Design methods and geometric modelling of scaffolds for bone tissue engineering

Every year, thousand of surgical treatments are performed in order to fix up or completely substitute, where possible, organs or tissues affected by degenerative diseases. Patients with these kind of illnesses stay long times waiting for a donor that could replace, in a short time, the damaged organ or the tissue. The lack of biological alternates, related to conventional surgical treatments as autografts, allografts, e xenografts, led the researchers belonging to different areas to collaborate to find out innovative solutions. This research brought to a new discipline able to merge molecular biology, biomaterial, engineering, biomechanics and, recently, design and architecture knowledges. This discipline is named Tissue Engineering (TE) and it represents a step forward towards the substitutive or regenerative medicine. One of the major challenge of the TE is to design and develop, using a biomimetic approach, an artificial 3D anatomy scaffold, suitable for cells adhesion that are able to proliferate and differentiate themselves as consequence of the biological and biophysical stimulus offered by the specific tissue to be replaced. Nowadays, powerful instruments allow to perform analysis day by day more accurateand defined on patients that need more precise diagnosis and treatments.Starting from patient specific information provided by TC (Computed Tomography) microCT and MRI(Magnetic Resonance Imaging), an image-based approach can be performed in order to reconstruct the site to be replaced. With the aid of the recent Additive Manufacturing techniques that allow to print tridimensional objects with sub millimetric precision, it is now possible to practice an almost complete control of the parametrical characteristics of the scaffold: this is the way to achieve a correct cellular regeneration. In this work, we focalize the attention on a branch of TE known as Bone TE, whose the bone is main subject. Bone TE combines osteoconductive and morphological aspects of the scaffold, whose main properties are pore diameter, structure porosity and interconnectivity. The realization of the ideal values of these parameters represents the main goal of this work: here we'll a create simple and interactive biomimetic design process based on 3D CAD modeling and generative algorithmsthat provide a way to control the main properties and to create a structure morphologically similar to the cancellous bone. Two different typologies of scaffold will be compared: the first is based on Triply Periodic MinimalSurface (T.P.M.S.) whose basic crystalline geometries are nowadays used for Bone TE scaffolding; the second is based on using Voronoi's diagrams and they are more often used in the design of decorations and jewellery for their capacity to decompose and tasselate a volumetric space using an heterogeneous spatial distribution (often frequent in nature). In this work, we will show how to manipulate the main properties (pore diameter, structure porosity and interconnectivity) of the design TE oriented scaffolding using the implementation of generative algorithms: "bringing back the nature to the nature".

