Restoring function after neuromuscular trauma: novel paradigms for enhancing volitional control of neural activity in untethered environments and vHAB, a gamified therapy platform

Thesis (Ph.D.)--University of Washington, 2016-08

Synthetic Polymer and Microbubble Systems for Gene Delivery to the Brain

Thesis (Ph.D.)--University of Washington, 2016-08

Nucleic Acid Diagnostics using Isotachophoresis and Isothermal Amplification

Thesis (Ph.D.)--University of Washington, 2016-08

Prediction of Sudden Cardiac Arrest for Patients with Congestive Heart Failure

Thesis (Ph.D.)--University of Washington, 2016-07

Handling Heterogeneity in Collaborative Networked Surgical Simulators

Stand-alone and networked surgical virtual reality based simulators have been proposed as means to train surgical skills with or without a supervisor nearby the student or trainee -- However, surgical skills teaching in medicine schools and hospitals is changing, requiring the development of new tools to focus on: (i) importance of mentors role, (ii) teamwork skills and (iii) remote training support -- For these reasons, a surgical simulator should not only allow the training involving a student and an instructor that are located remotely, but also the collaborative training of users adopting different medical roles during the training sesión -- Collaborative Networked Virtual Surgical Simulators (CNVSS) allow collaborative training of surgical procedures where remotely located users with different surgical roles can take part in the training session -- To provide successful training involving good collaborative performance, CNVSS should handle heterogeneity factors such as users’ machine capabilities and network conditions, among others -- Several systems for collaborative training of surgical procedures have been developed as research projects -- To the best of our knowledge none has focused on handling heterogeneity in CNVSS -- Handling heterogeneity in this type of collaborative sessions is important because not all remotely located users have homogeneous internet connections, nor the same interaction devices and displays, nor the same computational resources, among other factors -- Additionally, if heterogeneity is not handled properly, it will have an adverse impact on the performance of each user during the collaborative sesión -- In this document, the development of a context-aware architecture for collaborative networked virtual surgical simulators, in order to handle the heterogeneity involved in the collaboration session, is proposed -- To achieve this, the following main contributions are accomplished in this thesis: (i) Which and how infrastructure heterogeneity factors affect the collaboration of two users performing a virtual surgical procedure were determined and analyzed through a set of experiments involving users collaborating, (ii) a context-aware software architecture for a CNVSS was proposed and implemented -- The architecture handles heterogeneity factors affecting collaboration, applying various adaptation mechanisms and finally, (iii) A mechanism for handling heterogeneity factors involved in a CNVSS is described, implemented and validated in a set of testing scenarios

Image-Guided Precision Manipulation of Cells and Nanoparticles in Microfluidics

Manipulation of single cells and particles is important to biology and nanotechnology. Our electrokinetic (EK) tweezers manipulate objects in simple microfluidic devices using gentle fluid and electric forces under vision-based feedback control. In this dissertation, I detail a user-friendly implementation of EK tweezers that allows users to select, position, and assemble cells and nanoparticles. This EK system was used to measure attachment forces between living breast cancer cells, trap single quantum dots with 45 nm accuracy, build nanophotonic circuits, and scan optical properties of nanowires. With a novel multi-layer microfluidic device, EK was also used to guide single microspheres along complex 3D trajectories. The schemes, software, and methods developed here can be used in many settings to precisely manipulate most visible objects, assemble objects into useful structures, and improve the function of lab-on-a-chip microfluidic systems.

