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  • Public Library of Science (PLoS)
  • Wiley-Blackwell
  • 2010-2014  (5,202)
  • 2012  (5,202)
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  • 2010-2014  (5,202)
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  • 1
    Publication Date: 2021-01-07
    Description: The elemental fluxes and heat flow associated with large aquifer systems can be significant both at local and at regional scales. In fact, large amounts of heat transported by regional groundwater flow can affect the subsurface thermal regime, and the amount of matter discharged towards the surface by large spring systems can be significant relative to the elemental fluxes of surface waters. The Narni-Amelia regional aquifer system (Central Italy) discharges more than 13 m3 sec)1 of groundwater characterised by a slight thermal anomaly, high salinity and high pCO2. During circulation in the regional aquifer, groundwater reacts with the host rocks (dolostones, limestones and evaporites) and mixes with deep CO2-rich fluids of mantle origin. These processes transfer large amounts of dissolved substances, in particular carbon dioxide, and a considerable amount of heat towards the surface. Because practically all the water circulating in the Narni-Amelia system is discharged by few large springs (Stifone-Montoro), the mass and energy balance of these springs can give a good estimation of the mass and heat transported from the entire system towards the surface. By means of a detailed mass and balance of the aquifer and considering the soil CO2 fluxes measured from the main gas emission of the region, we computed a total CO2 discharge of about 7.8 · 109 mol a)1 for the whole Narni-Amelia system. Finally, considering the enthalpy difference between infiltrating water and water discharged by the springs, we computed an advective heat transfer related to groundwater flow of 410 ± 50 MW.
    Description: Published
    Description: 182-196
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: 4.5. Studi sul degassamento naturale e sui gas petroliferi
    Description: JCR Journal
    Description: reserved
    Keywords: carbon dioxide degassing ; heat flow ; regional aquifer ; 04. Solid Earth::04.02. Exploration geophysics::04.02.01. Geochemical exploration ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
    Publication Date: 2020-12-14
    Description: We study the implications of a recently published mass balance of the Greenland ice sheet (GrIS), derived from repeated surface elevation measurements from NASA’s ice cloud and land elevation satellite (ICESat) for the time period between 2003 and 2008. To characterize the effects of this new, high-resolution GrIS mass balance, we study the time-variations of various geophysical quantities in response to the current mass loss. They include vertical uplift and subsidence, geoid height variations, global patterns of sea level change (or fingerprints), and regional sea level variations along the coasts of Greenland. Long-wavelength uplifts and gravity variations in response to current or past ice thickness variations are obtained solving the sea level equation, which accounts for both the elastic and the viscoelastic components of deformation. To capture the short-wavelength components of vertical uplift in response to current ice mass loss, which is not resolved by satellite gravity observations, we have specifically developed a high-resolution regional elastic rebound (ER) model. The elastic component of vertical uplift is combined with estimates of the viscoelastic displacement fields associated with the process of glacial-isostatic adjustment (GIA), according to a set of published ice chronologies and associated mantle rheological profiles. We compare the sensitivity of global positioning system (GPS) observations along the coasts of Greenland to the ongoing ER and GIA. In notable contrast with past reports, we show that vertical velocities obtained by GPS data from five stations with sufficiently long records and from one tide gauge at the GrIS margins can be reconciled with model predictions based on the ICE-5G deglaciation model and the ER associated with the new ICESat-derived mass balance.
    Description: Published
    Description: 1457-1474
    Description: 3.3. Geodinamica e struttura dell'interno della Terra
    Description: JCR Journal
    Description: restricted
    Keywords: Sea level change ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
    Publication Date: 2021-06-22
    Description: The building materials of the Theatre of Marcellus, 44–11 BCE, reflect Roman builders’ careful selections of tuff and travertine for dimension stone and volcanic aggregates for pozzolanic concretes. The vitric–lithic–crystal Tufo Lionato tuff dimension stone contains a high proportion of lava lithic fragments, which increase its compressive strength and decrease water sorption, enhancing durability. Sophisticated installations of travertine dimension stone reinforce the tuff masonry, which is integrated with durable concrete walls and barrel vaults. The pozzolanic mortars of the concretes contain harenae fossiciae mainly from the intermediate alteration facies of the mid-Pleistocene, scoriaceous Pozzolane Rosse pyroclastic flow. They have pervasive interpenetrating pozzolanic cements, including strätlingite, similar to highquality, imperial era mortars. Concrete walls are faced with refined Tufo Lionato opus reticulatum and tufelli, and opus testaceum of fired, greyish-yellow brick. The exploratory concrete masonry, which includes some of the earliest examples of brick facings and strätlingite cements in Rome, and the integration of these materials in complex architectural elements and internal spaces, reflect the highly skilled workmanship, rigorous work-site management and technical supervision of Roman builders trained in republican era methods and materials.
    Description: Published
    Description: 728–742
    Description: JCR Journal
    Description: restricted
    Keywords: VOLCANIC TUFF MASONRY ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
    Publication Date: 2017-04-04
    Description: We propose a method to introduce a refined representation of the ground motion in the framework of the Probabilistic Seismic Hazard Analysis (PSHA). This study is especially oriented to the incorporation of a priori information about source parameters, by focusing on the directivity effect and its influence on seismic hazard maps. Two strategies have been followed. One considers the seismic source as an extended source, and it is valid when the PSHA seismogenetic sources are represented as fault segments. We show that the incorporation of variables related to the directivity effect can lead to variations up to 30% of the hazard level, in terms of spectral acceleration response at 5 sec., exceeding probability of 10% in 50 years. The second one concerns the more general problem of the seismogenetic areas, where each point is a seismogenetic source having the same chance of enucleate a seismic event. In our proposition the point source is associated to the rupture-related parameters, defined using a statistical description. As an example, we consider a source point of an area characterized by strike slip faulting style. With the introduction of the directivity correction the modulation of the hazard map reaches values up to 100%. The introduction of directivity does not increase uniformly the hazard level, but acts more like a redistribution of the estimation that is consistent with the fault orientation. A general increase appears only when no a-priori information is available. However, nowadays good a-priori knowledge exists on style of faulting, dip and orientation of faults associated to the majority of the seismogenetic zones of the present seismic hazard maps. Following this method, all the information collected may be easily converted to obtain a more comprehensive and meaningful probabilistic Seismic Hazard formulation.
    Description: Published
    Description: 616-626
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: reserved
    Keywords: Earthquake ground motion ; Earthquake source observation ; Probabilistic Seismic Hazard ; 04. Solid Earth::04.06. Seismology::04.06.11. Seismic risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
    Publication Date: 2017-04-04
    Description: The occurrence of crystallized and glassy melt inclusions (MI) in high-grade, partially melted metapelites and metagraywackes has opened up new possibilities to investigate anatectic processes. The present study focuses on three case studies: khondalites from the Kerala Khondalite Belt (India), the Ronda migmatites (Spain), and the Barun Gneiss (Nepal Himalaya). The results of a detailed microstructural investigation are reported, along with some new microchemical data on the bulk composition of MI. These inclusions were trapped within peritectic garnet and ilmenite during crystal growth and are therefore primary inclusions. They are generally isometric and very small in size, mostly £15 lm, and only rarely reaching 30 lm; they occur in clusters. In most cases inclusions are crystallized ( nanogranites ) and contain a granitic phase assemblage with quartz, feldspar and one or two mica depending on the particular case study, commonly with accessory phases (mainly zircon, apatite, rutile). In many cases the polycrystalline aggregates that make up the nanogranites show igneous microstructures, e.g. granophyric intergrowths, micrographic quartz in K-feldspar and cuneiform rods of quartz in plagioclase. Further evidence for the former presence of melt within the investigated inclusions consists of melt pseudomorphs, similar to those recognized at larger scale in the host migmatites. Moreover, partially crystallized inclusions are locally abundant and together with very small (£8 lm) glassy inclusions may occur in the same clusters. Both crystallized and partially crystallized inclusions often display a diffuse nanoporosity, which may contain fluids, depending on the case study. After entrapment, inclusions underwent limited microstructural modifications, such as shape maturation, local necking down processes, and decrepitation (mainly in the Barun Gneiss), which did not influence their bulk composition. Re-homogenized nanogranites and glassy inclusions show a leucogranitic and peraluminous composition, consistent with the results of partial melting experiments on metapelites and metagraywackes. Anatectic MI should therefore be considered as a new and important opportunity to understand the partial melting processes.
    Description: Published
    Description: 303-322
    Description: 3.5. Geologia e storia dei vulcani ed evoluzione dei magmi
    Description: JCR Journal
    Description: restricted
    Keywords: garnet ; melt inclusions ; melt microstructures ; migmatites ; nanogranite ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
    Publication Date: 2017-04-03
    Description: Campi Flegrei collapse caldera (Italy) is a high-risk volcanic area located close to Naples and includes part of the densely populated city. This area is characterised by large up and down ground displacements. The last large uplift episode caused 3.5 m of cumulative vertical displacement at the centre of the town of Pozzuoli, during the period 1969–1984. Up and down ground movements in this area often occur without intercurring eruptions and are similar to what is observed at other calderas worldwide. Here, however, they appear more evident and amplified. Understanding the mechanism of such movements is crucial for hazard assessment and eruption forecast, mainly due to this densely populated area. This paper presents a detailed model for ground displacements due to deep fluid injection in shallower layers. Such a model explains in a natural way the occurrence of uplift and subsidence without eruptions. We show that it is possible to fit observed ground deformation in this area with a thermofluid dynamical model. The model obtained is also consistent with other observations like microgravity changes, changes in CO2 flux, etc. Here, we suggest that significant uplift and subsidence at calderas can be due to effects of deep fluid injections other than magma. At Campi Flegrei, however, a partial magmatic contribution at the origin of the observed episodes cannot be excluded.
    Description: Published
    Description: 833–847
    Description: JCR Journal
    Description: restricted
    Keywords: Numerical approximations and analysis; Hydrothermal systems; Explosive volcanism; Calderas ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 7
    Publication Date: 2017-04-04
    Description: Two direct search methods, simulated annealing and neighbourhood algorithm, are applied to the inversion of the viscosity profile of the mantle using relative sea level time-histories for the Hudson Bay region. In problems characterized by a low-dimensional model space (Nd = 2 in this study), the two inversion methods show comparable performances. When a larger number of dimensions is involved (specifically Nd = 6), we directly show that simulated annealing is less effective than neighbourhood algorithm in overcoming the obstacles that are found in the model space when our specific data set is employed. This study confirms that modifications of the conventional Monte Carlo inversion method, such as simulated annealing and neighbourhood algorithm, are viable tools to determine the viscosity profile of the mantle, which, until recently, has been mainly tackled by means of linearized techniques.
    Description: Published
    Description: 890-900
    Description: 3.3. Geodinamica e struttura dell'interno della Terra
    Description: JCR Journal
    Description: restricted
    Keywords: mantle viscosity ; simulated annealing ; neighbourhood algorithm ; postglacial rebound ; 04. Solid Earth::04.01. Earth Interior::04.01.03. Mantle and Core dynamics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
    Publication Date: 2017-04-03
    Description: In the first part of this work, we make use of two non-parametric statistical pattern recognition algorithms and a multiple regression analysis to analyse seismic clusters occur ring around Mount Etna, Italy. The aim is to determine if the onset of flank eruptions at Mount Etna is linked to variations in the regional seismicity at a timescale of few weeks. From the analysis, we find that the discrimination between clusters preceding flank eruptions and clusters not related in time to flank activity is mainly linked to the volume output of the previous flank eruption, in some cases together with the time elapsed from its end. Instead, we do not find any difference in the seismicity features characterizing different types of clusters, except for a very small contribution of the number of seismic events in the clusters. This result does not confirm the existence, suggested in the past, of a direct link between the regional state of stress at a timescale of few weeks and the occurrence of flank eruptions on Mount Etna volcano. On the contrary, the result suggests that a prominent role in the flank eruption occur rence is played by the re-charging of the feeding system. In the second part of this study we analyse the relationship between the magma volume erupted in an eruption and the interevent time following it, finding that a ‘time-predictable model’ satisfactorily describes the occurrence of eruptions at Mount Etna in the last decades. The latter analysis is car ried out both on the flank eruption catalogue only, and on the complete catalogue of flank and summit eruptions, with comparable results.
    Description: Published
    Description: 1203–1218
    Description: JCR Journal
    Description: restricted
    Keywords: flank eruptions ; Mount Etna volcano ; regional tectonic stress ; statistical pattern recognition ; time predictability ; 05. General::05.01. Computational geophysics::05.01.04. Statistical analysis
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
    Publication Date: 2017-04-03
    Description: In this paper, we present a significant update of the Italian present-day stress data compilation not only to improve the knowledge on the tectonic setting of the region or to constrain future geodynamic models, but also to understand the mechanics of processes linked to faulting and earthquakes. In this paper, we have analysed, revised and collected new contemporary stress data from borehole breakouts and we have assembled earthquake and fault data. In total, 206 new quality-ranked entries complete the definition of the horizontal stress orientation and tectonic regime in some areas, and bring new information mainly in Sicily and along the Apenninic belt. Now the global Italian data set consists of 715 data points, including 499 of A–C quality, representing an increase of 37 per cent compared to the previous compilation. The alignment of horizontal stresses measured in some regions, closely matches the ∼N–S first- order stress field orientation of ongoing relative crustal motions between Eurasia and Africa plates. The Apenninic belt shows a diffuse extensional stress regime indicating a ∼NE–SW direction of extension, that we interpret as related to a second-order stress field. The horizontal stress rotations observed in peculiar areas reflect a complex interaction between first-order stress field and local effects revealing the importance of the tectonic structure orientations. In particular, in Sicily the new data delineate a more complete tectonic picture evidencing adjacent areas characterized by distinct stress regime: northern offshore of Sicily and in the Hyblean plateau the alignment of horizontal stresses is consistent with the crustal motions, whereas different directions have been observed along the belt and foredeep.
    Description: Published
    Description: 705–716
    Description: 3.2. Tettonica attiva
    Description: JCR Journal
    Description: restricted
    Keywords: Downhole methods; Seismicity and tectonics; Crustal structure; Europe. ; borehole breakouts, earthquakes, faults ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress
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  • 10
    Publication Date: 2017-04-04
    Description: In this study, we investigate the rupture history of the April 6th 2009 (Mw 6.1) L’Aquila normal faulting earthquake by using a nonlinear inversion of strong motion, GPS and DInSAR data. Both the separate and joint inversion solutions reveal a complex rupture process and a heterogeneous slip distribution. Slip is concentrated in two main asperities: a smaller shallow patch of slip located up-dip from the hypocenter and a second deeper and larger asperity located southeastward along strike direction. The key feature of the source process emerging from our inverted models concerns the rupture history, which is characterized by two distinct stages. The first stage begins with rupture nucleation and with up-dip propagation at relatively high (∼ 4.0 km/s), but still sub-shear, rupture velocity. The second stage starts nearly 2.0÷2.5 seconds after nucleation and it is characterized by the along strike rupture propagation. The largest and deeper asperity fails during this stage of the rupture process. The rupture velocity is larger in the up-dip than in the along-strike direction. The up-dip and along-strike rupture propagation are separated in time and associated with a Mode II and a Mode III crack, respectively. The comparison between the source models inferred in this study with the Poisson ratio anomalies in the crustal volume containing the fault plane (Di Stefano et al., 2011) allows the interpretation of the delay in along-strike rupture propagation in terms of a structural control of the rupture history. Our results show that the L’Aquila earthquake featured a very complex rupture, with strong spatial and temporal heterogeneities suggesting a strong frictional and/or structural control of the rupture process.
    Description: Published
    Description: 607-621
    Description: 3.1. Fisica dei terremoti
    Description: JCR Journal
    Description: restricted
    Keywords: Inverse theory;Earthquake dynamics;Earthquake ground motions;Earthquake source observations;Body waves;Rheology and friction of fault zones ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 11
    Publication Date: 2017-04-04
    Description: We investigate shear wave polarization in the Hayward fault zone near Niles Canyon, Fremont, CA. Waveforms of 12 earthquakes recorded by a seven-accelerometer seismic array around the fault are analysed to clarify directional site effects in the fault damage zone. The analysis is performed in the frequency domain through H/V spectral ratios with horizontal components rotated from 0◦ to 180◦, and in the time domain using the eigenvectors and eigenvalues of the covariance matrix method employing three component records. The near-fault ground motion tends to be polarized in the horizontal plane. At two on-fault stations where the local strike is N160◦, ground motion polarization is oriented N88 ± 19◦ and N83 ± 32◦, respectively. At a third on-fault station, the motion is more complex with horizontal polarization varying in different frequency bands. However, a polarization of N86 ± 7◦, similar to the results at the other two on-fault stations, is found in the frequency band 6–8 Hz. The predominantly high-angle polarization from the fault strike at the Hayward Fault is consistent with similar results at the Parkfield section of the San Andreas Fault and the Val d’Agri area (a Quaternary extensional basin) in Italy. In all these cases, comparisons of the observed polarization directions with models of fracture orientation based on the fault movement indicate that the dominant horizontal polarization is near-orthogonal to the orientation of the expected predominant cracking direction. The results help to develop improved connections between fault mechanics and near-fault ground motion.
