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6. Analysis of germline-driven ancestry-associated gene expression in cancers

Author

Chambwe, Nyasha, Sayaman, Rosalyn W, Hu, Donglei, Huntsman, Scott, Network, The Cancer Genome Analysis, Carrot-Zhang, Jian, Berger, Ashton C, Han, Seunghun, Meyerson, Matthew, Damrauer, Jeffrey S, Hoadley, Katherine A, Felau, Ina, Demchok, John A, Mensah, Michael KA, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Knijnenburg, Theo A, Robertson, A Gordon, Yau, Christina, Benz, Christopher, Huang, Kuan-lin, Newberg, Justin Y, Frampton, Garrett M, Mashl, R Jay, Ding, Li, Romanel, Alessandro, Demichelis, Francesca, Zhou, Wanding, Laird, Peter W, Shen, Hui, Wong, Christopher K, Stuart, Joshua M, Lazar, Alexander J, Le, Xiuning, Oak, Ninad, Kemal, Anab, Caesar-Johnson, Samantha, Zenklusen, Jean C, Ziv, Elad, Beroukhim, Rameen, and Cherniack, Andrew D

Subjects
Biological Sciences, Health Sciences, Genetics, Human Genome, Biotechnology, Cancer, Good Health and Well Being, Gene Expression, Germ Cells, Humans, Neoplasms, Quantitative Trait Loci, RNA, Messenger, Cancer Genome Analysis Network, Bioinformatics, Computer sciences, Genomics, RNAseq, Sequence analysis
Abstract

Differential mRNA expression between ancestry groups can be explained by both genetic and environmental factors. We outline a computational workflow to determine the extent to which germline genetic variation explains cancer-specific molecular differences across ancestry groups. Using multi-omics datasets from The Cancer Genome Atlas (TCGA), we enumerate ancestry-informative markers colocalized with cancer-type-specific expression quantitative trait loci (e-QTLs) at ancestry-associated genes. This approach is generalizable to other settings with paired germline genotyping and mRNA expression data for a multi-ethnic cohort. For complete details on the use and execution of this protocol, please refer to Carrot-Zhang et al. (2020), Robertson et al. (2021), and Sayaman et al. (2021).

Published
2022

10. The Imaging X-Ray Polarimetry Explorer (IXPE): Pre-Launch

Author

Weisskopf, Martin C., Soffitta, Paolo, Baldini, Luca, Ramsey, Brian D., O'Dell, Stephen L., Romani, Roger W., Matt, Giorgio, Deininger, William D., Baumgartner, Wayne H., Bellazzini, Ronaldo, Costa, Enrico, Kolodziejczak, Jeffery J., Latronico, Luca, Marshall, Herman L., Muleri, Fabio, Bongiorno, Stephen D., Tennant, Allyn, Bucciantini, Niccolo, Dovciak, Michal, Marin, Frederic, Marscher, Alan, Poutanen, Juri, Slane, Pat, Turolla, Roberto, Kalinowski, William, Di Marco, Alessandro, Fabiani, Sergio, Minuti, Massimo, La Monaca, Fabio, Pinchera, Michele, Rankin, John, Sgro', Carmelo, Trois, Alessio, Xie, Fei, Alexander, Cheryl, Allen, D. Zachery, Amici, Fabrizio, Andersen, Jason, Antonelli, Angelo, Antoniak, Spencer, Attina', Primo, Barbanera, Mattia, Bachetti, Matteo, Baggett, Randy M., Bladt, Jeff, Brez, Alessandro, Bonino, Raffaella, Boree, Christopher, Borotto, Fabio, Breeding, Shawn, Brienza, Daniele, Bygott, H. Kyle, Caporale, Ciro, Cardelli, Claudia, Carpentiero, Rita, Castellano, Simone, Castronuovo, Marco, Cavalli, Luca, Cavazzuti, Elisabetta, Ceccanti, Marco, Centrone, Mauro, Citraro, Saverio, Amico, Fabio D', D'Alba, Elisa, Di Gesu, Laura, Del Monte, Ettore, Dietz, Kurtis L., Di Lalla, Niccolo', Di Persio, Giuseppe, Dolan, David, Donnarumma, Immacolata, Evangelista, Yuri, Ferrant, Kevin, Ferrazzoli, Riccardo, Ferrie, MacKenzie, Footdale, Joseph, Forsyth, Brent, Foster, Michelle, Garelick, Benjamin, Gunji, Shuichi, Gurnee, Eli, Head, Michael, Hibbard, Grant, Johnson, Samantha, Kelly, Erik, Kilaru, Kiranmayee, Lefevre, Carlo, Roy, Shelley Le, Loffredo, Pasqualino, Lorenzi, Paolo, Lucchesi, Leonardo, Maddox, Tyler, Magazzu, Guido, Maldera, Simone, Manfreda, Alberto, Mangraviti, Elio, Marengo, Marco, Marrocchesi, Alessandra, Massaro, Francesco, Mauger, David, McCracken, Jeffrey, McEachen, Michael, Mize, Rondal, Mereu, Paolo, Mitchell, Scott, Mitsuishi, Ikuyuki, Morbidini, Alfredo, Mosti, Federico, Nasimi, Hikmat, Negri, Barbara, Negro, Michela, Nguyen, Toan, Nitschke, Isaac, Nuti, Alessio, Onizuka, Mitch, Oppedisano, Chiara, Orsini, Leonardo, Osborne, Darren, Pacheco, Richard, Paggi, Alessandro, Painter, Will, Pavelitz, Steven D., Pentz, Christina, Piazzolla, Raffaele, Perri, Matteo, Pesce-Rollins, Melissa, Peterson, Colin, Pilia, Maura, Profeti, Alessandro, Puccetti, Simonetta, Ranganathan, Jaganathan, Ratheesh, Ajay, Reedy, Lee, Root, Noah, Rubini, Alda, Ruswick, Stephanie, Sanchez, Javier, Sarra, Paolo, Santoli, Francesco, Scalise, Emanuele, Sciortino, Andrea, Schroeder, Christopher, Seek, Tim, Sosdian, Kalie, Spandre, Gloria, Speegle, Chet O., Tamagawa, Toru, Tardiola, Marcello, Tobia, Antonino, Thomas, Nicholas E., Valerie, Robert, Vimercati, Marco, Walden, Amy L., Weddendorf, Bruce, Wedmore, Jeffrey, Welch, David, Zanetti, Davide, and Zanetti, Francesco

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

Scheduled to launch in late 2021, the Imaging X-ray Polarimetry Explorer (IXPE) is a NASA Small Explorer Mission in collaboration with the Italian Space Agency (ASI). The mission will open a new window of investigation - imaging X-ray polarimetry. The observatory features 3 identical telescopes each consisting of a mirror module assembly with a polarization-sensitive imaging X-ray detector at the focus. A coilable boom, deployed on orbit, provides the necessary 4-m focal length. The observatory utilizes a 3-axis-stabilized spacecraft which provides services such as power, attitude determination and control, commanding, and telemetry to the ground. During its 2-year baseline mission, IXPE will conduct precise polarimetry for samples of multiple categories of X-ray sources, with follow-on observations of selected targets.

