Using digital RNA counting and flow cytometry to compare mRNA with protein expression in acute leukemias.

BACKGROUND: The diagnosis of malignant hematologic diseases has become increasingly complex during the last decade. It is based on the interpretation of results from different laboratory analyses, which range from microscopy to gene expression profiling. Recently, a method for the analysis of RNA phenotypes has been developed, the nCounter technology (Nanostring® Technologies), which allows for simultaneous quantification of hundreds of RNA molecules in biological samples. We evaluated this technique in a Swiss multi-center study on eighty-six samples from acute leukemia patients. METHODS: mRNA and protein profiles were established for normal peripheral blood and bone marrow samples. Signal intensities of the various tested antigens with surface expression were similar to those found in previously performed Affymetrix microarray analyses. Acute leukemia samples were analyzed for a set of twenty-two validated antigens and the Pearson Correlation Coefficient for nCounter and flow cytometry results was calculated. RESULTS: Highly significant values between 0.40 and 0.97 were found for the twenty-two antigens tested. A second correlation analysis performed on a per sample basis resulted in concordant results between flow cytometry and nCounter in 44-100% of the antigens tested (mean = 76%), depending on the number of blasts present in a sample, the homogeneity of the blast population, and the type of leukemia (AML or ALL). CONCLUSIONS: The nCounter technology allows for fast and easy depiction of a mRNA profile from hematologic samples. This technology has the potential to become a valuable tool for the diagnosis of acute leukemias, in addition to multi-color flow cytometry.

CFD Simulation of Two-phase and Three-phase Flows in Internal-loop Airlift

Airlift reactors are pneumatically agitated reactors that have been widely used in chemical, petrochemical, and bioprocess industries, such as fermentation and wastewater treatment. Computational Fluid Dynamics (CFD) has become more popular approach for design, scale-up and performance evaluation of such reactors. In the present work numerical simulations for internal-loop airlift reactors were performed using the transient Eulerian model with CFD package, ANSYS Fluent 12.1. The turbulence in the liquid phase is described using κ- ε the model. Global hydrodynamic parameters like gas holdup, gas velocity and liquid velocity have been investigated for a range of superficial gas velocities, both with 2D and 3D simulations. Moreover, the study of geometry and scale influence on the reactor have been considered. The results suggest that both, geometry and scale have significant effects on the hydrodynamic parameters, which may have substantial effects on the reactor performance. Grid refinement and time-step size effect have been discussed. Numerical calculations with gas-liquid-solid three-phase flow system have been carried out to investigate the effect of solid loading, solid particle size and solid density on the hydrodynamic characteristics of internal loop airlift reactor with different superficial gas velocities. It was observed that averaged gas holdup is significantly decreased with increasing slurry concentration. Simulations show that the riser gas holdup decreases with increase in solid particle diameter. In addition, it was found that the averaged solid holdup increases in the riser section with the increase of solid density. These produced results reveal that CFD have excellent potential to simulate two-phase and three-phase flow system.

Horizontal Slug Flow in a Large-Size Pipeline: Experimentation and Modeling

The knowledge of the slug flow characteristics is very important when designing pipelines and process equipment. When the intermittences typical in slug flow occurs, the fluctuations of the flow variables bring additional concern to the designer. Focusing on this subject the present work discloses the experimental data on slug flow characteristics occurring in a large-size, large-scale facility. The results were compared with data provided by mechanistic slug flow models in order to verify their reliability when modelling actual flow conditions. Experiments were done with natural gas and oil or water as the liquid phase. To compute the frequency and velocity of the slug cell and to calculate the length of the elongated bubble and liquid slug one used two pressure transducers measuring the pressure drop across the pipe diameter at different axial locations. A third pressure transducer measured the pressure drop between two axial location 200 m apart. The experimental data were compared with results of Camargo's1 algorithm (1991, 1993), which uses the basics of Dukler & Hubbard's (1975) slug flow model, and those calculated by the transient two-phase flow simulator OLGA.

