195 results on '"Morgan, MB"'
Search Results
2. Comprehensive molecular characterization of human colon and rectal cancer
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Collisson, Eric, Muzny, DM, Bainbridge, MN, Chang, K, Dinh, HH, Drummond, JA, Fowler, G, Kovar, CL, Lewis, LR, Morgan, MB, and Newsham, IF
- Abstract
To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) unde
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- 2012
3. Integrated genomic analyses of ovarian carcinoma
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Bell, D, Berchuck, A, Birrer, M, Chien, J, Cramer, DW, Dao, F, Dhir, R, DiSaia, P, Gabra, H, Glenn, P, Godwin, AK, Gross, J, Hartmann, L, Huang, M, Huntsman, DG, Iacocca, M, Imielinski, M, Kalloger, S, Karlan, BY, Levine, DA, Mills, GB, Morrison, C, Mutch, D, Olvera, N, Orsulic, S, Park, K, Petrelli, N, Rabeno, B, Rader, JS, Sikic, BI, Smith-McCune, K, Sood, AK, Bowtell, D, Penny, R, Testa, JR, Chang, K, Creighton, CJ, Dinh, HH, Drummond, JA, Fowler, G, Gunaratne, P, Hawes, AC, Kovar, CL, Lewis, LR, Morgan, MB, Newsham, IF, Santibanez, J, Reid, JG, Trevino, LR, Wu, Y-Q, Wang, M, Muzny, DM, Wheeler, DA, Gibbs, RA, Getz, G, Lawrence, MS, Cibulskis, K, Sivachenko, AY, Sougnez, C, Voet, D, Wilkinson, J, Bloom, T, Ardlie, K, Fennell, T, Baldwin, J, Nichol, R, Fisher, S, Gabriel, S, Lander, ES, Ding, L, Fulton, RS, Koboldt, DC, McLellan, MD, Wylie, T, Walker, J, O’Laughlin, M, Dooling, DJ, Fulton, L, Abbott, R, Dees, ND, Zhang, Q, Kandoth, C, Wendl, M, Schierding, W, Shen, D, Harris, CC, Schmidt, H, Kalicki, J, Delehaunty, KD, Fronick, CC, Demeter, R, Cook, L, Wallis, JW, Lin, L, Magrini, VJ, Hodges, JS, Eldred, JM, Smith, SM, Pohl, CS, and Vandin, F
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Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Oncology and Carcinogenesis ,Cancer Genomics ,Biotechnology ,Women's Health ,Ovarian Cancer ,Cancer ,Rare Diseases ,Breast Cancer ,Genetic Testing ,Human Genome ,2.1 Biological and endogenous factors ,Aged ,Carcinoma ,DNA Methylation ,Female ,Gene Dosage ,Gene Expression Profiling ,Gene Expression Regulation ,Neoplastic ,Genomics ,Humans ,MicroRNAs ,Middle Aged ,Mutation ,Ovarian Neoplasms ,RNA ,Messenger ,Cancer Genome Atlas Research Network ,General Science & Technology - Abstract
A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients' lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade serous ovarian adenocarcinomas and the DNA sequences of exons from coding genes in 316 of these tumours. Here we report that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1, BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three microRNA subtypes, four promoter methylation subtypes and a transcriptional signature associated with survival duration, and shed new light on the impact that tumours with BRCA1/2 (BRCA1 or BRCA2) and CCNE1 aberrations have on survival. Pathway analyses suggested that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in serous ovarian cancer pathophysiology.
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- 2011
4. Integrated genomic analyses of ovarian carcinoma
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Bell, D, Berchuck, A, Birrer, M, Chien, J, Cramer, DW, Dao, F, Dhir, R, DiSaia, P, Gabra, H, Glenn, P, Godwin, AK, Triche, T, Berman, BP, Van den Berg, DJ, Buckley, J, Baylin, SB, Zhang, J, Spellman, PT, Purdom, E, Iacocca, M, Shelton, T, Voet, D, Neuvial, P, Bengtsson, H, Jakkula, LR, Durinck, S, Han, J, Dorton, S, Marr, H, Zhang, H, Choi, YG, Wang, V, Wilkinson, J, Nguyen, H, Wang, NJ, Imielinski, M, Ngai, J, Conboy, JG, Parvin, B, Feiler, HS, Speed, TP, Gray, JW, Wu, CJ, Bloom, T, Levine, DA, Li, L, Socci, ND, Liang, Y, Taylor, BS, Kalloger, S, Schultz, N, Borsu, L, Lash, AE, Brennan, C, Ardlie, K, Viale, A, Shukla, S, Grimm, D, Sander, C, Ladanyi, M, Hoadley, KA, Meng, S, Du, Y, Karlan, BY, Shi, Y, Fennell, T, Cibulskis, K, Lawrence, MS, Meyerson, M, Hatfield, M, Mills, GB, Sivachenko, A, Jing, R, Park, RW, Liu, Y, Park, PJ, Ramos, AH, Noble, M, Chin, L, Carter, H, Kim, D, Morris, S, Winckler, W, Karchin, R, Morrison, C, Baldwin, J, Korkola, JE, Yena, P, Heiser, LM, Getz, G, Cho, RJ, Hu, Z, Gabriel, S, Mutch, D, Cerami, E, Rhodes, P, Olshen, A, Verhaak, RGW, Lander, ES, Reva, B, Antipin, Y, Shen, R, Olvera, N, Mankoo, P, Sheridan, R, Ciriello, G, Sherman, M, Chang, WK, Bernanke, JA, Hayes, DN, Carter, SL, Haussler, D, Orsulic, S, Benz, CC, Paulauskis, J, Stuart, JM, Zhang, N, Benz, SC, Sanborn, JZ, Vaske, CJ, Mermel, CH, Zhu, J, Szeto, C, Scott, GK, Yau, C, Rabeno, B, Ding, L, Park, K, Balu, S, Perou, CM, Saksena, G, Wilkerson, MD, Millis, S, Kahn, A, Turman, YJ, Fulton, RS, Onofrio, RC, Greene, JM, Sfeir, R, Jensen, MA, Chen, J, Whitmore, J, Alonso, S, Jordan, J, Chu, A, Rader, JS, Koboldt, DC, Zang, D, Gross, J, Barker, A, Compton, C, Eley, G, Ferguson, M, Fielding, P, Gerhard, DS, Myles, R, McLellan, MD, Schaefer, C, Helms, EB, Shaw, KRM, Sikic, BI, Vaught, J, Vockley, JB, Good, PJ, Guyer, MS, Ozenberger, B, Wylie, T, Peterson, J, Thomson, E, Smith-McCune, K, Sood, AK, Bowtell, D, Hubbard, D, Penny, R, Testa, JR, Chang, K, Walker, J, Dinh, HH, Drummond, JA, Fowler, G, Zhou, X, Gunaratne, P, Hawes, AC, Kovar, CL, Lewis, LR, Gupta, S, Morgan, MB, O'Laughlin, M, Newsham, IF, Santibanez, J, Reid, JG, Trevino, LR, Wu, J, Wu, Y-Q, Wang, M, Muzny, DM, Wheeler, DA, Gibbs, RA, Crenshaw, A, Sivachenko, AY, Topal, MD, Sougnez, C, Dooling, DJ, Fulton, L, Akbani, R, Abbott, R, Dees, ND, Zhang, Q, Kandoth, C, Wendl, M, Schierding, W, Shen, D, Harris, CC, Baggerly, KA, Schmidt, H, Wilson, RK, Kalicki, J, Delehaunty, KD, Fronick, CC, Demeter, R, Cook, L, Wallis, JW, Lin, L, Magrini, VJ, Yung, WK, Hodges, JS, Protopopov, A, Eldred, JM, Smith, SM, Pohl, CS, Vandin, F, Raphael, BJ, Weinstock, GM, Mardis, R, Kim, TM, Hartmann, L, Perna, I, Xiao, Y, Ren, G, Sathiamoorthy, N, Petrelli, N, Lee, E, Kucherlapati, R, Absher, DM, Huang, M, Waite, L, Sherlock, G, Brooks, JD, Li, JZ, Weinstein, JN, Xu, J, Myers, RM, Laird, PW, Cope, L, Herman, JG, Shen, H, Huntsman, DG, Weisenberger, DJ, Noushmehr, H, Pan, F, Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., and Meyerson, Matthew L.
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endocrine system diseases ,Serous carcinoma ,Messenger ,Gene Dosage ,Cancer Genome Atlas Research Network ,GYNECOLOGIC-ONCOLOGY-GROUP ,GRADE SEROUS CARCINOMA ,0302 clinical medicine ,Ovarian carcinoma ,Aged ,Carcinoma ,DNA Methylation ,Female ,Gene Expression Profiling ,Gene Expression Regulation, Neoplastic ,Humans ,MicroRNAs ,Middle Aged ,Mutation ,Ovarian Neoplasms ,RNA, Messenger ,Genomics ,Multidisciplinary ,Genetics ,HYBRID SELECTION ,0303 health sciences ,female genital diseases and pregnancy complications ,3. Good health ,Multidisciplinary Sciences ,Serous fluid ,BRCA MUTATION CARRIERS ,030220 oncology & carcinogenesis ,DNA methylation ,PARP inhibitor ,Science & Technology - Other Topics ,General Science & Technology ,Biology ,Article ,03 medical and health sciences ,CLEAR-CELL CARCINOMA ,MD Multidisciplinary ,microRNA ,HIGH-THROUGHPUT ANNOTATION ,medicine ,DRIVER MUTATIONS ,Gene ,030304 developmental biology ,Neoplastic ,Science & Technology ,MUTANT-CELLS ,SOMATIC MUTATIONS ,medicine.disease ,CANCER STATISTICS ,Gene Expression Regulation ,Cancer research ,RNA ,Ovarian cancer - Abstract
A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients’ lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade serous ovarian adenocarcinomas and the DNA sequences of exons from coding genes in 316 of these tumours. Here we report that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1, BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three microRNA subtypes, four promoter methylation subtypes and a transcriptional signature associated with survival duration, and shed new light on the impact that tumours with BRCA1/2 (BRCA1 or BRCA2) and CCNE1 aberrations have on survival. Pathway analyses suggested that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in serous ovarian cancer pathophysiology., National Institutes of Health (U.S.) (Grant U54HG003067), National Institutes of Health (U.S.) (Grant U54HG003273), National Institutes of Health (U.S.) (Grant U54HG003079), National Institutes of Health (U.S.) (Grant U24CA126543), National Institutes of Health (U.S.) (Grant U24CA126544), National Institutes of Health (U.S.) (Grant U24CA126546), National Institutes of Health (U.S.) (Grant U24CA126551), National Institutes of Health (U.S.) (Grant U24CA126554), National Institutes of Health (U.S.) (Grant U24CA126561), National Institutes of Health (U.S.) (Grant U24CA126563), National Institutes of Health (U.S.) (Grant U24CA143882), National Institutes of Health (U.S.) (Grant U24CA143731), National Institutes of Health (U.S.) (Grant U24CA143835), National Institutes of Health (U.S.) (Grant U24CA143845), National Institutes of Health (U.S.) (Grant U24CA143858), National Institutes of Health (U.S.) (Grant U24CA144025), National Institutes of Health (U.S.) (Grant U24CA143866), National Institutes of Health (U.S.) (Grant U24CA143867), National Institutes of Health (U.S.) (Grant U24CA143848), National Institutes of Health (U.S.) (Grant U24CA143843), National Institutes of Health (U.S.) (Grant R21CA135877)
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- 2010
5. Genome sequence of the pea aphid Acyrthosiphon pisum
- Author
