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Robust transcriptional indicators of immune cell death revealed by spatiotemporal transcriptome analyses

Molecular Plant 2022年第6期15卷 1059-1075页

作者： Jose Salguero-Linares Irene Serrano Nerea Ruiz-Solani Marta Salas-Gómez Ujjal Jyoti Phukan Victor Manuel González MartíBernardo-Faura marc valls David Rengel Nuria S.Coll Centre for Research in Agricultural Genomics(CRAG) CSIC-IRTA-UAB-UBCampus UABBellaterra08193 BarcelonaSpain LIPM Universitéde ToulouseINRACNRS84195 Castanet-TolosanFrance INRAE GeT-PlaGeGenotoul31326 Castanet-TolosanFrance Department of Genetics Universitat de Barcelona08028 BarcelonaSpain Consejo Superior de Investigaciones Científicas(CSIC) BarcelonaSpain Department of Plant Molecular Biology and Physiology.Albrechtvon Haller Institute for Plant Sciences niversity of GottingenJulia-Lermontowa-Weg3.37077 GottingenGrmany Institut de Phammacologie et de Biologie Structurale IPBS Universite deToulouse CNRSUPSBP 64182205 route de Nartxonne310077 Toulouse Cedex 04France

Recognition of a pathogen by the plant immune system often triggers a form of regulated cell death traditionally known as the hypersensitive response(HR).This type of cell death occurs precisely at the site of pathogen recognition,and it is restricted to a few cells.Extensive research has shed light on how plant immune receptors are mechanistically activated.However,two central key questions remain largely unresolved:how does cell death zonation take place,and what are the mechanisms that underpin this phenomenon?Consequently,bona fide transcriptional indicators of HR are lacking,which prevents deeper insight into its mechanisms before cell death becomes macroscopic and precludes early or live observation.In this study,to identify the transcriptional indicators of HR we used the paradigmatic Arabidopsis thaliana–Pseudomonas syringae pathosystem and performed a spatiotemporally resolved gene expression analysis that compared infected cells that will undergo HR upon pathogen recognition with bystander cells that will stay alive and activate immunity.Our data revealed unique and time-dependent differences in the repertoire of differentially expressed genes,expression profiles,and biological processes derived from tissue undergoing HR and that of its surroundings.Furthermore,we generated a pipeline based on concatenated pairwise comparisons between time,zone,and treatment that enabled us to define 13 robust transcriptional HR markers.Among these genes,the promoter of an uncharacterized AAA-ATPase was used to obtain a fluorescent reporter transgenic line that displays a strong spatiotemporally resolved signal specifically in cells that will later undergo pathogen-triggered cell death.This valuable set of genes can be used to define cells that are destined to die upon infection with HR-triggering bacteria,opening new avenues for specific and/or high-throughput techniques to study HR processes at a single-cell level.

关键词： Arabidopsis thaliana cell death indicator effector-triggered immunity hypersensitive response pattern-triggered immunity plant immunity Pseudomonas syringae

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Microbial phenolic metabolites are associated with better frontal lobe cognition

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Food Science and Human Wellness 2024年

作者： Inés Domínguez-López Isabella Parilli-Moser Anna Vallverdú-Queralt Anna Tresserra-Rimbau Cinta valls-Pedret Zenaida Vázquez-Ruiz Olga Casta?er Ramon Estruch Emili Ros Rosa M.Lamuela-Raventós Lipid Clinic Endocrinology and Nutrition Service Institut d'Investigacions Biomèdiques August Pi i Sunyer Hospital Clínic 08036 Barcelona Spain Unit of Cardiovascular Risk and Nutrition Institut Hospital del Mar de Investigaciones Médicas (IMIM) Department of Preventive Medicine and Public Health University of Navarra Departament de Nutrició Ciències de l'Alimentació i Gastronomía Facultat de Farmacia Universitat de Barcelon (UB) Av.de Joan XXII Department of Endocrinology Hospital Clinic IDIBAPS Barcelona Spain Department of Internal Medicine Hospital Clinic Institut d'Investigació Biomèdica August Pi i Sunyer (IDIBAPS) University of Barcelona CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN) Instituto de Salud Carlos III Institut de Nutrició i Seguretat Alimentària (INSA) Universitat de Barcelona (UB)

With increasing life expectancy， neurodegenerative diseases have become one of the leading causes of ill-health in the elderly. Preventive strategies include following healthy diets， such as the Mediterranean diet， which is particularly rich in polyphenols， bioactive compounds with neuroprotective properties. The aim of this study was to assess the association of microbial phenolic metabolites (MPM) with cognition. This cross-sectional analysis was performed with 200 participants of the PREDIMED trial (Barcelona-Clinic recruitment center). A novel method based on liquid chromatography coupled to mass spectrometry was used to identify urinary MPM (protocatechuic acid， enterodiol glucuronide， enterolactone glucuronide， urolithin B glucuronide， and vanillic acid glucuronide)， and cognitive function was evaluated with neuropsychological tests. Multivariable-adjusted ordinary least squares regression was used to assess the associations between cognitive function and MPM， and a score was calculated as the weighted sum of MPM. A higher MPM score was associated with better frontal lobe function. Among individual metabolites， vanillic acid glucuronide was correlated with frontal cognitive performance. Participants with higher concentrations of vanillic acid glucuronide and urolithin B glucuronide obtained better scores in the Color Trail Test part 2. A higher score for urinary multi-MPM was associated with better frontal cognitive performance in an older Mediterranean population.

