Efficacy of DNA amplification in tissue biopsy samples to improve the detection of invasive fungal disease

AbstractThe performance of a pan-fungal PCR-based technique was evaluated to assess the aetiology of invasive fungal diseases (IFDs). A total of 89 formalin-fixed paraffin-embedded biopsy samples from 84 patients with proven IFD were studied. Culture of tissue was performed in 68 (81%) patients. The sensitivities of the PCR-based technique and microbiological culture of tissues were 89% and 56%, respectively (p <0.01). According to PCR results, Aspergillus species accounted for 67%, Candida species for 13%, zygomycetes for 11%, and rare and emerging fungi for 9%. Aspergillus species were significantly associated with lung samples (79.6%, p <0.01), Mucorales were associated with skin/subcutaneous samples, and Candida species were associated with gastrointestinal samples. Regarding biopsy samples with Aspergillus species, Aspergillus fumigatus DNA was detected in 43 of 50 (86%), and Aspergillus flavus in six of 50 (12%). PCR was positive in 24 of 30 (80%) cases with negative culture. In nine of the 84 patients, the PCR technique failed to amplify the DNA. Six also had negative cultures, and in the remaining three cases culture was positive (Rhizopus microsporus, Rhizopus arrhizus, and Sakseneae vasiformis), suggesting that the PCR technique was not as effective in amplifying the DNA of some species of Zygomycetes. In five cases, there was no correlation between culture results and those obtained with DNA amplification, indicating the possibility of a mixed infection or the presence of colonizer/contaminant microorganisms. In summary, PCR-based techniques for DNA amplification should be implemented in histopathology and microbiology departments, as they appear to be complementary to conventional methods for IFD detection

Shapes of the 192,190^{192,190}Pb ground states from beta decay studies using the total absorption technique

The beta decay of $^{192,190}$Pb has been studied using the total absorption technique at the ISOLDE(CERN) facility. The beta-decay strength deduced from the measurements, combined with QRPA theoretical calculations, allow us to infer that the ground states of the $^{192,190}$Pb isotopes are spherical. These results represent the first application of the shape determination method using the total absorption technique for heavy nuclei and in a region where there is considerable interest in nuclear shapes and shape effects

Quantum-Aware Software Defined Networks

Software Defined Networks (SDN) represent a major paradigm change in communications networks. It provides a level of abstraction and independence from the traditional networking practice that allows for a fast path of innovation and, specifically, opens new opportunities for Quantum Key Distribution (QKD) networks. In this contribution we explore the implications of this paradigm for the deployment of QKD in practice from the point of view of telecommunications? providers, network equipment manufacturers and applied research and development. We propose a generic quantum-aware SDN architecture and two applications, a generic end to end encryption one and other for the network infrastructure itself

Ab Initio Calculation of the Lattice Distortions induced by Substitutional Ag- and Cu- Impurities in Alkali Halide Crystals

An ab initio study of the doping of alkali halide crystals (AX: A = Li, Na, K, Rb; X = F, Cl, Br, I) by ns2 anions (Ag- and Cu-) is presented. Large active clusters with 179 ions embedded in the surrounding crystalline lattice are considered in order to describe properly the lattice relaxation induced by the introduction of substitutional impurities. In all the cases considered, the lattice distortions imply the concerted movement of several shells of neighbors. The shell displacements are smaller for the smaller anion Cu-, as expected. The study of the family of rock-salt alkali halides (excepting CsF) allows us to extract trends that might be useful at a predictive level in the study of other impurity systems. Those trends are presented and discussed in terms of simple geometric arguments.Comment: LaTeX file. 8 pages, 3 EPS pictures. New version contains calculations of the energy of formation of the defects with model clusters of different size

Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction

[EN] Understanding the nature of pathogen host interaction may help improve strawberry (Fragaria x anahassa) cultivars. Plant resistance to pathogenic agents usually operates through a complex network of defense mechanisms mediated by a diverse array of signaling molecules. In strawberry, resistance to a variety of pathogens has been reported to be mostly polygenic and quantitatively inherited, making it difficult to associate molecular markers with disease resistance genes. Colletotrichum acutaturn spp. is a major strawberry pathogen, and completely resistant cultivars have not been reported. Moreover, strawberry defense network components and mechanisms remain largely unknown and poorly understood. Assessment of the strawberry response to C. acutatum included a global transcript analysis, and acidic hormones SA and JA measurements were analyzed after challenge with the pathogen. Induction of transcripts corresponding to the SA and JA signaling pathways and key genes controlling major steps within these defense pathways was detected. Accordingly, SA and JA accumulated in strawberry after infection. Contrastingly, induction of several important SA, JA, and oxidative stress-responsive defense genes, including FaPR1-1, FaLOX2, FaJAR1, FaPDF1, and FaGST1, was not detected, which suggests that specific branches in these defense pathways (those leading to FaPR1-2, FaPR2-1, FaPR2-2, FaAOS, FaPR5, and FaPR10) were activated. Our results reveal that specific aspects in SA and JA dependent signaling pathways are activated in strawberry upon interaction with C. acutatum. Certain described defense-associated transcripts related to these two known signaling pathways do not increase in abundance following infection. This finding suggests new insight into a specific putative molecular strategy for defense against this pathogen.Authors are grateful to Dr. JM Lopez-Aranda (IFAPA-Centro de Churriana) for providing micropropagated strawberry plants and to Nicolas Garcia-Caparros for technical assistance. Authors also want to thank Kevin M. Folta for his insightful comments on the paper. This work was supported by Junta de Andalucia, Spain [Proyectos de Excelencia P07-AGR-02482/P12-AGR-2174, and grants to Grupo-BIO278].Amil-Ruiz, F.; Garrido-Gala, J.; Gadea Vacas, J.; Blanco-Portales, R.; Munoz-Merida, A.; Trelles, O.; De Los Santos, B.... (2016). Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction. Frontiers in Plant Science. 7(1036). https://doi.org/10.3389/fpls.2016.01036S71036Acosta, I. F., & Farmer, E. E. (2010). Jasmonates. The Arabidopsis Book, 8, e0129. doi:10.1199/tab.0129Al-Shahrour, F., Diaz-Uriarte, R., & Dopazo, J. (2004). FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics, 20(4), 578-580. doi:10.1093/bioinformatics/btg455Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403-410. doi:10.1016/s0022-2836(05)80360-2Amil-Ruiz, F., Blanco-Portales, R., Muñoz-Blanco, J., & Caballero, J. L. (2011). The Strawberry Plant Defense Mechanism: A Molecular Review. Plant and Cell Physiology, 52(11), 1873-1903. doi:10.1093/pcp/pcr136Amil-Ruiz, F., Garrido-Gala, J., Blanco-Portales, R., Folta, K. M., Muñoz-Blanco, J., & Caballero, J. L. (2013). Identification and Validation of Reference Genes for Transcript Normalization in Strawberry (Fragaria × ananassa) Defense Responses. PLoS ONE, 8(8), e70603. doi:10.1371/journal.pone.0070603Arroyo, F. T., Moreno, J., García-Herdugo, G., Santos, B. D. los, Barrau, C., Porras, M., … Romero, F. (2005). Ultrastructure of the early stages of Colletotrichum acutatum infection of strawberry tissues. Canadian Journal of Botany, 83(5), 491-500. doi:10.1139/b05-022Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., … Sherlock, G. