Assessing the Validity of Brain Glucose Concentration Measurement Using Microdialysis

Brain functions, such as learning, orchestrating locomotion, memory recall, and processing information, all require glucose as a source of energy. During these functions, the glucose concentration decreases as the glucose is being consumed by brain cells. By measuring this drop in concentration, it is possible to determine which parts of the brain are used during specific functions and consequently, how much energy the brain requires to complete the function. One way to measure in vivo brain glucose levels is with a microdialysis probe. The drawback of this analytical procedure, as with many steadystate fluid flow systems, is that the probe fluid will not reach equilibrium with the brain fluid. Therefore, brain concentration is inferred by taking samples at multiple inlet glucose concentrations and finding a point of convergence. The goal of this thesis is to create a three-dimensional, time-dependent, finite element representation of the brainprobe system in COMSOL 4.2 that describes the diffusion and convection of glucose. Once validated with experimental results, this model can then be used to test parameters that experiments cannot access. When simulations were run using published values for physical constants (i.e. diffusivities, density and viscosity), the resulting glucose model concentrations were within the error of the experimental data. This verifies that the model is an accurate representation of the physical system. In addition to accurately describing the experimental brain-probe system, the model I created is able to show the validity of zero-net-flux for a given experiment. A useful discovery is that the slope of the zero-net-flux line is dependent on perfusate flow rate and diffusion coefficients, but it is independent of brain glucose concentrations. The model was simplified with the realization that the perfusate is at thermal equilibrium with the brain throughout the active region of the probe. This allowed for the assumption that all model parameters are temperature independent. The time to steady-state for the probe is approximately one minute. However, the signal degrades in the exit tubing due to Taylor dispersion, on the order of two minutes for two meters of tubing. Given an analytical instrument requiring a five μL aliquot, the smallest brain process measurable for this system is 13 minutes.

Use of a 3D perfusion bioreactor with osteoblasts and osteoblast/endothelial cell co-cultures to improve tissue-engineered bone

The delivery of oxygen, nutrients, and the removal of waste are essential for cellular survival. Culture systems for 3D bone tissue engineering have addressed this issue by utilizing perfusion flow bioreactors that stimulate osteogenic activity through the delivery of oxygen and nutrients by low-shear fluid flow. It is also well established that bone responds to mechanical stimulation, but may desensitize under continuous loading. While perfusion flow and mechanical stimulation are used to increase cellular survival in vitro, 3D tissue-engineered constructs face additional limitations upon in vivo implantation. As it requires significant amounts of time for vascular infiltration by the host, implants are subject to an increased risk of necrosis. One solution is to introduce tissue-engineered bone that has been pre-vascularized through the co-culture of osteoblasts and endothelial cells on 3D constructs. It is unclear from previous studies: 1) how 3D bone tissue constructs will respond to partitioned mechanical stimulation, 2) how gene expression compares in 2D and in 3D, 3) how co-cultures will affect osteoblast activity, and 4) how perfusion flow will affect co-cultures of osteoblasts and endothelial cells. We have used an integrated approach to address these questions by utilizing mechanical stimulation, perfusion flow, and a co-culture technique to increase the success of 3D bone tissue engineering. We measured gene expression of several osteogenic and angiogenic genes in both 2D and 3D (static culture and mechanical stimulation), as well as in 3D cultures subjected to perfusion flow, mechanical stimulation and partitioned mechanical stimulation. Finally, we co-cultured osteoblasts and endothelial cells on 3D scaffolds and subjected them to long-term incubation in either static culture or under perfusion flow to determine changes in gene expression as well as histological measures of osteogenic and angiogenic activity. We discovered that 2D and 3D osteoblast cultures react differently to shear stress, and that partitioning mechanical stimulation does not affect gene expression in our model. Furthermore, our results suggest that perfusion flow may rescue 3D tissue-engineered constructs from hypoxic-like conditions by reducing hypoxia-specific gene expression and increasing histological indices of both osteogenic and angiogenic activity. Future research to elucidate the mechanisms behind these results may contribute to a more mature bone-like structure that integrates more quickly into host tissue, increasing the potential of bone tissue engineering.