Physiologie eines erlernten Körpermodells in Drosophila melanogaster

In der vorliegenden Dissertation wird ein Körpergrößengedächtnis untersucht. Es wird dargestellt, wie diese Information über die Reichweite der Fliege beim Lückenklettern unter kotrollierten Umweltbedingungen erworben und prozessiert wird. Zusätzlich wird geklärt, welche biochemischen Signale benötigt werden, um daraus ein lang anhalten-des Gedächtnis zu formen. Adulte Fliegen sind in der Lage, ihre Körperreichweite zu lernen. Naive Fliegen, die in der Dunkelheit gehalten wurden, versuchen erfolglos, zu breite Lücken zu überqueren, während visuell erfahrene Fliegen die Kletterversuche an ihre Körpergröße anpassen. Erfahrene kleine Fliegen scheinen Kenntnis ihres Nachteils zu haben. Sie kehren an Lückenbreiten um, welche ihre größeren Artgenos-sen durchaus noch versuchen. Die Taufliegen lernen die größenabhängige Reichweite über die visuelle Rückmeldung während des Laufens (aus Parallaxenbewegung). Da-bei reichen 15 min in strukturierter, heller Umgebung aus. Es gibt keinen festgelegten Beginn der sensiblen Phase. Nach 2 h ist das Gedächtnis jedoch konsolidiert und kann durch Stress nicht mehr zerstört oder durch sensorische Eingänge verändert werden. Dunkel aufgezogene Fliegen wurden ausgewählten Streifenmustern mit spezifischen Raumfrequenzen ausgesetzt. Nur die Insekten, welche mit einem als „optimal“ klassi-fizierten Muster visuell stimuliert wurden, sind in der Lage, die Körperreichweite einzu-schätzen, indem die durchschnittliche Schrittlänge in Verbindung mit der visuellen Wahrnehmung gebracht wird. Überraschenderweise ist es sogar mittels partieller Kompensation der Parallaxen möglich, naive Fliegen so zu trainieren, dass sie sich wie kleinere Exemplare verhalten. Da die Experimente ein Erlernen der Körperreich-weite vermuten lassen, wurden lernmutante Stämme beim Lückenüberwinden getes-tet. Sowohl die Ergebnisse von rut1- und dnc1-Mutanten, als auch das defizitäre Klet-tern von oc1-Fliegen ließ eine Beteiligung der cAMP-abhängigen Lernkaskade in der Protocerebralbrücke (PB) vermuten. Rettungsexperimente der rut1- und dnc1-Hinter-gründe kartierten das Gedächtnis in unterschiedliche Neuronengruppen der PB, wel-che auch für die visuelle Ausrichtung des Kletterns benötigt werden. Erstaunlicher-weise haben laterale lokale PB-Neurone und PFN-Neurone (Projektion von der PB über den fächerförmigen Körper zu den Noduli) verschiedene Erfordernisse für cAMP-Signale. Zusammenfassend weisen die Ergebnisse darauf hin, dass hohe Mengen an cAMP/PKA-Signalen in den latero-lateralen Elementen der PB benötigt werden, wäh-rend kolumnäre PFN-Neurone geringe oder keine Mengen an cAMP/PKA erfordern. Das Körperreichweitengedächtnis ist vermutlich das am längsten andauernde Ge-dächtnis in Drosophila. Wenn es erst einmal konsolidiert ist hält es länger als drei Wo-chen.rnAußerdem kann die Fruchtliege Drosophila melanogaster trainiert werden, die kom-plexe motorische Aufgabe des Lückenkletterns zu optimieren. Die trainierten Fliegen werden erfolgreicher und schneller beim Überqueren von Lücken, welche größer sind als sie selbst. Dabei existiert eine Kurzeitkomponente (STM), die 40 min nach dem ersten Training anhält. Nach weiteren vier Trainingsdurchläufen im Abstand von 20 min wird ein Langzeitgedächtnis (LTM) zum Folgetag geformt. Analysen mit Mutati-onslinien wiesen eine Beteiligung der cAMP-abhängigen Lernkaskade an dieser Ge-dächtnisform auf. Rettungsexperimente des rut2080-Hintergrunds kartierten sowohl das STM, als auch das LTM in PFN-Neuronen. Das STM kann aber ebenso in den alpha- und beta- Loben der Pilzkörper gerettet werden.rnLetztendlich sind wildtypische Fliegen sogar in der Lage, sich an einen Verlust eines Mittelbeintarsuses und dem einhergehenden Fehlen des Adhäsionsorgans am Tarsusende anzupassen. Das Klettern wird zwar sofort schlechter, erholt sich aber bis zum Folgetag wieder auf ein normales Niveau. Dieser neue Zustand erfordert ein Ge-dächtnis für die physischen Möglichkeiten, die nur durch plastische Veränderungen im Nervensystem des Insekts erreicht werden können.

Investigation of petabyte-scale data transfer performances with PhEDEx for the CMS experiment

PhEDEx, the CMS transfer management system, during the first LHC Run has moved about 150 PB and currently it is moving about 2.5 PB of data per week over the Worldwide LHC Computing Grid (WLGC). It was designed to complete each transfer required by users at the expense of the waiting time necessary for its completion. For this reason, after several years of operations, data regarding transfer latencies has been collected and stored into log files containing useful analyzable informations. Then, starting from the analysis of several typical CMS transfer workflows, a categorization of such latencies has been made with a focus on the different factors that contribute to the transfer completion time. The analysis presented in this thesis will provide the necessary information for equipping PhEDEx in the future with a set of new tools in order to proactively identify and fix any latency issues. PhEDEx, il sistema di gestione dei trasferimenti di CMS, durante il primo Run di LHC ha trasferito all’incirca 150 PB ed attualmente trasferisce circa 2.5 PB di dati alla settimana attraverso la Worldwide LHC Computing Grid (WLCG). Questo sistema è stato progettato per completare ogni trasferimento richiesto dall’utente a spese del tempo necessario per il suo completamento. Dopo svariati anni di operazioni con tale strumento, sono stati raccolti dati relativi alle latenze di trasferimento ed immagazzinati in log files contenenti informazioni utili per l’analisi. A questo punto, partendo dall’analisi di una ampia mole di trasferimenti in CMS, è stata effettuata una suddivisione di queste latenze ponendo particolare attenzione nei confronti dei fattori che contribuiscono al tempo di completamento del trasferimento. L’analisi presentata in questa tesi permetterà di equipaggiare PhEDEx con un insieme di utili strumenti in modo tale da identificare proattivamente queste latenze e adottare le opportune tattiche per minimizzare l’impatto sugli utenti finali.

