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  • Oxford University Press  (22,888)
  • Molecular Diversity Preservation International  (21,713)
  • Public Library of Science (PLoS)  (9,424)
  • 2015-2019  (54,025)
  • 1930-1934
  • 2016  (54,025)
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  • 2015-2019  (54,025)
  • 1930-1934
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  • 1
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    Oxford University Press
    Publication Date: 2017-04-04
    Description: We provide an updated present-day stress map for the Italian territory. Following the World Stress Map (WSM) Project guidelines, we list the different stress indicators, explaining the criteria used to select data. We discuss the data, which will also be included in the 2016 release of the WSM, highlighting the areas for which we have added stress information. Our map displays the minimum horizontal stress orientations inferred from crustal stress indicators down to 40 km depth using data of A–C quality, updated for earthquakes until December 2015. We have completely reviewed all data, and the data set now contains 855 entries, in contrast to the previous 715. The number of data with A–C quality of 630 corresponds to an increase of 26 per cent relative to the previous data set. In particular, the new data set contains the results of the analysis of borehole breakouts, critically reviewed data from earthquake focal mechanisms, data concerning active faults, formal inversions of focal mechanisms of seismic sequences or of restricted areas and one stress determination from overcoring. The new data set defines the stress field in areas not well covered by the previous data: the region north to the Po Plain and the central Adriatic sea, both characterized by a thrust- and strike-faulting regime, the northern Sicilian belt with a prevailing normal-faulting regime, and the Ionian sea with a strike-slip regime.
    Description: Published
    Description: 1525-1531
    Description: 2T. Tettonica attiva
    Description: JCR Journal
    Description: restricted
    Keywords: Seismicity and tectonics ; Dynamics: seismotectonics ; Crustal structure ; Europe ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
    Publication Date: 2017-04-04
    Description: Although there are many methods for investigating tectonic structures, many faults remain hidden, and they can endanger the life and property of people living along them. The slopes of volcanoes are covered with such hidden faults, near which strong earthquakes and gas releases can appear. Revealing hidden faults can therefore contribute significantly to the protection of people living in volcanic areas. In the study, seven different techniques were used for making measurements of in-soil radon concentrations in order to search for hidden faults on the SE flank of the Mt. Etna volcano. These reported methods had previously been proved to be useful tools for investigating fault structures. The main aim of the experiment presented here was to evaluate the usability of these methods in the geological conditions of the Mt. Etna region, and to find the best place for continual radon monitoring using a permanent station in the near future.
    Description: Published
    Description: 70-73
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: restricted
    Keywords: Mt. Etna ; soil gas ; hidden faults ; radon ; 04. Solid Earth::04.02. Exploration geophysics::04.02.01. Geochemical exploration
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 3
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    Oxford University Press
    In:  EPIC3ICES Journal of Marine Science, Oxford University Press, 73, pp. 772-782, ISSN: 1054-3139
    Publication Date: 2016-11-30
    Description: Global warming and ocean acidification are among the most important stressors for aquatic ecosystems in the future. To investigate their direct and indirect effects on a near-natural plankton community, a multiple-stressor approach is needed. Hence, we set up mesocosms in a full-factorial design to study the effects of both warming and high CO2 on a Baltic Sea autumn plankton community, concentrating on the impacts on microzooplankton (MZP). MZP abundance, biomass, and species composition were analysed over the course of the experiment. We observed that warming led to a reduced time-lag between the phytoplankton bloom and an MZP biomass maximum. MZP showed a significantly higher growth rate and an earlier biomass peak in the warm treatments while the biomass maximum was not affected. Increased pCO2 did not result in any significant effects on MZP biomass, growth rate, or species composition irrespective of the temperature, nor did we observe any significant interactions between CO2 and temperature. We attribute this to the high tolerance of this estuarine plankton community to fluctuations in pCO2, often resulting in CO2 concentrations higher than the predicted end-of-century concentration for open oceans. In contrast, warming can be expected to directly affect MZP and strengthen its coupling with phytoplankton by enhancing its grazing pressure.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 4
    Publication Date: 2022-05-25
    Description: Author Posting. © Crown Copyright, 2015. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 204 (2016): 1-20, doi:10.1093/gji/ggv416.
    Description: The Canada Basin and the southern Alpha-Mendeleev ridge complex underlie a significant proportion of the Arctic Ocean, but the geology of this undrilled and mostly ice-covered frontier is poorly known. New information is encoded in seismic wide-angle reflections and refractions recorded with expendable sonobuoys between 2007 and 2011. Velocity–depth samples within the sedimentary succession are extracted from published analyses for 142 of these records obtained at irregularly spaced stations across an area of 1.9E + 06 km2. The samples are modelled at regional, subregional and station-specific scales using an exponential function of inverse velocity versus depth with regionally representative parameters determined through numerical regression. With this approach, smooth, non-oscillatory velocity–depth profiles can be generated for any desired location in the study area, even where the measurement density is low. Practical application is demonstrated with a map of sedimentary thickness, derived from seismic reflection horizons interpreted in the time domain and depth converted using the velocity–depth profiles for each seismic trace. A thickness of 12–13 km is present beneath both the upper Mackenzie fan and the middle slope off of Alaska, but the sedimentary prism thins more gradually outboard of the latter region. Mapping of the observed-to-predicted velocities reveals coherent geospatial trends associated with five subregions: the Mackenzie fan; the continental slopes beyond the Mackenzie fan; the abyssal plain; the southwestern Canada Basin; and, the Alpha-Mendeleev magnetic domain. Comparison of the subregional velocity–depth models with published borehole data, and interpretation of the station-specific best-fitting model parameters, suggests that sandstone is not a predominant lithology in any of the five subregions. However, the bulk sand-to-shale ratio likely increases towards the Mackenzie fan, and the model for this subregion compares favourably with borehole data for Miocene turbidites in the eastern Gulf of Mexico. The station-specific results also indicate that Quaternary sediments coarsen towards the Beaufort-Mackenzie and Banks Island margins in a manner that is consistent with the variable history of Laurentide Ice Sheet advance documented for these margins. Lithological factors do not fully account for the elevated velocity–depth trends that are associated with the southwestern Canada Basin and the Alpha-Mendeleev magnetic domain. Accelerated porosity reduction due to elevated palaeo-heat flow is inferred for these regions, which may be related to the underlying crustal types or possibly volcanic intrusion of the sedimentary succession. Beyond exploring the variation of an important physical property in the Arctic Ocean basin, this study provides comparative reference for global studies of seismic velocity, burial history, sedimentary compaction, seismic inversion and overpressure prediction, particularly in mudrock-dominated successions.
    Keywords: Numerical approximations and analysis ; Spatial analysis ; Controlled source seismology ; Acoustic properties ; Sedimentary basin processes ; Large igneous provinces ; Crustal structure ; Arctic region
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 7 (2015): 3207-3225, doi:10.1093/gbe/evv210.
    Description: High-throughput sequencing of reduced representation libraries obtained through digestion with restriction enzymes—generically known as restriction site associated DNA sequencing (RAD-seq)—is a common strategy to generate genome-wide genotypic and sequence data from eukaryotes. A critical design element of any RAD-seq study is knowledge of the approximate number of genetic markers that can be obtained for a taxon using different restriction enzymes, as this number determines the scope of a project, and ultimately defines its success. This number can only be directly determined if a reference genome sequence is available, or it can be estimated if the genome size and restriction recognition sequence probabilities are known. However, both scenarios are uncommon for nonmodel species. Here, we performed systematic in silico surveys of recognition sequences, for diverse and commonly used type II restriction enzymes across the eukaryotic tree of life. Our observations reveal that recognition sequence frequencies for a given restriction enzyme are strikingly variable among broad eukaryotic taxonomic groups, being largely determined by phylogenetic relatedness. We demonstrate that genome sizes can be predicted from cleavage frequency data obtained with restriction enzymes targeting “neutral” elements. Models based on genomic compositions are also effective tools to accurately calculate probabilities of recognition sequences across taxa, and can be applied to species for which reduced representation data are available (including transcriptomes and neutral RAD-seq data sets). The analytical pipeline developed in this study, PredRAD (https://github.com/phrh/PredRAD), and the resulting databases constitute valuable resources that will help guide the design of any study using RAD-seq or related methods.
    Description: This research was supported by the Office of Ocean Exploration and Research of the National Oceanic and Atmospheric Administration (NA09OAR4320129 to T.S.); the Division of Ocean Sciences of the National Science Foundation (OCE-1131620 to T.S.); the Astrobiology Science and Technology for Exploring Planets program of the National Aeronautics and Space Administration (NNX09AB76G to T.S.); and the Academic Programs Office (Ocean Ventures Fund to S.H.), the Ocean Exploration Institute (Fellowship support to T.M.S.), and the Ocean Life Institute of the Woods Hole Oceanographic Institution (internal grant to T.M.S. and S.H.).
    Keywords: RAD-seq ; Reduced representation sequencing ; PredRAD ; Experimental design ; Genome size prediction ; Restriction recognition sequence probability
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 6
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 44 (2016): e157, doi:10.1093/nar/gkw738.
    Description: Site-directed RNA editing (SDRE) is a strategy to precisely alter genetic information within mRNAs. By linking the catalytic domain of the RNA editing enzyme ADAR to an antisense guide RNA, specific adenosines can be converted to inosines, biological mimics for guanosine. Previously, we showed that a genetically encoded iteration of SDRE could target adenosines expressed in human cells, but not efficiently. Here we developed a reporter assay to quantify editing, and used it to improve our strategy. By enhancing the linkage between ADAR's catalytic domain and the guide RNA, and by introducing a mutation in the catalytic domain, the efficiency of converting a UAG premature termination codon (PTC) to tryptophan (UGG) was improved from ∼11% to ∼70%. Other PTCs were edited, but less efficiently. Numerous off-target edits were identified in the targeted mRNA, but not in randomly selected endogenous messages. Off-target edits could be eliminated by reducing the amount of guide RNA with a reduction in on-target editing. The catalytic rate of SDRE was compared with those for human ADARs on various substrates and found to be within an order of magnitude of most. These data underscore the promise of site-directed RNA editing as a therapeutic or experimental tool.
    Description: National Institutes of Health [1R0111223855, 1R01NS64259]; Cystic Fibrosis Foundation Therapeutics [Rosent14XXO]; Infrastructural support was provided by the National Institutes of Health [NIGMS 1P20GM103642, NIMHD 8G12-MD007600]; National Science Foundation [DBI 0115825, DBI 1337284]; Department of Defense [52680-RT-ISP].
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 7
    Publication Date: 2017-04-04
    Description: During volcanic eruptions, measurements of the rate at which magma is erupted underpin hazard assessments. For eruptions dominated by the effusion of lava, estimates are often made using satellite data; here, in a case study at Mount Etna (Sicily), we make the first measurements based on terrestrial laser scanning (TLS), and we also include explosive products. During the study period (17–21 July 2012), regular Strombolian explosions were occurring within the Bocca Nuova crater, producing a ~50 m-high scoria cone and a small lava flow field. TLS surveys over multi-day intervals determined a mean cone growth rate (effusive and explosive products) of ~0.24 m3·s−1. Differences between 0.3-m resolution DEMs acquired at 10-minute intervals captured the evolution of a breakout lava flow lobe advancing at 0.01–0.03 m3·s−1. Partial occlusion within the crater prevented similar measurement of the main flow, but integrating TLS data with time-lapse imagery enabled lava viscosity (7.4 × 105 Pa·s) to be derived from surface velocities and, hence, a flux of 0.11 m3·s−1 to be calculated. Total dense rock equivalent magma discharge estimates are ~0.1–0.2 m3·s−1 over the measurement period and suggest that simultaneous estimates from satellite data are somewhat overestimated. Our results support the use of integrated TLS and time-lapse photography for ground-truthing space-based measurements and highlight the value of interactive image analysis when automated approaches, such as particle image velocimetry (PIV), fail.
    Description: Published
    Description: 14967 - 14987
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: open
    Keywords: lava flow; scoria cone; effusion rate; terrestrial laser scanning; time-lapse photography; Mt. Etna ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
    Publication Date: 2022-05-26
    Description: Author Posting. © Oxford University Press, 2016. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 205 (2016): 728-743, doi:10.1093/gji/ggw044.
    Description: While elasticity is a defining characteristic of the Earth's lithosphere, it is often ignored in numerical models of long-term tectonic processes in favour of a simpler viscoplastic description. Here we assess the consequences of this assumption on a well-studied geodynamic problem: the growth of normal faults at an extensional plate boundary. We conduct 2-D numerical simulations of extension in elastoplastic and viscoplastic layers using a finite difference, particle-in-cell numerical approach. Our models simulate a range of faulted layer thicknesses and extension rates, allowing us to quantify the role of elasticity on three key observables: fault-induced topography, fault rotation, and fault life span. In agreement with earlier studies, simulations carried out in elastoplastic layers produce rate-independent lithospheric flexure accompanied by rapid fault rotation and an inverse relationship between fault life span and faulted layer thickness. By contrast, models carried out with a viscoplastic lithosphere produce results that may qualitatively resemble the elastoplastic case, but depend strongly on the product of extension rate and layer viscosity U × ηL. When this product is high, fault growth initially generates little deformation of the footwall and hanging wall blocks, resulting in unrealistic, rigid block-offset in topography across the fault. This configuration progressively transitions into a regime where topographic decay associated with flexure is fully accommodated within the numerical domain. In addition, high U × ηL favours the sequential growth of multiple short-offset faults as opposed to a large-offset detachment. We interpret these results by comparing them to an analytical model for the fault-induced flexure of a thin viscous plate. The key to understanding the viscoplastic model results lies in the rate-dependence of the flexural wavelength of a viscous plate, and the strain rate dependence of the force increase associated with footwall and hanging wall bending. This behaviour produces unrealistic deformation patterns that can hinder the geological relevance of long-term rifting models that assume a viscoplastic rheology.
    Description: This work was supported by NSF grants OCE-11-54238 (JAO, MDB), EAR-10-10432 (MDB) and OCE-11-55098 (GI), as well as a WHOI Deep Exploration Institute grant and start-up support from the University of Idaho (EM).
    Keywords: Mid-ocean ridge processes ; Continental tectonics: extensional ; Lithospheric flexure ; Mechanics, theory, and modelling
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 4 (2016): cow014, doi:10.1093/conphys/cow014.
    Description: Reproduction of mysticete whales is difficult to monitor, and basic parameters, such as pregnancy rate and inter-calving interval, remain unknown for many populations. We hypothesized that baleen plates (keratinous strips that grow downward from the palate of mysticete whales) might record previous pregnancies, in the form of high-progesterone regions in the sections of baleen that grew while the whale was pregnant. To test this hypothesis, longitudinal baleen progesterone profiles from two adult female North Atlantic right whales (Eubalaena glacialis) that died as a result of ship strike were compared with dates of known pregnancies inferred from calf sightings and post-mortem data. We sampled a full-length baleen plate from each female at 4 cm intervals from base (newest baleen) to tip (oldest baleen), each interval representing ∼60 days of baleen growth, with high-progesterone areas then sampled at 2 or 1 cm intervals. Pulverized baleen powder was assayed for progesterone using enzyme immunoassay. The date of growth of each sampling location on the baleen plate was estimated based on the distance from the base of the plate and baleen growth rates derived from annual cycles of stable isotope ratios. Baleen progesterone profiles from both whales showed dramatic elevations (two orders of magnitude higher than baseline) in areas corresponding to known pregnancies. Baleen hormone analysis shows great potential for estimation of recent reproductive history, inter-calving interval and general reproductive biology in this species and, possibly, in other mysticete whales.
    Description: This work was supported by the Eppley Foundation for Research, the National Oceanographic and Atmospheric Administration Marine Mammal Health and Stranding Program and the Woods Hole Oceanographic Institution Ocean Life Institute.
    Keywords: Baleen ; Cetacea ; Marine mammals ; Pregnancy ; Progesterone ; Reproduction
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2016. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 205 (2016): 785-795, doi:10.1093/gji/ggw036.
