ALBERT

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉An analytical solution is derived concerning the linear run-up for any given initial wave generated over a sloping bathymetry. Due to the simplicity of the linear formulation, complex transformations are unnecessary, hence the shoreline motion is directly obtained in terms of the initial wave. This result supports not only maximum run-up invariance between linear and nonlinear theories but also the time evolution of shoreline motion and velocity, exhibiting good agreement with the nonlinear theory. The present formulation also allows quantifying the shoreline motion numerically from a customized initial waveform, including non-smooth functions. This is useful for numerical tests, laboratory experiments or realistic cases in which the initial disturbance might be retrieved from seismic data rather than using a theoretical model. It is also shown that the run-up calculation for the real case studied is consistent with the field observations.〈/span〉

Description: We present a theoretical solution for the water wave elevation along the shoreline and a closed formula is derived for the runup distribution in the 2+1 dimensional (2 spatial + 1 temporal) linear case. An integral transform method is used to solve the linear shallow water wave equations for a sloping beach model extended along the coastline. At large regional scale, this simple bathymetry model gives a good approximation for the seafloor geometry along the Chilean subduction zone. In the bidimensional problem, for special cases, we found an analytic expression for the runup distribution along the shoreline that includes the obliquity of the incident incoming wave approaching the coast. Our solution establishes that obliquity can reduce maximum runup in important ways. It suggests that the distribution along the shoreline is determined mainly by the maximum unidimensional runup modulated, by a function controlling the horizontal extent of the incident wave parallel to the shoreline. This function was introduced to include the physical expected boundedness of the leading wave approaching the shore. Our theoretical solution was applied to model the runup generated by the 2010, M w 8.8 Maule mega-thrust earthquake. The model fits rather well the runup to first-order. The theoretical solution proposed in this study also provides new insights to the near-field tsunami discriminant formula proposed by Okal & Synolakis.

Description: A general method of solution for the runup evolution and some analytical results concerning a more general bathymetry than a canonical sloping beach model are presented. We studied theoretically the water wave elevation and runup generated on a continuous piecewise linear bathymetry, by solving analytically the linear shallow water wave equations in the 1+1 dimensional case. Non-horizontal linear segments are assumed and we develop an specific matrix propagator scheme, similar to the ones used in the propagation of elastic seismic wave fields in layered media, to obtain an exact integral form for the runup. A general closed expression for the maximum runup was computed analytically via the Cauchy's residue Theorem for an incident solitary wave and isosceles leading-depression N wave in the case of n + 1 linear segments. It is already known that maximum run-up strongly depends only on the closest slope to the shore, although this has not been mathematically demonstrated yet for arbitraries bathymetries. Analytical and numerical verifications were done to check the validity of the asymptotic maximum runup and we provided the mathematical and bathymetrical conditions that must be satisfied by the model to obtain correct asymptotic solutions. We applied our model to study the runup evolution on a more realistic bathymetry than a canonical sloping beach model. The seabed in a Chilean subduction zone was approximated—from the trench to the shore—by two linear segments adjusting the continental slope and shelf. Assuming an incident solitary wave, the two linear segment bathymetry generates a larger runup than the simple sloping beach model. We also discussed about the differences in the runup evolution computed numerically from incident leading-depression and leading-elevation isosceles N waves. In the latter case, the water elevation at the shore shows a symmetrical behaviour in terms of theirs waveforms. Finally, we applied our solution to study the resonance effects due to the bathymetry modelled by linear segments, which is in agreement with published studies and numerical tests.

Description: : SeDuS is the first flexible and user-friendly forward-in-time simulator of patterns of molecular evolution within segmental duplications undergoing interlocus gene conversion and crossover. SeDuS introduces known features of interlocus gene conversion such as biased directionality and dependence on local sequence identity. Additionally, it includes aspects such as different selective pressures acting upon copy number and flexible crossover distributions. A graphical user interface allows fast fine-tuning of relevant parameters and straightforward real-time analysis of the evolution of duplicates. Availability and implementation: SeDuS is implemented in C++ and can be run via command line or through a graphical user interface developed using Qt C++. Source code and binary executables for Linux, OS X and Windows are freely available at www.biologiaevolutiva.org/sedus/ . A tutorial with a detailed description of implementation, parameters and output files is available online. Contact: arcadi.navarro@upf.edu

Description: Thymocyte differentiation is a complex process involving well-defined sequential developmental stages that ultimately result in the generation of mature T-cells. In this study, we analyzed DNA methylation and gene expression profiles at successive human thymus developmental stages. Gain and loss of methylation occurred during thymocyte differentiation, but DNA demethylation was much more frequent than de novo methylation and more strongly correlated with gene expression. These changes took place in CpG-poor regions and were closely associated with T-cell differentiation and TCR function. Up to 88 genes that encode transcriptional regulators, some of whose functions in T-cell development are as yet unknown, were differentially methylated during differentiation. Interestingly, no reversion of accumulated DNA methylation changes was observed as differentiation progressed, except in a very small subset of key genes (RAG1, RAG2, CD8A, PTCRA, etc.), indicating that methylation changes are mostly unique and irreversible events. Our study explores the contribution of DNA methylation to T-cell lymphopoiesis and provides a fine-scale map of differentially methylated regions associated with gene expression changes. These can lay the molecular foundations for a better interpretation of the regulatory networks driving human thymopoiesis.

Description: : The open-source platform openBIS (open Biology Information System) offers an Electronic Laboratory Notebook and a Laboratory Information Management System (ELN-LIMS) solution suitable for the academic life science laboratories. openBIS ELN-LIMS allows researchers to efficiently document their work, to describe materials and methods and to collect raw and analyzed data. The system comes with a user-friendly web interface where data can be added, edited, browsed and searched. Availability and implementation: The openBIS software, a user guide and a demo instance are available at https://openbis-eln-lims.ethz.ch . The demo instance contains some data from our laboratory as an example to demonstrate the possibilities of the ELN-LIMS ( Ottoz et al. , 2014 ). For rapid local testing, a VirtualBox image of the ELN-LIMS is also available. Contact: brinn@ethz.ch or fabian.rudolf@bsse.ethz.ch

Description: Medusa production in cubozoans may be associated with reduced-salinity waters. Asexual reproduction of Carybdea sp. differed at different salinities. The metamorphosis of Carybdea sp. polyps into medusae was accelerated at low salinity (32), while more polyps were budded from the original polyp at the highest salinity (38), probably due to prolonged metamorphosis. High-nutrient river discharge may provide favorable conditions for Carybdea sp. blooms.

Description: Plant Reactome ( http://plantreactome.gramene.org/ ) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX.