@phdthesis{Somody2023, author = {Somody, Joseph Christian Campbell}, title = {Leveraging deep learning for identification and structural determination of novel protein complexes from \(in\) \(situ\) electron cryotomography of \(Mycoplasma\) \(pneumoniae\)}, doi = {10.25972/OPUS-31344}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-313447}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2023}, abstract = {The holy grail of structural biology is to study a protein in situ, and this goal has been fast approaching since the resolution revolution and the achievement of atomic resolution. A cell's interior is not a dilute environment, and proteins have evolved to fold and function as needed in that environment; as such, an investigation of a cellular component should ideally include the full complexity of the cellular environment. Imaging whole cells in three dimensions using electron cryotomography is the best method to accomplish this goal, but it comes with a limitation on sample thickness and produces noisy data unamenable to direct analysis. This thesis establishes a novel workflow to systematically analyse whole-cell electron cryotomography data in three dimensions and to find and identify instances of protein complexes in the data to set up a determination of their structure and identity for success. Mycoplasma pneumoniae is a very small parasitic bacterium with fewer than 700 protein-coding genes, is thin enough and small enough to be imaged in large quantities by electron cryotomography, and can grow directly on the grids used for imaging, making it ideal for exploratory studies in structural proteomics. As part of the workflow, a methodology for training deep-learning-based particle-picking models is established. As a proof of principle, a dataset of whole-cell Mycoplasma pneumoniae tomograms is used with this workflow to characterize a novel membrane-associated complex observed in the data. Ultimately, 25431 such particles are picked from 353 tomograms and refined to a density map with a resolution of 11 {\AA}. Making good use of orthogonal datasets to filter search space and verify results, structures were predicted for candidate proteins and checked for suitable fit in the density map. In the end, with this approach, nine proteins were found to be part of the complex, which appears to be associated with chaperone activity and interact with translocon machinery. Visual proteomics refers to the ultimate potential of in situ electron cryotomography: the comprehensive interpretation of tomograms. The workflow presented here is demonstrated to help in reaching that potential.}, subject = {Kryoelektronenmikroskopie}, language = {en} } @article{StebaniBlaimerZableretal.2023, author = {Stebani, Jannik and Blaimer, Martin and Zabler, Simon and Neun, Tilmann and Pelt, Dani{\"e}l M. and Rak, Kristen}, title = {Towards fully automated inner ear analysis with deep-learning-based joint segmentation and landmark detection framework}, series = {Scientific Reports}, volume = {13}, journal = {Scientific Reports}, doi = {10.1038/s41598-023-45466-9}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-357411}, year = {2023}, abstract = {Automated analysis of the inner ear anatomy in radiological data instead of time-consuming manual assessment is a worthwhile goal that could facilitate preoperative planning and clinical research. We propose a framework encompassing joint semantic segmentation of the inner ear and anatomical landmark detection of helicotrema, oval and round window. A fully automated pipeline with a single, dual-headed volumetric 3D U-Net was implemented, trained and evaluated using manually labeled in-house datasets from cadaveric specimen (N = 43) and clinical practice (N = 9). The model robustness was further evaluated on three independent open-source datasets (N = 23 + 7 + 17 scans) consisting of cadaveric specimen scans. For the in-house datasets, Dice scores of 0.97 and 0.94, intersection-over-union scores of 0.94 and 0.89 and average Hausdorf distances of 0.065 and 0.14 voxel units were achieved. The landmark localization task was performed automatically with an average localization error of 3.3 and 5.2 voxel units. A robust, albeit reduced performance could be attained for the catalogue of three open-source datasets. Results of the ablation studies with 43 mono-parametric variations of the basal architecture and training protocol provided task-optimal parameters for both categories. Ablation studies against single-task variants of the basal architecture showed a clear performance beneft of coupling landmark localization with segmentation and a dataset-dependent performance impact on segmentation ability.