29 research outputs found

    Ground Extraction from 3D Lidar Point Clouds

    Get PDF
    © 2018 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works Pomares, A., Martínez, J.L., Mandow, A., Martínez, M.A., Morán, M., Morales, J. Ground extraction from 3D lidar point clouds with the Classification Learner App (2018) 26th Mediterranean Conference on Control and Automation, Zadar, Croatia, June 2018, pp.400-405. DOI: PendingGround extraction from three-dimensional (3D) range data is a relevant problem for outdoor navigation of unmanned ground vehicles. Even if this problem has received attention with specific heuristics and segmentation approaches, identification of ground and non-ground points can benefit from state-of-the-art classification methods, such as those included in the Matlab Classification Learner App. This paper proposes a comparative study of the machine learning methods included in this tool in terms of training times as well as in their predictive performance. With this purpose, we have combined three suitable features for ground detection, which has been applied to an urban dataset with several labeled 3D point clouds. Most of the analyzed techniques achieve good classification results, but only a few offer low training and prediction times.This work was partially supported by the Spanish project DPI 2015- 65186-R. The publication has received support from Universidad de Málaga, Campus de Excelencia Andalucía Tech

    NLRP3 inflammasome activation and symptom burden in KRAS-mutated CMML patients is reverted by IL-1 blocking therapy

    Full text link
    Chronic myelomonocytic leukemia (CMML) is frequently associated with mutations in the rat sarcoma gene (RAS), leading to worse prognosis. RAS mutations result in active RAS-GTP proteins, favoring myeloid cell proliferation and survival and inducing the NLRP3 inflammasome together with the apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), which promote caspase-1 activation and interleukin (IL)-1(3 release. Here, we report, in a cohort of CMML patients with mutations in KRAS, a constitutive activation of the NLRP3 inflammasome in monocytes, evidenced by ASC oligomerization and IL-1(3 release, as well as a specific inflammatory cytokine signature. Treatment of a CMML patient with a KRASG12D mutation using the IL-1 receptor blocker anakinra inhibits NLRP3 inflammasome activation, reduces monocyte count, and improves the patient's clinical status, enabling a stem cell transplant. This reveals a basal inflammasome activation in RAS-mutated CMML patients and suggests potential therapeutic applications of NLRP3 and IL-1 blockers

    TLR4, but Neither Dectin-1 nor Dectin-2, Participates in the Mollusk Hemocyanin-Induced Proinflammatory Effects in Antigen-Presenting Cells From Mammals

    Get PDF
    Funding This study was supported by CONICYT-CHILE FONDECYT Regular Grant 1151337 to MB. FONDAP 15130011 to SL. CONICYT-CHILE National Ph.D. Fellowships were awarded to JJ (CONICYT-PCHA/Doctorado Nacional/2013-21130683) and to JO-Q (CONICYT-PFCHA/Doctorado Nacional/2017-21171588). FS holds a postdoctoral fellowship from the National Commission for Scientific and Technological Research (CONICYT), Chile. Funding was provided by the Wellcome Trust (102705, 097377), the MRC Centre for Medical Mycology and the University of Aberdeen (MR/N006364/1) to GB. Acknowledgments We thank Dr. María Rosa Bono, Dr. Sergio Vargas, and Dr. Juan Carlos Aguillón from Universidad de Chile and Dr. Mónica Imarai from Universidad de Santiago, Chile for helpful comments.Peer reviewedPublisher PD

    First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.)

    Full text link
    [EN] Background: Zucchini fruit set can be limited due to unfavourable environmental conditions in off-seasons crops that caused ineffective pollination/fertilization. Parthenocarpy, the natural or artificial fruit development without fertilization, has been recognized as an important trait to avoid this problem, and is related to auxin signalling. Nevertheless, differences found in transcriptome analysis during early fruit development of zucchini suggest that other complementary pathways could regulate fruit formation in parthenocarpic cultivars of this species. The development of next-generation sequencing technologies (NGS) as RNA-sequencing (RNA-seq) opens a new horizon for mapping and quantifying transcriptome to understand the molecular basis of pathways that could regulate parthenocarpy in this species. The aim of the current study was to analyze fruit transcriptome of two cultivars of zucchini, a non-parthenocarpic cultivar and a parthenocarpic cultivar, in an attempt to identify key genes involved in parthenocarpy. Results: RNA-seq analysis of six libraries (unpollinated, pollinated and auxin treated fruit in a non-parthenocarpic and parthenocarpic cultivar) was performed mapping to a new version of C. pepo transcriptome, with a mean of 92% success rate of mapping. In the non-parthenocarpic cultivar, 6479 and 2186 genes were differentially expressed (DEGs) in pollinated fruit and auxin treated fruit, respectively. In the parthenocarpic cultivar, 10,497 in pollinated fruit and 5718 in auxin treated fruit. A comparison between transcriptome of the unpollinated fruit for each cultivar has been performed determining that 6120 genes were differentially expressed. Annotation analysis of these DEGs revealed that cell cycle, regulation of transcription, carbohydrate metabolism and coordination between auxin, ethylene and gibberellin were enriched biological processes during pollinated and parthenocarpic fruit set. Conclusion: This analysis revealed the important role of hormones during fruit set, establishing the activating role of auxins and gibberellins against the inhibitory role of ethylene and different candidate genes that could be useful as markers for parthenocarpic selection in the current breeding programs of zucchini.Research worked is supported by the project RTA2014-00078 from the Spanish Institute of Agronomy Research INIA (Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria) and also PP.AVA.AVA201601.7, FEDER y FSE (Programa Operativo FSE de Andalucia 2007-2013 "Andalucia se mueve con Europa"). TPV is supported by a FPI scholarship from RTA2011-00044-C02-01/02 project of INIA. The funding agencies were not involved in the design of the study, collection, analysis, and interpretation of data and in writing the manuscript.Pomares-Viciana, T.; Del Rio-Celestino, M.; Roman, B.; Die, J.; Picó Sirvent, MB.; Gómez, P. (2019). First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.). BMC Plant Biology. 19:1-20. https://doi.org/10.1186/s12870-019-1632-2S12019Varga A, Bruinsma J. Tomato. In: Monselise SP, editor. CRC Handbook of Fruit Set and Development. Boca Raton: CRC Press; 1986. p. 461–80.Nepi M, Cresti L, Guarnieri M, Pacini E. Effect of relative humidity on water content, viability and carbohydrate profile of Petunia hybrid and Cucurbita pepo pollen. Plant Syst Evol. 2010;284:57–64.Gustafson FG. Parthenocarpy: natural and artificial. Bot Rev. 1942;8:599–654.Robinson RW, Reiners S. Parthenocarpy in summer squash. Hortscience. 1999;34:715–7.Pomares-Viciana T, Die J, Del Río-Celestino M, Román B, Gómez P. Auxin signalling regulation during induced and parthenocarpic fruit set in zucchini. Mol Breeding. 2017;37:56.Ozga JA, Reinecke DM. Hormonal interactions in fruit development. J Plant Growth Regul. 2003;22:73–81.Kim IS, Okubo H, Fujieda K. Endogenous levels of IAA in relation to parthenocarpy in cucumber (Cucumis sativus L). Sci Hortic. 1992;52:1–8.Olimpieri I, Siligato F, Caccia R, Mariotti L, Ceccarelli N, Soressi GP, et al. Tomato fruit set driven by pollination or by the parthenocarpic fruit allele are mediated by transcriptionally regulated gibberellin biosynthesis. Planta. 2007;226:877–88.Cui L, Zhang T, Li J, Lou Q, Chen J. Cloning and expression analysis of Cs-TIR1/AFB2: the fruit development-related genes of cucumber (Cucumis sativus L.). Acta Physiol Plant. 2014;36:139–49.De Jong M, Wolters-Arts J, Feron R, Mariani C, Vriezen WH. The Solanum lycopersicum auxin response factor 7 (SlARF7) regulates auxin signalling during tomato fruit set and development. Plant J. 2009;57:160–70.Wang H, Jones B, Li Z, Frasse P, Delalande C, Regad F, Chaabouni S, Latché A, Pech JC, Bouzayen M. The tomato aux/IAA transcription factor IAA9 is involved in fruit development and leaf morphogenesis. Plant Cell. 2005;17(10):2676–92.Goetz M, Vivian-Smith A, Johnson SD, Koltunow AM. AUXIN RESPONSE FACTOR 8 is a negative regulator of fruit initiation in Arabidopsis. Plant Cell. 2006;18(8):1873–86.Mazzucato A, Cellini F, Bouzayen M, Zouine M, Mila I, Minoia S et al. A TILLING allele of the tomato aux/IAA9 gene offers new insights into fruit set mechanisms and perspectives for breeding seedless tomatoes. Mol Breeding. 2015; 35(22):1-15.Blanca J, Cañizares J, Roig C, Ziarsolo P, Nuez F, Picó B. Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics. 2011;12:104.Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57–63.Da Fonseca RR, Albrechtsen A, Themudo GE, Ramos-Madrigal J, Sibbesen JA, Maretty L, et al. Next-generation biology: sequencing and data analysis approaches for non-model organisms. Mar Genomics. 2016;30:3–13.Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 2016;17:13.Li J, Cui ZWJ, Zhang T, Guo Q, Xu J, Li J, et al. Transcriptome comparison of global distinctive features between pollination and parthenocarpic fruit set reveals transcriptional phytohormone cross-talk in cucumber (Cucumis sativus L). Plant Cell Physiol. 2014;55(7):1325–42.Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23):3150–2.Montero-Pau J, Blanca J, Bombarely A, Ziarsolo P, Esteras C, Martí-Gómez C, et al. De novo assembly of the zucchini genome reveals a whole genome duplication associated with the origin of the Cucurbita genus. Plant Biotechnol J. 2017. https://doi.org/10.1111/pbi.12860 .Vriezen WH, Feron R, Maretto F, Keijman J, Mariani C. Changes in tomato ovary transcriptome demonstrate complex hormonal regulation of fruit set. New Phytol. 