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Empowering industrial research with shared biomedical vocabularies

drUG dISCOVErY TOdAY 2011年第21-22期16卷 940-947页

作者： Harland, Lee Larminie, Christopher Sansone, Susanna-Assunta Popa, Sorana Marshall, M. Scott Braxenthaler, Michael Cantor, Michael Filsell, Wendy Forster, Mark J. Huang, Enoch Matern, Andreas Musen, Mark Saric, Jasmin Slater, Ted Wilson, Jabe Lynch, Nick Wise, John dix, Ian Connected Discovery Ltd London WC1N 3AX England GlaxoSmithKline Computat Biol Stevenage SG1 2NY Herts England Univ Oxford Stand & Data Sharing Infrastruct Team E Res Ctr Oxford OX1 3QG England AstraZeneca R&D Knowledge Management & Informat Sci R&D Informat S-43183 Molndal Sweden Leiden Univ Med Ctr Dept Med Stat & Bioinformat NL-2333 ZC Leiden Netherlands Hoffmann LaRoche Inc Pharma Res & Early Dev Nutley NJ 07710 USA Pfizer Worldwide Res & Dev New York NY 10017 USA Unilever R&D Sharnbrook MK44 1LQ Beds England Syngenta R&D Informat Syst Int Res Ctr Jealotts Hill RG42 6EX Berks England Pfizer Worldwide Res & Dev Cambridge MA 02140 USA Thomson Reuters Life Sci Boston MA 02210 USA Stanford Univ Stanford CA 94305 USA Boehringer Ingelheim Pharma GmbH & Co KG Sci Informat Ctr D-88397 Biberach Germany Merck Sharp & Dohme Corp Boston MA 02115 USA Elsevier Pharma & Biotech Grp Sci & Technol Corp Markets London NW1 7BY England AstraZeneca UK Macclesfield SK10 4TG Cheshire England AstraZeneca Knowledge Management & Informat Sci R&D Informat Macclesfield SK10 4TJ Cheshire England

The life science industries (including pharmaceuticals, agrochemicals and consumer goods) are exploring new business models for research and development that focus on external partnerships. In parallel, there is a desire to make better use of data obtained from sources such as human clinical samples to inform and support early research programmes. Success in both areas depends upon the successful integration of heterogeneous data from multiple providers and scientific domains, something that is already a major challenge within the industry. This issue is exacerbated by the absence of agreed standards that unambiguously identify the entities, processes and observations within experimental results. In this article we highlight the risks to future productivity that are associated with incomplete biological and chemical vocabularies and suggest a new model to address this long-standing issue.

关键词： MEdICAL research INdUSTrIAL research VOCABULArY rESEArCH & development data integration (Computer science) INFOrMATION resources

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Survival analysis using inverse probability of treatment weighted methods based on the generalized propensity score

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PHArMACEUTICAL STATISTICS 2010年第1期9卷 21-34页

作者： Sugihara, Masahiro Dauchi Sankyo Co Ltd Clin Data & Biostat Dept R&D Div Shinagawa Ku Tokyo 1408710 Japan Tokyo Inst Technol Dept Ind Engn & Management Tokyo 152 Japan

In survival analysis, treatment effects are commonly evaluated based on survival curves and hazard ratios as causal treatment effects. In observational studies, these estimates may be biased due to confounding factors. The inverse probability of treatment weighted (IPTW) method based on the propensity score is one of the approaches utilized to adjust for confounding factors between binary treatment groups. As a generalization of this methodology, we developed an exact formula for an IPTW log-rank test based on the generalized propensity score for survival data. This makes it possible to compare the group differences of IPTW Kaplan Meier estimators of survival curves using an IPTW log-rank test for multi-valued treatments. As causal treatment effects, the hazard ratio can be estimated using the IPTW approach. If the treatments correspond to ordered levels of a treatment, the proposed method can be easily extended to the analysis of treatment effect patterns with contrast statistics. In this paper, the proposed method is illustrated with data from the Kyushu Lipid Intervention Study (KLIS), which investigated the primary preventive effects of pravastatin on coronary heart disease (CHd). The results of the proposed method suggested that pravastatin treatment reduces the risk of CHd and that compliance to pravastatin treatment is important for the prevention of CHd. Copyright (C) 2009 John Wiley & Sons, Ltd.

