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Sample records for quantitative biome reconstruction

  1. Global middle Pliocene biome reconstruction: A data/model synthesis

    NASA Astrophysics Data System (ADS)

    Haywood, Alan M.; Valdes, Paul J.; Francis, Jane E.; Sellwood, Bruce W.

    2002-12-01

    The middle Pliocene warm interval (ca. 3 Ma BP) has been extensively studied. However, our knowledge concerning the global distribution of middle Pliocene biomes remains far from complete. This paper presents the results from a "first attempt" at simulating the distribution of different mid-Pliocene biomes using an advanced numerical general circulation climate model (Hadley Centre Atmospheric Model Version 3) and the BIOME 4 vegetation model. The modeling indicates that during the middle Pliocene the geographical coverage of tundra type biomes may have been significantly reduced compared with the present day in the Northern Hemisphere. High-latitude forests expand in the place of tundra forms of vegetation. Total area covered by forest increases for the Pliocene case compared with the present day. Arid deserts become less prevalent in the Pliocene scenario and are replaced by tropical xerophytic shrublands and savanna-type vegetation. These results compare favorably with geological data in general and with the U.S. Geological Survey's PRISM2 middle Pliocene vegetation reconstruction, although data/model inconsistencies are apparent. Although some of these inconsistencies relate to the weaknesses of the climate and biome model employed, others identify deficiencies in the extant geological data set or the interpretation of this data. This modeled biome reconstruction will serve as a useful vehicle for aiding in future comparisons between geological data on middle Pliocene biomes and model predictions.

  2. Biomes.

    ERIC Educational Resources Information Center

    Web Feet K-8, 2001

    2001-01-01

    This annotated subject guide to Web sites and additional resources focuses on biomes. Specifies age levels for resources that include Web sites, CD-ROMs and software, videos, books, audios, and magazines; includes professional resources; and presents a relevant class activity. (LRW)

  3. Biomes.

    ERIC Educational Resources Information Center

    Web Feet K-8, 2001

    2001-01-01

    This annotated subject guide to Web sites and additional resources focuses on biomes. Specifies age levels for resources that include Web sites, CD-ROMs and software, videos, books, audios, and magazines; includes professional resources; and presents a relevant class activity. (LRW)

  4. Pollen-based biome reconstructions over the past 18,000 years and atmospheric CO2 impacts on vegetation in equatorial mountains of Africa

    NASA Astrophysics Data System (ADS)

    Izumi, K.; Lézine, A.-M.

    2016-11-01

    This paper presents a quantitative vegetation reconstruction, based on a biomization procedure, of two mountain sites in the west (Bambili; 5°56‧ N, 10°14‧ E, 2273 m) and east (Rusaka; 3°26‧ S, 29°37‧ E, 2070 m) Congo basin in equatorial Africa during the last 18,000 years. These reconstructions clarify the response of vegetation to changes in climate, atmospheric pressure, and CO2 concentrations. Two major events characterize the biome changes at both sites: the post-glacial development of all forest biomes ca. 14,500 years ago and their rapid collapse during the last millennium. The rates of forest development between the biomes are different; a progressive expansion of lowland biomes and an abrupt expansion of montane biomes. The trends of pollen diagrams and biome affinity scores are not always consistent in some periods such as the Younger Dryas interval and end of the Holocene Humid Period, because the biomization method is not a simple summarization of the pollen data, but also takes biodiversity into consideration. Our sensitivity experiment and inverse-vegetation modeling approach show that changes in atmospheric CO2 concentration unequally influence vegetation in different local environments. The study also suggests that the biome changes prior to the Holocene result from both changes in the atmospheric CO2 concentration and climate. The development of warm-mixed forest from xerophtic vegetation results from increases in atmospheric CO2 concentration and near-surface air temperature. Difference in local dryness results in the different biome distributions, with more forest-type biomes at Bambili and more grass/shrub-type biomes at Rusaka.

  5. Holocene Biomes and Climate Reconstruction of Northwestern Mexico Based on High Resolution Pollen Data

    NASA Astrophysics Data System (ADS)

    Ortega-Rosas, C. I.; Guiot, J.; Peñalba, C.

    2005-12-01

    New paleovegetation and paleoclimate data from the Sierra Madre Occidental (SMO) in northwestern Mexico are presented. This work involves three main studies: 1) the fossil pollen analysis of five Holocene peat bogs located at different altitudes (1500 to 2000 m) inside the states of Sonora and Chihuahua; 2) the modern pollen analysis across an altitudinal transect (28° latitude north) from the Sonoran desert towards the highlands of the temperate SMO; and 3) the climatic and biomes reconstruction using Plant Functional Types and Biomization methods. For this last study a modern pollen dataset of 630 sites across the NW Mexico and the SW United States was compiled from different sources (North American Pollen Dataset, Latin-American Pollen Dataset, personal data, and different scientific papers). For the biomization method (Prentice et al., 1996); we have modified the pollen-PFT and PFT-Biomes assignation of Thompson and Anderson (2000) for a better representation of the modern vegetation of NW Mexico. The biomes reconstructed from the modern pollen sites let us to validate the reconstruction method and then his application to the fossil sites. The preliminary results of biome reconstruction from the pollen fossil records shows during the early Holocene that a Cool conifer forest was well distributed at 1700 m, and possibly lower elevation, at the SMO while today this biome is present only at altitudes higher than 2000 m in the Chihuahua state, the annual temperature reconstructed were at less of 2°C colder than today, but annual precipitation was 300 mm/yr lower than the actual (800 mm/yr). The middle Holocene at 6000 yr BP is marked by the installation of the warm mixed forest biome at 1700 m elevation, similar to present vegetation in the region. While at higher elevations (1900 m) the cool conifer forest was still present at the middle Holocene. The increasing in temperature characterize the period from 6000 to 4000 yr BP being more marked at 6000 yr BP with 3

  6. Pollen-based biome reconstructions for Latin America at 0, 6000 and 18 000 radiocarbon years

    NASA Astrophysics Data System (ADS)

    Marchant, R.; Harrison, S. P.; Hooghiemstra, H.; Markgraf, V.; van Boxel, J. H.; Ager, T.; Almeida, L.; Anderson, R.; Baied, C.; Behling, H.; Berrio, J. C.; Burbridge, R.; Björck, S.; Byrne, R.; Bush, M. B.; Cleef, A. M.; Duivenvoorden, J. F.; Flenley, J. R.; de Oliveira, P.; van Geel, B.; Graf, K. J.; Gosling, W. D.; Harbele, S.; van der Hammen, T.; Hansen, B. C. S.; Horn, S. P.; Islebe, G. A.; Kuhry, P.; Ledru, M.-P.; Mayle, F. E.; Leyden, B. W.; Lozano-García, S.; Melief, A. B. M.; Moreno, P.; Moar, N. T.; Prieto, A.; van Reenen, G. B.; Salgado-Labouriau, M. L.; Schäbitz, F.; Schreve-Brinkman, E. J.; Wille, M.

    2009-02-01

    The biomisation method is used to reconstruct Latin American vegetation at 6000±500 and 18 000±1000 radiocarbon years before present (14C yr BP) from pollen data. Tests using modern pollen data from 381 samples derived from 287 locations broadly reproduce potential natural vegetation. The strong temperature gradient associated with the Andes is recorded by a transition from high altitude cool grass/shrubland and cool mixed forest to mid-altitude cool temperate rain forest, to tropical dry, seasonal and rain forest at low altitudes. Reconstructed biomes from a number of sites do not match the potential vegetation due to local factors such as human impact, methodological artefacts and mechanisms of pollen representivity of the parent vegetation. At 6000±500 14C yr BP 255 samples are analysed from 127 sites. Differences between the modern and the 6000±500 14C yr BP reconstruction are comparatively small. Patterns of change relative to the modern reconstruction are mainly to biomes characteristic of drier climate in the north of the region with a slight more mesic shift in the south. Cool temperate rain forest remains dominant in western South America. In northwestern South America a number of sites record transitions from tropical seasonal forest to tropical dry forest and tropical rain forest to tropical seasonal forest. Sites in Central America also show a change in biome assignment to more mesic vegetation, indicative of greater plant available moisture, e.g. on the Yucatán peninsula sites record warm evergreen forest, replacing tropical dry forest and warm mixed forest presently recorded. At 18 000±1000 14C yr BP 61 samples from 34 sites record vegetation that reflects a generally cool and dry environment. Cool grass/shrubland prevalent in southeast Brazil, Amazonian sites record tropical dry forest, warm temperate rain forest and tropical seasonal forest. Southernmost South America is dominated by cool grass/shrubland, a single site retains cool temperate

  7. Pollen-based biome reconstructions for Latin America at 0, 6000 and 18 000 radiocarbon years

    USGS Publications Warehouse

    Marchant, R.; Harrison, S.P.; Hooghiemstra, H.; Markgraf, Vera; Van Boxel, J. H.; Ager, T.; Almeida, L.; Anderson, R.; Baied, C.; Behling, H.; Berrio, J.C.; Burbridge, R.; Bjorck, S.; Byrne, R.; Bush, M.B.; Cleef, A.M.; Duivenvoorden, J.F.; Flenley, J.R.; De Oliveira, P.; Van Geel, B.; Graf, K.J.; Gosling, W.D.; Harbele, S.; Van Der Hammen, T.; Hansen, B.C.S.; Horn, S.P.; Islebe, G.A.; Kuhry, P.; Ledru, M.-P.; Mayle, F.E.; Leyden, B.W.; Lozano-Garcia, S.; Melief, A.B.M.; Moreno, P.; Moar, N.T.; Prieto, A.; Van Reenen, G. B.; Salgado-Labouriau, M. L.; Schasignbitz, F.; Schreve-Brinkman, E. J.; Wille, M.

    2009-01-01

    The biomisation method is used to reconstruct Latin American vegetation at 6000±500 and 18 000±1000 radiocarbon years before present (14C yr BP) from pollen data. Tests using modern pollen data from 381 samples derived from 287 locations broadly reproduce potential natural vegetation. The strong temperature gradient associated with the Andes is recorded by a transition from high altitude cool grass/shrubland and cool mixed forest to mid-altitude cool temperate rain forest, to tropical dry, seasonal and rain forest at low altitudes. Reconstructed biomes from a number of sites do not match the potential vegetation due to local factors such as human impact, methodological artefacts and mechanisms of pollen representivity of the parent vegetation.

    At 6000±500 14C yr BP 255 samples are analysed from 127 sites. Differences between the modern and the 6000±500 14C yr BP reconstruction are comparatively small. Patterns of change relative to the modern reconstruction are mainly to biomes characteristic of drier climate in the north of the region with a slight more mesic shift in the south. Cool temperate rain forest remains dominant in western South America. In northwestern South America a number of sites record transitions from tropical seasonal forest to tropical dry forest and tropical rain forest to tropical seasonal forest. Sites in Central America also show a change in biome assignment to more mesic vegetation, indicative of greater plant available moisture, e.g. on the Yucat??n peninsula sites record warm evergreen forest, replacing tropical dry forest and warm mixed forest presently recorded.

    At 18 000±1000 14C yr BP 61 samples from 34 sites record vegetation that reflects a generally cool and dry environment. Cool grass/shrubland prevalent in southeast Brazil, Amazonian sites record tropical dry forest, warm temperate rain forest and tropical seasonal forest. Southernmost South America is dominated by cool grass/shrubland, a single site

  8. Pollen-based biome reconstructions for Latin America at 0, 6000 and 18 000 radiocarbon years

    USGS Publications Warehouse

    Marchant, R.; Harrison, S.P.; Hooghiemstra, H.; Markgraf, Vera; Van Boxel, J. H.; Ager, T.; Almeida, L.; Anderson, R.; Baied, C.; Behling, H.; Berrio, J.C.; Burbridge, R.; Bjorck, S.; Byrne, R.; Bush, M.B.; Cleef, A.M.; Duivenvoorden, J.F.; Flenley, J.R.; De Oliveira, P.; Van Geel, B.; Graf, K.J.; Gosling, W.D.; Harbele, S.; Van Der Hammen, T.; Hansen, B.C.S.; Horn, S.P.; Islebe, G.A.; Kuhry, P.; Ledru, M.

    2009-01-01

    The biomisation method is used to reconstruct Latin American vegetation at 6000±500 and 18 000±1000 radiocarbon years before present (14C yr BP) from pollen data. Tests using modern pollen data from 381 samples derived from 287 locations broadly reproduce potential natural vegetation. The strong temperature gradient associated with the Andes is recorded by a transition from high altitude cool grass/shrubland and cool mixed forest to mid-altitude cool temperate rain forest, to tropical dry, seasonal and rain forest at low altitudes. Reconstructed biomes from a number of sites do not match the potential vegetation due to local factors such as human impact, methodological artefacts and mechanisms of pollen representivity of the parent vegetation. At 6000±500 14C yr BP 255 samples are analysed from 127 sites. Differences between the modern and the 6000±500 14C yr BP reconstruction are comparatively small. Patterns of change relative to the modern reconstruction are mainly to biomes characteristic of drier climate in the north of the region with a slight more mesic shift in the south. Cool temperate rain forest remains dominant in western South America. In northwestern South America a number of sites record transitions from tropical seasonal forest to tropical dry forest and tropical rain forest to tropical seasonal forest. Sites in Central America also show a change in biome assignment to more mesic vegetation, indicative of greater plant available moisture, e.g. on the Yucat??n peninsula sites record warm evergreen forest, replacing tropical dry forest and warm mixed forest presently recorded. At 18 000±1000 14C yr BP 61 samples from 34 sites record vegetation that reflects a generally cool and dry environment. Cool grass/shrubland prevalent in southeast Brazil, Amazonian sites record tropical dry forest, warm temperate rain forest and tropical seasonal forest. Southernmost South America is dominated by cool grass/shrubland, a single site retains cool temperate

  9. Colombian vegetation at the Last Glacial Maximum: a comparison of model- and pollen-based biome reconstructions

    NASA Astrophysics Data System (ADS)

    Marchant, Robert; Boom, Arnoud; Behling, Hermann; Hooghiemstra, Henry; Melief, Bert; van Geel, Bas; van der Hammen, Thomas; Wille, Michael

    2004-10-01

    Colombian vegetation, at the ecological level of the biome, is reconstructed at the Last Glacial Maximum (LGM) using two methods. A reconstruction of modern biomes shows that, for the majority of the sites, the pollen data accurately reflect the potential vegetation, even though much of the original vegetation has been transformed by agricultural practices. At 18 000 14C yr BP a generally cool and dry environment is reflected in biome assignments of cold mixed forests, cool evergreen forests and cool grassland/shrub, the latter extending to lower altitudes than presently recorded. Differential responses of the vegetation to climatic shifts are related to changes in moisture sources and the importance of edaphic control on the vegetation. Secondly, biomes at the LGM are also investigated by applying a vegetation model (BIOME-3) set to operate at CO2 levels of 200 ppmV and with climatic data from 12 meteorological stations that encompass a range of environments within Colombia. At lower altitudes it is apparent that moisture is the dominant control on driving vegetation change whereas temperature becomes more important at higher altitudes. The combined reconstruction of biome-scale vegetation dynamics in Colombia allows an understanding of the environmental controls on these to be developed that demonstrates the need to invoke different factors to explain the vegetation change rather than a uniform reduction in temperature or moisture. Copyright

  10. Pollen-based biome reconstructions for Colombia at 3000, 6000, 9000, 12 000, 15 000 and 18 000 14C yr ago: Late Quaternary tropical vegetation dynamics

    NASA Astrophysics Data System (ADS)

    Marchant, Robert; Behling, Hermann; Berrio, Juan-Carlos; Cleef, Antoine; Duivenvoorden, Joost; Hooghiemstra, Henry; Kuhry, Peter; Melief, Bert; Schreve-Brinkman, Elisabeth; van Geel, Bas; van der Hammen, Thomas; van Reenen, Guido; Wille, Michael

    2002-02-01

    Colombian biomes are reconstructed at 45 sites from the modern period extending to the Last Glacial Maximum (LGM). The basis for our reconstruction is pollen data assigned to plant functional types and biomes at six 3000-yr intervals. A reconstruction of modern biomes is used to check the treatment of the modern pollen data set against a map of potential vegetation. This allows the biomes reconstructed at past periods to be assessed relative to the modern situation. This process also provides a check on the a priori assignment of pollen taxa to plant functional types and biomes. For the majority of the sites, the pollen data accurately reflect the potential vegetation, even though much of the original vegetation has been transformed by agricultural practices. At 18 000 14C yr BP, a generally cool and dry environment is reflected in biome, assignments of cold mixed forests, cool evergreen forests and cool grassland-shrub; the latter extending to lower altitudes than presently recorded. This signal is strongly recorded at 15 000 and 12 000 14C yr BP, the vegetation at these times also reflecting a relatively cool and dry environment. At 9000 14C yr BP there is a shift to biomes thought to result from slightly cooler environmental conditions. This trend is reversed by 6000 14C yr BP; most sites, within a range of different environmental settings, recording a shift to more xeric biome types. There is an expansion of steppe and cool mixed-forest biomes, replacing tropical dry forest and cool grassland-shrub biomes, respectively. These changes in biome assignments from the modern situation can be interpreted as a biotic response to mid-Holocene climatic aridity. At 3000 14C yr BP the shift is mainly to biomes characteristic of slightly more mesic environmental conditions.There are a number of sites that do not change biome assignment relative to the modern reconstruction, although the affinities that these sites have to a specific biome do change. These anomalies are

  11. Pollen-based biome reconstructions for Latin America at 0, 6000 and 18 000 radiocarbon years ago

    NASA Astrophysics Data System (ADS)

    Marchant, R.; Cleef, A.; Harrison, S. P.; Hooghiemstra, H.; Markgraf, V.; van Boxel, J.; Ager, T.; Almeida, L.; Anderson, R.; Baied, C.; Behling, H.; Berrio, J. C.; Burbridge, R.; Björck, S.; Byrne, R.; Bush, M.; Duivenvoorden, J.; Flenley, J.; de Oliveira, P.; van Geel, B.; Graf, K.; Gosling, W. D.; Harbele, S.; van der Hammen, T.; Hansen, B.; Horn, S.; Kuhry, P.; Ledru, M.-P.; Mayle, F.; Leyden, B.; Lozano-García, S.; Melief, A. M.; Moreno, P.; Moar, N. T.; Prieto, A.; van Reenen, G.; Salgado-Labouriau, M.; Schäbitz, F.; Schreve-Brinkman, E. J.; Wille, M.

    2009-12-01

    The biomisation method is used to reconstruct Latin American vegetation at 6000±500 and 18 000±1000 radiocarbon years before present (14C yr BP) from pollen data. Tests using modern pollen data from 381 samples derived from 287 locations broadly reproduce potential natural vegetation. The strong temperature gradient associated with the Andes is recorded by a transition from high altitude cool grass/shrubland and cool mixed forest to mid-altitude cool temperate rain forest, to tropical dry, seasonal and rain forest at low altitudes. Reconstructed biomes from a number of sites do not match the potential vegetation due to local factors such as human impact, methodological artefacts and mechanisms of pollen representivity of the parent vegetation. At 6000±500 14C yr BP 255 samples are analysed from 127 sites. Differences between the modern and the 6000±500 14C yr BP reconstruction are comparatively small; change relative to the modern reconstruction are mainly to biomes characteristic of drier climate in the north of the region with a slight more mesic shift in the south. Cool temperate rain forest remains dominant in western South America. In northwestern South America a number of sites record transitions from tropical seasonal forest to tropical dry forest and tropical rain forest to tropical seasonal forest. Sites in Central America show a change in biome assignment, but to more mesic vegetation, indicative of greater plant available moisture, e.g. on the Yucatán peninsula sites record warm evergreen forest, replacing tropical dry forest and warm mixed forest presently recorded. At 18 000±1000 14C yr BP 61 samples from 34 sites record vegetation reflecting a generally cool and dry environment. Cool grass/shrubland is prevalent in southeast Brazil whereas Amazonian sites record tropical dry forest, warm temperate rain forest and tropical seasonal forest. Southernmost South America is dominated by cool grass/shrubland, a single site retains cool temperate rain

  12. Pollen-based biome reconstructions for Latin America at 0, 6000 and 18 000 radiocarbon years ago

    USGS Publications Warehouse

    Marchant, R.; Cleef, A.; Harrison, S.P.; Hooghiemstra, H.; Markgraf, Vera; Van Boxel, J.; Ager, T.; Almeida, L.; Anderson, R.; Baied, C.; Behling, H.; Berrio, J.C.; Burbridge, R.; Bjorck, S.; Byrne, R.; Bush, M.; Duivenvoorden, J.; Flenley, J.; De Oliveira, P.; Van Gee, B.; Graf, K.; Gosling, W.D.; Harbele, S.; Van Der Hammen, T.; Hansen, B.; Horn, S.; Kuhry, P.; Ledru, M.-P.; Mayle, F.; Leyden, B.; Lozano-Garcia, S.; Melief, A.M.; Moreno, P.; Moar, N.T.; Prieto, A.; Van Reenen, G.; Salgado-Labouriau, M.; Schabitz, F.; Schreve-Brinkman, E. J.; Wille, M.

    2009-01-01

    The biomisation method is used to reconstruct Latin American vegetation at 6000??500 and 18 000??1000 radiocarbon years before present ( 14C yr BP) from pollen data. Tests using modern pollen data from 381 samples derived from 287 locations broadly reproduce potential natural vegetation. The strong temperature gradient associated with the Andes is recorded by a transition from high altitude cool grass/shrubland and cool mixed forest to mid-altitude cool temperate rain forest, to tropical dry, seasonal and rain forest at low altitudes. Reconstructed biomes from a number of sites do not match the potential vegetation due to local factors such as human impact, methodological artefacts and mechanisms of pollen representivity of the parent vegetation. At 6000??500 14C yr BP 255 samples are analysed from 127 sites. Differences between the modern and the 6000??500 14C yr BP reconstruction are comparatively small; change relative to the modern reconstruction are mainly to biomes characteristic of drier climate in the north of the region with a slight more mesic shift in the south. Cool temperate rain forest remains dominant in western South America. In northwestern South America a number of sites record transitions from tropical seasonal forest to tropical dry forest and tropical rain forest to tropical seasonal forest. Sites in Central America show a change in biome assignment, but to more mesic vegetation, indicative of greater plant available moisture, e.g. on the Yucat??n peninsula sites record warm evergreen forest, replacing tropical dry forest and warm mixed forest presently recorded. At 18 000??1000 14C yr BP 61 samples from 34 sites record vegetation reflecting a generally cool and dry environment. Cool grass/shrubland is prevalent in southeast Brazil whereas Amazonian sites record tropical dry forest, warm temperate rain forest and tropical seasonal forest. Southernmost South America is dominated by cool grass/shrubland, a single site retains cool temperate rain

  13. Quantitative comparison of the in situ microbial communities in different biomes

    SciTech Connect

    White, D.C. |; Ringelberg, D.B.; Palmer, R.J.

    1995-12-31

    A system to define microbial communities in different biomes requires the application of non-traditional methodology. Classical microbiological methods have severe limitations for the analysis of environmental samples. Pure-culture isolation, biochemical testing, and/or enumeration by direct microscopic counting are not well suited for the estimation of total biomass or the assessment of community composition within environmental samples. Such methods provide little insight into the in situ phenotypic activity of the extant microbiota since these techniques are dependent on microbial growth and thus select against many environmental microorganisms which are non- culturable under a wide range of conditions. It has been repeatedly documented in the literature that viable counts or direct counts of bacteria attached to sediment grains are difficult to quantitative and may grossly underestimate the extent of the existing community. The traditional tests provide little indication of the in situ nutritional status or for evidence of toxicity within the microbial community. A more recent development (MIDI Microbial Identification System), measure free and ester-linked fatty acids from isolated microorganisms. Bacterial isolates are identified by comparing their fatty acid profiles to the MIKI database which contains over 8000 entries. The application of the MIKI system to the analysis of environmental samples however, has significant drawbacks. The MIDI system was developed to identify clinical microorganisms and requires their isolation and culture on trypticase soy agar at 27{degrees}C. Since many isolates are unable to grow at these restrictive growth conditions, the system does not lend itself to identification of some environmental organisms. A more applicable methodology for environmental microbial analysis is based on the liquid extrication and separation of microbial lipids from environmental samples, followed by quantitative analysis using gas chromatography/

  14. Quantifying modern biomes based on surface pollen data in China

    NASA Astrophysics Data System (ADS)

    Chen, Yu; Ni, Jian; Herzschuh, Ulrike

    2010-12-01

    Large-scale surface pollen records and reconstructions of modern biomes are a necessary prerequisite for the understanding of past vegetation and climate changes, especially in large countries such as China which is subject to a variety of climatic regimes and has experienced long-term intensive anthropogenic disturbances. An updated surface pollen data set consisting of 2324 samples and 737 taxa is used to reconstruct biome distribution in China according to a newly established and well-tested global classification of plant functional types, based on the regional assessment of pollen taxa and the quantitative pollen-biome assignment method of biomization. Nineteen reconstructed types of biome present a reasonable reflection of the latitudinal and altitudinal distributions of modern vegetation in China. Incorrect assignment has previously occurred in some biomes, for example among the cold and cool temperate coniferous forests and mixed forest, among warm-temperate evergreen forest, mixed forest and tropical forests, and among temperate shrubland, grassland, desert and tundra biomes. Mega-biomes, grouped for the same bioclimatic zones, result in a better reconstruction than the nineteen separate biome types. The correct assignments increased from 68.8% to 80.6%. However, comparison of pollen-based biome reconstructions to climate-driven vegetation simulations performed using the global vegetation model BIOME4 indicates a low correlation rate (only 24.8%), suggesting that more needs to be done to combine palaeoenvironmental data with model simulations of past vegetation changes. The misassignment of surface pollen to modern biomes usually occurs in areas which have similar bioclimatic features and vegetation types and for biomes which share the same plant functional types. These mis-matches often occur in mountainous regions where transitional vegetation zones occur on hill slopes at mid-altitudes. Our new modern biome reconstruction for China is more robust and

  15. A quantitative assessment of a terrestrial biosphere model's data needs across North American biomes

    NASA Astrophysics Data System (ADS)

    Dietze, Michael C.; Serbin, Shawn P.; Davidson, Carl; Desai, Ankur R.; Feng, Xiaohui; Kelly, Ryan; Kooper, Rob; LeBauer, David; Mantooth, Joshua; McHenry, Kenton; Wang, Dan

    2014-03-01

    Terrestrial biosphere models are designed to synthesize our current understanding of how ecosystems function, test competing hypotheses of ecosystem function against observations, and predict responses to novel conditions such as those expected under climate change. Reducing uncertainties in such models can improve both basic scientific understanding and our predictive capacity, but rarely are ecosystem models employed in the design of field campaigns. We provide a synthesis of carbon cycle uncertainty analyses conducted using the Predictive Ecosystem Analyzer ecoinformatics workflow with the Ecosystem Demography model v2. This work is a synthesis of multiple projects, using Bayesian data assimilation techniques to incorporate field data and trait databases across temperate forests, grasslands, agriculture, short rotation forestry, boreal forests, and tundra. We report on a number of data needs that span a wide array of diverse biomes, such as the need for better constraint on growth respiration, mortality, stomatal conductance, and water uptake. We also identify data needs that are biome specific, such as photosynthetic quantum efficiency at high latitudes. We recommend that future data collection efforts balance the bias of past measurements toward aboveground processes in temperate biomes with the sensitivities of different processes as represented by ecosystem models. ©2014. American Geophysical Union. All Rights Reserved.

  16. Biomes of western North America at 18,000, 6000 and 0 14C yr BP reconstructed from pollen and packrat midden data

    USGS Publications Warehouse

    Thompson, R.S.; Anderson, K.H.

    2000-01-01

    A new compilation of pollen and packrat midden data from western North America provides a refined reconstruction of the composition and distribution of biomes in western North America for today and for 6000 and 18,000 radiocarbon years before present (14C yr BP). Modern biomes in western North America are adequately portrayed by pollen assemblages from lakes and bogs. Forest biomes in western North America share many taxa in their pollen spectra and it can be difficult to discriminate among these biomes. Plant macrofossils from packrat middens provide reliable identification of modern biomes from arid and semiarid regions, and this may also be true in similar environments in other parts of the world. However, a weighting factor for trees and shrubs must be used to reliably reconstruct modern biomes from plant macrofossils. A new biome, open conifer woodland, which includes eurythermic conifers and steppe plants, was defined to categorize much of the current and past vegetation of the semiarid interior of western North America. At 6000 14C yr BP, the forest biomes of the coastal Pacific North-west and the desert biomes of the South-west were in near-modern positions. Biomes in the interior Pacific North-west differed from those of today in that taiga prevailed in modern cool/cold mixed forests. Steppe was present in areas occupied today by open conifer woodland in the northern Great Basin, while in the central and southern Rocky Mountains forests grew where steppe grows today. During the mid-Holocene, cool conifer forests were expanded in the Rocky Mountains (relative to today) but contracted in the Sierra Nevada. These differences from the forests of today imply different climatic histories in these two regions between 6000 14C yr BP and today. At 18,000 14C yr BP, deserts were absent from the South-west and the coverage of open conifer woodland was greatly expanded relative to today. Steppe and tundra were present in much of the region now covered by forests in

  17. Towards reconstructing herbaceous biome dynamics and associated precipitation in Africa: insights from the classification of grass morphological traits

    NASA Astrophysics Data System (ADS)

    Pasturel, Marine; Alexandre, Anne; Novello, Alice; Moctar Dieye, Amadou; Wele, Abdoulaye; Paradis, Laure; Hely, Christelle

    2014-05-01

    Inter-tropical herbaceous ecosystems occupy a 1/5th of terrestrial surface, a half of the African continent, and are expected to extend in the next decades. Dynamic of these ecosystems is simulated with poor accuracy by Dynamic Global Vegetation Models (DGVMs). One of the bias results from the fact that the diversity of the grass layer dominating these herbaceous ecosystems is poorly taken into account. Mean annual precipitation and the length of the dry season are the main constrains of the dynamics of these ecosystems. Conversely, changes in vegetation affect the water cycle. Inaccuracy in herbaceous ecosystem simulation thus impacts simulations of the water cycle (including precipitation) and vice versa. In order to increase our knowledge of the relationships between grass morphological traits, taxonomy, biomes and climatic niches in Western and South Africa, a 3-step methodology was followed: i) values of culm height, leaf length and width of dominant grass species from Senegal were gathered from flora and clustered using the Partition Around Medoids (PAM) method; ii) trait group ability to sign climatic domains and biomes was assessed using Kruskal-Wallis tests; iii) genericity and robustness of the trait groups were evaluated through their application to Chadian and South African botanical datasets. Results show that 8 grass trait groups are present either in Senegal, Chad or South Africa. These 8 trait groups are distributed along mean annual precipitation and dry season length gradients. The combination of three of them allow to discriminate mean annual precipitation domains (<250, 250-600, 600-1000 and >1000 mm) and herbaceous biomes (steppes, savannas, South African grasslands and Nama-Karoo). With these results in hand, grass Plant Functional Types (PFTs) of the DGMV LPJ-GUESS will be re-parameterized and particular attention will be given to the herbaceous biomass assigned to each grass trait group. Simultaneously, relationships between grass trait

  18. Quantitative tomography simulations and reconstruction algorithms

    SciTech Connect

    Martz, H E; Aufderheide, M B; Goodman, D; Schach von Wittenau, A; Logan, C; Hall, J; Jackson, J; Slone, D

    2000-11-01

    X-ray, neutron and proton transmission radiography and computed tomography (CT) are important diagnostic tools that are at the heart of LLNLs effort to meet the goals of the DOE's Advanced Radiography Campaign. This campaign seeks to improve radiographic simulation and analysis so that radiography can be a useful quantitative diagnostic tool for stockpile stewardship. Current radiographic accuracy does not allow satisfactory separation of experimental effects from the true features of an object's tomographically reconstructed image. This can lead to difficult and sometimes incorrect interpretation of the results. By improving our ability to simulate the whole radiographic and CT system, it will be possible to examine the contribution of system components to various experimental effects, with the goal of removing or reducing them. In this project, we are merging this simulation capability with a maximum-likelihood (constrained-conjugate-gradient-CCG) reconstruction technique yielding a physics-based, forward-model image-reconstruction code. In addition, we seek to improve the accuracy of computed tomography from transmission radiographs by studying what physics is needed in the forward model. During FY 2000, an improved version of the LLNL ray-tracing code called HADES has been coupled with a recently developed LLNL CT algorithm known as CCG. The problem of image reconstruction is expressed as a large matrix equation relating a model for the object being reconstructed to its projections (radiographs). Using a constrained-conjugate-gradient search algorithm, a maximum likelihood solution is sought. This search continues until the difference between the input measured radiographs or projections and the simulated or calculated projections is satisfactorily small. We developed a 2D HADES-CCG CT code that uses full ray-tracing simulations from HADES as the projector. Often an object has axial symmetry and it is desirable to reconstruct into a 2D r-z mesh with a limited

  19. Surface reconstruction of Pt(001) quantitatively revisited

    NASA Astrophysics Data System (ADS)

    Hammer, R.; Meinel, K.; Krahn, O.; Widdra, W.

    2016-11-01

    The complex hexagonal reconstructions of the (001) surfaces of platinum and gold have been under debate for decades. Here, the structural details of the Pt(001) reconstruction have been quantitatively reinvestigated by combining the high resolving power of scanning tunneling microscopy (STM) and spot profile analysis low energy electron diffraction (SPA-LEED). In addition, LEED simulations based on a Moiré approach have been applied. Annealing temperatures around 850 °C yield a superstructure that approaches a commensurable c (26.6 ×118 ) substrate registry. It evolves from a Moiré-like buckling of a compressed hexagonal top layer (hex) where atomic rows of the hex run parallel to atomic rows of the square substrate. Annealing at 920 °C stimulates a continuous rotation of the hex where all angles between ±0.7° are simultaneously realized. At temperatures around 1080 °C, the nonrotated hex coexists with a hex that is rotated by about 0.75°. Annealing at temperatures around 1120 °C yield a locking of the hex in fixed rotation angles of 0.77°, 0.88°, and 0.94°. At temperatures around 1170 °C, the Pt(001)-hex-R 0.94° prevails as the energetically most favored form of the rotated hex.

  20. Resistance reconstructed estimation of total peripheral resistance from computationally derived cardiac output - biomed 2013.

    PubMed

    Hill, Labarron K; Sollers Iii, John J; Thayer, Julian F

    2013-01-01

    Efficient functioning of the peripheral vasculature is an essential component in healthy cardiovascular regulation. Alterations in this functioning have been linked to the etiology and pathophysiological course of cardiovascular disease (CVD), especially hypertension. Given its significant role in the maintenance of both healthy and pathological blood pressure, total peripheral resistance (TPR), an index of the vasoconstrictive and elastic properties of the peripheral vasculature, has received much attention in this regard. However, obtaining a reliable estimate of TPR remains a complex and costly endeavor, primarily due to the necessity for sophisticated instrumentation as well as associated limitations in deriving cardiac output (CO). We have previously described a simple estimation method for CO using only arterial blood pressure and heart rate (Hill et al, 2012). In the present study we extend this technique to the estimation of TPR using beat-to-beat blood pressure data from the same sample of 67 young (mean age = 20.04± 2.8), healthy men (n = 30) and women (n = 37). Estimated TPR (TPRest) was calculated from the computationally-derived estimate of CO and mean arterial pressure (MAP). Correlation between TPR obtained via the validated Model-Flow technique and TPRest was moderate (r =.73, p <. 000) and stronger in men (r =.78, p <. 000) compared to women (r =.66, p <. 001). These data further suggest that reconstructed measures of hemodynamic functioning may be validly and adequately estimated from limited data sources.

  1. Multigrid-based reconstruction algorithm for quantitative photoacoustic tomography

    PubMed Central

    Li, Shengfu; Montcel, Bruno; Yuan, Zhen; Liu, Wanyu; Vray, Didier

    2015-01-01

    This paper proposes a multigrid inversion framework for quantitative photoacoustic tomography reconstruction. The forward model of optical fluence distribution and the inverse problem are solved at multiple resolutions. A fixed-point iteration scheme is formulated for each resolution and used as a cost function. The simulated and experimental results for quantitative photoacoustic tomography reconstruction show that the proposed multigrid inversion can dramatically reduce the required number of iterations for the optimization process without loss of reliability in the results. PMID:26203371

  2. Quantitative reconstructions in palaeolimnology: new paradigm or sick science?

    NASA Astrophysics Data System (ADS)

    Juggins, Steve

    2013-03-01

    Quantitative reconstructions from biological proxies have revolutionised palaeolimnology but the methodology is not without problems. The most important of these result from attempts to reconstruct non-causal environmental variables and from the effects of secondary variables. Non-causal variables act as surrogates for often unknown or unquantified ecological factors and the method assumes that these relationships are invariant in space and time. This assumption is almost never met and examples of diatom models for water depth and summer temperature demonstrate how violation leads to spurious and misleading reconstructions. In addition, comparison of published species optima indicate that a number of models have little or no predictive power outside their current spatial setting. Finally, experiments using simulated training sets of known properties demonstrate how changes in secondary "nuisance" variables can lead to large, consistent, and interpretable trends in a reconstruction that are completely spurious and independent of any real change in the reconstructed variable. These problems pervade many quantitative reconstructions in palaeolimnology and other disciplines. Palaeoecologists must give greater attention to what can and cannot be reconstructed and explicitly address the dangers of reconstructing surrogate and confounded variables if our reconstructions are to remain credible.

  3. Quantitative photoacoustic image reconstruction improves accuracy in deep tissue structures.

    PubMed

    Mastanduno, Michael A; Gambhir, Sanjiv S

    2016-10-01

    Photoacoustic imaging (PAI) is emerging as a potentially powerful imaging tool with multiple applications. Image reconstruction for PAI has been relatively limited because of limited or no modeling of light delivery to deep tissues. This work demonstrates a numerical approach to quantitative photoacoustic image reconstruction that minimizes depth and spectrally derived artifacts. We present the first time-domain quantitative photoacoustic image reconstruction algorithm that models optical sources through acoustic data to create quantitative images of absorption coefficients. We demonstrate quantitative accuracy of less than 5% error in large 3 cm diameter 2D geometries with multiple targets and within 22% error in the largest size quantitative photoacoustic studies to date (6cm diameter). We extend the algorithm to spectral data, reconstructing 6 varying chromophores to within 17% of the true values. This quantitiative PA tomography method was able to improve considerably on filtered-back projection from the standpoint of image quality, absolute, and relative quantification in all our simulation geometries. We characterize the effects of time step size, initial guess, and source configuration on final accuracy. This work could help to generate accurate quantitative images from both endogenous absorbers and exogenous photoacoustic dyes in both preclinical and clinical work, thereby increasing the information content obtained especially from deep-tissue photoacoustic imaging studies.

  4. Quantitative photoacoustic image reconstruction improves accuracy in deep tissue structures

    PubMed Central

    Mastanduno, Michael A.; Gambhir, Sanjiv S.

    2016-01-01

    Photoacoustic imaging (PAI) is emerging as a potentially powerful imaging tool with multiple applications. Image reconstruction for PAI has been relatively limited because of limited or no modeling of light delivery to deep tissues. This work demonstrates a numerical approach to quantitative photoacoustic image reconstruction that minimizes depth and spectrally derived artifacts. We present the first time-domain quantitative photoacoustic image reconstruction algorithm that models optical sources through acoustic data to create quantitative images of absorption coefficients. We demonstrate quantitative accuracy of less than 5% error in large 3 cm diameter 2D geometries with multiple targets and within 22% error in the largest size quantitative photoacoustic studies to date (6cm diameter). We extend the algorithm to spectral data, reconstructing 6 varying chromophores to within 17% of the true values. This quantitiative PA tomography method was able to improve considerably on filtered-back projection from the standpoint of image quality, absolute, and relative quantification in all our simulation geometries. We characterize the effects of time step size, initial guess, and source configuration on final accuracy. This work could help to generate accurate quantitative images from both endogenous absorbers and exogenous photoacoustic dyes in both preclinical and clinical work, thereby increasing the information content obtained especially from deep-tissue photoacoustic imaging studies. PMID:27867695

  5. Impact of reconstruction parameters on quantitative I-131 SPECT

    NASA Astrophysics Data System (ADS)

    van Gils, C. A. J.; Beijst, C.; van Rooij, R.; de Jong, H. W. A. M.

    2016-07-01

    Radioiodine therapy using I-131 is widely used for treatment of thyroid disease or neuroendocrine tumors. Monitoring treatment by accurate dosimetry requires quantitative imaging. The high energy photons however render quantitative SPECT reconstruction challenging, potentially requiring accurate correction for scatter and collimator effects. The goal of this work is to assess the effectiveness of various correction methods on these effects using phantom studies. A SPECT/CT acquisition of the NEMA IEC body phantom was performed. Images were reconstructed using the following parameters: (1) without scatter correction, (2) with triple energy window (TEW) scatter correction and (3) with Monte Carlo-based scatter correction. For modelling the collimator-detector response (CDR), both (a) geometric Gaussian CDRs as well as (b) Monte Carlo simulated CDRs were compared. Quantitative accuracy, contrast to noise ratios and recovery coefficients were calculated, as well as the background variability and the residual count error in the lung insert. The Monte Carlo scatter corrected reconstruction method was shown to be intrinsically quantitative, requiring no experimentally acquired calibration factor. It resulted in a more accurate quantification of the background compartment activity density compared with TEW or no scatter correction. The quantification error relative to a dose calibrator derived measurement was found to be  <1%,-26% and 33%, respectively. The adverse effects of partial volume were significantly smaller with the Monte Carlo simulated CDR correction compared with geometric Gaussian or no CDR modelling. Scatter correction showed a small effect on quantification of small volumes. When using a weighting factor, TEW correction was comparable to Monte Carlo reconstruction in all measured parameters, although this approach is clinically impractical since this factor may be patient dependent. Monte Carlo based scatter correction including accurately simulated CDR

  6. Impact of reconstruction parameters on quantitative I-131 SPECT.

    PubMed

    van Gils, C A J; Beijst, C; van Rooij, R; de Jong, H W A M

    2016-07-21

    Radioiodine therapy using I-131 is widely used for treatment of thyroid disease or neuroendocrine tumors. Monitoring treatment by accurate dosimetry requires quantitative imaging. The high energy photons however render quantitative SPECT reconstruction challenging, potentially requiring accurate correction for scatter and collimator effects. The goal of this work is to assess the effectiveness of various correction methods on these effects using phantom studies. A SPECT/CT acquisition of the NEMA IEC body phantom was performed. Images were reconstructed using the following parameters: (1) without scatter correction, (2) with triple energy window (TEW) scatter correction and (3) with Monte Carlo-based scatter correction. For modelling the collimator-detector response (CDR), both (a) geometric Gaussian CDRs as well as (b) Monte Carlo simulated CDRs were compared. Quantitative accuracy, contrast to noise ratios and recovery coefficients were calculated, as well as the background variability and the residual count error in the lung insert. The Monte Carlo scatter corrected reconstruction method was shown to be intrinsically quantitative, requiring no experimentally acquired calibration factor. It resulted in a more accurate quantification of the background compartment activity density compared with TEW or no scatter correction. The quantification error relative to a dose calibrator derived measurement was found to be  <1%,-26% and 33%, respectively. The adverse effects of partial volume were significantly smaller with the Monte Carlo simulated CDR correction compared with geometric Gaussian or no CDR modelling. Scatter correction showed a small effect on quantification of small volumes. When using a weighting factor, TEW correction was comparable to Monte Carlo reconstruction in all measured parameters, although this approach is clinically impractical since this factor may be patient dependent. Monte Carlo based scatter correction including accurately simulated CDR

  7. Accuracy of quantitative reconstructions in SPECT/CT imaging

    NASA Astrophysics Data System (ADS)

    Shcherbinin, S.; Celler, A.; Belhocine, T.; van der Werf, R.; Driedger, A.

    2008-09-01

    The goal of this study was to determine the quantitative accuracy of our OSEM-APDI reconstruction method based on SPECT/CT imaging for Tc-99m, In-111, I-123, and I-131 isotopes. Phantom studies were performed on a SPECT/low-dose multislice CT system (Infinia-Hawkeye-4 slice, GE Healthcare) using clinical acquisition protocols. Two radioactive sources were centrally and peripherally placed inside an anthropometric Thorax phantom filled with non-radioactive water. Corrections for attenuation, scatter, collimator blurring and collimator septal penetration were applied and their contribution to the overall accuracy of the reconstruction was evaluated. Reconstruction with the most comprehensive set of corrections resulted in activity estimation with error levels of 3-5% for all the isotopes.

  8. Single-stage reconstruction algorithm for quantitative photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Haltmeier, Markus; Neumann, Lukas; Rabanser, Simon

    2015-06-01

    The development of efficient and accurate image reconstruction algorithms is one of the cornerstones of computed tomography. Existing algorithms for quantitative photoacoustic tomography (qPAT) currently operate in a two-stage procedure: first an inverse source problem for the acoustic wave propagation is solved, whereas in a second step the optical parameters are estimated from the result of the first step. Such an approach has several drawbacks. In this paper we therefore propose the use of single-stage reconstruction algorithms for qPAT, where the optical parameters are directly reconstructed from the observed acoustical data. In that context we formulate the image reconstruction problem of qPAT as a single nonlinear inverse problem by coupling the radiative transfer equation with the acoustic wave equation. The inverse problem is approached by Tikhonov regularization with a convex penalty in combination with the proximal gradient iteration for minimizing the Tikhonov functional. We present numerical results, where the proposed single-stage algorithm shows an improved reconstruction quality at a similar computational cost.

  9. Concluding Report: Quantitative Tomography Simulations and Reconstruction Algorithms

    SciTech Connect

    Aufderheide, M B; Martz, H E; Slone, D M; Jackson, J A; Schach von Wittenau, A E; Goodman, D M; Logan, C M; Hall, J M

    2002-02-01

    In this report we describe the original goals and final achievements of this Laboratory Directed Research and Development project. The Quantitative was Tomography Simulations and Reconstruction Algorithms project (99-ERD-015) funded as a multi-directorate, three-year effort to advance the state of the art in radiographic simulation and tomographic reconstruction by improving simulation and including this simulation in the tomographic reconstruction process. Goals were to improve the accuracy of radiographic simulation, and to couple advanced radiographic simulation tools with a robust, many-variable optimization algorithm. In this project, we were able to demonstrate accuracy in X-Ray simulation at the 2% level, which is an improvement of roughly a factor of 5 in accuracy, and we have successfully coupled our simulation tools with the CCG (Constrained Conjugate Gradient) optimization algorithm, allowing reconstructions that include spectral effects and blurring in the reconstructions. Another result of the project was the assembly of a low-scatter X-Ray imaging facility for use in nondestructive evaluation applications. We conclude with a discussion of future work.

  10. Quantitative image quality evaluation for cardiac CT reconstructions

    NASA Astrophysics Data System (ADS)

    Tseng, Hsin-Wu; Fan, Jiahua; Kupinski, Matthew A.; Balhorn, William; Okerlund, Darin R.

    2016-03-01

    Maintaining image quality in the presence of motion is always desirable and challenging in clinical Cardiac CT imaging. Different image-reconstruction algorithms are available on current commercial CT systems that attempt to achieve this goal. It is widely accepted that image-quality assessment should be task-based and involve specific tasks, observers, and associated figures of merits. In this work, we developed an observer model that performed the task of estimating the percentage of plaque in a vessel from CT images. We compared task performance of Cardiac CT image data reconstructed using a conventional FBP reconstruction algorithm and the SnapShot Freeze (SSF) algorithm, each at default and optimal reconstruction cardiac phases. The purpose of this work is to design an approach for quantitative image-quality evaluation of temporal resolution for Cardiac CT systems. To simulate heart motion, a moving coronary type phantom synchronized with an ECG signal was used. Three different percentage plaques embedded in a 3 mm vessel phantom were imaged multiple times under motion free, 60 bpm, and 80 bpm heart rates. Static (motion free) images of this phantom were taken as reference images for image template generation. Independent ROIs from the 60 bpm and 80 bpm images were generated by vessel tracking. The observer performed estimation tasks using these ROIs. Ensemble mean square error (EMSE) was used as the figure of merit. Results suggest that the quality of SSF images is superior to the quality of FBP images in higher heart-rate scans.

  11. Quantitative analysis of the reconstruction performance of interpolants

    NASA Technical Reports Server (NTRS)

    Lansing, Donald L.; Park, Stephen K.

    1987-01-01

    The analysis presented provides a quantitative measure of the reconstruction or interpolation performance of linear, shift-invariant interpolants. The performance criterion is the mean square error of the difference between the sampled and reconstructed functions. The analysis is applicable to reconstruction algorithms used in image processing and to many types of splines used in numerical analysis and computer graphics. When formulated in the frequency domain, the mean square error clearly separates the contribution of the interpolation method from the contribution of the sampled data. The equations provide a rational basis for selecting an optimal interpolant; that is, one which minimizes the mean square error. The analysis has been applied to a selection of frequently used data splines and reconstruction algorithms: parametric cubic and quintic Hermite splines, exponential and nu splines (including the special case of the cubic spline), parametric cubic convolution, Keys' fourth-order cubic, and a cubic with a discontinuous first derivative. The emphasis in this paper is on the image-dependent case in which no a priori knowledge of the frequency spectrum of the sampled function is assumed.

  12. Quantitative Monte Carlo-based holmium-166 SPECT reconstruction.

    PubMed

    Elschot, Mattijs; Smits, Maarten L J; Nijsen, Johannes F W; Lam, Marnix G E H; Zonnenberg, Bernard A; van den Bosch, Maurice A A J; Viergever, Max A; de Jong, Hugo W A M

    2013-11-01

    Quantitative imaging of the radionuclide distribution is of increasing interest for microsphere radioembolization (RE) of liver malignancies, to aid treatment planning and dosimetry. For this purpose, holmium-166 ((166)Ho) microspheres have been developed, which can be visualized with a gamma camera. The objective of this work is to develop and evaluate a new reconstruction method for quantitative (166)Ho SPECT, including Monte Carlo-based modeling of photon contributions from the full energy spectrum. A fast Monte Carlo (MC) simulator was developed for simulation of (166)Ho projection images and incorporated in a statistical reconstruction algorithm (SPECT-fMC). Photon scatter and attenuation for all photons sampled from the full (166)Ho energy spectrum were modeled during reconstruction by Monte Carlo simulations. The energy- and distance-dependent collimator-detector response was modeled using precalculated convolution kernels. Phantom experiments were performed to quantitatively evaluate image contrast, image noise, count errors, and activity recovery coefficients (ARCs) of SPECT-fMC in comparison with those of an energy window-based method for correction of down-scattered high-energy photons (SPECT-DSW) and a previously presented hybrid method that combines MC simulation of photopeak scatter with energy window-based estimation of down-scattered high-energy contributions (SPECT-ppMC+DSW). Additionally, the impact of SPECT-fMC on whole-body recovered activities (A(est)) and estimated radiation absorbed doses was evaluated using clinical SPECT data of six (166)Ho RE patients. At the same noise level, SPECT-fMC images showed substantially higher contrast than SPECT-DSW and SPECT-ppMC+DSW in spheres ≥ 17 mm in diameter. The count error was reduced from 29% (SPECT-DSW) and 25% (SPECT-ppMC+DSW) to 12% (SPECT-fMC). ARCs in five spherical volumes of 1.96-106.21 ml were improved from 32%-63% (SPECT-DSW) and 50%-80% (SPECT-ppMC+DSW) to 76%-103% (SPECT-fMC). Furthermore

  13. Quantitative Monte Carlo-based holmium-166 SPECT reconstruction

    SciTech Connect

    Elschot, Mattijs; Smits, Maarten L. J.; Nijsen, Johannes F. W.; Lam, Marnix G. E. H.; Zonnenberg, Bernard A.; Bosch, Maurice A. A. J. van den; Jong, Hugo W. A. M. de; Viergever, Max A.

    2013-11-15

    Purpose: Quantitative imaging of the radionuclide distribution is of increasing interest for microsphere radioembolization (RE) of liver malignancies, to aid treatment planning and dosimetry. For this purpose, holmium-166 ({sup 166}Ho) microspheres have been developed, which can be visualized with a gamma camera. The objective of this work is to develop and evaluate a new reconstruction method for quantitative {sup 166}Ho SPECT, including Monte Carlo-based modeling of photon contributions from the full energy spectrum.Methods: A fast Monte Carlo (MC) simulator was developed for simulation of {sup 166}Ho projection images and incorporated in a statistical reconstruction algorithm (SPECT-fMC). Photon scatter and attenuation for all photons sampled from the full {sup 166}Ho energy spectrum were modeled during reconstruction by Monte Carlo simulations. The energy- and distance-dependent collimator-detector response was modeled using precalculated convolution kernels. Phantom experiments were performed to quantitatively evaluate image contrast, image noise, count errors, and activity recovery coefficients (ARCs) of SPECT-fMC in comparison with those of an energy window-based method for correction of down-scattered high-energy photons (SPECT-DSW) and a previously presented hybrid method that combines MC simulation of photopeak scatter with energy window-based estimation of down-scattered high-energy contributions (SPECT-ppMC+DSW). Additionally, the impact of SPECT-fMC on whole-body recovered activities (A{sup est}) and estimated radiation absorbed doses was evaluated using clinical SPECT data of six {sup 166}Ho RE patients.Results: At the same noise level, SPECT-fMC images showed substantially higher contrast than SPECT-DSW and SPECT-ppMC+DSW in spheres ≥17 mm in diameter. The count error was reduced from 29% (SPECT-DSW) and 25% (SPECT-ppMC+DSW) to 12% (SPECT-fMC). ARCs in five spherical volumes of 1.96–106.21 ml were improved from 32%–63% (SPECT-DSW) and 50%–80

  14. DISQOVER the Landcover - R based tools for quantitative vegetation reconstruction

    NASA Astrophysics Data System (ADS)

    Theuerkauf, Martin; Couwenberg, John; Kuparinen, Anna; Liebscher, Volkmar

    2016-04-01

    Quantitative methods have gained increasing attention in the field of vegetation reconstruction over the past decade. The DISQOVER package implements key tools in the R programming environment for statistical computing. This implementation has three main goals: 1) Provide a user-friendly, transparent, and open implementation of the methods 2) Provide full flexibility in all parameters (including the underlying pollen dispersal model) 3) Provide a sandbox for testing the sensitivity of the methods. We illustrate the possibilities of the package with tests of the REVEALS model and of the extended downscaling approach (EDA). REVEALS (Sugita 2007) is designed to translate pollen data from large lakes into regional vegetation composition. We applied REVEALSinR on pollen data from Lake Tiefer See (NE-Germany) and validated the results with historic landcover data. The results clearly show that REVEALS is sensitive to the underlying pollen dispersal model; REVEALS performs best when applied with the state of the art Lagrangian stochastic dispersal model. REVEALS applications with the conventional Gauss model can produce realistic results, but only if unrealistic pollen productivity estimates are used. The EDA (Theuerkauf et al. 2014) employs pollen data from many sites across a landscape to explore whether species distributions in the past were related to know stable patterns in the landscape, e.g. the distribution of soil types. The approach had so far only been implemented in simple settings with few taxa. Tests with EDAinR show that it produces sharp results in complex settings with many taxa as well. The DISQOVER package is open source software, available from disqover.uni-greifswald.de. This website can be used as a platform to discuss and improve quantitative methods in vegetation reconstruction. To introduce the tool we plan a short course in autumn of this year. This study is a contribution to the Virtual Institute of Integrated Climate and Landscape Evolution

  15. Methodological basis for quantitative reconstruction of air temperature and sunshine from pollen assemblages in Arctic Canada and Greenland

    NASA Astrophysics Data System (ADS)

    Fréchette, Bianca; de Vernal, Anne; Guiot, Joël; Wolfe, Alexander P.; Miller, Gifford H.; Fredskild, Bent; Kerwin, Micheal W.; Richard, Pierre J. H.

