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4. Quantitative test of thermal field theory for Bose-Einstein condensates

Author

Morgan, S. A., Rusch, M., Hutchinson, D. A. W., and Burnett, K.

Subjects
Condensed Matter
Abstract

We present numerical results from a full second order quantum field theory of Bose-Einstein condensates applied to the 1997 JILA experiment [D. S. Jin et al., Phys. Rev. Lett. Vol. 78, 764 (1997)]. Good agreement is found for the energies and decay rates for both the lowest-energy m = 2 and m = 0 modes. The anomalous behaviour of the m = 0 mode is due to experimental perturbation of the non-condensate. The theory includes the coupled dynamics of the condensate and thermal cloud, the anomalous pair average and all relevant finite size effects., Comment: 4 pages, 3 figures. Uses revtex4, amsmath, amssymb and psfrag

Published
2003
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8. MLL rearrangements impact outcome in HOXA-deregulated T-lineage acute lymphoblastic leukemia: a Children’s Oncology Group Study

Author

Matlawska-Wasowska, K, Kang, H, Devidas, M, Wen, J, Harvey, R C, Nickl, C K, Ness, S A, Rusch, M, Li, Y, Onozawa, M, Martinez, C, Wood, B L, Asselin, B L, Chen, I-M, Roberts, K G, Baruchel, A, Soulier, J, Dombret, H, Zhang, J, Larson, R S, Raetz, E A, Carroll, W L, Winick, N J, Aplan, P D, Loh, M L, Mullighan, C G, Hunger, S P, Heerema, N A, Carroll, A J, Dunsmore, K P, and Winter, S S

Published
2016
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13. Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia

Author

Waanders, E., Gu, Z., Dobson, S.M., Antić, Ž., Crawford, J.C., Ma, X., Edmonson, M.N., Payne-Turner, D., Vorst, M. van de, Jongmans, M.C.J., McGuire, I., Zhou, X., Wang, J, Shi, L., Pounds, S., Pei, D., Cheng, C., Song, G., Fan, Y., Shao, Y., Rusch, M., McCastlain, K., Yu, J., Boxtel, R. van, Blokzijl, F., Iacobucci, I., Roberts, K.G., Wen, J., Wu, G., Ma, J, Easton, J., Neale, G., Olsen, S.R., Nichols, K.E., Pui, C.H., Zhang, J., Evans, W.E., Relling, M.V., Yang, J.J., Thomas, P.G., Dick, J.E., Kuiper, R.P., Mullighan, C.G., Waanders, E., Gu, Z., Dobson, S.M., Antić, Ž., Crawford, J.C., Ma, X., Edmonson, M.N., Payne-Turner, D., Vorst, M. van de, Jongmans, M.C.J., McGuire, I., Zhou, X., Wang, J, Shi, L., Pounds, S., Pei, D., Cheng, C., Song, G., Fan, Y., Shao, Y., Rusch, M., McCastlain, K., Yu, J., Boxtel, R. van, Blokzijl, F., Iacobucci, I., Roberts, K.G., Wen, J., Wu, G., Ma, J, Easton, J., Neale, G., Olsen, S.R., Nichols, K.E., Pui, C.H., Zhang, J., Evans, W.E., Relling, M.V., Yang, J.J., Thomas, P.G., Dick, J.E., Kuiper, R.P., and Mullighan, C.G.

Abstract

Item does not contain fulltext, Relapse of acute lymphoblastic leukemia (ALL) remains a leading cause of childhood death. Prior studies have shown clonal mutations at relapse often arise from relapse-fated subclones that exist at diagnosis. However, the genomic landscape, evolutionary trajectories and mutational mechanisms driving relapse are incompletely understood. In an analysis of 92 cases of relapsed childhood ALL, incorporating multimodal DNA and RNA sequencing, deep digital mutational tracking and xenografting to formally define clonal structure, we identify 50 significant targets of mutation with distinct patterns of mutational acquisition or enrichment. CREBBP, NOTCH1, and Ras signaling mutations rose from diagnosis subclones, whereas variants in NCOR2, USH2A and NT5C2 were exclusively observed at relapse. Evolutionary modeling and xenografting demonstrated that relapse-fated clones were minor (50%), major (27%) or multiclonal (18%) at diagnosis. Putative second leukemias, including those with lineage shift, were shown to most commonly represent relapse from an ancestral clone rather than a truly independent second primary leukemia. A subset of leukemias prone to repeated relapse exhibited hypermutation driven by at least three distinct mutational processes, resulting in heightened neoepitope burden and potential vulnerability to immunotherapy. Finally, relapse-driving sequence mutations were detected prior to relapse using deep digital PCR at levels comparable to orthogonal approaches to monitor levels of measurable residual disease. These results provide a genomic framework to anticipate and circumvent relapse by earlier detection and targeting of relapse-fated clones.

Published
2020

15. Degradation and transformation of fluoroquinolones by microorganisms with special emphasis on ciprofloxacin

Author

Rusch, M., Spielmeyer, A., Zorn, H., Hamscher, G., and Publica

Abstract

Although internationally recognized as the ""highest priority critically important antimicrobials,"" fluoroquinolones are extensively used in both human and veterinary medicine. Poor metabolism and recalcitrance of fluoroquinolones have led to their worldwide presence in municipal wastewaters as well as in manure and, consequently, in several environmental compartments. Being one of the most widely used fluoroquinolones in human medicine and, aside from that, the main metabolite of the veterinary drug enrofloxacin, ciprofloxacin is the most frequently detected fluoroquinolone in effluents of European wastewater treatment plants. Due to serious global concerns about the increasing emergence of bacterial (multi)resistances toward the highly efficient fluoroquinolones, special attention has been paid to their environmental degradation by various microorganisms. This review summarizes research on microbial transformation and degradation of fluoroquinolones with special emphasis on ciprofloxacin, presents an overview of the main ciprofloxacin biotransformation products, and takes a closer look at their biological relevance. Furthermore, own data, experiences, and publications gathered from our recent research in the field are acknowledged.

