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  • American Institute of Physics  (185,826)
  • Periodicals Archive Online (PAO)  (57,353)
  • Annual Reviews
  • Copernicus
  • 2020-2023  (10)
  • 2005-2009  (95,537)
  • 1990-1994  (74,020)
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  • 1
    Publication Date: 2020-12-14
    Description: In this study we present an intercomparison of measurements of very low water vapor column content obtained with a Ground-Based Millimeter-wave Spectrometer (GBMS), Vaisala RS92k radiosondes, a Raman Lidar, and an IR Fourier Transform Spectrometer. These sets of measurements were carried out during the primary field campaign of the ECOWAR (Earth COoling by WAter vapor Radiation) project which took place on the Western Italian Alps from 3 to 16 March, 2007.
    Description: Published
    Description: 135-138
    Description: 1.8. Osservazioni di geofisica ambientale
    Description: N/A or not JCR
    Description: open
    Keywords: Precipitable Water Vapor ; ECOWAR ; IR and Millimeter-Wave Spectroscopy ; 01. Atmosphere::01.01. Atmosphere::01.01.01. Composition and Structure ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
    Publication Date: 2017-04-04
    Description: COST (Co-operation in the field of Scientific and Technical Research) is an important instrument supporting co-operation among scientists and researchers across Europe now joining 35 member countries. Scientific projects in the COST framework are called COST Actions and have the objectives embodied in their respective Memorandum of Understanding (MoU). The main objectives of the COST Actions within the European ionospheric and radio propagation community have been: to study the influence of upper atmospheric conditions on terrestrial and Earthspace communications, to develop methods and techniques to improve existing and generate new ionospheric and propagation models over Europe for telecommunication and navigation applications and to transfer the results to the appropriate national and international organizations, institutions and industry dealing with the modern communication systems. This paper summarises in brief the background and historical context of four ionospheric COST Actions and outlines their main objectives and results. In addition, the paper discusses the dissemination of the results and the collaboration among the participating institutions and researchers.
    Description: DRS Codem Systems Ball Aerospace Corporation University of Massachusetts Lowell
    Description: Published
    Description: Lowell, Massachusetts, U.S.A., April 29, 2007
    Description: 3.9. Fisica della magnetosfera, ionosfera e meteorologia spaziale
    Description: open
    Keywords: Physics of the Ionosphere ; 01. Atmosphere::01.02. Ionosphere::01.02.99. General or miscellaneous ; 05. General::05.07. Space and Planetary sciences::05.07.02. Space weather
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Conference paper
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  • 3
    Publication Date: 2017-04-04
    Description: Volcanoes represent an important natural source of several trace elements to the atmosphere. For some species (e.g., As, Cd, Pb and Se) they may be the main natural source and thereby strongly influencing geochemical cycles from the local to the global scale. Mount Etna is one of the most actively degassing volcanoes in the world, and it is considered to be, on the long-term average, the major atmospheric point source of many environmental harmful compounds. Their emission occurs either through continuous passive degassing from open-conduit activity or through sporadic paroxysmal eruptive activity, in the form of gases, aerosols or particulate. To estimate the environmental impact of magma-derived trace metals and their depositions processes, rainwater and snow samples were collected at Mount Etna area. Five bulk collectors have been deployed at various altitudes on the upper flanks around the summit craters of the volcano; samples were collected every two week for a period of one year and analyzed for the main chemical-physical parameters (electric conductivity and pH) and for major and trace elements concentrations. Chemical analysis of rainwater clearly shows that the volcanic contribution is always prevailing in the sampling site closest to the summit crater (about 1.5 km). In the distal sites (5.5-10 km from the summit) and downwind of the summit craters, the volcanic contribution is also detectable but often overwhelmed by anthropogenic or other natural (seawater spray, geogenic dust) contributions. Volcanic contribution may derive from both dry and wet deposition of gases and aerosols from the volcanic plume, but sometimes also from leaching of freshly emitted volcanic ashes. In fact, in our background site (7.5 km in the upwind direction) volcanic contribution has been detected only following an ash deposition event. About 30 samples of fresh snow were collected in the upper part of the volcano, during the winters 2006 and 2007 to estimate deposition processes at high altitude during cold periods. Some of the samples were collected immediately after a major explosive event from the summit craters to understand the interaction between snow and fresh erupted ash. Sulphur, Chlorine and Fluorine, are the major elements that prevailingly characterize the volcanic contribution in atmospheric precipitation on Mount Etna, but high concentrations of many trace elements are also detected in the studied samples. In particular, bulk deposition samples display high concentration of Al, Fe, Ti, Cu, As, Rb, Pb, Tl, Cd, Cr, U and Ag, in the site most exposed to the volcanic emissions: median concentration values are about two orders of magnitude higher than those measured in our background site. Also in the snow samples the volcanic signature is clearly detectable and decreases with distance from the summit craters. Some of the analysed elements display very high enrichment values with respect to the average crust and, in the closest site to the summit craters, also deposition values higher than those measured in polluted urban or industrial sites.
    Description: Published
    Description: Vienna, Austria
    Description: 4.5. Degassamento naturale
    Description: open
    Keywords: Mt. Etna ; trace elements ; rainwater ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 03. Hydrosphere::03.03. Physical::03.03.01. Air/water/earth interactions ; 03. Hydrosphere::03.04. Chemical and biological::03.04.03. Chemistry of waters
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Oral presentation
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  • 4
    Publication Date: 2017-04-04
    Description: Improving the constraints on the atmospheric fate and depletion rates of acidic compounds persistently emitted by non-erupting (quiescent) volcanoes is important for quantitatively predicting the environmental impact of volcanic gas plumes. Here, we present new experimental data coupled with modelling studies to investigate the chemical processing of acidic volcanogenic species during tropospheric dispersion. Diffusive tube samplers were deployed at Mount Etna, a very active open-conduit basaltic volcano in eastern Sicily, and Vulcano Island, a closed-conduit quiescent volcano in the Aeolian Islands (northern Sicily). Sulphur dioxide (SO2), hydrogen sulphide (H2S), hydrogen chloride (HCl) and hydrogen fluoride (HF) concentrations in the volcanic plumes (typically several minutes to a few hours old) were repeatedly determined at distances from the summit vents ranging from 0.1 to ~10 km, and under different environmental conditions. At both volcanoes, acidic gas concentrations were found to decrease exponentially with distance from the summit vents (e.g., SO2 decreases from ~10,000 μg/m3 at 0.1 km from Etna’s vents down to ~7 _μg/m3 at ~10km distance), reflecting the atmospheric dilution of the plume within the acid gas-free background troposphere. Conversely, SO2/HCl, SO2/HF, and SO2/H2S ratios in the plume showed no systematic changes with plume aging, and fit source compositions within analytical error. Assuming that SO2 losses by reaction are small during short-range atmospheric transport within quiescent (ash-free) volcanic plumes, our observations suggest that, for these short transport distances, atmospheric reactions for H2S and halogens are also negligible. The one-dimensional model MISTRA was used to simulate quantitatively the evolution of halogen and sulphur compounds in the plume of Mt. Etna. Model predictions support the hypothesis of minor HCl chemical processing during plume transport, at least in cloud-free conditions. Larger variations in the modelled SO2/HCl ratios were predicted under cloudy conditions, due to heterogeneous chlorine cycling in the aerosol phase. The modelled evolution of the SO2/H2S ratios is found to be substantially dependent on whether or not the interactions of H2S with halogens are included in the model. In the former case, H2S is assumed to be oxidized in the atmosphere mainly by OH, which results in minor chemical loss for H2S during plume aging and produces a fair match between modelled and measured SO2/H2S ratios. In the latter case, fast oxidation of H2S by Cl leads to H2S chemical lifetimes in the early plume of a few seconds, and thus SO2 to H2S ratios that increase sharply during plume transport. This disagreement between modelled and observed plume compositions suggests that more in-detail kinetic investigations are required for a proper evaluation of H2S chemical processing in volcanic plumes.
