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Article ; Online: A Simple-to-Use R Package for Mimicking Study Data by Simulations.

Koliopanos, Giorgos / Ojeda, Francisco / Ziegler, Andreas

2023 Volume 62, Issue 3-04, Page(s) 119–129

Abstract: ... to introduce the simple-to-use R package Mock Data Generation (modgo) that may be used for simulating data ... modgo's flexibility was demonstrated on several expansions.: Conclusion: The R package modgo is useful ...

Abstract	Background: Data protection policies might prohibit the transfer of existing study data to interested research groups. To overcome legal restrictions, simulated data can be transferred that mimic the structure but are different from the existing study data. Objectives: The aim of this work is to introduce the simple-to-use R package Mock Data Generation (modgo) that may be used for simulating data from existing study data for continuous, ordinal categorical, and dichotomous variables. Methods: The core is to combine rank inverse normal transformation with the calculation of a correlation matrix for all variables. Data can then be simulated from a multivariate normal and transferred back to the original scale of the variables. Unique features of modgo are that it allows to change the correlation between variables, to perform perturbation analysis, to handle multicenter data, and to change inclusion/exclusion criteria by selecting specific values of one or a set of variables. Simulation studies on real data demonstrate the validity and flexibility of modgo. Results: modgo mimicked the structure of the original study data. Results of modgo were similar with those from two other existing packages in standard simulation scenarios. modgo's flexibility was demonstrated on several expansions. Conclusion: The R package modgo is useful when existing study data may not be shared. Its perturbation expansion permits to simulate truly anonymized subjects. The expansion to multicenter studies can be used for validating prediction models. Additional expansions can support the unraveling of associations even in large study data and can be useful in power calculations.
MeSH term(s)	Computer Simulation ; Computer Security
Language	English
Publishing date	2023-03-07
Publishing country	Germany
Document type	Journal Article
ZDB-ID	3500-2
ISSN	2511-705X ; 0026-1270
ISSN (online)	2511-705X
ISSN	0026-1270
DOI	10.1055/a-2048-7692
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Article: A Simple-to-Use R Package for Mimicking Study Data by Simulations

Koliopanos, Giorgos / Ojeda, Francisco / Ziegler, Andreas

Methods of Information in Medicine

2023 Volume 62, Issue 03/04, Page(s) 119–129

Abstract	Background: Data protection policies might prohibit the transfer of existing study data to interested research groups. To overcome legal restrictions, simulated data can be transferred that mimic the structure but are different from the existing study data. Objectives: The aim of this work is to introduce the simple-to-use R package Mock Data Generation (modgo) that may be used for simulating data from existing study data for continuous, ordinal categorical, and dichotomous variables. Methods: The core is to combine rank inverse normal transformation with the calculation of a correlation matrix for all variables. Data can then be simulated from a multivariate normal and transferred back to the original scale of the variables. Unique features of modgo are that it allows to change the correlation between variables, to perform perturbation analysis, to handle multicenter data, and to change inclusion/exclusion criteria by selecting specific values of one or a set of variables. Simulation studies on real data demonstrate the validity and flexibility of modgo. Results: modgo mimicked the structure of the original study data. Results of modgo were similar with those from two other existing packages in standard simulation scenarios. modgo's flexibility was demonstrated on several expansions. Conclusion: The R package modgo is useful when existing study data may not be shared. Its perturbation expansion permits to simulate truly anonymized subjects. The expansion to multicenter studies can be used for validating prediction models. Additional expansions can support the unraveling of associations even in large study data and can be useful in power calculations.
Keywords	data privacy ; perturbation analysis ; statistical disclosure control ; synthetic data ; validation study
Language	English
Publishing date	2023-03-07
Publisher	Georg Thieme Verlag KG
Publishing place	Stuttgart ; New York
Document type	Article
ZDB-ID	3500-2
ISSN	2511-705X ; 0026-1270
ISSN (online)	2511-705X
ISSN	0026-1270
DOI	10.1055/a-2048-7692
Database	Thieme publisher's database

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Article ; Online: Affordable Prices Without Threatening the Oncological R&D Pipeline-An Economic Experiment on Transparency in Price Negotiations.

Franzen, Nora / Ziegler, Andreas / Romagnoli, Giorgia / Retèl, Valesca P / Offerman, Theo J S / van Harten, Wim H

Cancer research communications

2022 Volume 2, Issue 1, Page(s) 49–57

Abstract: ... to be affordable while sufficiently incentivizing research and development (R&D) investments. A proposed ... solution is increased transparency. Proponents argue that price and R&D cost confidentiality are drivers ... discounts which make treatments affordable; moreover, pharmaceutical companies argue that R&D investments ...