Published
2019

17. Genomic subtyping and therapeutic targeting of acute erythroleukemia

Author

Iacobucci, I., Wen, J., Meggendorfer, M., Choi, J. K., Shi, L., Pounds, S. B., Carmichael, C. L., Masih, K. E., Morris, S. M., Lindsley, R. C., Janke, L. J., Alexander, T. B., Song, G., Qu, C., Li, Y., Payne-Turner, D., Tomizawa, D., Kiyokawa, N., Valentine, M., Valentine, V., Basso, G., Locatelli, Franco, Enemark, E. J., Kham, S. K. Y., Yeoh, A. E. J., Ma, X., Zhou, X., Sioson, E., Rusch, M., Ries, R. E., Stieglitz, E., Hunger, S. P., Wei, A. H., To, L. B., Lewis, I. D., D'Andrea, R. J., Kile, B. T., Brown, A. L., Scott, H. S., Hahn, C. N., Marlton, P., Pei, D., Cheng, C., Loh, M. L., Ebert, B. L., Meshinchi, S., Haferlach, T., Mullighan, C. G., Locatelli F. (ORCID:0000-0002-7976-3654), Iacobucci, I., Wen, J., Meggendorfer, M., Choi, J. K., Shi, L., Pounds, S. B., Carmichael, C. L., Masih, K. E., Morris, S. M., Lindsley, R. C., Janke, L. J., Alexander, T. B., Song, G., Qu, C., Li, Y., Payne-Turner, D., Tomizawa, D., Kiyokawa, N., Valentine, M., Valentine, V., Basso, G., Locatelli, Franco, Enemark, E. J., Kham, S. K. Y., Yeoh, A. E. J., Ma, X., Zhou, X., Sioson, E., Rusch, M., Ries, R. E., Stieglitz, E., Hunger, S. P., Wei, A. H., To, L. B., Lewis, I. D., D'Andrea, R. J., Kile, B. T., Brown, A. L., Scott, H. S., Hahn, C. N., Marlton, P., Pei, D., Cheng, C., Loh, M. L., Ebert, B. L., Meshinchi, S., Haferlach, T., Mullighan, C. G., and Locatelli F. (ORCID:0000-0002-7976-3654)

Abstract

Acute erythroid leukemia (AEL) is a high-risk leukemia of poorly understood genetic basis, with controversy regarding diagnosis in the spectrum of myelodysplasia and myeloid leukemia. We compared genomic features of 159 childhood and adult AEL cases with non-AEL myeloid disorders and defined five age-related subgroups with distinct transcriptional profiles: adult, TP53 mutated; NPM1 mutated; KMT2A mutated/rearranged; adult, DDX41 mutated; and pediatric, NUP98 rearranged. Genomic features influenced outcome, with NPM1 mutations and HOXB9 overexpression being associated with a favorable prognosis and TP53, FLT3 or RB1 alterations associated with poor survival. Targetable signaling mutations were present in 45% of cases and included recurrent mutations of ALK and NTRK1, the latter of which drives erythroid leukemogenesis sensitive to TRK inhibition. This genomic landscape of AEL provides the framework for accurate diagnosis and risk stratification of this disease, and the rationale for testing targeted therapies in this high-risk leukemia.

Published
2019

19. Efficient Reduction of Antibacterial Activity and Cytotoxicity of Fluoroquinolones by Fungal-Mediated N-Oxidation

Author

Rusch, M., Spielmeyer, A., Meissner, J., Kietzmann, M., Zorn, H., Hamscher, G., and Publica

Abstract

Extensive usage of fluoroquinolone antibiotics in livestock results in their occurrence in manure and subsequently in the environment. Fluoroquinolone residues may promote bacterial resistance and are toxic to plants and aquatic organisms. Moreover, fluoroquinolones may enter the food chain through plant uptake, if manure is applied as fertilizer. Thus, the presence of fluoroquinolones in the environment may pose a threat to human and ecological health. In this study, the biotransformation of enrofloxacin, marbofloxacin, and difloxacin by the fungus X. longipes (Xylaria) was investigated. The main metabolites were unequivocally identified as the respective N-oxides by mass spectrometry and nuclear magnetic resonance spectroscopy. Fungal mediated N-oxidation of fluoroquinolones led to a 77-90% reduction of the initial antibacterial activity. In contrast to their respective parent compounds, N-oxides showed low cytotoxic potential and had a reduced impact on cell proliferation. Thus, biotransformation by X. longipes may represent an effective method for inactivating fluoroquinolones.

