Use of phycoerythrin and allophycocyanin for fluorescence resonance energy transfer analyzed by flow cytometry: advantages and limitations.

BACKGROUND: This study validates the use of phycoerythrin (PE) and allophycocyanin (APC) for fluorescence energy transfer (FRET) analyzed by flow cytometry. METHODS: FRET was detected when a pair of antibody conjugates directed against two noncompetitive epitopes on the same CD8alpha chain was used. FRET was also detected between antibody conjugate pairs specific for the two chains of the heterodimeric alpha (4)beta(1) integrin. Similarly, the association of T-cell receptor (TCR) with a soluble antigen ligand was detected by FRET when anti-TCR antibody and MHC class I/peptide complexes (<<tetramers>>) were used. RESULTS: FRET efficiency was always less than 10%, probably because of steric effects associated with the size and structure of PE and APC. Some suggestions are given to take into account this and other effects (e.g., donor and acceptor concentrations) for a better interpretation of FRET results obtained with this pair of fluorochromes. CONCLUSIONS: We conclude that FRET assays can be carried out easily with commercially available antibodies and flow cytometers to study arrays of multimolecular complexes.

Spreading due to heterogeneity in two-phase flow

Postprint (published version)

Orchestration signals in the classroom: managing the jigsaw collaborative learning flow

The orchestration of collaborative learning processes in face-to-facephysical settings, such as classrooms, requires teachers to coordinate students indicating them who belong to each group, which collaboration areas areassigned to each group, and how they should distribute the resources or roles within the group. In this paper we present an Orchestration Signal system,composed of wearable Personal Signal devices and an Orchestration Signal manager. Teachers can configure color signals in the manager so that they are transmitted to the wearable devices to indicate different orchestration aspects.In particular, the paper describes how the system has been used to carry out a Jigsaw collaborative learning flow in a classroom where students received signals indicating which documents they should read, in which group they were and in which area of the classroom they were expected to collaborate. The evaluation results show that the proposed system facilitates a dynamic, visual and flexible orchestration.

Effects of a nonpressor dose of neuropeptide Y on cardiac output, regional blood flow distribution and plasma renin, vasopressin and catecholamine levels.

Neuropeptide Y (NPY) is a peptide with vasoconstrictor properties known to be present in the central nervous system as well as in sympathetic nerve endings and the adrenal medulla. The purposes of this study were to investigate in normotensive conscious rats the effects of nonpressor doses of NPY on cardiac output and regional blood flow distribution (using radiolabeled microspheres) as well as on plasma renin activity, plasma catecholamine and vasopressin levels. NPY (0.1 microgram/min) infused i.v. for 30 min modified neither blood pressure nor heart rate. Cardiac index was at comparable levels in NPY- as in vehicle-treated rats (17.7 +/- 1.6, n = 8, vs. 21.3 +/- 0.9 ml/min/100 g, n = 8, mean +/- S.E.M.). There was no significant difference in regional blood flow distribution between the two groups of rats, except for the large intestine (0.42 +/- 0.06 vs. 0.71 +/- 0.1 ml/min/g in NPY- and vehicle-treated rats, respectively, P less than .05). Basal plasma renin activity and catecholamine levels were not modified by NPY whereas plasma vasopressin levels were lower (P less than .05) in rats given NPY (0.76 +/- 0.3 pg/ml, n = 8) than in those having received the vehicle (2.2 +/- 0.4 pg/ml).(ABSTRACT TRUNCATED AT 250 WORDS)

Scale Effects in Hydraulic Model Tests of Rock Protected Structures, HR-119, 1970

A laboratory investigation was undertaken to determine the limiting model Reynolds number above which the scour behavior of rock protected structures can be reproduced in hydraulic models scaled according to the Froude criterion. A submerged jet was passed over an initially full scour pocket containing uniform glass spheres and the rate of scour was measured as a function of time. The dimensions of the scour pocket and jet and the particle diameters were varied as needed to maintain strict geometric similarity. For each of two different Froude numbers the Reynolds number was varied over a wide range. The normalized scour rate was found to be practically independent of the Reynolds number, R, (based on the jet velocity and particle diameter) at values of R above about 2.5 x 10^3, and to decrease with Rat smaller values. A grid placed in the jet was found to have a very strong effect on the scour rate. In an attempt to explain the effect of R on the scour behavior, turbulent pressure and velocity fluctuations were measured in air flows and water flows, respectively, over rigid scour pockets having the same geometry as those formed in the scour experiments. The normalized spectra of the fluctuations were found to be nearly independent of R, but the flow pattern was found to be very sensitive to the inlet condition, the jet deflecting upward or downward in a not wholly explainable manner. This indicates that scour behavior can be modeled only if the approach flow is also accurately modeled.

