Stefan Weber | University of Bern (original) (raw)
Papers by Stefan Weber
Biophysical Journal, 2001
Structural changes in Escherichia coli DNA photolyase induced by binding of a (cis,syn)-cyclobuta... more Structural changes in Escherichia coli DNA photolyase induced by binding of a (cis,syn)-cyclobutane pyrimidine dimer (CPD) are studied by continuous-wave electron paramagnetic resonance and electron-nuclear double resonance spectroscopies, using the flavin adenine dinucleotide (FAD) cofactor in its neutral radical form as a naturally occurring electron spin probe. The electron paramagnetic resonance/electron-nuclear double resonance spectral changes are consistent with a large distance (Ն0.6 nm) between the CPD lesion and the 7,8-dimethyl isoalloxazine ring of FAD, as was predicted by recent model calculations on photolyase enzyme-substrate complexes. Small shifts of the isotropic proton hyperfine coupling constants within the FAD's isoalloxazine moiety can be understood in terms of the cofactor binding site becoming more nonpolar because of the displacement of water molecules upon CPD docking to the enzyme. Molecular orbital calculations of hyperfine couplings using density functional theory, in conjunction with an isodensity polarized continuum model, are presented to rationalize these shifts in terms of the changed polarity of the medium surrounding the FAD cofactor.
PloS one, 2018
To facilitate precise local ablation of hepatocellular carcinoma (HCC) in a setting of combined a... more To facilitate precise local ablation of hepatocellular carcinoma (HCC) in a setting of combined ablation and transarterial chemoembolization (TACE), we evaluated accuracy and efficiency of a novel technique for navigated positioning of ablation probes using intrahepatic tumor referencing and electromagnetic (EM) guidance, in a porcine model. An angiographic wire with integrated EM reference sensor at its tip was inserted via a transarterial femoral access and positioned in the vicinity of artificial liver tumors. The resulting offset distance between the tumor center and the intrahepatic endovascular EM reference was calculated. Subsequently, EM tracked ablation probes were inserted percutaneously and navigated toward the tumor center, relying on continuous EM guidance via the intrahepatic reference. Targeting accuracy was assessed as the Euclidean distance between the tip of the ablation probe and the tumor center (Target Positioning Error, TPE). Procedural efficiency was assessed ...
2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10, 2010
This paper presents an automated solution for precise detection of fiducial screws from three-dim... more This paper presents an automated solution for precise detection of fiducial screws from three-dimensional (3D) Computerized Tomography (CT)/Digital Volume Tomography (DVT) data for image-guided ENT surgery. Unlike previously published solutions, we regard the detection of the fiducial screws from the CT/DVT volume data as a pose estimation problem. We thus developed a model-based solution. Starting from a user-supplied initialization, our solution detects the fiducial screws by iteratively matching a computer aided design (CAD) model of the fiducial screw to features extracted from the CT/DVT data. We validated our solution on one conventional CT dataset and on five DVT volume datasets, resulting in a total detection of 24 fiducial screws. Our experimental results indicate that the proposed solution achieves much higher reproducibility and precision than the manual detection. Further comparison shows that the proposed solution produces better results on the DVT dataset than on the conventional CT dataset.
Hearing Research, 2010
Hypothesis: That the transmission paths of air and bone-conducted sound around, into and through ... more Hypothesis: That the transmission paths of air and bone-conducted sound around, into and through a human head can be accurately predicted by a three-dimensional acoustic wave propagation computational model. Background: Bone-conducted sound is the limiting factor in current hearing protection designs for very high noise environments such as those encountered by maintainers of military aircraft. The University of Illinois had developed a three-dimensional acoustic wave propagation model for the computation of sound
Annals of biomedical engineering, Jan 26, 2018
During robotic cochlear implantation a drill trajectory often passes at submillimeter distances f... more During robotic cochlear implantation a drill trajectory often passes at submillimeter distances from the facial nerve due to close lying critical anatomy of the temporal bone. Additional intraoperative safety mechanisms are thus required to ensure preservation of this vital structure in case of unexpected navigation system error. Electromyography based nerve monitoring is widely used to aid surgeons in localizing vital nerve structures at risk of injury during surgery. However, state of the art neuromonitoring systems, are unable to discriminate facial nerve proximity within submillimeter ranges. Previous work demonstrated the feasibility of utilizing combinations of monopolar and bipolar stimulation threshold measurements to discretize facial nerve proximity with greater sensitivity and specificity, enabling discrimination between safe (> 0.4 mm) and unsafe (< 0.1 mm) trajectories during robotic cochlear implantation (in vivo animal model). Herein, initial clinical validation...