VMC++ validation for photon beams in the energy range of 20-1000 keV

In high energy teletherapy, VMC++ is known to be a very accurate and efficient Monte Carlo (MC) code. In principle, the MC method is also a powerful dose calculation tool in other areas in radiation oncology, e.g., brachytherapy or orthovoltage radiotherapy. However, VMC++ is not validated for the low-energy range of such applications. This work aims in the validation of the VMC++ MC code for photon beams in the energy range between 20 and 1000 keV.

Monte Carlo dose calculation improvements for low energy electron beams using eMC

The electron Monte Carlo (eMC) dose calculation algorithm in Eclipse (Varian Medical Systems) is based on the macro MC method and is able to predict dose distributions for high energy electron beams with high accuracy. However, there are limitations for low energy electron beams. This work aims to improve the accuracy of the dose calculation using eMC for 4 and 6 MeV electron beams of Varian linear accelerators. Improvements implemented into the eMC include (1) improved determination of the initial electron energy spectrum by increased resolution of mono-energetic depth dose curves used during beam configuration; (2) inclusion of all the scrapers of the applicator in the beam model; (3) reduction of the maximum size of the sphere to be selected within the macro MC transport when the energy of the incident electron is below certain thresholds. The impact of these changes in eMC is investigated by comparing calculated dose distributions for 4 and 6 MeV electron beams at source to surface distance (SSD) of 100 and 110 cm with applicators ranging from 6 x 6 to 25 x 25 cm(2) of a Varian Clinac 2300C/D with the corresponding measurements. Dose differences between calculated and measured absolute depth dose curves are reduced from 6% to less than 1.5% for both energies and all applicators considered at SSD of 100 cm. Using the original eMC implementation, absolute dose profiles at depths of 1 cm, d(max) and R50 in water lead to dose differences of up to 8% for applicators larger than 15 x 15 cm(2) at SSD 100 cm. Those differences are now reduced to less than 2% for all dose profiles investigated when the improved version of eMC is used. At SSD of 110 cm the dose difference for the original eMC version is even more pronounced and can be larger than 10%. Those differences are reduced to within 2% or 2 mm with the improved version of eMC. In this work several enhancements were made in the eMC algorithm leading to significant improvements in the accuracy of the dose calculation for 4 and 6 MeV electron beams of Varian linear accelerators.

Comparison of monte carlo collimator transport methods for photon treatment planning in radiotherapy

The aim of this work was a Monte Carlo (MC) based investigation of the impact of different radiation transport methods in collimators of a linear accelerator on photon beam characteristics, dose distributions, and efficiency. Thereby it is investigated if it is possible to use different simplifications in the radiation transport for some clinical situations in order to save calculation time.

The Swiss IMRT dosimetry intercomparison using a thorax phantom

In 2008, a national intensity modulated radiation therapy (IMRT) dosimetry intercomparison was carried out for all 23 radiation oncology institutions in Switzerland. It was the aim to check the treatment chain focused on the planning, dose calculation, and irradiation process.

