Genetic structure and gene flow of Eugenia dysenterica natural populations

This study was carried out to assess the genetic variability of ten "cagaita" tree (Eugenia dysenterica) populations in Southeastern Goiás. Fifty-four randomly amplified polymorphic DNA (RAPD) loci were used to characterize the population genetic variability, using the analysis of molecular variance (AMOVA). A phiST value of 0.2703 was obtained, showing that 27.03% and 72.97% of the genetic variability is present among and within populations, respectively. The Pearson correlation coefficient (r) among the genetic distances matrix (1 - Jaccard similarity index) and the geographic distances were estimated, and a strong positive correlation was detected. Results suggest that these populations are differentiating through a stochastic process, with restricted and geographic distribution dependent gene flow.

Symmetric periodic orbits near heteroclinic loops at infinity for a class of polynomial vector fields

For polynomial vector fields in R3, in general, it is very difficult to detect the existence of an open set of periodic orbits in their phase portraits. Here, we characterize a class of polynomial vector fields of arbitrary even degree having an open set of periodic orbits. The main two tools for proving this result are, first, the existence in the phase portrait of a symmetry with respect to a plane and, second, the existence of two symmetric heteroclinic loops.

Symmetric periodic orbits near a heteroclinic loop in R3 formed by two singular points, a semistable periodic orbit and their invariant manifolds

In this paper we consider C1 vector fields X in R3 having a “generalized heteroclinic loop” L which is topologically homeomorphic to the union of a 2–dimensional sphere S2 and a diameter connecting the north with the south pole. The north pole is an attractor on S2 and a repeller on . The equator of the sphere is a periodic orbit unstable in the north hemisphere and stable in the south one. The full space is topologically homeomorphic to the closed ball having as boundary the sphere S2. We also assume that the flow of X is invariant under a topological straight line symmetry on the equator plane of the ball. For each n ∈ N, by means of a convenient Poincar´e map, we prove the existence of infinitely many symmetric periodic orbits of X near L that gives n turns around L in a period. We also exhibit a class of polynomial vector fields of degree 4 in R3 satisfying this dynamics.

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.

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 (&lt;&lt;tetramers&gt;&gt;) 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)

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.

Modelling ecological niches with support vector machines

1. The ecological niche is a fundamental biological concept. Modelling species' niches is central to numerous ecological applications, including predicting species invasions, identifying reservoirs for disease, nature reserve design and forecasting the effects of anthropogenic and natural climate change on species' ranges. 2. A computational analogue of Hutchinson's ecological niche concept (the multidimensional hyperspace of species' environmental requirements) is the support of the distribution of environments in which the species persist. Recently developed machine-learning algorithms can estimate the support of such high-dimensional distributions. We show how support vector machines can be used to map ecological niches using only observations of species presence to train distribution models for 106 species of woody plants and trees in a montane environment using up to nine environmental covariates. 3. We compared the accuracy of three methods that differ in their approaches to reducing model complexity. We tested models with independent observations of both species presence and species absence. We found that the simplest procedure, which uses all available variables and no pre-processing to reduce correlation, was best overall. Ecological niche models based on support vector machines are theoretically superior to models that rely on simulating pseudo-absence data and are comparable in empirical tests. 4. Synthesis and applications. Accurate species distribution models are crucial for effective environmental planning, management and conservation, and for unravelling the role of the environment in human health and welfare. Models based on distribution estimation rather than classification overcome theoretical and practical obstacles that pervade species distribution modelling. In particular, ecological niche models based on machine-learning algorithms for estimating the support of a statistical distribution provide a promising new approach to identifying species' potential distributions and to project changes in these distributions as a result of climate change, land use and landscape alteration.

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.

Classification of very high spatial resolution imagery using mathematical morphology and support vector machines

We investigate the relevance of morphological operators for the classification of land use in urban scenes using submetric panchromatic imagery. A support vector machine is used for the classification. Six types of filters have been employed: opening and closing, opening and closing by reconstruction, and opening and closing top hat. The type and scale of the filters are discussed, and a feature selection algorithm called recursive feature elimination is applied to decrease the dimensionality of the input data. The analysis performed on two QuickBird panchromatic images showed that simple opening and closing operators are the most relevant for classification at such a high spatial resolution. Moreover, mixed sets combining simple and reconstruction filters provided the best performance. Tests performed on both images, having areas characterized by different architectural styles, yielded similar results for both feature selection and classification accuracy, suggesting the generalization of the feature sets highlighted.

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.