Published
2017

20. Excitations of Bose-Einstein condensates at finite temperatures

Author

Rusch, M, Rusch, Martin, and Burnett, K

Subjects
Bose-Einstein gas
Abstract

Recent experimental observations of collective excitations of Bose condensed atomic vapours have stimulated interest in the microscopic description of the dynamics of a Bose-Einstein condensate confined in an external potential. We present a finite temperature field theory for collective excitations of trapped Bose-Einstein condensates and use a finite-temperature linear response formalism, which goes beyond the simple mean-field approximation of the Gross-Pitaevskii equation. The effect of the non-condensed thermal atoms we include using perturbation theory in a quasiparticle basis. This presents a simple scheme to understand the interaction between condensate and non-condensed atoms and enables us to include the effect the condensate has on collision dynamics. At first we limit our treatment to the case of a spatially homogeneous Bose gas. We include the effect of pair and triplet anomalous averages and thus obtain a gapless theory for the excitations of a weakly interacting system, which we can link to well known results for Landau and Beliaev damping rates. A gapless theory for trapped systems with a static thermal component follows straightforwardly. We then investigate finite temperature excitations of a condensate in a spherically symmetric harmonic trap. We avoid approximations to the density of states and thus emphasise finite size aspects of the problem. We show that excitations couple strongly to a restricted number of modes, giving rise to resonance structure in their frequency spectra. Where possible we derive energy shifts and lifetimes of excitations. For one particular mode, the breathing mode, the effects of the discreteness of the system are sufficiently pronounced that the simple picture of an energy shift and width fails. Experiments in spherical traps have recently become feasible and should be able to test our detailed quantitative predictions.

Published
2016

24. Femtosecond site-selective probing of energy relaxing excitons in poly(phenylenevinylene):...

Author

Kersting, R., Mollay, B., Rusch, M., Wenisch, J., Leising, G., and Kauffmann, H.F.

Subjects
PHENYL compounds, COMPLEX compounds, PHOTOLUMINESCENCE
Abstract

Demonstrates that site-selective probing methods give strong evidence to the concept that the photoluminescence in poly(phenylenevinylene) results from molecular elementary excitations which undergo a non-Markovian hopping process. Optical spectra and transient instrumentations; Pulse luminescence responses computed as trial functions for fitting the femtosecond data.

Published
1997
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25. Pediatric non–Down syndrome acute megakaryoblastic leukemia is characterized by distinct genomic subsets with varying outcomes

Author

Rooij, J.D. (Johan) de, Branstetter, C. (Cristyn), Ma, J. (Jing), Li, Y. (Yongjin), Walsh, M.P. (Michael P), Cheng, J. (Jinjun), Obulkasim, A. (Askar), Dang, J. (Jinjun), Easton, J. (John), Verboon, P. (Peter), Mulder, H.L. (Heather L), Zimmermann, M. (Martin), Koss, C. (Cary), Gupta, P. (Pankaj), Edmonson, M. (Michael), Rusch, M. (Michael), Lim, J.Y.S. (Joshua Yew Suang), Reinhardt, K. (Katarina), Pigazzi, M. (Martina), Song, G. (Guangchun), Yeoh, A.E.J. (Allen E. J.), Shih, L.-Y. (Lee-Yung), Liang, D. (Der), Halene, S. (Stephanie), Krause, D.S. (Diane S), Zhang, J. (Jinghui), Downing, J.R. (James), Locatelli, F. (Franco), Reinhardt, D. (Dirk), Heuvel-Eibrink, M.M. (Marry) van den, Zwaan, C.M. (Michel), Fornerod, M.W.J. (Maarten), Gruber, T.A. (Tanja A), Rooij, J.D. (Johan) de, Branstetter, C. (Cristyn), Ma, J. (Jing), Li, Y. (Yongjin), Walsh, M.P. (Michael P), Cheng, J. (Jinjun), Obulkasim, A. (Askar), Dang, J. (Jinjun), Easton, J. (John), Verboon, P. (Peter), Mulder, H.L. (Heather L), Zimmermann, M. (Martin), Koss, C. (Cary), Gupta, P. (Pankaj), Edmonson, M. (Michael), Rusch, M. (Michael), Lim, J.Y.S. (Joshua Yew Suang), Reinhardt, K. (Katarina), Pigazzi, M. (Martina), Song, G. (Guangchun), Yeoh, A.E.J. (Allen E. J.), Shih, L.-Y. (Lee-Yung), Liang, D. (Der), Halene, S. (Stephanie), Krause, D.S. (Diane S), Zhang, J. (Jinghui), Downing, J.R. (James), Locatelli, F. (Franco), Reinhardt, D. (Dirk), Heuvel-Eibrink, M.M. (Marry) van den, Zwaan, C.M. (Michel), Fornerod, M.W.J. (Maarten), and Gruber, T.A. (Tanja A)

Abstract

Acute megakaryoblastic leukemia (AMKL) is a subtype of acute myeloid leukemia (AML) in which cells morphologically resemble abnormal megakaryoblasts. While rare in adults, AMKL accounts for 4–15% of newly diagnosed childhood AML cases. AMKL in individuals without Down syndrome (non-DS-AMKL) is frequently associated with poor clinical outcomes. Previous efforts have identified chimeric oncogenes in a substantial number of

Published
2017
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26. Pediatric non-Down syndrome acute megakaryoblastic leukemia is characterized by distinct genomic subsets with varying outcomes

