Input: Task: pass the claim using the given text. Claim: Beauveria bassiana is used as a biocontrol agent against various pests. [SEP] Text: Co-expression analysis identified 332 genes with expression levels differentially correlated to OpS1 and OpS3 between red and non-red strains, including several Zn(2)-Cys(6), b-ZIP and other transcription factors. These included genes that were both positively and negatively correlated with OpS1 and OpS3 expression, representing potential positive and negative regulators of oosporein gene expression and production. Most showed no correlation in non-red strains, suggesting novel transcription factor activity or co-regulation in red strains. Furthermore, the Velvet protein-encoding gene VeA, a master regulator of secondary metabolism (37), was differentially co-expressed with both genes, showing negative expression correlation in both red and non-red strains. and Differential expression analysis identified 23 upregulated and 51 downregulated genes in UAMH 298-UVR (Fig. 3A) compared to the UAMH wildtype strain. The differentially expressed genes were significantly enriched for eight GO terms (Fig. 3C), including vitamin binding (FDR < 0. 012), extracellular region (FDR < 0. 039) and pathogenesis (FDR < 0. 0029). Two genes encoding glucose repressible protein Grg1 were downregulated in UAMH 298-UVR, and a gene with a heme-dependent catalase-like domain was upregulated. Two glutathione-S-transferase genes were upregulated, one of which was OpS6 of the oosporein BGC. Additionally, the oosporein BGC gene laccase 2 (OpS5) was upregulated. In the UAMH 299-UVR strain, 82 genes were upregulated and 89 were downregulated compared to UAMH 299 (Fig. 3B). 12 GO terms were significantly enriched among these differentially expressed genes (Fig. 3D), including pathogenesis (FDR < 4. 15e-7), monooxygenase activity (FDR < 0. 046), tetrapyrrole binding (FDR < 0. 046), and extracellular region (FDR < 0. 026). Two multicopper oxidase genes were differentially expressed, including the laccase 2 gene (OpS5). [SEP] Justify:

Output: The text does not address the claim as it focuses on gene expression analysis and does not mention Beauveria bassiana or its role as a biocontrol agent against pests. Therefore, the text is considered irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Stress management techniques can improve mental health and resilience. [SEP] Text: Our findings highlight the importance to reduce psychosocial work stress and to foster resilience in order to promote mental health in working parents during the pandemic and thereby ultimately benefiting the mental health of the entire family. Availability of data and materials The dataset analysed during the current study is not publicly available due to legal and ethical constraints. Public sharing of participant data was not included in the informed consent of the study. All enquiries about access to data should be sent to the corresponding author. All requests to access data will be handled in accordance with the of the Faculty of Medicine of the Technische Universität Dresden. AbbreviationsCI: confidence interval CD-RISC: Connor-: on Parenting, Work, and (“Dzu Elternschaft, Arbeit und Mentaler Gesundheit”) EPDS: : effort-reward imbalance LHD: lifetime history of depression WHO: : work-privacy conflict 51. Geneva; 2020 [cited 2020 Nov 20]. Available from: Online-Befragung von Beschäftigten: den Arbeitsalltag verändert hat. IAB-Kurzbericht 13. Nürnberg: Institut für Arbeitsmarkt- und Berufsforschung; 2020. p. 13. 17. 2020 [cited 2020 Nov 21]. Available from: K, et al. Community, work, and family in times of COVID-19. Fam. 2020;23(3):247–52. 92. 29. p. 24–35. 306. 95. V, Steudte-Schmiedgen S, Kopp M, Förster A, Altus C, Schier C, et al. The impact of parental role distributions, work participation, and stress factors on family health-related outcomes: study protocol of the prospective multi-method cohort “Dresden study on parenting, work, and mental health” (DREAM). Front Psychol. 2019;10:1–26. p. 1–141. 38. 2018. 2018. pdf? __blob=publicationFile. . Behind closed doors: The surge in mental distress of parents. 2020. [cited 2020 Nov 20]. Available from: Three job-related stress models and depression: a population-based study. Psychiatr Epidemiol. [SEP] Justify:

Output: The text corroborates the claim by stating that reducing psychosocial work stress and fostering resilience are important for promoting mental health, especially in working parents during the pandemic. This supports the idea that effective stress management can lead to improved mental health outcomes.


Input: Task: contrast the claim using the given text. Claim: Regenerative medicine can improve healing times for certain injuries. [SEP] Text: In addition, the daily monitoring of fingertip capillary blood glucose revealed that the effect of decreasing blood glucose by dgHPSCs-ERRγ cell transplantation could maintained at least for one and half months (Table 3). The exact duration of the effects of stem cell transplantations still needs to be determined further because the patient will take the second course of treatment using stem cell transplantation afterwards. The glucose challenge tests before and after stem cell transplantations did not show significant improvements both for insulin and C-peptide secretions (Table 2). These data demonstrated that transplantations of dgHPSCs-ERRγ cells could potentially replace exogenous insulin administration and restore the functions of the patient’s pancreatic β cells. The follow-up visit of the patient The patient reported that he had a transient fever after the transplantations of about 1x108 cells, and the body temperature reached up to 37°C. The fever faded away next day. 26 of 2018, about 50 days after the last transplantation, the patient described that he felt stronger physically, and his knees felt much better, he could exercise much longer than before and did not feel tired. His gross amount of food per meal did not change, but his body weight decreased slightly. In a word, his overall physical conditions were improved obviously. 2 diabetes is an increasing threat to human health span, and diabetes incidence and prevalence increase with the age. Approximately 25. 9% of Americans of 65 years or older have diabetes, whereas, 9. 3% of those in the general population. 3 In addition, diabetes is a major risk factor for premature onset of multiple age-related conditions, including renal dysfunction, cardiovascular disease, stroke, impaired wound healing, infection, depression, and cognitive decline. 25–27 Although, almost one hundred years ago, Banting et al. ,1 confirmed that administration of exogenous insulin can decrease blood glucose levels and improve the symptoms of diabetes, the administration of exogenous insulin cannot maintain blood glucose levels within the narrow physiological range and further protect from development of various diabetic complications, because normal pancreatic β cells adjust insulin secretion continually in response to varying blood glucose levels. 2 Therefore, to develop novel strategies for diabetes treatment to restore the normal functions of pancreatic β cells is critical to finally cure diabetes and protect from diabetic complications development. [SEP] Justify:

Output: The text contrasts the claim by discussing the effects of dgHPSCs-ERRγ cell transplantation, highlighting that while glucose levels were managed and the patient reported feeling stronger physically, there was no significant improvement in certain relevant medical markers post-transplant. The mention of the patient's improvement in physical condition suggests some benefit, but the overall lack of notable changes in blood tests may indicate that regenerative medicine does not always lead to improved healing times, especially considering the complexities of diabetes treatment mentioned in the text.


Input: Task: pass the claim using the given text. Claim: Beauveria bassiana is used as a biocontrol agent against various pests. [SEP] Text: The conidial pigment biosynthesis scytalone dehydratase Arp1 was downregulated, and the DNA replication complex GINS subunit Sld5 was upregulated. Additionally, a gene encoding a MAC1 interacting protein involved in stress response was downregulated in UAMH 299-UVR. Eight genes were differentially expressed in both UV resistant derivatives, including UDP-glucosyltransferase, laccase 2 and glutathione-s-transferase. These three genes were all upregulated in both strains. DiscussionBB virulence is highly variable and displays an extremely broad host range (26, 38); however, a lack of characteristic phenotypic variation within the species has made phylogenetic delineation difficult (39). With the increasing accessibility of genome sequencing, phylogenomic techniques are being used to infer evolutionary relationships between strains (33, 39). The genome assemblies and annotations generated for this work are highly complete in the gene space, providing confidence that they contain the necessary information for comparative analyses. Phylogenetic analysis of shared BUSCO sequences placed the eight BB strains into two distinct groups. UAMH 298 and UAMH 298-UVR clustered with the group I strains and were placed in group I accordingly, and this cluster of strains was examined as a unit for increased virulence and oosporein production. Oosporein was transiently detected in UAMH 298-UVR and may have been produced in the UAMH 298 strain below the limit of detection during the collection times. Interestingly, the red strains formed a clade with B. pseudobassiana rather than the reference BB strain. The B. pseudobassiana species was first described by Rehner et al. in 2011, using a multilocus phylogeny of 68 Beauveria strains based on the partial gene sequences of Rpb1, Rpb2, Tef 1-a and the nuclear intergenic region Bloc (39). As the name suggests, B. pseudobassiana is phenotypically similar to B. bassiana, and has also been studied for its entomopathogenic properties (40, 41), but has slightly smaller conidia. Further investigation using whole genome annotations would be necessary to confirm the phylogenetic placement of the red strains and B. [SEP] Justify:

Output: The text does not address the claim directly; instead, it discusses genetic expressions and phylogenetic relationships among different Beauveria strains, including B. bassiana and B. pseudobassiana. While it mentions the entomopathogenic properties of B. pseudobassiana, it does not state that Beauveria bassiana is explicitly used as a biocontrol agent.


