH) ‘forehead’. 4 In a stress system, an unstressed lexical word is usually ruled out, i. e. there must be one prominent syllable/mora within a word. In prosodic typology, a stress system and a tone system constitute two distinct linguistic types and a pitch-accent system is regarded as a hybrid of the two, not a distinct ‘type’ (Hyman 2006). As a typological hybrid, then, the various prosodic systems which are collectively called pitch-accent systems of Japonic languages may show a considerable internal variation, and the variation can be captured in terms of what kind of stress-like features and tone-like features are present in the system. languages exhibit a feature which is characteristic of tone languages, i. e. the paradigmatic choice between specific tonal melodies for each lexeme, e. g. between ‘Level’ and ‘Rising’ in (Western Japanese), or between ‘Level’ and ‘Falling’ in (Kyūshū Japanese). Tone as is found in these systems is called ‘word tone’ (Hayata 1998), as the domain of the paradigmatic tonal contrast is the word rather than the syllable/mora. However, these systems still show a stress-like character in that a certain mora/syllable is specified as prominent, i. e. accented, although the nature and function of accent differs between the two languages.

Output: pass


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: The rate of infection transmission: β is expressed in terms of the basic reproductive ratio of the pathogen R0 [31]. R0 corresponds to the average number of secondary infections produced by an infected individual in an otherwise susceptible population and can be understood as the fitness of the pathogen: for a pathogen to invade the population, R0 must be >1. In our model R0 has been calculated as: where and are determined numerically using the system of ordinary differential equations (see section 2. iii) assuming no infection. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 1. Parameters used and their default values. S* is the number of susceptible individuals, i. e. the number of individuals that are not vaccinated before the emergence of the infection. In our model, people can have two different opinions regarding vaccination which implies two different probabilities to accept the vaccine. Thus the number of susceptible individuals S* depends on the number of individuals who either have a positive or a negative opinion before the emergence of the infectious disease, i. e. where and represent the population equilibrium of the number of susceptible individuals in the absence of disease. The information relating to the costs of infection and vaccination: This information, available to everyone, is assumed to be summarized by a function of the number of the past and present individuals who have suffered negative side effects from infection and vaccination. This information is used by all individuals in order to measure the relating costs of infection and vaccination, respectively denoted CI and CV. We supposed that this information is generated and memorized by all individuals at a rate δI and δV. We also assumed that the information is forgotten at a rate f. At any given point in time, the number of infected individuals is determined by the history of vaccine uptake in the population. Thus, the costs of infection and vaccination depend on both the history of vaccine uptake and the number of infected individuals. The rate of vaccination: Only susceptible individuals can take up vaccination and the decision to vaccinate depends on both an individual opinion and the costs of infection and vaccination. Individuals with a positive opinion vaccinate at the rate θp; individuals with a negative opinion vaccinate at the rate θn. υp and υn represent the maximum rate at which individuals can be vaccinated.

Output: pass


Input: Claim: Epigenetics studies how gene expression can be modified by environmental factors. [SEP] Text: The fact that the effect of an external stimulation can be compensated by the interaction structure among genes (compare Fig. 4A with 4B) allows to raise the hypothesis that evolution might favor network structures that are less severely influenced by changes in environmental conditions. The reason for this may be an increased robustness of these systems because for different external signals the system exhibits essentially the same dynamical behavior. Previous studies investigating the robustness of gene networks focused on the elimination of interactions, (see, e. g. , Jeong et al. , 2000; Stelling et al. , 2004; Kitano, 2007; Emmert-Streib & Dehmer, 2009; Wagner, 2005; Wagner, 2007), and not on changes of external signals, as in this study. For this reason the observed effect in our study presents a new and potentially important factor that deserves more attention in future studies. would like to thank Ricardo de Matos Simoes, Benjamin Haibe-Kains and for fruitful discussions. For our numerical simulations we used R (R Team, 2008). Emmert-Streib is an for PeerJ. Frank Emmert-Streib conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper. work has been supported by the Center for (CCRCB), Queen’s University Belfast. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 2010. Inferring the conservative causal core of gene regulatory networks. BMC 4:132 Altay G, Emmert-Streib F. 2011. of gene networks on their inference: analysis of C3NET. 6:31 Blais A, Dynlacht B. 2005. Constructing transcriptional regulatory networks. Genes and Development 19(13):1499-511 Chen L. 1999. Combinatorial gene regulation by eukaryotic transcription factors. in 9(1):48-55. 1997. Ratio-based decisions and the quantitative analysis of cdna microarray images. Journal of 2(4):364-374 Consortium IHGS. 2004. Finishing the euchromatic sequence of the human genome. Nature 431(7011):931-945 Cover T, Thomas J. 1991. & Sons, Inc de R, Emmert-Streib F. 2011.