Standardizing admission and discharge processes to improve patient flow: A cross sectional study

Background: The aim of this study was to evaluate how hospital capacity was managed focusing on standardizing the admission and discharge processes. Methods: This study was set in a 900-bed university affiliated hospital of the National Health Service, near Barcelona (Spain). This is a cross-sectional study of a set of interventions which were gradually implemented between April and December 2008. Mainly, they were focused on standardizing the admission and discharge processes to improve patient flow. Primary administrative data was obtained from the 2007 and 2009 Hospital Database. Main outcome measures were median length of stay, percentage of planned discharges, number of surgery cancellations and median number of delayed emergency admissions at 8:00¿am. For statistical bivariate analysis, we used a Chi-squared for linear trend for qualitative variables and a Wilcoxon signed ranks test and a Mann¿Whitney test for non-normal continuous variables. Results:The median patients' global length of stay was 8.56 days in 2007 and 7.93 days in 2009 (p<0.051). The percentage of patients admitted the same day as surgery increased from 64.87% in 2007 to 86.01% in 2009 (p<0.05). The number of cancelled interventions due to lack of beds was 216 patients in 2007 and 42 patients in 2009. The median number of planned discharges went from 43.05% in 2007 to 86.01% in 2009 (p<0.01). The median number of emergency patients waiting for an in-hospital bed at 8:00¿am was 5 patients in 2007 and 3 patients in 2009 (p<0.01). Conclusions: In conclusion, standardization of admission and discharge processes are largely in our control. There is a significant opportunity to create important benefits for increasing bed capacity and hospital throughput.

Flow-targeted inversion-prepared b-TFE coronary MR angiography: initial results in patients.

PURPOSE: Visualization of coronary blood flow in the right and left coronary system in volunteers and patients by means of a modified inversion-prepared bright-blood coronary magnetic resonance angiography (cMRA) sequence. MATERIALS AND METHODS: cMRA was performed in 14 healthy volunteers and 19 patients on a 1.5 Tesla MR system using a free-breathing 3D balanced turbo field echo (b-TFE) sequence with radial k-space sampling. For magnetization preparation a slab selective and a 2D selective inversion pulse were used for the right and left coronary system, respectively. cMRA images were evaluated in terms of clinically relevant stenoses (< 50 %) and compared to conventional catheter angiography. Signal was measured in the coronary arteries (coro), the aorta (ao) and in the epicardial fat (fat) to determine SNR and CNR. In addition, maximal visible vessel length, and vessel border definition were analyzed. RESULTS: The use of a selective inversion pre-pulse allowed direct visualization of the coronary blood flow in the right and left coronary system. The measured SNR and CNR, vessel length, and vessel sharpness in volunteers (SNR coro: 28.3 +/- 5.0; SNR ao: 37.6 +/- 8.4; CNR coro-fat: 25.3 +/- 4.5; LAD: 128.0 cm +/- 8.8; RCA: 74.6 cm +/- 12.4; Sharpness: 66.6 % +/- 4.8) were slightly increased compared to those in patients (SNR coro: 24.1 +/- 3.8; SNR ao: 33.8 +/- 11.4; CNR coro-fat: 19.9 +/- 3.3; LAD: 112.5 cm +/- 13.8; RCA: 69.6 cm +/- 16.6; Sharpness: 58.9 % +/- 7.9; n.s.). In the patient study the assessment of 42 coronary segments lead to correct identification of 10 clinically relevant stenoses. CONCLUSION: The modification of a previously published inversion-prepared cMRA sequence allowed direct visualization of the coronary blood flow in the right as well as in the left coronary system. In addition, this sequence proved to be highly sensitive regarding the assessment of clinically relevant stenotic lesions.

Development of Stage-Discharge Relations for Ungaged Bridge Waterways in Western Iowa, TR-567, 2010

Stage-discharge relations constitute a viable, alternative technique for estimating accurately flow for ungaged sites. In this research, we have utilized pressure transducers and Large Scale Particle Image Velocimetry techniques to develop stage-discharge relations at eleven sites in the Hungry Canyon Area (HCA) of southwestern Iowa under different hydrologic conditions. We have employed these data to calibrate and verify an established hydrologic model and then we have used this model to provide a stage discharge relation for different hydrologic conditions (i.e. rating curves). The benefits of the project are numerous including that the discharge data will be used for a number of purposes, including operational decision making in the HCA about the design of water-control and conveyance structures, input for hydraulic and hydrologic models, and calculation of sediment and other water quality constituents transport and “loads”, and for decision making. This project has also pointed out the difficulties in measuring flows in ungaged streams with ice jams, steep banks, erodible beds, and floating debris.

Autonomous Measurements of Bridge Pier and Abutment Scour using Motion-Sensing Radio Transmitters, TR-595, 2010

Two portable Radio Frequency IDentification (RFID) systems (made by Texas Instruments and HiTAG) were developed and tested for bridge scour monitoring by the Department of Civil and Environmental Engineering at the University of Iowa (UI). Both systems consist of three similar components: 1) a passive cylindrical transponder of 2.2 cm in length (derived from transmitter/responder); 2) a low frequency reader (~134.2 kHz frequency); and 3) an antenna (of rectangular or hexagonal loop). The Texas Instruments system can only read one smart particle per time, while the HiTAG system was successfully modified here at UI by adding the anti-collision feature. The HiTAG system was equipped with four antennas and could simultaneously detect 1,000s of smart particles located in a close proximity. A computer code was written in C++ at the UI for the HiTAG system to allow simultaneous, multiple readouts of smart particles under different flow conditions. The code is written for the Windows XP operational system which has a user-friendly windows interface that provides detailed information regarding the smart particle that includes: identification number, location (orientation in x,y,z), and the instance the particle was detected.. These systems were examined within the context of this innovative research in order to identify the best suited RFID system for performing autonomous bridge scour monitoring. A comprehensive laboratory study that included 142 experimental runs and limited field testing was performed to test the code and determine the performance of each system in terms of transponder orientation, transponder housing material, maximum antenna-transponder detection distance, minimum inter-particle distance and antenna sweep angle. The two RFID systems capabilities to predict scour depth were also examined using pier models. The findings can be summarized as follows: 1) The first system (Texas Instruments) read one smart particle per time, and its effective read range was about 3ft (~1m). The second system (HiTAG) had similar detection ranges but permitted the addition of an anti-collision system to facilitate the simultaneous identification of multiple smart particles (transponders placed into marbles). Therefore, it was sought that the HiTAG system, with the anti-collision feature (or a system with similar features), would be preferable when compared to a single-read-out system for bridge scour monitoring, as the former could provide repetitive readings at multiple locations, which could help in predicting the scour-hole bathymetry along with maximum scour depth. 2) The HiTAG system provided reliable measures of the scour depth (z-direction) and the locations of the smart particles on the x-y plane within a distance of about 3ft (~1m) from the 4 antennas. A Multiplexer HTM4-I allowed the simultaneous use of four antennas for the HiTAG system. The four Hexagonal Loop antennas permitted the complete identification of the smart particles in an x, y, z orthogonal system as function of time. The HiTAG system can be also used to measure the rate of sediment movement (in kg/s or tones/hr). 3) The maximum detection distance of the antenna did not change significantly for the buried particles compared to the particles tested in the air. Thus, the low frequency RFID systems (~134.2 kHz) are appropriate for monitoring bridge scour because their waves can penetrate water and sand bodies without significant loss of their signal strength. 4) The pier model experiments in a flume with first RFID system showed that the system was able to successfully predict the maximum scour depth when the system was used with a single particle in the vicinity of pier model where scour-hole was expected. The pier model experiments with the second RFID system, performed in a sandbox, showed that system was able to successfully predict the maximum scour depth when two scour balls were used in the vicinity of the pier model where scour-hole was developed. 5) The preliminary field experiments with the second RFID system, at the Raccoon River, IA near the Railroad Bridge (located upstream of 360th street Bridge, near Booneville), showed that the RFID technology is transferable to the field. A practical method would be developed for facilitating the placement of the smart particles within the river bed. This method needs to be straightforward for the Department of Transportation (DOT) and county road working crews so it can be easily implemented at different locations. 6) Since the inception of this project, further research showed that there is significant progress in RFID technology. This includes the availability of waterproof RFID systems with passive or active transponders of detection ranges up to 60 ft (~20 m) within the water–sediment column. These systems do have anti-collision and can facilitate up to 8 powerful antennas which can significantly increase the detection range. Such systems need to be further considered and modified for performing automatic bridge scour monitoring. The knowledge gained from the two systems, including the software, needs to be adapted to the new systems.

