Search

Your search keyword '"Schultz, Andre"' showing total 100 results
Start Over Author "Schultz, Andre" Publication Type Academic Journals
100 results on '"Schultz, Andre"'

2. Distinct Hodgkin lymphoma subtypes defined by noninvasive genomic profiling

Author

Alig, Stefan K., Shahrokh Esfahani, Mohammad, Garofalo, Andrea, Li, Michael Yu, Rossi, Cédric, Flerlage, Tim, Flerlage, Jamie E., Adams, Ragini, Binkley, Michael S., Shukla, Navika, Jin, Michael C., Olsen, Mari, Telenius, Adèle, Mutter, Jurik A., Schroers-Martin, Joseph G., Sworder, Brian J., Rai, Shinya, King, Daniel A., Schultz, Andre, Bögeholz, Jan, Su, Shengqin, Kathuria, Karan R., Liu, Chih Long, Kang, Xiaoman, Strohband, Maya J., Langfitt, Deanna, Pobre-Piza, Kristine Faye, Surman, Sherri, Tian, Feng, Spina, Valeria, Tousseyn, Thomas, Buedts, Lieselot, Hoppe, Richard, Natkunam, Yasodha, Fornecker, Luc-Matthieu, Castellino, Sharon M., Advani, Ranjana, Rossi, Davide, Lynch, Ryan, Ghesquières, Hervé, Casasnovas, Olivier, Kurtz, David M., Marks, Lianna J., Link, Michael P., André, Marc, Vandenberghe, Peter, Steidl, Christian, Diehn, Maximilian, and Alizadeh, Ash A.

Published
2024
Full Text
View/download PDF

6. Inferring gene expression from cell-free DNA fragmentation profiles

Author

Esfahani, Mohammad Shahrokh, Hamilton, Emily G., Mehrmohamadi, Mahya, Nabet, Barzin Y., Alig, Stefan K., King, Daniel A., Steen, Chloé B., Macaulay, Charles W., Schultz, Andre, Nesselbush, Monica C., Soo, Joanne, Schroers-Martin, Joseph G., Chen, Binbin, Binkley, Michael S., Stehr, Henning, Chabon, Jacob J., Sworder, Brian J., Hui, Angela B-Y, Frank, Matthew J., Moding, Everett J., Liu, Chih Long, Newman, Aaron M., Isbell, James M., Rudin, Charles M., Li, Bob T., Kurtz, David M., Diehn, Maximilian, and Alizadeh, Ash A.

Published
2022
Full Text
View/download PDF

7. Survival of people with cystic fibrosis in Australia

Author

Ruseckaite, Rasa, Salimi, Farhad, Earnest, Arul, Bell, Scott C., Douglas, Tonia, Frayman, Katherine, Keatley, Lucy, King, Susannah, Kotsimbos, Tom, Middleton, Peter G., Morey, Sue, Mulrennan, Siobhain, Schultz, Andre, Wainwright, Claire, Ward, Nathan, Wark, Peter, and Ahern, Susannah

Published
2022
Full Text
View/download PDF

9. Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA

Author

Kurtz, David M., Soo, Joanne, Co Ting Keh, Lyron, Alig, Stefan, Chabon, Jacob J., Sworder, Brian J., Schultz, Andre, Jin, Michael C., Scherer, Florian, Garofalo, Andrea, Macaulay, Charles W., Hamilton, Emily G., Chen, Binbin, Olsen, Mari, Schroers-Martin, Joseph G., Craig, Alexander F. M., Moding, Everett J., Esfahani, Mohammad S., Liu, Chih Long, Dührsen, Ulrich, Hüttmann, Andreas, Casasnovas, René-Olivier, Westin, Jason R., Roschewski, Mark, Wilson, Wyndham H., Gaidano, Gianluca, Rossi, Davide, Diehn, Maximilian, and Alizadeh, Ash A.

Published
2021
Full Text
View/download PDF

10. A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily

Author

Korkut, Anil, Zaidi, Sobia, Kanchi, Rupa S, Rao, Shuyun, Gough, Nancy R, Schultz, Andre, Li, Xubin, Lorenzi, Philip L, Berger, Ashton C, Robertson, Gordon, Kwong, Lawrence N, Datto, Mike, Roszik, Jason, Ling, Shiyun, Ravikumar, Visweswaran, Manyam, Ganiraju, Rao, Arvind, Shelley, Simon, Liu, Yuexin, Ju, Zhenlin, Hansel, Donna, de Velasco, Guillermo, Pennathur, Arjun, Andersen, Jesper B, O'Rourke, Colm J, Ohshiro, Kazufumi, Jogunoori, Wilma, Nguyen, Bao-Ngoc, Li, Shulin, Osmanbeyoglu, Hatice U, Ajani, Jaffer A, Mani, Sendurai A, Houseman, Andres, Wiznerowicz, Maciej, Chen, Jian, Gu, Shoujun, Ma, Wencai, Zhang, Jiexin, Tong, Pan, Cherniack, Andrew D, Deng, Chuxia, Resar, Linda, Network, The Cancer Genome Atlas Research, Caesar-Johnson, Samantha J, Demchok, John A, Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L, Hutter, Carolyn M, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Zhang, Jiashan, Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I, Kim, Jaegil, Lawrence, Michael S, Lin, Pei, Meier, Sam, Noble, Michael S, Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M, Hegde, Apurva M, Li, Jun, Liang, Han, Liu, Wenbin, and Lu, Yiling

Subjects
Biological Sciences, Genetics, Cancer, Human Genome, Biotechnology, Cancer Genomics, 2.1 Biological and endogenous factors, Bone Morphogenetic Protein 5, DNA Methylation, Humans, MicroRNAs, Mutation Rate, Neoplasms, Receptor, Transforming Growth Factor-beta Type I, Signal Transduction, Smad Proteins, Transforming Growth Factor beta, Cancer Genome Atlas Research Network, DNA methylation, Pan-Cancer, TCGA, TGF-β, TGF-β pathway, The Cancer Genome Atlas, cancer, microRNA, mutation hotspot, transcription, Biochemistry and Cell Biology, Biochemistry and cell biology
Abstract

We present an integromic analysis of gene alterations that modulate transforming growth factor β (TGF-β)-Smad-mediated signaling in 9,125 tumor samples across 33 cancer types in The Cancer Genome Atlas (TCGA). Focusing on genes that encode mediators and regulators of TGF-β signaling, we found at least one genomic alteration (mutation, homozygous deletion, or amplification) in 39% of samples, with highest frequencies in gastrointestinal cancers. We identified mutation hotspots in genes that encode TGF-β ligands (BMP5), receptors (TGFBR2, AVCR2A, and BMPR2), and Smads (SMAD2 and SMAD4). Alterations in the TGF-β superfamily correlated positively with expression of metastasis-associated genes and with decreased survival. Correlation analyses showed the contributions of mutation, amplification, deletion, DNA methylation, and miRNA expression to transcriptional activity of TGF-β signaling in each cancer type. This study provides a broad molecular perspective relevant for future functional and therapeutic studies of the diverse cancer pathways mediated by the TGF-β superfamily.

Published
2018

11. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

Author

Campbell, Joshua D, Yau, Christina, Bowlby, Reanne, Liu, Yuexin, Brennan, Kevin, Fan, Huihui, Taylor, Alison M, Wang, Chen, Walter, Vonn, Akbani, Rehan, Byers, Lauren Averett, Creighton, Chad J, Coarfa, Cristian, Shih, Juliann, Cherniack, Andrew D, Gevaert, Olivier, Prunello, Marcos, Shen, Hui, Anur, Pavana, Chen, Jianhong, Cheng, Hui, Hayes, D Neil, Bullman, Susan, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I, Sadeghi, Sara, Mungall, Karen L, Robertson, A Gordon, Benz, Christopher, Schultz, Andre, Kanchi, Rupa S, Gay, Carl M, Hegde, Apurva, Diao, Lixia, Wang, Jing, Ma, Wencai, Sumazin, Pavel, Chiu, Hua-Sheng, Chen, Ting-Wen, Gunaratne, Preethi, Donehower, Larry, Rader, Janet S, Zuna, Rosemary, Al-Ahmadie, Hikmat, Lazar, Alexander J, Flores, Elsa R, Tsai, Kenneth Y, Zhou, Jane H, Rustgi, Anil K, Drill, Esther, Shen, Ronglei, Wong, Christopher K, Network, The Cancer Genome Atlas Research, Caesar-Johnson, Samantha J, Demchok, John A, Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L, Hutter, Carolyn M, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Zhang, Jiashan, Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I, Kim, Jaegil, Lawrence, Michael S, Lin, Pei, Meier, Sam, Noble, Michael S, Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, and Zhang, Wei

Subjects
Biological Sciences, Infectious Diseases, Cancer, Sexually Transmitted Infections, Cancer Genomics, Genetics, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, Carcinoma, Squamous Cell, Cell Line, Tumor, DNA Methylation, Epithelial-Mesenchymal Transition, Gene Expression Regulation, Neoplastic, Genomics, Humans, Metabolic Networks and Pathways, Polymorphism, Genetic, Cancer Genome Atlas Research Network, bladder carcinoma with squamous differentiation, cervical squamous cell carcinoma, esophageal squamous cell carcinoma, genomics, head and neck squamous cell carcinoma, human papillomavirus, lung squamous cell carcinoma, proteomics, transcriptomics, Biochemistry and Cell Biology, Medical Physiology, Biological sciences
Abstract

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the ΔNp63 oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support possibilities for molecular classification and therapeutic approaches.