    Description: Published
    Description: 1255–1272
    Description: JCR Journal
    Description: open
    Keywords: Earthquake ground motions. ; Interface waves ; Site effects ; 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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  • 12
    Publication Date: 2017-04-04
    Description: We present the results of a multi-temporal, differential interferometric synthetic aperture radar (DInSAR) analysis aiming to identify active surface deformation phenomena in southeastern Sicily. The study area has been chosen because of its strong seismicity, high concentration of industrial and agricultural activities, and high density of people living in the coastal area. Furthermore, the morphology, lithology and climatic feature of this sector of the Hyblean foreland are suitable for an interferometric analysis, providing a high coherence over the area. We used the Small BAseline Subset (SBAS) multitemporal DInSAR technique from Berardino et al., 2002, to calculate mean ground velocity maps and displacement time series from a large data set of European Remote Sensing Satellites (ERS 1-2) images spanning the time period 1992-2000. The reliability of the DInSAR results was tested calculating the EastSAR and UpSAR values over two permanent global positioning system (GPS) stations in the area, and comparing them with the EastGPS and UpGPS values. The residuals between GPS and DInSAR velocities were 1 and 0.6 mm/yr for the Up and East components, respectively. Four main subsiding areas, previously undetected, have been identified, in correspondence of the towns of Augusta, Siracusa, Priolo, and Villasmundo. The observed deformation phenomena are located within coastal structural basins, filled with Pleistocene and Holocence deposits, except the Villasmundo land subsidence which is located on the Hyblean plateau. The measured deformation rates reach values up to -18 mm/yr in Augusta, -6 mm/yr in Siracusa, -5 mm/yr in Villasmundo and -4.5 mm/yr in Priolo. The examination of velocity profiles, time series, and geological data allows us to relate all the detected deformation patterns primarily to groundwater over-exploitation. A multi-dimensional interpolation with kriging was performed to obtain a field subsidence map. A first order elastic deformation model was used to simulate the peculiar features of the Villasmundo subsidence
    Description: ASI-SIGRIS project. ESA Cat1 3769. MIUR Fondo per il sostegno dei giovani.
    Description: Published
    Description: 273-286
    Description: 1.10. TTC - Telerilevamento
    Description: JCR Journal
    Description: partially_open
    Keywords: subsidence ; InSAR ; 05. General::05.08. Risk::05.08.02. Hydrogeological risk
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  • 13
    Publication Date: 2017-04-04
    Description: We have analysed the history of seismic activity in the region of L'Aquila to compare the 2009 sequence with previous ones. Historical catalogues are exhaustive for large shocks, but not for small earthquakes and swarms. Our original compilation highlights repeated seismic sequences from 1315 ad to present. In the 20th century, at least 23 sequences affected the Abruzzi region, 8 of which were very close to L'Aquila. In previous centuries, we found evidence of at least 13 sequences around L'Aquila, with maximum magnitude ∼4 to ∼5. Only three sequences were followed by stronger shocks (1461, 1703 and 2009). However, many strong events of the region (1349, 1762, 1915, 1950) were not preceded by foreshocks. We describe here the last of these sequences (1985) showing its strong similarity with the 2009 one, except its final evolution (no large event in 1985). Our analysis suggests that seismic sequences alone cannot be considered straight forerunners of incoming strong events.
    Description: Published
    Description: 52–61
    Description: 3.1. Fisica dei terremoti
    Description: JCR Journal
    Description: reserved
    Keywords: L’Aquila earthquake ; 04. Solid Earth::04.06. Seismology::04.06.01. Earthquake faults: properties and evolution
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  • 14
    Publication Date: 2017-04-04
    Description: An improved method based on equilibrium partitioning between water samples and an inert host gas, introduced after sampling, is proposed for determining multiple species of dissolved gases in brackish water. The method itself, and the most convenient equations for describing gas solubilities in brackish waters, is described in detail. The method allows the rapid characterization of several sites and represents a useful tool for geochemical surveys. A comparison between replicate samples analyzed using different procedures demonstrates the efficiency of the method and indicates that the abundances of the main dissolved gases can be obtained, which can then be used to determine underlying geochemical processes. A Microsoft Excel worksheet is provided to easily calculate the concentration of dissolved gas species.
    Description: Published
    Description: 236-244
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: JCR Journal
    Description: restricted
    Keywords: brackish thermal waters ; dissolved gases ; 03. Hydrosphere::03.03. Physical::03.03.01. Air/water/earth interactions
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  • 15
    Publication Date: 2017-04-04
    Description: The present-day sea level variations and geodetically observed ground deformations in the Mediterranean area are normally ascribed to the combined effect of tectonic or human-driven subsidence and postglacial uplift as a result of the melting of the major Pleistocene ice sheets. However, another potential cause of deformation, only marginally considered to date, is the melting of the glacier that covered the Alps during the last glacial maximum (LGM). The aim of this paper is to predict the long-term sea level variations induced by the melting of both the late-Pleistocene and Alpine ice sheets and compare our results with the relative sea level (RSL) observations available in the Mediterranean region. This task is accomplished solving the sea level equation (SLE) for a spherically symmetric viscoelastic Earth. Our analysis shows that the melting of the Alpine glacier has marginally affected the Holocene sea level variations in the near-field sites in southern France (Marseilles and Roussillon) and the central Tyrrhenian sea (Civitavecchia), and that the RSL predictions are significantly sensitive to the chronology of the remote ice aggregates. The computations, which are performed using a specific mantle viscosity profile consistent with global observations of RSL rise, show that the uplift rate driven by the Alpine isostatic readjustment may account for up to 1/3 of the rates observed at GPS stations in the western portion of the chain. Our results suggest that a thorough modelization of both near- and far-field ice sheets is necessary to gain a better insight into the present-day deformations and sea level variations in the Mediterranean region.
    Description: Published
    Description: 137-147
    Description: 3.3. Geodinamica e struttura dell'interno della Terra
    Description: JCR Journal
    Description: restricted
    Keywords: Alpine glacier ; glacial rebound ; mantle viscosity ; sea level variations ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics
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  • 16
    Publication Date: 2017-04-04
    Description: Although characterized by low seismicity, the Monferrato area of north-western Italy was affected by earthquakes, of magnitude M5.1 and M4.8, in 2000 and 2001. At the same time, marked changes were recorded in water temperature and chemistry in several wells within the epicentral area. In May 2004, an automatic network for the continuous monitoring of groundwater was installed in selected wells to study the phenomenon. Here, we report on data collected during a 3-year period of groundwater monitoring. During the first year, episodes of water heating (by up to 20°C) were observed in one monitored well. The temporal analysis of the seismic activity recorded in the area revealed as almost all seismic events occurred during the period of elevated water temperatures. The similar timing of earthquakes and groundwater-temperature anomalies suggests that both may be triggered by the same processes acting in the crust.
    Description: Published
    Description: 142-149
    Description: JCR Journal
    Description: reserved
    Keywords: groundwater monitoring ; pore fluid pressure; ; tectonic stress ; 03. Hydrosphere::03.02. Hydrology::03.02.02. Hydrological processes: interaction, transport, dynamics ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring
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  • 17
    Publication Date: 2020-02-24
    Description: Integration of geologic, geomorphologic and seismologic data sets is used to reconstruct the recent tectonic evolution and active deformation pattern in the Val d’Agri area, located in the seismically active axial sector of the Southern Apennines (Italy). The western portion of the Apennines thrust belt has been affected by Pliocene–Quaternary extension during easterly roll-back and crustal delamination of the Adriatic slab. The bulk of Quaternary extension has been accommodated bySW-dipping oblique and normal faults,which have attained mature morphologic and structural features and, nowadays, separate mountain ranges from intermontane basins. However, in the present seismogenic belt, coseismic faulting locally occurs on NE-dipping structures, which might cut the inherited Pleistocene landscape. In theVal d’Agri basin, in spite of the large Early–Middle Pleistocene, displacement occurred on SW-dipping faults bordering its eastern flank, our investigations show that the recent basin evolution has been controlled by a NE-dipping fault system (Monti della Maddalena fault system, MMFS). This fault system cuts across the Monti della Maddalena range, west of the Agri valley and has not yet created an evident tectonic landscape. Notwithstanding, fault motion since the Middle Pleistocene might explain geomorphologic and hydrographic anomalies of the Agri river and its valley, where fault-controlled subsidence has captured the river course and produced an aggrading plain within a regional uplift context. Recent and ongoing motion is documented by fault scarplets in loose deposits, 14C ages of palaeosols and the spatial relation with low to moderate instrumental seismicity. Results from fault kinematic analysis are compatible with fault-plane solutions of local and regional seismic events, and indicate ∼NE–SW oriented extension. Recognition of the MMFS as a potential seismogenic fault increases the longitudinal extent of the NE-dipping, morphologically immature seismic sources in the Southern Apennines and argues against the range-bounding fault model for active extension in the region. The regional size of the NE-dipping seismogenic belt may result from impingement of a mantle wedge beneath the Apenninic chain and possibly track the external front of crustal delamination.
    Description: Published
    Description: 591-609
    Description: 3.2. Tettonica attiva
    Description: JCR Journal
    Description: reserved
    Keywords: active tectonics ; crustal deformation ; earthquakes ; geomorphology ; normal faulting ; Southern Italy ; 04. Solid Earth::04.04. Geology::04.04.01. Earthquake geology and paleoseismology ; 04. Solid Earth::04.04. Geology::04.04.03. Geomorphology ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 18
    Publication Date: 2020-02-24
    Description: After an earthquake, rapid, real-time assessment of hazards such as ground shaking and tsunami potential is important for early warning and emergency response. Tsunami potential depends on seafloor displacement, which is related to the length, L, width, W, mean slip, D, and depth, z, of earthquake rupture. Currently, the primary discriminant for tsunami potential is the centroid-moment tensor magnitude, MCMT, representing the seismic potency LWD, and w estimated through an indirect, inversion procedure. The obtained MCMT and the implied LWD w value vary with the depth of faulting, assumed earth model and other factors, and is only available 30 min or more after an earthquake. The use of more direct procedures for hazard assessment, when available, could avoid these problems and aid in effective early warning. Here we present a direct procedure for rapid assessment of earthquake tsunami potential using two, simple measures on P-wave seismograms—the dominant period on the velocity records, Td, and the likelihood that the high-frequency, apparent rupture-duration, T0, exceeds 50–55 s. T0 can be related to the critical parameters L and z, while Td may be related to W, D or z. For a set of recent, large earthquakes, we show that the period-duration product T T gives more information on tsunami impact and size than MCMT and other currently used d0w discriminants. All discriminants have difficulty in assessing the tsunami potential for oceanic strike-slip and backarc or upper plate, intraplate earthquake types. Our analysis and results suggest that tsunami potential is not directly related to the potency LWD from the ‘seismic’ faulting model, as is assumed with the use of the MCMT discriminant. Instead, knowledge of w rupture length, L, and depth, z, alone can constrain well the tsunami potential of an earthquake, with explicit determination of fault width, W, and slip, D, being of secondary importance. With available real-time seismogram data, rapid calculation of the direct, period-duration discriminant can be completed within 6–10 min after an earthquake occurs and thus can aid in effective and reliable tsunami early warning.
    Description: Published
    Description: 283-291
    Description: JCR Journal
    Description: restricted
    Keywords: earthquake dynamics ; earthquake source observation ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring
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  • 19
    Publication Date: 2020-02-24
    Description: This article analyzes the ocean forecast response to surface vector wind (SVW) distributions generated by a Bayesian hierarchical model (BHM) developed in Part I of this series. A new method for ocean ensemble forecasting (OEF), the socalled BHM-SVW-OEF, is described. BHM-SVW realizations are used to produce and force perturbations in the ocean state during 14 day analysis and 10 day forecast cycles of the Mediterranean Forecast System (MFS). The BHM-SVW-OEF ocean response spread is amplified at the mesoscales and in the pycnocline of the eddy field. The new method is compared with an ensemble response forced by European Centre for Medium-Range Weather Forecasts (ECMWF) ensemble prediction system (EEPS) surface winds, and with an ensemble forecast started from perturbed initial conditions derived froman ad hoc thermocline intensified random perturbation (TIRP) method. The EEPS-OEF shows spread on basin scales while the TIRP-OEF response is mesoscale-intensified as in the BHM-SVW-OEF response. TIRP-OEF perturbations fill more of the MFS domain, while the BHM-SVW-OEF perturbations are more location-specific, concentrating ensemble spread at the sites where the ocean-model response to uncertainty in the surface wind forcing is largest.
    Description: Published
    Description: 879–893
    Description: JCR Journal
    Description: embargoed_20140501
    Keywords: forecast uncertainty ; 03. Hydrosphere::03.01. General::03.01.03. Global climate models
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  • 20
    Publication Date: 2020-03-16
    Description: Post-seismic relaxation is known to occur after large or moderate earthquakes, on time scales ranging from days to years or even decades. In general, long-term deformation following seismic events has been detected by means of standard geodetic measurements, although seismic instruments are only used to estimate short timescale transient processes. Albeit inertial seismic sensors are also sensitive to rotation around their sensitive axes, the recording of very slow inclination of the ground surface at their standard output channels is practically impossible, because of their design characteristics. However, modern force-balance, broad- band seismometers provide the possibility to detect and measure slow surface inclination, through the analysis of the mass position signal. This output channel represents the integral of the broad-band velocity and is generally considered only for state-of-health diagnostics. In fact, the analysis of mass position data recorded at the time of the 2009 April 6, L’Aquila (MW = 6.3) earthquake, by a closely located STS-2 seismometer, evidenced the occurrence of a very low frequency signal, starting right at the time of the seismic event. This waveform is only visible on the horizontal components and is not related to the usual drift coupled with the temperature changes. This analysis suggests that the observed signal is to be ascribed to slowly developing ground inclination at the station site, caused by post-seismic relaxation following the main shock. The observed tilt reached 1.7 × 10−5 rad in about 2 months. This estimate is in very good agreement with the geodetic observations, giving comparable tilt magnitude and direction at the same site. This study represents the first seismic analysis ever for the mass position signal, suggesting useful applications for usually neglected data.
    Description: Published
    Description: 1717-1724
    Description: 3.1. Fisica dei terremoti
    Description: JCR Journal
    Description: restricted
    Keywords: Seismic cycle ; Earthquake source observations ; 04. Solid Earth::04.06. Seismology::04.06.03. Earthquake source and dynamics
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  • 21
    Publication Date: 2017-04-03
    Description: On 2009 April 6 a Mw = 6.3 earthquake struck the Abruzzi region (Central Italy) and caused severe destruction in L’Aquila and the surrounding area. In this work we present a Finite Element analysis of the event based on a realistic complex 3-D model, accounting for topographic relief and rheological heterogeneities deduced from local tomography. Finite Element computed Green’s functions were implemented in a linear inversion of GPS coseismic displacements, to retrieve the slip distribution on the rupture plane. The inverted slip models basically agree with previous studies carried out on homogeneous domains, but reveal the presence of a single high slip patch, whereas half-space or 1-D approaches obtain a more complex slip pattern. Our results point out that the introduction of 3-D features significantly influences the obtained source model, suggesting a trade-off between domain complexities and source details.
    Description: Published
    Description: 1339–1358
    Description: 3.3. Geodinamica e struttura dell'interno della Terra
    Description: JCR Journal
    Description: restricted
    Keywords: Numerical approximations and analysis ; Seismicity and tectonics ; Dynamics and mechanics of faulting ; L'Aquila earthquake ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics
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  • 22
    Publication Date: 2017-04-04
    Description: The accurate determination of locations and magnitudes of seismic events in a monitored region is important for many scientific, industrial and military studies and applications; for these purposes a wide variety of seismic networks are deployed throughout the world. It is crucial to know the performance of these networks not only in detecting and locating seismic events of different sizes throughout a specified source region, but also by evaluating their location errors as a function of the magnitude and source location. In this framework, we have developed a method for evaluating network performance in surface and borehole seismic monitoring. For a specified network geometry, station characteristics and a target monitoring volume, the method determines the lowest magnitude of events that the seismic network is able to detect (Mw detect), and locate (Mw loc) and estimates the expected location and origin time errors for a specified magnitude. Many of the features related to the seismic signal recorded at a single station are considered in this methodology, including characteristics of the seismic source, the instrument response, the ambient noise level, wave propagation in a layered, anelastic medium and uncertainties on waveform measures and the velocity model. We applied this method to two different network typologies: a local earthquake monitoring network, Irpinia Seismic Network (ISNet), installed along the Campania-Lucania Apennine chain in Southern Italy, and a hypothetic borehole network for monitoring microfractures induced during the hydrocarbon extraction process in an oil field. The method we present may be used to aid in enhancing existing networks and/or understanding their capabilities, such as for the ISNet case study, or to optimally design the network geometry in specific target regions, as for the borehole network example.
    Description: Published
    Description: 793-806
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: restricted
    Keywords: Earthquake ground motions ; Computational seismology ; 04. Solid Earth::04.06. Seismology::04.06.10. Instruments and techniques
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 23
    Publication Date: 2017-04-03
    Description: Computing the magnitude of an earthquake requires correcting for the propagation effects from the source to the receivers. This is often accomplished by performing numerical simulations using a suitable Earth model. In this work, the energy magnitude Me is considered and its determination is performed using theoretical spectral amplitude decay functions over teleseismic distances based on the global Earth model AK135Q. Since the high frequency part (above the corner frequency) of the source spectrum has to be considered in computing Me, the influence of propagation and site effects may not be negligible and they could bias the single station Me estimations. Therefore, in this study we assess the inter- and intrastation distributions of errors by considering the Me residuals computed for a large data set of earthquakes recorded at teleseismic distances by seismic stations deployed worldwide. To separate the inter- and intrastation contribution of errors, we apply a maximum likelihood approach to the Me residuals. We show that the interstation errors (describing a sort of site effect for a station) are within ±0.2 magnitude units for most stations and their spatial distribution reflects the expected lateral variation affecting the velocity and attenuation of the Earth's structure in the uppermost layers, not accounted for by the 1-D AK135Q model. The variance of the intrastation error distribution (describing the record-to-record component of variability) is larger than the interstation one (0.240 against 0.159), and the spatial distribution of the errors is not random but shows specific patterns depending on the source-to-station paths. The set of coefficients empirically determined may be used in the future to account for the heterogeneities of the real Earth not considered in the theoretical calculations of the spectral amplitude decay functions used to correct the recorded data for propagation effects.
