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@article{abdul-mutakabbirTeachingOldClass2019,
title = {Teaching an {{Old Class New Tricks}}: {{A Novel Semi-Synthetic Aminoglycoside}}, {{Plazomicin}}},
shorttitle = {Teaching an {{Old Class New Tricks}}},
author = {{Abdul-Mutakabbir}, Jacinda C. and Kebriaei, Razieh and Jorgensen, Sarah C. J. and Rybak, Michael J.},
year = {2019},
month = mar,
journal = {Infectious Diseases and Therapy},
pages = {16},
issn = {2193-8229, 2193-6382},
doi = {10.1007/s40121-019-0239-0},
urldate = {2019-03-24},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Abdul-Mutakabbir/abdul-mutakabbir_2019_teaching_an_old_class_new_tricks_-_a_novel_semi-synthetic_aminoglycoside,.pdf}
}
@article{acharyaDiagnosticToolPopulation2016,
title = {A Diagnostic Tool for Population Models Using Non-Compartmental Analysis: {{The}} Ncappc Package for {{R}}},
shorttitle = {A Diagnostic Tool for Population Models Using Non-Compartmental Analysis},
author = {Acharya, Chayan and Hooker, Andrew C. and T{\"u}rky{\i}lmaz, G{\"u}lbeyaz Y{\i}ld{\i}z and J{\"o}nsson, Siv and Karlsson, Mats O.},
year = {2016},
month = apr,
journal = {Comput Methods Programs Biomed},
volume = {127},
pages = {83--93},
issn = {01692607},
doi = {10.1016/j.cmpb.2016.01.013},
urldate = {2023-04-04},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Acharya/acharya_2016_a_diagnostic_tool_for_population_models_using_non-compartmental_analysis_-_the.pdf}
}
@misc{AddressingResistanceAntibiotics,
title = {Addressing {{Resistance To Antibiotics In Pluralistic Health Systems}}},
publisher = {Koninklijke Brill NV},
doi = {10.1163/2210-7975_HRD-0148-2015012},
urldate = {2019-03-10},
langid = {english},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/addressing_resistance_to_antibiotics_in_pluralistic_health_systems.pdf}
}
@article{agoramDevelopmentEvaluationPopulation2006,
title = {Development and Evaluation of a Population Pharmacokinetic-Pharmacodynamic Model of Darbepoetin Alfa in Patients with Nonmyeloid Malignancies Undergoing Multicycle Chemotherapy},
author = {Agoram, Balaji and Heatherington, Anne C. and Gastonguay, Marc R.},
year = {2006},
month = sep,
journal = {AAPS J},
volume = {8},
number = {3},
pages = {E552-E563},
issn = {1550-7416},
doi = {10.1208/aapsj080364},
urldate = {2023-06-27},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Agoram/agoram_2006_development_and_evaluation_of_a_population_pharmacokinetic-pharmacodynamic.pdf}
}
@book{agrestiCategoricalDataAnalysis2013,
title = {Categorical Data Analysis},
author = {Agresti, Alan},
year = {2013},
series = {Wiley Series in Probability and Statistics},
edition = {3rd ed},
number = {792},
publisher = {Wiley},
address = {Hoboken, NJ},
abstract = {"A classic in its own right, this book continues to provide an introduction to modern generalized linear models for categorical variables. The text emphasizes methods that are most commonly used in practical application, such as classical inferences for two- and three-way contingency tables, logistic regression, loglinear models, models for multinomial (nominal and ordinal) responses, and methods for repeated measurement and other forms of clustered, correlated response data. Chapter headings remain essentially with the exception of a new one on Bayesian inference for parametric models. Other major changes include an expansion of clustered data, new research on analysis of data sets with robust variables, extensive discussions of ordinal data, more on interpretation, and additional exercises throughout the book. R and SAS are now showcased as the software of choice. An author web site with solutions, commentaries, software programs, and data sets is available"--},
isbn = {978-0-470-46363-5},
lccn = {QA278 .A353 2013},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Agresti/agresti_2013_categorical_data_analysis.pdf}
}
@book{ahoAWKProgrammingLanguage1988,
title = {The {{AWK}} Programming Language},
author = {Aho, Alfred V. and Kernighan, Brian W. and Weinberger, Peter J.},
year = {1988},
publisher = {Addison-Wesley Pub. Co},
address = {Reading, Mass},
isbn = {978-0-201-07981-4},
langid = {english},
lccn = {QA76.73.A95 A35 1988},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Aho/aho_1988_the_awk_programming_language.pdf}
}
@article{ainsworthAerosporinAntibioticProduced1947,
title = {`{{Aerosporin}}', an {{Antibiotic Produced}} by {{Bacillus}} Aerosporus {{Greer}}},
author = {Ainsworth, G C and Brown, Annie M and Brownlee, G},
year = {1947},
month = aug,
journal = {Nature},
volume = {160},
number = {4060},
pages = {263--263},
issn = {1476-4687},
doi = {10.1038/160263a0},
abstract = {A Bacterium isolated from the soil of a market garden in Surrey during February 1946 and afterwards from a Yorkshire soil and from the air has been found to produce an antibiotic of possible therapeutic importance for which, as it appears to be hitherto undescribed, the name `Aerosporin'* is proposed. The production and properties of aerosporin are under investigation by a group of workers at the Wellcome Physiological Research Laboratories, and the purpose of the present communication is to direct attention to certain aspects of these studies, the results of which will be published in detail elsewhere.},
annotation = {ZSCC: 0000211},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Ainsworth/ainsworth_1947_‘aerosporin’,_an_antibiotic_produced_by_bacillus_aerosporus_greer.pdf}
}
@article{akaikeNewLookStatistical1974,
title = {A New Look at the Statistical Model Identification},
author = {Akaike, Hirotugu},
year = {1974},
month = dec,
journal = {IEEE Transactions on Automatic Control},
volume = {19},
number = {6},
pages = {716--723},
issn = {0018-9286},
doi = {10.1109/TAC.1974.1100705},
abstract = {The history of the development of statistical hypothesis testing in time series analysis is reviewed briefly and it is pointed out that the hypothesis testing procedure is not adequately defined as the procedure for statistical model identification. The classical maximum likelihood estimation procedure is reviewed and a new estimate minimum information theoretical criterion (AIC) estimate (MAICE) which is designed for the purpose of statistical identification is introduced. When there are several competing models the MAICE is defined by the model and the maximum likelihood estimates of the parameters which give the minimum of AIC defined by AIC = (-2)log-(maximum likelihood) + 2(number of independently adjusted parameters within the model). MAICE provides a versatile procedure for statistical model identification which is free from the ambiguities inherent in the application of conventional hypothesis testing procedure. The practical utility of MAICE in time series analysis is demonstrated with some numerical examples.},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Akaike/akaike_1974_a_new_look_at_the_statistical_model_identification.pdf}
}
@article{albaAntibioticResistanceHelicobacter2017,
title = {Antibiotic Resistance in {{Helicobacter}} Pylori:},
shorttitle = {Antibiotic Resistance in {{Helicobacter}} Pylori},
author = {Alba, Claudio and Blanco, Ana and Alarc{\'o}n, Teresa},
year = {2017},
month = oct,
journal = {Curr Opin Infect Dis},
volume = {30},
number = {5},
pages = {489--497},
issn = {0951-7375},
doi = {10.1097/QCO.0000000000000396},
