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  • Computational Methods  (26)
  • 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion  (16)
  • Oxford University Press  (26)
  • Springer  (16)
  • Annual Reviews
  • International Union of Crystallography (IUCr)
  • 2010-2014  (42)
  • 1955-1959
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  • 1
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    Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: Combinatorial transcription factor (TF) binding is essential for cell-type-specific gene regulation. However, much remains to be learned about the mechanisms of TF interactions, including to what extent constrained spacing and orientation of interacting TFs are critical for regulatory element activity. To examine the relative prevalence of the ‘enhanceosome’ versus the ‘TF collective’ model of combinatorial TF binding, a comprehensive analysis of TF binding site sequences in large scale datasets is necessary. We developed a motif-pair discovery pipeline to identify motif co-occurrences with preferential distance(s) between motifs in TF-bound regions. Utilizing a compendium of 289 mouse haematopoietic TF ChIP-seq datasets, we demonstrate that haematopoietic-related motif-pairs commonly occur with highly conserved constrained spacing and orientation between motifs. Furthermore, motif clustering revealed specific associations for both heterotypic and homotypic motif-pairs with particular haematopoietic cell types. We also showed that disrupting the spacing between motif-pairs significantly affects transcriptional activity in a well-known motif-pair—E-box and GATA, and in two previously unknown motif-pairs with constrained spacing—Ets and Homeobox as well as Ets and E-box. In this study, we provide evidence for widespread sequence-specific TF pair interaction with DNA that conforms to the ‘enhanceosome’ model, and furthermore identify associations between specific haematopoietic cell-types and motif-pairs.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
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    Dynalign II: common secondary structure prediction for RNA homologs with domain insertions (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: Homologous non-coding RNAs frequently exhibit domain insertions, where a branch of secondary structure is inserted in a sequence with respect to its homologs. Dynamic programming algorithms for common secondary structure prediction of multiple RNA homologs, however, do not account for these domain insertions. This paper introduces a novel dynamic programming algorithm methodology that explicitly accounts for the possibility of inserted domains when predicting common RNA secondary structures. The algorithm is implemented as Dynalign II, an update to the Dynalign software package for predicting the common secondary structure of two RNA homologs. This update is accomplished with negligible increase in computational cost. Benchmarks on ncRNA families with domain insertions validate the method. Over base pairs occurring in inserted domains, Dynalign II improves accuracy over Dynalign, attaining 80.8% sensitivity (compared with 14.4% for Dynalign) and 91.4% positive predictive value (PPV) for tRNA; 66.5% sensitivity (compared with 38.9% for Dynalign) and 57.0% PPV for RNase P RNA; and 50.1% sensitivity (compared with 24.3% for Dynalign) and 58.5% PPV for SRP RNA. Compared with Dynalign, Dynalign II also exhibits statistically significant improvements in overall sensitivity and PPV. Dynalign II is available as a component of RNAstructure, which can be downloaded from http://rna.urmc.rochester.edu/RNAstructure.html .
    Keywords: Computational Methods
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  • 3
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    MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-01
    Description: Determining the taxonomic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects research across the fields of environmental, clinical and evolutionary microbiology. Here, we introduce MyTaxa, a homology-based bioinformatics framework to classify metagenomic and genomic sequences with unprecedented accuracy. The distinguishing aspect of MyTaxa is that it employs all genes present in an unknown sequence as classifiers, weighting each gene based on its (predetermined) classifying power at a given taxonomic level and frequency of horizontal gene transfer. MyTaxa also implements a novel classification scheme based on the genome-aggregate average amino acid identity concept to determine the degree of novelty of sequences representing uncharacterized taxa, i.e. whether they represent novel species, genera or phyla. Application of MyTaxa on in silico generated (mock) and real metagenomes of varied read length (100–2000 bp) revealed that it correctly classified at least 5% more sequences than any other tool. The analysis also showed that ~10% of the assembled sequences from human gut metagenomes represent novel species with no sequenced representatives, several of which were highly abundant in situ such as members of the Prevotella genus. Thus, MyTaxa can find several important applications in microbial identification and diversity studies.
    Keywords: Computational Methods
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  • 4
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    Identifying RNA-binding residues based on evolutionary conserved structural and energetic features (2014)
    Oxford University Press
    Details
    Publication Date: 2014-02-11
    Description: Increasing numbers of protein structures are solved each year, but many of these structures belong to proteins whose sequences are homologous to sequences in the Protein Data Bank. Nevertheless, the structures of homologous proteins belonging to the same family contain useful information because functionally important residues are expected to preserve physico-chemical, structural and energetic features. This information forms the basis of our method, which detects RNA-binding residues of a given RNA-binding protein as those residues that preserve physico-chemical, structural and energetic features in its homologs. Tests on 81 RNA-bound and 35 RNA-free protein structures showed that our method yields a higher fraction of true RNA-binding residues (higher precision) than two structure-based and two sequence-based machine-learning methods. Because the method requires no training data set and has no parameters, its precision does not degrade when applied to ‘novel’ protein sequences unlike methods that are parameterized for a given training data set. It was used to predict the ‘unknown’ RNA-binding residues in the C-terminal RNA-binding domain of human CPEB3. The two predicted residues, F430 and F474, were experimentally verified to bind RNA, in particular F430, whose mutation to alanine or asparagine nearly abolished RNA binding. The method has been implemented in a webserver called DR_bind1, which is freely available with no login requirement at http://drbind.limlab.ibms.sinica.edu.tw .
    Keywords: Computational Methods
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  • 5
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    Complete RNA inverse folding: computational design of functional hammerhead ribozymes (2014)
    Oxford University Press
    Details
    Publication Date: 2014-10-10
    Description: Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic acid molecules, using our recent algorithm, RNAiFold , which can determine all RNA sequences whose minimum free energy secondary structure is a user-specified target structure. Using RNAiFold , we design ten cis -cleaving hammerhead ribozymes, all of which are shown to be functional by a cleavage assay. We additionally use RNAiFold to design a functional cis -cleaving hammerhead as a modular unit of a synthetic larger RNA. Analysis of kinetics on this small set of hammerheads suggests that cleavage rate of computationally designed ribozymes may be correlated with positional entropy, ensemble defect, structural flexibility/rigidity and related measures. Artificial ribozymes have been designed in the past either manually or by SELEX (Systematic Evolution of Ligands by Exponential Enrichment); however, this appears to be the first purely computational design and experimental validation of novel functional ribozymes. RNAiFold is available at http://bioinformatics.bc.edu/clotelab/RNAiFold/ .
