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Book ; Thesis: Der DICOM-Standard in der Kardiologie als Basis für die Interoperabilität medizinischer Bildsysteme und die Entwicklung eines vernetzten Bildarchivs

Becker, Tim

(Berichte aus der medizinischen Informatik und Bioinformatik)

2002

Author's details	Tim Becker
Series title	Berichte aus der medizinischen Informatik und Bioinformatik
Keywords	Kardiologie ; DICOM ; Archivsystem ; Bildbanksystem
Subject	Bilddatenbanksystem ; Elektronisches Archivierungssystem ; Archivierungssystem ; Cardiologie ; Cardiology
Language	German
Size	171 S. : Ill., graph. Darst., 21 cm
Publisher	Shaker
Publishing place	Aachen
Publishing country	Germany
Document type	Book ; Thesis
Thesis / German Habilitation thesis	Kiel, Univ., Diss., 2002
HBZ-ID	HT013935449
ISBN	3-8322-0348-6 ; 978-3-8322-0348-1
Database	Catalogue ZB MED Medicine, Health

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Article: Advanced In Vivo Prediction by Introducing Biphasic Dissolution Data into PBPK Models.

Denninger, Alexander / Becker, Tim / Westedt, Ulrich / Wagner, Karl G

Pharmaceutics

2023 Volume 15, Issue 7

Abstract: Coupling biorelevant in vitro dissolution with in silico physiological-based pharmacokinetic (PBPK) tools represents a promising method to describe and predict the in vivo performance of drug candidates in formulation development including non-passive ... ...

Abstract	Coupling biorelevant in vitro dissolution with in silico physiological-based pharmacokinetic (PBPK) tools represents a promising method to describe and predict the in vivo performance of drug candidates in formulation development including non-passive transport, prodrug activation, and first-pass metabolism. The objective of the present study was to assess the predictability of human pharmacokinetics by using biphasic dissolution results obtained with the previously established BiPHa+ assay and PBPK tools. For six commercial drug products, formulated by different enabling technologies, the respective organic partitioning profiles were processed with two PBPK in silico modeling tools, namely PK-Sim and GastroPlus
Language	English
Publishing date	2023-07-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527217-2
ISSN	1999-4923
ISSN	1999-4923
DOI	10.3390/pharmaceutics15071978
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Using item response theory to appraise key feature examinations for clinical reasoning.

Zegota, Simon / Becker, Tim / Hagmayer, York / Raupach, Tobias

Medical teacher

2022 Volume 44, Issue 11, Page(s) 1253–1259

Abstract: Background: Validation of examinations is usually based on classical test theory. In this study, we analysed a key feature examination according to item response theory and compared the results with those of a classical test theory approach.: Methods!# ...

Abstract	Background: Validation of examinations is usually based on classical test theory. In this study, we analysed a key feature examination according to item response theory and compared the results with those of a classical test theory approach. Methods: Over the course of five years, 805 fourth-year undergraduate students took a key feature examination on general medicine consisting of 30 items. Analyses were run according to a classical test theory approach as well as using item response theory. Classical test theory analyses are reported as item difficulty, discriminatory power, and Cronbach's alpha while item response theory analyses are presented as item characteristics curves, item information curves and a test information function. Results: According to classical test theory findings, the examination was labelled as easy. Analyses according to item response theory more specifically indicated that the examination was most suited to identify struggling students. Furthermore, the analysis allowed for adapting the examination to specific ability ranges by removing items, as well as comparing multiple samples with varying ability ranges. Conclusions: Item response theory analyses revealed results not yielded by classical test theory. Thus, both approaches should be routinely combined to increase the information yield of examination data.
MeSH term(s)	Humans ; Educational Measurement/methods ; Clinical Reasoning ; Psychometrics
Language	English
Publishing date	2022-06-02
Publishing country	England
Document type	Journal Article
ZDB-ID	424426-6
ISSN	1466-187X ; 0142-159X
ISSN (online)	1466-187X
ISSN	0142-159X
DOI	10.1080/0142159X.2022.2077716
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Discovery of novel eGFR-associated multiple independent signals using a quasi-adaptive method.

Ghasemi, Sahar / Becker, Tim / Grabe, Hans J / Teumer, Alexander

Frontiers in genetics

2022 Volume 13, Page(s) 997302

Abstract: A decreased estimated glomerular filtration rate (eGFR) leading to chronic kidney disease is a significant public health problem. Kidney function is a heritable trait, and recent application of genome-wide association studies (GWAS) successfully ... ...

