Ishihama, Akira; Shimada, Tomohiro; Yamazaki, Yukiko
Bacterial genomes are transcribed by DNA-dependent RNA polymerase (RNAP), which achieves gene selectivity through interaction with sigma factors that recognize promoters, and transcription factors (TFs) that control the activity and specificity of RNAP holoenzyme. To understand the molecular mechanisms of transcriptional regulation, the identification of regulatory targets is needed for all these factors. We then performed genomic SELEX screenings of targets under the control of each sigma factor and each TF. Here we describe the assembly of 156 SELEX patterns of a total of 116 TFs performed in the presence and absence of effector ligands. The results reveal several novel concepts: (i) each TF regulates more targets than hitherto recognized; (ii) each promoter is regulated by more TFs than hitherto recognized; and (iii) the binding sites of some TFs are located within operons and even inside open reading frames. The binding sites of a set of global regulators, including cAMP receptor protein, LeuO and Lrp, overlap with those of the silencer H-NS, suggesting that certain global regulators play an anti-silencing role. To facilitate sharing of these accumulated SELEX datasets with the research community, we compiled a database, ‘Transcription Profile of Escherichia coli’ (www.shigen.nig.ac.jp/ecoli/tec/). PMID:26843427
Wang, Xiaoling; Liu, Xuepeng; Sun, Yuefeng; An, Juan; Zhang, Jing; Chen, Hongchao
Former studies, the methods for estimating the ventilation time are all empirical in construction schedule simulation. However, in many real cases of construction schedule, the many factors have impact on the ventilation time. Therefore, in this paper the 3D unsteady quasi-single phase models are proposed to optimize the ventilation time with different tunneling lengths. The effect of buoyancy is considered in the momentum equation of the CO transport model, while the effects of inter-phase drag, lift force, and virtual mass force are taken into account in the momentum source of the dust transport model. The prediction by the present model for airflow in a diversion tunnel is confirmed by the experimental values reported by Nakayama [Nakayama, In-situ measurement and simulation by CFD of methane gas distribution at a heading faces, Shigen-to-Sozai 114 (11) (1998) 769-775]. The construction ventilation of the diversion tunnel of XinTangfang power station in China is used as a case. The distributions of airflow, CO and dust in the diversion tunnel are analyzed. A theory method for GIS-based dynamic visual simulation for the construction processes of underground structure groups is presented that combines cyclic operation network simulation, system simulation, network plan optimization, and GIS-based construction processes' 3D visualization. Based on the ventilation time the construction schedule of the diversion tunnel is simulated by the above theory method.
Wang, Xiaoling; Liu, Xuepeng; Sun, Yuefeng; An, Juan; Zhang, Jing; Chen, Hongchao
Former studies, the methods for estimating the ventilation time are all empirical in construction schedule simulation. However, in many real cases of construction schedule, the many factors have impact on the ventilation time. Therefore, in this paper the 3D unsteady quasi-single phase models are proposed to optimize the ventilation time with different tunneling lengths. The effect of buoyancy is considered in the momentum equation of the CO transport model, while the effects of inter-phase drag, lift force, and virtual mass force are taken into account in the momentum source of the dust transport model. The prediction by the present model for airflow in a diversion tunnel is confirmed by the experimental values reported by Nakayama [Nakayama, In-situ measurement and simulation by CFD of methane gas distribution at a heading faces, Shigen-to-Sozai 114 (11) (1998) 769-775]. The construction ventilation of the diversion tunnel of XinTangfang power station in China is used as a case. The distributions of airflow, CO and dust in the diversion tunnel are analyzed. A theory method for GIS-based dynamic visual simulation for the construction processes of underground structure groups is presented that combines cyclic operation network simulation, system simulation, network plan optimization, and GIS-based construction processes' 3D visualization. Based on the ventilation time the construction schedule of the diversion tunnel is simulated by the above theory method. PMID:19081188
Yamazaki, Yukiko; Niki, Hironori; Kato, Jun-ichi
