TY - JOUR A1 - Dawood, Peter A1 - Breuer, Felix A1 - Stebani, Jannik A1 - Burd, Paul A1 - Homolya, István A1 - Oberberger, Johannes A1 - Jakob, Peter M. A1 - Blaimer, Martin T1 - Iterative training of robust k‐space interpolation networks for improved image reconstruction with limited scan specific training samples JF - Magnetic Resonance in Medicine N2 - To evaluate an iterative learning approach for enhanced performance of robust artificial‐neural‐networks for k‐space interpolation (RAKI), when only a limited amount of training data (auto‐calibration signals [ACS]) are available for accelerated standard 2D imaging. Methods In a first step, the RAKI model was tailored for the case of limited training data amount. In the iterative learning approach (termed iterative RAKI [iRAKI]), the tailored RAKI model is initially trained using original and augmented ACS obtained from a linear parallel imaging reconstruction. Subsequently, the RAKI convolution filters are refined iteratively using original and augmented ACS extracted from the previous RAKI reconstruction. Evaluation was carried out on 200 retrospectively undersampled in vivo datasets from the fastMRI neuro database with different contrast settings. Results For limited training data (18 and 22 ACS lines for R = 4 and R = 5, respectively), iRAKI outperforms standard RAKI by reducing residual artifacts and yields better noise suppression when compared to standard parallel imaging, underlined by quantitative reconstruction quality metrics. Additionally, iRAKI shows better performance than both GRAPPA and standard RAKI in case of pre‐scan calibration with varying contrast between training‐ and undersampled data. Conclusion RAKI benefits from the iterative learning approach, which preserves the noise suppression feature, but requires less original training data for the accurate reconstruction of standard 2D images thereby improving net acceleration. KW - complex‐valued machine learning KW - data augmentation KW - deep learning KW - GRAPPA KW - parallel imaging KW - RAKI Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-312306 VL - 89 IS - 2 SP - 812 EP - 827 ER - TY - JOUR A1 - Triphan, Simon M. F. A1 - Jobst, Bertram J. A1 - Anjorin, Angela A1 - Sedlaczek, Oliver A1 - Wolf, Ursula A1 - Terekhov, Maxim A1 - Hoffmann, Christian A1 - Ley, Sebastian A1 - Düber, Christoph A1 - Biederer, Jürgen A1 - Kauczor, Hans-Ulrich A1 - Jakob, Peter M. A1 - Wielpütz, Mark O. T1 - Reproducibility and comparison of oxygen-enhanced T\(_1\) quantification in COPD and asthma patients JF - PLoS ONE N2 - T\(_1\) maps have been shown to yield useful diagnostic information on lung function in patients with chronic obstructive pulmonary disease (COPD) and asthma, both for native T\(_1\) and ΔT\(_1\), the relative reduction while breathing pure oxygen. As parameter quantification is particularly interesting for longitudinal studies, the purpose of this work was both to examine the reproducibility of lung T\(_1\) mapping and to compare T\(_1\) found in COPD and asthma patients using IRSnapShotFLASH embedded in a full MRI protocol. 12 asthma and 12 COPD patients (site 1) and further 15 COPD patients (site 2) were examined on two consecutive days. In each patient, T\(_1\) maps were acquired in 8 single breath-hold slices, breathing first room air, then pure oxygen. Maps were partitioned into 12 regions each to calculate average values. In asthma patients, the average T\(_{1,RA}\) = 1206ms (room air) was reduced to T\(_{1,O2}\) = 1141ms under oxygen conditions (ΔT\(_1\) = 5.3%, p < 5⋅10\(^{−4})\), while in COPD patients both native T\(_{1,RA}\) = 1125ms was significantly shorter (p < 10\(^{−3})\) and the relative reduction to T\(_{1,O2}\) = 1081ms on average ΔT\(_1\) = 4.2%(p < 10\(^{−5}\)). On the second day, with T\(_{1,RA}\) = 1186ms in asthma and T\(_{1,RA}\) = 1097ms in