Published
2018

12. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

Author

Berger, Ashton C, Korkut, Anil, Kanchi, Rupa S, Hegde, Apurva M, Lenoir, Walter, Liu, Wenbin, Liu, Yuexin, Fan, Huihui, Shen, Hui, Ravikumar, Visweswaran, Rao, Arvind, Schultz, Andre, Li, Xubin, Sumazin, Pavel, Williams, Cecilia, Mestdagh, Pieter, Gunaratne, Preethi H, Yau, Christina, Bowlby, Reanne, Robertson, A Gordon, Tiezzi, Daniel G, Wang, Chen, Cherniack, Andrew D, Godwin, Andrew K, Kuderer, Nicole M, Rader, Janet S, Zuna, Rosemary E, Sood, Anil K, Lazar, Alexander J, Ojesina, Akinyemi I, Adebamowo, Clement, Adebamowo, Sally N, Baggerly, Keith A, Chen, Ting-Wen, Chiu, Hua-Sheng, Lefever, Steve, Liu, Liang, MacKenzie, Karen, Orsulic, Sandra, Roszik, Jason, Shelley, Carl Simon, Song, Qianqian, Vellano, Christopher P, Wentzensen, Nicolas, Network, The Cancer Genome Atlas Research, Caesar-Johnson, Samantha J, Demchok, John A, Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L, Hutter, Carolyn M, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Zhang, Jiashan, Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I, Kim, Jaegil, Lawrence, Michael S, Lin, Pei, Meier, Sam, Noble, Michael S, Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M, Ju, Zhenlin, Li, Jun, Liang, Han, and Ling, Shiyun

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Women's Health, Cancer, Cancer Genomics, Precision Medicine, Genetics, Human Genome, Breast Cancer, 4.1 Discovery and preclinical testing of markers and technologies, Breast Neoplasms, DNA Copy Number Variations, Databases, Genetic, Female, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Gene Regulatory Networks, Genetic Predisposition to Disease, Genital Neoplasms, Female, Humans, Mutation, Organ Specificity, Prognosis, RNA, Long Noncoding, Receptors, Estrogen, Cancer Genome Atlas Research Network, TCGA, The Cancer Genome Atlas, breast cancer, cervical cancer, gynecologic cancer, omics, ovarian cancer, pan-gynecologic, uterine cancer, uterine carcinosarcoma, Neurosciences, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. We found 61 somatic copy-number alterations (SCNAs) and 46 significantly mutated genes (SMGs). Eleven SCNAs and 11 SMGs had not been identified in previous TCGA studies of the individual tumor types. We found functionally significant estrogen receptor-regulated long non-coding RNAs (lncRNAs) and gene/lncRNA interaction networks. Pathway analysis identified subtypes with high leukocyte infiltration, raising potential implications for immunotherapy. Using 16 key molecular features, we identified five prognostic subtypes and developed a decision tree that classified patients into the subtypes based on just six features that are assessable in clinical laboratories.

Published
2018

17. A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis.

Author

Noren, David P, Long, Byron L, Norel, Raquel, Rrhissorrakrai, Kahn, Hess, Kenneth, Hu, Chenyue Wendy, Bisberg, Alex J, Schultz, Andre, Engquist, Erik, Liu, Li, Lin, Xihui, Chen, Gregory M, Xie, Honglei, Hunter, Geoffrey AM, Boutros, Paul C, Stepanov, Oleg, DREAM 9 AML-OPC Consortium, Norman, Thea, Friend, Stephen H, Stolovitzky, Gustavo, Kornblau, Steven, and Qutub, Amina A

Subjects
DREAM 9 AML-OPC Consortium, Humans, Amyotrophic Lateral Sclerosis, Proteome, Treatment Outcome, Risk Assessment, Sensitivity and Specificity, Reproducibility of Results, Algorithms, Outcome and Process Assessment (Health Care), Crowdsourcing, Biomarkers, Outcome and Process Assessment, Health Care, Outcome and Process Assessment, Health Care, Mathematical Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

Acute Myeloid Leukemia (AML) is a fatal hematological cancer. The genetic abnormalities underlying AML are extremely heterogeneous among patients, making prognosis and treatment selection very difficult. While clinical proteomics data has the potential to improve prognosis accuracy, thus far, the quantitative means to do so have yet to be developed. Here we report the results and insights gained from the DREAM 9 Acute Myeloid Prediction Outcome Prediction Challenge (AML-OPC), a crowdsourcing effort designed to promote the development of quantitative methods for AML prognosis prediction. We identify the most accurate and robust models in predicting patient response to therapy, remission duration, and overall survival. We further investigate patient response to therapy, a clinically actionable prediction, and find that patients that are classified as resistant to therapy are harder to predict than responsive patients across the 31 models submitted to the challenge. The top two performing models, which held a high sensitivity to these patients, substantially utilized the proteomics data to make predictions. Using these models, we also identify which signaling proteins were useful in predicting patient therapeutic response.

Published
2016

18. Efficacy of oral amoxicillin–clavulanate or azithromycin for non-severe respiratory exacerbations in children with bronchiectasis (BEST-1): a multicentre, three-arm, double-blind, randomised placebo-controlled trial

Author

Goyal, Vikas, Grimwood, Keith, Ware, Robert S, Byrnes, Catherine A, Morris, Peter S, Masters, I Brent, McCallum, Gabrielle B, Binks, Michael J, Smith-Vaughan, Heidi, O'Grady, Kerry-Ann F, Champion, Anita, Buntain, Helen M, Schultz, André, Chatfield, Mark, Torzillo, Paul J, and Chang, Anne B

Published
2019
Full Text
View/download PDF

20. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

Author

Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Gonzalez, Ana Maria Angulo, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, onathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Pinero, Edna M. Mora, Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Jr., Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Campbell, Joshua D., Brennan, Kevin, Taylor, Alison M., Wang, Chen, Walter, Vonn, Byers, Lauren Averett, Coarfa, Cristian, Gevaert, Olivier, Prunello, Marcos, Chen, Jianhong, Cheng, Hui, Bullman, Susan, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I., Mungall, Karen L., Schultz, Andre, Gay, Carl M., Hegde, Apurva, Diao, Lixia, Ma, Wencai, Sumazin, Pavel, Chiu, Hua-Sheng, Chen, Ting-Wen, Gunaratne, Preethi, Donehower, Larry, Rader, Janet S., Flores, Elsa R., Tsai, Kenneth Y., Zhou, Jane H., Rustgi, Anil K., Drill, Esther, Shen, Ronglei, Pickering, Curtis R., Chen, Zhong, and Van Waes, Carter

Published
2018
Full Text
View/download PDF

21. Cough in Children and Adults: Diagnosis, Assessment and Management (CICADA). Summary of an updated position statement on chronic cough in Australia.