Coarse Graining to Invesitigate Peptide-Lipid Interactions

Experimental characterization of molecular details is challenging, and although single molecule experiments have gained prominence, oligomer characterization remains largely unexplored. The ability to monitor the time evolution of individual molecules while they self assemble is essential in providing mechanistic insights about biological events. Molecular dynamics (MD) simulations can fill the gap in knowledge between single molecule experiments and ensemble studies like NMR, and are increasingly used to gain a better understanding of microscopic properties. Coarse-grained (CG) models aid in both exploring longer length and time scale molecular phenomena, and narrowing down the key interactions responsible for significant system characteristics. Over the past decade, CG techniques have made a significant impact in understanding physicochemical processes. However, the realm of peptide-lipid interfacial interactions, primarily binding, partitioning and folding of amphipathic peptides, remains largely unexplored compared to peptide folding in solution. The main drawback of existing CG models is the inability to capture environmentally sensitive changes in dipolar interactions, which are indigenous to protein folding, and lipid dynamics. We have used the Drude oscillator approach to incorporate structural polarization and dipolar interactions in CG beads to develop a minimalistic peptide model, WEPPROM (Water Explicit Polarizable PROtein Model), and a lipid model WEPMEM (Water Explicit Polarizable MEmbrane Model). The addition of backbone dipolar interactions in a CG model for peptides enabled us to achieve alpha-beta secondary structure content de novo, without any added bias. As a prelude to studying amphipathic peptide-lipid membrane interactions, the balance between hydrophobicity and backbone dipolar interactions in driving ordered peptide aggregation in water and at a hydrophobic-hydrophilic interface, was explored. We found that backbone dipole interactions play a crucial role in driving ordered peptide aggregation, both in water and at hydrophobic-hydrophilic interfaces; while hydrophobicity is more relevant for aggregation in water. A zwitterionic (POPC: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and an anionic lipid (POPS: 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine) are used as model lipids for WEPMEM. The addition of head group dipolar interactions in lipids significantly improved structural, dynamic and dielectric properties of the model bilayer. Using WEPMEM and WEPPROM, we studied membrane-induced peptide folding of a cationic antimicrobial peptide with anticancer activity, SVS-1. We found that membrane-induced peptide folding is driven by both (a) cooperativity in peptide self interaction and (b) cooperativity in membrane-peptide interactions. The dipolar interactions between the peptide and the lipid head-groups contribute to stabilizing folded conformations. The role of monovalent ion size and peptide concentration in driving lipid domain formation in anionic/zwitterionic lipid mixtures was also investigated. Our study suggest monovalent ion size to be a crucial determinant of interaction with lipid head groups, and hence domain formation in lipid mixtures. This study reinforces the role of dipole interactions in protein folding, lipid membrane properties, membrane induced peptide folding and lipid domain formation. Therefore, the models developed in this thesis can be used to explore a multitude of biomolecular processes, both at longer time-scales and larger system sizes.

THE ROLE OF THE MECHANICAL ENVIRONMENT ON CANCER CELL TRANSMIGRATION AND MRNA LOCALIZATION

Most cancer-related deaths are due to metastasis formation, the ability of cancer cells to break away from the primary tumor site, transmigrate through the endothelium, and form secondary tumors in distant areas. Many studies have identified links between the mechanical properties of the cellular microenvironment and the behavior of cancer cells. Cells may experience heterogeneous microenvironments of varying stiffness during tumor progression, transmigration, and invasion into the basement membrane. In addition to mechanical factors, the localization of RNAs to lamellipodial regions has been proposed to play an important part in metastasis. This dissertation provides a quantitative evaluation of the biophysical effects on cancer cell transmigration and RNA localization. In the first part of this dissertation, we sought to compare cancer cell and leukocyte transmigration and investigate the impact of matrix stiffness on transmigration process. We found that cancer cell transmigration includes an additional step, ‘incorporation’, into the endothelial cell (EC) monolayer. During this phase, cancer cells physically displace ECs and spread into the monolayer. Furthermore, the effects of subendothelial matrix stiffness and endothelial activation on cancer cell incorporation are cell-specific, a notable difference from the process by which leukocytes transmigrate. Collectively, our results provide mechanistic insights into tumor cell extravasation and demonstrate that incorporation into the endothelium is one of the earliest steps. In the next part of this work, we investigated how matrix stiffness impacts RNA localization and its relevance to cancer metastasis. In migrating cells, the tumor suppressor protein, adenomatous polyposis coli (APC) targets RNAs to cellular protrusions. We observed that increasing stiffness promotes the peripheral localization of these APC-dependent RNAs and that cellular contractility plays a role in regulating this pathway. We next investigated the mechanism underlying the effect of substrate stiffness and cellular contractility. We found that contractility drives localization of RNAs to protrusions through modulation of detyrosinated microtubules, a network of modified microtubules that associate with, and are required for localization of APC-dependent RNAs. These results raise the possibility that as the matrix environment becomes stiffer during tumor progression, it promotes the localization of RNAs and ultimately induces a metastatic phenotype.