COPD, observed values were slightly shorter on average in all patient groups. ΔT\(_1\) reduction was the least repeatable parameter and varied from day to day by up to 23% in individual asthma and 30% in COPD patients. While for both patient groups T\(_1\) was below the values reported for healthy subjects, the T\(_1\) and ΔT\(_1\) found in asthmatics lies between that of the COPD group and reported values for healthy subjects, suggesting a higher blood volume fraction and better ventilation. However, it could be demonstrated that lung T\(_1\) quantification is subject to notable inter-examination variability, which here can be attributed both to remaining contrast agent from the previous day and the increased dependency of lung T\(_1\) on perfusion and thus current lung state. KW - Medicine KW - Chronic obstrusive pulmonary disease KW - Asthma KW - Oxygen KW - Magnetic resonance imaging KW - Breathing KW - Pulmonary imaging KW - Protons KW - Diagnostic medicine Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-171833 VL - 12 IS - 2 ER - TY - JOUR A1 - Gotschy, Alexander A1 - Bauer, Wolfgang R. A1 - Winter, Patrick A1 - Nordbeck, Peter A1 - Rommel, Eberhard A1 - Jakob, Peter M. A1 - Herold, Volker T1 - Local versus global aortic pulse wave velocity in early atherosclerosis: An animal study in ApoE\(^{-/-}\) mice using ultrahigh field MRI JF - PLoS ONE N2 - Increased aortic stiffness is known to be associated with atherosclerosis and has a predictive value for cardiovascular events. This study aims to investigate the local distribution of early arterial stiffening due to initial atherosclerotic lesions. Therefore, global and local pulse wave velocity (PWV) were measured in ApoE\(^{-/-}\) and wild type (WT) mice using ultrahigh field MRI. For quantification of global aortic stiffness, a new multi-point transit-time (TT) method was implemented and validated to determine the global PWV in the murine aorta. Local aortic stiffness was measured by assessing the local PWV in the upper abdominal aorta, using the flow/area (QA) method. Significant differences between age matched ApoE\(^{-/-}\) and WT mice were determined for global and local PWV measurements (global PWV: ApoE\(^{-/-}\): 2.7 ±0.2m/s vs WT: 2.1±0.2m/s, P<0.03; local PWV: ApoE\(^{-/-}\): 2.9±0.2m/s vs WT: 2.2±0.2m/s, P<0.03). Within the WT mouse group, the global PWV correlated well with the local PWV in the upper abdominal aorta (R\(^2\) = 0.75, P<0.01), implying a widely uniform arterial elasticity. In ApoE\(^{-/-}\) animals, however, no significant correlation between individual local and global PWV was present (R\(^2\) = 0.07, P = 0.53), implying a heterogeneous distribution of vascular stiffening in early atherosclerosis. The assessment of global PWV using the new multi-point TT measurement technique was validated against a pressure wire measurement in a vessel phantom and showed excellent agreement. The experimental results demonstrate that vascular stiffening caused by early atherosclerosis is unequally distributed over the length of large vessels. This finding implies that assessing heterogeneity of arterial stiffness by multiple local measurements of PWV might be more sensitive than global PWV to identify early atherosclerotic lesions. KW - MRI KW - Atherosclerosis KW - Aorta KW - Stiffness KW - Measurement KW - Time measurement KW - Magnetic resonance imaging KW - Mouse models KW - Systole Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-171824 VL - 12 IS - 2 ER - TY - JOUR A1 - Kaireit, Till F. A1 - Sorrentino, Sajoscha A. A1 - Renne, Julius A1 - Schoenfeld, Christian A1 - Voskrebenzev, Andreas A1 - Gutberlet, Marcel A1 - Schulz, Angela A1 - Jakob, Peter M. A1 - Hansen, Gesine A1 - Wacker, Frank A1 - Welte, Tobias A1 - Tümmler, Burkhard A1 - Vogel-Claussen, Jens T1 - Functional lung MRI for regional monitoring of patients with cystic