2008;177:60–76.Tang N, Deng W, Hu G, Hu N, Li Z. Transcriptome profiling reveals the regulatory mechanism underlying pollination dependent and parthenocarpic fruit set mainly mediated by auxin and gibberellin. PLoS One. 2015;10(4):e0125355.Li J, Yan S, Yang W, Li Y, Xia M, Chen Z, et al. Transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus L.). Sci Rep. 2015;26(5):8031.Mironov V, De Veylder L, Van Montagu M, Inze D. Cyclin-dependent kinases and cell division in plants- the nexus. Plant Cell. 1999;11(4):509–22.Perrot-Rechenmann C. Cellular responses to auxin: division versus expansion. Cold Spring Harb Perspect Biol. 2010;2(5):a001446.De Veylder L, Beeckman T, Beemster GT, Krols L, Terras F, Landrieu I, et al. Functional analysis of cyclin-dependent kinase inhibitors of Arabidopsis. Plant Cell. 2001;13:1653–68.Nieuwland J, Menges M, Murray JAH. The plant cyclins. In: Inze D, editor. Cell cycle control and plant development, vol. 2007. Oxford: Wiley-Blackwell Publishing; 2007. p. 33–61.Menges M, Samland AK, Planchais S, Murray JA. The D-type cyclin CYCD3;1 is limiting for the G1-to-S-phasetransition in Arabidopsis. Plant Cell. 2006;18:893–906.Boruc J, Mylle E, Duda M, De Clercq R, Rombauts S, Geelen D, et al. Systematic localization of the Arabidopsis core cell cycle proteins reveals novel cell division complexes. Plant Physiol. 2010;152(2):553–65.Sampedro J, Cosgrove DJ. The expansin superfamily. Genome Biol. 2005;6:242.Esmon CA, Tinsley AG, Ljung K, Sandberg G, Hearne LB, Liscum E. A gradient of auxin and auxin-dependent transcription precedes tropic growth responses. Proc Natl Acad Sci. 2006;103:236–41.De Folter S, Busscher J, Colombo L, Losa A, Angenent GC. Transcript profiling of transcription factors genes during siliques development in Arabidopsis. Plant Mol Bio. 2004;56:351–3662004.Son O, Cho HY, Kim MR, Lee H, Lee MS, Song E, et al. Induction of a homeodomain-leucine zipper gene by auxin is inhibited by cytokinin in Arabidopsis roots. Biochem Biophys Res Commun. 2005;326(1):203–9.Olsson ASB, Engstroem P, Seoderman E. The homeobox genes ATHB12 and ATHB7 encode potential regulators of growth in response to water deficit in Arabidopsis. Plant Mol Biol. 2004;55:663–77.Merrow SB, Hopp RJ. Storage effects on winter squashes. Associations between the sugar and starch content of and the degree of preference for winter squashes. J Agric Food Chem. 1961;9:321–6.Berg JM, Tymoczko JL, Stryer L. Carbohydrates. In: Freeman WH, editor. Biochemistry. 5th ed. New York: W H Freeman; 2002.Prabhakar V, Löttgert T, Gigolashvili T, Bell K, Flügge UI, Häusler RE. Molecular and functional characterization of the plastid-localized phosphoenolpyruvate enolase (ENO1) from Arabidopsis thaliana. FEBS Lett. 2009;583(6):983–91.Rius SP, Casati P, Iglesias AA, Gomez-Casati DF. Characterization of Arabidopsis lines deficient in GAPC-1, a cytosolic NAD-dependent glyceraldehyde-3-phosphate dehydrogenase. Plant Physiol. 2008;148(3):1655–67.Van der Linde K, Gutsche N, Leffers HM, Lindermayr C, Müller B, Holtgrefe S, et al. Regulation of plant cytosolic aldolase functions by redox-modifications. Plant Physiol Biochem. 2011;49(9):946–57.Lim H, Cho MH, Jeon JS, Bhoo SH, Kwon YK, Hahn TR. Altered expression of pyrophosphate: fructose-6-phosphate 1-phosphotransferase affects the growth of transgenic Arabidopsis plants. Mol Cells. 2009;27(6):641–9.Baud S, Wuillème S, Dubreucq B, De Almeida A, Vuagnat C, Lepiniec L, et al. Function of plastidial pyruvate kinases in seeds of Arabidopsis thaliana. Plant J. 2007;52:405–19.De Jong M, Mariani C, Vriezen WH. The role of auxin and gibberellin in tomato fruit set. J Exp Bot. 2009;60(5):1523–32.Martínez C, Manzano S, Megías Z, Garrido D, Picó B, Jamilena M. Involvement of ethylene biosynthesis and signalling in fruit set and early fruit development in zucchini squash (Cucurbita pepo L.). BMC Plant Biol. 2013;13:139.Serrani JC, Fos M, Atarés A, Garcia-martinez JL. Effect of gibberellin and auxin on parthenocarpic fruit growth induction in the cv. micro-tom of tomato. J Plant Growth Regul. 2007;26:211–21.Mapelli S. Changes in cytokinin in the fruits of parthenocarpic and normal tomatoes. Plant Sci Lett. 1981;22:227–33.Ulmasov T, Hagen G, Guilfoyle TJ. Activation and repression of transcription by auxin-response factors. Proc Natl Acad Sci U S A. 1999;96:5844–9.Ulmasov T, Hagen G, Guilfoyle TJ. Dimerization and DNA binding of auxin response factors. Plant J. 1999;19:309–19.Tiwari SB, Hagen G, Guilfoyle TJ. Aux/IAA proteins contain a potent transcriptional repression domain. Plant Cell. 2004;16:533–43.Switzenberg JA, Beaudry RM, Grumet R. Effect of CRC:: etr1-1 transgene expression on ethylene production, sex expression, fruit set and fruit ripening in transgenic melon (Cucumis melo L.). Transgenic Res. 2015;24(3):497-507.Nitsch LM, Oplaat C, Feron R, Ma Q, Wolters-Arts M, Hedden P, et al. Abscisic acid levels in tomato ovaries are regulated by LeNCED1 and SlCYP707A1. Planta. 2009;229(6):1335–46.Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods. 2008;5(7):621–8.Robinson MD, McCarthy DJ, Smyth GK. Edger: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2008;26(1):139–40.Raza K, Mishra A. A novel anticlustering filtering algorithm for the prediction of genes as a drug target. Am J Bio Engi. 2012;2(5):206–11.Van Iterson M, Boer JM, Menezes RX. Filtering, FDR and power. BMCBioinformatics. 2010;11:450.Conesa A, Götz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21:3674–6.Berardini TZ, Reiser L, Li D, Mezheritsky Y, Muller R, Strait E, Huala E. The Arabidopsis information resource: making and mining the “gold standard” annotated reference plant genome. Genesis. 2015. https://doi.org/10.1002/dvg.22877 .Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL. Nucleic Acids Res. 2000;28(1):45–8.Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL. NCBI BLAST: a better web interface. Nucleic Acids Res. 2008;36:W5–9.Wyatt LE, Strickler SR, Mueller LA, Mazourek M. An acorn squash (Cucurbita pepo ssp. ovifera) fruit and seed transcriptome as a resource for the study of fruit traits in Cucurbita. Hortic Res. 2015;2:14070. https://doi.org/10.1038/hortres.2014.70 .Zhang A, Ren GA, Sun YA, Guo H, Zhang SA, Zhang FA, et al. A high-density genetic map for anchoring genome sequences and identifying QTLs associated with dwarf vine in pumpkin (Cucurbita maxima Duch.). BMC Genomics. 2015;16:1101.Finn RD, Attwood TK, Babbit AB, Bork P, Bridge AJ, Chang HY. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. https://doi.org/10.1093/nar/gkw1107 .Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Sherlock G. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25(1):25–9.Kanehisa M, Araki M, Goto S, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36:480–4