    Description: Published
    Description: 1444-1454
    Description: JCR Journal
    Description: restricted
    Keywords: time series analysis ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 24
    Publication Date: 2017-04-04
    Description: The monitoring of crustal motions in Northern Victoria Land (NVL) of Antarctica by means of episodic GPS stations (EGPSs) provides an accurate and dense (∼50-km spaced) velocity field. The data, gathered starting in Austral summer 1999, derive from a series of benchmarks belonging to the Victoria Land Network for DEFormation control (VLNDEF) geodetic network. The velocity uncertainties are checked on the basis of length and returning time of the episodic surveys, to obtain a meaningful strain rate field by means of a least-square computation where the contribution of a GPS station is weighted by the inverse square of its velocity error. The study shows that the NVL is characterized by a complex kinematics and that, although three subregions with different prevailing deformational behaviour can be recognized, the single blocks cannot be resolved because too few stations exist. Only features having 150–200 km size at least can be recognized. Moreover, it is demonstrated that an appropriate data processing of EGPS data can lead to an accurate evaluation of the strain rate field even in a harsh environment like Antarctica.
    Description: Published
    Description: 851-862
    Description: 3.3. Geodinamica e struttura dell'interno della Terra
    Description: JCR Journal
    Description: reserved
    Keywords: Time-series analysis ; Satellite geodesy ; Geomorphology ; Antarctica ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics
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  • 25
    Publication Date: 2017-04-04
    Description: The Gulf of Manfredonia and the Tavoliere Plain have experienced intense human colonization since the neolithic times. There is past evidence in the study area of a Roman-age settlement historically known as Salapia, probably located close to the salt-production ponds. In particular, several portions of a partly submerged ancient pier-like structure were found close to Torre Pietra town. This structure has been interpreted as a portion of a dragged-ship channel that connected the town of Salapia to the sea. In this article we discuss the results of a high-resolution geophysical prospecting of the Margherita di Savoia offshore archaeological site (Puglia, Italy). We collected magnetic gradiometric and bathymetric data to map the submerged remains of Salapia harbour. We found evidence of an offshore projection of a Torre Pietra pier-like structure, identifying the direction of the ship channel and possibly the location of the harbour’s defensive post
    Description: Published
    Description: 89-101
    Description: 3.4. Geomagnetismo
    Description: JCR Journal
    Description: restricted
    Keywords: Marine magnetic survey; ; Manfredonia Gulf ; Roman archaeological finds ; buried ruins ; analytic signal; ; horizontal gradient ; 04. Solid Earth::04.05. Geomagnetism::04.05.04. Magnetic anomalies ; 05. General::05.01. Computational geophysics::05.01.01. Data processing
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  • 26
    Publication Date: 2017-04-04
    Description: The overall picture of Mount Etna deformation emerging since a couple of decades of geodetic surveys shows effects of magma accumulation, characterized by inflation/deflation cycle, accompanied by a sliding instability of the southeast flank, whose manifestation is an increase in the horizontal deformation away from the volcano summit. This is a very interesting case to test whether advanced models, taking into account topography, internal structure and frictional rheology, may contribute to a better understanding of the complex interplay among mechanical response, magmatic activity and gravitational load occurring in a volcanic system. Using finite element numerical models we make predictions of surface displacements associated with a simple expansion source and with a dike like vertical discontinuity. A new methodology is developed to initalize the lithostatic stress field according to the material and geometrical complexities of the models considered. Our results show that, while an amplification of the horizontal displacement can be easily obtained up to a maximum distance of 10 km from the source, we have not been able to find any onfiguration to extend further this signal. For the case of Mount Etna this suggests that the large horizontal displacements observed in the east flank along the coast cannot be directly related to magma accumulation below the volcano's summit.
    Description: Published
    Description: 939-953
    Description: 3.3. Geodinamica e struttura dell'interno della Terra
    Description: JCR Journal
    Description: partially_open
    Keywords: Numerical solutions ; Space geodetic surveys ; Elasticity and anelasticity ; Eruption mechanisms and flow emplacement ; Volcanic hazards and risks ; 04. Solid Earth::04.01. Earth Interior::04.01.02. Geological and geophysical evidences of deep processes
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 27
    Publication Date: 2017-04-04
    Description: The Solfatara is one of the major volcanoes of the Phlegrean Fields (Campi Flegrei) volcanic complex, and it is located in a densely populated area a few kilometres west of the city of Naples. It is an active resurgent caldera that has been characterized by a rich history of surface–ground deformation and soil diffuse degassing and fumarolic emissions, which are indications of the top of a hydrothermal plume. A seismic survey was completed in May 2009 for the characterization of the main subsurface features of the Solfatara. Using the complete data set, we have carried out surface wave inversion with high spatial resolution. A classical minimization of a least-squares objective function was first computed to retrieve the dispersion curves of the surface waves. Then, the fitting procedure between the data and a three-sedimentlayer forward model was carried out (to a depth of 7 m), using an improved version of the neighbourhood algorithm. The inversion results indicate a NE-SW fault, which is not visible at the surface. This was confirmed by a temperature survey conducted in 2010. A passive seismic experiment localized the ambient noise sources that correlate well with the areas of high CO2 flux and high soil temperatures. Finally, considering that the intrinsic attenuation is proportional to the frequency, a centroid analysis provides an overview of the attenuation of the seismic waves, which is closely linked to the petrophysical properties of the rock. These different approaches that merge complete active and passive seismic data with soil temperature and CO2 flux maps confirm the presence of the hydrothermal system plume. Some properties of the top of the plume are indicated and localized.
    Description: Published
    Description: 1725–1733
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: 4.5. Studi sul degassamento naturale e sui gas petroliferi
    Description: JCR Journal
    Description: restricted
    Keywords: Inverse theory ; Tomography ; Hydrothermal systems ; Europe ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases ; 04. Solid Earth::04.04. Geology::04.04.11. Instruments and techniques ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry
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  • 28
    Publication Date: 2017-04-04
    Description: The magnetic properties (first-order reversal curves, ferromagnetic resonance and decomposition of saturation remanent magnetization acquisition) of Magnetovibrio blakemorei, a cultivated marine magnetotactic bacterium, differ from those of other magnetotactic species from sediments deposited in lakes and marine habitats previously studied. This finding suggests that magnetite produced by some magnetotactic bacteria retains magnetic properties in relation to the crystallographic structure of the magnetic phase produced and thus might represent a ‘magnetic fingerprint’ for a specific magnetotactic bacterium. The use of this fingerprint is a non-destructive, new technology that might allow for the identification and presence of specific species or types of magnetotactic bacteria in certain environments such as sediments.
    Description: Published
    Description: 664-668
    Description: 1.8. Osservazioni di geofisica ambientale
    Description: 2.2. Laboratorio di paleomagnetismo
    Description: 3.8. Geofisica per l'ambiente
    Description: JCR Journal
    Description: restricted
    Keywords: batteri magnetotattici ; magnetite ; 03. Hydrosphere::03.01. General::03.01.06. Paleoceanography and paleoclimatology ; 04. Solid Earth::04.05. Geomagnetism::04.05.09. Environmental magnetism
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 29
    Publication Date: 2017-10-06
    Description: In this study we have determined detailed Vp and Vs seismic velocity models of the Ionian lithosphere subducting beneath the Tyrrhenian basin and of the surrounding mantle, by applying a post-processing technique to a large sample of local earthquake tomography studies. Our seismic velocity models permit us to infer the presence of low velocity anomalies within the slab, which we interpret as regions that are partially hydrated by fluids released during the subduction process. A petrological interpretation of the velocity anomalies gives new details on the magmatism of the volcanic Aeolian arc. Furthermore our velocity models provide a more detailed description of the boundary of the slab and its connection with the large seismically active Tindari-Letojanni strike slip system. Finally these results allow describing in detail some features of the slab as the presence of lateral and vertical tears. In conclusion, the obtained models provide some constraints for inferences on mantle circulation, and on the geodynamical evolution of the central-western Mediterranean.
    Description: Published
    Description: 751-764
    Description: 2.5. Laboratorio per lo sviluppo di sistemi di rilevamento sottomarini
    Description: JCR Journal
    Description: reserved
    Keywords: Tomography, petrology, Ionian slab ; 04. Solid Earth::04.06. Seismology::04.06.07. Tomography and anisotropy
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  • 30
    Publication Date: 2020-02-24
    Description: A Bayesian hierarchical model (BHM) is developed to estimate surface vector wind (SVW) fields and associated uncertainties over the Mediterranean Sea. The BHM–SVW incorporates data-stage inputs from analyses and forecasts of the European Centre for Medium-Range Weather Forecasts (ECMWF) and SVW retrievals from the QuikSCAT data record. The process-model stage of the BHM–SVW is based on a Rayleigh friction equation model for surface winds. Dynamical interpretations of posterior distributions of the BHM–SVW parameters are discussed. Ten realizations from the posterior distribution of the BHM–SVW are used to force the data-assimilation step of an experimental ensemble ocean forecast system for the Mediterranean Sea in order to create a set of ensemble initial conditions. The sequential data-assimilation method of the Mediterranean forecast system (MFS) is adapted to the ensemble implementation. Analyses of sample ensemble initial conditions for a single data-assimilation period in MFS are presented to demonstrate the multivariate impact of the BHM–SVW ensemble generation methodology. Ensemble initial-condition spread is quantified by computing standard deviations of ocean state variable fields over the ten ensemble members. The methodological findings in this article are of two kinds. From the perspective of statistical modelling, the process-model development is more closely related tophysicalbalances than inpreviousworkwithmodels for the SVW.Fromthe ocean forecast perspective, the generation of ocean ensemble initial conditions via BHM is shown to be practical for operational implementation in an ensemble ocean forecast system. Phenomenologically, ensemble spread generated via BHM–SVW occurs on ocean mesoscale time- and space-scales, in close association with strong synoptic-scale wind-forcing events. A companion article describes the impacts of the BHM–SVW ensemble method on the ocean forecast in comparisons with more traditional ensemble methods.
    Description: Published
    Description: 858–878
    Description: JCR Journal
    Description: embargoed_20140501
    Keywords: QuikSCAT surface winds ; 03. Hydrosphere::03.01. General::03.01.05. Operational oceanography
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  • 31
    Publication Date: 2020-02-24
    Description: In this study, new intensity prediction equations are derived for Central Asia, considering about 6000 intensity data points from 66 earthquakes encompassing the surface-wave magnitude range of 4.6–8.3. The suitability of the functional form used for constructing the model is assessed by comparing its predictions with those achieved through a non-parametric model. The parametric regressions are performed considering different measures of the source-to-site distance, namely the hypocentral, epicentral and the extended distance metrics. The latter is defined as the minimum distance from the site to a line crossing the epicentres, oriented along the strike of the earthquake and having a length estimated from the event’s magnitude. Although the extended distance is introduced as a preliminary attempt to improve the prediction capability of the model by considering the finiteness of the fault extension, the standard deviation of the residual distribution obtained considering the extended distance (σ = 0.734) does not show an improvement with respect to the results for the epicentral distance (σ = 0.737). The similarity of the two models in term of average residuals is also confirmed by comparing the interevent errors obtained for the two regressions, obtaining very similar values for all earthquakes but the 1911, M 8.2 Kemin event. In particular, different evidences suggest that the magnitude of this event could be overestimated by about half a magnitude unit. Regarding the variability of the residual distribution, all the three considered components (i.e. interevent, interlocation and record-to-record variances) are not negligible, although the largest contribution is related to the record-to-record variability, suggesting that both source and propagation as well as site effects not captured by the considered model influence the spatial variability of the intensity values.
    Description: Published
    Description: 327–337
    Description: JCR Journal
    Description: restricted
    Keywords: Earthquake ground motions ; 05. General::05.01. Computational geophysics::05.01.99. General or miscellaneous
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  • 32
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    Wiley-Blackwell
    In:  EPIC3Oxidative Stress in Aquatic Ecosystems, Abele, D., Zenteno-Savin, T, Vasquez-Medina, J. (Eds) Oxidatve Stress in Aquatic Ecosystems, Blackwell-Wiley., Oxford UK, Wiley-Blackwell, 15 p., pp. 141 -156, ISBN: 978-1-4443-3548-4
    Publication Date: 2019-07-16
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 33
    Publication Date: 2014-04-17
    Description: Compensatory dynamics, overyielding and statistical averaging are mechanisms promoting the temporal stability of natural communities. Using the model of European intertidal rocky shore assemblages and collating 17 datasets, we investigated how the strength of these stability-enhancing mechanisms varies with latitude and how it can be altered by the loss of habitat-formers (e.g. canopy-forming macroalgae). Community stability decreased with increasing latitude, mostly as a consequence of a greater synchronization of species fluctuations. Statistical averaging and overyielding (i.e. richness effects) promoted stability, but their strength did not vary with latitude. The experimental removal of macroalgal canopies caused a strengthening of the statistical averaging effect that was consistent across the latitudinal gradient investigated. Nonetheless, the loss of canopies depressed stability by enhancing the synchronization of species fluctuations on southernmost shores, while it had weak effects on shores at higher latitudes. Variation in life-history traits among canopy-forming species and/or in prevailing environmental conditions across a gradient of latitude could underlie variable effects of habitat-formers on species fluctuations. Our study shows i) that the stability of intertidal assemblages and strength of compensatory dynamics varies with latitude, ii) that canopy-forming macroalgae, exerting a strong control on understorey species, can influence the strength of compensatory dynamics and iii) that biological forcing (i.e. facilitation) can be as important as environmental forcing in enhancing the synchronization of species fluctuations.
    Repository Name: EPIC Alfred Wegener Institut
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  • 34
    Publication Date: 2021-12-15
    Description: Some of the most structurally innovative concrete vaults built in imperial Rome employed lightweight volcanic rocks to reduce the lateral thrust on the supporting walls, the most famous being the Pantheon. Roman concrete (opus caementicium) was made up of mortar binding together pieces of large aggregate (caementa) usually ranging from 10 to 20 cm long, which were hand laid in the mortar (as opposed to being poured as is typical in modern concrete), so that it resembles mortared rubble. A key aspect of the development of large-scale concrete vaulting was the ability to regulate the weight of the ingredients in order to reduce the weight of the vaults and to control the forces within the structure. The volcanic environment along the west coast of Italy provided numerous stones of different weights and physical properties from which the builders could choose (Fig. 1), including pumice and scoria, which were the most common choices for the lightweight caementa of the most innovative vaulted structures. Because these materials were produced by many of the Italian volcanoes, our goal was to establish the provenance of those used in vaults in Rome in order to understand better the supply network. We first used thin sections to narrow the potential sources and then we submitted selected samples to X-ray fluorescence
    Description: Published
    Description: 707-727
    Description: JCR Journal
    Description: restricted
    Keywords: concrete vault ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 35
    Publication Date: 2022-05-24
    Description: Series of multiple main shocks that develop on adjacent faults is a typical way in which active extension is accommodated in the Apennines of Italy. This behaviour is explained by fault interaction that occurs at a scale ranging from seconds to days, yielding a space–time clustering of earthquakes, termed as earthquake storms. We show that the seismic energy released by historical earthquakes in central Apennines is clustered into two main small time periods, around 600 and 300 years ago, during which a great portion of the normal faulting belt failed. We favour the hypothesis that clustering results from sudden input of deep fluids into the brittle upper crust. The roughly 300 years periodicity and the 3–4 mm year−1 of tectonic extension suggest that earthquake storms need to be taken into account in seismic hazard scenarios.
    Description: Published
    Description: 300–306
    Description: JCR Journal
    Description: restricted
    Keywords: Apennines ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 36
    Publication Date: 2022-06-08
    Description: Although no deterministic and reliable earthquake precursor is known to date, we are steadily gaining insight into probabilistic forecasting that draws on space–time characteristics of earthquake clustering. Clustering-based models aiming to forecast earthquakes within the next 24 hours are under test in the global project ‘Collaboratory for the Study of Earthquake Predictability’ (CSEP). The 2011 March 11 magnitude 9.0 Tohoku-Oki earthquake in Japan provides a unique opportunity to test the existing 1-day CSEP models against its unprecedentedly active aftershock sequence. The original CSEP experiment performs tests after the catalogue is finalized to avoid bias due to poor data quality. However, this study differs from this tradition and uses the preliminary catalogue revised and updated by the Japan Meteorological Agency (JMA), which is often incomplete but is immediately available. This study is intended as a first step towards operability-oriented earthquake forecasting in Japan. Encouragingly, at least one model passed the test in most combinations of the target day and the testing method, although the models could not take account of the megaquake in advance and the catalogue used for forecast generation was incomplete. However, it can also be seen that all models have only limited forecasting power for the period immediately after the quake. Our conclusion does not change when the preliminary JMAcatalogue is replaced by the finalized one, implying that the models perform stably over the catalogue replacement and are applicable to operational earthquake forecasting. However, we emphasize the need of further research on model improvement to assure the reliability of forecasts for the days immediately after the main quake. Seismicity is expected to remain high in all parts of Japan over the coming years. Our results present a way to answer the urgent need to promote research on time-dependent earthquake predictability to prepare for subsequent large earthquakes in the near future in Japan.
    Description: Published
    Description: 653-658
    Description: 3.1. Fisica dei terremoti
    Description: JCR Journal
    Description: restricted
    Keywords: Time-series analysis ; Probabilistic forecasting ; Seismicity and tectonics ; Computational seismology ; Statistical seismology ; Asia ; 04. Solid Earth::04.06. Seismology::04.06.02. Earthquake interactions and probability
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 37
    Publication Date: 2022-06-10
    Description: A multi-proxy record is presented for approximately the last 4500 cal a BP from Lake Shkodra, Albania/Montenegro. Lithological analyses, C/N ratio and δ13C of the organic and inorganic carbon component suggest that organic matter and bulk carbonate are predominantly authigenic. The δ18O record of bulk carbonate indicates the presence of two prominent wet periods: one at ca. 4300 cal a BP and one at ca. 2500–2000 cal a BP. The latter phase is also found in southern Spain and Central Italy, and represents a prominent event in the western and central Mediterranean. In the last 2000 years, four relatively wet intervals occurred between ca. 1800 and 1500 cal a BP (150–450 AD), 1350–1250 (600–700 AD), 1100–800 (850–1150 AD), and at ca. 90 cal a BP (1860 AD). Between ca. 4100 and 2500 cal a BP δ18O values are relatively high, with three prominent peaks indicating drier conditions at ca. 4100–4000 cal a BP, ca. 3500 and at ca. 3300 cal a BP. Four additional drier events are identified at 1850 (ca. 100 AD), 1400 (ca. 550 AD), 1150 (800 AD) and ca.750 cal a BP (1200 AD). The pollen record does not show changes in accordance with these episodes owing to the poor sensitivity of vegetation in this area, which is dominated by an orographic rainfall effect and where changes in altitudinal vegetation belts do not affect the pollen rain in the lake catchment. However, since ca. 900 cal a BP a significant decrease in the percentage arboreal pollen and in pollen concentrations suggest major deforestation produced by human activities. Copyright © 2012 John Wiley & Sons, Ltd.