    Description: An L-configured, three-component short period seismic array was deployed on the Ross Ice Shelf, Antarctica during November 2014. Polarization analysis of ambient noise data from these stations shows linearly polarized waves for frequency bands between 0.2 and 2 Hz. A spectral peak at about 1.6 Hz is interpreted as the resonance frequency of the water column and is used to estimate the water layer thickness below the ice shelf. The frequency band from 4 to 18 Hz is dominated by Rayleigh and Love waves propagating from the north that, based on daily temporal variations, we conclude were generated by field camp activity. Frequency–slowness plots were calculated using beamforming. Resulting Love and Rayleigh wave dispersion curves were inverted for the shear wave velocity profile within the firn and ice to ∼150 m depth. The derived density profile allows estimation of the pore close-off depth and the firn–air content thickness. Separate inversions of Rayleigh and Love wave dispersion curves give different shear wave velocity profiles within the firn. We attribute this difference to an effective anisotropy due to fine layering. The layered structure of firn, ice, water and the seafloor results in a characteristic dispersion curve below 7 Hz. Forward modelling the observed Rayleigh wave dispersion curves using representative firn, ice, water and sediment structures indicates that Rayleigh waves are observed when wavelengths are long enough to span the distance from the ice shelf surface to the seafloor. The forward modelling shows that analysis of seismic data from an ice shelf provides the possibility of resolving ice shelf thickness, water column thickness and the physical properties of the ice shelf and underlying seafloor using passive-source seismic data.
    Description: PDB, AD and PG were supported by NSF Grant PLR 1246151. RAS was supported by NSF Grant PLR-1246416. DAW, RA and AN were supported under NSF Grants PLR-1142518, 1141916 and 1142126, respectively. PDB also received support from the California Department of Parks and Recreation, Division of Boating and Waterways under contract 11-106-107.
    Keywords: Glaciology ; Surface waves and free oscillations ; Seismic anisotropy ; Antarctica
    Repository Name: Woods Hole Open Access Server
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  • 11
    Publication Date: 2022-05-26
    Description: © International Council for the Exploration of the Sea, 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ICES Journal of Marine Science 73 (2016): 1839-1850, doi: 10.1093/icesjms/fsw086.
    Description: For terrestrial and marine benthic ecologists, landscape ecology provides a framework to address issues of complexity, patchiness, and scale—providing theory and context for ecosystem based management in a changing climate. Marine pelagic ecosystems are likewise changing in response to warming, changing chemistry, and resource exploitation. However, unlike spatial landscapes that migrate slowly with time, pelagic seascapes are embedded in a turbulent, advective ocean. Adaptations from landscape ecology to marine pelagic ecosystem management must consider the nature and scale of biophysical interactions associated with organisms ranging from microbes to whales, a hierarchical organization shaped by physical processes, and our limited capacity to observe and monitor these phenomena across global oceans. High frequency, multiscale, and synoptic characterization of the 4-D variability of seascapes are now available through improved classification methods, a maturing array of satellite remote sensing products, advances in autonomous sampling of multiple levels of biological complexity, and emergence of observational networks. Merging of oceanographic and ecological paradigms will be necessary to observe, manage, and conserve species embedded in a dynamic seascape mosaic, where the boundaries, extent, and location of features change with time.
    Description: This work was supported by NASA grant NNX14AP62A “National Marine Sanctuaries as Sentinel Sites for a Demonstration Marine Biodiversity Observation Network (MBON)” funded under the National Ocean Partnership Program (NOPP RFP NOAA-NOS-IOOS-2014-2003803 in partnership between NOAA, BOEM, and NASA), the NOAA Integrated Ocean Observing System (IOOS) Program Office, and the LenFest Ocean Program.
    Keywords: Biodiversity ; Conservation ; Landscape ; Ocean observations ; Pelagic ; Phytoplankton ; Seascape
    Repository Name: Woods Hole Open Access Server
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  • 12
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    Public Library of Science (PLoS)
    Publication Date: 2016-07-12
    Description: by Eva R. M. Joosten, Shihab A. Shamma, Christian Lorenzi, Peter Neri Sound waveforms convey information largely via amplitude modulations (AM). A large body of experimental evidence has provided support for a modulation (bandpass) filterbank. Details of this model have varied over time partly reflecting different experimental conditions and diverse datasets from distinct task strategies, contributing uncertainty to the bandwidth measurements and leaving important issues unresolved. We adopt here a solely data-driven measurement approach in which we first demonstrate how different models can be subsumed within a common ‘cascade’ framework, and then proceed to characterize the cascade via system identification analysis using a single stimulus/task specification and hence stable task rules largely unconstrained by any model or parameters. Observers were required to detect a brief change in level superimposed onto random level changes that served as AM noise; the relationship between trial-by-trial noisy fluctuations and corresponding human responses enables targeted identification of distinct cascade elements. The resulting measurements exhibit a dynamic complex picture in which human perception of auditory modulations appears adaptive in nature, evolving from an initial lowpass to bandpass modes (with broad tuning, Q∼1) following repeated stimulus exposure.
    Print ISSN: 1553-734X
    Electronic ISSN: 1553-7358
    Topics: Biology , Computer Science
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  • 13
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    Public Library of Science (PLoS)
    Publication Date: 2016-07-12
    Description: by Bihai Shi, Cui Zhang, Caihuan Tian, Jin Wang, Quan Wang, Tengfei Xu, Yan Xu, Carolyn Ohno, Robert Sablowski, Marcus G. Heisler, Klaus Theres, Ying Wang, Yuling Jiao Shoot branching requires the establishment of new meristems harboring stem cells; this phenomenon raises questions about the precise regulation of meristematic fate. In seed plants, these new meristems initiate in leaf axils to enable lateral shoot branching. Using live-cell imaging of leaf axil cells, we show that the initiation of axillary meristems requires a meristematic cell population continuously expressing the meristem marker SHOOT MERISTEMLESS ( STM ). The maintenance of STM expression depends on the leaf axil auxin minimum. Ectopic expression of STM is insufficient to activate axillary buds formation from plants that have lost leaf axil STM expressing cells. This suggests that some cells undergo irreversible commitment to a developmental fate. In more mature leaves, REVOLUTA ( REV ) directly up-regulates STM expression in leaf axil meristematic cells, but not in differentiated cells, to establish axillary meristems. Cell type-specific binding of REV to the STM region correlates with epigenetic modifications. Our data favor a threshold model for axillary meristem initiation, in which low levels of STM maintain meristematic competence and high levels of STM lead to meristem initiation.
    Print ISSN: 1553-7390
    Electronic ISSN: 1553-7404
    Topics: Biology
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  • 14
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    Public Library of Science (PLoS)
    Publication Date: 2016-07-12
    Description: by Lauren A. Richardson Our first ever Open Highlights explores recent Open Access research into the complex relationship between host and pathogen during the course of an infection, and the factors that determine its eventual outcome.
    Print ISSN: 1544-9173
    Electronic ISSN: 1545-7885
    Topics: Biology
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  • 15
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    Public Library of Science (PLoS)
    Publication Date: 2016-07-12
    Description: by Cuncong Zhong, Anna Edlund, Youngik Yang, Jeffrey S. McLean, Shibu Yooseph Analyses of metagenome data (MG) and metatranscriptome data (MT) are often challenged by a paucity of complete reference genome sequences and the uneven/low sequencing depth of the constituent organisms in the microbial community, which respectively limit the power of reference-based alignment and de novo sequence assembly. These limitations make accurate protein family classification and abundance estimation challenging, which in turn hamper downstream analyses such as abundance profiling of metabolic pathways, identification of differentially encoded/expressed genes, and de novo reconstruction of complete gene and protein sequences from the protein family of interest. The profile hidden Markov model (HMM) framework enables the construction of very useful probabilistic models for protein families that allow for accurate modeling of position specific matches, insertions, and deletions. We present a novel homology detection algorithm that integrates banded Viterbi algorithm for profile HMM parsing with an iterative simultaneous alignment and assembly computational framework. The algorithm searches a given profile HMM of a protein family against a database of fragmentary MG/MT sequencing data and simultaneously assembles complete or near-complete gene and protein sequences of the protein family. The resulting program, HMM-GRASPx, demonstrates superior performance in aligning and assembling homologs when benchmarked on both simulated marine MG and real human saliva MG datasets. On real supragingival plaque and stool MG datasets that were generated from healthy individuals, HMM-GRASPx accurately estimates the abundances of the antimicrobial resistance (AMR) gene families and enables accurate characterization of the resistome profiles of these microbial communities. For real human oral microbiome MT datasets, using the HMM-GRASPx estimated transcript abundances significantly improves detection of differentially expressed (DE) genes. Finally, HMM-GRASPx was used to reconstruct comprehensive sets of complete or near-complete protein and nucleotide sequences for the query protein families. HMM-GRASPx is freely available online from http://sourceforge.net/projects/hmm-graspx.
    Print ISSN: 1553-734X
    Electronic ISSN: 1553-7358
    Topics: Biology , Computer Science
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  • 16
    Publication Date: 2016-07-12
    Description: by Dazhe Meng, Manu Dubin, Pei Zhang, Edward J. Osborne, Oliver Stegle, Richard M. Clark, Magnus Nordborg The extent to which epigenetic variation affects complex traits in natural populations is not known. We addressed this question using transcriptome and DNA methylation data from a sample of 135 sequenced A. thaliana accessions. Across individuals, expression was significantly associated with cis -methylation for hundreds of genes, and many of these associations remained significant after taking SNP effects into account. The pattern of correlations differed markedly between gene body methylation and transposable element methylation. The former was usually positively correlated with expression, and the latter usually negatively correlated, although exceptions were found in both cases. Finally, we developed graphical models of causality that adapt to a sample with heavy population structure, and used them to show that while methylation appears to affect gene expression more often than expression affects methylation, there is also strong support for both being independently controlled. In conclusion, although we find clear evidence for epigenetic regulation, both the number of loci affected and the magnitude of the effects appear to be small compared to the effect of SNPs.
    Print ISSN: 1553-7390
    Electronic ISSN: 1553-7404
    Topics: Biology
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  • 17
    Publication Date: 2016-07-12
    Description: by Minghua Nie, Emily Arner, John Prudden, Lana Schaffer, Steven Head, Michael N. Boddy Posttranslational modifications (PTMs) provide dynamic regulation of the cellular proteome, which is critical for both normal cell growth and for orchestrating rapid responses to environmental stresses, e.g. genotoxins. Key PTMs include ubiquitin, the Small Ubiquitin-like MOdifier SUMO, and phosphorylation. Recently, SUMO-targeted ubiquitin ligases (STUbLs) were found to integrate signaling through the SUMO and ubiquitin pathways. In general, STUbLs are recruited to target proteins decorated with poly-SUMO chains to ubiquitinate them and drive either their extraction from protein complexes, and/or their degradation at the proteasome. In fission yeast, reducing or preventing the formation of SUMO chains can circumvent the essential and DNA damage response functions of STUbL. This result indicates that whilst some STUbL "targets" have been identified, the crucial function of STUbL is to antagonize SUMO chain formation. Herein, by screening for additional STUbL suppressors, we reveal crosstalk between the serine/threonine phosphatase PP2A-Pab1 B55 and the SUMO pathway. A hypomorphic Pab1 B55 mutant not only suppresses STUbL dysfunction, but also mitigates the phenotypes associated with deletion of the SUMO protease Ulp2, or mutation of the STUbL cofactor Rad60. Together, our results reveal a novel role for PP2A-Pab1 B55 in modulating SUMO pathway output, acting in parallel to known critical regulators of SUMOylation homeostasis. Given the broad evolutionary functional conservation of the PP2A and SUMO pathways, our results could be relevant to the ongoing attempts to therapeutically target these factors.
    Print ISSN: 1553-7390
    Electronic ISSN: 1553-7404
    Topics: Biology
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  • 18
    Publication Date: 2016-07-12
    Description: by Edoardo Pasolli, Duy Tin Truong, Faizan Malik, Levi Waldron, Nicola Segata Shotgun metagenomic analysis of the human associated microbiome provides a rich set of microbial features for prediction and biomarker discovery in the context of human diseases and health conditions. However, the use of such high-resolution microbial features presents new challenges, and validated computational tools for learning tasks are lacking. Moreover, classification rules have scarcely been validated in independent studies, posing questions about the generality and generalization of disease-predictive models across cohorts. In this paper, we comprehensively assess approaches to metagenomics-based prediction tasks and for quantitative assessment of the strength of potential microbiome-phenotype associations. We develop a computational framework for prediction tasks using quantitative microbiome profiles, including species-level relative abundances and presence of strain-specific markers. A comprehensive meta-analysis, with particular emphasis on generalization across cohorts, was performed in a collection of 2424 publicly available metagenomic samples from eight large-scale studies. Cross-validation revealed good disease-prediction capabilities, which were in general improved by feature selection and use of strain-specific markers instead of species-level taxonomic abundance. In cross-study analysis, models transferred between studies were in some cases less accurate than models tested by within-study cross-validation. Interestingly, the addition of healthy (control) samples from other studies to training sets improved disease prediction capabilities. Some microbial species (most notably Streptococcus anginosus ) seem to characterize general dysbiotic states of the microbiome rather than connections with a specific disease. Our results in modelling features of the “healthy” microbiome can be considered a first step toward defining general microbial dysbiosis. The software framework, microbiome profiles, and metadata for thousands of samples are publicly available at http://segatalab.cibio.unitn.it/tools/metaml.