Author

De Rooij, J. D. E., Branstetter, C., Ma, J., Li, Y., Walsh, M. P., Cheng, J., Obulkasim, A., Dang, J., Easton, J., Verboon, L. J., Mulder, H. L., Zimmermann, M., Koss, C., Gupta, P., Edmonson, M., Rusch, M., Lim, J. Y. S., Reinhardt, K., Pigazzi, M., Song, G., Yeoh, A. E. J., Shih, L. -Y., Liang, D. -C., Halene, S., Krause, D. S., Zhang, J., Downing, J. R., Locatelli, Franco, Reinhardt, D., Van Den Heuvel-Eibrink, M. M., Zwaan, C. M., Fornerod, M., Gruber, T. A., Locatelli F. (ORCID:0000-0002-7976-3654), De Rooij, J. D. E., Branstetter, C., Ma, J., Li, Y., Walsh, M. P., Cheng, J., Obulkasim, A., Dang, J., Easton, J., Verboon, L. J., Mulder, H. L., Zimmermann, M., Koss, C., Gupta, P., Edmonson, M., Rusch, M., Lim, J. Y. S., Reinhardt, K., Pigazzi, M., Song, G., Yeoh, A. E. J., Shih, L. -Y., Liang, D. -C., Halene, S., Krause, D. S., Zhang, J., Downing, J. R., Locatelli, Franco, Reinhardt, D., Van Den Heuvel-Eibrink, M. M., Zwaan, C. M., Fornerod, M., Gruber, T. A., and Locatelli F. (ORCID:0000-0002-7976-3654)

Abstract

Acute megakaryoblastic leukemia (AMKL) is a subtype of acute myeloid leukemia (AML) in which cells morphologically resemble abnormal megakaryoblasts. While rare in adults, AMKL accounts for 4-15% of newly diagnosed childhood AML cases. AMKL in individuals without Down syndrome (non-DS-AMKL) is frequently associated with poor clinical outcomes. Previous efforts have identified chimeric oncogenes in a substantial number of non-DS-AMKL cases, including RBM15-MKL1, CBFA2T3-GLIS2, KMT2A gene rearrangements, and NUP98-KDM5A. However, the etiology of 30-40% of cases remains unknown. To better understand the genomic landscape of non-DS-AMKL, we performed RNA and exome sequencing on specimens from 99 patients (75 pediatric and 24 adult). We demonstrate that pediatric non-DS-AMKL is a heterogeneous malignancy that can be divided into seven subgroups with varying outcomes. These subgroups are characterized by chimeric oncogenes with cooperating mutations in epigenetic and kinase signaling genes. Overall, these data shed light on the etiology of AMKL and provide useful information for the tailoring of treatment.

Published
2017

28. Deregulation of DUX4 and ERG in acute lymphoblastic leukemia.

Author

Zhang, J., McCastlain, K., Yoshihara, H., Xu, B., Chang, Y., Churchman, M., Wul, G., Li, Y., Wei, L., Iacobucci, I., Liu, Y., Qu, C., Wen, J., Edmonsonl, M., Payne-Turner, D., Kaufmann, K.B., Takayanagi, S., Wienholds, E., Waanders, E., Ntziachristos, P., Bakogianni, S., Wang, J.J., Aifantis, I., Roberts, K.G., Ma, J, Song, G., Easton, J., Mulder, H., Chen, X., Newman, S., Ma, X., Rusch, M., Gupta, P., Boggs, K., Vadodaria, B., Dalton, J., et al., Zhang, J., McCastlain, K., Yoshihara, H., Xu, B., Chang, Y., Churchman, M., Wul, G., Li, Y., Wei, L., Iacobucci, I., Liu, Y., Qu, C., Wen, J., Edmonsonl, M., Payne-Turner, D., Kaufmann, K.B., Takayanagi, S., Wienholds, E., Waanders, E., Ntziachristos, P., Bakogianni, S., Wang, J.J., Aifantis, I., Roberts, K.G., Ma, J, Song, G., Easton, J., Mulder, H., Chen, X., Newman, S., Ma, X., Rusch, M., Gupta, P., Boggs, K., Vadodaria, B., Dalton, J., and et al.

Abstract

Item does not contain fulltext

Published
2016

30. Untersuchung der Fette

Author

Großfeld, J., Höglund, O., Schellenberg, H., Morgenstern, F. v., Schellbach, H., Adam, F., Wildi, H., Raalte, A. v., Klostermann, M., Quast, H., Sundberg, Th., Miermeister, A., Bruhns, G., Schmidt, A., Kraus, E. J., Wissemann, F., Bertram, S. H., Täufel, K., Rusch, M., Waterman, H. I., van Westen, H. A., Thomas, A. W., Mattikow, M., Dömötör, J., and Steiner, O.

Published
1930
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33. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia

Author

Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, Payne-Turner D, Easton J, Chen X, Wang J, Rusch M, Lu C, Chen SC, Wei L, Collins-Underwood JR, Ma J, Roberts KG, Pounds SB, Ulyanov A, Becksfort J, Gupta P, Huether R, Kriwacki RW, Parker M, McGoldrick DJ, Zhao D, Alford D, Espy S, Bobba KC, Song G, Pei D, Cheng C, Roberts S, Barbato MI, Campana D, Coustan-Smith E, Shurtleff SA, Raimondi SC, Kleppe M, Cools J, Shimano KA, Hermiston ML, Doulatov S, Eppert K, Laurenti E, Notta F, Dick JE, Basso G, Hunger SP, and Loh

