Table 1_Repurposing of the small-molecule adrenoreceptor-inhibitor carvedilol for treatment of the fibrotic lung.xlsx by Maria Jordan (10265489)

“…</p>Conclusion<p>Herein, carvedilol demonstrated significant anti-fibrotic effects on human lung fibroblasts in vitro, thus presenting great potential as an anti-IPF treatment. …”

Ubiquitin degradation of the Ribonuclease H2 subunit B Rnh2B regulates the virulence of <i>Cryptococcus neoformans</i> by Meng-Ru Guo (21375491)

“…Using an iTRAQ-based proteomic strategy, we recognized Ribonuclease H2 subunit B (Rnh2B) as a target substrate for Cdc4. …”

Data Sheet 2_Rutin ameliorates LPS-induced acute lung injury in mice by inhibiting the cGAS-STING-NLRP3 signaling pathway.docx by Xin Zhou (54275)

“…</p>Results<p>The proteomic profiling of lung tissues from LPS-challenged mice identified significant dysregulation of proteins integral to the cGAS-STING cascade and pyroptotic processes. …”

Data Sheet 1_Rutin ameliorates LPS-induced acute lung injury in mice by inhibiting the cGAS-STING-NLRP3 signaling pathway.docx by Xin Zhou (54275)

“…</p>Results<p>The proteomic profiling of lung tissues from LPS-challenged mice identified significant dysregulation of proteins integral to the cGAS-STING cascade and pyroptotic processes. …”

Data Sheet 1_Tcirg1 deficiency delays osteoarthritis progression by impairing lysosome acidification and peripheral accumulation in osteoclasts.docx by Rui Sun (177521)

“…</p>Results and discussion<p>Proteomic analysis revealed that TCIRG1 was significantly upregulated in the WBR compared to NWBR of subchondral bone in OA patients, with functional enrichment analysis indicating TCIRG1 correlation with lysosome-related biological processes. …”

Table 1_Xinfeng Capsule inhibits oxidative stress via regulating the PPARγ/ Hmgcs2 signaling pathway in lung tissue of adjuvant arthritis rats.docx by Ping-Heng Zhang (21785162)

“…Furthermore, XFC-containing serum suppressed TGF-β1–induced proliferation of lung fibroblasts, promoted PPARγ expression, and significantly decreased the levels of interleukin-6, tumor necrosis factor-α, reactive oxygen species, nicotinamide adenine dinucleotide phosphate oxidase 4, HMGCS2, collagen type I α 1, collagen type III α 1, and α-smooth muscle actin (P < 0.01). …”

Figure 3 from Synergistic Effects of PARP Inhibition and Cholesterol Biosynthesis Pathway Modulation by Anna Rutkowska (19676837)

“…Niraparib decreases CYP51A1 (lanosterol 14α-demethylase) enzyme levels (Supplementary Fig. …”

The expression of PAX7 and MYOD1 correlate with differential expression of diverse chemokines in HuMuSC. by Katharine Striedinger (15503387)

“…Using linear regression PAX7 slope varies significantly p = 0.0001 and MYOD1 slope also varies significantly p = 0.05 n = 3 <b>(b)</b> Heat map displaying the expression levels of all cytokine protein detected in HuMuSC from collection as they activate progressively at day 0, day 3 and day 6 <i>in vitro</i>, using the high throughput proteomic Multiplex assay. …”

Data Sheet 1_An active ingredient from the combination of Corydalis Rhizoma and Paeoniae Radix Alba relieves chronic compression injury-induced pain in rats by ameliorating AR/Mboa... by Ze-Ming Wang (9572399)

“…</p>Results<p>The results demonstrated that YB60 significantly decreased inflammatory cytokine levels both in cellular models and rat serum, while concurrently elevating pain thresholds in CCI rats. …”

<b>Exercise alters molecular profiles of inflammation and substrate metabolism in human white adipose tissue</b> by Maria Pino (6944198)

“…<p dir="ltr">White adipose tissue (WAT) plays a significant role in whole-body energy homeostasis, and its excess typifies obesity. …”

Data Sheet 1_Identification of the malonylation modification in Staphylococcus aureus and insight into the regulators in biofilm formation.xlsx by Xiaoyan Yu (319080)

“…</p>Methods<p>In this study, we analyzed the dynamic changes of protein malonylation of Staphylococcus aureus (S. aureus) DC15 during biofilm formation based on antibody affinity enrichment combined with quantitative proteomics.</p>Results<p>Quantitative profiling identified 2,833 malonylated sites across 788 proteins, with significant enrichment in biofilm-associated proteins. …”