Author

Marchant, Julie M, Chang, Anne B, Kennedy, Emma, King, David, Perret, Jennifer L, Schultz, Andre, Toombs, Maree R, Versteegh, Lesley, Dharmage, Shyamali C, Dingle, Rebecca, Fitzerlakey, Naomi, George, Johnson, Holland, Anne, Rigby, Debbie, Mann, Jennifer, Mazzone, Stuart, O'Brien, Mearon, O'Grady, Kerry‐Ann, Petsky, Helen L, and Pham, Jonathan

Abstract

Introduction: Cough is the most common symptom leading to medical consultation. Chronic cough results in significant health care costs, impairs quality of life, and may indicate the presence of a serious underlying condition. Here, we present a summary of an updated position statement on cough management in the clinical consultation. Main recommendations: Assessment of children and adults requires a focused history of chronic cough to identify any red flag cough pointers that may indicate an underlying disease. Further assessment with examination should include a chest x‐ray and spirometry (when age > 6 years). Separate paediatric and adult diagnostic management algorithms should be followed. Management of the underlying condition(s) should follow specific disease guidelines, as well as address adverse environmental exposures and patient/carer concerns. First Nations adults and children should be considered a high risk group. The full statement from the Thoracic Society of Australia and New Zealand and Lung Foundation Australia for managing chronic cough is available at https://lungfoundation.com.au/resources/cicada‐full‐position‐statement. Changes in management as a result of this statement: Algorithms for assessment and diagnosis of adult and paediatric chronic cough are recommended.High quality evidence supports the use of child‐specific chronic cough management algorithms to improve clinical outcomes, but none exist in adults.Red flags that indicate serious underlying conditions requiring investigation or referral should be identified.Early and effective treatment of chronic wet/productive cough in children is critical.Culturally specific strategies for facilitating the management of chronic cough in First Nations populations should be adopted.If the chronic cough does not resolve or is unexplained, the patient should be referred to a respiratory specialist or cough clinic. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

29. End-of-Treatment Response Assessment after Frontline Therapy for Aggressive B-Cell Lymphoma: Landmark Comparison of a Singular PET/CT Scan Versus Ultrasensitive Circulating Tumor DNA

Author

Roschewski, Mark, Lindenberg, Liza, Mena, Esther, Lakhotia, Rahul, Melani, Christopher, Steinberg, Seth M., Schultz, Andre, Hogan, Gregory, Chabon, Jake J., Close, Sandra, Diehn, Maximilian, Sworder, Brian J., Kurtz, David M., Alizadeh, Ash A., and Wilson, Wyndham H.

Published
2023
Full Text
View/download PDF

32. Genomic, Transcriptional, and Immunological Validation of Distinct Molecular Subtypes of Classic Hodgkin Lymphoma through Tissue-Based and Noninvasive Methods

Author

Alig, Stefan K., Shahrokh Esfahani, Mohammad, Garofalo, Andrea, Li, Michael Yu, Rossi, Cédric, Flerlage, Timothy, Flerlage, Jamie E., Adams, Ragini, Binkley, Michael S., Shukla, Navika, Jin, Michael, Olsen, Mari, Telenius, Adele, Mutter, Jurik A, Schroers-Martin, Joseph, Sworder, Brian J., Rai, Shinya, King, Daniel, Schultz, Andre, Bögeholz, Jan Lukas, Su, Shengqin, Kathuria, Karan R, Liu, Chih Long, Kang, Xiaoman, Langfitt, Deanna M., Pobre-Piza, Kristine Faye, Tian, Feng, Strohband, Maya J., Spina, Valeria, Tousseyn, Thomas, Buedts, Lieselot, Fornecker, Luc-Matthieu, Castellino, Sharon M., Advani, Ranjana H., Rossi, Davide, Lynch, Ryan C, Ghesquieres, Herve, Casasnovas, Olivier, Kurtz, David M., Marks, Lianna J., Link, Michael P., Andre, Marc, Vandenberghe, Peter, Steidl, Christian, Diehn, Maximilian, and Alizadeh, Ash A.

Published
2023
Full Text
View/download PDF

34. Frequency of protracted bacterial bronchitis and management pre‐respiratory referral.

Author

Lau, Gloria T Y, Laird, Pamela, Stevenson, Paul G, and Schultz, Andre

Abstract

Aim: To determine the frequency of protracted bacterial bronchitis (PBB) in children referred to tertiary care with chronic cough and describe management prior to referral. Methods: A retrospective cohort study of all new patients with a history of ≥4 weeks of cough seen at the only tertiary paediatric outpatient respiratory service in Western Australia between July 2018 and June 2019. Medical records were reviewed until a final diagnosis was documented or otherwise for a period of 18 months. Results: PBB was the most common cause and comprised 37.9% of all children referred to tertiary respiratory care with chronic cough. In children with PBB, the median cough duration at the time of first specialist review was 5.1 months (IQR 2.1–12.0 months). The most common referral source of PBB was primary practice (40.9%) and the most common working diagnosis pre‐referral was asthma (15.9%). Seventy‐eight percent of children with PBB had an ongoing cough at their first respiratory review, and of these, only 13.5% had been prescribed 4 weeks of antibiotics prior to their respiratory review. Asthma treatment had been prescribed for 34.0% of children with PBB. Conclusion: PBB is the most common cause of chronic cough in children referred to tertiary respiratory care and is frequently misdiagnosed and undertreated pre‐referral. There is a need to facilitate diagnosis and optimal management of PBB in primary care, which could result in earlier symptom resolution and potentially limit disease progression to bronchiectasis. [ABSTRACT FROM AUTHOR]

Published
2022
Full Text
View/download PDF

36. Viral cfDNA Profiling Reveals Distinct EBV Subtypes and Stratifies Risk in Hodgkin Lymphomas

Author

Garofalo, Andrea, Alig, Stefan K., Schroers-Martin, Joseph, Shyam, Ragini Malika, Olsen, Mari, Kurtz, David M., Rossi, Cédric, Schultz, Andre, Kathuria, Karan R., Liu, Chih Long, Spina, Valeria, Flerlage, Jamie E., Castellino, Sharon M., Advani, Ranjana H., Rossi, Davide, Lynch, Ryan C., Casasnovas, Olivier, Marks, Lianna J., Link, Michael P., Andre, Marc, Vandenberghe, Peter, Steidl, Christian, Diehn, Maximilian, and Alizadeh, Ash A.

Published
2022
Full Text
View/download PDF

37. Distinct Molecular Subtypes of Classic Hodgkin Lymphoma Identified By Comprehensive Noninvasive Profiling

Author

Alig, Stefan K., Shahrokh Esfahani, Mohammad, Li, Michael Y., Adams, Ragini Malika, Garofalo, Andrea, Jin, Michael C., Olsen, Mari, Telenius, Adèle, Sworder, Brian, Schroers-Martin, Joseph, King, Daniel A., Rossi, Cédric, Schultz, Andre, Kathuria, Karan R., Liu, Chih Long, Spina, Valeria, Buedts, Lieselot, Flerlage, Jamie E., Castellino, Sharon M., Advani, Ranjana H., Rossi, Davide, Lynch, Ryan C., Casasnovas, Olivier, Kurtz, David M., Marks, Lianna J., Link, Michael P., André, Marc, Vandenberghe, Peter, Steidl, Christian, Diehn, Maximilian, and Alizadeh, Ash A.

Published
2022
Full Text
View/download PDF

39. Infections and Progression of Structural Lung Disease in Children with Cystic Fibrosis.

Author

Breuer, Oded, Schultz, Andre, Garratt, Luke W., Turkovic, Lidija, Rosenow, Tim, Murray, Conor P., Karpievitch, Yuliya V., Akesson, Lauren, Dalton, Samuel, Sly, Peter D., Ranganathan, Sarath, Stick, Stephen M., and Caudri, Daan

Subjects
ASPERGILLOSIS, CYSTIC fibrosis in children, LUNG diseases, BRONCHIECTASIS, RESPIRATORY infections, DISEASE progression, COMPUTED tomography, COMPARATIVE studies, CYSTIC fibrosis, LONGITUDINAL method, FUNGAL lung diseases, RESEARCH methodology, MEDICAL cooperation, RESEARCH, EVALUATION research, ODDS ratio, DISEASE complications
Abstract