urldate = {2019-03-13},
abstract = {Metronidazole and clarithromycin resistance rates are alarming although they vary among populations. Tetracycline and amoxicillin-resistance are very low in most countries. H. pylori resistance can be detected by phenotypic or by molecular methods. Different break points may be used when performing an antimicrobial susceptibility test, so comparing resistance among different populations is challenging. Genomic techniques open new possibilities in the diagnosis of H. pylori, and the detection of H. pylori and its antimicrobial resistance in faeces is an interesting approach. Eradication rates are dependent on the susceptibility of the strain to metronidazole and clarithromycin, being lower in patients infected with a resistant strain.},
langid = {english},
keywords = {Unimportant},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Alba/alba_2017_antibiotic_resistance_in_helicobacter_pylori.pdf}
}
@article{allenFindingAlternativesAntibiotics2014,
title = {Finding Alternatives to Antibiotics},
shorttitle = {Finding Alternatives to Antibiotics},
author = {Allen, Heather K. and Trachsel, Julian and Looft, Torey and Casey, Thomas A.},
year = {2014},
month = sep,
journal = {Ann N Y Acad Sci},
volume = {1323},
number = {1},
pages = {91--100},
issn = {00778923},
doi = {10.1111/nyas.12468},
urldate = {2019-03-10},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Allen/allen_2014_finding_alternatives_to_antibiotics_-_finding_alternatives_to_antibiotics.pdf}
}
@article{ambroseAntibacterialDrugDevelopment2017,
title = {Antibacterial Drug Development Program Successes and Failures: A Pharmacometric Explanation},
shorttitle = {Antibacterial Drug Development Program Successes and Failures},
author = {Ambrose, Paul G},
year = {2017},
month = oct,
journal = {Curr Opin Pharmacol},
volume = {36},
pages = {1--7},
issn = {14714892},
doi = {10.1016/j.coph.2017.06.002},
urldate = {2019-03-10},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Ambrose/ambrose_2017_antibacterial_drug_development_program_successes_and_failures_-_a_pharmacometric.pdf}
}
@article{ambroseFrequentistBayesianPharmacometricBased2012,
title = {Frequentist and {{Bayesian Pharmacometric-Based Approaches To Facilitate Critically Needed New Antibiotic Development}}: {{Overcoming Lies}}, {{Damn Lies}}, and {{Statistics}}},
shorttitle = {Frequentist and {{Bayesian Pharmacometric-Based Approaches To Facilitate Critically Needed New Antibiotic Development}}},
author = {Ambrose, Paul G. and Hammel, Jeffrey P. and Bhavnani, Sujata M. and Rubino, Christopher M. and {Ellis-Grosse}, Evelyn J. and Drusano, George L.},
year = {2012},
month = mar,
journal = {Antimicrob Agents Chemother},
volume = {56},
number = {3},
pages = {1466--1470},
issn = {0066-4804, 1098-6596},
doi = {10.1128/AAC.01743-10},
urldate = {2019-03-08},
langid = {english},
keywords = {Done},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Ambrose/ambrose_2012_frequentist_and_bayesian_pharmacometric-based_approaches_to_facilitate.pdf}
}
@incollection{andornoHumanDignityHuman2014,
title = {Human {{Dignity}} and {{Human Rights}}},
booktitle = {Handbook of {{Global Bioethics}}},
author = {Andorno, Roberto},
editor = {{ten Have}, Henk A.M.J. and Gordijn, Bert},
year = {2014},
pages = {45--57},
publisher = {Springer Netherlands},
address = {Dordrecht},
doi = {10.1007/978-94-007-2512-6_66},
urldate = {2019-10-23},
isbn = {978-94-007-2511-9 978-94-007-2512-6},
langid = {english},
keywords = {Philosophy course},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Andorno/andorno_2014_human_dignity_and_human_rights.pdf}
}
@article{aokiModelSelectionAveraging2017,
title = {Model Selection and Averaging of Nonlinear Mixed-Effect Models for Robust Phase {{III}} Dose Selection},
author = {Aoki, Yasunori and R{\"o}shammar, Daniel and Hamr{\'e}n, Bengt and Hooker, Andrew C.},
year = {2017},
month = dec,
journal = {J Pharmacokinet Pharmacodyn},
volume = {44},
number = {6},
pages = {581--597},
issn = {1567-567X, 1573-8744},
doi = {10.1007/s10928-017-9550-0},
urldate = {2023-04-04},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Aoki/aoki_2017_model_selection_and_averaging_of_nonlinear_mixed-effect_models_for_robust_phase.pdf}
}
@article{aokiPreconditioningNonlinearMixed2016,
title = {Preconditioning of {{Nonlinear Mixed Effects Models}} for {{Stabilisation}} of {{Variance-Covariance Matrix Computations}}},
author = {Aoki, Yasunori and Nordgren, Rikard and Hooker, Andrew C.},
year = {2016},
month = mar,
journal = {AAPS J},
volume = {18},
number = {2},
pages = {505--518},
issn = {1550-7416},
doi = {10.1208/s12248-016-9866-5},
urldate = {2019-03-09},
abstract = {As the importance of pharmacometric analysis increases, more and more complex mathematical models are introduced and computational error resulting from computational instability starts to become a bottleneck in the analysis. We propose a preconditioning method for non-linear mixed effects models used in pharmacometric analyses to stabilise the computation of the variance-covariance matrix. Roughly speaking, the method reparameterises the model with a linear combination of the original model parameters so that the Hessian matrix of the likelihood of the reparameterised model becomes close to an identity matrix. This approach will reduce the influence of computational error, for example rounding error, to the final computational result. We present numerical experiments demonstrating that the stabilisation of the computation using the proposed method can recover failed variance-covariance matrix computations, and reveal non-identifiability of the model parameters.},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Aoki/aoki_2016_preconditioning_of_nonlinear_mixed_effects_models_for_stabilisation_of.pdf}
}
@book{armitageEncyclopediaBiostatistics2005,
title = {Encyclopedia of {{Biostatistics}}},
editor = {Armitage, P. and Colton, Theodore},
year = {2005},
edition = {2nd ed},
publisher = {John Wiley},
address = {Chichester, West Sussex, England ; Hoboken, NJ},
isbn = {978-0-470-84907-1},
lccn = {RA409 .E53 2005},
annotation = {OCLC: ocm57168526},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/Armitage/armitage_2005_encyclopedia_of_biostatistics.pdf}
}
@article{arthurAntibioticsVentilatorassociatedPneumonia2016,
title = {Antibiotics for Ventilator-Associated Pneumonia},
author = {Arthur, Lauren E and Kizor, Russell S and Selim, Adrian G and {van Driel}, Mieke L and Seoane, Leonardo},
editor = {{Cochrane Acute Respiratory Infections Group}},
year = {2016},
month = oct,
journal = {Cochrane Database Syst Rev},
issn = {14651858},
doi = {10.1002/14651858.CD004267.pub4},
urldate = {2019-03-09},
abstract = {Background Ventilator-associated pneumonia (VAP) is a significant cause of morbidity and mortality, complicating the medical course of approximately 10\% of mechanically-ventilated patients, with an estimated attributable mortality of 13\%. To treat VAP empirically, the American Thoracic Society currently recommends antibiotic therapy based on the patients' risk of colonisation by an organism with multidrug resistance. The selection of initial antibiotic therapy in VAP is important, as inappropriate initial antimicrobial treatment is associated with higher mortality and longer hospital stay in intensive care unit (ICU) patients.},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Arthur/arthur_2016_antibiotics_for_ventilator-associated_pneumonia.pdf}