    Print ISSN: 1553-734X
    Electronic ISSN: 1553-7358
    Topics: Biology , Computer Science
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  • 19
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2016-07-12
    Description: by Anja S. Ziegler, Simon J. McIlroy, Poul Larsen, Mads Albertsen, Aviaja A. Hansen, Nicolas Heinen, Per Halkjær Nielsen Membrane fouling presents the greatest challenge to the application of membrane bioreactor (MBR) technology. Formation of biofilms on the membrane surface is the suggested cause, yet little is known of the composition or dynamics of the microbial community responsible. To gain an insight into this important question, we applied 16S rRNA gene amplicon sequencing with a curated taxonomy and fluorescent in situ hybridization to monitor the community of a pilot-scale MBR carrying out enhanced biological nitrogen and phosphorus removal with municipal wastewater. In order to track the dynamics of the fouling process, we concurrently investigated the communities of the biofilm, MBR bulk sludge, and the conventional activated sludge system used to seed the MBR system over several weeks from start-up. As the biofilm matured the initially abundant betaproteobacterial genera Limnohabitans , Hydrogenophaga and Malikia were succeeded by filamentous Chloroflexi and Gordonia as the abundant species. This study indicates that, although putative pioneer species appear, the biofilm became increasingly similar to the bulk community with time. This suggests that the microbial population in bulk water will largely determine the community structure of the mature biofilm.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 20
    Publication Date: 2016-07-12
    Description: by Petra E. Verburg, Graeme Tucker, Wendy Scheil, Jan Jaap H. M. Erwich, Gus A. Dekker, Claire Trelford Roberts Objectives Sexual inequality starts in utero . The contribution of biological sex to the developmental origins of health and disease is increasingly recognized. The aim of this study was to assess and interpret sexual dimorphisms for three major adverse pregnancy outcomes which affect the health of the neonate, child and potentially adult. Methods Retrospective population-based study of 574,358 South Australian singleton live births during 1981–2011. The incidence of three major adverse pregnancy outcomes [preterm birth (PTB), pregnancy induced hypertensive disorders (PIHD) and gestational diabetes mellitus (GDM)] in relation to fetal sex was compared according to traditional and fetus-at-risk (FAR) approaches. Results The traditional approach showed male predominance for PTB [20–24 weeks: Relative Risk (RR) M/F 1.351, 95%-CI 1.274–1.445], spontaneous PTB [25–29 weeks: RR M/F 1.118, 95%-CI 1.044–1.197%], GDM [RR M/F 1.042, 95%-CI 1.011–1.074], overall PIHD [RR M/F 1.053, 95%-CI 1.034–1.072] and PIHD with term birth [RR M/F 1.074, 95%-CI 1.044–1.105]. The FAR approach showed that males were at increased risk for PTB [20–24 weeks: RR M/F 1.273, 95%-CI 1.087–1.490], for spontaneous PTB [25–29 weeks: RR M/F 1.269, 95%-CI 1.143–1.410] and PIHD with term birth [RR M/F 1.074, 95%-CI 1.044–1.105%]. The traditional approach demonstrated female predominance for iatrogenic PTB [25–29 weeks: RR M/F 0.857, 95%-CI 0.780–0.941] and PIHD associated with PTB [25–29 weeks: RR M/F 0.686, 95%-CI 0.581–0.811]. The FAR approach showed that females were at increased risk for PIHD with PTB [25–29 weeks: RR M/F 0.779, 95%-CI 0.648–0.937]. Conclusions This study confirms the presence of sexual dimorphisms and presents a coherent framework based on two analytical approaches to assess and interpret the sexual dimorphisms for major adverse pregnancy outcomes. The mechanisms by which these occur remain elusive, but sex differences in placental gene expression and function are likely to play a key role. Further research on sex differences in placental function and maternal adaptation to pregnancy is required to delineate the causal molecular mechanisms in sex-specific pregnancy outcome. Identifying these mechanisms may inform fetal sex specific tailored antenatal and neonatal care.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 21
    Publication Date: 2016-07-12
    Description: by Harald Schrem, Valentin Schneider, Marlene Kurok, Alon Goldis, Maren Dreier, Alexander Kaltenborn, Wilfried Gwinner, Marc Barthold, Jan Liebeneiner, Markus Winny, Jürgen Klempnauer, Moritz Kleine Background The aim of this study is to identify independent pre-transplant cancer risk factors after kidney transplantation and to assess the utility of G-chart analysis for clinical process control. This may contribute to the improvement of cancer surveillance processes in individual transplant centers. Patients and Methods 1655 patients after kidney transplantation at our institution with a total of 9,425 person-years of follow-up were compared retrospectively to the general German population using site-specific standardized-incidence-ratios (SIRs) of observed malignancies. Risk-adjusted multivariable Cox regression was used to identify independent pre-transplant cancer risk factors. G-chart analysis was applied to determine relevant differences in the frequency of cancer occurrences. Results Cancer incidence rates were almost three times higher as compared to the matched general population (SIR = 2.75; 95%-CI: 2.33–3.21). Significantly increased SIRs were observed for renal cell carcinoma (SIR = 22.46), post-transplant lymphoproliferative disorder (SIR = 8.36), prostate cancer (SIR = 2.22), bladder cancer (SIR = 3.24), thyroid cancer (SIR = 10.13) and melanoma (SIR = 3.08). Independent pre-transplant risk factors for cancer-free survival were age 62.6 years (p = 0.001, HR: 1.29), polycystic kidney disease other than autosomal dominant polycystic kidney disease (ADPKD) (p = 0.001, HR: 0.68), high body mass index in kg/m 2 (p
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 22
    Publication Date: 2016-07-12
    Description: by Prasamit Saurav Baruah, Myriam Beauchemin, Josée Hébert, Richard Bertrand Bcl-xL proteins undergo dynamic phosphorylation/dephosphorylation on Ser49 and Ser62 residues during mitosis. The expression of Bcl-xL(S49A), (S62A) and dual (S49/62A) phosphorylation mutants in tumor cells lead to severe mitotic defects associated with multipolar spindle, chromosome lagging and bridging, and micro-, bi- and multi-nucleated cells. Because the above observations were made in tumor cells which already display genomic instability, we now address the question: will similar effects occur in normal human diploid cells? We studied normal human diploid BJ foreskin fibroblast cells expressing Bcl-xL (wild type), (S49A), (S49D), (S62A), (S62D) and the dual-site (S49/62A) and (S49/62D) mutants. Cells expressing S49 and/or S62 phosphorylation mutants showed reduced kinetics of cell population doubling. These effects on cell population doubling kinetics correlated with early outbreak of senescence with no impact on the cell death rate. Senescent cells displayed typical senescence-associated phenotypes including high-level of senescence-associated β-galactosidase activity, interleukin-6 (IL-6) secretion, tumor suppressor p53 and cyclin-dependent kinase inhibitor p21Waf1/Cip1 activation as well as γH2A.X-associated nuclear chromatin foci. Fluorescence in situ hybridization analysis and Giemsa-banded karyotypes revealed that the expression of Bcl-xL phosphorylation mutants in normal diploid BJ cells provoked chromosome instability and aneuploidy. These findings suggest that dynamic Bcl-xL(S49) and (S62) phosphorylation/dephosphorylation cycles are important in the maintenance of chromosome integrity during mitosis in normal cells. They could impact future strategies aiming to develop and identify compounds that could target not only the anti-apoptotic domain of Bcl-xL protein, but also its mitotic domain for cancer therapy.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 23
    Publication Date: 2016-07-12
    Description: by Vera Kloten, Martin Schlensog, Julian Eschenbruch, Janina Gasthaus, Janina Tiedemann, Jolein Mijnes, Timon Heide, Till Braunschweig, Ruth Knüchel, Edgar Dahl NDRG2 , a member of the N-myc downstream-regulated gene family, is thought to be a putative tumor suppressor gene with promising clinical impact in breast cancer. Since breast cancer comprises heterogeneous intrinsic subtypes with distinct clinical outcomes we investigated the pivotal role of NDRG2 in basal-type breast cancers. Based on subtype classified tumor (n = 45) and adjacent normal tissues (n = 17) we examined NDRG2 mRNA expression and CpG-hypermethylation, whose significance was further validated by independent data sets from The Cancer Genome Atlas (TCGA). In addition, NDRG2 protein expression was evaluated immunohistochemically using a tissue micro array (TMA, n = 211). In vitro , we investigated phenotypic effects caused by NDRG2 silencing in the basal A-like HCC1806 as well as NDRG2 over-expression in basal A-like BT20 compared to luminal-type MCF7 breast cancer cells. Our tissue collections demonstrated an overall low NDRG2 mRNA expression in breast cancer subtypes compared to normal breast tissue in line with an increased CpG-hypermethylation in breast cancer tissue. Independent TCGA data sets verified a significant (P
    Electronic ISSN: 1932-6203
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  • 24
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2016-07-12
    Description: by Viorica Ionut, Orison O. Woolcott, Hasmik J. Mkrtchyan, Darko Stefanovski, Morvarid Kabir, Malini S. Iyer, Huiwen Liu, Ana V. B. Castro, Qiang Wu, Josiane L. Broussard, Cathryn M. Kolka, Isaac Asare-Bediako, Richard N. Bergman Background Exenatide’s effects on glucose metabolism have been studied extensively in diabetes but not in pre-diabetes. Objective We examined the chronic effects of exenatide alone on glucose metabolism in pre-diabetic canines. Design and Methods After 10 weeks of high-fat diet (HFD), adult dogs received one injection of streptozotocin (STZ, 18.5 mg/kg). After induction of pre-diabetes, while maintained on HFD, animals were randomized to receive either exenatide (n = 7) or placebo (n = 7) for 12 weeks. β-Cell function was calculated from the intravenous glucose tolerance test (IVGTT, expressed as the acute insulin response, AIR G ), the oral glucose tolerance test (OGTT, insulinogenic index) and the graded-hyperglycemic clamp (clamp insulinogenic index). Whole-body insulin sensitivity was assessed by the IVGTT. At the end of the study, pancreatic islets were isolated to assess β-cell function in vitro . Results OGTT: STZ caused an increase in glycemia at 120 min by 22.0% (interquartile range, IQR, 31.5%) (P = 0.011). IVGTT: This protocol also showed a reduction in glucose tolerance by 48.8% (IQR, 36.9%) (P = 0.002). AIR G decreased by 54.0% (IQR, 40.7%) (P = 0.010), leading to mild fasting hyperglycemia (P = 0.039). Exenatide, compared with placebo, decreased body weight (P
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 25
    Publication Date: 2016-07-12
    Description: by Ha Young Kim, Eun Jin Jang, ByeongJu Park, Tae-Young Kim, Soon-Ae Shin, Yong-Chan Ha, Sunmee Jang Background Asian-specific prediction models for estimating individual risk of osteoporotic fractures are rare. We developed a Korean fracture risk prediction model using clinical risk factors and assessed validity of the final model. Methods A total of 718,306 Korean men and women aged 50–90 years were followed for 7 years in a national system-based cohort study. In total, 50% of the subjects were assigned randomly to the development dataset and 50% were assigned to the validation dataset. Clinical risk factors for osteoporotic fracture were assessed at the biennial health check. Data on osteoporotic fractures during the follow-up period were identified by ICD-10 codes and the nationwide database of the National Health Insurance Service (NHIS). Results During the follow-up period, 19,840 osteoporotic fractures were reported (4,889 in men and 14,951 in women) in the development dataset. The assessment tool called the Korean Fracture Risk Score (KFRS) is comprised of a set of nine variables, including age, body mass index, recent fragility fracture, current smoking, high alcohol intake, lack of regular exercise, recent use of oral glucocorticoid, rheumatoid arthritis, and other causes of secondary osteoporosis. The KFRS predicted osteoporotic fractures over the 7 years. This score was validated using an independent dataset. A close relationship with overall fracture rate was observed when we compared the mean predicted scores after applying the KFRS with the observed risks after 7 years within each 10th of predicted risk. Conclusion We developed a Korean specific prediction model for osteoporotic fractures. The KFRS was able to predict risk of fracture in the primary population without bone mineral density testing and is therefore suitable for use in both clinical setting and self-assessment. The website is available at http://www.nhis.or.kr.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 26
    Publication Date: 2016-07-12
    Description: by Cecilia Ma, Eva Monsma This paper examines the factor structure and measurement invariance of the Task and Ego Orientation in Sport Questionnaire (TEOSQ) across American and Chinese samples. Results based on the mean and covariance structure analyses supported configural invariance, metric invariance and scalar invariance across groups. Latent means analyses revealed that American sample had significantly higher mean scores on task and ego orientations than the Chinese sample. The findings suggest that the TEOSQ is a valid and reliable instrument in assessing achievement motivation across these two diverse populations.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 27
    Publication Date: 2016-07-12
    Description: by Lin Yang, Liangping Xia, Yan Wang, Shaodong Hong, Haiyang Chen, Shaobo Liang, Peijian Peng, Yong Chen Background Poor nutritional status is associated with progression and advanced disease in patients with cancer. The prognostic nutritional index (PNI) may represent a simple method of assessing host immunonutritional status. This study was designed to investigate the prognostic value of the PNI for distant metastasis-free survival (DMFS) in patients with nasopharyngeal carcinoma (NPC). Methods A training cohort of 1,168 patients with non-metastatic NPC from two institutions was retrospectively analyzed. The optimal PNI cutoff value for DMFS was identified using the online tool “Cutoff Finder”. DMFS was analyzed using stratified and adjusted analysis. Propensity score-matched analysis was performed to balance baseline characteristics between the high and low PNI groups. Subsequently, the prognostic value of the PNI for DMFS was validated in an external validation cohort of 756 patients with NPC. The area under the receiver operating characteristics curve (AUC) was calculated to compare the discriminatory ability of different prognostic scores. Results The optimal PNI cutoff value was determined to be 51. Low PNI was significantly associated with poorer DMFS than high PNI in univariate analysis (P
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 28
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2016-07-12
    Description: by Hung Yuan Chen, Yen Ling Chiu, Shih Ping Hsu, Mei Fen Pai, Ju Yeh Yang, Yu Sen Peng Background Fractures are a common morbidity that lead to worse outcomes in dialysis patients. Fetuin A inhibits vascular calcification (VC), potentially promotes bone mineralization and its level positively correlates with bone mineral density in the general population. On the other hand, the presence of VC is associated with low bone volume in dialysis patients. Whether the fetuin A level and VC can predict the occurrence of fractures in dialysis patients remains unknown. Methods We performed this prospective, observational cohort study including 685 dialysis patients (629 hemodialysis and 56 peritoneal dialysis) from a single center in Taiwan for a median follow-up period of 3.4 years. The baseline fetuin A level and status of presence of aortic arch calcification (VC) and incidence of major fractures (hip, pelvis, humerus, proximal forearm, lower leg or vertebrae) were assessed using adjusted Cox proportional hazards models, recursive partitioning analysis and competing risk models. Results Overall, 177 of the patients had major fractures. The incidence rate of major fractures was 3.29 per 100 person-years. In adjusted analyses, the patients with higher baseline fetuin A levels had a lower incidence of fractures (adjusted hazard ratio (HR), 0.3; 95% CI, 0.18‒0.5, fetuin A tertile 3 vs . tertile 1 and HR, 0.52; 95% CI, 0.34‒0.78, tertile 2 vs . tertile 1). The presence of aortic arch calcification (VC) independently predicted the occurrence of fractures (adjusted HR, 1.95; 95% CI, 1.34‒2.84) as well. When accounting for death as an event in competing risk models, the patients with higher baseline fetuin A levels remained to have a lower incidence of fractures (SHR, 0.31; 95% CI, 0.17‒0.56, fetuin A tertile 3 vs . tertile 1 and 0.51; 95% CI, 0.32‒0.81, tertile 2 vs . tertile 1). Interpretations Lower baseline fetuin A levels and the presence of VC were independently linked to higher risk of incident fractures in prevalent dialysis patients.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 29
    Publication Date: 2016-07-13
    Description: Although phosphorus limitation is common in freshwaters and bacteria are known to use dissolved organic phosphorus (DOP), little is known about how efficiently DOP compounds are taken up by individual bacterial taxa. Here, we assessed bacterial uptake of three model DOP substrates in two mountain lakes and examined whether DOP uptake followed concentration-dependent patterns. We determined bulk uptake rates by the bacterioplankton and examined bacterial taxon-specific substrate uptake patterns using microautoradiography combined with catalyzed reporter deposition–fluorescence in situ hybridization. Our results show that in the oligotrophic alpine lake, bacteria took up ATP, glucose-6-phosphate and glycerol-3-phosphate to similar extents (mean 29.7 ± 4.3% Bacteria ), whereas in the subalpine mesotrophic lake, ca. 40% of bacteria took up glucose-6-phosphate, but only ~20% took up ATP or glycerol-3-phosphate. In both lakes, the R-BT cluster of Betaproteobacteria (lineage of genus Limnohabitans ) was over-represented in glucose-6-phosphate and glycerol-3-phosphate uptake, whereas AcI Actinobacteria were under-represented in the uptake of those substrates. Alphaproteobacteria and Bacteroidetes contributed to DOP uptake proportionally to their in situ abundance. Our results demonstrate that R-BT Betaproteobacteria are the most active bacteria in DOP acquisition, whereas the abundant AcI Actinobacteria may either lack high affinity DOP uptake systems or have reduced phosphorus requirements.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
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  • 30
    Publication Date: 2016-07-13
    Description: Earlier studies show that the proliferation of phytoplankton viruses can be inhibited by depletion of soluble reactive phosphorus (SRP; orthophosphate). In natural marine waters, phytoplankton phosphorus (P) availability is, however, largely determined by the supply rate of SRP (e.g. through remineralization) and potentially by the source of P as well (i.e. the utilization of soluble non-reactive P; SNP). Here we show how a steady low supply of P (mimicking natural P recycling) to virally infected P-limited Micromonas pusilla stimulates virus proliferation. Independent of the degree of P limitation prior to infection (0.32 and 0.97μ max chemostat cultures), SRP supply resulted in 2-fold higher viral burst sizes (viruses lysed per host cell) as compared with no addition (P starvation). Delaying these spikes during the infection cycle showed that the added SRP was utilized for extra M. pusilla virus (MpV) production far into the lytic cycle (18 h post-infection). Moreover, P-limited M. pusilla utilized several SNP compounds with high efficiency and with the same extent of burst size stimulation as for SRP. Finally, addition of virus-free MpV lysate (representing a complex SNP mixture) to newly infected cells enhanced MpV production, implicating host-associated alkaline phosphatase activity, and highlighting its important role in oligotrophic environments.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
