226,701 Works

Additional file 1: of Genome-wide transcriptional adaptation to salt stress in Populus

Jin-Gui Liu, Xiao Han, Tong Yang, Wen-Hui Cui, Ai-Min Wu, Chun-Xiang Fu, Bai-Chen Wang & Li-Jun Liu
Figure S1. Whole plant responses along the time-course of NaCl treatments. a, plants with no salt treatment; b, plants treated with 100 mM NaCl; c, plants treated with 100 mM NaCl followed with 3 days recovery, and then treated with 200 mM NaCl; d, plants treated with 200 mM NaCl directly. Photos were taken at the time points indicated on the left side. (JPG 17970 kb)

Additional file 1: of Use of estimated glomerular filtration rate to predict incident chronic kidney disease in patients at risk of cardiovascular disease: a retrospective study

Saif Al-Shamsi, Abderrahim Oulhaj, Dybesh Regmi & Romona Govender
Nomogram to predict the development of chronic kidney disease stages 3–5 at 5 years with a worked example. Instruction for use: locate a patient characteristic, such as history of diabetes, HbA1c, eGFR, and cholesterol levels, on the corresponding axis to determine the points the patient receives for each characteristic. Add the points of each characteristic and locate the sum on the total points axis. Draw a line straight down to identify the patient’s probability of...

Additional file 1: of Use of estimated glomerular filtration rate to predict incident chronic kidney disease in patients at risk of cardiovascular disease: a retrospective study

Saif Al-Shamsi, Abderrahim Oulhaj, Dybesh Regmi & Romona Govender
Nomogram to predict the development of chronic kidney disease stages 3–5 at 5 years with a worked example. Instruction for use: locate a patient characteristic, such as history of diabetes, HbA1c, eGFR, and cholesterol levels, on the corresponding axis to determine the points the patient receives for each characteristic. Add the points of each characteristic and locate the sum on the total points axis. Draw a line straight down to identify the patient’s probability of...

Additional file 9: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S9. Overall survival between CRCs with high and low load of tumor-assocated neutrophils (TAN load), using combined CRC samples from the TCGA-COAD and READ datasets, respectively. The patients were separated into high and low TAN load, based on the median number of TANs. (JPG 19 kb)

Additional file 8: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S8. CIBERSORT analysis results (in silico flow cytometry) depict the fractional representation of 22 hematopoietic cell types present in the gene expression profile of each cytolytic subset in colon (COAD) and rectal (READ) cancers, respectively. Columns represent cell types from the signature genes file and rows represent the deconvolution results for each tumor sample within each cytolytic subgroup. Filtering was set at p = 0.05 with 1000 permutations during analysis. All results are reported...

Additional file 8: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S8. CIBERSORT analysis results (in silico flow cytometry) depict the fractional representation of 22 hematopoietic cell types present in the gene expression profile of each cytolytic subset in colon (COAD) and rectal (READ) cancers, respectively. Columns represent cell types from the signature genes file and rows represent the deconvolution results for each tumor sample within each cytolytic subgroup. Filtering was set at p = 0.05 with 1000 permutations during analysis. All results are reported...

Additional file 9: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S9. Overall survival between CRCs with high and low load of tumor-assocated neutrophils (TAN load), using combined CRC samples from the TCGA-COAD and READ datasets, respectively. The patients were separated into high and low TAN load, based on the median number of TANs. (JPG 19 kb)

Additional file 5: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S5. Top 25 mutually exclusive ( 1 log10 p-value) gene pairs in COAD and READ, using pair-wise Fisher’s exact test. The red arrow indicates significant mutual exclusivity between BRAF and APC in COAD. (JPG 530 kb)

Additional file 6: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S6. MATH scores did not correlate with the number of classically defined neoepitopes (CDN) or alternatively defined neoepitopes (ADN) neoepitopes in CRC. (JPG 474 kb)

Additional file 6: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S6. MATH scores did not correlate with the number of classically defined neoepitopes (CDN) or alternatively defined neoepitopes (ADN) neoepitopes in CRC. (JPG 474 kb)

Additional file 2: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S2. Enrichment of selected immune-related gene sets in CYT-high colon (COAD) and rectum (READ) adenocarcinomas. A. Cytolytic-high tumors show increased enrichment of gene sets from activated, cytolytic CD8+ T-cell populations and PD1high CD8 T-cells [38, 39]. B. Gene set variation analysis (GSVA) of known immune-related gene sets shows statistically significant increase in CYT-high colon and rectal tumors. (JPG 2337 kb)

Additional file 3: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S3. Gene set variation analysis (GSVA) of known immune-related gene sets (e.g., BIOCARTA_CTL_PATHWAY; TCYTOTOXIC_PATHWAY; TCRA_PATHWAY; THELPER_PATHWAY; PD1_SIGNALING; PRODUCING_DENDRITIC_CELL) showed statistically significant increase in CRCs identified as CYT-high, based on the expression of GZMA and PRF1. (JPG 1293 kb)

Additional file 4: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S4. APC and KRAS mutation types across the two CRC datasets and association with the cytolytic index, showing no statistically significant correlation between APC or KRAS mutations and CYT-high or -low subsets. (JPG 1232 kb)