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics, 25(1), 25-29. doi:10.1038/75556Aviv, D. H., Rustérucci, C., Iii, B. F. H., Dietrich, R. A., Parker, J. E., & Dangl, J. L. (2002). Runaway cell death, but not basal disease resistance, inlsd1is SA- andNIM1/NPR1-dependent. The Plant Journal, 29(3), 381-391. doi:10.1046/j.0960-7412.2001.01225.xBak, S., Beisson, F., Bishop, G., Hamberger, B., Höfer, R., Paquette, S., & Werck-Reichhart, D. (2011). Cytochromes P450. The Arabidopsis Book, 9, e0144. doi:10.1199/tab.0144Baniwal, S. K., Bharti, K., Chan, K. Y., Fauth, M., Ganguli, A., Kotak, S., … von Koskull-DÖring, P. (2004). Heat stress response in plants: a complex game with chaperones and more than twenty heat stress transcription factors. Journal of Biosciences, 29(4), 471-487. doi:10.1007/bf02712120Bhattacharjee, S. (2012). The Language of Reactive Oxygen Species Signaling in Plants. Journal of Botany, 2012, 1-22. doi:10.1155/2012/985298Birkenbihl, R. P., Diezel, C., & Somssich, I. E. (2012). Arabidopsis WRKY33 Is a Key Transcriptional Regulator of Hormonal and Metabolic Responses toward Botrytis cinerea Infection. Plant Physiology, 159(1), 266-285. doi:10.1104/pp.111.192641Caarls, L., Pieterse, C. M. J., & Van Wees, S. C. M. (2015). How salicylic acid takes transcriptional control over jasmonic acid signaling. Frontiers in Plant Science, 6. doi:10.3389/fpls.2015.00170Casado-Díaz, A., Encinas-Villarejo, S., Santos, B. de los, Schilirò, E., Yubero-Serrano, E.-M., Amil-Ruíz, F., … Caballero, J.-L. (2006). Analysis of strawberry genes differentially expressed in response to Colletotrichum infection. Physiologia Plantarum, 128(4), 633-650. doi:10.1111/j.1399-3054.2006.00798.xCharng, Y., Liu, H., Liu, N., Chi, W., Wang, C., Chang, S., & Wang, T. (2006). A Heat-Inducible Transcription Factor, HsfA2, Is Required for Extension of Acquired Thermotolerance in Arabidopsis. Plant Physiology, 143(1), 251-262. doi:10.1104/pp.106.091322Chung, S. H., Rosa, C., Scully, E. D., Peiffer, M., Tooker, J. F., Hoover, K., … Felton, G. W. (2013). Herbivore exploits orally secreted bacteria to suppress plant defenses. Proceedings of the National Academy of Sciences, 110(39), 15728-15733. doi:10.1073/pnas.1308867110Curry, K. J., Abril, M., Avant, J. B., & Smith, B. J. (2002). Strawberry Anthracnose: Histopathology of Colletotrichum acutatum and C. fragariae. Phytopathology®, 92(10), 1055-1063. doi:10.1094/phyto.2002.92.10.1055Debode, J., Van Hemelrijck, W., Baeyen, S., Creemers, P., Heungens, K., & Maes, M. (2009). Quantitative detection and monitoring ofColletotrichum acutatumin strawberry leaves using real-time PCR. Plant Pathology, 58(3), 504-514. doi:10.1111/j.1365-3059.2008.01987.xDempsey, D. A., & Klessig, D. F. (2012). SOS – too many signals for systemic acquired resistance? Trends in Plant Science, 17(9), 538-545. doi:10.1016/j.tplants.2012.05.011Dodds, P. N., & Rathjen, J. P. (2010). Plant immunity: towards an integrated view of plant–pathogen interactions. Nature Reviews Genetics, 11(8), 539-548. doi:10.1038/nrg2812Doehlemann, G., Wahl, R., Horst, R. J., Voll, L. M., Usadel, B., Poree, F., … Kämper, J. (2008). Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis. The Plant Journal, 56(2), 181-195. doi:10.1111/j.1365-313x.2008.03590.xDong, X. (2004). NPR1, all things considered. Current Opinion in Plant Biology, 7(5), 547-552. doi:10.1016/j.pbi.2004.07.005Durgbanshi, A., Arbona, V., Pozo, O., Miersch, O., Sancho, J. V., & Gómez-Cadenas, A. (2005). Simultaneous Determination of Multiple Phytohormones in Plant Extracts by Liquid Chromatography−Electrospray Tandem Mass Spectrometry. Journal of Agricultural and Food Chemistry, 53(22), 8437-8442. doi:10.1021/jf050884bEl Oirdi, M., El Rahman, T. A., Rigano, L., El Hadrami, A., Rodriguez, M. C., Daayf, F., … Bouarab, K. (2011). Botrytis cinerea Manipulates the Antagonistic Effects between Immune Pathways to Promote Disease Development in Tomato. The Plant Cell, 23(6), 2405-2421. doi:10.1105/tpc.111.083394Encinas-Villarejo, S., Maldonado, A. M., Amil-Ruiz, F., de los Santos, B., Romero, F., Pliego-Alfaro, F., … Caballero, J. L. (2009). Evidence for a positive regulatory role of strawberry (Fragaria×ananassa) Fa WRKY1 and Arabidopsis At WRKY75 proteins in resistance. Journal of Experimental Botany, 60(11), 3043-3065. doi:10.1093/jxb/erp152Freeman, S., Horowitz, S., & Sharon, A. (2001). Pathogenic and Nonpathogenic Lifestyles in Colletotrichum acutatum from Strawberry and Other Plants. Phytopathology®, 91(10), 986-992. doi:10.1094/phyto.2001.91.10.986Freeman, S., Katan, T., & Shabi, E. (1998). Characterization of Colletotrichum Species Responsible for Anthracnose Diseases of Various Fruits. Plant Disease, 82(6), 596-605. doi:10.1094/pdis.1998.82.6.596Gfeller, A., Dubugnon, L., Liechti, R., & Farmer, E. E. (2010). Jasmonate Biochemical Pathway. Science Signaling, 3(109), cm3-cm3. doi:10.1126/scisignal.3109cm3Grellet-Bournonville, C. F., Martinez-Zamora, M. G., Castagnaro, A. P., & Díaz-Ricci, J. C. (2012). Temporal accumulation of salicylic acid activates the defense response against Colletotrichum in strawberry. Plant Physiology and Biochemistry, 54, 10-16. doi:10.1016/j.plaphy.2012.01.019Guidarelli, M., Carbone, F., Mourgues, F., Perrotta, G., Rosati, C., Bertolini, P., & Baraldi, E. (2011). Colletotrichum acutatum interactions with unripe and ripe strawberry fruits and differential responses at histological and transcriptional levels. Plant Pathology, 60(4), 685-697. doi:10.1111/j.1365-3059.2010.02423.xHeidrich, K., Wirthmueller, L., Tasset, C., Pouzet, C., Deslandes, L., & Parker, J. E. (2011). Arabidopsis EDS1 Connects Pathogen Effector Recognition to Cell Compartment-Specific Immune Responses. Science, 334(6061), 1401-1404. doi:10.1126/science.1211641Horowitz, S., Freeman, S., & Sharon, A. (2002). Use of Green Fluorescent Protein-Transgenic Strains to Study Pathogenic and Nonpathogenic Lifestyles in Colletotrichum acutatum. Phytopathology®, 92(7), 743-749. doi:10.1094/phyto.2002.92.7.743Ikeda, M., Mitsuda, N., & Ohme-Takagi, M. (2011). Arabidopsis HsfB1 and HsfB2b Act as Repressors of the Expression of Heat-Inducible Hsfs But Positively Regulate the Acquired Thermotolerance. Plant Physiology, 157(3), 1243-1254. doi:10.1104/pp.111.179036Ikeda, M., & Ohme-Takagi, M. (2009). A Novel Group of Transcriptional Repressors in Arabidopsis. Plant and Cell Physiology, 50(5), 970-975. doi:10.1093/pcp/pcp048Khan, A. A., & Shih, D. S. (2004). Molecular cloning, characterization, and expression analysis of two class II chitinase genes from the strawberry plant. Plant Science, 166(3), 753-762. doi:10.1016/j.plantsci.2003.11.015Krinke, O., Ruelland, E., Valentová, O., Vergnolle, C., Renou, J.