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Roy SJ, Gilliham M, Berger B, Essah PA, Cheffings C, Miller AJ, Davenport RJ, Liu LH, Skynner MJ, Davies JM, Richardson P, Leigh RA, Tester M. Investigating glutamate receptor-like gene co-expression in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2008; 31:861-71. [PMID: 18284583 DOI: 10.1111/j.1365-3040.2008.01801.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
There is increasing evidence of the important roles of glutamate receptors (GLRs) in plant development and in adaptation to stresses. However, the studies of these putative ion channels, both in planta and in Xenopus oocytes, may have been limited by our lack of knowledge of possible GLR heteromer formation in plants. We have developed a modification of the single-cell sampling technique to investigate GLR co-expression, and thus potential heteromer formation, in single cells of Arabidopsis thaliana leaves. Micro-EXpression amplification (MEX) has allowed us to amplify gene transcripts from a single cell, enabling expression of up to 100 gene transcripts to be assayed. We measured, on average, the transcripts of five to six different AtGLRs in a single cell. However, no consistent patterns of co-expression or cell-type-specific expression were detected, except that cells sampled from the same plant showed similar expression profiles. The only discernible feature was the detection of AtGLR3.7 in every cell examined, an observation supported by GUS staining patterns in plants stably expressing promoter::uidA fusions. In addition, we found AtGLR3.7 expression in oocytes induces a Ba2+-, Ca2+- and Na+-permeable plasma membrane conductance.
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El-Serag HB, Wieman M, Richardson P. The use of acid-decreasing medication in veteran patients with gastro-oesophageal reflux disorder with and without Barrett's oesophagus. Aliment Pharmacol Ther 2008; 27:1293-9. [PMID: 18363892 DOI: 10.1111/j.1365-2036.2008.03690.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
AIM To examine use of acid-decreasing medications, especially proton pump inhibitors (PPIs), in patients with gastro-oesophageal reflux disorder (GERD) with and without Barrett's oesophagus (BO) in a large-scale study. METHODS We conducted a retrospective cohort study of patients with newly diagnosed BO (ICD-9 code 5302) and patients with GERD and no BO (ICD-9 53081, 5301) in Department of Veterans Affairs (VA) databases. Filled prescriptions for oral PPI and histamine2-receptor antagonists (H2RA) were identified in the VA Pharmacy Benefit Management database during 365 days following diagnosis. Groups with or without PPI or H2RA were compared in unadjusted and adjusted regression analyses. Chart review was used to validate diagnoses in a subset of patients with and without BO. RESULTS We evaluated 7732 patients with BO and 13 457 with GERD and no BO diagnosed between 1/2000 and 12/2002. At least one PPI prescription was filled during the first year following diagnosis in 91.5% of BO and 61.4% of non-BO patients (P < 0.0001), and one H2RA in 31.7% of BO and 59.4% of non-BO patients (P < 0.0001), respectively. However, 6.1% of BO patients were prescribed neither. Median duration for PPI filled prescriptions was twice as long for BO (221.7 vs. 106.9 days) compared with non-BO patients. The ratio of PPI or H2RA filled prescription days to available follow-up days among BO subjects was 0.66 (122.8 days were not covered with prescription for either), and 0.55 in GERD patients with no BO (165.0 days on neither). CONCLUSIONS Veterans Affairs patients with BO are 50% more likely to be prescribed a PPI than patients with GERD and no BO. However, on average, PPI prescriptions cover only 60% of follow-up time for BO patients.
