software validation

Summary

Summary: The act of testing the software for compliance with a standard.

Top Publications

  1. ncbi Comparison of dose calculation algorithms in phantoms with lung equivalent heterogeneities under conditions of lateral electronic disequilibrium
    P Carrasco
    Servei de Radiofísica i Radioprotecció, Hospital de la Santa Creu i Sant Pau, St Antoni Maria Claret 167, 08025 Barcelona, Spain
    Med Phys 31:2899-911. 2004
  2. pmc Ability of pharmacy clinical decision-support software to alert users about clinically important drug-drug interactions
    Kim R Saverno
    Department of Pharmacy Practice and Science, The University of Arizona College of Pharmacy, Tucson, Arizona 85721 0202, USA
    J Am Med Inform Assoc 18:32-7. 2011
  3. ncbi Accurate phylogenetic classification of variable-length DNA fragments
    Alice Carolyn McHardy
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, USA
    Nat Methods 4:63-72. 2007
  4. pmc SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms
    Tim Van den Bulcke
    ESAT SCD, KU Leuven, Kasteelpark Arenberg 10, B 3001 Heverlee, Belgium
    BMC Bioinformatics 7:43. 2006
  5. pmc First pass annotation of promoters on human chromosome 22
    M Scherf
    Institute of Mammalian Genetics, GSF National Research Center for Environment and Health, Neuherberg, Germany
    Genome Res 11:333-40. 2001
  6. pmc OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy
    G P S Raghava
    School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK
    BMC Bioinformatics 4:47. 2003
  7. pmc SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools
    Arthur Chun Chieh Shih
    Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan
    BMC Bioinformatics 7:103. 2006
  8. pmc Improved benchmarks for computational motif discovery
    Geir Kjetil Sandve
    Department of Computer and Information Science, Norwegian University of Science and Technology NTNU, Trondheim, Norway
    BMC Bioinformatics 8:193. 2007
  9. pmc DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment
    Amarendran R Subramanian
    University of Tubingen, Wilhelm Schickard Institut fur Informatik, Sand 13, 72076 Tubingen, Germany
    BMC Bioinformatics 6:66. 2005
  10. ncbi Artificial gene networks for objective comparison of analysis algorithms
    Pedro Mendes
    Virginia Bioinformatics Institute, USA
    Bioinformatics 19:ii122-9. 2003

Research Grants

Detail Information

Publications192 found, 100 shown here

  1. ncbi Comparison of dose calculation algorithms in phantoms with lung equivalent heterogeneities under conditions of lateral electronic disequilibrium
    P Carrasco
    Servei de Radiofísica i Radioprotecció, Hospital de la Santa Creu i Sant Pau, St Antoni Maria Claret 167, 08025 Barcelona, Spain
    Med Phys 31:2899-911. 2004
    ....
  2. pmc Ability of pharmacy clinical decision-support software to alert users about clinically important drug-drug interactions
    Kim R Saverno
    Department of Pharmacy Practice and Science, The University of Arizona College of Pharmacy, Tucson, Arizona 85721 0202, USA
    J Am Med Inform Assoc 18:32-7. 2011
    ..However, studies indicate these systems may miss some important interactions. The purpose of this study was to assess the performance of pharmacy CDS programs to detect clinically important DDIs...
  3. ncbi Accurate phylogenetic classification of variable-length DNA fragments
    Alice Carolyn McHardy
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, USA
    Nat Methods 4:63-72. 2007
    ..The method requires no more than 100 kb of training sequence for the creation of accurate models of sample-specific populations and can assign fragments >or=1 kb with high specificity...
  4. pmc SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms
    Tim Van den Bulcke
    ESAT SCD, KU Leuven, Kasteelpark Arenberg 10, B 3001 Heverlee, Belgium
    BMC Bioinformatics 7:43. 2006
    ....
  5. pmc First pass annotation of promoters on human chromosome 22
    M Scherf
    Institute of Mammalian Genetics, GSF National Research Center for Environment and Health, Neuherberg, Germany
    Genome Res 11:333-40. 2001
    ..Results are available on-line at http://genomatix.gsf.de/chr22/...
  6. pmc OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy
    G P S Raghava
    School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK
    BMC Bioinformatics 4:47. 2003
    ..The benchmark shows the current state-of-the art for alignment accuracy and provides a baseline against which new alignment algorithms may be judged...
  7. pmc SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools
    Arthur Chun Chieh Shih
    Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan
    BMC Bioinformatics 7:103. 2006
    ..Thus, a tool that allows cross comparison of the alignment results obtained by different tools simultaneously could help a biologist evaluate their correctness and accuracy...
  8. pmc Improved benchmarks for computational motif discovery
    Geir Kjetil Sandve
    Department of Computer and Information Science, Norwegian University of Science and Technology NTNU, Trondheim, Norway
    BMC Bioinformatics 8:193. 2007
    ..Therefore, robust assessment of motif discovery methods becomes important, both for validation of existing tools and for identification of promising directions for future research...
  9. pmc DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment
    Amarendran R Subramanian
    University of Tubingen, Wilhelm Schickard Institut fur Informatik, Sand 13, 72076 Tubingen, Germany
    BMC Bioinformatics 6:66. 2005
    ..However, it is often outperformed by these methods on data sets with global but weak similarity at the primary-sequence level...
  10. ncbi Artificial gene networks for objective comparison of analysis algorithms
    Pedro Mendes
    Virginia Bioinformatics Institute, USA
    Bioinformatics 19:ii122-9. 2003
    ..One way to objectively test such analysis algorithms is to apply them on computational gene network models for which the mechanisms are completely know...