-P., Taconnat, L., … Zachowski, A. (2007). Phosphatidylinositol 4-Kinase Activation Is an Early Response to Salicylic Acid in Arabidopsis Suspension Cells. Plant Physiology, 144(3), 1347-1359. doi:10.1104/pp.107.100842Kubigsteltig, I., Laudert, D., & Weiler, E. W. (1999). Structure and regulation of the Arabidopsis thaliana allene oxide synthase gene. Planta, 208(4), 463-471. doi:10.1007/s004250050583Leandro, L. F. S., Gleason, M. L., Nutter, F. W., Wegulo, S. N., & Dixon, P. M. (2001). Germination and Sporulation of Colletotrichum acutatum on Symptomless Strawberry Leaves. Phytopathology®, 91(7), 659-664. doi:10.1094/phyto.2001.91.7.659Leon-Reyes, A., Van der Does, D., De Lange, E. S., Delker, C., Wasternack, C., Van Wees, S. C. M., … Pieterse, C. M. J. (2010). Salicylate-mediated suppression of jasmonate-responsive gene expression in Arabidopsis is targeted downstream of the jasmonate biosynthesis pathway. Planta, 232(6), 1423-1432. doi:10.1007/s00425-010-1265-zLi, J., Brader, G., Kariola, T., & Tapio Palva, E. (2006). WRKY70 modulates the selection of signaling pathways in plant defense. The Plant Journal, 46(3), 477-491. doi:10.1111/j.1365-313x.2006.02712.xLi, J., Brader, G., & Palva, E. T. (2004). The WRKY70 Transcription Factor: A Node of Convergence for Jasmonate-Mediated and Salicylate-Mediated Signals in Plant Defense. The Plant Cell, 16(2), 319-331. doi:10.1105/tpc.016980Liu, P.-P., von Dahl, C. C., Park, S.-W., & Klessig, D. F. (2011). Interconnection between Methyl Salicylate and Lipid-Based Long-Distance Signaling during the Development of Systemic Acquired Resistance in Arabidopsis and Tobacco. Plant Physiology, 155(4), 1762-1768. doi:10.1104/pp.110.171694Lodha, T. D., & Basak, J. (2011). Plant–Pathogen Interactions: What Microarray Tells About It? Molecular Biotechnology, 50(1), 87-97. doi:10.1007/s12033-011-9418-2López-Ráez, J. A., Verhage, A., Fernández, I., García, J. M., Azcón-Aguilar, C., Flors, V., & Pozo, M. J. (2010). Hormonal and transcriptional profiles highlight common and differential host responses to arbuscular mycorrhizal fungi and the regulation of the oxylipin pathway. Journal of Experimental Botany, 61(10), 2589-2601. doi:10.1093/jxb/erq089Maas, J. L. (Ed.). (1998). Compendium of Strawberry Diseases, Second Edition. doi:10.1094/9780890546178Makowski, R. M. D., & Mortensen, K. (1998). Latent infections and penetration of the bioherbicide agent Colletotrichum gloeosporioides f. sp. malvae in non-target field crops under controlled environmental conditions. Mycological Research, 102(12), 1545-1552. doi:10.1017/s0953756298006960Maleck, K., Levine, A., Eulgem, T., Morgan, A., Schmid, J., Lawton, K. A., … Dietrich, R. A. (2000). The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nature Genetics, 26(4), 403-410. doi:10.1038/82521Marcel, S., Sawers, R., Oakeley, E., Angliker, H., & Paszkowski, U. (2010). Tissue-Adapted Invasion Strategies of the Rice Blast Fungus Magnaporthe oryzae. The Plant Cell, 22(9), 3177-3187. doi:10.1105/tpc.110.078048Ndamukong, I., Abdallat, A. A., Thurow, C., Fode, B., Zander, M., Weigel, R., & Gatz, C. (2007). SA-inducible Arabidopsis glutaredoxin interacts with TGA factors and suppresses JA-responsive PDF1.2 transcription. The Plant Journal, 50(1), 128-139. doi:10.1111/j.1365-313x.2007.03039.xPajerowska-Mukhtar, K. M., Wang, W., Tada, Y., Oka, N., Tucker, C. L., Fonseca, J. P., & Dong, X. (2012). The HSF-like Transcription Factor TBF1 Is a Major Molecular Switch for Plant Growth-to-Defense Transition. Current Biology, 22(2), 103-112. doi:10.1016/j.cub.2011.12.015Pe�a-Cort�s, H., Barrios, P., Dorta, F., Polanco, V., S�nchez, C., S�nchez, E., & Ram�rez, I. (2004). Involvement