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Rosenblatt J, Vasir B, Wu Z, Bissonnette A, MacNamara C, Uhl L, Lenahan C, Miller K, Joyce R, Levine J, Lowe K, Dombagoda D, Richardson P, Anderson K, Munshi N, Kufe D, Avigan D. 56: Vaccination with DC/MM Fusions in Conjunction with Stem Cell Transplantation. Biol Blood Marrow Transplant 2008. [DOI: 10.1016/j.bbmt.2007.12.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kramer JR, Davila JA, Miller ED, Richardson P, Giordano TP, El-Serag HB. The validity of viral hepatitis and chronic liver disease diagnoses in Veterans Affairs administrative databases. Aliment Pharmacol Ther 2008; 27:274-82. [PMID: 17996017 DOI: 10.1111/j.1365-2036.2007.03572.x] [Citation(s) in RCA: 225] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND The validity of International Classification of Diseases-9 codes for liver disease has not been determined. AIM To examine the accuracy of International Classification of Diseases-9 codes for cirrhosis with hepatitis C virus or alcoholic liver disease and HIV or hepatitis B virus coinfection with hepatitis C virus in Veterans Affairs data. METHODS We conducted a retrospective study comparing the Veterans Affairs administrative data with abstracted data from the Michael E. DeBakey VA Medical Center's medical records. We calculated the positive predictive value, negative predictive value, per cent agreement and kappa. RESULTS For cirrhosis codes, the positive predictive value (probability that cirrhosis is present among those with a code) and negative predictive value (probability that cirrhosis is absent among those without a code) were 90% and 87% with 88% agreement and kappa = 0.70. For hepatitis C virus codes, the positive predictive value and negative predictive value were 93% and 92%, yielding 92% agreement and kappa = 0.78. For alcoholic liver disease codes, the positive predictive value and negative predictive value were 71% and 98%, with 89% agreement and kappa = 0.74. All parameters for HIV coinfection with hepatitis C virus were >89%; however, the codes for hepatitis B virus coinfection had a positive predictive value of 43-67%. CONCLUSION These diagnostic codes (except hepatitis B virus) in Veterans Affairs administrative data are highly predictive of the presence of these conditions in medical records and can be reliably used for research.
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Avigan D, Rosenblatt J, Vasir B, Wu Z, Bissonnette A, MacNamara C, Uhl L, Lenahan C, Miller K, Joyce R, Levine J, Lowe K, Donbagoda D, Richardson P, Anderson K, Munshi N, Kufe D. 172: Phase I Study of Vaccination with Dendritic Cell Myeloma Fusions. Biol Blood Marrow Transplant 2008. [DOI: 10.1016/j.bbmt.2007.12.181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Saunders KJ, Johnston B, Richardson P, Cooper B, Hill AE, Jackson AJ, Magee A, McClelland JF, Shannon M, Wolsley CJ. What can this child see? Practical interpretation of visual acuity (VA) measures for parents and teachers of visually impaired children. Ophthalmic Physiol Opt 2008. [DOI: 10.1111/j.1475-1313.2007.00530_9.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ford ME, Kallen M, Richardson P, Matthiesen E, Cox V, Teng EJ, Cook KF, Petersen NJ. Effect of social support on informed consent in older adults with Parkinson disease and their caregivers. JOURNAL OF MEDICAL ETHICS 2008; 34:41-47. [PMID: 18156521 DOI: 10.1136/jme.2006.018192] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
PURPOSE To evaluate the effects of social support on comprehension and recall of consent form information in a study of Parkinson disease patients and their caregivers. DESIGN AND METHODS Comparison of comprehension and recall outcomes among participants who read and signed the consent form accompanied by a family member/friend versus those of participants who read and signed the consent form unaccompanied. Comprehension and recall of consent form information were measured at one week and one month respectively, using Part A of the Quality of Informed Consent Questionnaire (QuIC). RESULTS The mean age of the sample of 143 participants was 71 years (SD = 8.6 years). Analysis of covariance was used to compare QuIC scores between the intervention group (n = 70) and control group (n = 73). In the 1-week model, no statistically significant intervention effect was found (p = 0.860). However, the intervention status by patient status interaction was statistically significant (p = 0.012). In the 1-month model, no statistically significant intervention effect was found (p = 0.480). Again, however, the intervention status by patient status interaction was statistically significant (p = 0.040). At both time periods, intervention group patients scored higher (better) on the QuIC than did intervention group caregivers, and control group patients scored lower (worse) on the QuIC than did control group caregivers. IMPLICATIONS Social support played a significant role in enhancing comprehension and recall of consent form information among patients.
