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2. The Bread Wheat Reference Genome Sequence

Author

International Wheat Genome Sequencing Consortium, Rogers, Jane, Kole, Chittaranjan, Series Editor, Appels, Rudi, editor, Eversole, Kellye, editor, Feuillet, Catherine, editor, and Gallagher, Dusti, editor

Published
2024
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7. Biological imaging for adaptive bladder radiotherapy

Author

Rogers, Jane Ann

Subjects
QC Physics, RC Internal medicine, RC0254 Neoplasms. Tumors. Oncology (including Cancer)
Abstract

Outcomes for muscle-invasive bladder cancer (MIBC) have changed little over recent decades, with long term survival remaining around 50 % [1]. Standard radiotherapy treatment for MIBC involves resection of tumour followed by uniform radiotherapy to the whole bladder, as the residual tumour is not readily visible on conventional computed tomography (CT) imaging. This thesis investigates the use of diffusion-weighted MRI (DW-MRI) to enable a dose-escalated radiotherapy treatment, aiming to improve local control of MIBC. Geometrical distortion in DW-MRI was investigated via bladder-mimicking phantoms, and positional differences were quantified between DW-MRI, standard T2-weighted MRI, and CT. Deformable registration within a commercial radiotherapy treatment planning system was tested to see whether it could mitigate distortion. All markers were located within a maximum discrepancy of 5 mm (mean 3 mm). Open-source software designed to correct geometric distortion in DW-MRI was tested and produced improved results with a maximum of 1.8 mm (mean 1.3 mm). Tumours were simulated in 6 locations within the bladder on a CT dataset of a previously-treated MIBC patient. Expansions producing planning target volumes incorporated the findings from the phantom investigations, aiming to mimic the use of DW-MRI registered to CT. Escalated dose distributions were compared against the standard, using established dose-constraints for nearby sensitive organs. Maximum dose-escalations to 70 - 78 Gy were possible depending on tumour location. Poisson-based tumour control probability (TCP) models were fitted to MIBC trials data for radiotherapy-only and radio-chemotherapy treatments, and used to calculate TCP for all dose distributions. TCP increased 9.0 - 19.2 % depending on tumour location and model used. The feasibility of delivery of the dose distributions was assessed via dose-accumulation using cone beam CT. This work showed that the use of DW-MRI for planning and pre-treatment imaging of MIBC patients could isotoxically improve local control of MIBC.

Published
2019

9. Three biomarkers (HER2, PD‐L1, and microsatellite status) in a large cohort of metastatic gastroesophageal adenocarcinomas: The MD Anderson Cancer Center experience.

Author

Sewastjanow‐Silva, Matheus, Kwiatkowski, Evan, Yamashita, Kohei, Abdelhakeem, Ahmed, Yoshimura, Katsuhiro, Vicentini, Ernesto R., Pizzi, Melissa P., Jin, Jiankang, Fan, Yibo, Zou, Gengyi, Wang, Lingzhi, Yin, Feng, Dhar, Shilpa S., Blum Murphy, Mariela, Mares, Jeannette E., Li, Jenny J., Gan, Qiong, Waters, Rebecca E., Rogers, Jane E., and Ajani, Jaffer A.

Subjects
EPIDERMAL growth factor, OVERALL survival, ESOPHAGEAL tumors, REGRESSION analysis, SURVIVAL analysis (Biometry)
Abstract

Human epidermal growth factor receptor‐2 (HER2), programmed death‐ligand 1 (PD‐L1), and microsatellite (MS) status are well‐established biomarkers in gastroesophageal adenocarcinomas (GEAs). However, it is unclear how the combination of these biomarkers is associated with clinicopathological factors and prognosis. This retrospective study included baseline metastatic GEA patients who were tested for all three biomarkers (HER2, PD‐L1, and MS status) at the MD Anderson Cancer Center between 2012 and 2022. Stratification was performed according to the combination of biomarker profiles: triple negative (TN), single positive (SP), and multiple positive (MP). Comparative analyses of clinicopathological factors and survival using combinations of biomarkers were performed. Among the 698 GEA patients analyzed, 251 (36.0%) were classified as TN, 334 (47.9%) as SP, and 113 (16.1%) as MP. The MP group showed a significant association with tumors located in the esophagus (p <.001), well to moderate differentiation (p <.001), and the absence of signet ring cells (p <.001). In the survival analysis, MP group had a significantly longer overall survival (OS) compared to the other groups (MP vs. TN, p <.001 and MP vs. SP, p <.001). Multivariate Cox regression analysis revealed that MP serves as an independent positive prognostic indicator for OS (hazard ratio = 0.63, p <.01). Our findings indicate that MP biomarkers are associated with a favorable prognosis in metastatic GEA. These results are reflective of clinical practice and offer valuable insights into how therapeutics and future biomarkers could influence therapy/prognosis. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Targeted and combination immunotherapies using biologics for gastric cancer: the state-of-the-art

Author

Rogers, Jane E., Gan, Qiong, Waters, Rebecca E., Horak, Ashley A., and Ajani, Jaffer A.