Published
2012

34. The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias.

Author

Andersson, AK, Ma, J, Wang, J, Chen, X, Gedman, AL, Dang, J, Nakitandwe, J, Holmfeldt, L, Parker, M, Easton, J, Huether, R, Kriwacki, R, Rusch, M, Wu, G, Li, Y, Mulder, H, Raimondi, S, Pounds, S, Kang, G, Shi, L, Becksfort, J, Gupta, P, Payne-Turner, D, Vadodaria, B, Boggs, K, Yergeau, D, Manne, J, Song, G, Edmonson, M, Nagahawatte, P, Wei, L, Cheng, C, Pei, D, Sutton, R, Venn, NC, Chetcuti, A, Rush, A, Catchpoole, D, Heldrup, J, Fioretos, T, Lu, C, Ding, L, Pui, C-H, Shurtleff, S, Mullighan, CG, Mardis, ER, Wilson, RK, Gruber, TA, Zhang, J, Downing, JR, St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project, Andersson, AK, Ma, J, Wang, J, Chen, X, Gedman, AL, Dang, J, Nakitandwe, J, Holmfeldt, L, Parker, M, Easton, J, Huether, R, Kriwacki, R, Rusch, M, Wu, G, Li, Y, Mulder, H, Raimondi, S, Pounds, S, Kang, G, Shi, L, Becksfort, J, Gupta, P, Payne-Turner, D, Vadodaria, B, Boggs, K, Yergeau, D, Manne, J, Song, G, Edmonson, M, Nagahawatte, P, Wei, L, Cheng, C, Pei, D, Sutton, R, Venn, NC, Chetcuti, A, Rush, A, Catchpoole, D, Heldrup, J, Fioretos, T, Lu, C, Ding, L, Pui, C-H, Shurtleff, S, Mullighan, CG, Mardis, ER, Wilson, RK, Gruber, TA, Zhang, J, Downing, JR, and St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project

Abstract

Infant acute lymphoblastic leukemia (ALL) with MLL rearrangements (MLL-R) represents a distinct leukemia with a poor prognosis. To define its mutational landscape, we performed whole-genome, exome, RNA and targeted DNA sequencing on 65 infants (47 MLL-R and 18 non-MLL-R cases) and 20 older children (MLL-R cases) with leukemia. Our data show that infant MLL-R ALL has one of the lowest frequencies of somatic mutations of any sequenced cancer, with the predominant leukemic clone carrying a mean of 1.3 non-silent mutations. Despite this paucity of mutations, we detected activating mutations in kinase-PI3K-RAS signaling pathway components in 47% of cases. Surprisingly, these mutations were often subclonal and were frequently lost at relapse. In contrast to infant cases, MLL-R leukemia in older children had more somatic mutations (mean of 6.5 mutations/case versus 1.3 mutations/case, P = 7.15 × 10(-5)) and had frequent mutations (45%) in epigenetic regulators, a category of genes that, with the exception of MLL, was rarely mutated in infant MLL-R ALL.

Published
2015

35. Endocarditis due to Lactobacillus jensenii in a Salvin's Amazon parrot (Amazona autumnalis salvini)

Author

Foldenauer, Ulrike, Rusch, M, Simova-Curd, Stefka, Nitzl, Dagmar, Hoop, Richard K, Hatt, Jean-Michel, University of Zurich, and Foldenauer, Ulrike

Subjects
10253 Department of Small Animals, 2400 General Immunology and Microbiology, 570 Life sciences, biology, 1103 Animal Science and Zoology, 10082 Institute of Food Safety and Hygiene, 3403 Food Animals
Published
2009
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36. Impairments, activity limitations and participation restrictions: Prevalence and associations among persons living with HIV/AIDS in British Columbia

Author

Rusch, M., Nixon, S., Schilder, A., Braitstein, P., Chan, K., and Robert Hogg

Subjects
Adult, Male, participation restrictions, Psychometrics, Motor Activity, lcsh:Computer applications to medicine. Medical informatics, Disability Evaluation, Sickness Impact Profile, Surveys and Questionnaires, Activities of Daily Living, Confidence Intervals, Prevalence, Humans, Disabled Persons, Social Behavior, impairments, Acquired Immunodeficiency Syndrome, British Columbia, Research, Sick Role, Social Support, Middle Aged, activity limitations, CD4 Lymphocyte Count, disability, Socioeconomic Factors, disablement, Quality of Life, lcsh:R858-859.7, HIV/AIDS, Female
Abstract

Background. To measure the prevalence of and associations among impairments, activity limitations and participation restrictions in persons living with HIV in British Columbia to inform support and care programs, policy and research. Methods A cross-sectional population-based sample of persons living with HIV in British Columbia was obtained through an anonymous survey sent to members of the British Columbia Persons With AIDS Society. The survey addressed the experience of physical and mental impairments, and the experience and level of activity limitations and participation restrictions. Associations were measured in three ways: 1) impact of types of impairment on social restriction; 2) impact of specific limitations on social restriction; and 3) independent association of overall impairments and limitations on restriction levels. Logistic regression was used to measure associations with social restriction, while ordinal logistic regression was used to measure associations with a three-category measure of restriction level. Results The survey was returned by 762 (50.5%) of the BCPWA participants. Over ninety percent of the population experienced one or more impairments, with one-third reporting over ten. Prevalence of activity limitations and participation restrictions was 80.4% and 93.2%, respectively. The presence of social restrictions was most closely associated with mental function impairments (OR: 7.0 for impairment vs. no impairment; 95% CI: 4.7 - 10.4). All limitations were associated with social restriction. Among those with ≤ 200 CD4 cells/mm3, odds of being at a higher restriction level were lower among those on antiretrovirals (OR: 0.3 for antiretrovirals vs. no antiretrovirals; 95% CI: 0.1–0.9), while odds of higher restriction were increased with higher limitation (OR: 3.6 for limitation score of 1–5 vs. no limitation, 95%CI: 0.9–14.2; OR: 24.7 for limitation score > 5 vs. no limitation, 95%CI: 4.9–125.0). Among those with > 200 CD4 cells/mm3, the odds of higher restriction were increased with higher limitation (OR: 2.7 for limitation score of 1–5 vs. no limitation, 95%CI: 1.4–5.1; OR: 8.6 for limitation score > 5 vs. no limitation, 95%CI: 3.9–18.8), as well as by additional number of impairments (OR:1.2 for every additional impairment; 95% CI:1.1–1.3). Conclusions This population-based sample of people living with HIV has been experiencing extremely high rates of impairments, activity limitations and participation restrictions. Furthermore, the complex inter-relationships identified amongst the levels reveal lessons for programming, policy and research in terms of the factors that contribute most to a higher quality of life.

