PMC:7799378 / 16939-21781 JSONTXT

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    LitCovid-PubTator

    {"project":"LitCovid-PubTator","denotations":[{"id":"698","span":{"begin":54,"end":69},"obj":"Disease"},{"id":"699","span":{"begin":97,"end":113},"obj":"Disease"},{"id":"715","span":{"begin":567,"end":572},"obj":"Species"},{"id":"716","span":{"begin":690,"end":695},"obj":"Species"},{"id":"717","span":{"begin":744,"end":771},"obj":"Species"},{"id":"718","span":{"begin":201,"end":230},"obj":"Disease"},{"id":"719","span":{"begin":339,"end":348},"obj":"Disease"},{"id":"720","span":{"begin":573,"end":609},"obj":"Disease"},{"id":"721","span":{"begin":655,"end":671},"obj":"Disease"},{"id":"722","span":{"begin":730,"end":738},"obj":"Disease"},{"id":"723","span":{"begin":864,"end":882},"obj":"Disease"},{"id":"724","span":{"begin":900,"end":911},"obj":"Disease"},{"id":"725","span":{"begin":913,"end":919},"obj":"Disease"},{"id":"726","span":{"begin":921,"end":925},"obj":"Disease"},{"id":"727","span":{"begin":927,"end":942},"obj":"Disease"},{"id":"728","span":{"begin":948,"end":957},"obj":"Disease"},{"id":"729","span":{"begin":718,"end":723},"obj":"CellLine"},{"id":"742","span":{"begin":1176,"end":1180},"obj":"Gene"},{"id":"743","span":{"begin":1189,"end":1194},"obj":"Gene"},{"id":"744","span":{"begin":1329,"end":1333},"obj":"Gene"},{"id":"745","span":{"begin":998,"end":1001},"obj":"Chemical"},{"id":"746","span":{"begin":1006,"end":1009},"obj":"Chemical"},{"id":"747","span":{"begin":1245,"end":1255},"obj":"Chemical"},{"id":"748","span":{"begin":1534,"end":1549},"obj":"Disease"},{"id":"749","span":{"begin":1597,"end":1611},"obj":"Disease"},{"id":"750","span":{"begin":1628,"end":1657},"obj":"Disease"},{"id":"751","span":{"begin":1659,"end":1662},"obj":"Disease"},{"id":"752","span":{"begin":1672,"end":1687},"obj":"Disease"},{"id":"753","span":{"begin":1724,"end":1742},"obj":"Disease"},{"id":"773","span":{"begin":2030,"end":2038},"obj":"Gene"},{"id":"774","span":{"begin":2529,"end":2536},"obj":"Gene"},{"id":"775","span":{"begin":2572,"end":2577},"obj":"Gene"},{"id":"776","span":{"begin":1786,"end":1794},"obj":"Species"},{"id":"777","span":{"begin":1983,"end":1991},"obj":"Species"},{"id":"778","span":{"begin":2100,"end":2110},"obj":"Species"},{"id":"779","span":{"begin":2398,"end":2406},"obj":"Species"},{"id":"780","span":{"begin":1777,"end":1785},"obj":"Disease"},{"id":"781","span":{"begin":1844,"end":1852},"obj":"Disease"},{"id":"782","span":{"begin":1907,"end":1919},"obj":"Disease"},{"id":"783","span":{"begin":1925,"end":1934},"obj":"Disease"},{"id":"784","span":{"begin":1974,"end":1982},"obj":"Disease"},{"id":"785","span":{"begin":2075,"end":2083},"obj":"Disease"},{"id":"786","span":{"begin":2129,"end":2141},"obj":"Disease"},{"id":"787","span":{"begin":2143,"end":2153},"obj":"Disease"},{"id":"788","span":{"begin":2159,"end":2169},"obj":"Disease"},{"id":"789","span":{"begin":2389,"end":2397},"obj":"Disease"},{"id":"790","span":{"begin":2437,"end":2446},"obj":"Disease"},{"id":"791","span":{"begin":2648,"end":2656},"obj":"Disease"},{"id":"806","span":{"begin":3078,"end":3087},"obj":"Gene"},{"id":"807","span":{"begin":3153,"end":3158},"obj":"Gene"},{"id":"808","span":{"begin":3163,"end":3168},"obj":"Gene"},{"id":"809","span":{"begin":3295,"end":3331},"obj":"Gene"},{"id":"810","span":{"begin":3333,"end":3338},"obj":"Gene"},{"id":"811","span":{"begin":3495,"end":3500},"obj":"Gene"},{"id":"812","span":{"begin":3438,"end":3456},"obj":"Species"},{"id":"813","span":{"begin":3457,"end":3478},"obj":"Species"},{"id":"814","span":{"begin":3480,"end":3483},"obj":"Species"},{"id":"815","span":{"begin":2758,"end":2770},"obj":"Disease"},{"id":"816","span":{"begin":3219,"end":3244},"obj":"Disease"},{"id":"817","span":{"begin":3249,"end":3275},"obj":"Disease"},{"id":"818","span":{"begin":3559,"end":3564},"obj":"Disease"},{"id":"819","span":{"begin":3674,"end":3697},"obj":"Disease"},{"id":"841","