}, language = {en} } @article{PatzerKunzHuflageetal.2023, author = {Patzer, Theresa Sophie and Kunz, Andreas Steven and Huflage, Henner and Conrads, Nora and Luetkens, Karsten Sebastian and Pannenbecker, Pauline and Paul, Mila Marie and Erg{\"u}n, S{\"u}leyman and Bley, Thorsten Alexander and Grunz, Jan-Peter}, title = {Ultrahigh-resolution photon-counting CT in cadaveric fracture models: spatial frequency is not everything}, series = {Diagnostics}, volume = {13}, journal = {Diagnostics}, number = {10}, issn = {2075-4418}, doi = {10.3390/diagnostics13101677}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-319281}, year = {2023}, abstract = {In this study, the impact of reconstruction sharpness on the visualization of the appendicular skeleton in ultrahigh-resolution (UHR) photon-counting detector (PCD) CT was investigated. Sixteen cadaveric extremities (eight fractured) were examined with a standardized 120 kVp scan protocol (CTDI\(_{vol}\) 10 mGy). Images were reconstructed with the sharpest non-UHR kernel (Br76) and all available UHR kernels (Br80 to Br96). Seven radiologists evaluated image quality and fracture assessability. Interrater agreement was assessed with the intraclass correlation coefficient. For quantitative comparisons, signal-to-noise-ratios (SNRs) were calculated. Subjective image quality was best for Br84 (median 1, interquartile range 1-3; p ≤ 0.003). Regarding fracture assessability, no significant difference was ascertained between Br76, Br80 and Br84 (p > 0.999), with inferior ratings for all sharper kernels (p < 0.001). Interrater agreement for image quality (0.795, 0.732-0.848; p < 0.001) and fracture assessability (0.880; 0.842-0.911; p < 0.001) was good. SNR was highest for Br76 (3.4, 3.0-3.9) with no significant difference to Br80 and Br84 (p > 0.999). Br76 and Br80 produced higher SNRs than all kernels sharper than Br84 (p ≤ 0.026). In conclusion, PCD-CT reconstructions with a moderate UHR kernel offer superior image quality for visualizing the appendicular skeleton. Fracture assessability benefits from sharp non-UHR and moderate UHR kernels, while ultra-sharp reconstructions incur augmented image noise.}, language = {en} } @article{SchneiderHoehneSchneideretal.2022, author = {Schneider, Sonja Jasmin Maria and H{\"o}hne, Christian and Schneider, Martin and Schmitter, Marc}, title = {Photoacoustic tomography versus cone-beam computed tomography versus micro-computed tomography: Accuracy of 3D reconstructions of human teeth}, series = {PloS One}, volume = {17}, journal = {PloS One}, number = {12}, doi = {10.1371/journal.pone.0274818}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-301437}, year = {2022}, abstract = {Objectives In this in-vitro study, teeth were imaged using photoacoustic tomography (PAT), cone-beam computed tomography (CBCT), and micro-computed tomography (μ-CT). The study had aim: to identify the best wavelength for PAT images to determine the accuracy of the three imaging methods, and to determine whether PAT images of teeth can achieve acceptable reconstruction quality. Methods Nineteen human mandibular single-rooted incisors were extracted from patients with trauma or periodontitis. To determine the best wavelength for acquiring photoacoustic images, all 19 teeth were scanned in vitro with PAT, using different laser wavelengths between 680 and 960 nm. The images were analyzed using image analysis software. To assess the accuracy of PAT and compare it with the accuracy of CBCT, each tooth was also scanned in vitro using CBCT and the reference standard technique of μ-CT. Subsequently, three different three-dimensional models, one for each imaging technique, were created for each tooth. Finally, the three different three-dimensional models acquired for the same tooth were matched and analyzed regarding volume and surface. Results The highest quality tooth images were achieved using the 680 nm wavelength, which showed the best contrast ratio. The full geometry of the dental root (μ-CT compared with PAT) could be visualized with relative standard deviations of 0.12 mm for the surface and -7.33 mm3 for the volume (n = 19). The full geometry of the dental root (μ-CT compared with CBCT) could be visualized with relative standard deviations of 0.06 mm for the surface and -14.56 mm3 for the volume (n = 19). The difference between the PAT-μ-CT group and CBCT-μ-CT group regarding the total average of the root surface area was not significant (p>0.06). Conclusion Images, which were acquired using PAT at 680nm showed the best contrast ration, enabling the identification of dentin, cementum and the dental pulp. No significant differences were found between the PAT-μ-CT group and CBCT-μ-CT group regarding the total average of the RSA and the total volume. Thus, three-dimensional reconstructions based on in-vitro PAT are already of acceptable reconstruction quality.