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  • 31
    Publication Date: 2016-07-13
    Description: Earth's free oscillations excited by a mega-thrust earthquake were observed by a continent-scale array of groundwater monitoring sites for the first time. After the occurrence of the 2011 Tohoku M w 9.0 earthquake, water level records at 43 out of 216 wells in the China mainland revealed long-period free oscillation signals. In the time domain, these free oscillations exhibit globe circling Rayleigh surface waves. In some single wells, even the globe-circling Rayleigh wave R7 was visible, which travels three times around the Earth after the first arrival and appears about 10 hr after the earthquake occurrence in the present case. The spectral analysis shows that the principal oscillatory fluctuations seen in the water level records correspond to the spheroidal modes 0 S l ( l  = 2–31 for frequencies between 0.3 and 5.0 mHz) of the Earth's free oscillation. Especially at quiet sites, the spheroidal modes at very low frequencies (〈1.5 mHz) can be identified with high signal-to-noise ratios. Using signal enhancement methods (product spectrum over 43 wells), even the gravest modes of these oscillations can be detected. The results suggest that groundwater level arrays can be considered as a low-cost complementary tool to study the Earth's free oscillations excited by great earthquakes. Additionally, the site-specific aquifer response may provide further insight into local hydrogeological conditions.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 32
    Publication Date: 2016-07-13
    Description: We performed numerical simulations of the 2011 deep-seated Akatani landslide in central Japan to understand the dynamic evolution of friction of the landslide. By comparing the forces obtained from numerical simulation to those resolved from seismic waveform inversion, the coefficient of the friction during sliding was investigated in the range of 0.1–0.4. The simulation assuming standard Coulomb friction shows that the forces obtained by the seismic waveform inversion are well explained using a constant friction of μ = 0.3. A small difference between the residuals of Coulomb simulation and a velocity-dependent simulation suggests that the coefficient of friction over the volume is well constrained as 0.3 most of time during sliding. It suggests the sudden loss of shearing resistance at the onset of sliding, that is, sudden drop of the initial coefficient of friction in our model, which accelerates the deep-seated landslide. Our numerical simulation calibrated by seismic data provides the evolution of dynamic friction with a reasonable resolution in time, which is difficult to obtain from a conventional runout simulation, or seismic waveform inversion alone.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 33
    Publication Date: 2016-07-13
    Description: We explore thermal convection of a fluid with a temperature-dependent viscosity in a basally heated 3-D spherical shell using linear stability analyses and numerical experiments, while considering the application of our results to terrestrial planets. The inner to outer radius ratio of the shell f assumed in the linear stability analyses is in the range of 0.11–0.88. The critical Rayleigh number R c for the onset of thermal convection decreases by two orders of magnitude as f increases from 0.11 to 0.88, when the viscosity depends sensitively on the temperature, as is the case for real mantle materials. Numerical simulations carried out in the range of f  = 0.11–0.55 show that a thermal boundary layer (TBL) develops both along the surface and bottom boundaries to induce cold and hot plumes, respectively, when f is 0.33 or larger. However, for smaller f values, a TBL develops only on the bottom boundary. Convection occurs in the stagnant-lid regime where the root mean square velocity on the surface boundary is less than 1 per cent of its maximum at depth, when the ratio of the viscosity at the surface boundary to that at the bottom boundary exceeds a threshold that depends on f . The threshold decreases from 10 6.5 at f  = 0.11 to 10 4 at f  = 0.55. If the viscosity at the base of the convecting mantle is 10 20 –10 21  Pa s, the Rayleigh number exceeds R c for Mars, Venus and the Earth, but does not for the Moon and Mercury; convection is unlikely to occur in the latter planets unless the mantle viscosity is much lower than 10 20  Pa s and/or the mantle contains a strong internal heat source.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 34
    Publication Date: 2016-07-13
    Description: We introduce a technique to compute exact anelastic sensitivity kernels in the time domain using parsimonious disk storage. The method is based on a reordering of the time loop of time-domain forward/adjoint wave propagation solvers combined with the use of a memory buffer. It avoids instabilities that occur when time-reversing dissipative wave propagation simulations. The total number of required time steps is unchanged compared to usual acoustic or elastic approaches. The cost is reduced by a factor of 4/3 compared to the case in which anelasticity is partially accounted for by accommodating the effects of physical dispersion. We validate our technique by performing a test in which we compare the K α sensitivity kernel to the exact kernel obtained by saving the entire forward calculation. This benchmark confirms that our approach is also exact. We illustrate the importance of including full attenuation in the calculation of sensitivity kernels by showing significant differences with physical-dispersion-only kernels.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 35
    Publication Date: 2016-07-13
    Description: Subducting oceanic lithosphere is an example of a thin sheet-like object whose characteristic lateral dimension greatly exceeds its thickness. Here we exploit this property to derive a new hybrid boundary-integral/thin sheet (BITS) representation of subduction that combines in a single equation all the forces acting on the sheet: gravity, internal resistance to bending and stretching, and the tractions exerted by the ambient mantle. For simplicity, we limit ourselves to 2-D. We solve the BITS equations using a discrete Lagrangian approach in which the sheet is represented by a set of vertices connected by edges. Instantaneous solutions for the sinking speed of a slab attached to a trailing flat sheet obey a scaling law of the form V / V Stokes  = fct(St), where V Stokes is a characteristic Stokes sinking speed and St is the sheet's flexural stiffness. Time-dependent solutions for the evolution of the sheet's shape and thickness show that these are controlled by the viscosity ratio between the sheet and its surroundings. An important advantage of the BITS approach is the possibility of generalizing the sheet's rheology, either to a viscosity that varies along the sheet or to a non-Newtonian shear-thinning rheology.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 36
    Publication Date: 2016-07-13
    Description: Rock permeability is an important parameter for the formation evaluation. In this paper, a new method with streaming current is proposed to determine the sample permeability based on the electrokinetic effects, and is proved by the experimental measurements. Corresponding to this method, we have designed an experimental setup and a test system, then performed the streaming current (potential) and electro-osmosis pressure experiments with 23 sandstone samples at 0.05 mol l –1 NaCl solution. The streaming current (potential) coefficient and electro-osmosis pressure coefficient are obtained, respectively, with the experimental data at low frequencies with AC lock-in technique. The electrokinetic permeabilities are further calculated with these coefficients. The results are consistent well with the gas permeability measured with Darcy's law, which verifies the current method for estimating rock permeability. Our measurements are also analysed and compared with previous measurements. The results indicate that our method can reflect the essence of electrokinetic effects better and simplify the electrokinetic measurements as well. In addition, we discuss the influences of experimental artefacts (core holder and confining pressure installation) on the electrokinetic data. The results show that the trough phenomenon, appeared in frequency curves of streaming current (potential) coefficients, is induced by the resonance of the core-holder/vibrator system. This is important for the design of electrokinetic setup and the analysis of low-frequency response of the electrokinetic coupling coefficients.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
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    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 37
    Publication Date: 2016-07-13
    Description: Real Earth media are not perfectly elastic. Instead, they attenuate propagating mechanical waves. This anelastic phenomenon in wave propagation can be modeled by a viscoelastic mechanical model consisting of several standard linear solids. Using this viscoelastic model, we approximate a constant Q over a frequency band of interest. We use a four-element viscoelastic model with a trade-off between accuracy and computational costs to incorporate Q into 2-D time-domain first-order velocity–stress wave equations. To improve the computational efficiency, we limit the Q in the model to a list of discrete values between 2 and 1000. The related stress and strain relaxation times that characterize the viscoelastic model are pre-calculated and stored in a database for use by the finite-difference calculation. A viscoelastic finite-difference scheme that is second order in time and fourth order in space is developed based on the MacCormack algorithm. The new method is validated by comparing the numerical result with analytical solutions that are calculated using the generalized reflection/transmission coefficient method. The synthetic seismograms exhibit greater than 95 per cent consistency in a two-layer viscoelastic model. The dispersion generated from the simulation is consistent with the Kolsky–Futterman dispersion relationship.
    Keywords: Seismology
    Print ISSN: 0956-540X
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    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 38
    Publication Date: 2016-07-13
    Description: Seismology plays an important role in characterizing potential underground nuclear tests. Using broad-band digital seismic data from Northeast China, South Korea and Japan, we investigated the properties of the recent seismic event occurred in North Korea on 2016 January 6. Using a relative location method and choosing the previous 2006 explosion as the master event, the 2016 event was located within the North Korean nuclear test site, with its epicentre at latitude 41.3003°N and longitude 129.0678°E, approximately 900 m north and 500 m west of the previous event on 2013 February 12. Based on the error ellipse, the relocation uncertainty was approximately 70 m. Using the P / S spectral ratios, including Pg/Lg, Pn/Lg and Pn/Sn, as the discriminants, we identify the 2016 event as an explosion rather than an earthquake. The body-wave magnitude calculated from regional wave Lg is m b (Lg) equal to 4.7 ± 0.2. Adopting an empirical magnitude–yield relation, and assuming that the explosion is fully coupled and detonated at a normally scaled depth, we find that the seismic yield is about 4 kt, with the uncertainties allowing a range from 2 to 8 kt.
    Keywords: Express Letters, Seismology
    Print ISSN: 0956-540X
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    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 39
    Publication Date: 2016-07-13
    Description: After 83 yr, the great normal-faulting earthquake of 1933 March 2, which took place off the Japan Trench and produced a devastating tsunami on the Sanriku coast and damaging waves in Hawaii, remains the largest recorded normal-faulting earthquake. This study uses advanced methods to investigate this event using far-field seismological and tsunami data and complements a sister study by Uchida et al. which used exclusively arrival times at Japanese stations. Our relocation of the main shock (39.22°N, 144.45°E, with a poorly constrained depth of less than 40 km) places it in the outer trench slope, below a seafloor depth of ~6500 m, in a region of horst-and-graben structure, with fault scarps approximately parallel to the axis of the Japan Trench. Relocated aftershocks show a band of genuine shallow aftershocks parallel to the Japan Trench under the outer trench slope and a region of post-mainshock events landward of the trench axis that occur over roughly the same latitude range and are thought to be the result of stress transfer to the interplate thrust boundary following the normal-faulting rupture. Based on a combination of P -wave first motions and inversion of surface wave spectral amplitudes, we propose a normal-faulting focal mechanism ( = 200°, = 61° and = 271°) and a seismic moment M 0 = (7 ± 1) x 10 28 dyn cm ( M w = 8.5). A wide variety of data, including the distribution of isoseismals, the large magnitudes (up to 8.9) proposed by early investigators before the standardization of magnitude scales, estimates of energy-to-moment ratios and the tentative identification of a T wave at Pasadena (and possibly Riverside), clearly indicate that this seismic source was exceptionally rich in high-frequency wave energy, suggesting a large apparent stress and a sharp rise time, and consistent with the behaviour of many smaller shallow normal-faulting earthquakes. Hydrodynamic simulations based on a range of possible sources consistent with the above findings, including a compound rupture on two opposite-facing normal-faulting segments, are in satisfactory agreement with tsunami observations in Hawaii, where run-up reached 3 m, causing significant damage. This study emphasizes the need to include off-trench normal-faulting earthquake sources in global assessments of tsunami hazards emanating from the subduction of old and cold plates, whose total length of trenches exceed 20 000 km, even though only a handful of great such events are known with confidence in the instrumental record.
    Keywords: Seismology
    Print ISSN: 0956-540X
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    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 40
    Publication Date: 2016-07-13
    Description: Pointwise error estimates for the first-order div least-squares (LS) finite element method for second-order elliptic partial differential equations are presented. Direct flux approximation is considered as an important advantage of the LS method. However, there are no known pointwise error estimates for the direct flux approximation. In this paper, we provide optimal pointwise estimates which show local dependence of the error at a point and weak dependence of the global norm. As an elementary consequence of these estimates, we provide an asymptotic error expansion inequality. The inequality has applications to superconvergence and a posteriori estimates.
    Print ISSN: 0272-4979
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    Topics: Mathematics
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  • 41
    Publication Date: 2016-07-13
    Description: The first-order and higher-order derivatives of a function can be viewed as the solutions of Volterra integral equations of the first kind. In this paper we propose a fast multiscale solver for the numerical solution of the Tikhonov regularization of the Volterra equations. In association with the special form of the kernels, the matrices resulting from the discretization by multiscale bases are sparse. Moreover, they can be truncated using proper strategies with only a minor loss of accuracy. In the best case, the number of nonzero entries of the truncated matrices is linear with respect to the dimensions of the matrices. The accuracy of the solution from the solver is analysed theoretically and verified by numerical experiments.
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  • 42
    Publication Date: 2016-07-13
    Description: The finite element method with $\mathscr {Q}_p$ elements is applied to a singularly perturbed convection–diffusion problem on an L-shaped domain. As an effect of corner singularities the exact solution is not $H^2$ -regular. Therefore, we combine a layer-adapted Shishkin mesh with a special grading adapted to the corner singularity. On such meshes we prove error estimates and estimates for the closeness error which explicitly show the influence of the grading parameter $\mu$ . Hence, $\mu$ can be chosen such that optimal error bounds are obtained. Thereby, it turns out that in the problem studied the influence of the corner singularity becomes small if the perturbation parameter $\varepsilon$ decreases. Moreover, we conduct numerical experiments that verify the theoretical results.
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  • 43
    Publication Date: 2016-07-13
    Description: Pták's method of nondiscrete induction is based on the idea that in the analysis of iterative processes one should aim at rates of convergence as functions rather than just numbers, because functions may give convergence estimates that are tight throughout the iteration rather than just asymptotically. In this paper we motivate and prove a theorem on nondiscrete induction, originally due to Potra and Pták, and we apply it to the Newton iterations for computing the matrix polar decomposition and the matrix square root. Our goal is to illustrate the application of the method of nondiscrete induction in the finite-dimensional numerical linear algebra context. We show the sharpness of the resulting convergence estimate analytically for the polar decomposition iteration and on some examples for the square root iteration. We also discuss some of the method's limitations and possible extensions.
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  • 44
    Publication Date: 2016-07-13
    Description: We consider the numerical solution, by a Petrov–Galerkin finite-element method, of a singularly perturbed reaction–diffusion differential equation posed on the unit square. In Lin & Stynes (2012, A balanced finite element method for singularly perturbed reaction-diffusion problems. SIAM J. Numer. Anal. , 50 , 2729–2743), it is argued that the natural energy norm, associated with a standard Galerkin approach, is not an appropriate setting for analysing such problems, and there they propose a method for which the natural norm is ‘balanced’. In the style of a first-order system least squares method, we extend the approach of Lin & Stynes (2012, A balanced finite element method for singularly perturbed reaction-diffusion problems. SIAM J. Numer. Anal. , 50 , 2729–2743) by introducing a constraint which simplifies the associated finite-element space and the method's analysis. We prove robust convergence in a balanced norm on a piecewise-uniform (Shishkin) mesh, and present supporting numerical results. Finally, we demonstrate how the resulting linear systems are solved optimally using multigrid methods.
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  • 45
    Publication Date: 2016-07-13
    Description: The construction of tensor-product surface patches with a family of Pythagorean-hodograph (PH) isoparametric curves is investigated. The simplest nontrivial instances, interpolating four prescribed patch boundary curves, involve degree $(5,4)$ tensor-product surface patches $\bf{x}(u,v)$ whose $v=\hbox {constant}$ isoparametric curves are all spatial PH quintics. It is shown that the construction can be reduced to solving a novel type of quadratic quaternion equation, in which the quaternion unknown and its conjugate exhibit left and right coefficients, while the quadratic term has a coefficient interposed between them. A closed-form solution for this type of equation is derived, and conditions for the existence of solutions are identified. The surfaces incorporate three residual scalar freedoms which can be exploited to improve the interior shape of the patch. The implementation of the method is illustrated through a selection of computed examples.