    Keywords: Computational Methods
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  • 6
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    Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-27
    Description: While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an ‘accessory’ during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context.
    Keywords: Computational Methods
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  • 7
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    An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: The thermophilic fungus Chaetomium thermophilum holds great promise for structural biology. To increase the efficiency of its biochemical and structural characterization and to explore its thermophilic properties beyond those of individual proteins, we obtained transcriptomics and proteomics data, and integrated them with computational annotation methods and a multitude of biochemical experiments conducted by the structural biology community. We considerably improved the genome annotation of Chaetomium thermophilum and characterized the transcripts and expression of thousands of genes. We furthermore show that the composition and structure of the expressed proteome of Chaetomium thermophilum is similar to its mesophilic relatives. Data were deposited in a publicly available repository and provide a rich source to the structural biology community.
    Keywords: Computational Methods
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  • 8
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    Strain/species identification in metagenomes using genome-specific markers (2014)
    Oxford University Press
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    Publication Date: 2014-05-01
    Description: Shotgun metagenome sequencing has become a fast, cheap and high-throughput technology for characterizing microbial communities in complex environments and human body sites. However, accurate identification of microorganisms at the strain/species level remains extremely challenging. We present a novel k -mer-based approach, termed GSMer, that identifies genome-specific markers (GSMs) from currently sequenced microbial genomes, which were then used for strain/species-level identification in metagenomes. Using 5390 sequenced microbial genomes, 8 770 321 50-mer strain-specific and 11 736 360 species-specific GSMs were identified for 4088 strains and 2005 species (4933 strains), respectively. The GSMs were first evaluated against mock community metagenomes, recently sequenced genomes and real metagenomes from different body sites, suggesting that the identified GSMs were specific to their targeting genomes. Sensitivity evaluation against synthetic metagenomes with different coverage suggested that 50 GSMs per strain were sufficient to identify most microbial strains with ≥0.25 x coverage, and 10% of selected GSMs in a database should be detected for confident positive callings. Application of GSMs identified 45 and 74 microbial strains/species significantly associated with type 2 diabetes patients and obese/lean individuals from corresponding gastrointestinal tract metagenomes, respectively. Our result agreed with previous studies but provided strain-level information. The approach can be directly applied to identify microbial strains/species from raw metagenomes, without the effort of complex data pre-processing.
    Keywords: Computational Methods
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  • 9
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    Characterizing RNA ensembles from NMR data with kinematic models (2014)
    Oxford University Press
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    Publication Date: 2014-09-02
    Description: Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem–loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention.
    Keywords: Computational Methods
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  • 10
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    Quantitative models for accelerated protein dissociation from nucleosomal DNA (2014)
    Oxford University Press
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    Publication Date: 2014-09-02
    Description: Binding of transcription factors to their binding sites in promoter regions is the fundamental event in transcriptional gene regulation. When a transcription factor binding site is located within a nucleosome, the DNA has to partially unwrap from the nucleosome to allow transcription factor binding. This reduces the rate of transcription factor binding and is a known mechanism for regulation of gene expression via chromatin structure. Recently a second mechanism has been reported where transcription factor off-rates are dramatically increased when binding to target sites within the nucleosome. There are two possible explanations for such an increase in off-rate short of an active role of the nucleosome in pushing the transcription factor off the DNA: (i) for dimeric transcription factors the nucleosome can change the equilibrium between monomeric and dimeric binding or (ii) the nucleosome can change the equilibrium between specific and non-specific binding to the DNA. We explicitly model both scenarios and find that dimeric binding can explain a large increase in off-rate while the non-specific binding model cannot be reconciled with the large, experimentally observed increase. Our results suggest a general mechanism how nucleosomes increase transcription factor dissociation to promote exchange of transcription factors and regulate gene expression.
    Keywords: Computational Methods
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  • 11
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    SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples (2014)
    Oxford University Press
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    Publication Date: 2014-08-15
    Description: High-throughput sequencing technologies, including RNA-seq, have made it possible to move beyond gene expression analysis to study transcriptional events including alternative splicing and gene fusions. Furthermore, recent studies in cancer have suggested the importance of identifying transcriptionally altered loci as biomarkers for improved prognosis and therapy. While many statistical methods have been proposed for identifying novel transcriptional events with RNA-seq, nearly all rely on contrasting known classes of samples, such as tumor and normal. Few tools exist for the unsupervised discovery of such events without class labels. In this paper, we present SigFuge for identifying genomic loci exhibiting differential transcription patterns across many RNA-seq samples. SigFuge combines clustering with hypothesis testing to identify genes exhibiting alternative splicing, or differences in isoform expression. We apply SigFuge to RNA-seq cohorts of 177 lung and 279 head and neck squamous cell carcinoma samples from the Cancer Genome Atlas, and identify several cases of differential isoform usage including CDKN2A , a tumor suppressor gene known to be inactivated in a majority of lung squamous cell tumors. By not restricting attention to known sample stratifications, SigFuge offers a novel approach to unsupervised screening of genetic loci across RNA-seq cohorts. SigFuge is available as an R package through Bioconductor.
    Keywords: Computational Methods
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  • 12
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    Microzonation of Potenza (Southern Italy) in terms of spectral intensity ratio using joint analysis of earthquakes and ambient noise. (2013)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: A temporary seismic network composed of 11 stations was installed in the city of Potenza (Southern Italy) to record local and regional seismicity within the context of a national project funded by the Italian Department of Civil Protection (DPC). Some stations were moved after a certain time in order to increase the number of measurement points, leading to a total of 14 sites within the city by the end of the experiment. Recordings from 26 local earthquakes (Ml 2.2−3.8 ) were analyzed to compute the site responses at the 14 sites by applying both reference and non-reference site techniques. Furthermore, the Spectral Intensity (SI) for each local earthquake, as well as their ratios with respect to the values obtained at a reference site, were also calculated. In addition, a field survey of 233 single station noise measurements within the city was carried out to increase the information available at localities different from the 14 monitoring sites. By using the results of the correlation analysis between the horizontal-to-vertical spectral ratios computed from noise recordings (NHV) at the 14 selected sites and those derived by the single station noise measurements within the town as a proxy, the spectral intensity correction factors for site amplification obtained from earthquake analysis were extended to the entire city area. This procedure allowed us to provide a microzonation map of the urban area that can be directly used when calculating risk scenarios for civil defence purposes. The amplification factors estimated following this approach show values increasing along the main valley toward east where the detrital and alluvial complexes reach their maximum thickness.
