Learned simulation as the engine of physical scene understanding

La cognición humana evoca las habilidades del razonamiento, la comunicación y la interacción. Esto incluye la interpretación de la física del mundo real para comprender las leyes que subyacen en ella. Algunas teorías postulan la semejanza entre esta capacidad de razonamiento con simulaciones para interpretar la física de la escena, que abarca la percepción para la comprensión del estado físico actual, y el razonamiento acerca de la evolución temporal de un sistema dado. En este contexto se propone el desarrollo de un sistema para realizar simulación aprendida. Establecido un objetivo, el algoritmo se entrena para aprender una aproximación de la dinámica real, para construir así un gemelo digital del entorno. Entonces, el sistema de simulación emulará la física subyacente con información obtenida mediante observaciones de la escena. Para ello, se empleará una cámara estéreo para adquirir datos a partir de secuencias de video. El trabajo se centra los fenómenos oscilatorios de fluidos. Los fluidos están presentes en muchas de nuestras acciones diarias y constituyen un reto físico para el sistema propuesto. Son deformables, no lineales, y presentan un carácter disipativo dominante, lo que los convierte en un sistema complejo para ser aprendido. Además, sólo se tiene acceso a mediciones parciales de su estado ya que la cámara sólo proporciona información acerca de la superficie libre. El resultado es un sistema capaz de percibir y razonar sobre la dinámica del fluido. El gemelo digital cognitivo así construido proporciona una interpretación del estado del mismo para integrar su evolución en tiempo real, aprendiendo con información observada del gemelo físico. El sistema, entrenado originalmente para un líquido concreto, se adaptará a cualquier otro a través del aprendizaje por refuerzo produciendo así resultados precisos para líquidos desconocidos. Finalmente, se emplea la realidad aumentada (RA) para ofrecer una representación visual de los resultados, así como información adicional sobre el estado del líquido que no es accesible al ojo humano. Este objetivo se alcanza mediante el uso de técnicas de aprendizaje de variedades, y aprendizaje automático, como las redes neuronales, enriquecido con información física. Empleamos sesgos inductivos basados en el conocimiento de la termodinámica para desarrollar un sistema inteligente que cumpla con estos principios para dar soluciones con sentido sobre la dinámica. El problema abordado en esta tesis constituye una dificultad de primer orden en el desarrollo de sistemas robóticos destinados a la manipulación de fluidos. En acciones como el vertido o el movimiento, la oscilación de los líquidos juega un papel importante en el desarrollo de sistemas de asistencia a personas con movilidad reducida o aplicaciones industriales. Cognition evokes human abilities for reasoning, communication, and interaction. This includes the interpretation of real-world physics so as to understand its underlying laws. Theories postulate the similarity of human reasoning about these phenomena with simulations for physical scene understanding, which gathers perception for comprehension of the current dynamical state, and reasoning for time evolution prediction of a given system. In this context, we propose the development of a system for learned simulation. Given a design objective, an algorithm is trained to learn an approximation to the real dynamics to build a digital twin of the environment. Then, the underlying physics will be emulated with information coming from observations of the scene. For this purpose, we use a commodity camera to acquire data exclusively from video recordings. We focus on the sloshing problem as a benchmark. Fluids are widely present in several daily actions and portray a physically rich challenge for the proposed systems. They are highly deformable, nonlinear, and present a dominant dissipative behavior, making them a complex entity to be emulated. In addition, we only have access to partial measurements of their dynamical state, since a commodity camera only provides information about the free surface. The result is a system capable of perceiving and reasoning about the dynamics of the fluid. This cognitive digital twin provides an interpretation of the state of the fluid to integrate its dynamical evolution in real-time, updated with information observed from the real twin. The system, trained originally for one liquid, will be able to adapt itself to any other fluid through reinforcement learning and produce accurate results for previously unseen liquids. Augmented reality is used in the design of this application to offer a visual interpretation of the solutions to the user, and include information about the dynamics that is not accessible to the human eye. This objective is to be achieved through the use of manifold learning and machine learning techniques, such as neural networks, enriched with physics information. We use inductive biases based on the knowledge of thermodynamics to develop machine intelligence systems that fulfill these principles to provide meaningful solutions to the dynamics. This problem is considered one of the main targets in fluid manipulation for the development of robotic systems. Pursuing actions such as pouring or moving, sloshing dynamics play a capital role for the correct performance of aiding systems for the elderly or industrial applications that involve liquids. <br /