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Richards, S, Gibbs, RA, Gerardo, NM, Moran, N, Nakabachi, A, Stern, D, Tagu, D, Wilson, ACC, Muzny, D, Kovar, C, Cree, A, Chacko, J, Chandrabose, MN, Dao, MD, Dinh, HH, Gabisi, RA, Hines, S, Hume, J, Jhangian, SN, Joshi, V, Lewis, LR, Liu, Y-S, Lopez, J, Morgan, MB, Nguyen, NB, Okwuonu, GO, Ruiz, SJ, Santibanez, J, Wright, RA, Fowler, GR, Hitchens, ME, Lozado, RJ, Moen, C, Steffen, D, Warren, JT, Zhang, J, Nazareth, LV, Chavez, D, Davis, C, Lee, SL, Patel, BM, Pu, L-L, Bell, SN, Johnson, AJ, Vattathil, S, Jr, WRL, Shigenobu, S, Dang, PM, Morioka, M, Fukatsu, T, Kudo, T, Miyagishima, S-Y, Jiang, H, Worley, KC, Legeai, F, Gauthier, J-P, Collin, O, Zhang, L, Chen, H-C, Ermolaeva, O, Hlavina, W, Kapustin, Y, Kiryutin, B, Kitts, P, Maglott, D, Murphy, T, Pruitt, K, Sapojnikov, V, Souvorov, A, Thibaud-Nissen, F, Camara, F, Guigo, R, Stanke, M, Solovyev, V, Kosarev, P, Gilbert, D, Gabaldon, T, Huerta-Cepas, J, Marcet-Houben, M, Pignatelli, M, Moya, A, Rispe, C, Ollivier, M, Quesneville, H, Permal, E, Llorens, C, Futami, R, Hedges, D, Robertson, HM, Alioto, T, Mariotti, M, Nikoh, N, McCutcheon, JP, Burke, G, Kamins, A, Latorre, A, Moran, NA, Ashton, P, Calevro, F, Charles, H, Colella, S, Douglas, A, Jander, G, Jones, DH, Febvay, G, Kamphuis, LG, Kushlan, PF, Macdonald, S, Ramsey, J, Schwartz, J, Seah, S, Thomas, G, Vellozo, A, Cass, B, Degnan, P, Hurwitz, B, Leonardo, T, Koga, R, Altincicek, B, Anselme, C, Atamian, H, Barribeau, SM, de Vos, M, Duncan, EJ, Evans, J, Ghanim, M, Heddi, A, Kaloshian, I, Vincent-Monegat, C, Parker, BJ, Perez-Brocal, V, Rahbe, Y, Spragg, CJ, Tamames, J, Tamarit, D, Tamborindeguy, C, Vilcinskas, A, Bickel, RD, Brisson, JA, Butts, T, Chang, C-C, Christiaens, O, Davis, GK, Duncan, E, Ferrier, D, Iga, M, Janssen, R, Lu, H-L, McGregor, A, Miura, T, Smagghe, G, Smith, J, van der Zee, M, Velarde, R, Wilson, M, Dearden, P, Edwards, OR, Gordon, K, Hilgarth, RS, Jr, RSD, Srinivasan, D, Walsh, TK, Ishikawa, A, Jaubert-Possamai, S, Fenton, B, Huang, W, Rizk, G, Lavenier, D, Nicolas, J, Smadja, C, Zhou, J-J, Vieira, FG, He, X-L, Liu, R, Rozas, J, Field, LM, Ashton, PD, Campbell, P, Carolan, JC, Douglas, AE, Fitzroy, CIJ, Reardon, KT, Reeck, GR, Singh, K, Wilkinson, TL, Huybrechts, J, Abdel-latief, M, Robichon, A, Veenstra, JA, Hauser, F, Cazzamali, G, Schneider, M, Williamson, M, Stafflinger, E, Hansen, KK, Grimmelikhuijzen, CJP, Price, DRG, Caillaud, M, van Fleet, E, Ren, Q, Gatehouse, JA, Brault, V, Monsion, B, Diaz, J, Hunnicutt, L, Ju, H-J, Pechuan, X, Aguilar, J, Cortes, T, Ortiz-Rivas, B, Martinez-Torres, D, Dombrovsky, A, Dale, RP, Davies, TGE, Williamson, MS, Jones, A, Sattelle, D, Williamson, S, Wolstenholme, A, Cottret, L, Sagot, MF, Heckel, DG, Hunter, W, Consortium, IAG, Universitat de Barcelona, Princeton University, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Baylor College of Medicine (BCM), Baylor University, An algorithmic view on genomes, cells, and environments (BAMBOO), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), IAGC, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon, Eisen, Jonathan A., and Eisen, Jonathan A
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0106 biological sciences ,TANDEM REPEATS ,Genome, Insect ,Gene Transfer ,RRES175 ,Sequència genòmica ,Faculty of Science\Computer Science ,CPG METHYLATION ,01 natural sciences ,Genome ,Medical and Health Sciences ,International Aphid Genomics Consortium ,Biologiska vetenskaper ,Biology (General) ,GENE-EXPRESSION ,2. Zero hunger ,Genetics ,0303 health sciences ,Aphid ,Afídids ,General Neuroscience ,GENOME SEQUENCE ,food and beverages ,DROSOPHILA CIRCADIAN CLOCK ,Biological Sciences ,Genetics and Genomics/Microbial Evolution and Genomics ,INSECTE ,Genètica microbiana ,puceron ,APIS-MELLIFERA ,General Agricultural and Biological Sciences ,Infection ,symbiose ,Biotechnology ,Research Article ,VIRUS VECTORING ,175_Genetics ,SYMBIOTIC BACTERIA ,Gene Transfer, Horizontal ,QH301-705.5 ,ACYRTHOSIPHON PISUM ,Biology ,HOLOMETABOLOUS INSECTS ,HOST-PLANT ,010603 evolutionary biology ,PEA APHID ,INSECT-PLANT ,PHENOTYPIC PLASTICITY ,RAVAGEUR DES CULTURES ,SOCIAL INSECT ,General Biochemistry, Genetics and Molecular Biology ,Horizontal ,03 medical and health sciences ,Buchnera ,Gene family ,Life Science ,Animals ,Symbiosis ,Gene ,030304 developmental biology ,Whole genome sequencing ,General Immunology and Microbiology ,Annotation ,Genome sequence ,Agricultural and Veterinary Sciences ,175_Entomology ,Genètica animal ,Bacteriocyte ,génome ,gène ,Human Genome ,Biology and Life Sciences ,15. Life on land ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,REPETITIVE ELEMENTS ,DNA-SEQUENCES ,Acyrthosiphon pisum ,Genome Sequence ,Genetics and Genomics/Genome Projects ,Aphids ,PHEROMONE-BINDING ,Insect ,Developmental Biology ,[SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis - Abstract
The genome of the pea aphid shows remarkable levels of gene duplication and equally remarkable gene absences that shed light on aspects of aphid biology, most especially its symbiosis with Buchnera., Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems., Author Summary Aphids are common pests of crops and ornamental plants. Facilitated by their ancient association with intracellular symbiotic bacteria that synthesize essential amino acids, aphids feed on phloem (sap). Exploitation of a diversity of long-lived woody and short-lived herbaceous hosts by many aphid species is a result of specializations that allow aphids to discover and exploit suitable host plants. Such specializations include production by a single genotype of multiple alternative phenotypes including asexual, sexual, winged, and unwinged forms. We have generated a draft genome sequence of the pea aphid, an aphid that is a model for the study of symbiosis, development, and host plant specialization. Some of the many highlights of our genome analysis include an expanded total gene set with remarkable levels of gene duplication, as well as aphid-lineage-specific gene losses. We find that the pea aphid genome contains all genes required for epigenetic regulation by methylation, that genes encoding the synthesis of a number of essential amino acids are distributed between the genomes of the pea aphid and its symbiont, Buchnera aphidicola, and that many genes encoding immune system components are absent. These genome data will form the basis for future aphid research and have already underpinned a variety of genome-wide approaches to understanding aphid biology.
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- 2010
- Full Text
- View/download PDF
6. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development
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Renfree, MB, Papenfuss, AT, Deakin, JE, Lindsay, J, Heider, T, Belov, K, Rens, W, Waters, PD, Pharo, EA, Shaw, G, Wong, ESW, Lefèvre, CM, Nicholas, KR, Kuroki, Y, Wakefield, MJ, Zenger, KR, Wang, C, Ferguson-Smith, M, Nicholas, FW, Hickford, D, Yu, H, Short, KR, Siddle, HV, Frankenberg, SR, Chew, KY, Menzies, BR, Stringer, JM, Suzuki, S, Hore, TA, Delbridge, ML, Mohammadi, A, Schneider, NY, Hu, Y, O'Hara, W, Al Nadaf, S, Wu, C, Feng, ZP, Cocks, BG, Wang, J, Flicek, P, Searle, SMJ, Fairley, S, Beal, K, Herrero, J, Carone, DM, Suzuki, Y, Sugano, S, Toyoda, A, Sakaki, Y, Kondo, S, Nishida, Y, Tatsumoto, S, Mandiou, I, Hsu, A, McColl, KA, Lansdell, B, Weinstock, G, Kuczek, E, McGrath, A, Wilson, P, Men, A, Hazar-Rethinam, M, Hall, A, Davis, J, Wood, D, Williams, S, Sundaravadanam, Y, Muzny, DM, Jhangiani, SN, Lewis, LR, Morgan, MB, Okwuonu, GO, Ruiz, SJ, Santibanez, J, Nazareth, L, Cree, A, Fowler, G, Kovar, CL, Dinh, HH, Joshi, V, Jing, C, Lara, F, Thornton, R, Chen, L, Deng, J, Liu, Y, Shen, JY, Song, XZ, Edson, J, Troon, C, Thomas, D, Stephens, A, Yapa, L, Levchenko, T, Gibbs, RA, Cooper, DW, Speed, TP, Fujiyama, A, M Graves, JA, O'Neill, RJ, Renfree, MB, Papenfuss, AT, Deakin, JE, Lindsay, J, Heider, T, Belov, K, Rens, W, Waters, PD, Pharo, EA, Shaw, G, Wong, ESW, Lefèvre, CM, Nicholas, KR, Kuroki, Y, Wakefield, MJ, Zenger, KR, Wang, C, Ferguson-Smith, M, Nicholas, FW, Hickford, D, Yu, H, Short, KR, Siddle, HV, Frankenberg, SR, Chew, KY, Menzies, BR, Stringer, JM, Suzuki, S, Hore, TA, Delbridge, ML, Mohammadi, A, Schneider, NY, Hu, Y, O'Hara, W, Al Nadaf, S, Wu, C, Feng, ZP, Cocks, BG, Wang, J, Flicek, P, Searle, SMJ, Fairley, S, Beal, K, Herrero, J, Carone, DM, Suzuki, Y, Sugano, S, Toyoda, A, Sakaki, Y, Kondo, S, Nishida, Y, Tatsumoto, S, Mandiou, I, Hsu, A, McColl, KA, Lansdell, B, Weinstock, G, Kuczek, E, McGrath, A, Wilson, P, Men, A, Hazar-Rethinam, M, Hall, A, Davis, J, Wood, D, Williams, S, Sundaravadanam, Y, Muzny, DM, Jhangiani, SN, Lewis, LR, Morgan, MB, Okwuonu, GO, Ruiz, SJ, Santibanez, J, Nazareth, L, Cree, A, Fowler, G, Kovar, CL, Dinh, HH, Joshi, V, Jing, C, Lara, F, Thornton, R, Chen, L, Deng, J, Liu, Y, Shen, JY, Song, XZ, Edson, J, Troon, C, Thomas, D, Stephens, A, Yapa, L, Levchenko, T, Gibbs, RA, Cooper, DW, Speed, TP, Fujiyama, A, M Graves, JA, and O'Neill, RJ
- Abstract
Background: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development.Results: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements.Conclusions: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution. © 2011 Renfree et al.; licensee BioMed Central Ltd.
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- 2011
7. Erdheim–Chester Disease: A Histiocytic Disorder More Than Skin Deep
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Skinner, Matthew, primary, Briant, Michale, additional, and Morgan, MB, additional
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- 2011
- Full Text
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8. Just-in-Time Radiologist Decision Support: The Importance of PACS-Integrated Workflow.
