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Additional file 1: of Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

Philipp Rausch, Malte RĂźhlemann, Britt Hermes, Shauni Doms, Tal Dagan, Katja Dierking, Hanna Domin, Sebastian Fraune, Jakob Frieling, Ute Hentschel, Femke-Anouska Heinsen, Marc HĂśppner, Martin Jahn, Cornelia Jaspers, Kohar Kissoyan, Daniela Langfeldt, Ateequr Rehman, Thorsten Reusch, Thomas Roeder, Ruth Schmitz, Hinrich Schulenburg, Ryszard Soluch, Felix Sommer, Eva Stukenbrock, Nancy Weiland-BräUer … & John Baines
Supplementary Materials. (PDF 6900 kb)

Biological variation of immunological blood biomarkers in healthy individuals and quality goals for biomarker tests

Najib Aziz, Roger Detels, Joshua Quint, David Gjertson, Timothy Ryner & Anthony Butch
Abstract Background Cytokines, chemokines, adipocytokines, soluble cell receptors, and immune activation markers play an important role in immune responsiveness and can provide prognostic value since they reflect underlying conditions and disease states. This study was undertaken to investigate the components of biological variation for various laboratory tests of blood immunological biomarkers. Results Estimates of intra-individual coefficient of variation (CVI) and inter-individual coefficient of variation (CVG) were examined for blood immunological biomarkers. Biomarkers with CVI 40%...

Biological variation of immunological blood biomarkers in healthy individuals and quality goals for biomarker tests

Najib Aziz, Roger Detels, Joshua Quint, David Gjertson, Timothy Ryner & Anthony Butch
Abstract Background Cytokines, chemokines, adipocytokines, soluble cell receptors, and immune activation markers play an important role in immune responsiveness and can provide prognostic value since they reflect underlying conditions and disease states. This study was undertaken to investigate the components of biological variation for various laboratory tests of blood immunological biomarkers. Results Estimates of intra-individual coefficient of variation (CVI) and inter-individual coefficient of variation (CVG) were examined for blood immunological biomarkers. Biomarkers with CVI 40%...

Additional file 9: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Figure S4. Gene arrays from rectus abdominis muscle from secondary female cohort (n=64). Correlation matrix of T cells genes and muscle catabolic pathway genes. Strength of the correlation is represented by the size and color intensity of each spot, positive in blue and negative in red. Pearson correlation analysis. (DOCX 1449 kb)

Additional file 8: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Figure S3. Flow cytometry analyses done using FlowJoŠ software [FlowJo, LLC]. A. Gating strategy for the main cell population. B. Exclusion of doublets. C and F. Gating strategy for CD3 and CD11b positive populations. D and G. Stable flow stream for CD3 and CD11b. E and H. FMO controls for CD3 and CD11b. (PDF 443 kb)

Additional file 7: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Figure S2. Immunostaining of serial cross-sections of muscle tissue: CD11b+CD14+CD15+ cells (A) and laminin-dystrophin (B). Stained nuclei in blue. A.1 Original image with no brightness manipulation. A.2 and A.3 Brightness was increased to visually appreciate the location of the CD11b+CD14+CD15+ cell (arrow) on the endomysial area. B. Serial cross-section used to confirm the location of immune cells on the periphery of muscle fibers (endomysium). Asterisks mark muscle fibers used as a reference point, and immune...

Additional file 9: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Figure S4. Gene arrays from rectus abdominis muscle from secondary female cohort (n=64). Correlation matrix of T cells genes and muscle catabolic pathway genes. Strength of the correlation is represented by the size and color intensity of each spot, positive in blue and negative in red. Pearson correlation analysis. (DOCX 1449 kb)

Additional file 5: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Table S5. Negative univariate associations between T cell related genes and genes involved in muscle catabolic pathways of rectus abdominis muscle of secondary female cohort (n=64). (DOCX 25 kb)

Additional file 6: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Figure S1. Immunostaining of CD3+CD4+ (A), CD3+CD4- (B), CD3-CD4+ (C), CD11b+CD14-CD15- (D) and CD11b+CD14+CD15+ (E) cells. Immune cells pointed by the white arrow. A.1, B.1, C.1, D.1 and E.1 antibody detected by Alexa Flour® 647. A.2, B.2, C.2, D.2 and E.2 antibody detected by Alexa Flour® 568. D.3 and E.3 antibody detected by Alexa Flour® 488. A.3, B.3, C.3, D.4 and E.4 nuclear stain detected by DAPI. A.4. B.4, C.4, D.5 and E.5 Merged images....