Aprendizaje automatico de dinámica de fluidos mediante modelos de datos

Real-time fluid simulation is one of the challenges of credible simulation. Among their applications, simulation-based control of robots manipulating liquids is one of the main research topics. The slosh is of great importance in this field. We suggest a data-driven integrator for the sloshing dynamics able to run in real-time.La simulación de fluidos en tiempo real es uno de los retos de la simulación creíble y, entre sus aplicaciones, el control de robots para la manipulación de líquidos. Un fenómeno importante en este ámbito es la salpicadura, para el cual proponemos un integrador capaz de trabajar en tiempo real

Small RNA profiling reveals regulation of Arabidopsis miR168 and heterochromatic siRNA415 in response to fungal elicitors

Background: Small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs), have emerged as important regulators of eukaryotic gene expression. In plants, miRNAs play critical roles in development, nutrient homeostasis and abiotic stress responses. Accumulating evidence also reveals that sRNAs are involved in plant immunity. Most studies on pathogen-regulated sRNAs have been conducted in Arabidopsis plants infected with the bacterial pathogen Pseudomonas syringae, or treated with the flagelin-derived elicitor peptide flg22 from P. syringae. This work investigates sRNAs that are regulated by elicitors from the fungus Fusarium oxysporum in Arabidopsis. - Results: Microarray analysis revealed alterations on the accumulation of a set of sRNAs in response to elicitor treatment, including miRNAs and small RNA sequences derived from massively parallel signature sequencing. Among the elicitor-regulated miRNAs was miR168 which regulates ARGONAUTE1, the core component of the RNA-induced silencing complex involved in miRNA functioning. Promoter analysis in transgenic Arabidopsis plants revealed transcriptional activation of MIR168 by fungal elicitors. Furthermore, transgenic plants expressing a GFP-miR168 sensor gene confirmed that the elicitor-induced miR168 is active. MiR823, targeting Chromomethylase3 (CMT3) involved in RNA-directed DNA methylation (RdDM) was also found to be regulated by fungal elicitors. In addition to known miRNAs, microarray analysis allowed the identification of an elicitor-inducible small RNA that was incorrectly annotated as a miRNA. Studies on Arabidopsis mutants impaired in small RNA biogenesis demonstrated that this sRNA, is a heterochromatic-siRNA (hc-siRNA) named as siRNA415. Hc-siRNAs are known to be involved in RNA-directed DNA methylation (RdDM). SiRNA415 is detected in several plant species. - Conclusion: Results here presented support a transcriptional regulatory mechanism underlying MIR168 expression. This finding highlights the importance of miRNA functioning in adaptive processes of Arabidopsis plants to fungal infection. The results of this study also lay a foundation for the involvement of RdDM processes through the activity of siRNA415 and miR823 in mediating regulation of immune responses in Arabidopsis plants

Famílies botàniques de plantes medicinals

Facultat de Farmàcia, Universitat de Barcelona. Ensenyament: Grau de Farmàcia, Assignatura: Botànica Farmacèutica, Curs: 2013-2014, Coordinadors: Joan Simon, Cèsar Blanché i Maria Bosch.Els materials que aquí es presenten són els recull de 175 treballs d’una família botànica d’interès medicinal realitzats de manera individual. Els treballs han estat realitzat per la totalitat dels estudiants dels grups M-2 i M-3 de l’assignatura Botànica Farmacèutica durant els mesos d’abril i maig del curs 2013-14. Tots els treballs s’han dut a terme a través de la plataforma de GoogleDocs i han estat tutoritzats pel professor de l’assignatura i revisats i finalment co-avaluats entre els propis estudiants. L’objectiu principal de l’activitat ha estat fomentar l’aprenentatge autònom i col·laboratiu en Botànica farmacèutica

Hyperoxemia and excess oxygen use in early acute respiratory distress syndrome : Insights from the LUNG SAFE study