Abstract

ABSTRACTIntroductionGastric adenocarcinoma (GAC) remains a prevalent cancer worldwide and its incidence is increasing in South America. The heterogenous nature of GAC makes advances in management challenging.  Areas coveredDespite challenges, recent therapeutic targets are individualizing treatment. For localized disease with microsatellite-instability-high/deficient mismatch repair, immunotherapy is now an adopted practice. In the advanced unresectable setting, those harboring human epidermal growth factor receptor-2 (HER2) expression continue to be a separate entity.   Expert opinionFuture targets are developing. Among these include claudin 18.2 (CLDN18.2), fibroblast growth factor receptor 2b (FGFR2b), and trophoblast cell surface antigen-2 (TROP-2). FDA approval of zolbetuximab’s, an anti-CLDN 18.2 monoclonal antibody, is expected soon. Additionally, bemarituzumab, ananti-FGFR2b monoclonal antibody, has shown improvements in combination with chemotherapy in those with HER2 negative GAC with FGFR2 overexpression. This combination is now being investigated in a phase 3 trial. Lastly, TROP-2 has emerged as an exciting solid tumor target and study is expected in GAC. All three of these therapeutic targets have seen an abundance of drug development in recent years, and we anticipate newer targeted agents driving therapeutic decisions in GAC in the coming years.

Published
2024
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12. Performance benefits of atrium office building occupancy

Author

Rogers, Jane Brenda

Subjects
725
Abstract

The rationale of this study is to investigate the relationship between the design characteristics of atrium office buildings and the performance of the occupants leading to organisation effectiveness. A central theme is to understand the spatial configuration of the accommodation within and surrounding the atrium space and how this affects office worker behaviour. The background to this study was established through a comprehensive literature review that considered what is known about knowledge worker performance and workplace productivity and how these are measured from a behavioural perspective. The literature review established that there was a need to better understand the behaviour of office workers within the entire office building setting and presented the hypothesis of whether the particular design qualities of an atrium office design could enhance worker performance and organisational effectiveness by facilitating co-worker connectivity, a sense of community and employee well-being. Five office building and their occupants were studied during the research period using a mixed methods case study methodology which employed questionnaires, interviews, drawings, surveys and observations. Two of the office buildings were occupied by the same organisation and formed the foundation study. Crucially one of the office buildings had an atrium and the other did not. The comparative analysis resulted in several emerging themes that influenced the behaviour of the office workers within the atrium office building. These themes were then further tested in three subsequent case studies performed in owner occupied atrium office buildings of a similar size but with contrasting atrium designs and with occupants involved in different work purposes. These studies resulted in the derivation of several key design characteristics and spatial relationships that appeared to impact on worker performance and organisational effectiveness and which can be employed by designers and investors of office buildings towards the development of facilitating work environments.

Published
2016

15. Chemotherapy Plus Atezolizumab Pre- and Post-Resection in Localized Esophageal or Gastroesophageal Junction Adenocarcinomas: A Phase I/II Single-Arm Study

Author

Sewastjanow-Silva, Matheus, primary, Xiao, Lianchun, additional, Gonzalez, Graciela N., additional, Wang, Xuemei, additional, Hofstetter, Wayne, additional, Swisher, Stephen, additional, Mehran, Reza, additional, Sepesi, Boris, additional, Bhutani, Manoop S., additional, Weston, Brian, additional, Coronel, Emmanuel, additional, Waters, Rebecca E., additional, Rogers, Jane E., additional, Smith, Jackie, additional, Lyons, Larry, additional, Reilly, Norelle, additional, Yao, James C., additional, Ajani, Jaffer A., additional, and Murphy, Mariela Blum, additional

Published
2024
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16. SMARCA4 Mutations in Gastroesophageal Adenocarcinoma: An Observational Study via a Next-Generation Sequencing Panel

Author

Yamashita, Kohei, primary, Sewastjanow-Silva, Matheus, additional, Yoshimura, Katsuhiro, additional, Rogers, Jane E., additional, Rosa Vicentini, Ernesto, additional, Pool Pizzi, Melissa, additional, Fan, Yibo, additional, Zou, Gengyi, additional, Li, Jenny J., additional, Blum Murphy, Mariela, additional, Gan, Qiong, additional, Waters, Rebecca E., additional, Wang, Linghua, additional, and Ajani, Jaffer A., additional