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Morgan MB, Branstetter BF 4th, Clark C, House J, Baker D, and Harnsberger HR
- Abstract
PURPOSE: Decision support systems for radiologists can provide information during image interpretation that may efficiently improve diagnostic accuracy and increase radiologists' confidence. However, most decision support systems require radiologists to exit PACS, which may deter busy radiologists from pursuing decision support. The purpose of this study was to determine whether radiologists would use a PACS-integrated decision support tool more frequently than an equivalent nonintegrated system. METHODS: Forty-eight radiology residents were randomly assigned to one of two groups: the control group was provided access to a radiology clinical decision support tool via Web access, which required the resident to launch a Web browser from a desktop icon and then log in to the decision support application. The experimental group was provided access to the same tool but was allowed to launch from a PACS-integrated portal with automated login and authentication. Halfway through the 10-month study period, the groups were switched. The main outcome measure was the average number of decision support sessions initiated each month over the study period. RESULTS: The experimental (integrated) group had higher use than the control (nonintegrated) group by a factor of 3.0 (P < .05). When integrated access was removed from the experimental group, their use fell by 52%. When integrated access was granted to the control group, their use rose by only 20%. CONCLUSION: Integration with PACS improves radiologists' use of clinical decision support tools. Integrated access is critical at the time of initial deployment, or acceptance of the decision support tools may be undermined. [ABSTRACT FROM AUTHOR]
- Published
- 2011
9. 'Wet reads' in the age of PACS: technical and workflow considerations for a preliminary report system.
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Mates J, Branstetter BF, Morgan MB, Lionetti DM, and Chang PJ
- Abstract
Communication between clinicians, technologists, and radiologists has become more complex, with Picture Archiving and Communication Systems (PACS) now allowing the radiologist to be removed from the physical location of the patients and the site of imaging. With these changes, effective communication becomes an ongoing challenge. Efficient communication of study interpretations has also become a priority for radiologists as they struggle to maintain relevance and provide added value to patient care when clinicians have ready access to radiology images. The purpose of this paper is to share our experience in developing and implementing the Collaborative Notification System (CNS), a communication tool used to inform referring clinicians of urgent findings-a.k.a. 'wet reads.' The system utilizes a system of web pages integrated into PACS for the sending and receiving of succinct messages to provide clinical information at the point of need. A second system of pager alerts provides notification of the need for such communication through a relatively unintrusive, one-way, acknowledged alert system. The CNS provides asynchronous, integrated communication for the reporting of urgent and emergent radiology findings in a complex, geographically distributed medical environment. [ABSTRACT FROM AUTHOR]
- Published
- 2007
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10. The radiology dashboard: a user's guide to a 'high-performance' PACS.
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Morgan MB and Chang PJ
- Abstract
As the use of digital image management grows, radiology systems and infrastructures have become increasingly complex. The authors describe the use of a 'digital dashboard' with real-time, context-specific information that allows for efficient system management and clinical workflow. [ABSTRACT FROM AUTHOR]
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- 2005
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11. Nonresponsiveness to anticholinesterase agents in patients with MuSK-antibody-positive MG.
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Hatanaka Y, Hemmi S, Morgan MB, Scheufele ML, Claussen GC, Wolfe GI, and Oh SJ
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- 2005
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12. Morning report. Blood diarrhea years after resection of a rib.
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Adelman HM, Wallach PM, Altus P, Morgan MB, and Truitt CA
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- 1996
13. Neutrophilic dermatosis revisited: An initial presentation of lupus?
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Pavlidakey P, Mills O, Bradley S, Casey J, and Morgan MB
- Published
- 2012
14. Letter to the Editor re: 'The radiology digital dashboard: effects on report turnaround time.'.
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Branstetter BF and Morgan MB
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- 2009
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15. Caveolin expression in adult renal tumors.
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Carrion R, Morgan BE, Tannenbaum M, Salup R, Morgan MB, Carrion, Rafael, Morgan, Beale E, Tannenbaum, Myron, Salup, Raoul, and Morgan, Michael B
- Abstract
Histopathological criteria are usually sufficient for the accurate distinction of benign form malignant renal tumors. A minority of cases however, poses a vexing diagnostic dilemma. Recent studies suggest that caveolin, a scaffolding cell membrane protein may prove helpful in predicting the behavior of these neoplasms. We analyzed a series of 40 renal tumors of which 7 were clear cell and 6 granular Renal Cell Carcinomas (RCC), 10 cases of Papillary Carcinoma (PCC), 4 cases of Chromophobe Renal cell carcinomas (CRCR), 11 cases of Oncocytomas (OC) and 2 cases of Collecting Duct Carcinomas (CDC). The distribution of immunoreactivity was analyzed by quantifying caveolin cell membrane staining in each case. There was a statistically significant difference in the expression of caveolin-1 between oncocytoma with a mean labeling index of 91.7 and the cases of malignant renal tumors with a mean labeling index of 26.9 for RCC, 24 for CDC, 21 for CRCR, and 19.2 for PCC. The results suggest an association between loss of caveolin expression among malignant renal tumors that might be useful in distinguishing oncocytoma from malignant renal tumors and possibly implicates this peptide in their pathogenesis. [ABSTRACT FROM AUTHOR]
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- 2003
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16. Somatic mutations affect key pathways in lung adenocarcinoma
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Aldi T. Kraja, Brian H. Dunford-Shore, Tittu Mathew, Otis Hall, Barbara A. Weir, Timothy Fennell, William Pao, Jack A. Roth, Alicia Hawes, Heidi Greulich, Steven E. Scherer, Xiaoqi Shi, Giovanni Tonon, Manuel L. Gonzalez-Garay, Yuzhu Tang, Mark B. Orringer, Qunyuan Zhang, Bruce E. Johnson, Li Ding, David G. Beer, Amit Dutt, Margaret R. Spitz, Carrie A. Haipek, Michael A. Province, Yiming Zhu, Liuda Ziaugra, Lucian R. Chirieac, Ken Chen, Rachel Abbott, William D. Travis, George M. Weinstock, Harold E. Varmus, Lucinda Fulton, Daniel C. Koboldt, Kristian Cibulskis, Carrie Sougnez, Christopher S. Sawyer, Richard A. Gibbs, Bradley A. Ozenberger, Thomas J. Giordano, Heather Schmidt, Ling Lin, Jennifer Baldwin, Elaine R. Mardis, Rick Meyer, Tracie L. Miner, David E. Larson, Ignacio I. Wistuba, Jiqiang Yao, Margaret Morgan, Andrew C. Chang, Akihiko Yoshizawa, Shalini N. Jhangiani, Xiaojun Zhao, David A. Wheeler, Stephen R. Broderick, Jody S. Robinson, Kerstin Clerc, Eric S. Lander, Richard K. Wilson, Ginger A. Fewell, Hua Shen, David J. Dooling, Robert S. Fulton, Aleksandar Milosavljevic, John R. Osborne, Gad Getz, Donna M. Muzny, Yanru Ren, Wendy Winckler, Roman K. Thomas, Mark A. Watson, Peter J. Good, Sacha N. Sander, Megan Hanna, Michael D. McLellan, Ginger A. Metcalf, Brian Ng, Michael C. Wendl, Lora Lewis, Seth D. Crosby, Michael C. Zody, Matthew Meyerson, Robert C. Onofrio, Michael S. Lawrence, Marc Ladanyi, Aniko Sabo, Craig Pohl, Stacey Gabriel, Tammi L. Vickery, Ding, L, Getz, G, Wheeler, Da, Mardis, Ea, Mclellan, Md, Cibulskis, K, Sougnez, C, Greulich, H, Muzny, Dm, Morgan, Mb, Fulton, L, Fulton, R, Zhang, Q, Wendl, Mc, Lawrence, M, Larson, De, Chen, K, Dooling, Dj, Sabo, A, Hawes, Ac, Shen, H, Jhangiani, Sh, Lewis, Lr, Hall, O, Zhu, Y, Mathew, T, Ren, Y, Yao, J, Scherer, Se, Clerc, K, Metcalf, Ga, Ng, B, Milosavljevic, A, Gonzalez-Garay, Ml, Osborne, Jr, Meyer, R, Shi, X, Tang, Y, Koboldt, Dc, Lin, L, Abbott, R, Miner, Tl, Pohl, C, Fewell, G, Haipek, C, Schmidt, H, Dunford-Shore, Bh, Kraja, A, Crosby, Sd, Sawyer, C, Vickery, T, Sander, S, Robinson, J, Winckler, W, Baldwin, J, Chirieac, Lr, Dutt, A, Fennell, T, Hanna, M, Johnson, Be, Onofrio, Rc, Thomas, Rk, Tonon, G, Weir, Ba, Zhao, X, Ziaugra, L, Zody, Mc, Giordano, T, Orringer, Mb, Roth, Ja, Spitz, Mr, Wistuba, Ii, Ozenberger, B, Good, Pj, Chang, Ac, Beer, Dg, Watson, Ma, Ladanyi, M, Broderick, S, Yoshizawa, A, Travis, Wd, Pao, W, Province, Ma, Weinstock, Gm, Varmus, He, Gabriel, Sb, Lander, E, Gibbs, Ra, Meyerson, M, and Wilson, Rk.
- Subjects
Male ,Genetics ,Mutation ,Lung Neoplasms ,Multidisciplinary ,Tumor suppressor gene ,DNA repair ,Gene Dosage ,Adenocarcinoma, Bronchiolo-Alveolar ,Biology ,medicine.disease ,medicine.disease_cause ,Article ,Gene Expression Regulation, Neoplastic ,Germline mutation ,Proto-Oncogenes ,medicine ,Humans ,Adenocarcinoma ,Female ,Genes, Tumor Suppressor ,Carcinogenesis ,Lung cancer ,Gene - Abstract
Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers--including NF1, APC, RB1 and ATM--and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment.
- Published
- 2008
17. Pembrolizumab plus chemotherapy in frontline treatment of advanced ovarian cancer: Clinical and translational results from a phase 2 trial.