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  • 46
    Publication Date: 2016-07-13
    Description: Interior eigenvalues of bounded scattering objects can be rigorously characterized from multi-static and multi-frequency far field data, that is, from the behaviour of scattered waves far away from the object. This characterization, the so-called inside–outside duality, holds for various types of penetrable and impenetrable scatterers and is based on the behaviour of a particular eigenvalue of the far field operator. It naturally leads to a numerical algorithm for computing interior eigenvalues of a scatterer that does not require shape or physical properties of the scatterer as input. Since the nonlinear inverse problem to compute such interior eigenvalues from far field data is ill-posed, we propose a regularizing algorithm that is shown to converge as the noise level of the far field data tends to zero. We illustrate feasibility and accuracy of our algorithm by numerical experiments where we compute interior transmission eigenvalues and Robin eigenvalues of the Laplacian in three-dimensional domains from scattering data of these domains due to plane incident waves.
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  • 47
    Publication Date: 2016-07-13
    Description: During the last centuries, populations of marine megafauna—such as seabirds, turtles, and mammals—were intensively exploited. At present, other threats such as bycatch and pollution affect these species, which play key ecological roles in marine ecosystems as apex consumers and/or nutrient transporters. This study analyses the distribution of six megafaunal species ( Chelonia mydas , Caretta caretta , Dermochelys coriacea , Thalassarche melanophris , Otaria flavescens , and Arctocephalus australis ) coexisting in the Southwestern Atlantic to discuss their protection in terms of current management strategies in the region. Through the prediction of the species potential distributions and their relation to bathymetry, sea temperature and oceanographic fronts, key ecological areas are defined from a multi-taxa perspective. Information on the distribution of 70 individuals (18 sea turtles, 19 albatrosses, and 33 otariids) was obtained through satellite tracking conducted during 2007–2013 and analysed using a Geographic Information System and maximum entropy models. During the autumn–winter period, megafaunal species were distributed over the continental shelves of Argentina, Uruguay, and Brazil, mainly over the Argentine Exclusive Economic Zone and the Argentina-Uruguay Common Fishing Zone. Despite some differences, all megafaunal species seems to have similar environmental requirements during the autumn–winter period. Mostly waters shallower than 50 m were identified as key ecological areas, with the Río de la Plata as the habitat with the highest suitability for all the species. This area is highly productive and sustains the main coastal fisheries of Uruguay and Argentina, yet its role as a key ecological area for megafaunal species has been underestimated until now. This approach provides a basis to analyse the effect of anthropic activities on megafaunal species through risk maps and, ultimately, to generate knowledge to improve national and bi-national management plans between Argentina and Uruguay.
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    Topics: Biology , Geosciences , Physics
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  • 48
    Publication Date: 2016-07-13
    Description: In the North Sea flatfish fishery, electric pulse trawls have been introduced to replace the conventional mechanical method. Pulse trawls reduce the fuel consumption, reduce adverse impact on the ecosystem but cause injuries in gadoids. We describe the design and electrical properties of pulse trawls currently in use and study the behavioural response and injuries in cod exposed to electrical pulses under controlled conditions. Pulse trawls operate at an average power of 0.7 kW m –1 beam length and a duty cycle of ~2%. The electric field is heterogeneous with highest field strength occurring close to the conductors. Cod were exposed to three different pulse types for a range of field strengths, frequencies, and duty cycles. Two size classes were tested representing cod that escape through the meshes (11–17 cm) and market-sized cod that are retained in the net (34–56 cm). Cod exposed to a field strength of ≥37 V m –1 responded by moderate-to-strong muscular contractions. Some of the large cod ( n = 260) developed haemorrhages and fractures in the spine, and haemal and neural arches in the tail part of the body. The probability of injuries increased with field strength and decreased when frequency was increased from 100 to 180 Hz. None of the small cod ( n = 132) were injured and all survived. The field strength at the lateral boundaries of the trawl was too low to inflict injuries in cod.
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  • 49
    Publication Date: 2016-07-13
    Description: A coupled biophysical model is used to explore the physical controls involved in the timing of the spring phytoplankton bloom in fjords. Observations from Rivers Inlet, British Columbia, are used to force and evaluate the model. It is found that the interannual variation in timing is due primarily to variations in retention, in particular, to variations in horizontal advection out of the fjord. The two dominant processes are (i) strong outflow winds rapidly advecting the surface layer and thus the phytoplankton population out of the fjord and (ii) losses due to high river flux increasing the estuarine circulation. Both processes delay the timing of spring bloom. Smaller effects on the interannual variation are due to increased wind mixing which deepens the mixing layer and reduces light to phytoplankton, and increased river flow which increases the stratification and decreases the mixing layer depth. Observed interannual variations in cloudiness were small. Strong outflow winds are common in winter along the British Columbia coast, but generally cease after the spring wind transition. Thus, observed interdecadal variations in the spring transition date probably imply strong variations in the timing of spring phytoplankton blooms in British Columbia fjords.
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  • 50
    Publication Date: 2016-07-13
    Description: Since "balanced harvest" was proposed in 2010 as a possible tool in the operationalization of the ecosystem approach to fisheries (EAF), the concept gained extensive international attention. Because maintaining ecosystem structure and achieving maximum sustainable yields have become two of the key international legal obligations in fisheries management, balanced harvest is as topical as ever. An international workshop on balanced harvest, organized by the IUCN Fisheries Expert Group at FAO headquarters in 2014, reviewed the progress in the field and discussed its prospects and challenges. Several articles in this theme set, mostly based on presentations from the workshop, discuss ecological, economical, legal, social, and operational issues surrounding the key management goals. Progress is being made on understanding of the theoretical underpinnings of balanced harvest and its practical feasibility. Yet, a basic debate on the concept of balanced harvest continues. To move the EAF forward, we anticipate and encourage further research and discussion on balanced harvest and similar ideas.
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  • 51
    Publication Date: 2016-07-13
    Description: Sampling of euphausiids is difficult because of their intermediate size between macrozooplankton and micronekton. The Barents Sea is one of the few marine areas where there have been long-term studies of euphausiids. We have examined three monitoring datasets on euphausiids and consider likely sources of errors associated with the sampling. Results indicated a high degree of patchiness in the distribution of euphausiids, even at the largest scale of sampling with a pelagic trawl. This indicates that euphausiids may occur in large, but infrequent, swarms that have a low probability of being sampled by small nets. The mean biomass of euphausiids sampled with MOCNESS was 2 g wet weight m –2 integrated over the water column, which is an underestimate due to avoidance of large individuals. The mean biomass obtained with pelagic trawl in the upper 60 m of water at night during an autumn survey was 10 g wet weight m –2 . The plankton net on bottom trawl collected mean and median density of euphausiids (0.1–0.2 g wet weight m –3 ) near bottom during a winter survey similar to the values found with pelagic trawl in the upper layer during autumn. The mean density for the autumn survey showed an increase from 2000 to 2011, while the winter survey showed generally a decrease from 2000–2007 to 2011. The increase in the autumn series coincided with a general warming trend presumably with a larger influx of euphausiids with Atlantic water, notably of Meganyctiphanes norvegica . In contrast, the decline during winter may reflect a decrease, particularly of Thysanoessa raschii in the southeastern Barents Sea in the most recent years. Improvements in sampling gears combined with more and better use of acoustical and optical technologies offer great promise for improved monitoring and quantification of the roles of euphausiids in the Barents Sea ecosystem.
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  • 52
    Publication Date: 2016-07-13
    Description: Balanced fishing proposes a considerable change to current fisheries management to increase overall biomass harvested while reducing the ecosystem impacts of large-scale fisheries. However, to date, the work to a large degree has focused on simplified models, which exclude much of the variability in real ecosystems, as well as basing harvesting rates on a perfect, but unrealistic, knowledge on stock productivity. Furthermore, the published studies have avoided examining the practicalities of implementing balanced fishing in a real world. This has resulted in a gap that remains to be overcome before balanced fishing can be considered a viable management strategy for large marine ecosystems. We discuss variability in recruitment, in biology and life history characteristics, in data quality, and in fishing practice and management, and their implications for implementation of balanced fishing, using examples from the Barents Sea. We try to outline the complexities that need to be investigated as a precursor to moving balanced fishing from an academic exercise to a practical management scheme. Given the difficulties in moving to "full" balanced fishing, we highlight the importance of investigating to what extent benefits can be gained by implementing only the most achievable parts of a balanced fishing regime.
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  • 53
    Publication Date: 2016-07-13
    Description: European eel ( Anguilla anguilla ) is considered as critical endangered and even under the best circumstances it may take decades before the stock recovers. Estimation of eel escapement biomass, B escapement , is of critical importance to evaluate management schemes and to predict the recovery potential for the eel stock. Westerberg and Wickström (2015. Stock assessment of eels in the Baltic: reconciling survey estimates to achieve quantitative analysis. ICES Journal of Marine Science, 73: 75–83) attempt to estimate potential B escapement based on the assumptions that all elvers at the entrance of the Baltic also migrate into the Baltic Sea and that natural mortality is low under the whole growth stage (close to 0.02 at the age of 10 years and older). As a consequence, Westerberg and Wickström estimated the present potential B escapement at ~10–20 000 tonnes and fishing mortality close to 0.05–0.10, while it was also suggested that other sources of anthropogenic mortality may reduce the actual escapement to unknown levels. Here we argue that these conclusions are entirely speculative and contradicted by tagging experiment and fishery data, which instead indicate a much higher fishing mortality (mortality induced by legal professional fishery) rates and a considerably smaller eel biomass.
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  • 54
    Publication Date: 2016-07-13
    Description: Discard bans have been proposed as part of management policies aimed at balanced harvest (BH). Nationwide discard bans exist in several countries, including Chile, the European Union, Norway, and New Zealand. We analysed experiences from these countries to determine whether or not discard bans are in contradiction with BH, based on six aspects: policy objectives, species/sizes applicability, accompanying technical measures, at-sea monitoring and control, and possible impacts. When discard bans are fully implemented, fishing operations change to more selective fishing, typically targeting bigger individuals of main commercial species. This is consistent with the primary objective of many discard policies, i.e. to reduce unwanted catch. In contrast, proponents of BH argue that broader catch diversity, a product of a widespread harvest strategy, should be sought to avoid major impacts on the ecosystem. Our analysis demonstrates that the scope of discard bans is often limited to main commercial species, although usually they can be extended to include more ecosystem components. Some of the policies examined also prohibit the use of unwanted catches for human consumption, thus limiting their effective use. However, the implementation of discard bans requires high levels of at-sea monitoring and effective control, and/or strong incentives to fish more selectively, neither of which applied in most cases examined. We conclude that if discard bans were set differently, they could contribute to fishery management policies aiming at BH. Their goals should be in line with BH, i.e. to reach a wider global harvest pattern, or at least be established within management regimes that promote high compliance. Finally, the extent to which a discard ban contributes to achieve BH depends also on the relative importance of the ecosystem benthic and megafauna components.
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  • 55
    Publication Date: 2016-07-13
    Description: Using a large dataset of US offices we analyse the relationship between investors’ distance to their assets and the effective rent of these assets, and study the extent to which property managers can influence this relationship. We construct hedonic rent models to control for other known rent determinants. It turns out that proximity matters: holding everything else constant, investors located closely to their office buildings are able to extract significantly higher effective rents from these assets, especially if these buildings are of low quality. This effect is due to significant differences in occupancy levels. Interestingly, property managers can affect this relationship, mitigating the adverse effects of investor distance on effective office rents. Especially if the owner does not reside in the same state as the building, external property management is of importance, most prominently so for class-B office buildings.
    Keywords: G11 - Portfolio Choice ; Investment Decisions, R12 - Size and Spatial Distributions of Regional Economic Activity, R32 - Other Production and Pricing Analysis, R33 - Nonagricultural and Nonresidential Real Estate Markets
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    Topics: Geography , Economics
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  • 56
    Publication Date: 2016-07-13
    Description: This article draws on extensive fieldwork conducted in Central Asia to explore food exports to Russia. It takes its theoretical starting point in global value chain theory and pinpoints chain entry barriers relating to financing, transportation and standards. The article also proposes rethinking the aspects of territoriality and institutional context, and suggests their integration into one concept, or rather a process of contextualizing territories. In doing so, the article argues for a methodology that not only examines current events, but also captures change as particularly important in what we term the territory in transition examined here.
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    Topics: Geography , Economics
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  • 57
    Publication Date: 2016-07-13
    Description: This article proposes a quantitative analysis of the interdependencies between port specialization and regional specialization across the world. A global database is elaborated, covering about 360 port regions in both developed and developing countries. One goal is to verify how interdependent port traffic and regional characteristics are, in a context of increasingly flexible commodity and value chains. Despite the aggregated dimension of available data and the heterogeneity of local situations, the main results confirm the affinity between the primary sector and raw materials traffic, and between the tertiary sector and general cargo traffic, whereas the industrial sector offers mixed evidence. This allows us to address fundamental questions raised by both economic geography and regional science about transport and local development. The global typology of port regions points to certain regularities in their spatial distribution, and the article discusses the policy implications of particular cases.
    Keywords: L90 - General, O18 - Regional, Urban, and Rural Analyses, R40 - General
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  • 58
    Publication Date: 2016-07-13
    Description: This article examines various upgrading and downgrading repositioning firm strategies within global value chains (GVCs) or global production networks (GPNs). It builds upon recent evidence that the mode of governance could vary profoundly among firms engaged in the same GVC/GPN. Therefore, the relevance of particular types of upgrading that were originally derived from the ideal types of GVC/GPN governance will be reconsidered. It is argued that the existing dissonance in the literature over possibilities for functional upgrading can be attributed to the different modes of governance that can exist within a particular GVC/GPN and to the diverse nature of functional upgrading. Consequently, a typology of functional upgrading is outlined, and it is argued that these different types vary significantly according to their probability and potential risk-benefit ratios. The article also introduces passive, adaptive and strategic downgrading and outlines their potential negative and positive effects on firms.
    Keywords: F63 - Economic Development, L23 - Organization of Production, L60 - General
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  • 59
    Publication Date: 2016-07-13
    Description: As nations continue to grapple with growing infrastructure demand, financial markets will play an increasingly prominent role in the landscape for urban infrastructure. Yet existing literature tends to depict the ‘financialization’ of urban infrastructure assets as a restless move towards market efficiency aided by the growing transparency of financial information. This article offers a different view, showing how the spatial richness of financial data for infrastructure has progressed towards what we term a more permanent state of ‘informational translucency’. We draw on 53 interviews with participants in the market for infrastructure investment to present this more complicated picture of infrastructure finance, thereby elaborating a more granular understanding of how information flows through and shapes financial market geography. From this we propose a relational model that contributes to theoretical understandings of how financial products are intermediated over time and space.
    Keywords: O18 - Regional, Urban, and Rural Analyses
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  • 60
    Publication Date: 2016-07-13
    Description: The provisions in the Habitats Directive relating to protection of sites establish a triumvirate of decision-makers: administrative authority, scientific advisor and judiciary. This article examines the relationship between these decision-makers as developed in recent case law, both at a European Union (EU) and national level. It argues that reference to the goal of environmental protection obscures the allocation of power among these actors, and that to truly understand the resulting system, we must acknowledge the differing norms which motivate each of these actors. In particular, it argues that we must consider the judiciary as an actor within the decision-making process, and should examine the role of the principles of judicial review and EU law in shaping this. It highlights that there are currently conflicts within the process, and that the principles of judicial review cannot provide a successful mechanism to manage these conflicts without an explicit consideration of the values ‘hidden’ therein.