Estimating traveltimes and groundwater flow patterns using 3D time-lapse crosshole ERT imaging of electrical resistivity fluctuations induced by infiltrating river water

The infiltration of river water into aquifers is of high relevance to drinking-water production and is a key driver of biogeochemical processes in the hyporheic and riparian zone, but the distribution and quantification of the infiltrating water are difficult to determine using conventional hydrological methods (e.g., borehole logging and tracer tests). By time-lapse inverting crosshole ERT (electrical resistivity tomography) monitoring data, we imaged groundwater flow patterns driven by river water infiltrating a perialpine gravel aquifer in northeastern Switzerland. This was possible because the electrical resistivity of the infiltrating water changed during rainfall-runoff events. Our time-lapse resistivity models indicated rather complex flow patterns as a result of spatially heterogeneous bank filtration and aquifer heterogeneity. The upper part of the aquifer was most affected by the river infiltrate, and the highest groundwater velocities and possible preferential flow occurred at shallow to intermediate depths. Time series of the reconstructed resistivity models matched groundwater electrical resistivity data recorded on borehole loggers in the upper and middle parts of the aquifer, whereas the resistivity models displayed smaller variations and delayed responses with respect to the logging data. in the lower part. This study demonstrated that crosshole ERT monitoring of natural electrical resistivity variations of river infiltrate could be used to image and quantify 3D bank filtration and aquifer dynamics at a high spatial resolution.

Fluid dynamical prediction of changed v1-flow at energies available at the CERN Large Hadron Collider

Substantial collective flow is observed in collisions between lead nuclei at Large Hadron Collider (LHC) as evidenced by the azimuthal correlations in the transverse momentum distributions of the produced particles. Our calculations indicate that the global v1-flow, which at RHIC peaked at negative rapidities (named third flow component or antiflow), now at LHC is going to turn toward forward rapidities (to the same side and direction as the projectile residue). Potentially this can provide a sensitive barometer to estimate the pressure and transport properties of the quark-gluon plasma. Our calculations also take into account the initial state center-of-mass rapidity fluctuations, and demonstrate that these are crucial for v1 simulations. In order to better study the transverse momentum flow dependence we suggest a new"symmetrized" vS1(pt) function, and we also propose a new method to disentangle global v1 flow from the contribution generated by the random fluctuations in the initial state. This will enhance the possibilities of studying the collective Global v1 flow both at the STAR Beam Energy Scan program and at LHC.

Optimization of particle bombardment parameters for the genetic transformation of Brazilian maize inbred lines

The objective of this work was to develop a genetic transformation system for tropical maize genotypes via particle bombardment of immature zygotic embryos. Particle bombardment was carried out using a genetic construct with bar and uidA genes under control of CaMV35S promoter. The best conditions to transform maize tropical inbred lines L3 and L1345 were obtained when immature embryos were cultivated, prior to the bombardment, in higher osmolarity during 4 hours and bombarded at an acceleration helium gas pressure of 1,100 psi, two shots per plate, and a microcarrier flying distance of 6.6 cm. Transformation frequencies obtained using these conditions ranged from 0.9 to 2.31%. Integration of foreign genes into the genome of maize plants was confirmed by Southern blot analysis as well as bar and uidA gene expressions. The maize genetic transformation protocol developed in this work will possibly improve the efficiency to produce new transgenic tropical maize lines expressing desirable agronomic characteristics.