}
@article{asin-prietoApplicationsPharmacokineticPharmacodynamic2015,
title = {Applications of the Pharmacokinetic/Pharmacodynamic ({{PK}}/{{PD}}) Analysis of Antimicrobial Agents},
author = {{As{\'i}n-Prieto}, Eduardo and {Rodr{\'i}guez-Gasc{\'o}n}, Alicia and Isla, Arantxazu},
year = {2015},
month = may,
journal = {Journal of Infection and Chemotherapy},
volume = {21},
number = {5},
pages = {319--329},
issn = {1341321X},
doi = {10.1016/j.jiac.2015.02.001},
urldate = {2021-01-16},
langid = {english},
annotation = {ZSCC: 0000146},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Asín-Prieto/asin-prieto_2015_applications_of_the_pharmacokinetic-pharmacodynamic_(pk-pd)_analysis_of.pdf}
}
@article{associationNationalisedDrugCompanies2019,
title = {Nationalised Drug Companies May Be Needed to 'Fix Antibiotics Market'},
author = {Association, Press},
year = {2019},
month = mar,
journal = {The Guardian},
issn = {0261-3077},
urldate = {2019-06-03},
abstract = {UK's superbug tsar Lord Jim O'Neill compares idea to way banks were taken over after 2008 financial crash},
chapter = {Business},
langid = {british},
file = {/Users/vrognas/.config/Zotero/storage/C76KTKLI/nationalised-drug-companies-may-be-needed-to-fix-antibiotics-market.html}
}
@article{atkinsonAugmentedRenalClearance2018,
title = {Augmented Renal Clearance},
author = {Atkinson, Arthur J.},
year = {2018},
journal = {Transl Clin Pharmacol},
volume = {26},
number = {3},
pages = {111},
issn = {2289-0882, 2383-5427},
doi = {10.12793/tcp.2018.26.3.111},
urldate = {2024-08-16},
langid = {english},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/Atkinson/atkinson_2018_augmented_renal_clearance.pdf}
}
@article{aulinBiomarkerguidedIndividualizationAntibiotic2021,
title = {Biomarker-guided Individualization of Antibiotic Therapy},
author = {Aulin, Linda B.S. and {de Lange}, Dylan W. and Saleh, Mohammed A.A. and {van der Graaf}, Piet H. and V{\"o}ller, Swantje and {Coen van Hasselt}, J.G.},
year = {2021},
month = feb,
journal = {Clin Pharmacol Ther},
pages = {cpt.2194},
issn = {0009-9236, 1532-6535},
doi = {10.1002/cpt.2194},
urldate = {2021-02-14},
langid = {english},
annotation = {ZSCC: 0000000},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Aulin/aulin_2021_biomarker‐guided_individualization_of_antibiotic_therapy.pdf}
}
@techreport{australiangovernment:departmentofhealththerapeuticgoodsadministrationAustralianClinicalTrial2021,
title = {Australian Clinical Trial Handbook: {{Guidance}} on Conducting Clinical Trials in {{Australia}} Using `Unapproved' Therapeutic Goods},
author = {{Australian Government: Department of Health, Therapeutic Goods Administration}},
year = {2021},
month = aug,
number = {v2.4},
langid = {english},
keywords = {nosource}
}
@article{bachComparingPerformanceFirstorder2021,
title = {Comparing the Performance of First-Order Conditional Estimation ({{FOCE}}) and Different Expectation--Maximization ({{EM}}) Methods in {{NONMEM}}: Real Data Experience with Complex Nonlinear Parent-Metabolite Pharmacokinetic Model},
author = {Bach, Thanh and An, Guohua},
year = {2021},
month = apr,
journal = {J Pharmacokinet Pharmacodyn},
volume = {48},
number = {4},
pages = {581--595},
doi = {10.1007/s10928-021-09753-0},
abstract = {First-order conditional estimation (FOCE) has been the most frequently used estimation method in NONMEM, a leading program for population pharmacokinetic/pharmacodynamic modeling. However, with growing data complexity, the performance of FOCE is challenged by long run time, convergence problem and model instability. In NONMEM 7, expectation-maximization (EM) estimation methods and FOCE with FAST option (FOCE FAST) were introduced. In this study, we compared the performance of FOCE, FOCE FAST, and two EM methods, namely importance sampling (IMP) and stochastic approximation expectation-maximization (SAEM), utilizing the rich pharmacokinetic data of oxfendazole and its two metabolites obtained from the first-in-human single ascending dose study in healthy adults. All methods yielded similar parameter estimates, but great differences were observed in parameter precision and modeling time. For simpler models (i.e., models of oxfendazole and/or oxfendazole sulfone), FOCE and FOCE FAST were more efficient than EM methods with shorter run time and comparable parameter precision. FOCE FAST was about two times faster than FOCE but it was prone to premature termination. For the most complex model (i.e., model of all three analytes, one of which having high level of data below quantification limit), FOCE failed to reliably assess parameter precision, while parameter precision obtained by IMP and SAEM was similar with SAEM being the faster method. IMP was more sensitive to model misspecification; without pre-systemic metabolism, IMP analysis failed to converge. With parallel computing introduced in NONMEM 7.2, modeling speed increased less than proportionally with the increase in the number of CPUs from 1 to 16.},
pmid = {33884580},
annotation = {MAG ID: 3155307402},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bach/bach_2021_comparing_the_performance_of_first-order_conditional_estimation_(foce)_and.pdf}
}
@article{badilloIntroductionMachineLearning2020,
title = {An {{Introduction}} to {{Machine Learning}}},
author = {Badillo, Solveig and Banfai, Balazs and Birzele, Fabian and Davydov, Iakov I. and Hutchinson, Lucy and Kam-Thong, Tony and Siebourg-Polster, Juliane and Steiert, Bernhard and Zhang, Jitao David},
year = {2020},
month = mar,
journal = {Clin Pharmacol Ther},
pages = {cpt.1796},
issn = {0009-9236, 1532-6535},
doi = {10.1002/cpt.1796},
urldate = {2020-03-06},
langid = {english},
annotation = {ZSCC: 0000007},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Badillo/badillo_2020_an_introduction_to_machine_learning.pdf}
}
@article{baeRbasedReproductionEstimation2016,
title = {R-Based Reproduction of the Estimation Process Hidden behind {{NONMEM}}{\textregistered} {{Part}} 2: {{First-order}} Conditional Estimation},
shorttitle = {R-Based Reproduction of the Estimation Process Hidden behind {{NONMEM}}{\textregistered} {{Part}} 2},
author = {Bae, Kyun-Seop and Yim, Dong-Seok},
year = {2016},
journal = {Transl Clin Pharmacol},
volume = {24},
number = {4},
pages = {161},
issn = {2289-0882, 2383-5427},
doi = {10.12793/tcp.2016.24.4.161},
urldate = {2019-03-09},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bae/bae_2016_r-based_reproduction_of_the_estimation_process_hidden_behind_nonmem®_part_2_-.pdf}
}
@article{bairy_using_2018,
title = {Using the {{Kinetic Estimating Glomerular Filtration Rate Equation}} for {{Estimating Glomerular Filtration Rate}} and {{Detecting Acute Kidney Injury}}: {{A Pilot Study}}},
shorttitle = {Using the {{Kinetic Estimating Glomerular Filtration Rate Equation}} for {{Estimating Glomerular Filtration Rate}} and {{Detecting Acute Kidney Injury}}},
author = {Bairy, Manohar and See, Faith H. W. and Lim, Ru Sin},
year = {2018},
journal = {Nephron},
volume = {140},
number = {4},
pages = {231--239},
issn = {1660-8151, 2235-3186},
doi = {10.1159/000492439},
urldate = {2023-02-13},
langid = {english},
pmid = {30231255},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bairy/bairy_2018_using_the_kinetic_estimating_glomerular_filtration_rate_equation_for_estimating.pdf}