    Granulocyte-macrophage colony stimulatory factor enhances the pro-inflammatory response of interferon-γ-treated macrophages to pseudomonas aeruginosa infection

    Get PDF
    Pseudomonas aeruginosa is an opportunistic pathogen that can cause severe infections at compromised epithelial surfaces, such those found in burns, wounds, and in lungs damaged by mechanical ventilation or recurrent infections, particularly in cystic fibrosis (CF) patients. CF patients have been proposed to have a Th2 and Th17-biased immune response suggesting that the lack of Th1 and/or over exuberant Th17 responses could contribute to the establishment of chronic P. aeruginosa infection and deterioration of lung function. Accordingly, we have observed that interferon (IFN)-γ production by peripheral blood mononuclear cells from CF patients positively correlated with lung function, particularly in patients chronically infected with P. aeruginosa. In contrast, IL-17A levels tended to correlate negatively with lung function with this trend becoming significant in patients chronically infected with P. aeruginosa. These results are in agreement with IFN-γ and IL-17A playing protective and detrimental roles, respectively, in CF. In order to explore the protective effect of IFN-γ in CF, the effect of IFN-γ alone or in combination with granulocyte-macrophage colony-stimulating factor (GM-CSF), on the ability of human macrophages to control P. aeruginosa growth, resist the cytotoxicity induced by this bacterium or promote inflammation was investigated. Treatment of macrophages with IFN-γ, in the presence and absence of GM-CSF, failed to alter bacterial growth or macrophage survival upon P. aeruginosa infection, but changed the inflammatory potential of macrophages. IFN-γ caused up-regulation of monocyte chemoattractant protein-1 (MCP-1) and TNF-α and down-regulation of IL-10 expression by infected macrophages. GM-CSF in combination with IFN-γ promoted IL-6 production and further reduction of IL-10 synthesis. Comparison of TNF-α vs. IL-10 and IL-6 vs. IL-10 ratios revealed the following hierarchy in regard to the pro-inflammatory potential of human macrophages infected with P. aeruginosa: untreated < treated with GM-CSF < treated with IFN-γ < treated with GM-CSF and IFN-γ

