Supplementary Material 1

Supplemental material, sj-pdf-3-msj-10.1177_13524585221134213 for Cerebrospinal fluid kappa free light chains for the diagnosis of multiple sclerosis: A systematic review and meta-analysis by Harald Hegen, Janette Walde, Klaus Berek, Georgina Arrambide, Sharmilee Gnanapavan, Batia Kaplan, Michael Khalil, Ruba Saadeh, Charlotte Teunissen, Hayrettin Tumani, Luisa M Villar, Maria Alice V Willrich, Henrik Zetterberg and Florian Deisenhammer in Multiple Sclerosis Journal

Figure 2. Phylogenetic tree of bacterial MAGs with representation of different categories of Eukaryotic-like proteins (ELPs) from a) P. lutea and b) I. palifera. From inner to outer, Innermost circle represents MAGs color coded at bacterial class level, heatmap represents different ELP categories (Inner to outer: HEAT repeats; WD domain repeats, WD40; Ankyrin Repeats, ARPs; and Tetratricopeptide repeats, TPRs) and Bar plot represent total ELP counts in MAGs. Bars colored in “sky blue” represent MAGs...

Figure 3. Phylogenetic tree of bacterial MAGs representing functional pathways based on nitrogen, sulphur and anoxygenic photosynthesis KEGG modules in a) P. lutea and b) I. palifera. From inner to outer ring, Innermost circle represents MAGs color coded at bacterial class level. Heatmap represents different KEGG modules (from inner to outer) for Nitrogen metabolism (M000175, M00524, M00529, M00530 and M00531), Sulfur metabolism (M00596, M00176 and M00595) and Anoxygenic photosynthesis (M00597). MAGs with at least one...

Additional file 1: Supplementary preclinical and clinical information.

This includes all the figures, scripts and command-line parameters used for the analysis presented in the manuscript Genomic view of archaeal and bacterial diversity in skeleton of coral Porites lutea and Isopora palifera
1. Figure 1. Phylogenetic trees of Metagenome-assembled genomes (MAGs) recovered from P. lutea and I. palifera skeleton. a) 376 bacterial MAGs, with genome completeness, GC content, and genes-of-interest and b) 17 archaeal MAGs with the presence of ammonia oxidising gene AmoA....

Additional file 1: Table S1. Included publication in analysis of the research question. Table S2. Excluded references and reason for exclusion.

Background:There is limited and inconsistent information on the prevalence of cognitive impairment in neuromyelitis optica spectrum disorders (NMOSD).Objective:To assess cognitive performance and changes over time in NMOSD.Methods:This study included data from 217 aquaporin-4-IgG-seropositive (80%) and double-seronegative NMOSD patients. Cognitive functions measured by Symbol Digit Modalities Test (SDMT), Paced Auditory Serial-Addition Task (PASAT), and/or Multiple Sclerosis Inventory Cognition (MuSIC) were standardized against normative data (N = 157). Intraindividual cognitive performance at 1- and 2-year follow-up was...

Statistical analyses

Genetic variation for resistance and disease tolerance has been described in a range of species. In Drosophila melanogaster, genetic variation in mortality following systemic Drosophila C virus (DCV) infection is driven by large-effect polymorphisms in the restriction factor pastrel (pst). However, it is unclear if pst contributes to disease tolerance. We investigated systemic DCV challenges spanning nine orders of magnitude, in males and females of 10 Drosophila Genetic Reference Panel lines carrying either a susceptible...

qPCR primers, model parameter estimates

Supplemental material, sj-doc-1-msj-10.1177_13524585231155639 for Cerebrospinal fluid–related tissue damage in multiple sclerosis patients with iron rim lesions by Matthias Wittayer, Claudia E Weber, Maximilian Kittel, Michael Platten, Lucas Schirmer, Hayrettin Tumani, Achim Gass and Philipp Eisele in Multiple Sclerosis Journal

Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the...

Insects are under pressure from agricultural intensification. To protect pollinators, conservation measures such as the EU agri-environment schemes (AES) promote planting wildflowers along fields. However, this can potentially alter disease ecology by serving as transmission hubs or by diluting infections. We tested this by measuring plant-pollinator interactions and virus infections (DWV-A, DWV-B and ABPV) across pollinator communities in agricultural landscapes over a year. AES had a direct effect on DWV-B, reducing prevalence and load in...

Supplemental material, sj-pdf-18-msj-10.1177_13524585221134213 for Cerebrospinal fluid kappa free light chains for the diagnosis of multiple sclerosis: A systematic review and meta-analysis by Harald Hegen, Janette Walde, Klaus Berek, Georgina Arrambide, Sharmilee Gnanapavan, Batia Kaplan, Michael Khalil, Ruba Saadeh, Charlotte Teunissen, Hayrettin Tumani, Luisa M Villar, Maria Alice V Willrich, Henrik Zetterberg and Florian Deisenhammer in Multiple Sclerosis Journal