Rationale: Recent data show that Aspergillus species are prevalent respiratory infections in children with cystic fibrosis (CF). The biological significance of these infections is unknown.Objectives: We aimed to evaluate longitudinal associations between Aspergillus infections and lung disease in young children with CF.Methods: Longitudinal data on 330 children participating in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis surveillance program between 2000 and 2018 who underwent annual chest computed tomography (CT) imaging and BAL were used to determine the association between Aspergillus infections and the progression of structural lung disease. Results were adjusted for the effects of other common infections, associated variables, and repeated visits. Secondary outcomes included inflammatory markers in BAL, respiratory symptoms, and admissions for exacerbations.Measurements and Main Results:Haemophilus influenzae, Staphylococcus aureus, Pseudomonas aeruginosa, and Aspergillus infections were all associated with worse CT scores in the same year (Poverall < 0.05). Only P. aeruginosa and Aspergillus were associated with progression in CT scores in the year after an infection and worse CT scores at the end of the observation period. P. aeruginosa was most significantly associated with development of bronchiectasis (difference, 0.9; 95% confidence interval, 0.3-1.6; P = 0.003) and Aspergillus with trapped air (difference, 3.2; 95% confidence interval, 1.0-5.4; P = 0.004). Aspergillus infections were also associated with markers of neutrophilic inflammation (P < 0.001) and respiratory admissions risk (P = 0.008).Conclusions: Lower respiratory Aspergillus infections are associated with the progression of structural lung disease in young children with CF. This study highlights the need to further evaluate early Aspergillus species infections and the feasibility, risk, and benefit of eradication regimens. [ABSTRACT FROM AUTHOR]

Published
2020
Full Text
View/download PDF

40. Regional centres conduct food challenges with outcomes equivalent to a tertiary pediatric hospital.

Author

Preece, Kahn, Ang, Melanie, Barker, Daniel, Craig, Angela, Schultz, Andre, Sinclair, Jan, Smiley, Richard, Smolnicki, Marie, Sutherland, Melanie, Townend, Tom, and Sampson, Hugh

Subjects
CHILDREN'S hospitals, ALLIED health personnel, FOOD allergy
Abstract

The open-label food challenge format was standardized to the ASCIA oral food challenge protocols.[2] Objective published criteria[3] were then used to assess the challenge outcome with anaphylaxis designated to reactions involving the respiratory and/or cardiovascular system. "Confirm allergy" indicates a child who has been identified as sensitized but not eaten the challenge food; "Confirm resolution" indicates a child who has a history of immediate reaction to the challenge food but is being assess for food allergy resolution. Clinical reaction was seen in 24% of patients challenged with anaphylaxis documented in 41 patients (15% of all those reacting and 3.6% of all challenges). [Extracted from the article]

Published
2019
Full Text
View/download PDF

41. Changing Prevalence of Lower Airway Infections in Young Children with Cystic Fibrosis.

Author

Breuer, Oded, Schultz, Andre, Turkovic, Lidija, de Klerk, Nicholas, Keil, Anthony D., Brennan, Siobhain, Harrison, Joanne, Robertson, Colin, Robinson, Philip J., Sly, Peter D., Ranganathan, Sarath, Stick, Stephen M., and Caudri, Daan

Abstract

Rationale: Historical studies suggest that airway infection in cystic fibrosis initiates with Staphylococcus aureus and Haemophilus influenzae, with later emergence of Pseudomonas aeruginosa. Aspergillus species are regarded as relatively infrequent, late-occurring infections.Objectives: To assess the prevalence and change in prevalence of early lower airway infections in a modern cohort of children with cystic fibrosis.Methods: All infants diagnosed with cystic fibrosis after newborn screening participating in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) cohort study between 2000 and 2018 were included. Participants prospectively underwent BAL at 3-6 months, 1 year, and annually up to 6 years of age. Lower airway infection prevalence was described. Changes in prevalence patterns were assessed longitudinally using generalized estimating equations controlling for age and repeated visits.Measurements and Main Results: A total of 380 infants underwent 1,759 BALs. The overall prevalence and median age of first acquisition of the most common infections were as follows: S. aureus, 11%, 2.5 years; P. aeruginosa, 8%, 2.4 years; Aspergillus species, 11%, 3.2 years; and H. influenzae, 9%, 3.1 years. During the study, a significant decrease in prevalence of P. aeruginosa (P < 0.001) and S. aureus (P < 0.001) was observed with a significant change toward more aggressive treatment. Prevalence of Aspergillus infections did not significantly change (P = 0.669).Conclusions:Aspergillus species and P. aeruginosa are commonly present in the lower airways from infancy. The decrease in prevalence of P. aeruginosa and S. aureus since 2000, coinciding with a more aggressive therapeutic approach, has resulted in Aspergillus becoming the most commonly isolated pathogen in young children. Further research is warranted to understand the implication of these findings. [ABSTRACT FROM AUTHOR]

Published
2019
Full Text
View/download PDF

43. Multi‐centre ethics and research governance review can impede non‐interventional clinical research.

Author

Duplancic, Christine, Crough, Tania, Bell, Scott C., Thomson, Rachel, Wainwright, Claire, Clements, Archie, Floto, Andres, Rogers, Geraint, Sly, Peter, Burr, Lucy, Feather, Iain, Moloney, Susan, Grimwood, Keith, Bye, Peter, Belessis, Yvonne, Selvadurai, Hiran, Schultz, Andre, Mulrennan, Siobhain, Stock, David, and Beggs, Sean

Subjects
CYSTIC fibrosis, ETHICS committees, MEDICAL cooperation, MEDICAL protocols, MEDICAL research, RESEARCH, RESEARCH ethics, INSTITUTIONAL review boards, PARTICIPANT-researcher relationships
Abstract

Background: The inter‐jurisdictional National Mutual Acceptance (NMA) scheme for Human Research Ethics Committee (HREC) approvals of human research is designed to reduce the reported delays and costs of ethical review. Introduction of the NMA set forth an uncoupling of the ethics and governance review processes, permitting a single ethical review for multiple sites, while continuing separate governance review for each centre covering financial and operational aspects of the research project. Aim: To compare the time required to gain ethics and governance approvals in Australia for a non‐interventional investigator‐led study from December 2015 to approval times for an earlier pre‐NMA study utilising a similar study design and study sites and evaluate the effect that the NMA has had on total approval time for non‐interventional multi‐centre projects. Methods: We recorded the time taken to obtain ethics and governance approval at 16 sites for our nationwide low‐risk non‐interventional study looking at the prevalence and aetiology of non‐tuberculous mycobacterial infection in people with cystic fibrosis in Australia. Results: Applications were submitted to three hospitals and one university HREC to conduct our study at 16 hospital sites, HREC approval took from 16 to 79 days (median 28). Subsequent site‐specific governance approval at 15 hospital sites took 23–225 days (median 83). The entire process of gaining ethical and governance approval to conduct the study at 16 sites took 24 months at an estimated cost of AU$56000 (US$ 42 000). Conclusion: Lengthy governance approval processes negate benefits gained from centralised ethics review under the NMA. [ABSTRACT FROM AUTHOR]

Published
2019
Full Text
View/download PDF

44. Trial Refresh: A Case for an Adaptive Platform Trial for Pulmonary Exacerbations of Cystic Fibrosis.

Author

Schultz, Andre, Marsh, Julie A., Saville, Benjamin R., Norman, Richard, Middleton, Peter G., Greville, Hugh W., Bellgard, Matthew I., Berry, Scott M., and Snelling, Tom

Subjects
CYSTIC fibrosis, CLINICAL trials, CONSUMER preferences, EARLY death, BURKHOLDERIA infections, LUNG diseases, PSEUDOMONAS aeruginosa infections
Abstract

Cystic fibrosis is a genetic disease typically characterized by progressive lung damage and premature mortality. Pulmonary exacerbations, or flare-ups of the lung disease, often require hospitalization for intensive treatment. Approximately 25% of patients with cystic fibrosis do not recover their baseline lung function after pulmonary exacerbations. There is a relative paucity of evidence to inform treatment strategies for exacerbations. Compounding this lack of evidence, there are a large number of treatment options already as well as becoming available. This results in significant variability between medication regimens prescribed by different physicians, treatment centers and regions with potentially adverse impact to patients. The conventional strategy is to undertake essential randomized clinical trials to inform treatment decisions and improve outcomes for patients with exacerbations. However, over the past several decades, clinical trials have generally failed to provide information critical to improved treatment and management of exacerbations. Bayesian adaptive platform trials hold the promise of addressing clinical uncertainties and informing treatment. Using modeling and response adaptive randomization, they allow for the evaluation of multiple treatments across different management domains, and progressive improvement in patient outcomes throughout the course of the trial. Bayesian adaptive platform trials require substantial amounts of preparation. Basic preparation includes extensive stakeholder involvement including elicitation of consumer preferences and clinician understanding of the research topic, defining the research questions, determining the best outcome measures, delineating study sub-groups, in depth statistical modeling, designing end-to-end digital solutions seamlessly supporting clinicians, researchers and patients, constructing randomisation algorithms and importantly, defining pre-determined intra-study end-points. This review will discuss the motivation and necessary steps required to embark on a Bayesian adaptive platform trial to optimize medication regimens for the treatment of pulmonary exacerbations of cystic fibrosis. [ABSTRACT FROM AUTHOR]