The Profiling of Escherichia coli Chromosome (PEC) database (http://www.shigen.nig.ac.jp/ecoli/pec/) is designed to allow E. coli researchers to efficiently access information from functional genomics studies. The database contains two principal types of data: gene essentiality and a large collection of E. coli genetic research resources. The essentiality data are based on data compilation from published single-gene essentiality studies and on cell growth studies of large-deletion mutants. Using the circular and linear viewers for both whole genomes and the minimal genome, users can not only gain an overview of the genome structure but also retrieve information on contigs, gene products, mutants, deletions, and so forth. In particular, genome-wide exhaustive mutants are an essential resource for studying E. coli gene functions. Although the genomic database was constructed independently from the genetic resources database, users may seamlessly access both types of data. In addition to these data, the PEC database also provides a summary of homologous genes of other bacterial genomes and of protein structure information, with a comprehensive interface. The PEC is thus a convenient and useful platform for contemporary E. coli researchers. PMID:18392982
Ishihama, Akira; Shimada, Tomohiro; Yamazaki, Yukiko
Bacterial genomes are transcribed by DNA-dependent RNA polymerase (RNAP), which achieves gene selectivity through interaction with sigma factors that recognize promoters, and transcription factors (TFs) that control the activity and specificity of RNAP holoenzyme. To understand the molecular mechanisms of transcriptional regulation, the identification of regulatory targets is needed for all these factors. We then performed genomic SELEX screenings of targets under the control of each sigma factor and each TF. Here we describe the assembly of 156 SELEX patterns of a total of 116 TFs performed in the presence and absence of effector ligands. The results reveal several novel concepts: (i) each TF regulates more targets than hitherto recognized; (ii) each promoter is regulated by more TFs than hitherto recognized; and (iii) the binding sites of some TFs are located within operons and even inside open reading frames. The binding sites of a set of global regulators, including cAMP receptor protein, LeuO and Lrp, overlap with those of the silencer H-NS, suggesting that certain global regulators play an anti-silencing role. To facilitate sharing of these accumulated SELEX datasets with the research community, we compiled a database, 'Transcription Profile of Escherichia coli' (www.shigen.nig.ac.jp/ecoli/tec/). PMID:26843427
Miki, Takeyoshi; Yamamoto, Yoshihiro; Matsuda, Hideo
We developed a novel, simple, high-throughput method for isolation of genome-wide transposon insertion mutants of Escherichia coli K-12. The basic idea of the method is to randomly disrupt the genes on the DNA fragments cloned on the Kohara library by inserting a mini-transposon first, and then transfer the disrupted genes from the lambda vector to the E. coli chromosome by homologous recombination. Using this method, we constructed a set of 8402 Km(r) cis-diploid mutants harboring a mini-Tn10 insertion mutation and the corresponding wild-type gene on a chromosome, as well as a set of 6954 haploid mutants derived from the cis-diploid mutants. The major advantage of the strategy used is that the indispensable genes or sites for growth can be identified. Preliminary results suggest that 415 open reading frames are indispensable for growth in E. coli cells. A total of 6404 haploid mutants were deposited to Genetic Strains Research Center, National Institute of Genetics, Japan (Chapter 26) and are available for public distribution upon request (http://shigen.lab.nig.ac.jp/ecoli/strain/nbrp/resource.jsp). PMID:18392969
JOGMEC, as a member of research group for resources assessment of Research Consortium for Methane Hydrate Resources in Japan (MH21), is conducting resources assessment of methane hydrates (MHs) offshore surrounding Japan. The interpretation of 3-D seismic data acquired by geophysical vessel 'Shigen', which is owned by Agency for Natural Resources and Energy, are carried out. And MH concentrated zones are being extracted. This study is an introduction for the case example of interpretation of 3-D seismic data in the area which have not been drilled. The characteristic of 3-D seismic data in this study area shows fold structure, which undulates severalfold. In addition, some faults are interpreted, which does not show the large displacement, are seen. Bottom Simulating Reflector (BSR) is very visible continuously. Clear velocity contrast in the boundary between above and below of BSR and the high velocity anomaly above BSR are confirmed in the high density velocity analysis profile. MHs are assumed to exist in sand heterogeneously because the velocity distribution in the extracted zones is inhomogeneous. In the results of geomorphological analysis, channel deposits and mid submarine fan deposits, which are located above BSR, are presumed the sediments which bear sand. Thus the extracted zones are estimated MH concentrated zones. As above, even the area has not been drilled, the extraction of MH concentrated zones can be estimated by the interpretation of the seismic data, the result of the high density velocity analysis, and the distribution of sand by geomorphological analysis. These results will be useful for the plan of the future drilling programme. This introduction is the example of 3-D seismic survey area. It will become a useful information for 3-D seismic survey plan by performing similar interpretation in 2-D seismic survey lines.