    Description: Published
    Description: 493-516
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: restricted
    Keywords: site effect ; seismic noise ; spectral intensity ; correlation ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 13
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    TrAp: a tree approach for fingerprinting subclonal tumor composition (2013)
    Oxford University Press
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    Publication Date: 2013-09-26
    Description: Revealing the clonal composition of a single tumor is essential for identifying cell subpopulations with metastatic potential in primary tumors or with resistance to therapies in metastatic tumors. Sequencing technologies provide only an overview of the aggregate of numerous cells. Computational approaches to de-mix a collective signal composed of the aberrations of a mixed cell population of a tumor sample into its individual components are not available. We propose an evolutionary framework for deconvolving data from a single genome-wide experiment to infer the composition, abundance and evolutionary paths of the underlying cell subpopulations of a tumor. We have developed an algorithm (TrAp) for solving this mixture problem. In silico analyses show that TrAp correctly deconvolves mixed subpopulations when the number of subpopulations and the measurement errors are moderate. We demonstrate the applicability of the method using tumor karyotypes and somatic hypermutation data sets. We applied TrAp to Exome-Seq experiment of a renal cell carcinoma tumor sample and compared the mutational profile of the inferred subpopulations to the mutational profiles of single cells of the same tumor. Finally, we deconvolve sequencing data from eight acute myeloid leukemia patients and three distinct metastases of one melanoma patient to exhibit the evolutionary relationships of their subpopulations.
    Keywords: Computational Methods
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  • 14
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    Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery (2013)
    Oxford University Press
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    Publication Date: 2013-04-02
    Description: MicroRNAs (miRNAs) constitute an important class of small regulatory RNAs that are derived from distinct hairpin precursors (pre-miRNAs). In contrast to mature miRNAs, which have been characterized in numerous genome-wide studies of different organisms, research on global profiling of pre-miRNAs is limited. Here, using massive parallel sequencing, we have performed global characterization of both mouse mature and precursor miRNAs. In total, 87 369 704 and 252 003 sequencing reads derived from 887 mature and 281 precursor miRNAs were obtained, respectively. Our analysis revealed new aspects of miRNA/pre-miRNA processing and modification, including eight Ago2-cleaved pre-miRNAs, eight new instances of miRNA editing and exclusively 5' tailed mirtrons. Furthermore, based on the sequences of both mature and precursor miRNAs, we developed a miRNA discovery pipeline, miRGrep, which does not rely on the availability of genome reference sequences. In addition to 239 known mouse pre-miRNAs, miRGrep predicted 41 novel ones with high confidence. Similar as known ones, the mature miRNAs derived from most of these novel loci showed both reduced abundance following Dicer knockdown and the binding with Argonaute2. Evaluation on data sets obtained from Caenorhabditis elegans and Caenorhabditis sp.11 demonstrated that miRGrep could be widely used for miRNA discovery in metazoans, especially in those without genome reference sequences.
    Keywords: Computational Methods
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  • 15
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    Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts (2013)
    Oxford University Press
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    Publication Date: 2013-09-26
    Description: It is a challenge to classify protein-coding or non-coding transcripts, especially those re-constructed from high-throughput sequencing data of poorly annotated species. This study developed and evaluated a powerful signature tool, Coding-Non-Coding Index (CNCI), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. CNCI is effective for classifying incomplete transcripts and sense–antisense pairs. The implementation of CNCI offered highly accurate classification of transcripts assembled from whole-transcriptome sequencing data in a cross-species manner, that demonstrated gene evolutionary divergence between vertebrates, and invertebrates, or between plants, and provided a long non-coding RNA catalog of orangutan. CNCI software is available at http://www.bioinfo.org/software/cnci .
    Keywords: Computational Methods
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  • 16
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    r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data (2013)
    Oxford University Press
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    Publication Date: 2013-07-16
    Description: The coupling of chromosome conformation capture (3C) with next-generation sequencing technologies enables the high-throughput detection of long-range genomic interactions, via the generation of ligation products between DNA sequences, which are closely juxtaposed in vivo . These interactions involve promoter regions, enhancers and other regulatory and structural elements of chromosomes and can reveal key details of the regulation of gene expression. 3C-seq is a variant of the method for the detection of interactions between one chosen genomic element (viewpoint) and the rest of the genome. We present r3Cseq , an R/Bioconductor package designed to perform 3C-seq data analysis in a number of different experimental designs. The package reads a common aligned read input format, provides data normalization, allows the visualization of candidate interaction regions and detects statistically significant chromatin interactions, thus greatly facilitating hypothesis generation and the interpretation of experimental results. We further demonstrate its use on a series of real-world applications.
    Keywords: Computational Methods
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  • 17
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    The recording stations of the Italian strong motion network: geological information and site classification (2012)
    Springer
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    Publication Date: 2020-10-26
    Description: One of the main objectives of the ITACA (ITalian ACcelerometric Archive) strong motion database, promoted by the Italian Department of Civil Protection, was to improve the characterization of the recording sites from a geological and geophysical point of view and to provide their seismic classification according to the seismic norms pertinent to Italy, namely the Eurocode 8 and the National Technical Norms for Constructions. A standard format to summarize the available information for the recording stations was first produced, in terms of a technical report dynamically linked to the database, i.e., some of the relevant information is automatically updated when the corresponding fields of the database are modified. Then, an important activity of collection, qualification and synthesis of available data was carried out, especially for stations that recorded the strongest earthquakes in Italy in the last 40 years, and for which a relevant number of studies have been published. In spite of this activity, among the more than 700 strong motion stations present in the ITACA database, only a limited number of them could be characterized by quantitative information on subsurface soil properties. For this reason, a dual seismic site classification criterion was implemented, either based on the standard Vs,30 scheme, or, in the absence of such information, based on an expert opinion supported by shallow geology maps, mostly at 1:100,000 scale, and when available on the H/V ratios calculated on recordings. Owing to the relevance in the Italian geographic and morphological context, a special care was also given to the topographic classification of stations, based on suitable criteria developed within a GIS environment.