Chem Phys Lett, 2004
Selective optimization of different isotopomers in an ionization process with shaped fs-laser pul... more Selective optimization of different isotopomers in an ionization process with shaped fs-laser pulses is presented for 23Na 39K/ 23Na 41K. By employing evolution strategies in a closed feedback loop a considerably high enhancement by a total factor of about 25 of one isotope compared to the other and reversed is measured. Surprisingly, vibrational levels of differing electronic states are utilized for the different isotopomer selections. Our approach generally allows to influence vibrational wave functions by coherent interaction with the corresponding spectral pulse components on the fs-time scale.
Proceedings of Spie the International Society For Optical Engineering, Feb 1, 2009
We are developing a linear array of micromirrors designed for optical, femtosecond laser pulse sh... more We are developing a linear array of micromirrors designed for optical, femtosecond laser pulse shaping. It is a bulkmicromachined device, capable of retarding or diminishing certain laser frequencies in order to perform phase and amplitude modulation within a frequency band spanning the UV to the near-infrared. The design consists of a linear array of mirrors fixed on either side by springs. They feature two degrees of freedom: Out-of-plane motion for phase shifting and rotational motion for binary amplitude modulation, both realized using vertical comb drives. The first applications will include femtosecond discrimination experiments on biomolecules.
MOEMS and Miniaturized Systems X, 2011
Shaping light with microtechnology components has been possible for many years. The Texas Instrum... more Shaping light with microtechnology components has been possible for many years. The Texas Instruments digital micromirror device (DMD) and all types of adaptive optics systems are very sophisticated tools, well established and widely used. Here we present, however, two very dedicated systems, where one is an extremely simple MEMS-based tunable diffuser, while the second device is complex micromirror array with
Annales françaises d'Oto-rhino-laryngologie et de Pathologie Cervico-faciale, 2014
Nature communications, 2015
Group 13 M(I) compounds often disproportionate into M(0) and M(III). Here, however, we show that ... more Group 13 M(I) compounds often disproportionate into M(0) and M(III). Here, however, we show that the reaction of the M(I) salt of the weakly coordinating alkoxyaluminate [Ga(I)(C6H5F)2](+)[Al(OR(F))4](-) (R(F)=C(CF3)3) with 2,2'-bipyridine (bipy) yields the paramagnetic and distorted octahedral [Ga(bipy)3](2+)(•){[Al(OR(F))4](-)}2 complex salt. While the latter appears to be a Ga(II) compound, both, EPR and DFT investigations assign a ligand-centred [Ga(III){(bipy)3}(•)](2+) radical dication. Surprisingly, the application of the heavier homologue [(I)n(I)(C6H5F)2](+)[Al(OR(F))4](-) leads to aggregation and formation of the homonuclear cationic triangular and rhombic [In3(bipy)6](3+), [In3(bipy)5](3+) and [In4(bipy)6](4+) metal atom clusters. Typically, such clusters are formed under strongly reductive conditions. Analysing the unexpected redox-neutral cationic cluster formation, DFT studies suggest a stepwise formation of the clusters, possibly via their triplet state and furthe...