Abstract	The high prices of innovative medicines endanger access to care worldwide. Sustainable prices need to be affordable while sufficiently incentivizing research and development (R&D) investments. A proposed solution is increased transparency. Proponents argue that price and R&D cost confidentiality are drivers of high prices. On the contrary, supporters of confidentiality claim that confidentiality enables targeted discounts which make treatments affordable; moreover, pharmaceutical companies argue that R&D investments would suffer with more transparency. Despite the political relevance, limited empirical evidence exists on the effects of transparency regulations. We contribute to fill this gap with an experiment where we replicate the EU pharmaceutical market in a laboratory setting. In a randomized controlled study, we analyzed how participants, 400 students located in four European countries, negotiated in the current system of
MeSH term(s)	Humans ; Drug Costs ; Negotiating ; Costs and Cost Analysis ; Research ; Pharmaceutical Preparations
Chemical Substances	Pharmaceutical Preparations
Language	English
Publishing date	2022-01-27
Publishing country	United States
Document type	Randomized Controlled Trial ; Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2767-9764
ISSN (online)	2767-9764
DOI	10.1158/2767-9764.CRC-21-0031
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Article: <i>firebehavioR</i>: An R Package for Fire Behavior and Danger Analysis

Ziegler, Justin P / Hoffman, Chad M / Mell, William

Fire. 2019 July 13, v. 2, no. 3

2019

Abstract: ... to the R programming language. We also highlight supporting data objects and functions to predict inputs ... using R, a free-and-open-source programming language, include freedom to adapt calculations to suit ...

Abstract	Wildland fire and ecological researchers use empirical and semi-empirical modeling systems to assess fire behavior and danger. This technical note describes the firebehavioR package, a porting of two fire behavior modeling systems, Crown Fire Initiation and Spread and a Rothermel-based framework, to the R programming language. We also highlight supporting data objects and functions to predict inputs required for fire behavior estimation. Last, this package contains functions for fifteen indices to express fire danger using weather and/or fuels observations. Specific advantages of predicting fire behavior using R, a free-and-open-source programming language, include freedom to adapt calculations to suit users’ needs, transparency of source code, and reduction of workflow inefficiencies, thereby aiding in sophisticated fire behavior analyses.
Keywords	computer software ; fire behavior ; fire hazard ; fuels (fire ecology) ; prediction ; semi-empirical models ; weather ; wildfires
Language	English
Dates of publication	2019-0713
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ISSN	2571-6255
DOI	10.3390/fire2030041
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: Data and R code for the paper The potential of future foods for sustainable and healthy diets

Parodi, Alejandro / Leip, Adrian / de Boer, Imke / Siegers, Petronella M. / Ziegler, Friederike / Temme, Liesbeth / Herrero, Mario / Tuomisto, Hanna / Valin, Hugo / van Middelaar, Corina / van Loon, Joop / van Zanten, Hannah

2021

Abstract: Contains data and R code for analysis and visualizations of the study The potential of future foods ...

Abstract	Contains data and R code for analysis and visualizations of the study The potential of future foods for sustainable and healthy diets
Keywords	Diets ; GHG ; LCA ; future foods ; land use ; livestock ; minerals ; protein ; seafood ; vitamins
Publisher	Wageningen University & Research
Publishing country	nl
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: High enantioselective Novozym 435-catalyzed esterification of (R,S)-flurbiprofen monitored with a chiral stationary phase.

Siódmiak, Tomasz / Mangelings, Debby / Vander Heyden, Yvan / Ziegler-Borowska, Marta / Marszałł, Michał Piotr

Applied biochemistry and biotechnology

2015 Volume 175, Issue 5, Page(s) 2769–2785

Abstract: ... in the enzymatic kinetic resolution of (R,S)-flurbiprofen by enantioselective esterification. Successful ... chromatographic separation with well-resolved peaks of (R)- and (S)-flurbiprofen and their esters was achieved ... The high values of enantiomeric ratio (E in the range of 51.3-90.5) of the esterification of (R,S ...