    Description: Published
    Description: 1441-1450
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: 4.5. Degassamento naturale
    Description: JCR Journal
    Description: open
    Keywords: Mt. Etna ; volcanic gas plumes ; tropospheric processing ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
    Publication Date: 2017-04-04
    Description: After some short test surveys, during the 2004–2005 summer expedition in Antarctica, a geomagnetic French-Italian observatory was installed on the plateau (geographic coordinates: 75.1 S, 123.4 E; corrected geomagnetic coordinates: 88.9 S, 54.3 E; UT=LT−8) very close to the geomagnetic pole. In this paper we present some peculiarities of the daily variation as observed at this polar cap observatory during the years 2005 and 2006, taking into account the different Loyd seasons and different interplanetary magnetic field conditions. Some interesting results emerge from the analysis, confirming the dependence of the daily variation (and of the associated polar current systems) on the IMF Bz and By components. In particular the analysis showed that different Bz conditions correspond to different contribution to daily variation of ionospheric and field aligned currents, while particular By conditions lead to a time shift of the diurnal variation, indicating an asymmetry with respect to the noon meridian.
    Description: Published
    Description: 2045–2051
    Description: 3.9. Fisica della magnetosfera, ionosfera e meteorologia spaziale
    Description: 1.6. Osservazioni di geomagnetismo
    Description: JCR Journal
    Description: reserved
    Keywords: Geomagnetism and paleomagnetism (Time variations, diurnal to secular) ; Magnetospheric physics (Polar cap phenomena; Solar wind-magnetosphere interactions) ; 01. Atmosphere::01.03. Magnetosphere::01.03.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    American Institute of Physics
    Publication Date: 2020-02-24
    Description: A high-resolution Fabry–Perot interferometer was inserted in a feedback loop which, by monitoring elements of the fringe pattern, keeps the position of the transmitting window fixed with respect to a given line, taking into account the instability of the radiation source which would produce a wander of the line itself and the noise affecting the tuning of the receiving interferometer. The system, in this preliminary form, is able to lock itself and maintain its position indefinitely for slow and moderately fast varying disturbances.
    Description: Published
    Description: 2940-2944
    Description: 1.7. Osservazioni di alta e media atmosfera
    Description: JCR Journal
    Description: reserved
    Keywords: FABRY-PEROT ; INTERFEROMETER ; SERVOMECHANISMS ; FEEDBACK ; 01. Atmosphere::01.01. Atmosphere::01.01.08. Instruments and techniques
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
    Publication Date: 2022-04-19
    Description: The late Pleistocene Yedoma Ice Complex is an ice-rich and organic-bearing type of permafrost deposit widely distributed across Beringia and is assumed to be especially prone to deep degradation with warming temperature, which is a potential tipping point of the climate system. To better understand Yedoma formation, its local characteristics, and its regional sedimentological composition, we compiled the grain-size distributions (GSDs) of 771 samples from 23 Yedoma locations across the Arctic; samples from sites located close together were pooled to form 17 study sites. In addition, we studied 160 samples from three non-Yedoma ice-wedge polygon and floodplain sites for the comparison of Yedoma samples with Holocene depositional environments. The multimodal GSDs indicate that a variety of sediment production, transport, and depositional processes were involved in Yedoma formation. To disentangle these processes, a robust endmember modeling analysis (rEMMA) was performed. Nine robust grain-size endmembers (rEMs) characterize Yedoma deposits across Beringia. The study sites of Yedoma deposits were finally classified using cluster analysis. The resulting four clusters consisted of two to five sites that are distributed randomly across northeastern Siberia and Alaska, suggesting that the differences are associated with rather local conditions. In contrast to prior studies suggesting a largely aeolian contribution to Yedoma sedimentation, the wide range of rEMs indicates that aeolian sedimentation processes cannot explain the entire variability found in GSDs of Yedoma deposits. Instead, Yedoma sedimentation is controlled by local conditions such as source rocks and weathering processes, nearby paleotopography, and diverse sediment transport processes. Our findings support the hypothesis of a polygenetic Yedoma origin involving alluvial, fluvial, and niveo-aeolian transport; accumulation in ponding waters; and in situ frost weathering as well as postdepositional processes of solifluction, cryoturbation, and pedogenesis. The characteristic rEM composition of the Yedoma clusters will help to improve how grain-size-dependent parameters in permafrost models and soil carbon budgets are considered. Our results show the characteristic properties of ice-rich Yedoma deposits in the terrestrial Arctic. Characterizing and quantifying site-specific past depositional processes is crucial for elucidating and understanding the trajectories of this unique kind of ice-rich permafrost in a warmer future.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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  • 8
    Publication Date: 2022-05-25
    Description: Author Posting. © Annual Reviews, 2003. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Environment and Resources 28 (2003): 521-558, doi:10.1146/annurev.energy.28.011503.163443.
    Description: Agriculture and industrial development have led to inadvertent changes in the natural carbon cycle. As a consequence, concentrations of carbon dioxide and other greenhouse gases have increased in the atmosphere and may lead to changes in climate. The current challenge facing society is to develop options for future management of the carbon cycle. A variety of approaches has been suggested: direct reduction of emissions, deliberate manipulation of the natural carbon cycle to enhance sequestration, and capture and isolation of carbon from fossil fuel use. Policy development to date has laid out some of the general principles to which carbon management should adhere. These are summarized as: how much carbon is stored, by what means, and for how long. To successfully manage carbon for climate purposes requires increased understanding of carbon cycle dynamics and improvement in the scientific capabilities available for measurement as well as for policy needs. The specific needs for scientific information to underpin carbon cycle management decisions are not yet broadly known. A stronger dialogue between decision makers and scientists must be developed to foster improved application of scientific knowledge to decisions. This review focuses on the current knowledge of the carbon cycle, carbon measurement capabilities (with an emphasis on the continental scale) and the relevance of carbon cycle science to carbon sequestration goals.
