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Hinterwimmer S, Gotthardt M, von Eisenhart-Rothe R, Sauerland S, Siebert M, Vogl T, Eckstein F, Graichen H. In vivo contact areas of the knee in patients with patellar subluxation. J Biomech 2005; 38:2095-101. [PMID: 16084210 DOI: 10.1016/j.jbiomech.2004.09.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2004] [Indexed: 11/20/2022]
Abstract
OBJECTIVE Ex vivo studies have suggested that cartilage contact areas and pressure are of high clinical relevance in the etiology of osteoarthritis in patients with patellar subluxation. The aims of this study were therefore to validate in vivo measurements of contact areas with 3D open magnetic resonance imaging (MRI), and to study knee joint contact areas in patients with patellar subluxation at different angles of knee flexion in comparison with healthy subjects. METHODS 3D-MRI data sets of 12 healthy volunteers and eight patients with patellar subluxation were acquired using a standard clinical (1.5 T) and an open (0.2 T) MRI scanner. We compared femoro-patellar and femoro-tibial contact areas obtained with two different sequences from open MRI [dual-echo-steady-state (DESS) and fast-low-angle-shot (FLASH) sequences] with those derived from standard clinical 1.5 T MRI. We then analyzed differences in joint contact areas between healthy subjects and patients with patellar subluxation at 0 degree, 30 degrees, and 90 degrees of knee flexion using open MRI. RESULTS The correlation of the size of contact areas from open MRI with standard clinical MRI data ranged from r = 0.52 to 0.92. Open-MRI DESS displayed a smaller overestimation of joint contact areas (+21% in the femoro-patellar, +12% in the medial femoro-tibial, and +19% in the lateral femoro-tibial compartment) than FLASH (+40%, +37%, +30%, respectively). The femoro-patellar contact areas in patients were significantly reduced in comparison with healthy subjects (-47% at 0 degree, -56% at 30 degrees, and -42% at 90 degrees of flexion; all p < 0.01), whereas no significant difference was observed in femoro-tibial contact areas. CONCLUSIONS Open MRI allows one to quantify joint contact areas of the knee with reasonable accuracy, if an adequate pulse sequence is applied. The technique permits one to clearly identify differences between patients with patellar subluxation and healthy subjects at different flexion angles, demonstrating a significant reduction and lateralization of contact areas in patients. In the future, application of this in vivo technique is of particular interest for monitoring the efficacy of different types of surgical and conservative treatment options for patellar subluxation.
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McWalter EJ, Wirth W, Siebert M, von Eisenhart-Rothe RMO, Hudelmaier M, Wilson DR, Eckstein F. Use of novel interactive input devices for segmentation of articular cartilage from magnetic resonance images. Osteoarthritis Cartilage 2005; 13:48-53. [PMID: 15639637 DOI: 10.1016/j.joca.2004.09.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2004] [Accepted: 09/24/2004] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To study the effect of new interactive computer input devices on cartilage segmentation in terms of time, consistency between input devices, and precision in quantitative magnetic resonance imaging (qMRI). DESIGN We compared two new input devices, an interactive digitizing tablet and an interactive touch-sensitive screen, to a traditional mouse. Medial tibial and patellar cartilage of six healthy and six osteoarthritic knees were segmented using each input device. Cartilage volume, surface area and mean thickness were assessed using a validated algorithm and used to determine consistency and precision. Segmentation time was also measured. RESULTS Segmenting with an interactive touch-sensitive screen reduced segmentation time by 15% when compared to the traditional mouse but we found no significant difference in segmentation time between the interactive digitizing tablet and the traditional mouse. We found no difference in consistency or precision of cartilage volume, mean thickness or surface area between the three input devices tested. CONCLUSIONS We conclude that measurements of cartilage made using articular cartilage segmentation from MR images are independent of the input device chosen for user interaction.