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Lacy M, Richardson P, Gertz M, Dispenzieri A, Greipp P, Witzig T, Schlossman R, Sidor C, Anderson K, Rajkumar S. Novel therapy with 2-methoxyestradiol (2ME2) for the treatment of relapsed and plateau phase multiple myeloma. J Clin Oncol 2007. [DOI: 10.1200/jco.2007.25.18_suppl.8108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
8108 Background: 2-methoxyestradiol (2ME2) is a natural endogenous product of estradiol metabolism with anti-angiogenic and anti-neoplastic properties that has demonstrated activity against multiple myeloma cell lines and xenografts in immunocompromised mice. We report results of the first phase II clinical trial of 2ME2 in pts with relapsed and plateau phase myeloma. Methods: This trial was designed with a one-stage design to accrue 60 pts in the setting of relapsed and plateau phase myeloma. 2ME2 was administered orally at a dose of 1000 mg daily. After the first 39 pts were accrued, based on the results of ongoing phase I trials, the dose of 2ME2 was increased to 800 mg twice daily for the remaining patients. Pts who were already on study at that point were also allowed to escalate their dose to 800 mg twice daily. The primary endpoint was overall response rate. Responses were assessed using Eastern Cooperative Oncology Group criteria. Results: Sixty patients were treated at Mayo Clinic and Dana Farber Cancer Institute. Median age was 60 years (range, 28–99). Thirty-one patients had relapsed/refractory myeloma and 29 patients had plateau phase myeloma. Median number of prior therapies was 4 including stem cell transplant (48%), thalidomide (62%), bortezomib (6%) and lenalidomide (3%). Therapy was well tolerated. Adverse events were anemia (35%), fatigue (35%), nausea (25%), diarrhea (20%), hot flashes (20%), headache (17%), muscle cramps (15%), and upper respiratory tract infection (15%). Most toxicities were mild (grade 1–2). Estimated progression-free survival rates for all pts at one, two, and three years are 24%, 16%, and 9% respectively. Three pts with plateau phase disease, have been on study for over 4 years without progression at 50, 60, and 63 months. Response assessment is ongoing; so far, whilst no partial responses have been seen, prolonged stable disease has been observed in 3 pts (5%). Conclusions: 2ME2 is a novel agent that appears to be safe and well tolerated. Although no responses have been seen, prolonged stable disease in some pts is promising. Preliminary pharmacokinetic data indicate that the dose of 2ME2 used in this study may be inadequate, and a new formulation with significantly better bioavailability will be tested soon in this patient population. No significant financial relationships to disclose.
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Echart C, Iacobelli M, Richardson P, Mitsiades C, Ignoni T, Ferro L, Eissner G. Pre-clinical evidence for an anti-tumor activity of defibrotide, a DNA-based, endothelium stabilizing drug. J Clin Oncol 2007. [DOI: 10.1200/jco.2007.25.18_suppl.14144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
14144 Background: Defibrotide (DF) is a mixture of polydeoxyribonucleotides with anti-thrombotic activity. Next to endothelium stabilization, recent data suggest anti-neoplastic properties of DF modulating interactions of tumor cells with their microenvironment. We investigated whether DF regulates expression and activity of heparanase, an enzyme critically involved in breaking down extracellular barriers and releasing growth factors linked to tumor invasion and angiogenesis. Methods: Heparanase expression was tested by RT-PCR and flow cytometry with multiple myeloma (MM) and microvascular endothelial cells. Heparanase activity was measured in cellular extracts with a heparan-degrading enzymatic assay. Serum degradation products of DF were identified by SEC-HPLC. The anti-angiogenic potential of DF was tested in vitro using a kit with human microvascular endothelial cells forming tubes across a layer of fibroblasts. In vivo, DF was tested in the dorsal skin-fold chamber assay in mice after inoculation of human gastric cancer cells. Proliferation was assessed by trypan blue exclusion. Results: We demonstrate a striking downregulation of expression and enzymatic activity of heparanase in endothelial as well as MM cells. In contrast, the degradation products of DF failed to exert any biological activity, suggesting that the intact mixture of deoxyoligonucleotides is responsible for the anti-tumor effect. We could also show that DF prevents (tumor) angiogenesis in vitro and in vivo. Western blots suggest that DF reduces phosphorylation-activation of p70S6 kinase, a key target in the mTOR pathway linked to angiogenesis. In addition, DF does not influence proliferation of vascular or tumor cells, rather acts via selective inhibition of tube formation of endothelial cells. Conclusion: In the present report we provide evidence for an anti-tumor activity of DF. DF inhibits (tumor) vessel formation and heparanase activity, and thus should be considered as an anti-cancer agent. [Table: see text]