    2008-06-01

    This study presents a modern database including 831 pollen assemblages from lakes of the Boreal, Subarctic and Arctic biomes of North America and Greenland, and corresponding temperature, sunshine and precipitation. Pollen data include the 39 most common vascular taxa (18 woody plants and 21 herbs). Multivariate ordinations using correspondence analysis (CA) and canonical correspondence analysis (CCA) reveal that temperature and sunshine account, respectively, for 45.5% and 44.4% of the variance within pollen assemblages, whereas precipitation only accounts for 10.2% of total variance. CCA further demonstrates that the climatic information encapsulated in pollen assemblages is not the same for the three biomes. In the Boreal biome, precipitation and temperature account for most of the variance, whereas sunshine and precipitation are more determinant in the Subarctic biome, and the temperature and sunshine seem to exert the main control on the pollen distribution in the Arctic biome. The modern analogue technique (MAT) and CCA regressions were tested for reconstructing climate parameters. MAT yields better results than CCA regressions and validation tests indicate a root mean square error (RMSE) of 1.35 °C for July air temperature, 2.3% for July sunshine, 3.10 °C for January air temperature and 143 mm for annual precipitation. Two examples of reconstructions are presented from recent (<450 years) lake-sediment cores of eastern Baffin Island, Arctic Canada and southwest Greenland. They demonstrate that July air temperature and July sunshine can be reconstructed independently from Arctic pollen assemblages, but January air temperature and annual precipitation must be interpreted with caution. They also suggest that reconstruction of past sunshine variations can serve to document climate changes at synoptic scale including the North Atlantic Oscillation (NAO).

  16. QUANTITATIVE PALEOCLIMATE RECONSTRUCTIONS FROM THE MELVILLE PENINSULA, NUNAVUT, CANADA

    NASA Astrophysics Data System (ADS)

    Adams, J. K.; Finkelstein, S. A.

    2009-12-01

    : Staurosira construens var. venter from 650 to 330 yrs BP may indicate the Little Ice Age (LIA) on the Peninsula, which closely coincides temporally with proxy-based reconstructions of the LIA from Boothia Peninsula to the west. Changes consistent with recent warming of SP02 began 225 yrs BP, including increased diatom concentration and increased species richness from pre-industrial maximum of 28 to 51 species in the modern assemblage. About 160 yrs BP, species richness increases in SP04 from pre-industrial maximum of 20 to 37 species in the modern assemblage. The diatom genera Achnanthes and Cymbella diversify in the past century, while Cyclotella spp. appear in SP04 44 yrs BP and SP02 -20 yrs BP (AD 1970), indicating longer ice-free seasons. Diatom-inferred quantitative pH reconstructions using transfer functions for the two study lakes did not indicate significant change in the Holocene despite assemblage changes. The lack of sensitivity in the transfer functions may be due to the need for high taxonomic resolution when analyzing fossil and modern diatoms (particularly Fragilarioids which dominate many Arctic lakes), or pervasive human impacts in the Arctic leading to a lack of modern analogues for fossil assemblages.

  17. Quantitative tectonic reconstructions of Zealandia based on crustal thickness estimates

    NASA Astrophysics Data System (ADS)

    Grobys, Jan W. G.; Gohl, Karsten; Eagles, Graeme

    2008-01-01

    Zealandia is a key piece in the plate reconstruction of Gondwana. The positions of its submarine plateaus are major constraints on the best fit and breakup involving New Zealand, Australia, Antarctica, and associated microplates. As the submarine plateaus surrounding New Zealand consist of extended and highly extended continental crust, classic plate tectonic reconstructions assuming rigid plates and narrow plate boundaries fail to reconstruct these areas correctly. However, if the early breakup history shall be reconstructed, it is crucial to consider crustal stretching in a plate-tectonic reconstruction. We present a reconstruction of the basins around New Zealand (Great South Basin, Bounty Trough, and New Caledonia Basin) based on crustal balancing, an approach that takes into account the rifting and thinning processes affecting continental crust. In a first step, we computed a crustal thickness map of Zealandia using seismic, seismological, and gravity data. The crustal thickness map shows the submarine plateaus to have a uniform crustal thickness of 20-24 km and the basins to have a thickness of 12-16 km. We assumed that a reconstruction of Zealandia should close the basins and lead to a most uniform crustal thickness. We used the standard deviation of the reconstructed crustal thickness as a measure of uniformity. The reconstruction of the Campbell Plateau area shows that the amount of extension in the Bounty Trough and the Great South Basin is far smaller than previously thought. Our results indicate that the extension of the Bounty Trough and Great South Basin occurred simultaneously.

  18. North American Biome

    USDA-ARS?s Scientific Manuscript database

    The North America biome includes the major ecoregions that make up the land area of Canada, the United States, Mexico, and countries in Central America. The biome is bordered to the north by the Arctic Ocean, to the east by the Atlantic Ocean, to the west and south by the Pacific Ocean, and to the s...

  19. Application study of transport intensity equation in quantitative phase reconstruction

    NASA Astrophysics Data System (ADS)

    Song, Xiaojun; Cheng, Wei; Wei, Chunjuan; Xue, Liang; Liu, Weijing; Bai, Baodan; Chu, Fenghong

    2016-10-01

    In order to improve detection speed and accuracy of biological cells, a quantitative non-interference optical phase recovery method is proposed in commercial microscope, taking the red blood cells as the classical phase objects. Three bright field micrographs were collected in the experiment. Utilizing the transport intensity equation (TIE), the quantitative phase distributions of red blood cell are gained and agree well with the previous optical phase models. Analysis shows that the resolution of introduced system reaches sub-micron. This method not only quickly gives quantitative phase distribution of cells, but also measures a large number of cells simultaneously. So it is potential in the use of real-time observing and quantitative analyzing of cells in vivo.

  20. Quantitative Reconstructions of Beringian Climates from Pollen Assemblages

    NASA Astrophysics Data System (ADS)

    Gajewski, K.; Sawada, M. C.; Viau, A. E.

    2004-12-01

    We reconstructed mean July temperature for the past 30 000 years at Zagoskin Lake (Ager. 2003. Quat Res 60:19) using the Modern Analogue Technique (MAT). Calibration was done using a dataset of 4549 modern pollen samples from across North America, with a pollen sum of 106 pollen taxa. Reconstructed temperatures show a cold full-glacial, warming in the late-glacial and early Holocene and a warm Holocene. Experimentation showed the results are robust with respect to various decisions that can be made in application of the method. Although many of the samples in the full-glacial could be considered non-analogue, the temperatures estimated are reasonable, and comparable to those estimated at samples that are considered analogue. Further, these samples are not greatly deviant when ordinated with modern samples from northern Canada and Alaska.

  1. Reconstructing palaeoclimatic variables from fossil pollen using boosted regression trees: comparison and synthesis with other quantitative reconstruction methods

    NASA Astrophysics Data System (ADS)

    Salonen, J. Sakari; Luoto, Miska; Alenius, Teija; Heikkilä, Maija; Seppä, Heikki; Telford, Richard J.; Birks, H. John B.

    2014-03-01

    We test and analyse a new calibration method, boosted regression trees (BRTs) in palaeoclimatic reconstructions based on fossil pollen assemblages. We apply BRTs to multiple Holocene and Lateglacial pollen sequences from northern Europe, and compare their performance with two commonly-used calibration methods: weighted averaging regression (WA) and the modern-analogue technique (MAT). Using these calibration methods and fossil pollen data, we present synthetic reconstructions of Holocene summer temperature, winter temperature, and water balance changes in northern Europe. Highly consistent trends are found for summer temperature, with a distinct Holocene thermal maximum at ca 8000-4000 cal. a BP, with a mean Tjja anomaly of ca +0.7 °C at 6 ka compared to 0.5 ka. We were unable to reconstruct reliably winter temperature or water balance, due to the confounding effects of summer temperature and the great between-reconstruction variability. We find BRTs to be a promising tool for quantitative reconstructions from palaeoenvironmental proxy data. BRTs show good performance in cross-validations compared with WA and MAT, can model a variety of taxon response types, find relevant predictors and incorporate interactions between predictors, and show some robustness with non-analogue fossil assemblages.

  2. Quantitative Reconstructions of 3D Chemical Nanostructures in Nanowires.

    PubMed

    Rueda-Fonseca, P; Robin, E; Bellet-Amalric, E; Lopez-Haro, M; Den Hertog, M; Genuist, Y; André, R; Artioli, A; Tatarenko, S; Ferrand, D; Cibert, J

    2016-03-09

    Energy dispersive X-ray spectrometry is used to extract a quantitative 3D composition profile of heterostructured nanowires. The analysis of hypermaps recorded along a limited number of projections, with a preliminary calibration of the signal associated with each element, is compared to the intensity profiles calculated for a model structure with successive shells of circular, elliptic, or faceted cross sections. This discrete tomographic technique is applied to II-VI nanowires grown by molecular beam epitaxy, incorporating ZnTe and CdTe and their alloys with Mn and Mg, with typical size down to a few nanometers and Mn or Mg content as low as 10%.

  3. Comparison of reconstruction methods and quantitative accuracy in Siemens Inveon PET scanner

    NASA Astrophysics Data System (ADS)

    Ram Yu, A.; Kim, Jin Su; Kang, Joo Hyun; Moo Lim, Sang

    2015-04-01

    concentrations for radioactivity Our data collectively showed that OSEM 2D reconstruction method provides quantitatively accurate reconstructed PET data results.

  4. Optimal reconstruction and quantitative image features for computer-aided diagnosis tools for breast CT.

    PubMed

    Lee, Juhun; Nishikawa, Robert M; Reiser, Ingrid; Boone, John M

    2017-05-01

    The purpose of this study is to determine the optimal representative reconstruction and quantitative image feature set for a computer-aided diagnosis (CADx) scheme for dedicated breast computer tomography (bCT). We used 93 bCT scans that contain 102 breast lesions (62 malignant, 40 benign). Using an iterative image reconstruction (IIR) algorithm, we created 37 reconstructions with different image appearances for each case. In addition, we added a clinical reconstruction for comparison purposes. We used image sharpness, determined by the gradient of gray value in a parenchymal portion of the reconstructed breast, as a surrogate measure of the image qualities/appearances for the 38 reconstructions. After segmentation of the breast lesion, we extracted 23 quantitative image features. Using leave-one-out-cross-validation (LOOCV), we conducted the feature selection, classifier training, and testing. For this study, we used the linear discriminant analysis classifier. Then, we selected the representative reconstruction and feature set for the classifier with the best diagnostic performance among all reconstructions and feature sets. Then, we conducted an observer study with six radiologists using a subset of breast lesions (N = 50). Using 1000 bootstrap samples, we compared the diagnostic performance of the trained classifier to those of the radiologists. The diagnostic performance of the trained classifier increased as the image sharpness of a given reconstruction increased. Among combinations of reconstructions and quantitative image feature sets, we selected one of the sharp reconstructions and three quantitative image feature sets with the first three highest diagnostic performances under LOOCV as the representative reconstruction and feature set for the classifier. The classifier on the representative reconstruction and feature set achieved better diagnostic performance with an area under the ROC curve (AUC) of 0.94 (95% CI = [0.81, 0.98]) than those of the

  5. Quantitative study on exact reconstruction sampling condition by verifying solution uniqueness in limited-view CT.

    PubMed

    Yan, Bin; Zhang, Wenkun; Li, Lei; Zhang, Hanming; Wang, Linyuan

    2016-10-01

    In limited-view computed tomography reconstruction, iterative image reconstruction with sparsity-exploiting methods, such as total variation (TV) minimization, inspired by compressive sensing, potentially claims large reductions in sampling requirements. However, a quantitative notion of this claim is non-trivial because of the ill-defined reduction in sampling achieved by the sparsity-exploiting method. In this paper, exact reconstruction sampling condition for limited-view problem is studied by verifying the uniqueness of solution in TV minimization model. Uniqueness is tested by solving a convex optimization problem derived from the sufficient and necessary condition of solution uniqueness. Through this method, the sufficient sampling number of exact reconstruction is quantified for any fixed phantom and settled geometrical parameter in the limited-view problem. This paper provides a reference to quantify the sampling condition. Three phantoms are tested to study the sampling condition of limited view exact reconstruction in this paper. The experiment results show the quantified sampling number and indicate that an object would be accurately reconstructed as the scanning range becomes narrower by increasing sampling number. The increased samplings compensate for the deficiency of the projection angle. However, the lower bound of the scanning range corresponding to three different phantoms are presented, in which an exact reconstruction cannot be obtained once the projection angular is narrowed to this extent no matter how to increase sampling. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  6. An efficient polyenergetic SART (pSART) reconstruction algorithm for quantitative myocardial CT perfusion

    SciTech Connect

    Lin, Yuan Samei, Ehsan

    2014-02-15

    Purpose: In quantitative myocardial CT perfusion imaging, beam hardening effect due to dense bone and high concentration iodinated contrast agent can result in visible artifacts and inaccurate CT numbers. In this paper, an efficient polyenergetic Simultaneous Algebraic Reconstruction Technique (pSART) was presented to eliminate the beam hardening artifacts and to improve the CT quantitative imaging ability. Methods: Our algorithm made threea priori assumptions: (1) the human body is composed of several base materials (e.g., fat, breast, soft tissue, bone, and iodine); (2) images can be coarsely segmented to two types of regions, i.e., nonbone regions and noniodine regions; and (3) each voxel can be decomposed into a mixture of two most suitable base materials according to its attenuation value and its corresponding region type information. Based on the above assumptions, energy-independent accumulated effective lengths of all base materials can be fast computed in the forward ray-tracing process and be used repeatedly to obtain accurate polyenergetic projections, with which a SART-based equation can correctly update each voxel in the backward projecting process to iteratively reconstruct artifact-free images. This approach effectively reduces the influence of polyenergetic x-ray sources and it further enables monoenergetic images to be reconstructed at any arbitrarily preselected target energies. A series of simulation tests were performed on a size-variable cylindrical phantom and a realistic anthropomorphic thorax phantom. In addition, a phantom experiment was also performed on a clinical CT scanner to further quantitatively validate the proposed algorithm. Results: The simulations with the cylindrical phantom and the anthropomorphic thorax phantom showed that the proposed algorithm completely eliminated beam hardening artifacts and enabled quantitative imaging across different materials, phantom sizes, and spectra, as the absolute relative errors were reduced

  7. An efficient polyenergetic SART (pSART) reconstruction algorithm for quantitative myocardial CT perfusion

    SciTech Connect

    Lin, Yuan Samei, Ehsan

    2014-02-15

    Purpose: In quantitative myocardial CT perfusion imaging, beam hardening effect due to dense bone and high concentration iodinated contrast agent can result in visible artifacts and inaccurate CT numbers. In this paper, an efficient polyenergetic Simultaneous Algebraic Reconstruction Technique (pSART) was presented to eliminate the beam hardening artifacts and to improve the CT quantitative imaging ability. Methods: Our algorithm made threea priori assumptions: (1) the human body is composed of several base materials (e.g., fat, breast, soft tissue, bone, and iodine); (2) images can be coarsely segmented to two types of regions, i.e., nonbone regions and noniodine regions; and (3) each voxel can be decomposed into a mixture of two most suitable base materials according to its attenuation value and its corresponding region type information. Based on the above assumptions, energy-independent accumulated effective lengths of all base materials can be fast computed in the forward ray-tracing process and be used repeatedly to obtain accurate polyenergetic projections, with which a SART-based equation can correctly update each voxel in the backward projecting process to iteratively reconstruct artifact-free images. This approach effectively reduces the influence of polyenergetic x-ray sources and it further enables monoenergetic images to be reconstructed at any arbitrarily preselected target energies. A series of simulation tests were performed on a size-variable cylindrical phantom and a realistic anthropomorphic thorax phantom. In addition, a phantom experiment was also performed on a clinical CT scanner to further quantitatively validate the proposed algorithm. Results: The simulations with the cylindrical phantom and the anthropomorphic thorax phantom showed that the proposed algorithm completely eliminated beam hardening artifacts and enabled quantitative imaging across different materials, phantom sizes, and spectra, as the absolute relative errors were reduced

  8. Holocene changes in vegetation composition in northern Europe: why quantitative pollen-based vegetation reconstructions matter

    NASA Astrophysics Data System (ADS)

    Marquer, Laurent; Gaillard, Marie-José; Sugita, Shinya; Trondman, Anna-Kari; Mazier, Florence; Nielsen, Anne Birgitte; Fyfe, Ralph M.; Odgaard, Bent Vad; Alenius, Teija; Birks, H. John B.; Bjune, Anne E.; Christiansen, Jörg; Dodson, John; Edwards, Kevin J.; Giesecke, Thomas; Herzschuh, Ulrike; Kangur, Mihkel; Lorenz, Sebastian; Poska, Anneli; Schult, Manuela; Seppä, Heikki

    2014-04-01

    We present pollen-based reconstructions of the spatio-temporal dynamics of northern European regional vegetation abundance through the Holocene. We apply the Regional Estimates of VEgetation Abundance from Large Sites (REVEALS) model using fossil pollen records from eighteen sites within five modern biomes in the region. The eighteen sites are classified into four time-trajectory types on the basis of principal components analysis of both the REVEALS-based vegetation estimates (RVs) and the pollen percentage (PPs). The four trajectory types are more clearly separated for RVs than PPs. Further, the timing of major Holocene shifts, rates of compositional change, and diversity indices (turnover and evenness) differ between RVs and PPs. The differences are due to the reduction by REVEALS of biases in fossil pollen assemblages caused by different basin size, and inter-taxonomic differences in pollen productivity and dispersal properties. For example, in comparison to the PPs, the RVs show an earlier increase in Corylus and Ulmus in the early-Holocene and a more pronounced increase in grassland and deforested areas since the mid-Holocene. The results suggest that the influence of deforestation and agricultural activities on plant composition and abundance from Neolithic times was stronger than previously inferred from PPs. Relative to PPs, RVs show a more rapid compositional change, a largest decrease in turnover, and less variable evenness in most of northern Europe since 5200 cal yr BP. All these changes are primarily related to the strong impact of human activities on the vegetation. This study demonstrates that RV-based estimates of diversity indices, timing of shifts, and rates of change in reconstructed vegetation provide new insights into the timing and magnitude of major human disturbance on Holocene regional vegetation, features that are critical in the assessment of human impact on vegetation, land-cover, biodiversity, and climate in the past.

  9. Quantitative SPECT/CT reconstruction for 177Lu and 177Lu/90Y targeted radionuclide therapies

    NASA Astrophysics Data System (ADS)

    Shcherbinin, S.; Piwowarska-Bilska, H.; Celler, A.; Birkenfeld, B.

    2012-09-01

    We investigated the quantitative accuracy of SPECT/CT imaging studies as would be performed before and after targeted radionuclide therapy (TRT) using phantom experiments with (i) 99mTc, (ii) 177Lu and (iii) 90Y/177Lu. While the experiment with 99mTc imitated a diagnostic scan, the experiments with 177Lu and 90Y/177Lu modeled post-therapy acquisitions. At the next stage, we reconstructed images from pre- and post-therapy patient studies. The data were first reconstructed using two methods with limited corrections for the physics effects. Then, to generate quantitatively accurate absolute activity distributions, we applied a hybrid (model-based and window-based) reconstruction strategy where some of the physics effects were accurately modeled while corrections for other effects were empirical and based on information obtained from the projection data. The accuracies of absolute activity recovered by the hybrid method from the six phantom experiments were very similar to each other and acceptable for potential use in TRT. When measured in identical regions of interest, the 99mTc activity was reconstructed with errors ranging between -3.3% and 2.9%, while the 177Lu activity was reconstructed from experiments with 177Lu and 90Y/177Lu with errors ranging between -1.6% and 1.6%. The reconstruction algorithms with limited corrections led to larger and case-specific errors as might have been expected. From a clinical prospective, our results showed that physics-based reconstructions improved resolution of images corresponding to both diagnostic scans with 99mTc and post-therapy scans with 177Lu. Our analysis of patient study demonstrated that lack of corrections led to overestimation of activities in organs and tumor by 29-39% for the diagnostic scan with 99mTc and by 105-218% for post-therapy scan with 177Lu.

  10. Quantitative comparison of OSEM and penalized likelihood image reconstruction using relative difference penalties for clinical PET

    NASA Astrophysics Data System (ADS)

    Ahn, Sangtae; Ross, Steven G.; Asma, Evren; Miao, Jun; Jin, Xiao; Cheng, Lishui; Wollenweber, Scott D.; Manjeshwar, Ravindra M.

    2015-08-01

    Ordered subset expectation maximization (OSEM) is the most widely used algorithm for clinical PET image reconstruction. OSEM is usually stopped early and post-filtered to control image noise and does not necessarily achieve optimal quantitation accuracy. As an alternative to OSEM, we have recently implemented a penalized likelihood (PL) image reconstruction algorithm for clinical PET using the relative difference penalty with the aim of improving quantitation accuracy without compromising visual image quality. Preliminary clinical studies have demonstrated visual image quality including lesion conspicuity in images reconstructed by the PL algorithm is better than or at least as good as that in OSEM images. In this paper we evaluate lesion quantitation accuracy of the PL algorithm with the relative difference penalty compared to OSEM by using various data sets including phantom data acquired with an anthropomorphic torso phantom, an extended oval phantom and the NEMA image quality phantom; clinical data; and hybrid clinical data generated by adding simulated lesion data to clinical data. We focus on mean standardized uptake values and compare them for PL and OSEM using both time-of-flight (TOF) and non-TOF data. The results demonstrate improvements of PL in lesion quantitation accuracy compared to OSEM with a particular improvement in cold background regions such as lungs.

  11. Optimization of Bayesian Emission tomographic reconstruction for region of interest quantitation

    SciTech Connect

    Qi, Jinyi

    2003-01-10

    Region of interest (ROI) quantitation is an important task in emission tomography (e.g., positron emission tomography and single photon emission computed tomography). It is essential for exploring clinical factors such as tumor activity, growth rate, and the efficacy of therapeutic interventions. Bayesian methods based on the maximum a posteriori principle (or called penalized maximum likelihood methods) have been developed for emission image reconstructions to deal with the low signal to noise ratio of the emission data. Similar to the filter cut-off frequency in the filtered backprojection method, the smoothing parameter of the image prior in Bayesian reconstruction controls the resolution and noise trade-off and hence affects ROI quantitation. In this paper we present an approach for choosing the optimum smoothing parameter in Bayesian reconstruction for ROI quantitation. Bayesian reconstructions are difficult to analyze because the resolution and noise properties are nonlinear and object-dependent. Building on the recent progress on deriving the approximate expressions for the local impulse response function and the covariance matrix, we derived simplied theoretical expressions for the bias, the variance, and the ensemble mean squared error (EMSE) of the ROI quantitation. One problem in evaluating ROI quantitation is that the truth is often required for calculating the bias. This is overcome by using ensemble distribution of the activity inside the ROI and computing the average EMSE. The resulting expressions allow fast evaluation of the image quality for different smoothing parameters. The optimum smoothing parameter of the image prior can then be selected to minimize the EMSE.

  12. Quantitative Reconstruction of Holocene Climates of Canadian Arctic and Greenland from pollen assemblages

    NASA Astrophysics Data System (ADS)

    Whitmore, J.; Gajewski, K.

    2004-05-01

    Ice cores have provided key records of the late-Quaternary climates of the North American Arctic. However, these are spatially restricted and are available only in the glaciated eastern Arctic and Greenland. Ten pollen diagrams are available from Banks, Prince of Wales, Somerset, Ellesmere and Baffin Island describe the changes in the postglacial vegetation. These pollen assemblages, along with other proxy-climate data, have been interpreted as indicating a relatively warm early Holocene with a cooling in the past several 1000 years. However, quantitative reconstructions of the magnitude of temperature change have been hampered by lack of a sufficiently extensive modern calibration dataset. A new modern pollen dataset has recently been prepared, permitting the quantitative reconstructions of summer conditions across the Arctic. We use the modern pollen dataset, along with high-resolution estimates of July temperatures to estimate the magnitude of the Holocene climate changes across the Arctic and compare these results to the ice core records.

  13. Objective evaluation of reconstruction methods for quantitative SPECT imaging in the absence of ground truth.

    PubMed

    Jha, Abhinav K; Song, Na; Caffo, Brian; Frey, Eric C

    2015-04-13

    Quantitative single-photon emission computed tomography (SPECT) imaging is emerging as an important tool in clinical studies and biomedical research. There is thus a need for optimization and evaluation of systems and algorithms that are being developed for quantitative SPECT imaging. An appropriate objective method to evaluate these systems is by comparing their performance in the end task that is required in quantitative SPECT imaging, such as estimating the mean activity concentration in a volume of interest (VOI) in a patient image. This objective evaluation can be performed if the true value of the estimated parameter is known, i.e. we have a gold standard. However, very rarely is this gold standard known in human studies. Thus, no-gold-standard techniques to optimize and evaluate systems and algorithms in the absence of gold standard are required. In this work, we developed a no-gold-standard technique to objectively evaluate reconstruction methods used in quantitative SPECT when the parameter to be estimated is the mean activity concentration in a VOI. We studied the performance of the technique with realistic simulated image data generated from an object database consisting of five phantom anatomies with all possible combinations of five sets of organ uptakes, where each anatomy consisted of eight different organ VOIs. Results indicate that the method provided accurate ranking of the reconstruction methods. We also demonstrated the application of consistency checks to test the no-gold-standard output.

  14. Objective evaluation of reconstruction methods for quantitative SPECT imaging in the absence of ground truth

    NASA Astrophysics Data System (ADS)

    Jha, Abhinav K.; Song, Na; Caffo, Brian; Frey, Eric C.

    2015-03-01

    Quantitative single-photon emission computed tomography (SPECT) imaging is emerging as an important tool in clinical studies and biomedical research. There is thus a need for optimization and evaluation of systems and algorithms that are being developed for quantitative SPECT imaging. An appropriate objective method to evaluate these systems is by comparing their performance in the end task that is required in quantitative SPECT imaging, such as estimating the mean activity concentration in a volume of interest (VOI) in a patient image. This objective evaluation can be performed if the true value of the estimated parameter is known, i.e. we have a gold standard. However, very rarely is this gold standard known in human studies. Thus, no-gold-standard techniques to optimize and evaluate systems and algorithms in the absence of gold standard are required. In this work, we developed a no-gold-standard technique to objectively evaluate reconstruction methods used in quantitative SPECT when the parameter to be estimated is the mean activity concentration in a VOI. We studied the performance of the technique with realistic simulated image data generated from an object database consisting of five phantom anatomies with all possible combinations of five sets of organ uptakes, where each anatomy consisted of eight different organ VOIs. Results indicate that the method pro- vided accurate ranking of the reconstruction methods. We also demonstrated the application of consistency checks to test the no-gold-standard output.

  15. Biomization and quantitative climate reconstruction techniques in northwestern Mexico—With an application to four Holocene pollen sequences

    NASA Astrophysics Data System (ADS)

    Ortega-Rosas, C. I.; Guiot, J.; Peñalba, M. C.; Ortiz-Acosta, M. E.

    2008-04-01

    New paleovegetation and paleoclimatic reconstructions from the Sierra Madre Occidental (SMO) in northwestern Mexico are presented. This work involves climate and biome reconstruction using Plant Functional Types (PFT) assigned to pollen taxa. We used fossil pollen data from four Holocene peat bogs located at different altitudes (1500-2000 m) at the border region of Sonora and Chihuahua at around 28° N latitude (Ortega-Rosas, C.I. 2003. Palinología de la Ciénega de Camilo: datos para la historia de la vegetación y el clima del Holoceno medio y superior en el NW de la Sierra Madre Occidental, Sonora, Mexico. Master Thesis, Universidad Nacional Autónoma de México, México D.F.; Ortega-Rosas, C.I., Peñalba, M.C., Guiot, J. Holocene altitudinal shifts in vegetation belts and environmental changes in the Sierra Madre Occidental, Northwestern Mexico. Submitted for publication of Palaeobotany and Palynology). The closest modern pollen data come from pollen analysis across an altitudinal transect from the Sonoran Desert towards the highlands of the temperate SMO at the same latitude (Ortega-Rosas, C.I. 2003. Palinología de la Ciénega de Camilo: datos para la historia de la vegetación y el clima del Holoceno medio y superior en el NW de la Sierra Madre Occidental, Sonora, Mexico. Master Thesis, Universidad Nacional Autónoma de México, México D.F.). An additional modern pollen dataset of 400 sites across NW Mexico and the SW United States was compiled from different sources (Davis, O.K., 1995. Climate and vegetation pattern in surface samples from arid western U.S.A.: application to Holocene climatic reconstruction. Palynology 19, 95-119, North American Pollen Database, Latin-American Pollen Database, personal data, and different scientific papers). For the biomization method (Prentice, I.C., Guiot, J., Huntley, B., Jolly, D., Cheddadi, R., 1996. Reconstructing biomes from paleoecological data: a general method and its application to European pollen data at 0 and

  16. Quantitative Paleoclimate Reconstruction From Pollen Assemblages Preserved in Arctic Lake Sediments

    NASA Astrophysics Data System (ADS)

    Frechette, B.; de Vernal, A.; Wolfe, A. P.; Fredskild, B.; Kerwin, M. W.; Miller, G. H.; Richard, P. J.

    2004-05-01

    Surface sediment pollen assemblages from 390 lakes in northwestern Canada, northern Québec, the Canadian Arctic Archipelago and Greenland have been analyzed in order to provide modern analogs for quantitative paleoclimatic reconstruction. This represents a modern environmental gradient spanning 2400 mm of mean annual precipitation, 14.7° C of July temperature, and 32.7° C of January temperature. The modern pollen data includes relative frequencies of the 35 most common taxa. Correspondance analysis (CA) was used to explore spatial distribution of pollen assemblages and relationships with climatic parameters. The CA demonstrates a clear latitudinal pattern, with Axis 1 (27.1% of variance) positively and disgnificantly correlated (r=0.85) with July air temperature. The use of closest modern analogues for quantitative paleoclimatic reconstruction was evaluated by estimating modern climate from surface pollen spectra. The best results were obtained using a chord distance dissimilarity metric and the 5 closest analogues. Observed versus estimated modern variables produced root-mean-squared errors of prediction (RMSEP) of ±1.98° C and ±0.71° C for the January and July temperatures, respectively, and ±175.32 mm for annual precipitation. Detailed pollen analyses and paleoclimate reconstructions have been undertaken on Holocene sediments from two well dated lake cores on Cumberland Peninsula, Baffin Island. Squared chord distances between successive pollen spectra were first used to identify times of rapid vegetation change. Notable transitions occurred at 8000, 3000 and 500 cal BP. Although climate reconstructions from both sites indicate some local differences, there are generally consistent features on a regional scale, including a progressive 1.5° C decrease in July temperature since 8000 cal BP, a progressive 5° C increase in January temperature since 7000 cal BP and an increase in annual precipitation. These reconstructions are therefore consistent with a

  17. Dynamic vegetation modeling of tropical biomes during Heinrich events

    NASA Astrophysics Data System (ADS)

    Handiani, Dian Noor; Paul, André; Dupont, Lydie M.

    2010-05-01

    changed from warm temperate forest during the last glacial maximum to the grassland and dry shrubland, suggesting a drier climate during Heinrich event 1. In south-western Africa savanna and dry woodland changed into boreal forest and boreal-temperate forest suggesting wetter conditions. The biomes diagnosed from the control-run, were compared to the modern vegetation reconstruction of BIOME 4 (http://www.bridge.bris.ac.uk/resources/Databases/BIOMES_data). Consistent biome patterns were simulated for the tropical forests of western and south-western Africa and the grasslands of northern Africa. On the other hand, in southern Europe, where the BIOME 4 vegetation reconstruction is dominated by warm temperate and temperate forest, our model shows a strong bias towards the grassland.

  18. Quantitative fractography by digital image processing: NIH Image macro tools for stereo pair analysis and 3-D reconstruction.

    PubMed

    Hein, L R

    2001-10-01

    A set of NIH Image macro programs was developed to make qualitative and quantitative analyses from digital stereo pictures produced by scanning electron microscopes. These tools were designed for image alignment, anaglyph representation, animation, reconstruction of true elevation surfaces, reconstruction of elevation profiles, true-scale elevation mapping and, for the quantitative approach, surface area and roughness calculations. Limitations on time processing, scanning techniques and programming concepts are also discussed.

  19. Quantitative reconstruction of climate variability during the Eemian (Merkinė) and Weichselian (Nemunas) in Lithuania

    NASA Astrophysics Data System (ADS)

    Šeirienė, Vaida; Kühl, Norbert; Kisielienė, Dalia

    2014-07-01

    Little is known concerning climate changes in the Eastern Baltic region during the last interglacial-glacial cycle and in particular, climate changes during the Weichselian. In this study, a quantitative reconstruction of the mean January and July temperature for the Medininkai-117 site in Lithuania is presented. The reconstruction is based on pollen and plant macrofossils from this site, which reveal that the vegetation was characteristic of many northern Europe sites during the Eemian and Early Weichselian. Gradual evolution of the vegetation suggests that relatively uniform climate conditions existed during the Eemian. Our reconstructions support the view of a relatively stable Eemian, with short cooling phases of low amplitude. A strong increase in temperature was apparent during the beginning of the interglacial and decrease during the transition to the Weichselian. Reconstructed July temperatures of the Eemian interglacial were approximately 2 °C higher than today (18.5 °C; today: 16.2 °C) and were similar to today for January (- 5.2 °C; today: - 5.1 °C). July temperatures during the Early Weichselian were only ~ 2°C lower than during the Eemian, whereas the January temperatures gradually decreased. Winter temperatures were relatively high (above - 10 °C) during the Early Weichselian.

  20. Quantitative characterization, classification and reconstruction of oocyst shapes of Eimeria species from cattle.

    PubMed

    Sommer, C

    1998-01-01

    This study reports on morphological variability of Eimeria species, which may be given either by drawings or as quantitative data. The drawings may be used to facilitate identification by eye of 'unknown' Eimeria specimens, whereas quantitative data may serve as a reference set for identification by multivariate statistical techniques. The morphology of 810 Eimeria specimens was defined in binary (b/w) digital images by pixels of their oocyst outline. A Fourier transform of pixel positions yielded size and shape features. To classify coccidia, the quantitative data were employed in an agglomerative clustering by average linkage algorithm with equal weight assigned to size and shape. An inverse Fourier transform served to reconstruct oocyst outlines, i.e. outlines of average shape and size, from mean values of features in resulting clusters. Clusters were subsequently identified based on their average morphology by comparison with drawings of species in an earlier taxonomical work. Five hundred oocyst outlines were simulated for each cluster representing a species, and shape/size variability was presented in contour diagrams. Differences in species shapes, and correspondence in length and width, were seen after reconstruction by inverse Fourier transform and comparison with earlier studies.

  1. Quantitative Reconstruction of Grassland and Forest Cover in Southern Sweden Inferred from Fossil Pollen Records

    NASA Astrophysics Data System (ADS)

    Brostrom, A.; Gaillard, M.; Sugita, S.

    2001-12-01

    When reconstructing past land-cover changes induced by humans at local to regional scales, primary interest is to quantify vegetation cover of forest and grassland. Fossil pollen records have great potential in that respect. However, quantitative reconstruction using pollen always require well-established pollen/vegetation relationship in the region of interest. In particular, pollen productivity and dispersal are two major factors, controlling the pollen representation of the surrounding vegetation in a basin (lake or bog), thus need a better understanding. Based on empirical studies in the ancient cultural landscape of southern Sweden, we have obtained pollen productivity estimates (PPE) for major taxa relevant for that region. These PPE show that arboreal taxa produce 10-40 times as much pollen as non-arboreal taxa. Considering significant input of background pollen dominated by arboreal taxa the area of open grassland in the past could often be underestimated when estimated directly from non-arboreal pollen percentages in fossil pollen records. To better understand the problem, we compare quantitative estimates of vegetation cover inferred from fossil pollen records in two regions of southern Sweden, where vegetation composition and structure are significantly different. One region is dominated by cultivated and grazed open-land with scattered wood patches (OPEN), while the other region is mostly forested with scattered patches of cultivated and grazed land (SEMI-OPEN). The reconstruction follows the "Landscape Reconstruction Algorithm" (LRA) approach, which estimates vegetation cover within a given catchment area around the pollen site using PPE and estimates of background pollen for that region. The results are compared to the historical records in the region at several time horizons to validate the LRA approach. Our results show that open grassland cover is always underrepresented when only NAP percentages are used, with various degrees depending on regional

  2. Evolution of the indoor biome.

    PubMed

    Martin, Laura J; Adams, Rachel I; Bateman, Ashley; Bik, Holly M; Hawks, John; Hird, Sarah M; Hughes, David; Kembel, Steven W; Kinney, Kerry; Kolokotronis, Sergios-Orestis; Levy, Gabriel; McClain, Craig; Meadow, James F; Medina, Raul F; Mhuireach, Gwynne; Moreau, Corrie S; Munshi-South, Jason; Nichols, Lauren M; Palmer, Clare; Popova, Laura; Schal, Coby; Täubel, Martin; Trautwein, Michelle; Ugalde, Juan A; Dunn, Robert R

    2015-04-01

    Few biologists have studied the evolutionary processes at work in indoor environments. Yet indoor environments comprise approximately 0.5% of ice-free land area--an area as large as the subtropical coniferous forest biome. Here we review the emerging subfield of 'indoor biome' studies. After defining the indoor biome and tracing its deep history, we discuss some of its evolutionary dimensions. We restrict our examples to the species found in human houses--a subset of the environments constituting the indoor biome--and offer preliminary hypotheses to advance the study of indoor evolution. Studies of the indoor biome are situated at the intersection of evolutionary ecology, anthropology, architecture, and human ecology and are well suited for citizen science projects, public outreach, and large-scale international collaborations. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Disturbance maintains alternative biome states.

    PubMed

    Dantas, Vinícius de L; Hirota, Marina; Oliveira, Rafael S; Pausas, Juli G

    2016-01-01

    Understanding the mechanisms controlling the distribution of biomes remains a challenge. Although tropical biome distribution has traditionally been explained by climate and soil, contrasting vegetation types often occur as mosaics with sharp boundaries under very similar environmental conditions. While evidence suggests that these biomes are alternative states, empirical broad-scale support to this hypothesis is still lacking. Using community-level field data and a novel resource-niche overlap approach, we show that, for a wide range of environmental conditions, fire feedbacks maintain savannas and forests as alternative biome states in both the Neotropics and the Afrotropics. In addition, wooded grasslands and savannas occurred as alternative grassy states in the Afrotropics, depending on the relative importance of fire and herbivory feedbacks. These results are consistent with landscape scale evidence and suggest that disturbance is a general factor driving and maintaining alternative biome states and vegetation mosaics in the tropics.

  4. Biomes computed from simulated climatologies

    NASA Astrophysics Data System (ADS)

    Claussen, Martin; Esch, Monika

    1994-01-01

    The biome model of Prentice et al. (1992a) is used to predict global patterns of potential natural plant formations, or biomes, from climatologies simulated by ECHAM, a model used for climate simulations at the Max-Planck-Institut fur Meteorologie. This study is undertaken in order to show the advantage of this biome model in diagnosing the performance of a climate model and assessing effects of past and future climate changes predicted by a climate model. Good overall agreement is found between global patterns of biomes computed from observed and simulated data of present climate. But there are also major discrepancies indicated by a difference in biomes in Australia, in the Kalahari Desert, and in the Middle West of North America. These discrepancies can be traced back to failures in simulated rainfall as well as summer or winter temperatures. Global patterns of biomes computed from an ice age simulation reveal that North America, Europe, and Siberia should have been covered largely by tundra and taiga, whereas only small differences are seen for the tropical rain forests. A potential northeast shift of biomes is expected from a simulation with enhanced C02 concentration according to the IPCC Scenario A. Little change is seen in the tropical rain forest and the Sahara. Since the biome model used is not capable of predicting changes in vegetation patterns due to a rapid climate change, the latter simulation has to be taken as a prediction of changes in conditions favourable for the existence of certain biomes, not as a prediction of a future distribution of biomes.[/ab

  5. Biomes computed from simulated climatologies

    SciTech Connect

    Claussen, M.; Esch, M.

    1994-01-01

    The biome model of Prentice et al. is used to predict global patterns of potential natural plant formations, or biomes, from climatologies simulated by ECHAM, a model used for climate simulations at the Max-Planck-Institut fuer Meteorologie. This study undertaken in order to show the advantage of this biome model in diagnosing the performance of a climate model and assessing effects of past and future climate changes predicted by a climate model. Good overall agreement is found between global patterns of biomes computed from observed and simulated data of present climate. But there are also major discrepancies indicated by a difference in biomes in Australia, in the Kalahari Desert, and in the Middle West of North America. These discrepancies can be traced back to in simulated rainfall as well as summer or winter temperatures. Global patterns of biomes computed from an ice age simulation reveal that North America, Europe, and Siberia should have been covered largely by tundra and taiga, whereas only small differences are for the tropical rain forests. A potential northeast shift of biomes is expected from a simulation with enhanced CO{sub 2} concentration according to the IPCC Scenario A. Little change is seen in the tropical rain forest and the Sahara. Since the biome model used is not capable of predicting chances in vegetation patterns due to a rapid climate change, the latter simulation to be taken as a prediction of chances in conditions favourable for the existence of certain biomes, not as a reduction of a future distribution of biomes. 15 refs., 8 figs., 2 tabs.

  6. Applicability of a set of tomographic reconstruction algorithms for quantitative SPECT on irradiated nuclear fuel assemblies

    NASA Astrophysics Data System (ADS)

    Jacobsson Svärd, Staffan; Holcombe, Scott; Grape, Sophie

    2015-05-01

    A fuel assembly operated in a nuclear power plant typically contains 100-300 fuel rods, depending on fuel type, which become strongly radioactive during irradiation in the reactor core. For operational and security reasons, it is of interest to experimentally deduce rod-wise information from the fuel, preferably by means of non-destructive measurements. The tomographic SPECT technique offers such possibilities through its two-step application; (1) recording the gamma-ray flux distribution around the fuel assembly, and (2) reconstructing the assembly's internal source distribution, based on the recorded radiation field. In this paper, algorithms for performing the latter step and extracting quantitative relative rod-by-rod data are accounted for. As compared to application of SPECT in nuclear medicine, nuclear fuel assemblies present a much more heterogeneous distribution of internal attenuation to gamma radiation than the human body, typically with rods containing pellets of heavy uranium dioxide surrounded by cladding of a zirconium alloy placed in water or air. This inhomogeneity severely complicates the tomographic quantification of the rod-wise relative source content, and the deduction of conclusive data requires detailed modelling of the attenuation to be introduced in the reconstructions. However, as shown in this paper, simplified models may still produce valuable information about the fuel. Here, a set of reconstruction algorithms for SPECT on nuclear fuel assemblies are described and discussed in terms of their quantitative performance for two applications; verification of fuel assemblies' completeness in nuclear safeguards, and rod-wise fuel characterization. It is argued that a request not to base the former assessment on any a priori information brings constraints to which reconstruction methods that may be used in that case, whereas the use of a priori information on geometry and material content enables highly accurate quantitative assessment, which

  7. Proxy-to-proxy calibration: increasing the temporal resolution of quantitative climate reconstructions.

    PubMed

    von Gunten, Lucien; D'Andrea, William J; Bradley, Raymond S; Huang, Yongsong

    2012-01-01

    High-resolution paleoclimate reconstructions are often restricted by the difficulties of sampling geologic archives in great detail and the analytical costs of processing large numbers of samples. Using sediments from Lake Braya Sø, Greenland, we introduce a new method that provides a quantitative high-resolution paleoclimate record by combining measurements of the alkenone unsaturation index (U37(K)) with non-destructive scanning reflectance spectroscopic measurements in the visible range (VIS-RS). The proxy-to-proxy (PTP) method exploits two distinct calibrations: the in situ calibration of U37(K) to lake water temperature and the calibration of scanning VIS-RS data to down core U37(K) data. Using this approach, we produced a quantitative temperature record that is longer and has 5 times higher sampling resolution than the original U37(K) time series, thereby allowing detection of temperature variability in frequency bands characteristic of the AMO over the past 7,000 years.

  8. Proxy-to-proxy calibration: Increasing the temporal resolution of quantitative climate reconstructions

    PubMed Central

    von Gunten, Lucien; D'Andrea, William J.; Bradley, Raymond S.; Huang, Yongsong

    2012-01-01

    High-resolution paleoclimate reconstructions are often restricted by the difficulties of sampling geologic archives in great detail and the analytical costs of processing large numbers of samples. Using sediments from Lake Braya Sø, Greenland, we introduce a new method that provides a quantitative high-resolution paleoclimate record by combining measurements of the alkenone unsaturation index () with non-destructive scanning reflectance spectroscopic measurements in the visible range (VIS-RS). The proxy-to-proxy (PTP) method exploits two distinct calibrations: the in situ calibration of to lake water temperature and the calibration of scanning VIS-RS data to down core data. Using this approach, we produced a quantitative temperature record that is longer and has 5 times higher sampling resolution than the original time series, thereby allowing detection of temperature variability in frequency bands characteristic of the AMO over the past 7,000 years. PMID:22934132

  9. Pollen-inferred quantitative reconstruction of the Holocene climate in the central Mediterranean area (Italy)

    NASA Astrophysics Data System (ADS)

    Peyron, O.; Magny, M.; Combourieu-nebout, N.; Goring, S.; Joannin, S.; de Beaulieu, J.-L.; Brugapaglia, E.; Dormoy, I.; Drescher-schneider, R.; Galop, D.; Ortu, E.; Sadori, L.

    2012-04-01

    The Mediterranean area is particularly sensitive to short-term climate change due to its intermediate position between the higher-latitude and lower-latitude climate systems. Consequently, future climate change can be expected to be particularly strong in this region and will likely have a strong impact on terrestrial ecosystems. Therefore a growing interest has been focused on the climate study of the last 15,000 years in the Mediterranean area. This study presents new pollen-based climate reconstructions of Holocene precipitation and temperature for four high-resolution pollen sequences from north to south of Italy: - Lake Ledro, Northern Italy (Magny et al., 2009; Joannin et al, in prep), - Lake Accesa, central-Italy (Magny et al., 2007; Drescher-Schneider et al., 2007; Vannière et al., 2008; Peyron et al., 2011) - Trifoglietti, Southern Italy (Joannin et al., in prep) - Pergusa, Sicily (Sadori and Narcisi, 2001; Magny et al., 2011) We aim to reconstruct quantitatively the climate changes in central Mediterranean during the Holocene and distinguish the patterns, trends and main changes along a latitudinal gradient. We also aim to test the reconstruction of the precipitation seasonality which can be validated by independent proxies obtained for same records, i.e. lake-levels, charcoal/fires (Magny et al., 2011; Vannière et al., 2011). To provide the climatic reconstruction, we use both the Modern Analogues Technique (MAT), and the recent Non-Metric Multidimensional Scaling/Generalized Additive Model method (NMDS/GAM) developed by Goring et al. (2009). Reconstructed annual and winter precipitations show a Holocene optimum at 9000-6000 cal BP for all sites, and an aridification trend starting around 4500 cal BP. The summer signal is different, underlining different patterns from North to South. Summer temperatures were cool during the Early Holocene and show a trend consistent with previous results for Southern Europe (Davis and Brewer, 2009). In order to test

  10. Quantitative assessment of lesion detection accuracy, resolution, and reconstruction algorithms in neutron stimulated emission computed tomography.

    PubMed

    Lakshmanan, Manu N; Kapadia, Anuj J

    2012-07-01

    We present a quantitative analysis of the image quality obtained using filtered back-projection (FBP) with Ram-Lak filtering and maximum likelihood-expectation maximization (ML-EM)-with no post-reconstruction filtering in either case-in neutron stimulated emission computed tomography (NSECT) imaging using Monte Carlo simulations in the context of clinically relevant models of liver iron overload. The ratios of pixel intensities for several regions of interest and lesion shape detection using an active-contours segmentation algorithm are assessed for accuracy across different scanning configurations and reconstruction algorithms. The modulation transfer functions (MTFs) are also computed for the cases under study and are applied to determine a minimum detectable lesion spacing as a form of sensitivity analysis. The accuracy of NSECT imaging in measuring relative tissue concentration is presented for simulated clinical liver cases. When using the 15th iteration, ML-EM provides at least 25% better resolution than FBP and proves to be highly robust under low-signal high-noise conditions prevalent in NSECT. However, FBP gives more accurate lesion pixel intensity ratios and size estimates in some cases; due to advantages provided by both reconstruction algorithms, it is worth exploring the development of an algorithm that is a hybrid of the two. We also show that NSECT imaging can be used to accurately detect 3-cm lesions in backgrounds that are a significant fraction (one-quarter) of the concentration of the lesion, down to a 4-cm spacing between lesions.

  11. Quantitative image reconstruction for total-body PET imaging using the 2-meter long EXPLORER scanner

    NASA Astrophysics Data System (ADS)

    Zhang, Xuezhu; Zhou, Jian; Cherry, Simon R.; Badawi, Ramsey D.; Qi, Jinyi

    2017-03-01

    The EXPLORER project aims to build a 2 meter long total-body PET scanner, which will provide extremely high sensitivity for imaging the entire human body. It will possess a range of capabilities currently unavailable to state-of-the-art clinical PET scanners with a limited axial field-of-view. The huge number of lines-of-response (LORs) of the EXPLORER poses a challenge to the data handling and image reconstruction. The objective of this study is to develop a quantitative image reconstruction method for the EXPLORER and compare its performance with current whole-body scanners. Fully 3D image reconstruction was performed using time-of-flight list-mode data with parallel computation. To recover the resolution loss caused by the parallax error between crystal pairs at a large axial ring difference or transaxial radial offset, we applied an image domain resolution model estimated from point source data. To evaluate the image quality, we conducted computer simulations using the SimSET Monte-Carlo toolkit and XCAT 2.0 anthropomorphic phantom to mimic a 20 min whole-body PET scan with an injection of 25 MBq 18F-FDG. We compare the performance of the EXPLORER with a current clinical scanner that has an axial FOV of 22 cm. The comparison results demonstrated superior image quality from the EXPLORER with a 6.9-fold reduction in noise standard deviation comparing with multi-bed imaging using the clinical scanner.

  12. Quantitative image reconstruction for total-body PET imaging using the 2-meter long EXPLORER scanner.

    PubMed

    Zhang, Xuezhu; Zhou, Jian; Cherry, Simon R; Badawi, Ramsey D; Qi, Jinyi

    2017-03-21

    The EXPLORER project aims to build a 2 meter long total-body PET scanner, which will provide extremely high sensitivity for imaging the entire human body. It will possess a range of capabilities currently unavailable to state-of-the-art clinical PET scanners with a limited axial field-of-view. The huge number of lines-of-response (LORs) of the EXPLORER poses a challenge to the data handling and image reconstruction. The objective of this study is to develop a quantitative image reconstruction method for the EXPLORER and compare its performance with current whole-body scanners. Fully 3D image reconstruction was performed using time-of-flight list-mode data with parallel computation. To recover the resolution loss caused by the parallax error between crystal pairs at a large axial ring difference or transaxial radial offset, we applied an image domain resolution model estimated from point source data. To evaluate the image quality, we conducted computer simulations using the SimSET Monte-Carlo toolkit and XCAT 2.0 anthropomorphic phantom to mimic a 20 min whole-body PET scan with an injection of 25 MBq (18)F-FDG. We compare the performance of the EXPLORER with a current clinical scanner that has an axial FOV of 22 cm. The comparison results demonstrated superior image quality from the EXPLORER with a 6.9-fold reduction in noise standard deviation comparing with multi-bed imaging using the clinical scanner.

  13. Real-time quantitative phase reconstruction in off-axis digital holography using multiplexing.

    PubMed

    Girshovitz, Pinhas; Shaked, Natan T

    2014-04-15

    We present a new approach for obtaining significant speedup in the digital processing of extracting unwrapped phase profiles from off-axis digital holograms. The new technique digitally multiplexes two orthogonal off-axis holograms, where the digital reconstruction, including spatial filtering and two-dimensional phase unwrapping on a decreased number of pixels, can be performed on both holograms together, without redundant operations. Using this technique, we were able to reconstruct, for the first time to our knowledge, unwrapped phase profiles from off-axis holograms with 1 megapixel in more than 30 frames per second using a standard single-core personal computer on a MATLAB platform, without using graphic-processing-unit programming or parallel computing. This new technique is important for real-time quantitative visualization and measurements of highly dynamic samples and is applicable for a wide range of applications, including rapid biological cell imaging and real-time nondestructive testing. After comparing the speedups obtained by the new technique for holograms of various sizes, we present experimental results of real-time quantitative phase visualization of cells flowing rapidly through a microchannel.