Published
2024
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17. Direct Clinical Pharmacist-Patient Telephone Follow-Up: A Focus on GI Medical Oncology Symptom Management

Author

Rogers, Jane E., primary, Zadlo, Jennifer, additional, Leung, Cheuk Hong, additional, Nguyen, Van, additional, Leung, Michael, additional, Mace, Morgan, additional, Covert, Wendy, additional, Smack, Makenna, additional, Sirisaengtaksin, Amanda, additional, Diao, Stacy, additional, Fang, Zhou, additional, and Landgraf Oholendt, Andrea, additional

Published
2024
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20. Brain metastases in patients with upper gastrointestinal cancer is associated with proximally located adenocarcinoma and lymph node metastases

Author

Harada, Kazuto, Hwang, Hyunsoo, Wang, Xuemei, Abdelhakeem, Ahmed, Iwatsuki, Masaaki, Murphy, Mariela A. Blum, Maru, Dipen M., Weston, Brian, Lee, Jeffrey H., Rogers, Jane E., Trail, Allison, Shanbhag, Namita, Zhao, Meina, Bhutani, Manoop S., Nguyen, Quynh-Nhu, Swisher, Stephen G., Ikoma, Naruhiko, Das, Prajnan, Hofstetter, Wayne L., Badgwell, Brian D., and Ajani, Jaffer A.

Published
2020
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21. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

Author

Consortium, The International Wheat Genome Sequencing, Mayer, Klaus FX, Rogers, Jane, Doležel, Jaroslav, Pozniak, Curtis, Eversole, Kellye, Feuillet, Catherine, Gill, Bikram, Friebe, Bernd, Lukaszewski, Adam J, Sourdille, Pierre, Endo, Takashi R, Kubaláková, Marie, Číhalíková, Jarmila, Dubská, Zdeňka, Vrána, Jan, Šperková, Romana, Šimková, Hana, Febrer, Melanie, Clissold, Leah, McLay, Kirsten, Singh, Kuldeep, Chhuneja, Parveen, Singh, Nagendra K, Khurana, Jitendra, Akhunov, Eduard, Choulet, Frédéric, Alberti, Adriana, Barbe, Valérie, Wincker, Patrick, Kanamori, Hiroyuki, Kobayashi, Fuminori, Itoh, Takeshi, Matsumoto, Takashi, Sakai, Hiroaki, Tanaka, Tsuyoshi, Wu, Jianzhong, Ogihara, Yasunari, Handa, Hirokazu, Maclachlan, P Ron, Sharpe, Andrew, Klassen, Darrin, Edwards, David, Batley, Jacqueline, Olsen, Odd-Arne, Sandve, Simen Rød, Lien, Sigbjørn, Steuernagel, Burkhard, Wulff, Brande, Caccamo, Mario, Ayling, Sarah, Ramirez-Gonzalez, Ricardo H, Clavijo, Bernardo J, Wright, Jonathan, Pfeifer, Matthias, Spannagl, Manuel, Martis, Mihaela M, Mascher, Martin, Chapman, Jarrod, Poland, Jesse A, Scholz, Uwe, Barry, Kerrie, Waugh, Robbie, Rokhsar, Daniel S, Muehlbauer, Gary J, Stein, Nils, Gundlach, Heidrun, Zytnicki, Matthias, Jamilloux, Véronique, Quesneville, Hadi, Wicker, Thomas, Faccioli, Primetta, Colaiacovo, Moreno, Stanca, Antonio Michele, Budak, Hikmet, Cattivelli, Luigi, Glover, Natasha, Pingault, Lise, Paux, Etienne, Sharma, Sapna, Appels, Rudi, Bellgard, Matthew, Chapman, Brett, Nussbaumer, Thomas, Bader, Kai Christian, Rimbert, Hélène, Wang, Shichen, Knox, Ron, Kilian, Andrzej, Alaux, Michael, Alfama, Françoise, Couderc, Loïc, Guilhot, Nicolas, Viseux, Claire, Loaec, Mikaël, Keller, Beat, and Praud, Sebastien

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Human Genome, Bread, Chromosomes, Plant, Evolution, Molecular, Gene Order, Genetic Variation, Genome, Plant, Molecular Sequence Annotation, Phylogeny, Plant Proteins, Polyploidy, Sequence Analysis, DNA, Transcriptome, Triticum, International Wheat Genome Sequencing Consortium, General Science & Technology
Abstract