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Hinterwimmer S, von Eisenhart-Rothe R, Siebert M, Welsch F, Vogl T, Graichen H. Patella kinematics and patello-femoral contact areas in patients with genu varum and mild osteoarthritis. Clin Biomech (Bristol, Avon) 2004; 19:704-10. [PMID: 15288456 DOI: 10.1016/j.clinbiomech.2004.04.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Accepted: 04/30/2004] [Indexed: 02/07/2023]
Abstract
BACKGROUND Patients with genu varum of the knee and moderate to severe osteoarthritis often suffer from additional symptoms of the patello-femoral joint. These patients have a poor prognosis following high tibial osteotomy. It is unclear whether varus knees with only mild femoro-tibial osteoarthritis are also associated with alterations of patella biomechanics, and affect the prognosis of intended high tibial osteotomy. METHODS Fifteen patients with genu varum and mild osteoarthritis and 15 healthy volunteers were assessed in an open MRI-scanner. 3D-GRE sequences of the knee were obtained in 0 degrees, 30 degrees and 90 degrees with and without activity of the extensor muscles. After segmentation of patella, femur, tibia and the adjacent cartilage, a patella-based local coordinate system was established. Femoral and tibial reference points allowed definition of the spatial position of the patella. Contact areas were defined by intersection of opposing cartilage volumes. FINDINGS No significant differences in patella kinematics and patello-femoral contact areas could be found (P > 0.05) between varus knees with mild osteoarthritis and healthy knees either at different flexion angles or under extending muscle activity. INTERPRETATION In knees with genu varum and mild medial osteoarthritis we could detect no alterations in patello-femoral kinematics. Since the alterations of patients with genu varum and mild osteoarthritis are restricted to the medial femoro-tibial joint high tibial osteotomy might be successful.
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von Eisenhart-Rothe R, Siebert M, Bringmann C, Vogl T, Englmeier KH, Graichen H. A new in vivo technique for determination of 3D kinematics and contact areas of the patello-femoral and tibio-femoral joint. J Biomech 2004; 37:927-34. [PMID: 15111080 DOI: 10.1016/j.jbiomech.2003.09.034] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2003] [Indexed: 10/26/2022]
Abstract
Patello-femoral disorders are often caused by changes of patello-femoral and/or tibio-femoral kinematics. However, until now there has been no quantitative in vivo technique, that is able to obtain 3D kinematics and contact areas of all knee compartments simultaneously on a non-invasive basis. The aim of this study was therefore to develop and apply a technique which allows for determination of 3D kinematics and contact areas of the patello-femoral and tibio-femoral joint during different knee flexion angles and under neuromuscular activation patterns. One knee of each of the 10 healthy volunteers was examined in an open MR system under flexing isometric muscle activity at 30 degrees and 90 degrees. Three-dimensional kinematics and contact areas of the patello-femoral and tibio-femoral joints were analyzed by 3D image postprocessing. The reproducibility of the imaging technique yielded a coefficient of variation of 4.6% for patello-femoral, 4.7% for femoro-tibial displacement and 8.6% for contact areas. During knee flexion (30-90 degrees ), patella tilt (opened to medial) decreased (8.8+/-3.4 degrees vs. 4.6+/-3.1 degrees, p<0.05), while lateral patellar shift increased significantly (1.6+/-2.3mm vs. 3.4+/-3.0mm, p<0.05). Furthermore, a significant posterior translation and external rotation of the femur relative to the tibia was observed. Patello-femoral contact areas increased significantly in size (134+/-60mm(2) vs. 205+/-96 mm(2)) during knee flexion. This technique shows a high reproducibility and provides physiologic in vivo data of 3D kinematics and contact areas of the patello-femoral and the tibio-femoral joint during knee flexion. This allows for advanced in vivo diagnostics, and may help to improve therapy of patello-femoral disorders in the future.
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von Eisenhart-Rothe R, Bringmann C, Siebert M, Reiser M, Englmeier KH, Eckstein F, Graichen H. Femoro-tibial and menisco-tibial translation patterns in patients with unilateral anterior cruciate ligament deficiency--a potential cause of secondary meniscal tears. J Orthop Res 2004; 22:275-82. [PMID: 15013085 DOI: 10.1016/j.orthres.2003.08.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/18/2003] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To analyze menisco-tibial and femoro-tibial translation patterns in healthy and ACL-deficient knees in different knee flexion angles under muscle activity. METHODS The ACL-deficient and contralateral healthy knees of 10 patients were examined with an open MRI system at 30 degrees and 90 degrees of knee flexion, under isometric contraction of the extensors or flexor muscle groups. Translations between the tibia, the femoral condyles and the menisci were analyzed by three-dimensional image postprocessing. RESULTS Posterior translation of the femur and menisci relative to the tibia occurred during knee flexion (30-90 degrees) in all knees. In ACL-deficient knees, posterior translation of the medial femoral condyle (+1.3 +/- 3.8 mm) was significantly larger than in healthy knee (-0.9 +/- 2.9 mm; p<0.05), while the translation pattern of the menisci was similar (med. meniscus 0.6 +/- 2.3 mm vs. 0.6 +/- 2.7 mm). Under isometric contraction of the extensors (relative to the flexor muscle group), an increased posterior position of the femur and menisci was observed at 30 degrees knee flexion, but not at 90 degrees. This applied to ACL-deficient and healthy knees. CONCLUSIONS This study shows a significant increase of translation of the medial femoral condyle in ACL-deficient knees, whereas menisco-tibial translation remains almost unchanged. This difference in translation patterns indicates that the posterior horn of the medial meniscus might encounter shear, potentially explaining the high rate of secondary medial meniscal tears in patients with ACL-deficiency.