  11. pmc Sensitivity and selectivity in protein structure comparison
    Michael L Sierk
    Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
    Protein Sci 13:773-85. 2004
    ..These results help quantify the statistical distinction between analogous and homologous structures, and provide a benchmark for structure comparison statistics...
  12. ncbi Quantification of left ventricular volumes and ejection fraction from gated 99mTc-MIBI SPECT: MRI validation and comparison of the Emory Cardiac Tool Box with QGS and 4D-MSPECT
    Wolfgang M Schaefer
    Department of Nuclear Medicine, University Hospital, Aachen University of Technology, Germany
    J Nucl Med 46:1256-63. 2005
    ..Furthermore, software-specific characteristics of ECTB were analyzed in comparison with 4D-MSPECT and Quantitative Gated SPECT (QGS) results (all relative to cMRI)...
  13. ncbi Validation of 4D-MSPECT and QGS for quantification of left ventricular volumes and ejection fraction from gated 99mTc-MIBI SPET: comparison with cardiac magnetic resonance imaging
    Claudia S A Lipke
    Department of Nuclear Medicine, University Hospital, Aachen University of Technology, Pauwelsstrasse 30, 52074, Aachen, Germany
    Eur J Nucl Med Mol Imaging 31:482-90. 2004
    ..However, algorithm-varying underestimation of LVEF should be accounted for in the clinical context and limits interchangeable use of software...
  14. pmc Gene structure prediction and alternative splicing analysis using genomically aligned ESTs
    Z Kan
    Center for Computational Biology, Washington University, St. Louis, Missouri 63110, USA
    Genome Res 11:889-900. 2001
    ..Furthermore, the evolutionary conservation of alternative splicing between human and mouse was analyzed using an EST-based approach. (See http://stl.wustl.edu/~zkan/TAP/)..
  15. pmc Fast and sensitive multiple alignment of large genomic sequences
    Michael Brudno
    Department of Computer Science, Stanford University, Stanford, CA 94305, USA
    BMC Bioinformatics 4:66. 2003
    ..In a first step, a fast search program identifies a chain of strong local sequence similarities. In a second step, regions between these anchor points are aligned using a slower but more accurate method...
  16. pmc A new protein linear motif benchmark for multiple sequence alignment software
    Emmanuel Perrodou
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, Department of Structural Biology and Genomics, F 67400 Illkirch, France
    BMC Bioinformatics 9:213. 2008
    ..As a consequence, poor motif alignment quality is hindering efforts to detect new LMs...
  17. ncbi Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays
    Yoseph Barash
    School of Computer Science and Engineering, Hebrew University, Jerusalem, 91904, Israel
    Bioinformatics 20:839-46. 2004
    ..For the effect of the SQ on the signal we evaluate the overabundance of differentially expressed genes using various statistical significance tests...
  18. ncbi MaxSub: an automated measure for the assessment of protein structure prediction quality
    N Siew
    Department of Chemistry, Ben Gurion University, Beer Sheva 84015, Israel
    Bioinformatics 16:776-85. 2000
    ..Such a method should (a) produce one single number that measures the quality of a predicted model and (b) perform similarly to human-expert evaluations...
  19. pmc An automated method for finding molecular complexes in large protein interaction networks
    Gary D Bader
    Samuel Lunenfeld Research Institute, MT, Sinai Hospital, Toronto ON Canada M5G 1X5, Dept, of Biochemistry, University of Toronto, Toronto ON Canada M5S 1A8
    BMC Bioinformatics 4:2. 2003
    ..As the size of the interaction set increases, databases and computational methods will be required to store, visualize and analyze the information in order to effectively aid in knowledge discovery...
  20. pmc Human-mouse alignments with BLASTZ
    Scott Schwartz
    Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Genome Res 13:103-7. 2003
    ..This work describes BLASTZ, its modifications, the hardware environment on which we run it, and several empirical studies to validate its results...
  21. pmc CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes
    Nikhat Zafar
    School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 4E3, Manassas, VA 20110 USA
    BMC Bioinformatics 3:12. 2002
    ..A major challenge is to analyze and to mine data from these databases, especially whole genomes. There is a need for computational tools that look globally at genomes for data mining...
  22. ncbi A protocol for building and evaluating predictors of disease state based on microarray data
    Lodewyk F A Wessels
    Department of Mediamatics, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology Mekelweg 4, 2628 CD Delft, The Netherlands
    Bioinformatics 21:3755-62. 2005
    ..However, there is, as yet, no objective way to evaluate whether a new approach truly improves on the current state of the art. In addition no 'standard' computational approach has emerged which enables robust outcome prediction...
  23. ncbi Quantification of left ventricular volumes and ejection fraction from gated 99mTc-MIBI SPECT: MRI validation of the EXINI heart software package
    Oliver H Winz
    Department of Nuclear Medicine, University Hospital, Aachen University of Technology, Aachen, Germany
    Clin Physiol Funct Imaging 29:89-94. 2009
    ..Cardiac magnetic resonance imaging (cMRI) was used as reference. Furthermore, effects of perfusion defects and image quality in SPECT on correlation between gated SPECT and magnetic resonance imaging were investigated...
  24. ncbi FDA final guidance on software validation
    Maria Donawa
    Donawa and Associates Ltd, an Aventor Partner, Via Fonte di Fauno 22, 1 00153 Rome, Italy
    Med Device Technol 13:20-4. 2002
    ..This article discusses a recently published final FDA guidance document on software validation and the reasons for its importance.
  25. ncbi Prediction of the subcellular location of prokaryotic proteins based on the hydrophobicity index of amino acids
    Z P Feng
    Department of Physics, Tianjin University, 300072, Tianjin, PR China
    Int J Biol Macromol 28:255-61. 2001
    ..This work would be useful for a systematic analysis of the great amounts of prokaryotic genome sequences. The computer programs used in this paper are available on request via email...