Monte Carlo Dose Calculation on Deforming Anatomy

This article presents the implementation and validation of a dose calculation approach for deforming anatomical objects. Deformation is represented by deformation vector fields leading to deformed voxel grids representing the different deformation scenarios. Particle transport in the resulting deformed voxels is handled through the approximation of voxel surfaces by triangles in the geometry implementation of the Swiss Monte Carlo Plan framework. The focus lies on the validation methodology which uses computational phantoms representing the same physical object through regular and irregular voxel grids. These phantoms are chosen such that the new implementation for a deformed voxel grid can be compared directly with an established dose calculation algorithm for regular grids. Furthermore, separate validation of the aspects voxel geometry and the density changes resulting from deformation is achieved through suitable design of the validation phantom. We show that equivalent results are obtained with the proposed method and that no statistically significant errors are introduced through the implementation for irregular voxel geometries. This enables the use of the presented and validated implementation for further investigations of dose calculation on deforming anatomy.

Monte Carlo implementation, validation, and characterization of a 120 leaf MLC

Recently, the new high definition multileaf collimator (HD120 MLC) was commercialized by Varian Medical Systems providing high resolution in the center section of the treatment field. The aim of this work is to investigate the characteristics of the HD120 MLC using Monte Carlo (MC) methods.

Validation of the Swiss Monte Carlo Plan for a static and dynamic 6 MV photon beam

Monte Carlo (MC) based dose calculations can compute dose distributions with an accuracy surpassing that of conventional algorithms used in radiotherapy, especially in regions of tissue inhomogeneities and surface discontinuities. The Swiss Monte Carlo Plan (SMCP) is a GUI-based framework for photon MC treatment planning (MCTP) interfaced to the Eclipse treatment planning system (TPS). As for any dose calculation algorithm, also the MCTP needs to be commissioned and validated before using the algorithm for clinical cases. Aim of this study is the investigation of a 6 MV beam for clinical situations within the framework of the SMCP. In this respect, all parts i.e. open fields and all the clinically available beam modifiers have to be configured so that the calculated dose distributions match the corresponding measurements. Dose distributions for the 6 MV beam were simulated in a water phantom using a phase space source above the beam modifiers. The VMC++ code was used for the radiation transport through the beam modifiers (jaws, wedges, block and multileaf collimator (MLC)) as well as for the calculation of the dose distributions within the phantom. The voxel size of the dose distributions was 2mm in all directions. The statistical uncertainty of the calculated dose distributions was below 0.4%. Simulated depth dose curves and dose profiles in terms of [Gy/MU] for static and dynamic fields were compared with the corresponding measurements using dose difference and γ analysis. For the dose difference criterion of ±1% of D(max) and the distance to agreement criterion of ±1 mm, the γ analysis showed an excellent agreement between measurements and simulations for all static open and MLC fields. The tuning of the density and the thickness for all hard wedges lead to an agreement with the corresponding measurements within 1% or 1mm. Similar results have been achieved for the block. For the validation of the tuned hard wedges, a very good agreement between calculated and measured dose distributions was achieved using a 1%/1mm criteria for the γ analysis. The calculated dose distributions of the enhanced dynamic wedges (10°, 15°, 20°, 25°, 30°, 45° and 60°) met the criteria of 1%/1mm when compared with the measurements for all situations considered. For the IMRT fields all compared measured dose values agreed with the calculated dose values within a 2% dose difference or within 1 mm distance. The SMCP has been successfully validated for a static and dynamic 6 MV photon beam, thus resulting in accurate dose calculations suitable for applications in clinical cases.

A virtual source model for kilo-voltage cone beam CT: source characteristics and model validation

The purpose of this investigation was to study the source characteristics of a clinical kilo-voltage cone beam CT unit and to develop and validate a virtual source model that could be used for treatment planning purposes.

Bioabsorbable pins for treatment of osteochondral fractures of the knee after acute patella dislocation in children and young adolescents

A retrospective study was performed on the use of bioabsorbable pins in the fixation of osteochondral fractures (OCFs) after traumatic patellar dislocation in children. Eighteen children (13 females, 5 males) aged 11 to 15 years (mean age 13.1 years) with osteochondral fracture (OCF) of the knee joint were treated at the authors' institution. Followup ranged from 22 months to 5 years. Diagnosis was verified by X-ray and magnetic resonance imaging (MRI) of the knee and patella. In seven patients the osteochondral fragment was detached from the patella and in 11 it was detached from the lateral femoral condyle. All patients were subjected to open reduction and fixation of the lesion with bioabsorbable pins. Postoperatively, the knee was immobilized in a cast and all patients were mobilized applying a standardized protocol. Bone consolidation was successful in 17 of the 18 patients. Bioabsorbable pins reliably fix OCF in children and adolescents, demonstrating a high incidence of consolidation of the detached osteochondral fragment in short- and middle-term followup without requiring further operative procedures.