Output: corroborate


Input: Claim: The majority of world languages are tonal, meaning that pitch or tone can change the meaning of a word. [SEP] Text: Dabei setzt man auf den „redaktionellen Mehrwert“ (Bernet 2010: 110) für ein Produkt oder eine Dienstleistung. ← 23 | 24 →Die für den Beitrag ausgewählten Beauty-Blogs sind auf der Grundlage der benannten Charakteristika als private Blogs einzuordnen und häufig in übergeordnete Plattformen eingebunden. Da sie in enger Beziehung zu Unternehmen stehen, können sich diese ebenso von privaten Blogs in Hinblick auf die Markenkommunikation einen Mehrwert erhoffen. 4. 1. IrritationenDie bereits angesprochenen Modi des Medienumgangs, Sozial- und Systemintegration, lassen sich zunächst vor dem Hintergrund der Irritation von Systemen fassen. ist es, dass der Übergang zur funktionalen Differenzierung „die Irritierbarkeit der Gesellschaft steigert, ihre Fähigkeit, auf Veränderungen der Umwelt rasch zu reagieren, zunehmen läßt […]. “ (1998: 789) Weiterhin wird zum formuliert: „Er hat seinen theoretischen Ort in der These eines Zusammenhangs von operativer Schließung (Autopoiesis) und struktureller Kopplung von System und Umwelt. “ (Luhmann 1998: 790) Umweltwirkungen „determinieren“ nicht, sie werden mit systemeigenen Operationen verarbeitet. „Irritation ist danach ein Systemzustand, der zur Fortsetzung der autopoietischen Operationen des Systems anregt.

Output: pass


Input: Claim: Cognitive biases can significantly influence decision-making. [SEP] Text: Specifically, we investigate the same range of parameter values (Table 1) for the five nested models in order to be able to detect the effect of each element (Table 2): Model 1: a classic SIR model without the belief component. Model 2: a model that characterizes individuals by both their epidemiological status and their opinion. Vaccination rate is fixed (θp = υp; θn = υn) and individuals with a positive opinion vaccinate more quickly than those with a negative opinion (υp > vn). By doing so, vaccination behaviour is a function of opinion but not confirmation bias (μp = μn = 1), i. e. the difference in vaccination rates between individuals with opposed opinions is not a function of the number of infected individuals and vaccination coverage. The rate of opinion change is also fixed (Ω = ωp→n = Ω′ = ωn→p). Model 3: This model includes the globally available information on the number of individuals suffering negative side effects from the infection CI and vaccination CV. This enables to calculate the epidemiological costs. Model 4: This model includes confirmation bias, i. e. the biased perception of costs by individual opinion. 1–3 confirmation bias is not considered so μ = μ′ regardless of the opinion of individuals. Model 5: This model includes conformism and corresponds to the full model. 1–4, conformism is not considered so cp = cn = 1. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 2. Components of the different nested models. Numerical simulation. We performed all simulations using Mathematica 9. 0 [33]. First, 500 susceptible positive individuals and 500 susceptible negative individuals are introduced. We ran 100 000 iterations with a time step of 10−4, the number of iterations needed to reach a stable equilibrium, to determine the number of susceptible individuals ( and ) and calculate the rate of infection transmission β with R0 in the absence of disease. Second, after β was obtained, we introduced two infected individuals, one of each opinion (N = 1002 individuals). We ran 1,000 000 iterations with a time step of 10−4 which corresponds to 100 time units (e. g. 100 years), to ensure that we capture the complete dynamic.

Output: pass