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Commentary on 'Physics-informed deep learning parameterization of ocean vertical mixing improves climate simulations' by Zhu et al.

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National Science Review 2022年第8期9卷 11-12页

作者： Gustau Camps-valls Image Processing Laboratory (IPL) Universitat de València

Climate models constitute an essential tool to understand our planet, as they implement the laws of physics describing the ocean, land and atmosphere dynamics. However, resolving processes at fine resolutions constitute an important computational botleneck. Parameterization(or closure) approximates such(e.g. turbulent) processes that cannot be resolved in climate models.

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PHASE PORTRAITS OF THE LESLIE-GOWER SYSTEM

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Acta Mathematica Scientia 2022年第5期42卷 1734-1742页

作者： Jaume LLIBRE Claudia valls Departament de Matematiques Universitat Autonoma de Barcelona08193BellaterraBarcelonaCataloniaSpain Departamento de Matematica Instituto Superior TecnicoUniversidade de LisboaAu.Rovisco Pais 1049-001LisboaPortugal

In this paper we characterize the phase portraits of the Leslie-Gower model for competition among species.We give the complete description of their phase portraits in the Poincarédisc(i.e.,in the compactification of R^(2) adding the circle S1 of the infinity)modulo topological equivalence.It is well-known that the equilibrium point of the Leslie-Gower model in the interior of the positive quadrant is a global attractor in this open quadrant,and in this paper we characterize where the orbits attracted by this equilibrium born.

关键词： predator-prey models Leslie-Gower system Poincare compactification global phaseportraits

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Soil and vegetation water content identify the main terrestrial ecosystem changes

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National Science Review 2023年第5期10卷 167-179页

作者： Diego Bueso Maria Piles Philippe Ciais Jean-Pierre Wigneron álvaro Moreno-Martínez Gustau Camps-valls Image Processing Laboratory Universitat de València Laboratoire des Sciences du Climat et de l'Environnement Université Paris Saclay INRA Centre de Bordeaux Aquitaine Image Processing Laboratory Universitat deValència

Environmental change is a consequence of many interrelated factors.How vegetation responds to natural and human activity still needs to be well establishe d,quantified and understood.Re cent satellite missions providing hydrologic and ecological indicators enable better monitoring of Earth system changes,yet there is no automatic way to address this issue directly from observations.Here,we develop an observation-based methodology to capture evidence of changes in global terrestrial ecosystems and attribute these changes to natural or anthropogenic activity.We use the longest time record of global microwave L-band soil moisture and vegetation optical depth as satellite data and build spatially explicit maps of change in soil and vegetation water content and biomass reflecting large ecosystem changes during the last decade,2010-20.Regions of prominent trends(from-8% to 9% per year) are observed,especially in humid and semi-arid climates.We further combine such trends with land cover change maps,vegetation greenness and precipitation variability to assess their relationship with major documented ecosystem changes.Several regions emerge from our results.They cluster changes according to human activity drivers,including deforestation(Amazon,Central Africa) and wildfires(East Australia),artificial reforestation(South-East China),abandonment of farm fields(Central Russia) and climate shifts related to changes in precipitation variability(East Africa,North America and Central Argentina).Using the high sensitivity of soil and vegetation water content to ecosystem changes,microwave satellite observations enable us to quantify and attribute global vegetation responses to climate or anthropogenic activities as a direct measure of environmental changes and the mechanisms driving them.

关键词： soil moisture vegetation water content ecosystem trend remote sensing soil moisture and ocean salinity satellite

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A Feature Selection Strategy to Optimize Retinal Vasculature Segmentation

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Computers, Materials & Continua 2022年第2期70卷 2971-2989页

作者： Jose Escorcia-Gutierrez Jordina Torrents-Barrena Margarita Gamarra Natasha Madera Pedro Romero-Aroca Aida valls Domenec Puig Electronic and Telecommunications Engineering Program Universidad Autónoma del CaribeBarranquilla080001Colombia Department of Computational Science and Electronic Universidad de la CostaCUCBarranquilla080001Colombia Ophthalmology Service Universitari Hospital Sant JoanInstitut de Investigacio Sanitaria Pere VirgiliReus43201Spain Departament d’Enginyeria Informàtica i Matemàtiques Escola Tècnica Superior d’EnginyeriaUniversitat Rovira i VirgiliTarragona43007Spain