Modeling of Liquid-Solid Flow in Industrial Scale

In the present work, liquid-solid flow in industrial scale is modeled using the commercial software of Computational Fluid Dynamics (CFD) ANSYS Fluent 14.5. In literature, there are few studies on liquid-solid flow in industrial scale, but any information about the particular case with modified geometry cannot be found. The aim of this thesis is to describe the strengths and weaknesses of the multiphase models, when a large-scale application is studied within liquid-solid flow, including the boundary-layer characteristics. The results indicate that the selection of the most appropriate multiphase model depends on the flow regime. Thus, careful estimations of the flow regime are recommended to be done before modeling. The computational tool is developed for this purpose during this thesis. The homogeneous multiphase model is valid only for homogeneous suspension, the discrete phase model (DPM) is recommended for homogeneous and heterogeneous suspension where pipe Froude number is greater than 1.0, while the mixture and Eulerian models are able to predict also flow regimes, where pipe Froude number is smaller than 1.0 and particles tend to settle. With increasing material density ratio and decreasing pipe Froude number, the Eulerian model gives the most accurate results, because it does not include simplifications in Navier-Stokes equations like the other models. In addition, the results indicate that the potential location of erosion in the pipe depends on material density ratio. Possible sedimentation of particles can cause erosion and increase pressure drop as well. In the pipe bend, especially secondary flows, perpendicular to the main flow, affect the location of erosion.

Automated two-dimensional separation flow system with electrochemical preconcentration, stripping, capillary electrophoresis and contactless conductivity detection for trace metal ion analysis

This paper describes the automation of a fully electrochemical system for preconcentration, cleanup, separation and detection, comprising the hyphenation of a thin layer electrochemical flow cell with CE coupled with contactless conductivity detection (CE-C(4)D). Traces of heavy metal ions were extracted from the pulsed-flowing sample and accumulated on a glassy carbon working electrode by electroreduction for some minutes. Anodic stripping of the accumulated metals was synchronized with hydrodynamic injection into the capillary. The effect of the angle of the slant polished tip of the CE capillary and its orientation against the working electrode in the electrochemical preconcentration (EPC) flow cell and of the accumulation time were studied, aiming at maximum CE-C(4)D signal enhancement. After 6 min of EPC, enhancement factors close to 50 times were obtained for thallium, lead, cadmium and copper ions, and about 16 for zinc ions. Limits of detection below 25 nmol/L were estimated for all target analytes but zinc. A second separation dimension was added to the CE separation capabilities by staircase scanning of the potentiostatic deposition and/or stripping potentials of metal ions, as implemented with the EPC-CE-C(4)D flow system. A matrix exchange between the deposition and stripping steps, highly valuable for sample cleanup, can be straightforwardly programmed with the multi-pumping flow management system. The automated simultaneous determination of the traces of five accumulable heavy metals together with four non-accumulated alkaline and alkaline earth metals in a single run was demonstrated, to highlight the potentiality of the system.

Pressure drop correlation for oil-refrigerant R134a mixture flashing flow in a small diameter tube

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Numerical analysis of refrigerant flow along non-adiabatic capillary tubes using a two-fluid model

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A transmission line model developed directly in phase domain

The phases of a transmission line are tightly coupled due to mutual impedances and admittances of the line. One way to accomplish the calculations of currents and voltages in multi-phase lines consists in representing them in modal domain, where its n coupled phases are represented by their n propagation modes. The separation line in their modes of propagation is through the use of a modal transformation matrix whose columns are eigenvectors associated with the parameters of the line. Usually, this matrix is achieved through numerical methods which do not allow the achievement of an analytical model for line developed directly in the phases domain. This work will show an analytical model for phase currents and voltages of the line and results it will be applied to a hypothetical two-phase. It will be shown results obtained with that will be compared to results obtained using a classical model. © 2012 IEEE.

A transmission line model developed directly in phase domain

The phases of a transmission line are tightly coupled due to mutual impedances and admittances of the line. One way to accomplish the calculations of currents and voltages in multi phase lines consists in representing them in modal domain, where its n coupled phases are represented by their n propagation modes. The separation line in their modes of propagation is through the use of a modal transformation matrix whose columns are eigenvectors associated with the parameters of the line. Usually, this matrix is achieved through numerical methods which do not allow the achievement of an analytical model for line developed directly in the phases domain. This work will show an analytical model for phase currents and voltages of the line and results it will be applied to a hypothetical two-phase. It will be shown results obtained with that will be compared to results obtained using a classical model © 2003-2012 IEEE.

A distributed-parameters transmission line model developed directly in the phase domain

This article shows a transmission line model developed directly in the phase domain. The proposed model is based on the relationships between the phase currents and voltages at both the sending and receiving ends of a single-phase line. These relationships, established using an ABCD matrix, were extended to multi-phase lines. The proposed model was validated by using it to represent a transmission line during short-and open-circuit tests. The results obtained with the proposed model were compared with results obtained with a classical model based on modal decomposition. These comparisons show that proposed model was correctly developed. © 2013 Taylor and Francis Group, LLC.