    Description: Published
    Description: 1779-1796
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: open
    Keywords: ITACA database ; Strong motion station ; General characterization ; Site classification ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring ; 05. General::05.02. Data dissemination::05.02.02. Seismological data ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 18
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    Frequency variation in site response as observed from strong motion data of the L’Aquila (2009) seismic sequence (2012)
    Springer
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    Publication Date: 2017-04-04
    Description: Previous works based mainly on strong-motion recordings of large Japanese earthquakes showed that site amplification and soil fundamental frequency could vary over long and short time scales. These phenomena were attributed to non-linear soil behaviour: the starting fundamental frequency and amplification were both instantaneously decreasing and then recovering for a time varying from few seconds to several months. The recent April 6, 2009 earthquake (M W 6.3), occurred in the L’Aquila district (central Italy), gave us the possibility to test hypotheses on time variation of amplification function and soil fundamental frequency, thanks to the recordings provided by a pre-existing strong-motion array and by a large number of temporary stations. We investigated the intra- and inter-event soil frequency variations through different spectral analyses, including time-frequency spectral ratios and S-Transform (Stockwell et al. in IEEE Trans Signal Process 44:998–1001, 1996). Finally, analyses on noise recordings were performed, in order to study the soil behaviour in linear conditions. The results provided puzzling evidences. Concerning the long time scale, little variation was observed at the permanent stations of the Aterno Valley array. As for the short time-scale variation, the evidence was often contrasting, with some station showing a time-varying behavior, while others did not change their frequency with respect to the one evaluated from noise measurements. Even when a time-varying fundamental frequency was observed, it was difficult to attribute it to a classical, softening non-linear behaviour. Even for the strongest recorded shocks, with peak ground acceleration reaching 0.7 g, variations in frequency and amplitude seems not relevant from building design standpoint. The only exception seems to be the site named AQV, where the analyses evidence a fundamental frequency of the soil shifting from 3 Hz to about 1.5 Hz during the mainshock.
    Description: Published
    Description: 869-892
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: open
    Keywords: Strong motion ; Subsoil non-linearity ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 19
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    Separation of source and site effects by Generalized Inversion Technique using the aftershock recordings of the 2009 L'Aquila earthquake (2012)
    Springer
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    Publication Date: 2017-04-04
    Description: We exploit S-wave spectral amplitudes from 112 aftershocks (3.0 ≤ ML ≤ 5.3) of the L’Aquila 2009 seismic sequence recorded at 23 temporary stations in the epicentral area to estimate the source parameters of these events, the seismic attenuation characteristics and the site amplification effects at the recording sites. The spectral attenuation curves exhibit a very fast decay in the first few kilometers that could be attributed to the large attenuation of waves traveling trough the highly heterogeneous and fractured crust in the fault zone of the L’Aquila mainshock. The S-waves total attenuation in the first 30 km can be parameterized by a quality factor QS(f) = 23f^0.58 obtained by fixing the geometrical spreading to 1/R. The source spectra can be satisfactorily modeled using the omega-square model that provides stress drops between 0.3 and 60 MPa with a mean value of 3.3±2.8 MPa. The site responses show a large variability over the study area and significant amplification peaks are visible in the frequency range from 1 to more than 10 Hz. Finally, the vertical component of the motion is amplified at a number of sites where, as a consequence, the horizontal-to-vertical spectral ratios (HVSR) method fails in detecting the amplitude levels and in few cases the resonance frequencies.
    Description: Published
    Description: 717-739
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: reserved
    Keywords: Generalized Inversion Technique ; 2009 L'Aquila earthquake ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Proposal for a soil classification based on parameters alternative or complementary to Vs,30 (2012)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: The selection of specific elastic response spectra according to soil categories is the easiest way to account for site effects in engineering projects and general-purpose hazard maps. Most of the international seismic codes make use of the average shear wave velocity of the upper 30 m (Vs,30) to discriminate soil categories, although some doubts arose about the capability of Vs,30 to predict actual soil amplification. In this work we propose two soil classifications in which the soil fundamental frequency (f0) becomes either an alternative or a complement to Vs,30. The performance of the derived categorizations is achieved through the estimation of the standard deviation associated to ground motion prediction equations of acceleration response spectra, considering recordings extracted from the Italian strong motion data base. The results indicate that there is a significant reduction of the standard deviation when the classification is based on the couple of variables Vs,30–f0, although a classification based of the single f0 also leads to satisfactory results, comparable with those obtained assuming a classification scheme based on Vs,30.
    Description: Published
    Description: 1877-1898
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: reserved
    Keywords: site effects ; soil classification ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Foreword to the special issue on the ITACA strong motion database (2012)
    Springer
    Details
    Publication Date: 2020-02-24
    Description: The S1 pecial Issue of the Bulletin of Earthquake Engineering devoted to the new 2 Italian strong motion database ITACA (ITalian ACelerometric Archive) is introduced in this 3 foreword. An overview of the papers published in this issue is presented, providing an idea of 4 the number of problems encountered in the compilation of a database as rich of information 5 as ITACA, of the solutions adopted and of the possible research and practical applications. 6 Most of the contents, though specifically addressed to ITACA and to its accelerograms, can 7 be usefully thought of as an exemplification of approaches and methods that can be used for, 8 and extended to, similar databases in other countries
    Description: Published
    Description: 1717-1721
    Description: 5.2. TTC - Banche dati di sismologia strumentale
    Description: JCR Journal
    Description: reserved
    Keywords: Strong motion database ; ITACA ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Seismic response of L’Aquila downtown from comparison between 2D synthetics spectral ratios of SH, P-SV and Rayleigh waves and observations of the 2009 earthquake sequence (2012)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: We have studied two velocity-depth models with the aim of outlining the behavior of a velocity reversal in the top layer, which is associated with the stiff Brecce de L’Aquila unit (BrA). In this setting, the SMTH model is topped by a layer with about 2:1 impedance contrast with the underlying layer while the NORV model has no velocity reversal. We have simulated the propagation of SH and P-SV wavefields in the range 0–10 Hz for incidence 0◦ –90◦ . Earthquake spectral ratios of the horizontal and vertical components at six sites in L’Aquila downtown are compared to corresponding syn- thetics spectral ratios. The vertical component of P-SV synthetics enables us to investigate a remarkable amplification effect seen in the vertical component of the recorded strong motion. Sites AQ04 and AQ05 are best matched by synthetics from the NORV model while FAQ5 and AQ06 have a better match with synthetics spectral ratios from the SMTH model. All simulations show this behavior systematically, with horizontal and near-horizontal incident waves predicting the overall pattern of matches more clearly than vertical and near-vertical incidence. The model inferences are in agreement with new geological data reporting lateral passages in the top layer from the stiff BrA to softer sediments. Matches are good in terms of frequency of the first amplification peak and of spectral amplitude: the horizontal compo-nents have spectral ratio peaks predominantly at 0.5 Hz in the simulations and at 0.7 Hz in the data, both with amplitudes of 4, while the vertical component spectral ratios reach values of 6 at frequencies of about 1 Hz in both data and simulations. The vertical component spectral ratios are very well matched using Rayleigh waves with incidence at 90◦ . The NORV model without the velocity reversal predicts spectral ratio peaks for the horizontal components at frequencies up to 6 Hz. The reversal of velocity acts as a low-pass frequency filter on the horizontal components reducing the amplification effect of the sediment filled valley.