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Stewart AK, Chang H, Trudel S, Anderson KC, Richardson P, Alsina M, Reece D, Young S, Sable-Hunt A, Li Z, Keats J, Van Wier S, Ahmann G, Price-Troska T, Giusti K, Bergsagel PL, Chesi M, Fonseca R. Diagnostic evaluation of t(4;14) in multiple myeloma and evidence for clonal evolution. Leukemia 2007; 21:2358-9. [PMID: 17568814 PMCID: PMC3882151 DOI: 10.1038/sj.leu.2404800] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Tasker R, Richardson P, Rewcastle B, Emmers R. Anatomical Correlation of Detailed Sensory Mapping of the Human Thalamus. Stereotact Funct Neurosurg 2007. [DOI: 10.1159/000103056] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Durie BGM, Harousseau JL, Miguel JS, Bladé J, Barlogie B, Anderson K, Gertz M, Dimopoulos M, Westin J, Sonneveld P, Ludwig H, Gahrton G, Beksac M, Crowley J, Belch A, Boccadaro M, Turesson I, Joshua D, Vesole D, Kyle R, Alexanian R, Tricot G, Attal M, Merlini G, Powles R, Richardson P, Shimizu K, Tosi P, Morgan G, Rajkumar SV. Erratum: International uniform response criteria for multiple myeloma. Leukemia 2007. [DOI: 10.1038/sj.leu.2404582] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abraham NS, El-Serag HB, Hartman C, Richardson P, Deswal A. Cyclooxygenase-2 selectivity of non-steroidal anti-inflammatory drugs and the risk of myocardial infarction and cerebrovascular accident. Aliment Pharmacol Ther 2007; 25:913-24. [PMID: 17402995 DOI: 10.1111/j.1365-2036.2007.03292.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
AIM To assess degree of cyclooxygenase-2 (COX-2) selectivity of a non-steroidal anti-inflammatory drug (NSAID) and risk of myocardial infarction (MI) or cerebrovascular accident (CVA). METHODS Prescription fill data were linked to medical records of a merged VA-Medicare dataset. NSAIDs were categorized by Cox-2 selectivity. Incidence of CVA and MI within 180 days of index prescription was assessed using Cox-proportional hazards models adjusted for gender, race, cardiovascular and pharmacological risk factors and propensity for prescription of highly COX-2 selective NSAIDs. RESULTS Of 384,322 patients (97.5% men and 85.4% white), 79.4% were prescribed a poorly selective, 16.4% a moderately selective and 4.2% a highly selective NSAID. There were 985 incident cases of MI and 586 cases of CVA in >145 870 person-years. Highly selective agents had the highest rate of MI (12.3 per 1000 person-years; [95% CI: 12.2-12.3]) and CVA (8.1 per 1000 person-years; [95% CI: 8.0-8.2]). Periods without NSAID exposure were associated with lowest risk. In adjusted models, highly selective COX-2 selective NSAIDs were associated with a 61% increase in CVA and a 47% increase in MI, when compared with poorly selective NSAIDs. CONCLUSIONS The risk of MI and CVA increases with any NSAID. Highly COX-2 selective NSAIDs confer the greatest risk.
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Durie BGM, Harousseau JL, Miguel JS, Bladé J, Barlogie B, Anderson K, Gertz M, Dimopoulos M, Westin J, Sonneveld P, Ludwig H, Gahrton G, Beksac M, Crowley J, Belch A, Boccadaro M, Turesson I, Joshua D, Vesole D, Kyle R, Alexanian R, Tricot G, Attal M, Merlini G, Powles R, Richardson P, Shimizu K, Tosi P, Morgan G. Erratum: International uniform response criteria for multiple myeloma. Leukemia 2006. [DOI: 10.1038/sj.leu.2404428] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A, Pavlova N, Karamychev V, Polouchine N, Shakhova V, Grigoriev I, Lou Y, Rohksar D, Lucas S, Huang K, Goodstein DM, Hawkins T, Plengvidhya V, Welker D, Hughes J, Goh Y, Benson A, Baldwin K, Lee JH, Díaz-Muñiz I, Dosti B, Smeianov V, Wechter W, Barabote R, Lorca G, Altermann E, Barrangou R, Ganesan B, Xie Y, Rawsthorne H, Tamir D, Parker C, Breidt F, Broadbent J, Hutkins R, O'Sullivan D, Steele J, Unlu G, Saier M, Klaenhammer T, Richardson P, Kozyavkin S, Weimer B, Mills D. Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A 2006; 103:15611-6. [PMID: 17030793 PMCID: PMC1622870 DOI: 10.1073/pnas.0607117103] [Citation(s) in RCA: 944] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.