Ohyanagi, Hajime; Ebata, Toshinobu; Huang, Xuehui; Gong, Hao; Fujita, Masahiro; Mochizuki, Takako; Toyoda, Atsushi; Fujiyama, Asao; Kaminuma, Eli; Nakamura, Yasukazu; Feng, Qi; Wang, Zi-Xuan; Han, Bin; Kurata, Nori
The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/. PMID:26578696
The installation and operation of an OSI seismic aftershock monitoring system (SAMS) is bound by strict time constraints: 30+ small arrays must be set up within days, and data screening must cope with the daily seismogram input. This is a significant challenge since any potential, single ML -2.0 aftershock from a potential nuclear test must be detected and discriminated against a variety of higher-amplitude noise bursts. No automated approach can handle this task to date; thus some 200 traces of 24/7 data must be screened manually with a time resolution sufficient to recover signals of just a few sec duration, and with tiny amplitudes just above the threshold of ambient noise. Previous tests confirmed that this task can not be performed by time-domain signal screening via established seismological processing software, e.g. PITSA, SEISAN, or GEOTOOLS. Instead, we introduced 'SonoView', a seismic diagnosis tool based on a compilation of array traces into super-sonograms. Several hours of cumulative array data can be displayed at once on a single computer screen - without sacrifying the necessary detectability of few-sec signals. Then 'TraceView' will guide the analyst to select the relevant traces with best SNR, and 'HypoLine' offers some interactive, graphical location tools for fast epicenter estimates and source signature identifications. A previous release of this software suite was successfully applied at IFE08 in Kasakhstan, and supported the seismic sub-team of OSI in its timely report compilation.
Maria Mendez Martinez, Luz de; Portillo, Mercy
We studied the geographic area located in the central part of El Salvador, between the San Salvador Volcano (Quezaltepec) and Ilopango Lake. Its latitude is between 13 deg. 36' and 13 deg. 54', and longitude is between -89 deg. 18' and -88 deg. 57'. This area is directly affected by the WNW axis, the most prominent weak tectonic system in the region. Our research aimed to determine the focal mechanisms of seisms occurring in the studied area between 1994 and March 2005. Our analysis provided information about displacement types of the geological faults, using the wave impulse P method and computer applications ARCGIS and SEISAN, with the subroutine FOCMEC. Information of the studied seisms was obtained from the National Service of Territorial Studies (SNET) database. Geographic models used in the preparation of maps are from the geographic information system of the School of Physics at the University of El Salvador. The 37 focal mechanisms on the map of faults were identified in digital seismographs to determinate the arrival polarity of the wave P for each seism station. Data from the focal mechanisms were analyzed and correlated with their replications. The analysis allowed us to identify evidences to consider the fault continuity not reported by the last geological mission in El Salvador conducted in the 1970s. The fault continuity is located northwest of the studied geographical area, between San Salvador City and the San Salvador Volcano. The compression and strain axes for this area are two main horizontal force axes. The average orientation for the strain axis is NNE-SSW, and WNW-SEE for the compression axis. There is also important seismic activity in the Ilopango Lake and surrounding area. However, data did not allow us to make any inference. The tensors distribution resulted in a high dispersion corresponding to typical fauces models.