    Description: The National Center for Atmospheric Research is supported by the National Science Foundation.
    Keywords: Carbon sequestration ; Measurement techniques ; Climate ; Kyoto protocol
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 9
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    Annual Reviews
    Publication Date: 2022-05-25
    Description: Author Posting. © Annual Reviews, 2006. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Fluid Mechanics 38 (2006): 395-425, doi:10.1146/annurev.fluid.38.050304.092129.
    Description: Over the past four decades, the combination of in situ and remote sensing observations has demonstrated that long nonlinear internal solitary-like waves are ubiquitous features of coastal oceans. The following provides an overview of the properties of steady internal solitary waves and the transient processes of wave generation and evolution, primarily from the point of view of weakly nonlinear theory, of which the Korteweg-de Vries equation is the most frequently used example. However, the oceanographically important processes of wave instability and breaking, generally inaccessible with these models, are also discussed. Furthermore, observations often show strongly nonlinear waves whose properties can only be explained with fully nonlinear models.
    Description: KRH acknowledges support from NSF and ONR and an Independent Study Award from the Woods Hole Oceanographic Institution. WKM acknowledges support from NSF and ONR, which has made his work in this area possible, in close collaboration with former graduate students at Scripps Institution of Oceanography and MIT.
    Keywords: Solitary waves ; Nonlinear waves ; Stratified flow ; Physical Oceanography
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 10
    Publication Date: 2022-05-25
    Description: First published online as a Review in Advance on October 24, 2005. (Some corrections may occur before final publication online and in print)
    Description: Author Posting. © Annual Reviews, 2005. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Physiology 68 (2006): 22.1-22.29, doi:10.1146/annurev.physiol.68.040104.105418.
    Description: Superfast muscles of vertebrates power sound production. The fastest, the swimbladder muscle of toadfish, generates mechanical power at frequencies in excess of 200 Hz. To operate at these frequencies, the speed of relaxation has had to increase approximately 50-fold. This increase is accomplished by modifications of three kinetic traits: (a) a fast calcium transient due to extremely high concentration of sarcoplasmic reticulum (SR)-Ca2+ pumps and parvalbumin, (b) fast off-rate of Ca2+ from troponin C due to an alteration in troponin, and (c) fast cross-bridge detachment rate constant (g, 50 times faster than that in rabbit fast-twitch muscle) due to an alteration in myosin. Although these three modifications permit swimbladder muscle to generate mechanical work at high frequencies (where locomotor muscles cannot), it comes with a cost: The high g causes a large reduction in attached force-generating cross-bridges, making the swimbladder incapable of powering low-frequency locomotory movements. Hence the locomotory and sound-producing muscles have mutually exclusive designs.
    Description: This work was made possible by support from NIH grants AR38404 and AR46125 as well as the University of Pennsylvania Research Foundation.
    Keywords: Parvalbumin ; Ca2+ release ; Ca2+ uptake ; Cross-bridges ; Adaptation ; Sound production ; Whitman Center
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 11
    Publication Date: 2022-01-10
    Description: The mid-Pliocene warm period (3.264–3.025 Ma) is the most recent geological period during which atmospheric CO2 levels were similar to recent historical values (∼400 ppm). Several proxy reconstructions for the mid-Pliocene show highly reduced zonal sea surface temperature (SST) gradients in the tropical Pacific Ocean, indicating an El Niño-like mean state. However, past modelling studies do not show these highly reduced gradients. Efforts to understand mid-Pliocene climate dynamics have led to the Pliocene Model Intercomparison Project (PlioMIP). Results from the first phase (PlioMIP1) showed clear El Niño variability (albeit significantly reduced) and did not show the greatly reduced time-mean zonal SST gradient suggested by some of the proxies. In this work, we study El Niño–Southern Oscillation (ENSO) variability in the PlioMIP2 ensemble, which consists of additional global coupled climate models and updated boundary conditions compared to PlioMIP1. We quantify ENSO amplitude, period, spatial structure and “flavour”, as well as the tropical Pacific annual mean state in mid-Pliocene and pre-industrial simulations. Results show a reduced ENSO amplitude in the model-ensemble mean (−24 %) with respect to the pre-industrial, with 15 out of 17 individual models showing such a reduction. Furthermore, the spectral power of this variability considerably decreases in the 3–4-year band. The spatial structure of the dominant empirical orthogonal function shows no particular change in the patterns of tropical Pacific variability in the model-ensemble mean, compared to the pre-industrial. Although the time-mean zonal SST gradient in the equatorial Pacific decreases for 14 out of 17 models (0.2 ∘C reduction in the ensemble mean), there does not seem to be a correlation with the decrease in ENSO amplitude. The models showing the most “El Niño-like” mean state changes show a similar ENSO amplitude to that in the pre-industrial reference, while models showing more “La Niña-like” mean state changes generally show a large reduction in ENSO variability. The PlioMIP2 results show a reasonable agreement with both time-mean proxies indicating a reduced zonal SST gradient and reconstructions indicating a reduced, or similar, ENSO variability.
    Repository Name: EPIC Alfred Wegener Institut
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  • 12
    Publication Date: 2022-01-10
    Description: The mid-Pliocene (∼3 Ma) is one of the most recent warm periods with high CO2 concentrations in the atmosphere and resulting high temperatures, and it is often cited as an analog for near-term future climate change. Here, we apply a moisture budget analysis to investigate the response of the large-scale hydrological cycle at low latitudes within a 13-model ensemble from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2). The results show that increased atmospheric moisture content within the mid-Pliocene ensemble (due to the thermodynamic effect) results in wetter conditions over the deep tropics, i.e., the Pacific intertropical convergence zone (ITCZ) and the Maritime Continent, and drier conditions over the subtropics. Note that the dynamic effect plays a more important role than the thermodynamic effect in regional precipitation minus evaporation (PmE) changes (i.e., northward ITCZ shift and wetter northern Indian Ocean). The thermodynamic effect is offset to some extent by a dynamic effect involving a northward shift of the Hadley circulation that dries the deep tropics and moistens the subtropics in the Northern Hemisphere (i.e., the subtropical Pacific). From the perspective of Earth's energy budget, the enhanced southward cross-equatorial atmospheric transport (0.22 PW), induced by the hemispheric asymmetries of the atmospheric energy, favors an approximately 1∘ northward shift of the ITCZ. The shift of the ITCZ reorganizes atmospheric circulation, favoring a northward shift of the Hadley circulation. In addition, the Walker circulation consistently shifts westward within PlioMIP2 models, leading to wetter conditions over the northern Indian Ocean. The PlioMIP2 ensemble highlights that an imbalance of interhemispheric atmospheric energy during the mid-Pliocene could have led to changes in the dynamic effect, offsetting the thermodynamic effect and, hence, altering mid-Pliocene hydroclimate.
