Multi-level emulation of tsunami simulations over Cilacap, South Java, Indonesia

Carrying out a Probabilistic Tsunami Hazard Assessment (PTHA) requires a large number of simulations done at a high resolution. Statistical emulation builds a surrogate to replace the simulator and thus reduces computational costs when propagating uncertainties from the earthquake sources to the tsunami inundations. To reduce further these costs, we propose here to build emulators that exploit multiple levels of resolution and a sequential design of computer experiments. By running a few tsunami simulations at high resolution and many more simulations at lower resolutions we are able to provide realistic assessments whereas, for the same budget, using only the high resolution tsunami simulations do not provide a satisfactory outcome. As a result, PTHA can be considered with higher precision using the highest spatial resolutions, and for impacts over larger regions. We provide an illustration to the city of Cilacap in Indonesia that demonstrates the benefit of our approach

Comparison of the histological and immunohistochemical features of the thymus in young- and elderly-onset myasthenia gravis without thymoma

ArticleJOURNAL OF CLINICAL NEUROSCIENCE. 14(2): 110-115 (2007)journal articl

Phenological phases of flowering in hop (Humulus lupulus L.) and their correspondence with microsporogenesis and microgametogenesis

[EN] Hop (Humulus Lupulus L.) suffered, as many other crops, a shrinkage of its intraspecific agrobiodiversity. Biotechnological methods of breeding would offer new opportunities to produce improved varieties with interesting phytochemical profiles and adaptable to the challenging conditions of climate change. Doubled haploid (DH) technology could be a useful tool to increase hop agrobiodiversity but, unfortunately, there is a complete lack of information about hop flower biology. For this reason, the main aim of this work is the study of the different phenological phases of flowering in hop and the corresponding developmental stages of microspores/pollen grains contained therein. The results obtained allowed the identification of morphological markers (anther and flower bud length), easy and fast to measure, that would speed up the selection of flower buds containing the highest percentage of vacuolated microspores and young pollen, the stages considered in most species as the most responsive to androgenesis. A further result, derived from the flower bud and anther microscopical observation, evidenced the increase of lupulin glands on bud and anther surface as the bud proceeds in development from microsporogenesis to microgametogenesis.This work was supported by Spanish MINECO [grant number AGL2017-88135-R to JMSS] jointly funded by FEDER.Liberatore, C.; Calabuig-Serna, A.; Rodolfi, M.; Chiancone, B.; Seguí-Simarro, JM. (2019). Phenological phases of flowering in hop (Humulus lupulus L.) and their correspondence with microsporogenesis and microgametogenesis. Scientia Horticulturae. 256:1-6. https://doi.org/10.1016/j.scienta.2019.108639S16256Easterling, K. A., Pitra, N. J., Jones, R. J., Lopes, L. G., Aquino, J. R., Zhang, D., … Bass, H. W. (2018). 3D Molecular Cytology of Hop (Humulus lupulus) Meiotic Chromosomes Reveals Non-disomic Pairing and Segregation, Aneuploidy, and Genomic Structural Variation. Frontiers in Plant Science, 9. doi:10.3389/fpls.2018.01501Nagel, J., Culley, L. K., Lu, Y., Liu, E., Matthews, P. D., Stevens, J. F., & Page, J. E. (2008). EST Analysis of Hop Glandular Trichomes Identifies an O-Methyltransferase That Catalyzes the Biosynthesis of Xanthohumol. The Plant Cell, 20(1), 186-200. doi:10.1105/tpc.107.055178Parra-Vega, V., González-García, B., & Seguí-Simarro, J. M. (2012). Morphological markers to correlate bud and anther development with microsporogenesis and microgametogenesis in pepper (Capsicum annuum L.). Acta Physiologiae Plantarum, 35(2), 627-633. doi:10.1007/s11738-012-1104-xPatzak, J., Nesvadba, V., Henychová, A., & Krofta, K. (2010). Assessment of the genetic diversity of wild hops (Humulus lupulus L.) in Europe using chemical and molecular analyses. Biochemical Systematics and Ecology, 38(2), 136-145. doi:10.1016/j.bse.2009.12.023Patzak, J., Nesvadba, V., Krofta, K., Henychova, A., Marzoev, A. I., & Richards, K. (2010). Evaluation of genetic variability of wild hops (Humulus lupulus L.) in Canada and the Caucasus region by chemical and molecular methods. Genome, 53(7), 545-557. doi:10.1139/g10-024Salas, P., Rivas-Sendra, A., Prohens, J., & Seguí-Simarro, J. M. (2011). Influence of the stage for anther excision and heterostyly in embryogenesis induction from eggplant anther cultures. Euphytica, 184(2), 235-250. doi:10.1007/s10681-011-0569-9Seguí-Simarro, J. M. (2010). Androgenesis Revisited. The Botanical Review, 76(3), 377-404. doi:10.1007/s12229-010-9056-6Seguí-Simarro, J. M., & Nuez, F. (2005). Meiotic metaphase I to telophase II as the most responsive stage during microspore development for callus induction in tomato (Solanum lycopersicum) anther cultures. Acta Physiologiae Plantarum, 27(4), 675-685. doi:10.1007/s11738-005-0071-xSHEPHARD, H. L., PARKER, J. S., DARBY, P., & AINSWORTH, C. C. (2000). Sexual development and sex chromosomes in hop. New Phytologist, 148(3), 397-411. doi:10.1046/j.1469-8137.2000.00771.xXie, W., Xiong, W., Pan, J., Ali, T., Cui, Q., Guan, D., … Davis, S. J. (2018). Decreases in global beer supply due to extreme drought and heat. Nature Plants, 4(11), 964-973. doi:10.1038/s41477-018-0263-