N, R.; Ec, M.
The permanent Seismological Observatory was established in 1997 at Maitri in Central Dronning Maud Land, East Antarctica (70 °45' South 11 °43' East) primarily to monitor the seismicity in and around Antarctica, the space and time distribution of earthquake occurrences and obtain hypocentral parameters, magnitudes of earthquakes, velocity inversion for underground structure and earthquake source mechanism. The observatory has been upgraded during 25th Indian Silver Jubilee Scientific Expedition to Antarctica (December 2005 to February 2007) and 26th Indian Antarctic Expedition (IAE) with the new generation Geotech KS-2000M Seismometer and Smart 24R digitizer. During the 27th IAE the Seismic Observatory was further upgraded by adding Reftek 130 seismic system. Uninterrupted good quality digital Broad Band Seismic data is continuously being acquired. The SEISAN 8.1 software was used for final processing and analysis of about 300 earthquakes recorded. During the year 2006 the tele-seismic events, and quite a number of regional earthquakes of the order of 4 to 6.0 magnitude within Antarctic Plate, 23 in South Sandwich Islands, 7 in Scotia Sea, 2 in Macqurie Islands and 23 in Mid Oceanic Ridges in the Indian Ocean were recorded. 48 earthquakes of the magnitude above 4.5 from the nearby South Indian Ocean, South of South Africa, Chile, Argentina, Bolivia and about 40 earthquakes of the magnitude above 5.0 from the Indonesian Region were analysed. An earthquake of magnitude Ms=7.3 from the seismically active region of South Sandwich Islands Δ =16.5 °, Mb=7.8 earthquake from Tonga Islands and Mb=7.2 earthquake from Java were the large earthquakes that were recorded. Along with this the MOHO depth beneath MAIT was also estimated to be about 40km using receiver function analysis. All the analysed monthly data was reported to the I.S.C., U.K.,Global Data Centre for the final processing and inclusion in the yearly ISC Seismic Bulletin. The increasing seismic activity in
Blanco Chia, J. F.; Poveda, E.; Pedraza, P.
The latest seismological equipment and data processing instrumentation installed at the Colombia Seismological Network (RSNC) are described. System configuration, network operation, and data management are discussed. The data quality and the new seismological products are analyzed. The main purpose of the network is to monitor local seismicity with a special emphasis on seismic activity surrounding the Colombian Pacific and Caribbean oceans, for early warning in case a Tsunami is produced by an earthquake. The Colombian territory is located at the South America northwestern corner, here three tectonic plates converge: Nazca, Caribbean and the South American. The dynamics of these plates, when resulting in earthquakes, is continuously monitored by the network. In 2012, the RSNC registered in 2012 an average of 67 events per day; from this number, a mean of 36 earthquakes were possible to be located well. In 2010 the network was also able to register an average of 67 events, but it was only possible to locate a mean of 28 earthquakes daily. This difference is due to the expansion of the network. The network is made up of 84 stations equipped with different kind of broadband 40s, 120s seismometers, accelerometers and short period 1s sensors. The signal is transmitted continuously in real-time to the Central Recording Center located at Bogotá, using satellite, telemetry, and Internet. Moreover, there are some other stations which are required to collect the information in situ. Data is recorded and processed digitally using two different systems, EARTHWORM and SEISAN, which are able to process and share the information between them. The RSNC has designed and implemented a web system to share the seismological data. This innovative system uses tools like Java Script, Oracle and programming languages like PHP to allow the users to access the seismicity registered by the network almost in real time as well as to download the waveform and technical details. The coverage
Rojas, W.; Camacho, E. I.; Marroquín, G.; Molina, E.; Talavera, E.; Benito, M. B.; Lindholm, C.