  14. Experimental investigation of target and transducer effects on quantitative image reconstruction in photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Gamelin, John K.; Aguirre, Andres C.; Huang, Fei; Maurudis, Anastasios; Castillo, Diego; Wang, Lihong V.; Zhu, Quing

    2007-02-01

    In principle, absorbed energy profiles can be exactly reconstructed from photoacoustic measurements on a closed surface. Clinical applications, however, involve compromises due to transducer focus, frequency characteristics, and incomplete measurement apertures. These tradeoffs introduce artifacts and errors in reconstructed absorption distributions that affect quantitative interpretations as well as qualitative contrast between features. The quantitative effects of target geometry, limited measurement surfaces, and bandpass transducer frequency response have been investigated using a ring transducer system designed for small animal imaging. The directionality of photoacoustic radiation is shown to increase with target aspect ratio, producing proportionate overestimates of absorption values for two-dimension apertures less than approximately 150 degrees. For all target geometries and orientations, mean absorption values approach the full view values for hemicircular measurement surfaces although the true spatial uniformity is recovered only with the complete surface. The bandpass transducer frequency spectrum produces a peaked amplitude response biased toward spatial features ranging from 1 to 8 times the system resolution. We discuss the implications of these results for design of clinical systems.

  15. Intervertebral disc segmentation and volumetric reconstruction from peripheral quantitative computed tomography imaging.

    PubMed

    Wong, Alexander; Mishra, Akshaya; Yates, Justin; Fieguth, Paul; Clausi, David A; Callaghan, Jack P

    2009-11-01

    An automatic system for segmenting and constructing volumetric representations of excised intervertebral discs from peripheral quantitative computed tomography (PQCT) imagery is presented. The system is designed to allow for automatic quantitative analysis of progressive herniation damage to the intervertebral discs under flexion/extension motions combined with a compressive load. Automatic segmentation and volumetric reconstruction of intervertebral disc from PQCT imagery is a very challenging problem due to factors such as streak artifacts and unclear material density separation between contrasted intervertebral disc and surrounding bone in the PQCT imagery, as well as the formation of multiple contrasted regions under axial scans. To address these factors, a novel multiscale level set approach based on the Mumford-Shah energy functional in iterative bilateral scale space is employed to segment the intervertebral disc regions from the PQCT imagery. A Delaunay triangulation is then performed based on the set of points associated with the intervertebral disc regions to construct the volumetric representation of the intervertebral disc. Experimental results show that the proposed system achieves segmentation and volumetric reconstructions of intervertebral discs with mean absolute distance error below 0.8 mm when compared to ground truth measurements. The proposed system is currently in operational use as a visualization tool for studying progressive intervertebral disc damage.

  16. Quantitative reconstructions of annual rainfall in Africa 6000 years ago: Model-data comparison

    NASA Astrophysics Data System (ADS)

    Peyron, Odile; Jolly, Dominique; Braconnot, Pascale; Bonnefille, Raymonde; Guiot, JoëL.; Wirrmann, Denis; Chalié, FrançOise

    2006-12-01

    This paper provides the first set of quantitative reconstructions of annual precipitation for mid-Holocene Africa, based on pollen data. The estimates of precipitation are based on 85 pollen sites 14C dated at 6000 ± 500 years B.P and distributed over the whole of Africa. To improve the reliability of the pollen-based climate reconstruction, two methods are used: the "modern analogues technique" (MAT) and the "plant functional types" (PFT) methods. We then conduct a model-data comparison for five distinct regions, allowing an evaluation of model outputs (the Sahara-Sahel, the eastern Sahara, western equatorial Africa, East Africa, and Madagascar). The pollen-inferred reconstructions are compared with 21 mid-Holocene simulations yielded by Atmospheric General Circulation Models (AGCMs), and coupled ocean-atmosphere-vegetation models (OAVGCMs). The large-scale feature of the hydrological changes is shown to be well captured by most of the models. Data show that during the mid-Holocene, the Sahara was considerably wetter than today (+200 to +700 mm/yr). The results reinforce the conclusion that the AGCMs significantly underestimate this precipitation increase in the Sahara whereas the OAVGCM simulations are in accordance with the data. Our results show that vegetation and ocean feedbacks do not have a strong impact in the intertropical zone and that models fail to properly reproduce the climatic conditions in East Africa and Madagascar. The model-data comparison also suggests that the lengthening of the dry season during boreal winter in the west equatorial region is a robust feature although the pollen-based reconstruction shows no change or only slight drying there.

  17. Impact of PET/CT image reconstruction methods and liver uptake normalization strategies on quantitative image analysis.

    PubMed

    Kuhnert, Georg; Boellaard, Ronald; Sterzer, Sergej; Kahraman, Deniz; Scheffler, Matthias; Wolf, Jürgen; Dietlein, Markus; Drzezga, Alexander; Kobe, Carsten

    2016-02-01

    In oncological imaging using PET/CT, the standardized uptake value has become the most common parameter used to measure tracer accumulation. The aim of this analysis was to evaluate ultra high definition (UHD) and ordered subset expectation maximization (OSEM) PET/CT reconstructions for their potential impact on quantification. We analyzed 40 PET/CT scans of lung cancer patients who had undergone PET/CT. Standardized uptake values corrected for body weight (SUV) and lean body mass (SUL) were determined in the single hottest lesion in the lung and normalized to the liver for UHD and OSEM reconstruction. Quantitative uptake values and their normalized ratios for the two reconstruction settings were compared using the Wilcoxon test. The distribution of quantitative uptake values and their ratios in relation to the reconstruction method used were demonstrated in the form of frequency distribution curves, box-plots and scatter plots. The agreement between OSEM and UHD reconstructions was assessed through Bland-Altman analysis. A significant difference was observed after OSEM and UHD reconstruction for SUV and SUL data tested (p < 0.0005 in all cases). The mean values of the ratios after OSEM and UHD reconstruction showed equally significant differences (p < 0.0005 in all cases). Bland-Altman analysis showed that the SUV and SUL and their normalized values were, on average, up to 60 % higher after UHD reconstruction as compared to OSEM reconstruction. OSEM and HD reconstruction brought a significant difference for SUV and SUL, which remained constantly high after normalization to the liver, indicating that standardization of reconstruction and the use of comparable SUV measurements are crucial when using PET/CT.

  18. The development and application of a diatom-based quantitative reconstruction technique in forensic science.

    PubMed

    Horton, Benjamin P; Boreham, Steve; Hillier, Caroline

    2006-05-01

    Diatoms are a group of unicellular algae that have been recorded and classified for over 200 years and have been used in a range of applications in forensic science. We have developed a quantitative diatom-based reconstruction technique to confirm drowning as a cause of death and localize the site of drowning in two recent, high-profile, case studies. In both case studies we collected diatom samples from the local and/or regional area to act as a control in the examination of diatom assemblages associated with lungs and clothing. In Case Study 1 the modern analog technique suggested that all lung and clothing samples have statistically significant similarities to control samples from shallow water habitats. In Case Study 2, the analog matching suggested that the majority of lung samples show a statistically significant relationship to samples from a pond, indicating that this was the drowning medium.

  19. Postoperative Quantitative Assessment of Reconstructive Tissue Status in Cutaneous Flap Model using Spatial Frequency Domain Imaging

    PubMed Central

    Yafi, Amr; Vetter, Thomas S; Scholz, Thomas; Patel, Sarin; Saager, Rolf B; Cuccia, David J; Evans, Gregory R; Durkin, Anthony J

    2010-01-01

    Background The purpose of this study is to investigate the capabilities of a novel optical wide-field imaging technology known as Spatial Frequency Domain Imaging (SFDI) to quantitatively assess reconstructive tissue status. Methods Twenty two cutaneous pedicle flaps were created on eleven rats based on the inferior epigastric vessels. After baseline measurement, all flaps underwent vascular ischemia, induced by clamping the supporting vessels for two hours (either arterio-venous or selective venous occlusions) normal saline was injected to the control flap, and hypertonic hyperoncotic saline solution to the experimental flap. Flaps were monitored for two hours after reperfusion. The SFDI system was used for quantitative assessment of flap status over the duration of the experiment. Results All flaps demonstrated a significant decline in oxy-hemoglobin and tissue oxygen saturation in response to occlusion. Total hemoglobin and deoxy-hemoglobin were markedly increased in the selective venous occlusion group. After reperfusion and the solutions were administered, oxy-hemoglobin and tissue oxygen saturation in those flaps that survived gradually returned to the baseline levels. However, flaps for which oxy-hemoglobin and tissue oxygen saturation didn’t show any signs of recovery appeared to be compromised and eventually became necrotic within 24–48 hours in both occlusion groups. Conclusion SFDI technology provides a quantitative, objective method to assess tissue status. This study demonstrates the potential of this optical technology to assess tissue perfusion in a very precise and quantitative way, enabling wide-field visualization of physiological parameters. The results of this study suggest that SFDI may provide a means for prospectively identifying dysfunctional flaps well in advance of failure. PMID:21200206

  20. Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors

    PubMed Central

    Rey-Villamizar, Nicolas; Merouane, Amine; Lu, Yanbin; Mukherjee, Amit; Trett, Kristen; Chong, Peter; Harris, Carolyn; Shain, William; Roysam, Badrinath

    2015-01-01

    Motivation: The arbor morphologies of brain microglia are important indicators of cell activation. This article fills the need for accurate, robust, adaptive and scalable methods for reconstructing 3-D microglial arbors and quantitatively mapping microglia activation states over extended brain tissue regions. Results: Thick rat brain sections (100–300 µm) were multiplex immunolabeled for IBA1 and Hoechst, and imaged by step-and-image confocal microscopy with automated 3-D image mosaicing, producing seamless images of extended brain regions (e.g. 5903 × 9874 × 229 voxels). An over-complete dictionary-based model was learned for the image-specific local structure of microglial processes. The microglial arbors were reconstructed seamlessly using an automated and scalable algorithm that exploits microglia-specific constraints. This method detected 80.1 and 92.8% more centered arbor points, and 53.5 and 55.5% fewer spurious points than existing vesselness and LoG-based methods, respectively, and the traces were 13.1 and 15.5% more accurate based on the DIADEM metric. The arbor morphologies were quantified using Scorcioni’s L-measure. Coifman’s harmonic co-clustering revealed four morphologically distinct classes that concord with known microglia activation patterns. This enabled us to map spatial distributions of microglial activation and cell abundances. Availability and implementation: Experimental protocols, sample datasets, scalable open-source multi-threaded software implementation (C++, MATLAB) in the electronic supplement, and website (www.farsight-toolkit.org). http://www.farsight-toolkit.org/wiki/Population-scale_Three-dimensional_Reconstruction_and_Quanti-tative_Profiling_of_Microglia_Arbors Contact: broysam@central.uh.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25701570

  1. Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors.

    PubMed

    Megjhani, Murad; Rey-Villamizar, Nicolas; Merouane, Amine; Lu, Yanbin; Mukherjee, Amit; Trett, Kristen; Chong, Peter; Harris, Carolyn; Shain, William; Roysam, Badrinath

    2015-07-01

    The arbor morphologies of brain microglia are important indicators of cell activation. This article fills the need for accurate, robust, adaptive and scalable methods for reconstructing 3-D microglial arbors and quantitatively mapping microglia activation states over extended brain tissue regions. Thick rat brain sections (100-300 µm) were multiplex immunolabeled for IBA1 and Hoechst, and imaged by step-and-image confocal microscopy with automated 3-D image mosaicing, producing seamless images of extended brain regions (e.g. 5903 × 9874 × 229 voxels). An over-complete dictionary-based model was learned for the image-specific local structure of microglial processes. The microglial arbors were reconstructed seamlessly using an automated and scalable algorithm that exploits microglia-specific constraints. This method detected 80.1 and 92.8% more centered arbor points, and 53.5 and 55.5% fewer spurious points than existing vesselness and LoG-based methods, respectively, and the traces were 13.1 and 15.5% more accurate based on the DIADEM metric. The arbor morphologies were quantified using Scorcioni's L-measure. Coifman's harmonic co-clustering revealed four morphologically distinct classes that concord with known microglia activation patterns. This enabled us to map spatial distributions of microglial activation and cell abundances. Experimental protocols, sample datasets, scalable open-source multi-threaded software implementation (C++, MATLAB) in the electronic supplement, and website (www.farsight-toolkit.org). http://www.farsight-toolkit.org/wiki/Population-scale_Three-dimensional_Reconstruction_and_Quanti-tative_Profiling_of_Microglia_Arbors broysam@central.uh.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. Quantitative methods for reconstructing tissue biomechanical properties in optical coherence elastography: a comparison study

    PubMed Central

    Han, Zhaolong; Li, Jiasong; Singh, Manmohan; Wu, Chen; Liu, Chih-hao; Wang, Shang; Idugboe, Rita; Raghunathan, Raksha; Sudheendran, Narendran; Aglyamov, Salavat R.; Twa, Michael D.; Larin, Kirill V.

    2015-01-01

    We present a systematic analysis of the accuracy of five different methods for extracting the biomechanical properties of soft samples using optical coherence elastography (OCE). OCE is an emerging noninvasive technique, which allows assessing biomechanical properties of tissues with a micrometer spatial resolution. However, in order to accurately extract biomechanical properties from OCE measurements, application of proper mechanical model is required. In this study, we utilize tissue-mimicking phantoms with controlled elastic properties and investigate the feasibilities of four available methods for reconstructing elasticity (Young’s modulus) based on OCE measurements of an air-pulse induced elastic wave. The approaches are based on the shear wave equation (SWE), the surface wave equation (SuWE), Rayleigh-Lamb frequency equation (RLFE), and finite element method (FEM), Elasticity values were compared with uniaxial mechanical testing. The results show that the RLFE and the FEM are more robust in quantitatively assessing elasticity than the other simplified models. This study provides a foundation and reference for reconstructing the biomechanical properties of tissues from OCE data, which is important for the further development of noninvasive elastography methods. PMID:25860076

  3. Improved dose-volume histogram estimates for radiopharmaceutical therapy by optimizing quantitative SPECT reconstruction parameters

    NASA Astrophysics Data System (ADS)

    Cheng, Lishui; Hobbs, Robert F.; Segars, Paul W.; Sgouros, George; Frey, Eric C.

    2013-06-01

    In radiopharmaceutical therapy, an understanding of the dose distribution in normal and target tissues is important for optimizing treatment. Three-dimensional (3D) dosimetry takes into account patient anatomy and the nonuniform uptake of radiopharmaceuticals in tissues. Dose-volume histograms (DVHs) provide a useful summary representation of the 3D dose distribution and have been widely used for external beam treatment planning. Reliable 3D dosimetry requires an accurate 3D radioactivity distribution as the input. However, activity distribution estimates from SPECT are corrupted by noise and partial volume effects (PVEs). In this work, we systematically investigated OS-EM based quantitative SPECT (QSPECT) image reconstruction in terms of its effect on DVHs estimates. A modified 3D NURBS-based Cardiac-Torso (NCAT) phantom that incorporated a non-uniform kidney model and clinically realistic organ activities and biokinetics was used. Projections were generated using a Monte Carlo (MC) simulation; noise effects were studied using 50 noise realizations with clinical count levels. Activity images were reconstructed using QSPECT with compensation for attenuation, scatter and collimator-detector response (CDR). Dose rate distributions were estimated by convolution of the activity image with a voxel S kernel. Cumulative DVHs were calculated from the phantom and QSPECT images and compared both qualitatively and quantitatively. We found that noise, PVEs, and ringing artifacts due to CDR compensation all degraded histogram estimates. Low-pass filtering and early termination of the iterative process were needed to reduce the effects of noise and ringing artifacts on DVHs, but resulted in increased degradations due to PVEs. Large objects with few features, such as the liver, had more accurate histogram estimates and required fewer iterations and more smoothing for optimal results. Smaller objects with fine details, such as the kidneys, required more iterations and less

  4. Improved dose-volume histogram estimates for radiopharmaceutical therapy by optimizing quantitative SPECT reconstruction parameters.

    PubMed

    Cheng, Lishui; Hobbs, Robert F; Segars, Paul W; Sgouros, George; Frey, Eric C

    2013-06-07

    In radiopharmaceutical therapy, an understanding of the dose distribution in normal and target tissues is important for optimizing treatment. Three-dimensional (3D) dosimetry takes into account patient anatomy and the nonuniform uptake of radiopharmaceuticals in tissues. Dose-volume histograms (DVHs) provide a useful summary representation of the 3D dose distribution and have been widely used for external beam treatment planning. Reliable 3D dosimetry requires an accurate 3D radioactivity distribution as the input. However, activity distribution estimates from SPECT are corrupted by noise and partial volume effects (PVEs). In this work, we systematically investigated OS-EM based quantitative SPECT (QSPECT) image reconstruction in terms of its effect on DVHs estimates. A modified 3D NURBS-based Cardiac-Torso (NCAT) phantom that incorporated a non-uniform kidney model and clinically realistic organ activities and biokinetics was used. Projections were generated using a Monte Carlo (MC) simulation; noise effects were studied using 50 noise realizations with clinical count levels. Activity images were reconstructed using QSPECT with compensation for attenuation, scatter and collimator-detector response (CDR). Dose rate distributions were estimated by convolution of the activity image with a voxel S kernel. Cumulative DVHs were calculated from the phantom and QSPECT images and compared both qualitatively and quantitatively. We found that noise, PVEs, and ringing artifacts due to CDR compensation all degraded histogram estimates. Low-pass filtering and early termination of the iterative process were needed to reduce the effects of noise and ringing artifacts on DVHs, but resulted in increased degradations due to PVEs. Large objects with few features, such as the liver, had more accurate histogram estimates and required fewer iterations and more smoothing for optimal results. Smaller objects with fine details, such as the kidneys, required more iterations and less

  5. The effects of iterative reconstruction and kernel selection on quantitative computed tomography measures of lung density.

    PubMed

    Rodriguez, Alfonso; Ranallo, Frank N; Judy, Philip F; Fain, Sean B

    2017-06-01

    To determine the effects of iterative reconstruction (IR) and high-frequency kernels on quantitative computed tomography (qCT) density measures at reduced X-ray dose. The COPDGene 2 Phantom (CTP 698, The Phantom Laboratory, Salem, NY) with four embedded lung mimicking foam densities (12lb, 20lb, and 4lb), as well as water, air, and acrylic reference inserts, was imaged using a GE 64 slice CT750 HD scanner in helical mode with four current-time products ranging from 12 to 100 mAs. The raw acquired data were reconstructed using standard (STD - low frequency) and Bone (high frequency) kernels with filtered back projection (FBP), 100% ASiR, and Veo reconstruction algorithms. The reference density inserts were manually segmented using Slicer3D (www.slicer.org), and the mean, standard deviation, and histograms of the segmented regions were generated using Fiji (http://fiji.sc/Fiji) for each reconstruction. Measurements of threshold values placed on the cumulative frequency distribution of voxels determined by these measured histograms at 5%, PD5phant , and 15%, PD15phant , (analogous to the relative area below -950 HU (RA-950) and percent density 15 (PD15) in human lung emphysema quantification, respectively), were also performed. The use of high-resolution kernels in conjunction with ASiR and Veo did not significantly affect the mean Hounsfield units (HU) of each of the density standards (< 4 HU deviation) and current-time products within the phantom when compared with the STD+FBP reconstruction conventionally used in clinical applications. A truncation of the scanner reported HU values at -1024 that shifts the mean toward more positive values was found to cause a systematic error in lower attenuating regions. Use of IR drove convergence toward the mean of measured histograms (~100-137% increase in the number measured voxels at the mean of the histogram), while the combination of Bone+ASiR preserved the standard deviation of HU values about the mean compared to STD

  6. Quantitative Metabolome Analysis Based on Chromatographic Peak Reconstruction in Chemical Isotope Labeling Liquid Chromatography Mass Spectrometry.

    PubMed

    Huan, Tao; Li, Liang

    2015-07-21

    Generating precise and accurate quantitative information on metabolomic changes in comparative samples is important for metabolomics research where technical variations in the metabolomic data should be minimized in order to reveal biological changes. We report a method and software program, IsoMS-Quant, for extracting quantitative information from a metabolomic data set generated by chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS). Unlike previous work of relying on mass spectral peak ratio of the highest intensity peak pair to measure relative quantity difference of a differentially labeled metabolite, this new program reconstructs the chromatographic peaks of the light- and heavy-labeled metabolite pair and then calculates the ratio of their peak areas to represent the relative concentration difference in two comparative samples. Using chromatographic peaks to perform relative quantification is shown to be more precise and accurate. IsoMS-Quant is integrated with IsoMS for picking peak pairs and Zero-fill for retrieving missing peak pairs in the initial peak pairs table generated by IsoMS to form a complete tool for processing CIL LC-MS data. This program can be freely downloaded from the www.MyCompoundID.org web site for noncommercial use.

  7. Neurolucida Lucivid versus Neurolucida camera: A quantitative and qualitative comparison of three-dimensional neuronal reconstructions.

    PubMed

    Anderson, Kaeley; Yamamoto, Erin; Kaplan, Joshua; Hannan, Markus; Jacobs, Bob

    2010-02-15

    A critical issue in quantitative neuromorphology is the accuracy and subsequent reliability of the tracing techniques employed to characterize neuronal components. Historically, the camera lucida was the only option for such investigations. In 1987, MBF Bioscience, Inc. (Williston, VT) developed the integrative Neurolucida computer-microscope system, replacing the camera lucida drawing tube with a Lucivid cathode ray tube, thereby allowing computer overlays directly on the view through microscope oculars. Subsequent advances in digital cameras have allowed the Lucivid system to be replaced so that microscope images can be traced by viewing the digital image on a computer monitor. Indeed, the camera systems now outsell Lucivid systems 9 to 1 (J. Glaser, personal communication, 08/2008). Nevertheless, researchers seldom note which of these configurations are being used (which may confound the accuracy of data sharing), and there have been no published comparisons of the Lucivid and camera configurations. The present study thus assesses the relative accuracy of these two hardware configurations by examining reconstructions of human pyramidal neurons. We report significant differences with respect to dendritic spines, with the camera estimates of spine counts being greater than those obtained with the Lucivid system. Potential underlying reasons (e.g., magnification, illumination, and resolution, as well as observer ergonomic differences between the two systems) for these quantitative findings are explored here, along with qualitative observations on the relative strengths of each configuration. Copyright 2009 Elsevier B.V. All rights reserved.

  8. Bayesian Quantitative Trait Locus Mapping Based on Reconstruction of Recent Genetic Histories

    PubMed Central

    Gasbarra, Dario; Pirinen, Matti; Sillanpää, Mikko J.; Arjas, Elja

    2009-01-01

    We assume that quantitative measurements on a considered trait and unphased genotype data at certain marker loci are available on a sample of individuals from a background population. Our goal is to map quantitative trait loci by using a Bayesian model that performs, and makes use of, probabilistic reconstructions of the recent unobserved genealogical history (a pedigree and a gene flow at the marker loci) of the sampled individuals. This work extends variance component-based linkage analysis to settings where the unobserved pedigrees are considered as latent variables. In addition to the measured trait values and unphased genotype data at the marker loci, the method requires as an input estimates of the population allele frequencies and of a marker map, as well as some parameters related to the population size and the mating behavior. Given such data, the posterior distribution of the trait parameters (the number, the locations, and the relative variance contributions of the trait loci) is studied by using the reversible-jump Markov chain Monte Carlo methodology. We also introduce two shortcuts related to the trait parameters that allow us to do analytic integration, instead of stochastic sampling, in some parts of the algorithm. The method is tested on two simulated data sets. Comparisons with traditional variance component linkage analysis and association analysis demonstrate the benefits of our approach in a gene mapping context. PMID:19620396

  9. Molecular phylogenetics reveals a pattern of biome conservatism in New World anchovies (family Engraulidae).

    PubMed

    Bloom, Devin D; Lovejoy, N R

    2012-04-01

    Evolutionary transitions between marine and freshwater biomes are relatively rare events, yielding a widespread pattern of biome conservatism among aquatic organisms. We investigated biome transitions in anchovies (Engraulidae), a globally distributed clade of economically important fishes. Most anchovy species are near-shore marine fishes, but several exclusively freshwater species are known from tropical rivers of South America and were previously thought to be the product of six or more independent freshwater invasions. We generated a comprehensive molecular phylogeny for Engraulidae, including representatives from 15 of 17 currently recognized genera. Our data support previous hypotheses of higher-level relationships within Engraulidae, but show that most New World genera are not monophyletic and in need of revision. Ancestral character reconstruction reveals that New World freshwater anchovies are the product of a single marine to freshwater transition, supporting a pattern of biome conservatism. We argue that competition is the principal mechanism that regulates aquatic biome transitions on a continental scale.

  10. An analysis of quantitative measurements of drainage exudate using negative suction in 96 microtia ear reconstructions.

    PubMed

    Xu, Zhicheng; Zhang, Ruhong; Zhang, Qun; Xu, Feng

    2012-01-01

    Negative suction drainage is commonly used for the prevention of seromas or hematomas in auricular reconstruction surgery; however, there are few reports regarding the quantitative measurement of negative suction and its relation to disposed time, patient age or microtia type. In the present study, the authors recorded the volume of suction exudate in microtia reconstruction and elaborate on the relevant details of controlling negative suction. A negative suction drainage system was applied in 96 microtia patients between 2007 and 2010. Two small polyethylene drains were inserted adjacent to the concha and the scapha, respectively. The volume of exudate was recorded for three days after surgery and was analyzed according to disposed time, patient age and microtia type. The drains were removed on the third postoperative day, when only a small amount of exudate remained. A significant change in drainage was observed over three days postoperatively, and the quantity decreased progressively on the third postoperative day. Comparison of age groups showed that the volume of drainage from adults was greater than that from children or adolescents in the first two postoperative days, regardless of whether the drains were inserted in the scapha or concha. No statistical differences were found on the third postoperative day. A comparison of drain types revealed no statistically significant differences between scapha and concha drains three days postoperatively. The analysis demonstrated that drainage quantity is related to disposed time and patient age, but not to microtia type. The authors recommend removal of suction drains on the third postoperative day. Moreover, individualized negative suction treatment according to age or microtia type provides a safe and consistent approach to achieving acceptable results and fewer complications.

  11. A quantitative reconstruction of changes in relative humidity during the Younger Dryas in Western Europe

    NASA Astrophysics Data System (ADS)

    Rach, O.; Kahmen, A.; Brauer, A.; Sachse, D.

    2013-12-01

    Hydroclimatic changes have a profound effect on terrestrial ecosystems from regional to continental scales. However, past hydrological changes linked to abrupt climate shifts and their effect on terrestrial ecosystems are not well understood due to the lack of direct quantitative hydrological reconstructions. In addition, most paleoclimate proxies record the environmental response to hydrological variations, such as vegetation changes inferred by changes in pollen abundance, rather than hydroclimatic change itself. Over the last decade hydrogen isotope ratios (δD value) of lipid biomarkers have emerged as a novel and direct hydrological proxy, since it aims to reconstruct the δD values of the water source used by photosynthetic organisms. However, the hydrogen isotope ratio of source water (such as precipitation) is an integrated signal of condensation temperature, moisture pathway, precipitation amount and evaporation. As such, it is difficult to separate a single parameter, for example relative humidity, required for a true quantitative interpretation. Here we present a novel approach to quantify changes in relative humidity (Δrh) based on the hydrogen isotope composition of terrestrial and aquatic n-alkanes. In this proof-of-concept study we generate a high-resolution Δrh record for the Younger Dryas period (YD) of Western Europe from Lake Meerfelder Maar, (MFM, Germany). We use aquatic macrophyte biomarker δD values as a recorder of lake water δD (aq), which represents an integrated annual precipitation signal, and terrestrial leaf wax n-alkane δD values (terr) as a record of leaf-water evapotranspiration. Therefore we consider the isotopic difference between δDterr and δDaq (ɛterr-aq) as a measure of mean leaf water enrichment (ΔL), which is mainly controlled by relative humidity and temperature. By employing a modified and parameterized Craig-Gordon leaf-water model we are able to extract past changes in relative humidity from a sedimentary record

  12. Tropical grassy biomes: linking ecology, human use and conservation.

    PubMed

    Lehmann, Caroline E R; Parr, Catherine L

    2016-09-19

    Tropical grassy biomes (TGBs) are changing rapidly the world over through a coalescence of high rates of land-use change, global change and altered disturbance regimes that maintain the ecosystem structure and function of these biomes. Our theme issue brings together the latest research examining the characterization, complex ecology, drivers of change, and human use and ecosystem services of TGBs. Recent advances in ecology and evolution have facilitated a new perspective on these biomes. However, there continues to be controversies over their classification and state dynamics that demonstrate critical data and knowledge gaps in our quantitative understanding of these geographically dispersed regions. We highlight an urgent need to improve ecological understanding in order to effectively predict the sensitivity and resilience of TGBs under future scenarios of global change. With human reliance on TGBs increasing and their propensity for change, ecological and evolutionary understanding of these biomes is central to the dual goals of sustaining their ecological integrity and the diverse services these landscapes provide to millions of people.This article is part of the themed issue 'Tropical grassy biomes: linking ecology, human use and conservation'. © 2016 The Author(s).

  13. Tropical grassy biomes: linking ecology, human use and conservation

    PubMed Central

    Parr, Catherine L.

    2016-01-01

    Tropical grassy biomes (TGBs) are changing rapidly the world over through a coalescence of high rates of land-use change, global change and altered disturbance regimes that maintain the ecosystem structure and function of these biomes. Our theme issue brings together the latest research examining the characterization, complex ecology, drivers of change, and human use and ecosystem services of TGBs. Recent advances in ecology and evolution have facilitated a new perspective on these biomes. However, there continues to be controversies over their classification and state dynamics that demonstrate critical data and knowledge gaps in our quantitative understanding of these geographically dispersed regions. We highlight an urgent need to improve ecological understanding in order to effectively predict the sensitivity and resilience of TGBs under future scenarios of global change. With human reliance on TGBs increasing and their propensity for change, ecological and evolutionary understanding of these biomes is central to the dual goals of sustaining their ecological integrity and the diverse services these landscapes provide to millions of people. This article is part of the themed issue ‘Tropical grassy biomes: linking ecology, human use and conservation’. PMID:27502385

  14. Practical reconstruction protocol for quantitative (90)Y bremsstrahlung SPECT/CT.

    PubMed

    Siman, W; Mikell, J K; Kappadath, S C

    2016-09-01

    To develop a practical background compensation (BC) technique to improve quantitative (90)Y-bremsstrahlung single-photon emission computed tomography (SPECT)/computed tomography (CT) using a commercially available imaging system. All images were acquired using medium-energy collimation in six energy windows (EWs), ranging from 70 to 410 keV. The EWs were determined based on the signal-to-background ratio in planar images of an acrylic phantom of different thicknesses (2-16 cm) positioned below a (90)Y source and set at different distances (15-35 cm) from a gamma camera. The authors adapted the widely used EW-based scatter-correction technique by modeling the BC as scaled images. The BC EW was determined empirically in SPECT/CT studies using an IEC phantom based on the sphere activity recovery and residual activity in the cold lung insert. The scaling factor was calculated from 20 clinical planar (90)Y images. Reconstruction parameters were optimized in the same SPECT images for improved image quantification and contrast. A count-to-activity calibration factor was calculated from 30 clinical (90)Y images. The authors found that the most appropriate imaging EW range was 90-125 keV. BC was modeled as 0.53× images in the EW of 310-410 keV. The background-compensated clinical images had higher image contrast than uncompensated images. The maximum deviation of their SPECT calibration in clinical studies was lowest (<10%) for SPECT with attenuation correction (AC) and SPECT with AC + BC. Using the proposed SPECT-with-AC + BC reconstruction protocol, the authors found that the recovery coefficient of a 37-mm sphere (in a 10-mm volume of interest) increased from 39% to 90% and that the residual activity in the lung insert decreased from 44% to 14% over that of SPECT images with AC alone. The proposed EW-based BC model was developed for (90)Y bremsstrahlung imaging. SPECT with AC + BC gave improved lesion detectability and activity quantification compared to SPECT with AC

  15. Triple Oxygen and Deuterium Isotopes in Gypsum Hydration Water for Quantitative Paleo-humidity Reconstructions

    NASA Astrophysics Data System (ADS)

    Gázquez, F.; Evans, N. P.; Herwartz, D.; Bauska, T. K.; Morellon, M.; Surma, J.; Moreno, A.; Staubwasser, M.; Valero-Garces, B. L.; Hodell, D. A.

    2016-12-01

    Variations in atmospheric relative humidity (RH) and precipitation may have driven major ecological and sociocultural changes during the Quaternary but quantitative proxies for RH are scarce and difficult to calibrate. The isotopic composition of lake water (δ17O, δ18O and δD, and derived d-excess and 17Oexcess) is sensitive to changes in atmospheric RH and temperature. Because 17Oexcess is less sensitive to temperature effects than the d-excess during evaporation, combining 17Oexces and d-excess provide information about the relative effects of humidity and temperature change in the hydrological cycle. Here we demonstrate how the isotope ratios of hydration water measured in gypsum from lake sediments can be used to reconstruct past changes in RH. We present stable isotopes of gypsum hydration water from two lake systems across the last deglaciation. In Lake Estanya (NE, Spain) the 17Oexcess and d-excess of the paleo-lake water indicates that evaporation of water during the Younger Dryas (ca. 12 kyr BP) occurred under RH conditions of 40-45%. Environmental humidity gradually increased over the Preboreal period and stabilised at 70-75% during the Holocene until present. In Lake Peten-Itza (Guatemala), the isotopic values of the paleo-lake waters during the Late Glacial can be explained by a lowering of atmospheric RH by 10% and cooling of temperature by 5oC compared with modern conditions. Our results demonstrate that the coupled measurement of 17Oexcess and d-excess of gypsum hydration water in lake sediments can provide a useful quantitative proxy for paleo-humidity.

  16. Deconvolution of two-dimensional NMR spectra by fast maximum likelihood reconstruction: application to quantitative metabolomics.

    PubMed

    Chylla, Roger A; Hu, Kaifeng; Ellinger, James J; Markley, John L

    2011-06-15

    We have developed an algorithm called fast maximum likelihood reconstruction (FMLR) that performs spectral deconvolution of 1D-2D NMR spectra for the purpose of accurate signal quantification. FMLR constructs the simplest time-domain model (e.g., the model with the fewest number of signals and parameters) whose frequency spectrum matches the visible regions of the spectrum obtained from identical Fourier processing of the acquired data. We describe the application of FMLR to quantitative metabolomics and demonstrate the accuracy of the method by analysis of complex, synthetic mixtures of metabolites and liver extracts. The algorithm demonstrates greater accuracy (0.5-5.0% error) than peak height analysis and peak integral analysis with greatly reduced operator intervention. FMLR has been implemented in a Java-based framework that is available for download on multiple platforms and is interoperable with popular NMR display and processing software. Two-dimensional (1)H-(13)C spectra of mixtures can be acquired with acquisition times of 15 min and analyzed by FMLR in the range of 2-5 min per spectrum to identify and quantify constituents present at concentrations of 0.2 mM or greater.

  17. Decadally resolved quantitative temperature reconstruction spanning 5.6 ka at Kurupa Lake, Arctic Alaska

    NASA Astrophysics Data System (ADS)

    Boldt, B. R.; Kaufman, D. S.; Briner, J. P.

    2012-12-01

    Pre-instrumental quantitative temperature records, fundamental for placing recent warming in the context of long-term, natural climate variability, are scarce in Arctic Alaska. New non-destructive high-resolution core scanning methods provide a means of constructing downcore inference models for various paleoclimate signals. Here we use visible reflectance spectroscopy (VIS-RS) to measure organic pigment (chlorophyll derivative) concentration in sediments from Kurupa Lake to quantitatively reconstruct air temperature in the north-central Brooks Range, Alaska during the past 5.6 ka. Kurupa Lake (N 68.35°, W -154.61°) is 29.7 km2, 40 m at maximum depth, and is fed by several tributaries, including meltwater from eight rapidly disappearing cirque glaciers. A 6.2-m-long core composed of finely laminated (sub-mm to 5 cm) coarse-grained clays to medium-grained silts was collected in 2010 from the primary depocenter of Kurupa Lake (depth = 34 m). The age model for the core is based on six radiocarbon ages and a Pu profile to capture the 1963 spike and 1953 onset of Pu deposition from atmospheric weapons testing. The split-core face was scanned with a Konica Minolta CM-2600d spectrometer at 2 mm intervals, corresponding to 1-2 years. The relative absorption band depth at 660-670 nm (RABD660-670) was used to quantify total sedimentary organic pigments (primarily diagenetic products of chlorophyll-a) as a proxy for primary productivity. Gridded temperature data from the NCEP reanalysis dataset were used for this study because regional weather stations in the Brooks Range are scarce and records discontinuous. The gridded data perform well in this area and are highly correlated (r = 0.88) with the instrumental record from Barrow. Mean May-through-October (warm half-year) temperature (5-year smoothed) from NCEP reanalysis data (130 years) correlates with inferred organic pigment content from Kurupa Lake (r = 0.76, p < 0.001). We chose k-fold cross-validation (k = 10) to

  18. Quantitative assessment of rest and acetazolamide CBF using quantitative SPECT reconstruction and sequential administration of (123)I-iodoamphetamine: comparison among data acquired at three institutions.

    PubMed

    Yamauchi, Miho; Imabayashi, Etsuko; Matsuda, Hiroshi; Nakagawara, Jyoji; Takahashi, Masaaki; Shimosegawa, Eku; Hatazawa, Jun; Suzuki, Michiyasu; Iwanaga, Hideyuki; Fukuda, Kenji; Iihara, Koji; Iida, Hidehiro

    2014-11-01

    A recently developed technique which reconstructs quantitative images from original projection data acquired using existing single-photon emission computed tomography (SPECT) devices enabled quantitative assessment of cerebral blood flow (CBF) at rest and after acetazolamide challenge. This study was intended to generate a normal database and to investigate its inter-institutional consistency. The three institutions carried out a series of SPECT scanning on 32 healthy volunteers, following a recently proposed method that involved dual administration of (123)I-iodoamphetamine during a single SPECT scan. Intra-institute and inter-institutional variations of regional CBF values were evaluated both at rest and after acetazolamide challenge. Functional images were pooled for both rest and acetazolamide CBF, and inter-institutional difference was evaluated among these images using two independent software programs. Quantitative assessment of CBF images at rest and after acetazolamide was successfully achieved with the given protocol in all institutions. Intra-institutional variation of CBF values at rest and after acetazolamide was consistent with previously reported values. Quantitative CBF values showed no significant difference among institutions in all regions, except for a posterior cerebral artery region after acetazolamide challenge in one institution which employed SPECT device with lowest spatial resolution. Pooled CBF images at rest and after acetazolamide generated using two software programs showed no institutional differences after equalization of the spatial resolution. SPECT can provide reproducible images from projection data acquired using different SPECT devices. A common database acquired at different institutions may be shared among institutions, if images are reconstructed using a quantitative reconstruction program, and acquired by following a standardized protocol.

  19. Biome representational in silico karyotyping

    PubMed Central

    Muthappan, Valliammai; Lee, Aaron Y.; Lamprecht, Tamara L.; Akileswaran, Lakshmi; Dintzis, Suzanne M.; Lee, Choli; Magrini, Vincent; Mardis, Elaine R.; Shendure, Jay; Van Gelder, Russell N.

    2011-01-01

    Metagenomic characterization of complex biomes remains challenging. Here we describe a modification of digital karyotyping—biome representational in silico karyotyping (BRISK)—as a general technique for analyzing a defined representation of all DNA present in a sample. BRISK utilizes a Type IIB DNA restriction enzyme to create a defined representation of 27-mer DNAs in a sample. Massively parallel sequencing of this representation allows for construction of high-resolution karyotypes and identification of multiple species within a biome. Application to normal human tissue demonstrated linear recovery of tags by chromosome. We apply this technique to the biome of the oral mucosa and find that greater than 25% of recovered DNA is nonhuman. DNA from 41 microbial species could be identified from oral mucosa of two subjects. Of recovered nonhuman sequences, fewer than 30% are currently annotated. We characterized seven prevalent unknown sequences by chromosome walking and find these represent novel microbial sequences including two likely derived from novel phage genomes. Application of BRISK to archival tissue from a nasopharyngeal carcinoma resulted in identification of Epstein-Barr virus infection. These results suggest that BRISK is a powerful technique for the analysis of complex microbiomes and potentially for pathogen discovery. PMID:21324882

  20. Biome representational in silico karyotyping.

    PubMed

    Muthappan, Valliammai; Lee, Aaron Y; Lamprecht, Tamara L; Akileswaran, Lakshmi; Dintzis, Suzanne M; Lee, Choli; Magrini, Vincent; Mardis, Elaine R; Shendure, Jay; Van Gelder, Russell N

    2011-04-01

    Metagenomic characterization of complex biomes remains challenging. Here we describe a modification of digital karyotyping-biome representational in silico karyotyping (BRISK)-as a general technique for analyzing a defined representation of all DNA present in a sample. BRISK utilizes a Type IIB DNA restriction enzyme to create a defined representation of 27-mer DNAs in a sample. Massively parallel sequencing of this representation allows for construction of high-resolution karyotypes and identification of multiple species within a biome. Application to normal human tissue demonstrated linear recovery of tags by chromosome. We apply this technique to the biome of the oral mucosa and find that greater than 25% of recovered DNA is nonhuman. DNA from 41 microbial species could be identified from oral mucosa of two subjects. Of recovered nonhuman sequences, fewer than 30% are currently annotated. We characterized seven prevalent unknown sequences by chromosome walking and find these represent novel microbial sequences including two likely derived from novel phage genomes. Application of BRISK to archival tissue from a nasopharyngeal carcinoma resulted in identification of Epstein-Barr virus infection. These results suggest that BRISK is a powerful technique for the analysis of complex microbiomes and potentially for pathogen discovery.

  1. Assessment of quantitative Holocene temperature reconstructions based on multiple proxies from the sediment record of Lake Loitsana, Sokli, NE Finland

    NASA Astrophysics Data System (ADS)

    Shala, S.; Helmens, K. F.; Luoto, T. P.; Salonen, J. S.; Väliranta, M.; Weckström, J.

    2014-12-01

    Four biotic proxies (pollen, plant macrofossils chironomids and diatoms) are employed to quantitatively reconstruct variations in mean July air temperatures (Tjul) at Lake Loitsana, NE Finland, during the Holocene. The aim: assessing the reliability of these temperature reconstructions and the timing of highest Tjul. The reconstructed Tjul values are evaluated in relation to local-scale/site-specific processes associated to the Holocene lake development at Loitsana, as these factors have been shown to significantly influence the fossil assemblages found in the Lake Loitsana sediments. Our study shows that the reconstructions are influenced, at least to some extent, by local factors, and highlights the benefit of using multi-proxy data in Holocene climate reconstructions. While pollen-based temperatures follow the classical trend of gradually increasing early Holocene Tjul with a mid-Holocene maximum July warming, the aquatic/wetland assemblages reconstruct higher than present Tjul already during the early Holocene, i.e. at the peak of summer insolation. We conclude that the relatively low early Holocene July temperatures recorded by the terrestrial pollen are the result of site-specific factors possibly combined with a delayed response of the terrestrial ecosystem compared to the aquatic ecosystem.

  2. Quantitative computed tomography and cranial burr holes: a model to evaluate the quality of cranial reconstruction in humans.

    PubMed

    Worm, Paulo Valdeci; Ferreira, Nelson Pires; Ferreira, Marcelo Paglioli; Kraemer, Jorge Luiz; Lenhardt, Rene; Alves, Ronnie Peterson Marcondes; Wunderlich, Ricardo Castilho; Collares, Marcus Vinicius Martins

    2012-05-01

    Current methods to evaluate the biologic development of bone grafts in human beings do not quantify results accurately. Cranial burr holes are standardized critical bone defects, and the differences between bone powder and bone grafts have been determined in numerous experimental studies. This study evaluated quantitative computed tomography (QCT) as a method to objectively measure cranial bone density after cranial reconstruction with autografts. In each of 8 patients, 2 of 4 surgical burr holes were reconstructed with autogenous wet bone powder collected during skull trephination, and the other 2 holes, with a circular cortical bone fragment removed from the inner table of the cranial bone flap. After 12 months, the reconstructed areas and a sample of normal bone were studied using three-dimensional QCT; bone density was measured in Hounsfield units (HU). Mean (SD) bone density was 1535.89 (141) HU for normal bone (P < 0.0001), 964 (176) HU for bone fragments, and 453 (241) HU for bone powder (P < 0.001). As expected, the density of the bone fragment graft was consistently greater than that of bone powder. Results confirm the accuracy and reproducibility of QCT, already demonstrated for bone in other locations, and suggest that it is an adequate tool to evaluate cranial reconstructions. The combination of QCT and cranial burr holes is an excellent model to accurately measure the quality of new bone in cranial reconstructions and also seems to be an appropriate choice of experimental model to clinically test any cranial bone or bone substitute reconstruction.

  3. The widespread distribution of a Group I alkenone-producing haptophyte: Implications for quantitative temperature reconstructions

    NASA Astrophysics Data System (ADS)

    Richter, N.; Longo, W. M.; Amaral-Zettler, L. A.; Huang, Y.

    2016-12-01

    Isochysidales haptophytes uniquely produce unsaturated long-chain ketones called alkenones that are commonly applied to marine paleoclimate records. Recent efforts are extending alkenones as temperature proxies for continental environments; however, these systems are more complex due to the greater diversity of haptophyte species in these environments. Saline lakes, for instance, often contain multiple alkenone-producing species, making it difficult to obtain quantitative paleotemperature estimates. Recent findings point to the ubiquity of a distinct alkenone-producing Group I haptophyte that dominate the alkenones in freshwater, alkaline lakes. The purpose of this study was to confirm the presence of the Group I haptophyte in a suite of global freshwater, alkaline lakes that contain its alkenone signature: dominant C37:4 alkenones and tri-unsaturated ketone isomers. We have identified this signature in numerous lakes from North America, Europe, Asia, and the North Atlantic Islands. We have surveyed surface lake sediments for Group I haptophyte phylotypes using next-generation DNA amplicon sequencing targeting the hypervariable regions in the large and small-subunit ribosomal RNA gene. In addition, we used five lakes with distinct limnic and catchment characteristics from the North Slope of Alaska as model systems to monitor lake conditions that induce Group I haptophyte blooms. We collected multiple water column and surface sediment samples for alkenone and DNA analyses to track changes in haptophytes during the spring season. Lake ice-cover change and water column profiles monitored changes in lake stratification and isothermal mixing. These data will strengthen the springtime temperature calibration reported in a previous study by our group, thereby validating an accurate method for continental temperature reconstructions.

  4. Movement of Viruses between Biomes

    PubMed Central

    Sano, Emiko; Carlson, Suzanne; Wegley, Linda; Rohwer, Forest

    2004-01-01

    Viruses are abundant in all known ecosystems. In the present study, we tested the possibility that viruses from one biome can successfully propagate in another. Viral concentrates were prepared from different near-shore marine sites, lake water, marine sediments, and soil. The concentrates were added to microcosms containing dissolved organic matter as a food source (after filtration to allow 100-kDa particles to pass through) and a 3% (vol/vol) microbial inoculum from a marine water sample (after filtration through a 0.45-μm-pore-size filter). Virus-like particle abundances were then monitored using direct counting. Viral populations from lake water, marine sediments, and soil were able to replicate when they were incubated with the marine microbes, showing that viruses can move between different ecosystems and propagate. These results imply that viruses can laterally transfer DNA between microbes in different biomes. PMID:15466522

  5. Quantitative evaluation of ASiR image quality: an adaptive statistical iterative reconstruction technique

    NASA Astrophysics Data System (ADS)

    Van de Casteele, Elke; Parizel, Paul; Sijbers, Jan

    2012-03-01

    Adaptive statistical iterative reconstruction (ASiR) is a new reconstruction algorithm used in the field of medical X-ray imaging. This new reconstruction method combines the idealized system representation, as we know it from the standard Filtered Back Projection (FBP) algorithm, and the strength of iterative reconstruction by including a noise model in the reconstruction scheme. It studies how noise propagates through the reconstruction steps, feeds this model back into the loop and iteratively reduces noise in the reconstructed image without affecting spatial resolution. In this paper the effect of ASiR on the contrast to noise ratio is studied using the low contrast module of the Catphan phantom. The experiments were done on a GE LightSpeed VCT system at different voltages and currents. The results show reduced noise and increased contrast for the ASiR reconstructions compared to the standard FBP method. For the same contrast to noise ratio the images from ASiR can be obtained using 60% less current, leading to a reduction in dose of the same amount.

  6. Developing a chironomid training set for western South America (South-Central Chile): potential for quantitative temperature reconstructions

    NASA Astrophysics Data System (ADS)

    Araneda, A.; Larocque-Tobler, I.; Torrejon, F.; Grosjean, M.; Jana-Pinninghoff, P.; Ortega, C.; Urrutia, R.

    2012-12-01

    Quantitative climate reconstructions of the last two millennia are a fundamental issue in order to compare the current trends in climate observed nowadays. At global scale most of the climate reconstructions have been developed for the Northern Hemisphere, while for the Southern Hemisphere quantitative reconstructions are very rare and very limited geographically. The recognition of such disparity has generated among other research initiatives the LOTRED-SA Long-Term climate Reconstruction and Dynamics of (southern) South America, a collaborative, high-resolution multi-proxy approach within the framework of the IGBP-PAGES program. In this context our work presents the results of a 50-lakes training set in Central-Southern Chile developed with the aim to generate a basis for quantitative chironomid-inferred temperature reconstructions for this part of the continent. Chironomids (Insecta: Diptera) are aquatic insects that develop a great proportion of their life cycle as larvae in aquatic ecosystems. Several studies, developed mainly in the Northern Hemisphere, have proven their usefulness in reconstructing past climate due to the larvae's relationship to temperature. The training set developed here includes lakes located between 34 and 48 S, covering a broad temperature (as latitudinal) gradient. The surface (0-1 cm) sediment of each lake was sampled and chironomids, organic matter and nutrient were analyzed. Water analyses included the measurement of 10 variables (AirT, WBT, WST, N-tot, P-tot, Fe, Na, pH among others). In order to identify the most important variables explaining the highest variance in the chironomid assemblages, ordinations analyses were performed. A preliminary DCA analysis indicated, according to the length of gradients smaller than 3 STD, that a linear model was more appropriate for further analysis. Hence a RDA analysis was applied to the environmental and species data, indicating that the most important variables to determine chironomid

  7. Biosphere 2's Marsh Biome

    NASA Technical Reports Server (NTRS)

    Molnar, Jennifer; Goodridge, Kelven

    1997-01-01

    The Marsh Biome, which was modeled after the mangroves and marshes of southwest Florida, has an area of 441.2 sq m separated into three hydrologically independent sections: the Freshwater, Oligohaline and Salt Marshes. The divisions are made based on their salinity (approximately 0, 4, and 34 ppt. respectively), but they also contain different biological communities. The Freshwater and Oligohaline Marshes are mostly filled with various grasses and several trees, while the Salt Marsh houses regions of red, black, and white mangroves (Rhizophora mangle, Avicennia germinans, and Languncularia racemosa respectively). Overall, there are an estimated 80 species of plants within the biome. Water in the Salt Marsh follows a meandering stream from the algal turf scrubbers (apparatuses that clean the water of its nutrients and heavy metals while increasing dissolved oxygen levels) which have an outlet in the Salt Marsh section near sites 4 and 5 to the Fringing Red Mangrove section. The sections of the Salt Marsh are separated by walls of concrete with openings to allow the stream to flow through. Throughout this study, conducted through the months of June and July, many conditions within the biome remained fairly constant. The temperature was within a degree or two of 25 C, mostly depending on whether the sample site was in direct sunlight or shaded. The pH throughout the Salt Marsh was 8.0 +/- 0.2, and the lower salinity waters only dropped below this soon after rains. The water rdepth and dissolved oxygen varied, however, between sites.

  8. Post-reconstruction non-local means filtering methods using CT side information for quantitative SPECT.

    PubMed

    Chun, Se Young; Fessler, Jeffrey A; Dewaraja, Yuni K

    2013-09-07

    Quantitative SPECT techniques are important for many applications including internal emitter therapy dosimetry where accurate estimation of total target activity and activity distribution within targets are both potentially important for dose–response evaluations. We investigated non-local means (NLM) post-reconstruction filtering for accurate I-131 SPECT estimation of both total target activity and the 3D activity distribution. We first investigated activity estimation versus number of ordered-subsets expectation–maximization (OSEM) iterations. We performed simulations using the XCAT phantom with tumors containing a uniform and a non-uniform activity distribution, and measured the recovery coefficient (RC) and the root mean squared error (RMSE) to quantify total target activity and activity distribution, respectively. We observed that using more OSEM iterations is essential for accurate estimation of RC, but may or may not improve RMSE. We then investigated various post-reconstruction filtering methods to suppress noise at high iteration while preserving image details so that both RC and RMSE can be improved. Recently, NLM filtering methods have shown promising results for noise reduction. Moreover, NLM methods using high-quality side information can improve image quality further. We investigated several NLM methods with and without CT side information for I-131 SPECT imaging and compared them to conventional Gaussian filtering and to unfiltered methods. We studied four different ways of incorporating CT information in the NLM methods: two known (NLM CT-B and NLM CT-M) and two newly considered (NLM CT-S and NLM CT-H). We also evaluated the robustness of NLM filtering using CT information to erroneous CT. NLM CT-S and NLM CT-H yielded comparable RC values to unfiltered images while substantially reducing RMSE. NLM CT-S achieved −2.7 to 2.6% increase of RC compared to no filtering and NLM CT-H yielded up to 6% decrease in RC while other methods yielded lower

  9. Post-reconstruction non-local means filtering methods using CT side information for quantitative SPECT

    NASA Astrophysics Data System (ADS)

    Chun, Se Young; Fessler, Jeffrey A.; Dewaraja, Yuni K.