Published
2019
Full Text
View/download PDF

45. Reply to Turnbull and to Hulme.

Author

Breuer, Oded, Schultz, Andre, Turkovic, Lidija, de Klerk, Nicholas, Keil, Anthony D., Brennan, Siobhain, Harrison, Joanne, Robertson, Colin, Robinson, Philip J., Sly, Peter D., Ranganathan, Sarath, Stick, Stephen M., and Caudri, Daan

Subjects
ASPERGILLOSIS, CYSTIC fibrosis in children, RESPIRATORY infections in children
Published
2020
Full Text
View/download PDF

47. Proceedings of the 23rd Paediatric Rheumatology European Society Congress: part two: Genoa, Italy. 28 September – 01 October 2016

Author

Lomakina, Olga, Alekseeva, Ekaterina, Valieva, Sania, Bzarova, Tatiana, Nikishina, Irina, Zholobova, Elena, Rodionovskaya, Svetlana, Kaleda, Maria, Nakagishi, Yasuo, Shimizu, Masaki, Mizuta, Mao, Yachie, Akihiro, Sugita, Yuko, Okamoto, Nami, Shabana, Kousuke, Murata, Takuji, Tamai, Hiroshi, Smith, Eve M., Yin, Peng, Jorgensen, Andrea L., Beresford, Michael W., Eleuteri, Antonio, Goilav, Beatrice, Lewandowski, Laura, Phuti, Angel, Wahezi, Dawn, Rubinstein, Tamar, Jones, Caroline, Newland, Paul, Marks, Stephen, Corkhill, Rachel, Ekdawy, Diana, Pilkington, Clarissa, Tullus, Kjell, Putterman, Chaim, Scott, Chris, Fisher, Antony C., Jorgensen, Andrea, Batu, Ezgi Deniz, Kosukcu, Can, Taskiran, Ekim, Akman, Sema, Ozturk, Kubra, Sozeri, Betul, Unsal, Erbil, Ekinci, Zelal, Bilginer, Yelda, Alikasifoglu, Mehmet, Ozen, Seza, Lythgoe, Hanna, Brunner, Hermine I., Gulati, Gaurav, Jones, Jordan T., Altaye, Mekibib, Eaton, Jamie, Difrancesco, Mark, Yeo, Joo Guan, Leong, Jingyao, Bathi, Loshinidevi D/O Thana, Arkachaisri, Thaschawee, Albani, Salvatore, Abdelrahman, Nagla, Beresford, Michael W, Leone, Valentina, Groot, Noortje, Shaikhani, D., Bultink, I. E. M., Bijl, M., Dolhain, R. J. E. M., Teng, Y. K. O., Zirkzee, E., de Leeuw, K., Fritsch-Stork, R., Kamphuis, S. S. M., Wright, Rachael D., Abdawani, Reem, Al Shaqshi, Laila, Al Zakwani, Ibrahim, Gormezano, Natali W., Kern, David, Pereira, Oriany L., Esteves, Gladys C. C., Sallum, Adriana M., Aikawa, Nadia E., Pereira, Rosa M., Silva, Clovis A., Bonfa, Eloisa, Beckmann, Jessica, Bartholomä, Nora, Venhoff, Nils, Henneke, Philipp, Salzer, Ulrich, Janda, Ales, Boteanu, Alina Lucica, Corral, Sandra Garrote, Giraldo, Alberto Sifuentes, Gámir, Mariluz Gámir, Mendoza, Antonio Zea, Adrovic, Amra, Dedeoglu, Reyhan, Sahin, Sezgin, Barut, Kenan, Koka, Aida, Oztunc, Funda, Kasapcopur, Ozgur, Rodriguez-Lozano, Ana Luisa, Rivas-Larrauri, Francisco, de la Puente, Silvestre García, Alves, Andressa G. F., Giacomin, Maria F. D. A., Farhat, Juliana, Braga, Alfésio L. F., Sallum, Adriana M. E., Campos, Lúcia M. D. A., Pereira, Luiz A. A., Lichtenfels, Ana J. D. F. C., Silva, Clóvis A., Farhat, Sylvia C. L., Acar, Banu, Ozcakar, Z. Birsin, Çakar, Nilgün, Uncu, Nermin, Gür, Gökçe, Özdel, Semanur, Yalçınkaya, Fatoş, Scott, Christiaan, Brice, Nicky, Nourse, Peter, Arango, Christine, Mosquera, Angela C., Malagon, Clara, Sakamoto, Ana P., Silva, Marco F. C. D., Lopes, Ananadreia S., Russo, Gleice C. S., Sallum, Adriana E. M., Kozu, Katia, Bonfá, Eloisa, Saad-Magalhães, Claudia, Pereira, Rosa M. R., Len, Claudio A., Terreri, Maria T., Suri, Deepti, Didel, Siyaram, Rawat, Amit, Singh, Surjit, Maritsi, Despoina, Onoufriou, MArgarita, Vougiouka, Olga, Tsolia, Maria, Bosak, Edi Paleka, Vidović, Mandica, Lamot, Mirta, Lamot, Lovro, Harjaček, Miroslav, Van Nieuwenhove, Erika, Liston, Adrian, Wouters, Carine, Tahghighi, Fatemeh, Ziaee, Vahid, Raeeskarami, Seid-Reza, Aguiar, Francisca, Pereira, Sandra, Rodrigues, Mariana, Moura, Cláudia, Rocha, Gustavo, Guimarães, Hercília, Brito, Iva, Fonseca, Rita, Horneff, Gerd, Klein, Ariane, Minden, Kirsten, Huppertz, Hans-Iko, Weller-Heinemann, Frank, Kuemmerle-Deschner, Jasmin, Haas, J-Peter, Hospach, Anton, Menendez-Castro, Ricardo, Huegle, Boris, Haas, Johannes-Peter, Swart, Joost, Giancane, Gabriella, Bovis, Francesca, Castagnola, Elio, Groll, Andreas, Lovell, Daniel J., Wolfs, Tom, Hofer, Michael, Panaviene, Violeta, Nielsen, Susan, Anton, Jordi, Uettwiller, Florence, Stanevicha, Valda, Trachana, Maria, Marafon, Denise Pires, Ailioaie, Constantin, Tsitsami, Elena, Kamphuis, Sylvia, Herlin, Troels, Doležalová, Pavla, Susic, Gordana, Flatø, Berit, Sztajnbok, Flavio, Pistorio, Angela, Martini, Alberto, Wulffraat, Nico, Ruperto, Nicolino, Gattorno, Marco, Brucato, Antonio, Finetti, Martina, Lazaros, George, Maestroni, Silvia, Carraro, Mara, Cumetti, Davide, Carobbio, Alessandra, Lorini, Monia, Rimini, Alessandro, Marcolongo, Renzo, Valenti, Anna, Erre, Gian Luca, Belli, Riccardo, Gaita, Fiorenzo, Sormani, Maria Pia, Imazio, Massimo, Abinun, Mario, Smith, Nicola, Rapley, Tim, McErlane, Flora, Kearsley-Fleet, Lianne, Hyrich, Kimme L., Foster, Helen, Tzaribachev, Nikolay, Zeft, Andrew, Cimaz, Rolando, Bohnsack, John, Griffin, Thomas, Carrasco, Ruy, Dare, Jason, Foeldvari, Ivan, Vehe, Richard, Simon, Teresa, Brunner, Hermine, Verazza, S., Davì, S., Consolaro, A., Insalaco, A., Gerloni, V., Cimaz, R., Zulian, F., Pastore, S., Corona, F., Conti, G., Barone, P., Cattalini, M., Cortis, E., Breda, L., Olivieri, A. N., Civino, A., Podda, R., Rigante, D., La Torre, F., D’Angelo, G., Jorini, M., Gallizzi, R., Maggio, M. C., Consolini, R., De Fanti, A., Alpigiani, M. G., Martini, A., Ravelli, A., Kısaarslan, Aysenur Pac, Gunduz, Zubeyde, Dusunsel, Ruhan, Dursun, Ismail, Poyrazoglu, Hakan, Kuchinskaya, Ekaterina, Abduragimova, Farida, Kostik, Mikhail, Sundberg, Erik, Omarsdottir, Soley, Klevenvall, Lena, Erlandsson-Harris, Helena, Basbozkurt, Gokalp, Erdemli, Ozge, Simsek, Dogan, Yazici, Fatih, Karsioglu, Yildirim, Tezcaner, Aysen, Keskin, Dilek, Ozkan, Huseyin, Acikel, Cengizhan, Demirkaya, Erkan, Orbán, Ilonka, Sevcic, Krisztina, Brodszky, Valentin, Kiss, Emese, Tekko, Ismaiel A., Rooney, Madeleine, McElnay, James, Taggart, Cliff, McCarthy, Helen, Donnelly, Ryan F., Slatter, Mary, Nademi, Zohreh, Friswell, Mark, Jandial, Sharmila, Flood, Terence, Hambleton, Sophie, Gennery, Andrew, Cant, Andrew, Duong, Phoi-Ngoc, Koné-Paut, Isabelle, Filocamo, Giovanni, Gamir, María Luz, Sanner, Helga, Carenini, Laura, Topdemir, Mesut, Karslioglu, Yildirim, Gok, Faysal, Tsurikova, Nadezhda, Ligostaeva, Elena, Ramchurn, Navdha R., Kostareva, O., Nikishina, I., Arsenyeva, S., Rodionovskaya, S., Kaleda, M., Alexeev, D., Dursun, Ismail Dursun, Murias, Sara, Barral, Estefania, Alcobendas, Rosa, Enriquez, Eugenia, Remesal, Agustin, de Inocencio, Jaime, Castro, Tania M., Lotufo, Simone A., Freye, Tatjana, Carlomagno, Raffaella, Zumbrunn, Thomas, Bonhoeffer, Jan, Schneider, Elvira