    Description: Published
    Description: 780-789
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: Lake Shkodra ; late Holocene ; Mediterranean ; palaeoclimate ; stable isotopes ; 03. Hydrosphere::03.01. General::03.01.06. Paleoceanography and paleoclimatology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 38
    Publication Date: 2022-05-24
    Description: Two different free-air gravity datasets from the Apennines have been analysed in the frequency domain to investigate the mechanisms of support of topography. At short wavelength (λ〈150 km) the best fit between the observed and the calculated admittance gives a value of the elastic thickness of 3.7 km. The observed behaviour of the admittance at larger wavelengths (λ〉150 km) shows that such topography is not supported by elastic stresses in the lithosphere but is dynamically supported by mantle convection. The distribution of gravity anomalies and topography suggests that the mantle is rising beneath the main topographic bulge of the Apennines and that this flow is maintained by buoyancy forces, rather than being driven by movement of the subducted slab.
    Description: Published
    Description: 228-233
    Description: 3.3. Geodinamica e struttura dell'interno della Terra
    Description: JCR Journal
    Description: reserved
    Keywords: Dynamic Topography ; Gravity ; Apennines ; 04. Solid Earth::04.03. Geodesy::04.03.03. Gravity and isostasy
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 39
    Publication Date: 2022-05-24
    Description: GPS measurements on Mount St. Helens spanning the 2004.00-2010.85 time interval, encompassing the 2004-2008 dome-building eruption, were analyzed. First, a local reference frame was derived in order to isolate the volcanic ground deformation from the background tectonic pattern related to the interactions between the Pacific, Juan de Fuca and North American plates. Secondly, the resulting ground deformation patterns were modelled to constrain magmatic sources. Results suggest a vertically elongated magma chamber centred at 8 - 9 km depth beneath the summit area that deflated during the beginning of the dome growth and inflated since January 2008, evidencing that a primary magma reservoir was active both during and after the eruption in a magmatic system persistent over the time.
    Description: Published
    Description: 148-155
    Description: 1.3. TTC - Sorveglianza geodetica delle aree vulcaniche attive
    Description: JCR Journal
    Description: restricted
    Keywords: Mount St. Helens ; Ground deformation modelling ; local reference frame ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 40
    Publication Date: 2022-05-24
    Description: The early Cenozoic, which is punctuated by several negative carbon isotope excursions (CIEs), was a time of climatic and oceanographic transition from ’Greenhouse’ to ’Icehouse’ conditions. The occurrence of a 0.5& CIE starting at the top of Chron C27n (TC27N) is reconfirmed with stable isotope data from Zumaia (Spain) and Bjala (Bulgaria) localities. Spectral analysis on respective carbonate ⁄magnetic susceptibility proxy records substantiates the orbital cyclostratigraphy allowing correlation to a high-resolution benthic foraminifera isotope record from ODP Pacific Site 1209, that indicates a coeval 2 C transient warming. The hyperthermal event lasts 200 ka, contrasting with other short-lived events from the Eocene, and displays a relatively rapid onset and a longer tailing back to pre-event values similar to the Palaeocene–Eocene Thermal Maximum (PETM), though lower in amplitude. That a causal trigger for the TC27N event may be the onset of volcanism in the North Atlantic Igneous Province (NAIP) can be inferred from a 200-m-thick lava pile erupted during C27n ⁄ C26r polarity transition in the E Greenland margin.
    Description: Published
    Description: 477-486
    Description: 2.2. Laboratorio di paleomagnetismo
    Description: JCR Journal
    Description: reserved
    Keywords: hyperthermal ; isotope excursion ; TC27N event ; Zumaia ; 03. Hydrosphere::03.01. General::03.01.06. Paleoceanography and paleoclimatology ; 04. Solid Earth::04.04. Geology::04.04.08. Sediments: dating, processes, transport ; 04. Solid Earth::04.04. Geology::04.04.10. Stratigraphy
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 41
    Publication Date: 2022-06-10
    Description: Earthquake forecasts are usually underinformed, and can be plagued by uncertainty in terms of the most appropriate model, and parameter values used in that model. In this paper, we explore the application of two different models to the same seismogenic area. The first is a renewal model based on the characteristic earthquake hypothesis that uses historical/palaeoseismic recurrence times, and fixed rupture geometries. The hazard rate is modified by the Coulomb static stress change caused by nearby earthquakes that occurred since the latest characteristic earthquake. The second model is a very simple earthquake simulator based on plate-motion, or fault-slip rates and adoption of a Gutenberg–Richter magnitude–frequency distribution. This information is commonly available even if historical and palaeoseismic recurrence data are lacking. The intention is to develop and assess a simulator that has a very limited parameter set that could be used to calculate earthquake rates in settings that are not as rich with observations of large-earthquake recurrence behaviour as the Nankai trough. We find that the use of convergence rate as a primary constraint allows the simulator to replicate much of the spatial distribution of observed segmented rupture rates along the Nankai, Tonankai and Tokai subduction zones. Although we note rate differences between the two forecast methods in the Tokai zone, we also see enough similarities between simulations and observations to suggest that very simple earthquake rupture simulations based on empirical data and fundamental earthquake laws could be useful forecast tools in information-poor settings.
    Description: Published
    Description: 1673-1688
    Description: 3.1. Fisica dei terremoti
    Description: JCR Journal
    Description: restricted
    Keywords: Time series analysis ; Spatial analysis ; Probability distributions ; Seismic cycle ; Earthquake interaction ; forecasting, and prediction ; Statistical seismology. ; 04. Solid Earth::04.06. Seismology::04.06.02. Earthquake interactions and probability ; 04. Solid Earth::04.06. Seismology::04.06.05. Historical seismology ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 42
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    Wiley-Blackwell
    In:  EPIC3Oxidative Stress in Aquatic Ecosystems, Oxidative Stress in Aquatic Ecosystems, Wiley-Blackwell, 18 p., pp. 263-280, ISBN: 978-1-4443-3548-4
    Publication Date: 2023-06-21
    Description: The chapter will summarize and critically review metabolic responses to environmental stress and stress effects on energy budgets in mollusks. Metabolic adaptations to environmental stress will be analyzed including alternative energy conserving pathways, aerobic/anaerobic transitions and metabolic arrest. Their role in the efficient use of energy substrates and in the maintenance of cellular homeostasis and redox status will be discussed. General stress effects on energy budget at different organization levels (from the cell to the whole-organism) will be analyzed including energy uptake, assimilation, conversion and expenditure, as well as the metabolic costs associated with stress resistance (including antioxidant protection, chaperone function and damage repair). We will compare metabolic responses to moderate and extreme levels of environmental stressors using temperature, ocean acidification, salinity, oxygen deficiency and toxic metal stress as examples. This chapter will also outline the future research directions to improve our understanding of the stress effects on bioenergetics in mollusks and other invertebrates. Keywords: Stress, metabolic adaptation, metabolic arrest, bioenergetics, cellular defense, energy trade-offs
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 43
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    Wiley-Blackwell
    In:  EPIC3Oxidative Stress in Aquatic Ecosystems, Oxidative Stress in Aquatic Ecosystems, Oxford, Wiley-Blackwell, 524 p., pp. 115-126, ISBN: 978 1 4443 3548 4
    Publication Date: 2023-06-21
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 44
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    Wiley-Blackwell
    In:  EPIC3Wiley-Blackwell, ISBN: 9781444335484
    Publication Date: 2023-06-21
    Repository Name: EPIC Alfred Wegener Institut
    Type: Book , peerRev
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  • 45
    Publication Date: 2023-02-10
    Description: The Indonesian island of Sumatra, located in one of the most active zones of the Pacific Ring of Fire, is characterized by a chain of subduction-zone volcanoes which extend the entire length of the island. As a group of volcanic geochemists, we embarked upon a five-week sampling expedition to these exotic, remote, and in part explosive volcanoes (SAGE 2010; Sumatran Arc Geochemical Expedition). We set out to collect rock and gas samples from 17 volcanic centres from the Sumatran segment of the Sunda arc system, with the aim of obtaining a regionally significant sample set that will allow quantification of the respective roles of mantle versus crustal sources to magma genesis along the strike of the arc. Here we document our geological journey through Sumatra’s unpredictable terrain, including the many challenges faced when working on active volcanoes in pristine tropical climes.
    Description: Swedish Science Foundation (VR), Scripps Institution of Oceanography, Istituto Nazionale di Geofisica e Vulcanologia (INGV), Upp-sala University Centre for Natural Disaster Science (CNDS) and Otterborgska donationsfonden
    Description: Published
    Description: 64-70
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: N/A or not JCR
    Description: restricted
    Keywords: Sumatra ; Indonesia ; geochemisty ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 46
    Publication Date: 2024-02-07
    Description: Phylogeographic patterns and sex-biased dispersal were studied in riverine populations of West Indian (Trichechus manatus) and Amazonian manatees (T. inunguis) in South America, using 410bp D-loop (Control Region, Mitochondrial DNA) sequences and 15 nuclear microsatellite loci. This multi-locus approach was key to disentangle complex patterns of gene flow among populations. D-loop analyses revealed population structuring among all Colombian rivers for T. manatus, while microsatellite data suggested no structure. Two main populations of T. inunguis separating the Colombian and Peruvian Amazon were supported by analysis of the D-loop and microsatellite data. Overall, we provide molecular evidence for differences in dispersal patterns between sexes, demonstrating male-biased gene flow dispersal in riverine manatees. These results are in contrast with previously reported levels of population structure shown by microsatellite data in marine manatee populations, revealing low habitat restrictions to gene flow in riverine habitats, and more significant dispersal limitations for males in marine environments. © 2012 Satizábal et al.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 47
    Publication Date: 2024-05-09
    Description: In this paper, we propose a new model of the crustal structure and seismotectonics for central Sicily (southern Italy) through the analysis of the depth distribution and kinematics of the instrumental seismicity, occurring during the period from 1983 to 2010, and its comparison with individual geological structures that may be active in the area. The analysed data set consists of 392 earthquakes with local magnitudes ranging from 1.0 to 4.7. We defined a new, detailed 1-D velocity model to relocate the earthquakes that occurred in central Sicily, and we calculated a Moho depth of 37 km and a mean VP/VS ratio of 1.73. The relocated seismic events are clustered mainly in the area north of Caltanissetta (e.g. Mainland Sicily) and in the northeastern sector (Madonie Mountains) of the study area; only minor and greatly dispersed seismicity is located in the western sector, near Belice, and along the southern coast, between Gela and Sciacca. The relocated hypocentral distribution depicts a bimodal pattern: 50 per cent of the events occur within the upper crust at depths less than ~16 km, 40 per cent of the events occur within the middle and depth crust, at depths between 16 and 32 km, and the remaining 10 per cent occur at subcrustal depths. The energy release pattern shows a similar depth distribution. On the basis of the kinematic analysis of 38 newly computed focal plane solutions, two major geographically distinct seismotectonic domains are distinguished: the Madonie Mountain domain, with prevalent extensional and extensional-oblique kinematics associated with upper crust Late Pliocene–Quaternary faulting, and the Mainland Sicily domain, with prevalent compressional and compressional-oblique kinematics associated with thrust faulting, at mid to deep crust depth, along the north-dipping Sicilian Basal Thrust (SBT). The stress inversion of the Mainland Sicily focal solutions integrated with neighbouring mechanisms available in the literature highlights a regional homogeneous compressional tensor, with a subhorizontal NNW–SSE-striking σ1 axis. In addition, on the basis of geodetic data, the Mainland Sicily domain may be attributed to the SSE-ward thrusting of the Mainland Sicily block along the SBT plane. Seismogenic shearing along the SBT at mid-crustal depths was responsible for the unexpected Belice 1968 earthquake (Mw 6.1), with evident implications in terms of hazard assessment.
    Description: Published
    Description: 1237-2252
    Description: 1.1. TTC - Monitoraggio sismico del territorio nazionale
    Description: 3.2. Tettonica attiva
    Description: 3.3. Geodinamica e struttura dell'interno della Terra
    Description: 5.2. TTC - Banche dati di sismologia strumentale
    Description: JCR Journal
    Description: restricted
    Keywords: Seismicity and tectonics ; Continental tectonics: compressional ; Dynamics: seismotectonics ; Crustal structure ; Europe ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous ; 04. Solid Earth::04.06. Seismology::04.06.01. Earthquake faults: properties and evolution ; 04. Solid Earth::04.06. Seismology::04.06.03. Earthquake source and dynamics ; 04. Solid Earth::04.07. Tectonophysics::04.07.99. General or miscellaneous ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics ; 04. Solid Earth::04.07. Tectonophysics::04.07.04. Plate boundaries, motion, and tectonics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 48
    Publication Date: 2012-12-26
    Description: by Ping-Ping Yao, Lei Qian, Yong Xia, Fang Xu, Zhang-Nv Yang, Rong-Hui Xie, Xiao Li, Wei-Feng Liang, Xiao-Xiao Huang, Zhi-Yong Zhu, Han-Ping Zhu A reliable disease model mimicking Enterovirus 71 (EV71) infection in humans is essential for understanding pathogenesis and for developing a safe and effective vaccine. Commonly used rodent models including mouse or rat models are not suitable for vaccine evaluation because the rodents are resistant to EV71 infection after they reach the age of 6 days. In this study, 21-day-old gerbils inoculated intraperitoneally (IP) with a non mouse-adapted EV71 strain developed neurological lesion-related signs including hind limb paralysis, slowness, ataxia and lethargy similar to those of central nervous system (CNS) infection of EV71 in humans. The infected gerbils eventually died of the neurological lesions and EV71 could be isolated from lung, liver, spleen, kidney, heart, spinal cord, brain cortex, brainstem and skeletal muscle. Significantly high virus replication was detected in spinal cord, brainstem and skeletal muscle by cellular analysis, real-time quantitative PCR (RT-PCR) and immunohistochemical staining. Histopathologic changes such as neuronal degeneration, neuronal loss and neuronophagia were observed in spinal cord, brain cortex, brainstem, and skeletal muscle along with necrotizing myositis and splenic atrophy. Gerbils that received two doses of inactive whole-virus vaccine showed no EV71-specific symptoms after challenged with EV71. In contrast, gerbils that received mock vaccination died of EV71-induced neuropathology after challenged with EV71. The result indicates that gerbils can serve as a reliable disease model for evaluating safety and efficacy of EV71 vaccine.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 49
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2012-12-27
    Description: by Anna Ligasová, Dmytro Strunin, Radek Liboska, Ivan Rosenberg, Karel Koberna A new method of the light microscopy detection of BrdU-labeled DNA in situ is described. It is based on the oxidative attack at the deoxyribose moiety by copper(I) in the presence of oxygen, which leads to the abstraction of hydrogen atom from deoxyribose culminating in the elimination of the nucleobase, scission of the nucleic-acid strand and formation of frequent gaps. The gaps allow the reaction of the antibodies with the commonly used markers of replication (e.g. 5-bromo-2′-deoxyuridine), which are otherwise masked. The method developed makes it possible to detect nuclear and mitochondrial DNA replication efficiently. In most cases, it does not inhibit effective protein detections and in addition enables simultaneous localization of newly-synthesized RNA. The alternative presently-used methods result in protein denaturation and/or extensive DNA cleavage followed by the DNA-bound proteins peeling off.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 50
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2012-12-27
    Description: by Francesca Collu, Matteo Ceccarelli, Paolo Ruggerone Ligand-receptor interactions are at the basis of the mediation of our physiological responses to a large variety of ligands, such as hormones, neurotransmitters and environmental stimulants, and their tuning represents the goal of a large variety of therapies. Several molecular details of these interactions are still largely unknown. In an effort to shed some light on this important issue, we performed a computational study on the interaction of two related compounds differing by a single methyl group (clozapine and desmethylclozapine) with a -opioid receptor. According to experiments, desmethylclozapine is more active than clozapine, providing a system well suited for a comparative study. We investigated stable configurations of the two drugs inside the receptor by simulating their escape routes by molecular dynamics simulations. Our results point out that the action of the compounds might be related to the spatial and temporal distribution of the affinity sites they visit during their permanency. Moreover, no particularly pronounced structural perturbations of the receptor were detected during the simulations, reinforcing the idea of a strong dynamical character of the interaction process, with an important role played by the solvent in addition.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 51
    Publication Date: 2012-12-27
    Description: by Qiang Feng, Xia Zou, Ling Lu, Yun Li, Yunzhang Liu, Jianfeng Zhou, Cunming Duan REDD1/redd1 is a stress-response gene that is induced under various stressful conditions such as hypoxia, DNA damage, and energy stress. The increased REDD1 inhibits mTOR signaling and cell growth. Here we report an unexpected role of Redd1 in regulating dorsoventral patterning in zebrafish embryos and the underlying mechanisms. Zebrafish redd1 mRNA is maternally deposited. Although it is ubiquitously detected in many adult tissues, its expression is highly tissue-specific and dynamic during early development. Hypoxia and heat shock strongly induce redd1 expression in zebrafish embryos. Knockdown of Redd1 using two independent morpholinos results in dorsalized embryos and this effect can be rescued by injecting redd1 mRNA. Forced expression of Redd1 ventralizes embryos. Co-expression of Redd1 with Wnt3a or a constitutively active form of β-catenin suggests that Redd1 alters dorsoventral patterning by antagonizing the Wnt/β-catenin signaling pathway. These findings have unraveled a novel role of Redd1 in early development by antagonizing Wnt/β-catenin signaling.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 52
    facet.materialart.