    Repository Name: EPIC Alfred Wegener Institut
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  • 13
    Publication Date: 2021-12-14
    Description: The Italian earthquake waveform data are collected here in a dataset suited for machine learning analysis (ML) applications. The dataset consists of nearly 1.2 million three-component (3C) waveform traces from about 50 000 earthquakes and more than 130 000 noise 3C waveform traces, for a total of about 43 000 h of data and an average of 21 3C traces provided per event. The earthquake list is based on the Italian Seismic Bulletin (http://terremoti.ingv.it/bsi, last access: 15 February 2020​​​​​​​) of the Istituto Nazionale di Geofisica e Vulcanologia between January 2005 and January 2020, and it includes events in the magnitude range between 0.0 and 6.5. The waveform data have been recorded primarily by the Italian National Seismic Network (network code IV) and include both weak- (HH, EH channels) and strong-motion (HN channels) recordings. All the waveform traces have a length of 120 s, are sampled at 100 Hz, and are provided both in counts and ground motion physical units after deconvolution of the instrument transfer functions. The waveform dataset is accompanied by metadata consisting of more than 100 parameters providing comprehensive information on the earthquake source, the recording stations, the trace features, and other derived quantities. This rich set of metadata allows the users to target the data selection for their own purposes. Much of these metadata can be used as labels in ML analysis or for other studies. The dataset, assembled in HDF5 format, is available at http://doi.org/10.13127/instance (Michelini et al., 2021).
    Description: Published
    Description: 5509–5544
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 14
    Publication Date: 2022-10-27
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Sherwood, C. R., van Dongeren, A., Doyle, J., Hegermiller, C. A., Hsu, T.-J., Kalra, T. S., Olabarrieta, M., Penko, A. M., Rafati, Y., Roelvink, D., van der Lugt, M., Veeramony, J., & Warner, J. C. Modeling the morphodynamics of coastal responses to extreme events: what shape are we in? Annual Review of Marine Science, 14, (2022): 457–492, https://doi.org/10.1146/annurev-marine-032221-090215.
    Description: This review focuses on recent advances in process-based numerical models of the impact of extreme storms on sandy coasts. Driven by larger-scale models of meteorology and hydrodynamics, these models simulate morphodynamics across the Sallenger storm-impact scale, including swash,collision, overwash, and inundation. Models are becoming both wider (as more processes are added) and deeper (as detailed physics replaces earlier parameterizations). Algorithms for wave-induced flows and sediment transport under shoaling waves are among the recent developments. Community and open-source models have become the norm. Observations of initial conditions (topography, land cover, and sediment characteristics) have become more detailed, and improvements in tropical cyclone and wave models provide forcing (winds, waves, surge, and upland flow) that is better resolved and more accurate, yielding commensurate improvements in model skill. We foresee that future storm-impact models will increasingly resolve individual waves, apply data assimilation, and be used in ensemble modeling modes to predict uncertainties.
    Description: All authors except D.R. were partially supported by the IFMSIP project, funded by US Office of Naval Research grant PE 0601153N under contracts N00014-17-1-2459 (Deltares), N00014-18-1-2785 (University of Delaware), N0001419WX00733 (US Naval Research Laboratory, Monterey), N0001418WX01447 (US Naval Research Laboratory, Stennis Space Center), and N0001418IP00016 (US Geological Survey). C.R.S., C.A.H., T.S.K., and J.C.W. were supported by the US Geological Survey Coastal/Marine Hazards and Resources Program. A.v.D. and M.v.d.L. were supported by the Deltares Strategic Research project Quantifying Flood Hazards and Impacts. M.O. acknowledges support from National Science Foundation project OCE-1554892.
    Keywords: Coastal morphodynamics ; Extreme storms ; Coastal modeling ; Sandy coasts ; Waves ; Sediment transport
    Repository Name: Woods Hole Open Access Server
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  • 15
    Publication Date: 2022-10-24
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
    Publication Date: 2022-06-29
    Description: We developed a new version of the Alfred Wegener Institute Climate Model (AWI-CM3), which has higher skills in representing the observed climatology and better computational efficiency than its predecessors. Its ocean component FESOM2 has the multi-resolution functionality typical for unstructured-mesh models while still featuring a scalability and efficiency similar to regular-grid models. The atmospheric component OpenIFS (CY43R3) enables the use of latest developments in the numerical weather prediction community in climate sciences. In this paper we describe the coupling of the model components and evaluate the model performance on a variable resolution (25–125 km) ocean mesh and a 61 km atmosphere grid, which serves as a reference and starting point for other on-going research activities with AWI-CM3. This includes the exploration of high and variable resolution, the development of a full Earth System Model as well as the creation of a new sea ice prediction system. At this early development stage and with the given coarse to medium resolutions, the model already features above CMIP6-average skills in representing the climatology and competitive model throughput. Finally we identify remaining biases and suggest further improvements to be made to the model.
    Repository Name: EPIC Alfred Wegener Institut
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  • 17
    Publication Date: 2022-09-23
    Repository Name: EPIC Alfred Wegener Institut
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  • 18
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    Copernicus
    In:  EPIC3On the true and the perceived minor interactions of dissolved phosphate and dissolved sulphate and some other constituents with the Alkalinity of oceanic seawater, EGUsphere [preprint], Copernicus
    Publication Date: 2022-08-08
    Repository Name: EPIC Alfred Wegener Institut
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  • 19
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    American Institute of Physics
    Publication Date: 2022-05-26
    Description: Author Posting. © American Institute of Physics, 2009. This article is posted here by permission of American Institute of Physics for personal use, not for redistribution. The definitive version was published in Physics Today 62 n.11 (2009): 39-44.