Published
2004
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39. C11ORF95-RELA FUSIONS DRIVE ONCOGENIC NF-KB SIGNALING IN EPENDYMOMA

Author

Gilbertson, R., primary, Parker, M., additional, Mohankumar, K. M., additional, Punchihewa, C., additional, Weinlich, R., additional, Dalton, J. D., additional, Li, Y., additional, Lee, R., additional, Tatevossian, R. G., additional, Phoenix, T. N., additional, Thiruvenkatam, R., additional, White, E., additional, Tang, B., additional, Orisme, W., additional, Gupta, K., additional, Rusch, M., additional, Chen, X., additional, Nagahawhatta, P., additional, Hedlund, E., additional, Finkelstein, D., additional, Wu, G., additional, Shurtleff, S., additional, Easton, J., additional, Boggs, K., additional, Yergeau, D., additional, Vadodaria, B., additional, Mulder, H. L., additional, Becksford, J., additional, Gupta, P., additional, Huether, R., additional, Ma, J., additional, Song, G., additional, Gajjar, A., additional, Merchant, T., additional, Boop, F., additional, Smith, A. A., additional, Ding, L., additional, Lu, C., additional, Ochoa, K., additional, Zhao, D., additional, Fulton, R. S., additional, Fulton, L. L., additional, Mardis, E. R., additional, Wilson, R. K., additional, Downing, J. R., additional, Green, D. R., additional, Zhang, J., additional, Ellison, D. W., additional, and Gilbertson, R. J., additional

Published
2014
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40. A recurrent germline PAX5 mutation confers susceptibility to pre-B cell acute lymphoblastic leukemia

Author

Shah, S., Schrader, K.A., Waanders, E., Timms, A.E., Vijai, J., Miething, C., Wechsler, J., Yang, J., Hayes, J., Klein, R.J., Zhang, J., Wei, L., Wu, G., Rusch, M., Nagahawatte, P., Ma, J, Chen, S.C., Song, G., Cheng, J., Meyers, P., Bhojwani, D., Jhanwar, S., Maslak, P., Fleisher, M., Littman, J., Offit, L., Rau-Murthy, R., Fleischut, M.H., Corines, M., Murali, R., Gao, X., Manschreck, C., Kitzing, T., Murty, V.V., Raimondi, S.C., Kuiper, R.P., Simons, A., Schiffman, J.D., Onel, K., Plon, S.E., Wheeler, D.A., Ritter, D., Ziegler, D.S., Tucker, K., Sutton, R., Chenevix-Trench, G., Li, J., Huntsman, D.G., Hansford, S., Senz, J., Walsh, T., Lee (Helen Dowling Instituut), M. van der, Hahn, C.N., Roberts, K.G., King, M.C., Lo, S.M., Levine, R.L., Viale, A., Socci, N.D., Nathanson, K.L., Scott, H.S., Daly, M., Lipkin, S.M., Lowe, S.W., Downing, J.R., Altshuler, D., Sandlund, J.T., Horwitz, M.S., Mullighan, C.G., Offit, K., Shah, S., Schrader, K.A., Waanders, E., Timms, A.E., Vijai, J., Miething, C., Wechsler, J., Yang, J., Hayes, J., Klein, R.J., Zhang, J., Wei, L., Wu, G., Rusch, M., Nagahawatte, P., Ma, J, Chen, S.C., Song, G., Cheng, J., Meyers, P., Bhojwani, D., Jhanwar, S., Maslak, P., Fleisher, M., Littman, J., Offit, L., Rau-Murthy, R., Fleischut, M.H., Corines, M., Murali, R., Gao, X., Manschreck, C., Kitzing, T., Murty, V.V., Raimondi, S.C., Kuiper, R.P., Simons, A., Schiffman, J.D., Onel, K., Plon, S.E., Wheeler, D.A., Ritter, D., Ziegler, D.S., Tucker, K., Sutton, R., Chenevix-Trench, G., Li, J., Huntsman, D.G., Hansford, S., Senz, J., Walsh, T., Lee (Helen Dowling Instituut), M. van der, Hahn, C.N., Roberts, K.G., King, M.C., Lo, S.M., Levine, R.L., Viale, A., Socci, N.D., Nathanson, K.L., Scott, H.S., Daly, M., Lipkin, S.M., Lowe, S.W., Downing, J.R., Altshuler, D., Sandlund, J.T., Horwitz, M.S., Mullighan, C.G., and Offit, K.

Abstract

Contains fulltext : 126772.pdf (publisher's version ) (Closed access), Somatic alterations of the lymphoid transcription factor gene PAX5 (also known as BSAP) are a hallmark of B cell precursor acute lymphoblastic leukemia (B-ALL), but inherited mutations of PAX5 have not previously been described. Here we report a new heterozygous germline variant, c.547G>A (p.Gly183Ser), affecting the octapeptide domain of PAX5 that was found to segregate with disease in two unrelated kindreds with autosomal dominant B-ALL. Leukemic cells from all affected individuals in both families exhibited 9p deletion, with loss of heterozygosity and retention of the mutant PAX5 allele at 9p13. Two additional sporadic ALL cases with 9p loss harbored somatic PAX5 substitutions affecting Gly183. Functional and gene expression analysis of the PAX5 mutation demonstrated that it had significantly reduced transcriptional activity. These data extend the role of PAX5 alterations in the pathogenesis of pre-B cell ALL and implicate PAX5 in a new syndrome of susceptibility to pre-B cell neoplasia.