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2012-12-27
    Description: by Claudia Figueroa-Romero, Junguk Hur, Diane E. Bender, Colin E. Delaney, Michael D. Cataldo, Andrea L. Smith, Raymond Yung, Douglas M. Ruden, Brian C. Callaghan, Eva L. Feldman Amyotrophic lateral sclerosis (ALS) is a terminal disease involving the progressive degeneration of motor neurons within the motor cortex, brainstem and spinal cord. Most cases are sporadic (sALS) with unknown causes suggesting that the etiology of sALS may not be limited to the genotype of patients, but may be influenced by exposure to environmental factors. Alterations in epigenetic modifications are likely to play a role in disease onset and progression in ALS, as aberrant epigenetic patterns may be acquired throughout life. The aim of this study was to identify epigenetic marks associated with sALS. We hypothesize that epigenetic modifications may alter the expression of pathogenesis-related genes leading to the onset and progression of sALS. Using ELISA assays, we observed alterations in global methylation (5 mC) and hydroxymethylation (5 HmC) in postmortem sALS spinal cord but not in whole blood. Loci-specific differentially methylated and expressed genes in sALS spinal cord were identified by genome-wide 5mC and expression profiling using high-throughput microarrays. Concordant direction, hyper- or hypo-5mC with parallel changes in gene expression (under- or over-expression), was observed in 112 genes highly associated with biological functions related to immune and inflammation response. Furthermore, literature-based analysis identified potential associations among the epigenes. Integration of methylomics and transcriptomics data successfully revealed methylation changes in sALS spinal cord. This study represents an initial identification of epigenetic regulatory mechanisms in sALS which may improve our understanding of sALS pathogenesis for the identification of biomarkers and new therapeutic targets.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 53
    Publication Date: 2012-12-27
    Description: by Wen-Yang Tsai, Szu-Chia Hsieh, Chih-Yun Lai, Hong-En Lin, Vivek R. Nerurkar, Wei-Kung Wang Background The envelope (E) protein of dengue virus (DENV) is the major immunogen for dengue vaccine development. At the C-terminus are two α-helices (EH1 and EH2) and two transmembrane domains (ET1 and ET2). After synthesis, E protein forms a heterodimer with the precursor membrane (prM) protein, which has been shown as a chaperone for E protein and could prevent premature fusion of E protein during maturation. Recent reports of enhancement of DENV infectivity by anti-prM monoclonal antibodies (mAbs) suggest the presence of prM protein in dengue vaccine is potentially harmful. A better understanding of prM-E interaction and its effect on recognition of E and prM proteins by different antibodies would provide important information for future design of safe and effective subunit dengue vaccines. Methodology/Principal Findings In this study, we examined a series of C-terminal truncation constructs of DENV4 prME, E and prM. In the absence of E protein, prM protein expressed poorly. In the presence of E protein, the expression of prM protein increased in a dose-dependent manner. Radioimmunoprecipitation, sucrose gradient sedimentation and pulse-chase experiments revealed ET1 and EH2 were involved in prM-E interaction and EH2 in maintaining the stability of prM protein. Dot blot assay revealed E protein affected the recognition of prM protein by an anti-prM mAb; truncation of EH2 or EH1 affected the recognition of E protein by several anti-E mAbs, which was further verified by capture ELISA. The E protein ectodomain alone can be recognized well by all anti-E mAbs tested. Conclusions/Significance A C-terminal domain (EH2) of DENV E protein can affect the expression and stability of its chaperone prM protein. These findings not only add to our understanding of the interaction between prM and E proteins, but also suggest the ectodomain of E protein alone could be a potential subunit immunogen without inducing anti-prM response.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 54
    Publication Date: 2012-12-27
    Description: by Quancheng Zhou, Guihua Sheng The thermal decomposition of Perilla frutescens polysaccharide was examined by thermogravimetry, differential thermogravimetry, and differential thermal analysis. The results showed that the mass loss of the substance proceeded in three steps. The first stage can be attributed to the expulsion of the water from ambient temperature to 182°C. The second stage corresponded to devolatilization from 182°C to 439°C. The residue slowly degraded in the third stage. The weight loss in air is faster than that in nitrogen, because the oxygen in air accelerated the pyrolytic reaction speed reaction. The heating rate significantly affected the pyrolysis of the sample. Similar activation energies of the degradation process (210–211 kJ mol −1 ) were obtained by the FWO, KAS, and Popescu techniques. According to Popescu mechanism functions, the possible kinetic model was estimated to be Avrami–Erofeev 20 g ( α ) = [−ln(1– α )] 4 .
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 55
    Publication Date: 2012-12-27
    Description: by Linda Irvine, Donald W. Falconer, Claire Jones, Ian W. Ricketts, Brian Williams, Iain K. Crombie Background Process evaluation is essential in developing, piloting and evaluating complex interventions. This often involves observation of intervention delivery and interviews with study participants. Mobile telephone interventions involve no face to face contact, making conventional process evaluation difficult. This study assesses the utility of novel techniques for process evaluation involving no face to face contact. Methods Text messages were delivered to 34 disadvantaged men as part of a feasibility study of a brief alcohol intervention. Process evaluation focused on delivery of the text messages and responses received from study participants. The computerized delivery system captured data on receipt of the messages. The text messages, delivered over 28 days, included nine which asked questions. Responses to these questions served as one technique for process evaluation by ascertaining the nature of engagement with the study and with steps on the causal chain to behavior change. Results A total of 646 SMS text messages were sent to participants. Of these, 613 messages (95%) were recorded as delivered to participants’ telephones. 88% of participants responded to messages that asked questions. There was little attenuation in responses to the questions across the intervention period. Content analysis of the responses revealed that participants engaged with text messages, thought deeply about their content and provided carefully considered personal responses to the questions. Conclusions Socially disadvantaged men, a hard to reach population, engaged in a meaningful way over a sustained period with an interactive intervention delivered by text message. The novel process measures used in the study are unobtrusive, low cost and collect real-time data on all participants. They assessed the fidelity of delivery of the intervention and monitored retention in the study. They measured levels of engagement and identified participants’ reactions to components of the intervention. These methods provide a valuable addition to conventional process evaluation techniques.
    Electronic ISSN: 1932-6203
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  • 56
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    In: PLoS ONE
    Publication Date: 2012-12-27
    Description: by Golnar Karimian, Manon Buist-Homan, Bojana Mikus, Robert H. Henning, Klaas Nico Faber, Han Moshage Conclusion Angiotensin II protects hepatocytes from bile salt-induced apoptosis through a combined activation of PI3-kinase, MAPKs, PKC pathways and inhibition of bile salt-induced ER stress. Our results suggest a mechanism for the observed hepatocyte-toxicity of Sartans (angiotensin receptor blockers, ARBs) in some patients with chronic liver injury.
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  • 57
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    In: PLoS ONE
    Publication Date: 2012-12-27
    Description: by Nuria Kotecki, Nicolas Penel, Antoine Adenis, Charles Ferte, Stéphanie Clisant Background The diagnosis of tumour progression or progressive disease (PD) is a key element for designing and interpreting contemporary phase II trials. In some cases, PD is stated by the physician and is not formally confirmed by imaging. Purpose In this study, we intend to analyze the value of the PD based on clinical judgment and the risk of overestimating the occurrence of PD by clinical judgment. Methods We have conducted a single-centre retrospective study to analyse the diagnostic accuracy of this clinical judgment compared to planned imaging including all patients enrolled in our institution in phase II trials investigating systemic treatments for advanced solid tumours between January 2008 and November 2010. Results The positive predictive value (PPV) and the specificity of clinical judgment of PD was very high (〉90%). Conclusions According to this study, the clinical judgment of PD is highly predictive of radiological PD as assessed, for example, by RECIST. Physicians do not overestimate PD occurence. Clinical judgment of PD could be taken into account in the definition of PD.
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  • 58
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    In: PLoS ONE
    Publication Date: 2012-12-27
    Description: by Aziza El Harchi, Dario Melgari, Yi Hong Zhang, Henggui Zhang, Jules C. Hancox Background The familial Short QT Syndrome (SQTS) is associated with an increased risk of cardiac arrhythmia and sudden death. Gain-of-function mutations in the hERG K + channel protein have been linked to variant 1 of the SQTS. A hERG channel pore (T618I) mutation has recently been identified in families with heritable SQTS. This study aimed to determine effects of the T618I-hERG mutation on (i) hERG current (I hERG ) elicited by ventricular action potentials; (ii) the sensitivity of I hERG to inhibition by four clinically used antiarrhythmic drugs. Methods Electrophysiological recordings of I hERG were made at 37°C from HEK 293 cells expressing wild-type (WT) or T618I hERG. Whole-cell patch clamp recording was performed using both conventional voltage clamp and ventricular action potential (AP) clamp methods. Results Under conventional voltage-clamp, WT I hERG peaked at 0-+10 mV, whilst for T618I I hERG maximal current was right-ward shifted to ∼ +40 mV. Voltage-dependent activation and inactivation of T618I I hERG were positively shifted (respectively by +15 and ∼ +25 mV) compared to WT I hERG . The I hERG ‘window’ was increased for T618I compared to WT hERG. Under ventricular AP clamp, maximal repolarising WT I hERG occurred at ∼ -30 mV, whilst for T618I hERG peak I hERG occurred earlier during AP repolarisation, at ∼ +5 mV. Under conventional voltage clamp, half-maximal inhibitory concentrations (IC 50 ) for inhibition of I hERG tails by quinidine, disopyramide, D-sotalol and flecainide for T618I hERG ranged between 1.4 and 3.2 fold that for WT hERG. Under action potential voltage clamp, T618I IC 50 s ranged from 1.2 to 2.0 fold the corresponding IC 50 values for WT hERG. Conclusions The T618I mutation produces a more modest effect on repolarising I hERG than reported previously for the N588K-hERG variant 1 SQTS mutation. All drugs studied here appear substantially to retain their ability to inhibit I hERG in the setting of the SQTS-linked T618I mutation.
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  • 59
    Publication Date: 2012-12-27
    Description: by Adelene Ai-Lian Song, Janna Ong Abdullah, Mohd. Puad Abdullah, Norazizah Shafee, Roohaida Othman, Ee-Fun Tan, Normah Mohd. Noor, Abdul Rahim Raha Isoprenoids are a large and diverse group of metabolites with interesting properties such as flavour, fragrance and therapeutic properties. They are produced via two pathways, the mevalonate pathway or the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway. While plants are the richest source of isoprenoids, they are not the most efficient producers. Escherichia coli and yeasts have been extensively studied as heterologous hosts for plant isoprenoids production. In the current study, we describe the usage of the food grade Lactococcus lactis as a potential heterologous host for the production of sesquiterpenes from a local herbaceous Malaysian plant, Persicaria minor (synonym Polygonum minus ). A sesquiterpene synthase gene from P. minor was successfully cloned and expressed in L. lactis . The expressed protein was identified to be a β-sesquiphellandrene synthase as it was demonstrated to be functional in producing β-sesquiphellandrene at 85.4% of the total sesquiterpenes produced based on in vitro enzymatic assays. The recombinant L. lactis strain developed in this study was also capable of producing β-sesquiphellandrene in vivo without exogenous substrates supplementation. In addition, overexpression of the strain’s endogenous 3-hydroxy-3-methylglutaryl coenzyme-A reductase (HMGR), an established rate-limiting enzyme in the eukaryotic mevalonate pathway, increased the production level of β-sesquiphellandrene by 1.25–1.60 fold. The highest amount achieved was 33 nM at 2 h post-induction.
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  • 60
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    In: PLoS ONE
    Publication Date: 2012-12-27
    Description: by Larisa R. G. DeSantis, Blaine W. Schubert, Jessica R. Scott, Peter S. Ungar The saber-toothed cat, Smilodon fatalis , and American lion, Panthera atrox , were among the largest terrestrial carnivores that lived during the Pleistocene, going extinct along with other megafauna ∼12,000 years ago. Previous work suggests that times were difficult at La Brea (California) during the late Pleistocene, as nearly all carnivores have greater incidences of tooth breakage (used to infer greater carcass utilization) compared to today. As Dental Microwear Texture Analysis (DMTA) can differentiate between levels of bone consumption in extant carnivores, we use DMTA to clarify the dietary niches of extinct carnivorans from La Brea. Specifically, we test the hypothesis that times were tough at La Brea with carnivorous taxa utilizing more of the carcasses. Our results show no evidence of bone crushing by P. atrox , with DMTA attributes most similar to the extant cheetah, Acinonyx jubatus , which actively avoids bone. In contrast, S. fatalis has DMTA attributes most similar to the African lion Panthera leo , implying that S. fatalis did not avoid bone to the extent previously suggested by SEM microwear data. DMTA characters most indicative of bone consumption (i.e., complexity and textural fill volume) suggest that carcass utilization by the extinct carnivorans was not necessarily more complete during the Pleistocene at La Brea; thus, times may not have been “tougher” than the present. Additionally, minor to no significant differences in DMTA attributes from older (∼30–35 Ka) to younger (∼11.5 Ka) deposits offer little evidence that declining prey resources were a primary cause of extinction for these large cats.
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  • 61
    Publication Date: 2012-12-27
    Description: by Feng Qu, Cai-Sheng Wu, Jin-Feng Hou, Ying Jin, Jin-Lan Zhang Background Hypersensitivity diseases are associated with many severe human illnesses, including leprosy and tuberculosis. Emerging evidence suggests that the pathogenesis and pathological mechanisms of treating these diseases may be attributable to sphingolipid metabolism. Methods High performance liquid chromatography-tandem mass spectrometry was employed to target and measure 43 core sphingolipids in the plasma, kidneys, livers and spleens of BALB/c mice from four experimental groups: control, delayed-type hypersensitivity (DTH) model, DTH+triptolide, and control+triptolide. Orthogonal partial least squares discriminant analysis (OPLS-DA) was used to identify potential biomarkers associated with variance between groups. Relationships between the identified biomarkers and disease markers were evaluated by Spearman correlation. Results As a treatment to hypersensitivity disease, triptolide significantly inhibit the ear swelling and recover the reduction of splenic index caused by DTH. The sphingolipidomic result revealed marked alterations in sphingolipid levels between groups that were associated with the effects of the disease and triptolide treatment. Based on this data, 23 potential biomarkers were identified by OPLS-DA, and seven of these biomarkers correlated markedly with the disease markers (p
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  • 62
    Publication Date: 2012-12-28
    Description: by Maria Kalyuga, David Gallego-Ortega, Heather J. Lee, Daniel L. Roden, Mark J. Cowley, C. Elizabeth Caldon, Andrew Stone, Stephanie L. Allerdice, Fatima Valdes-Mora, Rosalind Launchbury, Aaron L. Statham, Nicola Armstrong, M. Chehani Alles, Adelaide Young, Andrea Egger, Wendy Au, Catherine L. Piggin, Cara J. Evans, Anita Ledger, Tilman Brummer, Samantha R. Oakes, Warren Kaplan, Julia M. W. Gee, Robert I. Nicholson, Robert L. Sutherland, Alexander Swarbrick, Matthew J. Naylor, Susan J. Clark, Jason S. Carroll, Christopher J. Ormandy We have previously shown that during pregnancy the E-twenty-six (ETS) transcription factor ELF5 directs the differentiation of mammary progenitor cells toward the estrogen receptor (ER)-negative and milk producing cell lineage, raising the possibility that ELF5 may suppress the estrogen sensitivity of breast cancers. To test this we constructed inducible models of ELF5 expression in ER positive luminal breast cancer cells and interrogated them using transcript profiling and chromatin immunoprecipitation of DNA followed by DNA sequencing (ChIP-Seq). ELF5 suppressed ER and FOXA1 expression and broadly suppressed ER-driven patterns of gene expression including sets of genes distinguishing the luminal molecular subtype. Direct transcriptional targets of ELF5, which included FOXA1 , EGFR , and MYC , accurately classified a large cohort of breast cancers into their intrinsic molecular subtypes, predicted ER status with high precision, and defined groups with differential prognosis. Knockdown of ELF5 in basal breast cancer cell lines suppressed basal patterns of gene expression and produced a shift in molecular subtype toward the claudin-low and normal-like groups. Luminal breast cancer cells that acquired resistance to the antiestrogen Tamoxifen showed greatly elevated levels of ELF5 and its transcriptional signature, and became dependent on ELF5 for proliferation, compared to the parental cells. Thus ELF5 provides a key transcriptional determinant of breast cancer molecular subtype by suppression of estrogen sensitivity in luminal breast cancer cells and promotion of basal characteristics in basal breast cancer cells, an action that may be utilised to acquire antiestrogen resistance.
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  • 63
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    Publication Date: 2012-12-28
    Description: by Casey S. Greene, Olga G. Troyanskaya Modern experimental strategies often generate genome-scale measurements of human tissues or cell lines in various physiological states. Investigators often use these datasets individually to help elucidate molecular mechanisms of human diseases. Here we discuss approaches that effectively weight and integrate hundreds of heterogeneous datasets to gene-gene networks that focus on a specific process or disease. Diverse and systematic genome-scale measurements provide such approaches both a great deal of power and a number of challenges. We discuss some such challenges as well as methods to address them. We also raise important considerations for the assessment and evaluation of such approaches. When carefully applied, these integrative data-driven methods can make novel high-quality predictions that can transform our understanding of the molecular-basis of human disease.
