Johannes Wirth

Hof University of Applied Sciences

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Co-Authors

Anna Werbik

Jan Christian Mücke

Andreas Muth

Sahlgrenska University Hospital

Oliver Precht

René Peinl

Hof University of Applied Sciences

Franziska Herrmann

Boehringer Ingelheim (Germany)

Matthias Meier

Siemens Healthcare (Germany)

James P. Garnett

Newcastle University

Victoria Schroeder

Boehringer Ingelheim (Germany)

Matthew J. Thomas

Boehringer Ingelheim (Germany)

Cooperative Institutions

Friedrich-Alexander-Universität Erlangen-Nürnberg

Boehringer Ingelheim (Germany)

Technical University of Munich

Helmholtz Zentrum München

RWTH Aachen University

Boehringer Ingelheim (Australia)

German Centre for Cardiovascular Research

Klinikum rechts der Isar

Heidelberg University

Duke University

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Crystal structures of ternary complexes of archaeal B-family DNA polymerases

PLoS ONE (2017)

H.M. Kropp Karin Betz Johannes Wirth Kay Diederichs Andreas Marx

Archaeal B-family polymerases drive biotechnology by accepting a wide substrate range of chemically modified nucleotides. By now no structural data for archaeal B-family DNA polymerases in a closed, ternary complex are available, which would be the basis for developing next generation nucleotides. We present the ternary crystal structures of KOD and 9°N DNA polymerases complexed with DNA and the incoming dATP. The structures reveal a third metal ion in the active site, which was so far only observed for the eukaryotic B-family DNA polymerase δ and no other B-family DNA polymerase. The structures reveal a wide inner channel and numerous interactions with the template strand that provide space for modifications within the enzyme and may account for the high processivity, respectively. The crystal structures provide insights into the superiority over other DNA polymerases concerning the acceptance of modified nucleotides.

Processivity

DNA clamp

DNA polymerase II

Ternary complex

DNA polymerase I

10.1371/journal.pone.0188005

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Citations (45)

Crystal structure of lactate dehydrogenase from Eimeria maxima with NADH and oxamate

Johannes Wirth Cheng‐Yuan Xu Douglas L. Theobald

L-Lactate dehydrogenase

Eimeria maxima

10.2210/pdb6ct6/pdb

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Citations (0)

Automatic Speech Recognition in German: A Detailed Error Analysis

Johannes Wirth René Peinl

The amount of freely available systems for automatic speech recognition (ASR) based on neural networks is growing steadily, with equally increasingly reliable predictions. However, the evaluation of trained models is typically exclusively based on statistical metrics such as WER or CER, which do not provide any insight into the nature or impact of the errors produced when predicting transcripts from speech input. This work presents a selection of ASR model architectures that are pretrained on the German language and evaluates them on a benchmark of diverse test datasets. It identifies cross-architectural prediction errors, classifies those into categories and traces the sources of errors per category back into training data as well as other sources. Finally, it discusses solutions in order to create qualitatively better training datasets and more robust ASR systems.

Benchmark (surveying)

Training set

10.1109/coins54846.2022.9854978

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Citations (2)

8 Konzernsimulation und Konzernplanung

Schäffer-Poeschel eBooks (2021)

Johannes Wirth Andreas Muth Oliver Precht Anna Werbik Jan Christian Mücke

10.34156/9783791053790-443

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Exploiting High-Bandwidth Memory for FPGA-Acceleration of Inference on Sum-Product Networks

2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) (2022)