span":{"begin":4200,"end":4205},"obj":"Gene"},{"id":"842","span":{"begin":4523,"end":4527},"obj":"Gene"},{"id":"843","span":{"begin":4650,"end":4654},"obj":"Gene"},{"id":"844","span":{"begin":4694,"end":4698},"obj":"Gene"},{"id":"845","span":{"begin":3881,"end":3889},"obj":"Species"},{"id":"846","span":{"begin":3956,"end":3964},"obj":"Species"},{"id":"847","span":{"begin":4355,"end":4360},"obj":"Species"},{"id":"848","span":{"begin":4604,"end":4625},"obj":"Species"},{"id":"849","span":{"begin":4630,"end":4646},"obj":"Species"},{"id":"850","span":{"begin":4266,"end":4269},"obj":"Chemical"},{"id":"851","span":{"begin":4270,"end":4279},"obj":"Chemical"},{"id":"852","span":{"begin":4450,"end":4453},"obj":"Chemical"},{"id":"853","span":{"begin":4480,"end":4484},"obj":"Chemical"},{"id":"854","span":{"begin":3872,"end":3880},"obj":"Disease"},{"id":"855","span":{"begin":3947,"end":3955},"obj":"Disease"},{"id":"856","span":{"begin":3991,"end":3998},"obj":"Disease"},{"id":"857","span":{"begin":4084,"end":4092},"obj":"Disease"},{"id":"858","span":{"begin":4170,"end":4185},"obj":"Disease"},{"id":"859","span":{"begin":4342,"end":4347},"obj":"CellLine"},{"id":"86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NET formation and inflammasome activation in G6PD-deficiency and its possible effect on viral infections\nNeutrophils are among the key players in the immune system. The role of neutrophils in bacterial or fungal infection is well known, yet their influence on the anti-viral response has not been established [87]. In response to infection, stimulated neutrophils release chromosomal DNA for trapping and killing invading microbes. The chromatin trap is known as the neutrophil extracellular trap (NET). It mediates the control of viruses, such as seen with human HIV and chikungunya viral infections [88, 89], whereas it can contribute to other viral infections, including in non-human primates with SIV and Hep-2 cells infected with respiratory syncytial virus [90,91]. The cytotoxic effect on lung epithelium and endothelium has linked NETs to several pulmonary diseases, including acute lung injury, asthma, COPD, cystic fibrosis, and pneumonia [92].\nNET formation can be inhibited by NAC and DPI, indicating the involvement of oxidative stress and NOX. A metabolic shift towards the PPP is required for the NET formation induced by amyloid fibrils and PMA [93]. G6PD-derived NADPH can serve as a substrate for NOX, which generates superoxide and stimulates NET formation [17]. Neutrophils from individuals with the G6PD Taiwan-Hakka variant are equally effective as normal individuals regarding NET formation [94]. However, defective NET formation and NOX activity are observed in neutrophils of individuals with severe G6PD deficiency [95]. The absence of NET formation is found in NOX deficiency associated with chronic granulomatous disease (CGD). Severe G6PD deficiency may mimic impaired NOX resulting in dysfunctional NETs.\nElevated NET levels are found in COVID-19 patients [96]. NET formation is considered as a driver of COVID-19, since NET formation may contribute to tissue damage, organ injury, and mortality as indicated by autopsy specimens from COVID-19 patients [97]. The by-product of NETs, such as elastase, is involved in the pathogenesis of COVID-19 by facilitating SARS-CoV-2 entry and causing hypertension, thrombosis, and vasculitis [98–100]. The tissue damage leading to excessive oxidative stress creates a vicious cycle by increasing NET formation and distressing adaptive immunity [101]. Increased NETs are associated with hyperinflammation and in COVID-19 patients they amplify the severity and mortality associated with the disease. Targeting NETs and its feedback loop, with elastase, DNase-1, or inhibitory peptides as well as IL-1β, are potential therapeutic interventions for reducing the severity of COVID-19 [102,103].