An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

Published
2014

23. 2474. Emergence of Candida auris in Michigan

Author

McNamara, Sara E, primary, Brennan, Brenda M, additional, Mach, Niki, additional, McGuire, Nicole, additional, Sturgis, Margaret, additional, Rogers, Jane E, additional, Malani, Anurag, additional, and Pogue, jason M, additional

Published
2023
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25. Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study

Author

Abathina, Amadou, Abubakar, Ismaela, Achidi, Eric, Agbenyega, Tsiri, Aiyegbo, Mohammed, Akoto, Alex, Allen, Angela, Allen, Stephen, Amenga-Etego, Lucas, Amodu, Folakemi, Amodu, Olukemi, Anchang-Kimbi, Judith, Ansah, Nana, Ansah, Patrick, Ansong, Daniel, Antwi, Sampson, Anyorigiya, Thomas, Apinjoh, Tobias, Asafo-Agyei, Emmanuel, Asoala, Victor, Atuguba, Frank, Auburn, Sarah, Bah, Abdou, Bamba, Kariatou, Bancone, Germana, Band, Gavin, Barnwell, David, Barry, Abdoulaye, Bauni, Evasius, Besingi, Richard, Bojang, Kalifa, Bougouma, Edith, Bull, Susan, Busby, George, Camara, Abdoulie, Camara, Landing, Campino, Susana, Carter, Richard, Carucci, Dan, Casals-Pascual, Climent, Ceesay, Ndey, Ceesay, Pa, Chau, Tran, Chuong, Ly, Clark, Taane, Clarke, Geraldine, Cole-Ceesay, Ramou, Conway, David, Cook, Katharine, Cook, Olivia, Cornelius, Victoria, Corran, Patrick, Correa, Simon, Cox, Sharon, Craik, Rachel, Danso, Bakary, Davis, Timothy, Day, Nicholas, Deloukas, Panos, Dembele, Awa, deVries, Jantina, Dewasurendra, Rajika, Diakite, Mahamadou, Diarra, Elizabeth, Dibba, Yaya, Diss, Andrea, Djimdé, Abdoulaye, Dolo, Amagana, Doumbo, Ogobara, Doyle, Alan, Drakeley, Chris, Drury, Eleanor, Duffy, Patrick, Dunstan, Sarah, Ebonyi, Augustine, Elhassan, Ahmed, Elhassan, Ibrahim, Elzein, Abier, Enimil, Anthony, Esangbedo, Pamela, Evans, Jennifer, Evans, Julie, Farrar, Jeremy, Fernando, Deepika, Fitzpatrick, Kathryn, Fullah, Janet, Garcia, Jacob, Ghansah, Anita, Gottleib, Michael, Green, Angie, Hart, Lee, Hennsman, Meike, Hien, Tran, Hieu, Nguyen, Hilton, Eliza, Hodgson, Abraham, Horstmann, Rolf, Hubbart, Christina, Hughes, Catherine, Hussein, Ayman, Hutton, Robert, Ibrahim, Muntaser, Ishengoma, Deus, Jaiteh, Jula, Jallow, Mariatou, Jallow, Muminatou, Jammeh, Kebba, Jasseh, Momodou, Jeffreys, Anna, Jobarteh, Amie, Johnson, Kimberly, Joseph, Sarah, Jyothi, Dushyanth, Kachala, David, Kamuya, Dorcas, Kanyi, Haddy, Karunajeewa, Harin, Karunaweera, Nadira, Keita, Momodou, Kerasidou, Angeliki, Khan, Aja, Kivinen, Katja, Kokwaro, Gilbert, Konate, Amadou, Konate, Salimata, Koram, Kwadwo, Kwiatkowski, Dominic, Laman, Moses, Le, Si, Leffler, Ellen, Lemnge, Martha, Lin, Enmoore, Ly, Alioune, Macharia, Alexander, MacInnis, Bronwyn, Mai, Nguyen, Makani, Julie, Malangone, Cinzia, Mangano, Valentina, Manjurano, Alphaxard, Manneh, Lamin, Manning, Laurens, Manske, Magnus, Marsh, Kevin, Marsh, Vicki, Maslen, Gareth, Maxwell, Caroline, Mbunwe, Eric, McCreight, Marilyn, Mead, Daniel, Mendy, Alieu, Mendy, Anthony, Mensah, Nathan, Michon, Pascal, Miles, Alistair, Miotto, Olivo, Modiano, David, Mohamed, Hiba, Molloy, Sile, Molyneux, Malcolm, Molyneux, Sassy, Moore, Mike, Moyes, Catherine, Mtei, Frank, Mtove, George, Mueller, Ivo, Mugri, Regina, Munthali, Annie, Mutabingwa, Theonest, Nadjm, Behzad, Ndi, Andre, Ndila, Carolyne, Newton, Charles, Niangaly, Amadou, Njie, Haddy, Njie, Jalimory, Njie, Madi, Njie, Malick, Njie, Sophie, Njiragoma, Labes, Nkrumah, Francis, Ntunthama, Neema, Nyika, Aceme, Nyirongo, Vysaul, O'Brien, John, Obu, Herbert, Oduro, Abraham, Ofori, Alex, Olaniyan, Subulade, Olaosebikan, Rasaq, Oluoch, Tom, Omotade, Olayemi, Oni, Olajumoke, Onykwelu, Emmanuel, Opi, Daniel, Orimadegun, Adebola, O'Riordan, Sean, Ouedraogo, Issa, Oyola, Samuel, Parker, Michael, Pearson, Richard, Pensulo, Paul, Peshu, Norbert, Phiri, Ajib, Phu, Nguyen, Pinder, Margaret, Pirinen, Matti, Plowe, Chris, Potter, Claire, Poudiougou, Belco, Puijalon, Odile, Quyen, Nguyen, Ragoussis, Ioannis, Ragoussis, Jiannis, Rasheed, Oba, Reeder, John, Reyburn, Hugh, Riley, Eleanor, Risley, Paul, Rockett, Kirk, Rodford, Joanne, Rogers, Jane, Rogers, William, Rowlands, Kate, Ruano-Rubio, Valentín, Sabally-Ceesay, Kumba, Sadiq, Abubacar, Saidy-Khan, Momodou, Saine, Horeja, Sakuntabhai, Anavaj, Sall, Abdourahmane, Sambian, David, Sambou, Idrissa, SanJoaquin, Miguel, Sepúlveda, Nuno, Shah, Shivang, Shelton, Jennifer, Siba, Peter, Silva, Nilupa, Simmons, Cameron, Simpore, Jaques, Singhasivanon, Pratap, Sinh, Dinh, Sirima, Sodiomon, Sirugo, Giorgio, Sisay-Joof, Fatoumatta, Sissoko, Sibiry, Small, Kerrin, Somaskantharajah, Elilan, Spencer, Chris, Stalker, Jim, Stevens, Marryat, Suriyaphol, Prapat, Sylverken, Justice, Taal, Bintou, Tall, Adama, Taylor, Terrie, Teo, Yik, Thai, Cao, Thera, Mahamadou, Titanji, Vincent, Toure, Ousmane, Troye-Blomberg, Marita, Usen, Stanley, Uyoga, Sophie, Vanderwal, Aaron, Wangai, Hannah, Watson, Renee, Williams, Thomas, Wilson, Michael, Wrigley, Rebecca, Yafi, Clarisse, Yamoah, Lawrence, Ndila, Carolyne M, Macharia, Alexander W, Nyutu, Gideon, Ojal, John, Shebe, Mohammed, Awuondo, Kennedy O, Mturi, Neema, Tsofa, Benjamin, Clark, Taane G, Kariuki, Silvia, Mackinnon, Margaret, Maitland, Kathryn, Kwiatkowski, Dominic P, Rockett, Kirk A, and Williams, Thomas N