}
@article{baldiniMaturationRateReticulocytes1960,
title = {The {{Maturation Rate}} of {{Reticulocytes}}},
author = {Baldini, Mario and Pannacciulli, Ivo},
year = {1960},
month = may,
journal = {Blood},
volume = {15},
number = {5},
pages = {614--629},
issn = {0006-4971},
doi = {10.1182/blood.V15.5.614.614},
urldate = {2022-02-21},
abstract = {An in vitro culture technic for the study of reticulocyte maturation was described. The method gave reproducible results and proved to be of value in the comparative study of reticulocyte maturation in blood disorders. By this method it was shown that variations in the reticulocyte maturation in vitro paralleled similar variations present in vivo.The maturation of reticulocytes from patients with different types of anemia was investigated. In some anemias the in vitro maturation of reticulocytes was prolonged, not only because younger reticulocytes were present in the blood, but also because the rate at which the reticulum substance disappeared was delayed. This was particularly evident in the anemia of chronic uremia, in Cooley's anemia and in pernicious anemia in relapse. In only occasional cases of hereditary spherocytosis and of autoimmune hemolytic anemia was the rate of reticulocyte maturation found to be moderately delayed. In patients with iron deficiency anemia or bleeding anemia it was always normal.From the above findings the following conclusions were derived:1. The reticulocyte number in the circulating blood is the resultant of three variables: (a) the rate of output of new reticulocytes from the bone marrow; (b) the stage of maturation at which reticulocytes are delivered into the peripheral circulation; (c) the rate of disappearance of the reticulum substance.2. The number of reticulocytes in the circulating blood cannot be indiscriminately used as a precise index of red cell production in erythrokinetics.3. There is good reason to believe that a defect in the rate at which the reticulocytes mature in the circulating blood is an index of a similar defect in the process of erythroblastic differentiation in the bone marrow.},
annotation = {ZSCC: 0000055},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/BALDINI/baldini-and-pannacciulli_1960_the-maturation-rate-of-reticulocytes.pdf}
}
@incollection{baptistaAugmentedRenalClearance2018,
title = {Augmented {{Renal Clearance}}},
booktitle = {Antibiotic {{Pharmacokinetic}}/{{Pharmacodynamic Considerations}} in the {{Critically Ill}}},
author = {Baptista, Jo{\~a}o Pedro},
editor = {Udy, Andrew A. and Roberts, Jason A. and Lipman, Jeffrey},
year = {2018},
pages = {125--150},
publisher = {Springer Singapore},
address = {Singapore},
doi = {10.1007/978-981-10-5336-8_7},
urldate = {2024-08-18},
isbn = {978-981-10-5335-1 978-981-10-5336-8},
langid = {english},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/Baptista/baptista_2018_augmented_renal_clearance.pdf}
}
@article{bardoMethodsNonproportionalHazards2024,
title = {Methods for Non-Proportional Hazards in Clinical Trials: {{A}} Systematic Review},
shorttitle = {Methods for Non-Proportional Hazards in Clinical Trials},
author = {Bardo, Maximilian and Huber, Cynthia and Benda, Norbert and Brugger, Jonas and Fellinger, Tobias and Galaune, Vaidotas and Heinz, Judith and Heinzl, Harald and Hooker, Andrew C and Klinglm{\"u}ller, Florian and K{\"o}nig, Franz and Mathes, Tim and Mittlb{\"o}ck, Martina and Posch, Martin and Ristl, Robin and Friede, Tim},
year = {2024},
month = jun,
journal = {Stat Methods Med Res},
volume = {33},
number = {6},
pages = {1069--1092},
issn = {0962-2802, 1477-0334},
doi = {10.1177/09622802241242325},
urldate = {2024-12-07},
abstract = {For the analysis of time-to-event data, frequently used methods such as the log-rank test or the Cox proportional hazards model are based on the proportional hazards assumption, which is often debatable. Although a wide range of parametric and non-parametric methods for non-proportional hazards has been proposed, there is no consensus on the best approaches. To close this gap, we conducted a systematic literature search to identify statistical methods and software appropriate under non-proportional hazard. Our literature search identified 907 abstracts, out of which we included 211 articles, mostly methodological ones. Review articles and applications were less frequently identified. The articles discuss effect measures, effect estimation and regression approaches, hypothesis tests, and sample size calculation approaches, which are often tailored to specific non-proportional hazard situations. Using a unified notation, we provide an overview of methods available. Furthermore, we derive some guidance from the identified articles.},
langid = {english},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/Bardo/bardo-et-al_2024_methods-for-non-proportional-hazards-in-clinical-t.pdf}
}
@article{bassettiNewAntibioticsBad2013,
title = {New Antibiotics for Bad Bugs: Where Are We?},
shorttitle = {New Antibiotics for Bad Bugs},
author = {Bassetti, Matteo and Merelli, Maria and Temperoni, Chiara and Astilean, Augusta},
year = {2013},
journal = {Ann Clin Microbiol Antimicrob},
volume = {12},
number = {1},
pages = {22},
issn = {1476-0711},
doi = {10.1186/1476-0711-12-22},
urldate = {2019-10-08},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bassetti/bassetti_2013_new_antibiotics_for_bad_bugs_-_where_are_we.pdf}
}
@article{bauerClinicalPharmacokineticsPharmacodynamics2014,
title = {Clinical {{Pharmacokinetics}} and {{Pharmacodynamics}}},
author = {Bauer, Larry A},
year = {2014},
pages = {24},
langid = {english},
annotation = {ZSCC: NoCitationData[s0]},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bauer/bauer_2014_clinical_pharmacokinetics_and_pharmacodynamics.pdf}
}
@article{bauerNONMEMTutorialPart2019,
title = {{{NONMEM Tutorial Part I}}: {{Description}} of {{Commands}} and {{Options}}, {{With Simple Examples}} of {{Population Analysis}}},
shorttitle = {{{NONMEM Tutorial Part I}}},
author = {Bauer, Robert J.},
year = {2019},
month = jun,
journal = {CPT Pharmacometrics Syst Pharmacol},
pages = {psp4.12404},
issn = {2163-8306, 2163-8306},
doi = {10.1002/psp4.12404},
urldate = {2019-06-17},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bauer/bauer_2019_nonmem_tutorial_part_i_-_description_of_commands_and_options,_with_simple.pdf}
}
@article{bauerNONMEMTutorialPart2019a,
title = {{{NONMEM Tutorial Part II}}: {{Estimation Methods}} and {{Advanced Examples}}},
author = {Bauer, Robert J.},
year = {2019},
month = may,
journal = {CPT Pharmacometrics Syst Pharmacol},
pages = {psp4.12422},
issn = {2163-8306, 2163-8306},
doi = {10.1002/psp4.12422},
urldate = {2019-06-06},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bauer/bauer_2019_nonmem_tutorial_part_ii_-_estimation_methods_and_advanced_examples.pdf;/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bauer/bauer_2019_nonmem_tutorial_part_ii_-_estimation_methods_and_advanced_examples2.pdf}
}
@article{bauerSurveyPopulationAnalysis2007,
title = {A Survey of Population Analysis Methods and Software for Complex Pharmacokinetic and Pharmacodynamic Models with Examples},
author = {Bauer, Robert J. and Guzy, Serge and Ng, Chee},
year = {2007},
month = mar,
journal = {AAPS J},
volume = {9},