Published
2021

12. Association of antenatal or neonatal SARS-COV-2 exposure with developmental and respiratory outcomes, and healthcare usage in early childhood: a national prospective cohort study

Author

Mactier, Helen, Draper, Elizabeth, Sharkey, Don, Doherty, Cora, Shorthose, Karen, Venkata, Nagendra, Cooper, Claire, Lee, Claire, Coke, Louise, Cane, Clare, Diaba, Cynthia, Narayanan, Sankara, Ramadan, Ghada, Capell, Alys, Jolley, Dan, Pullen, Jennifer, Wane, Rachel, Ingram, Liz, Garr, Rosaline, Millington, Amy, El-Bokle, Manal, Brock, Paula, Hammond, Bev, Milner, Matthew, Ojha, Shalini, Miller, Sarah, Grigsby, Stephanie, Blunden, Susara, Shephard, Ruth, Williams, Emma, Thyagarajan, Balamurugan, Crowley, Phillippa, Le Doare, Kirsty, Marler, Emily, Sinha, Ajay, Plaatjas, Nicolene, Smith, Dominic, Baker, Jennifer, Ali, Muhammad, Smith, Jennifer, Ranganne, Ranganath, Stanbury, Kate, Scorrer, Tim, LePoidevin, Alison, Westcar, Sharon, Maquinana, Myrna, O'Brien, Clare, Willson, Seren, Simkin, Jessica, Carmichael, Amy, Salter, Laura, Sharma, Bhavna, Dixon, Caroline, Brown, Janet, Jones, Amaryl, Townsend, Kate, Tanton, Emma, Fleming, Paul, Stacey, Fiona, Hutchinson, Richard, Plummer, Laura, Swaminathan, Louise, Bhatia, Charu, Dubber, Rebecca, Dixon, Jenny, Phillipson, Angela, Groombridge, Julie, Benn, Tracey, Johnson, Kathryn, Uryn, Lindsay, Salgia, Sanjay, Frankland, Lisa, Salmon, Caroline, Green, Asharee, Lek, Elizabeth, Rodal-Prieto, Nerea, Grindey, Julie, O'Connor, Grainne, Tebbal, Afaf, Cullinan, Sophie, Sugden, Paula, Piaggio, Umberto, Farmer, Sarah, Tudor, Daisy, Das, Ambalika, Nicholls, Donna, Lea, Charlotte, Bowen, Ruth, Mann, Rebecca, Turner, Georgina, Piyasena, Chinthika, Robinson, Joanna, Neeraj, Jain, Godwin, Gillian, Oduro, Bridget, Fernandez, Ramon, Gurusamy, Kalyana, Pilling, Liz, Mupanemunda, Richard, Didier, Sarah, Ellis, Jessica, James, Anitha, Bohin, Sandie, Bishop, Linda, Satodia, Prakash, Wild, Laura, Banerjee, Jayanta, Elliott, Sian, Forster, Amanda, Demitry, Albert, Kortsalioudaki, Christina, Woodhead, Amy, Barrow, Heather, Kotsia, Efygenia, Barnett, Madeleine, Thompson, Katharine, Jackson, Rebecca, Cornish, Rosie, Daskalopoulou, Zoe, Gale, Chris, Hurd, Madeleine, Johnson, Samantha, Knight, Marian, Kurinczuk, Jennifer J., Woodward, Kathryn, and Chakkarapani, Ela

Published
2024
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13. Emergency front-of-neck access in cardiac arrest: A scoping review

Author

Berg, Katherine M., Böttiger, Bernd W., Chia, Yew Woon, Crowley, Conor, D'Arrigo, Sonia, Deakin, Charles D., Fernando, Shannon M., Garg, Rakesh, Granfeldt, Asger, Grunau, Brian, Hirsch, Karen G., Holmberg, Mathias J., Lavonas, Eric, Leong, Carrie, Kudenchuk, Peter J., Morley, Peter, Moskowitz, Ari, Neumar, Robert, Nicholson, Tonia C., Nikolaou, Nikolaos, Nolan, Jerry P., O'Neil, Brian, Ohshimo, Shinichiro, Parr, Michael, Pocock, Helen, Sandroni, Claudio, Scquizzato, Tommaso, Skrifvars, Markus, Vlok, Neville, Welsford, Michelle, Zelop, Carolyn, Aljanoubi, Mohammed, Almazrua, Abdulkarim A., Johnson, Samantha, Drennan, Ian R, Reynolds, Joshua C., Soar, Jasmeet, and Couper, Keith

Published
2024
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15. ADHD symptoms and diagnosis in adult preterms: systematic review, IPD meta-analysis, and register-linkage study

Author

Robinson, Rachel, Girchenko, Polina, Pulakka, Anna, Heinonen, Kati, Lähdepuro, Anna, Lahti-Pulkkinen, Marius, Hovi, Petteri, Tikanmäki, Marjaana, Bartmann, Peter, Lano, Aulikki, Doyle, Lex W., Anderson, Peter J., Cheong, Jeanie L. Y., Darlow, Brian A., Woodward, Lianne J., Horwood, L. John, Indredavik, Marit S., Evensen, Kari Anne I., Marlow, Neil, Johnson, Samantha, de Mendonca, Marina Goulart, Kajantie, Eero, Wolke, Dieter, and Räikkönen, Katri

Published
2023
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16. Ultra Short Period Planets in K2 III: Neighbors are Common with 13 New Multi-Planet Systems and 10 Newly Validated Planets in Campaigns 0-8, 10

Author

Adams, Elisabeth R., Jackson, Brian, Johnson, Samantha, Ciardi, David R., Cochran, William D., Endl, Michael, Everett, Mark E., Furlan, Elise, Howell, Steve B., Jayanthi, Prasanna, MacQueen, Phillip J., Matson, Rachel A., Partyka-Worley, Ciera, Schlieder, Joshua, Scott, Nicholas J., Stanton, Sevio M., and Ziegler, Carl