Cannizzaro, Kaiser, Daniela, Hofer, Michaël, Hentgen, Véronique, Woerner, Andreas, Schwarz, Tobias, Klotsche, Jens, Niewerth, Martina, Ganser, Gerd, Jeyaratnam, Jerold, ter Haar, Nienke, Rigante, Donato, Dedeoglu, Fatma, Baris, Ezgi, Vastert, Sebastiaan, Frenkel, Joost, Hausmann, Jonathan S., Lomax, Kathleen G., Shapiro, Ari, Durrant, Karen L., Brogan, P. A., Hofer, M., Kuemmerle-Deschner, J. B., Lauwerys, B., Speziale, A., Leon, K., Wei, X., Laxer, R. M., Signa, Sara, Rusmini, Marta, Campione, Elena, Chiesa, Sabrina, Grossi, Alice, Omenetti, Alessia, Caorsi, Roberta, Viglizzo, Gianmaria, Ceccherini, Isabella, Federici, Silvia, Lachmann, Helen, Ruperto, Nicola, Vanoni, Federica, Gomes, Sonia Melo, Omoyinmi, Ebun, Arostegui, Juan I., Gonzalez-Roca, Eva, Eleftheriou, Despina, Klein, Nigel, Brogan, Paul, Volpi, Stefano, Santori, Elettra, Picco, Paolo, Pastorino, Claudia, Rice, Gillian, Tesser, Alessandra, Crow, Yanick, Candotti, Fabio, Sinoplu, Ada B., Yucel, Gozde, Pamuk, Gizem, Damian, Laura O., Lazea, Cecilia, Sparchez, Mihaela, Vele, Paulina, Muntean, Laura, Albu, Adriana, Rednic, Simona, Lazar, Calin, Mendonça, Leonardo O., Pontillo, Alessandra, Kalil, Jorge, Castro, Fabio M., Barros, Myrthes T., Pardeo, Manuela, Messia, Virginia, De Benedetti, Fabrizio, Insalaco, Antonella, Malighetti, Giorgia, Gorio, Chiara, Ricci, Francesca, Parissenti, Ilaria, Montesano, Paola, Bonafini, Barbara, Medeghini, Veronica, Cattalini, Marco, Giordano, Lucio, Zani, Giulia, Ferraro, Rosalba, Vairo, Donatella, Giliani, Silvia, Maggio, Maria Cristina, Luppino, Girolamo, Corsello, Giovanni, Fernandez, Maria Isabel Gonzalez, Montesinos, Berta Lopez, Vidal, Adriana Rodriguez, Gorospe, Juan I. Arostegui, Penades, Inmaculada Calvo, Rafiq, Nadia K., Wynne, Karen, Hussain, Khalid, Brogan, Paul A., Ang, Elizabeth, Ng, Nicholas, Kacar, Ayla, Gucenmez, Ozge Altug, Makay, Balahan, Unsal, Sevket Erbil, Sahin, Yasin, Kutlu, Tufan, Cullu-Cokugras, Fugen, Ayyildiz-Civan, Hasret, Erkan, Tulay, Al Zuhbi, Sana, Abdalla, Eiman, Russo, Ricardo A., Katsicas, María M., Minoia, Francesca, Ravelli, Angelo, Bhattad, Sagar, Gupta, Anju, Pandiarajan, Vignesh, Nada, Ritambhra, Tiewsoh, Kaara, Hawkins, Philip, Rowczenio, Dorota, Fingerhutova, Sarka, Franova, Jana, Prochazkova, Leona, Hlavackova, Eva, Dolezalova, Pavla, Evrengül, Havva, Yüksel, Selçuk, Doğan, Mustafa, Gürses, Dolunay, Evrengül, Harun, De Pauli, Silvia, Pastore, Serena, Bianco, Anna Monica, Severini, Giovanni Maria, Taddio, Andrea, Tommasini, Alberto, Salugina, Svetlana O., Fedorov, Evgeny, Kamenets, Elena, Zaharova, Ekaterina, Sleptsova, Tatiana, Alexeeva, Ekaterina, Savostyanov, Kirill, Pushkov, Alexander, Bzarova, Tatyana, Valieva, Saniya, Denisova, Rina, Isayeva, Kseniya, Chistyakova, Evgeniya, Soloshenko, Margarita, Kaschenko, Elena, Kaneko, Utako, Imai, Chihaya, Saitoh, Akihiko, Teixeira, Vitor A., Ramos, Filipa O., Costa, Manuela, Aviel, Yonatan Butbul, Fahoum, Shafe, Brik, Riva, Özçakar, Zeynep Birsin, Celikel, Banu Acar, Yalcinkaya, Fatos, Schiappapietra, Benedetta, Davi’, Sergio, Mongini, Federica, Giannone, Luisa, Bava, Cecilia, Alpigiani, Maria Giannina, Consolaro, Alessandro, Lazarevic, Dragana S., Vojinovic, Jelena, Basic, Jelena, Muratore, Valentina, Marzetti, Valentina, Quilis, Neus, Benavente, Belen Serrano, Alongi, Alessandra, Civino, Adele, Quartulli, Lorenzo, Januskeviciute, Giedre, van Dijkhuizen, Pieter, Groot, N., van Dijk, W., Kardolus, A., Suárez, Raul Gutiérrez, Nordal, Ellen B., Rypdal, Veronika G., Berntson, Lillemor, Ekelund, Maria, Aalto, Kristiina, Peltoniemi, Suvi, Zak, Marek, Glerup, Mia, Arnstad, Ellen D., Fasth, Anders, Rygg, Marite, Duarte, Ana Catarina, Sousa, Sandra, Teixeira, Lídia, Cordeiro, Ana, Santos, Mª José, Mourão, Ana Filipa, Santos, Maria José, Eusébio, Mónica, Lopes, Ana, Oliveira-Ramos, Filipa, Salgado, Manuel, Estanqueiro, Paula, Melo-Gomes, José, Martins, Fernando, Costa, José, Furtado, Carolina, Figueira, Ricardo, Branco, Jaime C., Fonseca, João E., Canhão, Helena, Mourão, Ana F., Santos, Maria Jose, Coda, Andrea, Cassidy, Samuel, West, Kerry, Hendry, Gordon, Grech, Debra, Jones, Julie, Hawke, Fiona, Grewal, Davinder Singh, Foley, Charlene, Killeen, Orla, MacDermott, Emma, Veale, Douglas, Fearon, Ursula, Konukbay, Dilek, Tarakci, Ela, Arman, Nilay, Şahin, Sezgin, Munro, Jane, Morgan, Esi, Riebschleger, Meredith, Horonjeff, Jennifer, Strand, Vibeke, Bingham, Clifton, Collante, Ma. Theresa M., Ganeva, Margarita, Stefanov, Stefan, Telcharova, Albena, Mihaylova, Dimitrina, Saraeva, Radoslava, Tzveova, Reni, Kaneva, Radka, Tsakova, Adelina, Temelkova, Katya, Picarelli, Maria Mercedes C., Danzmann, Luiz C., Barbé-Tuana, Florencia, Grun, Lucas K., Jones, Marcus H., Frković, Marijan, Ištuk, Karla, Birkić, Ika, Sršen, Saša, Jelušić, Marija, Easton, Alan, Quarmby, Rachael, Khubchandani, Raju, Chan, Mercedes, Srp, Radoslav, Kobrova, Katerina, Nemcova, Dana, Hoza, Jozef, Uher, Michal, Saifridova, Melania, Linkova, Lenka, Charuvanij, Sirirat, Leelayuwattanakul, Isree, Pacharapakornpong, Thita, Vallipakorn, Sakda A.-O., Lerkvaleekul, Butsabong, Vilaiyuk, Soamarat, Lanni, Stefano, Davì, Sergio, Cron, Randy Q., Passarelli, Chiara, Pisaneschi, Elisa, Novelli, Antonio, Bracaglia, Claudia, Caiello, Ivan, de Graaf, Kathy, Guilhot, Florence, Ferlin, Walter, Schulert, Grant, Grom, Alexi A., Nelson, Robert, de Min, Cristina, Holzinger, Dirk, Kessel, Christoph, Fall, Ndate, Grom, Alexei, de Jager, Wilco, Strippoli, Raffaele, Horne, Anna, Ehl, Stephan, Ammann, Sandra, Lehmberg, Kai, Beutel, Karin, Foell, Dirk, Horne, AnnaCarin, Pagani, Laura, Espada, Graciela, Gao, Yi-jin, Shenoi, Susan, Weitzman, Sheila, Prencipe, Giusi, Pascarella, Antonia, Ferlin, Walter G., Chatel, Laurence, Jacqmin, Philippe, De Graaf, Kathy, Ballabio, Maria, Johnson, Zoë, Lapeyre, Geneviève, de Benedetti, Fabrizio, Cristina, de Min, Wakiguchi, Hiroyuki, Hasegawa, Shunji, Hirano, Reiji, Okazaki, Fumiko, Nakamura, Tamaki, Kaneyasu, Hidenobu, Ohga, Shouichi, Yamazaki, Kazuko, Nozawa, Tomo, Kanetaka, Taichi, Ito, Shuichi, Yokota, Shumpei, McLellan, Kirsty, MacGregor, Ishbel, Martin, Neil, Davidson, Joyce, Hansmann, Sandra, Eikelberg, Andreas, Haug, Iris, Schuller, Sabrina, Benseler, Susanne M., Nazarova, Liliia S., Danilko, Kseniia V., Malievsky, Viktor A., Viktorova, Tatiana V., Mauro, Angela, Barnicoat, Angela, Hurst, Jane, Canham, Nathalie, Lacassagne, Sandrine, Wiener, Anastasia, Hügle, Boris, Denecke, Bernd, Costa-Filho, Ivan, Haas, Johannes Peter, Tenbrock, Klaus, Popp, David, Boltjes, Arjan, Rühle, Frank, Herresthal, Stefanie, van