Browsing by study line "Lääketieteellinen fysiikka ja biofysiikka"

In order to streamline the diagnosis process and increase the accessibility of both magnetic resonance imaging (MRI) and magnetoencephalocraphy (MEG), the department of Neuroscience and Biomedical Engineering at Aalto University is developing a new hybrid MEG--MRI device capable of performing both of these imaging methods. Both methods are measured using an array of Superconducting QUantum Interference Device (SQUID) magnetometers, which are extremely sensitive detectors capable of detecting the small magnetic fields generated by the human brain. However, the changing magnetic fields utilized in the MRI implementation cause eddy currents in the magnetically shielded walls of the MEG--MRI room, causing artefacts in the measured signals. In order to nullify these currents, an additional magnetic field of a specifically designed pulse waveform is fed into the room in a new technique called Dynamical Coupling for Additional dimeNsions (DynaCAN). To help in the development of DynaCAN, a program designed to detect and flag SQUIDs which saturate due to various different reasons, such as the induced eddy current fields, has been created and is presented in this work. This program finds saturated and faulty signals using four different Fault Detection Filters (FDFs) and tests if they are physically consistent with the signals of their neighboring detectors using Consistency Analysis (CA). It was found that the FDFs are able to find unambiguously faulty signals repeatably, while CA was more unreliable and was very susceptible to bad data present in the data set it was analysing.

Eye plaque radiotherapy is a treatment method of ocular tumors: A sealed radiation source is temporarily placed on the surface of the eye in day surgery. Compared to externally delivered conventional radiation treatments, more precisely targeted brachytherapy allows a higher dose in the target tissue while keeping the dose to healthy tissue relatively low. In Finland, all eye plaque treatments are centralised in Helsinki and brachytherapy of the eye is performed annually on approximately 70 patients. Patient specific anatomy takes into account determination of specific location and shape of the tumor in respect of radio-biologically critical structures of the eye. Until now, this has not been systematically modeled in dose calculation of eye plaque brachytherapy at HUS. The new version of Plaque Simulator, a 3D treatment simulation and modeling package for I-125, Pd-103, Ir-192 and Ru-106 plaque therapy of ocular tumors, enables importation and digitisation of patient imaging data (fundus imaging, CT and MRI) which consequently allows for systematically accurate estimation of dose distribution not only in the tumor but also in surrounding healthy tissues. The aim of this Master’s thesis is to prepare the new version of Plaque Simulator simulation and modeling package for clinical use in patient dose calculation at HUS. A comparison is done between the dose calculation method of the old and the new version of Plaque Simulator, and the dose calculation parameters as well as the plaque modeling parameters are reviewed. The function of the image-based dose calculation method is also tested with an anonymised patient treated for a tumor of a more peculiar shape. The absorbed dose to water on the central axis of the radiation source is measured experimentally for two individual I-125-seed along with Ru-106-CCB-, I-125-CCB-, and two I-125-COB-plaques. Experimental results are compared with the results obtained from Plaque Simulator. Individual I-125-seed is used to calibrate the detector at a distance of 10 mm, yielding to a calibration factor of 0.808. The use of the gold parameter in the dose calculation is justified, and a dosimetry modifier of Plaque Simulator is found to be 1.226 for I-125-plaques. Ru-106-plaque measurements are not calibrated, making them only relative. However, an excellent correspondence is observed between Ru-106-plaque dose calculations in Plaque Simulator and the manufacturer’s certificate. The measurements are normalized to the manufacturer’s certificate with a normalisation factor of 1.117.

Nanodiscs are a synthetic model system for studying the behavior of cell membranes. They are used in experimental biological research to understand structural and functional properties of membrane proteins. Their utility is chiefly due to their water solubility and a relative native lipid environment for membrane proteins compared to other synthetic membrane systems. Though membrane proteins are frequently solubilized and stabilized in a nanodisc environment, the physical conditions that they are exposed to in a nanodisc have not been studied in detail. Additionally, the dynamic behavior of transmembrane proteins in a nanodisc environment has not been characterized with respect to a more typical planar bilayer environment. The results presented in this thesis formulate an answer to these open questions through atomistic molecular dynamics simulations and machine learning methods. Nanodiscs and bilayer systems with identical lipid compositions are systematically studied, and separately, both types of systems with adenosine receptor A2AR to understand the differences between the model systems. The membrane environment in the two systems is characterized by two well understood physical properties: the order parameter, and the diffusion of lipids in the membrane. The results not only affirm previous studies of nanodiscs but also provide novel insights into the membrane environment of the nanodisc systems. Finally, with the help of machine learning methods, the dynamical behaviour of the protein is shown to be significantly altered in the nanodisc system when compared to a planar bilayer environment. Specifically, it is shown that the activation behavior of A2AR is dependent on model system used to reconstitute the protein.