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Fill UA, Zankl M, Petoussi-Henss N, Siebert M, Regulla D. Adult female voxel models of different stature and photon conversion coefficients for radiation protection. HEALTH PHYSICS 2004; 86:253-272. [PMID: 14982227 DOI: 10.1097/00004032-200403000-00003] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This paper describes the construction of three adult female voxel models, two whole-body and one from head to thighs, from computed tomographic data of 3 women of different stature. Voxel models (also called phantoms) are human models based on computed tomographic or magnetic resonance images obtained from high resolution continuous scans of a single individual. The gray-scale data or information content of the medical images are interpreted into tissues (i.e., organs), a process known as segmentation. The phantoms, consisting of millions of volume elements, called voxels, provide a three-dimensional representation of the human body and the spatial form of its constituent organs and structures. They were initially developed for radiation protection purposes to estimate the organ and effective doses and hence the risk to a person or population due to an irradiation. This paper also presents conversion coefficients for idealized geometries of external photon exposures of energies 10 keV-1 MeV for the three female models, calculated with a Monte Carlo code. Until now there were not any published data on conversion coefficients for explicit female voxel models. Such sets of conversion coefficients exist for voxel adult males or for MIRD-type male, female, and hermaphrodite models. Numerical differences of the calculated conversion coefficients for the voxel female models and MIRD-type models can amount up to 60% or more for external exposures and are due to the improved anatomical realism of the voxel models. The size of the model also has an effect on the conversion coefficients, particularly for deeper lying organs and energies below 200 keV. The three separate sets of conversion coefficients allow one to choose the most suitable model according to the size of the individual as well as to study the dosimetric variations due to the size of the model.
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Englmeier KH, Hellwig G, Griebel J, Delorme S, Siebert M, Brix G. Morpho-functional visualization of dynamic MR-mammography. Stud Health Technol Inform 2004; 107:838-41. [PMID: 15360930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
In view of an increasing use of breast MRI supplementing X-ray mammography, the purpose of this study was the development of a method for fast and efficient analysis of dynamic MR image series of the female breast. The image data sets were acquired with a saturation-recovery-turbo-FLASH sequence facilitating the detection of the kinetics of the contrast agent concentration in the whole breast with a high temporal and spatial resolution. In addition, a morphological 3D-FLASH data set was acquired. The dynamic image data sets were analyzed by tracer kinetic modeling in order to describe the physiological processes underlying the contrast enhancement in mathematical terms and thus enable the estimation of functional tissue specific parameters, reflecting the status of microcirculation. To display morphological and functional tissue information simultaneously, a multidimensional real-time visualization system (using 3D-texture mapping) was developed, which enables a practical and intuitive human-computer interface in virtual reality. The spatially differentiated representation of the computed functional tissue parameters superimposed on the anatomical information offers several possibilities: improved discernibility of contrast enhancement, inspection of the data volume in 3D-space and localization of lesions in space and thus fast and more natural recognition of topological coherencies. In a feasibility study, it could be demonstrated that multidimensional visualization of contrast enhancement in virtual reality is practical. Especially, detection and localization of multiple breast lesions may be an important application
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Englmeier KH, Hellwig G, Griebel J, Delorme S, Siebert M, Brix G. Dynamic MR-mammography in virtual reality. Stud Health Technol Inform 2003; 94:72-8. [PMID: 15455867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
In view of an increasing use of breast MRI supplementing X-ray mammography, the purpose of this study was the development of a method for fast and efficient analysis of dynamic MR image series of the female breast. The image data sets were acquired with a saturation-recovery-turbo-FLASH sequence facilitating the detection of the kinetics of the contrast agent concentration in the whole breast with. In addition, a morphological 3D-FLASH data set was acquired. The dynamic image data sets were analyzed by tracer kinetic modeling in order to describe the physiological processes underlying the contrast enhancement in mathematical terms and thus to enable the estimation of functional tissue specific parameters, reflecting the status of microcirculation. To display morphological and functional tissue information simultaneously, a multidimensional real-time visualization system (using 3D-texture mapping) was developed, which enables a practical and intuitive human-computer interface in virtual reality. The spatially differentiated representation of the computed functional tissue parameters superimposed on the anatomical information offers several possibilities: improved discernibility of contrast enhancement; inspection of the data volume in 3D-space using the features of rotation and transparency variation; localization of lesions in space and thus fast and more natural recognition of topological coherencies. In a feasibility study, it could be demonstrated that multidimensional visualization of contrast enhancement in virtual reality is a practicable idea. Especially, detection and localization of multiple breast lesions may be an important application.