Pore-scale modeling of two-phase flow instabilities in porous media

Les problèmes d'écoulements multiphasiques en média poreux sont d'un grand intérêt pour de nombreuses applications scientifiques et techniques ; comme la séquestration de C02, l'extraction de pétrole et la dépollution des aquifères. La complexité intrinsèque des systèmes multiphasiques et l'hétérogénéité des formations géologiques sur des échelles multiples représentent un challenge majeur pour comprendre et modéliser les déplacements immiscibles dans les milieux poreux. Les descriptions à l'échelle supérieure basées sur la généralisation de l'équation de Darcy sont largement utilisées, mais ces méthodes sont sujettes à limitations pour les écoulements présentant de l'hystérèse. Les avancées récentes en terme de performances computationnelles et le développement de méthodes précises pour caractériser l'espace interstitiel ainsi que la distribution des phases ont favorisé l'utilisation de modèles qui permettent une résolution fine à l'échelle du pore. Ces modèles offrent un aperçu des caractéristiques de l'écoulement qui ne peuvent pas être facilement observées en laboratoire et peuvent être utilisé pour expliquer la différence entre les processus physiques et les modèles à l'échelle macroscopique existants. L'objet premier de la thèse se porte sur la simulation numérique directe : les équations de Navier-Stokes sont résolues dans l'espace interstitiel et la méthode du volume de fluide (VOF) est employée pour suivre l'évolution de l'interface. Dans VOF, la distribution des phases est décrite par une fonction fluide pour l'ensemble du domaine et des conditions aux bords particulières permettent la prise en compte des propriétés de mouillage du milieu poreux. Dans la première partie de la thèse, nous simulons le drainage dans une cellule Hele-Shaw 2D avec des obstacles cylindriques. Nous montrons que l'approche proposée est applicable même pour des ratios de densité et de viscosité très importants et permet de modéliser la transition entre déplacement stable et digitation visqueuse. Nous intéressons ensuite à l'interprétation de la pression capillaire à l'échelle macroscopique. Nous montrons que les techniques basées sur la moyenne spatiale de la pression présentent plusieurs limitations et sont imprécises en présence d'effets visqueux et de piégeage. Au contraire, une définition basée sur l'énergie permet de séparer les contributions capillaires des effets visqueux. La seconde partie de la thèse est consacrée à l'investigation des effets d'inertie associés aux reconfigurations irréversibles du ménisque causé par l'interface des instabilités. Comme prototype pour ces phénomènes, nous étudions d'abord la dynamique d'un ménisque dans un pore angulaire. Nous montrons que, dans un réseau de pores cubiques, les sauts et reconfigurations sont si fréquents que les effets d'inertie mènent à différentes configurations des fluides. A cause de la non-linéarité du problème, la distribution des fluides influence le travail des forces de pression, qui, à son tour, provoque une chute de pression dans la loi de Darcy. Cela suggère que ces phénomènes devraient être pris en compte lorsque que l'on décrit l'écoulement multiphasique en média poreux à l'échelle macroscopique. La dernière partie de la thèse s'attache à démontrer la validité de notre approche par une comparaison avec des expériences en laboratoire : un drainage instable dans un milieu poreux quasi 2D (une cellule Hele-Shaw avec des obstacles cylindriques). Plusieurs simulations sont tournées sous différentes conditions aux bords et en utilisant différents modèles (modèle intégré 2D et modèle 3D) afin de comparer certaines quantités macroscopiques avec les observations au laboratoire correspondantes. Malgré le challenge de modéliser des déplacements instables, où, par définition, de petites perturbations peuvent grandir sans fin, notre approche numérique apporte de résultats satisfaisants pour tous les cas étudiés. - Problems involving multiphase flow in porous media are of great interest in many scientific and engineering applications including Carbon Capture and Storage, oil recovery and groundwater remediation. The intrinsic complexity of multiphase systems and the multi scale heterogeneity of geological formations represent the major challenges to understand and model immiscible displacement in porous media. Upscaled descriptions based on generalization of Darcy's law are widely used, but they are subject to several limitations for flow that exhibit hysteric and history- dependent behaviors. Recent advances in high performance computing and the development of accurate methods to characterize pore space and phase distribution have fostered the use of models that allow sub-pore resolution. These models provide an insight on flow characteristics that cannot be easily achieved by laboratory experiments and can be used to explain the gap between physical processes and existing macro-scale models. We focus on direct numerical simulations: we solve the Navier-Stokes equations for mass and momentum conservation in the pore space and employ the Volume Of Fluid (VOF) method to track the evolution of the interface. In the VOF the distribution of the phases is described by a fluid function (whole-domain formulation) and special boundary conditions account for the wetting properties of the porous medium. In the first part of this thesis we simulate drainage in a 2-D Hele-Shaw cell filled with cylindrical obstacles. We show that the proposed approach can handle very large density and viscosity ratios and it is able to model the transition from stable displacement to viscous fingering. We then focus on the interpretation of the macroscopic capillary pressure showing that pressure average techniques are subject to several limitations and they are not accurate in presence of viscous effects and trapping. On the contrary an energy-based definition allows separating viscous and capillary contributions. In the second part of the thesis we investigate inertia effects associated with abrupt and irreversible reconfigurations of the menisci caused by interface instabilities. As a prototype of these phenomena we first consider the dynamics of a meniscus in an angular pore. We show that in a network of cubic pores, jumps and reconfigurations are so frequent that inertia effects lead to different fluid configurations. Due to the non-linearity of the problem, the distribution of the fluids influences the work done by pressure forces, which is in turn related to the pressure drop in Darcy's law. This suggests that these phenomena should be taken into account when upscaling multiphase flow in porous media. The last part of the thesis is devoted to proving the accuracy of the numerical approach by validation with experiments of unstable primary drainage in a quasi-2D porous medium (i.e., Hele-Shaw cell filled with cylindrical obstacles). We perform simulations under different boundary conditions and using different models (2-D integrated and full 3-D) and we compare several macroscopic quantities with the corresponding experiment. Despite the intrinsic challenges of modeling unstable displacement, where by definition small perturbations can grow without bounds, the numerical method gives satisfactory results for all the cases studied.