    Description: Most species of large whales are endangered because for centuries whaling fleets have decimated their populations. In the late 1960s, marine-mammal biologists discovered that fishermen setting nets for tuna in the Pacific Ocean were killing more than 100,000 dolphins a year. The cause of marine-mammal conservation became so popular at the dawn of the environmental movement that one of the first environmental accomplishments of the US Congress was to enact the Marine Mammal Protection Act of 1972, which prohibits the killing or injuring of marine mammals. Today, small remnant populations of whales, such as the North Atlantic right whale, are threatened by entanglement in fishing gear and collisions by ships. Indeed, marine biologists have estimated that hundreds of thousands of marine mammals are killed each year in fishing gear. Inadvertent effects of human activities can pose a serious risk to coastal populations, as evidenced by the recent extinction of the Chinese river dolphin due to fishing, pollution, and overdevelopment of the Yangtze River. A few decades ago, conservation efforts focused on reducing the intentional hunting of marine mammals. Nowadays, when hunts for marine mammals are better controlled, the slow degradation of habitat from a combination of sources may have a bigger impact. For example, biologists have documented cases in which the effects of coastal development—including noise, pollution, and dredging—have caused marine mammals to abandon critical breeding habitat. Noise in particular is at issue in legal actions that have been brought against the US Navy for sonar exercises that may have caused whales to strand and die.
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    Publication Date: 2022-11-14
    Description: Changes in Southern Ocean export production have broad biogeochemical and climatic implications. Specifically, iron fertilization likely increased subantarctic nutrient utilization and enhanced the efficiency of the biological pump during glacials. However, past export production in the subantarctic Southeast Pacific is poorly documented, and its connection to Fe fertilization, potentially related to Patagonian Ice Sheet dynamics is unknown. We report on biological productivity changes over the past 400 ka, based on a combination of 230Thxs-normalized and stratigraphy-based mass accumulation rates of biogenic barium, organic carbon, biogenic opal, and calcium carbonate as indicators of paleo-export production in a sediment core upstream of the Drake Passage. In addition, we use fluxes of iron and lithogenic material as proxies for terrigenous matter, and thus potential micronutrient supply. Stratigraphy-based mass accumulation rates are strongly influenced by bottom-current dynamics, which result in variable sediment focussing or winnowing at our site. Carbonate is virtually absent in the core, except during peak interglacial intervals of the Holocene, and Marine Isotope Stages (MIS) 5 and 11, likely caused by transient decreases in carbonate dissolution. All other proxies suggest that export production increased during most glacial periods, coinciding with high iron fluxes. Such augmented glacial iron fluxes at the core site were most likely derived from glaciogenic input from the Patagonian Ice Sheet promoting the growth of phytoplankton. Additionally, glacial export production peaks are also consistent with northward shifts of the Subantarctic and Polar Fronts, which positioned our site south of the Subantarctic Front and closer to silicic acid-rich waters of the Polar Frontal Zone, as well as a with a decrease in the diatom utilization of Si relative to nitrate under Fe-replete conditions. However, glacial export production near the Drake Passage was lower than in the Atlantic and Indian sectors of the Southern Ocean, which may relate to complete consumption of silicic acid in the study area. Our results underline the importance of micro-nutrient fertilization through lateral terrigenous input from South America rather than aeolian transport, and exemplify the role of frontal shifts and nutrient limitation for past productivity changes in the Pacific entrance to the Drake Passage.
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    Notes: Toroidal DNA condensates have attracted the attention of biophysicists, biochemists, and polymer physicists for more than thirty years. In the biological community, the quest to understand DNA toroid formation has been motivated by its relevance to gene packing in certain viruses and by the potential use of DNA toroids in artificial gene delivery (e.g., gene therapy). In the physical sciences, DNA toroids are appreciated as a superb model system for studying particle formation by the collapse of a semiflexible, polyelectrolyte polymer. This review focuses on experimental studies from the past few years that have significantly increased our understanding of DNA toroid structure and the mechanism of their formation. Highlights include structural studies that show the DNA strands within toroids to be packed in an ideal hexagonal lattice, and also in regions with a nonhexagonal lattice that are required by the topological constraints associated with winding DNA into a toroid. Recent studies of DNA toroid formation have also revealed that toroid size limits result from a complex interplay between kinetic and thermodynamic factors that govern both toroid nucleation and growth. The work discussed in this review indicates that it will ultimately be possible to obtain substantial control over DNA toroid dimensions.
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    Notes: With genome sequencing nearing completion for the model organisms used in biomedical research, there is a rapidly growing appreciation that proteomics, the study of covalent modification to proteins, and transcriptional regulation will likely dominate the research headlines in the next decade. Protein methylation plays a central role in both of these fields, as several different residues (Arg, Lys, Gln) are methylated in cells and methylation plays a central role in the "histone code" that regulates chromatin structure and impacts transcription. In some cases, a single lysine can be mono-, di-, or trimethylated, with different functional consequences for each of the three forms. This review describes structural aspects of methylation of histone lysine residues by two enzyme families with entirely different structural scaffolding (the SET proteins and Dot1p) and methylation of protein arginine residues by PRMTs.
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    Notes: Potassium (K+) channels are tetrameric membrane-spanning proteins that provide a selective pore for the conductance of K+ across the cell membranes. These channels are most remarkable in their ability to discriminate K+ from Na+ by more than a thousandfold and conduct at a throughput rate near diffusion limit. The recent progress in the structural characterization of K+ channel provides us with a unique opportunity to understand their function at the atomic level. With their ability to go beyond static structures, molecular dynamics simulations based on atomic models can play an important role in shaping our view of how ion channels carry out their function. The purpose of this review is to summarize the most important findings from experiments and computations and to highlight a number of fundamental mechanistic questions about ion conduction and selectivity that will require further work.