    Description: Published
    Description: 761-781
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: reserved
    Keywords: site effect, 2D synthetic seismograms, spectral ratios, reversal of velocity, L'Aquila ; 01. Atmosphere::01.02. Ionosphere::01.02.05. Wave propagation ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Local variability of the ground shaking during the 2009 L’Aquila earthquake (April 6, 2009—Mw 6.3): the case study of Onna and Monticchio villages (2012)
    Springer
    Details
    Publication Date: 2022-05-24
    Description: The 2009 Mw 6.3 L’Aquila event caused extensive damage in the city of L’Aquila and in some small towns in its vicinity. The most severe damage was recognized SE of L’Aquila town along the Aterno river valley. Although building vulnerability and near-source effects are strongly responsible for the high level of destruction, site effects have been invoked to explain the damage heterogeneities and the similarities between the 2009 macroseismic field with the intensities of historical earthquakes. The small village of Onna is settled on quaternary alluvium and suffered during the L’Aquila event an extremely heavy damage in the masonry structures with intensity IX–X on the Mercalli-Cancani-Sieberg (MCS) scale. The village of Monticchio, far less than 1.3 km from Onna, is mostly situated on Meso- zoic limestone and suffered a smaller level of damaging (VI MCS). In the present paper, we analyze the aftershock recordings at seismic stations deployed in a small area of the middle-Aterno valley including Onna and Monticchio. The aim is to investigate local ampli-fication effects caused by the near-surface geology. Because the seismological stations are close together, vulnerability and near-source effects are assumed to be constant. The wave- form analysis shows that the ground motion at Onna is systematically characterized by large high-frequency content. The frequency resonance is varying from 2 to 3 Hz and it is related to alluvial sediments with a thickness of about 40 m that overlay a stiffer Pleistocene substrate. The ground motion recordings of Onna are well reproduced by the predictive equation for the Italian territory.
    Description: Published
    Description: 783-807
    Description: 2T. Sorgente Sismica
    Description: JCR Journal
    Description: reserved
    Keywords: L’Aquila 2009 earthquake · Site effects · Onna · Seismic microzoning · Ground motion prediction equations ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Macroseismic effects highlight site response in Rome and its geological signature (2012)
    Springer
    Details
    Publication Date: 2023-06-05
    Description: A detailed analysis of the earthquake effects on the urban area of Rome has been conducted for the L’Aquila sequence, which occurred in April 2009, by using an on-line macroseismic questionnaire. Intensity residuals calculated using the mainshock and four aftershocks are analyzed in the light of a very accurate and original geological reconstruction of the subsoil of Rome based on a large amount of wells. The aim of this work is to highlight ground motion amplification areas and to find a correlation with the geological settings at a sub-regional scale, putting in evidence the extreme complexity of the phenomenon and the difficulty of making a simplified model. Correlations between amplification areas and both near-surface and deep geology were found. Moreover, the detailed scale of investigation has permitted us to find a correlation between seismic amplification in recent alluvial settings and subsiding zones, and between heard seismic sound and Tiber alluvial sediments.
    Description: Published
    Description: 425-443
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: open
    Keywords: Earthquakes ; Intensity residuals ; Urban geosciences ; Macroseismic effects ; Amplification areas ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion ; 04. Solid Earth::04.06. Seismology::04.06.11. Seismic risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Efficient motif search in ranked lists and applications to variable gap motifs (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-22
    Description: Sequence elements, at all levels—DNA, RNA and protein, play a central role in mediating molecular recognition and thereby molecular regulation and signaling. Studies that focus on measuring and investigating sequence-based recognition make use of statistical and computational tools, including approaches to searching sequence motifs. State-of-the-art motif searching tools are limited in their coverage and ability to address large motif spaces. We develop and present statistical and algorithmic approaches that take as input ranked lists of sequences and return significant motifs. The efficiency of our approach, based on suffix trees, allows searches over motif spaces that are not covered by existing tools. This includes searching variable gap motifs—two half sites with a flexible length gap in between—and searching long motifs over large alphabets. We used our approach to analyze several high-throughput measurement data sets and report some validation results as well as novel suggested motifs and motif refinements. We suggest a refinement of the known estrogen receptor 1 motif in humans, where we observe gaps other than three nucleotides that also serve as significant recognition sites, as well as a variable length motif related to potential tyrosine phosphorylation.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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    Inference of modules associated to eQTLs (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-22
    Description: Cataloging the association of transcripts to genetic variants in recent years holds the promise for functional dissection of regulatory structure of human transcription. Here, we present a novel approach, which aims at elucidating the joint relationships between transcripts and single-nucleotide polymorphisms (SNPs). This entails detection and analysis of modules of transcripts, each weakly associated to a single genetic variant, together exposing a high-confidence association signal between the module and this ‘main’ SNP. To explore how transcripts in a module are related to causative loci for that module, we represent such dependencies by a graphical model. We applied our method to the existing data on genetics of gene expression in the liver. The modules are significantly more, larger and denser than found in permuted data. Quantification of the confidence in a module as a likelihood score, allows us to detect transcripts that do not reach genome-wide significance level. Topological analysis of each module identifies novel insights regarding the flow of causality between the main SNP and transcripts. We observe similar annotations of modules from two sources of information: the enrichment of a module in gene subsets and locus annotation of the genetic variants. This and further phenotypic analysis provide a validation for our methodology.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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    Phase variable genes of Campylobacter jejuni exhibit high mutation rates and specific mutational patterns but mutability is not the major determinant of population structure during host colonization (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-22