关键词： generalized propensity score IPTW observational study survival data

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Prediction of response to antiretroviral therapy by human experts and by the Euresist data-driven expert system (the EVE study)

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HIV MEdICINE 2011年第4期12卷 211-218页

作者： Zazzi, M. Kaiser, r. Sonnerborg, A. Struck, d. Altmann, A. Prosperi, M. rosen-Zvi, M. Petroczi, A. Peres, Y. Schuelter, E. Boucher, C. A. Brun-Vezinet, F. Harrigan, P. r. Morris, L. Obermeier, M. Perno, C-F Phanuphak, P. Pillay, d. Shafer, r. W. Vandamme, A-M van Laethem, K. Wensing, A. M. J. Lengauer, T. Incardona, F. Univ Siena Dept Mol Biol Policlin S Maria Scotte Microbiol Sect I-53100 Siena Italy Univ Cologne Inst Virol Cologne Germany Karolinska Inst Dept Infect Dis Stockholm Sweden CRP Sante Lab Retrovirol Luxembourg Luxembourg Max Planck Inst Informat Saarbrucken Germany Univ Cattolica Sacro Cuore Clin Infect Dis Rome Italy IBM Res Labs Machine Learning & Data Min Grp Haifa Israel Kingston Univ Sch Life Sci Kingston upon Thames KT1 2EE Surrey England IBM Res Labs Knowledge Management Grp Haifa Israel Erasmus Univ Dept Virol Erasmus Med Ctr NL-3000 DR Rotterdam Netherlands Hop Bichat Claude Bernard Virol Lab F-75877 Paris 18 France Univ British Columbia BC Ctr Excellence HIV AIDS Vancouver BC V5Z 1M9 Canada Natl Inst Communicable Dis AIDS Virus Res Unit Johannesburg South Africa Univ Munich Dept Virol Munich Germany Univ Roma Tor Vergata Dept Expt Med Rome Italy HIV NAT Thai Red Cross AIDS Res Ctr Bangkok Thailand UCL Dept Infect & Immun London England Stanford Univ Dept Med Div Infect Dis Stanford CA 94305 USA Katholieke Univ Leuven Rega Inst Med Res Leuven Belgium Univ Med Ctr Utrecht Dept Med Microbiol Utrecht Netherlands Informa SRL R&D Rome Italy

Objectives The Euresist expert system is a novel data-driven online system for computing the probability of 8-week success for any given pair of HIV-1 genotype and combination antiretroviral therapy regimen plus optional patient information. The objective of this study was to compare the Euresist system vs. human experts (EVE) for the ability to predict response to treatment. Methods The Euresist system was compared with 10 HIV-1 drug resistance experts for the ability to predict 8-week response to 25 treatment cases derived from the Euresist database validation data set. All current and past patient data were made available to simulate clinical practice. The experts were asked to provide a qualitative and quantitative estimate of the probability of treatment success. results There were 15 treatment successes and 10 treatment failures. In the classification task, the number of mislabelled cases was six for Euresist and 6-13 for the human experts [mean +/- standard deviation (Sd) 9.1 +/- 1.9]. The accuracy of Euresist was higher than the average for the experts (0.76 vs. 0.64, respectively). The quantitative estimates computed by Euresist were significantly correlated (Pearson r=0.695, P < 0.0001) with the mean quantitative estimates provided by the experts. However, the agreement among experts was only moderate (for the classification task, inter-rater kappa=0.355;for the quantitative estimation, mean +/- Sd coefficient of variation=55.9 +/- 22.4%). Conclusions With this limited data set, the Euresist engine performed comparably to or better than human experts. The system warrants further investigation as a treatment-decision support tool in clinical practice.