A two-fluid model for refrigerant flow through adiabatic capillary tubes

This work presents a numerical model to simulate refrigerant flow through capillary tubes, commonly used as expansion devices in refrigeration systems. The flow is divided in a single-phase region, where the refrigerant is in the subcooled liquid state, and a region of two-phase flow. The capillary tube is considered straight and horizontal. The flow is taken as one-dimensional and adiabatic. Steady-state condition is also assumed and the metastable flow phenomena are neglected. The two-fluid model, considering the hydrodynamic and thermal non-equilibrium between the liquid and vapor phases, is applied to the two-phase flow region. Comparisons are made with experimental measurements of the mass flow rate and pressure distribution along two capillary tubes working with refrigerant R-134a in different operating conditions. The results indicate that the present model provides a better estimation than the commonly employed homogeneous model. Some computational results referring to the quality, void fraction, velocities, and temperatures of each phase are presented and discussed.

Saturated flow boiling heat transfer and critical heat flux in small horizontal flattened tubes

This paper presents experimental results for flow boiling heat transfer coefficient and critical heat flux (CHF) in small flattened tubes. The tested flattened tubes have the same equivalent internal diameter of 2.2 mm, but different aspect height/width ratios (H/W) of 1/4, 1/2, 2 and 4. The experimental data were compared against results for circular tubes using R134a and R245fa as working fluids at a nominal saturation temperature of 31 degrees C. For mass velocities higher than 200 kg/m(2)s, the flattened and circular tubes presented similar heat transfer coefficients. Such a behavior is related to the fact that stratification effects are negligible under conditions of higher mass velocities. Heat transfer correlations from the literature, usually developed using only circular-channel experimental data, predicted the flattened tube results for mass velocities higher than 200 kg/m(2)s with mean absolute error lower than 20% using the equivalent diameter to account for the geometry effect. Similarly, the critical heat flux results were found to be independent of the tube aspect ratio when the same equivalent length was kept. Equivalent length is a new parameter which takes into account the channel heat transfer area. The CHF correlations for round tubes predicted the flattened tube data relatively well when using the equivalent diameter and length. Furthermore, a new proposed CHF correlation predicted the present flattened tube data with a mean absolute error of 5%. (C) 2012 Elsevier Ltd. All rights reserved.

Geometrical and kinematic properties of interfacial waves in stratified oil-water flow in inclined pipe

The stratified oil-water flow pattern is common in the petroleum industry, especially in offshore directional wells and pipelines. Previous studies have shown that the phenomenon of flow pattern transition in stratified flow can be related to the interfacial wave structure (problem of hydrodynamic instability). The study of the wavy stratified flow pattern requires the characterization of the interfacial wave properties, i.e., average shape, celerity and geometric properties (amplitude and wavelength) as a function of holdup, inclination angle and phases' relative velocity. However, the data available in the literature on wavy stratified flow is scanty, especially in inclined pipes and when oil is viscous. This paper presents new geometric and kinematic interfacial wave properties as a function of a proposed two-phase Froude number in the wavy-stratified liquid-liquid flow. The experimental work was conducted in a glass test line of 12 m and 0.026 m id., oil (density and viscosity of 828 kg/m(3) and 0.3 Pa s at 20 degrees C, respectively) and water as the working fluids at several inclinations from horizontal (-20 degrees, -10 degrees, 0 degrees, 10 degrees, 20 degrees). The results suggest a physical relation between wave shape and the hydrodynamic stability of the stratified liquid-liquid flow pattern. (C) 2011 Elsevier Inc. All rights reserved.