Input: Task: corroborate the claim using the given text. Claim: Depression can result from a combination of genetic, biological, and environmental factors. [SEP] Text: IntroductionResearch has consistently implicated the joint contribution of genetic and environmental risk factors in the pathogenesis of major depression. 1 The most prominent example refers to the debate on whether a 43-bp insertion/deletion polymorphism (5-) in the serotonin transporter gene2 moderates the association of life stress and depression. 3, 4, 5 Whereas numerous studies observed increased disease vulnerability in carriers of the 5-short (S) variant upon exposure to environmental adversity,4,6 recent meta-analyses have triggered an active controversy about whether this finding holds up. 7,8 Therefore, exploring systemic and molecular mechanisms underlying gene–environment (GxE) interactions seems to be of major importance to further advance this debate. 1,9On a systemic level, experimental studies investigating biological quantitative traits strongly support the hypothesis of elevated stress sensitivity in S allele carriers. 4 Among other biological alterations, the S allele has repeatedly been associated with elevated amygdala activity10,11 and increased cortisol secretion in response to a variety of aversive/stressful stimuli. 12,13 However, little is known about the molecular pathways mediating disease vulnerability. One hypothesis is that GxE interaction already takes place at the very early level of gene expression, in a way that 5-and life stress jointly convey stable changes in serotonin transporter (SERT) expression. In line with this, altered SERT expression profiles may constitute a putative mediator of GxE interaction as they have been commonly observed in depressed patients14, 15, 16 and stress-sensitive Rhesus macaques. 17,18The functional effects of 5-have been widely documented by in vitro studies, indicating that the S allele is associated with reduced SERT gene (SLC6A4) transcription in lymphoblast cell lines2,19 and decreased serotonin uptake in platelets. 20,21 In addition, transcriptional efficiency of the SERT gene was found to be influenced by an A/G single-nucleotide polymorphism (rs25531) located upstream of the 5-promoter variant within the greater repeat structure. 19 This has led to the distinction between the variants S, LA and LG, (tri-allelic classification of 5-) with the latter one being functionally similar to the S allele. 19 In contrast to in vitro studies, results obtained in vivo appear to be less conclusive regarding allele-specific SERT mRNA expression in peripheral cells22,23 and SERT availability in the human brain. [SEP] Justify:

Output: The text corroborates the claim by discussing the joint contributions of genetic and environmental risk factors in the pathogenesis of major depression. It highlights how genetic variations, such as the serotonin transporter gene, interact with environmental stressors, emphasizing the complexity of the causes of depression. The reference to systemic and molecular mechanisms further supports the idea that both genetic and environmental factors play crucial roles in depression.


Input: Task: contrast the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: misunderstand Figure 3A-B, the induction of a selected set of 8C genes is considerably more modest in naïve reprogrammed cells compared to that in the embryo, and the reprogramming cells may be expressing many genes that are not typical of this stage. Some other form of analysis would be required to prove that the transient cells are really equivalent to an 8C stage. Thank the reviewer for this important question. The statement that transcriptional network with eight-cell-stage-like characteristics was transiently activated during naïve reprograming was concluded based on the following observations: 1) 8-cell specific genes were significantly enriched in the cluster exhibiting transiently enhanced transcription activity during the late stages of naïve reprogramming, which could not be observed during primed reprogramming process. 2) Dissecting the dynamics of transposon elements (TEs) by similar strategy also revealed that 8C-TEs were transiently re-activated during naïve reprograming. 3) The H3K9me3 signals around the 8C-TEs exhibited a transiently decreased pattern at day 14, strongly correlated with the transiently increasing transcriptional activity of the 8C-TEs at that time point. Our results cannot reach the conclusion that the transient cells are equivalent to an 8C stage, and we apologize for the misleading. We would like to conclude that the specific pattern of 8C-transcripts wave that we observed suggests the emergence of gene network activation with the 8C-stage-like characteristics during naïve reprograming. 6) Subsection “8-cell-stage-like state was transiently established during naïve reprogramming”-again the significance of enrichment for genes involved in gamete generation is unclear here. The p-value of these genes related to gamete generation is 3. 784322e-08. We have added that in the revised manuscript. 7) Subsection “Dynamic changes in epigenetic modifications in the naïve reprogramming system” and Figure 5C - what genes are chosen for study here and why? Thank the reviewer for the question. The genes with both H3K4me3 and H3K27me3 modifications covered at least one time point in the promoter regions (+/- 2k of TSS) during the reprogramming process were chosen for our study. [SEP] Justify:

Output: The text contrasts the claim by indicating that the analysis of gene expression and the characteristics of naïve reprogrammed cells do not conclusively prove that the reprogrammed cells are equivalent to pluripotent stem cells at the 8-cell stage. It emphasizes that while certain 8-cell specific genes exhibit transient activation during reprogramming, the authors cannot definitively state that the cells are truly equivalent to the 8C stage, stating 'our results cannot reach the conclusion that the transient cells are equivalent to an 8C stage.' This suggests a limitation in the claim regarding the efficacy of cell reprogramming to achieve true pluripotency.


Input: Task: pass the claim using the given text. Claim: Beauveria bassiana is used as a biocontrol agent against various pests. [SEP] Text: pseudobassiana; however, these results show that the two isolate groups have undergone different evolutionary histories and demonstrate different virulence and oosporein production levels. Orthogroup analysis revealed a large amount of gene content variation among strains, particularly when comparing the red and non-red groups. Accessory orthogroups, which may have arisen through gene duplication and neofunctionalization or were lost in an ancestral species, provide unique capabilities not necessary to survival but potentially confer an evolutionary advantage. OGs unique to the red group were enriched for several GO terms including mycotoxin biosynthetic process and transmembrane transport, and therefore may contribute to increased toxin production and secretion, or differential expression of virulence-related genes in the red strains. Of note, the red strains contained several unique toxin-encoding genes, including four heat-labile enterotoxins and six genes containing the mycotoxin biosynthesis protein UstYa domain. Heat-labile enterotoxin is a compound produced by enterotoxigenic Escherichia coli that causes diarrhoeal diseases in animals. This toxin belongs to the same family as the cholera, pertussis and diphtheria toxins (42), and is hypothesized to provide an alternative mode of infection by compromising insect gut epithelium after ingestion of BB spores (43). In the phytopathogenic Ustilaginoidea virens, the ustYa gene is involved in the biosynthesis of a toxic cyclic tetrapeptide called ustiloxin A (44). Homologues of this gene are present in various filamentous fungi, and while their purpose is still unknown, they have been shown to be involved in ribosomal peptide synthesis in several Aspergilli species (45) and could therefore be involved in secondary metabolism. Biosynthetic gene cluster mining results further demonstrated the genomic variability between strains. More clusters were predicted in the red strains than the non-red strains, which could reflect an increased capacity for secondary metabolism and virulence. Notably, the BGC responsible for synthesizing the red pigment bikaverin in Fusarium species (46) was present only in the genomes of the red strains. Bikaverin exhibits antibiotic and antifungal activity (47) and could function similarly to oosporein by outcompeting organisms in the host microbiome during infection. [SEP] Justify:

Output: The text does not address the claim about Beauveria bassiana being used as a biocontrol agent. Instead, it discusses the genetic and biochemical characteristics of certain isolates, including toxin production and variations among strains, without providing information related to biocontrol applications against pests.


Input: Task: corroborate the claim using the given text. Claim: Depression can result from a combination of genetic, biological, and environmental factors. [SEP] Text: 24, 25, 26 Environmentally-induced changes in SERT expression may partly account for the observed inconsistencies27 but have been sparsely addressed in humans. Animal studies in various species provide first evidence that exposure to early adversity correlates with decreased SERT mRNA levels in the brain28,29 (but also see Gardner et al. 30) and in peripheral cells. 31 These long-term changes in SERT expression patterns may result from stable epigenetic modifications such as DNA methylation. 32 Recent studies using peripheral blood cells found that increased methylation levels within a 799-bp promoter-associated CpG island in SLC6A4 associate with both lower SERT mRNA levels23,33, 34, 35 and exposure to childhood trauma,23,36, 37, 38, 39 in some studies dependent on 5-genotype. 40 Such peripheral measures of gene expression and DNA methylation profiles have been increasingly recognized as informative biomarkers in psychiatric research. 41, 42, 43 Most important for the present study, epigenetic and transcriptional changes in response to environmental adversity appear to be system-wide44,45 and can thus potentially be tracked in easily obtainable blood cells. The present study aimed to investigate joint effects of 5-and environmental adversity across different developmental stages (prenatal, early, recent trauma/stressors) on peripheral SERT mRNA expression and DNA methylation within the promoter-associated island. As a potential molecular pathway of GxE-mediated disease vulnerability, we expected to find lowest SERT mRNA and highest SERT methylation levels in individuals carrying both the genetic (S allele) and environmental (stress/trauma) risk factor. Studies investigating long-term transcriptional signatures of early adversity implicitly assume that gene expression profiles are characterized by a trait-like component with substantial differences between individuals. Prior studies have generally confirmed a considerable intraindividual stability of genome-wide gene expression patterns over hours and months; however, they have also highlighted that stability varies across individual transcripts. 46,47 As intra- and interindividual variation in human SERT mRNA expression has, to the best of our knowledge, not explicitly been evaluated yet, we further conducted a small pilot study investigating respective patterns. Materials and methodsPilot studyFor the assessment of intra- and interindividual variation in SERT mRNA levels, we obtained SERT mRNA expression day profiles in eight healthy individuals (four females, mean age: 25. 0±3. [SEP] Justify:

Output: The text corroborates the claim by discussing the interplay between genetic and environmental factors, particularly through the expression of the SERT gene. It mentions that changes in SERT expression may correlate with environmental adversity and highlights studies indicating that both genetic predispositions and exposure to traumatic experiences can influence SERT mRNA levels. This directly supports the claim that depression can arise from a mix of genetic, biological, and environmental elements, particularly emphasizing the role of epigenetics in these processes.


Input: Task: contrast the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: , 2011) and chromosomal aberrations (Mayshar et al. , 2010). Genomic instability could have unpredictable and undesirable effects on the reprogrammed cells. Furthermore, induced pluripotent stem cells carry their epigenetic signatures from the original differentiated adult cells (Lister et al. , 2011). The reprogrammed cells, therefore, unlike embryonic stem cells, may not develop into some cell types. In addition, induced pluripotent stem cells can still cause immune reactions when transplanted allogeneically. The sources of adult stem cells are multiple and feasibly obtained from various adult tissues, such as bone marrow, blood, adipose tissue, teeth and testes (Table 1). These adult stem cells can be collected from the human body at anytime throughout life. This makes them readily available and does not raise the moral and ethical issues involved with the attainment of embryonic stem cells. Moreover, pluripotent adult stem cells can easily be isolated and purified by cell surface markers, such as CD49f, SSEA-3 and SSEA4 (Conrad et al. , 2008; Kuroda et al. , 2010; Kawanabe et al. , 2010; Notta et al. , 2011). The pluripotent status of these adult stem cells is naturally acquired and does not require reprogramming by the introduction of pluripotent transcriptional factors, thus eliminating the use of viral vectors and the chance of aberrant chromosomal changes. Furthermore, transplantation of mesenchymal stem cells and periodontal ligament-derived stem cells can be autogenic or allogeneic. Immuno-suppression is not necessary since mesenchymal stem cells have strong immunomodulatory properties against alloreactivity of T lymphocytes and dendritic cells (Chen et al. , 2011). Similarly, mesenchymal stem cells and periodontal ligament-derived stem cells inhibit the proliferation of peripheral blood mononuclear cells (Wada et al. , 2009). Spermatogonial stem cells, however, are killed by cytotoxic T lymphocytes after transplantation (Dressel et al. , 2009), whereas allogeneic hematopoietic stem cell transplantation induces graft-vs-host disease (Strober et al. , 2011). [SEP] Justify:

Output: The text contrasts the claim by discussing the characteristics of adult stem cells and specifically mentions that pluripotent adult stem cells naturally acquire their pluripotent status without the need for reprogramming through transcriptional factors. This indicates that scientists do not necessarily have to use cell reprogramming to create pluripotent stem cells from adult cells, as adult stem cells can possess pluripotent properties inherently.