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How JA, Dang M, Lee S, Fellman B, Westin SN, Sood AK, Fleming ND, Shafer A, Yuan Y, Liu J, Zhao L, Celestino J, Hajek R, Morgan MB, Parra ER, Laberiano Fernandez CD, Arrechedera CA, Solis Soto LM, Schmeler KM, Nick A, Lu KH, Coleman R, Wang L, and Jazaeri AA
- Subjects
- Humans, Female, Middle Aged, Aged, Tumor Microenvironment drug effects, Progression-Free Survival, Neoadjuvant Therapy adverse effects, Neoadjuvant Therapy methods, Adult, B7-H1 Antigen metabolism, Cytoreduction Surgical Procedures, Antibodies, Monoclonal, Humanized therapeutic use, Antibodies, Monoclonal, Humanized administration & dosage, Antibodies, Monoclonal, Humanized adverse effects, Ovarian Neoplasms drug therapy, Ovarian Neoplasms mortality, Ovarian Neoplasms pathology, Antineoplastic Combined Chemotherapy Protocols therapeutic use, Antineoplastic Combined Chemotherapy Protocols adverse effects, Paclitaxel administration & dosage, Paclitaxel therapeutic use, Paclitaxel adverse effects, Carboplatin administration & dosage, Carboplatin therapeutic use, Carboplatin adverse effects, Carcinoma, Ovarian Epithelial drug therapy, Carcinoma, Ovarian Epithelial mortality
- Abstract
Background: The efficacy and feasibility of pembrolizumab combined with chemotherapy in frontline management of advanced high-grade epithelial ovarian cancer (EOC) is unknown. Additionally, modification of the tumor microenvironment following neoadjuvant therapy is not well understood., Methods: In this single-arm phase 2 trial (this study was registered at ClinicalTrials.gov: NCT02520154), eligible patients received up to 4 cycles of neoadjuvant chemotherapy followed by interval cytoreduction, 3 cycles of adjuvant intravenous carboplatin/weekly paclitaxel/pembrolizumab, and finally maintenance pembrolizumab until progression or toxicity (maximum 20 cycles). The primary endpoint was progression-free survival (PFS). Secondary endpoints included feasibility, toxicity, and overall survival (OS). PD-L1 staining, multiplex immunofluorescence staining, RNA sequencing, reverse-phase protein array analyses were performed on pre- and post-chemotherapy samples., Findings: Thirty-one eligible patients were enrolled. Median PFS and OS was 14.88 (95% CI 12.39-23.00) and 57.43 months (95% CI 30.88-not reached), respectively. Among those with PD-L1 combined positive score (CPS) ≥10, the median PFS and OS were not reached compared to those with CPS <10 (10.50 and 30.90 months, respectively). Feasibility was met, with all patients completing their planned adjuvant cycles. Treatment discontinuation due to immune-related toxicity occurred in 6 patients (20%). Chemotherapy resulted in an infiltration of anti-tumor immune cells in the tumor microenvironment. Samples of patients with the best PFS demonstrated increased expression of NF-κB, TGF-β, and β-catenin signaling., Conclusions: Pembrolizumab with chemotherapy was feasible and resulted in PFS within the historical range for this EOC population. Patients with CPS ≥10 may benefit more from this regimen, and future studies should investigate this potential biomarker., Funding: This investigator-initiated trial was funded by Merck., Competing Interests: Declaration of interests S.N.W. reports grants from NIH, GOG Foundation, Cotinga Pharmaceuticals, Bayer, and ArQule during the conduct of the study. She also reports grants and personal fees from AstraZeneca, Clovis Oncology, GlaxoSmithKline/Tesaro, Roche/Genentech, and Novartis. She reports personal fees from Merck, Pfizer, Eisai, CIrculogene, Zentalis, and Agenus outside the submitted work. N.D.F. reports personal fees from Tesaro, Pfizer, Bristol Myers Squibb, and GlaxoSmithKline outside the submitted work. A.K.S. discloses the following competing interests: consulting (Merck, GSK, ImmunoGen, Iylon, Kiyatec, Astra Zeneca, Onxeo) and shareholder (BioPath). R.C. reports the following competing interests: consulting (Clovis Oncology, Genentech/Roche, AstraZeneca/MedImmune, Genmab, OncoMed, Immunogen, AbbVie, Agenus, Novocure, Merck, OncXerna Therapeutics, Alkermes, Gradalis, GlaxoSmithKline, Alkermes, Eisai, GOG Foundation, Karyopharm Therapeutics), employment (Vanium Group, US Oncology Network), leadership (Onsexo), stock and other ownership interests (McKesson/US Oncology Network), and research funding (AstraZeneca/MedImmune, Clovis Oncology, Merck, Roche/Genentech, Immunogen, Mirati Therapeutics, Amgen, Pfizer, Lilly, Regeneron, Alkermes, Karyopharm Therapeutics). A.A.J. reports personal fees from Gerson Lehrman Group, Guidepoint, Iovance advisory board, NuProbe, Simcere, PACT Pharma, Genentech-Roche, Eisai, Agenus, and Macrogenics. He also reports grants from AstraZeneca, Bristol Myers Squibb, Iovance, Aravive, Pfizer, Immatics US, Eli Lilly, and Merck, and stock/stock options from AvengeBio outside the submitted work., (Copyright © 2024 Elsevier Inc. All rights reserved.)
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- 2025
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18. Apocrine Breast Cancer With Psammoma Bodies in a Male Patient.
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Bashinskaya A, Baum EW, and Morgan MB
- Abstract
Introduction: While male breast carcinoma is a relatively uncommon occurrence, its incidence is on the rise, potentially attributed to sporadic pathophysiological mechanisms, primarily involving hormonal imbalances. Invasive apocrine carcinoma represents a small fraction of global breast malignancies, with limited instances reported among male patients in the literature. The clinical presentation of an apocrine breast carcinoma closely resembles that of other breast cancer subtypes, as it is most often described as a solitary ulcerative nodular lesion occupying a retro-areolar region of the breast. Herein, we describe a novel case of an apocrine male breast carcinoma metastasizing to the skin, given that past cases had presented ab initio in the subcutaneous breast tissue. Furthermore, we discuss the unusual histopathology encountered in this entity such as the presence of psammoma bodies., Case Presentation: In this case report, we outline the clinical presentation of an 80-year-old male with a history of prior breast cancer and mastectomy, performed 9 years before this dermatologic consultation. Upon a physical examination, a singular nodular lesion on his right breast was discovered, leading to a biopsy. Subsequent histological analysis identified an apocrine cell carcinoma characterized by numerous psammoma bodies, an unusual occurrence in breast tissue. Consequently, the patient received a diagnosis of relapsing breast apocrine carcinoma., Conclusion: Cutaneous metastases arising from apocrine breast carcinoma are infrequent in male patients. The precise diagnosis of invasive apocrine breast carcinoma hinges on the accurate identification of immunohistochemical markers and a clear morphological profile. A notable correlation has been observed, particularly in positive expressions of gross cystic disease fluid protein-15 (GCDFP-15) and androgen receptor. However, due to the rarity of this presentation, there is limited data on treatment modalities. Ongoing studies are investigating the potential role of anti-androgens in the treatment of apocrine breast carcinomas., Competing Interests: Conflicts of Interest: The authors declare they have no conflicts of interest., (© 2024 HCA Physician Services, Inc. d/b/a Emerald Medical Education.)
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- 2024
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19. Optimizing the Care of Patients With Colorectal Cancer in Clinical Practice.
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Morgan MB and Triglianos T
- Abstract
At JADPRO Live 2023, presenters emphasized the importance of increasing colorectal cancer screening in high-risk groups, reviewed guidelines in the adjuvant and metastatic setting, and outlined clinical and molecular profiles to consider when discussing and determining treatment options with patients., Competing Interests: Mary B. Morgan has no relevant financial relationships to disclose. Tammy Triglianos has served on the advisory board for Pfizer., (© 2024 BroadcastMed LLC.)
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- 2024
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20. Synergistic and antagonistic interactions of oxybenzone and ocean acidification: new insight into vulnerable cellular processes in non-calcifying anthozoans.
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Morgan MB, Williams J, Breeze B, English N, Higdon N, Onthank K, and Qualley DF
- Abstract
Cnidarians face significant threats from ocean acidification (OA) and anthropogenic pollutants such as oxybenzone (BP-3). The convergence of threats from multiple stressors is an important area to investigate because of potential significant synergistic or antagonistic interactions. Real-time quantitative PCR was performed to characterize the expression profiles of twenty-two genes of interest (GOI) in sea anemones ( Exaiptasia diaphana) exposed to one of four treatments: 1) 96 h of OA conditions followed by a 4 h exposure to 20 ppb BP-3; 2) Exposure to 4 h 20 ppb BP-3 without 96 h of OA; 3) Exposure to 96 h of OA alone; or 4) laboratory conditions with no exposure to BP-3 and/or OA. These 22 GOIs represent cellular processes associated with proton-dependent transport, sodium-dependent transport, metal cation binding/transport, extracellular matrix, amino acid metabolism/transport, immunity, and/or steroidogenesis. These 22 GOIs provide new insight into vulnerable cellular processes in non-calcifying anthozoans exposed to OA and BP-3. Expression profiles were categorized as synergistic, antagonistic, or additive of BP-3 in the presence of OA. Two GOIs were synergistic. Fifteen GOIs were antagonistic and the remaining five GOIs were additive in response to BP-3 in acidified seawater. A subset of these GOIs appear to be candidate biomarkers for future in situ investigations. In human health, proton-dependent monocarboxylate transporters (MCTs) are promising pharmacological targets and recognized as potential biomarkers. By comparison, these same MCTs appear to be targets of xenobiotic chemical pollutants in cnidarian physiology. In the presence of BP-3, a network of collagen synthesis genes are upregulated and antagonistic in their expression profiles. Cytochrome b561 is a critical protein required for collagen synthesis and in silico modeling demonstrates BP-3 binds in the pocket of cytochrome b561. Understanding the underlying molecular mechanisms of "drug-like" compounds such as BP-3 may lead to a more comprehensive interpretation of transcriptional expression profiles. The collective antagonistic responses of GOIs associated with collagen synthesis strongly suggests these GOIs should be considered candidate biomarkers of effect. GOIs with synergistic and additive responses represent candidate biomarkers of exposure. Results show the effects of OA and BP-3 are interactive with respect to their impact on cnidarians. This investigation offers mechanistic data that supports the expression profiles and underpins higher order physiological responses., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Morgan, Williams, Breeze, English, Higdon, Onthank and Qualley.)
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- 2024
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21. Ethics of Artificial Intelligence in Breast Imaging.
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Morgan MB and Mates JL
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- Beneficence, Ethics, Medical, Diagnostic Imaging, Artificial Intelligence, Social Justice
- Abstract
There is great interest in the development of artificial intelligence (AI) applications for medical imaging in general and specifically in breast imaging. Because of the scale of application and the potential for harm, there has been a parallel interest in assuring that these new technologies are scrutinized and applied in ethical ways. The four principles of autonomy, beneficence, non-maleficence, and justice are widely accepted as a framework for bioethical analysis. We incorporate a fifth principle of explicability (adapted from Floridi and Cowls) because of the unique considerations of AI. We review definitions of each of these principles and provide examples of their practical application to breast imaging., (© Society of Breast Imaging 2023. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2023
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22. Permanent Makeup Procedure Heralds the Development of Systemic Sarcoidosis.
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Bashinskaya A, Fernandez AD, and Morgan MB
- Abstract
Permanent cosmetic procedures including tattooing are determined as risk factors that prompt the development of cutaneous granulomatous conditions. Scar sarcoidosis is an uncommon manifestation of a systemic granulomatous disease with a few cases reported in the literature worldwide. Although the incidence rates of sarcoid lesions at sites of pigment deposition are low, granuloma formation can provoke a severe systemic inflammatory response. We report a 48-year-old Hispanic female with a new onset of scar sarcoidosis that progressed to a systemic condition. Erythematous maculopapular eruptions arose on her left eyebrow area at the sites of scars from cosmetic tattooing, prior to exacerbation of the small airway disease. Histopathologic examination revealed typical findings of cutaneous sarcoidosis, including non-caseating epithelioid granulomas. This case highlights the importance of early detection of cutaneous sarcoidosis in long-standing scars due to the associated risks of systemic sarcoidosis., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2022, Bashinskaya et al.)
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- 2022
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23. Multi-modal molecular programs regulate melanoma cell state.
- Author
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Andrews MC, Oba J, Wu CJ, Zhu H, Karpinets T, Creasy CA, Forget MA, Yu X, Song X, Mao X, Robertson AG, Romano G, Li P, Burton EM, Lu Y, Sloane RS, Wani KM, Rai K, Lazar AJ, Haydu LE, Bustos MA, Shen J, Chen Y, Morgan MB, Wargo JA, Kwong LN, Haymaker CL, Grimm EA, Hwu P, Hoon DSB, Zhang J, Gershenwald JE, Davies MA, Futreal PA, Bernatchez C, and Woodman SE
- Subjects
- DNA Methylation, Humans, Transcriptome, Melanoma metabolism, Melanoma pathology, MicroRNAs metabolism, RNA, Long Noncoding metabolism
- Abstract
Melanoma cells display distinct intrinsic phenotypic states. Here, we seek to characterize the molecular regulation of these states using multi-omic analyses of whole exome, transcriptome, microRNA, long non-coding RNA and DNA methylation data together with reverse-phase protein array data on a panel of 68 highly annotated early passage melanoma cell lines. We demonstrate that clearly defined cancer cell intrinsic transcriptomic programs are maintained in melanoma cells ex vivo and remain highly conserved within melanoma tumors, are associated with distinct immune features within tumors, and differentially correlate with checkpoint inhibitor and adoptive T cell therapy efficacy. Through integrative analyses we demonstrate highly complex multi-omic regulation of melanoma cell intrinsic programs that provide key insights into the molecular maintenance of phenotypic states. These findings have implications for cancer biology and the identification of new therapeutic strategies. Further, these deeply characterized cell lines will serve as an invaluable resource for future research in the field., (© 2022. The Author(s).)
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- 2022
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24. Sea Anemones Responding to Sex Hormones, Oxybenzone, and Benzyl Butyl Phthalate: Transcriptional Profiling and in Silico Modelling Provide Clues to Decipher Endocrine Disruption in Cnidarians.