    Description: Phase variation of surface structures occurs in diverse bacterial species due to stochastic, high frequency, reversible mutations. Multiple genes of Campylobacter jejuni are subject to phase variable gene expression due to mutations in polyC/G tracts. A modal length of nine repeats was detected for polyC/G tracts within C. jejuni genomes. Switching rates for these tracts were measured using chromosomally-located reporter constructs and high rates were observed for cj1139 (G8) and cj0031 (G9). Alteration of the cj1139 tract from G8 to G11 increased mutability 10-fold and changed the mutational pattern from predominantly insertions to mainly deletions. Using a multiplex PCR, major changes were detected in ‘on/off’ status for some phase variable genes during passage of C. jejuni in chickens. Utilization of observed switching rates in a stochastic, theoretical model of phase variation demonstrated links between mutability and genetic diversity but could not replicate observed population diversity. We propose that modal repeat numbers have evolved in C. jejuni genomes due to molecular drivers associated with the mutational patterns of these polyC/G repeats, rather than by selection for particular switching rates, and that factors other than mutational drift are responsible for generating genetic diversity during host colonization by this bacterial pathogen.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    eIF4E-binding protein regulation of mRNAs with differential 5'-UTR secondary structure: a polyelectrostatic model for a component of protein-mRNA interactions (2012)
    Oxford University Press
    Details
    Publication Date: 2012-09-13
    Description: Control of translation in eukaryotes is complex, depending on the binding of various factors to mRNAs. Available data for subsets of mRNAs that are translationally up- and down-regulated in yeast eIF4E-binding protein (4E-BP) deletion mutants are coupled with reported mRNA secondary structure measurements to investigate whether 5'-UTR secondary structure varies between the subsets. Genes with up-regulated translational efficiencies in the caf20 mutant have relatively high averaged 5'-UTR secondary structure. There is no apparent wide-scale correlation of RNA-binding protein preferences with the increased 5'-UTR secondary structure, leading us to speculate that the secondary structure itself may play a role in differential partitioning of mRNAs between eIF4E/4E-BP repression and eIF4E/eIF4G translation initiation. Both Caf20p and Eap1p contain stretches of positive charge in regions of predicted disorder. Such regions are also present in eIF4G and have been reported to associate with mRNA binding. The pattern of these segments, around the canonical eIF4E-binding motif, varies between each 4E-BP and eIF4G. Analysis of gene ontology shows that yeast proteins containing predicted disordered segments, with positive charge runs, are enriched for nucleic acid binding. We propose that the 4E-BPs act, in part, as differential, flexible, polyelectrostatic scaffolds for mRNAs.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Identification of activated cryptic 5' splice sites using structure profiles and odds measure (2012)
    Oxford University Press
    Details
    Publication Date: 2012-05-23
    Description: The activation of cryptic 5' splice sites (5' SSs) is often related to human hereditary diseases. The DNA-based mutation screening strategies are commonly used to recognize the cryptic 5' SSs, because features of the local DNA sequence can influence the choice of cryptic 5' SSs. To improve the identification of the cryptic 5' SSs, we developed a structure-based method, named SPO (structure profiles and odds measure), which combines two parameters, the structural feature derived from hydroxyl radical cleavage pattern and odds measure, to assess the likelihood of a cryptic 5' SS activation in competing with its paired authentic 5' SS. Compared to the current tools for identifying activated cryptic 5' SSs, the SPO algorithm achieves higher prediction accuracy than the other methods, including MaxEnt, MDD, Markov model, weight matrix model, Shapiro and Senapathy matrix, R i and G . In addition, the predicted SPO scores from the SPO algorithm exhibited a greater degree of correlation with the strength of cryptic 5' SS activation than that measured from the other seven methods. In conclusion, the SPO algorithm provides an optimal identification of cryptic 5' SSs, can be applied in designing mutagenesis experiments for various splicing events and may be helpful to investigate the relationship between structural variants and human hereditary diseases.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-10
    Description: The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about ‘legacy’ parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Automated 3D structure composition for large RNAs (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-08
    Description: Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Spacer-length dependence of programmed -1 or -2 ribosomal frameshifting on a U6A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting (2012)
    Oxford University Press
    Details
    Publication Date: 2012-09-27
    Description: Programmed –1 ribosomal frameshifting is employed in the expression of a number of viral and cellular genes. In this process, the ribosome slips backwards by a single nucleotide and continues translation of an overlapping reading frame, generating a fusion protein. Frameshifting signals comprise a heptanucleotide slippery sequence, where the ribosome changes frame, and a stimulatory RNA structure, a stem–loop or RNA pseudoknot. Antisense oligonucleotides annealed appropriately 3' of a slippery sequence have also shown activity in frameshifting, at least in vitro . Here we examined frameshifting at the U 6 A slippery sequence of the HIV gag/pol signal and found high levels of both –1 and –2 frameshifting with stem–loop, pseudoknot or antisense oligonucleotide stimulators. By examining –1 and –2 frameshifting outcomes on mRNAs with varying slippery sequence-stimulatory RNA spacing distances, we found that –2 frameshifting was optimal at a spacer length 1–2 nucleotides shorter than that optimal for –1 frameshifting with all stimulatory RNAs tested. We propose that the shorter spacer increases the tension on the mRNA such that when the tRNA detaches, it more readily enters the –2 frame on the U 6 A heptamer. We propose that mRNA tension is central to frameshifting, whether promoted by stem–loop, pseudoknot or antisense oligonucleotide stimulator.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Co-clustering phenome-genome for phenotype classification and disease gene discovery (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-24
    Description: Understanding the categorization of human diseases is critical for reliably identifying disease causal genes. Recently, genome-wide studies of abnormal chromosomal locations related to diseases have mapped 〉2000 phenotype–gene relations, which provide valuable information for classifying diseases and identifying candidate genes as drug targets. In this article, a regularized non-negative matrix tri-factorization (R-NMTF) algorithm is introduced to co-cluster phenotypes and genes, and simultaneously detect associations between the detected phenotype clusters and gene clusters. The R-NMTF algorithm factorizes the phenotype–gene association matrix under the prior knowledge from phenotype similarity network and protein–protein interaction network, supervised by the label information from known disease classes and biological pathways. In the experiments on disease phenotype–gene associations in OMIM and KEGG disease pathways, R-NMTF significantly improved the classification of disease phenotypes and disease pathway genes compared with support vector machines and Label Propagation in cross-validation on the annotated phenotypes and genes. The newly predicted phenotypes in each disease class are highly consistent with human phenotype ontology annotations. The roles of the new member genes in the disease pathways are examined and validated in the protein–protein interaction subnetworks. Extensive literature review also confirmed many new members of the disease classes and pathways as well as the predicted associations between disease phenotype classes and pathways.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
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    A global sampling approach to designing and reengineering RNA secondary structures (2012)
    Oxford University Press
    Details
    Publication Date: 2012-11-04