Additional file 7: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Figure S2. Immunostaining of serial cross-sections of muscle tissue: CD11b+CD14+CD15+ cells (A) and laminin-dystrophin (B). Stained nuclei in blue. A.1 Original image with no brightness manipulation. A.2 and A.3 Brightness was increased to visually appreciate the location of the CD11b+CD14+CD15+ cell (arrow) on the endomysial area. B. Serial cross-section used to confirm the location of immune cells on the periphery of muscle fibers (endomysium). Asterisks mark muscle fibers used as a reference point, and immune...

Additional file 8: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Figure S3. Flow cytometry analyses done using FlowJoŠ software [FlowJo, LLC]. A. Gating strategy for the main cell population. B. Exclusion of doublets. C and F. Gating strategy for CD3 and CD11b positive populations. D and G. Stable flow stream for CD3 and CD11b. E and H. FMO controls for CD3 and CD11b. (PDF 443 kb)

Additional file 3: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Table S3. Patient characteristics, secondary cohort with microarray analysis in rectus abdominis muscle. (DOCX 23 kb)

Additional file 4: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Table S4. Negative univariate associations (r=

Additional file 6: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Figure S1. Immunostaining of CD3+CD4+ (A), CD3+CD4- (B), CD3-CD4+ (C), CD11b+CD14-CD15- (D) and CD11b+CD14+CD15+ (E) cells. Immune cells pointed by the white arrow. A.1, B.1, C.1, D.1 and E.1 antibody detected by Alexa Flour® 647. A.2, B.2, C.2, D.2 and E.2 antibody detected by Alexa Flour® 568. D.3 and E.3 antibody detected by Alexa Flour® 488. A.3, B.3, C.3, D.4 and E.4 nuclear stain detected by DAPI. A.4. B.4, C.4, D.5 and E.5 Merged images....

Additional file 4: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Table S4. Negative univariate associations (r=

Additional file 3: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Table S3. Patient characteristics, secondary cohort with microarray analysis in rectus abdominis muscle. (DOCX 23 kb)

Additional file 2: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Table S2. Secondary antibody panel for immunohistochemistry with corresponding primary antibodies. (DOCX 20 kb)

Additional file 5: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Table S5. Negative univariate associations between T cell related genes and genes involved in muscle catabolic pathways of rectus abdominis muscle of secondary female cohort (n=64). (DOCX 25 kb)

Additional file 1: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Table S1. Primary antibody panel for immunohistochemistry. (DOCX 21 kb)

Additional file 2: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Table S2. Secondary antibody panel for immunohistochemistry with corresponding primary antibodies. (DOCX 20 kb)

Additional file 1: of Immunohistochemical phenotyping of T cells, granulocytes, and phagocytes in the muscle of cancer patients: association with radiologically defined muscle mass and gene expression

Ana Anoveros-Barrera, Amritpal Bhullar, Cynthia Stretch, Abha Dunichand-Hoedl, Karen Martins, Aja Rieger, David Bigam, Todd McMullen, Oliver Bathe, Charles Putman, Catherine Field, Vickie Baracos & Vera Mazurak
Table S1. Primary antibody panel for immunohistochemistry. (DOCX 21 kb)

CSF evidence of pericyte damage in Alzheimer’s disease is associated with markers of blood-brain barrier dysfunction and disease pathology

J. Miners, P. Kehoe, S. Love, H. Zetterberg & K. Blennow
Abstract Background We aimed to assess the relationship between levels of a cerebrospinal fluid (CSF) marker of pericyte damage, soluble platelet-derived growth factor receptor β (sPDGFRβ) and CSF markers of blood-brain barrier (BBB) integrity (CSF albumin and CSF/serum albumin ratio) and disease pathology (reduced CSF Aβ42 and elevated CSF total and phosphorylated tau) in Alzheimer’s disease (AD). Methods sPDGFRβ and albumin were measured by sandwich ELISA in ante-mortem CSF from 39 AD and 39 age-matched...

Assessment of the effect of angiotensin-converting enzyme inhibitors and angiotensin receptor blockers in peritoneal dialysis patients: a systematic review and meta-analysis on clinical trials

Minoru Ito, Yosuke Saka, Yusuke Kuroki, Kaoru Yasuda, Hiraku Tsujimoto, Yasushi Tsujimoto, Hidemichi Yuasa, Munekazu Ryuzaki, Yasuhiko Ito & Hidetomo Nakamoto
Abstract Background Renin-angiotensin system inhibitors (RASIs), either angiotensin-converting enzyme inhibitors or angiotensin receptor blockers, are widely used in patients with non-dialysis chronic kidney disease, as a renin-angiotensin system (RAS) blockade has renoprotective effects. Several studies show that preserving residual renal function is important for a better prognosis in peritoneal dialysis (PD) patients. Here, we systematically reviewed the beneficial or harmful effects of RAS blockade in PD patients. Methods PubMed, the Cochrane Library, Embase, the Ichushi...

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