  26. ncbi Limited accuracy of dose calculation for large fields at deep depths using the BrainSCAN v5.21 treatment planning system
    Wen C Hsi
    Department of Medical Physics, Rush University Medical Center, 1653 West Congress Parkway, Chicago, Illinois 60612, USA
    J Appl Clin Med Phys 6:12-8. 2005
    ..These large systematic errors were caused by using the tissue maximum ratio (TMR) in BrainSCAN v5.21 without considering increased field size as depth increased. These errors have been reported to BrainLAB...
  27. ncbi QUADOS intercomparison: a summary of photon and charged particle problems
    G Gualdrini
    ENEA ION IRP, Via dei Colli 16, I 40136 Bologna, Italy
    Radiat Prot Dosimetry 115:587-99. 2005
    ..This paper focuses on the analysis of the photon and charged particle problems. The neutron problems were presented in a paper at the NEUDOS9 conference...
  28. ncbi A comparison of skyshine computational methods
    Nolan E Hertel
    Neely Nuclear Research Center, George W Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
    Radiat Prot Dosimetry 116:525-33. 2005
    ....
  29. ncbi Skyshine analysis using energy and angular dependent dose-contribution fluxes obtained from air-over-ground adjoint calculation
    Mikio Uematsu
    Plant and System Planning Department, Toshiba Corporation, Shinsugita cho 8, Isogo ku, Yokohama 235 8523, Japan
    Radiat Prot Dosimetry 116:534-7. 2005
    ..Moreover, the present method supplies plenty of energy-angular dependent contribution flux data, which will be useful for detailed shielding design of facilities...
  30. ncbi Determination of ion and neutral loss compositions and deconvolution of product ion mass spectra using an orthogonal acceleration time-of-flight mass spectrometer and an ion correlation program
    Andrew H Grange
    U S EPA, ORD, NERL, Environmental Sciences Division, PO Box 93478, Las Vegas, NV 89193 3478, USA
    Rapid Commun Mass Spectrom 20:89-102. 2006
    ..Finally, two unidentified analytes were characterized, based on data published by others and using the ICP together with mass spectral interpretation...
  31. ncbi Comparison of synchrotron radiation calculations between analytical codes (STAC8, photon) and Monte Carlo codes (FLUKA, EGS4)
    J C Liu
    Radiation Protection Department, Stanford Linear Accelerator Center, MS 48, P O Box 20450, Stanford, CA 94309, USA
    Radiat Prot Dosimetry 116:658-61. 2005
    ..Some of these features have been implemented and benchmarked against Monte Carlo calculations. Reasonable agreements were found between the STAC8 and Monte Carlo calculations...
  32. ncbi An algorithm for independent verification of Gamma Knife treatment plans
    James Beck
    CancerCare Manitoba, Winnipeg, Manitoba R3E 0V9, Canada
    Med Phys 31:2780-4. 2004
    ..Large discrepancies were almost all associated with dose plans utilizing a large number of collimator plugs, for which the simplifying approximations used by the program are known to break down...
  33. ncbi Dosimetric evaluation of the clinical implementation of the first commercial IMRT Monte Carlo treatment planning system at 6 MV
    Emily Heath
    McGill University, Montreal H3G 1A4, Canada
    Med Phys 31:2771-9. 2004
    ..After matching the calculated and measured MLC leakage, simulations of static and dynamic MLC-defined fields using the most recent MLC model agreed to within 2% with measurements...
  34. ncbi Rendering complex scenes for psychophysics using RADIANCE: how accurate can you get?
    Alexa I Ruppertsberg
    Department of Optometry, University of Bradford, UK
    J Opt Soc Am A Opt Image Sci Vis 23:759-68. 2006
    ..RADIANCE recovers color gradients well but the results are shifted in color space. Currently, there is no better simulation alternative for achieving physical accuracy than by combining a spectral rendering method with RADIANCE...
  35. ncbi Comparison of a finite-element multigroup discrete-ordinates code with Monte Carlo for radiotherapy calculations
    Kent A Gifford
    The University of Texas M D Anderson Cancer Center, Box 1202, 1220 Holcombe Blvd, Houston, TX 77030, USA
    Phys Med Biol 51:2253-65. 2006
    ..Our data suggest that the presented deterministic code is as accurate as EGS4 and MCNPX for the transport geometries examined in this study...
  36. ncbi CSnrc: correlated sampling Monte Carlo calculations using EGSnrc
    Lesley A Buckley
    Ionizing Radiation Standards, National Research Council of Canada, Ottawa K1A OR6, Canada
    Med Phys 31:3425-35. 2004
    ..The calculations show that for a 1 mm diameter aluminum central electrode, the correction factor differs somewhat from the values used in both the IAEA TRS-398 code of practice and the AAPM's TG-51 protocol...
  37. ncbi Aircrew dosimetry using the Predictive Code for Aircrew Radiation Exposure (PCAIRE)
    B J Lewis
    Department of Chemistry and Chemical Engineering, Royal Military College of Canada, P O Box 17000, Stn Forces, Kingston, Ontario, Canada K7K 7B4
    Radiat Prot Dosimetry 116:320-6. 2005
    ..This model has been used to determine the significance of SEP exposure on a theoretical jet altitude flight during GLE 42...
  38. ncbi Parallelising the MARS15 code with MPI for shielding applications
    M A Kostin
    Fermi National Accelerator Laboratory, P O Box 500, MS 220, Batavia, Illinois 60510 0500, USA
    Radiat Prot Dosimetry 116:297-300. 2005
    ..It is scalable and demonstrates good performance. The general architecture of the code, specific uses of message passing and effects of a scheduling on the performance and fault tolerance are described...