Dynamic Coculture of a Prevascularized Engineered Bone Construct

The generation of functional, vascularized tissues is a key challenge for the field of tissue engineering. Before clinical implantations of tissue engineered bone constructs can succeed, in vitro fabrication needs to address limitations in large-scale tissue development, including controlled osteogenesis and an inadequate vasculature network to prevent necrosis of large constructs. The tubular perfusion system (TPS) bioreactor is an effective culturing method to augment osteogenic differentiation and maintain viability of human mesenchymal stem cell (hMSC)-seeded scaffolds while they are developed in vitro. To further enhance this process, we developed a novel osteogenic growth factors delivery system for dynamically cultured hMSCs using microparticles encapsulated in three-dimensional alginate scaffolds. In light of this increased differentiation, we characterized the endogenous cytokine distribution throughout the TPS bioreactor. An advantageous effect in the ‘outlet’ portion of the uniaxial growth chamber was discovered due to the system’s downstream circulation and the unique modular aspect of the scaffolds. This unique trait allowed us to carefully tune the differentiation behavior of specific cell populations. We applied the knowledge gained from the growth profile of the TPS bioreactor to culture a high-volume bone composite in a 3D-printed femur mold. This resulted in a tissue engineered bone construct with a volume of 200cm3, a 20-fold increase over previously reported sizes. We demonstrated high viability of the cultured cells throughout the culture period as well as early signs of osteogenic differentiation. Taking one step closer toward a viable implant and minimize tissue necrosis after implantation, we designed a composite construct by coculturing endothelial cells (ECs) and differentiating hMSCs, encouraging prevascularization and anastomosis of the graft with the host vasculature. We discovered the necessity of cell to cell proximity between the two cell types as well as preference for the natural cell binding capabilities of hydrogels like collagen. Notably, the results suggested increased osteogenic and angiogenic potential of the encapsulated cells when dynamically cultured in the TPS bioreactor, suggesting a synergistic effect between coculture and applied shear stress. This work highlights the feasibility of fabricating a high-volume, prevascularized tissue engineered bone construct for the regeneration of a critical size defect.

Avaliação da dose de radiação: angiotomografia coronariana - métodos retrospectivo e prospectivo

The aim of this study was to evaluate the effective dose received by patients undergoing CCTA in both acquisition methods in the period June 1st to October 30th, 2013. Data collection was performed at the Clínica Sabedotti in Ponta Grossa/PR, with General Electric Equipment VCT XT, 64 detections lines. The effective dose was measured from the thirty cases randomly selected of Picture Archival and Communication System – PACS, reported by Dose Lenght Product (DLP) equipment for each examination and the conversion factor (EDLP) set by the European Commission for cardiac region (EDLP = 0.014). The results showed significant differences in radiation dose delivered to the patient according to the employee acquisition method, Retrospective or Prospective of ECG.

Desenvolvimento de equipamento para estimular a propriocepção utilizando ímãs permanentes

This study developed the Magnetic Proprioceptive Stimulator – MPS at the Technological Federal University of Parana - UTFPR to stimulate, record and quantify the proprioceptive activity of the shoulder joint, using permanent magnets. A pilot study was conducted to investigate the proprioceptive stimulation generated by MPS. The results of this study show that the magnetic and mechanical forces generated by permanent magnets can change the static and dynamic stability of the shoulder joint. The angular changes of the shoulder joint during the stimulation of proprioception were photographed, videotaped and analyzed by vector editing program. The joint movements caused by the action of the magnets were recorded by an optical sensor installed in the MPS and displayed in a graphical interface for analyzing the proprioceptive dynamics. The study concluded that the Magnetic Proprioceptive Stimulator is safe, effective to stimulate proprioception and features high economic viability.

Desenvolvimento de equipamento para medir os intervalos R-R

This study aimed to develop a device to measure RR intervals, which have high correlation with the values of the gold standard device of electrocardiograph (ECG), by the time domain and frequency domain indices. To this end, a study was conducted with 18 students of Jiu-Jitsu, males with 35.5 ± 8.6 years, at least a weekly frequency of 3 times and one year training. The location was at the academy Gracie Barra de Curitiba PR. They underwent an examination at rest for a period of 7 minutes and then the results were converted into heart rate variability (HRV) and analyzed by the indexes in the time domain and the frequency domain. The results were compared statistically using the Pearson test and intraclass correlation (ICC) and according to them proves to be viable the development of this equipment, which is highly correlated and excellent reproducibility for measuring the RR intervals.

Medidas de concentração de radônio proveniente de argamassas de cimento portland, gesso e fosfogesso