of Jasmonic Acid and Derivatives in Plant Response to Pathogen and Insects and in Fruit Ripening. Journal of Plant Growth Regulation, 23(3), 246-260. doi:10.1007/s00344-004-0035-1Pernas, M., Ryan, E., & Dolan, L. (2010). SCHIZORIZA Controls Tissue System Complexity in Plants. Current Biology, 20(9), 818-823. doi:10.1016/j.cub.2010.02.062Pieterse, C. M. J., Leon-Reyes, A., Van der Ent, S., & Van Wees, S. C. M. (2009). Networking by small-molecule hormones in plant immunity. Nature Chemical Biology, 5(5), 308-316. doi:10.1038/nchembio.164Rahman, T. A. E., Oirdi, M. E., Gonzalez-Lamothe, R., & Bouarab, K. (2012). Necrotrophic Pathogens Use the Salicylic Acid Signaling Pathway to Promote Disease Development in Tomato. Molecular Plant-Microbe Interactions®, 25(12), 1584-1593. doi:10.1094/mpmi-07-12-0187-rRen, C.-M., Zhu, Q., Gao, B.-D., Ke, S.-Y., Yu, W.-C., Xie, D.-X., & Peng, W. (2008). Transcription Factor WRKY70 Displays Important but No Indispensable Roles in Jasmonate and Salicylic Acid Signaling. Journal of Integrative Plant Biology, 50(5), 630-637. doi:10.1111/j.1744-7909.2008.00653.xRietz, S., Stamm, A., Malonek, S., Wagner, S., Becker, D., Medina-Escobar, N., … Parker, J. E. (2011). Different roles of Enhanced Disease Susceptibility1 (EDS1) bound to and dissociated from Phytoalexin Deficient4 (PAD4) in Arabidopsis immunity. New Phytologist, 191(1), 107-119. doi:10.1111/j.1469-8137.2011.03675.xRobert-Seilaniantz, A., Grant, M., & Jones, J. D. G. (2011). Hormone Crosstalk in Plant Disease and Defense: More Than Just JASMONATE-SALICYLATE Antagonism. Annual Review of Phytopathology, 49(1), 317-343. doi:10.1146/annurev-phyto-073009-114447Cristina, M., Petersen, M., & Mundy, J. (2010). Mitogen-Activated Protein Kinase Signaling in Plants. Annual Review of Plant Biology, 61(1), 621-649. doi:10.1146/annurev-arplant-042809-112252Rouhier, N. (2006). Genome-wide analysis of plant glutaredoxin systems. Journal of Experimental Botany, 57(8), 1685-1696. doi:10.1093/jxb/erl001Ruepp, A. (2004). The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Research, 32(18), 5539-5545. doi:10.1093/nar/gkh894Rusterucci, C. (2001). The Disease Resistance Signaling Components EDS1 and PAD4 Are Essential Regulators of the Cell Death Pathway Controlled by LSD1 in Arabidopsis. THE PLANT CELL ONLINE, 13(10), 2211-2224. doi:10.1105/tpc.13.10.2211Sarowar, S., Zhao, Y., Soria-Guerra, R. E., Ali, S., Zheng, D., Wang, D., & Korban, S. S. (2011). Expression profiles of differentially regulated genes during the early stages of apple flower infection with Erwinia amylovora. Journal of Experimental Botany, 62(14), 4851-4861. doi:10.1093/jxb/err147Sasaki, Y. (2001). Monitoring of Methyl Jasmonate-responsive Genes in Arabidopsis by cDNA Macroarray: Self-activation of Jasmonic Acid Biosynthesis and Crosstalk with Other Phytohormone Signaling Pathways. DNA Research, 8(4), 153-161. doi:10.1093/dnares/8.4.153Schenk, P. M., Kazan, K., Manners, J. M., Anderson, J. P., Simpson, R. S., Wilson, I. W., … Maclean, D. J. (2003). Systemic Gene Expression in Arabidopsis during an Incompatible Interaction with Alternaria brassicicola. Plant Physiology, 132(2), 999-1010. doi:10.1104/pp.103.021683Simpson, D. W. (1991). Resistance toBotrytis cinereain pistillate genotypes of the cultivated strawberryFragaria ananassa. Journal of Horticultural Science, 66(6), 719-723. doi:10.1080/00221589.1991.11516203Shulaev, V., Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., … Mane, S. P. (2010). The genome of woodland strawberry (Fragaria