fibrosis JF - PLoS ONE N2 - Purpose To test quantitative functional lung MRI techniques in young adults with cystic fibrosis (CF) compared to healthy volunteers and to monitor immediate treatment effects of a single inhalation of hypertonic saline in comparison to clinical routine pulmonary function tests. Materials and methods Sixteen clinically stable CF patients and 12 healthy volunteers prospectively underwent two functional lung MRI scans and pulmonary function tests before and 2h after a single treatment of inhaled hypertonic saline or without any treatment. MRI-derived oxygen enhanced T1 relaxation measurements, fractional ventilation, first-pass perfusion parameters and a morpho-functional CF-MRI score were acquired. Results Compared to healthy controls functional lung MRI detected and quantified significantly increased ventilation heterogeneity in CF patients. Regional functional lung MRI measures of ventilation and perfusion as well as the CF-MRI score and pulmonary function tests could not detect a significant treatment effect two hours after a single treatment with hypertonic saline in young adults with CF (p>0.05). Conclusion This study shows the feasibility of functional lung MRI as a non-invasive, radiation-free tool for monitoring patients with CF. KW - Physics KW - Magnetic resonance imaging KW - Functional magnetic resonance imaging KW - Cystic fibrosis KW - Oxygen KW - Pulmonary imaging KW - Hypertonic KW - Pulmonary function KW - Quantum chronodynamics Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-172457 VL - 12 IS - 12 ER - TY - JOUR A1 - Straßer, Marion A1 - Schrauth, Joachim H. X. A1 - Dembski, Sofia A1 - Haddad, Daniel A1 - Ahrens, Bernd A1 - Schweizer, Stefan A1 - Christ, Bastian A1 - Cubukova, Alevtina A1 - Metzger, Marco A1 - Walles, Heike A1 - Jakob, Peter M. A1 - Sextl, Gerhard T1 - Calcium fluoride based multifunctional nanoparticles for multimodal imaging JF - Beilstein Journal of Nanotechnology N2 - New multifunctional nanoparticles (NPs) that can be used as contrast agents (CA) in different imaging techniques, such as photoluminescence (PL) microscopy and magnetic resonance imaging (MRI), open new possibilities for medical imaging, e.g., in the fields of diagnostics or tissue characterization in regenerative medicine. The focus of this study is on the synthesis and characterization of CaF\(_{2}\):(Tb\(^{3+}\),Gd\(^{3+}\)) NPs. Fabricated in a wet-chemical procedure, the spherical NPs with a diameter of 5–10 nm show a crystalline structure. Simultaneous doping of the NPs with different lanthanide ions, leading to paramagnetism and fluorescence, makes them suitable for MR and PL imaging. Owing to the Gd\(^{3+}\) ions on the surface, the NPs reduce the MR T\(_{1}\) relaxation time constant as a function of their concentration. Thus, the NPs can be used as a MRI CA with a mean relaxivity of about r = 0.471 mL·mg\(^{−1}\)·s\(^{−1}\). Repeated MRI examinations of four different batches prove the reproducibility of the NP synthesis and determine the long-term stability of the CAs. No cytotoxicity of NP concentrations between 0.5 and 1 mg·mL\(^{−1}\) was observed after exposure to human dermal fibroblasts over 24 h. Overall this study shows, that the CaF\(_{2}\):(Tb\(^{3+}\),Gd\(^{3+}\)) NPs are suitable for medical imaging. KW - calcium fluoride nanoparticles KW - magnetic resonance imaging (MRI) KW - multifunctional nanoparticles KW - multimodal imaging KW - photoluminescence Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-170657 VL - 8 ER - TY - JOUR A1 - Munz, Eberhard A1 - Jakob, Peter M. A1 - Borisjuk, Ljudmilla T1 - The potential of nuclear magnetic resonance to track lipids in planta JF - Biochimie N2 - Nuclear Magnetic Resonance (NMR) provides a highly flexible platform for non invasive analysis and imaging biological samples, since the manipulation of nuclear