Lukas M. Weber Johannes Wirth Lukas Sommer Andreas Koch

Due to the memory wall becoming increasingly problematic in high-performance computing, there is a steady push to improve memory architectures, mainly focusing on better bandwidth as well as latency. One of the results of this push is the development of High-Bandwidth Memory (HBM) which is an alternative to the regular DRAM typically used by accelerator-cards. This work adapts an existing accelerator architecture for inference on Sum-Product Networks (SPN) to exploit the HBM present on more recent high-performance FPGA-accelerator cards. The evaluation shows that the use of HBM enables almost linear scaling of the performance due to the embarrassingly parallel nature of batch-wise SPN inference. It is also shown that the only hindrance to this scaling is the limited bandwidth available for data-transfers between host and FPGA. Even with this bottleneck, the prior FPGA-based implementation is outperformed by up to 1.50x (geo.-mean 1.29x). Similarly, the CPU and GPU baselines are outperformed by up to 2.4x (geo.-mean 1.6x) and 8.4x (geo.-mean 6.9x) respectively. Based on the evaluation, the scaling potential of HBM-based FPGA-accelerators is explored to give an outlook on what is to come with future generations of PCIe-based interfaces.

Dram

Memory bandwidth

10.1109/ipdpsw55747.2022.00028

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5 Prozess der Konsolidierungsvorbereitung

Schäffer-Poeschel eBooks (2021)

Johannes Wirth Andreas Muth Oliver Precht Anna Werbik Jan Christian Mücke

10.34156/9783791053790-135

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Structural Evolution of GaO_x-Shell and Intermetallic Phases in Ga–Pt Supported Catalytically Active Liquid Metal Solutions

The Journal of Physical Chemistry Letters (2024)

Shaun A. Carl Johannes Will Nnamdi Madubuko Alexander Götz Thomas Przybilla

We present a comprehensive scale-bridging characterization approach for supported catalytically active liquid metal solutions (SCALMS) which combines lab-based X-ray microscopy, nano X-ray computed tomography (nano-CT), and correlative analytical transmission electron microscopy. SCALMS catalysts consist of low-melting alloy particles and have demonstrated high catalytic activity, selectivity, and long-term stability in propane dehydrogenation (PDH). We established an identical-location nano-CT workflow which allows us to reveal site-specific changes of Ga-Pt SCALMS before and after PDH. These observations are complemented by analytical transmission electron microscopy investigations providing information on the structure, chemical composition, and phase distribution of individual SCALMS particles. Key findings of this combined microscopic approach include (i) structural evolution of the SCALMS particles' GaO

Liquid metal

10.1021/acs.jpclett.3c03494

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Citations (2)

A polycomb-independent role of EZH2 in TGFβ1-damaged epithelium triggers a fibrotic cascade with mesenchymal cells

bioRxiv (Cold Spring Harbor Laboratory) (2020)

Huy Quang Le Matthew Alexander Hill Ines Kollak Wioletta Skrońska-Wąsek Victoria Schroeder

Abstract To restore organ homeostasis, a myriad of cell types need to activate rapid and transient programs to adjust cell fate decisions and elicit a collective behaviour. Characterisation of such programs are imperative to elucidate an organ’s regenerative capacity and its aberrant repair in disease. By modelling epithelial-mesenchymal crosstalk, we provide direct evidence for transforming growth factor β1 (TGFβ1)-damaged epithelium initiating a bi-directional fibrotic cascade with the mesenchyme. Strikingly, TGFβ1-damaged epithelia facilitates the release of Enhancer of Zester Homolog 2 (EZH2) from Polycomb Repressive Complex 2 (PRC2) to establish a novel fibrotic transcriptional complex of EZH2, RNA-polymerase II (POL2) and nuclear actin. Perturbing this complex by disrupting epithelial EZH2 or actomyosin remodelling abrogates the fibrotic crosstalk. The liberation of EZH2 from PRC2 is accompanied by an EZH2-EZH1 switch to preserve global H3K27me3 occupancy. Our results reveal an important non-canonical function of EZH2, paving the way for therapeutic interventions in fibrotic disease.

PRC2

Crosstalk

Cell fate determination

Mesenchyme

10.1101/2020.07.29.225300

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Citations (2)

Crystal structure of ancestral apicomplexan lactate dehydrogenase with sulfate and NADH4.

Douglas L. Theobald Johannes Wirth Scott Classen N. Perlmutter

L-Lactate dehydrogenase

10.2210/pdb6vdj/pdb

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