Diabetic retinopathy (DR) is a complication of diabetesmellitus thatappears in the retina. Clinitians use retina images to detect DR pathologicalsigns related to the occlusion of tiny blood vessels. Such occlusion brings adegenerative cycle between the breaking off and the new generation of thinnerand weaker blood vessels. This research aims to develop a suitable retinalvasculature segmentation method for improving retinal screening proceduresby means of computer-aided diagnosis systems. The blood vessel segmentationmethodology relies on an effective feature selection based on SequentialForward Selection, using the error rate of a decision tree classifier in theevaluation function. Subsequently, the classification process is performed bythree alternative approaches: artificial neural networks, decision trees andsupport vector machines. The proposed methodology is validated on threepublicly accessible datasets and a private one provided by Hospital Sant Joanof Reus. In all cases we obtain an average accuracy above 96% with a sensitivityof 72% in the blood vessel segmentation process. Compared with the state-ofthe-art, our approach achieves the same performance as other methods thatneed more computational power.Our method significantly reduces the numberof features used in the segmentation process from 20 to 5 dimensions. Theimplementation of the three classifiers confirmed that the five selected featureshave a good effectiveness, independently of the classification algorithm.

关键词： Diabetic retinopathy artificial neural networks decision trees support vector machines feature selection retinal vasculature segmentation

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Global Phase Portraits of Quadratic Systems with a Complex Ellipse as Invariant Algebraic Curve

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Acta Mathematica Sinica,English Series 2018年第5期34卷 801-811页

作者： Jaume LLIBRE Claudia valls Departament de Mateatiques Universitat Autonoma de Barcelona 08193 Bellaterra Barcelona Catalonia Spain Departamento de Matemdtica Instituto Superior Tecnico Universidade de Lisboa 1049-001 Lisboa Portugal

In this paper, we study a new class of quadratic systems and classify all its phase portraits. More precisely, we characterize the class of all quadratic polynomial differential systems in the plane having a complex ellipse x^2 ＋ y^2 ＋ 1 = 0 as invariant algebraic curve. We provide all the different topological phase portraits that this class exhibits in the Poincare disc.

关键词： Quadratic system complex ellipse invariant algebraic curves phase portrait Poincare disc

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Weierstrass Integrability of Complex Differential Equations

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Acta Mathematica Sinica,English Series 2021年第10期37卷 1497-1506页

作者： Jaume LLIBRE Claudia valls Departament de Matematiques Universitat Autonoma de Barcelona08193 BellaterraBarcelonaCataloniaSpain Departamento de Matematica Instituto Superior TecnicoUniversidade de LisboaAv.Rovisco Pais 1049–001LisboaPortugal

We characterize the complex differential equations of the form dy/dx=a_(n)(x)y^)n_+a_(n-1)(x)y^(n-1)+…+a_(1)(x)y+a_(0)(x) where a_(j)(x) are meromorphic functions in the variable x for j = 0,..., n that admit either ... 详细信息

关键词： Weierstrass first integrals Weierstrass inverse integrating factor complex differential equations

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Liouvillian and Analytic Integrability of the Quadratic Vector Fields Having an Invariant Ellipse

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Acta Mathematica Sinica,English Series 2014年第3期30卷 453-466页

作者： Jaume LLIBRE Claudia valls Departament de Matemàtiques Universitat Autònoma de Barcelona Departamento de Matemtica Instituto Superior TcnicoUniversidade Tcnica de Lisboa

We characterize the Liouvillian and analytic integrability of the quadratic polynomial vector fields in R2 having an invariant ellipse.More precisely,a quadratic system having an invariant ellipse can be written into the form x=x2＋y2-1＋y（ax＋by＋c）,y=x（ax＋by＋c）,and the ellipse becomes x2＋y2=1.We prove that（i） this quadratic system is analytic integrable if and only if a=0;（ii） if x2＋y2=1 is a periodic orbit,then this quadratic system is Liouvillian integrable if and only if x2＋y2=1 is not a limit cycle;and（iii） if x2＋y2=1 is not a periodic orbit,then this quadratic system is Liouvilian integrable if and only if a=0.

关键词： Liouvillian integrability quadratic planar polynomial vector fields invariant ellipse

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On the Darboux Integrability of the Hindmarsh–Rose Burster

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Acta Mathematica Sinica,English Series 2018年第6期34卷 947-958页

作者： Jaume LLIBRE Claudia valls Departament de Matematiques Universitat Autonoma de Barcelona 08193 BeUaterra Barcelona Catalonia Spain Departamento de Matematica Instituto Superior TecnicoUniversidade Tecnica de Lisboa Av. Rovisco Pals 1049-001 Lisboa Portugal

We study the Hindmarsh-Rose burster which can be described by the differential system x^·=y-x^3＋bx^2＋I-z,y^·=1-5x^2-y,z^·=μ（s（x-x0）-z）where b, I, μ, s, x0 are parameters. We characterize all its invariant algebraic surfaces and all its exponential factors for all values of the parameters. We also characterize its Darboux integrability in function of the parameters. These characterizations allow to study the global dynamics of the system when such invariant algebraic surfaces exist.

关键词： Polynomial integrability rational integrability Darboux polynomials Darboux first integrals invariant algebraic surfaces exponential factors Hindmarsh Rose burster

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