Input: Task: pass the claim using the given text. Claim: Beauveria bassiana is used as a biocontrol agent against various pests. [SEP] Text: Additionally, the virulence factor bassianolide was unique to the non-red strains and may contribute to the insecticidal activity in these strains. The differential content of biosynthetic gene clusters reveals that the genomic factors driving virulence are diverse and variable between BB strains. Further characterization of these biosynthetic gene clusters and their products is necessary to determine their role in BB virulence. Several genes of interest were identified through differential expression analysis between the UVR strains and their wild type parents. Many were involved in stress response, monooxyenase activity and copper metabolism, all of which are crucial to protecting against UV radiation and oxidative stress. A gene encoding a MAC1 interacting protein was downregulated in UAMH 299-UVR. This gene contains a CFEM domain, which is a fungal-specific protein domain involved in a variety of biological functions including cell wall and cell membrane maintenance (48). Early studies of MAC1 in Saccharomyces cerevisiae revealed that the protein is a transcription factor responsible for regulating genes required for copper metabolism and stress response (49), suggesting potential involvement in oxidative stress response. Two highly similar glucose-repressible protein encoding genes were downregulated in UAMH 298-UVR, one of which was annotated as Grg1. anserina, transcription of Grg1 was induced by carbon starvation and aging, and its expression was significantly lowered in a long-lived mutant with decreased cellular copper levels and oxidative stress. Downregulation of these glucose-repressible genes in UAMH 298-UVR could therefore be a result of decreased oxidative stress. Furthermore, upregulation of a heme-dependent catalase-like domain containing gene and two glutathione-s-transferase genes in UAMH 298-UVR could improve the strain’s ability to remove damaging reactive oxygen species (ROS). Testing individual variants using genetic engineering approaches such asCas9 editing would help to determine which variants specifically confer UV resistance. Given the phenotypic diversity between BB strains, it was originally hypothesized that the group I strains contained the oosporein BGC while the other strains did not. The core biosynthetic genes OpS1-OpS7 were identified in all eight strains by antiSMASH, suggesting that the high levels of oosporein production in the red strains are a result of regulatory factors or differential expression. [SEP] Justify:

Output: The text does not address the claim regarding the use of Beauveria bassiana as a biocontrol agent against pests. Instead, it discusses various aspects of the genetic expression and virulence factors in different strains of Beauveria bassiana, including genetic responses to stress and the potential roles of specific genes. Therefore, the text is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Depression can result from a combination of genetic, biological, and environmental factors. [SEP] Text: Individuals of mothers reporting at least one major stressful/traumatic life event during pregnancy were found to have lower SERT mRNA levels compared with those without maternal prenatal stress (F1,83=5. 54; P=0. 02; η2=0. 06). Furthermore, we observed a negative correlation between the number of prenatal maternal life stressors/trauma and SERT mRNA levels (r=−0. 27, P=0. 01). A similar reduction in SERT mRNA expression was seen in individuals reporting early traumatization (F1,131=4. 15; P=0. 04; η2=0. 03) when comparing the groups of participants with (mean CTQ score: 48. 88±4. 38) and without (mean CTQ score: 30. 69±8. 54) a history of child maltreatment. Within the overall sample, CTQ scores were inversely correlated with SERT mRNA levels (r=−0. 18; P=0. 04). In contrast, recently experienced stress had no effect on SERT mRNA levels (F1,131=1. 17; P=0. 19). Our findings further indicated that the S allele and prenatal/early adversity associate with decreased SERT expression in an additive manner as lowest levels were found in individuals carrying both the genetic and the environmental risk factor (prenatal stress: F2,82=3. 14; P=0. 05; η2=0. 07; early trauma: F2,130=4. 55; P=0. 01; η2=0. 07; Figure 2). Specifically, those individuals were found to have 32. 8% (prenatal stress) and 56. 3% (child maltreatment) lower SERT mRNA levels compared with the group without any of the two risk factors. Including a GxE interaction term in the general linear model did not incrementally increase the portion of variance explained by an additive model (prenatal stress: F1,81=0. 86; P=0. 36; early trauma: F1,129<0. 01, P=0. 99). Figure 2SERT mRNA expression levels (mean±s. e. m. ) calculated with the 2−2ΔΔCt method as a function of 5-genotype and (a) prenatal stress or (b) early trauma. [SEP] Justify:

Output: The text corroborates the claim by providing evidence that supports the role of both genetic and environmental factors in depression. It highlights how maternal stress during pregnancy and early trauma correlate with lower SERT mRNA levels, suggesting a biological response influenced by these environmental factors. Additionally, the mention of the interaction between genetic (the S allele) and environmental risk factors provides a clear link to the claim that depression can arise from a combination of multiple influences.


Input: Task: pass the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: 2007 Feb 23;128(4):747-62. 59. . Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development. 1987 Mar;99(3):371-82. 60. . Embryonic germ cells induce epigenetic reprogramming of somatic nucleus in hybrid cells. Embo J. 1997 Nov 3;16(21):6510-20. 61. Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature. 2008 Apr 17;452(7189):877-81. 62. Ohinata Y, Payer B, O' Blimp1 is a critical determinant of the germ cell lineage in mice. Nature. 2005 Jul 14;436(7048):207-13. 63. - The zinc finger transcriptional repressor Blimp1/Prdm1 is dispensable for early axis formation but is required for specification of primordial germ cells in the mouse. Development. 2005 Mar;132(6):1315-25. 64. Critical function of Prdm14 for the establishment of the germ cell lineage in mice. Nat Genet. 2008 Aug;40(8):1016-22. 65. Epiblast stem cell-based system reveals reprogramming synergy of germline factors. Cell. 2012 Apr 6;10(4):425-39. 66. A germ cell-specific gene, Prmt5, works in somatic cell reprogramming. J Biol Chem. 2011 Mar 25;286(12):10641-8. 67. Blimp1 associates with Prmt5 and directs histone arginine methylation in mouse germ cells. Biol. 2006;8(6):623-30. 68. DNA methylation is a primary mechanism for silencing postmigratory primordial germ cell genes in both germ cell and somatic cell lineages. Development. 2006 Sep;133(17):3411-8. 69. Reik W, Dean W. Back to the beginning. Nature. 2002 Nov 14;420(6912):127. 70. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature. 2010 Feb 25;463(7284):1101-5. 71. -Mahrt SK. [SEP] Justify:

Output: The text does not provide any relevant information about the process of cell reprogramming specifically related to adult cells or pluripotent stem cells. Instead, it focuses on various studies involving DNA methylation, embryonic development, and germ cell lineages, which do not directly support or contrast the claim about adult cell reprogramming.


Input: Task: pass the claim using the given text. Claim: Beauveria bassiana is used as a biocontrol agent against various pests. [SEP] Text: The transcriptome data corroborated this hypothesis, demonstrating high levels of upregulation of OpS1, OpS2, OpS4-OpS7 and OpS11 in the red strains, but the absence of upregulation for OpS3 raised additional questions about the regulation of this gene cluster. Surprisingly, some oosporein cluster genes were upregulated in the UVR strains as well. Since oosporein is a pigment, it could potentially play a role in absorbing UV radiation, thus protecting these strains from oxidative stress. Another pigment that is known to play a protective role in UV radiation is melanin. Some fungi use L-dopa as a starter molecule and a laccase enzyme for the biosynthesis of melanin (50), however, it remains to be seen whether the upregulated OpS5 is involved in the production of melanin in the UVR strains of BB. Regulation of the oosporein BGC is not well understood, but some regulatory factors have been identified. Bbmsn2, a zinc finger TF and stress response protein, negatively regulates oosporein in a pH-dependent manner (51). This protein is also required for fungal penetration through the insect cuticle (52). Unfortunately, the genetic mechanisms underlying oosporein repression by Bbmsn2 have not been elucidated. Another zinc finger TF BbSmr1 was identified as an upstream regulator of the oosporein BGC, likely through regulation of the OpS3 transcription factor (31). BbSmr1 was not differentially expressed, and Bbmsn2 was significantly upregulated in the red strains. Since Bbmsn2 acts as a repressor for oosporein production, upregulation of this gene should cause a decrease in oosporein synthesis, therefore contradicting with the observed phenotype of the red strains. Differential co-expression analysis identified several potential transcription factors involved in regulating the expression of OpS1 and OpS3. Many of these were Zn(2)-Cys(6) type TFs, which is the same type of TF as OpS3. These TFs may be involved in regulating oosporein gene cluster expression and oosporein production upstream of OpS3. [SEP] Justify:

