WarpPINN: Cine-MR image registration with physics-informed neural networks

Heart failure is typically diagnosed with a global function assessment, such as ejection fraction. However, these metrics have low discriminate power, failing to distinguish different types of this disease. Quantifying local deformations in the form of cardiac strain can provide helpful information, but it remains a challenge. In this work, we introduce WarpPINN, a physics-informed neural network to perform image registration to obtain local metrics of the heart deformation. We apply this method to cine magnetic resonance images to estimate the motion during the cardiac cycle. We inform our neural network of near-incompressibility of cardiac tissue by penalizing the jacobian of the deformation field. The loss function has two components: an intensity-based similarity term between the reference and the warped template images, and a regularizer that represents the hyperelastic behavior of the tissue. The architecture of the neural network allows us to easily compute the strain via automatic differentiation to assess cardiac activity. We use Fourier feature mappings to overcome the spectral bias of neural networks, allowing us to capture discontinuities in the strain field. We test our algorithm on a synthetic example and on a cine-MRI benchmark of 15 healthy volunteers. We outperform current methodologies both landmark tracking and strain estimation. We expect that WarpPINN will enable more precise diagnostics of heart failure based on local deformation information. Source code is available at https://github.com/fsahli/WarpPINN.Comment: 18 pages, 10 figure

Nuevos escenarios para la docencia universitaria : entornos híbridos y pedagogías emergentes.

Memorias del IX Simposio Internacional de Docencia Universitaria (SIDU)Los trabajos reunidos en esta Memoria representan una contribución importante al campo de la educación y de la docencia universitaria, en tanto muestran distintas maneras de responder a las problemáticas educativas cotidianas y presentan propuestas para afrontar los retos emergentes en el campo de la educación superior. Invitamos a los lectores a realizar una lectura atenta y crítica de los trabajos compilados en esta publicación. Estamos seguros de que este acercamiento propiciará la reflexión y el análisis riguroso de los objetos de estudio abordados por los autores, y estimulará la generación de nuevos proyectos de investigación, intervención e innovación educativa que incidan en el desarrollo de mejores prácticas de docencia en educación media superior y superior.Pimera edición digitaldoi.org/10.56019/EDU-CETYS.2024.182

Estabilidad para modelo de Light Sheet Fluorescence Microscopy 2D y extensión al caso tridimensional

Tesis para optar al grado de Magíster en Cienias de la Ingeniería, mención Matemáticas AplicadasMemoria para optar al título de Ingeniero Civil MatemáticoLa observación a escala celular de procesos biológicos de forma continua en el tiempo y en las tres dimensiones espaciales es uno de los grandes objetivos en la investigación científica para comprender aspectos esenciales de la vida. Además, la forma en que la observación es llevada a cabo debe ser, en lo posible, a una alta resolución, sobre largos períodos de tiempo y sin comprometer en gran medida aspectos fisiológicos del espécimen en cuestión. El Microscopio de Fluorescencia por Planos (en adelante LSFM por su nombre en inglés, Light Sheet Fluorescence Microscopy) es un microscopio de fluorescencia que observa el espécimen en estudio excitando con una fuente lumínica moléculas capaces de fluorescer (fluoróforos) que han sido colocadas previamente en la muestra etiquetando estructuras del espécimen en estudio y luego observando la luz fluorescente que estos emiten. Así, el microscopio tiene por objetivo observar la distribución de fluoróforos en el espécimen. A diferencia de otros microscopios de fluorescencia, la técnica usada por el LSFM para adquirir las imágenes cumple en gran medida los requerimientos mencionados y lo convierte en una herramienta esencial para la investigación en las áreas de biología celular y medicina molecular. Existen problemas inherentes a la mayoría de los fenómenos ópticos, tales como imperfec- ciones en las mediciones o el scattering producido sobre los fotones, efectos que distorsionan la imagen final obtenida y por tanto no es tan cercana a la distribución de fluoróforos original como gustaría. Esto último restringe el estudio biológico y por tanto se hace necesario un procedimiento que pueda corregir las imperfecciones en las mediciones. Para restaurar la imagen final se plantea un modelo físico matemático que explica cómo es formada la medición a partir de la distribución de fluoróforos. Se trabaja inicialmente con un modelo bidimensional el cual es estudiado teórica y numéricamente planteando el respectivo problema inverso: cómo recuperar la distribución a partir de las mediciones. Al respecto la unicidad del problema ya está demostrada mientras que se cuenta con una resolución numérica del problema bidimensional mediante la construcción de un sistema lineal. Los principales resultados de esta tesis se resumen primero en un resultado de estabilidad de tipo Lipschitz para el problema inverso de LSFM, el que a su vez se basa en un novedoso resultado de estabilidad del mismo tipo para recuperar la condición inicial (cuando es a soporte compacto) de la ecuación de calor en R n . En segundo lugar, desde el punto de vista numérico se establece la extensión del modelo al caso tridimensional considerando además el fenómeno de descalibración y una nueva idea para simular la difusión que presentan las imágenes. Finalmente, dado que el problema consiste en tratamiento de imágenes se aplican herramientas disponibles en el área de las redes neuronales para dar una solución al problema inverso bidimensional por esta vía como una alternativa al sistema lineal, con la esperanza de poder extender este enfoque al caso tridimensionalCONICYT Proyecto Fondecyt regular #1191903, CONICYT Proyecto Apoyo Financiamiento Basal PIA AFB-170001 y por CONICYT Proyecto Fondecyt #11170475. Esta tesis fue parcialmente apoyada por la infraestructura de supercómputo del NLHPC (ECM-02)