  39. ncbi Experimental validation of coincidence summing corrections computed by the ETNA software
    Marie Christine Lépy
    LNE LNHB, Laboratoire National Henri Becquerel, CEA Saclay, F 91191 Gif sur Yvette Cedex, France
    Appl Radiat Isot 64:1340-5. 2006
    ..The ETNA code is used to compute the corrections due to coincidence summing for the same geometries. The calculated values are compared to the experimental ones...
  40. ncbi Towards a heavy-ion transport capability in the MARS15 code
    N V Mokhov
    Fermi National Accelerator Laboratory, MS 220, Batavia, Illinois 60510 0500, USA
    Radiat Prot Dosimetry 116:104-8. 2005
    ..A brief description of new modules is given in comparison with experimental data...
  41. ncbi Validation of physics improvements for IMRT with a commercial treatment-planning system
    Patrick Cadman
    Medical Physics Department, Saskatoon Cancer Centre, 20 Campus Drive, Saskatoon, Saskatchewan, S7N 4H4, Canada
    J Appl Clin Med Phys 6:74-86. 2005
    ..8%) occurred in low-dose regions in the central part of the field. The disagreement may be due to the overresponse of film to scattered radiation in the low-dose regions, which have significant shielding by the MLCs...
  42. ncbi Validation of the Monte Carlo simulator GATE for indium-111 imaging
    K Assié
    UMR 678 INSERM UPMC, CHU Pitie Salpetriere, 91 Boulevard de l Hopital, 75634 Paris Cedex 13, France
    Phys Med Biol 50:3113-25. 2005
    ..The simulation of the cylindrical phantom closely reproduced the experimental data. These results suggest that GATE enables accurate simulation of (111)In SPECT acquisitions...
  43. ncbi NASA Space Radiation Transport Code Development Consortium
    Lawrence W Townsend
    Department of Nuclear Engineering, University of Tennessee, Knoxville, TN 37996 2300, USA
    Radiat Prot Dosimetry 116:118-22. 2005
    ..In this paper, we present an overview of the consortium members and the current status and future plans of consortium efforts to meet the research goals and objectives of this extensive undertaking...
  44. ncbi Commissioning and implementation of a stereotactic conformal radiotherapy technique using a general-purpose planning system
    M Amin Mosleh-Shirazi
    Joint Department of Physics, The Institute of Cancer Research and The Royal Marsden NHS Trust, Sutton, Surrey SM2 5PT, United Kingdom
    J Appl Clin Med Phys 5:1-14. 2004
    ..Verification field shielding reduced lens dose by 12 to 15 times. In conclusion, this customized system for planning and verification of pediatric SCRT provides a high level of precision as well as reasonable practical efficiency...
  45. ncbi Validation of a Monte Carlo simulation of the Philips Allegro/GEMINI PET systems using GATE
    F Lamare
    U650 INSERM, Laboratoire du Traitement de l information medicale LaTIM, CHU Morvan, Universite de Bretagne Occidentale, Brest, 29609, France
    Phys Med Biol 51:943-62. 2006
    ....
  46. ncbi Comparison of thermal neutron distributions within shield materials obtained by experiments, SN and Monte Carlo code calculations
    Yoshihiro Asano
    Japan Atomic Energy Research Institute, SPring 8, Mikazuki cho, Hyogo 679 5143, Japan
    Radiat Prot Dosimetry 116:284-9. 2005
    ..The ANISN calculations with the modified absorption cross sections reproduced the results of the MCNP5 fairly well...
  47. ncbi A dose-volume-based tool for evaluating and ranking IMRT treatment plans
    Moyed M Miften
    Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA
    J Appl Clin Med Phys 5:1-14. 2004
    ....
  48. ncbi A model that accounts for the interdependence of extent and severity in the automatic evaluation of myocardial defects
    Henrik Hussein El-Ali
    Department of Medical Radiation Physics, Clinical Sciences, Lund University, Sweden
    Nucl Med Commun 27:127-35. 2006
    ..This interdependence has been investigated in two commercially available analysis programs (AutoQUANT and 4D-MSPECT) using Monte Carlo-simulated SPECT data...
  49. pmc Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies
    Zihua Hu
    Center for Computational Research, Department of Biostatistics, University at Buffalo, Buffalo, NY 14260, USA
    BMC Bioinformatics 7:12. 2006
    ....
  50. ncbi Intercomparison on the usage of computational codes in radiation dosimetry
    R J Tanner
    NRPB, Chilton, Didcot, Oxon OX11 0RQ, UK
    Radiat Prot Dosimetry 110:769-80. 2004
    ..Eight problems were selected for their relevance to the radiation dosimetry community, three of which involve neutron transport. This paper focuses on the analysis of the neutron problems...
  51. ncbi ANDI-03: a genetic algorithm tool for the analysis of activation detector data to unfold high-energy neutron spectra
    Bhaskar Mukherjee
    Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, D 22607 Hamburg, Germany
    Radiat Prot Dosimetry 110:249-54. 2004
    ..9% (at shield top level) and +/-27.2% (behind a 60 cm thick concrete shield) with the same unfolded with the SAND-II code...
  52. pmc The development and validation of the Virtual Tissue Matrix, a software application that facilitates the review of tissue microarrays on line
    Catherine M Conway
    Medical Informatics Group, School of Biotechnology, Dublin City University, Dublin, Ireland
    BMC Bioinformatics 7:256. 2006
    ....
  53. ncbi Commissioning, evaluation, quality assurance and clinical application of a virtual micro MLC technique
    M Woo
    Department of Medical Physics, Toronto Sunnybrook Regional Cancer Centre, Toronto, Canada
    Med Phys 30:138-43. 2003
    ....