Central America (CA) is known as a seismically active region in which several historic destructive earthquakes have occurred. This fact has promoved the development of seismic hazard studies that provide necessary estimates for decision making and risk assessment efforts, requiring a complete and standardized seismic catalog. With this aim, several authors have contributed to the study of the historical seismicity of Central America (e.g. Grases, Feldaman; White y Harlow, 1993; White et al. 2004; Ambraseys y Adams, 2001; Peraldo y Montero, 1999), who complied historical data. A first catalogue was developed by Rojas (1993) that comprises the 1522 to 1993 period. This information was integrated in 2007, together with data from the International Seismological Centre (CASC) and the national catalogs of CA countries in a new regional catalogue. Since 2007 a continuous effort has been done in order to complete and update this CA earthquake catalog. In particular, two workshops were held in 2008 and 2011 in the Universidad Politécnica de Madrid (Spain), joining experts from the different CA countries who worked each one in its own catalogue covering the entire region and the border with northwestern Colombia and southern Mexico. These national catalogues were later integrated in a common regional catalogue in SEISAN format. At this aim it was necessary to solve some problems, like to avoid duplicity of events, specially close to the boundaries, to consider the different scales of magnitude adopted by different countries, to take into account the completeness by the different national networks, etc. Some solutions were adopted for obtaining a homogenized catalogue to Mw, containing historical and instrumental events with Mw > 3.5 from 1522 up to 2011. The catalogue updated to December 2007 was the basis for the first regional hazard study carried out by Benito et al., (2011) as part of the collaborative RESIS II project under coordination of NORSAR. The ones updated to
Perrot, J.; Goslin, J.; Dziak, R. P.; Haxel, J. H.; Maia, M. A.; Tisseau, C.; Royer, J.
The seismicity of the North Atlantic Ocean was recorded by the SIRENA array of 6 autonomous underwater hydrophones (AUH) moored within the SOFAR channel on the flanks of the Mid-Atlantic Ridge (MAR). The instruments were deployed north of the Azores Plateau between 40° and 50°N from June 2002 to September 2003. The low attenuation properties of the SOFAR channel for earthquake T-wave propagation result in a detection threshold reduction to a magnitude completeness level (Mc) of ~2.8, to be compared to a Mc~4.7 for MAR events recorded by land-based seismic networks. A spatio-temporal analysis was performed over the 1696 events localized inside the SIRENA array. For hydrophone-derived catalogs, the acoustic magnitude, or Source Level (SL), is used as a measure of earthquake size. The ''source level completeness'', above which the data set is complete, is SLc=208 dB. The SIRENA catalog was searched for swarms using the cluster software of the SEISAN distribution. A minimum SL of 210 dB was chosen to detect a possible mainshock, and all subsequent events within 40 days following the possible mainshock, located within a radius of 15 km from the mainshock were considered as events of the swarm. 15 km correspond to the maximum fault length in a slow-ridge context. 11 swarms with more than 15 events were detected along the MAR between 40°et 50°N during the SIRENA deployment. The maximum number of earthquakes in a swarm is 40 events. The SL vs. time distribution within each swarm allowed a first discrimination between the swarms occurring in a tectonic context and those which can be attributed to volcanic processes, the latter showing a more constant SL vs. time distribution. Moreover, the swarms occurring in a tectonic context show a "mainshock-afterschock" distribution of the cumulative number of events vs. time, fitting a Modified Omori Law. The location of tectonic and volcanic swarms correlates well with regions where a positive and negative Mantle Bouguer
Megies, T.; Barsch, R.; Beyreuther, M.; Krischer, L.; Wassermann, J. M.; ObsPy Development Team
