54 research outputs found
"On the northern border of Islam": an anthropological analysis and the international implications of the Chechnya conflict
No full textBoston University. University Professors Program Senior theses.PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at [email protected]. Thank you.2999-01-0
Quick regional centroid moment tensor solutions for the Emilia 2012 (northern Italy) seismic sequence
No full textIn May 2012, a seismic sequence struck the Emilia region (northern Italy). The mainshock, of Ml 5.9, occurred on May 20, 2012, at 02:03 UTC. This was preceded by a smaller Ml 4.1 foreshock some hours before (23:13 UTC on May 19, 2012) and followed by more than 2,500 earthquakes in the magnitude range from Ml 0.7 to 5.2. In addition, on May 29, 2012, three further strong earthquakes occurred, all with magnitude Ml ≥5.2: a Ml 5.8 earthquake in the morning (07:00 UTC), followed by two events within just 5 min of each other, one at 10:55 UTC (Ml 5.3) and the second at 11:00 UTC (Ml 5.2). For all of the Ml ≥4.0 earthquakes in Italy and for all of the Ml ≥4.5 in the Mediterranean area, an automatic procedure for the computation of a regional centroid moment tensor (RCMT) is triggered by an email alert. Within 1 h of the event, a manually revised quick RCMT (QRCMT) can be published on the website if the solution is considered stable. In particular, for the Emilia seismic sequence, 13 QRCMTs were determined and for three of them, those with M >5.5, the automatically computed QRCMTs fitted the criteria for publication without manual revision. Using this seismic sequence as a test, we can then identify the magnitude threshold for automatic publication of our QRCMTs.</p
Seismic wave modelling for large scale 3-D problems: method development and application to lateral heterogeneity imaging
No full textStandardization of seismic tomographic models and earthquake focal mechanisms data sets based on web technologies, visualization with keyhole markup language
No full textActive deformation and seismicity in the Southern Alps (Italy): The Montello hill as a case study
No full textThe Montello anticline is a morphotectonic feature of the east pede-mountain of the South Alpine Chain in northern Italy, which lies ca. 40 km northwest of Venice, Italy. The purpose of this study is to characterize the present-day crustal deformation and seismotectonics of the Montello area
through multi-parametric geophysical observations. We used new data obtained from the installation of a temporary network of 12 seismic stations and 6 GPS sites. The GPS observations indicate that there is ~1 mm/yr shortening across the Montello thrust. Sites located north of the Montello thrust front deviate from the ~NNW-ward Adria-Eurasia convergence direction, as they are constrained by a
relative rotation pole in northwestern Italy that has a NNE-ward motion trend. Over 18 months, seismographic recordings allowed us to locate 142 local seismic events with Ml 0.5-3.5 with good reliability (rms 0.80. The source focal solutions indicate that: (i) there is thrusting seismic activity on the basal, sub-horizontal, portion of the Montello structure; and (ii) strike-slip source kinematics prevail on the western edge of the Montello hill. Our observations on the source mechanisms and the measured crustal deformation confirm that the Montello thrust is tectonically active.Published95-1082T. Tettonica attivaJCR Journalrestricte
Somatic mutations alter the differentiation outcomes of iPSC-derived neurons
No full textThe use of induced pluripotent stem cells (iPSC) as models for development and human disease has enabled the study of otherwise inaccessible tissues. A remaining challenge in developing reliable models is our limited understanding of the factors driving irregular differentiation of iPSCs, particularly the impact of acquired somatic mutations. We leveraged data from a pooled dopaminergic neuron differentiation experiment of 238 iPSC lines profiled with single-cell RNA and whole-exome sequencing to study how somatic mutations affect differentiation outcomes. We found that deleterious somatic mutations in key developmental genes, notably the BCOR gene, are strongly associated with failure in dopaminergic neuron differentiation and a larger proliferation rate in culture. We further identified broad differences in cell type composition between incorrectly and successfully differentiating lines, as well as significant changes in gene expression contributing to the inhibition of neurogenesis. Our work calls for caution in interpreting differentiation-related phenotypes in disease-modeling experiments.Peer reviewe
dispel4py: An Open-Source Python library for Data-Intensive Seismology
No full textScientific workflows are a necessary tool for many scientific communities as they enable easy composition and execution of applications on computing resources while scientists can focus on their research without being distracted by the computation management. Nowadays, scientific communities (e.g. Seismology) have access to a large variety of computing resources and their computational problems are best addressed using parallel computing technology. However, successful use of these technologies requires a lot of additional machinery whose use is not straightforward for non-experts: different parallel frameworks (MPI, Storm, multiprocessing, etc.) must be used depending on the computing resources (local machines, grids, clouds, clusters) where applications are run. This implies that for achieving the best applications' performance, users usually have to change their codes depending on the features of the platform selected for running them. This work presents dispel4py, a new open-source Python library for describing abstract stream-based workflows for distributed data-intensive applications. Special care has been taken to provide dispel4py with the ability to map abstract workflows to different platforms dynamically at run-time. Currently dispel4py has four mappings: Apache Storm, MPI, multi-threading and sequential. The main goal of dispel4py is to provide an easy-to-use tool to develop and test workflows in local resources by using the sequential mode with a small dataset. Later, once a workflow is ready for long runs, it can be automatically executed on different parallel resources. dispel4py takes care of the underlying mappings by performing an efficient parallelisation. Processing Elements (PE) represent the basic computational activities of any dispel4Py workflow, which can be a seismologic algorithm, or a data transformation process. For creating a dispel4py workflow, users only have to write very few lines of code to describe their PEs and how they are connected by using Python, which is widely supported on many platforms and is popular in many scientific domains, such as