Reynolds-stress turbulence model in the KIVA code for engine simulation

A Reynolds-Stress Turbulence Model has been incorporated with success into the KIVA code, a computational fluid dynamics hydrocode for three-dimensional simulation of fluid flow in engines. The newly implemented Reynolds-stress turbulence model greatly improves the robustness of KIVA, which in its original version has only eddy-viscosity turbulence models. Validation of the Reynolds-stress turbulence model is accomplished by conducting pipe-flow and channel-flow simulations, and comparing the computed results with experimental and direct numerical simulation data. Flows in engines of various geometry and operating conditions are calculated using the model, to study the complex flow fields as well as confirm the model’s validity. Results show that the Reynolds-stress turbulence model is able to resolve flow details such as swirl and recirculation bubbles. The model is proven to be an appropriate choice for engine simulations, with consistency and robustness, while requiring relatively low computational effort.

Simulation of four stroke engine cycle for a 4 - valve pentroof engine in KIVA 3VR2

The main purpose of this project is to understand the process of engine simulation using the open source CFD code called KIVA. This report mainly discusses the simulation of the 4-valve Pentroof engine through KIVA 3VR2. KIVA is an open source FORTRAN code which is used to solve the fluid flow field in the engines with the transient 2D and 3D chemically reactive flow with spray. It also focuses on the complete procedure to simulate an engine cycle starting from pre- processing until the final results. This report will serve a handbook for the using the KIVA code.

Non-intrusive pressure measurement in microchannels

A non-intrusive interferometric measurement technique has been successfully developed to measure fluid compressibility in both gas and liquid phases via refractive index (RI) changes. The technique, consisting of an unfocused laser beam impinging a glass channel, can be used to separate and quantify cell deflection, fluid flow rates, and pressure variations in microchannels. Currently in fields such as microfluidics, pressure and flow rate measurement devices are orders of magnitude larger than the channel cross-sections making direct pressure and fluid flow rate measurements impossible. Due to the non-intrusive nature of this technique, such measurements are now possible, opening the door for a myriad of new scientific research and experimentation. This technique, adapted from the concept of Micro Interferometric Backscatter Detection (MIBD), boasts the ability to provide comparable sensitivities in a variety of channel types and provides quantification capability not previously demonstrated in backscatter detection techniques. Measurement sensitivity depends heavily on experimental parameters such as beam impingement angle, fluid volume, photodetector sensitivity, and a channel’s dimensional tolerances. The current apparatus readily quantifies fluid RI changes of 10-5 refractive index units (RIU) corresponding to pressures of approximately 14 psi and 1 psi in water and air, respectively. MIBD reports detection capability as low as 10-9 RIU and the newly adapted technique has the potential to meet and exceed this limit providing quantification in the place of detection. Specific device sensitivities are discussed and suggestions are provided on how the technique may be refined to provide optimal quantification capabilities based on experimental conditions.

Implementation of monotonic higher order upwind scheme in KIVA 4

KIVA is a FORTRAN code developed by Los Alamos national lab to simulate complete engine cycle. KIVA is a flow solver code which is used to perform calculation of properties in a fluid flow field. It involves using various numerical schemes and methods to solve the Navier-Stokes equation. This project involves improving the accuracy of one such scheme by upgrading it to a higher order scheme. The numerical scheme to be modified is used in the critical final stage calculation called as rezoning phase. The primitive objective of this project is to implement a higher order numerical scheme, to validate and verify that the new scheme is better than the existing scheme. The latest version of the KIVA family (KIVA 4) is used for implementing the higher order scheme to support handling the unstructured mesh. The code is validated using the traditional shock tube problem and the results are verified to be more accurate than the existing schemes in reference with the analytical result. The convection test is performed to compare the computational accuracy on convective transfer; it is found that the new scheme has less numerical diffusion compared to the existing schemes. A four valve pentroof engine, an example case of KIVA package is used as application to ensure the stability of the scheme in practical application. The results are compared for the temperature profile. In spite of all the positive results, the numerical scheme implemented has a downside of consuming more CPU time for the computational analysis. The detailed comparison is provided. However, in an overview, the implementation of the higher order scheme in the latest code KIVA 4 is verified to be successful and it gives better results than the existing scheme which satisfies the objective of this project.

LATTICE BOLTZMANN METHOD AND CELLULAR AUTOMATA SIMULATION OF PARTICLE MOTION AND DEPOSITION IN 2-D CASE

This technical report discusses the application of the Lattice Boltzmann Method (LBM) and Cellular Automata (CA) simulation in fluid flow and particle deposition. The current work focuses on incompressible flow simulation passing cylinders, in which we incorporate the LBM D2Q9 and CA techniques to simulate the fluid flow and particle loading respectively. For the LBM part, the theories of boundary conditions are studied and verified using the Poiseuille flow test. For the CA part, several models regarding simulation of particles are explained. And a new Digital Differential Analyzer (DDA) algorithm is introduced to simulate particle motion in the Boolean model. The numerical results are compared with a previous probability velocity model by Masselot [Masselot 2000], which shows a satisfactory result.