关键词： antiretroviral therapy drug resistance genotype HIV type 1 prediction systems

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Efficacy and Safety of Besifloxacin Ophthalmic Suspension 0.6% Compared with Moxifloxacin Ophthalmic Solution 0.5% for Treating Bacterial Conjunctivitis

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OPHTHALMOLOGY 2009年第9期116卷 1615-1623页

作者： Mcdonald, Marguerite B. Protzko, Eugene E. Brunner, Lynne S. Morris, Timothy W. Haas, Wolfgang Paterno, Michael r. Comstock, Timothy L. Usner, date W. Ophthalm Consultants Long Isl Corneal Specialist & Cataract & Refract Surg Lynbrook NY USA Seidenberg Protzko Eye Associates Bel Air MD USA Bausch & Lomb Inc R&D Microbiol & Sterilizat Sci Rochester NY USA Bausch & Lomb Inc Pharmaceut Clin Sci Rochester NY USA Bausch & Lomb Inc Global Stat & Data Management Rochester NY USA

Objective: To compare the clinical and antimicrobial efficacy of besifloxacin ophthalmic suspension 0.6% with that of moxifloxacin ophthalmic solution 0.5% for the treatment of bacterial conjunctivitis. design: Multicenter, randomized, double-masked, parallel-group, active-controlled, noninferiority study. Participants: Patients 1 year of age or older with clinical manifestations of bacterial conjunctivitis. Methods: Eligible patients were randomized to either besifloxacin suspension or moxifloxacin solution, instilled in the infected eye(s) 3 times daily for 5 days, and participated in study visits on days 1, 5 ( 1 day), and 8 (+1 day). Assessments included clinical evaluation of signs and symptoms, visual acuity, biomicroscopy, and culture of the infected eye(s) at each visit, as well as direct ophthalmoscopy on days 1 and 8. Main Outcome Measures: The primary efficacy end points were clinical resolution and microbial eradication of baseline bacterial infection on day 5 in patients with culture-confirmed bacterial conjunctivitis. Secondary end points included clinical resolution and microbial eradication on day 8, individual clinical outcomes, microbial and clinical outcomes by bacterial species, and safety. results: A total of 1161 patients (533 with culture-confirmed bacterial conjunctivitis) were randomized. Based on the 95% confidence interval (CI) of the difference, besifloxacin was noninferior to moxifloxacin for clinical resolution on day 5 (58.3% vs. 59.4%, respectively;95% CI, -9.48 to 7.29) and day 8 (84.5% vs. 84.0%, respectively, 95% CI, -5.6% to 6.75%) and for microbial eradication on day 5 (93.3% vs. 91.1 %, respectively, 95% CI, -2.44 to 6.74) and day 8 (87.3% vs. 84.7%;95% CI, -3.32 to 8.53). There was no statistically significant difference between the 2 treatment groups for either efficacy end points on days 5 or 8 (P>0.05). Besifloxacin and moxifloxacin were well tolerated. The cumulative frequency of ocular adverse events was similar between tr

关键词： Ophthalmology

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A Multi-criteria Convex Quadratic Programming model for credit data analysis

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dECISION SUPPOrT SYSTEMS 2008年第4期44卷 1016-1030页

作者： Peng, Yi Kou, Gang Shi, Yong Chen, Zhengxin Univ Elect Sci & Technol China Sch Management & Econ Chengdu 610054 Peoples R China Thomson Corp R&D Eagan MN 55123 USA Univ Nebraska Coll Informat Sci & Technol Omaha NE 68182 USA CAS Res Ctr Fictitious Econ & Data Sci Beijing 100080 Peoples R China

Speed and scalability are two essential issues in data mining and knowledge discovery. This paper proposed a mathematical programming model that addresses these two issues and applied the model to Credit Classification Problems. The proposed Multicriteria Convex Quadric Programming (MCQP) model is highly efficient (computing time complexity O(n(1.5-2))) and scalable to massive problems (size of O(10(9))) because it only needs to solve linear equations to find the global optimal solution. Kernel functions were introduced to the model to solve nonlinear problems. In addition, the theoretical relationship between the proposed MCQP model and SVM was discussed. (c) 2007 Elsevier B.V. All rights reserved.

关键词： data mining classification mathematical programming multiple criteria decision making multi-criteria convex quadric programming (MCQP)

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does Thermal Stress decrease Uterine Blood Flow in Hypertensive Pregnancies?