    Print ISSN: 0952-8873
    Electronic ISSN: 1464-374X
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Law
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  • 61
    Publication Date: 2016-07-13
    Description: One of the key issues in the current controversy over the hunting of wolves in Sweden is whether the wolf population has reached favourable conservation status (FCS). FCS is a legal concept, created and defined in law, but like many legal concepts within environmental law, can only be understood by reference to ecological concepts such as species viability. These ecological determinations in turn often require some sort of legal or policy judgment, such as how great an extinction risk is acceptable for a viable population. This article interrogates contested legal and ecological aspects of FCS and argues for how they might be applied to the Swedish wolf in potential litigation.
    Print ISSN: 0952-8873
    Electronic ISSN: 1464-374X
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Law
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  • 62
    Publication Date: 2016-07-13
    Description: This article extends research exploring progressive models of reproducing economic life by reporting on research into some of the infrastructure, practices and motivations for Islamic charitable giving in London. In so doing the article: (i) makes visible sets of values, practices and institutions usually hidden in an otherwise widely researched international financial centre; (ii) identifies multiple, hard-to-research civic actors who are mobilising diverse resources to address economic hardship and development needs; and (iii) considers how these charitable values, practices and agents contribute to contemporary thinking about progressive economic possibilities.
    Keywords: D14 - Personal Finance, O12 - Microeconomic Analyses of Economic Development
    Print ISSN: 1468-2702
    Electronic ISSN: 1468-2710
    Topics: Geography , Economics
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  • 63
    Publication Date: 2016-07-13
    Description: Within the regulatory space that exists at the intersection of UK company law and environmental regulation, the business community has generated its own environmental governance initiatives to address growing anxiety about companies’ externalised risk. Yet, there is currently nothing in law to prevent companies from frequently acting inconsistently with these voluntary unilateral assurances, which has led to widespread concern that environmental values are treated as merely instrumental to the dominant idea of achieving economic benefits for the company. This article examines a specific case for the legal facilitation of binding obligations owed to the environment, which require a company to make good on its previous commitments about environmental responsibility. It seeks to demonstrate that this is possible through the common law doctrine of estoppel, which can be opened up to prevent a company from acting inconsistently with its previous statements or actions about the governance of environmental risk.
    Print ISSN: 0952-8873
    Electronic ISSN: 1464-374X
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Law
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  • 64
    Publication Date: 2016-07-13
    Description: The aim of the article is to shed light on the particular issue of absence of judicial dialogue between the European Court of Human Rights (ECtHR) and the Court of Justice of the EU (CJEU) in the matter of environmental rights which represents a glaring exception to the generally cooperative disposition exhibited by the two courts in other domains linked to human rights protection. The article draws on this particular absence of judicial dialogue by examining the respective patterns of judicial reasoning employed by the CJEU and the ECtHR in cases before them that involve, or have a bearing on, environmental rights (substantive and procedural). Thus, the singular tendencies discernible in the ECtHR’s progressive jurisprudence in the field of environmental rights will be compared to CJEU’s jurisprudence relevant to environmental rights with the intention of detecting certain aspects in the CJEU’s approach which could further stand to be improved following the example of ECtHR’s activist environmental jurisprudence as a viable avenue for initiating the currently missing dialogue between the two courts in the matter of environmental rights.
    Print ISSN: 0952-8873
    Electronic ISSN: 1464-374X
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Law
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  • 65
    Publication Date: 2016-07-13
    Description: We estimate the impact of drug cartels and drug-related homicides on crime and perceptions of security in Mexico. Since the location where drug cartels operate might be endogenous, we combine the difference-in-difference estimator with instrumental variables. Using surveys on crime victimization we find that people living in areas that experienced drug-related homicides are more likely to take extra security precautions. Yet, these areas are also more likely to experience certain crimes, particularly thefts and extortions. In contrast, these crimes and perceptions of insecurity do not change in areas where cartels operate without leading to drug-related homicides.
    Keywords: C26 - Instrumental Variables (IV) Estimation, K49 - Other, R59 - Other
    Print ISSN: 1468-2702
    Electronic ISSN: 1468-2710
    Topics: Geography , Economics
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  • 66
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    Oxford University Press
    Publication Date: 2016-07-13
    Print ISSN: 0952-8873
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Law
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  • 67
    Publication Date: 2016-07-13
    Print ISSN: 0952-8873
    Electronic ISSN: 1464-374X
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Law
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  • 68
    Publication Date: 2016-07-13
    Print ISSN: 0952-8873
    Electronic ISSN: 1464-374X
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Law
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  • 69
    Publication Date: 2016-07-13
    Print ISSN: 0952-8873
    Electronic ISSN: 1464-374X
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Law
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  • 70
    Publication Date: 2016-07-13
    Description: by Zhenyu Yuan, Heiko Praxenthaler, Nassif Tabaja, Rubben Torella, Anette Preiss, Dieter Maier, Rhett A. Kovall Notch is a conserved signaling pathway that specifies cell fates in metazoans. Receptor-ligand interactions induce changes in gene expression, which is regulated by the transcription factor CBF1/Su(H)/Lag-1 (CSL). CSL interacts with coregulators to repress and activate transcription from Notch target genes. While the molecular details of the activator complex are relatively well understood, the structure-function of CSL-mediated repressor complexes is poorly defined. In Drosophila , the antagonist Hairless directly binds Su(H) (the fly CSL ortholog) to repress transcription from Notch targets. Here, we determine the X-ray structure of the Su(H)-Hairless complex bound to DNA. Hairless binding produces a large conformational change in Su(H) by interacting with residues in the hydrophobic core of Su(H), illustrating the structural plasticity of CSL molecules to interact with different binding partners. Based on the structure, we designed mutants in Hairless and Su(H) that affect binding, but do not affect formation of the activator complex. These mutants were validated in vitro by isothermal titration calorimetry and yeast two- and three-hybrid assays. Moreover, these mutants allowed us to solely characterize the repressor function of Su(H) in vivo.
    Print ISSN: 1544-9173
    Electronic ISSN: 1545-7885
    Topics: Biology
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  • 71
    Publication Date: 2016-07-13
    Description: by Camille Attané, Marie-Line Peyot, Roxane Lussier, Dongwei Zhang, Erik Joly, S. R. Murthy Madiraju, Marc Prentki Many metabolic studies employ tissue-specific gene knockout mice, which requires breeding of floxed gene mice, available mostly on C57BL/6N (NN) genetic background, with cre or Flp recombinase-expressing mice, available on C57BL/6J (JJ) background, resulting in the generation of mixed C57BL/6NJ (NJ) genetic background mice. Recent awareness of many genetic differences between NN and JJ strains including the deletion of nicotinamide nucleotide transhydrogenase ( nnt ), necessitates examination of the consequence of mixed NJ background on glucose tolerance, beta cell function and other metabolic parameters. Male mice with NN and NJ genetic background were fed with normal or high fat diets (HFD) for 12 weeks and glucose and insulin homeostasis were studied. Genotype had no effect on body weight and food intake in mice fed normal or high fat diets. Insulinemia in the fed and fasted states and after a glucose challenge was lower in HFD-fed NJ mice, even though their glycemia and insulin sensitivity were similar to NN mice. NJ mice showed mild glucose intolerance. Moreover, glucose- but not KCl-stimulated insulin secretion in isolated islets was decreased in HFD-fed NJ vs NN mice without changes in insulin content and beta cell mass. Under normal diet, besides reduced fed insulinemia, NN and NJ mice presented similar metabolic parameters. However, HFD-fed NJ mice displayed lower fed and fasted insulinemia and glucose-induced insulin secretion in vivo and ex vivo , as compared to NN mice. These results strongly caution against using unmatched mixed genetic background C57BL/6 mice for comparisons, particularly under HFD conditions.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 72
    Publication Date: 2016-07-13
    Description: by Jill A. Rahnert, Bin Zheng, Matthew B. Hudson, Myra E. Woodworth-Hobbs, S. Russ Price Muscle wasting associated with chronic diseases has been linked to decreased expression of PGC-1α and overexpression of PGC-1α counters muscle loss. CREB, in conjunction with the CREB-regulated transcription coactivator (CRTC2), is a positive modulator of PGC-1α transcription. We previously reported that PGC-1α expression is decreased in skeletal muscle of diabetic rats despite a high level of CREB phosphorylation (i.e., activation), suggesting that CRTC2-CREB signaling may be dysregulated. In this study, the relationship between CREB/CRTC signaling and PGC-1α expression was examined in L6 myotubes treated with dexamethasone (Dex, 48h) to induce atrophy. Dex decreased PGC-1α mRNA and protein as well as the levels of CRTC1 and CRTC2 in the nucleus. Dex also altered the nuclear levels of two known regulators of CRTC2 localization; the amount of calcinuerin catalytic A subunit (CnA) was decreased whereas SIK was increased. To assess PGC-1α transcription, muscle cells were transfected with a PGC-1α luciferase reporter plasmid (PGC-1α-Luc). Dex suppressed PGC-1α luciferase activity while both isobutylmethylxanthine (IBMX) and over-expression of CRTC1 or CRTC2 increased PGC-1α-Luc activity. Mutation of the CRE binding site from PGC-1α-Luc reporter attenuated the responses to both IBMX and the CRTC proteins. Consistent with the reporter gene results, overexpression of CRTC2 produced an increase in CRTC2 in the nucleus and in PGC-1α mRNA and PGC-1α protein. Overexpression of CRTC2 was not sufficient to prevent the decrease in PGC-1α mRNA or protein by Dex. In summary, these data suggest that attenuated CREB/CRTC signaling contributes to the decrease in PGC-1α expression during atrophy.
    Electronic ISSN: 1932-6203
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  • 73
    Publication Date: 2016-07-13
    Description: by Fatima Ochoa-Gonzalez, Alberto R. Cervantes-Villagrana, Julio C. Fernandez-Ruiz, Hilda S. Nava-Ramirez, Adriana C. Hernandez-Correa, Jose A. Enciso-Moreno, Julio E. Castañeda-Delgado
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 74
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2016-07-13
    Description: by Abdessamad Ababou, Vassilis Koronakis Gram-negative bacteria such as E . coli use tripartite efflux pumps such as AcrAB-TolC to expel antibiotics and noxious compounds. A key feature of the inner membrane transporter component, AcrB, is a short stretch of residues known as the gate/switch loop that divides the proximal and distal substrate binding pockets. Amino acid substitutions of the gate loop are known to decrease antibiotic resistance conferred by AcrB. Here we present two new AcrB gate loop variants, the first stripped of its bulky side chains, and a second in which the gate loop is removed entirely. By determining the crystal structures of the variant AcrB proteins in the presence and absence of erythromycin and assessing their ability to confer erythromycin tolerance, we demonstrate that the gate loop is important for AcrB export activity but is not required for erythromycin binding.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 75
    Publication Date: 2016-07-13
    Description: by Shou-Chieh Wang, Chin-Chin Huang, Cheng-Huang Shen, Lei-Chen Lin, Pei-Wen Zhao, Shih-Ying Chen, Yu-Chiao Deng, Yi-Wen Liu Bladder cancer is highly recurrent after therapy, which has an enormous impact on the health and financial condition of the patient. It is worth developing diagnostic tools for bladder cancer. In our previous study, we found that the bladder carcinogen BBN increased urothelial global DNA CpG methylation and decreased GSTM1 protein expression in mice. Here, the correlation of BBN-decreased GSTM1 and GSTM gene CpG methylation status was analyzed in mice bladders. BBN treatment decreased the protein and mRNA expression of GSTM1, and the CpG methylation ratio of GSTM1 gene promoter was slightly increased in mice bladders. Unlike mouse GSTM1, the human GSTM1 gene tends to be deleted in bladder cancers. Among 7 human bladder cancer cell lines, GSTM1 gene is really null in 6 cell lines except one, T24 cells. The CpG methylation level of GSTM1 was 9.9% and 5-aza-dC did not significantly increase GSTM1 protein and mRNA expression in T24 cells; however, the GSTM5 gene was CpG hypermethylated (65.4%) and 5-aza-dC also did not affect the methylation ratio and mRNA expression. However, in other cell lines without GSTM1, 5-aza-dC increased GSTM5 expression and decreased its CpG DNA methylation ratio from 84.6% to 61.5% in 5637, and from 97.4% to 75% in J82 cells. In summary, two biomarkers of bladder tumor were provided. One is the GSTM1 gene which is down-regulated in mice bladder carcinogenesis and is usually deleted in human urothelial carcinoma, while the other is the GSTM5 gene, which is inactivated by DNA CpG methylation.
    Electronic ISSN: 1932-6203
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  • 76
    Publication Date: 2016-07-13
    Description: by Anna Moretti, Michele Ghidini, Carmine De Angelis, Matteo Lambertini, Chiara Cremolini, Martina Imbimbo, Rossana Berardi, Massimo Di Maio, Stefano Cascinu, Nicla La Verde Background and objectives Relevant heterogeneity exists among Postgraduate Schools in Medical Oncology, also within the same country. In order to provide a comprehensive overview of the landscape of Italian Postgraduate Schools in Medical Oncology, the Italian Association of Medical Oncology (AIOM) undertook an online survey, inviting all the residents to describe their daily activities and to express their overall satisfaction about their programs. Methods A team composed of five residents and three consultants in medical oncology prepared a 38 items questionnaire that was published online in a reserved section, accessible through a link sent by e-mail. Residents were invited to anonymously fill in the questionnaire that included the following sub-sections: quality of teaching, clinical and research activity, overall satisfaction. Results Three-hundred and eleven (57%) out of 547 invited residents filled in the questionnaire. Two-hundred and twenty-three (72%) participants declared that attending lessons was frequently difficult and 153 (49%) declared they did not gain substantial improvement in their knowledge from them. Fifty-five percent stated that they did not receive lessons on palliative care. Their overall judgment about didactic activity was low in 63% of the interviewed. The satisfaction for clinical activity was in 86% of cases good: 84% recognized that, during the training period, they acquired a progressive independence on patients' management. About research activity, the majority (79%) of participants in the survey was actively engaged in managing patients included in clinical trials but the satisfaction level for the involvement in research activities was quite low (54%). Overall, 246 residents (79%) gave a positive global judgment of their Medical Oncology Schools. Conclusions The landscape of Italian Postgraduate Schools in Medical Oncology is quite heterogeneous across the country. Some improvements in the organization of teaching and in the access to research opportunity are needed; the perception about clinical activity and the overall judgment of the programs are quite satisfactory.
    Electronic ISSN: 1932-6203
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  • 77
    Publication Date: 2016-07-13
    Description: by Jian Song, Zhangxiong Liu, Huilong Hong, Yansong Ma, Long Tian, Xinxiu Li, Ying-Hui Li, Rongxia Guan, Yong Guo, Li-Juan Qiu Soybean seed coat exists in a range of colors from yellow, green, brown, black, to bicolor. Classical genetic analysis suggested that soybean seed color was a moderately complex trait controlled by multi-loci. However, only a couple of loci could be detected using a single biparental segregating population. In this study, a combination of association mapping and bulk segregation analysis was employed to identify genes/loci governing this trait in soybean. A total of 14 loci, including nine novel and five previously reported ones, were identified using 176,065 coding SNPs selected from entire SNP dataset among 56 soybean accessions. Four of these loci were confirmed and further mapped using a biparental population developed from the cross between ZP95-5383 (yellow seed color) and NY279 (brown seed color), in which different seed coat colors were further dissected into simple trait pairs (green/yellow, green/black, green/brown, yellow/black, yellow/brown, and black/brown) by continuously developing residual heterozygous lines. By genotyping entire F 2 population using flanking markers located in fine-mapping regions, the genetic basis of seed coat color was fully dissected and these four loci could explain all variations of seed colors in this population. These findings will be useful for map-based cloning of genes as well as marker-assisted breeding in soybean. This work also provides an alternative strategy for systematically isolating genes controlling relative complex trait by association analysis followed by biparental mapping.