Python enables the user to combine the possibilities of a full-blown programming language with the flexibility of an interactive scripting language. Its extensive standard library and many freely available high quality scientific modules cover most needs in developing scientific processing workflows. The goal of the ObsPy project (http://www.obspy.org) is to facilitate rapid application development for seismology by extending Python's capabilities to fit the specific needs that arise when working with seismological data. It provides read and write support for many common waveform file formats (e.g. MiniSEED, SAC, GSE2, SEISAN, ...) and metadata formats (e.g. SEED, Dataless SEED, XML-SEED, RESP, ...). Several available client modules make it possible to directly acquire waveform data and metadata as well as earthquake event data from data centers communicating with ArcLink (http://www.webdc.eu), Fissures (http://www.iris.edu/dhi) and SeisHub servers (http://www.seishub.org) and by connecting to webservices provided by IRIS (http://www.iris.edu/ws/) and NERIES (http://www.seismicportal.eu/). Finally there is a growing signal processing toolbox that covers many often needed routines for filtering, triggering, instrument correction/simulation, complex trace analysis, array analysis and many more. Recent additions to ObsPy include calculation of probabilistic power spectral densities, relative instrument calibration and wrappers for the IASPEI-tau traveltime package and IRIS's evalresp. In combination with well developed, free Python packages like NumPy (http://numpy.scipy.org), SciPy (http://scipy.org), IPython (http://ipython.scipy.org), Matplotlib (http://matplotlib.sourceforge.net) and PyQt (http://www.riverbankcomputing.co.uk/software/pyqt), ObsPy makes it possible to develop complete workflows in Python, ranging from reading/requesting data via signal analysis and data processing to visualization in GUI applications and output of modified or derived data. ObsPy is
Domingues, A.; Chamussa, J. R.; Antunes, E.; Custodio, S.; Silveira, M. M.; Helffrich, G. R.; Ferreira, A. M.; Fonseca, J. F.
Extensively investigated from the Red Sea to southern Tanzania, the East African Rift (EAR) structure is still unknown on its southern tip, Mozambique. The M7 Machaze earthquake of 2006, in central Mozambique, shed new light on the location of the rifting activity, motivating the current initiative. During 2011, project MOZART (funded by FCT, Lisbon, PI J. Fonseca) deployed a network of 30 broadband (120s) seismic stations from the SEIS-UK Pool in central Mozambique and NE South Africa, to investigate the structure of the southernmost section of the EAR through a number of techniques. We present preliminary results of data quality control based on full-waveform modeling, hypocentral locations, and regional structure based on the analysis of ambient noise. Data quality control based on full-waveform modeling relies on comparisons between MOZART waveform data and synthetic seismograms computed with a spectral element method (Komatitsch and Tromp, 2002). These comparisons allow an understanding of how well existing global 3D and 1D Earth models, which were built from independent data, explain MOZART data, and how suitable MOZART data are for waveform tomography. The 3D Earth model synthetics explain the surface wave phases well, but are more limited at matching amplitudes, showing that there is still scope for improvement of the Earth model. The 1D Earth PREM synthetics explain surface wave amplitudes broadly as well as the 3D Earth model, but lead to much poorer phase fits. We will also present preliminary results of the analysis of local seismicity. Local hypocenters are determined using the SEISAN software. The hypocenter inversion is a modified version of HYPOCENTER (Lienert et al., 1986, Lienert,1991, Lienert and Havskov, 1995). The current version uses different seismic phases for earthquake location. The hypocentral locations of small to moderate earthquakes help to identify the most seismically active regions. Finally, we present the first results of the
Yanik, K.; Tezel, T.
-mail, data reading from anywhere that has ethernet connection and store the results in same centre. The Earthqukae Analysis (EA) program was developed considering above facilities. Microsoft Visual Basic 6.0 and Microsoft GDI tools were used as a basement for program development. EA program can image five different seismic formats (gcf, suds, seisan, sac, nanometrics-y) without any conversion and use all seismic process facilities that are filtering (band-pass, low-pass, high-pass), fast fourier transform, offset adjustment etc.
Bernal-Olaya, R.; Mann, P.; Vargas, C. A.; Koulakov, I.