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Morgan MB, Ross J, Ellwanger J, Phrommala RM, Youngblood H, Qualley D, and Williams J
- Abstract
Endocrine disruption is suspected in cnidarians, but questions remain how occurs. Steroid sex hormones are detected in corals and sea anemones even though these animals do not have estrogen receptors and their repertoire of steroidogenic enzymes appears to be incomplete. Pathways associated with sex hormone biosynthesis and sterol signaling are an understudied area in cnidarian biology. The objective of this study was to identify a suite of genes that can be linked to exposure of endocrine disruptors. Exaiptasia diaphana were exposed to nominal 20ppb concentrations of estradiol (E2), testosterone (T), cholesterol, oxybenzone (BP-3), or benzyl butyl phthalate (BBP) for 4 h. Eleven genes of interest (GOIs) were chosen from a previously generated EST library. The GOIs are 17β-hydroxysteroid dehydrogenases type 14 ( 17β HSD14 ) and type 12 ( 17β HSD12 ), Niemann-Pick C type 2 ( NPC2 ), Equistatin ( EI ), Complement component C3 ( C3 ), Cathepsin L ( CTSL ), Patched domain-containing protein 3 ( PTCH3 ), Smoothened ( SMO ), Desert Hedgehog ( DHH ), Zinc finger protein GLI2 ( GLI2 ), and Vitellogenin ( VTG ). These GOIs were selected because of functional associations with steroid hormone biosynthesis; cholesterol binding/transport; immunity; phagocytosis; or Hedgehog signaling. Quantitative Real-Time PCR quantified expression of GOIs. In silico modelling utilized protein structures from Protein Data Bank as well as creating protein structures with SWISS-MODEL. Results show transcription of steroidogenic enzymes, and cholesterol binding/transport proteins have similar transcription profiles for E2, T, and cholesterol treatments, but different profiles when BP-3 or BBP is present. C3 expression can differentiate between exposures to BP-3 versus BBP as well as exposure to cholesterol versus sex hormones. In silico modelling revealed all ligands (E2, T, cholesterol, BBP, and BP-3) have favorable binding affinities with 17β HSD14, 17β HSD12, NPC2, SMO, and PTCH proteins. VTG expression was down-regulated in the sterol treatments but up-regulated in BP-3 and BBP treatments. In summary, these eleven GOIs collectively generate unique transcriptional profiles capable of discriminating between the five chemical exposures used in this investigation. This suite of GOIs are candidate biomarkers for detecting transcriptional changes in steroidogenesis, gametogenesis, sterol transport, and Hedgehog signaling. Detection of disruptions in these pathways offers new insight into endocrine disruption in cnidarians., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Morgan, Ross, Ellwanger, Phrommala, Youngblood, Qualley and Williams.)
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- 2022
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25. Knock down analysis reveals critical phases for specific oskar noncoding RNA functions during Drosophila oogenesis.
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Kenny A, Morgan MB, Mohr S, and Macdonald PM
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- Animals, Drosophila melanogaster genetics, Female, Oocytes, Oogenesis genetics, RNA, Untranslated, Drosophila genetics, Drosophila Proteins genetics
- Abstract
The oskar transcript, acting as a noncoding RNA, contributes to a diverse set of pathways in the Drosophila ovary, including karyosome formation, positioning of the microtubule organizing center (MTOC), integrity of certain ribonucleoprotein particles, control of nurse cell divisions, restriction of several proteins to the germline, and progression through oogenesis. How oskar mRNA acts to perform these functions remains unclear. Here, we use a knock down approach to identify the critical phases when oskar is required for three of these functions. The existing transgenic shRNA for removal of oskar mRNA in the germline targets a sequence overlapping a regulatory site bound by Bruno1 protein to confer translational repression, and was ineffective during oogenesis. Novel transgenic shRNAs targeting other sites were effective at strongly reducing oskar mRNA levels and reproducing phenotypes associated with the absence of the mRNA. Using GAL4 drivers active at different developmental stages of oogenesis, we found that early loss of oskar mRNA reproduced defects in karyosome formation and positioning of the MTOC, but not arrest of oogenesis. Loss of oskar mRNA at later stages was required to prevent progression through oogenesis. The noncoding function of oskar mRNA is thus required for more than a single event., (© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)
- Published
- 2021
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26. Different roles for the adjoining and structurally similar A-rich and poly(A) domains of oskar mRNA: Only the A-rich domain is required for oskar noncoding RNA function, which includes MTOC positioning.
- Author
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Kenny A, Morgan MB, and Macdonald PM
- Subjects
- Animals, Binding Sites genetics, Drosophila Proteins metabolism, Drosophila melanogaster genetics, Drosophila melanogaster metabolism, Oocytes metabolism, Oogenesis, Poly A genetics, Poly A metabolism, RNA Splicing genetics, RNA Splicing physiology, RNA, Messenger genetics, RNA, Messenger metabolism, 3' Untranslated Regions genetics, Drosophila Proteins genetics, Microtubule-Organizing Center metabolism
- Abstract
Drosophila oskar (osk) mRNA has both coding and noncoding functions, with the latter required for progression through oogenesis. Noncoding activity is mediated by the osk 3' UTR. Three types of cis elements act most directly and are clustered within the final ~120 nucleotides of the 3' UTR: multiple binding sites for the Bru1 protein, a short highly conserved region, and A-rich sequences abutting the poly(A) tail. Here we extend the characterization of these elements and their functions, providing new insights into osk noncoding RNA function and the makeup of the cis elements. We show that all three elements are required for correct positioning of the microtubule organizing center (MTOC), a defect not previously reported for any osk mutant. Normally, the MTOC is located at the posterior of the oocyte during previtellogenic stages of oogenesis, and this distribution underlies the strong posterior enrichment of many mRNAs transported into the oocyte from the nurse cells. When osk noncoding function was disrupted the MTOC was dispersed in the oocyte and osk mRNA failed to be enriched at the posterior, although transport to the oocyte was not affected. A previous study did not detect loss of posterior enrichment for certain osk mutants lacking noncoding activity (Kanke et al., 2015). This discrepancy may be due to use of imaging aimed at monitoring transport to the oocyte rather than posterior enrichment. Involvement in MTOC positioning suggests that the osk noncoding function may act in conjunction with genes whose loss has similar effects, and that osk function may extend to other processes requiring those genes. Further characterization of the cis elements required for osk noncoding function included completion of saturation mutagenesis of the most highly conserved region, providing critical information for evaluating the possible contribution of candidate binding factors. The 3'-most cis element is a cluster of A-rich sequences, the ARS. The close juxtaposition and structural similarity of the ARS and poly(A) tail raised the possibility that they comprise an extended A-rich element required for osk noncoding function. We found that absence of the poly(A) tail did not mimic the effects of mutation of the ARS, causing neither arrest of oogenesis nor mispositioning of osk mRNA in previtellogenic stage oocytes. Thus, the ARS and the poly(A) tail are not interchangeable for osk noncoding RNA function, suggesting that the role of the ARS is not in recruitment of Poly(A) binding protein (PABP), the protein that binds the poly(A) tail. Furthermore, although PABP has been implicated in transport of osk mRNA from the nurse cells to the oocyte, mutation of the ARS in combination with loss of the poly(A) tail did not disrupt transport of osk mRNA into the oocyte. We conclude that PABP acts indirectly in osk mRNA transport, or is associated with osk mRNA independent of an A-rich binding site. Although the poly(A) tail was not required for osk mRNA transport into the oocyte, its absence was associated with a novel osk mRNA localization defect later in oogenesis, potentially revealing a previously unrecognized step in the localization process., (Copyright © 2021 Elsevier Inc. All rights reserved.)
- Published
- 2021
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27. Whole-exome Sequencing in Penile Squamous Cell Carcinoma Uncovers Novel Prognostic Categorization and Drug Targets Similar to Head and Neck Squamous Cell Carcinoma.
- Author
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Chahoud J, Gleber-Netto FO, McCormick BZ, Rao P, Lu X, Guo M, Morgan MB, Chu RA, Martinez-Ferrer M, Eterovic AK, Pickering CR, and Pettaway CA
- Subjects
- Adult, Aged, Aged, 80 and over, Case-Control Studies, Computational Biology, Disease Management, Disease Susceptibility, Humans, Male, Middle Aged, Molecular Targeted Therapy, Mutation, Neoplasm Grading, Neoplasm Staging, Penile Neoplasms drug therapy, Penile Neoplasms mortality, Prognosis, Squamous Cell Carcinoma of Head and Neck drug therapy, Squamous Cell Carcinoma of Head and Neck mortality, Biomarkers, Tumor, Penile Neoplasms diagnosis, Penile Neoplasms genetics, Squamous Cell Carcinoma of Head and Neck diagnosis, Squamous Cell Carcinoma of Head and Neck genetics, Exome Sequencing
- Abstract
Purpose: Penile squamous cell carcinoma (PSCC) is rare with limited treatment options. We report the first whole-exome sequencing (WES) analysis and compare the molecular landscape of PSCC with other squamous cell carcinomas (SCC), with the goal to identify common novel targets., Experimental Design: PSCC and matched normal penile tissues from 34 prospectively followed patients, underwent genomic WES and human papilloma virus testing. We performed tumor mutation signature estimation by two methods, first to identify APOBEC-related mutation enrichments and second to classify PSCC-enriched mutational patterns based on their association with the Catalogue of Somatic Mutations in Cancer mutation signatures. We performed an extensive genomic comparison between our PSCC cohort and other SCCs in The Cancer Genome Atlas studies., Results: We identified that most PSCC samples showed enrichment for Notch pathway ( n = 24, 70.6%) alterations, comparable with head and neck squamous cell carcinoma (HNSC). PSCC mutation signatures are most comparable with HNSC signatures. PSCC samples showed an enrichment of two distinct mutational signatures, the first, associated with oncogenic activity of AID/APOBEC, and the second, associated with defective DNA mismatch repair and microsatellite instability. MP1 enrichment was positively correlated with increased tumor mutation burden (TMB; CC, 0.71; P < 0.0001) and correlated with significantly worse survival in comparison with those with the MP2 subset [HR, 10.2 (1.13-92.9); P = 0.039]. We show that a subset of PSCC (38%), with enrichment of APOBEC-related mutation signature, had significantly higher TMB and worse overall survival in comparison with non-APOBEC-enriched subset [HR, 2.41 (1.11-6.77); P = 0.042]., Conclusions: This study identified novel druggable targets and similarities in mutational signatures between PSCC and HNSC with potential clinical implications. See related commentary by McGregor and Sonpavde, p. 2375 ., (©2021 American Association for Cancer Research.)
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- 2021
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28. Opposing roles for Egalitarian and Staufen in transport, anchoring and localization of oskar mRNA in the Drosophila oocyte.
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Mohr S, Kenny A, Lam STY, Morgan MB, Smibert CA, Lipshitz HD, and Macdonald PM
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- Animals, Drosophila Proteins ultrastructure, Drosophila melanogaster genetics, Drosophila melanogaster growth & development, Inverted Repeat Sequences genetics, Mutation genetics, RNA-Binding Proteins ultrastructure, Drosophila Proteins genetics, Oocytes growth & development, RNA-Binding Proteins genetics
- Abstract
Localization of oskar mRNA includes two distinct phases: transport from nurse cells to the oocyte, a process typically accompanied by cortical anchoring in the oocyte, followed by posterior localization within the oocyte. Signals within the oskar 3' UTR directing transport are individually weak, a feature previously hypothesized to facilitate exchange between the different localization machineries. We show that alteration of the SL2a stem-loop structure containing the oskar transport and anchoring signal (TAS) removes an inhibitory effect such that in vitro binding by the RNA transport factor, Egalitarian, is elevated as is in vivo transport from the nurse cells into the oocyte. Cortical anchoring within the oocyte is also enhanced, interfering with posterior localization. We also show that mutation of Staufen recognized structures (SRSs), predicted binding sites for Staufen, disrupts posterior localization of oskar mRNA just as in staufen mutants. Two SRSs in SL2a, one overlapping the Egalitarian binding site, are inferred to mediate Staufen-dependent inhibition of TAS anchoring activity, thereby promoting posterior localization. The other three SRSs in the oskar 3' UTR are also required for posterior localization, including two located distant from any known transport signal. Staufen, thus, plays multiple roles in localization of oskar mRNA., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2021
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29. Applications of Artificial Intelligence in Breast Imaging.