spin allows the tailoring of experiments to maximize the informativeness of the data. MRI is capable of visualizing a holistic picture of the lipid storage in living plant/seed. This review has sought to explain how the technology can be used to acquire functional and physiological data from plant samples, and how to exploit it to characterize lipid deposition in vivo. At the same time, we have referred to the current limitations of NMR technology as applied to plants, and in particular of the difficulty of transferring methodologies optimized for animal/medical subjects to plant ones. A forward look into likely developments in the field is included, anticipating its key future role in the study of living plant. KW - coconut cocos-nucifera KW - H-1-NMR spectroscopy KW - NMR-spectroscopy KW - camelina-sativa KW - high-throughput KW - oil storage KW - seeds KW - accumulation KW - field KW - metabolism KW - NMR KW - Lipid KW - MRI KW - CSI KW - Plants KW - Seeds Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-186828 VL - 130 ER - TY - JOUR A1 - Biller, Armin A1 - Choli, Morwan A1 - Blaimer, Martin A1 - Breuer, Felix A. A1 - Jakob, Peter M. A1 - Bartsch, Andreas J. T1 - Combined Acquisition Technique (CAT) for Neuroimaging of Multiple Sclerosis at Low Specific Absorption Rates (SAR) JF - PLOS ONE N2 - Purpose: To compare a novel combined acquisition technique (CAT) of turbo-spin-echo (TSE) and echo-planar-imaging (EPI) with conventional TSE. CAT reduces the electromagnetic energy load transmitted for spin excitation. This radiofrequency (RF) burden is limited by the specific absorption rate (SAR) for patient safety. SAR limits restrict high-field MRI applications, in particular. Material and Methods: The study was approved by the local Medical Ethics Committee. Written informed consent was obtained from all participants. T2- and PD-weighted brain images of n = 40 Multiple Sclerosis (MS) patients were acquired by CAT and TSE at 3 Tesla. Lesions were recorded by two blinded, board-certificated neuroradiologists. Diagnostic equivalence of CAT and TSE to detect MS lesions was evaluated along with their SAR, sound pressure level (SPL) and sensations of acoustic noise, heating, vibration and peripheral nerve stimulation. Results: Every MS lesion revealed on TSE was detected by CAT according to both raters (Cohen's kappa of within-rater/across-CAT/TSE lesion detection kappa(CAT) = 1.00, at an inter-rater lesion detection agreement of kappa(LES) = 0.82). CAT reduced the SAR burden significantly compared to TSE (p<0.001). Mean SAR differences between TSE and CAT were 29.0 (+/- 5.7) % for the T2-contrast and 32.7 (+/- 21.9) % for the PD-contrast (expressed as percentages of the effective SAR limit of 3.2 W/kg for head examinations). Average SPL of CAT was no louder than during TSE. Sensations of CAT-vs. TSE-induced heating, noise and scanning vibrations did not differ. Conclusion: T2-/PD-CAT is diagnostically equivalent to TSE for MS lesion detection yet substantially reduces the RF exposure. Such SAR reduction facilitates high-field MRI applications at 3 Tesla or above and corresponding protocol standardizations but CAT can also be used to scan faster, at higher resolution or with more slices. According to our data, CAT is no more uncomfortable than TSE scanning. KW - registration KW - clinically isolated syndromes KW - brain images KW - MRI criteria KW - robust KW - optimization Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-117179 SN - 1932-6203 VL - 9 IS - 3 ER - TY - JOUR A1 - Schwender, Joerg A1 - Koenig, Christina A1 - Klapperstueck, Matthias A1 - Heinzel, Nicolas A1 - Munz, Eberhard A1 - Hebbelmann, Inga A1 - Hay, Jordan O. A1 - Denolf, Peter A1 - De Bodt, Stefanie A1 - Redestig, Henning A1 - Caestecker, Evelyne A1 - Jakob, Peter M. A1 - Borisjuk, Ljudmilla A1 - Rolletschek, Hardy T1 - Transcript