    2013-09-01

    Quantitative SPECT techniques are important for many applications including internal emitter therapy dosimetry where accurate estimation of total target activity and activity distribution within targets are both potentially important for dose-response evaluations. We investigated non-local means (NLM) post-reconstruction filtering for accurate I-131 SPECT estimation of both total target activity and the 3D activity distribution. We first investigated activity estimation versus number of ordered-subsets expectation-maximization (OSEM) iterations. We performed simulations using the XCAT phantom with tumors containing a uniform and a non-uniform activity distribution, and measured the recovery coefficient (RC) and the root mean squared error (RMSE) to quantify total target activity and activity distribution, respectively. We observed that using more OSEM iterations is essential for accurate estimation of RC, but may or may not improve RMSE. We then investigated various post-reconstruction filtering methods to suppress noise at high iteration while preserving image details so that both RC and RMSE can be improved. Recently, NLM filtering methods have shown promising results for noise reduction. Moreover, NLM methods using high-quality side information can improve image quality further. We investigated several NLM methods with and without CT side information for I-131 SPECT imaging and compared them to conventional Gaussian filtering and to unfiltered methods. We studied four different ways of incorporating CT information in the NLM methods: two known (NLM CT-B and NLM CT-M) and two newly considered (NLM CT-S and NLM CT-H). We also evaluated the robustness of NLM filtering using CT information to erroneous CT. NLM CT-S and NLM CT-H yielded comparable RC values to unfiltered images while substantially reducing RMSE. NLM CT-S achieved -2.7 to 2.6% increase of RC compared to no filtering and NLM CT-H yielded up to 6% decrease in RC while other methods yielded lower RCs

  10. Quantitative diet reconstruction of a Neolithic population using a Bayesian mixing model (FRUITS): The case study of Ostorf (Germany).

    PubMed

    Fernandes, Ricardo; Grootes, Pieter; Nadeau, Marie-Josée; Nehlich, Olaf

    2015-07-14

    The island cemetery site of Ostorf (Germany) consists of individual human graves containing Funnel Beaker ceramics dating to the Early or Middle Neolithic. However, previous isotope and radiocarbon analysis demonstrated that the Ostorf individuals had a diet rich in freshwater fish. The present study was undertaken to quantitatively reconstruct the diet of the Ostorf population and establish if dietary habits are consistent with the traditional characterization of a Neolithic diet. Quantitative diet reconstruction was achieved through a novel approach consisting of the use of the Bayesian mixing model Food Reconstruction Using Isotopic Transferred Signals (FRUITS) to model isotope measurements from multiple dietary proxies (δ(13) Ccollagen , δ(15) Ncollagen , δ(13) Cbioapatite , δ(34) Smethione , (14) Ccollagen ). The accuracy of model estimates was verified by comparing the agreement between observed and estimated human dietary radiocarbon reservoir effects. Quantitative diet reconstruction estimates confirm that the Ostorf individuals had a high protein intake due to the consumption of fish and terrestrial animal products. However, FRUITS estimates also show that plant foods represented a significant source of calories. Observed and estimated human dietary radiocarbon reservoir effects are in good agreement provided that the aquatic reservoir effect at Lake Ostorf is taken as reference. The Ostorf population apparently adopted elements associated with a Neolithic culture but adapted to available local food resources and implemented a subsistence strategy that involved a large proportion of fish and terrestrial meat consumption. This case study exemplifies the diversity of subsistence strategies followed during the Neolithic. Am J Phys Anthropol, 2015. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  11. Quantitative reconstruction of paleoclimate - Air and ground temperature tracking from Emigrant Pass Observatory

    NASA Astrophysics Data System (ADS)

    Chapman, D. S.; Bartlett, M. G.; Harris, R. N.

    2004-12-01

    Borehole temperature-depth profiles contain information about surface ground temperatures histories and provide a useful complement to proxy indicators of climate change. An inherent assumption in borehole temperature reconstructions is that air and ground temperatures are coupled through heat diffusion track each other at annual and longer periods. The Emigrant Pass Observatory (EPO), located in the Grouse Creek Mountains of northwestern Utah, is designed to test ground-air temperature tracking. Analyses of 10 years of observations at EPO demonstrate the following: 1) Ground temperatures track air temperatures at annual and longer periods exceptionally well at the site. Divergence between the observed temperatures at 1 m in the subsurface and air temperatures modeled as a boundary layer forcing is less than 0.04 K per annum. 2) Seasonal variations in incident solar radiation are ~200 Wm-2 leading to an average annual difference between ground and air temperatures, Δ Tg-a, of 2.55 K (±0.01) from 1993-2003. The temperature difference varies from -5 K to +10 K when averaged over a diurnal cycle, and from 2.50 K to 2.60 K over an annual cycle. However, inter-annual variations in insulation are less than 1 Wm-2; consequently, solar radiation is not observed to affect the inter-annual tracking at the site. 3) Model studies snow-ground thermal interactions at EPO demonstrate that seasonal snow cover can either warm or cool the ground relative to the annual mean air temperature and that the winter snow effect is an order of magnitude smaller than the summer radiation effect at the site. 4) Temperature observations at various depths within the granite and soils at the site allow us to make estimates of in-situ thermal diffusivity and its changes with time. The "apparent" thermal diffusivity of the upper meter of granite at EPO ranges from 0.88-0.98 x 10-6 m2s-1 while the soil varies from 0.57-0.68 x 10-6 m2s-1. The accumulation of data at EPO leads to a quantitative

  12. A quantitative reconstruction of organic matter and nutrient diagenesis in Mediterranean Sea sediments over the Holocene

    NASA Astrophysics Data System (ADS)

    Reed, Daniel C.; Slomp, Caroline P.; de Lange, Gert J.

    2011-10-01

    A multicomponent diagenetic model was developed and applied to reconstruct the conditions under which the most recent sapropel, S1, was deposited in the eastern Mediterranean Sea. Simulations demonstrate that bottom waters must have been anoxic and sulphidic during the formation of S1 and that organic matter deposition was approximately three times higher than at present. Nevertheless, most present day sediment and pore water profiles — with the exception of pyrite, iron oxyhydroxides, iron-bound phosphorus and phosphate — can be reproduced under a wide range of redox conditions during formation of S1 by varying the depositional flux of organic carbon. As a result, paleoredox indicators (e.g., C org:S ratio, C org:P org ratio, trace metals) are needed when assessing the contribution of oxygen-depletion and enhanced primary production to the formation of organic-rich layers in the geological record. Furthermore, simulations show that the organic carbon concentration in sediments is a direct proxy for export production under anoxic bottom waters. The model is also used to examine the post-depositional alteration of the organic-rich layer focussing on nitrogen, phosphorus, and organic carbon dynamics. After sapropel formation, remineralisation is dominated by aerobic respiration at a rate that is inversely proportional to the time since bottom waters became oxic once again. A sensitivity analysis was undertaken to identify the most pertinent parameters in regulating the oxidation of sapropels, demonstrating that variations in sedimentation rate, depositional flux of organic carbon during sapropel formation, bottom water oxygen concentration, and porosity have the largest impact. Simulations reveal that sedimentary nutrient cycling was markedly different during the formation of S1, as well as after reoxygenation of bottom waters. Accumulation of organic nitrogen in sediments doubled during sapropel deposition, representing a significant nitrogen sink. Following

  13. What do we need to measure, how much, and where? A quantitative assessment of terrestrial data needs across North American biomes through data-model fusion and sampling optimization

    NASA Astrophysics Data System (ADS)

    Dietze, M. C.; Davidson, C. D.; Desai, A. R.; Feng, X.; Kelly, R.; Kooper, R.; LeBauer, D. S.; Mantooth, J.; McHenry, K.; Serbin, S. P.; Wang, D.

    2012-12-01

    Ecosystem models are designed to synthesize our current understanding of how ecosystems function and to predict responses to novel conditions, such as climate change. Reducing uncertainties in such models can thus improve both basic scientific understanding and our predictive capacity, but rarely have the models themselves been employed in the design of field campaigns. In the first part of this paper we provide a synthesis of uncertainty analyses conducted using the Predictive Ecosystem Analyzer (PEcAn) ecoinformatics workflow on the Ecosystem Demography model v2 (ED2). This work spans a number of projects synthesizing trait databases and using Bayesian data assimilation techniques to incorporate field data across temperate forests, grasslands, agriculture, short rotation forestry, boreal forests, and tundra. We report on a number of data needs that span a wide array diverse biomes, such as the need for better constraint on growth respiration. We also identify other data needs that are biome specific, such as reproductive allocation in tundra, leaf dark respiration in forestry and early-successional trees, and root allocation and turnover in mid- and late-successional trees. Future data collection needs to balance the unequal distribution of past measurements across biomes (temperate biased) and processes (aboveground biased) with the sensitivities of different processes. In the second part we present the development of a power analysis and sampling optimization module for the the PEcAn system. This module uses the results of variance decomposition analyses to estimate the further reduction in model predictive uncertainty for different sample sizes of different variables. By assigning a cost to each measurement type, we apply basic economic theory to optimize the reduction in model uncertainty for any total expenditure, or to determine the cost required to reduce uncertainty to a given threshold. Using this system we find that sampling switches among multiple

  14. Quantitative reconstruction of PIXE-tomography data for thin samples using GUPIX X-ray emission yields

    NASA Astrophysics Data System (ADS)

    Michelet, C.; Barberet, Ph.; Devès, G.; Bouguelmouna, B.; Bourret, S.; Delville, M.-H.; Le Trequesser, Q.; Gordillo, N.; Beasley, D. G.; Marques, A. C.; Farau, R.; Toko, B. R.; Campbell, J.; Maxwell, J.; Moretto, Ph.; Seznec, H.

    2015-04-01

    We present here a new development of the TomoRebuild software package, to perform quantitative Particle Induced X-ray Emission Tomography (PIXET) reconstruction. X-ray yields are obtained from the GUPIX code. The GUPIX data base is available for protons up to 5 MeV and also in the 20-100 MeV energy range, deuterons up to 6 MeV, 3He and alphas up to 12 MeV. In this version, X-ray yields are calculated for thin samples, i.e. without simulating X-ray attenuation. PIXET data reconstruction is kept as long as possible independent from Scanning Transmission Ion Microscopy Tomography (STIMT). In this way, the local mass distribution (in g/cm3) of each X-ray emitting element is reconstructed in all voxels of the analyzed volume, only from PIXET data, without the need of associated STIMT data. Only the very last step of data analysis requires STIMT data, in order to normalize PIXET data to obtain concentration distributions, in terms of normalized mass fractions (in μg/g). For this, a noise correction procedure has been designed in ImageJ. Moreover sinogram or image misalignment can be corrected, as well as the difference in beam size between the two experiments. The main features of the TomoRebuild code, user friendly design and modular C++ implementation, were kept. The software package is portable and can run on Windows and Linux operating systems. An optional user-friendly graphic interface was designed in Java, as a plugin for the ImageJ graphic software package. Reconstruction examples are presented from biological specimens of Caenorhabditis elegans - a small nematode constituting a reference model for biology studies. The reconstruction results are compared between the different codes TomoRebuild, DISRA and JPIXET, and different reconstruction methods: Filtered BackProjection (FBP) and Maximum Likelihood Expectation Maximization (MLEM).

  15. Quantitative vertical zonation of salt-marsh foraminifera for reconstructing former sea level; an example from New Jersey, USA.

    NASA Astrophysics Data System (ADS)

    Kemp, Andrew C.; Horton, Benjamin P.; Vann, David R.; Engelhart, Simon E.; Grand Pre, Candace A.; Vane, Christopher H.; Nikitina, Daria; Anisfeld, Shimon C.

    2012-10-01

    We present a quantitative technique to reconstruct sea level from assemblages of salt-marsh foraminifera using partitioning around medoids (PAM) and linear discriminant functions (LDF). The modern distribution of foraminifera was described from 62 surface samples at three salt marshes in southern New Jersey. PAM objectively estimated the number and composition of assemblages present at each site and showed that foraminifera adhered to the concept of elevation-dependent ecological zones, making them appropriate sea-level indicators. Application of PAM to a combined dataset identified five distinctive biozones occupying defined elevation ranges, which were similar to those identified elsewhere on the U.S. mid-Atlantic coast. Biozone A had high abundances of Jadammina macrescens and Trochammina inflata; biozone B was dominated by Miliammina fusca; biozone C was associated with Arenoparrella mexicana; biozone D was dominated by Tiphotrocha comprimata and biozone E was dominated by Haplophragmoides manilaensis. Foraminiferal assemblages from transitional and high salt-marsh environments occupied the narrowest elevational range and are the most precise sea-level indicators. Recognition of biozones in sequences of salt-marsh sediment using LDFs provides a probabilistic means to reconstruct sea level. We collected a core to investigate the practical application of this approach. LDFs indicated the faunal origin of 38 core samples and in cross-validation tests were accurate in 54 of 56 cases. We compared reconstructions from LDFs and a transfer function. The transfer function provides smaller error terms and can reconstruct smaller RSL changes, but LDFs are well suited to RSL reconstructions focused on larger changes and using varied assemblages. Agreement between these techniques suggests that the approach we describe can be used as an independent means to reconstruct sea level or, importantly, to check the ecological plausibility of results from other techniques.

  16. Quantitative high-resolution rainfall reconstruction back to AD 750 from the varved sediments of Lake Oeschinen, northern Swiss Alps

    NASA Astrophysics Data System (ADS)

    Amann, Benjamin; Mauchle, Fabian; Grosjean, Martin

    2014-05-01

    Varved lake sediments are valuable natural paleoclimatic archives due to their potential to preserve climate variability through very long times and at annual resolution. Well-calibrated records from lake sediments are critically important for quantitative climate reconstructions but they remain a methodological and analytical challenge. While several comprehensive paleotemperature reconstructions have been developed across Europe, quantitative studies on rainfall are still scarce. Here we present a quantitative high-resolution warm season rainfall reconstruction from the varved sediments of proglacial Lake Oeschinen (north-western Swiss Alps) back to AD 750. Lake Oeschinen is a high-elevation lake (1580 m a.s.l.), 56-m deep, oligotrophic (< 5 % OM) and dimictic with an ice cover extending from December through early May. The lake was formed by a Holocene rock slide. We used shoreline and delta-fan surface samples in combination with sediment trap data to interpret the varve formation process. Data from these sediments fingerprint different sediment source areas and transport process from the watershed and confirm the instant response of sediment flux to rainfall. Erodible sediments from the northern part of the catchment (Tertiary Flysch) are transported after snowmelt and warm season rainfall, whereas sediments from the southern glaciated part (Mesozoic limestone) are mainly transported with glacial meltwater independent from rainfall. Based on a highly accurate, precise and reproducible chronology, we demonstrate that varve thickness can be used as quantitative predictor for boreal spring-summer (MJJA) rainfall (r = 0.60, p < 0.01, 3-yr filtered) for the calibration period AD 1901 - 2008. We use this calibration model to establish a spring-summer rainfall record back to AD 750. Our rainfall reconstruction compares well with independent early instrumental precipitation data for the north-western Swiss Alps back to AD 1760 (HISTALP data set). The rainfall

  17. A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

    PubMed Central

    Morales-Navarrete, Hernán; Segovia-Miranda, Fabián; Klukowski, Piotr; Meyer, Kirstin; Nonaka, Hidenori; Marsico, Giovanni; Chernykh, Mikhail; Kalaidzidis, Alexander; Zerial, Marino; Kalaidzidis, Yannis

    2015-01-01

    A prerequisite for the systems biology analysis of tissues is an accurate digital three-dimensional reconstruction of tissue structure based on images of markers covering multiple scales. Here, we designed a flexible pipeline for the multi-scale reconstruction and quantitative morphological analysis of tissue architecture from microscopy images. Our pipeline includes newly developed algorithms that address specific challenges of thick dense tissue reconstruction. Our implementation allows for a flexible workflow, scalable to high-throughput analysis and applicable to various mammalian tissues. We applied it to the analysis of liver tissue and extracted quantitative parameters of sinusoids, bile canaliculi and cell shapes, recognizing different liver cell types with high accuracy. Using our platform, we uncovered an unexpected zonation pattern of hepatocytes with different size, nuclei and DNA content, thus revealing new features of liver tissue organization. The pipeline also proved effective to analyse lung and kidney tissue, demonstrating its generality and robustness. DOI: http://dx.doi.org/10.7554/eLife.11214.001 PMID:26673893

  18. Biome Context and Lotic Ecosystem Rates

    NASA Astrophysics Data System (ADS)

    Dodds, W. K.; Rüegg, J.; Sheehan, K.; Song, C.; Ballantyne, F.; Baker, C.; Bowden, W. B.; Farrell, K.; Flinn, M. B.; Garcia, E.; Harms, T.; Jones, J.; Koenig, L.; Kominoski, J. S.; McDowell, W. H.; McMaster, D.; Parker, S.; Trentman, M. T.; Whiles, M.; Wollheim, W. M.; Argerich, A.; Penaluna, B.

    2015-12-01

    The stream biome gradient concept suggests that the biome in which a stream is embedded influences stream community structure and key ecosystem functions including primary production, community respiration, and nutrient uptake. We measured these key processes with whole-stream reach methods and smaller-scale incubations in numerous locations within stream networks across two years as part of a project on scaling ecosystem rates. Measurements were repeated across 7 biomes (tropical forest, tropical savanna, temperate deciduous forest, temperate rain forest, tallgrass prairie, boreal forest, and tundra). We found strong effects of light on primary production within and among biomes as a function of variable canopy among reaches and biomes. Community respiration and ammonium uptake were decoupled from light relative to gross primary production. Ammonium uptake rarely exhibited saturation with elevated concentrations, regardless of background concentrations or biome. We hypothesize that even though biomes exhibit major differences in gross primary production, the overall variation in community respiration and ammonium uptake is similar across biomes because respiration and uptake depend on carbon irrespective if it is derived from allochthonous or autochthonous inputs. Respiration and uptake are expected to vary depending upon factors not as tightly connected to the biome a stream is embedded in.

  19. Validation of a quantitative susceptibility mapping acquisition and reconstruction pipeline using a new iron sucrose based MR susceptibility phantom.

    PubMed

    Deverdun, Jeremy; Molino, François; Menjot de Champfleur, Nicolas; Le Bars, Emmanuelle

    2017-07-01

    Quantitative susceptibility mapping is a new technique and its processing pipeline has to be validated before clinical practice. We described an easy to build magnetic resonance (MR) susceptibility phantom based on iron sucrose. In a plastic container, Eppendorf tubes containing increasing iron sucrose concentration ranging from 0 to 60μg Fe/mL were inserted in an agarose gel. To estimate susceptibility, multiple coronal gradient echo acquisitions were performed with varying angle of the phantom relative to the B0 field, ranging from 30 to 90°. Quantitative susceptibility maps were reconstructed using the l1 and l2 norm of total variation using Split Bregman approach. Iron concentration was finally estimated from the susceptibility in the tubes. In l1norm susceptibility and estimated iron concentration were not different from the real values while l2norm underestimated the susceptibility. A correlation was found between the angle of the phantom and the difference between real and estimated iron concentrations. The results highlight the importance of this validation by emphasizing the effects of various reconstruction parameters as well as acquisition conditions. Using optimal parameters, the quantitative susceptibility mapping provides a very good estimation of the iron concentrations in the phantom. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  20. Pollen, biomes, forest successions and climate at Lake Barombi Mbo (Cameroon) during the last ca. 33 000 cal yr BP - a numerical approach

    NASA Astrophysics Data System (ADS)

    Lebamba, J.; Vincens, A.; Maley, J.

    2010-12-01

    The aim of this paper is to provide a more complete and precise interpretation of the 33 000 cal yr BP pollen sequence from Lake Barombi Mbo, southwestern Cameroon (4°39'45.75'' N, 9°23'51.63'' E, 303 m a.s.l.), based on a numerical approach allowing quantitative estimates of vegetation and climate. The biomisation method was applied on fossil pollen assemblages to reconstruct potential biomes and forest successional stages. The modern analogues (MAT) and the artificial neural networks (ANN) techniques were used to reconstruct mean annual rainfall (Pann), mean annual potential evapotranspiration (PETann) and a bioclimatic index α related to the vegetation stature. Our reconstructions testifies of a dense forested environment around Lake Barombi Mbo of mixed evergreen/semi-deciduous type during the most humid phases (highest rainfall and lowest evapotranspiration reconstructed values), but with a more pronounced semi-deciduous facies from ca. 6500 cal yr BP to present day related to increased seasonality. These forests display a mature character until ca. 2800 cal yr BP then become of secondary type during the last millennium probably linked to increased human interferences. Two episodes of fragmentation are evidenced synchronous with the lowest rainfall and highest potential evapotranspiration reconstructed values, the first one centered during the LGM, and the second one from ca. 3000 to ca. 1200 cal yr BP linked mainly to high seasonality. But, as shown by low scores of savanna potential biome and successional stage, open formations never largely extend in the Barombi Mbo basin, and were more probably enclosed inside the forest in form of savanna patches. Concerning the climatic reconstructions at Lake Barombi Mbo, The ANN appears to be the most reliable technique in spite of under-estimated values of Pann all along the sequence mainly due to a lack of modern pollen data from very humid areas in central Africa.

  1. Holocene biome shifts in the East Asian monsoon margin region

    NASA Astrophysics Data System (ADS)

    Dallmeyer, Anne; Claussen, Martin; Ni, Jian; Wang, Yongbo; Cao, Xianyong; Herzschuh, Ulrike

    2013-04-01

    East Asia is affected by three major atmospheric circulation systems determining the regional climate and vegetation distribution: The moisture advected by the Indian and East Asian monsoon support the growing of forest in large parts of Eastern China. The influence of the monsoon gets weaker further on the continent yielding a transition of forest to steppe and of steppe to desert in Central East Asia (e.g. Inner Mongolia) where the dry westerly winds prevail. Particularly in these transition zones, vegetation is supposed to be very sensitive to climate change and strong feedbacks are expected in case of climate and vegetation shifts due to large environmental changes (Feng et al., 2006). During mid-Holocene, cyclic variations in the Earth's orbit around the sun led to an enhancement of the Asian monsoon system probably causing strong shifts in the biome distribution. According to reconstructions, the steppe-forest margin moved to the northwest by about 500km (Yu et al., 2000) and the desert area in China and Inner Mongolia was substantially reduced compared to today (Feng et al., 2006). However, in the complex environment of Asia, the locally limited reconstructions may not portray the general vegetation change. To get a systematic overview on the spatial pattern of biome shifts in the Asian monsoon - westerly wind transition zone since mid-Holocene, we use the diagnostic vegetation model BIOME4 and force this model with climate anomalies from different transient Holocene climate simulations performed in coupled atmosphere-ocean-vegetation models. The main aims of this study are to a) get a consistent ensemble of possible changes in biome distribution since the mid-Holocene b) test the robustness of the simulated vegetation changes and quantify the differences between the models, and c) allow for a better comparison of simulated and reconstructed vegetation changes. Preliminary results confirm the general trend seen in the reconstructions. The simulations reveal

  2. Holocene relative sea-level change in Hiroshima Bay, Japan: A semi-quantitative reconstruction based on ostracodes

    USGS Publications Warehouse

    Yasuhara, Moriaki; Seto, Koji

    2006-01-01

    Holocene relative sea-level changes in Hiroshima Bay were reconstructed from fossil ostracodes from a core, using a semi-quantitative method. In Hiroshima Bay, relative sea level rose rapidly (about 25 m) between ca. 9000 cal yr BP and ca. 5800 cal yr BP, after which it gradually fell (about 5 m) to its present level. The peak in relative sea level occurred at ca. 5800 cal yr BP. The sea-level curve for Hiroshima Bay is similar to curves for tectonically stable areas of Japan (e.g., Osaka Bay). ?? by the Palaeontological Society of Japan.

  3. Quantitative analysis of the tree-ring width record features essential for paleoclimatic reconstructions

    NASA Astrophysics Data System (ADS)

    Datsenko, N. M.; Ivashchenko, N. N.; Sonechkin, D. M.; Yang, B.

    2010-10-01

    Tree-ring width records provide a primary data source for millennial paleoclimatic reconstructions. However, a problem exists connected with taking into consideration the complex age-dependence within these records. Analyzing a set of very long-lived trees of Sabina przewalskii Kom. from the Dulan area of the northeastern Tibetan Plateau, we found for the first time that the annual basal-radius increment is larger for the outermost rings in comparison with the inner rings, especially for very long-living trees. Neglecting this circumstance when the so-called regional curve standardization is used can distort paleoclimatic reconstructions.

  4. Phylogenetic biome conservatism on a global scale.

    PubMed

    Crisp, Michael D; Arroyo, Mary T K; Cook, Lyn G; Gandolfo, Maria A; Jordan, Gregory J; McGlone, Matt S; Weston, Peter H; Westoby, Mark; Wilf, Peter; Linder, H Peter

    2009-04-09

    How and why organisms are distributed as they are has long intrigued evolutionary biologists. The tendency for species to retain their ancestral ecology has been demonstrated in distributions on local and regional scales, but the extent of ecological conservatism over tens of millions of years and across continents has not been assessed. Here we show that biome stasis at speciation has outweighed biome shifts by a ratio of more than 25:1, by inferring ancestral biomes for an ecologically diverse sample of more than 11,000 plant species from around the Southern Hemisphere. Stasis was also prevalent in transocean colonizations. Availability of a suitable biome could have substantially influenced which lineages establish on more than one landmass, in addition to the influence of the rarity of the dispersal events themselves. Conversely, the taxonomic composition of biomes has probably been strongly influenced by the rarity of species' transitions between biomes. This study has implications for the future because if clades have inherently limited capacity to shift biomes, then their evolutionary potential could be strongly compromised by biome contraction as climate changes.

  5. Quantitative analysis of 3D stent reconstruction from a limited number of views in cardiac rotational angiography

    NASA Astrophysics Data System (ADS)

    Perrenot, Béatrice; Vaillant, Régis; Prost, Rémy; Finet, Gérard; Douek, Philippe; Peyrin, Françoise

    2007-03-01

    Percutaneous coronary angioplasty consists in conducting a guidewire carrying a balloon and a stent through the lesion and deploying the stent by balloon inflation. A stent is a small 3D complex mesh hardly visible in X-ray images : the control of stent deployment is difficult although it is important to avoid post intervention complications. In a previous work, we proposed a method to reconstruct 3D stent images from a set of 2D cone-beam projections acquired in rotational acquisition mode. The process involves a motion compensation procedure based on the position of two markers located on the guidewire in the 2D radiographic sequence. Under the hypothesis that the stent and markers motions are identical, the method was shown to generate a negligible error. If this hypothesis is not fulfilled, a solution could be to use only the images where motion is weakest, at the detriment of having a limiter number of views. In this paper, we propose a simulation based study of the impact of a limited number of views in our context. The chain image involved in the acquisition of X-ray sequences is first modeled to simulate realistic noisy projections of stent animated by a motion close to cardiac motion. Then, the 3D stent images are reconstructed using the proposed motion compensation method from gated projections. Two gating strategies are examined to select projection in the sequences. A quantitative analysis is carried out to assess reconstruction quality as a function of noise and acquisition strategy.

  6. Toward a rule-based biome model

    SciTech Connect

    Neilson, R.P.; King, G.A.; Koerper, G.

    1991-01-01

    Current projections of the response of the biosphere to global climatic change indicate as much as 50% to 90% spatial displacement of extratropical biomes. The mechanism of spatial shift could be dominated by either (1) competitive displacement of northern biomes by southern biomes, or (2) drought-induced dieback of areas susceptible to change. The current suite of global biosphere models cannot distinguish between these two processes, thus determining the need for a mechanistically based biome model. The model is in an early stage of development and will require several enhancements, including explicit simulation of potential evapotranspiration, extension to boreal and tropical biomes, a shift from steady-state to transient dynamics, and validation on other continents.

  7. Acquisition of quantitative physiological data and computerized image reconstruction using a single scan TV system

    NASA Technical Reports Server (NTRS)

    Baily, N. A.

    1976-01-01

    A single-scan radiography system has been interfaced to a minicomputer, and the combined system has been used with a variety of fluoroscopic systems and image intensifiers available in clinical facilities. The system's response range is analyzed, and several applications are described. These include determination of the gray scale for typical X-ray-fluoroscopic-television chains, measurement of gallstone volume in patients, localization of markers or other small anatomical features, determinations of organ areas and volumes, computer reconstruction of tomographic sections of organs in motion, and computer reconstruction of transverse axial body sections from fluoroscopic images. It is concluded that this type of system combined with a minimum of statistical processing shows excellent capabilities for delineating small changes in differential X-ray attenuation.

  8. Acquisition of quantitative physiological data and computerized image reconstruction using a single scan TV system

    NASA Technical Reports Server (NTRS)

    Baily, N. A.

    1976-01-01

    A single-scan radiography system has been interfaced to a minicomputer, and the combined system has been used with a variety of fluoroscopic systems and image intensifiers available in clinical facilities. The system's response range is analyzed, and several applications are described. These include determination of the gray scale for typical X-ray-fluoroscopic-television chains, measurement of gallstone volume in patients, localization of markers or other small anatomical features, determinations of organ areas and volumes, computer reconstruction of tomographic sections of organs in motion, and computer reconstruction of transverse axial body sections from fluoroscopic images. It is concluded that this type of system combined with a minimum of statistical processing shows excellent capabilities for delineating small changes in differential X-ray attenuation.

  9. Effects of sparse sampling in combination with iterative reconstruction on quantitative bone microstructure assessment

    NASA Astrophysics Data System (ADS)

    Mei, Kai; Kopp, Felix K.; Fehringer, Andreas; Pfeiffer, Franz; Rummeny, Ernst J.; Kirschke, Jan S.; Noël, Peter B.; Baum, Thomas

    2017-03-01

    The trabecular bone microstructure is a key to the early diagnosis and advanced therapy monitoring of osteoporosis. Regularly measuring bone microstructure with conventional multi-detector computer tomography (MDCT) would expose patients with a relatively high radiation dose. One possible solution to reduce exposure to patients is sampling fewer projection angles. This approach can be supported by advanced reconstruction algorithms, with their ability to achieve better image quality under reduced projection angles or high levels of noise. In this work, we investigated the performance of iterative reconstruction from sparse sampled projection data on trabecular bone microstructure in in-vivo MDCT scans of human spines. The computed MDCT images were evaluated by calculating bone microstructure parameters. We demonstrated that bone microstructure parameters were still computationally distinguishable when half or less of the radiation dose was employed.

  10. BrGDGT-based quantitative temperature reconstruction over the past 2000 years from an alpine lake in subtropical southwestern China

    NASA Astrophysics Data System (ADS)

    Feng, X.; Zhao, C.

    2016-12-01

    Understand the nature of climate change over the past 2000 years is important to predict future climate change, which would influenced by both anthropogenic and natural forcing. However, limited paleoclimate data have been reported for quantitative temperature reconstruction in the tropical and subtropical region, the source region of the major moisture and heat in global climate system. In this study, we report a quantitative temperature record inferred from branched GDGTs from a sediment core collected at a small alpine lake (Tiancai lake, 26°38'E, 99°43'N, 3898 m asl) in a remote location in subtropical southwestern China. The chronology is well established by both 210Pb and AMS-14C dating methods. We find a significant correlation between brGDGT distributions and instrumental mean annual air temperature (MAAT) (R2=0.84, p<0.001) over the past 60 years. We then establish a local instrumental calibration and apply it to the entire core for MAAT reconstruction over the past 2000 years. Our preliminary results show the reconstructed MAAT varies between 1.11 and 2.87° over the past 2000 years, similar to the instrumental MAAT( 2.24°). Our data indicate four warm intervals at 20-151AD, 373-520AD, 796-1306AD and after 1940AD, and four cold intervals at 182-340AD, 550-643AD, 1540-1736AD, 1810-1948AD. The warm period at 796-1306AD and the cold period at 1540-1736AD are likely corresponding with the Medieval Climate Anomaly (MCA) and the Little Ice Age (LIA), respectively, which is consistent with published data in northern China and the northern Hemisphere but shows a higher amplitude of temperature changes. Our result suggests coherent temperature changes in the subtropical and high-latitude northern hemisphere over the past 2000 years, and probably indicate more pronounced centennial-scale climate variations at high-altitude mountain regions.

  11. Relation between modern pollen rain, vegetation and climate in northern China: Implications for quantitative vegetation reconstruction in a steppe environment.

    PubMed

    Ge, Yawen; Li, Yuecong; Bunting, M Jane; Li, Bing; Li, Zetao; Wang, Junting

    2017-05-15

    Vegetation reconstructions from palaeoecological records depend on adequate understanding of relationships between modern pollen, vegetation and climate. A key parameter for quantitative vegetation reconstructions is the Relative Pollen Productivity (RPP). Differences in both environmental and methodological factors are known to alter the RPP estimated significantly, making it difficult to determine whether the underlying pollen productivity does actually vary, and if so, why. In this paper, we present the results of a replication study for the Bashang steppe region, a typical steppe area in northern China, carried out in 2013 and 2014. In each year, 30 surface samples were collected for pollen analysis, with accompanying vegetation survey using the "Crackles Bequest Project" methodology. Sampling designs differed slightly between the two years: in 2013, sites were located completely randomly, whilst in 2014 sampling locations were constrained to be within a few km of roads. There is a strong inter-annual variability in both the pollen and the vegetation spectra therefore in RPPs, and annual precipitation may be a key influence on these variations. The pollen assemblages in both years are dominated by herbaceous taxa such as Artemisia, Amaranthaceae, Poaceae, Asteraceae, Cyperaceae, Fabaceae and Allium. Artemisia and Amaranthaceae pollen are significantly over-represented for their vegetation abundance. Poaceae, Cyperaceae and Fabaceae seem to have under-represented pollen for vegetation with correspondingly lower RPPs. Asteraceae seems to be well-represented, with moderate RPPs and less annual variation. Estimated Relevant Source Area of Pollen (RSAP) ranges from 2000 to 3000m. Different sampling designs have an effect both on RSAP and RPPs and random sample selection may be the best strategy for obtaining robust estimates. Our results have implications for further pollen-vegetation relationship and quantitative vegetation reconstruction research in typical steppe

  12. Quantitative schlieren method for studying the wavefront reconstructed from a hologram

    SciTech Connect

    Lyalikov, A.M.

    1995-03-01

    A schlieren method is proposed for visualizing the deflection angles of the light beams reconstructed from a phase object hologram. The method is based on employing a stationary visualizing slit and selecting the image of a slit light source by a movable slit. This light source comprises several equidistant slit sources. Compensation for the aberrations of the hologram-recording system is considered. Experimental results of the evaluation tests showing the performance of the method developed are presented. 15 refs., 4 figs.

  13. Microfabric reconstruction via quantitative digital petrographic image analysis for weakly foliated gneisses

    NASA Astrophysics Data System (ADS)

    Yeh, Meng-Wan; Lin, Yu-Ling; Lee, Tung-Yi; Ji, Jian-Qing

    2013-03-01

    Detection and documentation of petro-structural features such as alignment features of minerals/grains, and extraction of such spatial property data are two fundamental steps for structural geology. Such tasks were mostly carried out manually. However, manual analysis is laborious and potentially biased. These drawbacks are less obvious when the foliation is well developed and the amount of platy mineral is higher. For samples with weakly developed foliation and low platy mineral content, automatic method is required for subjective interpretation. A semi-automatic computerized method of 3D foliation orientation reconstruction via two-dimensional petrographic-shape fabric analysis from serial oriented digital microphotograph has been developed and demonstrated in this study. The foliation is reconstructed by fitting a best fitting plane to the maximum modal peaks of micro textural parameters (SPO) for different mineral groups of platy and granular minerals from each thin section on a stereonet for four coarse grained biotite gneiss samples collected along the Jialie fault, SE Tibet, China. Regardless of platy or granular mineral aggregates, the reconstructed foliations showed similar orientation within 10° angular variation to the field measurement. The 10° angular variation can be maintained if the foliations are reconstructed by consecutive thin section groupings ≦ 50° angular intervals and a horizontal thin section. The angular spread increased to 30° for thin section groupings with > 50° to 100° angular intervals with a horizontal thin section. Major advantages of the computerized photometric methods demonstrated by this study are: the reduction of human prejudice and obtaining quantified and repeatable data sets.

  14. Performance comparison of two resolution modeling PET reconstruction algorithms in terms of physical figures of merit used in quantitative imaging.

    PubMed

    Matheoud, R; Ferrando, O; Valzano, S; Lizio, D; Sacchetti, G; Ciarmiello, A; Foppiano, F; Brambilla, M

    2015-07-01

    Resolution modeling (RM) of PET systems has been introduced in iterative reconstruction algorithms for oncologic PET. The RM recovers the loss of resolution and reduces the associated partial volume effect. While these methods improved the observer performance, particularly in the detection of small and faint lesions, their impact on quantification accuracy still requires thorough investigation. The aim of this study was to characterize the performances of the RM algorithms under controlled conditions simulating a typical (18)F-FDG oncologic study, using an anthropomorphic phantom and selected physical figures of merit, used for image quantification. Measurements were performed on Biograph HiREZ (B_HiREZ) and Discovery 710 (D_710) PET/CT scanners and reconstructions were performed using the standard iterative reconstructions and the RM algorithms associated to each scanner: TrueX and SharpIR, respectively. RM determined a significant improvement in contrast recovery for small targets (≤17 mm diameter) only for the D_710 scanner. The maximum standardized uptake value (SUVmax) increased when RM was applied using both scanners. The SUVmax of small targets was on average lower with the B_HiREZ than with the D_710. Sharp IR improved the accuracy of SUVmax determination, whilst TrueX showed an overestimation of SUVmax for sphere dimensions greater than 22 mm. The goodness of fit of adaptive threshold algorithms worsened significantly when RM algorithms were employed for both scanners. Differences in general quantitative performance were observed for the PET scanners analyzed. Segmentation of PET images using adaptive threshold algorithms should not be undertaken in conjunction with RM reconstructions. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  15. Quantitative Temperature Reconstructions from Holocene and Late Glacial Lake Sediments in the Tropical Andes using Chironomidae (non-biting midges)

    NASA Astrophysics Data System (ADS)

    Matthews-Bird, F.; Gosling, W. D.; Brooks, S. J.; Montoya, E.; Coe, A. L.

    2014-12-01

    Chironomidae (non-biting midges) is a family of two-winged aquatic insects of the order Diptera. They are globally distributed and one of the most diverse families within aquatic ecosystems. The insects are stenotopic, and the rapid turnover of species and their ability to colonise quickly favourable habitats means chironomids are extremely sensitive to environmental change, notably temperature. Through the development of quantitative temperature inference models chironomids have become important palaeoecological tools. Proxies capable of generating independent estimates of past climate are crucial to disentangling climate signals and ecosystem response in the palaeoecological record. This project has developed the first modern environmental calibration data set in order to use chironomids from the Tropical Andes as quantitative climate proxies. Using surface sediments from c. 60 lakes from Bolivia, Peru and Ecuador we have developed an inference model capable of reconstructing temperatures, with a prediction error of 1-2°C, from fossil assemblages. Here we present the first Lateglacial and Holocene chironomid-inferred temperature reconstructions from two sites in the tropical Andes. The first record, from a high elevation (4153 m asl) lake in the Bolivian Andes, shows persistently cool temperatures for the past 15 kyr, punctuated by warm episodes in the early Holocene (9-10 kyr BP). The chironomid-inferred Holocene temperature trends from a lake sediment record on the eastern Andean flank of Ecuador (1248 m asl) spanning the last 5 millennia are synchronous with temperature changes in the NGRIP ice core record. The temperature estimates suggest along the eastern flank of the Andes, at lower latitudes (~1°S), climate closely resemble the well-established fluctuations of the Northern Hemisphere for this time period. Late-glacial climate fluctuations across South America are still disputed with some palaeoecological records suggesting evidence for Younger Dryas

  16. Quantitative PET image reconstruction employing nested expectation-maximization deconvolution for motion compensation.

    PubMed

    Karakatsanis, Nicolas A; Tsoumpas, Charalampos; Zaidi, Habib

    2016-11-16

    Bulk body motion may randomly occur during PET acquisitions introducing blurring, attenuation-emission mismatches and, in dynamic PET, discontinuities in the measured time activity curves between consecutive frames. Meanwhile, dynamic PET scans are longer, thus increasing the probability of bulk motion. In this study, we propose a streamlined 3D PET motion-compensated image reconstruction (3D-MCIR) framework, capable of robustly deconvolving intra-frame motion from a static or dynamic 3D sinogram. The presented 3D-MCIR methods need not partition the data into multiple gates, such as 4D MCIR algorithms, or access list-mode (LM) data, such as LM MCIR methods, both associated with increased computation or memory resources. The proposed algorithms can support compensation for any periodic and non-periodic motion, such as cardio-respiratory or bulk motion, the latter including rolling, twisting or drifting. Inspired from the widely adopted point-spread function (PSF) deconvolution 3D PET reconstruction techniques, here we introduce an image-based 3D generalized motion deconvolution method within the standard 3D maximum-likelihood expectation-maximization (ML-EM) reconstruction framework. In particular, we initially integrate a motion blurring kernel, accounting for every tracked motion within a frame, as an additional MLEM modeling component in the image space (integrated 3D-MCIR). Subsequently, we replaced the integrated model component with a nested iterative Richardson-Lucy (RL) image-based deconvolution method to accelerate the MLEM algorithm convergence rate (RL-3D-MCIR). The final method was evaluated with realistic simulations of whole-body dynamic PET data employing the XCAT phantom and real human bulk motion profiles, the latter estimated from volunteer dynamic MRI scans. In addition, metabolic uptake rate Ki parametric images were generated with the standard Patlak method. Our results demonstrate significant improvement in contrast-to-noise ratio (CNR) and

  17. Acquisition of quantitative physiological data and computerized image reconstruction using a single scan TV system

    NASA Technical Reports Server (NTRS)

    Baily, N. A.

    1975-01-01

    Single scan operation of television X-ray fluoroscopic systems allow both analog and digital reconstruction of tomographic sections from single plan images. This type of system combined with a minimum of statistical processing showed excellent capabilities for delineating small changes in differential X-ray attenuation. Patient dose reduction is significant when compared to normal operation or film recording. Flat screen, low light level systems were both rugged and light in weight, making them applicable for a variety of special purposes. Three dimensional information was available from the tomographic methods and the recorded data was sufficient when used with appropriate computer display devices to give representative 3D images.

  18. Quantitative morphometry of the orbit in Chinese adults based on a three-dimensional reconstruction method

    PubMed Central

    Ji, Yongrong; Qian, Zanqun; Dong, Yang; Zhou, Huifang; Fan, Xianqun

    2010-01-01

    The three-dimensional (3D) reconstruction technique serves as a practical tool in diagnosis, surgical planning, and outcome prediction of plastic and reconstructive surgery. In our study, the morphologic features of the Chinese adult orbit were described by 11 anatomic parameters using a 3D reconstruction technique. Sixty-four Chinese adults were selected randomly from patients who had undergone craniofacial computed tomography (CT) scans to diagnose conditions other than craniofacial or orbital deformations. The morphologic parameters of orbit such as bony orbital volume, orbital foramen area and orbital rim perimeter were measured on 3D models using this technique. Differences between the two orbits and between the two sexes were investigated. The method of measurement showed high reproducibility of results. No difference between the two orbits was found. There were significant differences between men and women in all anatomic parameters other than orbital height. In men and women, respectively, mean bony orbital volume was 26.02 and 23.32 mL, mean orbital foramen area 11.80 and 11.10 cm2, mean orbital rim perimeter 12.65 and 12.20 cm, mean orbital height 33.35 and 33.22 mm, mean orbital width 40.02 and 38.00 mm; mean orbital floor length 47.93 and 46.18 mm, mean orbital roof length 52.93 and 50.89 mm, mean medial orbital wall length 46.43 and 44.41 mm, mean lateral orbital wall length 48.38 and 46.91 mm, mean intraorbital distance 27.18 and 25.11 mm, mean extra-orbital distance 98.77 and 93.69 mm. It is concluded that the measurements of these orbital parameters could be obtained from a 3D reconstruction method. The two orbits were symmetric based on orbital volume and other anatomic parameters. Orbital size was significantly smaller in women than in men; orbital height, however, was similar. The findings of the present study allow for quantification of the orbital features of Chinese adults and provide parameters for preoperative planning and prediction of

  19. Acquisition of quantitative physiological data and computerized image reconstruction using a single scan TV system

    NASA Technical Reports Server (NTRS)

    Baily, N. A.

    1975-01-01

    Single scan operation of television X-ray fluoroscopic systems allow both analog and digital reconstruction of tomographic sections from single plan images. This type of system combined with a minimum of statistical processing showed excellent capabilities for delineating small changes in differential X-ray attenuation. Patient dose reduction is significant when compared to normal operation or film recording. Flat screen, low light level systems were both rugged and light in weight, making them applicable for a variety of special purposes. Three dimensional information was available from the tomographic methods and the recorded data was sufficient when used with appropriate computer display devices to give representative 3D images.

  20. Mapping Foliar Traits Across Biomes Using Imaging Spectroscopy: A Synthesis

    NASA Astrophysics Data System (ADS)

    Townsend, P. A.; Singh, A.; Wang, Z.

    2016-12-01

    One of the great promises of imaging spectroscopy - also known as hyperspectral remote sensing - is the ability to map the spatial variation in foliar functional traits, such as nitrogen concentration, pigments, leaf structure, photosynthetic capacity and secondary biochemistry, that drive terrestrial ecosystem processes. A remote-sensing approach enables characterization of within- and between-biome variations that may be crucial to understanding ecosystem responses to pests, pathogens and environmental change. We provide a synthesis of the foliar traits that can be mapped from imaging spectroscopy, as well as an overview of both the major applications of trait maps derived from hyperspectral imagery and current gaps in our knowledge and capacity. Specifically, we make the case that a global imaging spectroscopy mission will provide unique and urgent measurements necessary to understand the response of agricultural and natural systems to rapid global changes. Finally, we present a quantitative framework to utilize imaging spectroscopy to characterize spatial and temporal variation in foliar traits within and between biomes. From this we can infer the dynamics of vegetation function across ecosystems, especially in transition zones and environmentally sensitive systems. Eventual launch of a global imaging spectroscopy mission will enable collection of narrowband VSWIR measurements that will help close major gaps in our understanding of biogeochemical cycles and improve representation of vegetated biomes in Earth system process models.

  1. Stochastic optical reconstruction microscopy-based relative localization analysis (STORM-RLA) for quantitative nanoscale assessment of spatial protein organization.

    PubMed

    Veeraraghavan, Rengasayee; Gourdie, Robert G

    2016-11-07

    The spatial association between proteins is crucial to understanding how they function in biological systems. Colocalization analysis of fluorescence microscopy images is widely used to assess this. However, colocalization analysis performed on two-dimensional images with diffraction-limited resolution merely indicates that the proteins are within 200-300 nm of each other in the xy-plane and within 500-700 nm of each other along the z-axis. Here we demonstrate a novel three-dimensional quantitative analysis applicable to single-molecule positional data: stochastic optical reconstruction microscopy-based relative localization analysis (STORM-RLA). This method offers significant advantages: 1) STORM imaging affords 20-nm resolution in the xy-plane and <50 nm along the z-axis; 2) STORM-RLA provides a quantitative assessment of the frequency and degree of overlap between clusters of colabeled proteins; and 3) STORM-RLA also calculates the precise distances between both overlapping and nonoverlapping clusters in three dimensions. Thus STORM-RLA represents a significant advance in the high-throughput quantitative assessment of the spatial organization of proteins. © 2016 Veeraraghavan and Gourdie. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  2. Stochastic optical reconstruction microscopy–based relative localization analysis (STORM-RLA) for quantitative nanoscale assessment of spatial protein organization

    PubMed Central

    Veeraraghavan, Rengasayee; Gourdie, Robert G.

    2016-01-01

    The spatial association between proteins is crucial to understanding how they function in biological systems. Colocalization analysis of fluorescence microscopy images is widely used to assess this. However, colocalization analysis performed on two-dimensional images with diffraction-limited resolution merely indicates that the proteins are within 200–300 nm of each other in the xy-plane and within 500–700 nm of each other along the z-axis. Here we demonstrate a novel three-dimensional quantitative analysis applicable to single-molecule positional data: stochastic optical reconstruction microscopy–based relative localization analysis (STORM-RLA). This method offers significant advantages: 1) STORM imaging affords 20-nm resolution in the xy-plane and <50 nm along the z-axis; 2) STORM-RLA provides a quantitative assessment of the frequency and degree of overlap between clusters of colabeled proteins; and 3) STORM-RLA also calculates the precise distances between both overlapping and nonoverlapping clusters in three dimensions. Thus STORM-RLA represents a significant advance in the high-throughput quantitative assessment of the spatial organization of proteins. PMID:27307586

  3. Quantitative reconstruction of thermal and dynamic characteristics of lava flow from surface thermal measurements

    NASA Astrophysics Data System (ADS)

    Korotkii, Alexander; Kovtunov, Dmitry; Ismail-Zadeh, Alik; Tsepelev, Igor; Melnik, Oleg

    2016-06-01

    We study a model of lava flow to determine its thermal and dynamic characteristics from thermal measurements of the lava at its surface. Mathematically this problem is reduced to solving an inverse boundary problem. Namely, using known conditions at one part of the model boundary we determine the missing condition at the remaining part of the boundary. We develop a numerical approach to the mathematical problem in the case of steady-state flow. Assuming that the temperature and the heat flow are prescribed at the upper surface of the model domain, we determine the flow characteristics in the entire model domain using a variational (adjoint) method. We have performed computations of model examples and showed that in the case of smooth input data the lava temperature and the flow velocity can be reconstructed with a high accuracy. As expected, a noise imposed on the smooth input data results in a less accurate solution, but still acceptable below some noise level. Also we analyse the influence of optimization methods on the solution convergence rate. The proposed method for reconstruction of physical parameters of lava flows can also be applied to other problems in geophysical fluid flows.

  4. Precision and accuracy of regional radioactivity quantitation using the maximum likelihood EM reconstruction algorithm

    SciTech Connect

    Carson, R.E.; Yan, Y.; Chodkowski, B.; Yap, T.K.; Daube-Witherspoon, M.E. )

    1994-09-01

    The imaging characteristics of maximum likelihood (ML) reconstruction using the EM algorithm for emission tomography have been extensively evaluated. There has been less study of the precision and accuracy of ML estimates of regional radioactivity concentration. The authors developed a realistic brain slice simulation by segmenting a normal subject's MRI scan into gray matter, white matter, and CSF and produced PET sinogram data with a model that included detector resolution and efficiencies, attenuation, scatter, and randoms. Noisy realizations at different count levels were created, and ML and filtered backprojection (FBP) reconstructions were performed. The bias and variability of ROI values were determined. In addition, the effects of ML pixel size, image smoothing and region size reduction were assessed. ML estimates at 1,000 iterations (0.6 sec per iteration on a parallel computer) for 1-cm[sup 2] gray matter ROIs showed negative biases of 6% [+-] 2% which can be reduced to 0% [+-] 3% by removing the outer 1-mm rim of each ROI. FBP applied to the full-size ROIs had 15% [+-] 4% negative bias with 50% less noise than ML. Shrinking the FBP regions provided partial bias compensation with noise increases to levels similar to ML. Smoothing of ML images produced biases comparable to FBP with slightly less noise. Because of its heavy computational requirements, the ML algorithm will be most useful for applications in which achieving minimum bias is important.

  5. Quantitative analysis of the cochlea using three-dimensional reconstruction based on microcomputed tomographic images.

    PubMed

    Shin, Kang-Jae; Lee, Ju-Young; Kim, Jeong-Nam; Yoo, Ja-Young; Shin, Chuog; Song, Wu-Chul; Koh, Ki-Seok

    2013-07-01

    The aim of this study was to provide data on various dimensions of the normal cochlea using three-dimensional reconstruction based on high-resolution micro-CT images. The petrous parts of 39 temporal bones were scanned by micro-computed tomography (CT) with a slice thickness of 35 μm. The micro-CT images were used in reconstructing three-dimensional volumes of the bony labyrinth using computer software. The volumes were used to measure 12 dimensions of the cochlea, and statistical analysis was carried out. The dimensions of cochleae varied widely between different specimens. The mean height and length of the cochlea were 3.8 and 9.7 mm, respectively. The angle between the basal and middle turns was slightly larger in males than in females, while none of the other 11 dimensions differed significantly between males and females. The cochlear accessory canals were observed in about half of the cases (51.3%). Correlation analysis among measured items revealed positive correlations among several of the measured dimensions. The present study could investigate the detailed anatomy of the normal cochlea using high-resolution imaging technologies. The results of the present study could be helpful for the precise diagnosis of congenital cochlear malformations and for producing optimized cochlear implants.

  6. 3800 Years of Quantitative Precipitation Reconstruction from the Northwest Yucatan Peninsula

    PubMed Central

    Carrillo-Bastos, Alicia; Islebe, Gerald A.; Torrescano-Valle, Nuria

    2013-01-01

    Precipitation over the last 3800 years has been reconstructed using modern pollen calibration and precipitation data. A transfer function was then performed via the linear method of partial least squares. By calculating precipitation anomalies, it is estimated that precipitation deficits were greater than surpluses, reaching 21% and <9%, respectively. The period from 50 BC to 800 AD was the driest of the record. The drought related to the abandonment of the Maya Preclassic period featured a 21% reduction in precipitation, while the drought of the Maya collapse (800 to 860 AD) featured a reduction of 18%. The Medieval Climatic Anomaly was a period of positive phases (3.8–7.6%). The Little Ice Age was a period of climatic variability, with reductions in precipitation but without deficits. PMID:24391940

  7. Quantitative Mass Density Image Reconstructed from the Complex X-Ray Refractive Index

    PubMed Central

    Mukaide, Taihei; Iida, Atsuo; Watanabe, Masatoshi; Takada, Kazuhiro; Noma, Takashi

    2015-01-01

    We demonstrate a new analytical X-ray computed tomography technique for visualizing and quantifying the mass density of materials comprised of low atomic number elements with unknown atomic ratios. The mass density was obtained from the experimentally observed ratio of the imaginary and real parts of the complex X-ray refractive index. An empirical linear relationship between the X-ray mass attenuation coefficient of the materials and X-ray energy was found for X-ray energies between 8 keV and 30 keV. The mass density image of two polymer fibers was quantified using the proposed technique using a scanning-type X-ray microbeam computed tomography system equipped with a wedge absorber. The reconstructed mass density agrees well with the calculated one. PMID:26114770

  8. Quantitative reconstruction of Holocene sea ice and sea surface temperature off West Greenland from the first regional diatom data set

    NASA Astrophysics Data System (ADS)

    Krawczyk, D. W.; Witkowski, A.; Moros, M.; Lloyd, J. M.; Høyer, J. L.; Miettinen, A.; Kuijpers, A.