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    Notes: Proteins have become accessible targets for chemical synthesis. The basic strategy is to use native chemical ligation, Staudinger ligation, or other orthogonal chemical reactions to couple synthetic peptides. The ligation reactions are compatible with a variety of solvents and proceed in solution or on a solid support. Chemical synthesis enables a level of control on protein composition that greatly exceeds that attainable with ribosome-mediated biosynthesis. Accordingly, the chemical synthesis of proteins is providing previously unattainable insight into the structure and function of proteins.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 415-440 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: A powerful approach to understanding protein enzyme catalysis is to examine the structural context of essential amino acid side chains whose deletion or modification negatively impacts catalysis. In principle, this approach can be even more powerful for RNA enzymes, given the wide variety and subtlety of functionally modified nucleotides now available. Numerous recent success stories confirm the utility of this approach to understanding ribozyme function. An anomaly, however, is the hammerhead ribozyme, for which the structural and functional data do not agree well, preventing a unifying view of its catalytic mechanism from emerging. To delineate the hammerhead structure-function comparison, we have evaluated and distilled the large body of biochemical data into a consensus set of functional groups unambiguously required for hammerhead catalysis. By examining the context of these functional groups within available structures, we have established a concise set of disagreements between the structural and functional data. The number and relative distribution of these inconsistencies throughout the hammerhead reaffirms that an extensive conformational rearrangement from the fold observed in the crystal structure must be necessary for cleavage to occur. The nature and energetic driving force of this conformational isomerization are discussed.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 399-414 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: The development of single-molecule detection and manipulation has allowed us to monitor the behavior of individual biological molecules and molecular complexes in real time. This approach significantly expands our capability to characterize complex dynamics of biological processes, allowing transient intermediate states and parallel kinetic pathways to be directly observed. Exploring this capability to elucidate complex dynamics, recent single-molecule experiments on RNA folding and catalysis have improved our understanding of the folding energy landscape of RNA and allowed us to better dissect complex RNA catalytic reactions, including translation by the ribosome.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 173-199 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Water plays a central role in the structures and properties of biomoleculesĐ??proteins, nucleic acids, and membranesĐ??and in their interactions with ligands and drugs. Over the past half century, our understanding of water has been advanced significantly owing to theoretical and computational modeling. However, like the blind men and the elephant, different models describe different aspects of water's behavior. The trend in water modeling has been toward finer-scale properties and increasing structural detail, at increasing computational expense. Recently, our labs and others have moved in the opposite direction, toward simpler physical models, focusing on more global propertiesĐ??water's thermodynamics, phase diagram, and solvation properties, for exampleĐ??and toward less computational expense. Simplified models can guide a better understanding of water in ways that complement what we learn from more complex models. One ultimate goal is more tractable models for computer simulations of biomolecules. This review gives a perspective from simple models on how the physical properties of waterĐ??as a pure liquid and as a solventĐ??derive from the geometric and hydrogen bonding properties of water.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 379-398 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Structural data on protein-DNA complexes provide clues for understanding the mechanism of protein-DNA recognition. Although the structures of a large number of protein-DNA complexes are known, the mechanisms underlying their specific binding are still only poorly understood. Analysis of these structures has shown that there is no simple one-to-one correspondence between bases and amino acids within protein-DNA complexes; nevertheless, the observed patterns of interaction carry important information on the mechanisms of protein-DNA recognition. In this review, we show how the patterns of interaction, either observed in known structures or derived from computer simulations, confer recognition specificity, and how they can be used to examine the relationship between structure and specificity and to predict target DNA sequences used by regulatory proteins.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 457-483 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The field of lymphatic research has been recently invigorated by the identification of genes and mechanisms that control various aspects of lymphatic development. We are beginning to understand how, starting from a subgroup of embryonic venous endothelial cells, the whole lymphatic system forms in a stepwise manner. The generation of genetically engineered mice with defects in different steps of the lymphangiogenic program has provided models that are increasing our understanding of the lymphatic system in health and disease. This knowledge, in turn, should lead to the development of better diagnostic methods and treatments of lymphatic disorders and tumor metastasis.
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    Annual Review of Materials Research 35 (2005), S. 127-142 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The preparation of skeletal catalysts is considered, with particular reference to the preparation of skeletal nickel and skeletal copper. Skeletal catalysts have physical properties that are highly desired for some industrial processes, and the means of controlling these properties to optimize performance is reviewed. The preparation can be affected by the initial alloy composition, the quenching process, the leaching procedure, aging and by the addition of promoters. These processes may affect either or both the chemical and physical characteristics of the catalysts. Preparation procedures need to be adjusted for individual reactions if optimal performance is required. The effect of the preparation conditions on the structure and catalytic performance of these systems is reviewed.
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    Annual Review of Materials Research 35 (2005), S. 167-207 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: We review here the theory of the early stages of oxidation of the (110) surface of Ni1x Alx, based on ab initio calculations using a plane-wave pseudopotential method. The clean surface and several oxidized surfaces have been investigated, with oxygen coverages up to 2ML of oxygen (1ML = 3 O atoms per 2 surface Al atoms). The theory to date is a description in terms of equilibrium thermodynamics, with a comparison of the free energies of several surfaces of different composition, implemented at the atomic scale. Three environmental parameters are singled out as control variables in this treatment, namely the alloy composition x (assumed to be near 0.5), the temperature T and the partial pressure of oxygen pO2. With certain reasonable approximations an analytic formula for the surface energy ?? is derived in terms of these variables and some constants that are calculated ab initio together with others that are derived from experimental thermodynamic tables. At oxygen pressures just above the threshold for bulk oxidation of NiAl, the calculations explain the observed formation of a thin film of alumina in place of NiAl surface layers, with the consequent dissolution of Ni into the bulk. Ab initio calculations illustrate how the energetics of supplying Al to the surface depends on bulk stoichiometry, which alters the relative stability of different surface oxidation states so as to favour oxidation more if the alloy is Al-rich than if it is Ni-rich.
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    Annual Review of Materials Research 35 (2005), S. 315-350 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: There is a pressing need for cleaner fuels (free or aromatics and of minimal sulfur content) or ones that convert chemical energy directly to electricity, silently and without production of noxious oxides and particulates; chemical, petrochemical and pharmaceutical processes that may be conducted in a one-step, solvent-free manner and that use air as the preferred oxidant; and industrial processes that minimize consumption of energy, production of waste, or the use of corrosive, explosive, volatile, and nonbiodegradable materials. All these needs and other desiderata, such as the in situ production and containment of aggressive and hazardous reagents, and the avoidance of use of ecologically harmful elements, may be achieved by designing the appropriate heterogeneous inorganic catalyst, which ideally should be cheap, readily preparable and fully characterizable, preferably under in situ reaction conditions. A range of nanoporous and nanoparticle catalysts that meet most of the stringent demands of sustainable development and responsible (clean) technology is described. Specific examples that are highlighted include the production of adipic acid (precursor of polyamides and urethanes) without the use of concentrated nitric acid nor the production of greenhouse gases such as nitrous oxide; the production of caprolactam (precursor of nylon) without the use of oleum and hydroxylamine sulfate; and the terminal oxyfunctionalization of linear alkanes in air. The topic of biocatalysis and sustainable development is also briefly discussed for the epoxidation of terpenes and fatty acid methyl esters; for the generation of polymers, polylactides, and polyesters; and for the production of 1,3-propanediol from corn.
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    Annual Review of Materials Research 35 (2005), S. 351-395 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This review covers the synthesis, characterization, and physico-chemical properties of microporous and mesoporous aluminophosphates and silicoaluminophosphates molecular sieves. Particular emphasis is given to the materials that have found applications as acid catalysts. We consider the evolution of the synthesis procedures from the first discoveries to the current methodologies and give perspectives for new possible synthesis strategies. Emphasis is given to the use of specially prepared precursors/reactants designed for the use as molecular sieves. Experimental (especially MAS-NMR and FTIR spectroscopy) and theoretical approaches to the description of the Si insertion into the ALPO framework and to the acidic properties of SAPOs and MeAPSOs materials are discussed.
