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December 2022

Report Orthopedic Surgery – Practical course

Biomedical Engineering Master Program, University of Bern

Final report

Abstract—As part of the orthopedic surgery practical course at the Sonnenhof Hospital in Bern, Switzerland, which took place from 12.09.2022 to 16.09.2022, students were asked to create a report of an examined / treated patient during this time period. This report presents a case of 52-year-old female which consulted the hospital due to occurring back pain. The following sections highlight the necessary theory to understand the specific case as well as the patient medical history – known as anamnese -, the patient examination procedure, discussion of the diagnosis, possible treatment options and long-term effects, and an ambulant filtration procedure of the back for pain relief.

Keywords - back pain, scoliosis, spine, thoracic vertebrae, disc herniation, facet joint filtration, VENUS® Skoliose system, VENUS® screw-shaft-fixation system

February 2022

Tissue Engineering study

Biomedical Engineering Master Program, University of Bern

Project title: Effects of carrier material and culture environment conditions on nucleus pulposus and annulus fibrosus cell cultures extracted from bovine intervertebral discs

Finn Bürki, Nicole Bernhardsgütter, Joshua Dan Spreng
Tissue Engineering Practical Course – Final Report, Biomedical Engineering, University of Bern

Abstract—The aim of this study is to investigate the effects of micro-environment conditions (such as oxygen concentration) on cell cultures regarding extra cellular matrix (ECM) production and cell viability, activity and proliferation (our hypotheses based on [24] are listed below and further discussed under 1 Introduction). Nucleus pulposus (NP) and annulus fibrosus (AF) cells were harvested from tails of young bovines (tissue obtained under compliance of the 3R principle from a local abattoir) and cultured in two different hydrogel scaffold materials (alginate and agarose). Based on research showing that 3D scaffold structures yield in conditions that are closer to the native tissue environment, carriers in three dimensions rather than in two dimensions were used. An additional aim of this study is to investigate if the two different cell types alter their physiological behaviour and development when exposed to different oxygen concentration. To obtain results in this regard we cultivated the NP and AF cells under both normoxia (21% oxygen concentration) and hypoxia (1.5% oxygen concentration). To quantify the amount of ECM produced, we determined the amount of gylcosaminoglyan (GAG) by performing a dimethylmethylene blue (DMMB) assay. To determine the cell activity, we performed an Alamar blue assay and to investigate the cell viability we measured the DNA content present in the different cell cultures. Furthermore, a real-time RT-qPCR, using both forward and reverse primers, for aggrecan (ACAN), collagen type 1 and 2, and HIF-1Alpha was done to establish the performance of ECM production. In a final step, thin layers of the cell culture carriers were created using a cryosection machine. These were transferred to microscopy slides which again were stained with Mayer's haematoxylin, eosin and Alcian blue for visual inspection purposes of the cells and their compartments. The histological sections were qualitatively analysed by visual inspection using an inverted microscope featuring a digital NIKON camera with live-view capability. We found that for both AF and NP cells in both carrier materials and under both conditions the DNA content production increased over the timespan. Overall, DNA content and GAG content have been found the highest in the combination alginate and hypoxia, suggesting that alginate is a more favourable carrier for these cells. Since the two cell types are native an avascular and therefore hypoxically conditioned environment, we expected that the cell cultures would strive more in these conditions compared to a normoxic situation. For future studies a longer incubation time might be preferred to investigate for significant differences among carrier materials and culture conditions.

Hypothesis 1: Different types of primary cells perform proliferation at a different speed.

Hypothesis 2: Different culture environment conditions influence how NP and AF cells proliferate, produce extra cellular matrix and how active they are.

Hypothesis 3: The two cell types respond differently to an alteration of oxygen concentration by producing different degrees of extra cellular matrix (ECM).


Keywords - Low back pain, intervertebral disk, bovine annulus fibrosus (AF) and nucleus pulposus (NP), hydrogels alginate / agarose, hypoxia / normoxia, RNA, DNA, GAG, DMMB, real-time RT-qPCR, aggrecan (ACAN), collagen type 1 and 2, HIF-1Alpha.

July 2018 - June 2019

Department for Diagnostic, Interventional and Pediatric Radiology (DIPR), University Hospital Inselspital Bern, Switzerland

Professor von Tengg-Kobligk | Dr. Bernd Jung
Research intern MR Physics

Project: 4D blood flow measurements using MRI systems

More details will follow.

March - May 2018

Prakash Lab, Department of Bioengineering, Stanford University, CA, USA

Professor Manu Prakash | Dr. Clarice Aiello
Research intern

Project: Building of a vacuum chamber for a frugal electron microscope

- Worked together with Dr. Clarice Demarchie Aiello on the assembly of an electron microscope.
- Assisted with mechanical assembly and problem solving for the vacuum chamber.
- Participated in lab safety and training programs (biological safety, chemical safety, mechanical / workshop safety, laser safety, emergency training)

March - May 2018

Molecular Imagining Instrumentation Laboratory (MIIL), Stanford Medicine, Stanford University, CA, USA

Professor Craig Levin | Brian J. Lee
Research intern

Project: Performance analysis of a liquid cooling system for the detector submodules of a PET insert for simultaneous PET / MRI imaging using simulation software

More details will follow.

June - July 2017

Molecular Imagining Instrumentation Laboratory (MIIL), Stanford Medicine, Stanford University, CA, USA

Professor Craig Levin | Brian J. Lee
Research intern

Project: Construction of a shielding enclosure with high RF shielding effictiveness for detectors of a PET insert for simulaneous PET / MRI imaging

I helped with the construction of the new shielding enclosure for the PET detectors for simultaneous PET and MRI scanning (applied phosphor copper mesh with two component epoxy to carbon fiber composite, built the enclosure together). Tested the shielding enclosure's upon RF permeability and gradient-induced eddy current performance in various experiments including bench tests (S21 measurements) using a network analyzer and MRI system tests (using gradient intense Echo Planar sequence images). Evaluated ghosting artifacts created by induced eddy currents using DIACOM Viewer 64 bit. Attended MRI safety program, weekly lab meetings and talks, wrote project report and gave a presentation to the MIIL group.

Fall 2017

Mathematics & Computer Science Department, Lake Forest College, IL, USA

CS Tutorial project: Sign Language recognition using Computer Vision Techniques

Abstract—In recent years, the science of computer vision has developed immensely. While new technology and methods bring complexity to the field, a comparative understanding of new and old methods is essential to understand how methods have evolved. With the case of static hand gesture recognition, many methods previously documented can give insight into how emerging methods may be refined and improved. With the use and training of the new Convolutional Neural Network (CNN) process, the sign language alphabet can be identified from a data set consisting images of the individual sign language alphabet hand gestures. To better understand the recognition process in CNNs, older methods can be compared with the results created by a CNN in order to understand the incorporated analytical engine. This paper contrasts the results of convolutional neural networks with the method of the k-th nearest neighbor applied to the images. This process allows the analysis of programmer and neural network interaction.