Tietokonetomografialla (TT) on ollut jo usean vuosikymmenen ajan tärkeä asema lääketieteellisenä kuvantamismenetelmänä, jolla pystytään tuottamaan tarkkoja leikekuvia kehon rakenteista. TT on historiansa aikana muuttunut ja kehittynyt menetelmänä teknologisten harppausten ansiosta. Kuvauksista on tullut nopeampia ja entistä tarkempia. Kaksoisenergiatietokonetomografia (KETT) on yksi TT-kuvantamisen kehitysaskel, jonka teoreettiset perusteet ovat olleet jo pitkään tiedossa, mutta joka on vasta viime vuosikymmenenä saanut enemmän sovelluskohteita. KETT lisää TT-kuvauksen materiaalierottelukykyä, mikä mahdollistaa tarkemman diagnostiikan ja vähentää jatkotutkimusten tarvetta. Laajempi KETT:n kliininen käyttö vaatii kuitenkin toimintatapojen muutosta ja pysyvän laadunvalvontaprotokollan muodostamista. Tämän maisterintutkielman tarkoituksena oli auttaa laadunvalvonnan kehittämistä HUS:n Diagnostiikkakeskuksessa kartoittamalla KETT-kuvausten toimintaa, kuvausparametrien vaikutusta tuloksiin ja laitekohtaisia eroja. Työhön kuuluvat mittaukset suunniteltiin ja toteutettiin yhdessä HUS:n Diagnostiikkakeskuksen Meilahden Tornisairaalan radiologian yksikön kanssa. Kuvauksissa käytettiin Siemens Healthineersin valmistamia SOMATOM Definition Flash - ja SOMATOM Force -laitteita sekä KETT-kuvantamiseen soveltuvaa testikappaletta. Mittauksissa tutkittiin testikappaleen pystysuuntaisen asettelun vaikutusta kuvauksista saataviin tuloksiin, materiaalien elektronitiheyden ja efektiivisen järjestysluvun määritystarkkuutta, varjoaineena käytetyn jodin pitoisuuden määritystarkkuutta ja kuvauksen annostason merkitystä. Työssä käytetyllä menetelmällä määritettiin testikappaleen materiaalien koostumuksellisia eroja. Tutkimuksen avulla voitiin havaita jodipitoisuuden määrittämisen olevan haasteellisempaa hyvin pienillä alueilla, mutta halkaisijaltaan 5 mm:n kokoisilla alueilla määritystarkkuus oli jo kohtalainen. Potilaan oikeanlaisen keskityksen ja kuvanlaadun havaittiin olevan erityisen tärkeää pehmytkudoksia kuvattaessa. Laitteiden välisten erojen todettiin olevan merkittävämpää eri laitemallien välillä kuin samanmallisten laitteiden välillä. Laadunvalvonnassa tulee ottaa huomioon laitteiden kalibraatio, jotta laitteiden välisiä eroja pystytään vähentämään. Jatkossa mittauksia tulee toteuttaa lisää mittausten välisen toistettavuuden varmistamiseksi.

This thesis examines the optical response of tuneable chiral plasmonic nanostructures in linear cross-polarization. Plasmonic gold-silver nanostructures composed of silver-coated gold nanorods, and dynamic DNA origami are investigated because of their optical properties of interest in the visible light wavelength region, and because of their controllable rotational asymmetry, which results in tuneable chirality in dimer structures. These plasmonic nanostructures present optical properties such as circular dichroism and optical rotatory dispersion. In this thesis we establish the relationship between perceived color, spectrometry, circular dichroism and optical rotatory dispersion of the samples, depending on the chiral geometry of the nanostructures within. The motivation is to predict perceived color from the chiral geometry of the nanostructures, which will enable visual detection for biosensing applications. Circular dichroism and optical rotatory dispersion give us detailed knowledge about the polarization state of a sample, but visible light detection and spectrometer measurements are more accessible and portable methods for characterizing the polarization state of a sample. We achieve color modulation from green to blue with the switching of chiral geometry, under cross-polarized white light. This has potential for biosensing applications, based on the perceived color change depending on the chiral geometry of the sample. The DNA origami structures react to the presence of an analyte by changing their chiral geometry. Possible applications in biosensing of analytes can be made more practical if the orientation of the DNA origami template can be determined from the perceived color or the transmission spectra, rather than from the less accessible circular dichroism or optical rotatory dispersion measurements.

In nuclear medicine, radiopharmaceuticals are administered to the patient to diagnose or treat various diseases. The radioactive activity of these radiopharmaceuticals is measured using a radionuclide calibrator. In this study, the response of a radionuclide calibrator in different measurement conditions was studied. Code system PENELOPE (2018) that applies Monte Carlo methods in electron and photon transport simulation was used to investigate the response as a function of photon energy emitted by the source, source location, source volume and source container type. These calculated results were compared to corresponding experimental results. Overall, the computational results conformed well with the experimental results. The computational energy-response followed a similar trend to the efficiency curve extracted from the manual of Capintec CRC-25R radionuclide calibrator. The response of the calibrator to a Tc-99m source as a function of both vertical and horizontal displacement was inspected, and the results indicated a cubic and exponential trend, respectively. In both cases, results present that there is an agreeing optimal depth range (14 - 23 cm) at which the source should be located. Within this range, the variation in response remains below 2 %. Furthermore, the central axis of the chamber was deemed horizontally optimal for measurements. In the radius range 0 - 2.1 cm, experimental results showed an increase of 4 % relative to the centre position. Corresponding calculated results presented an increase of about 3 %. The response as a function of volume and container type was calculated for Tc-99m and I-123 source, respectively. In the case of volume-response, computational results presented a decrease of around 0.5 % for volumes between 2 to 5 ml in a plastic syringe. Experimental methods showed a corresponding decrease no greater than 0.8 %. Measuring response in a 15C transparent glass vial instead of a 3 ml plastic syringe, showcased that the response is only 81 % and 75 % of that in the syringe in simulated and experimental results, respectively.