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Chauhan D, Velankar M, Brahmandam M, Hideshima T, Podar K, Richardson P, Schlossman R, Ghobrial I, Raje N, Munshi N, Anderson KC. A novel Bcl-2/Bcl-X(L)/Bcl-w inhibitor ABT-737 as therapy in multiple myeloma. Oncogene 2006; 26:2374-80. [PMID: 17016430 DOI: 10.1038/sj.onc.1210028] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Bcl-2 or Bcl-X(L) confers resistance to chemotherapy in multiple myeloma (MM). Here we characterized the effects of ABT-737, a potent small-molecule inhibitor of antiapoptotic proteins Bcl-2, Bcl-X(L) and Bcl-w with markedly higher affinity than previously reported compounds, on human MM cells. ABT-737 induces apoptosis in MM cells, including those resistant to conventional therapy. Examination of purified patient MM cells demonstrated similar results, without significant toxicity against normal peripheral blood mononuclear cells and MM bone marrow stromal cells. Importantly, ABT-737 decreases the viability of bortezomib-, dexamethasone-(Dex) and thalidomide-refractory patient MM cells. Additionally, ABT-737 abrogates MM cell growth triggered by interleukin-6 or insulin-like growth factor-1. Mechanistic studies show that ABT-737-induced apoptosis is associated with activation of caspase-8, caspase-9 and caspase-3, followed by poly(ADP-ribose) polymerase cleavage. Combining ABT-737 with proteasome inhibitor bortezomib, melphalan or dexamethasone induces additive anti-MM activity. Taken together, our study provides the rationale for clinical protocols evaluating ABT-737, alone and together with botezomib, mephalan or dexamethasone, to enhance MM cell killing, overcome drug resistance conferred by Bcl-2 and improve patient outcome in MM.
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Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006; 313:1596-604. [PMID: 16973872 DOI: 10.1126/science.1128691] [Citation(s) in RCA: 2578] [Impact Index Per Article: 143.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.
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Baxter RL, Baxter HC, Campbell GA, Grant K, Jones A, Richardson P, Whittaker G. Quantitative analysis of residual protein contamination on reprocessed surgical instruments. J Hosp Infect 2006; 63:439-44. [PMID: 16772103 DOI: 10.1016/j.jhin.2006.03.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Accepted: 03/10/2006] [Indexed: 11/20/2022]
Abstract
'Ready-for-use' instruments from surgical instrument trays were examined after routine cleaning and sterilization in a blinded study. These reprocessed instruments originated from five National Health Service hospital trust sterile service departments in England and Wales. Determination of residual protein and peptide contamination was carried out by acid stripping of the instrument surfaces, hydrolysis of the constituent amino acids and quantitative total amino acid analysis. One hundred and twenty instruments were analysed, and the median levels of residual protein contamination per instrument for the individual trays were 267, 260, 163, 456 and 756 microg. Scanning electron microscopy and energy dispersive X-ray spectroscopic analyses of the instruments showed that tissue deposits were localized on surfaces, but there was no significant correlation between overall protein soiling and instrument complexity. The highest levels of residual contamination were found on instruments used for tonsillectomy and adenoid surgery.