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Englmeier KH, Hellwig G, Griebel J, Delorme S, Siebert M, Brix G. Morphofunctional visualization of MR-mammography in virtual reality. Stud Health Technol Inform 2003; 95:27-32. [PMID: 14663958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
In view of an increasing use of breast MRI supplementing X-ray mammography, the purpose of this study was the development of a method for fast and efficient analysis of dynamic MR image series of the female breast. The dynamic image data sets were analyzed by tracer kinetic modeling in order to describe the physiological processes underlying the contrast enhancement in mathematical terms and thus to enable the estimation of functional tissue specific parameters, reflecting the status of microcirculation. To display morphological and functional tissue information simultaneously, a multidimensional real-time visualization system (using 3D-texture mapping) was developed, which enables a practical and intuitive human-computer interface in virtual reality.
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Tirsch WS, Keidel M, Siebert M, Perz S, Doktor L, Diener HC. [Nonlinear analysis of heart rate for objective assessment of cardiac autonomic dysfunction after craniocerebral trauma]. BIOMED ENG-BIOMED TE 2002; 43 Suppl 3:145-8. [PMID: 11776214 DOI: 10.1515/bmte.1998.43.s3.145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Schlake HP, Goldbrunner R, Siebert M, Behr R, Roosen K. Intra-Operative electromyographic monitoring of extra-ocular motor nerves (Nn. III, VI) in skull base surgery. Acta Neurochir (Wien) 2002; 143:251-61. [PMID: 11460913 DOI: 10.1007/s007010170105] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND Extraocular motor nerves (Nn. III, IV, VI) are at risk of damage during skull base surgery. A new recording technique was employed in 18 patients suffering from various skull base tumours in order to extend intra-operative EMG monitoring to the extra-ocular muscles. METHODS Selective intra-operative EMG recordings were obtained from extra-ocular muscles by placement of single-shafted bipolar needle electrodes under the guidance of B-mode ultrasound to visualise the needle tip within the target muscle in the orbital cavity. FINDINGS Following bipolar electrical stimulation, the oculomotor nerve (N.III) was intra-operatively identified in 5 out of 7 cases, and the abducens nerve (N.VI) in 12 out of 18 cases. Postoperative (3-6 months) oculomotor nerve function remained unchanged in 5 and improved in 2 patients. No permanent deterioration was observed. Abducens nerve function deteriorated in two patients and improved in one case, but remained unchanged in 15 cases. No side effects occurred. There was neither any distinct relation of ocular motor nerve function to the kind and extent of SMA ("spontaneous muscle activity") patterns, nor could such relationship be detected with concern to neurophysiological parameters (latencies, amplitudes) of electrically evoked CMAP ("compound muscle action potentials"). INTERPRETATION The EMG technique proposed proved to be mainly effective as a mapping tool for intra-operative localisation and identification of ocular motor nerves in skull base surgery. However, the predictive value of conventional neurophysiological parameters for clinical outcome, seems to be rather poor. Further studies on a larger number of patients are therefore required to develop new quantification techniques which enable an intra-operative prediction of ocular motor nerve deficits. Further efforts are also necessary to extend this technique to the trochlear nerve.
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Englmeier KH, Siebert M, Stammberger T, von Eisenhardt-Rothe R, Graichen H, Eckstein F, Reiser M. Quantitative image analysis of the cartilage in Virtual Reality. Stud Health Technol Inform 2002; 85:141-3. [PMID: 15458075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
The objective of this work is to develop image processing methods for analysing the morphology of the joint cartilage with magnetic resonance imaging. Quantitative data on the morphological distribution of the joint cartilage are of great interest for both research as well as for diagnosis. The cartilage thickness provides information on the local cartilage occurance and may therefore be helpful in early and objective diagnosing degenerative cartilage changes, monitoring the pathogenesis of osteoarthritis, and controlling the success of chondroprotective treatment. In biomechanics, the thickness distribution serves to analyse the functional adaptation or the compression of the cartilage under loading and may be used for numerical simulation of load transmission in the joint.