We define the length and geometry of eastward and southeastward-subducting slabs beneath northwestern South America in Colombia using ~100,000 earthquake events recorded by the Colombian National Seismic Network from 1993 to 2012. Methods include: hypocenter relocation, compilation of focal mechanisms, and P and S wave tomographic calculations performed using LOTOS and Seisan. The margins of Colombia include four distinct subduction zones based on slab dip: 1) in northern Colombia, 12-16-km-thick oceanic crust subducts at a modern GPS rate of 20 mm/yr in a direction of 110 degrees at a shallow angle of 8 degrees; as a result of its low dip, Pliocene-Pleistocene volcanic rocks are present 400 km from the frontal thrust; magmatic arc migration to the east records 800 km of subduction since 58 Ma ago (Paleocene) with shallow subduction of the Caribbean oceanic plateau starting ~24-33 Ma (Miocene); at depths of 90-150 km, the slab exhibits a negative velocity anomaly we associate with pervasive fracturing; 2) in the central Colombia-Panama area, we define an area of 30-km-thick crust of the Panama arc colliding/subducting at a modern 30/mm in a direction of 95 degrees; the length of this slab shows subduction/collision initiated after 20 Ma (Middle Miocene); we call this feature the Panama indenter since it has produced a V-shaped indentation of the Colombian margin and responsible for widespread crustal deformation and topographic uplift in Colombia; an incipient subduction area is forming near the Panama border with intermediate earthquakes at an eastward dip of 70 degrees to depths of ~150 km; this zone is not visible on tomographic images; 3) a 250-km-wide zone of Miocene oceanic crust of the Nazca plate flanking the Panama indenter subducts at a rate of 25 mm/yr in a direction of 55 degrees and at a normal dip of 40 degrees; the length of this slab suggests subduction began at ~5 Ma; 4) the Caldas tear defines a major dip change to the south where a 35 degrees
Ordaz, M.; Martinelli, F.; Meletti, C.; D'Amico, V.
CRISIS is a computer tool for probabilistic seismic hazard analysis (PSHA), whose development started in the late 1980's at the Instituto de Ingeniería, UNAM, Mexico. It started circulating outside the Mexican borders at the beginning of the 1990's, when it was first distributed as part of SEISAN tools. Throughout the years, CRISIS has been used for seismic hazard studies in several countries in Latin America (Mexico, Guatemala, Belize, El Salvador, Honduras, Nicaragua, Costa Rica, Panama, Colombia, Venezuela, Ecuador, Peru, Argentina and Chile), and in many other countries of the World. CRISIS has always circulated free of charge for non-commercial applications. It is worth noting that CRISIS has been mainly written by people that are, at the same time, PSHA practitioners. Therefore, the development loop has been relatively short, and most of the modifications and improvements have been made to satisfy the needs of the developers themselves. CRISIS has evolved from a rather simple FORTRAN code to a relatively complex program with a friendly graphical interface, able to handle a variety of modeling possibilities for source geometries, seismicity descriptions and ground motion prediction models (GMPM). We will describe some of the improvements made for the newest version of the code: CRISIS 2012.These improvements, some of which were made in the frame of the Italian research project INGV-DPC S2 (http://nuovoprogettoesse2.stru.polimi.it/), funded by the Dipartimento della Protezione Civile (DPC; National Civil Protection Department), include: A wider variety of source geometries A wider variety of seismicity models, including the ability to handle non-Poissonian occurrence models and Poissonian smoothed-seismicity descriptions. Enhanced capabilities for using different kinds of GMPM: attenuation tables, built-in models and generalized attenuation models. In the case of built-in models, there is, by default, a set ready to use in CRISIS, but additional custom GMPMs
Martín, R.; Carmona, E.; Almendros, J.; Serrano, I.; Villaseñor, A.; Galeano, J.
the seismic activity and an efficient seismo-volcanic surveillance. The data are processed and analyzed using the SEISAN database management software. In addition to the seismic network, we deployed a small-aperture seismic array south of Fumarole Bay. It is composed by 9 vertical and 1 three-component short-period stations. The 24-bit data acquisition system samples these 12 channels at 100 sps. There is also a permanent seismic station operating since 2008 and located near GdC, that is very useful for the preliminary evaluation of the seismicity at the start of the survey. This station is composed by a 16-s electrolytic seismometer (Eentec SP400) and a 24-bit datalogger (Eentec DR4000) sampling at 100 sps. During the 2010-2011 survey we identified 33 regional earthquakes, 80 volcano-tectonic (VT) earthquakes, and 929 long-period (LP) events. The volcanic alert system has remained green (the lowest level) at all times. The seismic activity has been similar to previous surveys and remained within limits that are normal for the island.