\nThe inflammasome is part of the innate immune system that regulates effector cells during inflammation [104–107]. Inflammasomes are cytosolic protein complexes consisting of multiple oligomeric molecules that detect cell-damaging agents and pathogenic factors by recognizing danger-associated molecular patterns (DAMP) and pathogen-associated molecular patterns (PAMP), respectively [104]. Through cleavage of pro-IL-1β and pro-IL-18, they promote the secretion of the active forms of IL-1β and IL-18. Long-term exposure of the host to viruses causes dysregulated inflammation and autoinflammatory disorders. Activation of the NLR family pyrin domain containing 3 (NLRP3) inflammasome is triggered by viral replication and leads to the destruction of viruses [105]. The murine coronavirus mouse hepatitis virus (MHV) activates NLRP3 inflammasomes and induces proinflammatory programmed cell death by panoptosis (pyroptosis, apoptosis, and necroptosis) [106,107]. The deleterious effects on the host due to inflammasome impairment indicate that balanced regulation of inflammasomes is crucial for the immune response and antiviral defense.\nInflammasome activation causes a cytokine storm in both SARS and COVID-19 patients [108]. It is proposed that the heterogeneous response in COVID-19 patients due to the lack of immune fitness fails to properly reduce inflammasome activation. This leads to enhanced severity of COVID-19, that is associated with a cytokine storm and extensive tissue damage [109]. G6PD deficiency downregulates IL-1β expression and impairs inflammasome activation upon LPS and ATP/nigericin stimulation in PBMCs (peripheral blood mononuclear cells) and THP-1 cells (human monocyte cell line) [110]. The impaired inflammasome activation is attributed to reduced ROS production via NOX, while H2O2 stimulates inflammasome activation in G6PD-knockdown THP-1 cells. This results in weaken bactericidal activity against Staphylococcus aureus and Escherichia coli in G6PD-knockdown THP-1 cells, indicating that G6PD is required for the maintenance of the innate immune response, inflammasome activation, and pathogen clearance through redox homeostasis [110]."}

    LitCovid-sentences

    {"project":"LitCovid-sentences","denotations":[{"id":"T141","span":{"begin":0,"end":113},"obj":"Sentence"},{"id":"T142","span":{"begin":114,"end":173},"obj":"Sentence"},{"id":"T143","span":{"begin":174,"end":323},"obj":"Sentence"},{"id":"T144","span":{"begin":324,"end":440},"obj":"Sentence"},{"id":"T145","span":{"begin":441,"end":512},"obj":"Sentence"},{"id":"T146","span":{"begin":513,"end":780},"obj":"Sentence"},{"id":"T147","span":{"begin":781,"end":963},"obj":"Sentence"},{"id":"T148","span":{"begin":964,"end":1066},"obj":"Sentence"},{"id":"T149","span":{"begin":1067,"end":1175},"obj":"Sentence"},{"id":"T150","span":{"begin":1176,"end":1290},"obj":"Sentence"},{"id":"T151","span":{"begin":1291,"end":1428},"obj":"Sentence"},{"id":"T152","span":{"begin":1429,"end":1555},"obj":"Sentence"},{"id":"T153","span":{"begin":1556,"end":1664},"obj":"Sentence"},{"id":"T154","span":{"begin":1665,"end":1743},"obj":"Sentence"},{"id":"T155","span":{"begin":1744,"end":1800},"obj":"Sentence"},{"id":"T156","span":{"begin":1801,"end":1997},"obj":"Sentence"},{"id":"T157","span":{"begin":1998,"end":2179},"obj":"Sentence"},{"id":"T158","span":{"begin":2180,"end":2328},"obj":"Sentence"},{"id":"T159","span":{"begin":2329,"end":2475},"obj":"Sentence"},{"id":"T160","span":{"begin":2476,"end":2667},"obj":"Sentence"},{"id":"T161","span":{"begin":2668,"end":2781},"obj":"Sentence"},{"id":"T162","span":{"begin":2782,"end":3057},"obj":"Sentence"},{"id":"T163","span":{"begin":3058,"end":3169},"obj":"Sentence"},{"id":"T164","span":{"begin":3170,"end":3276},"obj":"Sentence"},{"id":"T165","span":{"begin":3277,"end":3433},"obj":"Sentence"},{"id":"T166","span":{"begin":3434,"end":3630},"obj":"Sentence"},{"id":"T167","span":{"begin":3631,"end":3806},"obj":"Sentence"},{"id":"T168","span":{"begin":3807,"end":3896},"obj":"Sentence"},{"id":"T169","span":{"begin":3897,"end":4048},"obj":"Sentence"},{"id":"T170","span":{"begin":4049,"end":4169},"obj":"Sentence"},{"id":"T171","span":{"begin":4170,"end":4387},"obj":"Sentence"},{"id":"T172","span":{"begin":4388,"end":4550},"obj":"Sentence"},{"id":"T173","span":{"begin":4551,"end":4842},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Impaired