Additional file 5: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S5. Top 25 mutually exclusive ( 1 log10 p-value) gene pairs in COAD and READ, using pair-wise Fisher’s exact test. The red arrow indicates significant mutual exclusivity between BRAF and APC in COAD. (JPG 530 kb)

Additional file 2: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S2. Enrichment of selected immune-related gene sets in CYT-high colon (COAD) and rectum (READ) adenocarcinomas. A. Cytolytic-high tumors show increased enrichment of gene sets from activated, cytolytic CD8+ T-cell populations and PD1high CD8 T-cells [38, 39]. B. Gene set variation analysis (GSVA) of known immune-related gene sets shows statistically significant increase in CYT-high colon and rectal tumors. (JPG 2337 kb)

Additional file 4: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S4. APC and KRAS mutation types across the two CRC datasets and association with the cytolytic index, showing no statistically significant correlation between APC or KRAS mutations and CYT-high or -low subsets. (JPG 1232 kb)

Additional file 7: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S7. Expression of differentially expressed Treg markers in cytolytic subsets of colorectal cancer. (JPG 1825 kb)

Additional file 1: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S1. The voom function was used to transform the read counts into log counts per million (CPMs) while taking into account the mean-variance relationship in the data [68]. The mean-variance trend plots below were made to detect any genes that possibly varied in the data, and filtering of the low counts was performed adequately. (JPG 1492 kb)

Additional file 3: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S3. Gene set variation analysis (GSVA) of known immune-related gene sets (e.g., BIOCARTA_CTL_PATHWAY; TCYTOTOXIC_PATHWAY; TCRA_PATHWAY; THELPER_PATHWAY; PD1_SIGNALING; PRODUCING_DENDRITIC_CELL) showed statistically significant increase in CRCs identified as CYT-high, based on the expression of GZMA and PRF1. (JPG 1293 kb)

Additional file 7: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S7. Expression of differentially expressed Treg markers in cytolytic subsets of colorectal cancer. (JPG 1825 kb)

Additional file 1: of Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer

Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz Lucas Moreno, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos & Georgios Ayiomamitis
Figure S1. The voom function was used to transform the read counts into log counts per million (CPMs) while taking into account the mean-variance relationship in the data [68]. The mean-variance trend plots below were made to detect any genes that possibly varied in the data, and filtering of the low counts was performed adequately. (JPG 1492 kb)

MOESM1 of A novel CD147 inhibitor, SP-8356, reduces neointimal hyperplasia and arterial stiffness in a rat model of partial carotid artery ligation

Kisoo Pahk, Hyojin Noh, Chanmin Joung, Mi Jang, Hwa Song, Kyung Kim, Kihoon Han, Jong-Ik Hwang, Sungeun Kim & Won-Ki Kim
Additional file 1: Figure S1. Unstained and secondary antibody stained control images of neointimal hyperplasia. There were no specific signals in both neointima and media. In unstained image, autofluorescence was significantly observed only in elastic lamina. In secondary antibody stained images, 488 nm signals were observed in elastic lamina and 555 nm signals in tissue debris and the boundary of neointima. Scale bars, 100 μm. Magnification, × 100.

MOESM1 of A novel CD147 inhibitor, SP-8356, reduces neointimal hyperplasia and arterial stiffness in a rat model of partial carotid artery ligation

Kisoo Pahk, Hyojin Noh, Chanmin Joung, Mi Jang, Hwa Song, Kyung Kim, Kihoon Han, Jong-Ik Hwang, Sungeun Kim & Won-Ki Kim
Additional file 1: Figure S1. Unstained and secondary antibody stained control images of neointimal hyperplasia. There were no specific signals in both neointima and media. In unstained image, autofluorescence was significantly observed only in elastic lamina. In secondary antibody stained images, 488 nm signals were observed in elastic lamina and 555 nm signals in tissue debris and the boundary of neointima. Scale bars, 100 μm. Magnification, × 100.

MOESM5 of Dapagliflozin improves left ventricular remodeling and aorta sympathetic tone in a pig model of heart failure with preserved ejection fraction

Nannan Zhang, Bin Feng, Xuexing Ma, Kangyun Sun, Guidong Xu & Yafeng Zhou
Additional file 5: Fig. S2. Dapagliflozin had no significant effect on CO, LVEDD or LVESD in HFpEF pigs. CO, cardiac output; LVEDD, left ventricular end-diastolic dimension; LVESD, left ventricular end-systolic dimension. Values are expressed as the mean Âą SD. n = 10 pigs per group. Statistical analyses were performed by one-way ANOVA followed by the Bonferroni post hoc test. *p < 0.05 vs. the Normal group.

MOESM5 of Dapagliflozin improves left ventricular remodeling and aorta sympathetic tone in a pig model of heart failure with preserved ejection fraction

Nannan Zhang, Bin Feng, Xuexing Ma, Kangyun Sun, Guidong Xu & Yafeng Zhou
Additional file 5: Fig. S2. Dapagliflozin had no significant effect on CO, LVEDD or LVESD in HFpEF pigs. CO, cardiac output; LVEDD, left ventricular end-diastolic dimension; LVESD, left ventricular end-systolic dimension. Values are expressed as the mean Âą SD. n = 10 pigs per group. Statistical analyses were performed by one-way ANOVA followed by the Bonferroni post hoc test. *p < 0.05 vs. the Normal group.

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