Published
2018
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26. Potentially curable gastric adenocarcinoma treated without surgery

Author

Mizrak Kaya, Dilsa, Nogueras-Gonzáles, Graciela M., Harada, Kazuto, Amlashi, Fatemeh G., Thomas, Irene, Rogers, Jane E., Bhutani, Manoop S., Lee, Jeffrey H., Weston, Brian, Minsky, Bruce D., Estrella, Jeannelyn S., Blum Murphy, Mariela A., Matamoros, Aurelio, Jr., Devine, Catherine E., Das, Prajnan, Badgwell, Brian D., and Ajani, Jaffer A.

Published
2018
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29. Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution.

Author

Carbone, Lucia, Harris, R Alan, Vessere, Gery M, Mootnick, Alan R, Humphray, Sean, Rogers, Jane, Kim, Sung K, Wall, Jeffrey D, Martin, David, Jurka, Jerzy, Milosavljevic, Aleksandar, and de Jong, Pieter J

Subjects
Animals, Humans, Hylobates, Cytosine, Chromosome Mapping, Karyotyping, Evolution, Molecular, Species Specificity, DNA Methylation, Epigenesis, Genetic, Gene Rearrangement, Alu Elements, Synteny, Genome, Human, Models, Genetic, DNA Breaks, Epigenesis, Genetic, Evolution, Molecular, Genome, Human, Models, Genetics, Developmental Biology
Abstract

Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15-18 million years ago. The cause of this increased rate of chromosomal rearrangements is not known, nor is it known if genome architecture has a role. To address this question, we analyzed sequences spanning 57 breaks of synteny between northern white-cheeked gibbons (Nomascus l. leucogenys) and humans. We find that the breakpoint regions are enriched in segmental duplications and repeats, with Alu elements being the most abundant. Alus located near the gibbon breakpoints (

Published
2009

32. Nivolumab for previously treated unresectable metastatic anal cancer (NCI9673): a multicentre, single-arm, phase 2 study

Author

Morris, Van K, Salem, Mohamed E, Nimeiri, Halla, Iqbal, Syma, Singh, Preet, Ciombor, Kristen, Polite, Blase, Deming, Dustin, Chan, Emily, Wade, James L, Xiao, Lianchun, Bekaii-Saab, Tanios, Vence, Luis, Blando, Jorge, Mahvash, Armeen, Foo, Wai Chin, Ohaji, Chimela, Pasia, Manolo, Bland, Gail, Ohinata, Aki, Rogers, Jane, Mehdizadeh, Amir, Banks, Kimberly, Lanman, Richard, Wolff, Robert A, Streicher, Howard, Allison, James, Sharma, Padmanee, and Eng, Cathy

Published
2017
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34. Total Lesion Glycolysis Assessment Identifies a Patient Fraction With a High Cure Rate Among Esophageal Adenocarcinoma Patients Treated With Definitive Chemoradiation

Author

Harada, Kazuto, Wu, Carol C., Wang, Xuemei, Mizrak Kaya, Dilsa, Amlashi, Fatemeh G., Iwatsuki, Masaaki, Blum Murphy, Mariela A., Maru, Dipen M., Weston, Brian, Lee, Jeffrey H., Rogers, Jane E., Thomas, Irene, Shanbhag, Namita, Bhutani, Manoop S., Hofstetter, Wayne L., Nguyen, Quynh-Nhu, and Ajani, Jaffer A.

Published
2020
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35. Taxane-based or platinum-based combination chemotherapy given concurrently with radiation followed by surgery resulting in high cure rates in esophageal cancer patients

Author

Lopez, Anthony, Harada, Kazuto, Chen, Hsiang-Chun, Bhutani, Manoop S., Weston, Brian, Lee, Jeffrey H., Maru, Dipen M., Chin, Foo Wai, Rogers, Jane E., Thomas, Irene, Amlashi, Fatemeh G., Blum-Murphy, Mariela A., Rice, David C., Zhao, Meina, Hofstetter, Wayne L., Nguyen, Quynh, and Ajani, Jaffer A.

Published
2020
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37. Total Lesion Glycolysis Assessment Identifies a Patient Fraction With a High Cure Rate Among Esophageal Adenocarcinoma Patients Treated With Definitive Chemoradiation

Author

Harada, Kazuto, Wu, Carol C., Wang, Xuemei, Mizrak Kaya, Dilsa, Amlashi, Fatemeh G., Iwatsuki, Masaaki, Blum Murphy, Mariela A., Maru, Dipen M., Weston, Brian, Lee, Jeffrey H., Rogers, Jane E., Thomas, Irene, Shanbhag, Namita, Bhutani, Manoop S., Hofstetter, Wayne L., Nguyen, Quynh-Nhu, and Ajani, Jaffer A.

Published
2019
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38. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.

Author

Stein, Lincoln D, Bao, Zhirong, Blasiar, Darin, Blumenthal, Thomas, Brent, Michael R, Chen, Nansheng, Chinwalla, Asif, Clarke, Laura, Clee, Chris, Coghlan, Avril, Coulson, Alan, D'Eustachio, Peter, Fitch, David HA, Fulton, Lucinda A, Fulton, Robert E, Griffiths-Jones, Sam, Harris, Todd W, Hillier, LaDeana W, Kamath, Ravi, Kuwabara, Patricia E, Mardis, Elaine R, Marra, Marco A, Miner, Tracie L, Minx, Patrick, Mullikin, James C, Plumb, Robert W, Rogers, Jane, Schein, Jacqueline E, Sohrmann, Marc, Spieth, John, Stajich, Jason E, Wei, C, Willey, David, Wilson, Richard K, Durbin, Richard, and Waterston, Robert H

Subjects
Chromosomes, Artificial, Bacterial, Animals, Caenorhabditis, Caenorhabditis elegans, Proteins, MicroRNAs, RNA, Codon, RNA, Ribosomal, RNA, Transfer, RNA, Spliced Leader, Cluster Analysis, Models, Statistical, Chromosome Mapping, Physical Chromosome Mapping, Sequence Analysis, DNA, Genomics, Evolution, Molecular, Species Specificity, Interspersed Repetitive Sequences, Conserved Sequence, Protein Structure, Tertiary, Gene Library, Multigene Family, Open Reading Frames, Genome, Introns, Exons, Plasmids, Models, Genetic, Molecular Sequence Data, Biological Evolution, Chromosomes, Artificial, Bacterial, Ribosomal, Transfer, Spliced Leader, Models, Statistical, Sequence Analysis, DNA, Evolution, Molecular, Protein Structure, Tertiary, Genetic, Developmental Biology, Biological Sciences, Medical and Health Sciences, Agricultural and Veterinary Sciences
Abstract

The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes.