Abstract	A decreased estimated glomerular filtration rate (eGFR) leading to chronic kidney disease is a significant public health problem. Kidney function is a heritable trait, and recent application of genome-wide association studies (GWAS) successfully identified multiple eGFR-associated genetic loci. To increase statistical power for detecting independent associations in GWAS loci, we improved our recently developed quasi-adaptive method estimating SNP-specific alpha levels for the conditional analysis, and applied it to the GWAS meta-analysis results of eGFR among 783,978 European-ancestry individuals. Among known eGFR loci, we revealed 19 new independent association signals that were subsequently replicated in the United Kingdom Biobank (n = 408,608). These associations have remained undetected by conditional analysis using the established conservative genome-wide significance level of 5 × 10
Language	English
Publishing date	2022-10-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.997302
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: PSEUDo: Interactive Pattern Search in Multivariate Time Series with Locality-Sensitive Hashing and Relevance Feedback.

Yu, Yuncong / Kruyff, Dylan / Jiao, Jiao / Becker, Tim / Behrisch, Michael

IEEE transactions on visualization and computer graphics

2022 Volume 29, Issue 1, Page(s) 33–42

Abstract: We present PSEUDo, a visual pattern retrieval tool for multivariate time series. It aims to overcome the uneconomic (re-)training problem accompanying deep learning-based methods. Very high-dimensional time series emerge on an unprecedented scale due to ... ...

Abstract	We present PSEUDo, a visual pattern retrieval tool for multivariate time series. It aims to overcome the uneconomic (re-)training problem accompanying deep learning-based methods. Very high-dimensional time series emerge on an unprecedented scale due to increasing sensor usage and data storage. Visual pattern search is one of the most frequent tasks on time series. Automatic pattern retrieval methods often suffer from inefficient training data, a lack of ground truth labels, and a discrepancy between the similarity perceived by the algorithm and required by the user or the task. Our proposal is based on the query-aware locality-sensitive hashing technique to create a representation of multivariate time series windows. It features sub-linear training and inference time with respect to data dimensions. This performance gain allows an instantaneous relevance-feedback-driven adaption to converge to users' similarity notion. We demonstrate PSEUDo's performance in terms of accuracy, speed, steerability, and usability through quantitative benchmarks with representative time series retrieval methods and a case study. We find that PSEUDo detects patterns in high-dimensional time series efficiently, improves the result with relevance feedback through feature selection, and allows an understandable as well as user-friendly retrieval process.
Language	English
Publishing date	2022-12-16
Publishing country	United States
Document type	Journal Article
ISSN	1941-0506
ISSN (online)	1941-0506
DOI	10.1109/TVCG.2022.3209431
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Assessment of significance of conditionally independent GWAS signals.

Ghasemi, Sahar / Teumer, Alexander / Wuttke, Matthias / Becker, Tim

Bioinformatics (Oxford, England)

2021 Volume 37, Issue 20, Page(s) 3521–3529

Abstract: Motivation: Multiple independently associated SNPs within a linkage disequilibrium region are a common phenomenon. Conditional analysis has been successful in identifying secondary signals. While conditional association tests are limited to specific ... ...

Abstract	Motivation: Multiple independently associated SNPs within a linkage disequilibrium region are a common phenomenon. Conditional analysis has been successful in identifying secondary signals. While conditional association tests are limited to specific genomic regions, they are benchmarked with genome-wide scale criterion, a conservative strategy. Within the weighted hypothesis testing framework, we developed a 'quasi-adaptive' method that uses the pairwise correlation (r2) and physical distance (d) from the index association to construct priority functions G =G(r2, d), which assign an SNP-specific α-threshold to each SNP. Family-wise error rate (FWER) and power of the approach were evaluated via simulations based on real GWAS data. We compared a series of different G-functions. Results: Simulations under the null hypothesis on 1,100 primary SNPs confirmed appropriate empirical FWER for all G-functions. A G-function with optimal r2 = 0.3 between index and secondary SNP which down-weighted SNPs at higher distance step-wise-strong and gave more emphasis on d than on r2 had overall best power. It also gave the best results in application to the real datasets. As a proof of concept, 'quasi-adaptive' method was applied to GWAS on free thyroxine (FT4), inflammatory bowel disease (IBD) and human height. Application of the algorithm revealed 5 secondary signals in our example GWAS on FT4, 5 secondary signals in case of the IBD and 19 secondary signals on human height, that would have gone undetected with the established genome-wide threshold (α=5×10-8). Availability and implementation: https://github.com/sghasemi64/Secondary-Signal. Supplementary information: Supplementary data are available at Bioinformatics online.
Language	English
Publishing date	2021-05-10
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btab332
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Matching by OS Prognostic Score to Construct External Controls in Lung Cancer Clinical Trials.