Output: The text does not address the claim directly and instead discusses gene regulation in Beauveria bassiana and its genetic mechanisms. It focuses on aspects of transcription factors and their roles in gene expression related to pigments like oosporein and melanin, which are not clearly linked to the use of Beauveria bassiana as a biocontrol agent. Therefore, the text is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Depression can result from a combination of genetic, biological, and environmental factors. [SEP] Text: For completeness, we have further investigated associations of prenatal, early and recent life stress/trauma with SERT methylation levels within the CpG island by means of a partial principal component analysis, which overall revealed no significant results (3). DiscussionIn the light of overall conflicting findings on whether the 5-allele conveys disease vulnerability upon environmental adversity,7,8 this study aimed to explore molecular modifications, which possibly mediate GxE interaction. Here, we report that both the S allele and prenatal/early adversity associate with decreased peripheral SERT mRNA levels in an additive manner and, remarkably, account for a comparable amount of variance in SERT expression. These effects appeared to be largely independent of methylation profiles within the SLC6A4 promoter-associated CpG island. Our finding of lower SERT mRNA levels in S allele carriers closely parallels previous data from in vitro research2,19, 20, 21 but stands at variance with several brain imaging studies reporting mixed results regarding allele-specific SERT availability. 24, 25, 26 Besides inconsistencies related to methodological aspects (see Willeit et al. 62), SERT mRNA may simply reflect a more proximate measure of transcriptional activity than SERT availability. Indeed, research across different species has shown SERT mRNA to be subjected to complex post-transcriptional regulation, such as translational repression by miRNA. 63, 64, 65 In addition, our findings implicate that differential exposure to early adversity may either overshadow or pronounce allele-specific effects on in vivo SERT mRNA expression (Figure 2) and may thus have contributed to previously observed discrepancies. 22,23To date, the link between environmental adversity and persistent changes in SERT mRNA profiles has almost exclusively been addressed in non-human research. Specifically, maternal separation has been associated with lower raphé SERT mRNA levels in rodents28,29 and decreased SERT availability in non-human primates. 66 Likewise, Rhesus macaques exposed to maternal aggression were found to have reduced SERT mRNA levels in peripheral blood cells, indicating that stress-induced changes of SERT expression are not limited to the brain. 31 Our study complements and extends previous animal research by demonstrating long-term signatures of early adversity using easily accessible markers of human SERT expression. Here, we provide first evidence for reduced SERT mRNA levels in individuals exposed to maternal prenatal stress or child maltreatment. [SEP] Justify:

Output: The text corroborates the claim by discussing the interaction of genetic (S allele) and environmental factors (prenatal and early adversity) with SERT mRNA levels. It suggests that early adversity may impact genetic predispositions, thereby linking biological and environmental influences to changes in gene expression which could contribute to conditions like depression.


Input: Task: contrast the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogramming. J Biol Chem. 2004 Dec 10;279(50):52353-60. 72. Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature. 2007 May 24;447(7143):425-32. 73. and Through 5-Hydroxymethylcytosine. Science. 2012 Dec 13. 74. de. Early loss of Xist RNA expression and inactive X chromosome associated chromatin modification in developing primordial germ cells. PLoS One. 2007;2(9):e860. 75. . Expression of Polycomb-group genes in human ovarian follicles, oocytes and preimplantation embryos. Reproduction. 2005 Dec;130(6):883-8. 76. . Mouse embryonic germ (EG) cell lines: transmission through the germline and differences in the methylation imprint of insulin-like growth factor 2 receptor (Igf2r) gene compared with embryonic stem (ES) cell lines. Development. 1994 Nov;120(11):3197-204. 77. Epigenotype switching of imprintable loci in embryonic germ cells. Evol. 1998 Feb;207(8):551-61. 78. Monoallelic expression and methylation of imprinted genes in human and mouse embryonic germ cell lineages. . 2002 Aug 6;99(16):10599-604. 79. . Derivation of pluripotential embryonic stem cells from murine primordial germ cells in culture. Cell. 1992;70(5):841-7. 80. . Stem cells from primordial germ cells can reenter the germ line. Dev Biol. 1994 Feb;161(2):626-8. 81. Derivation of pluripotent stem cells from cultured human primordial germ cells. Proceedings of the of Sciences of the of America. 1998;95(23):13726-31. 82. . Bone morphogenetic protein 4 mediates human embryonic germ cell derivation. Dev. 2011 Feb;20(2):351-61. 83. [SEP] Justify:

Output: The text contrasts the claim as it primarily discusses epigenetic changes and pluripotent tissues without directly supporting the idea that scientists specifically use cell reprogramming to turn adult cells into pluripotent stem cells. The mention of pluripotent stem cells from primordial germ cells does not provide evidence for the claim about reprogramming adult cells.


Input: Task: pass the claim using the given text. Claim: Beauveria bassiana is used as a biocontrol agent against various pests. [SEP] Text: Extraction and detection of oosporein from Beauveria bassiana Eight morphologically similar BB strains, with variable pigmentation, were selected and grown to obtain detection limits for oosporein production. The starting fungal inoculum was reactivated using Czapex-medium, and incubated at 25oC for 4–6 weeks, or until conidial lawn is at its maximum. The conidia were harvested from the agar media, titered, and inoculated a 25 mL Czapex-(CDBYE) medium in a 250 mL Erlenmeyer flask to a final concentration of 1 x 107 conidia/mL and incubated at 28oC for 72–96 h at 175 rpm. After incubation, a 1 mL inoculum was used to inoculate a 250 mmedium in a 1000 mL Erlenmeyer flask and incubated at 28oC at 175 rpm. After 5 days of incubation, duplicate mycelial mixtures (2 x 30 mL) were harvested through centrifugation at 10,000 x g for 15 min at 4oC. The supernatant was transferred to a new sterile conical tube and the resulting mycelial pellet was washed twice with ice-cold TE buffer (10 mM Tris/1 mM EDTA, pH 8. 0), and the supernatant was combined with the previous sample. The mycelial cultures were incubated further, and the extraction process was carried out again after day 10 and 15. The supernatant was extracted with ethyl acetate (4 x 20 mL), concentrated in vacuo, and purified through high-performance liquid chromatography (HPLC). Oosporein concentration was detected using LC-MS through comparison to a previously synthesized standard (78). Lastly, the limit of detection of oosporein was performed using 10-fold serial dilutions and analyzed via LC-MS. DNA for BB strains were grown to establish high quality draft genome reference sequences. The starting fungal inoculum was obtained from frozen mycelial stocks and re-activated using Czapex-(CDAYE) medium, and incubated at 25oC for 4–6 weeks, or until the conidial lawn is at its maximum. [SEP] Justify:

Output: The text is irrelevant to the claim as it describes the extraction and detection of oosporein from Beauveria bassiana and details the methodology of fungal cultivation and analysis, without addressing the use of Beauveria bassiana as a biocontrol agent against pests.


Input: Task: corroborate the claim using the given text. Claim: Depression can result from a combination of genetic, biological, and environmental factors. [SEP] Text: This observation is strengthened by an inverse correlation between SERT mRNA levels and the magnitude of prenatal/early adversity within the overall sample. Strikingly, we observed no such effect for adult stressors/trauma, hinting towards a sensitive period in early development. 67Epigenetic modifications are considered a promising pathway mediating sustained changes of gene expression in response to early adversity. 32 Methylation profiles within a 799-bp CpG island in SLC6A4 have recently been associated with SERT transcription and are further responsive to environmental influences. 68 Several in vivo and in vitro studies found site-specific SERT methylation to promote gene silencing in transformed lymphoblast cell lines,23,33 peripheral blood mononucleated cells35 and buccal cells,34 in some studies depending on 5-. 40 Our results tentatively concur with previous observations by demonstrating negative correlations of SERT methylation and mRNA expression for 10 out of 83 CpG sites investigated. Although this association remained significant only for CpG9 after Bonferroni correction, the finding of 12% of CpG sites being functionally relevant on an uncorrected level is unlikely to result from chance (B(i⩾10|α=0. 05, n=83) <1%). Despite its putative role in transcriptional regulation, we found very limited evidence for SERT methylation mediating associations between environmental adversity and SERT mRNA expression. Regarding childhood trauma, our study conflicts with previous reports linking site-specific SERT methylation to a history of sexual abuse,23,36,37 childhood trauma39 and bullying victimization. 38 However, it is of note that no specific CpG site has yet been consistently associated with early adversity across previous studies. Variable findings may result from diversity of used cell populations, examined subregions, methylation detection methods (for example, quantitative mass spectroscopy, platform, pyrosequencing), type of trauma and lack of correction for multiple testing. Regarding prenatal stress, initial evidence has suggested a positive association between maternal depressed mood during the second trimester and the mean methylation within a subregion of the island (10 CpG sites). [SEP] Justify:

Output: The text corroborates the claim by discussing factors that contribute to depression, emphasizing the role of genetic (SERT mRNA levels), biological (epigenetic modifications), and environmental influences (prenatal/early adversity). It also highlights the complex interactions between these aspects, stating that early adversity can affect gene expression and that methylation profiles are responsive to environmental factors, aligning well with the claim that a combination of these factors can lead to depression.


Input: Task: pass the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: Regulation of stem cell pluripotency and differentiation involves a mutual regulatory circuit of the 4, and SOX2 pluripotency transcription factors with polycomb repressive complexes and stem cell microRNAs. Dev. 2009 Sep;18(7):1093-108. 84. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009 Jan 23;136(2):215-33. 85. Gangaraju VK, Lin H. MicroRNAs: key regulators of stem cells. Biol. 2009 Feb;10(2):116-25. 86. . Embryonic stem cell-specific MicroRNAs. Dev Cell. 2003 Aug;5(2):351-8. 87. Barroso-delJesus A, Romero-Lopez C, Lucena- Embryonic stem cell-specific miR302-367 cluster: human gene structure and functional characterization of its core promoter. Biol. 2008 Nov;28(21):6609-19. 88. . of from Stem Cells. PLoS one. 2010;5(5):e10480 of Undifferentiated and Cells. Dev. 2007 Dec;16(6):1003-16. 90. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell. 2008 Aug 8;134(3):521-33. 91. . MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature. 2008 Oct 23;455(7216):1124-8. 92. . Polycomb group proteins in cell cycle progression and cancer. Cell Cycle. 2004 Apr;3(4):396-400. 93. NF-kappaB-YY1-miR-29 regulatory circuitry in skeletal myogenesis and rhabdomyosarcoma. Cancer Cell. 2008 Nov 4;14(5):369-81. 94. -Revel CG, et al. MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Mol Biol. 2008 Mar;15(3):259-67. 95. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev. 2005 Feb 15;19(4):489-501. 96. . [SEP] Justify:

Output: The text does not reference cell reprogramming or the process of converting adult cells into pluripotent stem cells. Instead, it discusses regulatory mechanisms related to stem cell pluripotency and differentiation without directly supporting, contrasting, or addressing the claim.