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Morgan MB and Mates JL
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- Breast diagnostic imaging, Female, Humans, Artificial Intelligence, Breast Neoplasms diagnostic imaging, Image Interpretation, Computer-Assisted methods, Mammography methods
- Abstract
Artificial intelligence (AI) technology shows promise in breast imaging to improve both interpretive and noninterpretive tasks. AI-based screening triage may help identify normal examinations and AI-based computer-aided detection (AI-CAD) may increase cancer detection and reduce false positives. Risk assessment, quality assurance, and other workflow tasks may also be streamlined. AI adoption will depend on robust evidence of improved quality, increased efficiency, and cost-effectiveness. Reliance on AI will likely proceed through stages and will involve careful attention to its limitations to prevent overconfidence in its application., Competing Interests: Disclosure M.B. Morgan, consultant at Elsevier, Inc. No relevant conflicts of interest and no funding sources for this article. J.L. Mates, employee at Viz.ai. No relevant conflicts of interest and no funding sources for this article., (Copyright © 2020 Elsevier Inc. All rights reserved.)
- Published
- 2021
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30. Chronic inflammatory axonal polyneuropathy.
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Oh SJ, Lu L, Alsharabati M, Morgan MB, and King P
- Subjects
- Adolescent, Adult, Aged, Autoimmune Diseases of the Nervous System classification, Autoimmune Diseases of the Nervous System drug therapy, Autoimmune Diseases of the Nervous System physiopathology, Axons pathology, Azathioprine therapeutic use, Biopsy, Child, Child, Preschool, Chronic Disease, Cyclophosphamide therapeutic use, Cyclosporine therapeutic use, Electromyography, Female, Humans, Immunoglobulins, Intravenous therapeutic use, Immunologic Factors therapeutic use, Inflammation classification, Inflammation drug therapy, Inflammation physiopathology, Male, Middle Aged, Mycophenolic Acid therapeutic use, Neural Conduction, Polyneuropathies classification, Polyneuropathies drug therapy, Polyneuropathies physiopathology, Polyradiculoneuropathy, Chronic Inflammatory Demyelinating physiopathology, Sural Nerve pathology, Young Adult, Autoimmune Diseases of the Nervous System diagnosis, Inflammation diagnosis, Polyneuropathies diagnosis, Polyradiculoneuropathy, Chronic Inflammatory Demyelinating diagnosis
- Abstract
Objectives: Chronic inflammatory axonal polyneuropathy (CIAP) is defined on the basis of the clinical, electrophysiological and nerve biopsy findings and therapeutic responses of 'immunotherapy responding chronic axonal polyneuropathy (IR-CAP)'., Methods: The diagnosis of IR-CAP was made when all of three of the following mandatory criterion were met: (1) acquired, chronic progressive or relapsing symmetrical or asymmetrical polyneuropathy with duration of progression >2 months; (2) electrophysiological evidence of axonal neuropathy in at least two nerves without any evidence of 'strict criteria of demyelination'; and (3) definite responsiveness to immunotherapy., Results: Thirty-three patients with IR-CAP showed similar clinical features of chronic inflammatory demyelinating polyneuropathy (CIDP) except 'motor neuropathy subtype'. High spinal fluid protein was found in 27/32 (78%) cases. 'Inflammatory axonal neuropathy' was proven in 14 (45%) of 31 sural nerve biopsies., Discussions: IR-CAP could well be 'axonal CIDP' in view of clinical similarity, but not proven as yet. Thus, IR-CAP is best described as CIAP, a distinct entity that deserves its recognition in view of responsiveness to immunotherapy., Conclusion: Diagnosis of CIAP can be made by additional documentation of 'inflammation' by high spinal fluid protein or nerve biopsy in addition to the first two diagnostic criteria of IR-CAP., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. No commercial re-use. See rights and permissions. Published by BMJ.)
- Published
- 2020
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31. A Comparison of Apoptotic Activity for Follicular Unit Extraction Hair Grafts Stored in Different Holding Solutions.
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Rose PT, Nusbaum AG, Nusbaum BP, and Morgan MB
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- Cell Survival, Hair Follicle cytology, Humans, Immunohistochemistry, Male, Robotic Surgical Procedures, Alopecia surgery, Apoptosis genetics, Genes, bcl-2 genetics, Hair Follicle transplantation, Organ Preservation Solutions
- Published
- 2020
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32. Molecular Analysis of Clinically Defined Subsets of High-Grade Serous Ovarian Cancer.
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Lee S, Zhao L, Rojas C, Bateman NW, Yao H, Lara OD, Celestino J, Morgan MB, Nguyen TV, Conrads KA, Rangel KM, Dood RL, Hajek RA, Fawcett GL, Chu RA, Wilson K, Loffredo JL, Viollet C, Jazaeri AA, Dalgard CL, Mao X, Song X, Zhou M, Hood BL, Banskota N, Wilkerson MD, Te J, Soltis AR, Roman K, Dunn A, Cordover D, Eterovic AK, Liu J, Burks JK, Baggerly KA, Fleming ND, Lu KH, Westin SN, Coleman RL, Mills GB, Casablanca Y, Zhang J, Conrads TP, Maxwell GL, Futreal PA, and Sood AK
- Subjects
- Adult, Female, Gene Expression Profiling methods, Genomics methods, Humans, Metabolomics methods, Middle Aged, Ovarian Neoplasms genetics, Cystadenocarcinoma, Serous pathology, Ovarian Neoplasms metabolism, Ovarian Neoplasms pathology
- Abstract
The diversity and heterogeneity within high-grade serous ovarian cancer (HGSC), which is the most lethal gynecologic malignancy, is not well understood. Here, we perform comprehensive multi-platform omics analyses, including integrated analysis, and immune monitoring on primary and metastatic sites from highly clinically annotated HGSC samples based on a laparoscopic triage algorithm from patients who underwent complete gross resection (R0) or received neoadjuvant chemotherapy (NACT) with excellent or poor response. We identify significant distinct molecular abnormalities and cellular changes and immune cell repertoire alterations between the groups, including a higher rate of NF1 copy number loss, and reduced chromothripsis-like patterns, higher levels of strong-binding neoantigens, and a higher number of infiltrated T cells in the R0 versus the NACT groups., Competing Interests: Declaration of Interests A.A.J. consults with Roche/Genentech, Aravive, and Almac Group; has research funding from AstraZeneca, Pfizer, Bristol-Myers Squibb, Immatics, Iovance Biotherapeutics; honoraria from Gerson Lehrman Group; and travel support from AstraZeneca and MedImmune. K.R., A.D., and D.C. are employees of Akoya Biosciences. N.D.F. consults with Tesaro. S.N.W. has clinical research grants from AstraZeneca, ArQule, Bayer, Clovis Oncology, Cotinga Pharmaceuticals, NCCN, Novartis, Roche/Genentech, and Tesaro and consults with AstraZeneca, Circulogene, Clovis Oncology, Merck, Novartis, Pfizer, Roche/Genentech, Takeda, and Tesaro. R.L.C. has clinical research grants from AstraZeneca, Merck, Clovis Oncology, Genmab, Roche/Genentech, Janssen, V Foundation, and Gateway for Cancer Research and consults with AstraZeneca, Merck, Tesaro, Medivation, Clovis Oncology, Genmab, GamaMabs, Agenus, Regeneron, OncoQuest, OncoSec, Roche/Genentech, and Janssen. G.B.M. consults with AstraZeneca, ImmunoMet, Ionis, Nuevolution, PDX Phamaceuticals, SignalChem, Symphogen, and Tarveda Therapeutics; has stock options with Catena Pharmaceuticals, ImmunoMet, SignalChem, Spindletop Captial, and Tarveda Therapeutics; sponsored research from AstraZeneca, ImmunoMet, Pfizer, NanoString, and Tesaro and travel support from Chrysallis BioTherapeutics; and has licensed technology to NanoString and Myriad Genetics. Y.C.’s spouse owns stock in Celsion. T.P.C. consults with Thermo Fisher Scientific and has research funding from AbbVie. G.L.M. consults with Merck, Kiyatek, Renovia, and Tesaro and has research funding from Merck. A.K.S. consults with Merck and Kiyatec, has research funding from M-Trap, and is a shareholder of Bio-Path Holdings. All other authors declare no competing interests., (Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2020
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33. Ethics of Artificial Intelligence in Radiology: Summary of the Joint European and North American Multisociety Statement.
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Geis JR, Brady AP, Wu CC, Spencer J, Ranschaert E, Jaremko JL, Langer SG, Kitts AB, Birch J, Shields WF, van den Hoven van Genderen R, Kotter E, Gichoya JW, Cook TS, Morgan MB, Tang A, Safdar NM, and Kohli M
- Subjects
- Canada, Consensus, Europe, Humans, Radiologists ethics, Societies, Medical, United States, Artificial Intelligence ethics, Radiology ethics
- Abstract
This is a condensed summary of an international multisociety statement on ethics of artificial intelligence (AI) in radiology produced by the ACR, European Society of Radiology, RSNA, Society for Imaging Informatics in Medicine, European Society of Medical Imaging Informatics, Canadian Association of Radiologists, and American Association of Physicists in Medicine. AI has great potential to increase efficiency and accuracy throughout radiology, but it also carries inherent pitfalls and biases. Widespread use of AI-based intelligent and autonomous systems in radiology can increase the risk of systemic errors with high consequence and highlights complex ethical and societal issues. Currently, there is little experience using AI for patient care in diverse clinical settings. Extensive research is needed to understand how to best deploy AI in clinical practice. This statement highlights our consensus that ethical use of AI in radiology should promote well-being, minimize harm, and ensure that the benefits and harms are distributed among stakeholders in a just manner. We believe AI should respect human rights and freedoms, including dignity and privacy. It should be designed for maximum transparency and dependability. Ultimate responsibility and accountability for AI remains with its human designers and operators for the foreseeable future. The radiology community should start now to develop codes of ethics and practice for AI that promote any use that helps patients and the common good and should block use of radiology data and algorithms for financial gain without those two attributes., (Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2019
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34. Creation and Curation of the Society of Imaging Informatics in Medicine Hackathon Dataset.
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Kohli M, Morrison JJ, Wawira J, Morgan MB, Hostetter J, Genereaux B, Hussain M, and Langer SG
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- Humans, Societies, Medical, Datasets as Topic, Electronic Health Records, Medical Informatics methods
- Abstract
In order to support innovation, the Society of Imaging Informatics in Medicine (SIIM) elected to create a collaborative computing experience called a "hackathon." The SIIM Hackathon has always consisted of two components, the event itself and the infrastructure and resources provided to the participants. In 2014, SIIM provided a collection of servers to participants during the annual meeting. After initial server setup, it was clear that clinical and imaging "test" data were also needed in order to create useful applications. We outline the goals, thought process, and execution behind the creation and maintenance of the clinical and imaging data used to create DICOM and FHIR Hackathon resources.
- Published
- 2018
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35. Ditching the Disc: The Effects of Cloud-Based Image Sharing on Department Efficiency and Report Turnaround Times in Mammography.