Subjects
Astrophysics - Earth and Planetary Astrophysics
Abstract

Using the EVEREST photometry pipeline, we have identified 74 candidate ultra-short-period planets (orbital period P<1 d) in the first half of the K2 data (Campaigns 0-8 and 10). Of these, 33 candidates have not previously been reported. A systematic search for additional transiting planets found 13 new multi-planet systems, doubling the number known and representing a third (32%) of USPs. We also identified 30 companions, which have periods from 1.4 to 31 days (median 5.5 d). A third (36 of 104) of the candidate USPs and companions have been statistically validated or confirmed, 10 for the first time, including 7 USPs. Almost all candidates, and all validated planets, are small (radii Rp<=3 R_E) with a median radius of R_p=1.1 R_E; the validated and confirmed candidates have radii between 0.4 R_E and 2.4 R_E and periods from P=0.18 to 0.96 d. The lack of candidate (a) ultra-hot-Jupiters (R_p>10 R_E) and (b) short-period desert (3<=Rp<=10 R_E) planets suggests that both populations are rare, although our survey may have missed some of the very deepest transits. These results also provide strong evidence that we have not reached a lower limit on the distribution of planetary radius values for planets at close proximity to a star, and suggest that additional improvements in photometry techniques would yield yet more ultra-short-period planets. The large fraction of USPs in known multi-planet systems supports origins models that involve dynamical interactions with exterior planets coupled to tidal decay of the USP orbits., Comment: Accepted to PSJ (5/19/21)

Published
2020

17. Impact of COVID-19 on Access to Laboratories and Human Participants: Exercise Science Faculty Perspectives

Author

Stenson, Mary C., Fleming, Jessica K., Johnson, Samantha L., Caputo, Jennifer L., Spillios, Katherine E., and Mel, Astrid E.

Abstract

Restrictions due to the coronavirus (COVID-19) pandemic impacted the ability of faculty and students in exercise science to work in lab settings with human participants. The purpose of this study was to determine how exercise science faculty were impacted by COVID-19 restrictions with respect to access and use of exercise science lab and research facilities. Of the 100 surveyed participants categorized as requiring access to people and lab spaces (lab-based faculty), 61% (n = 61) reported decreased research productivity with 87% (n = 53) of those faculty in one or more of the following subdisciplines: exercise physiology, clinical exercise physiology, or biomechanics. Of all lab-based faculty, 40% (n = 40) participants reported having access to students and lab spaces and 55% (n = 55) indicated they were allowed to conduct in-person research. Of tenure-track lab-based faculty, 80% (n = 20) reported a decrease in research productivity, of which 60.0% (n = 12) identified as female. Among faculty with 5 or less years of teaching experience (n = 23), 69.6% (n = 16) reported a decrease in productivity, with 68.8% (n = 11) of those being female. All exercise science faculty surveyed reported issues with safety and social distancing, modified lab and research procedures, faculty workload, and research productivity. This information can be leveraged to create better infrastructure to support faculty and develop and implement strategies to reduce workload inequities.

Published
2022
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18. Health-Related Quality-of-Life Outcomes of Very Preterm or Very Low Birth Weight Adults: Evidence From an Individual Participant Data Meta-Analysis

Author

Bolbocean, Corneliu, van der Pal, Sylvia, van Buuren, Stef, Anderson, Peter J., Bartmann, Peter, Baumann, Nicole, Cheong, Jeanie L. Y., Darlow, Brian A., Doyle, Lex W., Evensen, Kari Anne I., Horwood, John, Indredavik, Marit S., Johnson, Samantha, Marlow, Neil, Mendonça, Marina, Ni, Yanyan, Wolke, Dieter, Woodward, Lianne, Verrips, Erik, and Petrou, Stavros

Published
2023
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20. Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway

Author

Carrot-Zhang, Jian, Yao, Xiaotong, Devarakonda, Siddhartha, Deshpande, Aditya, Damrauer, Jeffrey S, Silva, Tiago Chedraoui, Wong, Christopher K, Choi, Hyo Young, Felau, Ina, Robertson, A Gordon, Castro, Mauro AA, Bao, Lisui, Rheinbay, Esther, Liu, Eric Minwei, Trieu, Tuan, Haan, David, Yau, Christina, Hinoue, Toshinori, Liu, Yuexin, Shapira, Ofer, Kumar, Kiran, Mungall, Karen L, Zhang, Hailei, Lee, Jake June-Koo, Berger, Ashton, Gao, Galen F, Zhitomirsky, Binyamin, Liang, Wen-Wei, Zhou, Meng, Moorthi, Sitapriya, Berger, Alice H, Collisson, Eric A, Zody, Michael C, Ding, Li, Cherniack, Andrew D, Getz, Gad, Elemento, Olivier, Benz, Christopher C, Stuart, Josh, Zenklusen, JC, Beroukhim, Rameen, Chang, Jason C, Campbell, Joshua D, Hayes, D Neil, Yang, Lixing, Laird, Peter W, Weinstein, John N, Kwiatkowski, David J, Tsao, Ming S, Travis, William D, Khurana, Ekta, Berman, Benjamin P, Hoadley, Katherine A, Robine, Nicolas, Network, TCGA Research, Arora, Kanika, Shah, Minita, Shelton, Jennifer, Bowlby, Reanne, Friedl, Verena, Goldman, Mary, Craft, Brian, Heiman, David I, Hajirasouliha, Iman, Ricketts, Camir, Anur, Pavana, Chiotti, Kami E, Caesar-Johnson, Samantha J, Demchok, John A, Ferguson, Martin L, Kemal, Anab, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Spellman, Paul T, Raphael, Benjamin, Akbani, Rehan, Zhu, Jingchun, Jones, Steven JM, Shen, Hui, Meyerson, Matthew, Govindan, Ramaswamy, and Imielinski, Marcin

Subjects
Biological Sciences, Cancer, Lung, Biotechnology, Genetics, Rare Diseases, Human Genome, Lung Cancer, Good Health and Well Being, Adenocarcinoma of Lung, Humans, Kelch-Like ECH-Associated Protein 1, Lung Neoplasms, Tachykinins, Whole Genome Sequencing, TCGA Research Network, TCGA, driver, genome analysis, lung adenocarcinoma, noncoding, oncogene, precision oncology, structural variation, tumor suppressor, whole genome sequencing, Biochemistry and Cell Biology, Medical Physiology, Biological sciences
Abstract

RTK/RAS/RAF pathway alterations (RPAs) are a hallmark of lung adenocarcinoma (LUAD). In this study, we use whole-genome sequencing (WGS) of 85 cases found to be RPA(-) by previous studies from The Cancer Genome Atlas (TCGA) to characterize the minority of LUADs lacking apparent alterations in this pathway. We show that WGS analysis uncovers RPA(+) in 28 (33%) of the 85 samples. Among the remaining 57 cases, we observe focal deletions targeting the promoter or transcription start site of STK11 (n = 7) or KEAP1 (n = 3), and promoter mutations associated with the increased expression of ILF2 (n = 6). We also identify complex structural variations associated with high-level copy number amplifications. Moreover, an enrichment of focal deletions is found in TP53 mutant cases. Our results indicate that RPA(-) cases demonstrate tumor suppressor deletions and genome instability, but lack unique or recurrent genetic lesions compensating for the lack of RPAs. Larger WGS studies of RPA(-) cases are required to understand this important LUAD subset.