NET formation and inflammasome activation in G6PD-deficiency and its possible effect on viral infections\nNeutrophils are among the key players in the immune system. The role of neutrophils in bacterial or fungal infection is well known, yet their influence on the anti-viral response has not been established [87]. In response to infection, stimulated neutrophils release chromosomal DNA for trapping and killing invading microbes. The chromatin trap is known as the neutrophil extracellular trap (NET). It mediates the control of viruses, such as seen with human HIV and chikungunya viral infections [88, 89], whereas it can contribute to other viral infections, including in non-human primates with SIV and Hep-2 cells infected with respiratory syncytial virus [90,91]. The cytotoxic effect on lung epithelium and endothelium has linked NETs to several pulmonary diseases, including acute lung injury, asthma, COPD, cystic fibrosis, and pneumonia [92].\nNET formation can be inhibited by NAC and DPI, indicating the involvement of oxidative stress and NOX. A metabolic shift towards the PPP is required for the NET formation induced by amyloid fibrils and PMA [93]. G6PD-derived NADPH can serve as a substrate for NOX, which generates superoxide and stimulates NET formation [17]. Neutrophils from individuals with the G6PD Taiwan-Hakka variant are equally effective as normal individuals regarding NET formation [94]. However, defective NET formation and NOX activity are observed in neutrophils of individuals with severe G6PD deficiency [95]. The absence of NET formation is found in NOX deficiency associated with chronic granulomatous disease (CGD). Severe G6PD deficiency may mimic impaired NOX resulting in dysfunctional NETs.\nElevated NET levels are found in COVID-19 patients [96]. NET formation is considered as a driver of COVID-19, since NET formation may contribute to tissue damage, organ injury, and mortality as indicated by autopsy specimens from COVID-19 patients [97]. The by-product of NETs, such as elastase, is involved in the pathogenesis of COVID-19 by facilitating SARS-CoV-2 entry and causing hypertension, thrombosis, and vasculitis [98–100]. The tissue damage leading to excessive oxidative stress creates a vicious cycle by increasing NET formation and distressing adaptive immunity [101]. Increased NETs are associated with hyperinflammation and in COVID-19 patients they amplify the severity and mortality associated with the disease. Targeting NETs and its feedback loop, with elastase, DNase-1, or inhibitory peptides as well as IL-1β, are potential therapeutic interventions for reducing the severity of COVID-19 [102,103].\nThe inflammasome is part of the innate immune system that regulates effector cells during inflammation [104–107]. Inflammasomes are cytosolic protein complexes consisting of multiple oligomeric molecules that detect cell-damaging agents and pathogenic factors by recognizing danger-associated molecular patterns (DAMP) and pathogen-associated molecular patterns (PAMP), respectively [104]. Through cleavage of pro-IL-1β and pro-IL-18, they promote the secretion of the active forms of IL-1β and IL-18. Long-term exposure of the host to viruses causes dysregulated inflammation and autoinflammatory disorders. Activation of the NLR family pyrin domain containing 3 (NLRP3) inflammasome is triggered by viral replication and leads to the destruction of viruses [105]. The murine coronavirus mouse hepatitis virus (MHV) activates NLRP3 inflammasomes and induces proinflammatory programmed cell death by panoptosis (pyroptosis, apoptosis, and necroptosis) [106,107]. The deleterious effects on the host due to inflammasome impairment indicate that balanced regulation of inflammasomes is crucial for the immune response and antiviral defense.