Abstract	Lipases form Candida rugosa and Candida antarctica were tested for their application in the enzymatic kinetic resolution of (R,S)-flurbiprofen by enantioselective esterification. Successful chromatographic separation with well-resolved peaks of (R)- and (S)-flurbiprofen and their esters was achieved in one run on chiral stationary phases by high-performance liquid chromatography (HPLC). In this study screening of enzymes was performed, and Novozym 435 was selected as an optimal catalyst for obtaining products with high enantiopurity. Additionally, the influence of organic solvents (dichloromethane, dichloroethane, dichloropropane, and methyl tert-butyl ether), primary alcohols (methanol, ethanol, n-propanol, and n-butanol), reaction time, and temperature on the enantiomeric ratio and conversion was tested. The high values of enantiomeric ratio (E in the range of 51.3-90.5) of the esterification of (R,S)-flurbiprofen were obtained for all tested alcohols using Novozym 435, which have a great significance in the field of biotechnological synthesis of drugs. The optimal temperature range for the performed reactions was from 37 to 45 °C. As a result of the optimization, (R)-flurbiprofen methyl ester was obtained with a high optical purity, eep = 96.3 %, after 96 h of incubation. The enantiomeric ratio of the reaction was E = 90.5 and conversion was C = 35.7 %.
MeSH term(s)	Biocatalysis ; Candida/chemistry ; Candida/enzymology ; Chromatography, High Pressure Liquid/instrumentation ; Enzymes, Immobilized ; Esterification ; Flurbiprofen/chemistry ; Flurbiprofen/metabolism ; Fungal Proteins/chemistry ; Fungal Proteins/metabolism ; Kinetics ; Lipase/chemistry ; Lipase/metabolism ; Stereoisomerism ; Substrate Specificity
Chemical Substances	Enzymes, Immobilized ; Fungal Proteins ; Flurbiprofen (5GRO578KLP) ; Novozyme 435 (EC 3.1.1.-) ; Lipase (EC 3.1.1.3)
Language	English
Publishing date	2015-01-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	392344-7
ISSN	1559-0291 ; 0273-2289
ISSN (online)	1559-0291
ISSN	0273-2289
DOI	10.1007/s12010-014-1455-4
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Conference proceedings: ATOMIC – Ein R-Paket zur automatisierten Beurteilung von Genotyp-Callings

Schillert, Arne / Ziegler, Andreas

2012 , Page(s) 12gmds129

Event/congress	57. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e.V. (GMDS); GMDS 2012; Braunschweig; Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie; 2012
Keywords	Medizin, Gesundheit ; Genomweite Assoziationsstudien ; Qualitätskontrolle
Publishing date	2012-09-13
Publisher	German Medical Science GMS Publishing House; Düsseldorf
Document type	Conference proceedings
DOI	10.3205/12gmds129
Database	German Medical Science

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Article: Synthese und Charakterisierung der Spezies R–C7H7Cr(CO)3 mit R = CH3COCH2-, CH3CO(CH3)CH-, CH3COCHCH(CH3)2– / Synthesis and Characterization of the Species R-C7H7Cr(CO)3 with R = CH3COCH2-, CH3CO(CH3)CH - , CH3COCHCH(CH3)2–

Zahedi, Farhad / Manfred L. Ziegler

Zeitschrift für Naturforschung B. 2014 June 2, v. 34, no. 7

2014

Abstract: The species R-C₇H₇Cr(CO)₃ (R = -CH₂COCH₃ , -CH(CH₃)COCH₃ , -CH(CH)CH₃)₂COCH₃) have been synthesized ...

Abstract	The species R-C₇H₇Cr(CO)₃ (R = -CH₂COCH₃ , -CH(CH₃)COCH₃ , -CH(CH)CH₃)₂COCH₃) have been synthesized by reaction of [η⁷-C₇H₇Cr(CO)₃][BF₄] with suitable ketones in the presence of bases like OH- and F- , suggesting a nucleophilic addition of the enolate ion to the cycloheptatrienyl ligand. ¹H NMR spectra revealed the CH₃-CO-CH(CH₃) group being bonded to the cycloheptatriene ligand via the a-carbon atom of the ethyl group
Keywords	chemical reactions ; ketones ; ligands ; moieties ; nuclear magnetic resonance spectroscopy ; synthesis
Language	English
Dates of publication	2014-0602
Size	p. 918-920.
Publishing place	Verlag der Zeitschrift für Naturforschung
Document type	Article
ISSN	1865-7117
DOI	10.1515/znb-1979-0707
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Randomized controlled trial comparing highly purified (HP-hCG) and recombinant hCG (r-hCG) for triggering ovulation in ART.

Bellavia, Marina / de Geyter, Christian / Streuli, Isabelle / Ibecheole, Victoria / Birkhäuser, Martin H / Cometti, Barbara P S / de Ziegler, Dominique

Gynecological endocrinology : the official journal of the International Society of Gynecological Endocrinology

2013 Volume 29, Issue 2, Page(s) 93–97

Abstract: ... Choriogonadotrophin (HP-hCG) and recombinant hCG (r-hCG) both administered subcutaneously for triggering ovulation ... of retrieved oocytes was not inferior when HP-hCG was used as compared to r-hCG: the mean number was 13.3 (6.8) in HP ... hCG and 12.5 (5.8) in the r-hCG group (p = 0.49) with a 95% CI (-1.34, 2.77). Regarding the secondary ...