Published
2021

21. Faculty Perceptions of the Exercise Science Student Learning Experience during the Coronavirus Pandemic

Author

Caputo, Jennifer L., Mel, Astrid E., Stenson, Mary C., Fleming, Jessica K., Johnson, Samantha L., and Spillios, Katherine E.

Abstract

Significant disruptions in higher education course delivery occurred during the coronavirus (COVID-19) global pandemic. The implementation of emergency remote teaching (ERT) offered exercise science faculty a safe method to continue educating students in courses generally taught face-to-face. The purpose of this investigation was to explore faculty perceptions of their ERT efforts with respect to student successes, challenges, and faculty expectations. Through an electronic survey, participants (n = 112) from higher education institutions in 31 states and three Canadian provinces provided feedback on their perceptions of the student experience across 315 fall 2020 courses. Data analysis included a thematic analysis to identify themes and trends in participant responses. Faculty identified student adaptability, increased autonomy of learning, and maintenance of learning as successes. Also noted was the increased flexibility of alternative pedagogy methods. Participants perceived student challenges related to technology, time management, and well-being. Faculty perceived students expected increased accommodations and instructor responsiveness during fall 2020. While faculty and students were challenged to adapt during the global pandemic, the perceived ERT experiences during COVID-19 highlight the resiliency of higher education students and underscores changes needed by educational institutions to provide resources and training upon return to traditional education or in response to a future crisis.

Published
2021
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22. A systematic review of interventions for resuscitation following drowning

Author

Bierens, Joost, Bray, Janet, Abelairas-Gomez, Cristian, Barcala-Furelos, Roberto, Beerman, Stephen, Claesson, Andreas, Dunne, Cody, Fukuda, Tatsuma, Jayashree, Muralidharan, T Lagina, Anthony, Li, Lei, Mecrow, Tom, Morgan, Patrick, Schmidt, Andrew, Seesink, Jeroen, Sempsrott, Justin, Szpilman, David, Thom, Ogilvie, Tobin, Joshua, Webber, Jonathon, Johnson, Samantha, and Perkins, Gavin D

Published
2023
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23. Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer

Author

Carrot-Zhang, Jian, Chambwe, Nyasha, Damrauer, Jeffrey S, Knijnenburg, Theo A, Robertson, A Gordon, Yau, Christina, Zhou, Wanding, Berger, Ashton C, Huang, Kuan-lin, Newberg, Justin Y, Mashl, R Jay, Romanel, Alessandro, Sayaman, Rosalyn W, Demichelis, Francesca, Felau, Ina, Frampton, Garrett M, Han, Seunghun, Hoadley, Katherine A, Kemal, Anab, Laird, Peter W, Lazar, Alexander J, Le, Xiuning, Oak, Ninad, Shen, Hui, Wong, Christopher K, Zenklusen, Jean C, Ziv, Elad, Network, Cancer Genome Atlas Analysis, Aguet, Francois, Ding, Li, Demchok, John A, Mensah, Michael KA, Caesar-Johnson, Samantha, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Alfoldi, Jessica, Karczewski, Konrad J, MacArthur, Daniel G, Meyerson, Matthew, Benz, Christopher, Stuart, Joshua M, Cherniack, Andrew D, and Beroukhim, Rameen

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Genetics, Human Genome, Clinical Research, Cancer, Biotechnology, DNA Methylation, DNA-Binding Proteins, Ethnicity, F-Box-WD Repeat-Containing Protein 7, Gene Expression Regulation, Neoplastic, Genetic Predisposition to Disease, Genetics, Population, Genome, Human, Genomics, High-Throughput Nucleotide Sequencing, Humans, MicroRNAs, Mutation, Neoplasm Proteins, Neoplasms, Transcription Factors, Von Hippel-Lindau Tumor Suppressor Protein, Cancer Genome Atlas Analysis Network, TCGA, admixture, ancestry, cancer, eQTL, genomics, mRNA, methylation, miRNA, mutation, Neurosciences, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

We evaluated ancestry effects on mutation rates, DNA methylation, and mRNA and miRNA expression among 10,678 patients across 33 cancer types from The Cancer Genome Atlas. We demonstrated that cancer subtypes and ancestry-related technical artifacts are important confounders that have been insufficiently accounted for. Once accounted for, ancestry-associated differences spanned all molecular features and hundreds of genes. Biologically significant differences were usually tissue specific but not specific to cancer. However, admixture and pathway analyses suggested some of these differences are causally related to cancer. Specific findings included increased FBXW7 mutations in patients of African origin, decreased VHL and PBRM1 mutations in renal cancer patients of African origin, and decreased immune activity in bladder cancer patients of East Asian origin.

Published
2020

27. Developing a Simulated-Person Methodology Workshop: An Experiential Education Initiative for Educators and Simulators

Author

Peisachovich, Eva Hava, Nelles, L. J., Johnson, Samantha, Nicholson, Laura, Gal, Raya, Kerr, Barbara, Celia, Popovic, Epstein, Iris, and Da Silva, Celina

Abstract

Numerous forecasts suggest that professional-competence development depends on human encounters. Interaction between organizations, tasks, and individual providers influence human behaviour, affect organizations' or systems' performance, and are a key component of professional-competence development. Further, insufficient or ineffective communication between professionals is deemed a contributing factor to adverse events worldwide. This underscores the need to provide educators with the tools and education to embed methods in their teaching that will enable learners to effectively intervene in highly charged interpersonal situations and high-risk scenarios; these concerns highlight the value of realistic simulated-experiential approaches, such as the one proposed in this project. The first phase of this project involved conducting a three-day experiential workshop developed at a Canadian university to provide educators with knowledge and skills to work and effectively utilize simulators, enhancing pedagogical classroom practices for teaching undergraduate learners. This workshop's development resulted in numerous benefits. Participation in the workshop provided educators with opportunities for meaningful reflection on their teaching practice and the ability to apply this insight to optimize student learning. It provided theatre students, recruited as simulators as part of this interdisciplinary initiative, to expand their experiences and this will lead to an expanded practicum course for their program. There is now a group of simulators available to educators across the university to include in classroom activities, and lastly there are further iterations of this workshop available for faculty development. This paper reflects on the workshop experiences and the feedback obtained from the participants. Formal and informal feedback obtained provides an understanding of the participants' experiences.