number = {1},
pages = {E60-E83},
issn = {1550-7416},
doi = {10.1208/aapsj0901007},
urldate = {2020-11-10},
langid = {english},
annotation = {ZSCC: 0000206},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bauer/bauer_2007_a_survey_of_population_analysis_methods_and_software_for_complex.pdf}
}
@article{bauerTutorial$DESIGNNONMEM2021,
title = {Tutorial for \${{DESIGN}} in {{NONMEM}}: {{Clinical}} Trial Evaluation and Optimization},
shorttitle = {Tutorial for \${{DESIGN}} in {{NONMEM}}},
author = {Bauer, Robert J. and Hooker, Andrew C. and Mentre, France},
year = {2021},
month = dec,
journal = {CPT Pharmacometrics Syst Pharmacol},
volume = {10},
number = {12},
pages = {1452--1465},
issn = {2163-8306, 2163-8306},
doi = {10.1002/psp4.12713},
urldate = {2022-11-19},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bauer/bauer_2021_tutorial_for_$design_in_nonmem_-_clinical_trial_evaluation_and_optimization.pdf}
}
@misc{bealNONMEM74Users2019,
title = {{{NONMEM}} 7.4 Users Guides},
author = {Beal, Stuart L and Sheiner, Lewis B and Boeckmann, Alison J and Bauer, Robert J},
year = {2019},
address = {Gaithersburg, MD},
keywords = {nosource},
annotation = {ZSCC: NoCitationData[s0]}
}
@misc{bealNONMEM75Users2020,
title = {{{NONMEM}} 7.5 Users Guides},
author = {Beal, Stuart L and Sheiner, Lewis B and Boeckmann, Alison J and Bauer, Robert J},
year = {2020},
address = {Gaithersburg, MD},
keywords = {nosource},
annotation = {ZSCC: NoCitationData[s0]}
}
@article{bealWaysFitPK2001,
title = {Ways to {{Fit}} a {{PK Model}} with {{Some Data Below}} the {{Quantification Limit}}},
author = {Beal, Stuart L},
year = {2001},
journal = {J Pharmacokinet Pharmacodyn},
volume = {28},
number = {5},
pages = {481--504},
issn = {1567567X},
doi = {10.1023/a:1012299115260},
langid = {english},
keywords = {Read},
annotation = {PMID 11768292},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Beal/beal_ways_to_fit_a_pk_model_with_some_data_below_the_quantification_limit.pdf}
}
@article{beckettIntentiontotreatTransparencyRelated2016,
title = {Intention-to-Treat and Transparency of Related Practices in Randomized, Controlled Trials of Anti-Infectives},
author = {Beckett, Robert D. and Loeser, Kathryn C. and Bowman, Kathryn R. and Towne, Trent G.},
year = {2016},
month = aug,
journal = {BMC Med Res Methodol},
volume = {16},
number = {1},
issn = {1471-2288},
doi = {10.1186/s12874-016-0215-2},
urldate = {2019-03-21},
abstract = {Background Intention-to-treat (ITT) analysis is commonly recommended for use, due to its benefits on external validity, in randomized, controlled trials (RCTs). No published reports describe how ITT analysis, as well as alternative approaches, are used in anti-infective RCTs. The purpose of this study is to describe the extent to which ITT analysis and alternative data approaches are used, the practices used to handle missing subject data, and whether non-inferiority trials present both ITT and per protocol (PP) analyses. Results of this analysis will help guide end users of infectious diseases primary drug literature. Methods A cross-sectional study of RCTs of anti-infectives published from January 1, 2013 through December 31, 2014 was conducted. A PubMed search identified relevant articles published in five specialty infectious diseases journals and four general medical journals. Each article was reviewed by two independent investigators with discrepancies resolved by consensus. Descriptive statistics were used to quantify results. Results One hundred four articles met study criteria. The most common medication classes represented in the RCTs were hepatitis C antivirals (26~\%), antibacterials (25~\%), and antiretrovirals (21~\%). Thirty studies (29~\%) were non-inferiority trials. Most studies (77~\%) described use of ITT or modified ITT (mITT) in their methods. Of the ITT and mITT studies, most (73~\%) did not describe practices used to handle missing data. Most (97~\%) non-inferiority trials described use of ITT, mITT, or both; however, only 15 (50~\%) also described use of PP. Conclusions RCTs of anti-infectives commonly employ ITT and mITT. Most do not describe how missing data were addressed. Non-inferiority trials of anti-infectives do not consistently employ both ITT and PP populations. Electronic supplementary material The online version of this article (doi:10.1186/s12874-016-0215-2) contains supplementary material, which is available to authorized users.},
pmcid = {PMC4997732},
pmid = {27557676},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Beckett/beckett_2016_intention-to-treat_and_transparency_of_related_practices_in_randomized,.pdf}
}
@article{bellomoAcuteRenalFailure2004,
title = {Acute Renal Failure -- Definition, Outcome Measures, Animal Models, Fluid Therapy and Information Technology Needs: The {{Second International Consensus Conference}} of the {{Acute Dialysis Quality Initiative}} ({{ADQI}}) {{Group}}},
author = {Bellomo, Rinaldo and Ronco, Claudio and Kellum, John A and Mehta, Ravindra L and Palevsky, Paul},
year = {2004},
journal = {Crit Care},
volume = {8},
number = {4},
pages = {R204},
issn = {13648535},
doi = {10.1186/cc2872},
urldate = {2019-12-04},
keywords = {Important},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bellomo/bellomo_2004_acute_renal_failure_–_definition,_outcome_measures,_animal_models,_fluid.pdf}
}
@misc{benferhatElucidationPharmacokineticsPK2020,
title = {Elucidation of the Pharmacokinetics ({{PK}}) and Pharmacodynamics ({{PD}}) of a Drug Impacting the Erythropoietic System Using a Model-Based Pharmacometric Approach.},
author = {Benferhat, Amina},
year = {2020},
annotation = {ZSCC: NoCitationData[s0]},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Benferhat/benferhat_2020_elucidation_of_the_pharmacokinetics_(pk)_and_pharmacodynamics_(pd)_of_a_drug.pdf}
}
@misc{benferhatInvestigationPharmacokineticsPK2020,
title = {Investigation of the Pharmacokinetics ({{PK}}) and Pharmacodynamics ({{PD}}) of a Drug Acting on the Erythropoietic System Using a Pharmacometric Approach},
author = {Benferhat, Amina},
year = {2020},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Benferhat/benferhat_2020_investigation_of_the_pharmacokinetics_(pk)_and_pharmacodynamics_(pd)_of_a_drug.pdf}
}
@article{bergenPharmacokineticPharmacodynamicInvestigation2010,
title = {Pharmacokinetic/{{Pharmacodynamic Investigation}} of {{Colistin}} against {{Pseudomonas}} Aeruginosa {{Using}} an {{In Vitro Model}}},
author = {Bergen, Phillip J. and Bulitta, Jurgen B. and Forrest, Alan and Tsuji, Brian T. and Li, Jian and Nation, Roger L.},
year = {2010},
month = sep,
journal = {Antimicrob Agents Chemother},
volume = {54},
number = {9},
pages = {3783--3789},
issn = {0066-4804, 1098-6596},
doi = {10.1128/AAC.00903-09},
urldate = {2020-11-06},