Annals of biomedical engineering, Jan 10, 2015
Surgical robots have been proposed ex vivo to drill precise holes in the temporal bone for minima... more Surgical robots have been proposed ex vivo to drill precise holes in the temporal bone for minimally invasive cochlear implantation. The main risk of the procedure is damage of the facial nerve due to mechanical interaction or due to temperature elevation during the drilling process. To evaluate the thermal risk of the drilling process, a simplified model is proposed which aims to enable an assessment of risk posed to the facial nerve for a given set of constant process parameters for different mastoid bone densities. The model uses the bone density distribution along the drilling trajectory in the mastoid bone to calculate a time dependent heat production function at the tip of the drill bit. Using a time dependent moving point source Green's function, the heat equation can be solved at a certain point in space so that the resulting temperatures can be calculated over time. The model was calibrated and initially verified with in vivo temperature data. The data was collected in ...
A method is reported for creating, generating, and measuring parametrically shaped pulses for tim... more A method is reported for creating, generating, and measuring parametrically shaped pulses for time-bandwidth product >>5, which consists of a parametric pulse-shaping algorithm, a spatial light modulation system and a single shot interferometric characterization scheme (SEA TADPOLE) . The utilization of these tools marks the inception of a new method called SPECIFIC, shaped-pulse electric-field construction and interferometric characterization, capable of
This contribution presents an architecture, which enables collision-avoiding robot navigation in ... more This contribution presents an architecture, which enables collision-avoiding robot navigation in indoor-environments based on monocular visual information. This is achieved by neural linkage of image features with depth information, which can be extracted from the stream of visual data. A first approach only segments camera images into obstacle and passable underground regions with the exclusive help of suitably trained neural gases. An extended approach is introduced that merges the results of different segmenting procedures into a stable result. In this paper the efficiency of the algorithm will be described, problems in the real world application and their appropriate solutions will be pointed out.
This contribution presents an architecture, which enables collision-avoiding robot navigation in ... more This contribution presents an architecture, which enables collision-avoiding robot navigation in indoor-environments based on monocular visual information. This is achieved by neural linkage of image features with depth information, which can be extracted from the stream of visual data. A rst approach only segments camera images into obstacle and passable underground regions with the exclusive help of suitably trained neural gases. An extended approach is introduced that merges the results of different segmenting procedures into a stable result. In this paper the ef- ciency of the algorithm will be described, problems in the real world application and their appropriate solutions will be pointed out.
Biophysical Journal, 2001
Structural changes in Escherichia coli DNA photolyase induced by binding of a (cis,syn)-cyclobuta... more Structural changes in Escherichia coli DNA photolyase induced by binding of a (cis,syn)-cyclobutane pyrimidine dimer (CPD) are studied by continuous-wave electron paramagnetic resonance and electron-nuclear double resonance spectroscopies, using the flavin adenine dinucleotide (FAD) cofactor in its neutral radical form as a naturally occurring electron spin probe. The electron paramagnetic resonance/electron-nuclear double resonance spectral changes are consistent with a large distance (Ն0.6 nm) between the CPD lesion and the 7,8-dimethyl isoalloxazine ring of FAD, as was predicted by recent model calculations on photolyase enzyme-substrate complexes. Small shifts of the isotropic proton hyperfine coupling constants within the FAD's isoalloxazine moiety can be understood in terms of the cofactor binding site becoming more nonpolar because of the displacement of water molecules upon CPD docking to the enzyme. Molecular orbital calculations of hyperfine couplings using density functional theory, in conjunction with an isodensity polarized continuum model, are presented to rationalize these shifts in terms of the changed polarity of the medium surrounding the FAD cofactor.
PloS one, 2018
To facilitate precise local ablation of hepatocellular carcinoma (HCC) in a setting of combined a... more To facilitate precise local ablation of hepatocellular carcinoma (HCC) in a setting of combined ablation and transarterial chemoembolization (TACE), we evaluated accuracy and efficiency of a novel technique for navigated positioning of ablation probes using intrahepatic tumor referencing and electromagnetic (EM) guidance, in a porcine model. An angiographic wire with integrated EM reference sensor at its tip was inserted via a transarterial femoral access and positioned in the vicinity of artificial liver tumors. The resulting offset distance between the tumor center and the intrahepatic endovascular EM reference was calculated. Subsequently, EM tracked ablation probes were inserted percutaneously and navigated toward the tumor center, relying on continuous EM guidance via the intrahepatic reference. Targeting accuracy was assessed as the Euclidean distance between the tip of the ablation probe and the tumor center (Target Positioning Error, TPE). Procedural efficiency was assessed ...