Published
2017

28. Corrigendum to “2022 International Consensus on Cardiopulmonary Resuscitation and Emergency Cardiovascular Care Science With Treatment Recommendations: Summary From the Basic Life Support; Advanced Life Support; Pediatric Life Support; Neonatal Life Support; Education, Implementation, and Teams; and First Aid Task Forces” [Resuscitation 181 (2022) 208–288]

Author

Wyckoff, Myra H., primary, Greif, Robert, additional, Morley, Peter T., additional, Ng, Kee-Chong, additional, Olasveengen, Theresa M., additional, Singletary, Eunice M., additional, Soar, Jasmeet, additional, Cheng, Adam, additional, Drennan, Ian R., additional, Liley, Helen G., additional, Scholefield, Barnaby R., additional, Smyth, Michael A., additional, Welsford, Michelle, additional, Zideman, David A., additional, Acworth, Jason, additional, Aickin, Richard, additional, Andersen, Lars W., additional, Atkins, Diane, additional, Berry, David C., additional, Bhanji, Farhan, additional, Bierens, Joost, additional, Borra, Vere, additional, Böttiger, Bernd W., additional, Bradley, Richard N., additional, Bray, Janet E., additional, Breckwoldt, Jan, additional, Callaway, Clifton W., additional, Carlson, Jestin N., additional, Cassan, Pascal, additional, Castrén, Maaret, additional, Chang, Wei-Tien, additional, Charlton, Nathan P., additional, Chung, Sung Phil, additional, Considine, Julie, additional, Costa-Nobre, Daniela T., additional, Couper, Keith, additional, Couto, Thomaz Bittencourt, additional, Dainty, Katie N., additional, Davis, Peter G., additional, de Almeida, Maria Fernanda, additional, de Caen, Allan R., additional, Deakin, Charles D., additional, Djärv, Therese, additional, Donnino, Michael W., additional, Douma, Matthew J., additional, Duff, Jonathan P., additional, Dunne, Cody L., additional, Eastwood, Kathryn, additional, El-Naggar, Walid, additional, Fabres, Jorge G., additional, Fawke, Joe, additional, Finn, Judith, additional, Foglia, Elizabeth E., additional, Folke, Fredrik, additional, Gilfoyle, Elaine, additional, Goolsby, Craig A., additional, Granfeldt, Asger, additional, Guerguerian, Anne-Marie, additional, Guinsburg, Ruth, additional, Hirsch, Karen G., additional, Holmberg, Mathias J., additional, Hosono, Shigeharu, additional, Hsieh, Ming-Ju, additional, Hsu, Cindy H., additional, Ikeyama, Takanari, additional, Isayama, Tetsuya, additional, Johnson, Nicholas J., additional, Kapadia, Vishal S., additional, Daripa Kawakami, Mandira, additional, Kim, Han-Suk, additional, Kleinman, Monica, additional, Kloeck, David A., additional, Kudenchuk, Peter J., additional, Lagina, Anthony T., additional, Lauridsen, Kasper G., additional, Lavonas, Eric J., additional, Lee, Henry C., additional, (Jeffrey) Lin, Yiqun, additional, Lockey, Andrew S., additional, Maconochie, Ian K., additional, John Madar, R., additional, Hansen, Carolina Malta, additional, Masterson, Siobhan, additional, Matsuyama, Tasuku, additional, McKinlay, Christopher J.D., additional, Meyran, Daniel, additional, Morgan, Patrick, additional, Morrison, Laurie J., additional, Nadkarni, Vinay, additional, Nakwa, Firdose L., additional, Nation, Kevin J., additional, Nehme, Ziad, additional, Nemeth, Michael, additional, Neumar, Robert W., additional, Nicholson, Tonia, additional, Nikolaou, Nikolaos, additional, Nishiyama, Chika, additional, Norii, Tatsuya, additional, Nuthall, Gabrielle A., additional, O'Neill, Brian J., additional, Gene Ong, Yong-Kwang, additional, Orkin, Aaron M., additional, Paiva, Edison F., additional, Parr, Michael J., additional, Patocka, Catherine, additional, Pellegrino, Jeffrey L., additional, Perkins, Gavin D., additional, Perlman, Jeffrey M., additional, Rabi, Yacov, additional, Reis, Amelia G., additional, Reynolds, Joshua C., additional, Ristagno, Giuseppe, additional, Rodriguez-Nunez, Antonio, additional, Roehr, Charles C., additional, Rüdiger, Mario, additional, Sakamoto, Tetsuya, additional, Sandroni, Claudio, additional, Sawyer, Taylor L., additional, Schexnayder, Steve M., additional, Schmölzer, Georg M., additional, Schnaubelt, Sebastian, additional, Semeraro, Federico, additional, Skrifvars, Markus B., additional, Smith, Christopher M., additional, Sugiura, Takahiro, additional, Tijssen, Janice A., additional, Trevisanuto, Daniele, additional, Van de Voorde, Patrick, additional, Wang, Tzong-Luen, additional, Weiner, Gary M., additional, Wyllie, Jonathan P., additional, Yang, Chih-Wei, additional, Yeung, Joyce, additional, Nolan, Jerry P., additional, Berg, Katherine M., additional, Burdick, Madeline C., additional, Cartledge, Susie, additional, Dawson, Jennifer A., additional, Elgohary, Moustafa M., additional, Ersdal, Hege L., additional, Finan, Emer, additional, Flaatten, Hilde I., additional, Flores, Gustavo E., additional, Fuerch, Janene, additional, Garg, Rakesh, additional, Gately, Callum, additional, Goh, Mark, additional, Halamek, Louis P., additional, Handley, Anthony J., additional, Hatanaka, Tetsuo, additional, Hoover, Amber, additional, Issa, Mohmoud, additional, Johnson, Samantha, additional, Kamlin, C. Omar, additional, Ko, Ying-Chih, additional, Kule, Amy, additional, Leone, Tina A., additional, MacKenzie, Ella, additional, Macneil, Finlay, additional, Montgomery, William, additional, O'Dochartaigh, Domhnall, additional, Ohshimo, Shinichiro, additional, Palazzo, Francesco Stefano, additional, Picard, Christopher, additional, Quek, Bin Huey, additional, Raitt, James, additional, Ramaswamy, Viraraghavan V., additional, Scapigliati, Andrea, additional, Shah, Birju A., additional, Stewart, Craig, additional, Strand, Marya L., additional, Szyld, Edgardo, additional, Thio, Marta, additional, Topjian, Alexis A., additional, Udaeta, Enrique, additional, Vaillancourt, Christian, additional, Wetsch, Wolfgang A., additional, Wigginton, Jane, additional, Yamada, Nicole K., additional, Yao, Sarah, additional, Zace, Drieda, additional, and Zelop, Carolyn M., additional

Published
2024
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29. Long-Acting Injectable ART in Practice: A Mixed Methods Implementation Study Assessing the Feasibility of Using LAI ART in High Risk Populations and At Alternative Low Barrier Care Sites