Input: Task: pass the claim using the given text. Claim: Beauveria bassiana is used as a biocontrol agent against various pests. [SEP] Text: The conidia were harvested from the agar media, titered, and inoculated a 100 mbroth medium in a baffled 500 mL Erlenmeyer flask to a final concentration of 1 x 107 conidia/mL and incubated at 28oC for 72–96 h at 175 rpm. Mycelia were harvested through centrifugation at 5000 x g for 20 min at 4oC. The resulting mycelial pellet was washed twice with ice-cold TE buffer, and flash frozen in liquid nitrogen, and stored at -80oC until processing. Quality control analysis for bacterial contamination was performed for all samples. An aliquot of the mycelia was serially diluted ten-fold up to 1. 0 x 106 and all dilutions were spread-plated, in quadruplicate, on Agar () with 100 U/mL nystatin. Duplicate plates were incubated at either 28oC or 35oC for 28–72 h to assess the bacterial load. Frozen mycelial pellets were sent to the Laboratories, University of British Columbia, for DNA extraction. was isolated from lyophilized mycelium (~ 5 g) with a modified protocol of Doyle and Dickson (53). The modifications included adding 3% mercaptoethanol to the lysis extraction buffer, incubation at 60oC for 45 minutes and washing the initial pellet with 75% ethanol with 10 mM ammonium acetate. An additional solvent cleaning with 1:1 phenol:chloroform-isoamyl solution was included after incubation with RNAse and proteinase K at 37oC. The concentration and quality of DNA was verified with a Nanodrop 2000c (), Quantiflor () and 0. 8% agarose gel. 3–4 µg total DNA for all 8 strains was sent to Canada’s Centre for sequencing. microfluidic partitioned library was created using the Chromium system (10x ). Gel beads-in-Emulsion (GEMs) were produced by combining DNA, Master Mix, and partitioning oil in the 10x Controller instrument with the microfluidic [PN-120216] (10x Genomics). The DNA in each GEM underwent isothermic amplification as a barcode was added to each fragment. Barcoded fragments then underwent Illumina library construction, as per the Version 2 [PN-120229]. [SEP] Justify:

Output: The text is irrelevant to the claim because it focuses on the methodologies and protocols for DNA extraction and processing of mycelial samples without mentioning Beauveria bassiana's role as a biocontrol agent or its application against pests.


Input: Task: corroborate the claim using the given text. Claim: Depression can result from a combination of genetic, biological, and environmental factors. [SEP] Text: 72 Regarding SERT in particular, a recent brain imaging study73 indicates that peripheral SERT methylation is indeed an informative marker for in vivo serotonin synthesis. Even more importantly, environmentally induced modifications in gene expression and methylation patterns appear to be system-wide44,45 supporting the usefulness of peripheral markers for the present study. Lastly, the choice of analyzing whole blood was motivated by the fact that it is readily available, allows to stabilize RNA at the time of blood draw and, importantly, does not require transformation known to modify methylation profiles. 74 Despite these advantages, the heterogeneous mixture of cell types may constitute a potential confound, although expression levels of very few mRNA transcripts were found to depend on cell composition. 47In conclusion, our findings raise the assumption of lower SERT mRNA expression being a correlate of both the 5-allele and prenatal/early adversity. Strikingly, individuals carrying both the genetic and one of the environmental risk factors were found to have 32. 8% (maternal prenatal stress) and 56. 3% (child maltreatment) lower SERT mRNA levels compared with those without any risk factor. Sustained alterations in SERT expression profiles may in turn relate to changes in serotonergic functioning and thus constitute a possible molecular pathway mediating disease vulnerability as a function of GxE. In accordance with genome-wide transcriptomics analyses,46,47 preliminary evidence from our pilot study suggests that interindividual variability in SERT expression is substantially higher compared with intraindividual variation, thus highlighting the potential usefulness of this specific transcript as a biomarker. Although not without inconsistencies,75, 76, 77 numerous studies indeed suggest that lower SERT expression in the brain and periphery associates with major depression,14, 15, 16 treatment efficacy14,78,79 and increased stress sensitivity. 17,18 Since the mean age of onset for depression80 is slightly higher compared with the mean age of our sample, altered SERT expression levels could be discussed in terms of a premorbid risk factor for the development of stress-related psychopathology later in life. Future evaluation of such putative biomarkers of disease vulnerability in longitudinal designs may not only shed light on the pathogenesis of stress-related psychopathology but may also bear important implications for predictive testing. In line with this assumption, peripheral blood gene expression profiles measured in the third trimester of pregnancy have been found to reliably predict subsequent postpartum depression within a high-risk cohort. [SEP] Justify:

Output: The text corroborates the claim by discussing how both genetic factors (notably SERT expression) and environmental factors (such as maternal prenatal stress and child maltreatment) contribute to the understanding of depression. It highlights that individuals who carry specific genetic risks along with environmental stressors have markedly lower levels of SERT mRNA expression, suggesting a biological vulnerability influenced by both genetic and environmental components. This aligns with the claim that depression arises from a combination of these factors.


Input: Task: pass the claim using the given text. Claim: Scientists use cell reprogramming to turn adult cells into pluripotent stem cells. [SEP] Text: Bracken AP, Kleine- group proteins bind throughout the INK4A-ARF locus and are disassociated in senescent cells. Genes Dev. 2007 Mar 1;21(5):525-30. 122. Bypass of senescence by the polycomb group protein CBX8 through direct binding to the INK4A-ARF locus. Embo J. 2007 Mar 21;26(6):1637-48. 123. . EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. Embo J. 2003 Oct 15;22(20):5323-35. 124. - Epigenetic stem cell signature in cancer. Nat Genet. 2007 Feb;39(2):157-8. 125. Hedgehog signaling and Bmi-1 regulate self-renewal of normal and malignant human mammary stem cells. Cancer Res. 2006 Jun 15;66(12):6063-71. 126. . Increased expression of the polycomb group gene, EZH2, in transitional cell carcinoma of the bladder. Res. 2005 Dec 15;11(24 Pt 1):8570-6. 127. The putative tumor suppressor microRNA-101 modulates the cancer epigenome by repressing the polycomb group protein EZH2. Cancer Res. 2009 Mar 15;69(6):2623-9. information 1. Introduction2. Epigenetic control in pluripotent stem cells3. Epigenetic control in primordial germ cells and pluripotent embryonic germ cells4. MicroRNAs and stem cells5. Epigenetic regulation in progenitor and adult stem cells6. Epigenetic dysregulation in cancer stem cells7. ConclusionNomenclature1. Choose citation style Select style to clipboard Get citation 2. Choose citation style Select format Bibtex RIS Download citation 1. Choose citation style Select style to clipboard Get citation 2. Choose citation style Select format Bibtex RIS Download citation © 2013 The Author(s). Licensee IntechOpen. This 3. 0 License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Continue reading from the same book by by Published: 28 August 2013 0. 00 Local taxes (VAT) are calculated in later steps, if applicable. [SEP] Justify:

Output: The text does not address the claim about cell reprogramming or the process of turning adult cells into pluripotent stem cells. Instead, it discusses various aspects of epigenetic control and cancer stem cells without providing any supportive or contrasting information related to the claim.


Input: Task: pass the claim using the given text. Claim: Beauveria bassiana is used as a biocontrol agent against various pests. [SEP] Text: The resulting library was assessed for quality using the Agilent 2100 Bioanalyzer () and a DNA 1000 assay. The median insert size was 550 bp. The library was quantified using a Quant-iT dson a Qubit fluorometer () prior to library pooling and size corrected final molar concentration calculation for Illumina HiSeqX sequencing with paired-end 150 base reads. pipeline (v2. 1. 3) was run on the raw reads to perform read trimming, barcode error correction, whitelisting and barcode assignment (54). The reads were downsampled by barcode to 18 million reads (approximately 80X sequencing depth) for further analyses. De novo The genomes were assembled using Supernova v2. 1. 1 (55), which leverages the long-range information provided by linked reads. Since read coverages were higher than the recommended range of 38-56X for assembly, 15 million reads were selected (approximately 56X coverage) using --maxreads = 15000000. The output FASTA files were created using the --style = pseudohap option which generated a single record per scaffold, and scaffolds shorter than 1 kb were excluded from the final assembly. The draft genomes were polished by aligning 80X downsampled reads to their respective genomes using BWA-MEM v0. 7. 17r1188 (56, 57) and supplying these alignments to Pilon v1. 23. BUSCO v5. 1. 2 (58) was run to assess the genic completeness of the assemblies using the hypocreales_odb10 database in genome mode, and other assembly metrics were calculated with QUAST v5. 0. 2 (59). EDTA v1. 9. 4 (60) and RepeatModeler v2. 0. 1 (61) were used to identify and annotate repetitive sequences within the polished assemblies. The coding sequences of BB strain ARSEF 8028 (33) were supplied to EDTA to ensure that gene sequences were excluded from the resulting libraries. All identified repeats were merged with the RepBase (62) database of eukaryotic repeat sequences (v23. 12), and redundant sequences were removed using the cleanup_nested. pl script from EDTA (60). This custom repeat library was used as input for RepeatMasker v4. 1. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the technical details of genomic sequencing and assembly processes, particularly focusing on the methodologies and software used, without mentioning Beauveria bassiana or its application as a biocontrol agent against pests.


Input: Task: pass the claim using the given text. Claim: Depression can result from a combination of genetic, biological, and environmental factors. [SEP] Text: Success in identifying the correct model in these circumstances is consistent with the results of a larger set of simulations by Schadt et al. (2005), who found that the power to detect the correct model under similar circumstances was ∼80% when QTL explained as little as 1–2% of the variation in the less-affected trait. Confounding effects of incomplete QTL and trait detection: These simulations clearly show that not including all relevant QTL in the models can lead to incorrect functional predictions with multiple-trait QTL data. Much of the “signal” for detecting indirect QTL effects on traits in a network, whether the traits are gene expression or functional phenotypes, comes from the degree and pattern of residual correlations between trait values within QTL genotypic classes (Stein et al. 2003; Doss et al. 2005; Schadt et al. 2005). In the absence of common-environment effects, only the genetic component of trait variation in a pair of traits should be correlated if a set of genes affects both traits independently. When QTL effects on one trait are indirect effects of variation in an upstream trait, however, both genetic and environmental effects on the upstream trait will affect the downstream trait in the same manner, leading to similar correlations within and among QTL classes. If all QTL that jointly affect a set of traits are not included in the model, effects of the unobserved or excluded QTL will also result in residual correlations between traits. These residual correlations may generate false support for indirect models, with the trait having larger standardized QTL effects appearing to be upstream. Thus, analyses that test only a single QTL region for effects on a suite of polygenic traits are virtually guaranteed to place the traits in a common regulatory pathway, whether such a pathway exists or not. Even when all experimentally detected QTL regions are included in a model, some actual QTL are likely to be missed due to limited experimental power (Beavis 1994) and lead to correlated residuals. Testing of direct vs. indirect QTL path models has been suggested as a test of close linkage vs. pleiotropy with shared QTL regions, since the former are by definition independently regulated (Doss et al. 2005; Schadt et al. 2005). For this test to identify instances of close linkage effectively, however, these results show that all other QTL regions that jointly affect the two traits must be included in the model. [SEP] Justify:

Output: The text primarily discusses statistical models and methods related to Quantitative Trait Loci (QTL) in genetic studies but does not address the claim about depression resulting from genetic, biological, and environmental factors. Therefore, it does not corroborate, contrast, or provide any relevance to the claim.