Published
2013

41. A recurrent germline PAX5 mutation confers susceptibility to pre-B cell acute lymphoblastic leukemia

Author

Shah, S, Schrader, KA, Vijai, J, Miething, C, Hayes, J, Klein, RJ, Gao, X, Kitzing, T, Lowe, SW, Offit, K, Littman, J, Offit, L, Rau-Murthy, R, Fleischut, MH, Corines, M, Manschreck, C, Waanders, E, Wei, L, Ma, J, Chen, S-C, Song, G, Cheng, J, Raimondi, SC, Roberts, KG, Downing, JR, Mullighan, CG, Kuiper, RP, Simons, A, Timms, AE, Wechsler, J, Horwitz, MS, Yang, J, Zhang, J, Wu, G, Rusch, M, Nagahawatte, P, Meyers, P, Bhojwani, D, Sandlund, JT, Jhanwar, S, Murali, R, Maslak, P, Fleisher, M, Murty, VV, Schiffman, JD, Onel, K, Plon, SE, Wheeler, DA, Ritter, D, Ziegler, DS ; https://orcid.org/0000-0001-7451-7916, Sutton, R ; https://orcid.org/0000-0002-0188-6005, Tucker, K ; https://orcid.org/0000-0002-6452-9427, Chenevix-Trench, G, Li, J, Huntsman, DG, Hansford, S, Senz, J, Walsh, T, Lee, M, King, M-C, Hahn, CN, Scott, HS, Lo, SM, Levine, RL, Viale, A, Socci, ND, Nathanson, KL, Daly, M, Lipkin, SM, Altshuler, D, Shah, S, Schrader, KA, Vijai, J, Miething, C, Hayes, J, Klein, RJ, Gao, X, Kitzing, T, Lowe, SW, Offit, K, Littman, J, Offit, L, Rau-Murthy, R, Fleischut, MH, Corines, M, Manschreck, C, Waanders, E, Wei, L, Ma, J, Chen, S-C, Song, G, Cheng, J, Raimondi, SC, Roberts, KG, Downing, JR, Mullighan, CG, Kuiper, RP, Simons, A, Timms, AE, Wechsler, J, Horwitz, MS, Yang, J, Zhang, J, Wu, G, Rusch, M, Nagahawatte, P, Meyers, P, Bhojwani, D, Sandlund, JT, Jhanwar, S, Murali, R, Maslak, P, Fleisher, M, Murty, VV, Schiffman, JD, Onel, K, Plon, SE, Wheeler, DA, Ritter, D, Ziegler, DS ; https://orcid.org/0000-0001-7451-7916, Sutton, R ; https://orcid.org/0000-0002-0188-6005, Tucker, K ; https://orcid.org/0000-0002-6452-9427, Chenevix-Trench, G, Li, J, Huntsman, DG, Hansford, S, Senz, J, Walsh, T, Lee, M, King, M-C, Hahn, CN, Scott, HS, Lo, SM, Levine, RL, Viale, A, Socci, ND, Nathanson, KL, Daly, M, Lipkin, SM, and Altshuler, D

Abstract

Somatic alterations of the lymphoid transcription factor gene PAX5 (also known as BSAP) are a hallmark of B cell precursor acute lymphoblastic leukemia (B-ALL), but inherited mutations of PAX5 have not previously been described. Here we report a new heterozygous germline variant, c.547G>A (p.Gly183Ser), affecting the octapeptide domain of PAX5 that was found to segregate with disease in two unrelated kindreds with autosomal dominant B-ALL. Leukemic cells from all affected individuals in both families exhibited 9p deletion, with loss of heterozygosity and retention of the mutant PAX5 allele at 9p13. Two additional sporadic ALL cases with 9p loss harbored somatic PAX5 substitutions affecting Gly183. Functional and gene expression analysis of the PAX5 mutation demonstrated that it had significantly reduced transcriptional activity. These data extend the role of PAX5 alterations in the pathogenesis of pre-B cell ALL and implicate PAX5 in a new syndrome of susceptibility to pre-B cell neoplasia. © 2013 Nature America, Inc. All rights reserved.