Author

Fletcher, Laura, primary, Burrowes, Shana, additional, Sabin, Lora L., additional, McCann, Nicole, additional, Khan, Ghulam Karim, additional, Ruiz-Mercado, Glorimar, additional, Johnson, Samantha, additional, Kimmel, Simeon D., additional, Pierre, Cassandra, additional, and Drainoni, Mari-Lynn, additional

Published
2024
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30. 2022 International Consensus on Cardiopulmonary Resuscitation and Emergency Cardiovascular Care Science With Treatment Recommendations: Summary From the Basic Life Support; Advanced Life Support; Pediatric Life Support; Neonatal Life Support; Education, Implementation, and Teams; and First Aid Task Forces

Author

Burdick, Madeline C., Cartledge, Susie, Dawson, Jennifer A., Elgohary, Moustafa M., Ersdal, Hege L., Finan, Emer, Flaatten, Hilde I., Flores, Gustavo E., Fuerch, Janene, Garg, Rakesh, Gately, Callum, Goh, Mark, Halamek, Louis P., Handley, Anthony J., Hatanaka, Tetsuo, Hoover, Amber, Issa, Mohmoud, Johnson, Samantha, Kamlin, C. Omar, Ko, Ying-Chih, Kule, Amy, Leone, Tina A., MacKenzie, Ella, Macneil, Finlay, Montgomery, William, O’Dochartaigh, Domhnall, Ohshimo, Shinichiro, Stefano Palazzo, Francesco, Picard, Christopher, Quek, Bin Huey, Raitt, James, Ramaswamy, Viraraghavan V., Scapigliati, Andrea, Shah, Birju A., Stewart, Craig, Strand, Marya L., Szyld, Edgardo, Thio, Marta, Topjian, Alexis A., Udaeta, Enrique, Vaillancourt, Christian, Wetsch, Wolfgang A., Wigginton, Jane, Yamada, Nicole K., Yao, Sarah, Zace, Drieda, Zelop, Carolyn M., Wyckoff, Myra H., Greif, Robert, Morley, Peter T., Ng, Kee-Chong, Olasveengen, Theresa M., Singletary, Eunice M., Soar, Jasmeet, Cheng, Adam, Drennan, Ian R., Liley, Helen G., Scholefield, Barnaby R., Smyth, Michael A., Welsford, Michelle, Zideman, David A., Acworth, Jason, Aickin, Richard, Andersen, Lars W., Atkins, Diane, Berry, David C., Bhanji, Farhan, Bierens, Joost, Borra, Vere, Böttiger, Bernd W., Bradley, Richard N., Bray, Janet E., Breckwoldt, Jan, Callaway, Clifton W., Carlson, Jestin N., Cassan, Pascal, Castrén, Maaret, Chang, Wei-Tien, Charlton, Nathan P., Phil Chung, Sung, Considine, Julie, Costa-Nobre, Daniela T., Couper, Keith, Couto, Thomaz Bittencourt, Dainty, Katie N., Davis, Peter G., de Almeida, Maria Fernanda, de Caen, Allan R., Deakin, Charles D., Djärv, Therese, Donnino, Michael W., Douma, Matthew J., Duff, Jonathan P., Dunne, Cody L., Eastwood, Kathryn, El-Naggar, Walid, Fabres, Jorge G., Fawke, Joe, Finn, Judith, Foglia, Elizabeth E., Folke, Fredrik, Gilfoyle, Elaine, Goolsby, Craig A., Granfeldt, Asger, Guerguerian, Anne-Marie, Guinsburg, Ruth, Hirsch, Karen G., Holmberg, Mathias J., Hosono, Shigeharu, Hsieh, Ming-Ju, Hsu, Cindy H., Ikeyama, Takanari, Isayama, Tetsuya, Johnson, Nicholas J., Kapadia, Vishal S., Kawakami, Mandira Daripa, Kim, Han-Suk, Kleinman, Monica, Kloeck, David A., Kudenchuk, Peter J., Lagina, Anthony T., Lauridsen, Kasper G., Lavonas, Eric J., Lee, Henry C., Lin, Yiqun (Jeffrey), Lockey, Andrew S., Maconochie, Ian K., Madar, R. John, Malta Hansen, Carolina, Masterson, Siobhan, Matsuyama, Tasuku, McKinlay, Christopher J.D., Meyran, Daniel, Morgan, Patrick, Morrison, Laurie J., Nadkarni, Vinay, Nakwa, Firdose L., Nation, Kevin J., Nehme, Ziad, Nemeth, Michael, Neumar, Robert W., Nicholson, Tonia, Nikolaou, Nikolaos, Nishiyama, Chika, Norii, Tatsuya, Nuthall, Gabrielle A., O’Neill, Brian J., Gene Ong, Yong-Kwang, Orkin, Aaron M., Paiva, Edison F., Parr, Michael J., Patocka, Catherine, Pellegrino, Jeffrey L., Perkins, Gavin D., Perlman, Jeffrey M., Rabi, Yacov, Reis, Amelia G., Reynolds, Joshua C., Ristagno, Giuseppe, Rodriguez-Nunez, Antonio, Roehr, Charles C., Rüdiger, Mario, Sakamoto, Tetsuya, Sandroni, Claudio, Sawyer, Taylor L., Schexnayder, Steve M., Schmölzer, Georg M., Schnaubelt, Sebastian, Semeraro, Federico, Skrifvars, Markus B., Smith, Christopher M., Sugiura, Takahiro, Tijssen, Janice A., Trevisanuto, Daniele, Van de Voorde, Patrick, Wang, Tzong-Luen, Weiner, Gary M., Wyllie, Jonathan P., Yang, Chih-Wei, Yeung, Joyce, Nolan, Jerry P., and Berg, Katherine M.

Published
2022
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32. The Immune Landscape of Cancer

Author

Thorsson, Vésteinn, Gibbs, David L, Brown, Scott D, Wolf, Denise, Bortone, Dante S, Yang, Tai-Hsien Ou, Porta-Pardo, Eduard, Gao, Galen F, Plaisier, Christopher L, Eddy, James A, Ziv, Elad, Culhane, Aedin C, Paull, Evan O, Sivakumar, IK Ashok, Gentles, Andrew J, Malhotra, Raunaq, Farshidfar, Farshad, Colaprico, Antonio, Parker, Joel S, Mose, Lisle E, Vo, Nam Sy, Liu, Jianfang, Liu, Yuexin, Rader, Janet, Dhankani, Varsha, Reynolds, Sheila M, Bowlby, Reanne, Califano, Andrea, Cherniack, Andrew D, Anastassiou, Dimitris, Bedognetti, Davide, Mokrab, Younes, Newman, Aaron M, Rao, Arvind, Chen, Ken, Krasnitz, Alexander, Hu, Hai, Malta, Tathiane M, Noushmehr, Houtan, Pedamallu, Chandra Sekhar, Bullman, Susan, Ojesina, Akinyemi I, Lamb, Andrew, Zhou, Wanding, Shen, Hui, Choueiri, Toni K, Weinstein, John N, Guinney, Justin, Saltz, Joel, Holt, Robert A, Rabkin, Charles S, 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, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, and Broom, Bradley M