abundance on its own cannot be used to infer fluxes in central metabolism JF - Frontiers in Plant Science N2 - An attempt has been made to define the extent to which metabolic flux in central plant metabolism is reflected by changes in the transcriptome and metabolome, based on an analysis of in vitro cultured immature embryos of two oilseed rape (Brassica napus) accessions which contrast for seed lipid accumulation. Metabolic flux analysis (MFA) was used to constrain a flux balance metabolic model which included 671 biochemical and transport reactions within the central metabolism. This highly confident flux information was eventually used for comparative analysis of flux vs. transcript (metabolite). Metabolite profiling succeeded in identifying 79 intermediates within the central metabolism, some of which differed quantitatively between the two accessions and displayed a significant shift corresponding to flux. An RNA-Seq based transcriptome analysis revealed a large number of genes which were differentially transcribed in the two accessions, including some enzymes/proteins active in major metabolic pathways. With a few exceptions, differential activity in the major pathways (glycolysis, TCA cycle, amino acid, and fatty acid synthesis) was not reflected in contrasting abundances of the relevant transcripts. The conclusion was that transcript abundance on its own cannot be used to infer metabolic activity/fluxes in central plant metabolism. This limitation needs to be borne in mind in evaluating transcriptome data and designing metabolic engineering experiments. KW - oilseeds KW - lipid biosynthesis KW - heterotrophic arabidopsis cells KW - central carbon metabolism KW - gene-expression data KW - targeted metabolite profiling KW - central metabolism KW - flux balance analysis KW - C-13-metabolic flux analysis KW - Brassica napus KW - RNA-SEQ KW - developing oilseeds KW - saccharomyces cerevisiae KW - maize kernels KW - embryo KW - seed Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-114586 SN - 1664-462X N1 - Funding information: Bayer Crop Science NV; Deutsche Forschungsgemeinschaft [BO-1917/4-1]; U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division [DEACO298CH10886] VL - 5 ER - TY - JOUR A1 - Dasenbrook, Elliot C. A1 - Lu, Luan A1 - Donnola, Shannon A1 - Weaver, David E. A1 - Gulani, Viskas A1 - Jakob, Peter M. A1 - Konstan, Michael W. A1 - Flask, Chris A. T1 - Normalized T1 Magnetic Resonance Imaging for Assessment of Regional Lung Function in Adult Cystic Fibrosis Patients - A Cross-Sectional Study JF - PLOS ONE N2 - Background: Cystic fibrosis (CF) patients would benefit from a safe and effective tool to detect early-stage, regional lung disease to allow for early intervention. Magnetic Resonance Imaging (MRI) is a safe, non-invasive procedure capable of providing quantitative assessments of disease without ionizing radiation. We developed a rapid normalized T1 MRI technique to detect regional lung disease in early-stage CF patients. Materials and Methods: Conventional multislice, pulmonary T1 relaxation time maps were obtained for 10 adult CF patients with normal spirometry and 5 healthy non-CF control subjects using a rapid Look-Locker MRI acquisition (5 seconds/imaging slice). Each lung absolute T1 map was separated into six regions of interest (ROI) by manually selecting upper, central, and lower lung regions in the left and right lungs. In order to reduce the effects of subject-to-subject variation, normalized T1 maps were calculated by dividing each pixel in the absolute T1 maps by the mean T1 time in the central lung region. The primary outcome was the differences in mean normalized T1 values in the upper lung regions between CF patients with normal spirometry and healthy volunteers. Results: Normalized T1 (nT1) maps showed visibly reduced subject-to-subject variation in