Additional file 5: Figure S2. Median-joining network of Pv230 among eight geographically diverse populations. Haplotypes composed of nucleotide polymorphism in ICP of Pv230 with a frequency > 1 were used to create a median-joining network. Each node represents one haplotype, node size indicates haplotype frequency, and node color corresponds to the country of origin. Line length is proportional to genetic distance.

Additional file 2: Figure S1. Depletion of LARRPM promoted proliferation, repressed apoptosis and promoted migration and invasion of LUAD cells. A LARRPM expression in HCC827 cells with LARRPM stable depletion or control was detected by qRT-PCR. B Cell proliferation of HCC827 cells with LARRPM stable depletion or control was detected using CCK-8 assays. C Cell proliferation of HCC827 cells with LARRPM stable overexpression or control was detected using EdU incorporation assays. Scale bar: 100 µm....

Additional file 6: Fig. S5. Anti-CSF1 antibody abolished the effects of LARRPM on M2 macrophage infiltration. A THP-1 cells were subjected to transwell migration assays towards A549 cells with LARRPM overexpression or A549 control cells treated with anti-CSF1. Scale bar: 100 µm. B THP-1 cells were subjected to transwell migration assays towards HCC827 cells with LARRPM depletion or HCC827 control treated with anti-CSF1. Scale bar: 100 µm. C M1 and M2 polarization markers expression in...

Supplemental material, sj-jpg-1-ccn-10.1177_20597002221133183 for Neuroimaging correlates of syndromal depression following traumatic brain injury: A systematic review of the literature by Lisa N. Richey, Barry R. Bryant, Akshay Krieg, Michael J. C. Bray, Aaron I. Esagoff, Tejus Pradeep, Sahar Jahed, Licia P. Luna, Nicholas T. Trapp, Jaxon Adkins, Melissa B. Jones, Andrew Bledsoe, Daniel A. Stevens, Carrie Roper, Eric L. Goldwaser, LiAnn Morris, Emily Berich-Anastasio, Alexandra Pletnikova, Katie Lobner, Daniel J. Lee, Margo Lauterbach, Simon Ducharme,...

Additional file 3: Fig. S3. Annotation of DMCs. (A-C) The annotation of DMCs in the context of CpG (A), CHG (B) and CHH (C). (D) The distribution of DMC CpG islands (CGIs) and related regions. (E-F) The number of DMCs grouped by the differences in methylation levels in gene features (E) and regions in CGI context (F).

Additional file 4: Fig. S4. DNA methylation landscape. (A) The number of DMCs grouped by the differences in methylation levels per chromosome. (B-D) Manhattan plots showing the global distribution of DMCs in the context of CpG (B), CHG (C) and CHH (D). (E) DNA methylation landscape of chromosome 2.

Additional file 5: Fig. S5. Association between DNA methylation and gene expression levels. (A-B) Scatter plots showing correlation between gene expression level and promoter methylation level (A) and first exon (B). (C) Box plot showing promoter methylation level of genes grouped by expression levels. (D-F) Scatterplots and fitting curves of DNA methylation and relative gene expression of gene body methylation (D), exon methylation (E) and intron methylation (F). (G-I) MetGDE genes selected based on the...

Additional file 5: Figure S4. The correlation between LARRPM expression, 5hmC level at CSF1 promoter, CpG82 methylation level and CSF1 expression in LUAD tissues. A Correlation between CSF1 and LARRPM expression analysed using the TCGA LUAD data. r = − 0.3069, P < 0.0001 by Spearman correlation analysis. B Correlation between CSF1 and LARRPM expression analysed in our LUAD cohort. r = − 0.5774, P < 0.0001 by Spearman correlation analysis. C 5hmC levels of...

Additional file 7: Fig. S6. Depletion of LARRPM in LUAD cells enhanced the oncogenic roles of infiltrated M2 macrophages. A–F Conditioned medium (CM) was collected from co-culture of macrophages with HCC827 cells with LARRPM depletion or control HCC827 cells, or collected from only HCC827 cells with LARRPM depletion or control HCC827 cells. A Cell proliferation of HCC827 cells treated with the CM was detected using CCK-8 assays. B Cell proliferation of HCC827 cells treated with...

Additional file 4: Figure S1. Phylogenetic analysis of Pvs230 sequences from global P. vivax populations. The maximum-likelihood phylogenetic tree reconstructed based on alignment by ClustalW with bootstrap analysis to assess clade support (500 replicates) was shown for Pvs230 global isolates. The global isolates were clustered into three main groups, the branches of which are shown in red (group 1), green (group 2), and blue (group 3).

Additional file 1: Fig. S1 The distributions of variant allele frequencies (VAFs) of ARID1A, ARID1B, ARID2, PBRM1, SMARCA4, and SMARCB1. The median VAFs of the above genes were 16.1%, 13.4%, 13.3%, 17.2%, 15.2%, and 16.7%, respectively. Red solid line, median; black dotted line, quartiles.

Additional file 2: Fig. S2. Methylation status of differentially methylated sites. (A-B) Volcano plots showing DMCs in the context of CHG (A) and CHH (B). (C) Bar plots showing distribution of differences in methylation levels of DMCs.

Additional file 1. Fig. S1 Effect of lithium chloride 1mM for 7 days on telomere length in human-derived neural precursors cells (NPCs). Li: lithium treated; ns: not significant.