Input: Task: contrast the claim using the given text. Claim: All patients respond equally well to regenerative therapies. [SEP] Text: all stem cells are equally great donor single nucleotide polymorphisms snp may matter more than previously thought Submit manuscript. . . Advances in eISSN: 2572-8490 & Regenerative Medicine: Review 231. DOI: 10. 15406/atroa. 2017. 02. 00040 cell therapy has brought new opportunities for a wide range of human diseases that currently have no cure. Stable and sustainable stem cell sources have always been a key issue for all clinical applications and regenerative properties and host-insulting nature of stem cells are determined by several factors of allogeneic or even autologous donors. Most human diseases are considered multi factorial and complex, with a degree of genetic etiologies, which may potentially influence their stem cell characteristics. This mini-review will particularly discuss how genetic traits of donors, represented by single nucleotide polymorphisms (SNPs), may have impact on the quality/suitability of stem cells for a particular disease and the clinical outcomes, and try to propose some possible solutions in light of the latest advances in genome and stem cell technologies. Keywords: Stem cell; Donor; Single-nucleotide polymorphisms; Stem cell therapy Abbreviations HSC: Cells; ESC: Cells; MSC: Cells; HGP: Project; SNPs: Polymorphisms; HSCT: Cell Transplantation; : cell may provide new therapies for a wide range of human diseases Rapid advances in stem cell research in recent decade have brought revolutionary insights into modern biology and medicine, including cell functions, development and growth, maintenance of tissue homeostasis, tissue regeneration, aging/degeneration and diseases. 1,2 Most importantly, stem cell research holds the promise of developing new therapies for a wide range of human diseases. Numerous animal and human studies indicate that stem cell therapy are very promising and especially significant for the treatment of diseases that cannot be cured with conventional medicine. 3-6 Dated on late March of 2017, the number of stem cell-based clinical trials registered in (www. ClinicalTrials. gov) has nearly reached at 6000, a number probably greater than any other single therapeutic technique or approach, whereas the majority of the trials are understandably haematopoietic stem cells (HSC) and mesenchymal stem cells (MSC) that can be harvested from various tissue sources. [SEP] Justify:

Output: The text contrasts the claim by discussing the influence of genetic factors, specifically single nucleotide polymorphisms (SNPs), on the effectiveness of stem cells in therapy. It points out that 'genetic traits of donors, represented by SNPs, may have impact on the quality/suitability of stem cells for a particular disease and the clinical outcomes,' suggesting that patients do not respond equally well to regenerative therapies due to these differences.


Input: Task: pass the claim using the given text. Claim: Beauveria bassiana is used as a biocontrol agent against various pests. [SEP] Text: 1 (63) to annotate and soft-mask repetitive sequences in the polished genome assemblies. Evolutionary relationships between the strains were inferred using RAxML v8. 2. 12 (64). The BB reference strain ARSEF 2860 (32) and B. pseudobassiana strain KACC 47484 (unpublished; GenBank accession: GCA_003267905. 1) were also included in the analysis, as well as C. militaris strain CM01 (65), which was set as the outgroup with the -o option. Single-copy BUSCO sequences were used to generate the phylogeny as annotations were not available for the B. pseudobassiana genome assembly. Multiple sequence alignments were generated for the shared BUSCO sequences with MAFFT v7. 475 (66), selecting the appropriate strategy automatically (--auto), and the resulting amino acid alignments were concatenated into a single matrix. The phylogeny was generated from a rapid Bootstrap analysis and search for the best-scoring tree, using the model of amino acid substitution and 100 bootstrap replicates. Genome annotation was performed using the MAKER (v2. 31. 10) pipeline (67), which combines ab initio gene predictions and homology evidence. SNAP v2006-07-28 (68), GeneMark. hmm-E v3. 47 (69) and v3. 3. 3 (70) were used for ab initio gene prediction; SNAP and GeneMark were both trained on the UAMH 299 assembly, and Fusarium graminearum was used as the gene prediction species model for. CDS of BB strain ARSEF 8028 (33) were supplied as expressed sequence tag (EST) evidence and the UniProtKB/Swiss-Prot database of protein sequences (71) was used as protein homology evidence. The gene predictions were processed using Generator v2. 0. 1 (72), which added start and stop codons and removed transcripts with introns shorter than 10 bp or coding sequences shorter than 90 bp. Annotations that were missing a start and/or stop codon were then manually removed. The quality of the filtered annotations was assessed with GeneValidator v2. 1. 10 (73) using the TrEMBL database (71), and these scores were considered while selecting genes of interest in later analyses. [SEP] Justify:

Output: The text only discusses the analysis of genomic data, phylogenetic relationships, and gene prediction methodologies related to different fungal strains, including Beauveria bassiana. It does not provide any information about the use of Beauveria bassiana as a biocontrol agent or its effectiveness against pests, making it irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Depression can result from a combination of genetic, biological, and environmental factors. [SEP] Text: Advertisement intended for healthcare professionals in through your institution Filter Evolution, Medicine, and Public HealthThis issueEvolutionary Biology Biologyand search term Issue 1, 2024 (In Progress) Issue 1, 2023 Browse all Advance 10. 1093/emph/eov009 Published: 26 April 2015 10. 1093/emph/eov009 Select format. ris (Mendeley, Papers, Zotero). enw (EndNote). bibtex (BibTex). txt (Medlars, RefWorks) Download citation and Public HealthThis issueEvolutionary Biology Biologyand search term and Public HealthThis issueEvolutionary Biology Biologyand search term and objectives: Depression is a major medical problem diagnosed in an increasing proportion of people and for which commonly prescribed psychoactive drugs are frequently ineffective. Development of treatment options may be facilitated by an evolutionary perspective; several adaptive reasons for proneness to depression have been proposed. A common feature of many explanations is that depressive behaviour is a way to avoid costly effort where benefits are small and/or unlikely. However, this viewpoint fails to explain why low mood persists when the situation improves. We investigate whether a behavioural rule that is adapted to a stochastically changing world can cause inactivity which appears similar to the effect of depression, in that it persists after the situation has improved. Methodology: We develop an adaptive learning model in which an individual has repeated choices of whether to invest costly effort that may result in a net benefit. Investing effort also provides information about the current conditions and rates of change of the conditions. Results: An individual following the optimal behavioural strategy may sometimes remain inactive when conditions are favourable (i. e. when it would be better to invest effort) when it is poorly informed about the current environmental state. Initially benign conditions can predispose an individual to inactivity after a relatively brief period of negative experiences. Conclusions and implications: Our approach suggests that the antecedent factors causing depressed behaviour could go much further back in an individual s history than is currently appreciated. The insights from our approach have implications for the ongoing debate about best treatment options for patients with depressive symptoms. behavioural shutdown model, low mood, major depressive disorder, psychic pain hypothesis, reactive depressionPain or suffering of any kind, if long continued, causes depression and lessens the power of action, yet it is well adapted to make a creature guard against any greater or sudden evil. [SEP] Justify:

Output: The text corroborates the claim by discussing the multifaceted nature of depression, indicating that several adaptive reasons for proneness to depression have been proposed and suggesting that antecedent factors causing depressed behavior can include environmental influences, thus aligning with the claim's emphasis on the combination of genetic, biological, and environmental factors.


Input: Task: contrast the claim using the given text. Claim: All patients respond equally well to regenerative therapies. [SEP] Text: Knowledge of stem cell technologies and the potential clinical applications has on one hand become essential for increasing numbers of medical specialists. On the other hand, some critical issues regarding stem cell research has become prominent in order to obtain optimal outcomes in both experimental and clinical stem cell studies. Thus far, major types of stem cells, including embryonic stem cells (ESC), induced pluripotent stem cells (iSPC) with fantastically similar properties to ESC in many aspects, adult stem cells isolated from various adult tissues, stem cells harvested from fetal and the related tissues such as umbilical cord blood, Warton’s Jelly within umbilical cord, amnion and placental tissues, have comprehensively been analyzed, most of which are being clinically applied or currently studied for certain clinical conditions. 7,8 Among the adult stem cells that are extensively studied are bone marrow-derived HSC and MSC while the both stem cell types can be also isolated from other tissue origins, such as cord blood for HSC and many tissue origins for MSC. With regard to clinical transplantation, stem cell for clinical study or therapy can basically be either allogeneic or autologous, mainly depending on donor or tissue source availability as well as clinical conditions. All stem cell types harbor certain advantages over others but in the meanwhile can have some drawbacks and at present no single stem cell type reaches all criteria optimal for all clinical requirements. Therefore, a great deal of efforts in stem cell research continuously focuses on finding the most suitable stem cell types or sources for certain tissues/organs or disease types. In other words, in order to achieve the best outcomes for stem cell therapy, a number of factors and parameters should be taken into account, particularly in light of targeting the goal of Precision Medicine, an initiative and effort that aims to make advances in tailoring medical care to the individual on the genetic and molecular basis. 9 Understanding therapeutic mechanism of stem cells following in vivo transplantation has been the other major issue in stem cell research in order to enhance and optimize the therapeutic efficacy while minimizing the possible adverse effects. Although it is generally thought that the major mode of stem cell actions is through direct impacts like functional and/or architectural substitution of tissue loss as well as paracrine or cellular mechanisms supporting self-restoration of the diseased tissue or organ. These mechanisms, however, are poorly defined in any single particular stem cell- based therapy. [SEP] Justify:

Output: The text contrasts the claim by highlighting that different types of stem cells and their clinical applications have varying advantages and drawbacks. It suggests that no single stem cell type meets all criteria optimal for all clinical requirements, indicating that responses to regenerative therapies are not uniform among patients. Furthermore, it emphasizes that achieving the best outcomes depends on numerous factors and parameters, aligning with the concept of Precision Medicine, which seeks to tailor medical care to the individual. Therefore, the assertion that 'all patients respond equally well' is not supported by the complications and nuances discussed in the text.