    2017-01-01

    Holocene oceanographic conditions in Disko Bay, West Greenland, were reconstructed from high-resolution diatom records derived from two marine sediment cores. A modern data set composed of 35 dated surface sediment samples collected along the West Greenland coast accompanied by remote sensing data was used to develop a diatom transfer function to reconstruct April sea ice concentration (SIC) supported by July sea surface temperature (SST) in the area. Our quantitative reconstruction shows that oceanographic changes recorded throughout the last 11,000 years reflect seasonal interplay between spring (April SIC) and summer (July SST) conditions. Our records show clear correlation with climate patterns identified from ice core data from GISP2 and Agassiz-Renland for the early to middle Holocene. The early Holocene deglaciation of western Greenland Ice Sheet was characterized in Disko Bay by initial strong centennial-scale fluctuations in April SIC with amplitude of over 40%, followed by high April SIC and July SST. These conditions correspond to a general warming of the climate in the Northern Hemisphere. A decrease in April SIC and July SST was recorded during the Holocene Thermal Optimum reflecting more stable spring-summer conditions in Disko Bay. During the late Holocene, high April SIC characterized the Medieval Climate Anomaly, while high July SST prevailed during the Little Ice Age, supporting previously identified antiphase relationship between surface waters in West Greenland and climate in NW Europe. This antiphase pattern might reflect seasonal variations in regional oceanographic conditions and large-scale fluctuations within the North Atlantic Oscillation and Atlantic Meridional Overturning Circulation.

  9. Holocene local forest history at two sites in Småland, southern Sweden - insights from quantitative reconstructions using the Landscape Reconstruction Algorithm

    NASA Astrophysics Data System (ADS)

    Cui, Qiaoyu; Gaillard, Marie-José; Lemdahl, Geoffrey; Olsson, Fredrik; Sugita, Shinya

    2010-05-01

    Quantitative reconstruction of past vegetation using fossil pollen was long very problematic. It is well known that pollen percentages and pollen accumulation rates do not represent vegetation abundance properly because pollen values are influenced by many factors of which inter-taxonomic differences in pollen productivity and vegetation structure are the most important ones. It is also recognized that pollen assemblages from large sites (lakes or bogs) record the characteristics of the regional vegetation, while pollen assemblages from small sites record local features. Based on the theoretical understanding of the factors and mechanisms that affect pollen representation of vegetation, Sugita (2007a and b) proposed the Landscape Reconstruction Algorithm (LRA) to estimate vegetation abundance in percentage cover for well defined spatial scales. The LRA includes two models, REVEALS and LOVE. REVEALS estimates regional vegetation abundance at a spatial scale of 100 km x 100 km. LOVE estimates local vegetation abundance at the spatial scale of the relevant source area of pollen (RSAP sensu Sugita 1993) of the pollen site. REVEALS estimates are needed to apply LOVE in order to calculate the RSAP and the vegetation cover within the RSAP. The two models were validated theoretically and empirically. Two small bogs in southern Sweden were studied for pollen, plant macrofossil, charcoal, and coleoptera in order to reconstruct the local Holocene forest and fire history (e.g. Greisman and Gaillard 2009; Olsson et al. 2009). We applied the LOVE model in order to 1) compare the LOVE estimates with pollen percentages for a better understanding of the local forest history; 2) obtain more precise information on the local vegetation to explain between-sites differences in fire history. We used pollen records from two large lakes in Småland to obtain REVEALS estimates for twelve continuous 500-yrs time windows. Following the strategy of the Swedish VR LANDCLIM project (see Gaillard

  10. Lossless 3-D reconstruction and registration of semi-quantitative gene expression data in the mouse brain.

    PubMed

    Enlow, Matthew A; Ju, Tao; Kakadiaris, Ioannis A; Carson, James P

    2011-01-01

    As imaging, computing, and data storage technologies improve, there is an increasing opportunity for multiscale analysis of three-dimensional datasets (3-D). Such analysis enables, for example, microscale elements of multiple macroscale specimens to be compared throughout the entire macroscale specimen. Spatial comparisons require bringing datasets into co-alignment. One approach for co-alignment involves elastic deformations of data in addition to rigid alignments. The elastic deformations distort space, and if not accounted for, can distort the information at the microscale. The algorithms developed in this work address this issue by allowing multiple data points to be encoded into a single image pixel, appropriately tracking each data point to ensure lossless data mapping during elastic spatial deformation. This approach was developed and implemented for both 2-D and 3D registration of images. Lossless reconstruction and registration was applied to semi-quantitative cellular gene expression data in the mouse brain, enabling comparison of multiple spatially registered 3-D datasets without any augmentation of the cellular data. Standard reconstruction and registration without the lossless approach resulted in errors in cellular quantities of ∼ 8%.

  11. Lossless 3-D reconstruction and registration of semi-quantitative gene expression data in the mouse brain

    PubMed Central

    Enlow, Matthew A.; Ju, Tao; Kakadiaris, Ioannis A.; Carson, James P.

    2012-01-01

    As imaging, computing, and data storage technologies improve, there is an increasing opportunity for multiscale analysis of three-dimensional datasets (3-D). Such analysis enables, for example, microscale elements of multiple macroscale specimens to be compared throughout the entire macroscale specimen. Spatial comparisons require bringing datasets into co-alignment. One approach for co-alignment involves elastic deformations of data in addition to rigid alignments. The elastic deformations distort space, and if not accounted for, can distort the information at the microscale. The algorithms developed in this work address this issue by allowing multiple data points to be encoded into a single image pixel, appropriately tracking each data point to ensure lossless data mapping during elastic spatial deformation. This approach was developed and implemented for both 2-D and 3-D registration of images. Lossless reconstruction and registration was applied to semi-quantitative cellular gene expression data in the mouse brain, enabling comparison of multiple spatially registered 3-D datasets without any augmentation of the cellular data. Standard reconstruction and registration without the lossless approach resulted in errors in cellular quantities of ~ 8%. PMID:22256218

  12. Assessment of diffuse coronary artery disease by quantitative analysis of coronary morphology based upon 3-D reconstruction from biplane angiograms

    SciTech Connect

    Wahel, A.; Wellnhofer, E.; Mugaragu, I.; Sauer, H.U.; Oswald, H.; Fleck, E. |

    1995-06-01

    Quantitative evaluations on coronary vessel systems are of increasing importance in cardiovascular diagnosis, therapy planning, and surgical verification. Whereas local evaluations, such as stenosis analysis, are already available with sufficient accuracy, global evaluations of vessel segments or vessel subsystems are not yet common. Especially for the diagnosis of diffuse coronary artery diseases, the authors combined a 3-D reconstruction system operating on biplane angiograms with a length/volume calculation. The 3-D reconstruction results in a 3-D model of the coronary vessel system, consisting of the vessel skeleton and a discrete number of contours. To obtain an utmost accurate model, the authors focused on exact geometry determination. Several algorithms for calculating missing geometric parameters and correcting remaining geometry errors were implemented and verified. The length/volume evaluation can be performed either on single vessel segments, on a set of segments, or on subtrees. A volume model based on generalized elliptical conic sections is created for the selected segments. Volumes and lengths (measured along the vessel course) of those elements are summed up. In this way, the morphological parameters of a vessel subsystem can be set in relation to the parameters of the proximal segment supplying it. These relations allow objective assessments of diffuse coronary artery diseases.

  13. Glaciers and ice sheets as a biome.

    PubMed

    Anesio, Alexandre M; Laybourn-Parry, Johanna

    2012-04-01

    The tundra is the coldest biome described in typical geography and biology textbooks. Within the cryosphere, there are large expanses of ice in the Antarctic, Arctic and alpine regions that are not regarded as being part of any biome. During the summer, there is significant melt on the surface of glaciers, ice caps and ice shelves, at which point microbial communities become active and play an important role in the cycling of carbon and other elements within the cryosphere. In this review, we suggest that it is time to recognise the cryosphere as one of the biomes of Earth. The cryospheric biome encompasses extreme environments and is typified by truncated food webs dominated by viruses, bacteria, protozoa and algae with distinct biogeographical structures.

  14. Reconstructing Past Depositional and Diagenetic Processes through Quantitative Stratigraphic Analysis of the Martian Sedimentary Rock Record

    NASA Astrophysics Data System (ADS)

    Stack, Kathryn M.

    High-resolution orbital and in situ observations acquired of the Martian surface during the past two decades provide the opportunity to study the rock record of Mars at an unprecedented level of detail. This dissertation consists of four studies whose common goal is to establish new standards for the quantitative analysis of visible and near-infrared data from the surface of Mars. Through the compilation of global image inventories, application of stratigraphic and sedimentologic statistical methods, and use of laboratory analogs, this dissertation provides insight into the history of past depositional and diagenetic processes on Mars. The first study presents a global inventory of stratified deposits observed in images from the High Resolution Image Science Experiment (HiRISE) camera on-board the Mars Reconnaissance Orbiter. This work uses the widespread coverage of high-resolution orbital images to make global-scale observations about the processes controlling sediment transport and deposition on Mars. The next chapter presents a study of bed thickness distributions in Martian sedimentary deposits, showing how statistical methods can be used to establish quantitative criteria for evaluating the depositional history of stratified deposits observed in orbital images. The third study tests the ability of spectral mixing models to obtain quantitative mineral abundances from near-infrared reflectance spectra of clay and sulfate mixtures in the laboratory for application to the analysis of orbital spectra of sedimentary deposits on Mars. The final study employs a statistical analysis of the size, shape, and distribution of nodules observed by the Mars Science Laboratory Curiosity rover team in the Sheepbed mudstone at Yellowknife Bay in Gale crater. This analysis is used to evaluate hypotheses for nodule formation and to gain insight into the diagenetic history of an ancient habitable environment on Mars.

  15. Thresholds for boreal biome transitions

    PubMed Central

    Scheffer, Marten; Hirota, Marina; Holmgren, Milena; Van Nes, Egbert H.; Chapin, F. Stuart

    2012-01-01

    Although the boreal region is warming twice as fast as the global average, the way in which the vast boreal forests and tundras may respond is poorly understood. Using satellite data, we reveal marked alternative modes in the frequency distributions of boreal tree cover. At the northern end and at the dry continental southern extremes, treeless tundra and steppe, respectively, are the only possible states. However, over a broad intermediate temperature range, these treeless states coexist with boreal forest (∼75% tree cover) and with two more open woodland states (∼20% and ∼45% tree cover). Intermediate tree covers (e.g., ∼10%, ∼30%, and ∼60% tree cover) between these distinct states are relatively rare, suggesting that they may represent unstable states where the system dwells only transiently. Mechanisms for such instabilities remain to be unraveled, but our results have important implications for the anticipated response of these ecosystems to climatic change. The data reveal that boreal forest shows no gradual decline in tree cover toward its limits. Instead, our analysis suggests that it becomes less resilient in the sense that it may more easily shift into a sparse woodland or treeless state. Similarly, the relative scarcity of the intermediate ∼10% tree cover suggests that tundra may shift relatively abruptly to a more abundant tree cover. If our inferences are correct, climate change may invoke massive nonlinear shifts in boreal biomes. PMID:23236159

  16. Thresholds for boreal biome transitions.

    PubMed

    Scheffer, Marten; Hirota, Marina; Holmgren, Milena; Van Nes, Egbert H; Chapin, F Stuart

    2012-12-26

    Although the boreal region is warming twice as fast as the global average, the way in which the vast boreal forests and tundras may respond is poorly understood. Using satellite data, we reveal marked alternative modes in the frequency distributions of boreal tree cover. At the northern end and at the dry continental southern extremes, treeless tundra and steppe, respectively, are the only possible states. However, over a broad intermediate temperature range, these treeless states coexist with boreal forest (∼75% tree cover) and with two more open woodland states (∼20% and ∼45% tree cover). Intermediate tree covers (e.g., ∼10%, ∼30%, and ∼60% tree cover) between these distinct states are relatively rare, suggesting that they may represent unstable states where the system dwells only transiently. Mechanisms for such instabilities remain to be unraveled, but our results have important implications for the anticipated response of these ecosystems to climatic change. The data reveal that boreal forest shows no gradual decline in tree cover toward its limits. Instead, our analysis suggests that it becomes less resilient in the sense that it may more easily shift into a sparse woodland or treeless state. Similarly, the relative scarcity of the intermediate ∼10% tree cover suggests that tundra may shift relatively abruptly to a more abundant tree cover. If our inferences are correct, climate change may invoke massive nonlinear shifts in boreal biomes.

  17. Differential axial contrast of optical sections: laser microtomography and quantitative 3D reconstruction

    NASA Astrophysics Data System (ADS)

    Pogorelova, M. A.; Golichenkov, V. A.; Pogorelov, A. G.

    2014-03-01

    Specific features of the quantitative laser microtomography of biological samples are discussed. The method exhibits the main advantages of a confocal microscope (rapid measurement of a stack of parallel optical cross sections and accurate displacement of an object along the optical axis). A relatively high contrast is reached owing to the superposition of pairwise complementary images on neighboring cross sections. A simple and convenient algorithm for image processing does not require additional software and can be computerized using a conventional graphic editor. The applicability of the method is illustrated using volume measurements of a single cell of an early mouse embryo.

  18. The extent of forest in dryland biomes

    Treesearch

    Jean-Francois Bastin; Nora Berrahmouni; Alan Grainger; Danae Maniatis; Danilo Mollicone; Rebecca Moore; Chiara Patriarca; Nicolas Picard; Ben Sparrow; Elena Maria Abraham; Kamel Aloui; Ayhan Atesoglu; Fabio Attore; Caglar Bassullu; Adia Bey; Monica Garzuglia; Luis G. GarcÌa-Montero; Nikee Groot; Greg Guerin; Lars Laestadius; Andrew J. Lowe; Bako Mamane; Giulio Marchi; Paul Patterson; Marcelo Rezende; Stefano Ricci; Ignacio Salcedo; Alfonso Sanchez-Paus Diaz; Fred Stolle; Venera Surappaeva; Rene Castro

    2017-01-01

    Dryland biomes cover two-fifths of Earth’s land surface, but their forest area is poorly known. Here, we report an estimate of global forest extent in dryland biomes, based on analyzing more than 210,000 0.5-hectare sample plots through a photo-interpretation approach using large databases of satellite imagery at (i) very high spatial resolution and (ii) very high...

  19. Fiber tracking: A qualitative and quantitative comparison between four different software tools on the reconstruction of major white matter tracts.

    PubMed

    Christidi, Foteini; Karavasilis, Efstratios; Samiotis, Kostantinos; Bisdas, Sotirios; Papanikolaou, Nikolaos

    2016-01-01

    Diffusion tensor imaging (DTI) enables in vivo reconstruction of white matter (WM) pathways. Considering the emergence of numerous models and fiber tracking techniques, we herein aimed to compare, both quantitatively and qualitatively, the fiber tracking results of four DTI software (Brainance, Philips FiberTrak, DSI Studio, NordicICE) on the reconstruction of representative WM tracts. Ten healthy participants underwent 30-directional diffusion tensor imaging on a 3T-Philips Achieva TX MR-scanner. All data were analyzed by two independent sites of experienced raters with the aforementioned software and the following WM tracts were reconstructed: corticospinal tract (CST); forceps major (Fmajor); forceps minor (Fminor); cingulum bundle (CB); superior longitudinal fasciculus (SLF); inferior fronto-occipital fasciculus (IFOF). Visual inspection of the resulted tracts and statistical analysis (inter-rater and betweensoftware agreement; paired t-test) on fractional anisotropy (FA), axial and radial diffusivity (Daxial, Dradial) were applied for qualitative and quantitative evaluation of DTI software results. Qualitative evaluation of the extracted tracts confirmed anatomical landmarks at least for the core part of each tract, even though differences in the number of fibers extracted and the whole tract were evident, especially for the CST, Fmajor, Fminor and SLF. Descriptive values did not deviate from the expected range of values for healthy adult population. Substantial inter-rater agreement (intraclass correlation coefficient [ICC], Bland-Altman analysis) was found for all tracts (ICC; FA: 0.839-0.989, Daxial: 0.704-0.991, Dradial: 0.972-0.993). Low agreement for FA, Daxial and Dradial (ICC; Bland-Altman analysis) and significant paired t-test differences (p < 0.05) were detected regarding between-software agreement. Qualitative comparison of four different DTI software in addition to substantial inter-rater but poor between-software agreement highlight the

  20. A new peat bog testate amoeba transfer function and quantitative palaeohydrological reconstructions from southern Patagonia

    NASA Astrophysics Data System (ADS)

    van Bellen, S.; Mauquoy, D.; Payne, R.; Roland, T. P.; Hughes, P. D.; Daley, T. J.; Street-Perrot, F. A.; Loader, N.

    2013-12-01

    Testate amoebae have been used extensively as proxies for environmental change and palaeoclimate reconstructions in European and North American peatlands. The presence of these micro-organisms in surface samples is generally significantly linked to the local water table depth (WTD) and preservation of the amoeba shells downcore allows for millennial length water table reconstructions. Peat bog archive records in southern Patagonia are increasingly the focus of palaeoecological research due to the possibility of detecting changes in the Southern Westerlies. These Sphagnum magellanicum-dominated peat bogs are characterised by a wide range of water table depths, from wet hollows to high hummocks (>100 cm above the water table). Here we present the first transfer function for this region along with ~2k-year palaeorecords from local peat bogs. A modern dataset (155 samples) was sampled along transects from five bogs in 2012 and 2013. Measurements of WTD, pH and conductivity were taken for all samples. The transfer function model was based on the 2012 dataset, while the 2013 samples served as an independent test set to validate the model. Besides the standard leave-one-out cross-validation, we applied leave-one-site-out and leave-one transect-out cross-validation, which are effective means of verifying the degree of clustering in the dataset. To ensure that the environmental gradient had been evenly sampled we quantified the root-mean-squared error of prediction (RMSEP) individually for segments of this gradient. Ordinations showed a clear hydrological gradient in amoeba assemblages, with the dominant Assulina muscorum at the dry end and Amphitrema wrightianum and Difflugia globulosa at the wet end. Canonical correspondence analysis showed that WTD was the most important environmental variable, accounting for 18% of the variance in amoeba assemblages. A weighted averaging-partial least squares model showed best performance in cross-validation, using the 2013 data as an

  1. Quantitative paleoclimatic reconstructions from late Pleistocene plant macrofossils of the Yucca Mountain region

    USGS Publications Warehouse

    Thompson, R.S.; Anderson, K.H.; Bartlein, P.J.

    1999-01-01

    Plant macrofossil assemblages recovered from packrat (Neotoma) middens of late Pleistocene age from the present-day Mojave Desert of southern Nevada contain plant species that today live at higher elevations and/or farther north than the midden collection sites. Previous reconstructions of late Pleistocene climates from packrat midden assemblages in this region (Spaulding, 1985) assessed the minimum climatic differences from today by estimating the present-day climatic differences between the fossil midden sites and the nearest current occurrences of key plant species recovered from the Pleistocene middens. From this approach Spaulding (1985) concluded that although late Pleistocene temperatures were considerably below those of today, only modest increases in precipitation (relative to today) were necessary for these plant species to survive in the current Mojave Desert during the late Pleistocene.Spaulding's approach provided "state-of-the-art" results from an intensive careful examination of the best data available at the time. However, data and techniques developed since the mid-1980s suggest that there are two possible short-comings to this approach: 1) the use of lowest elevational and (frequently) most southerly occurrences of key plant species results in minimal estimates of the differences between Pleistocene and present-day climates, and 2) the instrumental climate data set available to Spaulding was limited in duration, non-standard in its method of collection, and indicated a modern climate wetter than the long-term historic mean, which resulted in relatively small apparent differences between late Pleistocene and present-day mean annual precipitation levels. In this report we use a more standard (close to the long-term mean) modern calibration period and a modern plant distribution data set that permits us to identify modern analogues for the Pleistocene vegetation. This reexamination permits a more robust reconstruction of the past climate, and results

  2. Biome-Level Biogeography of Streambed Microbiota▿

    PubMed Central

    Findlay, Robert H.; Yeates, Christine; Hullar, Meredith A. J.; Stahl, David A.; Kaplan, Louis A.

    2008-01-01

    A field study was conducted to determine the microbial community structures of streambed sediments across diverse geographic and climatic areas. Sediment samples were collected from three adjacent headwater forest streams within three biomes, eastern deciduous (Pennsylvania), southeastern coniferous (New Jersey), and tropical evergreen (Guanacaste, Costa Rica), to assess whether there is biome control of stream microbial community structure. Bacterial abundance, microbial biomass, and bacterial and microbial community structures were determined using classical, biochemical, and molecular methods. Microbial biomass, determined using phospholipid phosphate, was significantly greater in the southeastern coniferous biome, likely due to the smaller grain size, higher organic content, and lower levels of physical disturbance of these sediments. Microbial community structure was determined using phospholipid fatty acid (PLFA) profiles and bacterial community structure from terminal restriction fragment length polymorphism and edited (microeukaryotic PLFAs removed) PLFA profiles. Principal component analysis (PCA) was used to investigate patterns in total microbial community structure. The first principal component separated streams based on the importance of phototrophic microeukaryotes within the community, while the second separated southeastern coniferous streams from all others based on increased abundance of fungal PLFAs. PCA also indicated that within- and among-stream variations were small for tropical evergreen streams and large for southeastern coniferous streams. A similar analysis of bacterial community structure indicated that streams within biomes had similar community structures, while each biome possessed a unique streambed community, indicating strong within-biome control of stream bacterial community structure. PMID:18378660

  3. Paleopedological reconstruction and quantitative analysis of weathering processes in the Southern Piedmont Province

    SciTech Connect

    Feldman, S.B.; Zelazny, L.W. ); Pavich, M.J. )

    1992-01-01

    Soils and paleosols are commonly used to estimate ages of deposits and geomorphic surfaces, and to infer paleoenvironmental conditions during pedogenesis. Accurate interpretation of these and other parameters is currently limited, however, by considerable uncertainty in many fundamental areas of soils-geomorphic research. These include: (1) lack of accurate estimates of weathering rates for reliably-dated surfaces, (2) inability to quantitatively differentiate between the complex effects of climate vs. geomorphic age on weathering rates, processes, and pedogenic properties, and (3) difficulty in assessing which soil properties persist, alter, or become obliterated in the weathering environment as conditions change. In this paper, the authors discuss a method for assessing, on a regional basis, the quantitative relationships between climate, time, and weathering processes along a soil climosequence in the Southern Piedmont Province. Their approach involves sampling exclusively in areas of granitic plutons that exhibit a high degree of homogeneity with regard to total Fe content, bulk mineralogy, and absence of secondary phyllosilicates or sesquioxides. Independent age control is being established by [sup 10]Be dating, and analytical techniques include, in part, (1) geochemical speciation of soil solution and mineral equilibrium determination, (2) elemental analysis and mass balance calculations of elemental flux during pedogenesis, and (3) detailed analysis of Fe-oxide crystallinity, structure, and Al substitution using selective dissolution analysis, and both X-ray and differential X-ray diffraction.

  4. Quantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction

    PubMed Central

    Haraldsdóttir, H.S.; Thiele, I.; Fleming, R.M.T.

    2012-01-01

    Reaction directionality is a key constraint in the modeling of genome-scale metabolic networks. We thermodynamically constrained reaction directionality in a multicompartmental genome-scale model of human metabolism, Recon 1, by calculating, in vivo, standard transformed reaction Gibbs energy as a function of compartment-specific pH, electrical potential, and ionic strength. We show that compartmental pH is an important determinant of thermodynamically determined reaction directionality. The effects of pH on transport reaction thermodynamics are only seen to their full extent when metabolites are represented as pseudoisomer groups of multiple protonated species. We accurately predict the irreversibility of 387 reactions, with detailed propagation of uncertainty in input data, and manually curate the literature to resolve conflicting directionality assignments. In at least half of all cases, a prediction of a reversible reaction directionality is due to the paucity of compartment-specific quantitative metabolomic data, with remaining cases due to uncertainty in estimation of standard reaction Gibbs energy. This study points to the pressing need for 1), quantitative metabolomic data, and 2), experimental measurement of thermochemical properties for human metabolites. PMID:22768925

  5. Persistent Biomechanical Alterations After ACL Reconstruction Are Associated With Early Cartilage Matrix Changes Detected by Quantitative MR

    PubMed Central

    Amano, Keiko; Pedoia, Valentina; Su, Favian; Souza, Richard B.; Li, Xiaojuan; Ma, C. Benjamin

    2016-01-01

    Background: The effectiveness of anterior cruciate ligament (ACL) reconstruction in preventing early osteoarthritis is debated. Restoring the original biomechanics may potentially prevent degeneration, but apparent pathomechanisms have yet to be described. Newer quantitative magnetic resonance (qMR) imaging techniques, specifically T1ρ and T2, offer novel, noninvasive methods of visualizing and quantifying early cartilage degeneration. Purpose: To determine the tibiofemoral biomechanical alterations before and after ACL reconstruction using magnetic resonance imaging (MRI) and to evaluate the association between biomechanics and cartilage degeneration using T1ρ and T2. Study Design: Cohort study; Level of evidence, 2. Methods: Knee MRIs of 51 individuals (mean age, 29.5 ± 8.4 years) with unilateral ACL injuries were obtained prior to surgery; 19 control subjects (mean age, 30.7 ± 5.3 years) were also scanned. Follow-up MRIs were obtained at 6 months and 1 year. Tibial position (TP), internal tibial rotation (ITR), and T1ρ and T2 were calculated using an in-house Matlab program. Student t tests, repeated measures, and regression models were used to compare differences between injured and uninjured sides, observe longitudinal changes, and evaluate correlations between TP, ITR, and T1ρ and T2. Results: TP was significantly more anterior on the injured side at all time points (P < .001). ITR was significantly increased on the injured side prior to surgery (P = .033). At 1 year, a more anterior TP was associated with elevated T1ρ (P = .002) and T2 (P = .026) in the posterolateral tibia and with decreased T2 in the central lateral femur (P = .048); ITR was associated with increased T1ρ in the posteromedial femur (P = .009). ITR at 6 months was associated with increased T1ρ at 1 year in the posteromedial tibia (P = .029). Conclusion: Persistent biomechanical alterations after ACL reconstruction are related to significant changes in cartilage T1ρ and T2 at 1 year

  6. Towards a quantitative climate reconstruction linking meteorological, limnological and sedimentological datasets: the Lake Sanabria (NW Spain) case.

    NASA Astrophysics Data System (ADS)

    Rico-Herrero, María. Teresa; Giralt, Santiago; Valero-Garcés, Blas L.; Vega, José Carlos

    2010-05-01

    It is well-known that lacustrine sediment records constitute one of the best environmental sensors to reconstruct climate variability. Nevertheless, our knowledge of how the climate signal (precipitation, temperature, wind stress) is transferred from the atmosphere to the lake water masses (through the limnological variables such as pH, nutrient inputs or water chemistry) and to the sediments is very poor. Besides there are few reliable and temporal long limnological and/or meteorological datasets. This lack also prevents the conversion of these qualitative climate reconstructions into quantitative ones. Lake Sanabria (Zamora) is located in the northwestern of the Iberian Peninsula (42°07'30' N, 06°43'00' W), at 1.000 m a.s.l. It is the largest glacial lake (368 ha, 51 m of water depth at the deepest point and 96 Hm3 of water volume) in the Iberian Peninsula. The main water and sediments input and output is the Tera River. Monthly limnological (secchi disk, water temperature profiles, conductivity, pH, dissolved oxygen), nutrients (nitrates, silicon, total phosphorous, reactive phosphorous, total chlorophyll and a-chlorophyll), hydrological (Tera river discharge) and meteorological (precipitation and air temperature from the Ribadelago meteorological station) datasets covering the period 1992 - 2005 were employed to explore the relationships between the atmosphere and the Lake Sanabria hydrological balance, and the limnological variables. X-Ray Fluorescence (XRF) core scanner data of two gravity cores (SAN04-3A and SAN07-1M) allowed us to characterize with high resolution the evolution of the chemical composition of the uppermost sedimentary infill. SAN07-1M was dated using gamma-spectrometry (210Pb) and a key bed corresponding to the dam failure of the Vega de Tera Reservoir located upstream occurred in 1959 AD. The relationships between the sedimentological and limnological datasets allowed us to characterize the transference of the climate signal from the

  7. Quantitative analysis of free flap volume changes in head and neck reconstruction.

    PubMed

    Yamaguchi, Kazuaki; Kimata, Yoshihiro; Onoda, Satoshi; Mizukawa, Nobuyoshi; Onoda, Tomoo

    2012-10-01

    The purpose of this study was to determine whether free flap volume decreases or increases in the long-term postoperative period. We used a retrospective analysis of 17 patients to measure muscle and fat volume in free flap with 3-dimensional (3D) images using the AZE Virtual Place Lexus64. Seventeen patients underwent free flap reconstruction with rectus abdominis musculocutaneous flaps (n = 11) or anterolateral thigh flaps (n = 6). Median follow-up was 28.9 months (range, 2.1-48.4 months). Total flap volume was significantly decreased in flaps including ≥40% muscle (p = .011). Mean final muscle volume was 50% at an average of 12 months. Final fat volume was significantly higher for cases with no evidence of disease (mean, 116.7%) than for died-of-the-disease cases (mean, 70.3%; p = .007). Use of free flaps with a high ratio of fat to muscle is sustainable and can gain volume over time, as transplanted fat can increase depending on host condition. Copyright © 2011 Wiley Periodicals, Inc.

  8. Quantitative three-dimensional reconstruction: feasibility for studies of sexually dimorphic hypothalamic development in rats.

    PubMed

    Scallet, Andrew C; Meredith, John M

    2002-01-01

    The adult rat brain develops through an interplay of neuronal proliferation with programmed cell death. Sensory stimulation, as well as growth factors and steroids, may alter the balance between these competing processes. "Endocrine disrupters" (EDs) may do the same by mimicry or modulation of endogenous hormones. The sexually dimorphic nucleus (SDN) of the medial preoptic hypothalamus contains a high concentration of estrogen receptors (ERs). The SDN develops to a final adult volume, which may be used as an indication of the hormonal conditions during perinatal development. Although male rats have been repeatedly observed to have a greater adult SDN volume than female rats, variability between the actual measurements reported (both within and between laboratories) have been rather large. Exposure of female rats to testosterone (or excessive estradiol, beyond the binding capacity of alpha-fetoprotein) has been shown to masculinize them through a P450 aromatase that converts testosterone to estrogen in the SDN. Exposure of males to estradiol may feminize them at low doses through interference with the synthesis of their endogenous testosterone, which normally acts on SDN ERs following aromatization. We have employed computer-assisted reconstruction methods in order to render the SDN within the surrounding hypothalamus in 3-D for computation of its volume. Ongoing studies are investigating whether exposure through the diet to estrogenic endocrine disruptors such as genistein, nonylphenol, and ethinyl estradiol might produce effects similar to those of estradiol itself on the adult SDN.

  9. Multivariate clinical models and quantitative dipyridamole-thallium imaging to predict cardiac morbidity and death after vascular reconstruction

    SciTech Connect

    Lette, J.; Waters, D.; Lassonde, J.; Rene, P.; Picard, M.; Laurendeau, F.; Levy, R.; Cerino, M.; Nattel, S. )

    1991-08-01

    Patients with peripheral vascular disease have a high prevalence of coronary artery disease and are at increased risk for cardiac morbidity and death after vascular reconstruction. The present study was undertaken to assess the value of 18 clinical parameters, of 7 clinical scoring systems, and of quantitative dipyridamole-thallium imaging for predicting the occurrence of postoperative myocardial infarction or cardiac death. Vascular surgery was performed in 125 patients. Thirteen postoperative cardiac events occurred, including 10 cardiac deaths and 3 nonfatal infarctions. Clinical parameters were not useful in predicting postoperative outcome. All 63 patients with normal scan results or fixed perfusion defects underwent surgery uneventfully, whereas 21% (13/62) of patients with reversible defects had a postoperative cardiac complication. By use of quantitative scintigraphic indexes we found that patients with reversible defects could be stratified into intermediate and high-risk subgroups with postoperative event rates of 5% (2/47) and 85% (11/13), respectively, despite intensive postoperative monitoring and antianginal medication. Thus in patients unable to complete a standard exercise stress test, postoperative outcome cannot be predicted clinically, whereas dipyridamole-thallium imaging successfully identified all patients who had a postoperative cardiac event. By use of quantification we found that patients with reversible defects can be stratified into an intermediate risk subgroup that can undergo surgery with minimal complication rate and a high-risk subgroup that requires coronary angiography.

  10. Quantitative reconstruction of precipitation and runoff during MIS 5a, MIS 3a, and Holocene, arid China

    NASA Astrophysics Data System (ADS)

    Liu, Yuan; Li, Yu

    2016-09-01

    Marine oxygen isotope stage 5a (MIS 5a), MIS 3a, and Holocene were highlighted periods in paleoclimate studies. Many scientists have published a great number of studies in this regard, but they paid more attention to qualitative research, and there was often a lack of quantitative data. In this paper, based on chronological evidence from a paleolake in arid China, MIS 5a, MIS 3a, and Holocene lake area, the precipitation of the drainage area and the runoff of the inflowing rivers of the lake were reconstructed with ArcGIS spatial analysis software and the improved water and energy balance model which was calibrated by modern meteorological and hydrological data in the Shiyang River drainage basin. The results showed that the paleolake areas were 1824, 1124, and 628 km2 for MIS 5a, MIS 3a, and Holocene; meanwhile, the paleoprecipitation and runoff were 293.992-297.433, 271.105-274.294, and 249.431-252.373 mm and 29.103 × 108-29.496 × 108, 18.810 × 108-18.959 × 108, and 10.637 × 108-10.777 × 108 mm, respectively. The quantitative data can help us not only strengthen the understanding of paleoclimatic characteristics but also recognize the complexity and diversity of the climate system.

  11. Models and the paleo record of biome responses to glacial climate and CO2

    SciTech Connect

    Prentice; Colin, I.; Haxeltine

    1995-06-01

    Continental-scale reconstructions of the distribution of biomes at the last glacial maximum (LGM) indicate big changes, which can primarily be explained by climate. The climate was different from today mainly because of a combination of low concentrations of CO{sub 2} and other greenhouse gases and the presence of large continental ice sheets. Atmospheric general circulation model (AGCM) simulations, driven by these factors and linked to simple biome models in {open_quotes}diagnostic{close_quotes} mode, account for the broad outlines of the changes in vegetation patterns, including encroachment of C4 grasslands and savannas on what are now tropical forests. Physiological effects of low CO{sub 2} might also have played a role by altering the partitioning of precipitation to evapotranspiration and runoff, and altering the competitive balance of C3 and C4 plants. Such effects have not been quantified until recently, with the development of integrated biome/biochemistry models like those used in the VEMAP project. In these models, vegetation composition affects the coupled C and H{sub 2}O fluxes, which in turn influence the competitive balance of the constituent plant types. The relative importance of climatic and physiological effects of CO{sub 2} on biome distributions is a key issue for the future. This is gives added impetus to research that aims to exploit the potential of palaeo, data, through global data synthesis projects like BIOME 6000, to provide objective benchmarks against which to test models of the biosphere and climate.

  12. Quantitative reconstruction of past soil erosion in the Kirschgraben catchment (Spessart mountains, Central Europe)

    NASA Astrophysics Data System (ADS)

    Kranz, Annegret; Bork, Hans-Rudolf; Nelle, Oliver; Müller, Ulrich; Fuchs, Markus; Fuelling, Alexander

    2010-05-01

    An important problem in Holocene landscape reconstruction is quantifying the relative roles of climatic change and human impact. This project aims to quantify and mass-balance sediment flux in high temporal and spatial resolution, therefore a relatively small gully catchment (Kirschgraben) in the low mountain range Spessart (Germany, Lower Franconia) was chosen as a research area. The catchment is 42 ha in size and total relief is ~200 m. Bedrock is composed of Bunter Sandstone, large areas of which are loess mantled. In the intersection between Kirschgraben fan and the alluvial plain of the Elsava River a moated archaeological site was recently excavated. On the basis of process-based stratigraphy and preliminary chronology, a detailed sequence of landscape changes can be interpreted. Gully incision into Pleistocene sand and gravel sediments during early Holocene resulted in rapid fan development. Non-deposition on the fan surface and minor infilling of the gully system suggests relative catchment stability persisted during prehistoric times, at least until the early iron ages, when human occupation of the fan surface is first recorded. The first evidence of human impact, although minor, is represented by thin colluvial layers on the lower slopes during late Neolithic period. Subsequently, almost the entire catchment has been under agricultural use from the early medieval periods on, and well preserved within field terraces along ancient tenure borders. These features demonstrate widespread and intensive soil loss from the slopes, and eroded material is also preserved in various sediment traps within the catchment. Charcoal production in the catchment probably began at the same time as the widespread soil loss, and lasted until ca. 1900 AD. Anthracological investigations provide the opportunity to reconstruct the vegetation composition on a local scale, and is combined with paleobotanical macro remains and pollen analysis. Initial results indicate a rotating wood

  13. Quantitative reconstruction of paleo-Colorado-River profiles to test river integration and uplift models

    NASA Astrophysics Data System (ADS)

    Crow, R. S.; Karlstrom, K. E.; House, K.; Block, D.; Crossey, L. J.

    2015-12-01

    Spatial and temporal distribution of paleo Colorado River (CR) deposits form a primary dataset to better understand the evolution of a continental-scale river system and quantify regional uplift. We focus on the elevations of Bouse Formation, Bullhead Alluvium, and Chemehuevi Formation outcrops in the lower CR corridor taken from published maps and ongoing regional mapping efforts and the elevations of published and newly dated strath and fill terraces in Grand Canyon (GC). Our premise is that paleoprofile reconstruction can reveal overall incision magnitude, change in incision rates through time and space, fault dampened incision, and regional tilting due to differential epeirogenic uplift. Paleoprofile geometries were determined by projecting the elevation of dated CR deposits and bedrock straths onto a longitudinal valley profile using a semi-automated GIS routine. Base and top of deposits provide information about net bedrock incision and aggradation magnitude, respectively. In the lower CR corridor, the base of the ca. 4 Ma Bullhead Alluvium is subparallel to the modern CR, where not locally subsided, and projects to near sea level indicating little bedrock incision or surface uplift since 4 Ma. In GC paleoprofiles older than ca. 100 ka are above modern river level due to prolonged bedrock incision. Incision rates in western GC of ~100 m/Ma and 160 m/Ma in eastern GC necessitate ~400 m of differential block uplift across faults in the Lake Mead area and an additional ~240 m of epeirogenic mantle-driven surface uplift in eastern GC. Bedrock incision is locally dampened by fault-related folding associated with the Hurricane and Toroweap faults, but there is little regional uplift across these structures. Ongoing efforts focus on detailed geologic mapping and improved geochronology of defined paleoprofile segments to test depositional models for the Bouse, post-Bouse / pre-Bullhead uplift models, and further constrain differential uplift rates.

  14. The underestimated biodiversity of tropical grassy biomes.

    PubMed

    Murphy, Brett P; Andersen, Alan N; Parr, Catherine L

    2016-09-19

    For decades, there has been enormous scientific interest in tropical savannahs and grasslands, fuelled by the recognition that they are a dynamic and potentially unstable biome, requiring periodic disturbance for their maintenance. However, that scientific interest has not translated into widespread appreciation of, and concern about threats to, their biodiversity. In terms of biodiversity, grassy biomes are considered poor cousins of the other dominant biome of the tropics-forests. Simple notions of grassy biomes being species-poor cannot be supported; for some key taxa, such as vascular plants, this may be valid, but for others it is not. Here, we use an analysis of existing data to demonstrate that high-rainfall tropical grassy biomes (TGBs) have vertebrate species richness comparable with that of forests, despite having lower plant diversity. The Neotropics stand out in terms of both overall vertebrate species richness and number of range-restricted vertebrate species in TGBs. Given high rates of land-cover conversion in Neotropical grassy biomes, they should be a high priority for conservation and greater inclusion in protected areas. Fire needs to be actively maintained in these systems, and in many cases re-introduced after decades of inappropriate fire exclusion. The relative intactness of TGBs in Africa and Australia make them the least vulnerable to biodiversity loss in the immediate future. We argue that, like forests, TGBs should be recognized as a critical-but increasingly threatened-store of global biodiversity.This article is part of the themed issue 'Tropical grassy biomes: linking ecology, human use and conservation'. © 2016 The Author(s).

  15. The underestimated biodiversity of tropical grassy biomes

    PubMed Central

    Andersen, Alan N.; Parr, Catherine L.

    2016-01-01

    For decades, there has been enormous scientific interest in tropical savannahs and grasslands, fuelled by the recognition that they are a dynamic and potentially unstable biome, requiring periodic disturbance for their maintenance. However, that scientific interest has not translated into widespread appreciation of, and concern about threats to, their biodiversity. In terms of biodiversity, grassy biomes are considered poor cousins of the other dominant biome of the tropics—forests. Simple notions of grassy biomes being species-poor cannot be supported; for some key taxa, such as vascular plants, this may be valid, but for others it is not. Here, we use an analysis of existing data to demonstrate that high-rainfall tropical grassy biomes (TGBs) have vertebrate species richness comparable with that of forests, despite having lower plant diversity. The Neotropics stand out in terms of both overall vertebrate species richness and number of range-restricted vertebrate species in TGBs. Given high rates of land-cover conversion in Neotropical grassy biomes, they should be a high priority for conservation and greater inclusion in protected areas. Fire needs to be actively maintained in these systems, and in many cases re-introduced after decades of inappropriate fire exclusion. The relative intactness of TGBs in Africa and Australia make them the least vulnerable to biodiversity loss in the immediate future. We argue that, like forests, TGBs should be recognized as a critical—but increasingly threatened—store of global biodiversity. This article is part of the themed issue ‘Tropical grassy biomes: linking ecology, human use and conservation’. PMID:27502382

  16. Quantitative summer and winter temperature reconstructions from pollen and chironomid data in the Baltic-Belarus area

    NASA Astrophysics Data System (ADS)

    Veski, Siim; Seppä, Heikki; Stančikaitė, Migle; Zernitskaya, Valentina; Reitalu, Triin; Gryguc, Gražyna; Heinsalu, Atko; Stivrins, Normunds; Amon, Leeli; Vassiljev, Jüri; Heiri, Oliver

    2015-04-01

    Quantitative reconstructions based on fossil pollen and chironomids are widely used and useful for long-term climate variability estimations. The Lateglacial and early Holocene period (15-8 ka BP) in the Baltic-Belarus (BB) area between 60°-51° N was characterized by sudden shifts in climate due to various climate forcings affecting the climate of the northern hemisphere and North Atlantic, including the proximity of receding ice sheets. Climate variations in BB during the LG were eminent as the southern part of the region was ice free during the Last Glacial Maximum over 19 ka BP, whereas northern Estonia became ice free no sooner than 13 ka BP. New pollen based reconstructions of summer (May-to-August) and winter (December-to-February) temperatures between 15-8 ka BP along a S-N transect in the BB area display trends in temporal and spatial changes in climate variability. These results are completed by two chironomid-based July mean temperature reconstructions (Heiri et al. 2014). The magnitude of change compared with modern temperatures was more prominent in the northern part of BB area than in the southern part. The 4 °C winter and 2 °C summer warming at the start of GI-1 was delayed in the BB area and Lateglacial maximum temperatures were reached at ca 13.6 ka BP, being 4 °C colder than the modern mean. The Younger Dryas cooling in the area was 5 °C colder than present as inferred by all proxies (Veski et al. in press). In addition, our analyses show an early Holocene divergence in winter temperature trends with modern values reaching 1 ka earlier (10 ka BP) in southern BB compared to the northern part of the region (9 ka BP). Heiri, O., Brooks, S.J., Renssen, H., Bedford, A., Hazekamp, M., Ilyashuk, B., Jeffers, E.S., Lang, B., Kirilova, E., Kuiper, S., Millet, L., Samartin, S., Toth, M., Verbruggen, F., Watson, J.E., van Asch, N., Lammertsma, E., Amon, L., Birks, H.H., Birks, J.B., Mortensen, M.F., Hoek, W.Z., Magyari, E., Muñoz Sobrino, C., Seppä, H

  17. SU-E-I-41: Dictionary Learning Based Quantitative Reconstruction for Low-Dose Dual-Energy CT (DECT)

    SciTech Connect

    Xu, Q; Xing, L; Xiong, G; Elmore, K; Min, J

    2015-06-15

    Purpose: DECT collects two sets of projection data under higher and lower energies. With appropriates composition methods on linear attenuation coefficients, quantitative information about the object, such as density, can be obtained. In reality, one of the important problems in DECT is the radiation dose due to doubled scans. This work is aimed at establishing a dictionary learning based reconstruction framework for DECT for improved image quality while reducing the imaging dose. Methods: In our method, two dictionaries were learned respectively from the high-energy and lowenergy image datasets of similar objects under normal dose in advance. The linear attenuation coefficient was decomposed into two basis components with material based composition method. An iterative reconstruction framework was employed. Two basis components were alternately updated with DECT datasets and dictionary learning based sparse constraints. After one updating step under the dataset fidelity constraints, both high-energy and low-energy images can be obtained from the two basis components. Sparse constraints based on the learned dictionaries were applied to the high- and low-energy images to update the two basis components. The iterative calculation continues until a pre-set number of iteration was reached. Results: We evaluated the proposed dictionary learning method with dual energy images collected using a DECT scanner. We re-projected the projection data with added Poisson noise to reflect the low-dose situation. The results obtained by the proposed method were compared with that obtained using FBP based method and TV based method. It was found that the proposed approach yield better results than other methods with higher resolution and less noise. Conclusion: The use of dictionary learned from DECT images under normal dose is valuable and leads to improved results with much lower imaging dose.

  18. Defining functional biomes and monitoring their change globally.

    PubMed

    Higgins, Steven I; Buitenwerf, Robert; Moncrieff, Glenn R

    2016-11-01

    Biomes are important constructs for organizing understanding of how the worlds' major terrestrial ecosystems differ from one another and for monitoring change in these ecosystems. Yet existing biome classification schemes have been criticized for being overly subjective and for explicitly or implicitly invoking climate. We propose a new biome map and classification scheme that uses information on (i) an index of vegetation productivity, (ii) whether the minimum of vegetation activity is in the driest or coldest part of the year, and (iii) vegetation height. Although biomes produced on the basis of this classification show a strong spatial coherence, they show little congruence with existing biome classification schemes. Our biome map provides an alternative classification scheme for comparing the biogeochemical rates of terrestrial ecosystems. We use this new biome classification scheme to analyse the patterns of biome change observed over recent decades. Overall, 13% to 14% of analysed pixels shifted in biome state over the 30-year study period. A wide range of biome transitions were observed. For example, biomes with tall vegetation and minimum vegetation activity in the cold season shifted to higher productivity biome states. Biomes with short vegetation and low seasonality shifted to seasonally moisture-limited biome states. Our findings and method provide a new source of data for rigorously monitoring global vegetation change, analysing drivers of vegetation change and for benchmarking models of terrestrial ecosystem function. © 2016 John Wiley & Sons Ltd.

  19. Quantitative evaluation of an automatic segmentation method for 3D reconstruction of intervertebral scoliotic disks from MR images.

    PubMed

    Claudia, Chevrefils; Farida, Cheriet; Guy, Grimard; Marie-Claude, Miron; Carl-Eric, Aubin

    2012-08-02

    For some scoliotic patients the spinal instrumentation is inevitable. Among these patients, those with stiff curvature will need thoracoscopic disk resection. The removal of the intervertebral disk with only thoracoscopic images is a tedious and challenging task for the surgeon. With computer aided surgery and 3D visualisation of the interverterbral disk during surgery, surgeons will have access to additional information such as the remaining disk tissue or the distance of surgical tools from critical anatomical structures like the aorta or spinal canal. We hypothesized that automatically extracting 3D information of the intervertebral disk from MR images would aid the surgeons to evaluate the remaining disk and would add a security factor to the patient during thoracoscopic disk resection. This paper presents a quantitative evaluation of an automatic segmentation method for 3D reconstruction of intervertebral scoliotic disks from MR images. The automatic segmentation method is based on the watershed technique and morphological operators. The 3D Dice Similarity Coefficient (DSC) is the main statistical metric used to validate the automatically detected preoperative disk volumes. The automatic detections of intervertebral disks of real clinical MR images are compared to manual segmentation done by clinicians. Results show that depending on the type of MR acquisition sequence, the 3D DSC can be as high as 0.79 (±0.04). These 3D results are also supported by a 2D quantitative evaluation as well as by robustness and variability evaluations. The mean discrepancy (in 2D) between the manual and automatic segmentations for regions around the spinal canal is of 1.8 (±0.8) mm. The robustness study shows that among the five factors evaluated, only the type of MRI acquisition sequence can affect the segmentation results. Finally, the variability of the automatic segmentation method is lower than the variability associated with manual segmentation performed by different

  20. Quantitative evaluation of an automatic segmentation method for 3D reconstruction of intervertebral scoliotic disks from MR images

    PubMed Central

    2012-01-01

    Background For some scoliotic patients the spinal instrumentation is inevitable. Among these patients, those with stiff curvature will need thoracoscopic disk resection. The removal of the intervertebral disk with only thoracoscopic images is a tedious and challenging task for the surgeon. With computer aided surgery and 3D visualisation of the interverterbral disk during surgery, surgeons will have access to additional information such as the remaining disk tissue or the distance of surgical tools from critical anatomical structures like the aorta or spinal canal. We hypothesized that automatically extracting 3D information of the intervertebral disk from MR images would aid the surgeons to evaluate the remaining disk and would add a security factor to the patient during thoracoscopic disk resection. Methods This paper presents a quantitative evaluation of an automatic segmentation method for 3D reconstruction of intervertebral scoliotic disks from MR images. The automatic segmentation method is based on the watershed technique and morphological operators. The 3D Dice Similarity Coefficient (DSC) is the main statistical metric used to validate the automatically detected preoperative disk volumes. The automatic detections of intervertebral disks of real clinical MR images are compared to manual segmentation done by clinicians. Results Results show that depending on the type of MR acquisition sequence, the 3D DSC can be as high as 0.79 (±0.04). These 3D results are also supported by a 2D quantitative evaluation as well as by robustness and variability evaluations. The mean discrepancy (in 2D) between the manual and automatic segmentations for regions around the spinal canal is of 1.8 (±0.8) mm. The robustness study shows that among the five factors evaluated, only the type of MRI acquisition sequence can affect the segmentation results. Finally, the variability of the automatic segmentation method is lower than the variability associated with manual segmentation

  1. Quantitative reconstruction of temperature in northern Japan for the last 2000 years and the influential factors to determine climatic fluctuation

    NASA Astrophysics Data System (ADS)

    Kawahata, Hodaka; Hatta, Yoshiki; Ota, Yuki; Yoshida, Akihiro; Habu, Junko

    2016-04-01

    A coastal sedimentary core at St. 5 in Uchiura Bay in northern Japan provided an opportunity to quantitatively estimate terrestrial atmospheric temperatures (AT) using the alkenone proxy because of their strong correlation with summer sea surface temperatures (SSTs) (r2 >0.90). In other words, when we can estimate SST, we can reconstruct AT quantitatively at high time resolution (10-30 years for the last 2K). During the last two millennia, SSTs fluctuated by 4.9 °C before 20 century, reaching two maximum in 1820 AD (22.3°C) and 760 AD (22.0 °C) and two minima around 145 AD (17.4 °C) and 1080 AD (17.4 °C). The SST profile is generally consistent with those obtained from western and central Japan by us (3 sites) and from East Asia by Cook (2013) but shows some differences. Although the MWP (Medieval Warm Period) was not identified in this study because a cold climate prevailed in 990-1100 AD. Particularly low temperatures around 1000-1100 AD can be verified by historical documents from in and around the ancient capital city of Kyoto (Ishii, 2002). The reconstructed SOI (Southern Oscillation Index) data suggest that the equatorial Pacific was predominantly in an El Niño phase in 900-1200 AD. Under modern conditions, during an El Niño episode, the Pacific high is weakened, with reduced atmospheric pressure in the western North Pacific in the vicinity of Japan. This results in an enhanced Okhotsk high, which tends to be accompanied by a cold and cloudy/rainy summer in Japan. A cold climate was definitely observed in 1550-1700 AD, which almost corresponded to the LIA (Little Ice Age). A cold event around 1650 AD can be attributed to big eruptions at Komagatake. This resulted in severe cold type of famine, which is evidenced by historical documents. Because several factors, including external forcing (e.g., solar activity) and internal forcing (e.g., volcanic activity, ENSO, and the Asian monsoon), can affect the climate, we compared SST fluctuations with each of

  2. Phytolith carbon sequestration in global terrestrial biomes.

    PubMed

    Song, Zhaoliang; Liu, Hongyan; Strömberg, Caroline A E; Yang, Xiaomin; Zhang, Xiaodong

    2017-12-15

    Terrestrial biogeochemical carbon (C) sequestration is coupled with the biogeochemical silicon (Si) cycle through mechanisms such as phytolith C sequestration, but the size and distribution of the phytolith C sink remain unclear. Here, we estimate phytolith C sequestration in global terrestrial biomes. We used biome data including productivity, phytolith and silica contents, and the phytolith stability factor to preliminarily determine the size and distribution of the phytolith C sink in global terrestrial biomes. Total phytolith C sequestration in global terrestrial biomes is 156.7±91.6TgCO2yr(-1). Grassland (40%), cropland (35%), and forest (20%) biomes are the dominant producers of phytolith-based carbon; geographically, the main contributors are Asia (31%), Africa (24%), and South America (17%). Practices such as bamboo afforestation/reforestation and grassland recovery for economic and ecological purposes could theoretically double the above phytolith C sink. The potential terrestrial phytolith C sequestration during 2000-2099 under such practices would be 15.7-40.5PgCO2, equivalent in magnitude to the C sequestration of oceanic diatoms in sediments and through silicate weathering. Phytolith C sequestration contributes vitally to the global C cycle, hence, it is essential to incorporate plant-soil silica cycling in biogeochemical C cycle models. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. A quantitative technique to create a femoral tunnel at the averaged center of the anteromedial bundle attachment in anatomic double-bundle anterior cruciate ligament reconstruction

    PubMed Central

    2013-01-01

    Background In the anatomic double-bundle ACL reconstruction, 2 femoral tunnel positions are particularly critical to obtain better clinical results. Recently, a few studies have reported quantitative identification methods for posterolateral (PL) bundle reconstruction. Concerning anteromedial (AM) bundle reconstruction, however, no quantitative clinically available methods to insert a guide wire at the center of the direct attachment of the AM mid-substance fibers have been reported to date. Methods First, we determined the center of the femoral attachment of the AM mid-substance fibers using 38 fresh frozen cadaveric knees. Based on this anatomical sub-study, we developed a quantitative clinical technique to insert a guide wire at the averaged center for anatomic double-bundle ACL reconstruction. In the second clinical sub-study with 63 patients who underwent anatomic ACL reconstruction with this quantitative technique, we determined the center of an actually created AM tunnel. Then, we compared the results of the second sub-study with those of the first sub-study to validate the accuracy of the quantitative technique. In both the sub-studies, we determined the center of the anatomical attachment and the tunnel outlet using the “3-dimensional clock” system. The tunnel outlet was evaluated using the “transparent” 3-dimensional computed tomography. Results The averaged center of the direct attachment of the AM bundle midsubstance fibers was located on the cylindrical surface of the femoral intercondylar notch at “10:37” (or “1:23”) o’clock orientation in the distal view and at 5.0-mm from the proximal outlet of the intercondylar notch (POIN) in the lateral view. The AM tunnel actually created in ACL reconstruction was located at “10:41” (or “1:19”) o’clock orientation in the average and at 5.0-mm from the POIN. There was no significant difference between the 2 center locations. Conclusions The quantitative technique enabled us to easily

  4. Quantitative structure determination using grazing scattering of fast atoms: Oxygen-induced missing-row reconstruction of Mo(112)

    NASA Astrophysics Data System (ADS)

    Seifert, J.; Winter, H.