vesca). Nature Genetics, 43(2), 109-116. doi:10.1038/ng.740Song, W. C., Funk, C. D., & Brash, A. R. (1993). Molecular cloning of an allene oxide synthase: a cytochrome P450 specialized for the metabolism of fatty acid hydroperoxides. Proceedings of the National Academy of Sciences, 90(18), 8519-8523. doi:10.1073/pnas.90.18.8519Spoel, S. H., & Dong, X. (2012). How do plants achieve immunity? Defence without specialized immune cells. Nature Reviews Immunology, 12(2), 89-100. doi:10.1038/nri3141Spoel, S. H., Johnson, J. S., & Dong, X. (2007). Regulation of tradeoffs between plant defenses against pathogens with different lifestyles. Proceedings of the National Academy of Sciences, 104(47), 18842-18847. doi:10.1073/pnas.0708139104Staswick, P. E., & Tiryaki, I. (2004). The Oxylipin Signal Jasmonic Acid Is Activated by an Enzyme That Conjugates It to Isoleucine in Arabidopsis. The Plant Cell, 16(8), 2117-2127. doi:10.1105/tpc.104.023549Ten Hove, C. A., Willemsen, V., de Vries, W. J., van Dijken, A., Scheres, B., & Heidstra, R. (2010). SCHIZORIZA Encodes a Nuclear Factor Regulating Asymmetry of Stem Cell Divisions in the Arabidopsis Root. Current Biology, 20(5), 452-457. doi:10.1016/j.cub.2010.01.018Turner, J. G., Ellis, C., & Devoto, A. (2002). The Jasmonate Signal Pathway. The Plant Cell, 14(suppl 1), S153-S164. doi:10.1105/tpc.000679Tusher, V. G., Tibshirani, R., & Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences, 98(9), 5116-5121. doi:10.1073/pnas.091062498Uknes, S., Mauch-Mani, B., Moyer, M., Potter, S., Williams, S., Dincher, S., … Ryals, J. (1992). Acquired resistance in Arabidopsis. The Plant Cell, 4(6), 645-656. doi:10.1105/tpc.4.6.645Vargas, W. A., Martín, J. M. S., Rech, G. E., Rivera, L. P., Benito, E. P., Díaz-Mínguez, J. M., … Sukno, S. A. (2012). Plant Defense Mechanisms Are Activated during Biotrophic and Necrotrophic Development of Colletotricum graminicola in Maize. Plant Physiology, 158(3), 1342-1358. doi:10.1104/pp.111.190397Venugopal, S. C., Jeong, R.-D., Mandal, M. K., Zhu, S., Chandra-Shekara, A. C., Xia, Y., … Kachroo, P. (2009). Enhanced Disease Susceptibility 1 and Salicylic Acid Act Redundantly to Regulate Resistance Gene-Mediated Signaling. PLoS Genetics, 5(7), e1000545. doi:10.1371/journal.pgen.1000545Vlot, A. C., Liu, P.-P., Cameron, R. K., Park, S.-W., Yang, Y., Kumar, D., … Klessig, D. F. (2008). Identification of likely orthologs of tobacco salicylic acid-binding protein 2 and their role in systemic acquired resistance inArabidopsis thaliana. The Plant Journal, 56(3), 445-456. doi:10.1111/j.1365-313x.2008.03618.xWang, D., Amornsiripanitch, N., & Dong, X. (2006). A Genomic Approach to Identify Regulatory Nodes in the Transcriptional Network of Systemic Acquired Resistance in Plants. PLoS Pathogens, 2(11), e123. doi:10.1371/journal.ppat.0020123Wang, D. (2005). Induction of Protein Secretory Pathway Is Required for Systemic Acquired Resistance. Science, 308(5724), 1036-1040. doi:10.1126/science.1108791Wang, G.-F., Seabolt, S., Hamdoun, S., Ng, G., Park, J., & Lu, H. (2011). Multiple Roles of WIN3 in Regulating Disease Resistance, Cell Death, and Flowering Time in Arabidopsis. Plant Physiology, 156(3), 1508-1519. doi:10.1104/pp.111.176776Wiermer, M., Feys, B. J., & Parker, J. E. (2005). Plant immunity: the EDS1 regulatory node. Current Opinion in Plant Biology, 8(4), 383-389. doi:10.1016/j.pbi.2005.05.010Windram, O., Madhou, P., McHattie, S., Hill, C., Hickman, R., Cooke, E., … Denby, K. J. (2012). Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis. Th