\nInflammasome activation causes a cytokine storm in both SARS and COVID-19 patients [108]. It is proposed that the heterogeneous response in COVID-19 patients due to the lack of immune fitness fails to properly reduce inflammasome activation. This leads to enhanced severity of COVID-19, that is associated with a cytokine storm and extensive tissue damage [109]. G6PD deficiency downregulates IL-1β expression and impairs inflammasome activation upon LPS and ATP/nigericin stimulation in PBMCs (peripheral blood mononuclear cells) and THP-1 cells (human monocyte cell line) [110]. The impaired inflammasome activation is attributed to reduced ROS production via NOX, while H2O2 stimulates inflammasome activation in G6PD-knockdown THP-1 cells. This results in weaken bactericidal activity against Staphylococcus aureus and Escherichia coli in G6PD-knockdown THP-1 cells, indicating that G6PD is required for the maintenance of the innate immune response, inflammasome activation, and pathogen clearance through redox homeostasis [110]."}

    LitCovid-PD-HP

    {"project":"LitCovid-PD-HP","denotations":[{"id":"T27","span":{"begin":894,"end":911},"obj":"Phenotype"},{"id":"T28","span":{"begin":913,"end":919},"obj":"Phenotype"},{"id":"T29","span":{"begin":921,"end":925},"obj":"Phenotype"},{"id":"T30","span":{"begin":948,"end":957},"obj":"Phenotype"},{"id":"T31","span":{"begin":1041,"end":1057},"obj":"Phenotype"},{"id":"T32","span":{"begin":2129,"end":2141},"obj":"Phenotype"},{"id":"T33","span":{"begin":2159,"end":2169},"obj":"Phenotype"},{"id":"T34","span":{"begin":2219,"end":2235},"obj":"Phenotype"},{"id":"T35","span":{"begin":3463,"end":3472},"obj":"Phenotype"},{"id":"T36","span":{"begin":3840,"end":3854},"obj":"Phenotype"},{"id":"T37","span":{"begin":4120,"end":4134},"obj":"Phenotype"}],"attributes":[{"id":"A27","pred":"hp_id","subj":"T27","obj":"http://www.orpha.net/ORDO/Orphanet_178320"},{"id":"A28","pred":"hp_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/HP_0002099"},{"id":"A29","pred":"hp_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/HP_0006510"},{"id":"A30","pred":"hp_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A31","pred":"hp_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/HP_0025464"},{"id":"A32","pred":"hp_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/HP_0000822"},{"id":"A33","pred":"hp_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/HP_0002633"},{"id":"A34","pred":"hp_id","subj":"T34","obj":"http://purl.obolibrary.org/obo/HP_0025464"},{"id":"A35","pred":"hp_id","subj":"T35","obj":"http://purl.obolibrary.org/obo/HP_0012115"},{"id":"A36","pred":"hp_id","subj":"T36","obj":"http://purl.obolibrary.org/obo/HP_0033041"},{"id":"A37","pred":"hp_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/HP_0033041"}],"text":"Impaired NET formation and inflammasome activation in G6PD-deficiency and its possible effect on viral infections\nNeutrophils are among the key players in the immune system. The role of neutrophils in bacterial or fungal infection is well known, yet their influence on the anti-viral response has not been established [87]. In response to infection, stimulated neutrophils release chromosomal DNA for trapping and killing invading microbes. The chromatin trap is known as the neutrophil extracellular trap (NET). It mediates the control of viruses, such as seen with human HIV and chikungunya viral infections [88, 89], whereas it can contribute to other viral infections, including in non-human primates with SIV and Hep-2 cells infected with respiratory syncytial virus [90,91]. The cytotoxic effect on lung epithelium and endothelium has linked NETs to several pulmonary diseases, including acute lung injury, asthma, COPD, cystic fibrosis, and pneumonia [92].