2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10, 2010
This paper presents an automated solution for precise detection of fiducial screws from three-dim... more This paper presents an automated solution for precise detection of fiducial screws from three-dimensional (3D) Computerized Tomography (CT)/Digital Volume Tomography (DVT) data for image-guided ENT surgery. Unlike previously published solutions, we regard the detection of the fiducial screws from the CT/DVT volume data as a pose estimation problem. We thus developed a model-based solution. Starting from a user-supplied initialization, our solution detects the fiducial screws by iteratively matching a computer aided design (CAD) model of the fiducial screw to features extracted from the CT/DVT data. We validated our solution on one conventional CT dataset and on five DVT volume datasets, resulting in a total detection of 24 fiducial screws. Our experimental results indicate that the proposed solution achieves much higher reproducibility and precision than the manual detection. Further comparison shows that the proposed solution produces better results on the DVT dataset than on the conventional CT dataset.
Hearing Research, 2010
Hypothesis: That the transmission paths of air and bone-conducted sound around, into and through ... more Hypothesis: That the transmission paths of air and bone-conducted sound around, into and through a human head can be accurately predicted by a three-dimensional acoustic wave propagation computational model. Background: Bone-conducted sound is the limiting factor in current hearing protection designs for very high noise environments such as those encountered by maintainers of military aircraft. The University of Illinois had developed a three-dimensional acoustic wave propagation model for the computation of sound
Annals of biomedical engineering, Jan 26, 2018
During robotic cochlear implantation a drill trajectory often passes at submillimeter distances f... more During robotic cochlear implantation a drill trajectory often passes at submillimeter distances from the facial nerve due to close lying critical anatomy of the temporal bone. Additional intraoperative safety mechanisms are thus required to ensure preservation of this vital structure in case of unexpected navigation system error. Electromyography based nerve monitoring is widely used to aid surgeons in localizing vital nerve structures at risk of injury during surgery. However, state of the art neuromonitoring systems, are unable to discriminate facial nerve proximity within submillimeter ranges. Previous work demonstrated the feasibility of utilizing combinations of monopolar and bipolar stimulation threshold measurements to discretize facial nerve proximity with greater sensitivity and specificity, enabling discrimination between safe (> 0.4 mm) and unsafe (< 0.1 mm) trajectories during robotic cochlear implantation (in vivo animal model). Herein, initial clinical validation...
Chem Phys Lett, 2004
Selective optimization of different isotopomers in an ionization process with shaped fs-laser pul... more Selective optimization of different isotopomers in an ionization process with shaped fs-laser pulses is presented for 23Na 39K/ 23Na 41K. By employing evolution strategies in a closed feedback loop a considerably high enhancement by a total factor of about 25 of one isotope compared to the other and reversed is measured. Surprisingly, vibrational levels of differing electronic states are utilized for the different isotopomer selections. Our approach generally allows to influence vibrational wave functions by coherent interaction with the corresponding spectral pulse components on the fs-time scale.
Proceedings of Spie the International Society For Optical Engineering, Feb 1, 2009
We are developing a linear array of micromirrors designed for optical, femtosecond laser pulse sh... more We are developing a linear array of micromirrors designed for optical, femtosecond laser pulse shaping. It is a bulkmicromachined device, capable of retarding or diminishing certain laser frequencies in order to perform phase and amplitude modulation within a frequency band spanning the UV to the near-infrared. The design consists of a linear array of mirrors fixed on either side by springs. They feature two degrees of freedom: Out-of-plane motion for phase shifting and rotational motion for binary amplitude modulation, both realized using vertical comb drives. The first applications will include femtosecond discrimination experiments on biomolecules.
