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Additional file 1: Data S1. Participant characteristics. S1a: Characteristics of individuals with CSF Aβ1-42 and tau measurements available; S1b: Characteristics of individuals with CSF proteomic data. Data S2. Protein annotation and statistics of group comparisons of protein levels. Data S3a. Full list of GO biological processes associated with proteins that differ according to group and clinical stage. Data S3b. SynGO enriched synaptic cellular components and biological processes that differ according to group. Data S4a. Estimated marginal means of AD GWAS-based polygenic risk scores in controls, AD individuals with increased t-tau and AD individuals with normal t-tau. Data S4b. Top 1000 SNPS from GWAS on AD individuals with increased t-tau and normal t-tau in pooled ADNI and EMIF-AD MBD cohorts. Data S4c. Difference in MAGMA gene score between AD individuals with increased t-tau and normal t-tau based on t-tau GWAS in pooled ADNI and EMIF-AD MBD cohorts. Data S4d. Difference in GO biological process MAGMA geneset score between AD individuals with increased t-tau and normal t-tau based on t-tau GWAS in pooled ADNI and EMIF-AD MBD cohorts. Data S5a. Correlation between genetic risk score and CSF protein level in individuals with abnormal Aβ1-42. Data S5b. Association of the number of GMNC rs9877502-A risk alleles and number of APOE-e4 alleles with CSF protein concentrations in a linear model in individuals with AD. Data S5c. GO-BP processes enriched for proteins that have a positive or negative association with the number of rs9877502-A risk alleles in an additive model. Data S6. Annual change in imaging measures.

During spawning, adult Pacific salmonids (Oncorhynchus spp.) complete challenging upriver migrations during which energy and oxygen delivery must be partitioned into activities such as locomotion, maturation and spawning behaviours under the constraints of an individual's cardiac capacity. To advance our understanding of cardiac function in free-swimming fishes, we implanted migrating adult Chinook salmon (Oncorhynchus tshawytscha) collected near the mouth of the Sydenham River, Ontario, with heart rate (fH) biologgers that recorded fH every 3 min until these semelparous fish expired on spawning grounds several days later. Fundamental aspects of cardiac function were quantified, including resting, routine and maximum fH, as well as scope for fH (maximum−resting fH). Predictors of fH were explored using generalized least-squares regression, including water temperature, discharge, fish size and fish origin (wild versus hatchery). Heart rate was positively correlated with water temperature, which aligned closely with daily and seasonal shifts. Wild fish had slower resting heart rates than hatchery fish, which led to significantly higher scope for fH. Our findings suggest that wild salmon may have better cardiac capacity during migration than hatchery fish, potentially promoting migration success in wild fish.This article is part of the theme issue ‘Measuring physiology in free living animals (Part I)’.

Additional file 2: Dataset S1. Longitudinal microbial composition (relative abundance) in viremic controllers and non-controllers analyzed by MetaPhlAn2.0. Dataset S2. Raw bacterial protein counts at baseline in viremic controllers and non-controllers analysed using Scaffold Q+ software v4.9.0. Dataset S3. Raw gene counts at baseline in viremic controllers and non-controllers estimated using RSEM v1.3.0. Dataset S4. Soluble factors (normalized protein expression units) from the Olink inflammation panel at baseline in viremic controllers and non-controllers. Dataset S5. List of transcripts significantly correlated with the Bacteroidales:Clostridiales ratio adjusted for multiple comparisons (spearman’s rho and corresponding q-value<0.05 are reported). Dataset S6. Spearman’s correlation (rho=0.5) between viral reservoir (CA HIV-1 RNA and HIV-1 DNA), bacterial species (Bacteroidales and Clostrdiales), transcripts correlated with the ratio Bacteroidales / Clostridiales and differentially abundant microbial proteins (p<0.025). Dataset S7. Benjamini–Hochberg multiple hypothesis correction for unadjusted p-values ≤ 0.05 (metagenomics and metaproteomics datasets).

Appendix S3. Summary of species names, accession numbers, and Newick strings used in codon model analyses (XLSX 51 kb)

Additional file 1. Geographical, genetic, and kinetic parameter information for hybrids.

Additional file 3: Table S1. List of differentially expressed genes between controllers and non-controllers at baseline (adjusted p-value <0.1and log2 FoldChange = 0). Table S2. Detailed information of differentially expressed genes (DEGs) between controllers and non-controllers at baseline (adjusted p-value <0.1 and log2 FoldChange = 0). Table S3. GO terms from enrichment analysis (biological process) based on upregulated genes in viremic controllers (n. transcripts =15). Table S4. Enriched GO biological process terms of host transcripts significantly correlated with the ratio Bacteroidales/Clostridiales. Table S5. Enriched GO biological process terms of transcripts (n=453) significantly correlated with the ratio Bacteroidales/Clostridiales and viral reservoir (CA HIV-1 RNA and HIV-1 DNA). Table S6. Summary of shotgun metagenomics sequencing yield from longitudinally-collected fecal samples. Statistics of reads mapped to integrated gene catalog (IGC) are also shown.

Primary image data related to Quesnel-Vallières et al., 2016, Mol Cell: http://dx.doi.org/10.1016/j.molcel.2016.11.033

This Malab file solves the normal shock structure problem (figure no: 6 in the manuscript) for the CCR/NSF/Grad models.

Authors’ original file for figure 1

Additional file 9. Genetic and kinetic parameter information for Saccharomyces strains.