Publisher Copyright: © 2020 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.Background: Concerns exist regarding the prevalence and impact of unnecessary oxygen use in patients with acute respiratory distress syndrome (ARDS). We examined this issue in patients with ARDS enrolled in the Large observational study to UNderstand the Global impact of Severe Acute respiratory FailurE (LUNG SAFE) study. Methods: In this secondary analysis of the LUNG SAFE study, we wished to determine the prevalence and the outcomes associated with hyperoxemia on day 1, sustained hyperoxemia, and excessive oxygen use in patients with early ARDS. Patients who fulfilled criteria of ARDS on day 1 and day 2 of acute hypoxemic respiratory failure were categorized based on the presence of hyperoxemia (PaO2 > 100 mmHg) on day 1, sustained (i.e., present on day 1 and day 2) hyperoxemia, or excessive oxygen use (FIO2 ≥ 0.60 during hyperoxemia). Results: Of 2005 patients that met the inclusion criteria, 131 (6.5%) were hypoxemic (PaO2 < 55 mmHg), 607 (30%) had hyperoxemia on day 1, and 250 (12%) had sustained hyperoxemia. Excess FIO2 use occurred in 400 (66%) out of 607 patients with hyperoxemia. Excess FIO2 use decreased from day 1 to day 2 of ARDS, with most hyperoxemic patients on day 2 receiving relatively low FIO2. Multivariate analyses found no independent relationship between day 1 hyperoxemia, sustained hyperoxemia, or excess FIO2 use and adverse clinical outcomes. Mortality was 42% in patients with excess FIO2 use, compared to 39% in a propensity-matched sample of normoxemic (PaO2 55-100 mmHg) patients (P = 0.47). Conclusions: Hyperoxemia and excess oxygen use are both prevalent in early ARDS but are most often non-sustained. No relationship was found between hyperoxemia or excessive oxygen use and patient outcome in this cohort. Trial registration: LUNG-SAFE is registered with ClinicalTrials.gov, NCT02010073publishersversionPeer reviewe

Small RNA profiling reveals regulation of Arabidopsis miR168 and heterochromatic siRNA415 in response to fungal elicitors

Background: Small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs), have emerged as important regulators of eukaryotic gene expression. In plants, miRNAs play critical roles in development, nutrient homeostasis and abiotic stress responses. Accumulating evidence also reveals that sRNAs are involved in plant immunity. Most studies on pathogen-regulated sRNAs have been conducted in Arabidopsis plants infected with the bacterial pathogen Pseudomonas syringae, or treated with the flagelin-derived elicitor peptide flg22 from P. syringae. This work investigates sRNAs that are regulated by elicitors from the fungus Fusarium oxysporum in Arabidopsis. - Results: Microarray analysis revealed alterations on the accumulation of a set of sRNAs in response to elicitor treatment, including miRNAs and small RNA sequences derived from massively parallel signature sequencing. Among the elicitor-regulated miRNAs was miR168 which regulates ARGONAUTE1, the core component of the RNA-induced silencing complex involved in miRNA functioning. Promoter analysis in transgenic Arabidopsis plants revealed transcriptional activation of MIR168 by fungal elicitors. Furthermore, transgenic plants expressing a GFP-miR168 sensor gene confirmed that the elicitor-induced miR168 is active. MiR823, targeting Chromomethylase3 (CMT3) involved in RNA-directed DNA methylation (RdDM) was also found to be regulated by fungal elicitors. In addition to known miRNAs, microarray analysis allowed the identification of an elicitor-inducible small RNA that was incorrectly annotated as a miRNA. Studies on Arabidopsis mutants impaired in small RNA biogenesis demonstrated that this sRNA, is a heterochromatic-siRNA (hc-siRNA) named as siRNA415. Hc-siRNAs are known to be involved in RNA-directed DNA methylation (RdDM). SiRNA415 is detected in several plant species. - Conclusion: Results here presented support a transcriptional regulatory mechanism underlying MIR168 expression. This finding highlights the importance of miRNA functioning in adaptive processes of Arabidopsis plants to fungal infection. The results of this study also lay a foundation for the involvement of RdDM processes through the activity of siRNA415 and miR823 in mediating regulation of immune responses in Arabidopsis plants

Triplet-triplet sensitizing within pyrene-based COO-BODIPY: a breaking molecular platform for annihilating photon upconversion