Subjects
Biomedical and Clinical Sciences, Immunology, Cancer Genome Atlas Research Network
Abstract

(Immunity 48, 812–830.e1–e14; April 17, 2018) In the originally published version of this article, the authors neglected to include Younes Mokrab and Aaron M. Newman as co-authors and misspelled the names of authors Charles S. Rabkin and Ilya Shmulevich. The author names have been corrected here and online. In addition, the concluding sentence of the subsection “Immune Signature Compilation” in the Method Details in the original published article was deemed unclear because it did not specify differences among the gene set scoring methods. The concluding sentences now reads “Gene sets from Bindea et al., Senbabaoglu et al., and the MSigDB C7 collection were scored using single-sample gene set enrichment (ssGSEA) analysis (Barbie et al., 2009), as implemented in the GSVA R package (Hänzelmann et al., 2013). All other signatures were scored using methods found in the associated citations.”

Published
2019

34. 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, Cancer Genomics, Human Genome, Biotechnology, 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

41. Factors Affecting the Duration of Agricultural Marketing Orders.

Author

Johnson, Samantha R., Brady, Michael P., and McCluskey, Jill J.

Abstract

Marketing orders are government-supported cartels designed to help farmers by allowing them to set production quotas and quality standards. Given that, it is surprising that a growing number have been voluntarily terminated in recent decades by their constituent farmers. To better understand why, we construct a novel data set on the timing of initiation and termination of marketing orders active between 1974 and 2019 and estimate duration models to examine the impact of specific factors on marketing orders' probability of survival. We find that the most significant factor affecting marketing order persistence is whether the order had a corresponding marketing agreement. [ABSTRACT FROM AUTHOR]

Published
2024
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42. The impact of Chatbot-Assisted Self Assessment (CASA) on intentions for sexual health screening in people from minoritised ethnic groups at risk of sexually transmitted infections.

Author

Nadarzynski, Tom, Knights, Nicky, Husbands, Deborah, Graham, Cynthia A., Llewellyn, Carrie D., Buchanan, Tom, Montgomery, Ian, Khlafa, Nuha, Tichackova, Jana, Odeyemi, Riliwan, Johnson, Samantha, Jesuthas, Neomi, Tahia, Syeda, and Ridge, Damien

Abstract

Background: Sexually transmitted infections (STIs) present a significant global public health issue, with disparities in STI rates often observed across ethnic groups. The study investigates the impact of Chatbot-Assisted Self Assessment (CASA) on the intentions for sexual health screening within minoritised ethnic groups (MEGs) at risk of STIs as well as the subsequent use of a chatbot for booking STI screening. Methods: A simulation within-subject design was utilised to evaluate the effect of CASA on intentions for STI/HIV screening, concern about STIs, and attitudes towards STI screening. Screening intentions served as the dependent variable, while demographic and behavioural factors related to STI/HIV risk were the independent variables. ANCOVA tests were conducted to measure the impact of CASA on these perceptions. Results: Involving 548 participants (54% women, 66% black, average age = 30 years), the study found that CASA positively influenced screening intentions t (547) = −10.3, P < 0.001], concerns about STIs t (544) = −4.96, P < 0.001, and attitudes towards sexual health screening [ t (543) = −4.36, P < 0.001. Positive attitudes towards CASA were observed (mean, 13.30; s.d., 6.73; range, −17 to 21). About 72% of users who booked STI screening appointments via chatbot were from MEGs. Conclusion: CASA increased motivations for STI screening intentions among ethnically diverse communities. The intervention's non-judgemental nature and the chatbot's ability to emulate sexual history-taking were critical in fostering an environment conducive to behavioural intention change. The study's high acceptability indicates the potential for broader application in digital health interventions. However, the limitation of not tracking actual post-intervention behaviour warrants further investigation into CASA's real-world efficacy. Health disparities remain a pressing issue globally, and Chatbot-Assisted Self Assessment (CASA) may enhance sexual health screening intentions among minoritised ethnic groups at risk of sexually transmitted infections (STIs). This innovative study reveals that CASA significantly boosts screening intentions, alleviates concerns about STIs, and fosters positive attitudes towards sexual health screening. Importantly, these findings underscore the potential of artificial intelligence to bridge gaps in health care and contribute to the broader goal of achieving health equity, particularly in underserved communities. [ABSTRACT FROM AUTHOR]

Published
2024
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44. Assessing the Impacts of Pediatric Primary Care Parenting Interventions on EI Referrals through Linkage with a Public Health Database

Author

Mendelsohn, Alan L., Cates, Carolyn Brockmeyer, Huberman, Harris S., Johnson, Samantha B., Govind, Prashil, Kincler, Naomi, Rohatgi, Rashi, Weisleder, Adriana, Trogen, Brit, and Dreyer, Benard P.

Abstract

We sought to determine whether pediatric primary care interventions targeting positive parenting among low socioeconomic status mothers resulted in reduced referrals to the New York City Early Intervention Program (NYC-EIP). Participants in Building Blocks (BB) and the Video Interaction Project (VIP) were linked with the NYC-EIP administrative dataset to determine referrals. In all, 139 of 422 study participants (31.4%) meeting inclusion criteria were referred to the NYC-EIP. Although referrals did not differ overall by group (VIP 29.8%; BB 33.8%; control 35.3%), differences were found for mothers with education/literacy of seventh grade or higher (interaction p = 0.02). In that subgroup, VIP was associated with reduced referrals by age 3 years (22.4%; adjusted odds ratio 0.53; 95% confidence interval [0.29, 0.97]), compared with BB (35.0%) and controls (34.3%), with survival analysis showing reduced cumulative risk (p = 0.04). We conclude that VIP resulted in reduced referrals for early intervention evaluation among children of mothers with seventh-grade education or higher.