Loureiro, Hugo / Roller, Andreas / Schneider, Meike / Talavera-López, Carlos / Becker, Tim / Bauer-Mehren, Anna

Clinical pharmacology and therapeutics

2023 Volume 115, Issue 2, Page(s) 333–341

Abstract: External controls (eControls) leverage historical data to create non-randomized control arms. The lack of randomization can result in confounding between the experimental and eControl cohorts. To balance potentially confounding variables between the ... ...

Abstract	External controls (eControls) leverage historical data to create non-randomized control arms. The lack of randomization can result in confounding between the experimental and eControl cohorts. To balance potentially confounding variables between the cohorts, one of the proposed methods is to match on prognostic scores. Still, the performance of prognostic scores to construct eControls in oncology has not been analyzed yet. Using an electronic health record-derived de-identified database, we constructed eControls using one of three methods: ROPRO, a state-of-the-art prognostic score, or either a propensity score composed of five (5Vars) or 27 covariates (ROPROvars). We compared the performance of these methods in estimating the overall survival (OS) hazard ratio (HR) of 11 recent advanced non-small cell lung cancer. The ROPRO eControls had a lower OS HR error (median absolute deviation (MAD), 0.072, confidence interval (CI): 0.036-0.185), than the 5Vars (MAD 0.081, CI: 0.025-0.283) and ROPROvars eControls (MAD 0.087, CI: 0.054-0.383). Notably, the OS HR errors for all methods were even lower in the phase III studies. Moreover, the ROPRO eControl cohorts included, on average, more patients than the 5Vars (6.54%) and ROPROvars cohorts (11.7%). The eControls matched with the prognostic score reproduced the controls more reliably than propensity scores composed of the underlying variables. Additionally, prognostic scores could allow eControls to be built on many prognostic variables without a significant increase in the variability of the propensity score, which would decrease the number of matched patients.
MeSH term(s)	Humans ; Lung Neoplasms/drug therapy ; Carcinoma, Non-Small-Cell Lung/drug therapy ; Prognosis ; Proportional Hazards Models ; Propensity Score
Language	English
Publishing date	2023-11-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	123793-7
ISSN	1532-6535 ; 0009-9236
ISSN (online)	1532-6535
ISSN	0009-9236
DOI	10.1002/cpt.3109
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Article: Using item response theory to appraise key feature examinations for clinical reasoning

Zegota, Simon / Becker, Tim / Hagmayer, York / Raupach, Tobias

Medical Teacher

2022 Volume 44, Issue 11, Page(s) 1253–1259

Title translation	Verwendung der Item-Response-Theorie zur Beurteilung von Schlüsselmerkmalen bei Prüfungen zum klinischen Denken (DeepL)
Abstract	Background: Validation of examinations is usually based on classical test theory. In this study, we analysed a key feature examination according to item response theory and compared the results with those of a classical test theory approach. Methods: Over the course of five years, 805 fourth-year undergraduate students took a key feature examination on general medicine consisting of 30 items. Analyses were run according to a classical test theory approach as well as using item response theory. Classical test theory analyses are reported as item difficulty, discriminatory power, and Cronbach's alpha while item response theory analyses are presented as item characteristics curves, item information curves and a test information function. Results: According to classical test theory findings, the examination was labelled as easy. Analyses according to item response theory more specifically indicated that the examination was most suited to identify struggling students. Furthermore, the analysis allowed for adapting the examination to specific ability ranges by removing items, as well as comparing multiple samples with varying ability ranges. Conclusions: Item response theory analyses revealed results not yielded by classical test theory. Thus, both approaches should be routinely combined to increase the information yield of examination data.
Keywords	Berufliche Qualifikationsprüfung ; Classical Test Theory ; Item Response Theory ; Item-Response-Theorie ; Klassische Testtheorie ; Medical Education ; Medizinische Ausbildung ; Professional Examinations ; Testen ; Testing
Language	English
Document type	Article
ZDB-ID	424426-6
ISSN	1466-187X ; 0142-159X
ISSN (online)	1466-187X
ISSN	0142-159X
DOI	10.1080/0142159X.2022.2077716
Database	PSYNDEX

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Article ; Online: The exhaustive genomic scan approach, with an application to rare-variant association analysis.