Abstract	Background: A randomized controlled trial (RCT) comparing highly purified human Choriogonadotrophin (HP-hCG) and recombinant hCG (r-hCG) both administered subcutaneously for triggering ovulation in controlled ovarian stimulation (COS) for Assisted Reproductive Technology (ART). Methods: Multi-centre (n = 4), prospective, controlled, randomized, non-inferiority, parallel group, investigator blind design, including 147 patients. The trial was registered with www.clinicaltrials.gov, using the identifier: NCT00335569. The primary endpoint is the number of oocytes retrieved, while the secondary endpoints include embryo implantation, pregnancy and delivery rates as well as safety parameters. Results: The number of retrieved oocytes was not inferior when HP-hCG was used as compared to r-hCG: the mean number was 13.3 (6.8) in HP-hCG and 12.5 (5.8) in the r-hCG group (p = 0.49) with a 95% CI (-1.34, 2.77). Regarding the secondary outcomes, there were also no differences in fertilization rate at 57.3% (467/815) vs. 61.3% (482/787) (p = 0.11), the number of embryos available for transfer and cryopreservation (2PN stage) and implantation, pregnancy and delivery rates. Furthermore, there were no differences in the number and type of adverse events reported. HP-hCG was therefore not inferior to r-hCG. Conclusions: HP-hCG and r-hCG are equally efficient and safe for triggering ovulation in ART and, both being administered subcutaneously, equally practical and well tolerated by patients.
MeSH term(s)	Adult ; Birth Rate ; Chorionic Gonadotropin/adverse effects ; Chorionic Gonadotropin/chemistry ; Chorionic Gonadotropin/genetics ; Chorionic Gonadotropin/pharmacology ; Embryo Implantation ; Family Characteristics ; Female ; Fertility Agents, Female/administration & dosage ; Fertility Agents, Female/adverse effects ; Fertility Agents, Female/chemistry ; Fertility Agents, Female/pharmacology ; Fertilization in Vitro ; Humans ; Infertility, Female/etiology ; Infertility, Female/therapy ; Infertility, Male/physiopathology ; Injections, Subcutaneous ; Male ; Oocyte Retrieval ; Ovary/drug effects ; Ovulation Induction/methods ; Pregnancy ; Pregnancy Rate ; Recombinant Proteins/administration & dosage ; Recombinant Proteins/adverse effects ; Recombinant Proteins/pharmacology ; Single-Blind Method ; Sperm Injections, Intracytoplasmic ; Switzerland/epidemiology
Chemical Substances	Chorionic Gonadotropin ; Fertility Agents, Female ; Recombinant Proteins
Language	English
Publishing date	2013-02
Publishing country	England
Document type	Comparative Study ; Journal Article ; Multicenter Study ; Randomized Controlled Trial ; Research Support, Non-U.S. Gov't
ZDB-ID	639237-4
ISSN	1473-0766 ; 0951-3590
ISSN (online)	1473-0766
ISSN	0951-3590
DOI	10.3109/09513590.2012.730577
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Article: Enantioselective acetylation of (R,S)-atenolol: The use of Candida rugosa lipases immobilized onto magnetic chitosan nanoparticles in enzyme-catalyzed biotransformation

Sikora, Adam / Agata Tarczykowska / Dorota Chełminiak-Dudkiewicz / Marta Ziegler-Borowska / Michał Piotr Marszałł / Tomasz Siódmiak / Wiktor Dariusz Sroka

Journal of molecular catalysis. 2016 Dec., v. 134

2016

Abstract: ... for the direct resolution of (R,S)-atenolol. The used magnetic enzyme carriers possess on their surface new ...

Abstract	This paper describes the enzyme immobilization protocol as well as the enzymatic method for the direct resolution of (R,S)-atenolol. The used magnetic enzyme carriers possess on their surface new-synthetized chitosan derivatives with free amine groups distanced by ethyl or butyl chain. Additionally the catalytic activity of two types of commercially available lipases from Candida rugosa immobilized onto two different magnetic nanoparticles were compared. The highest values of enantioselectivity (E=66.9), enantiomeric excess of product (eep=94.1%) and conversion (c=41.84%) were obtained by using lipase from Candida rugosa OF immobilized onto Fe3O4-CS-EtNH2. The study confirmed that even after 5 reaction cycles the immobilized lipase maintain its high catalytic activity.
Keywords	acetylation ; biotransformation ; Candida rugosa ; carboxylic ester hydrolases ; catalytic activity ; chitosan ; enantiomers ; enzymatic treatment ; immobilized enzymes ; nanoparticles
Language	English
Dates of publication	2016-12
Size	p. 43-50.
Publishing place	Elsevier B.V.
Document type	Article
ISSN	1381-1177
DOI	10.1016/j.molcatb.2016.09.017
Database	NAL-Catalogue (AGRICOLA)

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