Wijk, Femke, Schultze, Joachim, Stoll, Monika, Klotz, Luisa, Vogl, Thomas, Roth, Johannes, Quesada-Masachs, Estefania, de la Sierra, Daniel Álvarez, Prat, Marina Garcia, Sánchez, Ana M. Marín, Borrell, Ricardo Pujol, Barril, Sara Marsal, Gallo, Mónica Martínez, Caballero, Consuelo Modesto, Chyzheuskaya, Iryna, Byelyaeva, Lyudmyla M., Filonovich, Rostislav M., Khrustaleva, Helena K., Zajtseva, Larisa I., Yuraga, Tamara M., Giner, Thomas, Hackl, Lukas, Albrecht, Julia, Würzner, Reinhard, Brunner, Juergen, Minute, Marta, Parentin, Fulvio, Nocerino, Agostino, Nørgaard, Mette, Alberdi-Saugstrup, Mikel, Zak, Marek S., Nielsen, Susan M., Nordal, Ellen, Müller, Klaus G., Avramovič, Mojca Zajc, Dolžan, Vita, Toplak, Nataša, Avčin, Tadej, Ruperto, N., Lovell, D. J., Wallace, C., Toth, M., Foeldvari, I., Bohnsack, J., Milojevic, D., Rabinovich, C., Kingsbury, D., Marzan, K., Quartier, P., Minden, K., Chalom, E., Horneff, G., Kuester, R. M., Dare, J., Heinrich, M., Kupper, H., Kalabic, J., Brunner, H. I., Burgos-Vargas, Ruben, Constantin, Tamas, Dehoorne, Joke, Stanevica, Valda, Kobusinska, Katarzyna, Zuber, Zbigniew, Mouy, Richard, Rumba-Rozenfelde, Ingrida, Job-Deslandre, Chantal, Pederson, Ronald, Bukowski, Jack, Hinnershitz, Tina, Vlahos, Bonnie, Keskitalo, Paula, Kangas, Salla, Vähäsalo, Paula, Valencia, Raul A. Chavez, Martino, David, Ponsonby, Anne-Louise, Chiaroni-Clarke, Rachel, Meyer, Braydon, Allen, Roger C., Akikusa, Jonathan D., Craig, Jeffrey M., Saffrey, Richard, Ellis, Justine A., Wallace, Carol, Uziel, Yosef, Sterba, Gary, Schneider, Rayfel, Russo, Ricardo, Ramanan, Athimalaipet V., Schmid, Jana Pachlopnik, Nichols, Kim E, Miettunen, Paivi, Kitoh, Toshiyuki, Ilowite, Norman T., Henter, Jan-Inge, Grom, Alexei A, Behrens, Edward M., Avcin, Tadej, Aricò, Maurizio, Grevich, Sriharsha, Lee, Peggy, Ringold, Sarah, Leroux, Brian, Leahey, Hannah, Yuasa, Megan, Foster, Jessica, Sokolove, Jeremy, Lahey, Lauren, Robinson, William, Newson, Joshua, Stevens, Anne, Shoop, Stephanie J. W., Verstappen, Suzanne M. M., Thomson, Wendy, McDonagh, Janet E., Beukelman, Timothy, Kimura, Yuki, Natter, Marc, Ilowite, Norm, Mieszkalski, Kelly, Burrell, Grendel, Best, Brian, Bristow, Helen, Carr, Shannon, Dennos, Anne, Kaufmann, Rachel, Schanberg, Laura, Simonini, Gabriele, Lancini, Francesca, Gerbaux, Margaux, Lê, Phu-Quoc, Goffin, Laurence, Badot, Valérie, La, Céline, Caspers, Laure, Willermain, François, Ferster, Alina, Ceci, Maria, Licciardi, Francesco, Turco, Marco, Santarelli, Francesca, Montin, Davide, Toppino, Claudia, Alizzi, Clotilde, Papia, Bruno, Vergara, Beatrice, Corpora, Umberto, Messina, Luca, Tsinti, Maria, Dermentzoglou, Vasiliko, Tziavas, Panagiotis, Perica, Marija, Bukovac, Lana Tambić, Çakan, Mustafa, Ayaz, Nuray Aktay, Keskindemirci, Gonca, Lang, Michael, Laing, Catherine, Benseler, Susanne, Gerschman, Tommy, Luca, Nadia, Schmeling, Heinrike, Dropol, Anastasia, Taiani, Jaymi, Johnson, Nicole, Rusted, Brian, Nalbanti, Panagiota, Pratsidou, Polyxeni, Pardalos, Grigoris, Tzimouli, Vasiliki, Taparkou, Anna, Stavrakidou, Maria, Papachristou, Fotios, Kanakoudi-Tsakalidou, Florence, Bale, Peter, Robinson, Emily, Palman, Jason, Ralph, Elizabeth, Gilmour, Kimberly, Heard, Clare, Wedderburn, Lucy R., Barrense-Dias, Yara, Gregory, Antonarakis, Amira, Dhouib, Paolo, Scolozzi, Sylviane, Hanquinet, Michaël, Hofer, Panko, Nataliya, Shokry, Salah, Rakovska, Liudmila, Pino, Sally, Diaz-Maldonado, Adriana, Guarnizo, Pilar, Torreggiani, Sofia, Cressoni, Paolo, Garagiola, Umberto, Di Landro, Giancarla, Farronato, Giampietro, Corona, Fabrizia, Bell, Samantha, Bhatti, Parveen, Nelson, Lee, Mueller, Beth A., Simon, T. A., Baheti, A., Ray, N., Guo, Z., Hazra, Anasuya, Stock, Thomas, Wang, Ronnie, Mebus, Charles, Alvey, Christine, Lamba, Manisha, Krishnaswami, Sriram, Conte, Umberto, Wang, Min, Kingsbury, Daniel, Koskova, Elena, Smolewska, Elzbieta, Vehe, Richard K., Lovell, Daniel, Kubota, Tomohiro, Yasumura, Junko, Kizawa, Toshitaka, Yashiro, Masato, Yamatou, Tsuyoshi, Yamasaki, Yuichi, Takei, Syuji, Kawano, Yoshifumi, Nykvist, Ulrika Järpemo, Magnusson, Bo, Wicksell, Rikard, Palmblad, Karin, Olsson, Gunnar L., Modaressi, Mohammadreza, Moradinejad, Mohammad-Hassan, Seraya, Valentina, Vitebskaya, Alisa, Moshe, Veronica, Amarilyo, Gil, Harel, Liora, Hashkes, Phillip J, Mendelson, Amir, Rabinowicz, Noa, Reis, Yonit, Dāvidsone, Zane, Lazareva, Arina, Šantere, Ruta, Bērziņa, Dace, Staņēviča, Valda, Varnier, Giulia Camilla, Maillard, Susan, Ferrari, Cristina, Zaffarano, Silvia, Wienke, Judith, Enders, Felicitas Bellutti, van den Hoogen, Lucas L., Mertens, Jorre S., Radstake, Timothy R., Hotten, Henny G., Fritsch, Ruth, Wedderburn, Lucy, Nistala, Kiran, Prakken, Berent, van Royen-Kerkhof, Annet, Alhemairi, Mohammad, Muzaffer, Mohammed, Van Dijkhuizen, Pieter, Deakin, Claire T., Simou, Stefania, De Iorio, Maria, Wu, Qiong, Amin, Tania, Dossetter, Lee, Campanilho-Marques, Raquel, Deakin, Claire, Pilkington, Clarissa A., Rosina, Silvia, Soponkanaporn, Sirisucha, Arıcı, Zehra S., Tuğcu, Gökçen D., Batu, Ezgi D., Sönmez, Hafize E., Doğru-Ersöz, Deniz, Talim, Beril, Kiper, Nural, Özen, Seza, Solyom, Alexander, Batu, Ezgi, Mitchell, John, Kariminejad, Ariana, Hadipour, Fatemeh, Hadipour, Zahra, Torcoletti, Marta, Agostoni, Carlo, Di Rocco, Maja, Tanpaiboon, Pranoot, Superti-Furga, Andrea, Bonafé, Luisa, Arslan, Nur, Guelbert, Norberto, Ehlert, Karoline, Grigelioniene, Giedre, Puri, Ratna, Schuchman, Edward, Gomez, Pilar, Gonzalez, Tatiana, Yepez, Ricardo, Vargas, Camilo, Fernanda, Falcini, Lepri, Gemma, Ferrari, Alessandra, Matucci-Cerinic, Marco, Meini, Antonella, Moneta, Gian Marco, Marasco, Emiliano, Nicolai, Rebecca, Bracci-Laudiero, Luisa, Kopchak, Olga, Mushkin, Alexander, Maletin, Alexey, Mosquera, Catalina, Amorim, Rita A., Molina, Juliana, Moreira, Gustavo, Santos, Flávia H., Fraga, Melissa, Keppeke, Livia, Silva, Vanessa M., Hirotsu, Camila, Tufik, Sergio, Terreri, Maria Teresa, Braga, Vinícius L., Fonseca, Maria Beatriz, Schinzel, Vania, Terreri, Maria Teresa R., Jorge, Liliana, Guerra, Liana, Junior, Edson Amaro, Castiglione, Maria Cristina, Tricarico, Alessandra, Boulter, Emily, Schultz, Andre, Murray, Kevin, Falcini, Fernanda, Stagi, Stefano, Bellucci, Eleonora, Grein, Ingrid H. R., Pileggi, Gecilmara, Pinto, Natália B. F., de Oliveira, Aline L., Belyaeva, Lyudmila, Filonovich, Rostislav, Khrustaleva, Helena, Zajtseva, Larisa, Ilisson, Jaanika, Pruunsild, Chris, Gilliaux, Olivier, Corazza, Francis, Lelubre, Christophe, Morel, Zoilo, C, Claudia Saad-Magalhães, Lira, Luis, Ladino, Mabel, Eraso, Ruth, Arroyo, Ivonne, Silva, Clovis, and Rose, Carlos