  54. ncbi Recent enhancements to the MARS15 code
    N V Mokhov
    Fermi National Accelerator Laboratory, MS 220, Batavia, IL 60510 0500, USA
    Radiat Prot Dosimetry 116:99-103. 2005
    ....
  55. ncbi A preliminary comparative study of two treatment planning systems developed for boron neutron capture therapy: MacNCTPlan and SERA
    C Wojnecki
    JRC of European Commission, HFR Unit, Petten, The Netherlands
    Med Phys 29:1710-5. 2002
    ..For the examples studied, it is found that the methods used for geometry representation (in MacNCTPlan) and for cross-section representation (in SERA) were found to impact directly on the accuracy of the calculated results...
  56. ncbi Technical note: overprediction of dose with default PRESTA-I boundary crossing in DOSXYZnrc and BEAMnrc
    B R B Walters
    Ionizing Radiation Standards, National Research Council of Canada, Ottawa, KIA OR6 Canada
    Med Phys 34:647-50. 2007
    ..As a result, the default boundary crossing algorithm in BEAMnrc will be changed to "exact" (single scattering)...
  57. ncbi Experimental verification of a Monte Carlo-based MLC simulation model for IMRT dose calculation
    Neelam Tyagi
    Department of Radiation Oncology, The University of Michigan, Ann Arbor, Michigan 48109 0010, USA
    Med Phys 34:651-63. 2007
    ..Various sources of uncertainties in these comparisons are discussed...
  58. ncbi Spread-out Bragg peak and monitor units calculation with the Monte Carlo code MCNPX
    J Herault
    Centre Antoine Lacassagne, Cyclotron Biomedical, 227 Avenue de la Lanterne, 06200 Nice, France
    Med Phys 34:680-8. 2007
    ..This determination of Monitor Units will be controlled by an independent semi-empirical calculation...
  59. ncbi An evaluation of automated homology modelling methods at low target template sequence similarity
    James A R Dalton
    Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
    Bioinformatics 23:1901-8. 2007
    ..However, on average Nest produces the best loops with an 8% improvement by mean RMSD compared to the loops generated by Builder...
  60. ncbi Computational framework for simulating fluorescence microscope images with cell populations
    Antti Lehmussola
    Institute of Signal Processing, Tampere University of Technology, FI 33101 Tampere, Finland
    IEEE Trans Med Imaging 26:1010-6. 2007
    ..The presented simulation framework, with several user-controllable parameters, forms a versatile tool for many kinds of validation tasks, and is freely available at http://www.cs.tut.fi/sgn/csb/simcep...
  61. ncbi A comparison of non-standard solvers for ODEs describing cellular reactions in the heart
    Mary C MacLachlan
    Simula Research Laboratory, Lysaker, Norway
    Comput Methods Biomech Biomed Engin 10:317-26. 2007
    ..In this paper we study the performance of three non-standard methods on two different cell models with comparable complexity but very different stiffness characteristics...
  62. ncbi A new validation method for X-ray mammogram registration algorithms using a projection model of breast X-ray compression
    John H Hipwell
    University College London, Centre for Medical Image Computing, London, WC1E 6BT U K
    IEEE Trans Med Imaging 26:1190-200. 2007
    ....
  63. ncbi VMC++ versus BEAMnrc: a comparison of simulated linear accelerator heads for photon beams
    F Hasenbalg
    Division of Medical Radiation Physics, Insel Hospital, University of Berne, Berne 3010, Switzerland
    Med Phys 35:1521-31. 2008
    ..4%. Dosimetrically, these phase space differences imply an agreement between both codes at the <1% level, making VMC++ head module suitable for full head simulations with considerable gain in efficiency and without loss of accuracy...
  64. pmc Assessment of the accuracy of an MCNPX-based Monte Carlo simulation model for predicting three-dimensional absorbed dose distributions
    U Titt
    The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
    Phys Med Biol 53:4455-70. 2008
    ..Hence, the Monte Carlo models of medium- and large-size double scattering proton-therapy nozzles were valid for proton beams in the 100 MeV-250 MeV interval...
  65. ncbi The bootstrap and cross-validation in neuroimaging applications: estimation of the distribution of extrema of random fields for single volume tests, with an application to ADC maps
    Roberto Viviani
    Department of Psychiatry III, University of Ulm, Germany
    Hum Brain Mapp 28:1075-88. 2007
    ..As case studies, we present parametric maps of lesions in patients suffering from stroke and glioblastoma at different stages of evolution...
  66. ncbi Incorporation of a combinatorial geometry package and improved scoring capabilities in the EGSnrc Monte Carlo Code system
    Margarida Fragoso
    Joint Department of Physics, The Royal Marsden NHS Trust and Institute of Cancer Research, Fulham Road, London SW3 6JJ, United Kingdom
    Med Phys 30:1076-85. 2003
    ..GenUC has been successfully applied to complex geometric setups, e.g., intracavitary brachytherapy applicators and was also benchmarked against the EGSnrc user code, DOSRZnrc...
  67. ncbi Software for image registration: algorithms, accuracy, efficacy
    Brian F Hutton
    Department of Medical Physics and Department of Nuclear Medicine and Ultrasound, Westmead Hospital, Sydney, Australia
    Semin Nucl Med 33:180-92. 2003
    ..Although hardware-based registration has now become possible by using dual-modality instruments, software-based registration will continue to play an important role in nuclear medicine...