MOEMS and Miniaturized Systems X, 2011
Shaping light with microtechnology components has been possible for many years. The Texas Instrum... more Shaping light with microtechnology components has been possible for many years. The Texas Instruments digital micromirror device (DMD) and all types of adaptive optics systems are very sophisticated tools, well established and widely used. Here we present, however, two very dedicated systems, where one is an extremely simple MEMS-based tunable diffuser, while the second device is complex micromirror array with
Annales françaises d'Oto-rhino-laryngologie et de Pathologie Cervico-faciale, 2014
Nature communications, 2015
Group 13 M(I) compounds often disproportionate into M(0) and M(III). Here, however, we show that ... more Group 13 M(I) compounds often disproportionate into M(0) and M(III). Here, however, we show that the reaction of the M(I) salt of the weakly coordinating alkoxyaluminate [Ga(I)(C6H5F)2](+)[Al(OR(F))4](-) (R(F)=C(CF3)3) with 2,2'-bipyridine (bipy) yields the paramagnetic and distorted octahedral [Ga(bipy)3](2+)(•){[Al(OR(F))4](-)}2 complex salt. While the latter appears to be a Ga(II) compound, both, EPR and DFT investigations assign a ligand-centred [Ga(III){(bipy)3}(•)](2+) radical dication. Surprisingly, the application of the heavier homologue [(I)n(I)(C6H5F)2](+)[Al(OR(F))4](-) leads to aggregation and formation of the homonuclear cationic triangular and rhombic [In3(bipy)6](3+), [In3(bipy)5](3+) and [In4(bipy)6](4+) metal atom clusters. Typically, such clusters are formed under strongly reductive conditions. Analysing the unexpected redox-neutral cationic cluster formation, DFT studies suggest a stepwise formation of the clusters, possibly via their triplet state and furthe...
Annals of biomedical engineering, Jan 10, 2015
Surgical robots have been proposed ex vivo to drill precise holes in the temporal bone for minima... more Surgical robots have been proposed ex vivo to drill precise holes in the temporal bone for minimally invasive cochlear implantation. The main risk of the procedure is damage of the facial nerve due to mechanical interaction or due to temperature elevation during the drilling process. To evaluate the thermal risk of the drilling process, a simplified model is proposed which aims to enable an assessment of risk posed to the facial nerve for a given set of constant process parameters for different mastoid bone densities. The model uses the bone density distribution along the drilling trajectory in the mastoid bone to calculate a time dependent heat production function at the tip of the drill bit. Using a time dependent moving point source Green's function, the heat equation can be solved at a certain point in space so that the resulting temperatures can be calculated over time. The model was calibrated and initially verified with in vivo temperature data. The data was collected in ...
A method is reported for creating, generating, and measuring parametrically shaped pulses for tim... more A method is reported for creating, generating, and measuring parametrically shaped pulses for time-bandwidth product >>5, which consists of a parametric pulse-shaping algorithm, a spatial light modulation system and a single shot interferometric characterization scheme (SEA TADPOLE) . The utilization of these tools marks the inception of a new method called SPECIFIC, shaped-pulse electric-field construction and interferometric characterization, capable of
This contribution presents an architecture, which enables collision-avoiding robot navigation in ... more This contribution presents an architecture, which enables collision-avoiding robot navigation in indoor-environments based on monocular visual information. This is achieved by neural linkage of image features with depth information, which can be extracted from the stream of visual data. A first approach only segments camera images into obstacle and passable underground regions with the exclusive help of suitably trained neural gases. An extended approach is introduced that merges the results of different segmenting procedures into a stable result. In this paper the efficiency of the algorithm will be described, problems in the real world application and their appropriate solutions will be pointed out.
This contribution presents an architecture, which enables collision-avoiding robot navigation in ... more This contribution presents an architecture, which enables collision-avoiding robot navigation in indoor-environments based on monocular visual information. This is achieved by neural linkage of image features with depth information, which can be extracted from the stream of visual data. A rst approach only segments camera images into obstacle and passable underground regions with the exclusive help of suitably trained neural gases. An extended approach is introduced that merges the results of different segmenting procedures into a stable result. In this paper the ef- ciency of the algorithm will be described, problems in the real world application and their appropriate solutions will be pointed out.