    El cultivo del caqui

    Get PDF
    En este libro se escribe del caqui en toda su amplitud, los mejores investigadores en las diferentes especialidades nos explican los resultados de la investigación y experiencias en fertirrigación, pies y variedades, sanidad vegetal, poda y postcosecha; acompañado y documentado de una amplia bibliografía de los investigadores de los principales países productores del mundo: China, Japón e Israel, e Italia, más que por su producción, por su continua y avanzada investigación. Este libro, fruto del trabajo de las diferentes líneas de investigación del producto, coordinada por el magnífico equipo de investigadores del IVIA, pone a disposición de la producción, postcosecha y comercialización todos los avances conocidos a nivel nacional e internacional

    TOXOPLASMOSIS IN MEXICO: EPIDEMIOLOGICAL SITUATION IN HUMANS AND ANIMALS

    Full text link

    Diseño de un Sistema de Aprendizaje Basado en Proyecto para el Máster Universitario en Automática y Robótica

    No full text
    El ABP (Aprendizaje Basado en Proyecto) es una metodología didáctica en la que el estudiante aprende los conceptos de una materia mediante la realización de un proyecto o resolución de un problema adecuadamente diseñado y formulado por el profesor. Diversos estudios muestran que el ABP fomenta habilidades muy importantes, tales como el trabajo en grupo, el aprendizaje autónomo, la planificación del tiempo, el trabajo por proyectos o la capacidad de expresión oral y escrita, y mejora la motivación del estudiante, lo que se traduce en un mejor rendimiento académico y una mayor persistencia en el estudio. Este tipo de experiencias pueden ser beneficiosas tanto para el alumnado, que desarrolla nuevas habilidades que se acaban de mencionar, como para el profesor, que debe adaptarse a las nuevas exigencias tanto del entorno académico que plantea la adaptación al EEES como del mercado de trabajo. En este trabajo se pretende utilizar la metodología ABP en cada una de las asignaturas relacionadas con la robótica dentro del Máster Universitario en Automática y Robótica, para diseñar, construir y programar un robot a lo largo del Máster. Cada una de las asignaturas implicadas en la red definirá cómo participará dentro del proyecto global. El alumno podrá adquirir las competencias de cada asignatura al mismo tiempo que trabaja en un proyecto de gran envergadura en el que se obtiene finalmente un robot real
    corecore