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Durie BGM, Harousseau JL, Miguel JS, Bladé J, Barlogie B, Anderson K, Gertz M, Dimopoulos M, Westin J, Sonneveld P, Ludwig H, Gahrton G, Beksac M, Crowley J, Belch A, Boccadaro M, Cavo M, Turesson I, Joshua D, Vesole D, Kyle R, Alexanian R, Tricot G, Attal M, Merlini G, Powles R, Richardson P, Shimizu K, Tosi P, Morgan G, Rajkumar SV. International uniform response criteria for multiple myeloma. Leukemia 2006; 20:1467-73. [PMID: 16855634 DOI: 10.1038/sj.leu.2404284] [Citation(s) in RCA: 2017] [Impact Index Per Article: 112.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
New uniform response criteria are required to adequately assess clinical outcomes in myeloma. The European Group for Blood and Bone Marrow Transplant/International Bone Marrow Transplant Registry criteria have been expanded, clarified and updated to provide a new comprehensive evaluation system. Categories for stringent complete response and very good partial response are added. The serum free light-chain assay is included to allow evaluation of patients with oligo-secretory disease. Inconsistencies in prior criteria are clarified making confirmation of response and disease progression easier to perform. Emphasis is placed upon time to event and duration of response as critical end points. The requirements necessary to use overall survival duration as the ultimate end point are discussed. It is anticipated that the International Response Criteria for multiple myeloma will be widely used in future clinical trials of myeloma.
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Abraham NS, Cohen DC, Rivers B, Richardson P. Validation of administrative data used for the diagnosis of upper gastrointestinal events following nonsteroidal anti-inflammatory drug prescription. Aliment Pharmacol Ther 2006; 24:299-306. [PMID: 16842456 DOI: 10.1111/j.1365-2036.2006.02985.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
AIMS To validate veterans affairs (VA) administrative data for the diagnosis of nonsteroidal anti-inflammatory drug (NSAID)-related upper gastrointestinal events (UGIE) and to develop a diagnostic algorithm. METHODS A retrospective study of veterans prescribed an NSAID as identified from the national pharmacy database merged with in-patient and out-patient data, followed by primary chart abstraction. Contingency tables were constructed to allow comparison with a random sample of patients prescribed an NSAID, but without UGIE. Multivariable logistic regression analysis was used to derive a predictive algorithm. Once derived, the algorithm was validated in a separate cohort of veterans. RESULTS Of 906 patients, 606 had a diagnostic code for UGIE; 300 were a random subsample of 11 744 patients (control). Only 161 had a confirmed UGIE. The positive predictive value (PPV) of diagnostic codes was poor, but improved from 27% to 51% with the addition of endoscopic procedural codes. The strongest predictors of UGIE were an in-patient ICD-9 code for gastric ulcer, duodenal ulcer and haemorrhage combined with upper endoscopy. This algorithm had a PPV of 73% when limited to patients >or=65 years (c-statistic 0.79). Validation of the algorithm revealed a PPV of 80% among patients with an overlapping NSAID prescription. CONCLUSIONS NSAID-related UGIE can be assessed using VA administrative data. The optimal algorithm includes an in-patient ICD-9 code for gastric or duodenal ulcer and gastrointestinal bleeding combined with a procedural code for upper endoscopy.
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Lonial S, Alsina M, Anderson KC, Richardson P, Stewart K, Fonseca R, Heise C, Fox J, Allen A, Michelson G. Phase I trial of chir-258 in multiple myeloma. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.17502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