Published
2013

42. An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia

Author

Gruber, T, Larson Gedman, A, Zhang, J, Koss, C, Marada, S, Ta, H, Chen, S, Su, X, Ogden, S, Dang, J, Wu, G, Gupta, V, Andersson, A, Pounds, S, Sh, L, Easton, J, Barbato, M, Mulder, H, Manne, J, Wang, J, Rusch, M, Ranade, S, Ganti, R, Parker, M, Ma, J, Radtke, I, Ding, L, Cazzaniga, G, Biondi, A, Kornblau, S, Ravandi, F, Kantarjian, H, Nimer, S, Döhner, K, Döhner, H, Ley, T, Ballerini, P, Shurtleff, S, Tomizawa, D, Adachi, S, Hayashi, Y, Tawa, A, Shih, L, Liang, D, Rubnitz, J, Pui, C, Mardis, E, Wilson, R, Downing, J, Gruber, TA, Koss, CS, Ta, HQ, Chen, SC, Ogden, SK, Andersson, AK, Barbato, MI, Mulder, HL, Kornblau, SM, Nimer, SD, Ley, TJ, Shih, LY, Liang, DC, Rubnitz, JE, Pui, CH, Mardis, ER, Wilson, RK, Downing, JR, BIONDI, ANDREA, Gruber, T, Larson Gedman, A, Zhang, J, Koss, C, Marada, S, Ta, H, Chen, S, Su, X, Ogden, S, Dang, J, Wu, G, Gupta, V, Andersson, A, Pounds, S, Sh, L, Easton, J, Barbato, M, Mulder, H, Manne, J, Wang, J, Rusch, M, Ranade, S, Ganti, R, Parker, M, Ma, J, Radtke, I, Ding, L, Cazzaniga, G, Biondi, A, Kornblau, S, Ravandi, F, Kantarjian, H, Nimer, S, Döhner, K, Döhner, H, Ley, T, Ballerini, P, Shurtleff, S, Tomizawa, D, Adachi, S, Hayashi, Y, Tawa, A, Shih, L, Liang, D, Rubnitz, J, Pui, C, Mardis, E, Wilson, R, Downing, J, Gruber, TA, Koss, CS, Ta, HQ, Chen, SC, Ogden, SK, Andersson, AK, Barbato, MI, Mulder, HL, Kornblau, SM, Nimer, SD, Ley, TJ, Shih, LY, Liang, DC, Rubnitz, JE, Pui, CH, Mardis, ER, Wilson, RK, Downing, JR, and BIONDI, ANDREA

Abstract

To define the mutation spectrum in non-Down syndrome acute megakaryoblastic leukemia (non-DS-AMKL), we performed transcriptome sequencing on diagnostic blasts from 14 pediatric patients and validated our findings in a recurrency/validation cohort consisting of 34 pediatric and 28 adult AMKL samples. Our analysis identified a cryptic chromosome 16 inversion (inv(16)(p13.3q24.3)) in 27% of pediatric cases, which encodes a CBFA2T3-GLIS2 fusion protein. Expression of CBFA2T3-GLIS2 in Drosophila and murine hematopoietic cells induced bone morphogenic protein (BMP) signaling and resulted in a marked increase in the self-renewal capacity of hematopoietic progenitors. These data suggest that expression of CBFA2T3-GLIS2 directly contributes to leukemogenesis

Published
2012

43. Transcriptome Sequence Analysis of Pediatric Acute Megakaryoblastic Leukemia Identifies An Inv(16)(p13.3;q24.3)-Encoded CBFA2T3-GLIS2 Fusion Protein As a Recurrent Lesion in 39% of Non-Infant Cases: A Report From the St. Jude Children's Research Hospital – Washington University Pediatric Cancer Genome Project

Author

Gruber, T, Gedman, A, Ta, H, Zhang, J, Koss, C, Chen, S, Su, X, Gupta, V, Ogden, S, Andersson, A, Easton, J, Wang, J, Rusch, M, Ding, L, Cazzaniga, G, Biondi, A, Kornblau, S, Ravandi, F, Kantarjian, H, Nimer, S, Doehner, K, Doehner, H, Ley, T, Shurtleff, S, Rubnitz, J, Pui, C, Mardis, E, Wilson, R, Downing, J, Downing, J., BIONDI, ANDREA, Gruber, T, Gedman, A, Ta, H, Zhang, J, Koss, C, Chen, S, Su, X, Gupta, V, Ogden, S, Andersson, A, Easton, J, Wang, J, Rusch, M, Ding, L, Cazzaniga, G, Biondi, A, Kornblau, S, Ravandi, F, Kantarjian, H, Nimer, S, Doehner, K, Doehner, H, Ley, T, Shurtleff, S, Rubnitz, J, Pui, C, Mardis, E, Wilson, R, Downing, J, Downing, J., and BIONDI, ANDREA

Published
2011

44. Enteropathogen Resource Integration Center (ERIC): Bioinformatics support for research on biodefense-relevant enterobacteria

Author

Glasner, JD, Plunkett, G, Anderson, BD, Baumler, DJ, Biehl, BS, Burland, V, Cabot, EL, Darling, AE, Mau, B, Neeno-Eckwall, EC, Pot, D, Qiu, Y, Rissman, AI, Worzella, S, Zaremba, S, Fedorko, J, Hampton, T, Liss, P, Rusch, M, Shaker, M, Shaull, L, Shetty, P, Thotakura, S, Whitmore, J, Blattner, FR, Greene, JM, Perna, NT, Glasner, JD, Plunkett, G, Anderson, BD, Baumler, DJ, Biehl, BS, Burland, V, Cabot, EL, Darling, AE, Mau, B, Neeno-Eckwall, EC, Pot, D, Qiu, Y, Rissman, AI, Worzella, S, Zaremba, S, Fedorko, J, Hampton, T, Liss, P, Rusch, M, Shaker, M, Shaull, L, Shetty, P, Thotakura, S, Whitmore, J, Blattner, FR, Greene, JM, and Perna, NT

Abstract

ERIC, the Enteropathogen Resource Integration Center (www.ericbrc.org), is a new web portal serving as a rich source of information about enterobacteria on the NIAID established list of Select Agents related to biodefense - diarrheagenic Escherichia coli, Shigella spp., Salmonella spp., Yersinia enterocolitica and Yersinia pestis. More than 30 genomes have been completely sequenced, many more exist in draft form and additional projects are underway. These organisms are increasingly the focus of studies using high-throughput experimental technologies and computational approaches. This wealth of data provides unprecedented opportunities for understanding the workings of basic biological systems and discovery of novel targets for development of vaccines, diagnostics and therapeutics. ERIC brings information together from disparate sources and supports data comparison across different organisms, analysis of varying data types and visualization of analyses in human and computer-readable formats. © 2007 The Author(s).

Published
2008

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