    Electronic ISSN: 1932-6203
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  • 78
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2016-07-13
    Description: by Yuki Murai, Yuko Yotsumoto When individuals are asked to reproduce intervals of stimuli that are intermixedly presented at various times, longer intervals are often underestimated and shorter intervals overestimated. This phenomenon may be attributed to the central tendency of time perception, and suggests that our brain optimally encodes a stimulus interval based on current stimulus input and prior knowledge of the distribution of stimulus intervals. Two distinct systems are thought to be recruited in the perception of sub- and supra-second intervals. Sub-second timing is subject to local sensory processing, whereas supra-second timing depends on more centralized mechanisms. To clarify the factors that influence time perception, the present study investigated how both sensory modality and timescale affect the central tendency. In Experiment 1, participants were asked to reproduce sub- or supra-second intervals, defined by visual or auditory stimuli. In the sub-second range, the magnitude of the central tendency was significantly larger for visual intervals compared to auditory intervals, while visual and auditory intervals exhibited a correlated and comparable central tendency in the supra-second range. In Experiment 2, the ability to discriminate sub-second intervals in the reproduction task was controlled across modalities by using an interval discrimination task. Even when the ability to discriminate intervals was controlled, visual intervals exhibited a larger central tendency than auditory intervals in the sub-second range. In addition, the magnitude of the central tendency for visual and auditory sub-second intervals was significantly correlated. These results suggest that a common modality-independent mechanism is responsible for the supra-second central tendency, and that both the modality-dependent and modality-independent components of the timing system contribute to the central tendency in the sub-second range.
    Electronic ISSN: 1932-6203
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  • 79
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2016-07-13
    Description: by Martin W. von Websky, Koji Kitamura, Isis Ludwig-Portugall, Christian Kurts, Maximilian von Laffert, Joel LeMaoult, Edgardo D. Carosella, Kareem Abu-Elmagd, Joerg C. Kalff, Nico Schäfer The non-classical MHC I paralogue HLA-G is expressed by cytotrophoblast cells and implicated with fetomaternal tolerance by downregulating the maternal adaptive and innate immune response against the fetus. HLA-G expression correlates with favorable graft outcome in humans and recently promising immunosuppressive effects of therapeutic HLA-G in experimental transplantation (skin allograft acceptance) were shown. Consequently, we examined this novel therapeutic approach in solid organ transplantation. In this study, therapeutic recombinant HLA-G5 was evaluated for the first time in a solid organ model of acute rejection (ACR) after orthotopic intestinal transplantation (ITX). Allogenic ITX was performed in rats (Brown Norway to Lewis) with and without HLA-G treatment. It was found that HLA-G treatment significantly reduced histologically proven ACR at both an early and late postoperative timepoint (POD 4/7), concomitant to a functionally preserved graft contractility at POD 7. Interestingly, graft infiltration by myeloperoxidase+ cells was significantly reduced at POD7 by HLA-G treatment. Moreover, HLA-G treatment showed an effect on the allogenic T-cell immune response as assessed by flow cytometry: The influx of recipient-derived CD8 + T-cells into the graft mesenteric lymphnodes at POD7 was significantly reduced while CD4 + populations were not affected. As a potential mechanism of action, an induction of T-reg populations in the mesenteric lymphnodes was postulated, but flow cytometric analysis of classical CD4 + /CD25 + /FoxP3 + T reg -cells showed no significant alteration by HLA-G treatment. The novel therapeutic approach using recombinant HLA-G5 reported herein demonstrates a significant immunosuppressive effect in this model of allogenic experimental intestinal transplantation. This effect may be mediated via inhibition of recipient-derived CD8 + T-cell populations either directly or by induction of non-classical T reg populations.
    Electronic ISSN: 1932-6203
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  • 80
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2016-07-13
    Description: by Nayana Wijayathilaka, Madhava Meegaskumbura Vocalizing behavior of frogs and toads, once quantified, is useful for systematics, rapid species identification, behavioral experimentation and conservation monitoring. But yet, for many lineages vocalizations remain unknown or poorly quantified, especially in diversity rich tropical regions. Here we provide a quantitative acoustical analysis for all four Sri Lankan congeners of the genus Microhyla . Three of these species are endemic to the island, but Microhyla ornata is regionally widespread. Two of these endemics, M . karunaratnei (Critically Endangered) and M . zeylanica (Endangered), are highly threatened montane isolates; the other, M . mihintalei , is relatively common across the dry lowlands. We recorded and analyzed 100 advertisement calls from five calling males for each species, except for M . zeylanica , which only had 53 calls from three males suitable for analyses. All four species call in choruses and their vocal repertoires are simple compared to most frogs. Their calls contain multiple pulses and no frequency modulation. We quantified eight call characters. Call duration and number of pulses were higher for the two montane isolates (inhabiting cooler habitats at higher altitudes) compared to their lowland congeners. Microhyla zeylanica has the longest call duration (of 1.8 ± 0.12 s) and the highest number of pulses (of 61–92 pulses). The smallest of the species, Microhyla karunaratnei (16.2–18.3 mm), has the highest mean dominant frequency (3.3 ± 0.14 kHz) and pulse rate (77 ± 5.8 pulses per second). The calls separate well in the Principal Component space: PC1 axis is mostly explained by the number of pulses per call and call duration; PC2 is mostly explained by the pulse rate. A canonical means plot of a Discriminant Function analysis shows non-overlapping 95% confidence ellipses. This suggests that some call parameters can be used to distinguish these species effectively. We provide detailed descriptions for eight call properties and compare these with congeners for which data is available. This work provides a foundation for comparative bioacoustic analyses and species monitoring while facilitating the systematics of Microhyla across its range.
    Electronic ISSN: 1932-6203
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  • 81
    Publication Date: 2016-07-13
    Description: by Rozalia Korbut, Foojan Mehrdana, Per Walter Kania, Marianne Halberg Larsen, Dorte Frees, Inger Dalsgaard, Louise von Gersdorff Jørgensen Immersion-vaccines (bacterins) are routinely used for aquacultured rainbow trout to protect against Yersinia ruckeri (Yr). During immersion vaccination, rainbow trout take up and process the antigens, which induce protection. The zebrafish was used as a model organism to study uptake mechanisms and subsequent antigen transport in fish. A genetically modified Yr was developed to constitutively express green fluorescent protein (GFP) and was used for bacterin production. Larval, juvenile and adult transparent zebrafish (tra:nac mutant) received a bath in the bacterin for up to 30 minutes. Samples were taken after 1 min, 15 min, 30 min, 2 h, 12 h and 24 h. At each sampling point fish were used for live imaging of the uptake using a fluorescence stereomicroscope and for immunohistochemistry (IHC). In adult fish, the bacterin could be traced within 30 min in scale pockets, skin, oesophagus, intestine and fins. Within two hours post bath (pb) Yr-antigens were visible in the spleen and at 24 h in liver and kidney. Bacteria were associated with the gills, but uptake at this location was limited. Antigens were rarely detected in the blood and never in the nares. In juvenile fish uptake of the bacterin was seen in the intestine 30 min pb and in the nares 2 hpb but never in scale pockets. Antigens were detected in the spleen 12 hpb. Zebrafish larvae exhibited major Yr uptake only in the mid-intestine enterocytes 24 hpb. The different life stages of zebrafish varied with regard to uptake locations, however the gut was consistently a major uptake site. Zebrafish and rainbow trout tend to have similar uptake mechanisms following immersion or bath vaccination, which points towards zebrafish as a suitable model organism for this aquacultured species.
    Electronic ISSN: 1932-6203
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  • 82
    Publication Date: 2016-07-13
    Description: by Seema Thakur, Rajesh K. Grover, Sanjay Gupta, Ajay K. Yadav, Bhudev C. Das Of several subtypes of breast cancer, triple negative breast cancer (TNBC) is a highly aggressive tumor that lacks expression of hormone receptors for estrogen, progesterone and human epidermal growth factor receptor 2 and shows a worst prognosis. The small noncoding RNAs (miRNAs) considered as master regulator of gene expression play a key role in cancer initiation, progression and drug resistance and have emerged as attractive molecular biomarkers for diagnosis, prognosis and treatment targets in cancer. We have done expression profiling of selected miRNAs in paired serum and tissue samples of TNBC patients and corresponding cell lines and compared with that of other subtypes, in order to identify novel serum miRNA biomarkers for early detection and progression of TNBC. A total of 85 paired tumor tissues and sera with an equal number of adjacent normal tissue margins and normal sera from age matched healthy women including tissue and sera samples from 15 benign fibroadenomas were employed for the study. We report for the first time an extremely high prevalence (73.9%) of TNBC in premenopausal women below 35 years of age and a significant altered expression of a panel of three specific oncogenic miRNAs- miR-21, miR-221, miR-210, and three tumor suppressor miRNAs- miR-195, miR-145 and Let-7a in both tissues and corresponding sera of TNBC patients when compared with triple positive breast cancer (TPBC) patients. While miR-21, miR-221 and miR-210 showed significant over-expression, miR-195 and miR-145 were downregulated and well correlated with various clinicopathological and demographic risk factors, tumor grade, clinical stage and hormone receptor status. Interestingly, despite being a known tumor suppressor, Let-7a showed a significant overexpression in TNBCs. It is suggested that this panel of six miRNA signature may serve as a minimally invasive biomarker for an early detection of TNBC patients.
    Electronic ISSN: 1932-6203
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  • 83
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2016-07-13
    Description: by Martin G. Schwacha, Meenakshi Rani, Susannah E. Nicholson, Aaron M. Lewis, Travis L. Holloway, Salvador Sordo, Andrew P. Cap Background Gamma delta T-cells have been shown to be important to the early immunoinflammatory response to injury, independent of infection. This unique T-cell population acts to regulate cell trafficking and the release of cytokines and growth factors. We propose this sterile inflammatory response is in part associated with damage associated molecular patterns (DAMPs) generated by major injury, such as burn, and mediated via toll-like receptors (TLRs). It is unknown whether DAMPs can activate resident γδ T-cells that reside in skin. Methods Gamma delta T-cells were isolated from the skin of male C57BL/6 mice by enzymatic digestion. Mitochondrial DAMPs (MTDs) were generated from mitochondria isolated from mouse livers by sonication and centrifugation. Dermal γδ T-cells were incubated with MTDs (0–500 μg/ml) for 24 hr and cells and supernatants were collected for analysis. Results MTDs activated dermal γδ T-cells, as evidenced by increased TLR2 and TLR4 expression following in vitro exposure. MTDs also induced the production of inflammatory cytokines (IL-1β, IL-6), and growth factors (PDGF and VEGF) by γδ T-cells. Conclusions These findings herein support the concept that MTDs released after tissue/cellular injury are capable of activating dermal γδ T-cells. We propose that the activation of this unique T-cell population is central in the initiation of sterile inflammation and also contributes to the subsequent healing processes.
    Electronic ISSN: 1932-6203
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  • 84
    Publication Date: 2016-07-13
    Description: by Tamaki Hayase Like various stressors, the addictive use of nicotine (NC) is associated with emotional symptoms such as anxiety and depression, although the underlying mechanisms have not yet been fully elucidated due to the complicated involvement of target neurotransmitter systems. In the elicitation of these emotional symptoms, the fundamental involvement of epigenetic mechanisms such as histone acetylation has recently been suggested. Furthermore, among the interacting neurotransmitter systems implicated in the effects of NC and stressors, the endocannabinoid (ECB) system is considered to contribute indispensably to anxiety and depression. In the present study, the epigenetic involvement of histone acetylation induced by histone deacetylase (HDAC) inhibitors was investigated in anxiety- and depression-related behavioral alterations caused by NC and/or immobilization stress (IM). Moreover, based on the contributing roles of the ECB system, the interacting influence of ECB ligands on the effects of HDAC inhibitors was evaluated in order to examine epigenetic therapeutic interventions. Anxiety-like (elevated plus-maze test) and depression-like (forced swimming test) behaviors, which were observed in mice treated with repeated (4 days) NC (subcutaneous 0.8 mg/kg) and/or IM (10 min), were blocked by the HDAC inhibitors sodium butyrate (SB) and valproic acid (VA). The cannabinoid type 1 (CB1) agonist ACPA (arachidonylcyclopropylamide; AC) also antagonized these behaviors. Conversely, the CB1 antagonist SR 141716A (SR), which counteracted the effects of AC, attenuated the anxiolytic-like effects of the HDAC inhibitors commonly in the NC and/or IM groups. SR also attenuated the antidepressant-like effects of the HDAC inhibitors, most notably in the IM group. From these results, the combined involvement of histone acetylation and ECB system was shown in anxiety- and depression-related behaviors. In the NC treatment groups, the limited influence of SR against the HDAC inhibitor-induced antidepressant-like effects may reflect the characteristic involvement of histone acetylation within the NC-related neurotransmitter systems other than the ECB system.
    Electronic ISSN: 1932-6203
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  • 85
    Publication Date: 2016-07-14
    Description: The fitness and survival of organisms ultimately depend on their feeding. Therefore, foraging behaviors should be selected to maximize cost-benefit ratio. Wind may restrict and modify animal movements increasing the cost of foraging, especially when the animal carries resources that intercept wind. We quantified the effect of wind on the foraging of leaf-cutting ants and evaluated whether this effect varies with 1) leaf fragment traits, such as area, mass, and shape, and 2) the characteristics of the foraging trail system. We also tested whether these ants show a short-term response to wind by selecting loads with characteristics that reduce wind interception, and a long-term response, by arranging the spatial design of the trail system in a way that reduces that effect. We found that in windy conditions, the speed of loaded ants was reduced by 55%, and ants were blown off the trail 28 times more than in windless conditions. However, wind only affected ants walking along trails that were perpendicular to wind direction or parallel upwind. Wind effect increased with area, mass, and shape of loads. At the short term, ants reduced the negative effect of wind by selecting smaller, lighter, or more elongated loads. However, trails showed no particular spatial distribution in relation to wind direction. This is the first study that quantifies the negative consequences of wind on leaf-cutting ants’ foraging and reports behaviors that can reduce this effect. Our work illustrates how short-term behavioral responses can mitigate the negative effect of an understudied environmental factor on ant foraging.
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  • 86
    Publication Date: 2016-07-14
    Description: The temporal partitioning hypothesis suggests that the evolution of different diel activity rhythms in animals might facilitate the coexistence between prey and predators. However, the temporal shift of habitat use induced by predation has rarely been observed. The study of such a mechanism is particularly relevant for introduced species because it might explain how native species can persist or decline in response to the presence of alien species. The introduction of fish into ponds inhabited by amphibians has severe consequences for their occurrence and abundance. Fish particularly affect an alternative newt phenotype, the paedomorph, which does not undergo metamorphosis and maintains larval traits such as gills at the adult stage. In a laboratory design, we assessed the diel patterns of habitat use in the 2 distinct morphological phenotypes of palmate newt ( Lissotriton helveticus ) in the presence or absence of goldfish ( Carassius auratus ). Both newt phenotypes avoided a risky habitat more in the presence than in the absence of fish. This habitat shift was more pronounced during the daytime (i.e., when the risk could be considered higher for the newts) than during nighttime. However, in contrast to metamorphs, paedomorphs showed less adaptive changes according to temporal risk and remained in their shelter for most of the time. Temporal and habitat partitioning at the diel scale between native and alien species might promote their coexistence, but diel change can also imply a cost in the overall reduction of the time allocated to essential activities, showing that species interactions remain complex.
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  • 87
    Publication Date: 2016-07-14
    Description: Translocation is an important conservation management tool. However, not all individuals are equally suited to translocation, and temperament traits (e.g., boldness, reactivity, exploration, sociability, and aggression) are likely to influence survival in a new environment. A few empirical studies have examined the consequences of personality differences on captive-bred translocated animals, but this has not been done for wild-caught animals. We compared behavioral responses to trapping, processing, holding, and release for 56 wild common brushtail possums ( Trichosurus vulpecula ). Twenty individuals were captured twice, once to attach radio-tracking collars, the second time (2 weeks later) for the translocation. Consistency of behavioral responses was compared between capture events and radio-tracking allowed estimates of pretranslocation home range, rest site selection, and foraging behavior. Survivors ( n = 10 survivors, 5 months later) were individuals showing the most fear or emotional reactivity during holding (less likely to have slept, eaten, defecated, or nested) and those that had the smallest home ranges and selected the safest den sites in their original habitat. Conversely, the greatest increase in body mass was recorded for individuals that had demonstrated "unsafe" behavior in their original habitat. To our knowledge, this is the first time this type of behavioral screening during handling and holding prior to release as part of a translocation has been undertaken. These methods have broad applicability for screening potential translocation candidates and are easily translated to a range of threatened and vulnerable animal species.