S1 excited-state dynamics of OMpCA and its hydrogen-bonded complexes

第30回化学反応討論会, 2014年6月4日-6日, イーグレひめじ(姫路

Impact of future tsunamis from the Java trench on household welfare: Merging geophysics and economics through catastrophe modelling

This paper presents the first end-to-end example of a risk model for loss of assets in households due to possible future tsunamis. There is a significant need for Government to assess the generic risk to buildings, and the concrete impact on the full range of assets of households, including the ones that are key to livelihoods such as agricultural land, fishing boats, livestock and equipment. Our approach relies on the Oasis Loss Modelling Framework to integrate hazard and risk. We first generate 25 representative events of tsunamigenic earthquakes off the Southern coast of Java, Indonesia. We then create a new vulnerability function based upon the Indonesian household survey STAR1 of how much assets have been reduced in each household after the 2004 tsunami. We run a multinomial logit regression to precisely allocate the probabilistic impacts to bins that correspond with levels of financial reduction in assets. We focus on the town of Cilacap for which we build loss exceedance curves, which represent the financial losses that may be exceeded at a range of future timelines, using future tsunami inundations over a surveyed layout and value of assets over the city. Our loss calculations show that losses increase sharply, especially for events with return periods beyond 250 years. These series of computations will allow more accurate investigations of impacts on livelihoods and thus will help design mitigation strategies as well as policies to minimize suffering from tsunamis.Lloyd's Tercentenary Research Foundation; Lighthill Risk Network; Alan Turing Institute project "Uncertainty Quantification of multi-scale and multiphysics computer models: applications to hazard and climate models", EPSRC EP/N510129/1; Royal Society, the United Kingdom CHL/R1/180173

Studi Karakter Morfologi dan Fisiologi Varietas Padi Toleran Terhadap Cekaman Kekeringan Pada Sistem Sawah

Water stress is one of factors which causes low yield of lowland. This study aimed to identify and characterize morphology and physiology of drought tolerant rice varieties. Experiments which have conducted: (i) Investigation of rice varieties tolerance to drought stress at early vegetative stage in the laboratory (ii) morphology and physiology characters of rice varieties to drought stress in the paddy field and (iii) determining the character of root of  rice tolerant to drought stress. The experimental design used was split plot design with 3 (three) replications, with drought stress as the main plot and the variety as sub-plot. The result of screening test at the laboratory using PEG (Polyethylene Glycol) which could characterize which rice varieties could be considered as drought tolerant varieties. Results showed that periods of drought increasing the proline content at Ciherang (25.38 μmol) and IPB 3S varieties (22.08 μmol) at 13 WAT (Week After Transplanting). The variety that has the highest total sugar content in the flowering stage is Rokan (289.38 mg.g-1DW) followed by Menthik Wangi (230.53 mg.g1DW), while the lowest sugar content in harvest found in Jatiluhur (17.14 mg.g-1DW) followed by Way Apo Buru (46.99 mg.g-1DW). Jatiluhur, Way Apo Buru and IPB 3S varieties have drought tolerant based on the root characteristic. Ciherang, IPB 3S, Way Apo Buru and Jatiluhur varieties were drought tolerant and potential to be used in paddy field

The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

Many cases of non-standard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The gain represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The loss represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is Codon Disappearance, where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the Unassigned Codon mechanism, the loss occurs first, whereas in the Ambiguous Intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. Codon disappearance is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense to sense reassignments cannot be explained by codon disappearance. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the Unassigned Codon and Ambiguous Intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.Comment: 53 pages (45 pages, including 4 figures + 8 pages of supplementary information). To appear in J.Mol.Evo

Genetic polymorphisms in glutathione-S-transferases are associated with anxiety and mood disorders in nicotine dependence

Nicotine dependence is associated with an increased risk of mood and anxiety disorders and suicide. The primary hypothesis of this study was to identify whether the polymorphisms of two glutathione-S-transferase enzymes (GSTM1 and GSTT1 genes) predict an increased risk of mood and anxiety disorders in smokers with nicotine dependence