    2016-05-01

    We present an extensive study on the structure of oxygen adsorbates on Mo(112) by means of grazing scattering of fast hydrogen and helium atoms and low-energy electron diffraction. For projectile energies less than 2 keV, fast atom diffraction provides information on the surface unit cell and on adsorption sites for low coverages. In the classical scattering regime, we employed so-called triangulation techniques where for an azimuthal rotation of the target axial surface channels are identified. From comparison with computer simulation positions of surface atoms can be derived. Aside from the detection scheme of projectile-induced electron emission, we present details for a new variant of triangulation based on the detection of angular distributions of scattered particles. The different sensitivity of the methods to the topmost surface layers allows us to efficiently set up structural models for four adsorbate phases for which contradicting models exist in literature. The c (4 ×2 ) phase is revealed to be one step in the formation of a missing-row reconstruction with p (1 ×2 ) unit cell. Our studies demonstrate the potential of grazing scattering of fast atoms for quantitative structure analysis.

  5. Reproducibility of R2 * and quantitative susceptibility mapping (QSM) reconstruction methods in the basal ganglia of healthy subjects.

    PubMed

    Santin, M D; Didier, M; Valabrègue, R; Yahia Cherif, L; García-Lorenzo, D; Loureiro de Sousa, P; Bardinet, E; Lehéricy, S

    2017-04-01

    The basal ganglia are key structures for motor, cognitive and behavioral functions. They undergo several changes with aging and disease, such as Parkinson's or Huntington's disease, for example. Iron accumulation in basal ganglia is often related to these diseases, which is conventionally monitored by the transverse relaxation rate (R2 *). Quantitative susceptibility mapping (QSM) is a novel contrast mechanism in MRI produced by adding information taken from the phase of the MR signal to its magnitude. It has been shown to be more sensitive to subtle changes in Parkinson's disease. In order to be applied widely to various pathologies, its reproducibility must be evaluated in order to assess intra-subject variability and to disseminate into clinical and pharmaceutical studies. In this work, we studied the reproducibility and sensitivity of several QSM techniques. Fourteen subjects were scanned four times, and QSM and R2 * images were reconstructed and registered. An atlas of the basal ganglia was used to automatically define regions of interest. We found that QSM measurements are indeed reproducible in the basal ganglia of healthy subjects and can be widely used as a replacement for R2 * mapping in iron-rich regions. This reproducibility study could lead to several lines of research in relaxometry and susceptibility measurements, in vivo iron load evaluation as well as pharmacological assessment and biomarker development. Copyright © 2016 John Wiley & Sons, Ltd.

  6. A quantitative assessment of the insertional footprints of the hip joint capsular ligaments and their spanning fibers for reconstruction.

    PubMed

    Telleria, Jessica J M; Lindsey, Derek P; Giori, Nicholas J; Safran, Marc R

    2014-04-01

    Quantitative descriptions of the hip joint capsular ligament insertional footprints have been reported. Using a three-dimensional digitizing system, and computer modeling, the area, and dimensions of the three main hip capsular ligaments and their insertional footprints were quantified in eight cadaveric hips. The iliofemoral ligament (ILFL) attaches proximally to the anterolateral supra-acetabular region (mean area = 4.2 cm(2)). The mean areas of the ILFL lateral and medial arm insertional footprints are 4.8 and 3.1 cm(2), respectively. The pubofemoral ligament (proximal footprint mean area = 1.4 cm(2)) blends with the medial ILFL anteriorly and the proximal ischiofemoral ligament (ISFL) distally without a distal bony insertion. The proximal and distal ISFL footprint mean areas are 6.4 and 1.2 cm(2), respectively. The hip joint capsular ligaments have consistent anatomic and insertional patterns. Quantification of the ligaments and their attachment sites may aid in improving anatomic repairs and reconstructions of the hip joint capsule using open and/or arthroscopic techniques.

  7. Quantitative image reconstruction for dual-isotope parathyroid SPECT/CT: phantom experiments and sample patient studies

    NASA Astrophysics Data System (ADS)

    Shcherbinin, S.; Chamoiseau, S.; Celler, A.

    2012-08-01

    We investigated the quantitative accuracy of the model-based dual-isotope single-photon emission computed tomography (DI-SPECT) reconstructions that use Klein-Nishina expressions to estimate the scattered photon contributions to the projection data. Our objective was to examine the ability of the method to recover the absolute activities pertaining to both radiotracers: Tc-99m and I-123. We validated our method through a series of phantom experiments performed using a clinical hybrid SPECT/CT camera (Infinia Hawkeye, GE Healthcare). Different activity ratios and different attenuating media were used in these experiments to create cross-talk effects of varying severity, which can occur in clinical studies. Accurate model-based corrections for scatter and cross-talk with CT attenuation maps allowed for the recovery of the absolute activities from DI-SPECT/CT scans with errors that ranged 0-10% for both radiotracers. The unfavorable activity ratios increased the computational burden but practically did not affect the resulting accuracy. The visual analysis of parathyroid patient data demonstrated that our model-based processing improved adenoma/background contrast and enhanced localization of small or faint adenomas.

  8. Correlation between average tissue depth data and quantitative accuracy of forensic craniofacial reconstructions measured by geometric surface comparison method.

    PubMed

    Lee, Won-Joon; Wilkinson, Caroline M; Hwang, Hyeon-Shik; Lee, Sang-Mi

    2015-05-01

    Accuracy is the most important factor supporting the reliability of forensic facial reconstruction (FFR) comparing to the corresponding actual face. A number of methods have been employed to evaluate objective accuracy of FFR. Recently, it has been attempted that the degree of resemblance between computer-generated FFR and actual face is measured by geometric surface comparison method. In this study, three FFRs were produced employing live adult Korean subjects and three-dimensional computerized modeling software. The deviations of the facial surfaces between the FFR and the head scan CT of the corresponding subject were analyzed in reverse modeling software. The results were compared with those from a previous study which applied the same methodology as this study except average facial soft tissue depth dataset. Three FFRs of this study that applied updated dataset demonstrated lesser deviation errors between the facial surfaces of the FFR and corresponding subject than those from the previous study. The results proposed that appropriate average tissue depth data are important to increase quantitative accuracy of FFR.

  9. Quantitative Features of Liver Lesions, Lung Nodules, and Renal Stones at Multi-Detector Row CT Examinations: Dependency on Radiation Dose and Reconstruction Algorithm.

    PubMed

    Solomon, Justin; Mileto, Achille; Nelson, Rendon C; Roy Choudhury, Kingshuk; Samei, Ehsan

    2016-04-01

    To determine if radiation dose and reconstruction algorithm affect the computer-based extraction and analysis of quantitative imaging features in lung nodules, liver lesions, and renal stones at multi-detector row computed tomography (CT). Retrospective analysis of data from a prospective, multicenter, HIPAA-compliant, institutional review board-approved clinical trial was performed by extracting 23 quantitative imaging features (size, shape, attenuation, edge sharpness, pixel value distribution, and texture) of lesions on multi-detector row CT images of 20 adult patients (14 men, six women; mean age, 63 years; range, 38-72 years) referred for known or suspected focal liver lesions, lung nodules, or kidney stones. Data were acquired between September 2011 and April 2012. All multi-detector row CT scans were performed at two different radiation dose levels; images were reconstructed with filtered back projection, adaptive statistical iterative reconstruction, and model-based iterative reconstruction (MBIR) algorithms. A linear mixed-effects model was used to assess the effect of radiation dose and reconstruction algorithm on extracted features. Among the 23 imaging features assessed, radiation dose had a significant effect on five, three, and four of the features for liver lesions, lung nodules, and renal stones, respectively (P < .002 for all comparisons). Adaptive statistical iterative reconstruction had a significant effect on three, one, and one of the features for liver lesions, lung nodules, and renal stones, respectively (P < .002 for all comparisons). MBIR reconstruction had a significant effect on nine, 11, and 15 of the features for liver lesions, lung nodules, and renal stones, respectively (P < .002 for all comparisons). Of note, the measured size of lung nodules and renal stones with MBIR was significantly different than those for the other two algorithms (P < .002 for all comparisons). Although lesion texture was significantly affected by the

  10. Toward a rule-based biome model (journal article)

    SciTech Connect

    Neilson, R.P.; King, G.A.; Koerper, G.

    1992-01-01

    The current projections of the response of the biosphere to global climatic change indicate as much as 50% to 90% spatial displacement of extratropical biomes. The mechanism of spatial shift could be dominated by either (1) competitive displacement of northern biomes by southern biomes, or (2) drought-induced dieback of areas susceptible to change. The current suite of global biosphere models cannot distinguish between these two processes, thus determining the need for a mechanistically based biome model.

  11. Changes in forest productivity across Alaska consistent with biome shift

    Treesearch

    Peter S.A. Beck; Glenn P. Juday; Claire Alix; Valerie A. Barber; Stephen E. Winslow; Emily E. Sousa; Patricia Heiser; James D. Herriges; Scott J. Goetz

    2011-01-01

    Global vegetation models predict that boreal forests are particularly sensitive to a biome shift during the 21st century. This shift would manifest itself first at the biome's margins, with evergreen forest expanding into current tundra while being replaced by grasslands or temperate forest at the biome's southern edge. We evaluated changes in forest...

  12. An integrated enhancement and reconstruction strategy for the quantitative extraction of actin stress fibers from fluorescence micrographs.

    PubMed

    Zhang, Zhen; Xia, Shumin; Kanchanawong, Pakorn

    2017-05-22

    The stress fibers are prominent organization of actin filaments that perform important functions in cellular processes such as migration, polarization, and traction force generation, and whose collective organization reflects the physiological and mechanical activities of the cells. Easily visualized by fluorescence microscopy, the stress fibers are widely used as qualitative descriptors of cell phenotypes. However, due to the complexity of the stress fibers and the presence of other actin-containing cellular features, images of stress fibers are relatively challenging to quantitatively analyze using previously developed approaches, requiring significant user intervention. This poses a challenge for the automation of their detection, segmentation, and quantitative analysis. Here we describe an open-source software package, SFEX (Stress Fiber Extractor), which is geared for efficient enhancement, segmentation, and analysis of actin stress fibers in adherent tissue culture cells. Our method made use of a carefully chosen image filtering technique to enhance filamentous structures, effectively facilitating the detection and segmentation of stress fibers by binary thresholding. We subdivided the skeletons of stress fiber traces into piecewise-linear fragments, and used a set of geometric criteria to reconstruct the stress fiber networks by pairing appropriate fiber fragments. Our strategy enables the trajectory of a majority of stress fibers within the cells to be comprehensively extracted. We also present a method for quantifying the dimensions of the stress fibers using an image gradient-based approach. We determine the optimal parameter space using sensitivity analysis, and demonstrate the utility of our approach by analyzing actin stress fibers in cells cultured on various micropattern substrates. We present an open-source graphically-interfaced computational tool for the extraction and quantification of stress fibers in adherent cells with minimal user input. This

  13. Can use of adaptive statistical iterative reconstruction reduce radiation dose in unenhanced head CT? An analysis of qualitative and quantitative image quality.

    PubMed

    Østerås, Bjørn Helge; Heggen, Kristin Livelten; Pedersen, Hans Kristian; Andersen, Hilde Kjernlie; Martinsen, Anne Catrine T

    2016-08-01

    Iterative reconstruction can reduce image noise and thereby facilitate dose reduction. To evaluate qualitative and quantitative image quality for full dose and dose reduced head computed tomography (CT) protocols reconstructed using filtered back projection (FBP) and adaptive statistical iterative reconstruction (ASIR). Fourteen patients undergoing follow-up head CT were included. All patients underwent full dose (FD) exam and subsequent 15% dose reduced (DR) exam, reconstructed using FBP and 30% ASIR. Qualitative image quality was assessed using visual grading characteristics. Quantitative image quality was assessed using ROI measurements in cerebrospinal fluid (CSF), white matter, peripheral and central gray matter. Additionally, quantitative image quality was measured in Catphan and vendor's water phantom. There was no significant difference in qualitative image quality between FD FBP and DR ASIR. Comparing same scan FBP versus ASIR, a noise reduction of 28.6% in CSF and between -3.7 and 3.5% in brain parenchyma was observed. Comparing FD FBP versus DR ASIR, a noise reduction of 25.7% in CSF, and -7.5 and 6.3% in brain parenchyma was observed. Image contrast increased in ASIR reconstructions. Contrast-to-noise ratio was improved in DR ASIR compared to FD FBP. In phantoms, noise reduction was in the range of 3 to 28% with image content. There was no significant difference in qualitative image quality between full dose FBP and dose reduced ASIR. CNR improved in DR ASIR compared to FD FBP mostly due to increased contrast, not reduced noise. Therefore, we recommend using caution if reducing dose and applying ASIR to maintain image quality.

  14. Can use of adaptive statistical iterative reconstruction reduce radiation dose in unenhanced head CT? An analysis of qualitative and quantitative image quality

    PubMed Central

    Heggen, Kristin Livelten; Pedersen, Hans Kristian; Andersen, Hilde Kjernlie; Martinsen, Anne Catrine T

    2016-01-01

    Background Iterative reconstruction can reduce image noise and thereby facilitate dose reduction. Purpose To evaluate qualitative and quantitative image quality for full dose and dose reduced head computed tomography (CT) protocols reconstructed using filtered back projection (FBP) and adaptive statistical iterative reconstruction (ASIR). Material and Methods Fourteen patients undergoing follow-up head CT were included. All patients underwent full dose (FD) exam and subsequent 15% dose reduced (DR) exam, reconstructed using FBP and 30% ASIR. Qualitative image quality was assessed using visual grading characteristics. Quantitative image quality was assessed using ROI measurements in cerebrospinal fluid (CSF), white matter, peripheral and central gray matter. Additionally, quantitative image quality was measured in Catphan and vendor’s water phantom. Results There was no significant difference in qualitative image quality between FD FBP and DR ASIR. Comparing same scan FBP versus ASIR, a noise reduction of 28.6% in CSF and between −3.7 and 3.5% in brain parenchyma was observed. Comparing FD FBP versus DR ASIR, a noise reduction of 25.7% in CSF, and −7.5 and 6.3% in brain parenchyma was observed. Image contrast increased in ASIR reconstructions. Contrast-to-noise ratio was improved in DR ASIR compared to FD FBP. In phantoms, noise reduction was in the range of 3 to 28% with image content. Conclusion There was no significant difference in qualitative image quality between full dose FBP and dose reduced ASIR. CNR improved in DR ASIR compared to FD FBP mostly due to increased contrast, not reduced noise. Therefore, we recommend using caution if reducing dose and applying ASIR to maintain image quality. PMID:27583169

  15. Dosimetry software Hermes Internal Radiation Dosimetry: from quantitative image reconstruction to voxel-level absorbed dose distribution.

    PubMed

    Hippeläinen, Eero T; Tenhunen, Mikko J; Mäenpää, Hanna O; Heikkonen, Jorma J; Sohlberg, Antti O

    2017-05-01

    The aim of this work is to validate a software package called Hermes Internal Radiation Dosimetry (HIRD) for internal dose assessment tailored for clinical practice. The software includes all the necessary steps to perform voxel-level absorbed dose calculations including quantitative reconstruction, image coregistration and volume of interest tools. The basics of voxel-level dosimetry methods and implementations to HIRD software are reviewed. Then, HIRD is validated using simulated SPECT/CT data and data from Lu-DOTATATE-treated patients by comparing absorbed kidney doses with OLINDA/EXM-based dosimetry. In addition, electron and photon dose components are studied separately in an example patient case. The simulation study showed that HIRD can reproduce time-activity curves accurately and produce absorbed doses with less than 10% error for the kidneys, liver and spleen. From the patient data, the absorbed kidney doses calculated using HIRD and using OLINDA/EXM were highly correlated (Pearson's correlation coefficient, r=0.98). From Bland-Altman plot analysis, an average absorbed dose difference of -2% was found between the methods. In addition, we found that in Lu-DOTATATE-treated patients, photons can contribute over 10% of the kidney's total dose and is partly because of cross-irradiation from high-uptake lesions close to the kidneys. HIRD is a straightforward voxel-level internal dosimetry software. Its clinical utility was verified with simulated and clinical Lu-DOTATATE-treated patient data. Patient studies also showed that photon contribution towards the total dose can be relatively high and voxel-level dose calculations can be valuable in cases where the target organ is in close proximity to high-uptake organs.

  16. Evaluating the efficacy of continuous quantitative characters for reconstructing the phylogeny of a morphologically homogeneous spider taxon (Araneae, Mygalomorphae, Antrodiaetidae, Antrodiaetus).

    PubMed

    Hendrixson, Brent E; Bond, Jason E

    2009-10-01

    The use of continuous quantitative characters for phylogenetic analyses has long been contentious in the systematics literature. Recent studies argue for and against their use, but there have been relatively few attempts to evaluate whether these characters provide an accurate estimate of phylogeny, despite the fact that a number of methods have been developed to analyze these types of data for phylogenetic inference. A tree topology will be produced for a given methodology and set of characters, but little can be concluded with regards to the accuracy of phylogenetic signal without an independent evaluation of those characters. We assess the performance of continuous quantitative characters for the mygalomorph spider genus Antrodiaetus, a group that is morphologically homogeneous and one for which few discrete (morphological) characters have been observed. Phylogenetic signal contained in continuous quantitative characters is compared to an independently derived phylogeny inferred on the basis of multiple nuclear and mitochondrial gene loci. Tree topology randomizations, regression techniques, and topological tests all demonstrate that continuous quantitative characters in Antrodiaetus conflict with the phylogenetic signal contained in the gene trees. Our results show that the use of continuous quantitative characters for phylogenetic reconstruction may be inappropriate for reconstructing Antrodiaetus phylogeny and indicate that due caution should be exercised before employing this character type in the absence of other independently derived sources of characters.

  17. Quantitative reconstruction of summer precipitation using a mid-Holocene δ13C common millet record from Guanzhong Basin, northern China

    NASA Astrophysics Data System (ADS)

    Yang, Qing; Li, Xiaoqiang; Zhou, Xinying; Zhao, Keliang; Sun, Nan

    2016-12-01

    To quantitatively reconstruct Holocene precipitation for particular geographical areas, suitable proxies and faithful dating controls are required. The fossilized seeds of common millet (Panicum miliaceum) are found throughout the sedimentary strata of northern China and are suited to the production of quantitative Holocene precipitation reconstructions: their isotopic carbon composition (δ13C) gives a measure of the precipitation required during the growing season of summer (here the interval from mid-June to September) and allows these seeds to be dated. We therefore used a regression function, as part of a systematic study of the δ13C of common millet, to produce a quantitative reconstruction of mid-Holocene summer precipitation in the Guanzhong Basin (107°40'-107°49' E, 33°39'-34°45' N). Our results showed that mean summer precipitation at 7.7-3.4 ka BP was 353 mm, ˜ 50 mm or 17 % higher than present levels, and the variability increased, especially after 5.2 ka BP. Maximum mean summer precipitation peaked at 414 mm during the period 6.1-5.5 ka BP, ˜ 109 mm (or 36 %) higher than today, indicating that the East Asian summer monsoon (EASM) peaked at this time. This work can provide a new proxy for further research into continuous paleoprecipitation sequences and the variability of summer precipitation, which will promote the further research into the relation between early human activity and environmental change.

  18. Global climate and the distribution of plant biomes.

    PubMed

    Woodward, F I; Lomas, M R; Kelly, C K

    2004-10-29

    Biomes are areas of vegetation that are characterized by the same life-form. Traditional definitions of biomes have also included either geographical or climatic descriptors. This approach describes a wide range of biomes that can be correlated with characteristic climatic conditions, or climatic envelopes. The application of remote sensing technology to the frequent observation of biomes has led to a move away from the often subjective definition of biomes to one that is objective. Carefully characterized observations of life-form, by satellite, have been used to reconsider biome classification and their climatic envelopes. Five major tree biomes can be recognized by satellites based on leaf longevity and morphology: needleleaf evergreen, broadleaf evergreen, needleleaf deciduous, broadleaf cold deciduous and broadleaf drought deciduous. Observations indicate that broadleaf drought deciduous vegetation grades substantially into broadleaf evergreen vegetation. The needleleaf deciduous biome occurs in the world's coldest climates, where summer drought and therefore a drought deciduous biome are absent. Traditional biome definitions are quite static, implying no change in their life-form composition with time, within their particular climatic envelopes. However, this is not the case where there has been global ingress of grasslands and croplands into forested vegetation. The global spread of grasses, a new super-biome, was probably initiated 30-45 Myr ago by an increase in global aridity, and was driven by the natural spread of the disturbances of fire and animal grazing. These disturbances have been further extended over the Holocene era by human activities that have increased the land areas available for domestic animal grazing and for growing crops. The current situation is that grasses now occur in most, if not all biomes, and in many areas they dominate and define the biome. Croplands are also increasing, defining a new and relatively recent component to the

  19. Investigating the quantitative fidelity of prospectively undersampled chemical shift imaging in muscular dystrophy with compressed sensing and parallel imaging reconstruction.

    PubMed

    Hollingsworth, Kieren G; Higgins, David M; McCallum, Michelle; Ward, Louise; Coombs, Anna; Straub, Volker

    2014-12-01

    Fat fraction measurement in muscular dystrophy has an important role to play in future therapy trials. Undersampled data acquisition reconstructed by combined compressed sensing and parallel imaging (CS-PI) can potentially reduce trial cost and improve compliance. These benefits are only gained from prospectively undersampled acquisitions. Eight patients with Becker muscular dystrophy were recruited and prospectively undersampled data at ratios of 3.65×, 4.94×, and 6.42× were acquired in addition to fully sampled data: equivalent coherent undersamplings were acquired for reconstruction with parallel imaging alone (PI). Fat fraction maps and maps of total signal were created using a combined compressed sensing/parallel imaging (CS-PI) reconstruction. The CS-PI reconstructions are of sufficient quality to allow muscle delineation at 3.65× and 4.94× undersampling but some muscles were obscured at 6.42×. When plotted against the fat fractions derived from fully sampled data, non-significant bias and 95% limits of agreement of 1.58%, 2.17% and 2.41% were found for the three CS-PI reconstructions, while a 3.36× PI reconstruction yields 2.78%, 1.8 times worse than the equivalent CS-PI reconstruction. Prospective undersampling and CS-PI reconstruction of muscle fat fraction mapping can be used to accelerate muscle fat fraction measurement in muscular dystrophy. © 2013 Wiley Periodicals, Inc.

  20. Qualitative and quantitative assessment of smoking-related lung disease: effect of iterative reconstruction on low-dose computed tomographic examinations.

    PubMed

    Hague, Cameron J; Krowchuk, Natasha; Alhassan, Donya; Ho, Kevin; Leipsic, Jonathon; Sin, Don D; Mayo, John R; Coxson, Harvey O

    2014-11-01

    The purpose of this research is to examine the role that differing levels of adaptive statistical iterative reconstruction (ASIR) have on the qualitative and quantitative assessment of smoking-related lung disease. Institutional board review approval was obtained. A total of 52 patients undergoing clinically indicated low-dose computed tomographic (CT) examinations of the chest (100 kVp, 65 mAs, mean radiation dose 1.0±0.12 mSv), with reconstruction of data with different levels of blended ASIR (0%, 40%, and 100%), were consented. Qualitative assessment of CT data sets was performed by 2 trained thoracic radiologists blinded to clinical history, spirometry, and quantitative data for the presence of emphysema (%/lung zone) and the degree of respiratory bronchiolitis. Quantitative analysis was performed (Apollo Image analysis, VIDA Diagnostics) to assess emphysema and airway measures of chronic obstructive pulmonary disease. The application of ASIR results in alterations in both qualitative and quantitative assessment of smoking-related lung disease. As levels of ASIR increased, both readers scored more respiratory bronchiolitis (P<0.05). At increased levels of ASIR (ie, 100% vs. 0%), the amount of emphysema measured (% below -950 HU) decreased, the number of airways measured diminished, and the airway thickness (Pi10mm) increased (P<0.001). The use of ASIR alters both the qualitative and quantitative assessment of smoking-related lung disease. Although a powerful tool to allow dose reduction, caution must be exercised when iterative reconstruction techniques are utilized when evaluating CT examinations for findings of chronic obstructive pulmonary disease.

  1. Significance of the Lateral Thoracic Artery in Pectoralis Major Musculocutaneous Flap Reconstruction: Quantitative Assessment of Blood Circulation Using Indocyanine Green Angiography.

    PubMed

    Miyazaki, Hidetaka; Igari, Kimihiro; Kudo, Toshifumi; Iwai, Toshinori; Wada, Yoshitaka; Takahashi, Yasuhiro; Inoue, Yoshinori; Asamura, Shinichi

    2017-11-01

    Free tissue transfer is the preferred reconstruction option in most major head and neck reconstructions. The pectoralis major muscle musculocutaneous (PMMC) flap is commonly used in salvage of necrotic free flaps and is the first choice for patients who are not candidates for free flaps. The lateral thoracic artery (LTA), which is thought to contribute to blood perfusion of the inferior and lateral mammary area, is not preserved in a conventionally harvested PMMC flap. With regard to blood supply, it has been suggested that the LTA should be preserved, in addition to the pectoral branch of the thoracoacromial artery, when a skin island is designed in the lower chest to attain a pedicle length sufficient for head and neck reconstruction. However, an effect on hemodynamic improvement using the LTA has not been shown quantitatively. In this study, we examined 8 patients with oral cancer who underwent reconstruction procedures with a bipedicle PMMC flap that included the LTA, in addition to the thoracoacromial artery. Intraoperative indocyanine green angiography was performed to examine circulation to the PMMC flap with or without LTA clamping after harvesting. After image processing, data were analyzed using a new quantitative perfusion assessment system with parameters that we recently established for assessment of peripheral arterial disease of the lower limbs. All patients had good clinical courses with whole-flap survival, no vascular insufficiency of the skin island, and no fistula formation. Intraoperative indocyanine green angiography showed an increased inflow rate into the skin island in an LTA-declamped condition in all cases, implying that the preserved LTA increased the blood supply to skin islands in the pectoralis major muscle. We conclude that preserving the LTA in a PMMC flap can increase blood perfusion and stabilize the vascularity of the flap, making the reconstruction more effective and reliable than with use of a conventionally harvested flap

  2. Surging wildfire activity in a grassland biome

    NASA Astrophysics Data System (ADS)

    Donovan, Victoria M.; Wonkka, Carissa L.; Twidwell, Dirac

    2017-06-01

    Rapid changes in wildfire patterns are documented globally, increasing pressure to identify regions that may experience increases in wildfire in future decades. Temperate grassland and savanna biomes were some of the most frequently burned regions on Earth; however, large wildfires have been largely absent from the Great Plains of North America over the last century. In this paper, we conduct an in-depth analysis of changes in large wildfire (>400 ha) regime characteristics over a 30 year period across the Great Plains. For the entire biome, (i) the average number of large wildfires increased from 33.4 ± 5.6 per year from 1985 to 1994 to 116.8 ± 28.8 wildfires per year from 2005 to 2014, (ii) total area burned by large wildfires increased 400%, (iii) over half the ecoregions had greater than a 70% probability of a large wildfire occurring in the last decade, and (iv) seasonality of large wildfires remained relatively similar.

  3. The extent of forest in dryland biomes.

    PubMed

    Bastin, Jean-François; Berrahmouni, Nora; Grainger, Alan; Maniatis, Danae; Mollicone, Danilo; Moore, Rebecca; Patriarca, Chiara; Picard, Nicolas; Sparrow, Ben; Abraham, Elena Maria; Aloui, Kamel; Atesoglu, Ayhan; Attore, Fabio; Bassüllü, Çağlar; Bey, Adia; Garzuglia, Monica; García-Montero, Luis G; Groot, Nikée; Guerin, Greg; Laestadius, Lars; Lowe, Andrew J; Mamane, Bako; Marchi, Giulio; Patterson, Paul; Rezende, Marcelo; Ricci, Stefano; Salcedo, Ignacio; Diaz, Alfonso Sanchez-Paus; Stolle, Fred; Surappaeva, Venera; Castro, Rene

    2017-05-12

    Dryland biomes cover two-fifths of Earth's land surface, but their forest area is poorly known. Here, we report an estimate of global forest extent in dryland biomes, based on analyzing more than 210,000 0.5-hectare sample plots through a photo-interpretation approach using large databases of satellite imagery at (i) very high spatial resolution and (ii) very high temporal resolution, which are available through the Google Earth platform. We show that in 2015, 1327 million hectares of drylands had more than 10% tree-cover, and 1079 million hectares comprised forest. Our estimate is 40 to 47% higher than previous estimates, corresponding to 467 million hectares of forest that have never been reported before. This increases current estimates of global forest cover by at least 9%. Copyright © 2017, American Association for the Advancement of Science.

  4. Biome Is Where the Art Is

    ERIC Educational Resources Information Center

    Gooden, Kelly

    2005-01-01

    The author is surprised every year when fifth-grade students react to the study of biomes as if they've never given any thought to the differences across parts of the world. Sure, they've all heard of the tropical rain forest and the desert, but it seems as though they think the rest of the world is just some undefined area with climate, animals,…

  5. Biome Is Where the Art Is

    ERIC Educational Resources Information Center

    Gooden, Kelly

    2005-01-01

    The author is surprised every year when fifth-grade students react to the study of biomes as if they've never given any thought to the differences across parts of the world. Sure, they've all heard of the tropical rain forest and the desert, but it seems as though they think the rest of the world is just some undefined area with climate, animals,…

  6. The Past is a Guide to the Future? Comparing Middle Pliocene Vegetation With Predicted Biome Distributions for the 21st Century

    NASA Astrophysics Data System (ADS)

    Salzmann, U.; Haywood, A. M.; Lunt, D. J.

    2007-12-01

    The Middle Pliocene geological stage, ca. 3.6 to 2.6 million years ago, represents an interval of time in which Earth experienced greater global warmth. In order to evaluate the degree to which the Middle Pliocene can be used as a 'test bed' for future warming, we compare a newly developed Middle Pliocene biome reconstruction with simulated global biome distributions for the mid and late 21st century. The Middle Pliocene biome reconstruction is based on an internally consistent dataset of 202 palaeobotanical sites and predictions from a state-of-the-art coupled climate-vegetation model (HadAM3-TRIFFID-BIOME4), the output of which is used to provide biome estimates for data sparse regions. For the Middle Pliocene, both the vegetation reconstruction and model predictions indicate a generally warmer and moister climate than today. Evergreen taiga as well as temperate forest and grasslands shifted northward resulting in a significantly reduced area of tundra vegetation. Warm-temperate forests (with subtropical taxa) spread in Middle and Eastern Europe and tropical savannas and woodland expanded in Africa and Australia at the expense of deserts. Middle Pliocene biome distributions are compared (globally and on a regional scale) with two new predictions of equilibrium vegetation conditions for the early 21st Century (around 2020, ~ 400ppmv CO2 in the atmosphere) and end of the 21st Century (~ 560ppmv CO2 in the atmosphere), to examine similarities and discrepancies in biome distributions. Our comparison between reconstruction and prediction will contribute to a better understanding of the past and future impact of increased atmospheric CO2 on vegetation and climate.

  7. A Comprehensive in vivo Kinematic, Quantitative MRI and Functional Evaluation Following ACL Reconstruction – a Comparison between Mini-Two Incision and Anteromedial Portal Femoral Tunnel Drilling

    PubMed Central

    Lansdown, Drew A.; Allen, Christina; Zaid, Musa; Wu, Samuel; Subburaj, Karupppasamy; Souza, Richard; Feeley, Brian T.; Li, Xiaojuan; Ma, C. Benjamin

    2015-01-01

    Introduction Multiple techniques are used for femoral tunnel drilling in ACL reconstruction, including the Mini-Two Incision method (MT) and Anteromedial Portal technique (AM). Both techniques allow for independent placement of the femoral tunnel, though there are no reports comparing kinematics and cartilage health after these reconstructions. We hypothesized that both techniques would result in the restoration of normal knee kinematics and show no evidence of early cartilage degeneration. Methods A total of 20 patients were evaluated one year after ACL reconstruction, including 10 patients after MT and 10 patients after AM. MR-imaging was acquired bilaterally with the knee loaded in extension and flexion to evaluate kinematics of the reconstructed knee compared to the normal knee. Quantitative cartilage imaging was obtained and compared to 10 matched control subjects. The Marx Activity Rating Scale and KOOS survey were administered. Results The tibia was positioned significantly more anteriorly in extension and flexion relative to the contralateral knee for the MT group. The tibial position in the AM group was not significantly different from the patient’s contralateral knee. T1ρ values in the central-medial tibia were significantly elevated in the MT group compared to the Control group. KOOS Symptom scores were significantly better for the MT group compared to the AM group. Conclusions We have observed in vivo differences in knee kinematics and early cartilage degeneration between patients following MT and AM ACL reconstruction. Both techniques allow for anatomic ACL reconstruction, though the MT group shows significant early differences compared to the patient’s normal knee. PMID:25982298

  8. Late Quaternary and future biome simulations for Alaska and Eastern Russia

    NASA Astrophysics Data System (ADS)

    Hendricks, Amy S.

    Arctic biomes across a region including Alaska and Eastern Russia were investigated using the BIOME4 biogeochemical and biogeography vegetation model. This study investigated past (the last 21,000 years), present, and future vegetation distributions in the study area, using climate forcing from five CMIP5 models (CCSM4, GISS-E2-R, MIROC-ESM, MPI-ESM, and MRI-CGCM3). The present-day BIOME4 simulations were generally consistent with current vegetation observations in the study region characterized by evergreen and deciduous taiga and shrub tundras. Paleoclimatological simulations were compared with pollen data samples collected in the study region. Pre-industrial biome simulations are generally similar to the modern reconstruction but differ by having more shrub tundra in both Russia and Alaska to the north, as well as less deciduous taiga in Alaska. Pre-industrial simulations were in good agreement with the pollen data. Mid-Holocene simulations place shrub tundras along the Arctic coast, and in some cases along the eastern coast of Russia. Simulations for the Mid-Holocene are in good agreement with pollen-based distributions of biomes. Simulations for the Last Glacial Maximum (LGM) show that the Bering Land Bridge was covered almost entirely by cushion forb, lichen and moss tundra, shrub tundra, and graminoid tundra. Three out of the five models' climate data produce evergreen and deciduous taiga in what is now southwestern Alaska, however the pollen data does not support this. The distributions of cushion forb, lichen, and moss tundra and graminoid tundra differ noticeably between models, while shrub tundra distributions are generally similar. Future simulations of BIOME4 based on the RCP8.5 climate scenario indicate a northward shift of the treeline and a significant areal decrease of shrub tundra and graminoid tundra regions in the 21st century. Intrusions of cool mixed, deciduous, and conifer forests above 60°N, especially in southwest Alaska, were notable

  9. Qualitative and Quantitative Evaluation of Blob-Based Time-of-Flight PET Image Reconstruction in Hybrid Brain PET/MR Imaging.

    PubMed

    Leemans, Eva L; Kotasidis, Fotis; Wissmeyer, Michael; Garibotto, Valentina; Zaidi, Habib

    2015-10-01

    Many neurological diseases affect small structures in the brain and, as such, reliable visual evaluation and accurate quantification are required. Recent technological developments made the clinical use of hybrid positron emission tomography/magnetic resonance (PET/MR) systems possible, providing both functional and anatomical information in a single imaging session. Nevertheless, there is a trade-off between spatial resolution and image quality (contrast and noise), which is dictated mainly by the chosen acquisition and reconstruction protocols. Image reconstruction algorithms using spherical symmetric basis functions (blobs) for image representation have a number of additional parameters that impact both the qualitative and quantitative image characteristics. Hence, a detailed investigation of the blob-based reconstruction characteristics using different parameters is needed to achieve optimal reconstruction results. This work evaluated the impact of a range of blob parameters on image quality and quantitative accuracy of brain PET images acquired on the Ingenuity Time-of-Flight (TOF) PET/MR system. Two different phantoms were used to simulate brain imaging applications. Image contrast and noise characteristics were assessed using an image quality phantom. Quantitative performance in a clinical setting was investigated using the Hoffman 3D brain phantom at various count levels. Furthermore, the visual quality of four clinical studies was scored blindly by two experienced physicians to qualitatively evaluate the influence of different reconstruction protocols, hereby providing indications on parameters producing the best image quality. Quantitative evaluation using the image quality phantom showed that larger basis function radii result in lower contrast recovery (∼2%) and lower variance levels (∼15%). The brain phantom and clinical studies confirmed these observations since lower contrast was seen between anatomical structures. High and low count statistics

  10. High-resolution 3D reconstruction of microtubule structures by quantitative multi-angle total internal reflection fluorescence microscopy

    NASA Astrophysics Data System (ADS)

    Jin, Luhong; Wu, Jian; Xiu, Peng; Fan, Jiannan; Hu, Miao; Kuang, Cuifang; Xu, Yingke; Zheng, Xiaoxiang; Liu, Xu

    2017-07-01

    Total internal reflection fluorescence microscopy (TIRFM) has been widely used in biomedical research to visualize cellular processes near the cell surface. In this study, a novel multi-angle ring-illuminated TIRFM system, equipped with two galvo mirrors that are on conjugate plan of a 4f optical system was developed. Multi-angle TIRFM generates images with different penetration depths through the controlled variation of the incident angle of illuminating laser. We presented a method to perform three-dimensional (3-D) reconstruction of microtubules from multi-angle TIRFM images. The performance of our method was validated in simulated microtubules with variable signal-to-noise ratios (SNR) and the axial resolution and accuracy of reconstruction were evaluated in selecting different numbers of illumination angles or in different SNR conditions. In U373 cells, we reconstructed the 3-D localization of microtubules near the cell surface with high resolution using over a hundred different angles. Theoretically, the presented TIRFM setup and 3-D reconstruction method can achieve 40 nm axial resolution in experimental conditions where SNR is as low as 2, with 35 different illumination angles. Moreover, our system and reconstruction method have the potential to be used in live cells to track membrane dynamics in 3-D.

  11. Quantitative comparison of the pivot shift test results before and after anterior cruciate ligament reconstruction by using the three-dimensional electromagnetic measurement system.

    PubMed

    Nagai, Kanto; Hoshino, Yuichi; Nishizawa, Yuichiro; Araki, Daisuke; Matsushita, Takehiko; Matsumoto, Tomoyuki; Takayama, Koji; Nagamune, Kouki; Kurosaka, Masahiro; Kuroda, Ryosuke

    2015-10-01

    Tibial acceleration during the pivot shift test is a potential quantitative parameter to evaluate rotational laxity of anterior cruciate ligament (ACL) insufficiency. However, clinical application of this measurement has not been fully examined. This study aimed to measure and compare tibial acceleration before and after ACL reconstruction (ACLR) in ACL-injured patients. We hypothesized tibial acceleration would be reduced by ACLR and tibial acceleration would be consistent in the same knee at different time points. Seventy ACL-injured patients who underwent ACLR were enrolled. Tibial acceleration during the pivot shift test was measured using an electromagnetic measurement system before ALCR and at the second-look arthroscopy 1 year post-operatively. Tibial acceleration was compared to clinical grading and between ACL-injured/ACL-reconstructed and contralateral knees. Pre-operative tibial acceleration was increased stepwise with the increase in clinical grading (P < 0.01). Tibial acceleration in ACL-injured knee (1.9 ± 1.2 m/s(2)) was larger than that in the contralateral knee (0.8 ± 0.3 m/s(2), P < 0.01), and reduced to 0.9 ± 0.3 m/s(2) post-operatively (P < 0.01). There was no difference between ACL-reconstructed and contralateral knee (n.s.). Tibial acceleration in contralateral knees was consistent pre- and post-operatively (n.s.). Tibial acceleration measurement demonstrated increased rotational laxity in ACL-injured knees and its reduction by ALCR. Additionally, consistent measurements were obtained in ACL-intact knees at different time points. Therefore, tibial acceleration during the pivot shift test could provide quantitative evaluation of rotational stability before and after ACL reconstruction. III.

  12. Toward a quantitative reconstruction of hypoxia from varve records in the large perialpin Lake Bourget over the last 150 years

    NASA Astrophysics Data System (ADS)

    Jenny, J.-P.; Arnaud, F.; Dorioz, J. M.; Giguet Covex, C.; Frossard, V.; Sabatier, P.; Millet, L.; Reyss, J. L.; Tachikawa, K.; Romeyer, O.; Pignol, C.; Mallet, E.; Perga, M. E.

    2012-04-01

    Hypoxia -defined as dissolved oxygen ≤2 mg/l- is a severe detrimental factor for aquatic environments. In lakes, despit the importance for management, it is generally still hard to estimate hypoxia because of the lack of appropriate proxies or restricted number of sample cores. In this study, by using (40) sediment core data from chosen depths, we propose to go a step further toward a quantitative reconstruction of hypoxia integrating the extension of hypoxic water layer, both through space (volume) and time (yearly value). For that we went a step further in using an existing proxy: varve preservation. It is generally well-adapted for hypoxia detection, but not yet developed for small scale time and space variations through a complete large lake basin. Varves preservation is the consequence of the death of most of benthic macro-organisms that normally mix-up first millimetres of sediments, due to oxygen depletion. In Lake Bourget recent laminated sediments correspond to biochemical varves. We assume that their preservation results from a threshold in dissolved oxygen concentrations induced by seasonal hypoxia. Chironomids, organic matter and Mn/Fe ratio (XRF) were used as complementary proxies of hypoxia to validate our assumptions concerning varves. Our results show that volume of hypoxia can be annually estimated according to varve records through lake. Volumes of hypoxia varied through time in the Lake Bourget. Sediments recorded first the onset of severe hypoxia in the deepest part of the basin (-140m) in AD 1935±1, corresponding to 11.103m3 of hypoxic waters. Then hypoxic surface progressively extended on the slope until reaching a maximum at -90m in AD 1960, leading to 306.103m3 of hypoxic waters. After a retreat dated to AD 1980, hypoxia seemed to re-extend until today. Those fluctuations over the "oscillating zone" of hypoxia (-90 to -133m) were compared with potential forcing factors. The onset of hypolimnetic hypoxia is commonly attributed to

  13. WE-FG-207B-12: Quantitative Evaluation of a Spectral CT Scanner in a Phantom Study: Results of Spectral Reconstructions

    SciTech Connect

    Duan, X; Arbique, G; Guild, J; Anderson, J; Yagil, Y

    2016-06-15

    Purpose: To evaluate the quantitative image quality of spectral reconstructions of phantom data from a spectral CT scanner. Methods: The spectral CT scanner (IQon Spectral CT, Philips Healthcare) is equipped with a dual-layer detector and generates conventional 80-140 kVp images and variety of spectral reconstructions, e.g., virtual monochromatic (VM) images, virtual non-contrast (VNC) images, iodine maps, and effective atomic number (Z) images. A cylindrical solid water phantom (Gammex 472, 33 cm diameter and 5 cm thick) with iodine (2.0-20.0 mg I/ml) and calcium (50-600 mg/ml) rod inserts was scanned at 120 kVp and 27 mGy CTDIvol. Spectral reconstructions were evaluated by comparing image measurements with theoretical values calculated from nominal rod compositions provided by the phantom manufacturer. The theoretical VNC was calculated using water and iodine basis material decomposition, and the theoretical Z was calculated using two common methods, the chemical formula method (Z1) and the dual-energy ratio method (Z2). Results: Beam-hardening-like artifacts between high-attenuation calcium rods (≥300 mg/ml, >800 HU) influenced quantitative measurements, so the quantitative analysis was only performed on iodine rods using the images from the scan with all the calcium rods removed. The CT numbers of the iodine rods in the VM images (50∼150 keV) were close to theoretical values with average difference of 2.4±6.9 HU. Compared with theoretical values, the average difference for iodine concentration, VNC CT number and effective Z of iodine rods were −0.10±0.38 mg/ml, −0.1±8.2 HU, 0.25±0.06 (Z1) and −0.23±0.07 (Z2). Conclusion: The results indicate that the spectral CT scanner generates quantitatively accurate spectral reconstructions at clinically relevant iodine concentrations. Beam-hardening-like artifacts still exist when high-attenuation objects are present and their impact on patient images needs further investigation. YY is an employee of Philips

  14. Investigation of the quantitative accuracy of 3D iterative reconstruction algorithms in comparison to filtered back projection method: a phantom study

    NASA Astrophysics Data System (ADS)

    Abuhadi, Nouf; Bradley, David; Katarey, Dev; Podolyak, Zsolt; Sassi, Salem

    2014-03-01

    Introduction: Single-Photon Emission Computed Tomography (SPECT) is used to measure and quantify radiopharmaceutical distribution within the body. The accuracy of quantification depends on acquisition parameters and reconstruction algorithms. Until recently, most SPECT images were constructed using Filtered Back Projection techniques with no attenuation or scatter corrections. The introduction of 3-D Iterative Reconstruction algorithms with the availability of both computed tomography (CT)-based attenuation correction and scatter correction may provide for more accurate measurement of radiotracer bio-distribution. The effect of attenuation and scatter corrections on accuracy of SPECT measurements is well researched. It has been suggested that the combination of CT-based attenuation correction and scatter correction can allow for more accurate quantification of radiopharmaceutical distribution in SPECT studies (Bushberg et al., 2012). However, The effect of respiratory induced cardiac motion on SPECT images acquired using higher resolution algorithms such 3-D iterative reconstruction with attenuation and scatter corrections has not been investigated. Aims: To investigate the quantitative accuracy of 3D iterative reconstruction algorithms in comparison to filtered back projection (FBP) methods implemented on cardiac SPECT/CT imaging with and without CT-attenuation and scatter corrections. Also to investigate the effects of respiratory induced cardiac motion on myocardium perfusion quantification. Lastly, to present a comparison of spatial resolution for FBP and ordered subset expectation maximization (OSEM) Flash 3D together with and without respiratory induced motion, and with and without attenuation and scatter correction. Methods: This study was performed on a Siemens Symbia T16 SPECT/CT system using clinical acquisition protocols. Respiratory induced cardiac motion was simulated by imaging a cardiac phantom insert whilst moving it using a respiratory motion motor

  15. Microbes to Biomes at Berkeley Lab

    SciTech Connect

    2015-10-28

    Microbes are the Earth's most abundant and diverse form of life. Berkeley Lab's Microbes to Biomes initiative -- which will take advantage of research expertise at the Joint Genome Institute, Advanced Light Source, Molecular Foundry, and the new computational science facility -- is designed to explore and reveal the interactions of microbes with one another and with their environment. Microbes power our planet’s biogeochemical cycles, provide nutrients to our plants, purify our water and are integral components in keeping the human body free of disease and may hold the key to the Earth’s future.

  16. Airborne remote sensing of forest biomes

    NASA Technical Reports Server (NTRS)

    Sader, Steven A.

    1987-01-01

    Airborne sensor data of forest biomes obtained using an SAR, a laser profiler, an IR MSS, and a TM simulator are presented and examined. The SAR was utilized to investigate forest canopy structures in Mississippi and Costa Rica; the IR MSS measured forest canopy temperatures in Oregon and Puerto Rico; the TM simulator was employed in a tropical forest in Puerto Rico; and the laser profiler studied forest canopy characteristics in Costa Rica. The advantages and disadvantages of airborne systems are discussed. It is noted that the airborne sensors provide measurements applicable to forest monitoring programs.

  17. Microbes to Biomes at Berkeley Lab

    ScienceCinema

    None

    2016-07-12

    Microbes are the Earth's most abundant and diverse form of life. Berkeley Lab's Microbes to Biomes initiative -- which will take advantage of research expertise at the Joint Genome Institute, Advanced Light Source, Molecular Foundry, and the new computational science facility -- is designed to explore and reveal the interactions of microbes with one another and with their environment. Microbes power our planet’s biogeochemical cycles, provide nutrients to our plants, purify our water and are integral components in keeping the human body free of disease and may hold the key to the Earth’s future.

  18. Levels of reconstruction as complementarity in mixed methods research: a social theory-based conceptual framework for integrating qualitative and quantitative research.

    PubMed

    Carroll, Linda J; Rothe, J Peter

    2010-09-01

    Like other areas of health research, there has been increasing use of qualitative methods to study public health problems such as injuries and injury prevention. Likewise, the integration of qualitative and quantitative research (mixed-methods) is beginning to assume a more prominent role in public health studies. Likewise, using mixed-methods has great potential for gaining a broad and comprehensive understanding of injuries and their prevention. However, qualitative and quantitative research methods are based on two inherently different paradigms, and their integration requires a conceptual framework that permits the unity of these two methods. We present a theory-driven framework for viewing qualitative and quantitative research, which enables us to integrate them in a conceptually sound and useful manner. This framework has its foundation within the philosophical concept of complementarity, as espoused in the physical and social sciences, and draws on Bergson's metaphysical work on the 'ways of knowing'. Through understanding how data are constructed and reconstructed, and the different levels of meaning that can be ascribed to qualitative and quantitative findings, we can use a mixed-methods approach to gain a conceptually sound, holistic knowledge about injury phenomena that will enhance our development of relevant and successful interventions.

  19. Levels of Reconstruction as Complementarity in Mixed Methods Research: A Social Theory-Based Conceptual Framework for Integrating Qualitative and Quantitative Research

    PubMed Central

    Carroll, Linda J.; Rothe, J. Peter

    2010-01-01

    Like other areas of health research, there has been increasing use of qualitative methods to study public health problems such as injuries and injury prevention. Likewise, the integration of qualitative and quantitative research (mixed-methods) is beginning to assume a more prominent role in public health studies. Likewise, using mixed-methods has great potential for gaining a broad and comprehensive understanding of injuries and their prevention. However, qualitative and quantitative research methods are based on two inherently different paradigms, and their integration requires a conceptual framework that permits the unity of these two methods. We present a theory-driven framework for viewing qualitative and quantitative research, which enables us to integrate them in a conceptually sound and useful manner. This framework has its foundation within the philosophical concept of complementarity, as espoused in the physical and social sciences, and draws on Bergson’s metaphysical work on the ‘ways of knowing’. Through understanding how data are constructed and reconstructed, and the different levels of meaning that can be ascribed to qualitative and quantitative findings, we can use a mixed-methods approach to gain a conceptually sound, holistic knowledge about injury phenomena that will enhance our development of relevant and successful interventions. PMID:20948937

  20. Quantitative analysis of the reconstruction errors of the currently popular algorithm of magnetic resonance electrical property tomography at the interfaces of adjacent tissues.

    PubMed

    Duan, Song; Xu, Chao; Deng, Guanhua; Wang, Jiajia; Liu, Feng; Xin, Sherman Xuegang

    2016-06-01

    This work quantitatively analyzed the reconstruction errors (REs) of electrical property (EP) images using a currently popular algorithm of magnetic resonance electrical property tomography (MREPT), which occurred along the tissue interfaces. Transmitted magnetic fields B1+ were acquired at 3 T using a birdcage coil loaded with a phantom consisting of various adjacent tissues. Homogeneous Helmholtz was employed to calculate the EP maps by Laplacian computation of central differences. The maps of absolute REs (aREs) and relative REs (rREs) were calculated. The maximum and mean rREs, in addition to rRE distributions at the interfaces, were presented. Reconstructed EP maps showed various REs along different interface boundaries. Among all the investigated tissue interfaces, the kidney-fat interface presented the maximum mean rREs for both conductivity and relative permittivity. The minimum mean rRE of conductivity was observed at the spleen-muscle interface, and the minimum mean rRE of relative permittivity was detected along the lung-heart interface. The mean rREs ranged from 0.3986 to 36.11 for conductivity and 0.2218 to 11.96 for relative permittivity. Overall, this research indicates that different REs occur at various tissue boundaries, as shown by the currently popular algorithm of MREPT. Thus, REs should be considered when applying MREPT to reconstruct the EP distributions inside the human body. Copyright © 2016 John Wiley & Sons, Ltd.