Portland cement being very common construction material has in its composition the natural gypsum. To decrease the costs of manufacturing, the cement industry is substituting the gypsum in its composition by small quantities of phosphogypsum, which is the residue generated by the production of fertilizers and consists essentially of calcium dihydrate and some impurities, such as fluoride, metals in general, and radionuclides. Currently, tons of phosphogypsum are stored in the open air near the fertilizer industries, causing contamination of the environment. The 226 Ra present in these materials, when undergoes radioactive decay, produces the 222Rn gas. This radioactive gas, when inhaled together with its decay products deposited in the lungs, produces the exposure to radiation and can be a potential cause of lung cancer. Thus, the objective of this study was to measure the concentration levels of 222Rn from cylindrical samples of Portland cement, gypsum and phosphogypsum mortar from the state of Paraná, as well as characterizer the material and estimate the radon concentration in an environment of hypothetical dwelling with walls covered by such materials. Experimental setup of 222Rn activity measurements was based on AlphaGUARD detector (Saphymo GmbH). The qualitative and quantitative analysis was performed by gamma spectrometry and EDXRF with Au and Ag targets tubes (AMPTEK), and Mo target (ARTAX) and mechanical testing with x- ray equipment (Gilardoni) and the mechanical press (EMIC). Obtained average values of radon activity from studied materials in the air of containers were of 854 ± 23 Bq/m3, 60,0 ± 7,2 Bq/m3 e 52,9 ± 5,4 Bq/m3 for Portland cement, gypsum and phosphogypsum mortar, respectively. These results extrapolated into the volume of hypothetical dwelling of 36 m3 with the walls covered by such materials were of 3366 ± 91 Bq/m3, 237 ± 28 Bq/m3 e 208 ± 21 Bq/m3for Portland cement, gypsum and phosphogypsum mortar, respectively. Considering the limit of 300 Bq/m3 established by the ICRP, it could be concluded that the use of Portland cement plaster in dwellings is not secure and requires some specific mitigation procedure. Using the results of gamma spectrometry there were calculated the values of radium equivalent activity concentrations (Raeq) for Portland cement, gypsum and phosphogypsum mortar, which were obtained equal to 78,2 ± 0,9 Bq/kg; 58,2 ± 0,9 Bq/kg e 68,2 ± 0,9 Bq/kg, respectively. All values of radium equivalent activity concentrations for studied samples are below the maximum level of 370 Bq/kg. The qualitative and quantitative analysis of EDXRF spectra obtained with studied mortar samples allowed to evaluate quantitate and the elements that constitute the material such as Ca, S, Fe, and others.

Numerical simulation of strain-adaptive bone remodelling in the ankle joint

Background: The use of artificial endoprostheses has become a routine procedure for knee and hip joints while ankle arthritis has traditionally been treated by means of arthrodesis. Due to its advantages, the implantation of endoprostheses is constantly increasing. While finite element analyses (FEA) of strain-adaptive bone remodelling have been carried out for the hip joint in previous studies, to our knowledge there are no investigations that have considered remodelling processes of the ankle joint. In order to evaluate and optimise new generation implants of the ankle joint, as well as to gain additional knowledge regarding the biomechanics, strain-adaptive bone remodelling has been calculated separately for the tibia and the talus after providing them with an implant. Methods: FE models of the bone-implant assembly for both the tibia and the talus have been developed. Bone characteristics such as the density distribution have been applied corresponding to CT scans. A force of 5,200 N, which corresponds to the compression force during normal walking of a person with a weight of 100 kg according to Stauffer et al., has been used in the simulation. The bone adaptation law, previously developed by our research team, has been used for the calculation of the remodelling processes. Results: A total bone mass loss of 2% in the tibia and 13% in the talus was calculated. The greater decline of density in the talus is due to its smaller size compared to the relatively large implant dimensions causing remodelling processes in the whole bone tissue. In the tibia, bone remodelling processes are only calculated in areas adjacent to the implant. Thus, a smaller bone mass loss than in the talus can be expected. There is a high agreement between the simulation results in the distal tibia and the literature regarding. Conclusions: In this study, strain-adaptive bone remodelling processes are simulated using the FE method. The results contribute to a better understanding of the biomechanical behaviour of the ankle joint and hence are useful for the optimisation of the implant geometry in the future.

Modelagem eletroquímica e do distúrbio ácido-básico em atletas de karatê participantes do campeonato mundial WKO 2014

The objective of this study was to analyze the electrochemical and acid-base disorders in high performance athletes during the World Karate Championship hosted by the WKO (World Karate Organization) in 2014. In this study 19 male athletes were analyzed (age 34 ± 8), black belts and with over 5 years of experience in the sport. Capillary blood samples from the digital pulp of the finger were collected in three stages: rest, 5 minutes after and 10 minutes after fighting (kumite). The sample was analyzed using blood gas analyzer GEM Premier 3000, using the parameters pH, Na+, K+, Ca2+, lactate e HCO3−. The values related to acid-base disturbance presented statistical differences (p <0.05) in most of the collected moments. The lactate levels found were 2.77 ± 0.97mmol / L in rest, 6.57 ± 2.1 for 5 minutes after and 4.06 ± 1.55 for 10 minutes after combat. The samples collected for the electrolytic markers showed no statistical differences in their values (p <0.05). Through the data collected, we conjecture that the sport can be characterized as a high-intensity exercise and with a predominance of the glycolytic system. The analysis of acid-base disturbance is an efficient method to assist in the control of training loads.