17502 Background: CHIR-258 is an orally active small molecule receptor tyrosine kinase (RTK) inhibitor which has potent activity against multiple RTKs involved in tumor growth and angiogenesis (IC50 ≤13 nM for FGFR, VEGFR, PDGFR, C-KIT, and FLT3). Approximately 15% of newly diagnosed MM patients harbor a t(4;14) translocation, which results in ectopic expression of FGFR3 and MMSET and is associated with poor treatment outcome [0]and reduced survival. CHIR-258 inhibits proliferation and induces apoptosis in FGFR3-expressing MM tumor xenografts as well as FGFR3-expressing primary MM cells (Trudel et al, Blood 2005). CHIR-258 was synergistic with dexamethasone (dex) in vitro. Methods: CHIR-258 was administered once daily in a dose-escalating phase 1 study to patients with relapsed/refractory MM. Drug tolerability and safety, pharmacokinetics (PK) and pharmacodynamics (PD) were assessed. Results: as of December 2005, 9 total pts have been treated (50, 100, and 200mg qd cohorts) [6M, 3F; median age: 58 (range: 44–68), median of 3 prior therapies(range:1–7)]. Prior tx: 9/9 pts-thalidomide; 8/9 -Velcade; 8/9-transplant; 8/9- had progressed through dex. 4 of 9 pts treated were FGFR3+ and 4 pts remain on study (3 are FGFR3+). No CR or PR have been observed; stable disease has been noted. CHIR-258 has been generally well tolerated, and most drug related AEs were CTC grade 1 or 2, including: headache, dysgeusia, fatigue and anorexia. No neuropathy. One DLT has been observed to date: neutropenia (200mg cohort). Five pts had dex added to CHIR-258 of which 3 are ongoing (all FGFR3+). FGFR3+ pts receiving dex and CHIR-258 have a greater decline in urine and serum paraproteins (pp) vs CHIR-258 alone. Plasma exposure and Cmax increased proportionally across the doses. Conclusions: CHIR-258 is a novel inhibitor of RTKs involved in MM growth and proliferation. FGFR3+ pts have a more marked reduction in pp than FGFR3- pts. CHIR-258 has generally been well tolerated and further accrual continues. [Table: see text]
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Pollak MN, Chapman JW, Shepherd L, Meng D, Richardson P, Wilson C, Orme B, Pritchard KI. Insulin resistance, estimated by serum C-peptide level, is associated with reduced event-free survival for postmenopausal women in NCIC CTG MA.14 adjuvant breast cancer trial. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.524] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
524 Background: NCIC CTG MA.14 is a randomized multi-centre trial of tamoxifen versus combined tamoxifen and octreotide LAR therapy in the adjuvant treatment of breast cancer in post-menopausal women. Planned secondary analyses included investigation of baseline metabolic factors that might influence survival. Laboratory and clinical studies indicate that insulin resistance is associated with adverse outcome in breast cancer. Insulin resistance elevates C-peptide levels. Methods: In MA.14, trial patients with stage I or II postmenopausal breast cancer were randomized from September, 1996 until July, 2000 to receive 20 mg tamoxifen PO daily for 5 years with/without the administration of the somatostatin analogue Octreotide LAR 90 mg depot injection monthly for 2 years. Event-free survival (EFS), the trial’s primary outcome measure, was defined as time from randomization to time of recurrence of primary disease, time of second malignancy or death due to any cause. We investigated the effect of baseline IGF-I, IGFBP-3, and C-peptide levels on EFS. Kaplan-Meier univariate and Cox step-wise multivariate regressions were performed with/without adjustment for the stratification factors of adjuvant chemotherapy, nodal status, and hormone receptor status, and included patient age (years) and tumour size (T-status). Results: These results are based on analysis of patient serum for the trial’s 667 patients. Median follow-up for those alive is 6.1 years; patients experienced 165 events. Higher C-peptide levels were associated with significantly worse EFS in adjusted, and unadjusted, univariate and multivariate analyses. Final efficacy analyses are expected within a few months. Updated analyses for the effects of baseline metabolic markers and body mass index on EFS will be presented. Conclusions: This is the largest data set, and the first clinical trial, linking higher serum C-peptide levels to adverse outcome in patients with early breast cancer. These results raise concern in the context of increasing population prevalence of insulin resistance. Potential novel adjuvant therapies exist as insulin resistance is modifiable. [Table: see text]