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    Annual Review of Materials Research 35 (2005), S. 51-73 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The diffusion-multiple approachĐ??the creation of composition gradients and intermetallic phases by long-term annealing of junctions of three or more phases/alloysĐ??enables the generation of a large number of phases and compositions for efficient mapping of phase diagrams, phase properties, and kinetics. With an efficiency much higher than that of a conventional approach, many critical materials data, which otherwise would be too time-consuming and expensive to acquire, can be obtained and employed to accelerate alloy design. The critical data for structural materials design include phase diagrams, diffusion coefficients, precipitation kinetics, solution-strengthening effects, and precipitation-strengthening effects. All these data can be obtained from diffusion multiples. The combination of the diffusion-multiple approach with the CALPHAD approach can impact computational design of structural materials. The diffusion-multiple approach can also be applied to combinatorial screening of functional materials having unique physical, chemical, or other properties when micro-scale measurement techniques are available for these properties. Examples are shown to illustrate the progress made to date on applying the diffusion-multiple approach to accelerated design/discovery of materials.
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    Annual Review of Materials Research 35 (2005), S. 505-538 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Renewable energy resources, of which wind energy is prominent, are part of the solution to the global energy problem. Wind turbine and the rotorblade concepts are reviewed, and loadings by wind and gravity as important factors for the fatigue performance of the materials are considered. Wood and composites are discussed as candidates for rotorblades. The fibers and matrices for composites are described, and their high stiffness, low density, and good fatigue performance are emphasized. Manufacturing technologies for composites are presented and evaluated with respect to advantages, problems, and industrial potential. The important technologies of today are prepreg (pre-impregnated) technology and resin infusion technology. The mechanical properties of fiber composite materials are discussed, with a focus on fatigue performance. Damage and materials degradation during fatigue are described. Testing procedures for documentation of properties are reviewed, and fatigue loading histories are discussed, together with methods for data handling and statistical analysis of (large) amounts of test data. Future challenges for materials in the field of wind turbines are presented, with a focus on thermoplastic composites, new structural materials concepts, new structural design aspects, structural health monitoring, and the coming trends and markets for wind energy.
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    Annual Review of Materials Research 35 (2005), S. 397-426 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This review illustrates how catalytically active molecular structures are created on oxide surfaces by attachment of metal complexes with subsequent structural transformation and molecular imprinting on the surfaces. Also discussed is how the designed surfaces are characterized in situ by physical techniques including conventional and time-resolved X-ray absorption fine structure. The structural transformation and molecular imprinting for attached metal complexes can provide a new class of catalytic materials with a high complexity for selective catalysis including shape-selective and asymmetric catalysis.
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    Annual Review of Materials Research 35 (2005), S. 29-49 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This paper describes the use of extended X-ray absorption fine structure spectroscopy (EXAFS) to examine the structure of molten salts and ionic liquids and species dissolved in them. The EXAFS theory is briefly described as are the methods by which EXAFS of these systems can be studied. A range of applications have used EXAFS to investigate the structure of metallic species in ionic liquids from extraction studies to catalysts. The area of structural investigations of ionic liquids is still being developed, although growing rapidly, whereas the structure of molten salts has been studied using EXAFS in more detail.
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    Annual Review of Materials Research 35 (2005), S. 539-569 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: In the nanoscience era, the properties of many exciting new materials and devices will depend on the details of their composition down to the level of single atoms. Thus the characterization of the structure and electronic properties of matter at the atomic scale is becoming ever more vital for economic and technological as well as for scientific reasons. The combination of atomic-resolution Z-contrast scanning transmission electron microscopy (STEM) and electron energy loss spectroscopy (EELS) represents a powerful method to link the atomic and electronic structure to macroscopic properties, allowing materials, nanoscale systems, and interfaces to be probed in unprecedented detail. Z-contrast STEM uses electrons that have been scattered to large angles for imaging. The relative intensity of each atomic column is roughly proportional to Z2, where Z is the atomic number. Recent developments in correcting the aberrations of the lenses in the electron microscope have pushed the achievable spatial resolution and the sensitivity for imaging and spectroscopy in the STEM into the sub-A??ngstrom (sub-A??) regime, providing a new level of insight into the structure/property relations of complex materials. Images acquired with an aberration-corrected instrument show greatly improved contrast. The signal-to-noise ratio is sufficiently high to allow sensitivity even to single atoms in both imaging and spectroscopy. This is a key achievement because the detection and measurement of the response of individual atoms has become a challenging issue to provide new insight into many fields, such as catalysis, ceramic materials, complex oxide interfaces, or grain boundaries. In this article, the state-of-the-art for the characterization of all of these different types of materials by means of aberration-corrected STEM and EELS are reviewed.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 47-79 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Mixed mating, in which hermaphrodite plant species reproduce by both self- and cross-fertilization, presents a challenging problem for evolutionary biologists. Theory suggests that inbreeding depression, the main selective factor opposing the evolution of selfing, can be purged with self-fertilization, a process that is expected to yield pure strategies of either outcrossing or selfing. Here we present updated evidence suggesting that mixed mating systems are frequent in seed plants. We outline the floral and pollination mechanisms that can lead to intermediate outcrossing, review the theoretical models that address the stability of intermediate outcrossing, and examine relevant empirical evidence. A comparative analysis of estimated inbreeding coefficients and outcrossing rates suggests that mixed mating often evolves despite strong inbreeding depression. The adaptive significance of mixed mating has yet to be fully explained for any species. Recent theoretical and empirical work suggests that future progress will come from a better integration of studies of floral mechanisms, genetics, and ecology, and recognition of how selective pressures vary in space and time.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 191-218 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: We explore empirical and theoretical evidence for the functional significance of plant-litter diversity and the extraordinary high diversity of decomposer organisms in the process of litter decomposition and the consequences for biogeochemical cycles. Potential mechanisms for the frequently observed litter-diversity effects on mass loss and nitrogen dynamics include fungi-driven nutrient transfer among litter species, inhibition or stimulation of microorganisms by specific litter compounds, and positive feedback of soil fauna due to greater habitat and food diversity. Theory predicts positive effects of microbial diversity that result from functional niche complementarity, but the few existing experiments provide conflicting results. Microbial succession with shifting enzymatic capabilities enhances decomposition, whereas antagonistic interactions among fungi that compete for similar resources slow litter decay. Soil-fauna diversity manipulations indicate that the number of trophic levels, species identity, and the presence of keystone species have a strong impact on decomposition, whereas the importance of diversity within functional groups is not clear at present. In conclusion, litter species and decomposer diversity can significantly influence carbon and nutrient turnover rates; however, no general or predictable pattern has emerged. Proposed mechanisms for diversity effects need confirmation and a link to functional traits for a comprehensive understanding of how biodiversity interacts with decomposition processes and the consequences of ongoing biodiversity loss for ecosystem functioning.