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Siebert M. Giving the industry a face. MEDICAL DEVICE TECHNOLOGY 2001; 12:36-7. [PMID: 15966145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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Siebert M, Krieg P, Lehmann WD, Marks F, Fürstenberger G. Enzymic characterization of epidermis-derived 12-lipoxygenase isoenzymes. Biochem J 2001; 355:97-104. [PMID: 11256953 PMCID: PMC1221716 DOI: 10.1042/0264-6021:3550097] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Substrate selectivity and other enzymic characteristics of two epidermis-derived lipoxygenases (LOXs), the epidermis-type (e) (12S)-LOX and (12R)-LOX, were compared with those of the platelet-type (p) (12S)-LOX. In contrast with p(12S)-LOX, e(12S)-LOX and (12R)-LOX exhibited no or very low reactivity towards the customary substrates linoleic acid and arachidonic acid but metabolized the corresponding fatty acid methyl esters, which, in contrast, were not accepted as substrates by p(12S)-LOX. Other esters of arachidonic acid and linoleic acid, including propan-2-yl and cholesterol esters, 1-palmitoyl-2-arachidonyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-linoleyl-sn-glycero-3-phosphoethanolamine, and ceramide 1 carrying an omega-linoleic acid ester, were not metabolized by these three LOX isoenzymes. Among various polyunsaturated fatty acids the isomeric eicosatrienoic acids were found to be oxygenated by e(12S)-LOX but not by (12R)-LOX. 4,7,10,13,16,19-Docosahexaenoic acid as a substrate was restricted to p(12S)-LOX. Variations in the pH and the Ca(2+) content of the incubation medium affected the catalytic potential only slightly. Whereas (12R)-LOX activity increased in the presence of Ca(2+) and with an acidic pH, Ca(2+) had no effect on p(12S)-LOX and e(12S)-LOX; an acidic pH decreased the catalytic activity of the latter two. However, the catalytic activity of the epidermis-type isoenzymes, but not of p(12S)-LOX, was found to be markedly increased in the presence of DMSO. Under these conditions, e(12S)-LOX and (12R)-LOX oxygenated 4,7,10,13,16,19-docosahexaenoic acid to 14-hydroxy-4,7,10,12,16,19-docosahexaenoic acid and 13-hydroxy-4,7,10,14,16,19-docosahexaenoic acid respectively. In addition, (9R)-hydroxyoctadeca-10,12-dienoic acid methyl ester was generated from linoleic acid methyl ester by (12R)-LOX. Independently of the substrate, the catalytic activity of e(12S)-LOX and (12R)-LOX was always at most 2% of that of p(12S)-LOX with arachidonic acid as substrate.
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Englmeier KH, Griebel J, Lucht R, Knopp M, Siebert M, Brix G. [Dynamic MR mammography. Multidimensional visualization of contrast medium enhancement in virtual reality]. Radiologe 2000; 40:262-6. [PMID: 10789125 DOI: 10.1007/s001170050667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND The purpose of this study was the development of a method for fast and efficient analysis of dynamic MR images of the female breast. The image data sets were acquired with a saturation-recovery turbo-FLASH sequence which enables the detection of the kinetics of the contrast agent concentration in the whole breast with a high temporal and spatial resolution. In addition, a morphologic 3D-FLASH data set was acquired. METHODS The dynamic image datasets were analyzed by a pharmacokinetic model which enables the representation of the relevant functional tissue information by two parameters. In order to display simultaneously morphologic and functional tissue information, we developed a multidimensional visualization system, which enables a practical and intuitive human-computer interface in virtual reality. DISCUSSIONS The developed system allows the fast and efficient analysis of dynamic MR data sets. An important clinical application is the localization and definition of multiple lesions of the female breast.
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Oldenburg MC, Siebert M. New Cleavase Fragment Length Polymorphism method improves the mutation detection assay. Biotechniques 2000; 28:351-7. [PMID: 10683747 DOI: 10.2144/00282pf02] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Cleavase Fragment Length Polymorphism (CFLP) analysis is a convenient, accurate and highly sensitive method for the detection and localization of nucleic acid mutations. The assay is well suited for high-throughput screening and can be used to detect mutations in known and unknown nucleic acid samples. A recent improvement in the CFLP assay termed "temperature ramping" or "ramping" is reported here. This procedural improvement eliminates the need for time and temperature optimizations before the actual sample analysis. In this study, we compare the CFLP ramping procedure to the conventional CFLP optimization procedure and demonstrate equal, and in some cases improved, detection of point mutations. With ramping, CFLP reactions are identical for all DNA fragments analyzed, which allows for increased sample throughput, decreased assay time and lower overall cost.
