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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Mealey, Nicole E.; O���Sullivan, Dylan E.; Peters, Cheryl E.; Heng, Daniel Y. C.; +1 Authors

    Additional file 6: Table S1. Comparison of COSMIC mutational signature contributions to non-seminomatous (n = 56) and seminomatous (n = 44) testicular tumors. Entries are number (proportion) of cases with a signature present above a threshold of 6% in each histologic group. P-values were calculated adjusting for age of onset * indicates statistical significance at a 0.05 level.

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    Novakovsky, Gherman; Saraswat, Manu; Fornes, Oriol; Mostafavi, Sara; +1 Authors

    Additional file 12: Table S1. Total number of ones, zeros and nulls in the sparse matrix for the 163 TFs used in this study.

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  • Xubiao Peng; Ebrima Gibbs; Silverman, Judith M; Cashman, Neil R; +1 Authors

    Supplemental material, sj-xlsx-3-smm-10.1177_09622802211002861 for A method for systematically ranking therapeutic drug candidates using multiple uncertain screening criteria by Xubiao Peng, Ebrima Gibbs, Judith M Silverman, Neil R Cashman and Steven S Plotkin in Statistical Methods in Medical Research

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Patel, Zain M.; Hughes, Timothy R.;

    Additional file 3 : Table S2. Exact file IDs and links to all data obtained from ENCODE and Roadmap Epigenome.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Wadsworth, Brennan J.; Decotret, Lisa R.; Villamil, Carlos; Yapp, Donald; +4 Authors

    A common feature of solid tumours that are resistant to therapy is the presence of regions with low oxygen content (i.e., hypoxia). Oxygen electrode studies suggest that localized prostate adenocarcinoma is commonly hypoxic, although conflicting data have been reported between immunohistochemical detection of hypoxia-induced proteins in biopsy specimens and positron emission tomography (PET) imaging of 18F-labeled hypoxia reporters. Although the 2-nitroimidazole 18F-EF5 is well-established to label hypoxic tumour cells in pre-clinical tumour models and clinical trials of multiple primary tumour sites, it has yet to be tested in prostate cancer. The purpose of this study was to evaluate the feasibility of using 18F-EF5 to detect hypoxia in clinical prostate tumours. Patients with localized adenocarcinoma of the prostate were recruited for pre-treatment 18F-EF5 PET scans. Immunohistochemistry was conducted on diagnostic biopsies to assess the expression of glucose transporter 1 (GLUT1), osteopontin (OPN), and carbonic anhydrase IX (CAIX). Immunoreactivity scores of staining intensity and frequency were used to indicate the presence of tumour hypoxia. We found low tumour-to-muscle ratios of 18F-EF5 uptake that were not consistent with tumour hypoxia, causing early termination of the study. However, we observed GLUT1 and OPN expression in all prostate tumour biopsies, indicating the presence of hypoxia in all tumours. Our data do not support the use of 18F-EF5 PET to detect hypoxia in prostate adenocarcinoma, and suggest the use of immunohistochemistry to quantify expression of the hypoxia-inducible proteins GLUT1 and OPN as indications of prostate tumour hypoxia.

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    Konwar, Chaini; Asiimwe, Rebecca; Inkster, Amy M.; Merrill, Sarah M.; +6 Authors

    Additional file 1: Table S1. List of candidate genes examined in the current study. Table S2. Results obtained from the sex-based expression analysis performed on the autosomal genes (segregated by tissues). Table S3. Results obtained from the sex-based expression analysis performed on the X-linked genes (segregated by tissues). Table S4. Results obtained from the sex-based DNA methylation analysis performed on the autosomal genes (segregated by tissues). Table S5. Results obtained from the sex-based DNA methylation analysis performed on the X-linked genes (segregated by tissues). Table S6. Results obtained from the exposure-based DNA methylation analysis performed on the autosomal genes (segregated by tissues).

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Azevedo Portilho, Nathalia; Saini, Deepak; Hossain, Ishtiaque; Sirois, Jacinthe; +2 Authors

    Additional file 4: Table S3. Mapping and conversion statistics for Whole Genome Bisulfite Sequencing data used in this publication.

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  • Choudhary, Neha; Scheiber, Hayden; Zhang, Jiale; Patrick, Brian O.; +2 Authors

    Related Article: Neha Choudhary, Hayden Scheiber, Jiale Zhang, Brian O. Patrick, María de Guadalupe Jaraquemada-Peláez, Chris Orvig|2021|Inorg.Chem.|60|12855|doi:10.1021/acs.inorgchem.1c01175

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    Azevedo Portilho, Nathalia; Saini, Deepak; Hossain, Ishtiaque; Sirois, Jacinthe; +2 Authors

    Additional file 3: Table S2. P-values for upregulation of indicated genes and transposons.