Published
2017
Full Text
View/download PDF

48. SAMMI: a semi-automated tool for the visualization of metabolic networks.

Author

Schultz, Andre and Akbani, Rehan

Abstract

Summary Here we present a browser-based Semi-Automated Metabolic Map Illustrator (SAMMI) for the visualization of metabolic networks. While automated features allow for easy network partitioning, navigation, and node positioning, SAMMI also offers a wide array of manual map editing features. This combination allows for fast, context-specific visualization of metabolic networks as well as the development of standardized, large-scale, visually appealing maps. The implementation of SAMMI with popular constraint-based modeling toolboxes also allows for effortless visualization of simulation results of genome-scale metabolic models. Availability and implementation SAMMI has been implemented as a standalone web-based tool and as plug-ins for the COBRA and COBRApy toolboxes. SAMMI and its COBRA plugins are available under the GPL 3.0 license and are available along with documentation, tutorials, and source code at www.SammiTool.com. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Published
2020
Full Text
View/download PDF

50. Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines.

Author

Zhao, Wei, Li, Jun, Chen, Mei-Ju M., Luo, Yikai, Ju, Zhenlin, Nesser, Nicole K., Johnson-Camacho, Katie, Boniface, Christopher T., Lawrence, Yancey, Pande, Nupur T., Davies, Michael A., Herlyn, Meenhard, Muranen, Taru, Zervantonakis, Ioannis K., von Euw, Erika, Schultz, Andre, Kumar, Shwetha V., Korkut, Anil, Spellman, Paul T., and Akbani, Rehan

Subjects
*CELL lines, *CANCER cells, *PROTEIN microarrays, *PROTEINS, *PROTEIN drugs
Abstract

Perturbation biology is a powerful approach to modeling quantitative cellular behaviors and understanding detailed disease mechanisms. However, large-scale protein response resources of cancer cell lines to perturbations are not available, resulting in a critical knowledge gap. Here we generated and compiled perturbed expression profiles of ∼210 clinically relevant proteins in >12,000 cancer cell line samples in response to ∼170 drug compounds using reverse-phase protein arrays. We show that integrating perturbed protein response signals provides mechanistic insights into drug resistance, increases the predictive power for drug sensitivity, and helps identify effective drug combinations. We build a systematic map of "protein-drug" connectivity and develop a user-friendly data portal for community use. Our study provides a rich resource to investigate the behaviors of cancer cells and the dependencies of treatment responses, thereby enabling a broad range of biomedical applications. • A large collection of cancer cell line protein responses to drug perturbations • Perturbed protein responses greatly increase predictive power for drug sensitivity • A systematic map of protein-drug connectivity was built based on response profiles • A user-friendly, interactive data portal was developed for community use Zhao et al. profile the protein responses of a large collection of cancer cell lines to drug perturbations using the RPPA platform and build a systematic protein-drug connectivity map. The integration of perturbed protein responses provides better prediction of drug sensitivity and insights into drug-resistance mechanisms and combination therapies. [ABSTRACT FROM AUTHOR]

Published
2020
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results