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Morgan MB, Young E, Harada S, Winkler N, Riegert J, Jones T, Hu N, and Stein M
- Subjects
- Data Warehousing, Female, Humans, Information Storage and Retrieval, Time Factors, Workflow, Breast Neoplasms diagnostic imaging, Cloud Computing, Efficiency, Organizational, Information Dissemination, Mammography, Radiology Department, Hospital organization & administration, Radiology Information Systems
- Abstract
In screening mammography, accessing prior examination images is crucial for accurate diagnosis and avoiding false-positives. When women visit multiple institutions for their screens, these "outside" examinations must be retrieved for comparison. Traditionally, prior images are obtained by faxing requests to other institutions and waiting for standard mail (film or CD-ROM), which can greatly delay report turnaround times. Recently, advancements in cloud-based image transfer technology have opened up more efficient options for examination transfer between institutions. The objective of this study was to evaluate the effect of cloud-based image transfer on mammography department workflow, time required to obtain prior images, and report turnaround times. Sixty screening examinations requiring prior images were placed into two groups (30 each). The control group used the standard institutional protocol for requesting prior images: faxing requests and waiting for mailed examinations. The experimental group used a cloud-based transfer for both requesting and receiving examinations. The mean number of days between examination request and examination receipt was measured for both groups and compared. The mean number of days from examination request to receipt was 6.08 days (SD 3.50) in the control group compared with 3.16 days (SD 3.95) in the experimental group. Using a cloud-based image transfer to obtain prior mammograms resulted in an average reduction of 2.92 days (P = .0361; 95% confidence interval 0.20-5.65) between examination request and receipt. This improvement in system efficiency is relevant for interpreting radiologists working to improve reporting times and for patients anxious to receive their mammography results., (Copyright © 2017 American College of Radiology. Published by Elsevier Inc. All rights reserved.)
- Published
- 2017
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36. Developing transcriptional profiles in Orbicella franksi exposed to copper: Characterizing responses associated with a spectrum of laboratory-controlled environmental conditions.
- Author
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Morgan MB, Edge SE, Venn AA, and Jones RJ
- Published
- 2017
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37. Informatics leaders in radiology: who they are and why you need them.
- Author
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Morgan MB, Meenan CD, Safdar NM, Nagy P, and Flanders AE
- Subjects
- Job Description, United States, Leadership, Medical Informatics organization & administration, Models, Organizational, Organizational Objectives, Radiology organization & administration, Radiology Information Systems organization & administration
- Abstract
IT in health care has evolved rapidly over the past 20 years. The rise of the computer is at the core of these changes. Most agree that although these technologies have revolutionized the practice of medicine, they have additionally fostered a data revolution that is simultaneously useful and disruptive. The effective use and implementation of the right IT tools are critical to the success of the imaging profession. This article serves as a guideline to radiologists on how to build an effective IT division within an imaging enterprise from the perspective of leadership, management, and human resources. We address the process for building an IT team from the ground up and also provide recommendations for modifying an existing IT group to make it more effective. Paramount to this discussion is the concept of the imaging informatics professional and the advantage this type of training brings to a radiology department. In addition, we focus on the critical role of the physician informaticist as a liaison to bridge gaps among the IT, medical, and administrative functions in an organization., (Copyright © 2014 American College of Radiology. Published by Elsevier Inc. All rights reserved.)
- Published
- 2014
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38. Next-generation sequencing identifies rare variants associated with Noonan syndrome.
- Author
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Chen PC, Yin J, Yu HW, Yuan T, Fernandez M, Yung CK, Trinh QM, Peltekova VD, Reid JG, Tworog-Dube E, Morgan MB, Muzny DM, Stein L, McPherson JD, Roberts AE, Gibbs RA, Neel BG, and Kucherlapati R
- Subjects
- Alleles, Genetic Association Studies, Humans, MAP Kinase Kinase 1 genetics, MAP Kinase Signaling System genetics, Neurofibromin 1 genetics, ras Proteins genetics, ras Proteins metabolism, High-Throughput Nucleotide Sequencing methods, Mutation genetics, Noonan Syndrome genetics
- Abstract
Noonan syndrome (NS) is a relatively common genetic disorder, characterized by typical facies, short stature, developmental delay, and cardiac abnormalities. Known causative genes account for 70-80% of clinically diagnosed NS patients, but the genetic basis for the remaining 20-30% of cases is unknown. We performed next-generation sequencing on germ-line DNA from 27 NS patients lacking a mutation in the known NS genes. We identified gain-of-function alleles in Ras-like without CAAX 1 (RIT1) and mitogen-activated protein kinase kinase 1 (MAP2K1) and previously unseen loss-of-function variants in RAS p21 protein activator 2 (RASA2) that are likely to cause NS in these patients. Expression of the mutant RASA2, MAP2K1, or RIT1 alleles in heterologous cells increased RAS-ERK pathway activation, supporting a causative role in NS pathogenesis. Two patients had more than one disease-associated variant. Moreover, the diagnosis of an individual initially thought to have NS was revised to neurofibromatosis type 1 based on an NF1 nonsense mutation detected in this patient. Another patient harbored a missense mutation in NF1 that resulted in decreased protein stability and impaired ability to suppress RAS-ERK activation; however, this patient continues to exhibit a NS-like phenotype. In addition, a nonsense mutation in RPS6KA3 was found in one patient initially diagnosed with NS whose diagnosis was later revised to Coffin-Lowry syndrome. Finally, we identified other potential candidates for new NS genes, as well as potential carrier alleles for unrelated syndromes. Taken together, our data suggest that next-generation sequencing can provide a useful adjunct to RASopathy diagnosis and emphasize that the standard clinical categories for RASopathies might not be adequate to describe all patients.
- Published
- 2014
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39. Pilomatrix carcinoma: 13 new cases and review of the literature with emphasis on predictors of metastasis.
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Herrmann JL, Allan A, Trapp KM, and Morgan MB
- Subjects
- Aged, Female, Humans, Lymphatic Metastasis, Male, Middle Aged, Neoplasm Invasiveness, Neoplasm Metastasis, Neoplasm Recurrence, Local epidemiology, Proportional Hazards Models, Retrospective Studies, Risk Factors, Hair Diseases pathology, Head and Neck Neoplasms pathology, Pilomatrixoma pathology, Skin Neoplasms pathology
- Abstract
Background: Pilomatrix carcinoma is a rare cutaneous tumor derived from follicular matrix cells with few cases documented in the literature., Objective: We sought to better characterize this tumor by analyzing its epidemiologic, clinical, and histopathologic features in 13 new cases and by reviewing the literature., Methods: All cases of pilomatrix carcinoma from a large regional dermatopathology practice were identified and analyzed by chart review for clinical and histopathologic characteristics. Similar characteristics were compiled from an additional 123 cases in the English-language literature. Cox proportional hazards regression models were used to determine risk factors associated with the development of metastasis for all identified metastatic tumors., Results: Our 13 tumors were most common in middle-aged to older white men and presented mostly on the head/neck. Histopathologically, tumors were asymmetric, were poorly circumscribed, were composed of basaloid and "ghost" cells, had frequent atypical mitoses, and had infrequent lymphovascular invasion. Wide excision was considered the most definitive treatment modality, but local recurrence was common. When analyzing all reported cases of metastasis using statistics, metastasis was significantly associated (hazard ratio 3.45, P < .0413) with local tumor recurrence., Limitations: The retrospective, single-center design and the reliance on electronic medical records are limitations., Conclusions: This study helps better characterize pilomatrix carcinoma and identifies potential predictors of metastasis., (Copyright © 2014 American Academy of Dermatology, Inc. Published by Mosby, Inc. All rights reserved.)
- Published
- 2014
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40. Vascular Quality of Life Questionnaire-6 facilitates health-related quality of life assessment in peripheral arterial disease.
- Author
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Nordanstig J, Wann-Hansson C, Karlsson J, Lundström M, Pettersson M, and Morgan MB
- Subjects
- Aged, Cognition, Critical Illness, Exercise Test instrumentation, Exercise Tolerance, Female, Geographic Information Systems, Hospitals, University, Humans, Intermittent Claudication physiopathology, Intermittent Claudication psychology, Intermittent Claudication therapy, Ischemia physiopathology, Ischemia psychology, Ischemia therapy, Male, Middle Aged, Peripheral Arterial Disease physiopathology, Peripheral Arterial Disease psychology, Peripheral Arterial Disease therapy, Predictive Value of Tests, Psychometrics, Reproducibility of Results, Severity of Illness Index, Sweden, Time Factors, Treatment Outcome, Walking, Intermittent Claudication diagnosis, Ischemia diagnosis, Peripheral Arterial Disease diagnosis, Quality of Life, Surveys and Questionnaires
- Abstract
Background: Most commonly used outcome measures in peripheral arterial disease (PAD) provide scarce information about achieved patient benefit. Therefore, patient-reported outcome measures have become increasingly important as complementary outcome measures. The abundance of items in most health-related quality of life instruments makes everyday clinical use difficult. This study aimed to develop a short version of the 25-item Vascular Quality of Life Questionnaire (VascuQoL-25), a PAD-specific health-related quality of life instrument., Methods: The study recruited 129 individuals with intermittent claudication and 71 with critical limb ischemia from two university hospitals. Participants were a mean age of 70 ± 9 years, and 57% were men. All patients completed the original VascuQoL when evaluated for treatment, and 127 also completed the questionnaire 6 months after a vascular procedure. The VascuQoL-25 was reduced based on cognitive interviews and psychometric testing. The short instrument, the VascuQoL-6, was tested using item-response theory, exploring structure, precision, item fit, and targeting. A subgroup of 21 individuals with intermittent claudication was also tested correlating the results of VascuQoL-6 to the actual walking capacity, as measured using global positioning system technology., Results: On the basis of structured psychometric testing, the six most informative items were selected (VascuQoL-6) and tested vs the original VascuQoL-25. The correlation between VascuQoL-25 and VascuQoL-6 was r = 0.88 before intervention, r = 0.96 after intervention, and the difference was r = 0.91 (P < .001). The Cronbach α for the VascuQoL-6 was .85 before and .94 after intervention. Cognitive interviews indicated that the responders considered all six items to be relevant and comprehensible. Rasch analysis was used to reduce response options from seven (VascuQoL-25) to four (VascuQoL-6). VascuQol-6 was shown to have high precision and discriminative properties. Item fit was excellent, with both "infit" and "outfit" between 0.7 and 1.3 for all six items. The standardized response mean after intervention was 1.15, indicating good responsiveness to clinical change. VascuQoL-6 results correlated strongly (r = 0.72; P < .001) with the actual measured walking ability (n = 21)., Conclusions: VascuQoL-6 is a valid and responsive instrument for the assessment of health-related quality of life in PAD. The main advantage is the compact format that offers a possibility for routine use in busy clinical settings., (Copyright © 2014 Society for Vascular Surgery. Published by Mosby, Inc. All rights reserved.)
- Published
- 2014
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41. Sub-lethal coral stress: detecting molecular responses of coral populations to environmental conditions over space and time.
- Author
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Edge SE, Shearer TL, Morgan MB, and Snell TW
- Subjects
- Alveolata physiology, Analysis of Variance, Animals, Environmental Monitoring, Gene Expression Profiling, Time Factors, Anthozoa genetics, Anthozoa metabolism, Ecosystem, Gene Expression Regulation, Stress, Physiological
- Abstract
In order for sessile organisms to survive environmental fluctuations and exposures to pollutants, molecular mechanisms (i.e. stress responses) are elicited. Previously, detrimental effects of natural and anthropogenic stressors on coral health could not be ascertained until significant physiological responses resulted in visible signs of stress (e.g. tissue necrosis, bleaching). In this study, a focused anthozoan holobiont microarray was used to detect early and sub-lethal effects of spatial and temporal environmental changes on gene expression patterns in the scleractinian coral, Montastraea cavernosa, on south Florida reefs. Although all colonies appeared healthy (i.e. no visible tissue necrosis or bleaching), corals were differentially physiologically compensating for exposure to stressors that varied over time. Corals near the Port of Miami inlet experienced significant changes in expression of stress responsive and symbiont (zooxanthella)-specific genes after periods of heavy precipitation. In contrast, coral populations did not demonstrate stress responses during periods of increased water temperature (up to 29°C). Specific acute and long-term localized responses to other stressors were also evident. A correlation between stress response genes and symbiont-specific genes was also observed, possibly indicating early processes involved in the maintenance or disruption of the coral-zooxanthella symbiosis. This is the first study to reveal spatially- and temporally-related variation in gene expression in response to different stressors of in situ coral populations, and demonstrates that microarray technology can be used to detect specific sub-lethal physiological responses to specific environmental conditions that are not visually detectable., (Copyright © 2012 Elsevier B.V. All rights reserved.)
- Published
- 2013
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42. Topical formulation engendered alteration in p53 and cyclobutane pyrimidine dimer expression in chronic photodamaged patients.