8 pags., 6 figs., 1 tab.We envisioned a new approach for achieving triplet-triplet annihilation-assisted photon upconversion based on the rational design of a heavy-atom-free, all-organic and photoactivatable triplet-triplet synergistic multichromophoric molecular assembly. This single molecular architecture is easily built by covalently anchoring triplet-annihilator units (pyrenes) to a triplet-photosensitizer moiety (BODIPY), to improve the effectiveness and probability of the required triplet-triplet energy transfer and the ulterior triplet-triplet annihilation. This unprecedented design takes advantage of the high synthetic accessibility and chemical versatility of the COO-BODIPY scaffold. The laser-induced photophysical characterization, assisted by computational simulations (quantum mechanics calculations at single molecular level and molecular dynamics in a solvent cage), identifies the key factors to finely control the intersystem crossing and reverse intersystem crossing probability, pivotal to improve energy transfer efficiency between the involved triplet states. Likewise, theoretical simulations highlight the relevance of the new photoactivable chromophoric design to promote intra- and inter-molecular triplet-triplet annihilation towards enhanced photon upconversion, yielding noticeable fluorescence from pyrene units even under unfavorable conditions (aerated solutions of low concentration at room temperature). The understanding of the complex dynamics sustained by this single molecular architecture could approach the next generation of chemically accessible and low-cost materials enabling fluorescence by photon upconversion mediated by triplet-triplet annihilation.Grant (PID2020-114755GB-C31, -C32 and -C33) funded by MCIN/AEI/10.13039/501100011033 and (IT1639-22) by Gobierno Vasco. E. D. R. thanks Gobierno Vasco for a postdoctoral contractPeer reviewe

Polar ammoniostyryls easily converting a clickable lipophilic BODIPY in an advanced plasma membrane probe

7 pags., 5 figs.A very simple, small and symmetric, but highly bright, photostable and functionalizable molecular probe for plasma membrane (PM) has been developed from an accessible, lipophilic and clickable organic dye based on BODIPY. To this aim, two lateral polar ammoniostyryl groups were easily linked to increase the amphiphilicity of the probe and thus its lipid membrane partitioning. Compared to the BODIPY precursor, the transversal diffusion across lipid bilayers of the ammoniostyryled BODIPY probe was highly reduced, as evidenced by fluorescence confocal microscopy on model membranes built up as giant unilamellar vesicles (GUVs). Moreover, the ammoniostyryl groups endow the new BODIPY probe with the ability to optically work (excitation and emission) in the bioimaging-useful red region, as shown by staining of the plasma membrane of living mouse embryonic fibroblasts (MEFs). Upon incubation, this fluorescent probe rapidly entered the cell through the endosomal pathway. By blocking the endocytic trafficking at 4 °C, the probe was confined within the PM of MEFs. Our experiments show the developed ammoniostyrylated BODIPY as a suitable PM fluorescent probe, and confirm the synthetic approach for advancing PM probes, imaging and science.Financial support from MICINN (PID2020-114755GB-C31, -C32 and C-33) and Basque Government (IT1639-22) is gratefully acknowledged by S. d. l. M., J. B. and I. G.-M. I. L.-M. acknowledge financial support from the Spanish Ministry of Science, Innovation and Universities through the grant PGC2018-097903-B-I00. This work was also supported by the TECNOLOGI´AS 2018 program, funded by the Regional Government of Madrid (Grant S2018/BAA-4403 SINOXPHOS-CM, to I. L-M.). S. S.-B. thanks the Regional Government of Madrid for an INVESTIGO contract. M. M.-U´. was recipient of a Sara Borrell fellowship (CD15/00190) financed by the Spanish Ministry of Health

Generation and characterization of the human iPSC line CABi001-A from a patient with retinitis pigmentosa caused by a novel mutation in PRPF31 gene

PRPF31 gene codes for a ubiquitously expressed splicing factor but mutations affect exclusively the retina, producing the progressive death of photoreceptor cells. We have identified a novel PRPF31 mutation in a patient with autosomal dominant retinitis pigmentosa. A blood sample was obtained and mononuclear cells were reprogrammed using the non-integrative Sendai virus to generate the cell line CABi001-A. The iPSC line has been characterized for pluripotency and differentiation capacity and will be differentiated toward photoreceptors and retinal pigment epithelium cells to study the molecular mechanism of the disease and test possible therapeutic strategies