Data Sheet 3_Identification of the malonylation modification in Staphylococcus aureus and insight into the regulators in biofilm formation.pdf by Xiaoyan Yu (319080)

“…</p>Methods<p>In this study, we analyzed the dynamic changes of protein malonylation of Staphylococcus aureus (S. aureus) DC15 during biofilm formation based on antibody affinity enrichment combined with quantitative proteomics.</p>Results<p>Quantitative profiling identified 2,833 malonylated sites across 788 proteins, with significant enrichment in biofilm-associated proteins. …”

Data Sheet 2_Identification of the malonylation modification in Staphylococcus aureus and insight into the regulators in biofilm formation.xlsx by Xiaoyan Yu (319080)

“…</p>Methods<p>In this study, we analyzed the dynamic changes of protein malonylation of Staphylococcus aureus (S. aureus) DC15 during biofilm formation based on antibody affinity enrichment combined with quantitative proteomics.</p>Results<p>Quantitative profiling identified 2,833 malonylated sites across 788 proteins, with significant enrichment in biofilm-associated proteins. …”

Data Sheet 1_Immune monitoring of trabectedin therapy in refractory soft tissue sarcoma patients - the IMMUNYON study.pdf by Paulo Rodrigues-Santos (3424613)

“…Gene expression analysis identified changes in BTRC (decreased), IFNA1 (increased), and IL9 (increased) in PD versus SD patients (p<0.05). …”

Growth and physiological response of Yulu <i>Hippophae rhamnoides</i> to drought stress and its omics analysis by Haipeng Chen (7228403)

“…The phenotypic traits and physiological indies were assessed and analyzed, while the roots were subjected by RNA-Seq transcriptome and Tandem Mass Tags (TMT) proteome analysis. Drought stress significantly reduced the plant height, ground diameter, root biomass and superoxide dismutase activity; however, the main root length increased. …”

FLEXI interactions with RNA-binding proteins. by Jun Yao (9646)

“…RNA-binding sites: I, within introns corresponding to FLEXIs; SS-I and SS-E, bimodally enriched across the 5’- and 3’ splice sites in unspliced pre-mRNAs with the midpoints in the intron or flanking exon (SS-I and SS-E, respectively; Figs <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1011416#pgen.1011416.g004" target="_blank">4A</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1011416#pgen.1011416.s011" target="_blank">S11</a>). mRNA levels, RBPs whose knockdown resulted in significant difference in mRNA levels (increased or decreased, DESeq2 |LFC|≥1, adjusted p≤0.05) from host gene of FLEXIs with a binding site for that RBP compared to those genes whose transcripts lacked a binding site for the same RBPs based on ENCODE RBP-knockdown datasets (p≤0.05 calculated by Fisher’s exact test; <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1011416#pgen.1011416.s013" target="_blank">S13 Fig</a>). …”

TRIM16 mediates secretory autophagy in head and neck cancer-associated fibroblasts by Thuc Ly (12832686)

“…Autophagy in CAFs is constitutive and independent of STAT3, MAPK1/ERK2-MAPK3/ERK1 and phosphoinositide 3-kinase (PI3K) signaling. Despite the significant role of secretory autophagy in CAFs, its molecular machinery has remained elusive. …”

Image 1_Vitamin K protects against lipopolysaccharide-induced intestinal inflammation in piglets by inhibiting the MAPK and PI3K-AKT pathways.pdf by Huakai Wang (505567)

“…</p>Results<p>Morphological analysis revealed that VK significantly restored the decreased villus height and ratio of villus height to crypt depth induced by LPS. …”

Rinderine suppresses African swine fever virus replication in porcine alveolar macrophages by dual targeting of membrane-associated profilin 1 and phosphatidylethanolamine by Di Liu (30843)

“…Structural prediction analysis, co-immunoprecipitation assay, and confocal microscopy demonstrate that RIN disrupts the interaction between PFN1 and actin, thereby decreasing the actin remodelling. Notably, untargeted metabolomics profiling and further experiments reveal that RIN reduces the phosphatidylethanolamine level derived from the glycerophospholipid metabolism pathway and decreases the membrane permeability of PAMs, contributing to its anti-ASFV activity. …”

Alteration of Ubiquitination in the Brain of ENOPH1 Knockout Mice after Early Ischemic Stroke by Yike Wu (20982007)

“…Our results showed that 4000 ubiquitination-modified sites in 1613 proteins were quantified, with 772 ubiquitinated sites in 464 proteins significantly decreasing or increasing after ENOPH1 knockout (fold change >1.5 or <1/1.5, <i>p</i> < 0.05). …”