}, language = {en} } @article{GietzenKunzLuetkensetal.2022, author = {Gietzen, Carsten Herbert and Kunz, Andreas Steven and Luetkens, Karsten Sebastian and Huflage, Henner and Christopoulos, Georgios and van Schoonhoven, J{\"o}rg and Bley, Thorsten Alexander and Schmitt, Rainer and Grunz, Jan-Peter}, title = {Evaluation of prestyloid recess morphology and ulnar-sided contrast leakage in CT arthrography of the wrist}, series = {BMC Musculoskeletal Disorders}, volume = {23}, journal = {BMC Musculoskeletal Disorders}, number = {1}, doi = {10.1186/s12891-022-05241-9}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-301113}, year = {2022}, abstract = {Background In wrist arthrograms, aberrant contrast material is frequently seen extending into the soft tissue adjacent to the ulnar styloid process. Since the prestyloid recess can mimic contrast leakage in CT arthrography, this study aims to provide a detailed analysis of its morphologic variability, while investigating whether actual ulnar-sided leakage is associated with injuries of the triangular fibrocartilage complex (TFCC). Methods Eighty-six patients with positive wrist trauma history underwent multi-compartment CT arthrography (40 women, median age 44.5 years). Studies were reviewed by two board-certified radiologists, who documented the morphology of the prestyloid recess regarding size, opening type, shape and position, as well as the presence or absence of ulnar-sided contrast leakage. Correlations between leakage and the presence of TFCC injuries were assessed using the mean square contingency coefficient (r\(_{ɸ}\)). Results The most common configuration of the prestyloid recess included a narrow opening (73.26\%; width 2.26 ± 1.43 mm), saccular shape (66.28\%), and palmar position compared to the styloid process (55.81\%). Its mean length and anterior-posterior diameter were 6.89 ± 2.36 and 5.05 ± 1.97 mm, respectively. Ulnar-sided contrast leakage was reported in 29 patients (33.72\%) with a mean extent of 12.30 ± 5.31 mm. Leakage occurred more often in patients with ulnar-sided TFCC injuries (r\(_{ɸ}\) = 0.480; p < 0.001), whereas no association was found for lesions of the central articular disc (r\(_{ɸ}\) = 0.172; p = 0.111). Conclusions Since ulnar-sided contrast leakage is more common in patients with peripheral TFCC injuries, distinction between an atypical configuration of the prestyloid recess and actual leakage is important in CT arthrography of the wrist.}, language = {en} } @article{SherifHeroldVoelkeretal.2015, author = {Sherif, Mohammad A. and Herold, Joerg and Voelker, Wolfram and Maniuc, Octavian and Ertl, Georg and Praast, Christian and Braun-Dullaeus, Ruediger Christian}, title = {Feasibility of a new method using two-dimensional transesophageal echocardiography for aortic annular sizing in patients undergoing transcatheter aortic valve implantation; a case-control study}, series = {BMC Cardiovascular Disorders}, volume = {15}, journal = {BMC Cardiovascular Disorders}, number = {78}, doi = {10.1186/s12872-015-0072-7}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-148328}, year = {2015}, abstract = {Background: Accurate preoperative assessment of the aortic annulus dimension is crucial for successful transcatheter aortic valve implantation (TAVI). In this study we validated a new method using two-dimensional transesophageal echocardiography (2D-TEE) for measurement of the aortic annulus prior to TAVI. Methods: We analysed 124 patients who underwent successful TAVI using a self-expandable prosthesis, divided equally into two groups; in the study group we used the cross sectional short axis 2D-TEE for measurement of the aortic annulus and in the control group we used the long axis 2D-TEE. Results: Both groups were comparable regarding the clinical parameters. On the other hand, patients in the study group had less left ventricular ejection fraction (38.9 \% versus 45.6 \%, p = 0.01). The aortic valve annulus was, although not statistically significant, smaller in the study group (21.58 versus 23.28 mm, p = 0.25). Post procedural quantification of the aortic regurgitation revealed that only one patient in both groups had severe aortic regurgitation (AR), in this patient the valve was implanted deep. The incidence of significant AR was higher in the control group (29.0 \% versus 12.9 \%, p = 0.027). Conclusions: Sizing of the aortic valve annulus using cross-sectional 2D-TEE offers a safe and plausible method for patients undergoing TAVI using the self-expandable prosthesis and is significantly superior to using long axis 2D-TEE.}, language = {en} }