Supplemental material, sj-pdf-17-msj-10.1177_13524585221134213 for Cerebrospinal fluid kappa free light chains for the diagnosis of multiple sclerosis: A systematic review and meta-analysis by Harald Hegen, Janette Walde, Klaus Berek, Georgina Arrambide, Sharmilee Gnanapavan, Batia Kaplan, Michael Khalil, Ruba Saadeh, Charlotte Teunissen, Hayrettin Tumani, Luisa M Villar, Maria Alice V Willrich, Henrik Zetterberg and Florian Deisenhammer in Multiple Sclerosis Journal

Supplemental material, sj-pdf-16-msj-10.1177_13524585221134213 for Cerebrospinal fluid kappa free light chains for the diagnosis of multiple sclerosis: A systematic review and meta-analysis by Harald Hegen, Janette Walde, Klaus Berek, Georgina Arrambide, Sharmilee Gnanapavan, Batia Kaplan, Michael Khalil, Ruba Saadeh, Charlotte Teunissen, Hayrettin Tumani, Luisa M Villar, Maria Alice V Willrich, Henrik Zetterberg and Florian Deisenhammer in Multiple Sclerosis Journal

Supplemental material, sj-pdf-1-msj-10.1177_13524585221134213 for Cerebrospinal fluid kappa free light chains for the diagnosis of multiple sclerosis: A systematic review and meta-analysis by Harald Hegen, Janette Walde, Klaus Berek, Georgina Arrambide, Sharmilee Gnanapavan, Batia Kaplan, Michael Khalil, Ruba Saadeh, Charlotte Teunissen, Hayrettin Tumani, Luisa M Villar, Maria Alice V Willrich, Henrik Zetterberg and Florian Deisenhammer in Multiple Sclerosis Journal

Supplemental material, sj-pdf-2-msj-10.1177_13524585221134213 for Cerebrospinal fluid kappa free light chains for the diagnosis of multiple sclerosis: A systematic review and meta-analysis by Harald Hegen, Janette Walde, Klaus Berek, Georgina Arrambide, Sharmilee Gnanapavan, Batia Kaplan, Michael Khalil, Ruba Saadeh, Charlotte Teunissen, Hayrettin Tumani, Luisa M Villar, Maria Alice V Willrich, Henrik Zetterberg and Florian Deisenhammer in Multiple Sclerosis Journal

Supplemental material, sj-pdf-5-msj-10.1177_13524585221134213 for Cerebrospinal fluid kappa free light chains for the diagnosis of multiple sclerosis: A systematic review and meta-analysis by Harald Hegen, Janette Walde, Klaus Berek, Georgina Arrambide, Sharmilee Gnanapavan, Batia Kaplan, Michael Khalil, Ruba Saadeh, Charlotte Teunissen, Hayrettin Tumani, Luisa M Villar, Maria Alice V Willrich, Henrik Zetterberg and Florian Deisenhammer in Multiple Sclerosis Journal

Supplemental material, sj-pdf-17-msj-10.1177_13524585221134213 for Cerebrospinal fluid kappa free light chains for the diagnosis of multiple sclerosis: A systematic review and meta-analysis by Harald Hegen, Janette Walde, Klaus Berek, Georgina Arrambide, Sharmilee Gnanapavan, Batia Kaplan, Michael Khalil, Ruba Saadeh, Charlotte Teunissen, Hayrettin Tumani, Luisa M Villar, Maria Alice V Willrich, Henrik Zetterberg and Florian Deisenhammer in Multiple Sclerosis Journal

Supplemental material, sj-pdf-10-msj-10.1177_13524585221134213 for Cerebrospinal fluid kappa free light chains for the diagnosis of multiple sclerosis: A systematic review and meta-analysis by Harald Hegen, Janette Walde, Klaus Berek, Georgina Arrambide, Sharmilee Gnanapavan, Batia Kaplan, Michael Khalil, Ruba Saadeh, Charlotte Teunissen, Hayrettin Tumani, Luisa M Villar, Maria Alice V Willrich, Henrik Zetterberg and Florian Deisenhammer in Multiple Sclerosis Journal

Additional file 3: Fig. S2. Differential methylation of CpG loci in the SOCS3 promoter in T-LGL samples. Comparison of CpG methylation (beta-value) for CpGs in the SOCS3 promoter between CD8+ memory cells (CD8mem) and T-LGLL samples (LGL). On top, adjusted p val of differential methylation analysis (dmpFDR, top left) and adjusted p value of differential variability analysis (dmVar, top right).

Additional file 5: Fig. S3B. Gene Ontology analysis of genes hyper- (A) and hypomethylated (B) of T-LGL patients. Significant Biological processes (GO database) enriched in genes associated with significantly differentially methylated CpG loci in T-LGL. Enrichment represented as odds ratio. Point size represents the gene count of each pathway. Enrichment p value obtained by overrepresentation analysis [30], represented by point color. B Gene Ontology analysis of hypomethylated genes in T-LGL.

Abstract Background The molecular pathogenesis of T-cell large granular lymphocytic leukemia (T-LGLL), a mature T-cell leukemia arising commonly from T-cell receptor αβ-positive CD8+ memory cytotoxic T cells, is only partly understood. The role of deregulated methylation in T-LGLL is not well known. We analyzed the epigenetic profile of T-LGLL cells of 11 patients compared to their normal counterparts by array-based DNA methylation profiling. For identification of molecular events driving the pathogenesis of T-LGLL, we compared...