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Chanan-Khan A, Richardson P, Alsina M, Lonial S, Krishnan A, Carroll M, Albitar M, Hannah AL, Johnson RG, Anderson K. Phase 1 clinical trial of KOS-953 + bortezomib (BZ) in relapsed refractory multiple myeloma (MM). J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.3066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3066 Background: KOS-953 (17-AAG in Cremophor) inhibits HSP90 chaperone function, resulting in disruption of protein complexes and proteasomal degradation. Single-agent 17-AAG is active in relapsed/refractory MM patients (pts) (ASH 2005 A#361), with a recommended dose ≥ 275 mg/m2. In vitro, BZ + KOS-953 show additive cytotoxicity of myeloma cells. Objectives: Define phase 2 dose of BZ+KOS-953 in pts with relapsed refractory MM. Determine PK of KOS-953 and its active metabolite. Evaluate proteasome inhibition in whole blood lysates and explore changes in intracellular signaling proteins in pt PBMCs and MM cells. Methods: Pts received BZ as IV bolus followed by 1-hour infusion KOS-953 twice weekly for 2 out of 3 weeks. Dose escalation occurred in a step-wise manner. PK and collection of surrogates are performed following the 1st and 4th infusion. Pts assessed for response by EBMT criteria. Results: 20 pts were enrolled in 4 cohorts: BZ+KOS-953 (mg/m2): 0.7+100 (n=3); 1.0+100 (n=3); 1.0+150 (n=8); and 1.3+150 (n=6), receiving a total of 103+ cycles (median 5 cycles; range <1 - 17). Demographics: 10F/10M; median age/KPS 64y/90; median # of prior regimens 4 (range 2–16); 75% prior BZ (5 with ≥2 prior BZ); 95% prior thalidomide; 15% prior lenalidomide; 70% prior SCT(s). DLT observed in Cohort 2 (n=1 grade 4 hepatotoxicity in a setting of congestive heart failure secondary to cardiac amyloidosis) and in Cohort 3 (n=1 pancreatitis). Other Grade 3–4 toxicity (1 each): thrombocytopenia with Herpes Zoster recurrence and pneumonia; septic thrombophlebitis. Drug-related toxicity (mild-to-moderate): diarrhea (n=8), fatigue (n=8), constipation (n=7), neuropathy (n=7), ↑AST (n=5), muscle cramps (n=5) and rash (n=4). PK similar to single-agent trial; stationary kinetics noted upon twice weekly dosing. 20S proteasome function (1.3 mg/m2, end of infusion): 50% decrease (similar to predicted values). Response was seen in 6 out of 12 BZ-refractory patients (1 nCR, 5 MR) and 3 out of 4 BZ-naïve pts (1 nCR, 2 MR). Conclusions: Dose escalation continues with no additive toxicity or PK interactions to date. Similar inhibition of the 20S proteasome is observed compared to BZ alone. Encouraging activity is seen in both BZ-naïve and BZ-refractory heavily pre-treated MM pts. [Table: see text]
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Anderson K, Richardson P, Chanan-Khan A, Schlossman R, Munshi N, Oaklander A, Heffner L, Hassoun H, Avigan D, Amato A. Single-agent bortezomib in previously untreated multiple myeloma (MM): Results of a phase II multicenter study. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.7504] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
7504 Background: Bortezomib is effective in relapsed and/or refractory MM. This trial evaluated its efficacy and safety as monotherapy in previously untreated MM. Methods: Pts with untreated, symptomatic MM were eligible, with pts receiving concomitant steroids, platelet count < 30 × 109/L, or grade > 2 peripheral neuropathy [PN] excluded. Endpoints included response rate (RR) [Bladé criteria], time to progression, safety, incidence/severity of PN, and effect of dose modifications on PN. Pts received bortezomib 1.3 mg/m2 (d1, 4, 8, 11 every 21d) for 8 cycles. Comprehensive neurologic evaluation including electrophysiologic testing [NCS] and skin biopsy was performed in a subset of pts (n = 34). Results: Sixty-six pts (47% with stage III MM) were treated and 60 pts are evaluable for response, with an overall RR of 38% (CR 10%, PR 28%). PN was reported in 55% (36/65) pts (23 grade 1, 12 grade 2). One pt with grade 3 PN was discontinued. Other common treatment-associated adverse events reported to date include grade 1–2 fatigue in 21% (6/29), and rash in 17% (5/29) pts. Preliminary analysis shows PN improved or resolved in 75% (6/8 pts, with available follow-up data) with dose reduction. At baseline, small-fiber neuropathy (SFN) was seen in 52% (17/33) and large fiber axonal neuropathy (LFN) occurred in 9% (3/34) pts by NCS. SFN worsened in 41% (7/17) pts with baseline SFN. After completion of treatment, new SFN was seen in 33% (8/24) pts and LFN in 17% (4/24) pts by NCS. Conclusion: Single agent bortezomib is active in newly diagnosed MM pts (CR 10%), has manageable toxicity and offers a steroid-sparing approach. Underlying SFN appears more common in MM than previously appreciated and can also develop during bortezomib therapy, with symptomatic PN improving with dose modification. [Table: see text]
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