  68. ncbi Benchmark of PENELOPE code for low-energy photon transport: dose comparisons with MCNP4 and EGS4
    Sung Joon Ye
    Department of Radiation Oncology, University of Alabama School of Medicine, 1824 6th Avenue South, Birmingham, AL 35294, USA
    Phys Med Biol 49:387-97. 2004
    ..However, the differences among the four datasets became negligible above 100 keV...
  69. ncbi Application of pulse mixing method in software coincidence counting
    Miroslav Havelka
    Czech Metrology Institute, Inspectorate for Ionizing Radiation, Radiova 1, Prague 102 00, Czech Republic
    Appl Radiat Isot 60:409-13. 2004
    ..The difference between the results obtained from both calculation methods applied on the data from the same measurement did not exceed 0.015%. The details of both methods and the results of their comparison are presented...
  70. ncbi Validation of the EGS usercode DOSE3D for internal beta dose calculation at the cellular and tissue levels
    J Coulot
    Service de Physique, Institut Gustave Roussy, 39 rue Camille Desmoulins F94805, Villejuif Cedex, France
    Phys Med Biol 48:2591-602. 2003
    ..Dose point-kernel calculations in water were compared to those published by Cross et al and Simpkin and Mackie. They confirm that DOSE3D is a reliable tool for cellular dosimetry in various geometric configurations...
  71. ncbi Efficient photon beam dose calculations using DOSXYZnrc with BEAMnrc
    I Kawrakow
    Ionizing Radiation Standards, National Research Council of Canada, Ottawa, K1A OR6, Canada
    Med Phys 33:3046-56. 2006
    ..This points towards eliminating the need for storing intermediate phase-space files...
  72. ncbi Development and validation of a BEAMnrc component module for accurate Monte Carlo modelling of the Varian dynamic Millennium multileaf collimator
    Emily Heath
    Medical Physics Unit, McGill University, 1650 Cedar Ave, Montreal H3G1A4, Canada
    Phys Med Biol 48:4045-63. 2003
    ....
  73. ncbi Monte Carlo dose voxel kernel calculations of beta-emitting and Auger-emitting radionuclides for internal dosimetry: A comparison between EGSnrcMP and EGS4
    Lidia Strigari
    Laboratory of Medical Physics and Expert Systems, National Cancer Institute Regina Elena, Rome, 00144 Italy
    Med Phys 33:3383-9. 2006
    ..For the voxel source, where doses were scored in the coarser spatial resolution, dose deposition in the central voxel is in good agreement for all the radionuclides; while surrounding voxels exhibit a slightly worse agreement...
  74. ncbi Flexible ligand docking using evolutionary algorithms: investigating the effects of variation operators and local search hybrids
    René Thomsen
    EVALife Group, Department of Computer Science, University of Aarhus, Ny Munkegade, Bldg 540, DK 8000 Aarhus C, Denmark
    Biosystems 72:57-73. 2003
    ..Furthermore, the DockEA proved to be more robust than the LGA (in terms of reproducing the results in several runs) on the more difficult problems with a high number of flexible torsion angles...
  75. ncbi Evaluation and comparison of gene clustering methods in microarray analysis
    Anbupalam Thalamuthu
    Department of Human Genetics, University of Pittsburgh, PA, USA
    Bioinformatics 22:2405-12. 2006
    ..Yet no comprehensive comparative study has been performed to evaluate the effectiveness of these methods...
  76. ncbi SCEW: a Microsoft Excel add-in for easy creation of survival curves
    Haseeb Ahmad Khan
    Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
    Comput Methods Programs Biomed 83:12-7. 2006
    ..The advantages of this program are simple data input, minimal procedural steps and the creation of survival curves in the familiar confines of Excel...
  77. ncbi Normality of oligonucleotide microarray data and implications for parametric statistical analyses
    Peter J Giles
    Department of Pathology, University of Wales College of Medicine, Heath Park, Cardiff CF14 4XN, UK
    Bioinformatics 19:2254-62. 2003
    ..However, these tests assume that the data follow a normal distribution. To date, the assumption that replicate expression values for any gene are normally distributed, has not been critically addressed for Affymetrix GeneChip data...
  78. ncbi Validation of radiographic simulation codes including x-ray phase effects for millimeter-size objects with micrometer structures
    Harry E Martz
    Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    J Opt Soc Am A Opt Image Sci Vis 24:169-78. 2007
    ..We conclude that the multislice method is not required for accurate simulation of greater than or equal to 8 keV x-ray radiographs of millimeter-size objects with micrometer structures...
  79. ncbi Assessing the quality of conformal treatment planning: a new tool for quantitative comparison
    J Menhel
    Oncology Institute, Sheba Medical Center, Tel Hashomer, 52621, Israel
    Phys Med Biol 51:5363-75. 2006
    ..The choice of plan was quick, simple and accurate using the new graphical representation...
  80. ncbi DNA fingerprinting of sister blastomeres from human IVF embryos
    Mandy G Katz
    Centre for Early Human Development, Monash Institute of Reproduction and Development, Monash University, Level 3, 27 31 Wright Street, Clayton 3168, Victoria, Australia
    Hum Reprod 17:752-9. 2002
    ..Previously published single cell DNA fingerprinting systems have been plagued by high rates of allele drop-out (ADO) and preferential amplification (PA) preventing clinical application in preimplantation genetic diagnosis...
  81. ncbi Microarray analysis reveals potential target genes of NF-kappaB2/p52 in LNCaP prostate cancer cells
    Nagalakshmi Nadiminty
    Department of Urology, University of California Davis Medical Center, Sacramento, California, USA
    Prostate 70:276-87. 2010
    ....
  82. ncbi The use of handheld computers in clinical trials
    Andreas Koop
    Institute for Medical Statistics, Informatics, and Epidemiology, University of Cologne, Cologne, Germany
    Control Clin Trials 23:469-80. 2002
    ..We conclude that mobile devices are very useful in most cases, especially when design and software validation aspects have been taken into account.