Kanoungi, George / Nothnagel, Michael / Becker, Tim / Drichel, Dmitriy

European journal of human genetics : EJHG

2020 Volume 28, Issue 9, Page(s) 1283–1291

Abstract: Region-based genome-wide scans are usually performed by use of a priori chosen analysis regions. Such an approach will likely miss the region comprising the strongest signal and, thus, may result in increased type II error rates and decreased power. Here, ...

Abstract	Region-based genome-wide scans are usually performed by use of a priori chosen analysis regions. Such an approach will likely miss the region comprising the strongest signal and, thus, may result in increased type II error rates and decreased power. Here, we propose a genomic exhaustive scan approach that analyzes all possible subsequences and does not rely on a prior definition of the analysis regions. As a prime instance, we present a computationally ultraefficient implementation using the rare-variant collapsing test for phenotypic association, the genomic exhaustive collapsing scan (GECS). Our implementation allows for the identification of regions comprising the strongest signals in large, genome-wide rare-variant association studies while controlling the family-wise error rate via permutation. Application of GECS to two genomic data sets revealed several novel significantly associated regions for age-related macular degeneration and for schizophrenia. Our approach also offers a high potential to improve genome-wide scans for selection, methylation, and other analyses.
Keywords	covid19
Language	English
Publishing date	2020-05-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1141470-4
ISSN	1476-5438 ; 1018-4813
ISSN (online)	1476-5438
ISSN	1018-4813
DOI	10.1038/s41431-020-0639-3
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Article ; Online: Use of digital teaching resources and predictors of medical student performance during the pandemic: A prospective study.

Seer, Michelle / Kampsen, Charlotte / Becker, Tim / Hobert, Sebastian / Anders, Sven / Raupach, Tobias

PloS one

2022 Volume 17, Issue 5, Page(s) e0268331

Abstract: Background: The coronavirus pandemic has led to increased use of digital teaching formats in medical education. A number of studies have assessed student satisfaction with these resources. However, there is a lack of studies investigating changes in ... ...

Abstract	Background: The coronavirus pandemic has led to increased use of digital teaching formats in medical education. A number of studies have assessed student satisfaction with these resources. However, there is a lack of studies investigating changes in student performance following the switch from contact to virtual teaching. Specifically, there are no studies linking student use of digital resources to learning outcome and examining predictors of failure. Methods: Student performance before (winter term 2019/20: contact teaching) and during (summer term 2020: no contact teaching) the pandemic was compared prospectively in a cohort of 162 medical students enrolled in the clinical phase of a five-year undergraduate curriculum. Use of and performance in various digital resources (case-based teaching in a modified flipped classroom approach; formative key feature examinations of clinical reasoning; daily multiple choice quizzes) was recorded in summer 2020. Student scores in summative examinations were compared to examination scores in the previous term. Associations between student characteristics, resource use and summative examination results were used to identify predictors of performance. Results: Not all students made complete use of the digital learning resources provided. Timely completion of tasks was associated with superior performance compared to delayed completion. Female students scored significantly fewer points in formative key feature examinations and digital quizzes. Overall, higher rankings within the student cohort (according to summative exams) in winter term 2019/20 as well as male gender predicted summative exam performance in summer 2020. Scores achieved in the first formative key feature examination predicted summative end-of-module exam scores. Conclusions: The association between timely completion of tasks as well as early performance in a module and summative exams might help to identify students at risk and offering help early on. The unexpected gender difference requires further study to determine whether the shift to a digital-only curriculum disadvantages female students.
MeSH term(s)	Curriculum ; Educational Measurement/methods ; Female ; Humans ; Learning ; Male ; Pandemics ; Prospective Studies ; Students, Medical ; Teaching
Language	English
Publishing date	2022-05-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0268331
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