Published
2003

39. Influence of induction chemotherapy in trimodality therapy-eligible oesophageal cancer patients: secondary analysis of a randomised trial

Author

Shimodaira, Yusuke, Slack, Rebecca S, Harada, Kazuto, Chen, Hsiang-Chun, Sagebiel, Tara, Bhutani, Manoop S, Lee, Jeffrey H, Weston, Brian, Elimova, Elena, Lin, Quan, Amlashi, Fatemeh G, Mizrak Kaya, Dilsa, Blum, Mariela A, Roth, Jack A, Swisher, Stephen G, Skinner, Heath D, Hofstetter, Wayne L, Rogers, Jane E, Mares, Jaennette, Thomas, Irene, Maru, Dipen M, Komaki, Ritsuko, Walsh, Garrett, and Ajani, Jaffer A

Published
2018
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40. Early Metabolic Change after Induction Chemotherapy Predicts Histologic Response and Prognosis in Patients with Esophageal Cancer: Secondary Analysis of a Randomized Trial

Author

Harada, Kazuto, Wang, Xuemei, Shimodaira, Yusuke, Sagebiel, Tara, Bhutani, Manoop S., Lee, Jeffrey H., Weston, Brian, Elimova, Elena, Lin, Quan, Amlashi, Fatemeh G., Mizrak Kaya, Dilsa, Lopez, Anthony, Blum Murphy, Mariela A., Roth, Jack A., Swisher, Stephen G., Skinner, Heath D., Hofstetter, Wayne L., Rogers, Jane E., Thomas, Irene, Maru, Dipen M., Komaki, Ritsuko, Walsh, Garrett, and Ajani, Jaffer A.

Published
2018
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45. Postpartum haemorrhage occurring in UK midwifery units: A national population-based case-control study to investigate incidence, risk factors and outcomes.

Author

Elkington, Madeline, Kurinczuk, Jennifer J., Pasupathy, Dharmintra, Plachcinski, Rachel, Rogers, Jane, Williams, Catherine, and Rowe, Rachel

Subjects
POSTPARTUM hemorrhage, THIRD stage of labor (Obstetrics), MIDWIFERY, CASE-control method, PREGNANCY complications, PUERPERAL disorders, EMBRYO transfer, OBSTETRICAL forceps
Abstract

Objectives: To estimate the incidence of, and investigate risk factors for, postpartum haemorrhage (PPH) requiring transfer to obstetric care following birth in midwifery units (MU) in the UK; to describe outcomes for women who experience PPH requiring transfer to obstetric care. Methods: We conducted a national population-based case-control study in all MUs in the UK using the UK Midwifery Study System (UKMidSS). Between September 2019 and February 2020, 1501 women with PPH requiring transfer to obstetric care following birth in an MU, and 1475 control women were identified. We used multivariable logistic regression, generating adjusted odds ratios (aORs) and 95% confidence intervals (CIs) to investigate risk factors for PPH requiring transfer to obstetric care. Results: The incidence of PPH requiring transfer to obstetric care following birth in an MU was 3.7% (95% CI 3.6%-3.9%). Factors independently associated with PPH requiring transfer to obstetric care were smoking during pregnancy (aOR = 0.73; 95% CI 0.56–0.94), nulliparity (aOR = 1.96; 95% CI 1.66–2.30), previous PPH (aOR = 2.67; 95% CI 1.67–4.25), complications in a previous pregnancy other than PPH (aOR = 2.40; 95% CI 1.25–4.60), gestational age ≥41 weeks (aOR = 1.36; 95% CI 1.10–1.69), instrumental birth (aOR = 2.69; 95% CI 1.53–4.72), third stage of labour ≥60 minutes (aOR = 5.56; 95% CI 3.93–7.88), perineal trauma (aOR = 4.67; 95% CI 3.16–6.90), and birthweight 3500-3999g (aOR = 1.71; 95% CI 1.42–2.07) or ≥4000g (aOR = 2.31; 95% CI 1.78–3.00). One in ten (10.6%) cases received a blood transfusion and one in five (21.0%) were admitted to higher level care. Conclusions: The risk factors identified in this study align with those identified in previous research and with current guidelines for women planning birth in an MU in the UK. Maternal outcomes after PPH were broadly reassuring and indicative of appropriate management. NHS organisations should ensure that robust guidelines are in place to support management of PPH in MUs. [ABSTRACT FROM AUTHOR]