  83. ncbi Validation by school nurses of the Nursing Intervention Classification for computer software
    S Redes
    Comput Nurs 15:333-8. 1997
    ..Of these, 53 direct care interventions were selected as used by more than 80% of the sample. Fifty interventions were not used by 100% of the sample. E-mail was a useful means to obtain a national sample and collect data...
  84. ncbi Using the Virtual Heart Model to validate the mode-switch pacemaker operation
    Zhihao Jiang
    Department of Electrical and System Engineering, University of Pennsylvania, USA
    Conf Proc IEEE Eng Med Biol Soc 2010:6690-3. 2010
    ..We have developed a timed-automata based Virtual Heart Model (VHM) to act as platform for medical device software validation and verification...
  85. ncbi A review of the FDA draft guidance document for software validation: guidance for industry
    K L Keatley
    Colorado Analytical Research and Development Corporation, Colorado Springs 80907, USA
    Qual Assur 7:49-55. 1999
    ..1) was issued by the United States Food and Drug Administration (FDA) to address the software validation requirement of the Quality System Regulation, 21 CFR Part 820, effective June 1, 1997...
  86. ncbi US quality system requirements for software validation
    M E Donawa
    Donawa and Associates Ltd, Rome, Italy
    Med Device Technol 9:17-20. 1998
    ..This article will discuss the contents of a recent FDA draft guidance document that may reduce this variability...
  87. ncbi CalcNTCP: a simple tool for computation of normal tissue complication probability (NTCP) associated with cancer radiotherapy
    Haseeb Ahmad Khan
    Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
    Int J Radiat Biol 83:717-20. 2007
    ..This study was aimed to develop a simple and user-friendly software for fast and accurate computation of normal tissue complication probability (NTCP) in accordance with the Lyman model...
  88. ncbi Belt worn control system and battery for the percutaneous model of the Jarvik 2000 heart
    R Jarvik
    Jarvik Heart, Inc, New York, NY 10019 6238, USA
    Artif Organs 23:487-9. 1999
    ..interference (EMI), to minimize susceptibility to electrostatic discharge, and to avoid the need for software validation. Manual control of pump speed is accomplished by a patient operated knob, according to physician ..
  89. ncbi Validation of dietary intake data in black women with type 2 diabetes
    Allison Amend
    Marymount University, Arlington, VA 22207, USA
    J Am Diet Assoc 107:112-7. 2007
    ..Additional modification and validity testing is warranted in this and other populations...
  90. ncbi Software development: resolving the conflict between speed and compliance
    D Jennings
    Trosolwg Systems and Software, Llansaint, UK
    Med Device Technol 20:21-3. 2009
    ..These techniques can help bring products to market more rapidly and cost-effectively because the production of compliance documentation is automated and ensures that quality control processes are strictly and demonstrably observed...
  91. ncbi An integrative analysis platform for multiple neural spike train data
    Yu Huang
    Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
    J Neurosci Methods 172:303-11. 2008
    ..Because the interface developed is very general and flexible, new analysis tools can be integrated effectively as required. MEA-Platform implies an ideal environment for integrative neuroscience research...
  92. ncbi Differences among Monte Carlo codes in the calculations of voxel S values for radionuclide targeted therapy and analysis of their impact on absorbed dose evaluations
    M Pacilio
    Department of Medical Physics, Azienda Ospedaliera S Camillo Forlanini, Piazza Forlanini 1, Rome 00151, Italy
    Med Phys 36:1543-52. 2009
    ....
  93. ncbi Criterion validity of a computer-based tutorial for teaching waist circumference self-measurement
    William Leland Elliott
    J Bodyw Mov Ther 12:133-45. 2008
    ..The results of this experiment suggest that the tested CBT is efficacious in teaching WC self-measurement. The tutorial could be used in the areas of health assessment, standardization, biomedical education and research...
  94. pmc A transcript finishing initiative for closing gaps in the human transcriptome
    Mari Cleide Sogayar
    Genome Res 14:1413-23. 2004
    ....
  95. pmc Validity of a new automated software program for visceral adipose tissue estimation
    E W Demerath
    Department of Community Health, Lifespan Health Research Center, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
    Int J Obes (Lond) 31:285-91. 2007
    ..Hippo Fat has yet to be independently validated against commonly used image analysis software programs...
  96. pmc A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
    Michelle L Green
    Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
    BMC Bioinformatics 5:76. 2004
    ..If a protein has not been assigned a specific function during the annotation process, any reaction catalyzed by that protein will appear as a missing enzyme or pathway hole in a Pathway/Genome database...
  97. ncbi Frequency and spectrum of errors in final radiology reports generated with automatic speech recognition technology
    Leslie E Quint
    Department of Radiology, University of Michigan Health System, Ann Arbor, Michigan MI 48109 0030, USA
    J Am Coll Radiol 5:1196-9. 2008
    ..The purpose of this study was to determine the frequency and spectrum of significant dictation errors in finalized radiology reports generated with speech recognition technology...
  98. ncbi Adaptive software for head-operated computer controls
    Edmund F LoPresti
    University of Pittsburgh, Pittsburgh, PA 15260, USA
    IEEE Trans Neural Syst Rehabil Eng 12:102-11. 2004
    ..In addition, five current head-control users evaluated the software in a real-world setting. One of these five subjects perceived an improvement in comparison to his current head-control system...
  99. pmc Basecalling with LifeTrace
    D Walther
    Incyte Genomics, Inc, Palo Alto, California 94304, USA
    Genome Res 11:875-88. 2001
    ..We also describe a new protocol for benchmarking that we believe better discerns basecaller performance differences than methods previously published...