Scherverhalten kolloidaler Lagenphasen in Rohrströmungen

Kolloidale Suspensionen aus identischen kugelförmigen, geladenen Partikeln in wässrigen Medien stellen ein ideales Modellsystem zur Untersuchung des Gleichgewichtsverhaltens, aber auch des Nicht-Gleichgewichtsverhaltens Weicher Materie dar. So bilden derartige Systeme bei hinreichend starker und langreichweitiger elektrostatischer Repulsion fluid und kristallin geordnete Strukturen aus, die wegen der weitreichenden Analogie zu atomar kondensierter Materie als kolloidale Fluide und Kristalle bezeichnet werden. Von großem Vorteil ist dabei die Möglichkeit zur kontrollierten Einstellung der Wechselwirkung und die gute optische Zugänglichkeit für Mikroskopie und Lichtstreuung sowie die Weichheit der Materialien, aufgrund derer sich auch Zustände fernab des mechanischen Gleichgewichts gezielt präparieren lassen. Themenstellung der vorliegenden Arbeit ist die Untersuchung des Phasenverhaltens und der Fließmechanismen kolloidaler Kristalle in einer Rohrströmung. Im ersten Teil der Arbeit wird gezeigt, dass beim Fluss durch eine zylindrische Röhre Mehrphasenkoexistenz auftritt, wobei ein polykristalliner Kern von einer isotropen Scherschmelze umgeben ist. Zusätzlich treten an der Grenze zwischen diesen Phasen und an der Rohrwand Phasen hexagonal geordneter übereinander hinweggleitender Lagen auf. Der Vergleich zwischen auf der Basis der Navier-Stokes-Gleichung theoretisch berechneten und gemessenen Geschwindigkeitsprofilen zeigt, dass jede dieser Phasen für sich Newtonsches Fließverhalten aufweist. Die Gesamtviskosität ist hingegen durch die mit dem Durchsatz veränderliche Phasenzusammensetzung Nicht-Newtonsch. Damit gelang es, die erstmalig von Würth beschriebene Scherverdünnung auf eine Veränderung der Phasenzusammensetzung zurückzuführen. Im zweiten Teil der Arbeit wurde erstmals das Fließverhalten der Lagenphasen mittels Lichtstreuung und Korrelationsanalyse untersucht. Dafür wurde ein im Prinzip einfacher, aber leistungsstarker Aufbau realisiert, der es erlaubt, die zeitliche Veränderung der Bragg-Reflexe der Lagenphase in radialer und azimutaler Richtung zu verfolgen und mittels Fourieranalyse zu analysieren. In Abhängigkeit vom Durchsatz geht die zunächst rastend gleitende Lagenphase in eine frei gleitende Lagenphase über, wobei charakteristische Veränderungen der Spektren sowie der Korrelationsfunktionen auftreten, die detailliert diskutiert werden. Der Übergang im Gleitmechanismus ist mit einem Verlust der Autokorrelation der Rotationskomponente der periodischen Intra-Lagenverzerrung verbunden, während die Kompressionskomponente erhalten bleibt. Bei hohen Durchflüssen lassen die Reflexbewegungen auf das Auftreten einer Eigenschwingung der frei gleitenden Lagen schließen. Diese Schwingung lässt sich als Rotationsbewegung, gekoppelt mit einer transversalen Auslenkung in Vortexrichtung, beschreiben. Die Ergebnisse erlauben eine detaillierte Diskussion von verschiedenen Modellvorstellungen anderer Autoren.

Thermal fluctuations and boundary conditions in the lattice Boltzmann method

The lattice Boltzmann method is a popular approach for simulating hydrodynamic interactions in soft matter and complex fluids. The solvent is represented on a discrete lattice whose nodes are populated by particle distributions that propagate on the discrete links between the nodes and undergo local collisions. On large length and time scales, the microdynamics leads to a hydrodynamic flow field that satisfies the Navier-Stokes equation. In this thesis, several extensions to the lattice Boltzmann method are developed. In complex fluids, for example suspensions, Brownian motion of the solutes is of paramount importance. However, it can not be simulated with the original lattice Boltzmann method because the dynamics is completely deterministic. It is possible, though, to introduce thermal fluctuations in order to reproduce the equations of fluctuating hydrodynamics. In this work, a generalized lattice gas model is used to systematically derive the fluctuating lattice Boltzmann equation from statistical mechanics principles. The stochastic part of the dynamics is interpreted as a Monte Carlo process, which is then required to satisfy the condition of detailed balance. This leads to an expression for the thermal fluctuations which implies that it is essential to thermalize all degrees of freedom of the system, including the kinetic modes. The new formalism guarantees that the fluctuating lattice Boltzmann equation is simultaneously consistent with both fluctuating hydrodynamics and statistical mechanics. This establishes a foundation for future extensions, such as the treatment of multi-phase and thermal flows. An important range of applications for the lattice Boltzmann method is formed by microfluidics. Fostered by the "lab-on-a-chip" paradigm, there is an increasing need for computer simulations which are able to complement the achievements of theory and experiment. Microfluidic systems are characterized by a large surface-to-volume ratio and, therefore, boundary conditions are of special relevance. On the microscale, the standard no-slip boundary condition used in hydrodynamics has to be replaced by a slip boundary condition. In this work, a boundary condition for lattice Boltzmann is constructed that allows the slip length to be tuned by a single model parameter. Furthermore, a conceptually new approach for constructing boundary conditions is explored, where the reduced symmetry at the boundary is explicitly incorporated into the lattice model. The lattice Boltzmann method is systematically extended to the reduced symmetry model. In the case of a Poiseuille flow in a plane channel, it is shown that a special choice of the collision operator is required to reproduce the correct flow profile. This systematic approach sheds light on the consequences of the reduced symmetry at the boundary and leads to a deeper understanding of boundary conditions in the lattice Boltzmann method. This can help to develop improved boundary conditions that lead to more accurate simulation results.