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Sander T, Olson S, Hall J, Siebert M, Grooms K, Heisler L, de Arruda M, Neri B. Comparison of detection platforms and post-polymerase chain reaction DNA purification methods for use in conjunction with Cleavase fragment length polymorphism analysis. Electrophoresis 1999. [PMID: 10380752 DOI: 10.1002/(sici)1522-2683(19990101)20:6<1131::aid-elps1131>3.0.co;2-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The removal of impurities and contaminants from PCR-amplified fragments is important for mutation detection methods which identify mutations based on shifts in electrophoretic mobility. This is particularly critical for assays and detection methods which use target DNA that is labeled prior to analysis and electrophoretic detection. We examined several procedures for purifying DNA amplified by the polymerase chain reaction (PCR) and their use in conjunction with a novel DNA scanning method, the Cleavase fragment length polymorphism (CFLP)* assay. In this study, a 480 bp DNA fragment, fluorescently labeled on the 5'-end of one strand, was amplified and subjected to various widely used purification procedures, including several commercially available clean-up kits. We demonstrate that visualization of the fluorescent label, as opposed to simple ethidium bromide staining, reveals the presence of considerable levels of labeled, truncated, amplification products. The various procedures were evaluated on the basis of their ability to remove these unwanted DNA fragments as well as on the degree to which they inhibited or promoted the CFLP reaction. Several procedures are recommended for use with CFLP analysis, including isopropanol precipitation, gel excision, and several commercially available spin columns. Concurrently, we evaluated (compared) a number of commonly used visualization platforms, including fluorescence imaging, chemiluminescence, and post-electrophoretic staining, for the ability to detect CFLP pattern changes. The advantages and disadvantages of different methods are discussed and amounts of DNA to be used for CFLP analysis on different detection platforms are recommended.
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Sander T, Olson S, Hall J, Siebert M, Grooms K, Heisler L, de Arruda M, Neri B. Comparison of detection platforms and post-polymerase chain reaction DNA purification methods for use in conjunction with Cleavase fragment length polymorphism analysis. Electrophoresis 1999; 20:1131-40. [PMID: 10380752 DOI: 10.1002/(sici)1522-2683(19990101)20:6<1131::aid-elps1131>3.0.co;2-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The removal of impurities and contaminants from PCR-amplified fragments is important for mutation detection methods which identify mutations based on shifts in electrophoretic mobility. This is particularly critical for assays and detection methods which use target DNA that is labeled prior to analysis and electrophoretic detection. We examined several procedures for purifying DNA amplified by the polymerase chain reaction (PCR) and their use in conjunction with a novel DNA scanning method, the Cleavase fragment length polymorphism (CFLP)* assay. In this study, a 480 bp DNA fragment, fluorescently labeled on the 5'-end of one strand, was amplified and subjected to various widely used purification procedures, including several commercially available clean-up kits. We demonstrate that visualization of the fluorescent label, as opposed to simple ethidium bromide staining, reveals the presence of considerable levels of labeled, truncated, amplification products. The various procedures were evaluated on the basis of their ability to remove these unwanted DNA fragments as well as on the degree to which they inhibited or promoted the CFLP reaction. Several procedures are recommended for use with CFLP analysis, including isopropanol precipitation, gel excision, and several commercially available spin columns. Concurrently, we evaluated (compared) a number of commonly used visualization platforms, including fluorescence imaging, chemiluminescence, and post-electrophoretic staining, for the ability to detect CFLP pattern changes. The advantages and disadvantages of different methods are discussed and amounts of DNA to be used for CFLP analysis on different detection platforms are recommended.
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O'Connell CD, Atha DH, Oldenburg MC, Tian J, Siebert M, Handrow R, Grooms K, Heisler L, de Arruda M. Detection of p53 gene mutations: analysis by single-strand conformation polymorphism and Cleavase fragment length polymorphism. Electrophoresis 1999; 20:1211-23. [PMID: 10380761 DOI: 10.1002/(sici)1522-2683(19990101)20:6<1211::aid-elps1211>3.0.co;2-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have generated a collection of clones containing single point mutations within the exon 5-9 hot spot regions of the p53 gene by using polymerase chain reaction (PCR) to amplify select regions of the gene from characterized cell lines. These clones were then used to address the sensitivity of mutation detection using slab-gel single-strand conformation polymorphism (SSCP) and Cleavase fragment length polymorphism (CFLP) assay systems. Both methods exhibited high sensitivities for the detection of mutations in cloned p53 mutations in this study: 97% for CFLP and 94% for SSCP. In addition to resulting in higher sensitivity of mutation detection, CFLP has the capability to analyze longer fragments. In this study, CFLP identified five intronic mutations which were not investigated in the exon-specific SSCP assay. These results agree with those found elsewhere and demonstrate that CFLP scanning can have practical advantages when used for the identification of sequence alterations within the p53 gene.
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Krieg P, Siebert M, Kinzig A, Bettenhausen R, Marks F, Fürstenberger G. Murine 12(R)-lipoxygenase: functional expression, genomic structure and chromosomal localization. FEBS Lett 1999; 446:142-8. [PMID: 10100631 DOI: 10.1016/s0014-5793(99)00196-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A cDNA, recently cloned (by Krieg et al. (1998)) from mouse skin, was shown to encode a 12(R)-lipoxygenase. When expressed in HEK cells, the recombinant protein converted methyl arachidonate into the corresponding 12-HETE ester which was shown to be the R-enantiomer by chiral phase chromatography. Neither arachidonic acid nor linoleic acid were substrates for the recombinant protein. The structure of the 12(R)-lipoxygenase gene is unique among all animal lipoxygenases in that it is divided into 15 exons and 14 introns spanning approximately 12.5 kb. By interspecific backcross analysis, the 12(R)-lipoxygenase gene was localized to the central region of mouse chromosome 11.