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  • 88
    Publication Date: 2016-07-14
    Description: The distribution and abundance of food resources are among the most important factors that influence animal behavioral strategies. Yet, spatial variation in feeding habitat quality is often difficult to assess with traditional methods that rely on extrapolation from plot survey data or remote sensing. Here, we show that maximum entropy species distribution modeling can be used to successfully predict small-scale variation in the distribution of 24 important plant food species for chimpanzees at Gombe National Park, Tanzania. We combined model predictions with behavioral observations to quantify feeding habitat quality as the cumulative dietary proportion of the species predicted to occur in a given location. This measure exhibited considerable spatial heterogeneity with elevation and latitude, both within and across main habitat types. We used model results to assess individual variation in habitat selection among adult chimpanzees during a 10-year period, testing predictions about trade-offs between foraging and reproductive effort. We found that nonswollen females selected the highest-quality habitats compared with swollen females or males, in line with predictions based on their energetic needs. Swollen females appeared to compromise feeding in favor of mating opportunities, suggesting that females rather than males change their ranging patterns in search of mates. Males generally occupied feeding habitats of lower quality, which may exacerbate energetic challenges of aggression and territory defense. Finally, we documented an increase in feeding habitat quality with community residence time in both sexes during the dry season, suggesting an influence of familiarity on foraging decisions in a highly heterogeneous landscape.
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  • 89
    Publication Date: 2016-07-14
    Description: Despite parents are equally related to all of their progeny, they may differentially invest in offspring that provide the highest fitness return. Sons and daughters can differ in reproductive value, especially in species where fitness is predicted by the expression of sexually selected traits. In many birds, offspring plumage coloration functions as a honest signal of individual quality, thus allowing parents to differentially invest in offspring of either sex accordingly. Here, we tested whether parents allocate different amounts of food depending on plumage color of their male and female offspring. As a model, we used the barn swallow ( Hirundo rustica ), a species where large among- and within-brood variation in ventral plumage color exists and male reproductive success varies according to ventral plumage coloration. We recorded the proportion of feedings obtained and body mass variation by dyads of same-sex and similar-sized nestlings subjected to either experimental darkening of their ventral plumage color or to a sham treatment. Plumage darkening enhanced food provisioning and body mass gain of males but not of females. Because darker ventral coloration is associated with larger reproductive success in male barn swallows, these results suggest that parents tune their effort toward more valuable male offspring that are likely to provide the greatest fitness returns. Our study thus suggests that parents are selected to differentially invest in offspring of either sex according to a trait expressed in early life, which is relevant to intrasexual competition for access to mates at sexual maturity.
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  • 90
    Publication Date: 2016-07-14
    Description: The iconic red hourglass of the black widow spiders (genus Latrodectus ) is traditionally considered an aposematic signal, yet experimental evidence is lacking. Here, we present data that suggest that black widow coloration may have evolved to be an aposematic signal that is more conspicuous to their vertebrate predators than to their insect prey. In choice experiments with wild birds, we found that the red-and-black coloration deters potential predators: Wild birds were ~3 times less likely to attack a black widow model with an hourglass than one without. Using visual-system appropriate models, we also found that a black widow’s red-and-black color combo is more apparent to a typical bird than a typical insect. Additionally, an ancestral reconstruction reveals that red dorsal coloration is ancestral in black widows and that at some point some North American widows lost their red dorsal coloration. Behaviorally, differences in red dorsal coloration between 2 North American species are accompanied by differences in microhabitat that affects how often a bird will view a black widow’s dorsal region. All observations are consistent with a cost–benefit trade-off of being more conspicuous to predators than to prey. We suggest that limiting detection by prey may help explain why red and black aposematic signals occur frequently in nature.
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  • 91
    Publication Date: 2016-07-14
    Description: While conducting a toxicity assessment of the antidepressant paroxetine (Paxil®), in wild-derived mice ( Mus musculus ), we observed that exposed dams (P 0 ) produced female biased litters (32:68 M:F). Though numerous experimental manipulations have induced sex ratio bias in mice, none have assessed the fitness of the offspring from these litters relative to controls. Here, we retrospectively analyze experimentally derived fitness data gathered for the purpose of toxicological assessment in light of 2 leading hypothesis (Trivers–Willard hypothesis [TWH] and cost of reproduction hypothesis [CRH]), seeking to test if this facultative sex ratio adjustment fits into an adaptive framework. Control F 1 males were heavier than F 1 females, but no differences in mass were detected between exposed F 1 males and females, suggesting that exposed dams did not save energy by producing fewer males, despite producing 29.2% lighter litters relative to controls. F 1 offspring of both treatments were released into seminatural enclosures where fitness was quantified. In enclosures, the relative reproductive success of F 1 -exposed males (compared with controls) was reduced by ~20% compared with the relative reproductive success of F 1 -exposed females. Thus, exposed dams increased their fitness by adjusting litters toward females who were less negatively affected by the exposure than males. Collectively, these data provide less support that the observed sex ratio bias results in energetic savings (CRH), and more support for the TWH because fitness was increased by biasing litters toward female offspring. These mammalian data are unique in their ability to support the TWH through the use of relevant fitness data.
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  • 92
    Publication Date: 2016-07-14
    Description: Understanding how seabirds and other central place foragers locate food resources represents a key step in predicting responses to changes in resource abundance and distribution. Where prey distributions are unpredictable and ephemeral, seabirds may gain up-to-date information by monitoring the direction of birds returning to the colony or by monitoring the foraging behavior of other birds through local enhancement. However, search strategies based on social information may require high population densities, raising concerns about the potential loss of information in declining populations. Our objectives were to explore the mechanisms that underpin effective search strategies based on social information under a range of population densities and different foraging conditions. Testing relevant hypotheses through field observation is challenging because of limitations in the ability to manipulate population densities and foraging conditions. We therefore developed a spatially explicit individual-based foraging model, informed by data on the movement and foraging patterns of seabirds foraging on pelagic prey, and used model simulations to investigate the mechanisms underpinning search strategies. Orientation of outbound headings in line with returning birds enables departing birds to avoid areas without prey even at relatively low population densities. The mechanisms underpinning local enhancement are more effective as population densities increase and may be facilitated by other mechanisms that concentrate individuals in profitable areas. For seabirds and other central place foragers foraging on unpredictable and ephemeral food resources, information is especially valuable when resources are spatially concentrated and may play an important role in mitigating poor foraging conditions.
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  • 93
    Publication Date: 2016-07-14
    Description: Experiments designed to quantify the effects of increasing numbers of carers on levels of offspring care are rare in cooperative breeding systems, where offspring are reared by individuals additional to the breeding pair. This paucity might stem from disagreement over the most appropriate manipulations necessary to elucidate these effects. Here, we perform both carer removal and brood enhancement experiments to test the effects of numbers of carers and carer:offspring ratios on provisioning rates in the cooperatively breeding chestnut-crowned babbler ( Pomatostomus ruficeps ). Removing carers caused linear reductions in overall brood provisioning rates. Further analyses failed to provide evidence that this effect was influenced by territory quality or disruption of group dynamics stemming from the removals. Likewise, adding nestlings to broods caused linear increases in brood provisioning rates, suggesting carers are responsive to increasing offspring demand. However, the 2 experiments did not generate quantitatively equivalent results: Each nestling received more food following brood size manipulation than carer removal, despite comparable carer:offspring ratios in each. Following an at-hatching split-design cross-fostering manipulation to break any links between prehatching maternal effects and posthatching begging patterns, we found that begging intensity increased in larger broods after controlling for metrics of hunger. These findings suggest that manipulation of brood size can, in itself, influence nestling provisioning rates when begging intensity is affected by scramble competition. We highlight that carer number and brood size manipulations are complimentary but not equivalent; adopting both can yield greater overall insight into carer effects in cooperative breeding systems.
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  • 94
    Publication Date: 2016-07-14
    Description: Dispersal affects the social contexts individuals experience by redistributing individuals in space, and the nature of social interactions can have important fitness consequences. During the vagrancy stage of natal dispersal, after an individual has left its natal site and before it has settled to breed, social affiliations might be predicted by opportunities to associate (e.g., distance in space and time between natal points of origin) or kin preferences. We investigated the social structure of a population of juvenile great tits ( Parus major ) and asked whether social affiliations during vagrancy were predicted by 1) the distance between natal nest-boxes, 2) synchrony in fledge dates, and 3) accounting for spatial and temporal predictors, whether siblings tended to stay together. We show that association strength was affected predominantly by spatial proximity at fledging and, to a lesser extent, temporal proximity in birth dates. Independently of spatial and temporal effects, sibling pairs associated more often than expected by chance. Our results suggest that the structure of the winter population is shaped primarily by limits to dispersal through incomplete population mixing. In addition, our results reveal kin structure, and hence the scope for fitness-related interactions between particular classes of kin. Both spatial-mediated and socially mediated population structuring can have implications for our understanding of the evolution of sociality.
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  • 95
    Publication Date: 2016-07-14
    Description: Cultural transmission in nonhuman animals is often sex biased, with females more frequently or efficiently learning cultural behaviors than males. The evolutionary origins of sex-biased cultural transmission have been a mystery, though it has been proposed that female offspring may gain greater reproductive benefit from cultural traits than sons—the "disparate benefits" hypothesis. I propose a different, "uniparental teaching," hypothesis where sex-biased transmission evolves in uniparental species if mothers teach, that is, invest in their offsprings’ learning. I show, with theoretical models, that mothers evolve to invest more in teaching daughters than sons because teaching daughters results in greater inclusive fitness benefits. Teaching a son gives him a reproductive benefit for one generation. However, I show that because daughters may teach future generations, teaching a daughter can be a better long-term investment. I also model the disparate benefits hypothesis and show that the uniparental teaching hypothesis better fits the empirical patterns of sex-biased transmission in the well-studied example of "sponging" in bottlenose dolphins. Uniparental teaching may also explain sex-biased transmission in other species, including chimpanzees. My findings suggest that controversial mechanisms of cultural transmission in nonhumans, such as teaching, may be inferred from population-level patterns of transmission even when it is difficult to observe transmission directly in the field or laboratory.
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  • 96
    Publication Date: 2016-07-14
    Description: Iteroparous organisms face a trade-off between reproduction and survival, but knowledge of whether how and when costs of long-term increases in workload are paid is scant. We increased locomotion costs for a whole year by equipping male great tits with a backpack during breeding, removing the backpacks 1 year later. We applied 3 different treatments: control (without backpack), light ("empty" backpack, 0.1g), and heavy ("full" backpack, 0.9g, ~5% of body mass). Backpacks were administered in 3 cohorts, and we monitored effects on mass of nestlings and the male, wing length, reproduction, and survival. Added mass had a negative effect on nestling mass in both the starting year of the experiment and 1 year later, but not on production of fledglings or recruits. In winter and the next breeding season, males equipped with heavy backpacks had a higher (net) body mass and had shorter third primary feathers than the other 2 groups. Heavy backpack males were less likely to sleep in a nest box in winter. Nest boxes are optimal roosting sites, and we interpret this finding as a treatment effect on success in competition over this resource. However, there was no effect of the manipulation on survival. Overall, we found no long-term fitness consequences, and we discuss possible explanations and implications for the "starvation–predation theory" of optimal body mass. However, we found short-term effects of carrying extra weight suggesting that behavioral studies using small devices should consider the effects of equipping small non-migratory passerines with devices such as transmitters.
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  • 97
    Publication Date: 2016-07-14
    Description: Behavior is usually the first line of defense against parasites. Antiparasite behaviors, such as grooming, or outright avoidance, have been shown to reduce the risk of parasitism in a wide variety of host–parasite systems. However, despite the central importance of antiparasite behavior, little is known about the extent to which prior exposure to parasites improves effectiveness. Here, we report the results of a 2-year study designed to test whether exposure to parasites can "prime" behavior, loosely analogous to priming of the immune system. We tested whether preening improves with experience by infesting captive-bred rock pigeons ( Columba livia ) with 2 common species of rock pigeon feather lice. We infested "primed" birds in Years 1 and 2 of the study and "nonprimed" birds only in Year 2. Birds with lice preened about a third more, on average, than birds without lice. Birds subsequently cleared of lice resumed preening at the same rate as birds that never had lice. Thus, our results confirm that preening is an inducible, reversible defense that is partly triggered by the presence of lice. Surprisingly, primed birds did not differ significantly from nonprimed birds in the overall rate or the efficacy of preening. Primed and nonprimed birds preened at similar rates and had similar numbers of lice at the end of the study. Our results therefore provide little evidence that antiparasite behavior improves with experience, at least in the case of preening as a defense against feather lice.
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  • 98
    Publication Date: 2016-07-14
    Description: Acoustic communication signals are often involved in mate-choice decisions. The decision for the best mating partner can become difficult when the available parameters of a signal are not positively correlated. Rational choice theory predicts that animals assign each signal a fixed value on a single dimension. The probability of choosing one signal over the other should be a monotonic function of the respective values and result in transitive choices. A violation of transitivity in choice behavior would suggest comparative rather than absolute decision making. Here, we tested the transitivity of preferences of female crickets for male calling songs. We conducted a series of binary choice experiments and compared their outcome to female preferences measured in no-choice experiments. To test transitivity, every choice pair had to differ in 2 parameters of the calling song. The parameter pairs used were 1) pulse rate and sound intensity, 2) chirp rate and sound intensity, and 3) pulse rate and chirp rate. The results revealed that females acted transitively if chirp rate and sound intensity or pulse rate and chirp rate of the patterns were varied. But females violated transitivity if pulse rate and sound intensity of signals differed as they mostly chose the louder pattern, although it was less attractive in the no-choice situation. This implies that sound intensity was weighted differently by females in the decision process in no-choice and choice experiments. The violation of transitivity suggests a comparative evaluation of available signals by female crickets.
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  • 99
    Publication Date: 2016-07-13
    Description: The motion of superfluid vortices in a neutron star crust is at the heart of most theories of pulsar glitches. Pinning of vortices to ions can decouple the superfluid from the crust and create a reservoir of angular momentum. Sudden large-scale unpinning can lead to an observable glitch. In this paper, we investigate the scattering of a free vortex off a pinning potential and calculate its mean free path, in order to assess whether unpinned vortices can skip multiple pinning sites and come close enough to their neighbours to trigger avalanches, or whether they simply hop from one pinning site to its neighbour, giving rise to a more gradual creep. We find that there is a significant range of parameter space in which avalanches can be triggered, thus supporting the hypothesis that they may lie at the origin of pulsar glitches. For realistic values of the pinning force and superfluid drag parameters, we find that avalanches are more likely in the higher density regions of the crust where pinning is stronger. Physical differences in stellar parameters, such as mass and temperature, may lead to a switch between creep-like motion and avalanches, explaining the different characteristics of glitching pulsars.
    Print ISSN: 0035-8711
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  • 100
    Publication Date: 2016-07-13
    Description: We present the results of the application of locally linear embedding (LLE) to reduce the dimensionality of dereddened and continuum subtracted near-infrared spectra using a combination of models and real spectra of massive protostars selected from the Red MSX Source survey data base. A brief comparison is also made with two other dimension reduction techniques; principal component analysis (PCA) and Isomap using the same set of spectra as well as a more advanced form of LLE, Hessian locally linear embedding. We find that whilst LLE certainly has its limitations, it significantly outperforms both PCA and Isomap in classification of spectra based on the presence/absence of emission lines and provides a valuable tool for classification and analysis of large spectral data sets.
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