    Description: The development of algorithms for designing artificial RNA sequences that fold into specific secondary structures has many potential biomedical and synthetic biology applications. To date, this problem remains computationally difficult, and current strategies to address it resort to heuristics and stochastic search techniques. The most popular methods consist of two steps: First a random seed sequence is generated; next, this seed is progressively modified (i.e. mutated) to adopt the desired folding properties. Although computationally inexpensive, this approach raises several questions such as (i) the influence of the seed; and (ii) the efficiency of single-path directed searches that may be affected by energy barriers in the mutational landscape. In this article, we present RNA-ensign , a novel paradigm for RNA design. Instead of taking a progressive adaptive walk driven by local search criteria, we use an efficient global sampling algorithm to examine large regions of the mutational landscape under structural and thermodynamical constraints until a solution is found. When considering the influence of the seeds and the target secondary structures, our results show that, compared to single-path directed searches, our approach is more robust, succeeds more often and generates more thermodynamically stable sequences. An ensemble approach to RNA design is thus well worth pursuing as a complement to existing approaches. RNA-ensign is available at http://csb.cs.mcgill.ca/RNAensign .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Functional impact bias reveals cancer drivers (2012)
    Oxford University Press
    Details
    Publication Date: 2012-11-25
    Description: Identifying cancer driver genes and pathways among all somatic mutations detected in a cohort of tumors is a key challenge in cancer genomics. Traditionally, this is done by prioritizing genes according to the recurrence of alterations that they bear. However, this approach has some known limitations, such as the difficulty to correctly estimate the background mutation rate, and the fact that it cannot identify lowly recurrently mutated driver genes. Here we present a novel approach, Oncodrive-fm, to detect candidate cancer drivers which does not rely on recurrence. First, we hypothesized that any bias toward the accumulation of variants with high functional impact observed in a gene or group of genes may be an indication of positive selection and can thus be used to detect candidate driver genes or gene modules. Next, we developed a method to measure this bias (FM bias) and applied it to three datasets of tumor somatic variants. As a proof of concept of our hypothesis we show that most of the highly recurrent and well-known cancer genes exhibit a clear FM bias. Moreover, this novel approach avoids some known limitations of recurrence-based approaches, and can successfully identify lowly recurrent candidate cancer drivers.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    The ITalian ACcelerometric Archive (ITACA): processing of strong-motion data (2011)
    Springer
    Details
    Publication Date: 2012-02-03
    Description: The Italian strong-motion database was created during a joint project between Istituto Nazionale di Geofisica e Vulcanologia (INGV, Italian Institute for Geophysics and Vulcanology) and Dipartimento della Protezione Civile (DPC, Italian Civil Protection). The aim of the project was the collection, homogenization and distribution of strong motion data acquired in Italy in the period 1972–2004 by different institutions, namely Ente Nazionale per l’Energia Elettrica (ENEL, Italian electricity company), Ente per le Nuove tecnologie, l’Energia e l’Ambiente (ENEA, Italian energy and environment organization) and DPC. Recently the strong-motion data relative to the 23th December 2009, Parma (Mw = 5.4 and Mw = 4.9) and to the April 2009 L’Aquila sequences (13 earthquakes with 4.1 ≤ Mw ≤ 6.3) were included in the Italian Accelerometric Archive (ITACA) database (beta release). The database contains 7,038 waveforms from analog and digital instruments, generated by 1.019 earthquakes with magnitude up to 6.9 and can be accessed on-line at the web site http://itaca. mi.ingv.it. The strong motion data are provided in the unprocessed and processed versions. This article describes the steps followed to process the acceleration time series recorded by analogue and digital instruments. The procedures implemented involve: baseline removal, instrumental correction, band pass filtering with acausal filters, integration of the corrected acceleration in order to obtain velocity and displacement waveforms, computation of accel- eration response spectra and strong motion parameters. This procedure is applied to each accelerogram and it is realised to preserve the low frequency content of the records.
    Description: Published
    Description: 1175-1187
    Description: 5.2. TTC - Banche dati di sismologia strumentale
    Description: JCR Journal
    Description: open
    Keywords: Strong motion ; processing ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Italian strong motion database relative to the period 1972–2004: motivations and aims (2011)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: The Italian Accelerometic Archive (ITACA) was created in 2007 during a joint project between the Italian Institute for Geophysics and Vulcanology (Istituto Nazionale di Geofisica e Vulcanologia, INGV) and the Italian Civil Protection (Dipartimento della Protezione Civile, DPC). The project, started in 2006, had the aim of filling the data gap of existing strong motion databases and facilitating strong motion data users in obtaining good quality waveforms, through the collection, homogenization and distribution of strong motion data acquired during the period 1972–2004 in Italy by different institutions (Ente Nazionale per l’Energia Elettrica, ENEL, Italian electricity company; Ente per le Nuove tecnologie, l’Energia e l’Ambiente, ENEA, Italian energy and environment organizationDPC). The compiled database contains 2,182 three-component waveforms generated by 1,008 earthquakes with a maximum moment magnitude of 6.9 (1980 Irpinia earthquake) and can be accessed on-line at the portal denominated ITACAat the site http://itaca.mi.ingv.it,where a wide range of search tools enables the user to interactively retrieve events, recording stations and waveforms with particular characteristics, whose parameters can be specified, as needed, through user friendly interfaces. A range of display options allows users to view data in different contexts, extract and download time series and spectral data. This article describes the state of the art up to 2006 and the activities which led to the completion of the project.
    Description: Published
    Description: 1159-1174
    Description: 5.2. TTC - Banche dati di sismologia strumentale
    Description: JCR Journal
    Description: open
    Keywords: strong motion ; database ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 38
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    Strong-Motion Networks in Italy and Their Efficient Use in the Derivation of Regional and Global Predictive Models (2011)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: Italy is a country characterized by high seismic hazard so strong-motion monitoring represents a relevant issue. Several strong-motion networks have been installed in the Italian territory during the last decades, with the aim of recording the ground motion generated by moderate to strong events or to monitor single regions. The collection of the strong-motion recordings of the Italian earthquakes was recently fulfilled and data are distributed through the ITACA database (http://itaca.mi.ingv.it). The new data set was used to develop a set of ground motion prediction equations (hereinafter GMPEs) for the Italian territory (Bindi et al., 2009), in order to update the well known GMPEs developed by Sabetta and Pugliese. The recent Mw 6.3 earthquake that occurred in central Italy on April 2009 and the upgrades of the ITACA database gave us the possibility to validate the predictive capability of the newly developed GMPEs and to explore the regional variability inside the Italian territory.