\nNET formation can be inhibited by NAC and DPI, indicating the involvement of oxidative stress and NOX. A metabolic shift towards the PPP is required for the NET formation induced by amyloid fibrils and PMA [93]. G6PD-derived NADPH can serve as a substrate for NOX, which generates superoxide and stimulates NET formation [17]. Neutrophils from individuals with the G6PD Taiwan-Hakka variant are equally effective as normal individuals regarding NET formation [94]. However, defective NET formation and NOX activity are observed in neutrophils of individuals with severe G6PD deficiency [95]. The absence of NET formation is found in NOX deficiency associated with chronic granulomatous disease (CGD). Severe G6PD deficiency may mimic impaired NOX resulting in dysfunctional NETs.\nElevated NET levels are found in COVID-19 patients [96]. NET formation is considered as a driver of COVID-19, since NET formation may contribute to tissue damage, organ injury, and mortality as indicated by autopsy specimens from COVID-19 patients [97]. The by-product of NETs, such as elastase, is involved in the pathogenesis of COVID-19 by facilitating SARS-CoV-2 entry and causing hypertension, thrombosis, and vasculitis [98–100]. The tissue damage leading to excessive oxidative stress creates a vicious cycle by increasing NET formation and distressing adaptive immunity [101]. Increased NETs are associated with hyperinflammation and in COVID-19 patients they amplify the severity and mortality associated with the disease. Targeting NETs and its feedback loop, with elastase, DNase-1, or inhibitory peptides as well as IL-1β, are potential therapeutic interventions for reducing the severity of COVID-19 [102,103].\nThe inflammasome is part of the innate immune system that regulates effector cells during inflammation [104–107]. Inflammasomes are cytosolic protein complexes consisting of multiple oligomeric molecules that detect cell-damaging agents and pathogenic factors by recognizing danger-associated molecular patterns (DAMP) and pathogen-associated molecular patterns (PAMP), respectively [104]. Through cleavage of pro-IL-1β and pro-IL-18, they promote the secretion of the active forms of IL-1β and IL-18. Long-term exposure of the host to viruses causes dysregulated inflammation and autoinflammatory disorders. Activation of the NLR family pyrin domain containing 3 (NLRP3) inflammasome is triggered by viral replication and leads to the destruction of viruses [105]. The murine coronavirus mouse hepatitis virus (MHV) activates NLRP3 inflammasomes and induces proinflammatory programmed cell death by panoptosis (pyroptosis, apoptosis, and necroptosis) [106,107]. The deleterious effects on the host due to inflammasome impairment indicate that balanced regulation of inflammasomes is crucial for the immune response and antiviral defense.\nInflammasome activation causes a cytokine storm in both SARS and COVID-19 patients [108]. It is proposed that the heterogeneous response in COVID-19 patients due to the lack of immune fitness fails to properly reduce inflammasome activation. This leads to enhanced severity of COVID-19, that is associated with a cytokine storm and extensive tissue damage [109]. G6PD deficiency downregulates IL-1β expression and impairs inflammasome activation upon LPS and ATP/nigericin stimulation in PBMCs (peripheral blood mononuclear cells) and THP-1 cells (human monocyte cell line) [110]. The impaired inflammasome activation is attributed to reduced ROS production via NOX, while H2O2 stimulates inflammasome activation in G6PD-knockdown THP-1 cells. This results in weaken bactericidal activity against Staphylococcus aureus and Escherichia coli in G6PD-knockdown THP-1 cells, indicating that G6PD is required for the maintenance of the innate immune response, inflammasome activation, and pathogen clearance through redox homeostasis [110]."}