Published
2023
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46. Supplementary Table 8 from Insertional Mutagenesis in Mice Deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 Reveals Cancer Gene Interactions and Correlations with Tumor Phenotypes

Author

Kool, Jaap, primary, Uren, Anthony G., primary, Martins, Carla P., primary, Sie, Daoud, primary, de Ridder, Jeroen, primary, Turner, Geoffrey, primary, van Uitert, Miranda, primary, Matentzoglu, Konstantin, primary, Lagcher, Wendy, primary, Krimpenfort, Paul, primary, Gadiot, Jules, primary, Pritchard, Colin, primary, Lenz, Jack, primary, Lund, Anders H., primary, Jonkers, Jos, primary, Rogers, Jane, primary, Adams, David J., primary, Wessels, Lodewyk, primary, Berns, Anton, primary, and van Lohuizen, Maarten, primary

Published
2023
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47. Data from Insertional Mutagenesis in Mice Deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 Reveals Cancer Gene Interactions and Correlations with Tumor Phenotypes

Author

Kool, Jaap, primary, Uren, Anthony G., primary, Martins, Carla P., primary, Sie, Daoud, primary, de Ridder, Jeroen, primary, Turner, Geoffrey, primary, van Uitert, Miranda, primary, Matentzoglu, Konstantin, primary, Lagcher, Wendy, primary, Krimpenfort, Paul, primary, Gadiot, Jules, primary, Pritchard, Colin, primary, Lenz, Jack, primary, Lund, Anders H., primary, Jonkers, Jos, primary, Rogers, Jane, primary, Adams, David J., primary, Wessels, Lodewyk, primary, Berns, Anton, primary, and van Lohuizen, Maarten, primary

Published
2023
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48. Supplementary Table 10 from Insertional Mutagenesis in Mice Deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 Reveals Cancer Gene Interactions and Correlations with Tumor Phenotypes

Author

Kool, Jaap, primary, Uren, Anthony G., primary, Martins, Carla P., primary, Sie, Daoud, primary, de Ridder, Jeroen, primary, Turner, Geoffrey, primary, van Uitert, Miranda, primary, Matentzoglu, Konstantin, primary, Lagcher, Wendy, primary, Krimpenfort, Paul, primary, Gadiot, Jules, primary, Pritchard, Colin, primary, Lenz, Jack, primary, Lund, Anders H., primary, Jonkers, Jos, primary, Rogers, Jane, primary, Adams, David J., primary, Wessels, Lodewyk, primary, Berns, Anton, primary, and van Lohuizen, Maarten, primary

Published
2023
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49. Supplementary Figure 1B from Insertional Mutagenesis in Mice Deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 Reveals Cancer Gene Interactions and Correlations with Tumor Phenotypes

Author

Kool, Jaap, primary, Uren, Anthony G., primary, Martins, Carla P., primary, Sie, Daoud, primary, de Ridder, Jeroen, primary, Turner, Geoffrey, primary, van Uitert, Miranda, primary, Matentzoglu, Konstantin, primary, Lagcher, Wendy, primary, Krimpenfort, Paul, primary, Gadiot, Jules, primary, Pritchard, Colin, primary, Lenz, Jack, primary, Lund, Anders H., primary, Jonkers, Jos, primary, Rogers, Jane, primary, Adams, David J., primary, Wessels, Lodewyk, primary, Berns, Anton, primary, and van Lohuizen, Maarten, primary

Published
2023
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50. Supplementary Table 6 from Insertional Mutagenesis in Mice Deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 Reveals Cancer Gene Interactions and Correlations with Tumor Phenotypes

Author

Kool, Jaap, primary, Uren, Anthony G., primary, Martins, Carla P., primary, Sie, Daoud, primary, de Ridder, Jeroen, primary, Turner, Geoffrey, primary, van Uitert, Miranda, primary, Matentzoglu, Konstantin, primary, Lagcher, Wendy, primary, Krimpenfort, Paul, primary, Gadiot, Jules, primary, Pritchard, Colin, primary, Lenz, Jack, primary, Lund, Anders H., primary, Jonkers, Jos, primary, Rogers, Jane, primary, Adams, David J., primary, Wessels, Lodewyk, primary, Berns, Anton, primary, and van Lohuizen, Maarten, primary

Published
2023
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