  1. Evolution of Philodendron (Araceae) species in Neotropical biomes

    PubMed Central

    Loss-Oliveira, Leticia; Sakuragui, Cassia; Soares, Maria de Lourdes

    2016-01-01

    Philodendron is the second most diverse genus of the Araceae, a tropical monocot family with significant morphological diversity along its wide geographic distribution in the Neotropics. Although evolutionary studies of Philodendron were conducted in recent years, the phylogenetic relationship among its species remains unclear. Additionally, analyses conducted to date suggested the inclusion of all American representatives of a closely-related genus, Homalomena, within the Philodendron clade. A thorough evaluation of the phylogeny and timescale of these lineages is thus necessary to elucidate the tempo and mode of evolution of this large Neotropical genus and to unveil the biogeographic history of Philodendron evolution along the Amazonian and Atlantic rainforests as well as open dry forests of South America. To this end, we have estimated the molecular phylogeny for 68 Philodendron species, which consists of the largest sampling assembled to date aiming the study of the evolutionary affinities. We have also performed ancestral reconstruction of species distribution along biomes. Finally, we contrasted these results with the inferred timescale of Philodendron and Homalomena lineage diversification. Our estimates indicate that American Homalomena is the sister clade to Philodendron. The early diversification of Philodendron took place in the Amazon forest from Early to Middle Miocene, followed by colonization of the Atlantic forest and the savanna-like landscapes, respectively. Based on the age of the last common ancestor of Philodendron, the species of this genus diversified by rapid radiations, leading to its wide extant distribution in the Neotropical region. PMID:27042390

  2. The effects of variable biome distribution on global climate

    SciTech Connect

    Noever, D.A.; Brittain, A.; Matsos, H.C.; Baskaran, S.; Obenhuber, D.

    1996-12-31

    In projecting climatic adjustments to anthropogenically elevated atmospheric carbon dioxide, most global climate models fix biome distribution to current geographic conditions. The authors develop a model that examines the albedo-related effects of biome distribution on global temperature. The model was tested on historical biome changes since 1860 and the results fit both the observed trend and order of magnitude change in global temperature. Once backtested in this way on historical data, the model is then used to generate an optimized future biome distribution which minimizes projected greenhouse effects on global temperature. Because of the complexity of this combinatorial search an artificial intelligence method, the genetic algorithm, was employed. The genetic algorithm assigns various biome distributions to the planet, then adjusts their percentage area and albedo effects to regulate or moderate temperature changes.

  3. Changes in forest productivity across Alaska consistent with biome shift.

    PubMed

    Beck, Pieter S A; Juday, Glenn P; Alix, Claire; Barber, Valerie A; Winslow, Stephen E; Sousa, Emily E; Heiser, Patricia; Herriges, James D; Goetz, Scott J

    2011-04-01

    Global vegetation models predict that boreal forests are particularly sensitive to a biome shift during the 21st century. This shift would manifest itself first at the biome's margins, with evergreen forest expanding into current tundra while being replaced by grasslands or temperate forest at the biome's southern edge. We evaluated changes in forest productivity since 1982 across boreal Alaska by linking satellite estimates of primary productivity and a large tree-ring data set. Trends in both records show consistent growth increases at the boreal-tundra ecotones that contrast with drought-induced productivity declines throughout interior Alaska. These patterns support the hypothesized effects of an initiating biome shift. Ultimately, tree dispersal rates, habitat availability and the rate of future climate change, and how it changes disturbance regimes, are expected to determine where the boreal biome will undergo a gradual geographic range shift, and where a more rapid decline.

  4. Climate-biomes, pedo-biomes and pyro-biomes: which world view explains the tropical forest - savanna boundary in South America?

    NASA Astrophysics Data System (ADS)

    Langan, Liam; Higgins, Steven; Scheiter, Simon

    2015-04-01

    Elucidating the drivers of broad vegetation formations improves our understanding of earth system functioning. The biome, defined primarily by the dominance of a particular growth strategy, is commonly employed to group vegetation into similar units. Predicting tropical forest and savanna biome boundaries in South America has proven difficult. Process based DGVMs (Dynamic global vegetation models) are our best tool to simulate vegetation patterns, make predictions for future changes and test theory, however, many DGVMs fail to accurately simulate the spatial distribution or indeed presence of the South American savanna biome which can result in large differences in modelled ecosystem structural properties. Evidence suggests fire plays a significant role in mediating these forest and savanna biome boundaries, however, fire alone does not appear to be sufficient to predict these boundaries in South America using DGVMs hinting at the presence of one or more missing environmental factors. We hypothesise that soil depth, which affects plant available water by determining maximum storage potential and influences temporal availability, may be one of these missing environmental factors. To test our hypothesis we use a novel vegetation model, the aDGVM2. This model has been specifically designed to allow plant trait strategies, constrained by trade-offs between traits, evolve based on the abiotic and biotic conditions where the resulting community trait suites are emergent properties of model dynamics. Furthermore it considers root biomass in multiple soil layers and therefore allows the consideration of alternative rooting strategies, which in turn allows us to explore in more detail the role of soil hydraulic factors in controlling biome boundary distributions. We find that changes in soil depth, interacting with fire, affect the relative dominance of tree and grass strategies and thus the presence and spatial distribution of forest and savanna biomes in South America

  5. Quantitative MR imaging evaluation of the cartilage thickness and subchondral bone area in patients with ACL-reconstructions 7 years after surgery.

    PubMed

    Andreisek, G; White, L M; Sussman, M S; Kunz, M; Hurtig, M; Weller, I; Essue, J; Marks, P; Eckstein, F

    2009-07-01

    To evaluate the cartilage thickness (ThC) and subchondral bone area (tAB) of the operated and contra-lateral non-operated (healthy) knees in patients with anterior cruciate ligament (ACL)-reconstruction 7 years after surgery using a quantitative and regional cartilage MR imaging (qMRI) technique. Charts of 410 patients with ACL-reconstructions were retrospectively reviewed. Fifty-two patients (male/female, 28/24; mean age, 33.3 years) were included. Patients underwent KT-1000 testing and qMRI of both knees using coronal fat-saturated 3D spoiled gradient-recalled echo (SPGR) sequences (TR/TE, 44/4 ms) at 1.5 T. Quantitative analyses of ThC and tAB in the femoro-tibial cartilage plates were performed using a subregional approach. In addition, qualitative and quantitative assessment of femoral condyle shapes was performed. t tests with Bonferroni corrections were used for statistical analysis of side-to-side differences between the operated and non-operated knees. KT-1000 testing was abnormal in 3/52 patients (6%). Lateral femoral tAB was significantly lower (-9.2%), and medial tibial tAB was significantly larger (+2%) in the operated vs non-operated knee (P<0.001). Regional and subregional ThC side-to-side differences were less than 0.1mm and, except for the external lateral femoral subregion, they were not statistically significant. Flattened and broader shapes of medial femoral condyles (P<0.001) were found in operated knees. No significant association of presence of cartilage or meniscus lesions at surgery with ThC 7 years post-operatively was found (P=0.06-0.98). There is evidence for changes in the tAB and femoral shape 7 years post-ACL-reconstruction, but no side-to-side differences in subregional ThC were found between the operated and contra-lateral non-operated knees.

  6. An Overview of the BIOMed Project.

    PubMed

    Mantas, John; Wageih, Mohamed A

    2017-01-01

    The purpose is to: 1) foster the national BioMedical Informatics (BMI) foundation aligning with the international medical informatics association (IMIA) in order to remodel the national strategies; 2) structure the BMHI strategic plans in Egypt and Jordan as models for other Arab States; 3) define the requirements for new joint EU-Mediterranean BMHI projects and initiatives; and 4) encourage and support the BMHI centres of excellence in Egypt and Jordan. BIOMed will synergistically apply up-to-date European and International methodologies & standards. The pre-defined challenges were integrating multiple segregated BMHI initiatives and policies; overcoming obstructions- socio, political, economic; recommendation adaptation, assessing the current and proposed solutions; defining the national health systems real demands; identifying different European best practices. Political instability in the Middle East after the Arab Spring in 2011 added further challenges as well as improved the importance of the EU-MENA (EU and Middle East and North Africa) cooperation.

  7. U.S. Tundra Biome-International Biological Program. U.S. Tundra Biome Publication List.

    DTIC Science & Technology

    1983-09-01

    Provisional checklist to the vascular, bryophyte , and lichen flora of Prudhoe Bay, Alaska. In Ecological Investigations of the Tundra Biome in the Prudhoe Bay...4040) /Bib 33-4561/ Rastorfer, J.R., H.J. Webster and D.K. Smith (1973) Floristic and ecologic studies of bryophytes of selected habitats at...57: 1025-1033. (2759) /Bib 31-1286/ Steere, W.C. (1976) Ecology , phytogeography, and floristics of arctic Alaskan bryophytes . Journal of Hattori

  8. Biome changes in Asia since the mid-Holocene - an analysis of different transient Earth system model simulations

    NASA Astrophysics Data System (ADS)

    Dallmeyer, Anne; Claussen, Martin; Ni, Jian; Cao, Xianyong; Wang, Yongbo; Fischer, Nils; Pfeiffer, Madlene; Jin, Liya; Khon, Vyacheslav; Wagner, Sebastian; Haberkorn, Kerstin; Herzschuh, Ulrike

    2017-02-01

    The large variety of atmospheric circulation systems affecting the eastern Asian climate is reflected by the complex Asian vegetation distribution. Particularly in the transition zones of these circulation systems, vegetation is supposed to be very sensitive to climate change. Since proxy records are scarce, hitherto a mechanistic understanding of the past spatio-temporal climate-vegetation relationship is lacking. To assess the Holocene vegetation change and to obtain an ensemble of potential mid-Holocene biome distributions for eastern Asia, we forced the diagnostic biome model BIOME4 with climate anomalies of different transient Holocene climate simulations performed in coupled atmosphere-ocean(-vegetation) models. The simulated biome changes are compared with pollen-based biome records for different key regions.In all simulations, substantial biome shifts during the last 6000 years are confined to the high northern latitudes and the monsoon-westerly wind transition zone, but the temporal evolution and amplitude of change strongly depend on the climate forcing. Large parts of the southern tundra are replaced by taiga during the mid-Holocene due to a warmer growing season and the boreal treeline in northern Asia is shifted northward by approx. 4° in the ensemble mean, ranging from 1.5 to 6° in the individual simulations, respectively. This simulated treeline shift is in agreement with pollen-based reconstructions from northern Siberia. The desert fraction in the transition zone is reduced by 21 % during the mid-Holocene compared to pre-industrial due to enhanced precipitation. The desert-steppe margin is shifted westward by 5° (1-9° in the individual simulations). The forest biomes are expanded north-westward by 2°, ranging from 0 to 4° in the single simulations. These results corroborate pollen-based reconstructions indicating an extended forest area in north-central China during the mid-Holocene. According to the model, the forest-to-non-forest and steppe

  9. Application of a New Grain-Based Reconstruction Algorithm to Microtomography Images for Quantitative Characterization and Flow Modeling

    DTIC Science & Technology

    2008-06-01

    resolution issues. Acknowledgments The core samples were obtained in a study funded by the Univer- sity of Texas at Dallas Quantitative Sedimentology ...Texas at Dallas before joining the Univer- sity of Houston. His research interests include deltaic sedimen- tology and sequence stratigraphy , the local...control of struc- ture on stratigraphy , and reservoir architecture of clastic depositional systems. He has authored or co-authored ap- proximately

  10. Return to Sport for Skeletally Immature Athletes After ACL Reconstruction: Preventing a Second Injury Using a Quality of Movement Assessment and Quantitative Measures to Address Modifiable Risk Factors.

    PubMed

    Graziano, Jessica; Chiaia, Theresa; de Mille, Polly; Nawabi, Danyal H; Green, Daniel W; Cordasco, Frank A

    2017-04-01

    Reinjury rates after anterior cruciate ligament reconstruction (ACLR) are highest among young athletes, who consequently suffer from low rates of return to play. Historically, quantitative measures have been used to determine readiness to return to sport; however, they do not assess modifiable risk factors related to the quality of movement. To determine the effectiveness of a criteria-based rehabilitation progression and return-to-sport criteria on efficient return to activity and prevention of second injury in young athletes post-ACLR. Case series; Level of evidence, 4. Between December 2010 and 2013, 42 skeletally immature athletes (mean chronologic age, 12 years; range, 10-15 years) who underwent ACLR using ipsilateral hamstring tendon autograft were prospectively evaluated. All athletes progressed through a criteria-based rehabilitation progression; were assessed at specific time frames for strength, biomechanical, and neuromuscular risk factors predictive of injury; and were provided targeted interventions. The final return to sport phase consisted of quantitative testing as well as a quality of movement assessment of several functional movements with progressive difficulty and sports-specific loading. Clearance for unrestricted activity was determined by achieving satisfactory results on both qualitative and quantitative assessments with consideration for the demands of each sport. The mean time for return to unrestricted competitive activity was 12 months. All but 3 (7%) athletes returned to their primary sport. Thirty-five athletes (83%) returned to unrestricted activity. Of the 6 (14%) who sustained a second injury, 3 (50%) were injured in sports they were not cleared for. All ACL reinjuries occurred in a cutting sport. Half of reinjuries occurred within 1 year of surgery, while the remaining occurred between 1 and 2 years. Eighty-three percent of reinjuries involved highly competitive cutting athletes. In our cohort, the combination of qualitative and

  11. Return to Sport for Skeletally Immature Athletes After ACL Reconstruction: Preventing a Second Injury Using a Quality of Movement Assessment and Quantitative Measures to Address Modifiable Risk Factors

    PubMed Central

    Graziano, Jessica; Chiaia, Theresa; de Mille, Polly; Nawabi, Danyal H.; Green, Daniel W.; Cordasco, Frank A.

    2017-01-01

    Background: Reinjury rates after anterior cruciate ligament reconstruction (ACLR) are highest among young athletes, who consequently suffer from low rates of return to play. Historically, quantitative measures have been used to determine readiness to return to sport; however, they do not assess modifiable risk factors related to the quality of movement. Purpose: To determine the effectiveness of a criteria-based rehabilitation progression and return-to-sport criteria on efficient return to activity and prevention of second injury in young athletes post-ACLR. Study Design: Case series; Level of evidence, 4. Methods: Between December 2010 and 2013, 42 skeletally immature athletes (mean chronologic age, 12 years; range, 10-15 years) who underwent ACLR using ipsilateral hamstring tendon autograft were prospectively evaluated. All athletes progressed through a criteria-based rehabilitation progression; were assessed at specific time frames for strength, biomechanical, and neuromuscular risk factors predictive of injury; and were provided targeted interventions. The final return to sport phase consisted of quantitative testing as well as a quality of movement assessment of several functional movements with progressive difficulty and sports-specific loading. Clearance for unrestricted activity was determined by achieving satisfactory results on both qualitative and quantitative assessments with consideration for the demands of each sport. Results: The mean time for return to unrestricted competitive activity was 12 months. All but 3 (7%) athletes returned to their primary sport. Thirty-five athletes (83%) returned to unrestricted activity. Of the 6 (14%) who sustained a second injury, 3 (50%) were injured in sports they were not cleared for. All ACL reinjuries occurred in a cutting sport. Half of reinjuries occurred within 1 year of surgery, while the remaining occurred between 1 and 2 years. Eighty-three percent of reinjuries involved highly competitive cutting athletes

  12. Continental European Eemian and early Würmian climate evolution: comparing signals using different quantitative reconstruction approaches based on pollen

    NASA Astrophysics Data System (ADS)

    Klotz, Stefan; Guiot, Joel; Mosbrugger, Volker

    2003-05-01

    Analyses of Eemian climate dynamics based on different reconstruction methods were conducted for several pollen sequences in the northern alpine foreland. The modern analogue and mutual climate sphere techniques used, which are briefly presented, complement one another with respect to comparable results. The reconstructions reveal the occurrence of at least two similar thermal periods, representing temperate oceanic conditions warmer and with a higher humidity than today. Intense changes of climate processes become obvious with a shift of winter temperatures of about 15 °C from the late Rissian to the first thermal optimum of the Eemian. The transition shows a pattern of summer temperatures and precipitation increasing more rapidly than winter temperatures. With the first optimum during the Pinus-Quercetum mixtum-Corylus phase (PQC) at an early stage of the Eemian and a second optimum period at a later stage, which is characterised by widespread Carpinus, climate gradients across the study area were less intense than today. Average winter temperatures vary between -1.9 and 0.4 °C (present-day -3.6 to 1.4 °C), summer temperatures between 17.8 and 19.6 °C (present-day 14 to 18.9 °C). The timberline expanded about 350 m when compared to the present-day limit represented by Pinus mugo. Whereas the maximum of temperature parameters is related to the first optimum, precipitation above 1100 mm is higher during the second warm period concomitant to somewhat reduced temperatures. Intermediate, smaller climate oscillations and a cooling becomes obvious, which admittedly represent moderate deterioration but not extreme chills. During the boreal semicontinental Eemian Pinus-Picea-Abies phase, another less distinct fluctuation occurs, initiating the oscillating shift from temperate to cold conditions.

  13. Detection and origin of different types of annual laminae in recent stalagmites from Zoolithencave, southern Germany: Evaluation of the potential for quantitative reconstruction of past precipitation variability

    NASA Astrophysics Data System (ADS)

    Riechelmann, Dana F. C.; Fohlmeister, Jens; Tjallingii, Rik; Jochum, Klaus Peter; Richter, Detlev K.; Brummer, Geert-Jan A.; Scholz, Denis

    2016-04-01

    An arrangement of three stalagmites from Zoolithencave (southern Germany) was analysed for different types of annual laminae using microscopic and geochemical methods. The speleothems show visible laminae (consisting of a pair of a clear and a brownish, pigmented layer) as well as fluorescent and elemental laminae. The growth periods of the speleothems were dated to AD 1800 to 1970 by detection of the 14C bomb peak, 14C-dating of a charcoal piece located below the speleothems, as well as counting of annual laminae. On the annual time-scale, the variability of Mg, Ba, and Sr is controlled by Prior Calcite Precipitation (PCP) resulting in lower values during the wet season (autumn/winter) and vice versa. Both, Y and P are enriched in the brownish, pigmented layers and are proxies for soil activity. However, both elemental concentrations are also influenced by detrital content superimposed on the signal resulting from soil activity. Proxies for detrital content are Al and Mn. Lamina thickness shows a significant correlation with the amount of precipitation of December of the previous year and January, February, March, April, May, and December of the current year (DJFMAMD) recorded at the nearby meteorological station Bamberg. Thus, lamina thickness is a proxy for past precipitation variability. This is confirmed by the good agreement with a precipitation reconstruction based on tree-ring width from the Bavarian forest. This highlights the potential of these speleothems for climate reconstruction at annual resolution (Riechelmann et al., submitted). Riechelmann, D.F.C, Fohlmeister, J., Tjallingii, R., Jochum, K.P., Richter, D.K., Brummer, G.-J. A., Scholz, D., submitted. Detection and origin of different types of annual laminae in recent stalagmites from Zoolithancave, southern Germany: Evaluation of the potential for quantitative reconstruction of past precipitation variability. Hydrology and Earth System Science Discussions.

  14. Quantitative comparison of cortical surface reconstructions from MP2RAGE and multi-echo MPRAGE data at 3 and 7 T.

    PubMed

    Fujimoto, Kyoko; Polimeni, Jonathan R; van der Kouwe, André J W; Reuter, Martin; Kober, Tobias; Benner, Thomas; Fischl, Bruce; Wald, Lawrence L

    2014-04-15

    The Magnetization-Prepared 2 Rapid Acquisition Gradient Echo (MP2RAGE) method achieves spatially uniform contrast across the entire brain between gray matter and surrounding white matter tissue and cerebrospinal fluid by rapidly acquiring data at two points during an inversion recovery, and then combining the two volumes so as to cancel out sources of intensity and contrast bias, making it useful for neuroimaging studies at ultrahigh field strengths (≥7T). To quantify the effectiveness of the MP2RAGE method for quantitative morphometric neuroimaging, we performed tissue segmentation and cerebral cortical surface reconstruction of the MP2RAGE data and compared the results with those generated from conventional multi-echo MPRAGE (MEMPRAGE) data across a group of healthy subjects. To do so, we developed a preprocessing scheme for the MP2RAGE image data to allow for automatic cortical segmentation and surface reconstruction using FreeSurfer and analysis methods to compare the positioning of the surface meshes. Using image volumes with 1mm isotropic voxels we found a scan-rescan reproducibility of cortical thickness estimates to be 0.15 mm (or 6%) for the MEMPRAGE data and a slightly lower reproducibility of 0.19 mm (or 8%) for the MP2RAGE data. We also found that the thickness estimates were systematically smaller in the MP2RAGE data, and that both the interior and exterior cortical boundaries estimated from the MP2RAGE data were consistently positioned within the corresponding boundaries estimated from the MEMPRAGE data. Therefore several measureable differences exist in the appearance of cortical gray matter and its effect on automatic segmentation methods that must be considered when choosing an acquisition or segmentation method for studies requiring cortical surface reconstructions. We propose potential extensions to the MP2RAGE method that may help to reduce or eliminate these discrepancies. Copyright © 2013 Elsevier Inc. All rights reserved.

  15. Quantitative and qualitative MR-imaging assessment of vastus medialis muscle volume loss in asymptomatic patients after anterior cruciate ligament reconstruction.

    PubMed

    Marcon, Magda; Ciritsis, Bernhard; Laux, Christoph; Nanz, Daniel; Fischer, Michael A; Andreisek, Gustav; Ulbrich, Erika J

    2015-08-01

    To quantitatively and qualitatively assess vastus medialis muscle atrophy in asymptomatic patients with anterior cruciate ligament reconstruction, using the nonoperated leg as control. Prospective Institutional Review Board approved study with written informed patient consent. Thirty-three asymptomatic patients (men, 21; women,12) with ACL-reconstruction underwent MR imaging of both legs (axial T1-weighted spin-echo and 3D spoiled dual gradient-echo sequences). Muscle volume and average fat-signal fraction (FSF) of the vastus medialis muscles were measured. Additionally, Goutallier classification was used to classify fatty muscle degeneration. Significant side differences were evaluated using the Wilcoxon test and, between volumes and FSF, using student t-tests with P-value < 0.05 and < 0.025, respectively. The muscle volume was significantly smaller in the operated (mean ± SD, 430.6 ± 119.6 cm(3) ; range, 197.3 to 641.7 cm(3) ) than in the nonoperated leg (479.5 ± 124.8 cm(3) ; 261.4 to 658.9 cm(3) ) (P < 0.001). Corresponding FSF was 6.3 ± 1.5% (3.9 to 9.2%) and 5.8 ± 0.9% (4.0 to 7.4%), respectively, with a nonsignificant (P > 0.025) difference. The relative muscle-volume and FSF differences were -10.1 ± 8.6% (7.1 to -30.1%) and 10.9 ± 29.4% (39.7 to 40.1%). The qualitative assessment revealed no significant differences (P > 0.1). A significant muscle volume loss of the vastus medialis muscle does exist in asymptomatic patients with ACL-reconstruction, but without fatty degeneration. © 2014 Wiley Periodicals, Inc.

  16. Pollen-based quantitative reconstructions of Holocene regional vegetation cover (plant-functional types and land-cover types) in Europe suitable for climate modelling.

    PubMed

    Trondman, A-K; Gaillard, M-J; Mazier, F; Sugita, S; Fyfe, R; Nielsen, A B; Twiddle, C; Barratt, P; Birks, H J B; Bjune, A E; Björkman, L; Broström, A; Caseldine, C; David, R; Dodson, J; Dörfler, W; Fischer, E; van Geel, B; Giesecke, T; Hultberg, T; Kalnina, L; Kangur, M; van der Knaap, P; Koff, T; Kuneš, P; Lagerås, P; Latałowa, M; Lechterbeck, J; Leroyer, C; Leydet, M; Lindbladh, M; Marquer, L; Mitchell, F J G; Odgaard, B V; Peglar, S M; Persson, T; Poska, A; Rösch, M; Seppä, H; Veski, S; Wick, L

    2015-02-01

    We present quantitative reconstructions of regional vegetation cover in north-western Europe, western Europe north of the Alps, and eastern Europe for five time windows in the Holocene [around 6k, 3k, 0.5k, 0.2k, and 0.05k calendar years before present (bp)] at a 1° × 1° spatial scale with the objective of producing vegetation descriptions suitable for climate modelling. The REVEALS model was applied on 636 pollen records from lakes and bogs to reconstruct the past cover of 25 plant taxa grouped into 10 plant-functional types and three land-cover types [evergreen trees, summer-green (deciduous) trees, and open land]. The model corrects for some of the biases in pollen percentages by using pollen productivity estimates and fall speeds of pollen, and by applying simple but robust models of pollen dispersal and deposition. The emerging patterns of tree migration and deforestation between 6k bp and modern time in the REVEALS estimates agree with our general understanding of the vegetation history of Europe based on pollen percentages. However, the degree of anthropogenic deforestation (i.e. cover of cultivated and grazing land) at 3k, 0.5k, and 0.2k bp is significantly higher than deduced from pollen percentages. This is also the case at 6k in some parts of Europe, in particular Britain and Ireland. Furthermore, the relationship between summer-green and evergreen trees, and between individual tree taxa, differs significantly when expressed as pollen percentages or as REVEALS estimates of tree cover. For instance, when Pinus is dominant over Picea as pollen percentages, Picea is dominant over Pinus as REVEALS estimates. These differences play a major role in the reconstruction of European landscapes and for the study of land cover-climate interactions, biodiversity and human resources. © 2014 The Authors Global Change Biology Published by John Wiley & Sons Ltd.

  17. BIOME: An Ecosystem Remote Sensor Based on Imaging Interferometry

    NASA Technical Reports Server (NTRS)

    Peterson, David L.; Hammer, Philip; Smith, William H.; Lawless, James G. (Technical Monitor)

    1994-01-01

    Until recent times, optical remote sensing of ecosystem properties from space has been limited to broad band multispectral scanners such as Landsat and AVHRR. While these sensor data can be used to derive important information about ecosystem parameters, they are very limited for measuring key biogeochemical cycling parameters such as the chemical content of plant canopies. Such parameters, for example the lignin and nitrogen contents, are potentially amenable to measurements by very high spectral resolution instruments using a spectroscopic approach. Airborne sensors based on grating imaging spectrometers gave the first promise of such potential but the recent decision not to deploy the space version has left the community without many alternatives. In the past few years, advancements in high performance deep well digital sensor arrays coupled with a patented design for a two-beam interferometer has produced an entirely new design for acquiring imaging spectroscopic data at the signal to noise levels necessary for quantitatively estimating chemical composition (1000:1 at 2 microns). This design has been assembled as a laboratory instrument and the principles demonstrated for acquiring remote scenes. An airborne instrument is in production and spaceborne sensors being proposed. The instrument is extremely promising because of its low cost, lower power requirements, very low weight, simplicity (no moving parts), and high performance. For these reasons, we have called it the first instrument optimized for ecosystem studies as part of a Biological Imaging and Observation Mission to Earth (BIOME).

  18. BIOME: An Ecosystem Remote Sensor Based on Imaging Interferometry

    NASA Technical Reports Server (NTRS)

    Peterson, David L.; Hammer, Philip; Smith, William H.; Lawless, James G. (Technical Monitor)

    1994-01-01

    Until recent times, optical remote sensing of ecosystem properties from space has been limited to broad band multispectral scanners such as Landsat and AVHRR. While these sensor data can be used to derive important information about ecosystem parameters, they are very limited for measuring key biogeochemical cycling parameters such as the chemical content of plant canopies. Such parameters, for example the lignin and nitrogen contents, are potentially amenable to measurements by very high spectral resolution instruments using a spectroscopic approach. Airborne sensors based on grating imaging spectrometers gave the first promise of such potential but the recent decision not to deploy the space version has left the community without many alternatives. In the past few years, advancements in high performance deep well digital sensor arrays coupled with a patented design for a two-beam interferometer has produced an entirely new design for acquiring imaging spectroscopic data at the signal to noise levels necessary for quantitatively estimating chemical composition (1000:1 at 2 microns). This design has been assembled as a laboratory instrument and the principles demonstrated for acquiring remote scenes. An airborne instrument is in production and spaceborne sensors being proposed. The instrument is extremely promising because of its low cost, lower power requirements, very low weight, simplicity (no moving parts), and high performance. For these reasons, we have called it the first instrument optimized for ecosystem studies as part of a Biological Imaging and Observation Mission to Earth (BIOME).

  19. Quantitative Proteomics-Based Reconstruction and Identification of Metabolic Pathways and Membrane Transport Proteins Related to Sugar Accumulation in Developing Fruits of Pear (Pyrus communis).

    PubMed

    Reuscher, Stefan; Fukao, Yoichiro; Morimoto, Reina; Otagaki, Shungo; Oikawa, Akira; Isuzugawa, Kanji; Shiratake, Katsuhiro

    2016-03-01

    During their 6 month development, pear (Pyrus communis) fruits undergo drastic changes in their morphology and their chemical composition. To gain a better understanding of the metabolic pathways and transport processes active during fruit development, we performed a time-course analysis using mass spectrometry (MS)-based protein identification and quantification of fruit flesh tissues. After pre-fractionation of the samples, 2,841 proteins were identified. A principal component analysis (PCA) separated the samples from seven developmental stages into three distinct clusters representing the early, mid and late developmental phase. Over-representation analysis of proteins characteristic of each developmental phase revealed both expected and novel biological processes relevant at each phase. A high abundance of aquaporins was detected in samples from fruits in the cell expansion stage. We were able quantitatively to reconstruct basic metabolic pathways such as the tricarboxylic acid (TCA) cycle, which indicates sufficient coverage to reconstruct other metabolic pathways. Most of the enzymes that presumably contribute to sugar accumulation in pear fruits could be identified. Our data indicate that invertases do not play a major role in the sugar conversions in developing pear fruits. Rather, sucrose might be broken down by sucrose synthases. Further focusing on sugar transporters, we identified several putative sugar transporters from diverse families which showed developmental regulation. In conclusion, our data set comprehensively describes the proteome of developing pear fruits and provides novel insights about sugar accumulation as well as candidate genes for key reactions and transport steps.

  20. Three-dimensional reconstruction and morphologic measurements of human embryonic hearts: a new diagnostic and quantitative method applicable to fetuses younger than 13 weeks of gestation

    PubMed Central

    Schleich, Jean-Marc; Dillenseger, Jean-Louis; Loeuillet, Laurence; Moulinoux, Jacques-Philippe; Almange, Claude

    2005-01-01

    Improvements in the diagnosis of congenital malformations explain the increasing early termination of pregnancies. Before 13 weeks of gestation, an accurate in vivo anatomical diagnosis cannot currently be made in all fetuses with the imaging instrumentation available. Anatomo-pathological examinations remain the gold standard to make accurate diagnoses, although they reach limits between 9 and 13 weeks of gestation. We present the first results of a methodology that can be applied routinely, using standard histological section, enabling the reconstruction, visual estimate and quantitative analysis of 13 weeks of age human embryonic cardiac structures. The cardiac blocks were fixed, included in paraffin and entirely sliced by a microtome. One slice out of 10 was topographically colored and digitized on an optical microscope. The cardiac volume was recovered by a semi-automatic realignment of the sections. Another semi-automatic procedure allowed extracting and labeling of the cardiac structures from the volume. The structures were studied with display tools, disclosing the internal and external cardiac components, and enabling the determination of size, thickness and precise position of the ventricles, atria and large vessels. This pilot study confirmed that a new 3-D reconstruction and visualization method enabled to make accurate diagnoses, including in embryos <13 weeks old. Its implementation at earlier stages of embryogenesis will provide a clearer view of cardiac development. PMID:16211458

  1. Holocene high-resolution quantitative summer temperature reconstruction based on subfossil chironomids from the southeast margin of the Qinghai-Tibetan Plateau

    NASA Astrophysics Data System (ADS)

    Zhang, Enlou; Chang, Jie; Cao, Yanmin; Sun, Weiwei; Shulmeister, James; Tang, Hongqu; Langdon, Peter G.; Yang, Xiangdong; Shen, Ji

    2017-06-01

    This paper reports the first quantitative summer (mean July) temperature reconstruction based on subfossil chironomids from the southeast margin of the Qinghai-Tibetan Plateau (QTP) covering the end of the last deglaciation and the entire Holocene, spanning 11,800 cal yr BP to the present. The record is based on 223 chironomid samples throughout a 927 cm sediment core providing a temporal resolution of ∼50 years per sample. We validate the record by applying several statistical reconstruction diagnostics and comparing with pollen and diatom records from the same sediment core. The record suggests the summer temperature varies by ∼2.5 °C across the entire period. A generally warmer period occurred between c.8500 and c.6000 cal yr BP and a cooling trend was initiated from c.5500 cal yr BP. The overall pattern broadly matches the summer insolation at 30°N and the Asian Summer Monsoon records from the surrounding regions suggesting that summer temperatures from the southeast margin of the QTP respond to insolation forcing and monsoon driven variability on a multi-millennial time scale. Modifications of this overall trend are observed on the finer temporal resolution and we suggest that solar activity could be an important mechanism driving the centennial-scale variability. It may have a strengthened effect in the late Holocene when the monsoon influence weakened. Further detailed investigation is needed to disentangle these effects on the climate change over the highlands of southwestern China.

  2. Global negative vegetation feedback to climate warming responses of leaf litter decomposition rates in cold biomes.

    PubMed

    Cornelissen, Johannes H C; van Bodegom, Peter M; Aerts, Rien; Callaghan, Terry V; van Logtestijn, Richard S P; Alatalo, Juha; Chapin, F Stuart; Gerdol, Renato; Gudmundsson, Jon; Gwynn-Jones, Dylan; Hartley, Anne E; Hik, David S; Hofgaard, Annika; Jónsdóttir, Ingibjörg S; Karlsson, Staffan; Klein, Julia A; Laundre, Jim; Magnusson, Borgthor; Michelsen, Anders; Molau, Ulf; Onipchenko, Vladimir G; Quested, Helen M; Sandvik, Sylvi M; Schmidt, Inger K; Shaver, Gus R; Solheim, Bjørn; Soudzilovskaia, Nadejda A; Stenström, Anna; Tolvanen, Anne; Totland, Ørjan; Wada, Naoya; Welker, Jeffrey M; Zhao, Xinquan

    2007-07-01

    Whether climate change will turn cold biomes from large long-term carbon sinks into sources is hotly debated because of the great potential for ecosystem-mediated feedbacks to global climate. Critical are the direction, magnitude and generality of climate responses of plant litter decomposition. Here, we present the first quantitative analysis of the major climate-change-related drivers of litter decomposition rates in cold northern biomes worldwide. Leaf litters collected from the predominant species in 33 global change manipulation experiments in circum-arctic-alpine ecosystems were incubated simultaneously in two contrasting arctic life zones. We demonstrate that longer-term, large-scale changes to leaf litter decomposition will be driven primarily by both direct warming effects and concomitant shifts in plant growth form composition, with a much smaller role for changes in litter quality within species. Specifically, the ongoing warming-induced expansion of shrubs with recalcitrant leaf litter across cold biomes would constitute a negative feedback to global warming. Depending on the strength of other (previously reported) positive feedbacks of shrub expansion on soil carbon turnover, this may partly counteract direct warming enhancement of litter decomposition.

  3. Beyond the climate envelope: using trait filtering models to predict biome boundaries from plant physiology.

    NASA Astrophysics Data System (ADS)

    Fisher, R.; Hoffmann, W. A.; Muszala, S.

    2014-12-01

    The introduction of second-generation dynamic vegetation models - which simulate the distribution of light resources between plant types along the vertical canopy profile, and therefore facilitate the representation of plant competition explicitly - is a large increase in the complexity and fidelity with which the terrestrial biosphere is abstracted into Earth System Models. In this new class of model, biome boundaries are predicted as the emergent properties of plant physiology, and are therefore sensitive to the high-dimensional parameterizations of plant functional traits. These new approaches offer the facility to quantitatively test ecophysiological hypotheses of plant distribution at large scales, a field which remains surprisingly under-developed. Here we describe experiments conducted with the Community Land Model Ecosystem Demography component, CLM(ED), in which we reduce the complexity of the problem by testing how individual plant functional trait changes to control the location of biome boundaries between functional types. Specifically, we investigate which physiological trade-offs determine the boundary between frequently burned savanna and forest biomes, and attempt to distinguish how each strategic life-history trade-off (carbon storage, bark investment, re-sprouting strategy) contributes towards the maintenance of sharp geographical gradients between fire adapted and typically inflammable closed canopy ecosystems. This study forms part of the planning for a model-inspired fire manipulation experiment at the cerrado-forest boundary in South-Eastern Brazil, and the results will be used to guide future data-collection and analysis strategies.

  4. Evaluation of bone bruises and associated cartilage in ACL injured and reconstructed knees using quantitative T1ρ MRI: One-year cohort study

    PubMed Central

    Theologis, Alexander A.; Kuo, Daniel; Cheng, Jonathan; Bolbos, Radu I.; Carballido-Gamio, Julio; Ma, C. Benjamin; Li, Xiaojuan

    2010-01-01

    Purpose To quantitate bone marrow edema-like lesions (BMEL) and the radiologic properties of cartilage in knees with acute anterior cruciate ligament (ACL) injuries using T1ρ MRI over a 1 year time period. Methods 9 patients with ACL injuries were studied. MRI were acquired within 8 weeks of the injury, after which ACL reconstruction surgery was performed. Images were then acquired 0.5, 6, and 12 months following reconstructions. The volume and signal intensity of BMEL were quantified at baseline and follow up exams. T1ρ values were quantified in cartilage overlying the BMEL (OC) and compared to surrounding cartilage (SC) at all time-points. Results BMEL were most commonly found in the lateral tibia and lateral femoral condyle. Nearly 50% of BMEL resolved over 1-year. The T1ρ values of the OC in the lateral tibia, medial tibia, and medial femoral condyle were elevated compared to respective regions in SC at all time points, significant only in the lateral tibia (P < 0.05). The opposite results were found in the lateral femoral condyle. For the medial tibia and medial femoral condyle, none of the time periods were significantly different. The percent increase in T1ρ values of OC in the lateral tibia was significantly correlated to BMEL-volume (r = 0.74, P < 0.05). At 1-year, the OC in the lateral tibia, medial tibia, and medial femoral condyle showed increased T1ρ values despite improvement of BMEL. Conclusions In patients following ACL tear and reconstruction, (1) the cartilage overlying BMEL in the lateral tibia experiences persistent T1ρ signal change immediately after acute injuries and at 1-year follow up despite BMEL improvement. (2) The superficial layers of the overlying cartilage demonstrate greater matrix damage than the deep layers, and (3) the volume of the BMEL may predict the severity of the overlying matrix's damage in the lateral tibia. T1ρ is capable of quantitatively and noninvasively monitoring this damage and detecting early cartilage

  5. TU-AB-BRA-04: Quantitative Radiomics: Sensitivity of PET Textural Features to Image Acquisition and Reconstruction Parameters Implies the Need for Standards

    SciTech Connect

    Nyflot, MJ; Yang, F; Byrd, D; Bowen, SR; Sandison, GA; Kinahan, PE

    2015-06-15

    Purpose: Despite increased use of heterogeneity metrics for PET imaging, standards for metrics such as textural features have yet to be developed. We evaluated the quantitative variability caused by image acquisition and reconstruction parameters on PET textural features. Methods: PET images of the NEMA IQ phantom were simulated with realistic image acquisition noise. 35 features based on intensity histograms (IH), co-occurrence matrices (COM), neighborhood-difference matrices (NDM), and zone-size matrices (ZSM) were evaluated within lesions (13, 17, 22, 28, 33 mm diameter). Variability in metrics across 50 independent images was evaluated as percent difference from mean for three phantom girths (850, 1030, 1200 mm) and two OSEM reconstructions (2 iterations, 28 subsets, 5 mm FWHM filtration vs 6 iterations, 28 subsets, 8.6 mm FWHM filtration). Also, patient sample size to detect a clinical effect of 30% with Bonferroni-corrected α=0.001 and 95% power was estimated. Results: As a class, NDM features demonstrated greatest sensitivity in means (5–50% difference for medium girth and reconstruction comparisons and 10–100% for large girth comparisons). Some IH features (standard deviation, energy, entropy) had variability below 10% for all sensitivity studies, while others (kurtosis, skewness) had variability above 30%. COM and ZSM features had complex sensitivities; correlation, energy, entropy (COM) and zone percentage, short-zone emphasis, zone-size non-uniformity (ZSM) had variability less than 5% while other metrics had differences up to 30%. Trends were similar for sample size estimation; for example, coarseness, contrast, and strength required 12, 38, and 52 patients to detect a 30% effect for the small girth case but 38, 88, and 128 patients in the large girth case. Conclusion: The sensitivity of PET textural features to image acquisition and reconstruction parameters is large and feature-dependent. Standards are needed to ensure that prospective trials

  6. Satellite- and pollen-based quantitative woody cover reconstructions for northern Asia: Verification and application to late-Quaternary pollen data

    NASA Astrophysics Data System (ADS)

    Tarasov, Pavel; Williams, John W.; Andreev, Andrei; Nakagawa, Takeshi; Bezrukova, Elena; Herzschuh, Ulrike; Igarashi, Yaeko; Müller, Stefanie; Werner, Kirstin; Zheng, Zhuo

    2007-12-01

    Accurate reconstruction of late-Quaternary vegetation cover is necessary for better understanding of past vegetation dynamics, the role of vegetation feedbacks in glacial-interglacial climate variations, and for validating vegetation and climate models. In this paper over 1700 surface-pollen spectra from the former Soviet Union, Mongolia, northern China, and northern Japan together with data from the Advanced Very High Resolution Radiometer (AVHRR) were used to calibrate modern-analogue method for quantitatively reconstructing past woody cover from fossil pollen data. The AVHRR-based estimates of woody cover percentages within a 21 × 21 km window around pollen sampling sites were attributed to the respective modern pollen spectra. Reconstructions of modern woody cover using the pollen data and best-modern-analogues (BMA) method matched well to the original AVHRR-based estimates, for both total woody cover ( r2 = 0.77) and its fractions, including broad-leaved ( r2 = 0.66), needle-leaved ( r2 = 0.79), deciduous ( r2 = 0.60) and evergreen ( r2 = 0.76) woody cover. Discrepancies in the pollen-AVHRR cross-validation may be caused by long-distance transport of arboreal pollen, patchy forest distributions, underrepresentation of Larix and Populus in pollen records, and errors in the AVHRR classification. The generally strong correlations encourage application of the modern-analogue approach for reconstructing late-Quaternary variations in vegetation cover from northern Asian fossil pollen records. At the last glacial maximum (LGM: ˜ 21,000 cal yr BP), areas presently occupied by boreal forest were much more open, suggesting a reduction in total woody cover to below 20% at most modern forest sites. Pollen records from northern and central Siberia suggest a rather quick spread of tree and shrub vegetation after 15,000 cal yr BP, presumably in response to increased summer insolation. Woody cover histories are spatially variable in the modern forest-steppe, where tree

  7. Sinogram Affirmed Iterative Reconstruction (SAFIRE) versus weighted filtered back projection (WFBP) effects on quantitative measure in the COPDGene 2 test object.

    PubMed

    Sieren, J P; Hoffman, E A; Fuld, M K; Chan, K S; Guo, J; Newell, J D

    2014-09-01

    Assessing pulmonary emphysema using Quantitative CT of the lung depends on accurate measures of CT density. Sinogram-Affirmed-Iterative-Reconstruction (SAFIRE) is a new approach for reconstructing CT data acquired at significantly lower doses. However, quantitative effects of this method remain unexplored. The authors investigated the effects on the median values of materials in the COPDGene2 test-object as a function of the reconstruction method [weighted filtered back projection (WFBP) versus SAFIRE], test-object size, dose, and material composition using a Siemens SOMATOM Definition FLASH CT scanner. The COPDGene2 test-object contains eight materials; acrylic, water, four foams (20 lb, 12 lb, lung-equivalent, and 4 lb emphysema-equivalent), internal and external-air. The test-object was scanned with three different outer ring sizes, simulating three different body habitus. There is an average size (36 cm) Ring A, large size (40 cm) Ring B, and small size Ring C (30 cm). The CT protocol used 120 kVp, 0.5 s rotation, 1.0 pitch, and a 0.6 slice collimation with progressively decreasing x-ray exposure values, 11.94-0.74 mGy. With a thorax length of 30 cm, the corresponding effective doses would be 5.01-0.31 mSv. The effects of using SAFIRE versus WFBP were assessed using a two tailed t-test for each ring size, material, and dose. Multivariable linear regression was used to evaluate the relative effects of ring size, material composition, dose, and reconstruction method on the measured median value in HU. SAFIRE versus WFBP, at the largest ring size and two lowest doses there was a significant difference in median values of 4 lb-foam, p<0.01. Using the smallest ring size at the lowest dose level there was a significant difference in the median value of 4 lb-foam, but the effect size was small, 1 HU. There is a significant difference in median values of both internal and external air using both the small and medium size rings at the three lowest dose levels, p<0

  8. Lacustrine turbidites as a tool for quantitative earthquake reconstruction: New evidence for a variable rupture mode in south central Chile

    NASA Astrophysics Data System (ADS)

    Moernaut, Jasper; Daele, Maarten Van; Heirman, Katrien; Fontijn, Karen; Strasser, Michael; Pino, Mario; Urrutia, Roberto; De Batist, Marc

    2014-03-01

    Understanding the long-term earthquake recurrence pattern at subduction zones requires continuous paleoseismic records with excellent temporal and spatial resolution and stable threshold conditions. South central Chilean lakes are typically characterized by laminated sediments providing a quasi-annual resolution. Our sedimentary data show that lacustrine turbidite sequences accurately reflect the historical record of large interplate earthquakes (among others the 2010 and 1960 events). Furthermore, we found that a turbidite's spatial extent and thickness are a function of the local seismic intensity and can be used for reconstructing paleo-intensities. Consequently, our multilake turbidite record aids in pinpointing magnitudes, rupture locations, and extent of past subduction earthquakes in south central Chile. Comparison of the lacustrine turbidite records with historical reports, a paleotsunami/subsidence record, and a marine megaturbidite record demonstrates that the Valdivia Segment is characterized by a variable rupture mode over the last 900 years including (i) full ruptures (Mw ~9.5: 1960, 1575, 1319 ± 9, 1127 ± 44), (ii) ruptures covering half of the Valdivia Segment (Mw ~9: 1837), and (iii) partial ruptures of much smaller coseismic slip and extent (Mw ~7.5-8: 1737, 1466 ± 4). Also, distant or smaller local earthquakes can leave a specific sedimentary imprint which may resolve subtle differences in seismic intensity values. For instance, the 2010 event at the Maule Segment produced higher seismic intensities toward southeastern localities compared to previous megathrust ruptures of similar size and extent near Concepción.

  9. Three-dimensional visual truth of the normal airway tree for use as a quantitative comparison to micro-CT reconstructions

    NASA Astrophysics Data System (ADS)

    Thiesse, Jacqueline; Reinhardt, Joseph M.; de Ryk, Jessica; Namati, Eman; Leinen, Jessica; Recheis, Wolfgang A.; Hoffman, Eric A.; McLennan, Geoffrey

    2005-04-01

    Mouse models are important for pulmonary research to gain insight into structure and function in normal and diseased states, thereby extending knowledge of human disease conditions. The flexibility of human disease induction into mice, due to their similar genome, along with their short gestation cycle makes mouse models highly suitable as investigative tools. Advancements in non-invasive imaging technology, with the development of micro-computed tomography (μ-CT), have aided representation of disease states in these small pulmonary system models. The generation ofμCT 3D airway reconstructions has to date provided a means to examine structural changes associated with disease. The degree of accuracy ofμCT is uncertain. Consequently, the reliability of quantitative measurements is questionable. We have developed a method of sectioning and imaging the whole mouse lung using the Large Image Microscope Array (LIMA) as the gold standard for comparison. Fixed normal mouse lungs were embedded in agarose and 250μm sections of tissue were removed while the remaining tissue block was imaged with a stereomicroscope. A complete dataset of the mouse lung was acquired in this fashion. Following planar image registration, the airways were manually segmented using an in-house built software program PASS. Amira was then used render the 3D isosurface from the segmentations. The resulting 3D model of the normal mouse airway tree developed from pathology images was then quantitatively assessed and used as the standard to compare the accuracy of structural measurements obtained from μ-CT.

  10. Climate Control of Photosynthetic Parameters across Biomes

    NASA Astrophysics Data System (ADS)

    Wei, S.; Yi, C.

    2011-12-01

    Meteorological tower networks measure net ecosystem exchange (NEE) of CO2, which is a balance between ecosystem respiration (Reco) and gross primary production (GPP). For understanding the mechanistic response of CO2 exchange to climate factors at process-level, it's necessary to separate NEE into its two components. A light-response analysis model (Ruimy, et al., 1995) has proved to be an efficient tool for this purpose. Principal light-response parameters-apparent quantum yield (α), photosynthetic capacity (Fmax) and ecosystem respiration (Reco) are important for modeling of CO2 exchange from regional scale to global domains using remote sensing. A major challenge lies in understanding how those parameters vary across biomes under different climatic conditions. So far, few large-sample studies have been conducted on this purpose. In our study, we partition seasonal NEE into photosynthesis and ecosystem respiration of 247 unique fluxnet sites, which represents over 900 site-years. Our results indicate that: (1) apparent quantum yield (α) of deciduous broadleaf forests and mixed forests is sensitive to seasonal temperature; (2) photosynthetic capacity (Fmax) of deciduous forests and evergreen broadleaf forests is controlled by Bowen Ratio; and (3) Ecosystem respiration of evergreen needle forests and mixed forests is controlled by temperature, while evergreen broadleaf forests controlled by Bowen Ratio. Our results also demonstrate that some relationships between photosynthetic parameters and climate controls are latitude dependent. Ecosystem respiration of croplands and deciduous broadleaf forests in high latitudes shows better temperature correlations than that in low latitudes; apparent quantum yield (α) of evergreen needle forests only display temperature control in latitudes above 40N. On biome-scale average, the magnitudes of photosynthetic capacity are categorized into two groups: (1) with high value (from 31.96 to 37.13 umol m-2s-1) of croplands

  11. Flow convergence flow rates from 3-dimensional reconstruction of color Doppler flow maps for computing transvalvular regurgitant flows without geometric assumptions: An in vitro quantitative flow study.

    PubMed

    Li, X; Shiota, T; Delabays, A; Teien, D; Zhou, X; Sinclair, B; Pandian, N G; Sahn, D J

    1999-12-01

    This study was designed to develop and test a 3-dimensional method for direct measurement of flow convergence (FC) region surface area and for quantitating regurgitant flows with an in vitro flow system. Quantitative methods for characterizing regurgitant flow events such as flow convergence with 2-dimensional color flow Doppler imaging systems have yielded variable results and may not be accurate enough to characterize those more complex spatial events. Four differently shaped regurgitant orifices were studied: 3 flat orifices (circular, rectangular, triangular) and a nonflat one mimicking mitral valve prolapse (all 4 orifice areas = 0.24 cm(2)) in a pulsatile flow model at 8 to 9 different regurgitant flow rates (10 to 50 mL/beat). An ultrasonic flow probe and meter were connected to the flow model to provide reference flow data. Video composite data from the color Doppler flow images of the FC were reconstructed after computer-controlled 180 degrees rotational acquisition was performed. FC surface area (S cm(2)) was calculated directly without any geometric assumptions by measuring parallel sliced flow convergence arc lengths through the FC volume and multiplying each by the slice thickness (2.5 to 3.2 mm) over 5 to 8 slices and then adding them together. Peak regurgitant flow rate (milliliters per second) was calculated as the product of 3-dimensional determined S (cm(2)) multiplied by the aliasing velocity (centimeters per second) used for color Doppler imaging. For all of the 4 shaped orifices, there was an excellent relationship between actual peak flow rates and 3-dimensional FC-calculated flow rates with the direct measurement of the surface area of FC (r = 0.99, mean difference = -7.2 to -0.81 mL/s, % difference = -5% to 0%), whereas a hemielliptic method implemented with 3 axial measurements of the flow convergence zone from 2-dimensional planes underestimated actual flow rate by mean difference = -39.8 to -18.2 mL/s, % difference = -32% to -17% for any

  12. Using an Exploratory Internet Activity & Trivia Game to Teach Students about Biomes

    ERIC Educational Resources Information Center

    Richardson, Matthew L.

    2009-01-01

    Students in life science classes need an introduction to biomes, including an introduction to the concept, key biotic and abiotic features of biomes, and geographic locations of biomes. In this activity, students in seventh- and eighth-grade science classes used a directed exploratory Internet activity to learn about biomes. The author tested…

  13. Using an Exploratory Internet Activity & Trivia Game to Teach Students about Biomes

    ERIC Educational Resources Information Center

    Richardson, Matthew L.

    2009-01-01

    Students in life science classes need an introduction to biomes, including an introduction to the concept, key biotic and abiotic features of biomes, and geographic locations of biomes. In this activity, students in seventh- and eighth-grade science classes used a directed exploratory Internet activity to learn about biomes. The author tested…

  14. A direct and quantitative three-dimensional reconstruction of the internal structure of disordered mesoporous carbon with tailored pore size.

    PubMed

    Balach, Juan; Soldera, Flavio; Acevedo, Diego F; Mücklich, Frank; Barbero, César A

    2013-06-01

    A new technique that allows direct three-dimensional (3D) investigations of mesopores in carbon materials and quantitative characterization of their physical properties is reported. Focused ion beam nanotomography (FIB-nt) is performed by a serial sectioning procedure with a dual beam FIB-scanning electron microscopy instrument. Mesoporous carbons (MPCs) with tailored mesopore size are produced by carbonization of resorcinol-formaldehyde gels in the presence of a cationic surfactant as a pore stabilizer. A visual 3D morphology representation of disordered porous carbon is shown. Pore size distribution of MPCs is determined by the FIB-nt technique and nitrogen sorption isotherm methods to compare both results. The obtained MPCs exhibit pore sizes of 4.7, 7.2, and 18.3 nm, and a specific surface area of ca. 560 m(2)/g.