abstract = {ABSTRACT Colistin plays a key role in treatment of serious infections by Pseudomonas aeruginosa . The aims of this study were to (i) identify the pharmacokinetic/pharmacodynamic (PK/PD) index (i.e., the area under the unbound concentration-time curve to MIC ratio [{\textflorin}AUC/MIC], the unbound maximal concentration to MIC ratio [{\textflorin} C max /MIC], or the cumulative percentage of a 24-h period that unbound concentrations exceed the MIC [{\textflorin} T {$>$}MIC ]) that best predicts colistin efficacy and (ii) determine the values for the predictive PK/PD index required to achieve various magnitudes of killing effect. Studies were conducted in a one-compartment in vitro PK/PD model for 24 h using P. aeruginosa ATCC 27853, PAO1, and the multidrug-resistant mucoid clinical isolate 19056 muc. Six intermittent dosing intervals, with a range of {\textflorin} C max colistin concentrations, and two continuous infusion regimens were examined. PK/PD indices varied from 0.06 to 18 for targeted {\textflorin} C max /MIC, 0.36 to 312 for {\textflorin}AUC/MIC, and 0 to 100\% for {\textflorin} T {$>$}MIC . A Hill-type model was fit to killing effect data, which were expressed as the log 10 ratio of the area under the CFU/ml curve for treated regimens versus control. With {\textflorin} C max values equal to or above the MIC, rapid killing was observed following the first dose; substantial regrowth occurred by 24 h with most regimens. The overall killing effect was best correlated with {\textflorin}AUC/MIC ( R 2 = 0.931) compared to {\textflorin} C max /MIC ( R 2 = 0.868) and {\textflorin} T {$>$}MIC ( R 2 = 0.785). The magnitudes of {\textflorin}AUC/MIC required for 1- and 2-log 10 reductions in the area under the CFU/ml curve relative to growth control were 22.6 and 30.4, 27.1 and 35.7, and 5.04 and 6.81 for ATCC 27853, PAO1, and 19056 muc, respectively. The PK/PD targets identified will assist in designing optimal dosing strategies for colistin.},
langid = {english},
annotation = {ZSCC: 0000161},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/Bergen/bergen_2010_pharmacokinetic-pharmacodynamic_investigation_of_colistin_against_pseudomonas.pdf}
}
@article{bergenPharmacokineticsPharmacodynamicsOld2012,
title = {Pharmacokinetics and Pharmacodynamics of 'old' Polymyxins: What Is New?},
shorttitle = {Pharmacokinetics and Pharmacodynamics of 'old' Polymyxins},
author = {Bergen, Phillip J. and Landersdorfer, Cornelia B. and Zhang, Jing and Zhao, Miao and Lee, Hee Ji and Nation, Roger L. and Li, Jian},
year = {2012},
month = nov,
journal = {Diagn Microbiol Infect Dis},
volume = {74},
number = {3},
pages = {213--223},
issn = {1879-0070},
doi = {10.1016/j.diagmicrobio.2012.07.010},
abstract = {'Old' colistin and polymyxin B are increasingly used as last-line therapy against multidrug-resistant Gram-negative bacteria Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. For intravenous administration, colistin is dosed as its inactive prodrug colistin methanesulfonate (sodium), while polymyxin B is used as its sulfate (active antibacterial). Over the last decade, significant progress has been made in understanding their chemistry, pharmacokinetics (PK), and pharmacodynamics (PD). The first scientifically based dosing suggestions are now available for colistin methanesulfonate to generate a desired target steady-state plasma concentration of formed colistin in various categories of critically ill patients. As simply increasing polymyxin dosage regimens is not an option for optimizing their PK/PD due to nephrotoxicity, combination therapy with other antibiotics has great potential to maximize the efficacy of polymyxins while minimizing emergence of resistance. We must pursue rational approaches to the use of polymyxins and other existing antibiotics through the application of PK/PD principles.},
langid = {english},
pmcid = {PMC3477253},
pmid = {22959816},
keywords = {Acinetobacter Infections,Anti-Bacterial Agents,Colistin,Drug Therapy Combination,Humans,Klebsiella Infections,Polymyxins,Pseudomonas Infections},
annotation = {ZSCC: 0000177},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/Bergen/bergen_2012_pharmacokinetics_and_pharmacodynamics_of_'old'_polymyxins_-_what_is_new.pdf}
}
@article{bergstrandPredictionCorrectedVisualPredictive2011,
title = {Prediction-{{Corrected Visual Predictive Checks}} for {{Diagnosing Nonlinear Mixed-Effects Models}}},
author = {Bergstrand, Martin and Hooker, Andrew C. and Wallin, Johan E. and Karlsson, Mats O.},
year = {2011},
month = jun,
journal = {AAPS J},
volume = {13},
number = {2},
pages = {143--151},
issn = {1550-7416},
doi = {10.1208/s12248-011-9255-z},
urldate = {2023-11-09},
abstract = {Informative diagnostic tools are vital to the development of useful mixed-effects models. The Visual Predictive Check (VPC) is a popular tool for evaluating the performance of population PK and PKPD models. Ideally, a VPC will diagnose both the fixed and random effects in a mixed-effects model. In many cases, this can be done by comparing different percentiles of the observed data to percentiles of simulated data, generally grouped together within bins of an independent variable. However, the diagnostic value of a VPC can be hampered by binning across a large variability in dose and/or influential covariates. VPCs can also be misleading if applied to data following adaptive designs such as dose adjustments. The prediction-corrected VPC (pcVPC) offers a solution to these problems while retaining the visual interpretation of the traditional VPC. In a pcVPC, the variability coming from binning across independent variables is removed by normalizing the observed and simulated dependent variable based on the typical population prediction for the median independent variable in the bin. The principal benefit with the pcVPC has been explored by application to both simulated and real examples of PK and PKPD models. The investigated examples demonstrate that pcVPCs have an enhanced ability to diagnose model misspecification especially with respect to random effects models in a range of situations. The pcVPC was in contrast to traditional VPCs shown to be readily applicable to data from studies with a priori and/or a posteriori dose adaptations.},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bergstrand/bergstrand_2011_prediction-corrected_visual_predictive_checks_for_diagnosing_nonlinear.pdf}
}
@article{bettiolChallengesSolutionsClinical2015,
title = {Challenges and {{Solutions}} for {{Clinical Development}} of {{New Antibacterial Agents}}: {{Results}} of a {{Survey}} among {{Pharmaceutical Industry Professionals}}},
shorttitle = {Challenges and {{Solutions}} for {{Clinical Development}} of {{New Antibacterial Agents}}},
author = {Bettiol, Esther and Wetherington, Jeffrey D. and Schmitt, Nicola and Harbarth, Stephan},
year = {2015},
month = jul,
journal = {Antimicrob Agents Chemother},
volume = {59},
number = {7},
pages = {3695--3699},
issn = {0066-4804, 1098-6596},
doi = {10.1128/AAC.00638-15},
urldate = {2019-03-08},
langid = {english},
keywords = {Done},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bettiol/bettiol_2015_challenges_and_solutions_for_clinical_development_of_new_antibacterial_agents_-.pdf}
}
@article{bhavnaniClinicalPharmacokineticPharmacodynamic2017,
title = {Clinical Pharmacokinetic--Pharmacodynamic Analyses: A Critical Element for Developing Antibacterial Agents},
shorttitle = {Clinical Pharmacokinetic--Pharmacodynamic Analyses},
author = {Bhavnani, Sujata M and Hammel, Jeffrey P},
year = {2017},
month = oct,
journal = {Curr Opin Pharmacol},
volume = {36},
pages = {124--129},
issn = {14714892},
doi = {10.1016/j.coph.2017.09.010},
urldate = {2019-03-10},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bhavnani/bhavnani_2017_clinical_pharmacokinetic–pharmacodynamic_analyses_-_a_critical_element_for.pdf}
}