comparison to conventional absolute T1 maps for healthy volunteers. An ROI analysis showed that the variation in the nT1 values in all regions was <= 2% of the mean. The primary outcome, the mean (SD) of the normalized T1 values in the upper right lung regions, was significantly lower in the CF subjects [.914 (.037)] compared to the upper right lung regions of the healthy subjects [.983 (.003)] [difference of .069 (95% confidence interval .032-.105); p=.001). Similar results were seen in the upper left lung region. Conclusion: Rapid normalized T1 MRI relaxometry obtained in 5 seconds/imaging slice may be used to detect regional early-stage lung disease in CF patients. KW - infants KW - disease KW - ventilation KW - infection KW - guidelines KW - diagnosis KW - children Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-128346 SN - 1932-6203 VL - 8 IS - 9 ER - TY - JOUR A1 - Nordbeck, Peter A1 - Bönhof, Leoni A1 - Hiller, Karl-Heinz A1 - Voll, Sabine A1 - Arias-Loza, Paula A1 - Seidlmaier, Lea A1 - Williams, Tatjana A1 - Ye, Yu-Xiang A1 - Gensler, Daniel A1 - Pelzer, Theo A1 - Ertl, Georg A1 - Jakob, Peter M. A1 - Bauer, Wolfgang R. A1 - Ritter, Oliver T1 - Impact of Thoracic Surgery on Cardiac Morphology and Function in Small Animal Models of Heart Disease: A Cardiac MRI Study in Rats JF - PLoS ONE N2 - Background Surgical procedures in small animal models of heart disease might evoke alterations in cardiac morphology and function. The aim of this study was to reveal and quantify such potential artificial early or long term effects in vivo, which might account for a significant bias in basic cardiovascular research, and, therefore, could potentially question the meaning of respective studies. Methods Female Wistar rats (n = 6 per group) were matched for weight and assorted for sham left coronary artery ligation or control. Cardiac morphology and function was then investigated in vivo by cine magnetic resonance imaging at 7 Tesla 1 and 8 weeks after the surgical procedure. The time course of metabolic and inflammatory blood parameters was determined in addition. Results Compared to healthy controls, rats after sham surgery showed a lower body weight both 1 week (267.5±10.6 vs. 317.0±11.3 g, n<0.05) and 8 weeks (317.0±21.1 vs. 358.7±22.4 g, n<0.05) after the intervention. Left and right ventricular morphology and function were not different in absolute measures in both groups 1 week after surgery. However, there was a confined difference in several cardiac parameters normalized to the body weight (bw), such as myocardial mass (2.19±0.30/0.83±0.13 vs. 1.85±0.22/0.70±0.07 mg left/right per g bw, p<0.05), or enddiastolic ventricular volume (1.31±0.36/1.21±0.31 vs. 1.14±0.20/1.07±0.17 µl left/right per g bw, p<0.05). Vice versa, after 8 weeks, cardiac masses, volumes, and output showed a trend for lower values in sham operated rats compared to controls in absolute measures (782.2±57.2/260.2±33.2 vs. 805.9±84.8/310.4±48.5 mg, p<0.05 for left/right ventricular mass), but not normalized to body weight. Matching these findings, blood testing revealed only minor inflammatory but prolonged metabolic changes after surgery not related to cardiac disease. Conclusion Cardio-thoracic surgical procedures in experimental myocardial infarction cause distinct alterations upon the global integrity of the organism, which in the long term also induce circumscribed repercussions on cardiac morphology and function. This impact has to be considered when analyzing data from respective animal studies and transferring these findings to conditions in patients. KW - heart rate KW - body weight KW - surgical and invasive medical procedures KW - magnetic resonance imaging KW - blood KW - vascular surgery KW - myocardial infarction KW - cardiac ventricles Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-130064 VL - 8 IS - 8 ER -