- Author
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Spencer JM, Morgan MB, Trapp KM, and Moon SD
- Subjects
- Administration, Cutaneous, Adult, Aged, Chronic Disease, DNA Damage drug effects, DNA Damage radiation effects, DNA Repair drug effects, DNA Repair radiation effects, Dermatologic Agents administration & dosage, Follow-Up Studies, Humans, Middle Aged, Prospective Studies, Pyrimidine Dimers metabolism, Skin Aging radiation effects, Treatment Outcome, Tumor Suppressor Protein p53 metabolism, Ultraviolet Rays adverse effects, Dermatologic Agents therapeutic use, Pyrimidine Dimers genetics, Skin Aging drug effects, Tumor Suppressor Protein p53 genetics
- Abstract
While the clinical attributes of photoaging are well characterized in the literature, the pathogenic mechanisms that underlie these changes are incompletely elucidated. At the molecular level, p53 tumor-suppressor gene product mediated excision repair of ultraviolet (UV)-induced DNA damage is a critical effector in xeroderma pigmentosum (XP) and potentially in conventional photoaging. We examined p53 activity and measured UV-induced DNA damage via cyclobutane pyrimidine dimers (CPDs) quantitatively in 20 volunteers before and after an 8-week, open-label prospective topical application of a proprietary DNA recovery serum (Celfix). There was a statistically significant decrease in immunohistochemically determined p53 and CPD levels. While these data are preliminary, the findings lend support to the theoretical possibility of a topical agent reversing the effects of photodamage at the molecular level and, potentially, an ameliorative outcome clinically.
- Published
- 2013
43. Deep resequencing and association analysis of schizophrenia candidate genes.
- Author
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Crowley JJ, Hilliard CE, Kim Y, Morgan MB, Lewis LR, Muzny DM, Hawes AC, Sabo A, Wheeler DA, Lieberman JA, Sullivan PF, and Gibbs RA
- Subjects
- Adolescent, Adult, Aged, Female, Gene Frequency, Genetic Association Studies, Genotype, Humans, Logistic Models, Male, Middle Aged, Young Adult, Genetic Predisposition to Disease genetics, Polymorphism, Single Nucleotide genetics, Schizophrenia genetics
- Published
- 2013
- Full Text
- View/download PDF
44. Electromyography tests in patients with implanted cardiac devices are safe regardless of magnet placement.
- Author
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Ohira M, Silcox J, Haygood D, Harper-King V, Alsharabati M, Lu L, Morgan MB, Young AM, Claussen GC, King PH, and Oh SJ
- Subjects
- Aged, Aged, 80 and over, Electromyography methods, Female, Humans, Magnets, Male, Middle Aged, Patient Safety, Defibrillators, Implantable adverse effects, Electromyography adverse effects, Pacemaker, Artificial adverse effects
- Abstract
Methods: We compared the problems or complications associated with electrodiagnostic testing in 77 patients with implanted cardiac devices. Thirty tests were performed after magnet placement, and 47 were performed without magnet application., Results: All electrodiagnostic tests were performed safely in all patients without any serious effect on the implanted cardiac devices with or without magnet placement. A significantly higher number of patient symptoms and procedure changes were reported in the magnet group (P < 0.013). No statistical difference was found in the testing difficulty or ECG changes., Conclusion: The magnet group patients had an approximately 11-fold greater risk of symptoms than those in the control group. Our data do not support a recommendation that magnet placement is necessary for routine electrodiagnostic testing in patients with implanted cardiac devices, as long as our general and specific guidelines are followed., (Copyright © 2012 Wiley Periodicals, Inc.)
- Published
- 2013
- Full Text
- View/download PDF
45. Different characteristic phenotypes according to antibody in myasthenia gravis.
- Author
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Oh SJ, Morgan MB, Lu L, Hatanaka Y, Hemmi S, Young A, and Claussen GC
- Subjects
- Adolescent, Adult, Age of Onset, Aged, Chi-Square Distribution, Cholinesterase Inhibitors therapeutic use, Electric Stimulation, Electromyography, Evoked Potentials, Motor physiology, Female, Humans, Immunoglobulins, Intravenous therapeutic use, Immunologic Factors therapeutic use, Longitudinal Studies, Male, Middle Aged, Myasthenia Gravis therapy, Neural Conduction physiology, Pyridostigmine Bromide therapeutic use, Receptor Protein-Tyrosine Kinases immunology, Receptors, Cholinergic immunology, Retrospective Studies, Young Adult, Autoantibodies metabolism, Myasthenia Gravis classification, Myasthenia Gravis immunology, Phenotype
- Abstract
Objectives: To find the characteristic phenotypes of 3 different types of myasthenia gravis (MG)., Methods: The clinical and electrophysiological features among 15 cases of muscle-specific kinase antibody positive (MuSK Ab+) MG, 59 cases of double seronegative (DSN) MG, and 161 cases of acetylcholine receptor antibody (AChR Ab)+ MG in the University of Alabama at Birmingham were compared., Results: AChR Ab was positive in 69% of cases and MuSK Ab in 6% of cases. MuSK Ab+ MG was more common (14%) in African Americans compared with whites (4%). AChR Ab+ MG is characterized by male predominance, later onset, a fewer cases of ocular MG, and a higher association with thymoma. DSN-MG is characterized by a greater prevalence of ocular MG, milder forms of MG with less number of crisis, and fewer abnormalities in the repetitive nerve stimulation test. MuSK Ab+ MG is characterized by younger age at onset, severe and bulbar forms of MG, predominant faciobulbar neck weakness, and a poor response to edrophonium, anticholinesterase, and intravenous immunoglobulin. Long-term outcome showed no difference among 3 types of MG., Conclusions: AChR Ab+ MG and DSN-MG are similar, with the exception of less severity in the latter. MuSK Ab+ MG has distinct clinical and electrophysiological features.
- Published
- 2012
- Full Text
- View/download PDF
46. Using Representational Difference Analysis to detect changes in transcript expression of Aiptasia genes after laboratory exposure to lindane.
- Author
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Morgan MB, Parker CC, Robinson JW, and Pierce EM
- Subjects
- Animals, DNA, Complementary metabolism, Endocrine Disruptors toxicity, Insecticides toxicity, Sea Anemones drug effects, Sea Anemones metabolism, Gene Expression drug effects, Hexachlorocyclohexane toxicity, Sea Anemones genetics, Water Pollutants, Chemical toxicity
- Abstract
Molecular stress responses to pesticide exposures represent an understudied area of cnidarian transcriptome investigations. The organochlorine pesticide lindane is known to disrupt normal neuron function. Cnidarians with simple nervous systems are recognized as sensitive indicators of water quality, yet nothing is known about cnidarian responses to lindane. Sea anemones (Aiptasia pallida) were exposed for 4h to lindane (20 μg/l). Because anemones have neurons and lindane is known to target neurons, it is anticipated that cnidarian stress responses will include changes in transcription of genes associated with neurons. Representational Difference Analysis (RDA) was utilized to isolate differentially transcribed genes in the anemones exposed to the pesticide. After two rounds of RDA hybridizations, 148 amplified fragments ranging in size from 150 to 800 bp were cloned. Sequencing and bioinformatic analyses of 106 clones revealed 56 different gene fragments. Virtual Northern dot blots were used as a preliminary screening tool to identify the most responsive RDA products. To further characterize the specificity of response, additional anemones were exposed to a series of lindane concentrations (0, 0.2, 2.0, 10, and 20 μg/l). Northern dot blots were subsequently used to develop expression profiles for selected RDA products over the range of pesticide concentrations. The seven most responsive RDA products represent genes with products associated with neuron development, immune responses, and Ca(2+) binding/transport. The resulting expression profiles illustrate that these RDA products exhibit various degrees of concentration specificity with some RDA products being significantly up-regulated at 20 μg/l while other RDA products are most responsive at concentrations <20 μg/l. Results also demonstrate how RDA can be used to identify potentially important biomarkers of organochlorine exposure while generating new hypotheses about important phenomena such as endocrine disruption in cnidarians., (Copyright © 2012 Elsevier B.V. All rights reserved.)
- Published
- 2012
- Full Text
- View/download PDF
47. Intravascular schwannoma.
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Gaudi S, Mills O, Goyette EF, and Morgan MB
- Subjects
- Biomarkers, Tumor analysis, Biopsy, Female, Humans, Immunohistochemistry, Middle Aged, Neurilemmoma chemistry, Predictive Value of Tests, Skin Neoplasms chemistry, Vascular Neoplasms chemistry, Veins pathology, Neurilemmoma pathology, Skin blood supply, Skin Neoplasms pathology, Vascular Neoplasms pathology
- Abstract
Schwannoma is defined as a benign nerve sheath neoplasm of Schwann cell origin. Cutaneous schwannoma typically manifests along the course of peripheral nerves as a solitary, well-defined, skin-colored nodule within the deep dermis or subcutis of the flexor aspects of the extremities. Schwannoma enlarges slowly and typically follows a benign course, with local recurrence and malignant transformation being exceedingly rare. Although involvement of the vasculature by neurofibroma has been rarely reported, intravascular schwannoma has not been documented to date. We present a unique case of cutaneous schwannoma, as confirmed by histological morphology and immunohistochemistry, within the dermal venous system. Presentation of this case is followed by a discussion of the differential diagnoses of schwannoma, the possible etiologies of the extension of this lesion into the vasculature, and the significance of such a phenomenon.
- Published
- 2011
- Full Text
- View/download PDF
48. Adapting to the new realities of radiology resident education.
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Branstetter BF 4th and Morgan MB
- Subjects
- Diagnostic Imaging statistics & numerical data, Faculty, Medical statistics & numerical data, Internship and Residency statistics & numerical data, Observer Variation, Radiology statistics & numerical data
- Published
- 2011
- Full Text
- View/download PDF
49. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.
- Author
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Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Patel HR, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SM, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, Graves JA, O'Neill RJ, Pask AJ, Forrest SM, and Worley KC
- Subjects
- Animals, Australia, Chromosome Mapping, Chromosomes, Mammalian genetics, Female, Gene Expression Regulation, Genome, Genomic Imprinting, In Situ Hybridization, Fluorescence, Macropodidae growth & development, MicroRNAs genetics, MicroRNAs metabolism, Molecular Sequence Data, Reproduction genetics, Sequence Alignment, Sequence Analysis, DNA, Biological Evolution, Macropodidae classification, Macropodidae genetics, Transcriptome genetics
- Abstract
Background: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development., Results: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements., Conclusions: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.
- Published
- 2011
- Full Text
- View/download PDF
50. Whole-genome sequencing for optimized patient management.
- Author
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Bainbridge MN, Wiszniewski W, Murdock DR, Friedman J, Gonzaga-Jauregui C, Newsham I, Reid JG, Fink JK, Morgan MB, Gingras MC, Muzny DM, Hoang LD, Yousaf S, Lupski JR, and Gibbs RA
- Subjects
- Adolescent, Decision Making, Female, Humans, Levodopa therapeutic use, Male, Pedigree, Treatment Outcome, Twins, Dizygotic genetics, Dystonic Disorders drug therapy, Dystonic Disorders genetics, Genome, Human, Patient Care, Sequence Analysis, DNA
- Abstract
Whole-genome sequencing of patient DNA can facilitate diagnosis of a disease, but its potential for guiding treatment has been under-realized. We interrogated the complete genome sequences of a 14-year-old fraternal twin pair diagnosed with dopa (3,4-dihydroxyphenylalanine)-responsive dystonia (DRD; Mendelian Inheritance in Man #128230). DRD is a genetically heterogeneous and clinically complex movement disorder that is usually treated with l-dopa, a precursor of the neurotransmitter dopamine. Whole-genome sequencing identified compound heterozygous mutations in the SPR gene encoding sepiapterin reductase. Disruption of SPR causes a decrease in tetrahydrobiopterin, a cofactor required for the hydroxylase enzymes that synthesize the neurotransmitters dopamine and serotonin. Supplementation of l-dopa therapy with 5-hydroxytryptophan, a serotonin precursor, resulted in clinical improvements in both twins.
- Published
- 2011
- Full Text
- View/download PDF
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