Mixing-cell boundary conditions and apparent mass balance errors for advective-dispersive solute transport

In many field or laboratory situations, well-mixed reservoirs like, for instance, injection or detection wells and gas distribution or sampling chambers define boundaries of transport domains. Exchange of solutes or gases across such boundaries can occur through advective or diffusive processes. First we analyzed situations, where the inlet region consists of a well-mixed reservoir, in a systematic way by interpreting them in terms of injection type. Second, we discussed the mass balance errors that seem to appear in case of resident injections. Mixing cells (MC) can be coupled mathematically in different ways to a domain where advective-dispersive transport occurs: by assuming a continuous solute flux at the interface (flux injection, MC-FI), or by assuming a continuous resident concentration (resident injection). In the latter case, the flux leaving the mixing cell can be defined in two ways: either as the value when the interface is approached from the mixing-cell side (MC-RT -), or as the value when it is approached from the column side (MC-RT +). Solutions of these injection types with constant or-in one case-distance-dependent transport parameters were compared to each other as well as to a solution of a two-layer system, where the first layer was characterized by a large dispersion coefficient. These solutions differ mainly at small Peclet numbers. For most real situations, the model for resident injection MC-RI + is considered to be relevant. This type of injection was modeled with a constant or with an exponentially varying dispersion coefficient within the porous medium. A constant dispersion coefficient will be appropriate for gases because of the Eulerian nature of the usually dominating gaseous diffusion coefficient, whereas the asymptotically growing dispersion coefficient will be more appropriate for solutes due to the Lagrangian nature of mechanical dispersion, which evolves only with the fluid flow. Assuming a continuous resident concentration at the interface between a mixing cell and a column, as in case of the MC-RI + model, entails a flux discontinuity. This flux discontinuity arises inherently from the definition of a mixing cell: the mixing process is included in the balance equation, but does not appear in the description of the flux through the mixing cell. There, only convection appears because of the homogeneous concentration within the mixing cell. Thus, the solute flux through a mixing cell in close contact with a transport domain is generally underestimated. This leads to (apparent) mass balance errors, which are often reported for similar situations and erroneously used to judge the validity of such models. Finally, the mixing cell model MC-RI + defines a universal basis regarding the type of solute injection at a boundary. Depending on the mixing cell parameters, it represents, in its limits, flux as well as resident injections. (C) 1998 Elsevier Science B.V. All rights reserved.

Intracranial meningiomas associated with cervical syringohydromyelia in a cat

Eine dreizehnjährige, weibliche, nicht kastrierte Hauskatze wurde zur chirurgischen Therapie eines multiplen Meningeoms in der Kleintierklinik des Tierspital Bern vorgestellt. Eine leichtgradige generalisierte Ataxie wurde beobachtet, die Propriozeption war generalisiert herabgesetzt und der Drohreflex war beidseitig reduziert. Es wurden eine prä- und eine postoperative Magnetrezonanztomographie durchgeführt. Drei supratentoriale extra-axiale Raumforderungen wurden diagnostiziert. Eine vierte Masse wurde infratentorial extra-axial über der linken zerebellären Hemisphere lokalisiert. Eine Herniation des kaudoventralen Kleinhirn (Vermis) von ungefähr einem Zentimeter Länge durch das Foramen magnum wurde beobachtet. Eine zervikale Syringohydromyelie wurde als Zufallsbefund diagnostiziert. Die Meningeome wurden durch 3 Kraniotomiestellen entfernt. Zwei Jahre nach der Operation ist die Katze normal. Anhand der vorhandenen Literatur wird die tumor-assoziierte Syringohydromyelie besprochen. Die Therapie der Syringohydromyelie sollte gegen den kausalen pathologischen Prozess (z.B. intrakranieller Tumor) für die Liquorzirkulationsstörung gerichtet sein.