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  • 64
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    Publication Date: 2012-12-28
    Description: by Dong-Yeon Cho, Yoo-Ah Kim, Teresa M. Przytycka Complex diseases are caused by a combination of genetic and environmental factors. Uncovering the molecular pathways through which genetic factors affect a phenotype is always difficult, but in the case of complex diseases this is further complicated since genetic factors in affected individuals might be different. In recent years, systems biology approaches and, more specifically, network based approaches emerged as powerful tools for studying complex diseases. These approaches are often built on the knowledge of physical or functional interactions between molecules which are usually represented as an interaction network. An interaction network not only reports the binary relationships between individual nodes but also encodes hidden higher level organization of cellular communication. Computational biologists were challenged with the task of uncovering this organization and utilizing it for the understanding of disease complexity, which prompted rich and diverse algorithmic approaches to be proposed. We start this chapter with a description of the general characteristics of complex diseases followed by a brief introduction to physical and functional networks. Next we will show how these networks are used to leverage genotype, gene expression, and other types of data to identify dysregulated pathways, infer the relationships between genotype and phenotype, and explain disease heterogeneity. We group the methods by common underlying principles and first provide a high level description of the principles followed by more specific examples. We hope that this chapter will give readers an appreciation for the wealth of algorithmic techniques that have been developed for the purpose of studying complex diseases as well as insight into their strengths and limitations.
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  • 65
    Publication Date: 2012-12-28
    Description: by Nitika Raychaudhuri, Raphaelle Dubruille, Guillermo A. Orsi, Homayoun C. Bagheri, Benjamin Loppin, Christian F. Lehner In Drosophila melanogaster , as in many animal and plant species, centromere identity is specified epigenetically. In proliferating cells, a centromere-specific histone H3 variant (CenH3), named Cid in Drosophila and Cenp-A in humans, is a crucial component of the epigenetic centromere mark. Hence, maintenance of the amount and chromosomal location of CenH3 during mitotic proliferation is important. Interestingly, CenH3 may have different roles during meiosis and the onset of embryogenesis. In gametes of Caenorhabditis elegans , and possibly in plants, centromere marking is independent of CenH3. Moreover, male gamete differentiation in animals often includes global nucleosome for protamine exchange that potentially could remove CenH3 nucleosomes. Here we demonstrate that the control of Cid loading during male meiosis is distinct from the regulation observed during the mitotic cycles of early embryogenesis. But Cid is present in mature sperm. After strong Cid depletion in sperm, paternal centromeres fail to integrate into the gonomeric spindle of the first mitosis, resulting in gynogenetic haploid embryos. Furthermore, after moderate depletion, paternal centromeres are unable to re-acquire normal Cid levels in the next generation. We conclude that Cid in sperm is an essential component of the epigenetic centromere mark on paternal chromosomes and it exerts quantitative control over centromeric Cid levels throughout development. Hence, the amount of Cid that is loaded during each cell cycle appears to be determined primarily by the preexisting centromeric Cid, with little flexibility for compensation of accidental losses.
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  • 66
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    Publication Date: 2012-12-28
    Description: by Mileidy W. Gonzalez, Maricel G. Kann Proteins do not function in isolation; it is their interactions with one another and also with other molecules (e.g. DNA, RNA) that mediate metabolic and signaling pathways, cellular processes, and organismal systems. Due to their central role in biological function, protein interactions also control the mechanisms leading to healthy and diseased states in organisms. Diseases are often caused by mutations affecting the binding interface or leading to biochemically dysfunctional allosteric changes in proteins. Therefore, protein interaction networks can elucidate the molecular basis of disease, which in turn can inform methods for prevention, diagnosis, and treatment. In this chapter, we will describe the computational approaches to predict and map networks of protein interactions and briefly review the experimental methods to detect protein interactions. We will describe the application of protein interaction networks as a translational approach to the study of human disease and evaluate the challenges faced by these approaches.
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  • 67
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    Publication Date: 2012-12-28
    Description: by Benjamin J. Raphael Differences between individual human genomes, or between human and cancer genomes, range in scale from single nucleotide variants (SNVs) through intermediate and large-scale duplications, deletions, and rearrangements of genomic segments. The latter class, called structural variants (SVs), have received considerable attention in the past several years as they are a previously under appreciated source of variation in human genomes. Much of this recent attention is the result of the availability of higher-resolution technologies for measuring these variants, including both microarray-based techniques, and more recently, high-throughput DNA sequencing. We describe the genomic technologies and computational techniques currently used to measure SVs, focusing on applications in human and cancer genomics.
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  • 68
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    Publication Date: 2012-12-28
    Description: by David S. Wishart “Big” molecules such as proteins and genes still continue to capture the imagination of most biologists, biochemists and bioinformaticians. “Small” molecules, on the other hand, are the molecules that most biologists, biochemists and bioinformaticians prefer to ignore. However, it is becoming increasingly apparent that small molecules such as amino acids, lipids and sugars play a far more important role in all aspects of disease etiology and disease treatment than we realized. This particular chapter focuses on an emerging field of bioinformatics called “chemical bioinformatics” – a discipline that has evolved to help address the blended chemical and molecular biological needs of toxicogenomics, pharmacogenomics, metabolomics and systems biology. In the following pages we will cover several topics related to chemical bioinformatics. First, a brief overview of some of the most important or useful chemical bioinformatic resources will be given. Second, a more detailed overview will be given on those particular resources that allow researchers to connect small molecules to diseases. This section will focus on describing a number of recently developed databases or knowledgebases that explicitly relate small molecules – either as the treatment, symptom or cause – to disease. Finally a short discussion will be provided on newly emerging software tools that exploit these databases as a means to discover new biomarkers or even new treatments for disease.
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  • 69
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    Publication Date: 2012-12-28
    Description: by Joshua C. Denny Abstract: The combination of improved genomic analysis methods, decreasing genotyping costs, and increasing computing resources has led to an explosion of clinical genomic knowledge in the last decade. Similarly, healthcare systems are increasingly adopting robust electronic health record (EHR) systems that not only can improve health care, but also contain a vast repository of disease and treatment data that could be mined for genomic research. Indeed, institutions are creating EHR-linked DNA biobanks to enable genomic and pharmacogenomic research, using EHR data for phenotypic information. However, EHRs are designed primarily for clinical care, not research, so reuse of clinical EHR data for research purposes can be challenging. Difficulties in use of EHR data include: data availability, missing data, incorrect data, and vast quantities of unstructured narrative text data. Structured information includes billing codes, most laboratory reports, and other variables such as physiologic measurements and demographic information. Significant information, however, remains locked within EHR narrative text documents, including clinical notes and certain categories of test results, such as pathology and radiology reports. For relatively rare observations, combinations of simple free-text searches and billing codes may prove adequate when followed by manual chart review. However, to extract the large cohorts necessary for genome-wide association studies, natural language processing methods to process narrative text data may be needed. Combinations of structured and unstructured textual data can be mined to generate high-validity collections of cases and controls for a given condition. Once high-quality cases and controls are identified, EHR-derived cases can be used for genomic discovery and validation. Since EHR data includes a broad sampling of clinically-relevant phenotypic information, it may enable multiple genomic investigations upon a single set of genotyped individuals. This chapter reviews several examples of phenotype extraction and their application to genetic research, demonstrating a viable future for genomic discovery using EHR-linked data.
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  • 70
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    Publication Date: 2012-12-28
    Description: by Konrad J. Karczewski, Roxana Daneshjou, Russ B. Altman There is great variation in drug-response phenotypes, and a “one size fits all” paradigm for drug delivery is flawed. Pharmacogenomics is the study of how human genetic information impacts drug response, and it aims to improve efficacy and reduced side effects. In this article, we provide an overview of pharmacogenetics, including pharmacokinetics (PK), pharmacodynamics (PD), gene and pathway interactions, and off-target effects. We describe methods for discovering genetic factors in drug response, including genome-wide association studies (GWAS), expression analysis, and other methods such as chemoinformatics and natural language processing (NLP). We cover the practical applications of pharmacogenomics both in the pharmaceutical industry and in a clinical setting. In drug discovery, pharmacogenomics can be used to aid lead identification, anticipate adverse events, and assist in drug repurposing efforts. Moreover, pharmacogenomic discoveries show promise as important elements of physician decision support. Finally, we consider the ethical, regulatory, and reimbursement challenges that remain for the clinical implementation of pharmacogenomics.
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  • 71
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    Publication Date: 2012-12-28
    Description: by Yang Ding, Sarah S. Sharpe, Andrew Masse, Daniel I. Goldman The sandfish lizard ( Scincus scincus ) swims within granular media (sand) using axial body undulations to propel itself without the use of limbs. In previous work we predicted average swimming speed by developing a numerical simulation that incorporated experimentally measured biological kinematics into a multibody sandfish model. The model was coupled to an experimentally validated soft sphere discrete element method simulation of the granular medium. In this paper, we use the simulation to study the detailed mechanics of undulatory swimming in a “granular frictional fluid” and compare the predictions to our previously developed resistive force theory (RFT) which models sand-swimming using empirically determined granular drag laws. The simulation reveals that the forward speed of the center of mass (CoM) oscillates about its average speed in antiphase with head drag. The coupling between overall body motion and body deformation results in a non-trivial pattern in the magnitude of lateral displacement of the segments along the body. The actuator torque and segment power are maximal near the center of the body and decrease to zero toward the head and the tail. Approximately 30% of the net swimming power is dissipated in head drag. The power consumption is proportional to the frequency in the biologically relevant range, which confirms that frictional forces dominate during sand-swimming by the sandfish. Comparison of the segmental forces measured in simulation with the force on a laterally oscillating rod reveals that a granular hysteresis effect causes the overestimation of the body thrust forces in the RFT. Our models provide detailed testable predictions for biological locomotion in a granular environment.
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  • 72
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    Publication Date: 2012-12-28
    Description: by William R. Holmes, Leah Edelstein-Keshet Eukaryotic cell motility involves complex interactions of signalling molecules, cytoskeleton, cell membrane, and mechanics interacting in space and time. Collectively, these components are used by the cell to interpret and respond to external stimuli, leading to polarization, protrusion, adhesion formation, and myosin-facilitated retraction. When these processes are choreographed correctly, shape change and motility results. A wealth of experimental data have identified numerous molecular constituents involved in these processes, but the complexity of their interactions and spatial organization make this a challenging problem to understand. This has motivated theoretical and computational approaches with simplified caricatures of cell structure and behaviour, each aiming to gain better understanding of certain kinds of cells and/or repertoire of behaviour. Reaction–diffusion (RD) equations as well as equations of viscoelastic flows have been used to describe the motility machinery. In this review, we describe some of the recent computational models for cell motility, concentrating on simulations of cell shape changes (mainly in two but also three dimensions). The problem is challenging not only due to the difficulty of abstracting and simplifying biological complexity but also because computing RD or fluid flow equations in deforming regions, known as a “free-boundary” problem, is an extremely challenging problem in applied mathematics. Here we describe the distinct approaches, comparing their strengths and weaknesses, and the kinds of biological questions that they have been able to address.
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  • 73
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    Publication Date: 2012-12-28
    Description: by Maria Victoria Schneider, Rafael C. Jimenez This article aims to introduce the nature of data integration to life scientists. Generally, the subject of data integration is not discussed outside the field of computational science and is not covered in any detail, or even neglected, when teaching/training trainees. End users (hereby defined as wet-lab trainees, clinicians, lab researchers) will mostly interact with bioinformatics resources and tools through web interfaces that mask the user from the data integration processes. However, the lack of formal training or acquaintance with even simple database concepts and terminology often results in a real obstacle to the full comprehension of the resources and tools the end users wish to access. Understanding how data integration works is fundamental to empowering trainees to see the limitations as well as the possibilities when exploring, retrieving, and analysing biological data from databases. Here we introduce a game-based learning activity for training/teaching the topic of data integration that trainers/educators can adopt and adapt for their classroom. In particular we provide an example using DAS (Distributed Annotation Systems) as a method for data integration.
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  • 74
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    Publication Date: 2012-12-28
    Description: by Xochitl C. Morgan, Curtis Huttenhower Humans are essentially sterile during gestation, but during and after birth, every body surface, including the skin, mouth, and gut, becomes host to an enormous variety of microbes, bacterial, archaeal, fungal, and viral. Under normal circumstances, these microbes help us to digest our food and to maintain our immune systems, but dysfunction of the human microbiota has been linked to conditions ranging from inflammatory bowel disease to antibiotic-resistant infections. Modern high-throughput sequencing and bioinformatic tools provide a powerful means of understanding the contribution of the human microbiome to health and its potential as a target for therapeutic interventions. This chapter will first discuss the historical origins of microbiome studies and methods for determining the ecological diversity of a microbial community. Next, it will introduce shotgun sequencing technologies such as metagenomics and metatranscriptomics, the computational challenges and methods associated with these data, and how they enable microbiome analysis. Finally, it will conclude with examples of the functional genomics of the human microbiome and its influences upon health and disease.
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  • 75
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    Publication Date: 2012-12-28
    Description: by Ranjan V. Mannige, Charles L. Brooks, Eugene I. Shakhnovich Despite progresses in ancestral protein sequence reconstruction, much needs to be unraveled about the nature of the putative last common ancestral proteome that served as the prototype of all extant lifeforms. Here, we present data that indicate a steady decline (oil escape) in proteome hydrophobicity over species evolvedness (node number) evident in 272 diverse proteomes, which indicates a highly hydrophobic (oily) last common ancestor (LCA). This trend, obtained from simple considerations (free from sequence reconstruction methods), was corroborated by regression studies within homologous and orthologous protein clusters as well as phylogenetic estimates of the ancestral oil content. While indicating an inherent irreversibility in molecular evolution, oil escape also serves as a rare and universal reaction-coordinate for evolution (reinforcing Darwin's principle of Common Descent), and may prove important in matters such as (i) explaining the emergence of intrinsically disordered proteins, (ii) developing composition- and speciation-based “global” molecular clocks, and (iii) improving the statistical methods for ancestral sequence reconstruction.
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  • 76
    Publication Date: 2012-12-28
    Description: by Oliver Ratmann, Gé Donker, Adam Meijer, Christophe Fraser, Katia Koelle A key priority in infectious disease research is to understand the ecological and evolutionary drivers of viral diseases from data on disease incidence as well as viral genetic and antigenic variation. We propose using a simulation-based, Bayesian method known as Approximate Bayesian Computation (ABC) to fit and assess phylodynamic models that simulate pathogen evolution and ecology against summaries of these data. We illustrate the versatility of the method by analyzing two spatial models describing the phylodynamics of interpandemic human influenza virus subtype A(H3N2). The first model captures antigenic drift phenomenologically with continuously waning immunity, and the second epochal evolution model describes the replacement of major, relatively long-lived antigenic clusters. Combining features of long-term surveillance data from the Netherlands with features of influenza A (H3N2) hemagglutinin gene sequences sampled in northern Europe, key phylodynamic parameters can be estimated with ABC. Goodness-of-fit analyses reveal that the irregularity in interannual incidence and H3N2's ladder-like hemagglutinin phylogeny are quantitatively only reproduced under the epochal evolution model within a spatial context. However, the concomitant incidence dynamics result in a very large reproductive number and are not consistent with empirical estimates of H3N2's population level attack rate. These results demonstrate that the interactions between the evolutionary and ecological processes impose multiple quantitative constraints on the phylodynamic trajectories of influenza A(H3N2), so that sequence and surveillance data can be used synergistically. ABC, one of several data synthesis approaches, can easily interface a broad class of phylodynamic models with various types of data but requires careful calibration of the summaries and tolerance parameters.
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  • 77
    Publication Date: 2012-12-28
    Description: by Jens Vindahl Kringelum, Claus Lundegaard, Ole Lund, Morten Nielsen The interaction between antibodies and antigens is one of the most important immune system mechanisms for clearing infectious organisms from the host. Antibodies bind to antigens at sites referred to as B-cell epitopes. Identification of the exact location of B-cell epitopes is essential in several biomedical applications such as; rational vaccine design, development of disease diagnostics and immunotherapeutics. However, experimental mapping of epitopes is resource intensive making in silico methods an appealing complementary approach. To date, the reported performance of methods for in silico mapping of B-cell epitopes has been moderate. Several issues regarding the evaluation data sets may however have led to the performance values being underestimated: Rarely, all potential epitopes have been mapped on an antigen, and antibodies are generally raised against the antigen in a given biological context not against the antigen monomer. Improper dealing with these aspects leads to many artificial false positive predictions and hence to incorrect low performance values. To demonstrate the impact of proper benchmark definitions, we here present an updated version of the DiscoTope method incorporating a novel spatial neighborhood definition and half-sphere exposure as surface measure. Compared to other state-of-the-art prediction methods, Discotope-2.0 displayed improved performance both in cross-validation and in independent evaluations. Using DiscoTope-2.0 , we assessed the impact on performance when using proper benchmark definitions. For 13 proteins in the training data set where sufficient biological information was available to make a proper benchmark redefinition, the average AUC performance was improved from 0.791 to 0.824. Similarly, the average AUC performance on an independent evaluation data set improved from 0.712 to 0.727. Our results thus demonstrate that given proper benchmark definitions, B-cell epitope prediction methods achieve highly significant predictive performances suggesting these tools to be a powerful asset in rational epitope discovery. The updated version of DiscoTope is available at www.cbs.dtu.dk/services/DiscoTope-2.0.
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  • 78
    Publication Date: 2012-12-28
    Description: by Federica Chiappori, Ivan Merelli, Giorgio Colombo, Luciano Milanesi, Giulia Morra Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD) modulate substrate recognition at the Substrate Binding Domain (SBD). Herein, a comparative analysis of an allosteric (Hsp70-DnaK) and a non-allosteric structural homolog (Hsp110-Sse1) of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.