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Schlake HP, Goldbrunner R, Milewski C, Siebert M, Behr R, Riemann R, Helms J, Roosen K. Technical developments in intra-operative monitoring for the preservation of cranial motor nerves and hearing in skull base surgery. Neurol Res 1999; 21:11-24. [PMID: 10048048 DOI: 10.1080/01616412.1999.11740885] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Although EMG recordings from mimic muscles have become the standard for intra-operative facial nerve monitoring, few data are available concerning other motor cranial nerves (MCN). Auditory brainstem responses (ABR) are a proven tool for intra-operative hearing preservation, but have their limitations, suggesting the application of supplementary methods. This paper describes new developments of MCN and cochlear nerve monitoring in skull base surgery. Up to 2 x 8 EMG channels were recorded after bipolar stimulation of MCN using concentric coaxial probes. A special software enabled event-dependent registrations of all signals exceeding a definable threshold level. Selective recordings from masticatory muscles (N.V) were obtained using rectangular Teflon-insulated needle electrodes. For oculomotor (Nn.III/ VI) nerve recordings bipolar needle electrodes were precisely placed by orbital ultrasound guidance. Lower cranial nerves were monitored inserting needle electrodes into the soft palate (N.IX), tongue (N.XII) and vocal muscles (N.X) during laryngoscopy using a special applicator. For ABR recordings, click stimuli (95 dB HL) were applied monaurally through insert earphones. Electrocochleography was simultaneously recorded as a near-field potential without averaging after promontory (transtympanic) electrode placement using otomicroscopy. Regarding the ABR biosignal, a characteristic response pattern was detected following bipolar electrical stimulation of the auditory nerve possibly useful for its intra-operative identification.
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Sommer S, Siebert M, Bechthold A, Heide L. Specific induction of secondary product formation in transgenic plant cell cultures using an inducible promoter. PLANT CELL REPORTS 1998; 17:891-896. [PMID: 30736563 DOI: 10.1007/s002990050504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This paper describes the artificial induction of secondary metabolite production in transgenic plant cell cultures using a recombinant, inducible plant promoter. The bacterial gene ubiC from Escherichia coli encodes the enzyme chorismate pyruvate lyase (CPL) which catalyses the conversion of chorismate to 4-hydroxybenzoate (4HB). This gene was fused to the tetracycline-inducible plant promoter Triple-Op. After transformation into Nicotiana tabacum W38 TET, transgenic cell cultures were established. Addition of chlorotetracycline to the medium led to specific induction of CPL activity. The optimal chlorotetracycline concentration was approximately 2 mg/l medium. Three to 5 h after induction, the ubiC mRNA concentration reached a maximum, while highest specific CPL activity was detected after 8 days. The artificial secondary metabolite 4HB was converted to glucosides, and their accumulation reached maximum levels after 5 weeks of subculture. The induction was reversible.
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Boyd G, Morice AH, Pounsford JC, Siebert M, Peslis N, Crawford C. An evaluation of salmeterol in the treatment of chronic obstructive pulmonary disease (COPD). Eur Respir J 1997; 10:815-21. [PMID: 9150318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The objectives of this study were to compare the efficacy and safety of salmeterol xinafoate (50 and 100 microg b.i.d.) with that of placebo, when added to existing therapy, in the treatment of patients with chronic obstructive pulmonary disease (COPD). Six hundred and seventy four patients were randomized to receive either salmeterol 50 microg b.i.d., salmeterol 100 microg b.i.d., or placebo treatment for a period of 16 weeks. The results showed a significant improvement in daily symptom scores noted for patients taking either 50 microg (p=0.043) or 100 microg b.i.d. salmeterol (p=0.01) compared with placebo, with a corresponding decrease in additional daytime salbutamol requirements for both salmeterol groups. The same pattern was reflected for night-time symptoms and additional salbutamol use. During treatment, forced expiratory volume in one second (FEV1) measurements improved significantly in each salmeterol group, with up to a 7% improvement observed at the end of the study. Although no difference was observed between treatment groups for the distance walked in 6 min, patients treated with salmeterol 50 microg b.i.d. were significantly less breathless than those treated with placebo after their 6 min walk, after 8 weeks (p=0.024) and 16 weeks (p=0.004) of therapy. Adverse events were similar in all three groups except for tremor, which was significantly higher in the 100 microg b.i.d. salmeterol group (p=0.005) compared both with 50 microg b.i.d. salmeterol and placebo. Salmeterol offered further positive improvement to the effect of therapy in patients with chronic obstructive pulmonary disease when added to their existing regimens. This clinical improvement was similar both with 50 and 100 microg b.i.d. dosage, although the group receiving 50 microg b.i.d. tolerated the drug better than those receiving 100 microg b.i.d. salmeterol.