Input: Task: pass the claim using the given text. Claim: Beauveria bassiana is used as a biocontrol agent against various pests. [SEP] Text: Functional annotations were assigned to protein sequences by running stages 4 and 5 of the EnTAP (74) pipeline (v0. 10. 7-beta), which included a similarity search to the Uniref90 (71) database followed by GO term and Pfam domain assignment using InterProScan v5. 30-69. 0 (75). Gene predictions that were not annotated by similarity search or gene family assignment were filtered out, and BUSCO (58) was run in protein mode to assess the completeness of the final gene annotations. Orthogroups were inferred from the protein sequences using OrthoFinder v2. 5. 1 (34) with default parameters. The longest isoform of each gene was supplied for this analysis. OGs were functionally annotated with terms and Pfam domains by selecting the most common terms and domains assigned to the genes included in each OG. Core orthogroups were identified as those that included one or more gene in every strain, and core, single-copy OGs were present in only one copy in each. Accessory OGs were identified as those present in two or more, but not all strains, and singleton OGs were those present only in one strain. Next, group-specific OGs were manually extracted by identifying those that included one or more genes from each strain of a given group, while not containing any genes from the strains in the other group. Functional relevance of orthogroup sets was assessed by performing GO enrichment analyses with clusterProfiler v3. 18. 1 (76). Benjamini & Hochberg’s false discovery rate (FDR) (77) was used to correct the p-values for multiple comparisons, and significantly enriched GO terms were identified at alpha = 0. 05. antiSMASH v5. 1. 2 (78) was used to identify biosynthetic gene clusters within the genomes using the --taxon fungi option. annotations were supplied using the --genefinding-gff3 option. The runs included active site finder analysis (--asf), and clusters were compared against a database of antiSMASH-predicted clusters (--cb-general), known gene clusters from the MIBiG database (--cb-knownclusters) and known subclusters (--cb-subclusters). [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses functional annotations, protein sequences, and various bioinformatics methods without mentioning Beauveria bassiana or its use as a biocontrol agent. There is no information that supports, contradicts, or addresses the claim about Beauveria bassiana.


Input: Task: corroborate the claim using the given text. Claim: Depression can result from a combination of genetic, biological, and environmental factors. [SEP] Text: 143] says, depression has some built-in pattern; it is a potential brain state organization and any of us are potential sufferers. It will have great phenotypic variability from person to person but still there will be commonalities; an experience of misery, low levels of explorative behaviour, loss of energy, negative self-organizations and perceptions of inferiority and poor assertiveness. Depression can vary in magnitude from mild to very severe [33]. In the most severe cases, it seems clear that the phenomenon is a form of illness. In less severe cases, it is not clear whether depressed experiences and behaviour are caused by a malfunction of the brain or the reaction of a healthy brain to the set of experiences. In this 0. 5, P(αf) = 0. 5). The decision to rest (rather than try) for numerous time steps can be induced by a sequence of failures (Fig. 2a). Following the first decision, the perceived probability that trying is likely to be rewarded declines because the individual experiences failure. Nothing is learned about the switching rate on this first update, but subsequent failures increase the perceived probability that the switching rate is low. After the first try, the individual sometimes chooses to rest. During these periods of resting, P(Eg) increases due to the possibility of conditions having switched during that period. P(αf) alters very little when resting, due to the small meta-switching probability, γ. Note that as the length of the sequence of failures increases, there is an increase in the duration of resting before the individual tries again; these numerous time steps of not trying would be regarded as increasing degrees of depression under Characterization 2. Figure 2. (a) Effect of a sequence of failures on the two probabilities P(Eg) and P(αf) for an individual following the optimal strategy, where the outcome of trying is fixed as a failure. Black markers indicate trying whereas white markers indicate resting. The values on each axis are each a sum of probabilities; at each data point, P(Eg) = P(Eg, αf) P(Eg, αs) and P(αf) = P(Eg, αf) + P(Eb, αf). (b) The effect of a sequence of failures depends strongly on how many successes were previously experienced. [SEP] Justify:

Output: The text corroborates the claim by discussing the variability of depression and indicating that it can result from different factors, including the brain's functioning and individual experiences. It mentions that depression can be influenced by a sequence of failures and their impact on the individual's state, suggesting an interplay between biological responses (brain state organization) and environmental factors (experiences of failure and misery). This suggests that both genetic and environmental variables contribute to the experience of depression.


Input: Task: contrast the claim using the given text. Claim: All patients respond equally well to regenerative therapies. [SEP] Text: The action mode of stem cells at the genetic and molecular level therefore have to be elucidated in order to understand the therapeutic mechanisms in sufficient depth. The success of a stem cell based therapy may be influenced by several donor-originated factors such as age, metabolic status, disease conditions, and in some cases, the genotype matching and disease susceptibility-related genetic background, which all have become recognized to probably alter stem cell characteristics in vivo and in vitro (proliferation, differentiation, homing and paracrine) and/or insulting host response. 10-12 As a starting point, we would in this mini-review like to only focus on the brief discussion on some experimental and potential aspects of how genetic background of donors could impact on the regenerative properties of stem cells and the clinical outcomes. Genetic traits of donors are represented in stem cells In the past decade, the extensive wealth of information obtained from the completion of Project (HGP) and numerous genome-wide associated studies (GWAS) has significantly enhanced our understanding of multi factorial and complex human diseases. 13-15 Particularly, thousands of single nucleotide polymorphisms (SNPs) have been identified, many of which are likely associated to various complex human diseases that were previously hypothesized to have genetic components. The resources of HGP and new genetic technologies have rapidly been evolving and its impact keeps continuously strengthening and forms the solid basis for the Initiative. We can now anticipate that as our understanding of genetic etiology of these diseases grows, future studies will further explore common or rare genetic variations contributing to diseases as well as many physiological and pathophysiological processes such as aging, tissue homeostasis and regeneration. 16,17 Genetic studies are rapidly expanding into stem cell research and regenerative medicine models and the study of stem cell genomics has been emerging to have wide implications in biology and possible therapeutic applications of stem cells. 18,19 Genetic traits at the DNA level are reflected in stem cells originated from a donor although transcriptome and epigenome may understandable vary in different tissue and cell types. One can analyze the genomes of stem cells from different individual donors for the purpose of identifying particular genetic traits in relation to cell phenotype of different stem cell types and their derived lineages. Current technologies have gradually become mature in many mainstream institutions and extending to RNA sequencing to detect gene expression and micro RNA expression, genomic DNA methylation and transcription factor binding site localizations. The field is rapidly expanding due to the dramatic decrease in the cost of sequencing genomes. [SEP] Justify:

Output: The text contrasts the claim by indicating that the success of stem cell-based therapies varies depending on several donor-originated factors such as age, metabolic status, disease conditions, and genetic background. This variation implies that not all patients respond equally well to these therapies.


Input: Task: pass the claim using the given text. Claim: Beauveria bassiana is used as a biocontrol agent against various pests. [SEP] Text: The fungal-specific by Islands of Sites () algorithm (79) was used to aid in the prediction of cluster regions by searching for conserved binding motifs in promoter regions using the --cassis option. The --cf-create-clusters option was used to find extra clusters, and Pfam and GO terms were mapped with --pfam2go. RNA for The starting fungal inoculum was reactivated from frozen mycelial stocks through spot inoculation at the centre of a PDA medium and incubated for 3–5 d at 25oC. A one-cm2 agar block was cored on to the mycelial culture and transferred to four different pigment inducing media: CDAYE (for red pigmentation), Agar (MEA; for yellow pigmentation), Agar (PDA; for yellow pigmentation), and 0. 25xAgar (SDA; for induction of conidiation). After comparative quality analysis of the cultures (i. e. , morphology, pigmentation response, and conidiation density), the conidia from 0. 25x SDA were harvested, titered, and inoculated in 25 mbroth medium in a 250 mL Erlenmeyer flask to a final concentration of 1. 0 x 107 conidia/mL and incubated for 72 h at 28oC at 175 rpm. The active mycelial culture was inoculated (10% v/v inoculum) in a 100 mbroth medium in a baffled 500 mL Erlenmeyer flask and incubated for 72–86 h at 28oC at 175 rpm. The mycelial slurries were harvested using a Release-GP vacuum filtration system (0. 22 µm, polyethersulfone membrane; Millipore-Sigma, USA). The mycelial mat was aseptically transferred to a pre-weighed 50 mL conical tube, flash frozen in liquid nitrogen, and stored at -80oC until processing. Quality control analysis was carried out, as described previously, for all the samples to determine bacterial contamination. The frozen mycelial mats were sent to the Laboratories, University of British Columbia, for RNA extraction. RNA biological replicates for each of the 8 isolates, for a total of 24 samples, were extracted for total RNA. [SEP] Justify:

Output: The text does not provide any information related to Beauveria bassiana being used as a biocontrol agent against pests. Instead, it discusses experimental methods involving fungal cultures and RNA extraction without mentioning any application in pest control.


Input: Task: corroborate the claim using the given text. Claim: Depression can result from a combination of genetic, biological, and environmental factors. [SEP] Text: However, in the real world, individuals are often ‘forced’ to experience the current environmental conditions, either through necessity (e. g. the need to find food to avoid starvation) or because they are coerced or encouraged (or, more simply, informed) by others. We therefore incorporated a fixed probability of being forced to try in any given time step, and allowed the strategy to take this probability into account (see Supplementary 5. The proportion of individuals under good conditions that choose to rest (when they have that choice) increases with the probability of forced attempts, both immediately following a success (solid line) and having already tried and succeeded at some point since conditions became good (dashed line)Open in new tabDownload slide Figure 6. The anticipated probability of forced attempts (labels on lines) affects the waiting time to the next attempt when those forced attempts do not occur. In the baseline case of no forced attempts, the asymptotic waiting time with respect to the number of failures is 13 resting periods; for a 50% probability of forced attempts this increases to 44 consecutive decisions to rest (i. e. much more depressed according to Characterization 2)Open in new tabDownload slideIt is possible that, having switched to good conditions and experienced success, a subsequent run of bad luck causes an individual to stop trying; this is shown as the dashed line in Fig. 5. Both mechanisms—a forced attempt, or success followed by bad luck—result in behaviour that, according to our most stringent Characterization 5, can be characterized as depression: a small fraction of individuals show inactivity when environmental conditions are good, despite having experienced success since environmental conditions became good. have used a simple model to show that seemingly depressed behaviour can arise from an optimal strategy when the individual has had an unfortunate series of experiences, and that the antecedent factors causing this reactive behaviour could go a long way back in an individual’s history. Depression has usually been viewed as a mental disorder that is maladaptive [35]. However, there have been a number of recent suggestions that depression represents an adaptive response to complex problems. [SEP] Justify:

Output: The text corroborates the claim by discussing how depression can arise from various environmental factors and circumstances, such as being 'forced' to act under certain conditions. It mentions that the antecedent factors causing reactive depressive behavior could stem from individual histories, highlighting the interplay of environmental conditions and personal experiences in contributing to depression.