in geosciences. Once, a dispel4py workflow is written, a user only has to select which mapping they would like to use, and everything else (parallelisation, distribution of data) is carried on by dispel4py without any cost to the user. Among all dispel4py features we would like to highlight the following: * The PEs are connected by streams and not by writing to and reading from intermediate files, avoiding many IO operations. * The PEs can be stored into a registry. Therefore, different users can recombine PEs in many different workflows. * dispel4py has been enriched with a provenance mechanism to support runtime provenance analysis. We have adopted the W3C-PROV data model, which is accessible via a prototypal browser-based user interface and a web API. It supports the users with the visualisation of graphical products and offers combined operations to access and download the data, which may be selectively stored at runtime, into dedicated data archives. dispel4py has been already used by seismologists in the VERCE project to develop different seismic workflows. One of them is the Seismic Ambient Noise Cross-Correlation workflow, which preprocesses and cross-correlates traces from several stations. First, this workflow was tested on a local machine by using a small number of stations as input data. Later, it was executed on different parallel platforms (SuperMUC cluster, and Terracorrelator machine), automatically scaling up by using MPI and multiprocessing mappings and up to 1000 stations as input data. The results show that the dispel4py achieves scalable performance in both mappings tested on different parallel platforms
The First Very Broadband Mediterranean Network: 30 Yr of Data and Seismological Research
No full textStarting in 1988, with the installation of the first broadband (BB) instrument in Italy, the
Mediterranean Very Broadband Seismographic Network (MedNet) program established
a backbone network of BB stations of the highest quality in the Mediterranean Sea
countries. The Mediterranean region is characterized by relevant and frequent seismic-
ity related to its complex tectonics, due to the convergence of two major plates, Africa
and Eurasia, and the involvement of other minor plates, as the Adriatic plate. Therefore,
the MedNet project became a scientific research infrastructure of excellence, able to fill
the gap of regional coverage when the availability of seismic BB instruments was still
scarce. The main characteristics of the MedNet network are the highest quality of the
seismographic instrumentation at remote sites and very low level of anthropogenic
noise with stable conditions of pressure and temperature. After 30 yr of recordings,
the MedNet program has proven that the early adoption of very BB instruments in
selected sites have been the best choice. A large number of studies benefited from
MedNet data, as seismic source computation and Earth structure reconstruction, at local
and global scale.
We present a concise overview of the contribution given by MedNet data in the
last three decades to motivate and financially support the existence of this valuable
infrastructure, and to further maintain this project.Published787–8021T. Struttura della TerraJCR Journa
Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation
No full textUnderstanding the contribution of neutral and adaptive evolutionary processes to population differences is often necessary for better-informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the world's rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species' evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to assess loci possibly under selection, and to evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation reflecting consistently low effective population sizes across time and limited genetic differentiation suggesting maintenance of gene flow following divergence. However, genome scans identified more than 2000 candidate SNPs for divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates natural selection has likely contributed to the evolution of population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effects of rarity, divergent selection suggests genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine.Funding provided by: USDA Health Protection Gene Conservation Program*Crossref Funder Registry ID: Award Number: Funding provided by: Western Wildlands Environmental Threats Assessment Center*Crossref Funder Registry ID: Award Number: Funding provided by: Morton Arboretum*Crossref Funder Registry ID: Award Number: Funding provided by: North Dakota Experimental Program to Stimulate Competitive Research*Crossref Funder Registry ID: Award Number: ND-EPSCoR NSF-IIA-1355466Funding provided by: NDSU Environmental and Conservation Sciences Graduate Program*Crossref Funder Registry ID: Award Number:All genetic data sets within this repository represent either do novo assembly or range-wide single-nucleotide polymorphisms (SNPs) obtained using the dDocent pipeline (Puritz et al. 2014a; Puritz et al. 2014b) for the critically endangered Torrey pine (Pinus torreyana Parry).
Filtering of data sets was either performed using VCFtools (Danecek et al. 2011) or customized R scripts (available upon request to the corresponding author). For details on how these datasets were generated, refer to the Materials and Methods section in the published manuscript.
References:
Puritz, J. B., Hollenbeck, C. M., & Gold, J. R. (2014a). dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms. PeerJ, 2, e431. doi:10.7717/peerj.431
Puritz, J. B., Matz, M. V, Toonen, R. J., Weber, J. N., Bolnick, D. I., & Bird, C. E. (2014b). Demystifying the RAD fad. Molecular Ecology, 23(24), 5937–5942. doi: 10.1111/mec.12965
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., … Group, 1000 Genomes Project Analysis. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156–2158. doi: 10.1093/bioinformatics/btr33
Common genetic variation drives molecular heterogeneity in human iPSCs
No full textInduced pluripotent stem cell (iPSC) technology has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterisation of many existing iPSC lines limits their potential use for research and therapy. Here, we describe the systematic generation, genotyping and phenotyping of 711 iPSC lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative (HipSci: http://www.hipsci.org). Our study outlines the major sources of genetic and phenotypic variation in iPSCs and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 5-46% of the variation in different iPSC phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of rare, genomic copy number mutations that are repeatedly observed in iPSC reprogramming and present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells.</p
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