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Boyd G, Morice AH, Pounsford JC, Siebert M, Peslis N, Crawford C. An evaluation of salmeterol in the treatment of chronic obstructive pulmonary disease (COPD). Eur Respir J 1997. [DOI: 10.1183/09031936.97.10040815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The objectives of this study were to compare the efficacy and safety of salmeterol xinafoate (50 and 100 microg b.i.d.) with that of placebo, when added to existing therapy, in the treatment of patients with chronic obstructive pulmonary disease (COPD). Six hundred and seventy four patients were randomized to receive either salmeterol 50 microg b.i.d., salmeterol 100 microg b.i.d., or placebo treatment for a period of 16 weeks. The results showed a significant improvement in daily symptom scores noted for patients taking either 50 microg (p=0.043) or 100 microg b.i.d. salmeterol (p=0.01) compared with placebo, with a corresponding decrease in additional daytime salbutamol requirements for both salmeterol groups. The same pattern was reflected for night-time symptoms and additional salbutamol use. During treatment, forced expiratory volume in one second (FEV1) measurements improved significantly in each salmeterol group, with up to a 7% improvement observed at the end of the study. Although no difference was observed between treatment groups for the distance walked in 6 min, patients treated with salmeterol 50 microg b.i.d. were significantly less breathless than those treated with placebo after their 6 min walk, after 8 weeks (p=0.024) and 16 weeks (p=0.004) of therapy. Adverse events were similar in all three groups except for tremor, which was significantly higher in the 100 microg b.i.d. salmeterol group (p=0.005) compared both with 50 microg b.i.d. salmeterol and placebo. Salmeterol offered further positive improvement to the effect of therapy in patients with chronic obstructive pulmonary disease when added to their existing regimens. This clinical improvement was similar both with 50 and 100 microg b.i.d. dosage, although the group receiving 50 microg b.i.d. tolerated the drug better than those receiving 100 microg b.i.d. salmeterol.
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Cramer LP, Siebert M, Mitchison TJ. Identification of novel graded polarity actin filament bundles in locomoting heart fibroblasts: implications for the generation of motile force. J Cell Biol 1997; 136:1287-305. [PMID: 9087444 PMCID: PMC2132518 DOI: 10.1083/jcb.136.6.1287] [Citation(s) in RCA: 247] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/1996] [Revised: 01/08/1997] [Indexed: 02/04/2023] Open
Abstract
We have determined the structural organization and dynamic behavior of actin filaments in entire primary locomoting heart fibroblasts by S1 decoration, serial section EM, and photoactivation of fluorescence. As expected, actin filaments in the lamellipodium of these cells have uniform polarity with barbed ends facing forward. In the lamella, cell body, and tail there are two observable types of actin filament organization. A less abundant type is located on the inner surface of the plasma membrane and is composed of short, overlapping actin bundles (0.25-2.5 microm) that repeatedly alternate in polarity from uniform barbed ends forward to uniform pointed ends forward. This type of organization is similar to the organization we show for actin filament bundles (stress fibers) in nonlocomoting cells (PtK2 cells) and to the known organization of muscle sarcomeres. The more abundant type of actin filament organization in locomoting heart fibroblasts is mostly ventrally located and is composed of long, overlapping bundles (average 13 microm, but can reach up to about 30 microm) which span the length of the cell. This more abundant type has a novel graded polarity organization. In each actin bundle, polarity gradually changes along the length of the bundle. Actual actin filament polarity at any given point in the bundle is determined by position in the cell; the closer to the front of the cell the more barbed ends of actin filaments face forward. By photoactivation marking in locomoting heart fibroblasts, as expected in the lamellipodium, actin filaments flow rearward with respect to substrate. In the lamella, all marked and observed actin filaments remain stationary with respect to substrate as the fibroblast locomotes. In the cell body of locomoting fibroblasts there are two dynamic populations of actin filaments: one remains stationary and the other moves forward with respect to substrate at the rate of the cell body. This is the first time that the structural organization and dynamics of actin filaments have been determined in an entire locomoting cell. The organization, dynamics, and relative abundance of graded polarity actin filament bundles have important implications for the generation of motile force during primary heart fibroblast locomotion.
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