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    Grisé, Kenneth N.; Bautista, Nelson X.; Jacques, Krystal; Coles, Brenda L. K.; +1 Authors

    Additional file 2: Ontario Institute for Cancer Research (OICR) Tool Compound Library.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Mealey, Nicole E.; O���Sullivan, Dylan E.; Peters, Cheryl E.; Heng, Daniel Y. C.; +1 Authors

    Additional file 6: Table S1. Comparison of COSMIC mutational signature contributions to non-seminomatous (n = 56) and seminomatous (n = 44) testicular tumors. Entries are number (proportion) of cases with a signature present above a threshold of 6% in each histologic group. P-values were calculated adjusting for age of onset * indicates statistical significance at a 0.05 level.

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    Novakovsky, Gherman; Saraswat, Manu; Fornes, Oriol; Mostafavi, Sara; +1 Authors

    Additional file 12: Table S1. Total number of ones, zeros and nulls in the sparse matrix for the 163 TFs used in this study.

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  • Xubiao Peng; Ebrima Gibbs; Silverman, Judith M; Cashman, Neil R; +1 Authors

    Supplemental material, sj-xlsx-3-smm-10.1177_09622802211002861 for A method for systematically ranking therapeutic drug candidates using multiple uncertain screening criteria by Xubiao Peng, Ebrima Gibbs, Judith M Silverman, Neil R Cashman and Steven S Plotkin in Statistical Methods in Medical Research

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    Patel, Zain M.; Hughes, Timothy R.;

    Additional file 3 : Table S2. Exact file IDs and links to all data obtained from ENCODE and Roadmap Epigenome.

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    Wadsworth, Brennan J.; Decotret, Lisa R.; Villamil, Carlos; Yapp, Donald; +4 Authors

    A common feature of solid tumours that are resistant to therapy is the presence of regions with low oxygen content (i.e., hypoxia). Oxygen electrode studies suggest that localized prostate adenocarcinoma is commonly hypoxic, although conflicting data have been reported between immunohistochemical detection of hypoxia-induced proteins in biopsy specimens and positron emission tomography (PET) imaging of 18F-labeled hypoxia reporters. Although the 2-nitroimidazole 18F-EF5 is well-established to label hypoxic tumour cells in pre-clinical tumour models and clinical trials of multiple primary tumour sites, it has yet to be tested in prostate cancer. The purpose of this study was to evaluate the feasibility of using 18F-EF5 to detect hypoxia in clinical prostate tumours. Patients with localized adenocarcinoma of the prostate were recruited for pre-treatment 18F-EF5 PET scans. Immunohistochemistry was conducted on diagnostic biopsies to assess the expression of glucose transporter 1 (GLUT1), osteopontin (OPN), and carbonic anhydrase IX (CAIX). Immunoreactivity scores of staining intensity and frequency were used to indicate the presence of tumour hypoxia. We found low tumour-to-muscle ratios of 18F-EF5 uptake that were not consistent with tumour hypoxia, causing early termination of the study. However, we observed GLUT1 and OPN expression in all prostate tumour biopsies, indicating the presence of hypoxia in all tumours. Our data do not support the use of 18F-EF5 PET to detect hypoxia in prostate adenocarcinoma, and suggest the use of immunohistochemistry to quantify expression of the hypoxia-inducible proteins GLUT1 and OPN as indications of prostate tumour hypoxia.

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    Konwar, Chaini; Asiimwe, Rebecca; Inkster, Amy M.; Merrill, Sarah M.; +6 Authors

    Additional file 1: Table S1. List of candidate genes examined in the current study. Table S2. Results obtained from the sex-based expression analysis performed on the autosomal genes (segregated by tissues). Table S3. Results obtained from the sex-based expression analysis performed on the X-linked genes (segregated by tissues). Table S4. Results obtained from the sex-based DNA methylation analysis performed on the autosomal genes (segregated by tissues). Table S5. Results obtained from the sex-based DNA methylation analysis performed on the X-linked genes (segregated by tissues). Table S6. Results obtained from the exposure-based DNA methylation analysis performed on the autosomal genes (segregated by tissues).

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    Azevedo Portilho, Nathalia; Saini, Deepak; Hossain, Ishtiaque; Sirois, Jacinthe; +2 Authors

    Additional file 4: Table S3. Mapping and conversion statistics for Whole Genome Bisulfite Sequencing data used in this publication.

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  • Choudhary, Neha; Scheiber, Hayden; Zhang, Jiale; Patrick, Brian O.; +2 Authors

    Related Article: Neha Choudhary, Hayden Scheiber, Jiale Zhang, Brian O. Patrick, María de Guadalupe Jaraquemada-Peláez, Chris Orvig|2021|Inorg.Chem.|60|12855|doi:10.1021/acs.inorgchem.1c01175

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    Azevedo Portilho, Nathalia; Saini, Deepak; Hossain, Ishtiaque; Sirois, Jacinthe; +2 Authors

    Additional file 3: Table S2. P-values for upregulation of indicated genes and transposons.

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    Grisé, Kenneth N.; Bautista, Nelson X.; Jacques, Krystal; Coles, Brenda L. K.; +1 Authors

    Additional file 2: Ontario Institute for Cancer Research (OICR) Tool Compound Library.

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