Jet fragmentation transverse momentum distributions in pp and p–Pb collisions at √sNN = 5.02 TeV

Jet fragmentation transverse momentum (jT) distributions are measured in proton-proton (pp) and proton-lead (p-Pb) collisions at sNN−−−√ = 5.02 TeV with the ALICE experiment at the LHC. Jets are reconstructed with the ALICE tracking detectors and electromagnetic calorimeter using the anti-kT algorithm with resolution parameter R=0.4 in the pseudorapidity range |η|<0.25. The jT values are calculated for charged particles inside a fixed cone with a radius R=0.4 around the reconstructed jet axis. The measured jT distributions are compared with a variety of parton-shower models. Herwig and PYTHIA 8 based models describe the data well for the higher jT region, while they underestimate the lower jT region. The jT distributions are further characterised by fitting them with a function composed of an inverse gamma function for higher jT values (called the "wide component"), related to the perturbative component of the fragmentation process, and with a Gaussian for lower jT values (called the "narrow component"), predominantly connected to the hadronisation process. The width of the Gaussian has only a weak dependence on jet transverse momentum, while that of the inverse gamma function increases with increasing jet transverse momentum. For the narrow component, the measured trends are successfully described by all models except for Herwig. For the wide component, Herwig and PYTHIA 8 based models slightly underestimate the data for the higher jet transverse momentum region. These measurements set constraints on models of jet fragmentation and hadronisation

Elliptic flow of electrons from beauty-hadron decays in Pb–Pb collisions at √sNN = 5.02 TeV

The elliptic flow of electrons from beauty hadron decays at midrapidity (|y| < 0.8) is measured in Pb-Pb collisions at sNN−−−√ = 5.02 TeV with the ALICE detector at the LHC. The azimuthal distribution of the particles produced in the collisions can be parameterized with a Fourier expansion, in which the second harmonic coefficient represents the elliptic flow, v2. The v2 coefficient is measured for the first time in transverse momentum (pT) range 1.3-6 GeV/c in the centrality class 30-50%. The measurement of electrons from beauty-hadron decays exploits their larger mean proper decay length cτ≈ 500 μm compared to that of charm hadrons and most of the other background sources. The v2 of electrons from beauty hadron decays at midrapidity is found to be positive with a significance of 3.75σ. The results provide insights on the degree of thermalization of beauty quarks in the medium. A model assuming full thermalization of beauty quarks is strongly disfavoured by the measurement at high pT, but is in agreement with the results at low pT. Transport models including substantial interactions of beauty quarks with an expanding strongly-interacting medium describe the measurement

Publisher Correction: Unveiling the strong interaction among hadrons at the LHC

Correction to: Nature https://doi.org/10.1038/s41586-020-3001-6Published online 09 December 2020 In Fig. 1c of this Article, owing to an error during the production process, the equation incorrectly began ‘C(k*, r*) = …’ instead of ‘C(k*) = …’. In addition, in affiliation 71 ‘Dipartimento di Fisica dell’Università degli studi di Bari Aldo Moro’ has been corrected to read ‘Dipartimento di Fisica dell’Università degli studi di Cagliari’. The original Article has been corrected online

Measurement of isolated photon–hadron correlations in √sNN = 5.02 TeV pp and p–Pb collisions