  100. ncbi Cognitive and usability engineering methods for the evaluation of clinical information systems
    Andre W Kushniruk
    Information Technology Division, Department of Mathematics and Statistics, York University, Toronto, Canada
    J Biomed Inform 37:56-76. 2004
    ..Emerging trends in the evaluation of complex information systems are discussed...
  101. ncbi Comparison of dose calculation algorithms for treatment planning in external photon beam therapy for clinical situations
    Tommy Knöös
    Radiation Physics, Lund University Hospital, S 221 85 Lund, Sweden
    Phys Med Biol 51:5785-807. 2006
    ..The more sophisticated models in the type b group exhibit changes in both absorbed dose and its distribution which are congruent with the simulations performed by Monte Carlo-based virtual accelerator...

Research Grants25

  1. MRI Parallel Excitation for Neuroimaging Applications
    Douglas C Noll; Fiscal Year: 2012
    ..abstract_text> ..
  2. Dynamic Peer Membership QA Software for Underserved Labs
    JACQUELINE COLEMAN; Fiscal Year: 2005
    ..of this concept are: 1) Develop a design requirements document that adheres to the FDA standards for software validation; 2) Develop a design plan (software blueprint) that meets the design requirements created in aim 1; 3) ..
  3. VOICE RESPONSE/INTERNET REGISTRATION AND RANDOM SYSTEM
    Herman Mitchell; Fiscal Year: 1999
    ..All modules will be formally validated to ensure compliance with FDA requirements for software validation. The aims of this grant are to finalize system requirements; design the architecture of the system; develop ..
  4. System for Cost Effective Clinical Trial Design
    Ronald Helms; Fiscal Year: 2003
    ..The aims of SCET Phase II are to build the system, validate it in compliance with FDA regulations for software validation, perform Beta testing at a range of target client organizations, and use the Beta test findings to produce ..
  5. PREVENTION INTERVENTIONS IN HISPANIC AND ANGLO CHILDREN
    Christine Kennedy; Fiscal Year: 2003
    ..abstract_text> ..
  6. Conference:Dental Informatics and Dental Research
    Titus Schleyer; Fiscal Year: 2002
    ....
  7. Realistic Phantom Series for OLINDA/EXM Version 2
    Michael Stabin; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  8. A Controlled Terminology for Diagnoses and Findings in General Dentistry
    Titus Schleyer; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  9. WFU_Pickatlas Interoperability
    Joseph Maldjian; Fiscal Year: 2008
    ..This project will build on the pickatlas software to provide automated neuroanatomical region of interest analyses for human imaging studies and studies of non-human primates. [unreadable] [unreadable]..
  10. Object-Centric Computational Model for Imaging Analysis
    Paul Yushkevich; Fiscal Year: 2008
    ..unreadable] [unreadable]..
  11. A Multifaceted Adaptive Testing Approach to Health Literacy in Older Adults
    David Kaufman; Fiscal Year: 2009
    ..The tool has the potential to be used to support research on health literacy, develop screening tools for clinicians and tailor health education materials for older adult patients and consumers at varying levels of literacy. ..
  12. BCI2000: SOFTWARE FOR BRAIN-COMPUTER INTERFACE RESEARCH
    Gerwin Schalk; Fiscal Year: 2009
    ..This project will greatly facilitate this development by improving and maintaining general-purpose BCI software and continuing to provide it to BCI research groups throughout the world. ..
  13. Temporal Clustering Analysis for Detection of Irregular Transient fMRI Activation
    VICTORIA MORGAN; Fiscal Year: 2009
    ....
  14. Sematic Relatedness for Active Medication Safety and Outcomes Surveillance
    Serguei V S Pakhomov; Fiscal Year: 2010
    ....
  15. Accessibility Enhancements for ITK-SNAP 3D Medical Image Segmentation Software
    Paul Yushkevich; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  16. A Multiethnic Internet Study on Menopausal Symptoms
    Eun Ok Im; Fiscal Year: 2008
    ....
  17. CREATING GUIDELINES THAT ADAPT TO LOCAL CONTEXTS
    Aziz Boxwala; Fiscal Year: 2003
    ..We will compare the acceptance of recommendations contained in guidelines that have been adapted to acceptance of recommendations contained in guidelines that have not been adapted. ..
  18. Telomere Length as a Marker of Cardiovascular Aging
    Ellen Demerath; Fiscal Year: 2005
    ..Telomeric DNA length may thus be found to be a valuable plasma biomarker for the prediction and monitoring of cardiovascular health and aging. ..
  19. New Methods for Improved Image-based Dosimetry
    Michael Stabin; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  20. DEVELOPMENT OF A VACCINE FOR HUMAN PERIODONTITIS
    ROY PAGE; Fiscal Year: 2001
    ..These observations will contribute in a major way to closing the gaps in our knowledge of the role of the host immune response in the pathogenesis of periodontitis. ..
  21. Integrated Tool for Biological Parametric Mapping
    Joseph Maldjian; Fiscal Year: 2007
    ....
  22. Prediction of Second Cancer Risks for Children Treated with Proton - vs. - Photon
    Wayne D Newhauser; Fiscal Year: 2010
    ..In the future, we expect that the lower-risk treatments will result in fewer second cancers and this will translate into longer, higher-quality lives for survivors of childhood cancer (presently 270,000 persons in the United States). ..
  23. Radiopharmaceutical Dosimetry Symposium
    Michael Stabin; Fiscal Year: 2002
    ..abstract_text> ..
  24. Cancer Pain Management-Decision Support Computer Program
    Eun Ok Im; Fiscal Year: 2007
    ..abstract_text> ..