Input: Task: contrast the claim using the given text. Claim: All patients respond equally well to regenerative therapies. [SEP] Text: Epigenomics has been extensively focusing on the epigenetic plasticity of ESC and iPSC and gradually expanding to adult stem cells. Single cell analysis has become a major method suggested for cancer research and for research in complex diseases like Alzheimer's disease and metabolic diseases. Further steps of stem cell genome analysis will also be to combine with single cell phenotypic analysis, and the connection between the phenotype and genotype of specific stem cells. 20-22 Stem cell-based analysis of the biology of a genetic variation currently provides tools for disease mechanism study, drug screening, and in some cases for the creation of replacement cells and organs. In many instances, the analysis is conducted in patient-derived stem cells, which represent the basis for personalized therapeutics. Such strategies in areas of neurodegenerative, bone, eye, blood and cardiovascular disease, diabetes, and obesity are being tested. 23,24 Considering the importance of SNPs in etiology of many multi factorial complex diseases, it would be highly reasonable for us to recommend that stem cells carrying with the suggested disease-causing or susceptible SNPs should NOT be transplanted onto the recipients to treat the same disease. It is just starting, however, to propose that the detection of SNPs is considered as a required indication for the selection of stem cell donors, particularly for haematological diseases (see below). Impact of donor SNPS on the outcome of haematopoietic stem cell transplantation beyond the HLA matching Haematopoietic stem cell transplantation (HSCT) remains the only cure for many malignant haematological diseases. HSCT could be either allogeneic or autologous. 25,26 Cryopreservation techniques now allow autologous bone marrow to be stored safely and indefinitely without catastrophic loss of stem cells on thawing. Umbilical cord blood from neonates contains substantial numbers of haematopoietic stem cells, which can be harvested at delivery, frozen, and then transplanted to patients after cell counts and virological screening are performed. Thousands of cord blood donations are normally stored in cord blood banks worldwide and information of their HLA types can be available readily for transplantation into a matched recipient without delays inherent in securing an adult donor. Similar to autologous bone marrow storage, cord blood bank also provides an opportunity, after long-term storage, for autologous cord transplantation. [SEP] Justify:

Output: The text contrasts the claim by discussing the variability in patient responses to therapies, particularly when mentioning the importance of SNPs (single nucleotide polymorphisms) in the etiology of complex diseases. It states that 'it would be highly reasonable for us to recommend that stem cells carrying with the suggested disease-causing or susceptible SNPs should NOT be transplanted onto the recipients to treat the same disease.' This suggests that not all patients will respond equally well, as genetic factors can significantly impact therapy outcomes.


Input: Task: pass the claim using the given text. Claim: Beauveria bassiana is used as a biocontrol agent against various pests. [SEP] Text: Starting with 2–5 g (with the exception UAX-29, which required 7–9 g), mycelium was ground with liquid nitrogen in a mortar and pestle to a fine powder. Kolosova et al. ’s RNA extraction protocol (80) was used to process 100–200 mg of ground tissue. Instead of drying the RNA pellet for three minutes at room temperature, the sample was spun for an additional 30 seconds, remaining liquid was removed with a micropipette tip and samples were air-dried for one minute. The final pellet was resuspended in 30 µl of Nuclease-Free water. Total RNA concentration was determined using a NanoDrop 1000 (ThermoFisher Scientific) and assessed for quality on an Agilent 2100 Bioanalyzer and Agilent RNA 6000 LabChips. Total RNA (37. 5 ng/µL) was sent to Canada’s Centre for sequencing. Qualities of total RNA samples were assessed using an and arrayed into a 96-well plate (ThermoFisher Scientific). Polyadenylated RNA was purified using the NEBNext Poly(A) m[E7490L] () from 1000 ng total RNA. Messenger RNA selection was performed using NEBd(T)25 beads (Biolabs) incubated at 65°C for five minutes, followed by snap-chilling at 4°C to denature RNA and facilitate binding of poly(A) mRNA to the beads. mRNA was eluted from the beads in from the NEBNext Poly(A) Kit (Biolabs) and incubated at 80°C for two minutes, then held at 25°C for two minutes. RNA binding buffer was added to allow the mRNA to re-bind to the beads, mixed 10 times and incubated at room temperature for five minutes. The sample plate was placed on the magnet and the supernatant discarded. The mRNA bound beads were washed twice, then cleared again on magnet. The supernatant was again discarded, and mRNA was eluted from the beads in 20 µL Tris buffer incubated at 80°C for two minutes. mRNA was transferred to a new 96-well plate. [SEP] Justify:

Output: The text does not address the claim regarding Beauveria bassiana or its use as a biocontrol agent against pests. Instead, it discusses a detailed RNA extraction and processing protocol, which is irrelevant to the context of biocontrol usage.


Input: Task: corroborate the claim using the given text. Claim: Depression can result from a combination of genetic, biological, and environmental factors. [SEP] Text: MENU E-submission en menu About the and 10. 5607/en. 2013. 22. 4. 235© Society for Brain and Involvement of Genetic an d in the Onset of DepressionToshitaka Nabeshima1,2* and Hyoung-Chun Kim31Department of Care and Sciences, of Pharmaceutical Sciences, Meijo University, 2of and Research, Nagoya 468-8503, Japan, 3Neuropsychopharmacology & Toxicology Program, College of Pharmacy, University, Chuncheon 200-701, KoreaCorrespondence to: *To whom correspondence should be addressed. TEL: 81-52-839-2756, FAX: 81-52-839-2756 e-mail: tnabeshi@ccalumni. meijo-u. ac. jpReceived: October 23, 2013; Revised: November 26, 2013; Accepted: December 2, 2013 to : -this 2. 7 trillion (USD 27 billion) [3]. Therefore, addressing depression represents an urgent challenge. This 1. 5 to 3 times higher [27, 28]. Research with identical twins has also shown that when one twin develops depression, the probability that the other twin will also develop depression is 25 to 93% [29]. These reports imply that in some cases, genetic factors may play a role in the onset of depression. Studies examining postmortem brains of patients with depression and using animal models of depression have implicated ATP-binding cassette sub-family B member 1 (ABCB1) [30], histone deacetylase (HDAC6) [31], a promoter region related to serotonin transporter gene transcription (5-TT LPR) [32, 33], neuritin [34], and disrupted in schizophrenia 1 (DISC1) [35] as candidate genes. Depression-like behavior can be observed in mice with a gene deficiency in melanoma-associated antigen D1 (MAGE-D1), a member of the family of melanoma-associated antigens, therefore, we have previously proposed that this molecule is also a candidate gene for the onset of depression [36]. [SEP] Justify:

Output: The text corroborates the claim by presenting evidence that genetic factors, as shown through research with identical twins and candidate genes associated with depression, play a significant role in the onset of depression. It discusses the hereditary aspect of depression and mentions specific genes that have been implicated, which aligns with the assertion that depression arises from a combination of genetic factors along with biological and potentially environmental factors.


Input: Task: contrast the claim using the given text. Claim: All patients respond equally well to regenerative therapies. [SEP] Text: 28,29 In most cases, however, allogeneic donors can be the choice only available. The most important factor affecting the outcome of allogeneic transplantation is the quality of the HLA match between donor and recipient and therefore patients subject to allogeneic HSCT will have to find a HLA-matching donor. The current mortality rate of HSCT, unfortunately, stands rather high at 30-80% although up-to-dated high-resolution HLA genotyping and matching techniques have improved the survival to a significant extent. 27,28 Despite stringent procedures to secure the best HLA matching between donors and recipients, life-threatening complications continue to occur in some cases after HSCT. Common complications post HSCT are relapse, GVHD, graft rejection and viral infection. Therefore, polymorphisms in other genes may also affect complications such as GVHD and the overall survival. In fact, numerous studies have been carried out in the past decade to suggest that a number of SNP located within genes for innate and adaptive immune responses, residual leukemia, allo-antigens, and drug metabolism, may be associated with HSCT outcomes. Studying SNPs in genes encoding co-stimulatory and other related molecules have particularly been proposed to help identify patients at risk for post-HSCT complications. SNPs within other genes have been included in the systematically analysis by different groups, such as CD274, CD40, CD154, CD28, 4, STAT4, IL-28, and VCAM, for their potential association with post-HSCT outcomes. 29-32 And, certain SNP variants do have been found to likely influence the expression level of corresponding genes. For instance, the TNFSF4C variant showed a higher affinity for the nuclear transcription factor Myb and increased percentage of TNFSF4-positive B cells after stimulation compared with CT or TT genotypes. 28 The question now raised is: whether genetic characteristics, of stem cell donors and recipients, should be used to tailor HSCT protocols with emphasis on determining GVHD prophylaxis. In parallel, a consensus terminology of clinical outcomes should be standardized, suggested for international multicentre studies, and adopted so that each center/country uses the same grading system for complications such as GVHD and infection. What should be noted is that in different phases of in inflammatory or anti-inflammatory genes could have different effects. [SEP] Justify:

Output: The text contrasts the claim by discussing the variability in outcomes for patients undergoing allogeneic transplantation. It explains that multiple factors affect the outcome, including the quality of HLA matches and the existence of genetic polymorphisms, which suggests that not all patients respond equally well to regenerative therapies. Specifically, it states that 'the most important factor affecting the outcome of allogeneic transplantation is the quality of the HLA match' and references varying mortality rates and complications that can occur, further indicating that individual differences among patients lead to different responses.