Supplemental material, sj-jpg-2-ccn-10.1177_20597002221133183 for Neuroimaging correlates of syndromal depression following traumatic brain injury: A systematic review of the literature by Lisa N. Richey, Barry R. Bryant, Akshay Krieg, Michael J. C. Bray, Aaron I. Esagoff, Tejus Pradeep, Sahar Jahed, Licia P. Luna, Nicholas T. Trapp, Jaxon Adkins, Melissa B. Jones, Andrew Bledsoe, Daniel A. Stevens, Carrie Roper, Eric L. Goldwaser, LiAnn Morris, Emily Berich-Anastasio, Alexandra Pletnikova, Katie Lobner, Daniel J. Lee, Margo Lauterbach, Simon Ducharme,...

Additional file 1: Fig. S1. DNA methylation level trends. (A) Bean plots showing the methylation level distribution of methylation sites in the context of CpG, CHG and CHH at genome wide scale. (B) The methylation level trends around gene features per sample. a = promoter (2 kb upstream of transcription start site); b = first exon; c = first intron; d = inner exons; e = inner introns; f = last exon; g = downstream...

Additional file 3: Fig. S3. Annotation of DMCs. (A-C) The annotation of DMCs in the context of CpG (A), CHG (B) and CHH (C). (D) The distribution of DMC CpG islands (CGIs) and related regions. (E-F) The number of DMCs grouped by the differences in methylation levels in gene features (E) and regions in CGI context (F).

Additional file 3: Figure S2. The correlation between LARRPM expression, 5hmC level at LINC00240 promoter, CpG43 methylation level and LINC00240 expression in LUAD tissues. A Correlation between LINC00240 and LARRPM expression analysed using the TCGA LUAD data. r = 0.6164, P < 0.0001 by Spearman correlation analysis. B Correlation between LINC00240 and LARRPM expression analyzed in our LUAD cohort. r = 0.5521, P < 0.0001 by Spearman correlation analysis. C 5hmC levels of CpG43 from...

Additional file 5: Figure S4. The correlation between LARRPM expression, 5hmC level at CSF1 promoter, CpG82 methylation level and CSF1 expression in LUAD tissues. A Correlation between CSF1 and LARRPM expression analysed using the TCGA LUAD data. r = − 0.3069, P < 0.0001 by Spearman correlation analysis. B Correlation between CSF1 and LARRPM expression analysed in our LUAD cohort. r = − 0.5774, P < 0.0001 by Spearman correlation analysis. C 5hmC levels of...

Additional file 2: Fig. S2 The progression-free survival (PFS) of patients receiving immune checkpoint inhibitor (ICI) treatment based on cancer types. The survival analysis was performed for individual cancer types that contained at least 10 cases in the SWI/SNF-mutant or SWI/SNF-non-mutant groups. The PFS of the SWI/SNF-mutant group was significantly superior to that of the SWI/SNF-non-mutant group in colorectal cancer (a) and gastric cancer (b), the same tendency was significant numerically by not statistically in...

Additional file 1: Fig. S1. DNA methylation level trends. (A) Bean plots showing the methylation level distribution of methylation sites in the context of CpG, CHG and CHH at genome wide scale. (B) The methylation level trends around gene features per sample. a = promoter (2 kb upstream of transcription start site); b = first exon; c = first intron; d = inner exons; e = inner introns; f = last exon; g = downstream...

Additional file 2: Fig. S2. Methylation status of differentially methylated sites. (A-B) Volcano plots showing DMCs in the context of CHG (A) and CHH (B). (C) Bar plots showing distribution of differences in methylation levels of DMCs.

Additional file 4: Fig. S4. DNA methylation landscape. (A) The number of DMCs grouped by the differences in methylation levels per chromosome. (B-D) Manhattan plots showing the global distribution of DMCs in the context of CpG (B), CHG (C) and CHH (D). (E) DNA methylation landscape of chromosome 2.

Additional file 4: Figure S3. LINC00240 repressed proliferation, induced apoptosis and inhibited migration and invasion of LUAD cells. A LINC00240 expression in A549 cells with LINC00240 stable overexpression or control was detected by qRT-PCR. B Cell proliferation of A549 cells with LINC00240 stable overexpression or control was detected using CCK-8 assays. C Cell proliferation of A549 cells with LINC00240 stable overexpression or control was detected using EdU incorporation assays. Scale bar: 100 µm. Red color...

Additional file 7: Fig. S6. Depletion of LARRPM in LUAD cells enhanced the oncogenic roles of infiltrated M2 macrophages. A–F Conditioned medium (CM) was collected from co-culture of macrophages with HCC827 cells with LARRPM depletion or control HCC827 cells, or collected from only HCC827 cells with LARRPM depletion or control HCC827 cells. A Cell proliferation of HCC827 cells treated with the CM was detected using CCK-8 assays. B Cell proliferation of HCC827 cells treated with...

Additional file 2: Fig. S2 The progression-free survival (PFS) of patients receiving immune checkpoint inhibitor (ICI) treatment based on cancer types. The survival analysis was performed for individual cancer types that contained at least 10 cases in the SWI/SNF-mutant or SWI/SNF-non-mutant groups. The PFS of the SWI/SNF-mutant group was significantly superior to that of the SWI/SNF-non-mutant group in colorectal cancer (a) and gastric cancer (b), the same tendency was significant numerically by not statistically in...