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American Journal of Perinatology 2008年第5期11卷 313-316页

作者： Jouko P. Pirhonen Kalevi K. Vähä-Eskeli Asko Seppänen Jouni Vuorinen risto U. Erkkola Department of Obstetrics and Gynecology Turku University Hospital (J.P.P. K.K.V.-E. R.U.E.) Rehabilitation Research Center of the Social Insurance Institution (A.S.) and Data Management and Biostatistics Orion Corporation Farmos R&D Pharmaceuticals (J.V.) Turku Finland

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Effect of severe renal failure and haemodialysis on the pharmacokinetics of levosimendan and its metabolites

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CLINICAL PHArMACOKINETICS 2007年第3期46卷 235-246页

作者： Puttonen, Jaakko Kantele, Sampo Kivikko, Matti Hakkinen, Sari Harjola, Veli-Pekka Koskinen, Petri Pentikainen, Pertti J. Orion Pharma Clin R&D FI-70701 Kuopio Finland Orion Pharma Dept Biostat & Data Management R&D Espoo Finland Orion Pharma Clin R&D Espoo Finland Orion Pharma Nonclin R&D Espoo Finland Univ Helsinki Cent Hosp Dept Med Div Nephrol Helsinki Finland

Background and objectives: Levosimendan is a calcium sensitiser developed for the treatment of congestive heart failure. It increases myocardial contractility, reduces the filling pressure and dilates both the peripheral and coronary vessels. The circulating metabolites of levosimendan, Or-1855 and Or-1896, are formed and eliminated slowly after intravenous administration of levosimendan. The aim of this study was to investigate the effect of impaired renal function and haemodialysis on the pharmacokinetics of levosimendan, Or-1855 and Or-1896. Study design: This study was an open-label, nonrandomised, phase I pharmacokinetic study. Levosimendan was administered as a single-dose infusion of 0.1 mu g/kg/minute for 24 hours. The follow-up period lasted 3 weeks. Study setting: Twenty-five patients were included: 12 patients with severe chronic renal failure (CrF) with creatinine clearance of < 30 mL/minute/1.73m(2) and 13 patients with end-stage renal disease (ESrd) undergoing haemodialysis. A group of 12 healthy subjects served as controls. results: Levosimendan, the parent drug, was eliminated rapidly from the plasma after discontinuation of its infusion, with an elimination half-life (t(1)/(2)) [mean standard error of mean] of 1.5 +/- 0.09 hours in ESrd patients undergoing haemodialysis, 1.0 +/- 0.2 hours in patients with severe CrF and 0.91 +/- 0.03 hours in healthy subjects. The t(1)/(2) of levosimendan was significantly longer (p < 0.001) in ESrd patients undergoing haemodialysis than in healthy subjects. The t(1)/(2) of Or-1855 and Or-1896 were 94.0 +/- 20.4 hours and 96.5 +/- 19.5 hours, respectively, in ESrd patients undergoing haemodialysis compared with 60.8 +/- 5.2 and 61.6 +/- 5.2 hours, respectively, in healthy subjects (p = not significant). The t(1)/(2) of Or-1855 was significantly longer (85.0 +/- 13.6 hours) in patients with severe CrF than in healthy subjects (60.8 5.2 hours, p < 0.05). The area under the plasma concentration-time curve (AUC) and the

关键词： Cardiotonic Agents Hydrazones Kidney Failure Chronic Pyridazines renaldialysis

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Sample size calculation for the Power Model for dose proportionality studies

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PHArMACEUTICAL STATISTICS 2007年第1期6卷 35-41页

作者： Sethuraman, Venkat S. Leonov, Sergei Squassante, Lisa Mitchell, Toni r. Hale, Michael d. Novartis Pharmaceut Biostat & Stat Reporting Florham Pk NJ 07932 USA GlaxoSmithKline Pharmaceut R&D Biomed Data Sci Philadelphia PA USA Amgen Inc Biostatistics Thousand Oaks CA USA

There are several approaches to assess or demonstrate pharmacokinetic dose proportionality. One statistical method is the traditional ANOVA model, where dose proportionality is evaluated using the bioequivalence limits. A more informative method is the mixed effects Power Model, where dose proportionality is assessed using a decision rule for the estimated slope. Here we propose analytical derivations of sample sizes for various designs (including crossover, incomplete block and parallel group designs) to be analysed according to the Power Model. Copyright (C) 2006 John Wiley & Sons, Ltd.