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  • 79
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    Publication Date: 2012-12-28
    Description: by Cameron W. Harvey, Huijing Du, Zhiliang Xu, Dale Kaiser, Igor Aranson, Mark Alber The formation of spore-filled fruiting bodies by myxobacteria is a fascinating case of multicellular self-organization by bacteria. The organization of Myxococcus xanthus into fruiting bodies has long been studied not only as an important example of collective motion of bacteria, but also as a simplified model for developmental morphogenesis. Sporulation within the nascent fruiting body requires signaling between moving cells in order that the rod-shaped self-propelled cells differentiate into spores at the appropriate time. Probing the three-dimensional structure of myxobacteria fruiting bodies has previously presented a challenge due to limitations of different imaging methods. A new technique using Infrared Optical Coherence Tomography (OCT) revealed previously unknown details of the internal structure of M. xanthus fruiting bodies consisting of interconnected pockets of relative high and low spore density regions. To make sense of the experimentally observed structure, modeling and computer simulations were used to test a hypothesized mechanism that could produce high-density pockets of spores. The mechanism consists of self-propelled cells aligning with each other and signaling by end-to-end contact to coordinate the process of differentiation resulting in a pattern of clusters observed in the experiment. The integration of novel OCT experimental techniques with computational simulations can provide new insight into the mechanisms that can give rise to the pattern formation seen in other biological systems such as dictyostelids, social amoeba known to form multicellular aggregates observed as slugs under starvation conditions.
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  • 80
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    Publication Date: 2012-12-28
    Description: by Tobias Wijshake, Liviu A. Malureanu, Darren J. Baker, Karthik B. Jeganathan, Bart van de Sluis, Jan M. van Deursen Mosaic Variegated Aneuploidy (MVA) syndrome is a rare autosomal recessive disorder characterized by inaccurate chromosome segregation and high rates of near-diploid aneuploidy. Children with MVA syndrome die at an early age, are cancer prone, and have progeroid features like facial dysmorphisms, short stature, and cataracts. The majority of MVA cases are linked to mutations in BUBR1 , a mitotic checkpoint gene required for proper chromosome segregation. Affected patients either have bi-allelic BUBR1 mutations, with one allele harboring a missense mutation and the other a nonsense mutation, or mono-allelic BUBR1 mutations combined with allelic variants that yield low amounts of wild-type BubR1 protein. Parents of MVA patients that carry single allele mutations have mild mitotic defects, but whether they are at risk for any of the pathologies associated with MVA syndrome is unknown. To address this, we engineered a mouse model for the nonsense mutation 2211insGTTA (referred to as GTTA) found in MVA patients with bi-allelic BUBR1 mutations. Here we report that both the median and maximum lifespans of the resulting BubR1 +/GTTA mice are significantly reduced. Furthermore, BubR1 +/GTTA mice develop several aging-related phenotypes at an accelerated rate, including cataract formation, lordokyphosis, skeletal muscle wasting, impaired exercise ability, and fat loss. BubR1 +/GTTA mice develop mild aneuploidies and show enhanced growth of carcinogen-induced tumors. Collectively, these data demonstrate that the BUBR1 GTTA mutation compromises longevity and healthspan, raising the interesting possibility that mono-allelic changes in BUBR1 might contribute to differences in aging rates in the general population.
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  • 81
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    Publication Date: 2012-12-28
    Description: by H. Deborah Chen, Mollie W. Jewett, Eduardo A. Groisman Changes in gene regulatory circuits often give rise to phenotypic differences among closely related organisms. In bacteria, these changes can result from alterations in the ancestral genome and/or be brought about by genes acquired by horizontal transfer. Here, we identify an allele of the ancestral transcription factor PmrA that requires the horizontally acquired pmrD gene product to promote gene expression. We determined that a single amino acid difference between the PmrA proteins from the human adapted Salmonella enterica serovar Paratyphi B and the broad host range S. enterica serovar Typhimurium rendered transcription of PmrA-activated genes dependent on the PmrD protein in the former but not the latter serovar. Bacteria harboring the serovar Typhimurium allele exhibited polymyxin B resistance under PmrA- or under PmrA- and PmrD-inducing conditions. By contrast, isogenic strains with the serovar Paratyphi B allele displayed PmrA-regulated polymyxin B resistance only when experiencing activating conditions for both PmrA and PmrD. We establish that the two PmrA orthologs display quantitative differences in several biochemical properties. Strains harboring the serovar Paratyphi B allele showed enhanced biofilm formation, a property that might promote serovar Paratyphi B's chronic infection of the gallbladder. Our findings illustrate how subtle differences in ancestral genes can impact the ability of horizontally acquired genes to confer new properties.
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  • 82
    Publication Date: 2012-12-28
    Description: by Roxana del Rio, Ryan D. McAllister, Nathan D. Meeker, Emma H. Wall, Jeffrey P. Bond, Vasileios C. Kyttaris, George C. Tsokos, Kenneth S. K. Tung, Cory Teuscher Experimental autoimmune orchitis (EAO), the principal model of non-infectious testicular inflammatory disease, can be induced in susceptible mouse strains by immunization with autologous testicular homogenate and appropriate adjuvants. As previously established, the genome of DBA/2J mice encodes genes that are capable of conferring dominant resistance to EAO, while the genome of BALB/cByJ mice does not and they are therefore susceptible to EAO. In a genome scan, we previously identified Orch3 as the major quantitative trait locus controlling dominant resistance to EAO and mapped it to chromosome 11. Here, by utilizing a forward genetic approach, we identified kinesin family member 1C ( Kif1c ) as a positional candidate for Orch3 and, using a transgenic approach, demonstrated that Kif1c is Orch3 . Mechanistically, we showed that the resistant Kif1cD2 allele leads to a reduced antigen-specific T cell proliferative response as a consequence of decreased MHC class II expression by antigen presenting cells, and that the L 578 →P 578 and S 1027 →P 1027 polymorphisms distinguishing the BALB/cByJ and DBA/2J alleles, respectively, can play a role in transcriptional regulation. These findings may provide mechanistic insight into how polymorphism in other kinesins such as KIF21B and KIF5A influence susceptibility and resistance to human autoimmune diseases.
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  • 83
    Publication Date: 2012-12-28
    Description: by Andrea Calixto, Juan S. Jara, Felipe A. Court Axonal degeneration is a key event in the pathogenesis of neurodegenerative conditions. We show here that mec-4d triggered axonal degeneration of Caenorhabditis elegans neurons and mammalian axons share mechanistical similarities, as both are rescued by inhibition of calcium increase, mitochondrial dysfunction, and NMNAT overexpression. We then explore whether reactive oxygen species (ROS) participate in axonal degeneration and neuronal demise. C. elegans dauers have enhanced anti-ROS systems, and dauer mec-4d worms are completely protected from axonal degeneration and neuronal loss. Mechanistically, downregulation of the Insulin/IGF-1-like signaling (IIS) pathway protects neurons from degenerating in a DAF-16/FOXO–dependent manner and is related to superoxide dismutase and catalase-increased expression. Caloric restriction and systemic antioxidant treatment, which decrease oxidative damage, protect C. elegans axons from mec-4d -mediated degeneration and delay Wallerian degeneration in mice. In summary, we show that the IIS pathway is essential in maintaining neuronal homeostasis under pro-degenerative stimuli and identify ROS as a key intermediate of neuronal degeneration in vivo . Since axonal degeneration represents an early pathological event in neurodegeneration, our work identifies potential targets for therapeutic intervention in several conditions characterized by axonal loss and functional impairment.
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  • 84
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    Publication Date: 2012-12-28
    Description: by Mark J. Bradshaw, Man C. Cheung, Daniel J. Ehrlich, Michael L. Smith The structural proteins of the extracellular matrix (ECM) form fibers with finely tuned mechanical properties matched to the time scales of cell traction forces. Several proteins such as fibronectin (Fn) and fibrin undergo molecular conformational changes that extend the proteins and are believed to be a major contributor to the extensibility of bulk fibers. The dynamics of these conformational changes have been thoroughly explored since the advent of single molecule force spectroscopy and molecular dynamics simulations but remarkably, these data have not been rigorously applied to the understanding of the time dependent mechanics of bulk ECM fibers. Using measurements of protein density within fibers, we have examined the influence of dynamic molecular conformational changes and the intermolecular arrangement of Fn within fibers on the bulk mechanical properties of Fn fibers. Fibers were simulated as molecular strands with architectures that promote either equal or disparate molecular loading under conditions of constant extension rate. Measurements of protein concentration within micron scale fibers using deep ultraviolet transmission microscopy allowed the simulations to be scaled appropriately for comparison to in vitro measurements of fiber mechanics as well as providing estimates of fiber porosity and water content, suggesting Fn fibers are approximately 75% solute. Comparing the properties predicted by single molecule measurements to in vitro measurements of Fn fibers showed that domain unfolding is sufficient to predict the high extensibility and nonlinear stiffness of Fn fibers with surprising accuracy, with disparately loaded fibers providing the best fit to experiment. This work shows the promise of this microstructural modeling approach for understanding Fn fiber properties, which is generally applicable to other ECM fibers, and could be further expanded to tissue scale by incorporating these simulated fibers into three dimensional network models.
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  • 85
    Publication Date: 2012-12-28
    Description: by Eric Röttinger, Paul Dahlin, Mark Q. Martindale Understanding the functional relationship between intracellular factors and extracellular signals is required for reconstructing gene regulatory networks (GRN) involved in complex biological processes. One of the best-studied bilaterian GRNs describes endomesoderm specification and predicts that both mesoderm and endoderm arose from a common GRN early in animal evolution. Compelling molecular, genomic, developmental, and evolutionary evidence supports the hypothesis that the bifunctional gastrodermis of the cnidarian-bilaterian ancestor is derived from the same evolutionary precursor of both endodermal and mesodermal germ layers in all other triploblastic bilaterian animals. We have begun to establish the framework of a provisional cnidarian “endomesodermal” gene regulatory network in the sea anemone, Nematostella vectensis , by using a genome-wide microarray analysis on embryos in which the canonical Wnt/ß-catenin pathway was ectopically targeted for activation by two distinct pharmaceutical agents (lithium chloride and 1-azakenpaullone) to identify potential targets of endomesoderm specification. We characterized 51 endomesodermally expressed transcription factors and signaling molecule genes (including 18 newly identified) with fine-scale temporal (qPCR) and spatial ( in situ ) analysis to define distinct co-expression domains within the animal plate of the embryo and clustered genes based on their earliest zygotic expression. Finally, we determined the input of the canonical Wnt/ß-catenin pathway into the cnidarian endomesodermal GRN using morpholino and mRNA overexpression experiments to show that NvTcf/canonical Wnt signaling is required to pattern both the future endomesodermal and ectodermal domains prior to gastrulation, and that both BMP and FGF (but not Notch) pathways play important roles in germ layer specification in this animal. We show both evolutionary conserved as well as profound differences in endomesodermal GRN structure compared to bilaterians that may provide fundamental insight into how GRN subcircuits have been adopted, rewired, or co-opted in various animal lineages that give rise to specialized endomesodermal cell types.
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  • 86
    Publication Date: 2012-12-29
    Description: by Thomas D. Pfister, Melinda Hollingshead, Robert J. Kinders, Yiping Zhang, Yvonne A. Evrard, Jiuping Ji, Sonny A. Khin, Suzanne Borgel, Howard Stotler, John Carter, Raymond Divelbiss, Shivaani Kummar, Yves Pommier, Ralph E. Parchment, Joseph E. Tomaszewski, James H. Doroshow Background Topoisomerase I (Top1) is a proven target for cancer therapeutics. Recent data from the Fluorouracil, Oxaliplatin, CPT-11: Use and Sequencing (FOCUS) trial demonstrated that nuclear staining of Top1 correlates with chemotherapeutic efficacy. Such a correlation may help identify patients likely to respond to Top1 inhibitors and illuminate their mechanism of action. Cellular response to Top1 inhibitors is complex, but Top1 target engagement is a necessary first step in this process. This paper reports the development and validation of a quantitative immunoassay for Top1 in tumors. Methodology/Principal Findings We have developed and validated a two-site enzyme chemiluminescent immunoassay for quantifying Top1 levels in tumor biopsies. Analytical validation of the assay established the inter-day coefficient of variation at 9.3%±3.4% and a 96.5%±7.3% assay accuracy. Preclinical fit-for-purpose modeling of topotecan time- and dose-effects was performed using topotecan-responsive and -nonresponsive xenografts in athymic nude mice. Higher baseline levels of Top1 were observed in topotecan-responsive than -nonresponsive tumors. Top1 levels reached a maximal decrease 4 to 7 hours following treatment of engrafted mice with topotecan and the indenoisoquinoline NSC 724998. Conclusions/Significance Our analysis of Top1 levels in control and treated tumors supports the previously proposed mechanism of action for Top1 inhibitor efficacy, wherein higher baseline Top1 levels lead to formation of more covalent-complex-dependent double-strand break damage and, ultimately, cell death. In contrast, xenografts with lower baseline Top1 levels accumulate fewer double-stand breaks, and may be more resistant to Top1 inhibitors. Our results support further investigation into the use of Top1 levels in tumors as a potential predictive biomarker. The Top1 immunoassay described in this paper has been incorporated into a Phase I clinical trial at the National Cancer Institute to assess pharmacodynamic response in tumor biopsies and determine whether baseline Top1 levels are predictive of response to indenoisoquinoline Top1 inhibitors.
    Electronic ISSN: 1932-6203
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  • 87
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    In: PLoS ONE
    Publication Date: 2012-12-29
    Description: by Lindsay Riley, Hua Zhou, Kenneth Lange, Janet S. Sinsheimer, Mary E Sehl Introduction Trastuzumab dramatically improves survival in breast cancer patients whose tumor overexpresses HER2. A subpopulation of cells in human breast tumors has been identified with characteristics of cancer stem cells. These breast cancer stem-like cells (BCSCs) rely on HER2 signaling for self-renewal, suggesting that HER2-targeted therapy targets BCSCs even when the bulk of the tumor does not overexpress HER2. In order to guide clinical trials examining HER2-targeted therapy in the adjuvant setting, we propose a mathematical model to examine BCSC population dynamics and predict optimal duration of therapy. Methods Varying the susceptibility of BCSCs to HER2-targeted therapy, we quantify the average time to extinction of BCSCs. We expand our model using stochastic simulation to include the partially differentiated tumor cells (TCs) that represent bulk tumor population and examine effects of plasticity on required duration of therapy. Results Lower susceptibility of BCSCs and increased rates of dedifferentiation entail longer extinction times, indicating a need for prolonged administration of HER2-targeted therapy. We predict that even when therapy does not appreciably reduce tumor size in the advanced cancer setting, it will eventually eradicate the tumor in the adjuvant setting as long as there is at least a modest effect on BCSCs. Conclusions We anticipate that our results will inform clinical trials of targeted therapies in planning the duration of therapy needed to eradicate BCSCs. Our predictions also address safety, as longer duration of therapy entails a greater potential impact on normal stem cells that may also be susceptible to stem cell-targeted therapies.
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  • 88
    Publication Date: 2012-12-29
    Description: by Mahir Karakas, Jens Baumert, Marcus E. Kleber, Barbara Thorand, Dhayana Dallmeier, Günther Silbernagel, Tanja B. Grammer, Wolfgang Rottbauer, Christa Meisinger, Thomas Illig, Winfried März, Wolfgang Koenig Background Elevated soluble (s) E-selectin levels have been associated with various cardiovascular diseases. Recently, genetic variants in the ABO blood group have been related to E-selectin levels in a small cohort of patients with type 1 diabetes. We evaluated whether this association is reproducible in two large samples of Caucasians. Methodology/ Principal Findings Data of the present study was drawn from the population-based MONICA/KORA Augsburg study (n = 1,482) and the patients-based LURIC study (n = 1,546). A high-density genotyping array (50K IBC Chip) containing single-nucleotide polymorphisms (SNPs) from E-selectin candidate genes selected on known biology of E-selectin metabolism, mouse genetic studies, and human genetic association studies, was used for genotyping. Linear regression analyses with adjustment for age and sex (and survey in KORA) were applied to assess associations between gene variants and sE-selectin concentrations. A number of 12 SNPs (in KORA) and 13 SNPs (in LURIC), all from the ABO blood group gene, were significantly associated with the log-transformed concentration of E-selectin. The strongest association was observed for rs651007 with a change of log-transformed sE-selectin per one copy of the minor allele of −0.37 ng/ml (p = 1.87×10 −103 ) in KORA and −0.35 ng/ml (p = 5.11×10 −84 ) in LURIC. Inclusion of rs651007 increased the explained sE-selectin variance by 0.256 in KORA and 0.213 in LURIC. All SNPs had minor allele frequencies above 20% showing a substantial gene variation. Conclusions/ Significance Our findings in two independent samples indicate that the genetic variants at the ABO locus affect sE-selectin levels. Since distinct genome-wide association studies linked the ABO gene with myocardial infarction (MI) in the presence of coronary atherosclerosis and with coronary artery disease, these findings may not only enhance our understanding of adhesion molecule biology, but may also provide a focus for several novel research avenues.
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  • 89
    Publication Date: 2012-12-29
    Description: by Hon-Yi Shi, Hao-Hsien Lee, Jinn-Tsong Tsai, Wen-Hsien Ho, Chieh-Fan Chen, King-Teh Lee, Chong-Chi Chiu Background Few studies of laparoscopic cholecystectomy (LC) outcome have used longitudinal data for more than two years. Moreover, no studies have considered group differences in factors other than outcome such as age and nonsurgical treatment. Additionally, almost all published articles agree that the essential issue of the internal validity (reproducibility) of the artificial neural network (ANN), support vector machine (SVM), Gaussian process regression (GPR) and multiple linear regression (MLR) models has not been adequately addressed. This study proposed to validate the use of these models for predicting quality of life (QOL) after LC and to compare the predictive capability of ANNs with that of SVM, GPR and MLR. Methodology/Principal Findings A total of 400 LC patients completed the SF-36 and the Gastrointestinal Quality of Life Index at baseline and at 2 years postoperatively. The criteria for evaluating the accuracy of the system models were mean square error (MSE) and mean absolute percentage error (MAPE). A global sensitivity analysis was also performed to assess the relative significance of input parameters in the system model and to rank the variables in order of importance. Compared to SVM, GPR and MLR models, the ANN model generally had smaller MSE and MAPE values in the training data set and test data set. Most ANN models had MAPE values ranging from 4.20% to 8.60%, and most had high prediction accuracy. The global sensitivity analysis also showed that preoperative functional status was the best parameter for predicting QOL after LC. Conclusions/Significance Compared with SVM, GPR and MLR models, the ANN model in this study was more accurate in predicting patient-reported QOL and had higher overall performance indices. Further studies of this model may consider the effect of a more detailed database that includes complications and clinical examination findings as well as more detailed outcome data.