Dynamical properties of liquid Al near melting. An orbital-free molecular dynamics study

The static and dynamic structure of liquid Al is studied using the orbital free ab-initio molecular dynamics method. Two thermodynamic states along the coexistence line are considered, namely T = 943 K and 1323 K for which X-ray and neutron scattering data are available. A new kinetic energy functional, which fulfills a number of physically relevant conditions is employed, along with a local first principles pseudopotential. In addition to a comparison with experiment, we also compare our ab-initio results with those obtained from conventional molecular dynamics simulations using effective interionic pair potentials derived from second order pseudopotential perturbation theory.Comment: 15 pages, 12 figures, 2 tables, submitted to PR

Ionic and electronic structure of sodium clusters up to N=59

We determined the ionic and electronic structure of sodium clusters with even electron numbers and 2 to 59 atoms in axially averaged and three-dimensional density functional calculations. A local, phenomenological pseudopotential that reproduces important bulk and atomic properties and facilitates structure calculations has been developed. Photoabsorption spectra have been calculated for $\mathrm{Na}_2$, $\mathrm{Na}_8$, and $\mathrm{Na}_9^+$ to $\mathrm{Na}_{59}^+$. The consistent inclusion of ionic structure considerably improves agreement with experiment. An icosahedral growth pattern is observed for $\mathrm{Na}_{19}^+$ to $\mathrm{Na}_{59}^+$. This finding is supported by photoabsorption data.Comment: To appear in Phys. Rev. B 62. Version with figures in better quality can be requested from the author

Perfil de los pacientes que acuden al médico internista para valoración de osteoporosis: registro OSTEOMED

Producción CientíficaAntecedentes y objetivo: La osteoporosis se considera un trastorno generalizado del esqueleto en el que existe una alteración de la resistencia ósea que predispone a la persona a un mayor riesgo de fractura. Este estudio transversal pretende recoger y presentar las principales características clínicas de los pacientes que acuden a la consulta de los médicos internistas en Espa˜na. Conocer estas características podría facilitar la puesta en marcha de planes de actuación para mejorar la atención de estos pacientes de manera más eficaz y eficiente. Material y métodos: A través del análisis del registro OSTEOMED (Osteoporosis en Medicina Interna), este trabajo presenta las principales características clínicas de los pacientes con osteoporosis que acudieron a las consultas de Medicina Interna en 23 centros hospitalarios espa˜noles entre 2012 y 2017. Se han analizado los motivos de consulta, los valores densitométricos, la presencia de comorbilidades, el tratamiento prescrito y otros factores relacionados con el estilo de vida. Resultados: En total se evaluó a 2.024 pacientes con osteoporosis (89,87% mujeres, 10,13% hombres). La edad media de los pacientes fue de 64,1 ± 12,1 a˜nos (mujeres, 64,7 ± 11,5 a˜nos; hombres, 61,2 ± 14,2 a˜nos). No hubo diferencia entre sexos en la historia de caídas recientes (9,1-6,7%), mientras que sí se apreció en la ingesta diaria de calcio de lácteos (553,8 ± 332,6 mg en mujeres vs. 450,2 ± 303,3 mg en hombres; p < 0,001) y en causas secundarias de osteoporosis(13% de hombres vs. 6,5% de mujeres; p < 0,001). En la muestra se observaron un total de 404fracturas (20%), destacando el número de fracturas vertebrales confirmadas (17,2%, 35,6% enhombres vs. 15,2% de las mujeres; p < 0,001). Una gran parte de los pacientes no recibía eltratamiento indicado y presentaba bajos niveles de actividad física y exposición solar. Un por-centaje importante de pacientes presentó comorbilidades asociadas, siendo las más frecuentesla hipertensión (32%) y la dislipidemia (28%).Conclusiones: Estos resultados definen el perfil del paciente con osteoporosis que acude a laconsulta de Medicina Interna en Espa˜na. Además, ponen de manifiesto el carácter multisistémicode esta entidad que junto con su elevada prevalencia determinan que las consultas específicasde Medicina Interna dedicadas a su manejo son el lugar adecuado para la atención de estos pacientes

Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants

Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling. © 2018 The Author(s).Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling. © 2018 The Author(s).Peer reviewe