Experimental Characterization and Quantification of Cement-Bentonite Interaction using Core Infiltration Techniques Coupled with X-ray Tomography

Deep geological storage of radioactive waste foresees cementitious materials as reinforcement of tunnels and as backfill. Bentonite is proposed to enclose spent fuel canisters and as drift seals. Sand/bentonite (s/b) is foreseen as backfill material of access galleries or as drift seals. The emplacement of cementitious material next to clay material generates an enormous chemical gradient in pore-water composition that drives diffusive solute transport. Laboratory studies and reactive transport modeling predicted significant mineral alteration at and near interfaces, mainly resulting in a decrease of porosity in bentonite. The goal of this thesis was to characterize and quantify the cement/bentonite interactions both spatially and temporally in laboratory experiments. A newly developed mobile X-ray transparent core infiltration device was used to perform X-ray computed tomography (CT) scans without interruption of running experiments. CT scans allowed tracking the evolution of the reaction plume and changes in core volume/diameter/density during the experiments. In total 4 core infiltration experiments were carried out for this study with the compacted and saturated cores consisting of MX-80 bentonite and sand/MX-80 bentonite mixture (s/b; 65/35%). Two different high-pH cementitious pore-fluids were infiltrated: a young (early) ordinary Portland cement pore-fluid (APWOPC; K+–Na+–OH-; pH 13.4; ionic strength 0.28 mol/kg) and a young ‘low-pH’ ESDRED shotcrete pore-fluid (APWESDRED; Ca2+–Na+–K+–formate; pH 11.4; ionic strength 0.11 mol/kg). The experiments lasted between 1 and 2 years. In both bentonite experiments, the hydraulic conductivity was strongly reduced after switching to high-pH fluids, changing eventually from an advective to a diffusion-dominated transport regime. The reduction was mainly induced by mineral precipitation and possibly partly also by high ionic strength pore-fluids. Both bentonite cores showed a volume reduction and a resulting transient flow in which pore-water was squeezed out during high-pH infiltration. The outflow chemistry was characterized by a high ionic strength, while chloride in the initial pore water got replaced as main anionic charge carrier by sulfate, originating from gypsum dissolution. The chemistry of the high-pH fluids got strongly buffered by the bentonite, consuming hydroxide and in case of APWESDRED also formate. Hydroxide got consumed by mineral reactions (saponite and possibly talc and brucite precipitation), while formate being affected by bacterial degradation. Post-mortem analysis showed reaction zones near the inlet of the bentonite core, characterized by calcium and magnesium enrichment, consisting predominately of calcite and saponite, respectively. Silica got enriched in the outflow, indicating dissolution of silicate-minerals, identified as preferentially cristobalite. In s/b, infiltration of APWOPC reduced the hydraulic conductivity strongly, while APWESDRED infiltration had no effect. The reduction was mainly induced by mineral precipitation and probably partly also by high ionic strength pore-fluids. Not clear is why the observed mineral precipitates in the APWESDRED experiment had no effect on the fluid flow. Both s/b cores showed a volume expansion along with decreasing ionic strengths of the outflow, due to mineral reactions or in case of APWESDRED infiltration also mediated by microbiological activity, consuming hydroxide and formate, respectively. The chemistry of the high-pH fluids got strongly buffered by the s/b. In the case of APWESDRED infiltration, formate reached the outflow only for a short time, followed by enrichment in acetate, indicating most likely biological activity. This was in agreement to post-mortem analysis of the core, observing black spots on the inflow surface, while the sample had a rotten-egg smell indicative of some sulfate reduction. Post-mortem analysis showed further in both cores a Ca-enrichment in the first 10 mm of the core due to calcite precipitation. Mg-enrichment was only observed in the APWOPC experiment, originating from newly formed saponite. Silica got enriched in the outflow of both experiments, indicating dissolution of silicate-minerals, identified in the OPC experiment as cristobalite. The experiments attested an effective buffering capacity for bentonite and s/b, a progressing coupled hydraulic-chemical sealing process and also the preservation of the physical integrity of the interface region in this setup with a total pressure boundary condition on the core sample. No complete pore-clogging was observed but the hydraulic conductivity got rather strongly reduced in 3 experiments, explained by clogging of the intergranular porosity (macroporosity). Such a drop in hydraulic conductivity may impact the saturation time of the buffer in a nuclear waste repository, although the processes and geometry will be more complex in repository situation.