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 445-466 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Investigation into model selection has a long history in the statistical literature. As model-based approaches begin dominating systematic biology, increased attention has focused on how models should be selected for distance-based, likelihood, and Bayesian phylogenetics. Here, we review issues that render model-based approaches necessary, briefly review nucleotide-based models that attempt to capture relevant features of evolutionary processes, and review methods that have been applied to model selection in phylogenetics: likelihood-ratio tests, AIC, BIC, and performance-based approaches.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 295-317 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: One of the greatest mass extinctions in Earth's history occurred at the end of the Cretaceous era, sixty-five million years (Myr) ago. Considerable evidence indicates that the impact of a large asteroid or comet was the ultimate cause of this extraordinary event. At the time of mass extinction, the organic flux to the deep sea collapsed, and production of calcium carbonate by marine plankton radically declined. These biogeochemical processes did not fully recover for a few million years. The drastic decline and long lag in final recovery of these processes are most simply explained as consequences of open-ocean ecosystem alteration by the mass extinction. If this explanation is correct, the extent and timing of marine biogeochemical recovery from the end-Cretaceous event was ultimately contingent on the extent and timing of open-ocean ecosystem recovery. The biogeochemical recovery may in turn have created new evolutionary opportunities for a diverse array of marine organisms.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 1-21 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Variation in the subtle differences between right and left sides of bilateral characters, or fluctuating asymmetry (FA), has long been considered to be primarily environmental in origin, and this has promoted its use as a measure of developmental instability (DI) in populations. There is little evidence for specific genes that govern FA per se. Numerous studies show that FA levels in various characters are influenced by dominance and especially epistatic interactions among genes. An epistatic genetic basis for FA may complicate its primary use in comparisons of DI levels in outbred or wild populations subjected or not subjected to various environmental stressors. Although the heritability of FA typically is very low or zero, epistasis can generate additive genetic variation for FA that may allow it to evolve especially in populations subjected to bottlenecks, hybridizations, or periods of rapid environmental changes caused by various stresses.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 419-444 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Understanding and predicting the dynamics of multispecies systems generally require estimates of interaction strength among species. Measuring interaction strength is difficult because of the large number of interactions in any natural system, long-term feedback, multiple pathways of effects between species pairs, and possible nonlinearities in interaction-strength functions. Presently, the few studies that extensively estimate interaction strength suggest that distributions of interaction strength tend to be skewed toward few strong and many weak interactions. Modeling studies indicate that such skewed patterns tend to promote system stability and arise during assembly of persistent communities. Methods for estimating interaction strength efficiently from traits of organisms, such as allometric relationships, show some promise. Methods for estimating community response to environmental perturbations without an estimate of interaction strength may also be of use. Spatial and temporal scale may affect patterns of interaction strength, but these effects require further investigation and new multispecies modeling frameworks. Future progress will be aided by development of long-term multispecies time series of natural communities, by experimental tests of different methods for estimating interaction strength, and by increased understanding of nonlinear functional forms.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 643-689 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Oysters have been introduced worldwide to 73 countries, but the ecological consequences of the introductions are not fully understood. Economically, introduced oysters compose a majority of oyster harvests in many areas. Oysters are ecosystem engineers that influence many ecological processes, such as maintenance of biodiversity, population and food web dynamics, and nutrient cycling. Consequently, both their loss, through interaction of overharvest, habitat degradation, disease, poor water quality, and detrimental species interactions, and their gain, through introductions, can cause complex changes in coastal ecosystems. Introductions can greatly enhance oyster population abundance and production, as well as populations of associated native species. However, introduced oysters are also vectors for non-native species, including disease-causing organisms. Thus, substantial population, community, and habitat changes have accompanied new oysters. In contrast, ecosystem-level consequences of oyster introductions, such as impacts on flow patterns, sediment and nutrient dynamics, and native bioengineering species, are not well understood. Ecological risk assessments for future introductions must emphasize probabilities of establishment, spread, and impacts on vulnerable species, communities, and ecosystem properties. Many characteristics of oysters lead to predictions that they would be successful, high-impact members of recipient ecosystems. This conclusion leaves open the discussion of whether such impacts are desirable in terms of restoration of coastal ecosystems, especially where restoration of native oysters is possible.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 219-242 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The multi-gene family that encodes ribosomal RNA (the rDNA) has been the subject of numerous review articles examining its structure and function, as well as its use as a molecular systematic marker. The purpose of this review is to integrate information about structural and functional aspects of rDNA that impact the ecology and evolution of organisms. We examine current understanding of the impact of length heterogeneity and copy number in the rDNA on fitness and the evolutionary ecology of organisms. We also examine the role that elemental ratios (biological stoichiometry) play in mediating the impact of rDNA variation in natural populations and ecosystems. The body of work examined suggests that there are strong reciprocal feedbacks between rDNA and the ecology of all organisms, from microbes to metazoans, mediated through increased phosphorus demand in organisms with high rRNA content.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 23-46 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Two consequences of terrestrial ectothermy (low energy needs and behavioral control of body temperatures) have had major consequences for the evolution of reptile life-history traits. For example, reproducing females can manipulate incubation temperatures and thus phenotypic traits of their offspring by retaining developing eggs in utero. This ability has resulted in multiple evolutionary transitions from oviparity to viviparity in cool-climate reptile populations. The spatial and temporal heterogeneity of operative temperatures in terrestrial habitats also has favored careful nest-site selection and a matching of embryonic reaction norms to thermal regimes during incubation (e.g., via temperature-dependent sex determination). Many of the life-history features in which reptiles differ from endothermic vertebratesĐ??such as their small offspring sizes, large litter sizes, and infrequent reproductionĐ??are direct consequences of ectothermy, reflecting freedom from heat-conserving constraints on body size and energy storage. Ectothermy confers immense flexibility, enabling a dynamic matching of life-history traits to local circumstances. This flexibility has generated massive spatial and temporal variation in life-history traits via phenotypic plasticity as well as adaptation. The diversity of life histories in reptiles can best be interpreted within a conceptual framework that views reptiles as low-energy, variable-temperature systems.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 541-562 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The continuous flow of genomic data is creating unprecedented opportunities for the reconstruction of molecular phylogenies. Access to whole-genome data means that phylogenetic analysis can now be performed at different genomic levels, such as primary sequences and gene order, allowing for reciprocal corroboration of the results. We critically review the different kinds of phylogenomic methods currently available, paying particular attention to method reliability. Our emphasis is on methods for the analysis of primary sequences because these are the most advanced. We discuss the important issue of statistical inconsistency and show how failing to fully capture the process of sequence evolution in the underlying models leads to tree reconstruction artifacts. We suggest strategies for detecting and potentially overcoming these problems. These strategies involve the development of better models, the use of an improved taxon sampling, and the exclusion of phylogenetically misleading data.
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