Reyes, C. G.; West, M. E.; McNutt, S. R.
The Waveform Suite, developed at the University of Alaska Geophysical Institute, is an open-source collection of MATLAB classes that provide a means to import, manipulate, display, and share waveform data while ensuring integrity of the data and stability for programs that incorporate them. Data may be imported from a variety of sources, such as Antelope, Winston databases, SAC files, SEISAN, .mat files, or other user-defined file formats. The waveforms being manipulated in MATLAB are isolated from their stored representations, relieving the overlying programs from the responsibility of understanding the specific format in which data is stored or retrieved. The waveform class provides an object oriented framework that simplifies manipulations to waveform data. Playing with data becomes easier because the tedious aspects of data manipulation have been automated. The user is able to change multiple waveforms simultaneously using standard mathematical operators and other syntactically familiar functions. Unlike MATLAB structs or workspace variables, the data stored within waveform class objects are protected from modification, and instead are accessed through standardized functions, such as get and set; these are already familiar to users of MATLAB’s graphical features. This prevents accidental or nonsensical modifications to the data, which in turn simplifies troubleshooting of complex programs. Upgrades to the internal structure of the waveform class are invisible to applications which use it, making maintenance easier. We demonstrate the Waveform Suite’s capabilities on seismic data from Okmok and Redoubt volcanoes. Years of data from Okmok were retrieved from Antelope and Winston databases. Using the Waveform Suite, we built a tremor-location program. Because the program was built on the Waveform Suite, modifying it to operate on real-time data from Redoubt involved only minimal code changes. The utility of the Waveform Suite as a foundation for large
Yavuz, Evrim; Çaka, Deniz; Tunç, Berna; Woith, Heiko; Gottfried Lühr, Birger; Barış, Şerif
Attenuation characteristic of seismic waves was determined using coda Q in the frame of MARsite (MARsite has received funding from the European Union's Seventh Programme for research, technological development and demonstration under grant agreement No 308417). Data from 82 earthquakes recorded in 2013-2014 in the Armutlu Peninsula and its vicinity by 9 ARNET seismic stations were used for processing. The earthquake magnitudes (Ml) and depths vary from 1.5 to 3.7 and 1.2-16.9 km, respectively. Epicentral distances closer than 90 km were selected to ensure better signal-to-noise ratios. Lapse times between 20 seconds and 40 seconds at intervals of 5 seconds were used for the calculation of the coda wave quality factor. The coda windows were filtered at central frequencies of 1.5, 3, 6, 9 and 12 Hz bandpass filter. To obtain reliable results, only data with signal-to-noise ratios greater than 5 and correlation coefficents higher than 0.7 were used. The SEISAN software and one of its subroutines (CODAQ) were used for data processing and analyses. In the whole study area, Qc=(51±4)f^(0.91±0.04) for 20 seconds, Qc=(77±7)f^(0.80±0.04) for 30 seconds and Qc=(112±13)f^(0.72±0.06) for 40 seconds lapse times are obtained for coda wave quality factor. The observed quality factor is dependent on frequency and lapse time. The results indicate that the upper lithosphere is more heterogeneous and seismically more active than the lower lithosphere as expected in the region which is tectonically complex refering to the effects of the North Anatolian Fault Zone. By considering earthquake clusters and recorded stations, the scattering area was drawn. The intersection of the scattered areas for 20 seconds lapse time is covering all stations. Quality factor in 1 Hz and frequency dependent values were calculated separately and for the intersection of all scattered areas. Calculated Qo and n values of the intersection area are 50 and 0.89, respectively. Hence, the Qo and n values