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  • 90
    Publication Date: 2012-12-29
    Description: by Stacie L. Lambert, Chin-Fen Yang, Zheng Liu, Rosemary Sweetwood, Jackie Zhao, Lily Cheng, Hong Jin, Jennifer Woo Background Toll-like receptor (TLR)4 agonists are known potent immunostimulatory compounds. These compounds can be formulated as part of novel adjuvants to enhance vaccine medicated immune responses. However, the contribution of the formulation to the innate in vivo activity of TLR4 agonist compounds is not well understood. Methodology and Principal Findings We evaluated synthetic TLR4 agonist Glucopyranosyl Lipid A (GLA) for its effects on molecular and cellular innate immune responses in the murine model. Microarray techniques were used to compare the responses to GLA in an aqueous formulation or in an oil-in-water Stable Emulsion formulation (GLA-SE) versus either SE alone or the mineral salt aluminum hydroxide (alum) at the muscle injection site over multiple timepoints. In contrast to the minimal gene upregulation induced by SE and alum, both GLA and GLA-SE triggered MyD88- and TRIF-dependent gene expression. Genes for chemokines, cytokine receptors, signaling molecules, complement, and antigen presentation were also strongly upregulated by GLA and GLA-SE. These included chemokines for T H 1-type T cells (CXCL9 and CXCL10) and mononuclear leukocytes (CCL2, CCL3) among others. GLA-SE induced stronger and more sustained gene upregulation than GLA in the muscle; GLA-SE induced genes were also detected in local draining lymph nodes and at lower levels in peripheral blood. Both GLA and GLA-SE resulted in increased cellular trafficking to the draining lymph nodes and upregulated MHC molecules and ICAM1 on local dendritic cells. GLA and GLA-SE transiently upregulated circulating MCP-1, TNFα, IFNγ and IP-10 in blood. Conclusions/Significance While GLA and GLA-SE activate a large number of shared innate genes and proteins, GLA-SE induces a quantitatively and qualitatively stronger response than GLA, SE or alum. The genes and proteins upregulated could be used to facilitate selection of appropriate adjuvant doses in vaccine formulations.
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  • 91
    Publication Date: 2012-12-29
    Description: by Lianne J. Woodward, Caron A. C. Clark, Samudragupta Bora, Terrie E. Inder Background Cerebral white matter abnormalities on term MRI are a strong predictor of motor disability in children born very preterm. However, their contribution to cognitive impairment is less certain. Objective Examine relationships between the presence and severity of cerebral white matter abnormalities on neonatal MRI and a range of neurocognitive outcomes assessed at ages 4 and 6 years. Design/Methods The study sample consisted of a regionally representative cohort of 104 very preterm (≤32 weeks gestation) infants born from 1998–2000 and a comparison group of 107 full-term infants. At term equivalent, all preterm infants underwent a structural MRI scan that was analyzed qualitatively for the presence and severity of cerebral white matter abnormalities, including cysts, signal abnormalities, loss of white matter volume, ventriculomegaly, and corpus callosal thinning/myelination. At corrected ages 4 and 6 years, all children underwent a comprehensive neurodevelopmental assessment that included measures of general intellectual ability, language development, and executive functioning. Results At 4 and 6 years, very preterm children without cerebral white matter abnormalities showed no apparent neurocognitive impairments relative to their full-term peers on any of the domain specific measures of intelligence, language, and executive functioning. In contrast, children born very preterm with mild and moderate-to-severe white matter abnormalities were characterized by performance impairments across all measures and time points, with more severe cerebral abnormalities being associated with increased risks of cognitive impairment. These associations persisted after adjustment for gender, neonatal medical risk factors, and family social risk. Conclusions Findings highlight the importance of cerebral white matter connectivity for later intact cognitive functioning amongst children born very preterm. Preterm born children without cerebral white matter abnormalities on their term MRI appear to be spared many of the cognitive impairments commonly associated with preterm birth. Further follow-up will be important to assess whether this finding persists into the school years.
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  • 92
    Publication Date: 2012-12-18
    Description: by Lynnae M. Smith, Mya C. Schiess, Mary P. Coffey, Andrea C. Klaver, David A. Loeffler α-synuclein is thought to play a key role in Parkinson’s disease (PD) because it is the major protein in Lewy bodies, and because its gene mutations, duplication, and triplication are associated with early-onset PD. There are conflicting reports as to whether serum and plasma concentrations of α-synuclein and anti-α-synuclein antibodies differ between PD and control subjects. The objectives of this study were to compare the levels of α-synuclein and its antibodies between individuals with typical PD (n = 14), atypical Parkinson syndromes (n = 11), idiopathic rapid eye movement sleep behavior disorder (n = 10), and healthy controls (n = 9), to assess the strength of association between these serum proteins, and to determine group sizes needed for a high probability (80% power) of detecting statistical significance for 25% or 50% differences between typical PD and control subjects for these measurements. Analysis of log-transformed data found no statistically significant differences between groups for either α-synuclein or its antibodies. The concentrations of these proteins were weakly correlated (Spearman rho = 0.16). In subjects with typical PD and atypical Parkinson syndromes, anti-α-synuclein antibody levels above 1.5 µg/ml were detected only in subjects with no more than four years of clinical disease. Power analysis indicated that 236 and 73 samples per group would be required for an 80% probability that 25% and 50% differences, respectively, in mean α-synuclein levels between typical PD and control subjects would be statistically significant; for anti-α-synuclein antibodies, 283 and 87 samples per group would be required. Our findings are consistent with those previous studies which suggested that serum concentrations of α-synuclein and its antibodies are not significantly altered in PD.
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  • 93
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    In: PLoS ONE
    Publication Date: 2012-12-18
    Description: by Jan Churan, Daniel Guitton, Christopher C. Pack Visual neurons have spatial receptive fields that encode the positions of objects relative to the fovea. Because foveate animals execute frequent saccadic eye movements, this position information is constantly changing, even though the visual world is generally stationary. Interestingly, visual receptive fields in many brain regions have been found to exhibit changes in strength, size, or position around the time of each saccade, and these changes have often been suggested to be involved in the maintenance of perceptual stability. Crucial to the circuitry underlying perisaccadic changes in visual receptive fields is the superior colliculus (SC), a brainstem structure responsible for integrating visual and oculomotor signals. In this work we have studied the time-course of receptive field changes in the SC. We find that the distribution of the latencies of SC responses to stimuli placed outside the fixation receptive field is bimodal: The first mode is comprised of early responses that are temporally locked to the onset of the visual probe stimulus and stronger for probes placed closer to the classical receptive field. We suggest that such responses are therefore consistent with a perisaccadic rescaling, or enhancement, of weak visual responses within a fixed spatial receptive field. The second mode is more similar to the remapping that has been reported in the cortex, as responses are time-locked to saccade onset and stronger for stimuli placed in the postsaccadic receptive field location. We suggest that these two temporal phases of spatial updating may represent different sources of input to the SC.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 94
    Publication Date: 2012-12-18
    Description: by Chengchao Zhou, Jie Chu, Jinan Liu, Ruoyan Gai Tobe, Hong Gen, Xingzhou Wang, Wengui Zheng, Lingzhong Xu Adherence to TB treatment is the most important requirement for efficient TB control. Migrant TB patients’ “migratory” nature affects the adherence negatively, which presents an important barrier for National TB Control Program in China. Therefore, TB control among migrants is of high importance.The aim of this study is to describe adherence to TB treatment among migrant TB patients and to identify factors associated with adherence. A total of 12 counties/districts of Shandong Province, China were selected as study sites. 314 confirmed smear positive TB patients were enrolled between August 2 nd 2008 and October 17 th 2008, 16% of whom were non-adherent to TB therapy. Risk factors for non-adherence were: the divorced or bereft of spouse, patients not receiving TB-related health education before chemotherapy, weak incentives for treatment adherence, and self supervision on treatment. Based on the risk factors identified, measures are recommended such as implementing health education for all migrant patients before chemotherapy and encouraging primary care workers to supervise patients.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 95
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2012-12-18
    Description: by Hong-Lim Kim, Ji Hyun Jeon, Tae-Hyung Koo, U-Young Lee, Eojin Jeong, Myung-Hoon Chun, Jung-Il Moon, Stephen C. Massey, In-Beom Kim In the mammalian retina, bipolar cells and ganglion cells which stratify in sublamina a of the inner plexiform layer (IPL) show OFF responses to light stimuli while those that stratify in sublamina b show ON responses. This functional relationship between anatomy and physiology is a key principle of retinal organization. However, there are at least three types of retinal neurons, including intrinsically photosensitive retinal ganglion cells (ipRGCs) and dopaminergic amacrine cells, which violate this principle. These cell types have light-driven ON responses, but their dendrites mainly stratify in sublamina a of the IPL, the OFF sublayer. Recent anatomical studies suggested that certain ON cone bipolar cells make axonal or ectopic synapses as they descend through sublamina a , thus providing ON input to cells which stratify in the OFF sublayer. Using immunoelectron microscopy with 3-dimensional reconstruction, we have identified axonal synapses of ON cone bipolar cells in the rabbit retina. Ten calbindin ON cone bipolar axons made en passant ribbon synapses onto amacrine or ganglion dendrites in sublamina a of the IPL. Compared to the ribbon synapses made by bipolar terminals, these axonal ribbon synapses were characterized by a broad postsynaptic element that appeared as a monad and by the presence of multiple short synaptic ribbons. These findings confirm that certain ON cone bipolar cells can provide ON input to amacrine and ganglion cells whose dendrites stratify in the OFF sublayer via axonal synapses. The monadic synapse with multiple ribbons may be a diagnostic feature of the ON cone bipolar axonal synapse in sublamina a . The presence of multiple ribbons and a broad postsynaptic density suggest these structures may be very efficient synapses. We also identified axonal inputs to ipRGCs with the architecture described above.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 96
    Publication Date: 2012-12-20
    Description: by Bryan Bedrosian, Derek Craighead, Ross Crandall Studies suggest hunter discarded viscera of big game animals (i.e., offal) is a source of lead available to scavengers. We investigated the incidence of lead exposure in bald eagles in Wyoming during the big game hunting season, the influx of eagles into our study area during the hunt, the geographic origins of eagles exposed to lead, and the efficacy of using non-lead rifle ammunition to reduce lead in eagles. We tested 81 blood samples from bald eagles before, during and after the big game hunting seasons in 2005–2010, excluding 2008, and found eagles had significantly higher lead levels during the hunt. We found 24% of eagles tested had levels indicating at least clinical exposure (〉60 ug/dL) during the hunt while no birds did during the non-hunting seasons. We performed driving surveys from 2009–2010 to measure eagle abundance and found evidence to suggest that eagles are attracted to the study area during the hunt. We fitted 10 eagles with satellite transmitters captured during the hunt and all migrated south after the cessation of the hunt. One returned to our study area while the remaining nine traveled north to summer/breed in Canada. The following fall, 80% returned to our study area for the hunting season, indicating that offal provides a seasonal attractant for eagles. We fitted three local breeding eagles with satellite transmitters and none left their breeding territories to feed on offal during the hunt, indicating that lead ingestion may be affecting migrants to a greater degree. During the 2009 and 2010 hunting seasons we provided non-lead rifle ammunition to local hunters and recorded that 24% and 31% of successful hunters used non-lead ammunition, respectively. We found the use of non-lead ammunition significantly reduced lead exposure in eagles, suggesting this is a viable solution to reduce lead exposure in eagles.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 97
    Publication Date: 2012-12-20
    Description: by Chandrashekhar T. Sreeramareddy, T. N. Sathyanarayana, H. N. Harsha Kumar Background Information about utilization of health services and associated factors are useful for improving service delivery to achieve universal health coverage. Methods Data on a sample of ever-married women from India Demographic and Health survey 2005–06 was used. Mothers of children aged 0–59 months were asked about child’s illnesses and type of health facilities where treatment was given during 15 days prior to the survey date. Type of health facilities were grouped as informal provider, public provider and private provider. Factors associated with utilization of health services for diarrhea and fever/cough was assessed according to Andersen’s health behavior model. Multinomial logistic regression analyses were done considering sampling weights for complex sampling design. Results A total of 48,679 of ever-married women reported that 9.1% 14.8% and 17.67% of their children had diarrhea, fever and cough respectively. Nearly one-third of the children with diarrhea and fever/cough did not receive any treatment. Two-thirds of children who received treatment were from private health care providers (HCPs). Among predisposing factors, children aged 1–2 years and those born at health facility (public/private) were more likely to be taken to any type of HCP during illness. Among enabling factors, as compared to poorer household, wealthier households were 2.5 times more likely to choose private HCPs for any illness. Children in rural areas were likely to be taken to any type of HCP for diarrhea but rural children were less likely to utilize private HCP for fever/cough. ‘Need’ factors i.e. children having severe symptoms were 2–3 times more likely to be taken to any type of HCP. Conclusion Private HCPs were preferred for treatment of childhood illnesses. Involvement of private HCPs may be considered while planning child health programs. Health insurance scheme for childhood illnesses may to protect economically weaker sections from out-of-pocket health expenditure during child illness.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 98
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2012-12-20
    Description: by Michael T. Cheeseman, Kate Vowell, Tertius A. Hough, Lynn Jones, Paras Pathak, Hayley E. Tyrer, Michelle Kelly, Roger Cox, Madhuri V. Warren, Jo Peters GNAS/Gnas encodes G s α that is mainly biallelically expressed but shows imprinted expression in some tissues. In Albright Hereditary Osteodystrophy (AHO) heterozygous loss of function mutations of GNAS can result in ectopic ossification that tends to be superficial and attributable to haploinsufficiency of biallelically expressed G s α. Oed-Sml is a point missense mutation in exon 6 of the orthologous mouse locus Gnas . We report here both the late onset ossification and occurrence of benign cutaneous fibroepithelial polyps in Oed-Sml . These phenotypes are seen on both maternal and paternal inheritance of the mutant allele and are therefore due to an effect on biallelically expressed G s α. The ossification is confined to subcutaneous tissues and so resembles the ossification observed with AHO. Our mouse model is the first with both subcutaneous ossification and fibroepithelial polyps related to G s α deficiency. It is also the first mouse model described with a clinically relevant phenotype associated with a point mutation in G s α and may be useful in investigations of the mechanisms of heterotopic bone formation. Together with earlier results, our findings indicate that G s α signalling pathways play a vital role in repressing ectopic bone formation.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 99
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2012-12-20
    Description: by Xavier Bosch, Cristina Hernández, Juan M. Pericas, Pamela Doti, Ana Marušić Background It is not clear which research misconduct policies are adopted by biomedical journals. This study assessed the prevalence and content policies of the most influential biomedical journals on misconduct and procedures for handling and responding to allegations of misconduct. Methods We conducted a cross-sectional study of misconduct policies of 399 high-impact biomedical journals in 27 biomedical categories of the Journal Citation Reports in December 2011. Journal websites were reviewed for information relevant to misconduct policies. Results Of 399 journals, 140 (35.1%) provided explicit definitions of misconduct. Falsification was explicitly mentioned by 113 (28.3%) journals, fabrication by 104 (26.1%), plagiarism by 224 (56.1%), duplication by 242 (60.7%) and image manipulation by 154 (38.6%). Procedures for responding to misconduct were described in 179 (44.9%) websites, including retraction, (30.8%) and expression of concern (16.3%). Plagiarism-checking services were used by 112 (28.1%) journals. The prevalences of all types of misconduct policies were higher in journals that endorsed any policy from editors’ associations, Office of Research Integrity or professional societies compared to those that did not state adherence to these policy-producing bodies. Elsevier and Wiley-Blackwell had the most journals included (22.6% and 14.8%, respectively), with Wiley journals having greater a prevalence of misconduct definition and policies on falsification, fabrication and expression of concern and Elsevier of plagiarism-checking services. Conclusions Only a third of top-ranking peer-reviewed journals had publicly-available definitions of misconduct and less than a half described procedures for handling allegations of misconduct. As endorsement of international policies from policy-producing bodies was positively associated with implementation of policies and procedures, journals and their publishers should standardize their policies globally in order to increase public trust in the integrity of the published record in biomedicine.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 100
    Publication Date: 2012-12-20
    Description: by Ru Li, Ehsan Khafipour, Denis O. Krause, Martin H. Entz, Teresa R. de Kievit, W. G. Dilantha Fernando It has been debated how different farming systems influence the composition of soil bacterial communities, which are crucial for maintaining soil health. In this research, we applied high-throughput pyrosequencing of V1 to V3 regions of bacterial 16S rRNA genes to gain further insight into how organic and conventional farming systems and crop rotation influence bulk soil bacterial communities. A 2×2 factorial experiment consisted of two agriculture management systems (organic versus conventional) and two crop rotations (flax-oat-fababean-wheat versus flax-alfalfa-alfalfa-wheat) was conducted at the Glenlea Long-Term Crop Rotation and Management Station, which is Canada’s oldest organic-conventional management study field. Results revealed that there is a significant difference in the composition of bacterial genera between organic and conventional management systems but crop rotation was not a discriminator factor. Organic farming was associated with higher relative abundance of Proteobacteria , while Actinobacteria and Chloroflexi were more abundant in conventional farming. The dominant genera including Blastococcus, Microlunatus, Pseudonocardia, Solirubrobacter, Brevundimonas, Pseudomonas , and Stenotrophomonas exhibited significant variation between the organic and conventional farming systems. The relative abundance of bacterial communities at the phylum and class level was correlated to soil pH rather than other edaphic properties. In addition, it was found that Proteobacteria and Actinobacteria were more sensitive to pH variation.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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