Generalized eMC implementation for Monte Carlo dose calculation of electron beams from different machine types

The electron Monte Carlo (eMC) dose calculation algorithm available in the Eclipse treatment planning system (Varian Medical Systems) is based on the macro MC method and uses a beam model applicable to Varian linear accelerators. This leads to limitations in accuracy if eMC is applied to non-Varian machines. In this work eMC is generalized to also allow accurate dose calculations for electron beams from Elekta and Siemens accelerators. First, changes made in the previous study to use eMC for low electron beam energies of Varian accelerators are applied. Then, a generalized beam model is developed using a main electron source and a main photon source representing electrons and photons from the scattering foil, respectively, an edge source of electrons, a transmission source of photons and a line source of electrons and photons representing the particles from the scrapers or inserts and head scatter radiation. Regarding the macro MC dose calculation algorithm, the transport code of the secondary particles is improved. The macro MC dose calculations are validated with corresponding dose calculations using EGSnrc in homogeneous and inhomogeneous phantoms. The validation of the generalized eMC is carried out by comparing calculated and measured dose distributions in water for Varian, Elekta and Siemens machines for a variety of beam energies, applicator sizes and SSDs. The comparisons are performed in units of cGy per MU. Overall, a general agreement between calculated and measured dose distributions for all machine types and all combinations of parameters investigated is found to be within 2% or 2 mm. The results of the dose comparisons suggest that the generalized eMC is now suitable to calculate dose distributions for Varian, Elekta and Siemens linear accelerators with sufficient accuracy in the range of the investigated combinations of beam energies, applicator sizes and SSDs.

Macro Monte Carlo for dose calculation of proton beams

Although the Monte Carlo (MC) method allows accurate dose calculation for proton radiotherapy, its usage is limited due to long computing time. In order to gain efficiency, a new macro MC (MMC) technique for proton dose calculations has been developed. The basic principle of the MMC transport is a local to global MC approach. The local simulations using GEANT4 consist of mono-energetic proton pencil beams impinging perpendicularly on slabs of different thicknesses and different materials (water, air, lung, adipose, muscle, spongiosa, cortical bone). During the local simulation multiple scattering, ionization as well as elastic and inelastic interactions have been taken into account and the physical characteristics such as lateral displacement, direction distributions and energy loss have been scored for primary and secondary particles. The scored data from appropriate slabs is then used for the stepwise transport of the protons in the MMC simulation while calculating the energy loss along the path between entrance and exit position. Additionally, based on local simulations the radiation transport of neutrons and the generated ions are included into the MMC simulations for the dose calculations. In order to validate the MMC transport, calculated dose distributions using the MMC transport and GEANT4 have been compared for different mono-energetic proton pencil beams impinging on different phantoms including homogeneous and inhomogeneous situations as well as on a patient CT scan. The agreement of calculated integral depth dose curves is better than 1% or 1 mm for all pencil beams and phantoms considered. For the dose profiles the agreement is within 1% or 1 mm in all phantoms for all energies and depths. The comparison of the dose distribution calculated using either GEANT4 or MMC in the patient also shows an agreement of within 1% or 1 mm. The efficiency of MMC is up to 200 times higher than for GEANT4. The very good level of agreement in the dose comparisons demonstrate that the newly developed MMC transport results in very accurate and efficient dose calculations for proton beams.

General Protocol for the Culture of Cells on Plasma-Coated Electrospun Scaffolds

As opposed to culture on standard tissue-treated plastic, cell culture on three-dimensional scaffolds impedes additional challenges with respect to substrate preparation, cell seeding, culture maintenance, and analysis. We herewith present a general route for the culture of primary cells, differentiated cells, or stem cells on plasma-coated, electrospun scaffolds. We describe a method to prepare and fix the scaffolds in culture wells and discuss a convenient method for cell seeding and subsequent analysis by scanning electron microscopy or immunohistology.