@article{bianPharmacokineticsPharmacodynamicsPeptide2022,
title = {Pharmacokinetics and Pharmacodynamics of Peptide Antibiotics},
author = {Bian, Xingchen and Qu, Xingyi and Zhang, Jing and Nang, Sue C. and Bergen, Phillip J. and Tony. Zhou, Qi and Chan, Hak-Kim and Feng, Meiqing and Li, Jian},
year = {2022},
month = apr,
journal = {Adv Drug Deliv Rev},
volume = {183},
pages = {114171},
issn = {0169409X},
doi = {10.1016/j.addr.2022.114171},
urldate = {2023-02-18},
abstract = {Antimicrobial resistance is a major global health challenge. As few new efficacious antibiotics will become available in the near future, peptide antibiotics continue to be major therapeutic options for treating infections caused by multidrug-resistant pathogens. Rational use of antibiotics requires optimisation of the pharmacokinetics and pharmacodynamics for the treatment of different types of infections. Toxicodynamics must also be considered to improve the safety of antibiotic use and, where appropriate, to guide therapeutic drug monitoring. This review focuses on the pharmacokinetics/pharmacodynamics/ toxicodynamics of peptide antibiotics against multidrug-resistant Gram-negative and Gram-positive pathogens. Optimising antibiotic exposure at the infection site is essential for improving their efficacy and minimising emergence of resistance.},
langid = {english},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/Bian/bian-et-al_2022_pharmacokinetics-and-pharmacodynamics-of-peptide-a.pdf}
}
@article{bilbao-meseguerAugmentedRenalClearance2018,
title = {Augmented {{Renal Clearance}} in {{Critically Ill Patients}}: {{A Systematic Review}}},
shorttitle = {Augmented {{Renal Clearance}} in {{Critically Ill Patients}}},
author = {{Bilbao-Meseguer}, Idoia and {Rodr{\'i}guez-Gasc{\'o}n}, Alicia and Barrasa, Helena and Isla, Arantxazu and Solin{\'i}s, Mar{\'i}a {\'A}ngeles},
year = {2018},
month = sep,
journal = {Clin Pharmacokinet},
volume = {57},
number = {9},
pages = {1107--1121},
issn = {0312-5963, 1179-1926},
doi = {10.1007/s40262-018-0636-7},
urldate = {2024-09-24},
langid = {english},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/Bilbao-Meseguer/bilbao-meseguer_2018_augmented_renal_clearance_in_critically_ill_patients_-_a_systematic_review.pdf}
}
@article{bjorkRevisedEquationsEstimating2011,
title = {Revised Equations for Estimating Glomerular Filtration Rate Based on the {{Lund-Malm{\"o} Study}} Cohort},
author = {Bj{\"o}rk, Jonas and Grubb, Anders and Sterner, Gunnar and Nyman, Ulf},
year = {2011},
month = may,
journal = {Scand J Clin Lab Invest},
volume = {71},
number = {3},
pages = {232--239},
issn = {0036-5513, 1502-7686},
doi = {10.3109/00365513.2011.557086},
urldate = {2020-09-25},
langid = {english},
annotation = {ZSCC: 0000054},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Björk/bjork_2011_revised_equations_for_estimating_glomerular_filtration_rate_based_on_the.pdf}
}
@article{bjornssonUseSerumCreatinine1979,
title = {Use of {{Serum Creatinine Concentrations}} to {{Determine Renal Function}}},
author = {Bjornsson, Thorir D},
year = {1979},
journal = {Clin Pharmacokinet},
volume = {4},
pages = {200--222},
langid = {english},
annotation = {ZSCC: NoCitationData[s0]},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bjornsson/bjornsson_1979_use_of_serum_creatinine_concentrations_to_determine_renal_function.pdf}
}
@article{boissonComparisonIntrapulmonarySystemic2014,
title = {Comparison of {{Intrapulmonary}} and {{Systemic Pharmacokinetics}} of {{Colistin Methanesulfonate}} ({{CMS}}) and {{Colistin}} after {{Aerosol Delivery}} and {{Intravenous Administration}} of {{CMS}} in {{Critically Ill Patients}}},
author = {Boisson, Matthieu and Jacobs, Matthieu and Gr{\'e}goire, Nicolas and Gobin, Patrice and Marchand, Sandrine and Couet, William and Mimoz, Olivier},
year = {2014},
month = dec,
journal = {Antimicrob Agents Chemother},
volume = {58},
number = {12},
pages = {7331--7339},
issn = {0066-4804, 1098-6596},
doi = {10.1128/AAC.03510-14},
urldate = {2020-10-20},
abstract = {ABSTRACT Colistin is an old antibiotic that has recently gained a considerable renewal of interest for the treatment of pulmonary infections due to multidrug-resistant Gram-negative bacteria. Nebulization seems to be a promising form of administration, but colistin is administered as an inactive prodrug, colistin methanesulfonate (CMS); however, differences between the intrapulmonary concentrations of the active moiety as a function of the route of administration in critically ill patients have not been precisely documented. In this study, CMS and colistin concentrations were measured on two separate occasions within the plasma and epithelial lining fluid (ELF) of critically ill patients ( n = 12) who had received 2 million international units (MIU) of CMS by aerosol delivery and then intravenous administration. The pharmacokinetic analysis was conducted using a population approach and completed by pharmacokinetic-pharmacodynamic (PK-PD) modeling and simulations. The ELF colistin concentrations varied considerably (9.53 to 1,137 mg/liter), but they were much higher than those in plasma (0.15 to 0.73 mg/liter) after aerosol delivery but not after intravenous administration of CMS. Following CMS aerosol delivery, typically, 9\% of the CMS dose reached the ELF, and only 1.4\% was presystemically converted into colistin. PK-PD analysis concluded that there was much higher antimicrobial efficacy after CMS aerosol delivery than after intravenous administration. These new data seem to support the use of aerosol delivery of CMS for the treatment of pulmonary infections in critical care patients.},
langid = {english},
annotation = {ZSCC: NoCitationData[s0]},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Boisson/boisson_2014_comparison_of_intrapulmonary_and_systemic_pharmacokinetics_of_colistin.pdf}
}
@article{bonateEffectCollinearityParameter1999,
title = {The {{Effect}} of {{Collinearity}} on {{Parameter Estimates}} in {{Nonlinear Mixed Effect Models}}},
author = {Bonate, Peter L.},
year = {1999},
month = may,
journal = {Pharm Res},
volume = {16},
number = {5},
pages = {709--717},
issn = {07248741},
doi = {10.1023/A:1018828709196},
urldate = {2024-12-06},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/Bonate/bonate_1999_the-effect-of-collinearity-on-parameter-estimates.pdf}
}
@book{bonatePharmacokineticpharmacodynamicModelingSimulation2011,
title = {Pharmacokinetic-Pharmacodynamic Modeling and Simulation},
author = {Bonate, Peter L.},
year = {2011},
edition = {2. ed},
publisher = {Springer},
address = {New York},
isbn = {978-1-4419-9484-4 978-1-4419-9485-1},
langid = {english},
annotation = {OCLC: 748651873},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bonate/bonate_2011_pharmacokinetic-pharmacodynamic_modeling_and_simulation.pdf}
}
@book{bonatePharmacokineticsDrugDevelopment2016,
title = {Pharmacokinetics in {{Drug Development}}: {{Problems}} and {{Challenges}} in {{Oncology}}, {{Volume}} 4},
shorttitle = {Pharmacokinetics in {{Drug Development}}},
editor = {Bonate, Peter L. and Howard, Danny R.},
year = {2016},
publisher = {Springer International Publishing},
address = {Cham},
doi = {10.1007/978-3-319-39053-6},
urldate = {2023-12-24},
isbn = {978-3-319-39051-2 978-3-319-39053-6},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bonate/bonate_2016_pharmacokinetics_in_drug_development_-_problems_and_challenges_in_oncology,.pdf}