Diversity in T cell costimulation by alpha4beta1 integrin

T cell activation requires antigen-specific T cell receptor signals that spatially and temporally coincide with a second costimulatory signal. CD28 and α4β1 integrin both function as T cell costimulators, but their individual mechanisms remain elusive. By directly comparing CD3-dependent functions and signaling pathways employed by these two costimulatory receptors, aspects of their individual signaling mechanisms are explored. We determined that CD28 and α4β1 integrins both use Src-family kinase Lck and MAPK Erk, but to different extents and functional ends. After identifying functional differences between CD28 and integrin costimulatory pathways, the focus of the study turned to integrin signaling in naïve and memory T cell subsets. CD45RO T cells are fully co-activated by natural β1 integrin ligands fibronectin (FN) and VCAM-1, β1 monoclonal antibody 33B6, as well as α4β1 monoclonal antibody 19H8 which binds a combinatorial epitope of the α4β1 heterodimer. While CD28 fully costimulates CD45RA T cells, the degree of activation from integrin ligands varies. FN costimulates CD3-dependent proliferation, IL-2 secretion, and early activation markers CD25 and CD69. However, β1 antibody 33B6, which binds to the same T cell integrins (α4β1 and α5β1) as natural ligand FN, failed to costimulate proliferation or IL-2 in the CD45RA subset, but retained the ability to regulate CD25 and CD69. Unique aspects of 19H8 signaling involve early Erk activation and IL-2 independent proliferation. Signaling defects through 33B6 ligation correlates with poor adhesion under fluid flow conditions, suggesting a cytoskeletal basis for signaling. All together, these data provide evidence for a mechanism of α4β1 integrin signaling and describe functional differences between naïve and memory T cells. ^

Chemistry of minerals from amphibole-chlorite veins of ODP Site 209-1270

We examined small-scale shear zones in drillcore samples of abyssal peridotites from the Mid-Atlantic Ridge. These shear zones are associated with veins consisting of chlorite + actinolite/tremolite assemblages, with accessory phases zircon and apatite, and they are interpreted as altered plagiogranite melt impregnations, which originate from hydrous partial melting of gabbroic intrusion in an oceanic detachment fault. Ti-in-zircon thermometry yields temperatures around 820°C for the crystallization of the evolved melt. Reaction path modeling indicates that the alteration assemblage includes serpentine of the adjacent altered peridotites. Based on the model results, we propose that formation of chlorite occurred at higher temperatures than serpentinization, thus leading to strain localization around former plagiogranites during alteration. The detachment fault represents a major pathway for fluids through the oceanic crust, as evidenced by extremely low d18O of altered plagiogranite veins (+3.0-4.2 per mil) and adjacent serpentinites (+ 2.6-3.7 per mil). The uniform oxygen isotope data indicate that fluid flow in the detachment fault system affected veins and adjacent host serpentinites likewise.

(Table 1) Summary of sampling points described and main petrographic, morphological and geochemical characteristics

Targeted sampling on the Dolgovskoy Mound (northern Shatsky Ridge) revealed the presence of spectacular laterally extensive and differently shaped authigenic carbonates. The sampling stations were selected based on sidescan sonar and profiler images that show patchy backscatter and irregular and discontinuous reflections in the near subsurface. The interpretation of acoustic data from the top part of the mound supports the seafloor observations and the sampling that revealed the presence of a complex subsurface plumbing system characterized by carbonates and gas. The crusts sampled consist of carbonate cemented layered hemipelagic sedimentary Unit 1 associated with several centimetres thick microbial mats. Three different carbonate morphologies were observed: (a) tabular slabs, (b) subsurface cavernous carbonates consisting of void chambers up to 20 cm**3 in size and (c) chimney and tubular conduits vertically oriented or forming a subhorizontal network in the subsurface. The methanogenic origin of the carbonates is established based on visual observations of fluids seepage structures, 13C depletion of the carbonates (d13C varying between -36.7 per mil and -27.4 per mil), and by thin carbonate layers present within the thick microbial mats. Laboratory experiments with a Hele-Shaw cell were conducted in order to simulate the gas seepage through contrasting grain size media present on the seafloor. Combined petrography, visual observations and sandbox simulations allowed a characterization of the dynamics and the structures of the plumbing system in the near subsurface. Based on sample observations and the experiments, three observed morphologies of authigenic carbonates are interpreted, respectively, as (a) Darcian porous flow through the finely laminated clayey/coccolith-rich layers, (b) gas accumulation chambers at sites where significant fluid escape was impeded by thicker clayey layers forming the laminated Unit1 and (c) focussed vertical fluid venting and subhorizontal migration of overpressured fluids released from (b). The Hele-Shaw cell experiments represent a promising tool for investigating shallow fluid flow pathways in marine systems.