    Description: Published
    Description: 53-70
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: reserved
    Keywords: strong motion data ; Prediction equation ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 39
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    Evaluation of site effects in the Aterno river valley (Central Italy) from aftershocks of the 2009 L'Aquila earthquake (2011)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: A temporary network of 33 seismic stations was deployed in the area struck by the 6th April 2009, Mw 6.3, L’Aquila earthquake (central Italy), with the aim to investigate the site amplification within the Aterno river Valley. The seismograms of 18 earthquakes recorded by 14 of the 33 stations were used to evaluate the average horizontal to vertical spectral ratio (HVSR) for each site and the standard horizontal spectral ratio (SSR) between a site and a reference station. The obtained results have been compared to the geological and geophysical information in order to explain the resonance frequencies and the amplification levels with respect to surface geology of the valley. The result indicate that there is no uniform pattern of amplification, due to the complex geologic setting, as the thickness and degree of cementation of the deposits is highly variable. As consequence, a large number of the local site response is observed, therefore it is very difficult to elaborate a unique model that can explain such a variability of the amplification.
    Description: Published
    Description: 697-715
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: partially_open
    Keywords: l'Aquila earthquake ; microzoning ; ground shaking ; site effects ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 40
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    Site effects “on the rock”: the case of Castelvecchio Subequo (L’Aquila, central Italy) (2011)
    Springer
    Details
    Publication Date: 2022-05-24
    Description: The April 6, 2009 L’Aquila earthquake was responsible for an “anomalous”, relatively high degree of damage (i.e. Is 7 MCS scale) at Castelvecchio Subequo (CS). Indeed, the village is located at source-to-site distance of about 40 km, and it is surrounded by other inhabited centres to which considerably lower intensities, i.e. Is 5-6, have been attributed. Moreover, the damage was irregularly distributed within CS, being mainly concentrated in the uppermost portion of the old village. Geophysical investigations (ambient seismic noise and weak ground motions analyses) revealed that site effects occurred at CS. Amplifications of the ground motion, mainly striking NE-SW, have been detected at the uppermost portion of the carbonate ridge on which the village is built. Geological/structural and geomechanical field surveys defined that the CS ridge is affected by sets of fractures, joints and shear planes – mainly roughly NW-SE and N-S trending – that are related to the deformation zone of the Subequana valley fault system and to transfer faults linking northward the mentioned tectonic feature with the Middle Aterno Valley fault system. In particular, our investigations highlight that seismic amplifications occur where joints set NW-SE trending are open. On the other hand, no amplification is seen in portions of the ridge where the bedrock is densely fractured but no open joints occur. The fracture opening seems related to the toppling tendency of the bedrock slabs, owing to the local geomorphic setting. These investigations suggest that the detected amplification of the ground motion is probably related to the polarization of the seismic waves along the Castelvecchio Subequo ridge, with the consequent oscillation of the rock slabs perpendicularly to the fractures azimuth.
    Description: Published
    Description: 841-868
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: open
    Keywords: Site effects ; Rock site ; Ambient seismic noise ; Structural characteristics ; Geomechanical analyses ; Jointing ; Castelvecchio Subequo ; 2009 L'Aquila earthquake ; central Italy ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 41
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    Suboceanic Rayleigh Waves in the 1755 Lisbon Earthquake (2010)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: Moderate-magnitude shallow earthquakes in the Atlantic Ocean, hundreds of kilometres southwest of Lisbon, can generate efficient suboceanic Rayleigh waves (SRW) that are well recorded in Portugal. Here we compare moderate-size earthquakes recorded by seismic stations in Portugal with the Tyrrhenian Sea earthquakes recorded in peninsular Italy where SRW were recently observed. In spite of a different behaviour of high frequencies due to the different tectonic setting of the two areas, similar results are found in the intermediate-period range, suggesting that this effect, if extrapolated to a magnitude larger than 8, could be devastating at regional distance in terms of ground motion amplitude and duration. Through 1D models, we explore the hypothesis that the high level of destruction and the long duration of shaking felt during the Great 1755 Lisbon earthquake were caused by SRW. In this preliminary study, we check the role of critical model parameters. We find that duration and amplitude are largest when the average thickness of the water layer is 2 km and shear-wave velocity of the ocean floor is close to the speed of sound in the water. Both conditions are realistic for a source in the Atlantic Ocean, few hundreds of kilometres southwest of Lisbon. Moreover, the propagation of SRW at regional distances accounts for durations of more than ten minutes as the effect of a single large earthquake.
    Description: Published
    Description: 283-295
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: open
    Keywords: ground motion ; surface waves ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 42
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    The role of alternating outcrops of sediments and basaltic lavas on seismic urban scenario: the study case of Catania, Italy (2010)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: Experimental data and numerical modelling were used to study the effect of local geology on the seismic response of the Catania area. The town extends on a marly clays bedrock and terraced deposits made up by coastal sands and alluvial conglomerates. This sedimentary substratum is deeply entrenched by paleo-valleys filled by lava flows and pyroclastics. Available borehole data and elastic parameters were used to reconstruct a geotechnical model in order to perfome 1D numerical modeling. Seismic urban scenarios were simulated considering destructive (Mw = 7.0), strong (Mw = 6.2) and moderate (Mw = 5.7) earthquakes to assess the shaking level of the different outcropping formations. For each scenario seven real accelerograms were selected from the European Strong Motion Database to assess the expected seismic input at the bedrock. PGA and spectral acceleration at different periods were obtained in the urban area through the equivalent linear numerical code EERA, and contour maps of different levels of shaking were drawn. Standard and horizontal-to-vertical spectral ratios were achieved making use of a dataset of 172 seismic events recorded at ten sites located on the main outcropping lithotypes. Spectral ratios inferred from earthquake data were compared with theoretical transfer functions. Both experimental and numerical results confirm the role of the geological and morphologic setting of Catania. Amplification of seismic motion mainly occurs in three different stratigraphic conditions: (a) sedimentary deposits mainly diffused in the south of the study area; (b) spots of soft sediments surrounded by lava flows; (c) intensely fractured and scoriaceous basaltic lavas.
    Description: In press
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: restricted
    Keywords: Scenario earthquake ; 1D modelling ; PGA values ; Earthquake records ; spectral ratios ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring ; 04. Solid Earth::04.06. Seismology::04.06.09. Waves and wave analysis
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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