This paper presents isolated photon-hadron correlations using pp and p-Pb data collected by the ALICE detector at the LHC. For photons with |η| < 0.67 and 12 < pT < 40 GeV/c, the associated yield of charged particles in the range |η| < 0.80 and 0.5 < pT < 10 GeV/c is presented. These momenta are much lower than previous measurements at the LHC. No significant difference between pp and p-Pb is observed, with PYTHIA 8.2 describing both data sets within uncertainties. This measurement constrains nuclear effects on the parton fragmentation in p-Pb collisions, and provides a benchmark for future studies of Pb-Pb collisions

J/ψ elliptic and triangular flow in Pb–Pb collisions at √sNN = 5.02 TeV

The inclusive J/ψ elliptic (v2) and triangular (v3) flow coefficients measured at forward rapidity (2.5 <y< 4) and the v2 measured at midrapidity (|y|< 0.9) in Pb-Pb collisions at sNN−−−√ = 5.02 TeV using the ALICE detector at the LHC are reported. The entire Pb-Pb data sample collected during Run 2 is employed, amounting to an integrated luminosity of 750 μb−1 at forward rapidity and 93 μb−1 at midrapidity. The results are obtained using the scalar product method and are reported as a function of transverse momentum pT and collision centrality. At midrapidity, the J/ψ v2 is in agreement with the forward rapidity measurement. The centrality averaged results indicate a positive J/ψ v3 with a significance of more than 5σ at forward rapidity in the pT range 2<pT<5 GeV/c. The forward rapidity v2, v3, and v3/v2 results at low and intermediate pT (pT≲8 GeV/c) exhibit a mass hierarchy when compared to pions and D mesons, while converging into a species-independent curve at higher pT. At low and intermediate pT, the results could be interpreted in terms of a later thermalization of charm quarks compared to light quarks, while at high pT, path-length dependent effects seem to dominate. The J/ψ v2 measurements are further compared to a microscopic transport model calculation. Using a simplified extension of the quark scaling approach involving both light and charm quark flow components, it is shown that the D-meson vn measurements can be described based on those for charged pions and J/ψ flow

Elliptic and triangular flow of (anti)deuterons in Pb–Pb collisions at √sNN = 5.02 TeV

The measurements of the (anti)deuterons elliptic flow (v2) and the first measurements of triangular flow (v3) in Pb-Pb collisions at a center-of-mass energy per nucleon-nucleon collisions sNN−−−√ = 5.02 TeV are presented. A mass ordering at low transverse momentum (pT) is observed when comparing these measurements with those of other identified hadrons, as expected from relativistic hydrodynamics. The measured (anti)deuterons v2 lies between the predictions from the simple coalescence and blast-wave models, which provide a good description of the data only for more peripheral and for more central collisions, respectively. The mass number scaling, which is violated for v2, is approximately valid for the (anti)deuterons v3. The measured v2 and v3 are also compared with the predictions from a coalescence approach with phase-space distributions of nucleons generated by iEBE-VISHNU with AMPT initial conditions coupled with UrQMD, and from a dynamical model based on relativistic hydrodynamics coupled to the hadronic afterburner SMASH. The model predictions are consistent with the data within the uncertainties in mid-central collisions, while a deviation is observed in central centrality intervals

Dielectron production in proton–proton and proton–lead collisions at √sNN = 5.02 TeV

The first measurements of dielectron production at midrapidity (|ηc|<0.8) in proton-proton and proton-lead collisions at sNN−−−√ = 5.02 TeV at the LHC are presented. The dielectron cross section is measured with the ALICE detector as a function of the invariant mass mee and the pair transverse momentum pT,ee in the ranges mee < 3.5 GeV/c2 and pT,ee < 8.0 GeV/c2, in both collision systems. In proton-proton collisions, the charm and beauty cross sections are determined at midrapidity from a fit to the data with two different event generators. This complements the existing dielectron measurements performed at s√ = 7 and 13 TeV. The slope of the s√ dependence of the three measurements is described by FONLL calculations. The dielectron cross section measured in proton-lead collisions is in agreement, within the current precision, with the expected dielectron production without any nuclear matter effects for e+e− pairs from open heavy-flavor hadron decays. For the first time at LHC energies, the dielectron production in proton-lead and proton-proton collisions are directly compared at the same sNN−−−√ via the dielectron nuclear modification factor RpPb. The measurements are compared to model calculations including cold nuclear matter effects, or additional sources of dielectrons from thermal radiation