Published
2020
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47. Comprehensive Characterization of Cancer Driver Genes and Mutations

Author

Bailey, Matthew H, Tokheim, Collin, Porta-Pardo, Eduard, Sengupta, Sohini, Bertrand, Denis, Weerasinghe, Amila, Colaprico, Antonio, Wendl, Michael C, Kim, Jaegil, Reardon, Brendan, Ng, Patrick Kwok-Shing, Jeong, Kang Jin, Cao, Song, Wang, Zixing, Gao, Jianjiong, Gao, Qingsong, Wang, Fang, Liu, Eric Minwei, Mularoni, Loris, Rubio-Perez, Carlota, Nagarajan, Niranjan, Cortés-Ciriano, Isidro, Zhou, Daniel Cui, Liang, Wen-Wei, Hess, Julian M, Yellapantula, Venkata D, Tamborero, David, Gonzalez-Perez, Abel, Suphavilai, Chayaporn, Ko, Jia Yu, Khurana, Ekta, Park, Peter J, Van Allen, Eliezer M, Liang, Han, Lawrence, Michael S, Godzik, Adam, Lopez-Bigas, Nuria, Stuart, Joshua M, Wheeler, David A, Getz, Gad, Chen, Amy, Lazar, Alexander J, Mills, Gordon B, Karchin, Rachel, Ding, Li, 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, Heiman, David I, 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, and Ling, Shiyun

Subjects
Biological Sciences, Biomedical and Clinical Sciences, MC3 Working Group, Cancer Genome Atlas Research Network, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

(Cell 173, 371–385.e1–e9; April 5, 2018) It has come to our attention that we made two errors in preparation of this manuscript. First, in the STAR Methods, under the subheading of “Hypermutators and Immune Infiltrates” within the “Quantification and Statistical Analysis” section, we inadvertently referred to Figures S7A–S7C for data corresponding to sample stratification by hypermutator status alone in the last sentence. It should have referred to Figure S6A–S6C. Second, the lists of highly frequent missense mutations for COAD (colon adenocarcinoma) and READ (rectum adenocarcinoma) displayed in Figure S7 were incorrect because when we ordered the mutations in the initial analysis, we mistakenly combined the two cancer types COAD and READ for analysis, despite the fact that they were listed as two separate cancer types in the x-axis of the figure. After re-ordering the mutations by frequency for COAD and READ independently, information on highly frequent missense mutations for each of these cancer types is different and updated now in the revised Figure S7. These errors don't change the major conclusions of the paper and have been corrected online. We apologize for any confusion they may have caused. [Figure-presented]

Published
2018

48. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

Author

Ricketts, Christopher J, De Cubas, Aguirre A, Fan, Huihui, Smith, Christof C, Lang, Martin, Reznik, Ed, Bowlby, Reanne, Gibb, Ewan A, Akbani, Rehan, Beroukhim, Rameen, Bottaro, Donald P, Choueiri, Toni K, Gibbs, Richard A, Godwin, Andrew K, Haake, Scott, Hakimi, A Ari, Henske, Elizabeth P, Hsieh, James J, Ho, Thai H, Kanchi, Rupa S, Krishnan, Bhavani, Kwiatkowski, David J, Lui, Wembin, Merino, Maria J, Mills, Gordon B, Myers, Jerome, Nickerson, Michael L, Reuter, Victor E, Schmidt, Laura S, Shelley, C Simon, Shen, Hui, Shuch, Brian, Signoretti, Sabina, Srinivasan, Ramaprasad, Tamboli, Pheroze, Thomas, George, Vincent, Benjamin G, Vocke, Cathy D, Wheeler, David A, Yang, Lixing, Kim, William Y, Robertson, A Gordon, Spellman, Paul, Rathmell, W Kimryn, Linehan, W Marston, 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, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Broom, Bradley M, Hegde, Apurva M, Ju, Zhenlin, Korkut, Anil, Li, Jun, Liang, Han, and Ling, Shiyun

Subjects
Biological Sciences, Cancer Genome Atlas Research Network, Biochemistry and Cell Biology, Medical Physiology, Biological sciences
Abstract

(Cell Reports 23, 313–326; April 3, 2018) In the originally published version of this article, the author list contained two errors. Specifically, David J. Kwiatkowski was misspelled as David J. Kwaitkowski, and William Y. Kim was inadvertently written as William T. Kim. Both names have been corrected online. The authors regret this error.

Published
2018

49. Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Author

Chiu, Hua-Sheng, Somvanshi, Sonal, Patel, Ektaben, Chen, Ting-Wen, Singh, Vivek P, Zorman, Barry, Patil, Sagar L, Pan, Yinghong, Chatterjee, Sujash S, 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, 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, and Anur, Pavana

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Breast Cancer, Human Genome, Cancer, Biotechnology, Women's Health, Genetics, Cancer Genomics, 2.1 Biological and endogenous factors, Cell Line, Cell Line, Tumor, Gene Expression Regulation, Neoplastic, Gene Regulatory Networks, Genes, Tumor Suppressor, Humans, Neoplasms, Oncogenes, RNA, Long Noncoding, Cancer Genome Atlas Research Network, RNA-binding proteins, cancer gene, interactome, lncRNA, microRNA, modulation, noncoding RNA, pan-cancer, regulation, Biochemistry and Cell Biology, Medical Physiology, Biological sciences
Abstract

Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles in cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling their effects on the activity of transcription factors, RNA-binding proteins, and microRNAs in 5,185 TCGA tumors and 1,019 ENCODE assays. Our predictions included hundreds of candidate onco- and tumor-suppressor lncRNAs (cancer lncRNAs) whose somatic alterations account for the dysregulation of dozens of cancer genes and pathways in each of 14 tumor contexts. To demonstrate proof of concept, we showed that perturbations targeting OIP5-AS1 (an inferred tumor suppressor) and TUG1 and WT1-AS (inferred onco-lncRNAs) dysregulated cancer genes and altered proliferation of breast and gynecologic cancer cells. Our analysis indicates that, although most lncRNAs are dysregulated in a tumor-specific manner, some, including OIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergistically dysregulate cancer pathways in multiple tumor contexts.

Published
2018

50. Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

Author

Seiler, Michael, Peng, Shouyong, Agrawal, Anant A, Palacino, James, Teng, Teng, Zhu, Ping, Smith, Peter G, 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, 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, and Spellman, Paul

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Cancer, Cancer Genomics, 2.1 Biological and endogenous factors, Cell Line, Tumor, Genes, Tumor Suppressor, Humans, Loss of Function Mutation, Mutation Rate, Neoplasms, Oncogenes, RNA Splicing, RNA Splicing Factors, Cancer Genome Atlas Research Network, FUBP1, RBM10, SF3B1, SRSF2, U2AF1, cancer, mutation, splicing, Biochemistry and Cell Biology, Medical Physiology, Biological sciences
Abstract

Hotspot mutations in splicing factor genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of RNA splicing in cancer. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome Atlas (TCGA), and we identified 119 splicing factor genes with significant non-silent mutation patterns, including mutation over-representation, recurrent loss of function (tumor suppressor-like), or hotspot mutation profile (oncogene-like). Furthermore, RNA sequencing analysis revealed altered splicing events associated with selected splicing factor mutations. In addition, we were able to identify common gene pathway profiles associated with the presence of these mutations. Our analysis suggests that somatic alteration of genes involved in the RNA-splicing process is common in cancer and may represent an underappreciated hallmark of tumorigenesis.

Published
2018

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