关键词： power model dose proportionality sample size mixed effects model pharmacokinetic parameters

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EPOCH-F: A Novel Salvage regimen for Multiple Myeloma Prior to reduced-Intensity Allogeneic Stem Cell Transplantation

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Blood 2008年第11期112卷 4328-4328页

作者： Saad Jamshed daniel Fowler Sattva Neelapu robert M. dean Seth M Steinberg Jeanne Odom Kelly Snow ronald E Gress Michael r Bishop Lombardi Comprehensive Cancer Center Washington DC USA Experimental Transplantation and Immunology Branch National Cancer Institute Bethesda MD USA Department of Lymphoma and Myeloma University of Texas M.D. Anderson Cancer Center Houston TX USA Cleveland Clinic Foundation Taussig Cancer Center R35 Cleveland OH USA National Cancer Institute National Institutes of Health Biostatistics and Data Management Section Center for Cancer Research Rockville MD USA

Variation in baseline host immune status contributes to inconsistent donor engraftment and may impede maximal graft-versus-myeloma effects after reduced-intensity allogeneic stem cell transplantation (rI-alloSCT) for advanced multiple myeloma. We performed a phase II study to determine the efficacy of a novel salvage regimen, EPOCH-F, which was designed to provide immune depletion and disease control prior to rI-alloSCT, in 22 patients with advanced multiple myeloma. EPOCH is an infusional chemotherapeutic regimen consisting of etoposide, vincristine and adriamycin, with prednisone, cyclophosphamide and fludarabine and given in 21 day cycles prior to rI-alloSCT. Patients received at least 1 and no more than 5 cycles of EPOCH-F gudied by peripheral blood Cd4+ T cell count. Pts achieving adequate lymphodepletion proceeded to rI-alloSCT; otherwise patients proceeded to rI-alloSCT after 5 cycles or if there was disease progression during EPOCH-F, regardless of Cd4 count. Median age was 53 years (range, 36–65); median time from initial therapy to transplant was 12 months (range, 2–168). Median number of prior therapies was 2 (range, 1–8), while 63% had chemotherapy sensitive disease. 68% of patients had received a novel agent. Patients received a median of 3 cycles (range, 1–5) of EPOCH-F. Therapy was well tolerated with manageable toxicities, mostly hematologic. Neutropenia (grade IV) was the most common toxicity seen in 77% of the administered cycles with only 6 episodes of neutropenic fever. Median lymphocyte count decreased from 1423/μL (range, 335–2788) to 519/μL (range, 102–1420); Cd4 count decreased from 320/μL (range, 130–1366) to 115/μL (range, 30–309). In 21 evaluable patients, the overall response rate to EPOCH-F was 22% and 68% had stable disease. 13% of patients achieved Cr/nCr. Only 1 patient progressed while on therapy. 20 patients received allograft from HLA matched sibling donors and were evaluable for engraftment. Median day 100 chimerism was 100% (rang

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Ibuprofen extrudate, a novel, rapidly dissolving ibuprofen formulation: relative bioavailability compared to ibuprofen lysinate and regular ibuprofen, and food effect on all formulations

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JOUrNAL OF CLINICAL PHArMACOLOGY 2005年第9期45卷 1055-1061页

作者： Klueglich, M ring, A Scheuerer, S Trommeshauser, d Schuijt, C Liepold, B Berndl, G Boehringer Ingelheim Pharma GmbH & Co KG Dept Project Management & R&D Human Pharmacol Ctr Ingelheim D-88397 Biberach Germany Boehringer Ingelheim Pharma GmbH & Co KG Dept Med Data Serv & Biostat D-88397 Biberach Germany Boehringer Ingelheim Pharma GmbH & Co KG Dept Pharmacokinet & Drug Metab D-88397 Biberach Germany Boehringer Ingelheim GmbH & Co KG Corp Dept Med Ingelheim Germany Abbott GmbH & Co KG Drug Delivery Business Unit Analyt Dev SOLIQS Ludwigshafen Germany Abbott GmbH & Co KG Drug Delivery Business Unit Pharmaceut Dev SOLIQS Ludwigshafen Germany

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