}
@article{bonateRecommendedReadingPopulation2005,
title = {Recommended Reading in Population Pharmacokinetic Pharmacodynamics},
author = {Bonate, Peter L.},
year = {2005},
month = jun,
journal = {AAPS J},
volume = {7},
number = {2},
pages = {E363-E373},
issn = {1550-7416},
doi = {10.1208/aapsj070237},
urldate = {2024-03-23},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bonate/bonate_2005_recommended_reading_in_population_pharmacokinetic_pharmacodynamics.pdf}
}
@article{bonateTrainingNextGeneration2023,
title = {Training the next Generation of Pharmacometric Modelers: A Multisector Perspective},
shorttitle = {Training the next Generation of Pharmacometric Modelers},
author = {Bonate, Peter L. and Barrett, Jeffrey S. and {Ait-Oudhia}, Sihem and Brundage, Richard and Corrigan, Brian and Duffull, Stephen and Gastonguay, Marc and Karlsson, Mats O. and Kijima, Shinichi and Krause, Andreas and Lovern, Mark and Riggs, Matthew M. and Neely, Michael and Ouellet, Daniele and Plan, Elodie L. and Rao, Gauri G. and Standing, Joseph and Wilkins, Justin and Zhu, Hao},
year = {2023},
month = aug,
journal = {J Pharmacokinet Pharmacodyn},
issn = {1567-567X, 1573-8744},
doi = {10.1007/s10928-023-09878-4},
urldate = {2023-09-24},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bonate/bonate_2023_training_the_next_generation_of_pharmacometric_modelers_-_a_multisector.pdf}
}
@article{bouchardComparisonMethodsEstimating2010,
title = {Comparison of Methods for Estimating Glomerular Filtration Rate in Critically Ill Patients with Acute Kidney Injury},
author = {Bouchard, J. and Macedo, E. and Soroko, S. and Chertow, G. M. and Himmelfarb, J. and Ikizler, T. A. and Paganini, E. P. and Mehta, R. L. and {DM, FACP, FASN. Program to Improve Care in Acute Renal Disease (PICARD)}},
year = {2010},
month = jan,
journal = {Nephrology Dialysis Transplantation},
volume = {25},
number = {1},
pages = {102--107},
issn = {0931-0509, 1460-2385},
doi = {10.1093/ndt/gfp392},
urldate = {2023-03-01},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Bouchard/bouchard_2010_comparison_of_methods_for_estimating_glomerular_filtration_rate_in_critically.pdf}
}
@article{boucher1020ProgressDevelopment2013,
title = {10 x '20 {{Progress--Development}} of {{New Drugs Active Against Gram-Negative Bacilli}}: {{An Update From}} the {{Infectious Diseases Society}} of {{America}}},
shorttitle = {10 x '20 {{Progress--Development}} of {{New Drugs Active Against Gram-Negative Bacilli}}},
author = {Boucher, H. W. and Talbot, G. H. and Benjamin, D. K. and Bradley, J. and Guidos, R. J. and Jones, R. N. and Murray, B. E. and Bonomo, R. A. and Gilbert, D. and {for the Infectious Diseases Society of America}},
year = {2013},
month = jun,
journal = {Clin Infect Dis},
volume = {56},
number = {12},
pages = {1685--1694},
issn = {1058-4838, 1537-6591},
doi = {10.1093/cid/cit152},
urldate = {2020-10-28},
langid = {english},
annotation = {ZSCC: NoCitationData[s0]},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/Boucher/boucher-et-al_2013_10-x-'20-progress--development-of-new-drugs-active.pdf}
}
@article{boucherBadBugsNo2009,
title = {Bad {{Bugs}}, {{No Drugs}}: {{No ESKAPE}}! {{An Update}} from the {{Infectious Diseases Society}} of {{America}}},
shorttitle = {Bad {{Bugs}}, {{No Drugs}}},
author = {Boucher, Helen~W. and Talbot, George~H. and Bradley, John~S. and Edwards, John~E. and Gilbert, David and Rice, Louis~B. and Scheld, Michael and Spellberg, Brad and Bartlett, John},
year = {2009},
month = jan,
journal = {Clin Infect Dis},
volume = {48},
number = {1},
pages = {1--12},
issn = {1058-4838, 1537-6591},
doi = {10.1086/595011},
urldate = {2019-01-31},
langid = {english},
keywords = {ab_pipeline,Done},
annotation = {ZSCC: 0004557},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/Boucher/boucher_2009_bad_bugs,_no_drugs_-_no_eskape!_an_update_from_the_infectious_diseases_society.pdf}
}
@article{boucherReplyPaulLeibovici2018,
title = {Reply to {{Paul}} and {{Leibovici}}},
author = {Boucher, Helen W and Ambrose, Paul G and Chambers, Henry F and Ebright, Richard H and Jezek, Amanda and Murray, Barbara E and Ostrowsky, Belinda and Rex, John H},
year = {2018},
month = jan,
journal = {J Infect Dis},
volume = {217},
number = {3},
pages = {509--510},
issn = {0022-1899, 1537-6613},
doi = {10.1093/infdis/jix537},
urldate = {2019-03-10},
langid = {english},
keywords = {Done},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/Boucher/boucher_2018_reply_to_paul_and_leibovici.pdf}
}
@article{boucherWhitePaperDeveloping2017,
title = {White {{Paper}}: {{Developing Antimicrobial Drugs}} for {{Resistant Pathogens}}, {{Narrow-Spectrum Indications}}, and {{Unmet Needs}}},
shorttitle = {White {{Paper}}},
author = {Boucher, Helen W and Ambrose, Paul G and Chambers, H F and Ebright, Richard H and Jezek, Amanda and Murray, Barbara E and Newland, Jason G and Ostrowsky, Belinda and Rex, John H and {on behalf of the Infectious Diseases Society of America}},
year = {2017},
month = jul,
journal = {J Infect Dis},
volume = {216},
number = {2},
pages = {228--236},
issn = {0022-1899, 1537-6613},
doi = {10.1093/infdis/jix211},
urldate = {2019-01-31},
langid = {english},
keywords = {Done},
annotation = {ZSCC: 0000057},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/Boucher/boucher_2017_white_paper_-_developing_antimicrobial_drugs_for_resistant_pathogens,.pdf}
}
@article{boxenbaumInterspeciesScalingAllometry1982,
title = {Interspecies Scaling, Allometry, Physiological Time, and the Ground Plan of Pharmacokinetics},
author = {Boxenbaum, Harold},
year = {1982},
month = apr,
journal = {J Pharmacokinet Biopharm},
volume = {10},
number = {2},
pages = {201--227},
issn = {0090-466X},
doi = {10.1007/BF01062336},
urldate = {2024-12-06},
copyright = {http://www.springer.com/tdm},
langid = {english},
file = {/Users/vrognas/Documents/2_projects/3_professional/phd/documents/literature/zotero/Boxenbaum/boxenbaum_1982_interspecies-scaling,-allometry,-physiological-tim.pdf}
}
@article{brandAuthorshipAttributionContribution2015,
title = {Beyond Authorship: Attribution, Contribution, Collaboration, and Credit},
shorttitle = {Beyond Authorship},
author = {Brand, Amy and Allen, Liz and Altman, Micah and Hlava, Marjorie and Scott, Jo},
year = {2015},
month = apr,
journal = {Learned Publishing},
volume = {28},
number = {2},
pages = {151--155},
issn = {09531513, 17414857},
doi = {10.1087/20150211},
urldate = {2019-03-13},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Brand/brand_2015_beyond_authorship_-_attribution,_contribution,_collaboration,_and_credit.pdf}
}
@article{braunerDistinguishingResistanceTolerance2016,
title = {Distinguishing between Resistance, Tolerance and Persistence to Antibiotic Treatment},
author = {Brauner, Asher and Fridman, Ofer and Gefen, Orit and Balaban, Nathalie Q.},
year = {2016},
month = may,
journal = {Nat Rev Microbiol},
volume = {14},
number = {5},
pages = {320--330},
issn = {1740-1526, 1740-1534},
doi = {10.1038/nrmicro.2016.34},
urldate = {2020-04-19},
langid = {english},
file = {/Users/vrognas/Library/Mobile Documents/com~apple~CloudDocs/PhD/documents/literature/zotero/AUTH/Brauner/brauner_2016_distinguishing_between_resistance,_tolerance_and_persistence_to_antibiotic.pdf}
}
@article{brendelMetricsExternalModel2006,