  15. The PRoViDE framework for the quantitative geologic analysis of reconstructed Martian terrain and outcrops

    NASA Astrophysics Data System (ADS)

    Traxler, Christoph; Hesina, Gerd; Barnes, Robert; Gupta, Sanjeev; Paar, Gerhard

    2016-04-01

    The EU-FP7 project PRoViDE (Planetary Robotics Vision Data Exploitation) assembled a major portion of the imaging data gathered so far from planetary surface missions into a unique 3D database, brought them into a spatial context and provides access to a complete set of 3D vision products. The processing chain (PRoViP) is able to generate novel 3D fusion products between HiRISE orbiter and multiple-station rover stereo imagery from NASA's Mars Exploration Rover - MER (Pancam, Navcam), and Mars Science Laboratory Curiosity - MSL (Mastcam). An important tool of the PRoViDE framework, using PRoViP multi-resolution 3D vision processing products, is called PRo3D. It is an interactive virtual environment for the scientific exploration and analysis of reconstructed Martian terrain and digital outcrop models. Data fusion is supported so that multiple models with different scales and geometric resolutions can be combined in one 3D scene. This allows studying both the large geological context, which usually is reconstructed from orbiter imagery, and small outcrop details originating from rover camera imagery. PRo3D allows the user to fluently move around and zoom to investigate features at different scales and perspectives, as well as providing various interactive analysis tools. Interpretations can be digitised directly onto the 3D surface, and simple measurements can be taken of the dimensions of the outcrop and sedimentary features. The 3D data allows for incorporation of the geometrical features of the sedimentary layers into the measurements to obtain the true dimensions of those features. Dip and strike is calculated within PRo3D from mapped bedding contacts and fracture traces, through which a best fit plane is created to derive the dip and strike vectors. Scientists can organize measurements and annotations according to their geological context in a hierarchical way. These tools have been tested on two case studies; Victoria Crater and Shaler. Victoria Crater, in the

  16. Do Distinct Biomes Influence the Cuticular Chemical Profile in Orchid Bees?

    PubMed

    Santos, A B; Nascimento, F S

    2017-02-17

    Cuticular chemical profiles of Euglossa cordata L. males were analyzed to test whether ecological predictors affect their composition and relative proportion. Males were collected in areas of Caatinga and Atlantic Forest from Brazil during two distinct seasonal periods. We found 48 compounds from the cuticular extracts of males, which consisted of hydrocarbons (71.39%), acetates (16.79%), esters (10.5%), alcohols and others (1.31%). We verified that when specimens were separated between biomes, they did not show a qualitative differentiation, but a small quantitative variation of compounds was found between some alkanes. We suggest that these results reflect stability of epicuticular compounds even under variable environmental conditions.

  17. Diverging responses of tropical Andean biomes under future climate conditions.

    PubMed

    Tovar, Carolina; Arnillas, Carlos Alberto; Cuesta, Francisco; Buytaert, Wouter

    2013-01-01

    Observations and projections for mountain regions show a strong tendency towards upslope displacement of their biomes under future climate conditions. Because of their climatic and topographic heterogeneity, a more complex response is expected for biodiversity hotspots such as tropical mountain regions. This study analyzes potential changes in the distribution of biomes in the Tropical Andes and identifies target areas for conservation. Biome distribution models were developed using logistic regressions. These models were then coupled to an ensemble of 8 global climate models to project future distribution of the Andean biomes and their uncertainties. We analysed projected changes in extent and elevational range and identified regions most prone to change. Our results show a heterogeneous response to climate change. Although the wetter biomes exhibit an upslope displacement of both the upper and the lower boundaries as expected, most dry biomes tend to show downslope expansion. Despite important losses being projected for several biomes, projections suggest that between 74.8% and 83.1% of the current total Tropical Andes will remain stable, depending on the emission scenario and time horizon. Between 3.3% and 7.6% of the study area is projected to change, mostly towards an increase in vertical structure. For the remaining area (13.1%-17.4%), there is no agreement between model projections. These results challenge the common believe that climate change will lead to an upslope displacement of biome boundaries in mountain regions. Instead, our models project diverging responses, including downslope expansion and large areas projected to remain stable. Lastly, a significant part of the area expected to change is already affected by land use changes, which has important implications for management. This, and the inclusion of a comprehensive uncertainty analysis, will help to inform conservation strategies in the Tropical Andes, and to guide similar assessments for other

  18. Diverging Responses of Tropical Andean Biomes under Future Climate Conditions

    PubMed Central

    Tovar, Carolina; Arnillas, Carlos Alberto; Cuesta, Francisco; Buytaert, Wouter

    2013-01-01

    Observations and projections for mountain regions show a strong tendency towards upslope displacement of their biomes under future climate conditions. Because of their climatic and topographic heterogeneity, a more complex response is expected for biodiversity hotspots such as tropical mountain regions. This study analyzes potential changes in the distribution of biomes in the Tropical Andes and identifies target areas for conservation. Biome distribution models were developed using logistic regressions. These models were then coupled to an ensemble of 8 global climate models to project future distribution of the Andean biomes and their uncertainties. We analysed projected changes in extent and elevational range and identified regions most prone to change. Our results show a heterogeneous response to climate change. Although the wetter biomes exhibit an upslope displacement of both the upper and the lower boundaries as expected, most dry biomes tend to show downslope expansion. Despite important losses being projected for several biomes, projections suggest that between 74.8% and 83.1% of the current total Tropical Andes will remain stable, depending on the emission scenario and time horizon. Between 3.3% and 7.6% of the study area is projected to change, mostly towards an increase in vertical structure. For the remaining area (13.1%–17.4%), there is no agreement between model projections. These results challenge the common believe that climate change will lead to an upslope displacement of biome boundaries in mountain regions. Instead, our models project diverging responses, including downslope expansion and large areas projected to remain stable. Lastly, a significant part of the area expected to change is already affected by land use changes, which has important implications for management. This, and the inclusion of a comprehensive uncertainty analysis, will help to inform conservation strategies in the Tropical Andes, and to guide similar assessments for

  19. Generality of leaf trait relationships: A test across six biomes

    SciTech Connect

    Reich, P.B.; Ellsworth, D.S.; Walters, M.B.; Vose, J.M.; Gresham, C.; Volin, J.C.; Bowman, W.D. |

    1999-09-01

    Convergence in interspecific leaf trait relationships across diverse taxonomic groups and biomes would have important evolutionary and ecological implications. Such convergence has been hypothesized to result from trade-offs that limit the combination of plant traits for any species. Here the authors address this issue by testing for biome differences in the slope and intercept of interspecific relationships among leaf traits: longevity, net photosynthetic capacity (A{sub max}), leaf diffusive conductance (G{sub S}), specific leaf area (SLA), and nitrogen (N) status, for more than 100 species in six distinct biomes of the Americas. The six biomes were: alpine tundra-subalpine forest ecotone, cold temperate forest-prairie ecotone, montane cool temperate forest, desert shrubland, subtropical forest, and tropical rain forest. Despite large differences in climate and evolutionary history, in all biomes mass-based leaf N (N{sub mass}), SLA, G{sub S}, and A{sub max} were positively related to one another and decreased with increasing leaf life span. The relationships between pairs of leaf traits exhibited similar slopes among biomes, suggesting a predictable set of scaling relationships among key leaf morphological, chemical, and metabolic traits that are replicated globally among terrestrial ecosystems regardless of biome or vegetation type. However, the intercept (i.e., the overall elevation of regression lines) of relationships between pairs of leaf traits usually differed among biomes. With increasing aridity across sites, species had greater A{sub max} for a given level of G{sub S} and lower SLA for any given leaf life span. Using principal components analysis, most variation among species was explained by an axis related to mass-based leaf traits (A{sub max}, N, and SLA) while a second axis reflected climate, G{sub S}, and other area-based leaf traits.

  20. Quantitative woody cover reconstructions from eastern continental Asia of the last 22 kyr reveal strong regional peculiarities

    NASA Astrophysics Data System (ADS)

    Tian, Fang; Cao, Xianyong; Dallmeyer, Anne; Ni, Jian; Zhao, Yan; Wang, Yongbo; Herzschuh, Ulrike

    2016-04-01

    We present a calibration-set based on modern pollen and satellite-based Advanced Very High Resolution Radiometer (AVHRR) observations of woody cover (including needleleaved, broadleaved and total tree cover) in eastern continental Asia, which shows good performance under cross-validation with the modern analogue technique (all the coefficients of determination between observed and predicted values are greater than 0.65). The calibration-set is used to reconstruct woody cover from a taxonomically harmonized and temporally standardized fossil pollen dataset (including 274 cores) with 500-year resolution over the last 22 kyr. The spatial range of forest has not noticeably changed in eastern continental Asia during the last 22 kyr, although woody cover has, especially at the margin of the eastern Tibetan Plateau and in the forest-steppe transition area of north-central China. Vegetation was sparse during the LGM in the present forested regions, but woody cover increased markedly at the beginning of the Bølling/Allerød period (B/A; ca. 14.5 ka BP) and again at the beginning of the Holocene (ca. 11.5 ka BP), and is related to the enhanced strength of the East Asian Summer Monsoon. Forest flourished in the mid-Holocene (ca. 8 ka BP) possibly due to favourable climatic conditions. In contrast, cover was stable in southern China (high cover) and arid central Asia (very low cover) throughout the investigated period. Forest cover increased in the north-eastern part of China during the Holocene. Comparisons of these regional pollen-based results with simulated forest cover from runs of a global climate model (for 9, 6 and 0 ka BP (ECHAM5/JSBACH ∼1.125° spatial resolution)) reveal many similarities in temporal change. The Holocene woody cover history of eastern continental Asia is different from that of other regions, likely controlled by different climatic variables, i.e. moisture in eastern continental Asia; temperature in northern Eurasia and North America.

  1. biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format.

    PubMed

    Ankenbrand, Markus J; Terhoeven, Niklas; Hohlfeld, Sonja; Förster, Frank; Keller, Alexander

    2016-01-01

    The Biological Observation Matrix (BIOM) format is widely used to store data from high-throughput studies. It aims at increasing interoperability of bioinformatic tools that process this data. However, due to multiple versions and implementation details, working with this format can be tricky. Currently, libraries in Python, R and Perl are available, whilst such for JavaScript are lacking. Here, we present a BioJS component for parsing BIOM data in all format versions. It supports import, modification, and export via a unified interface. This module aims to facilitate the development of web applications that use BIOM data. Finally, we demonstrate its usefulness by two applications that already use this component. Availability: https://github.com/molbiodiv/biojs-io-biom, https://dx.doi.org/10.5281/zenodo.218277.

  2. biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format

    PubMed Central

    Ankenbrand, Markus J.; Terhoeven, Niklas; Hohlfeld, Sonja; Förster, Frank; Keller, Alexander

    2017-01-01

    The Biological Observation Matrix (BIOM) format is widely used to store data from high-throughput studies. It aims at increasing interoperability of bioinformatic tools that process this data. However, due to multiple versions and implementation details, working with this format can be tricky. Currently, libraries in Python, R and Perl are available, whilst such for JavaScript are lacking. Here, we present a BioJS component for parsing BIOM data in all format versions. It supports import, modification, and export via a unified interface. This module aims to facilitate the development of web applications that use BIOM data. Finally, we demonstrate its usefulness by two applications that already use this component. Availability: https://github.com/molbiodiv/biojs-io-biom, https://dx.doi.org/10.5281/zenodo.218277 PMID:28105307

  3. Evaluation of the Quantitative Accuracy of 3D Reconstruction of Edentulous Jaw Models with Jaw Relation Based on Reference Point System Alignment

    PubMed Central

    Li, Weiwei; Yuan, Fusong; Lv, Peijun; Wang, Yong; Sun, Yuchun

    2015-01-01

    Objectives To apply contact measurement and reference point system (RPS) alignment techniques to establish a method for 3D reconstruction of the edentulous jaw models with centric relation and to quantitatively evaluate its accuracy. Methods Upper and lower edentulous jaw models were clinically prepared, 10 pairs of resin cylinders with same size were adhered to axial surfaces of upper and lower models. The occlusal bases and the upper and lower jaw models were installed in the centric relation position. Faro Edge 1.8m was used to directly obtain center points of the base surface of the cylinders (contact method). Activity 880 dental scanner was used to obtain 3D data of the cylinders and the center points were fitted (fitting method). 3 pairs of center points were used to align the virtual model to centric relation. An observation coordinate system was interactively established. The straight-line distances in the X (horizontal left/right), Y (horizontal anterior/posterior), and Z (vertical) between the remaining 7 pairs of center points derived from contact method and fitting method were measured respectively and analyzed using a paired t-test. Results The differences of the straight-line distances of the remaining 7 pairs of center points between the two methods were X: 0.074 ± 0.107 mm, Y: 0.168 ± 0.176 mm, and Z: −0.003± 0.155 mm. The results of paired t-test were X and Z: p >0.05, Y: p <0.05. Conclusion By using contact measurement and the reference point system alignment technique, highly accurate reconstruction of the vertical distance and centric relation of a digital edentulous jaw model can be achieved, which meets the design and manufacturing requirements of the complete dentures. The error of horizontal anterior/posterior jaw relation was relatively large. PMID:25659133

  4. Quantitative Analysis of Cardiac Tissue Including Fibroblasts Using Three-Dimensional Confocal Microscopy and Image Reconstruction: Towards a Basis for Electrophysiological Modeling

    PubMed Central

    Schwab, Bettina C.; Seemann, Gunnar; Lasher, Richard A.; Torres, Natalia S.; Wülfers, Eike M.; Arp, Maren; Carruth, Eric D.; Bridge, John H. B.; Sachse, Frank B.

    2014-01-01

    Electrophysiological modeling of cardiac tissue is commonly based on functional and structural properties measured in experiments. Our knowledge of these properties is incomplete, in particular their remodeling in disease. Here, we introduce a methodology for quantitative tissue characterization based on fluorescent labeling, 3-D scanning confocal microscopy, image processing and reconstruction of tissue micro-structure at sub-micrometer resolution. We applied this methodology to normal rabbit ventricular tissue and tissue from hearts with myocardial infarction. Our analysis revealed that the volume fraction of fibroblasts increased from 4.83 ± 0.42% (mean ± standard deviation) in normal tissue up to 6.51 ± 0.38% in myocardium from infarcted hearts. The myocyte volume fraction decreased from 76.20 ± 9.89% in normal to 73.48 ± 8.02% adjacent to the infarct. Numerical field calculations on 3-D reconstructions of the extracellular space yielded an extracellular longitudinal conductivity of 0.264 ± 0.082 S/m with an anisotropy ratio of 2.095 ± 1.11 in normal tissue. Adjacent to the infarct, the longitudinal conductivity increased up to 0.400 ± 0.051 S/m, but the anisotropy ratio decreased to 1.295 ± 0.09. Our study indicates an increased density of gap junctions proximal to both fibroblasts and myocytes in infarcted versus normal tissue, supporting previous hypotheses of electrical coupling of fibroblasts and myocytes in infarcted hearts. We suggest that the presented methodology provides an important contribution to modeling normal and diseased tissue. Applications of the methodology include the clinical characterization of disease-associated remodeling. PMID:23340590

  5. Quantitative Reconstruction of Sulfur Deposition Using a Mixing Model Based on Sulfur Isotope Ratios in Tree Rings.

    PubMed

    Ishida, Takuya; Tayasu, Ichiro; Takenaka, Chisato

    2015-11-01

    Quantification of sulfur (S) deposition is critical to deciphering the environmental archive of S in terrestrial ecosystems. Here we propose a mixing model that quantifies S deposition based on the S isotope ratio (δS) in tree rings. We collected samples from Japanese cedar ( D. Don) stumps from two sites: one near Yokkaichi City (YOK), which is well known for having the heaviest S air pollution in the world, and one at Inabu-cho (INA) in central Japan, which has been much less affected by air pollution. The δS profiles at both sites are consistent with S air pollution and contributions of anthropogenic S. The minimum value in YOK is lower than the δS values of anthropogenic S or any other possible source. Because the δS in the tree rings is affected by fractionation in the forest ecosystems, we used a mixing model to account for the isotope effects and to distinguish the sources of S. Based on the model results, we infer that the peak of S emissions at YOK occurred sometime between the late 1960s and early 1970s (489 mmol m yr). This estimated value is comparable with the highest reported values in Europe. This is the first quantitative estimate of anthropogenic input of S in forest systems based on δS in tree rings. Our results suggest that tree ring data can be used when monitoring stations of atmospheric S are lacking and that estimates of S deposition using δS in tree rings will advance our understanding of the local-scale S dynamics and the effect of human activities on it.

  6. Availability of latissimus dorsi minigraft in smile reconstruction for incomplete facial paralysis: quantitative assessment based on the optical flow method.

    PubMed

    Takushima, Akihiko; Harii, Kiyonori; Okazaki, Mutsumi; Ohura, Norihiko; Asato, Hirotaka

    2009-04-01

    Acute unilateral facial paralysis, such as occurs in Bell palsy and Hunt syndrome, is mostly a benign neurologic morbidity that resolves within a few months. However, incomplete or misdirected return of the affected nerve results in unfavorable cosmetic sequelae in some patients. Although functional problems such as lagophthalmos are rare, facial asymmetry on smiling resulting from a lack of mimetic muscle strength in the cheek is often psychologically annoying to patients. To obtain a more natural smile, the authors transfer latissimus dorsi muscle to assist in cheek movement. A small, thinned muscle (mini-latissimus dorsi) is sufficient for transplant in this situation. In this study, 96 patients with incomplete facial paralysis who underwent mini-latissimus dorsi transfer were examined. In this series, along with evaluation using the grading scale used in previous reports, preoperative and postoperative videos of 30 patients were analyzed for quantitative assessment using newly developed computer software. Temporary deterioration of paralysis was recognized in three cases but did not last more than a few months. Signs of transferred muscle contraction were recorded after 4 to 12 months among 91 patients. No apparent clinical signs of contraction were recognized in one patient, and four patients could not be followed postoperatively. The synchronized ratio of vertical movement and the symmetrical ratio of horizontal movement both in the cheek and in the lower lip between healthy and paralyzed sides among 30 patients were statistically improved. Statistical analysis using newly developed computer software revealed that a more symmetrical smile can be achieved by muscle transfer among patients with incomplete facial paralysis. Mini-latissimus dorsi transfer can avoid postoperative muscle bulkiness of the cheek and can achieve more natural cheek movement.

  7. Multiband radar characterization of forest biomes

    NASA Technical Reports Server (NTRS)

    Dobson, M. Craig; Ulaby, Fawwaz T.

    1990-01-01

    The utility of airborne and orbital SAR in classification, assessment, and monitoring of forest biomes is investigated through analysis of orbital synthetic aperature radar (SAR) and multifrequency and multipolarized airborne SAR imagery relying on image tone and texture. Preliminary airborne SAR experiments and truck-mounted scatterometer observations demonstrated that the three dimensional structural complexity of a forest, and the various scales of temporal dynamics in the microwave dielectric properties of both trees and the underlying substrate would severely limit empirical or semi-empirical approaches. As a consequence, it became necessary to develop a more profound understanding of the electromagnetic properties of a forest scene and their temporal dynamics through controlled experimentation coupled with theoretical development and verification. The concatenation of various models into a physically-based composite model treating the entire forest scene became the major objective of the study as this is the key to development of a series of robust retrieval algorithms for forest biophysical properties. In order to verify the performance of the component elements of the composite model, a series of controlled laboratory and field experiments were undertaken to: (1) develop techniques to measure the microwave dielectric properties of vegetation; (2) relate the microwave dielectric properties of vegetation to more readily measured characteristics such as density and moisture content; (3) calculate the radar cross-section of leaves, and cylinders; (4) improve backscatter models for rough surfaces; and (5) relate attenuation and phase delays during propagation through canopies to canopy properties. These modeling efforts, as validated by the measurements, were incorporated within a larger model known as the Michigan Microwave Canopy Scattering (MIMICS) Model.

  8. Calibrating Long-chain Diols for Quantitative Temperature Reconstructions in the High Elevation, Lacustrine Environments of the Sierra Nevada, Spain

    NASA Astrophysics Data System (ADS)

    Toney, J. L.; García-Alix, A.; Jimenez-Moreno, G.; Anderson, R. S.; Perez-Martinez, C.; Jimenez, L.

    2016-12-01

    High-alpine, oligotrophic lakes in the Sierra Nevada are sensitive archives of paleoclimate and paleoecology. In this study we present the first quantitative calibration of lacustrine long-chain diols to instrumental temperature anamoly data. The data suggest that the long-chain diol index (LDI) is linearly correlated with the regional temperature anomaly data (TA = 8.8997 x LDI - 2.1113, r2 = 0.65) over the past 165-years and that this correlation can accurately be applied downcore to reconstructure temperature change over the course of the Holocene. This study compares the newly generated diol-inferred temperature dataset with existing multiproxy records to show that the mid-Holocene transition that shows a step change in vegetation and humidity toward aridification was likely driven by an increased and sustained temperature anomaly of +1.5°C from 6.4 to 5.8ka. Major changes occurred with respect to biogeography and vegetation communities in the Sierra Nevada at this time, but until now, the drivers of change have been unclear. In addition to the diol-inferred temperature anomaly data, compound-specific stable H-isotopes of terrestrial and aquatic plant waxes indicate that this warm event was directly preceded by a brief cold excursion at Laguna de Rio Seco that likely reduced terrestrial plant development and enhanced input of meltwater - suggested by low lake-water H-isotope values. The diol-inferred temperatures suggest that meltwater lowered the lake water temperature with a -1.2°C anomaly from 6.6 to 6.4ka. This suggests that the subsequent warming over the next 600-years likely caused a local, extreme shift to higher temperatures due to the lack of buffering by meltwater once the year-on-year snowpack was depleted. Briefer warm anomalies occur at 5.5, 3.2, and 1.5ka, which correspond to know periods of reduced precipitation in the Mediterranean region (e.g., see discussion in Martin-Puertas et al. 2010, doi:10.5194/cpd-6-1655-2010). A similar, but more

  9. Modern Spatial Rainfall Rate is well Correlated with Coretop δ2Hdinosterol in the South Pacific Convergence Zone: A Tool for Quantitative Reconstructions of Rainfall Rate

    NASA Astrophysics Data System (ADS)

    Sear, D. A.; Maloney, A. E.; Nelson, D. B.; Sachs, J. P.; Hassall, J. D.; Langdon, P. G.; Prebble, M.; Richey, J. N.; Schabetsberger, R.; Sichrowsky, U.; Hope, G.

    2015-12-01

    The South Pacific Convergence Zone (SPCZ) is the Southern Hemisphere's most prominent precipitation feature extending southeastward 3000 km from Papua New Guinea to French Polynesia. Determining how the SPCZ responded to climate variations before the instrumental record requires the use of indirect indicators of rainfall. The link between the hydrogen isotopic composition of fluxes of water though the hydrologic cycle, lake water, and molecular fossil 2H/1H ratios make hydrogen isotopes a promising tool for improving our understanding of this important climate feature. An analysis of coretop sediment from freshwater lakes in the SPCZ region indicates that there is a strong spatial relationship between δ2Hdinosterol and mean annual precipitation rate. The objectives of this research are to use 2H/1H ratios of the biomarker dinosterol to develop an empirical relationship between δ2Hdinosterol and modern environmental rainfall rates so that we may quantitatively reconstruct several aspects of the SPCZ's hydrological system during the late Holocene. The analysis includes lake sediment coretops from the Solomon Islands, Wallis Island, Vanuatu, Tahiti, Samoa, New Caledonia, and the Cook Islands. These islands span range of average modern precipitation rates from 3 to 7 mm/day and the coretop sediment δ2Hdinosterol values range from -240‰ to -320‰. Applying this regional coretop calibration to dated sediment cores reveals that the mean annual position and/or intensity of the SPCZ has not been static during the past 2000 years.

  10. Modern Spatial Rainfall Rate is well Correlated with Coretop δ2Hdinosterol in the South Pacific Convergence Zone: a Tool for Quantitative Reconstructions

    NASA Astrophysics Data System (ADS)

    Maloney, A. E.; Nelson, D. B.; Sachs, J. P.; Hassall, J. D.; Sear, D. A.; Langdon, P. G.; Prebble, M.; Richey, J. N.; Schabetsberger, R.; Sichrowsky, U.; Hope, G.

    2016-02-01

    The South Pacific Convergence Zone (SPCZ) is the Southern Hemisphere's most prominent precipitation feature extending southeastward 3000 km from Papua New Guinea to French Polynesia. Determining how the SPCZ responded to climate variations before the instrumental record requires the use of indirect indicators of rainfall. The link between the hydrogen isotopic composition of water fluxes though the hydrologic cycle, lake water, and molecular fossil 2H/1H ratios make hydrogen isotopes a promising tool for improving our understanding of this important climate feature. An analysis of coretop sediment from freshwater lakes in the SPCZ region indicates that there is a strong spatial relationship between δ2Hdinosterol and mean annual precipitation rate. The objectives of this research are to use 2H/1H ratios of the biomarker dinosterol to develop an empirical relationship between δ2Hdinosterol and modern environmental rainfall rates so that we may quantitatively reconstruct several aspects of the SPCZ's hydrological system during the late Holocene. The analysis includes lake sediment coretops from the Solomon Islands, Wallis Island, Vanuatu, Tahiti, Samoa, New Caledonia, and the Cook Islands. These islands span range of average modern precipitation rates from 3 to 7 mm/day and the coretop sediment δ2Hdinosterol values range from -240‰ to -320‰. Applying this regional coretop calibration to dated sediment cores reveals that the mean annual position and/or intensity of the SPCZ has not been static during the past 2000 years.

  11. New insights into the role of hilar ectopic granule cells in the dentate gyrus based on quantitative anatomic analysis and three-dimensional reconstruction

    PubMed Central

    Scharfman, Helen E.; Pierce, Joseph P.

    2014-01-01

    SUMMARY The dentate gyrus is one of two main areas of the mammalian brain where neurons are born throughout adulthood, a phenomenon called postnatal neurogenesis. Most of the neurons that are generated are granule cells (GCs), the major principal cell type in the dentate gyrus. Some adult-born granule cells develop in ectopic locations, such as the dentate hilus. The generation of hilar ectopic granule cells (HEGCs) is greatly increased in several animal models of epilepsy and has also been demonstrated in surgical specimens from patients with intractable temporal lobe epilepsy (TLE). Herein we review the results of our quantitative neuroanatomic analysis of HEGCs that were filled with Neurobiotin following electrophysiologic characterization in hippocampal slices. The data suggest that two types of HEGCs exist, based on a proximal or distal location of the cell body relative to the granule cell layer, and based on the location of most of the dendrites, in the molecular layer or hilus. Three-dimensional reconstruction revealed that the dendrites of distal HEGCs can extend along the transverse and longitudinal axis of the hippocampus. Analysis of axons demonstrated that HEGCs have projections that contribute to the normal mossy fiber innervation of CA3 as well as the abnormal sprouted fibers in the inner molecular layer of epileptic rodents (mossy fiber sprouting). These data support the idea that HEGCs could function as a “hub” cell in the dentate gyrus and play a critical role in network excitability. PMID:22612815

  12. The potential of pollen-based quantitative vegetation reconstructions in studies of past human settlements and use of resources - examples from Europe

    NASA Astrophysics Data System (ADS)

    Gaillard, Marie-Jose; Cui, Qiao-Yu; Lemdahl, Geoffrey; Trondman, Anna-Kari

    2015-04-01

    approach - the Landscape Reconstruction Algorithm (LRA) (3, 4) - makes it possible to estimate the cover of plant taxa or landscape units at both regional and local spatial scales using pollen records. The LRA has been tested and applied in various types of studies in Europe in particular. Examples from Europe and Scandinavia show that pollen-based quantitative reconstructions of vegetation cover, in combination with other palaeoecological records such as insect and plant macroremains, show the great potential of such studies to provide new insights on the use of landscapes and vegetation by humans in the past and its environmental consequences at both regional and local spatial scales (5, 6). These results provide a new environmental framework for the discussion and testing of hypotheses based on archaeological data. (1) Berglund, B.E. (1991) Ecological Bulletins 41: 1-495. (2) Gaillard, M.-J. et al. (1994) Review of Palaeobotany and Palynology 82: 47-73. (3) Sugita, S. (2007a) The Holocene 17: 243-257. (4) Sugita, S. (2007b) The Holocene 17: 229-241. (5) Cui, Q.-Y. et al. (2014) Ecology and Evolution, doi: 10.1002/ece3.1198 (6) Trondman, A.-K. (2014) Global Change Biology, doi: 10.1111/gcb.12737

  13. Modelling insights on the partition of evapotranspiration components across biomes

    NASA Astrophysics Data System (ADS)

    Fatichi, Simone; Pappas, Christoforos

    2017-04-01

    Recent studies using various methodologies have found a large variability (from 35 to 90%) in the ratio of transpiration to total evapotranspiration (denoted as T:ET) across biomes or even at the global scale. Concurrently, previous results suggest that T:ET is independent of mean precipitation and has a positive correlation with Leaf Area Index (LAI). We used the mechanistic ecohydrological model, T&C, with a refined process-based description of soil resistance and a detailed treatment of canopy biophysics and ecophysiology, to investigate T:ET across multiple biomes. Contrary to observation-based estimates, simulation results highlight a well-constrained range of mean T:ET across biomes that is also robust to perturbations of the most sensitive parameters. Simulated T:ET was confirmed to be independent of average precipitation, while it was found to be uncorrelated with LAI across biomes. Higher values of LAI increase evaporation from interception but suppress ground evaporation with the two effects largely cancelling each other in many sites. These results offer mechanistic, model-based, evidence to the ongoing research about the range of T:ET and the factors affecting its magnitude across biomes.

  14. Phylogeny and cryptic diversity in geckos (Phyllopezus; Phyllodactylidae; Gekkota) from South America's open biomes.

    PubMed

    Gamble, Tony; Colli, Guarino R; Rodrigues, Miguel T; Werneck, Fernanda P; Simons, Andrew M

    2012-03-01

    The gecko genus Phyllopezus occurs across South America's open biomes: Cerrado, Seasonally Dry Tropical Forests (SDTF, including Caatinga), and Chaco. We generated a multi-gene dataset and estimated phylogenetic relationships among described Phyllopezus taxa and related species. We included exemplars from both described Phyllopezus pollicaris subspecies, P. p. pollicaris and P. p.przewalskii. Phylogenies from the concatenated data as well as species trees constructed from individual gene trees were largely congruent. All phylogeny reconstruction methods showed Bogertia lutzae as the sister species of Phyllopezus maranjonensis, rendering Phyllopezus paraphyletic. We synonymized the monotypic genus Bogertia with Phyllopezus to maintain a taxonomy that is isomorphic with phylogenetic history. We recovered multiple, deeply divergent, cryptic lineages within P. pollicaris. These cryptic lineages possessed mtDNA distances equivalent to distances among other gekkotan sister taxa. Described P. pollicaris subspecies are not reciprocally monophyletic and current subspecific taxonomy does not accurately reflect evolutionary relationships among cryptic lineages. We highlight the conservation significance of these results in light of the ongoing habitat loss in South America's open biomes. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. Discovery of a novel alkenone-producing haptophyte in freshwater and oligosaline lakes marks a new era for quantitative paleotemperature reconstruction

    NASA Astrophysics Data System (ADS)

    Huang, Y.; Longo, W. M.; Dillon, J. T.; D'Andrea, W. J.; Theroux, S.; Zheng, Y.; Richter, N.; Amaral-Zettler, L. A.

    2016-12-01

    spatial survey of the global distribution of lakes that contain the Group I haptophyte. The discovery of lakes that harbor Group I haptophytes in the EuroAsian continent, North America, and Cirum-North Atlantic islands paves the way for new quantitative paleotemperature reconstructions from lakes around the world.

  16. Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers.

    PubMed

    Saito, Mak A; McIlvin, Matthew R; Moran, Dawn M; Goepfert, Tyler J; DiTullio, Giacomo R; Post, Anton F; Lamborg, Carl H

    2014-09-05

    Marine primary productivity is strongly influenced by the scarcity of required nutrients, yet our understanding of these nutrient limitations is informed by experimental observations with sparse geographical coverage and methodological limitations. We developed a quantitative proteomic method to directly assess nutrient stress in high-light ecotypes of the abundant cyanobacterium Prochlorococcus across a meridional transect in the central Pacific Ocean. Multiple peptide biomarkers detected widespread and overlapping regions of nutritional stress for nitrogen and phosphorus in the North Pacific Subtropical Gyre and iron in the equatorial Pacific. Quantitative protein analyses demonstrated simultaneous stress for these nutrients at biome interfaces. This application of proteomic biomarkers to diagnose ocean metabolism demonstrated Prochlorococcus actively and simultaneously deploying multiple biochemical strategies for low-nutrient conditions in the oceans.

  17. Tropical grassy biomes: misunderstood, neglected, and under threat.

    PubMed

    Parr, Catherine L; Lehmann, Caroline E R; Bond, William J; Hoffmann, William A; Andersen, Alan N

    2014-04-01

    Tropical grassy biomes (TGBs) are globally extensive, provide critical ecosystem services, and influence the earth-atmosphere system. Yet, globally applied biome definitions ignore vegetation characteristics that are critical to their functioning and evolutionary history. Hence, TGB identification is inconsistent and misinterprets the ecological processes governing vegetation structure, with cascading negative consequences for biodiversity. Here, we discuss threats linked to the definition of TGB, the Clean Development Mechanism (CDM) and Reducing Emissions from Deforestation and Forest Degradation schemes (REDD+), and enhanced atmospheric CO2, which may facilitate future state shifts. TGB degradation is insidious and less visible than in forested biomes. With human reliance on TGBs and their propensity for woody change, ecology and evolutionary history are fundamental to not only the identification of TGBs, but also their management for future persistence. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. [Parameter sensitivity of simulating net primary productivity of Larix olgensis forest based on BIOME-BGC model].

    PubMed

    He, Li-hong; Wang, Hai-yan; Lei, Xiang-dong

    2016-02-01

    Model based on vegetation ecophysiological process contains many parameters, and reasonable parameter values will greatly improve simulation ability. Sensitivity analysis, as an important method to screen out the sensitive parameters, can comprehensively analyze how model parameters affect the simulation results. In this paper, we conducted parameter sensitivity analysis of BIOME-BGC model with a case study of simulating net primary productivity (NPP) of Larix olgensis forest in Wangqing, Jilin Province. First, with the contrastive analysis between field measurement data and the simulation results, we tested the BIOME-BGC model' s capability of simulating the NPP of L. olgensis forest. Then, Morris and EFAST sensitivity methods were used to screen the sensitive parameters that had strong influence on NPP. On this basis, we also quantitatively estimated the sensitivity of the screened parameters, and calculated the global, the first-order and the second-order sensitivity indices. The results showed that the BIOME-BGC model could well simulate the NPP of L. olgensis forest in the sample plot. The Morris sensitivity method provided a reliable parameter sensitivity analysis result under the condition of a relatively small sample size. The EFAST sensitivity method could quantitatively measure the impact of simulation result of a single parameter as well as the interaction between the parameters in BIOME-BGC model. The influential sensitive parameters for L. olgensis forest NPP were new stem carbon to new leaf carbon allocation and leaf carbon to nitrogen ratio, the effect of their interaction was significantly greater than the other parameter' teraction effect.

  19. Anthropogenic biomes: a key contribution to earth-system science

    Treesearch

    Lilian Alessa; F. Stuart Chapin

    2008-01-01

    Human activities now dominate most of the ice-free terrestrial surface. A recent article presents a classification and global map of human-influenced biomes of the world that provides a novel and potentially appropriate framework for projecting changes in earth-system dynamics.

  20. Convergence across biomes to a common rain-use efficiency.

    PubMed

    Huxman, Travis E; Smith, Melinda D; Fay, Philip A; Knapp, Alan K; Shaw, M Rebecca; Loik, Michael E; Smith, Stanley D; Tissue, David T; Zak, John C; Weltzin, Jake F; Pockman, William T; Sala, Osvaldo E; Haddad, Brent M; Harte, John; Koch, George W; Schwinning, Susan; Small, Eric E; Williams, David G

    2004-06-10

    Water availability limits plant growth and production in almost all terrestrial ecosystems. However, biomes differ substantially in sensitivity of aboveground net primary production (ANPP) to between-year variation in precipitation. Average rain-use efficiency (RUE; ANPP/precipitation) also varies between biomes, supposedly because of differences in vegetation structure and/or biogeochemical constraints. Here we show that RUE decreases across biomes as mean annual precipitation increases. However, during the driest years at each site, there is convergence to a common maximum RUE (RUE(max)) that is typical of arid ecosystems. RUE(max) was also identified by experimentally altering the degree of limitation by water and other resources. Thus, in years when water is most limiting, deserts, grasslands and forests all exhibit the same rate of biomass production per unit rainfall, despite differences in physiognomy and site-level RUE. Global climate models predict increased between-year variability in precipitation, more frequent extreme drought events, and changes in temperature. Forecasts of future ecosystem behaviour should take into account this convergent feature of terrestrial biomes.

  1. Anthropogenic biomes: a key contribution to earth-system science.

    PubMed

    Alessa, Lilian; Chapin, F Stuart

    2008-10-01

    Human activities now dominate most of the ice-free terrestrial surface. A recent article presents a classification and global map of human-influenced biomes of the world that provides a novel and potentially appropriate framework for projecting changes in earth-system dynamics.

  2. Climate control of terrestrial carbon exchange across biomes and continents

    Treesearch

    Chuixiang Yi; Daniel Ricciuto; Runze Li; John Wolbeck; Xiyan Xu; Mats Nilsson; John Frank; William J. Massman

    2010-01-01

    Understanding the relationships between climate and carbon exchange by terrestrial ecosystems is critical to predict future levels of atmospheric carbon dioxide because of the potential accelerating effects of positive climate-carbon cycle feedbacks. However, directly observed relationships between climate and terrestrial CO2 exchange with the atmosphere across biomes...

  3. User's Guide to Biome Information from the United States International Biological Program (IBP). First Edition.

    ERIC Educational Resources Information Center

    Hinckley, A. Dexter; Haug, Peter T.

    This publication is a guide to the biome research conducted under the International Biological Program. The guide lists biome researchers by interest and by biome as well as a central list. A site list, map, information sources section reporting abstracts, bibliographies, journals, books, evaluations, and data books are also included. Three…

  4. The effect of heterogeneous landscape dynamics on ecotone types at two convergent semi-arid biomes

    USDA-ARS?s Scientific Manuscript database

    Landscapes in biome transition zones consist of a mosaic of patches dominated or codominated by species from adjacent biomes. Shifts in the vegetation composition and dynamics of a biome transition zone depend upon the underlying patch dynamics of the ecotones between these dominant species. Landsca...

  5. User's Guide to Biome Information from the United States International Biological Program (IBP). First Edition.

    ERIC Educational Resources Information Center

    Hinckley, A. Dexter; Haug, Peter T.

    This publication is a guide to the biome research conducted under the International Biological Program. The guide lists biome researchers by interest and by biome as well as a central list. A site list, map, information sources section reporting abstracts, bibliographies, journals, books, evaluations, and data books are also included. Three…

  6. Importance of ecotone type to landscape dynamics at biome transition zones

    USDA-ARS?s Scientific Manuscript database

    Landscapes in biome transition zones consist of a mosaic of patches dominated or codominated by species from adjacent biomes. Shifts in the vegetation composition and dynamics of a biome transition zone depend upon the underlying patch dynamics of the ecotones between these dominant species. Landsc...

  7. Vegetation and Climate in the Pyrenean Mountains (southern France) during the Last 15000 Years Bp: a Pollen-Inferred Quantitative Reconstruction

    NASA Astrophysics Data System (ADS)

    Peyron, O.; Galop, D.

    2008-12-01

    Climatic linkages between the North Atlantic and west Europe areas have been investigated for the last 15,000 yrs from four high-temporal pollen records located in the western Pyrenees Mountains. Mountain areas are of particular interest because the vegetation is very sensitive to variations in climate and human impact, and also because the vegetation responses to climatic changes are more pronounced at higher altitudes than in the lowlands, and are well recorded in pollen sequences. In the Alps Mountains, the lateglacial and Holocene climate variations are now well known from numerous multi-proxies approaches. However no climate estimates are available in the Pyrenean Mountains (southern France). This study aim to test the sensitivity of the Pyrenean Mountains area to even short term and relatively weak climatic fluctuations recognised in the North Atlantic region. Here, we reconstruct the vegetation and the climate changes along an latitudinal/altitudinal gradient in the western part of the Pyrenees for the last 15,000 yrs BP from 4 high-resolution pollen records located from the oceanic shore to the central Pyrenees with a chronology established on 40 radiocarbon dates : from west to east, the Mouriscot lake record located near the ocean coast at 50m asl (43.45 N/1.55W), the Occabe record in Basque mountains located in the Iraty massif at 1300m (43.03N/1.10W); the Piet record at 1150m in the Ossau valley (42.88N/0.42W) and the Ech record located at lower altitude (600m) in the Lourdes basin (43.7N/0.08W) in the central part of the chain. From the 4 cores, the modern analogues technique has been used to obtain robust and precise quantitative estimates of the annual temperature, the mean temperature of the warmest/coldest month, total annual precipitation, and the ratio of real to potential evapotranspiration. Pollen-inferred climate estimates show that cold and dry conditions prevailed during the Oldest and Younger Dryas while temperate conditions are evidenced

  8. The isotope record of short- and long-term dietary changes in sheep tooth enamel: Implications for quantitative reconstruction of paleodiets

    NASA Astrophysics Data System (ADS)

    Zazzo, A.; Balasse, M.; Passey, B. H.; Moloney, A. P.; Monahan, F. J.; Schmidt, O.

    2010-06-01

    Quantitative reconstruction of paleodiet by means of sequential sampling and carbon isotope analysis in hypsodont tooth enamel requires a precise knowledge of the isotopic enrichment between dietary carbon and carbon from enamel apatite ( ɛD-E), as well as of the timing and duration of the enamel mineralization process (amelogenesis). To better constrain these parameters, we performed a series of controlled feeding experiments on sheep ranging in age from 6 to 24 months-old. Twenty-eight lambs and 14 ewes were fed isotopically distinct diets for different periods of time, and then slaughtered, allowing the timing and rate of molar growth to be determined. High resolution sampling and stable carbon isotope analysis of breath CO 2 performed on six individuals following a diet-switch showed that 70-90% of dietary carbon had turned over in less than 24 h. Sequential sampling and carbon isotopic analysis was performed on the first (M 1) and second (M 2) lower molars of four lambs as well as on the third lower molar (M 3) of 11 ewes. The changes in diet were recorded in all molars. We found that the length of enamel matrix apposition is approximately one-quarter of the final tooth length during crown extension, and that enamel maturation spans slightly less than 3 months in M 1, and 4 months in M 2 and M 3. Portions of enamel in equilibrium with dietary carbon were used to calculate ɛD-E values. Animals on grass silage diets had values similar to previous observations, whereas animal switched to pelleted corn diets had values ca. 4‰ lower, a pattern consistent with lower methane production observed for animals fed concentrate diets. The tooth enamel forward model of Passey and Cerling (2002) closely predicted the amplitude of isotope changes recorded in tooth enamel, but slightly underestimated the rate of isotope change, suggesting that the rate of accumulation of carbonate during maturation may not be constant over time. Although stable isotope profiles in tooth

  9. Aeolian particles in marine cores as a tool for quantitative high-resolution reconstruction of upwelling favorable winds along coastal Atacama Desert, Northern Chile

    NASA Astrophysics Data System (ADS)

    Flores-Aqueveque, Valentina; Alfaro, Stéphane; Vargas, Gabriel; Rutllant, José A.; Caquineau, Sandrine

    2015-05-01

    Upwelling areas play a major role in ocean biogeochemical cycles and ultimately in global climate, especially in higly productive regions as the South Eastern Pacific. This work is based on the analysis of the aeolian lithic particles accumulated in laminated sediments off Mejillones (23°S) in the eastern boundary Humboldt Current System. It proposes a high-resolution quantitative reconstruction of the upwelling-favorable southerly wind strength in the past ∼250 years, comparing its variability with changes in organic carbon export/preserved changes to the sea bottom. The increase of the intensity and variability in fluxes of particles larger than 35 μm and 100 μm since the second half of the 19th century and during the 20th century confirms a general strengthening of southerly winds in the region. Spectral analysis on the complete time-series of yearly depositional fluxes indicates that sedimentary variability can be explained by a combination of interannual (ENSO) to decadal (PDO) oscillations similar to the ones yielded by the analysis of the Interdecadal Pacific Oscillation index. However, when applied separately to the lithic fluxes of the first and last centuries of the time-series, the method shows that relative to the one of the interannual mode of variability, the influence of the decadal mode has increased in the recent period. Based on the presence/absence of particles with sizes larger than 35/100 μm, each year of the time series is classified as a 'Low wind' (<6 m/s), 'Intermediate wind' (6-8 m/s), or 'Strong wind' (10 to >12 m/s) year. From the AD 1754-1820 period to the AD 1878-1998 one, the proportion of Low and Intermediate wind years decreased from 12% and 74% to 3% and 68%, respectively, whereas the proportion of strong wind years increased from 14% to 29%. For these periods the mean organic carbon also increased 22%, stating the strong relation between export/preservation productivity rate and southerly wind intensity. In the recent period

  10. Tree mortality across biomes is promoted by drought intensity, lower wood density and higher specific leaf area.

    PubMed

    Greenwood, Sarah; Ruiz-Benito, Paloma; Martínez-Vilalta, Jordi; Lloret, Francisco; Kitzberger, Thomas; Allen, Craig D; Fensham, Rod; Laughlin, Daniel C; Kattge, Jens; Bönisch, Gerhard; Kraft, Nathan J B; Jump, Alistair S

    2017-04-01

    Drought events are increasing globally, and reports of consequent forest mortality are widespread. However, due to a lack of a quantitative global synthesis, it is still not clear whether drought-induced mortality rates differ among global biomes and whether functional traits influence the risk of drought-induced mortality. To address these uncertainties, we performed a global meta-analysis of 58 studies of drought-induced forest mortality. Mortality rates were modelled as a function of drought, temperature, biomes, phylogenetic and functional groups and functional traits. We identified a consistent global-scale response, where mortality increased with drought severity [log mortality (trees trees(-1)  year(-1) ) increased 0.46 (95% CI = 0.2-0.7) with one SPEI unit drought intensity]. We found no significant differences in the magnitude of the response depending on forest biomes or between angiosperms and gymnosperms or evergreen and deciduous tree species. Functional traits explained some of the variation in drought responses between species (i.e. increased from 30 to 37% when wood density and specific leaf area were included). Tree species with denser wood and lower specific leaf area showed lower mortality responses. Our results illustrate the value of functional traits for understanding patterns of drought-induced tree mortality and suggest that mortality could become increasingly widespread in the future. © 2017 John Wiley & Sons Ltd/CNRS.

  11. Quantitative photoacoustic tomography

    PubMed Central

    Yuan, Zhen; Jiang, Huabei

    2009-01-01

    In this paper, several algorithms that allow for quantitative photoacoustic reconstruction of tissue optical, acoustic and physiological properties are described in a finite-element method based framework. These quantitative reconstruction algorithms are compared, and the merits and limitations associated with these methods are discussed. In addition, a multispectral approach is presented for concurrent reconstructions of multiple parameters including deoxyhaemoglobin, oxyhaemoglobin and water concentrations as well as acoustic speed. Simulation and in vivo experiments are used to demonstrate the effectiveness of the reconstruction algorithms presented. PMID:19581254

  12. BIOME: A browser-aware search and order system

    NASA Technical Reports Server (NTRS)

    Grubb, Jon W.; Jennings, Sarah V.; Yow, Teresa G.; Daughterty, Patricia F.

    1996-01-01

    The Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC), which is associated with NASA's Earth Observing System Data and Information System (EOSDIS), provides access to a large number of tabular and imagery datasets used in ecological and environmental research. Because of its large and diverse data holdings, the challenge for the ORNL DAAC is to help users find data of interest from the hundreds of thousands of files available at the DAAC without overwhelming them. Therefore, the ORNL DAAC developed the Biogeochemical Information Ordering Management Environment (BIOME), a search and order system for the World Wide Web (WWW). The WWW provides a new vehicle that allows a wide range of users access to the data. This paper describes the specialized attributes incorporated into BIOME that allow researchers easy access to an otherwise bewildering array of data products.

  13. BIOME: A browser-aware search and order system

    SciTech Connect

    Grubb, J.W.; Jennings, S.V.; Yow, T.G.; Daugherty, P.F.

    1996-05-01

    The Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC), which is associated with NASA`s Earth Observing System Data and Information System (EOSDIS), provides access to a large number of tabular and imagery datasets used in ecological and environmental research. Because of its large and diverse data holdings, the challenge for the ORNL DAAC is to help users find data of interest from the hundreds of thousands of files available at the DAAC without overwhelming them. Therefore, the ORNL DAAC developed the Biogeochemical Information Ordering Management Environment (BIOME), a search and order system for the World Wide Web (WWW). The WWW provides a new vehicle that allows a wide range of users access to the data. This paper describes the specialized attributes incorporated into BIOME that allow researchers easy access to an otherwise bewildering array of data products.

  14. BIOME: A browser-aware search and order system

    NASA Technical Reports Server (NTRS)

    Grubb, Jon W.; Jennings, Sarah V.; Yow, Teresa G.; Daughterty, Patricia F.

    1996-01-01

    The Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC), which is associated with NASA's Earth Observing System Data and Information System (EOSDIS), provides access to a large number of tabular and imagery datasets used in ecological and environmental research. Because of its large and diverse data holdings, the challenge for the ORNL DAAC is to help users find data of interest from the hundreds of thousands of files available at the DAAC without overwhelming them. Therefore, the ORNL DAAC developed the Biogeochemical Information Ordering Management Environment (BIOME), a search and order system for the World Wide Web (WWW). The WWW provides a new vehicle that allows a wide range of users access to the data. This paper describes the specialized attributes incorporated into BIOME that allow researchers easy access to an otherwise bewildering array of data products.

  15. A dated phylogeny and collection records reveal repeated biome shifts in the African genus Coccinia (Cucurbitaceae).

    PubMed

    Holstein, Norbert; Renner, Susanne S

    2011-01-26

    Conservatism in climatic tolerance may limit geographic range expansion and should enhance the effects of habitat fragmentation on population subdivision. Here we study the effects of historical climate change, and the associated habitat fragmentation, on diversification in the mostly sub-Saharan cucurbit genus Coccinia, which has 27 species in a broad range of biota from semi-arid habitats to mist forests. Species limits were inferred from morphology, and nuclear and plastid DNA sequence data, using multiple individuals for the widespread species. Climatic tolerances were assessed from the occurrences of 1189 geo-referenced collections and WorldClim variables. Nuclear and plastid gene trees included 35 or 65 accessions, representing up to 25 species. The data revealed four species groups, one in southern Africa, one in Central and West African rain forest, one widespread but absent from Central and West African rain forest, and one that occurs from East Africa to southern Africa. A few individuals are differently placed in the plastid and nuclear (LFY) trees or contain two ITS sequence types, indicating hybridization. A molecular clock suggests that the diversification of Coccinia began about 6.9 Ma ago, with most of the extant species diversity dating to the Pliocene. Ancestral biome reconstruction reveals six switches between semi-arid habitats, woodland, and forest, and members of several species pairs differ significantly in their tolerance of different precipitation regimes. The most surprising findings of this study are the frequent biome shifts (in a relatively small clade) over just 6 - 7 million years and the limited diversification during and since the Pleistocene. Pleistocene climate oscillations may have been too rapid or too shallow for full reproductive barriers to develop among fragmented populations of Coccinia, which would explain the apparently still ongoing hybridization between certain species. Steeper ecological gradients in East Africa and

  16. A dated phylogeny and collection records reveal repeated biome shifts in the African genus Coccinia (Cucurbitaceae)

    PubMed Central

    2011-01-01

    Background Conservatism in climatic tolerance may limit geographic range expansion and should enhance the effects of habitat fragmentation on population subdivision. Here we study the effects of historical climate change, and the associated habitat fragmentation, on diversification in the mostly sub-Saharan cucurbit genus Coccinia, which has 27 species in a broad range of biota from semi-arid habitats to mist forests. Species limits were inferred from morphology, and nuclear and plastid DNA sequence data, using multiple individuals for the widespread species. Climatic tolerances were assessed from the occurrences of 1189 geo-referenced collections and WorldClim variables. Results Nuclear and plastid gene trees included 35 or 65 accessions, representing up to 25 species. The data revealed four species groups, one in southern Africa, one in Central and West African rain forest, one widespread but absent from Central and West African rain forest, and one that occurs from East Africa to southern Africa. A few individuals are differently placed in the plastid and nuclear (LFY) trees or contain two ITS sequence types, indicating hybridization. A molecular clock suggests that the diversification of Coccinia began about 6.9 Ma ago, with most of the extant species diversity dating to the Pliocene. Ancestral biome reconstruction reveals six switches between semi-arid habitats, woodland, and forest, and members of several species pairs differ significantly in their tolerance of different precipitation regimes. Conclusions The most surprising findings of this study are the frequent biome shifts (in a relatively small clade) over just 6 - 7 million years and the limited diversification during and since the Pleistocene. Pleistocene climate oscillations may have been too rapid or too shallow for full reproductive barriers to develop among fragmented populations of Coccinia, which would explain the apparently still ongoing hybridization between certain species. Steeper ecological

  17. Quantitative reconstructions of mid- to late holocene climate and vegetation in the north-eastern altai mountains recorded in lake teletskoye

    NASA Astrophysics Data System (ADS)

    Rudaya, Natalia; Nazarova, Larisa; Novenko, Elena; Andreev, Andrei; Kalugin, Ivan; Daryin, Andrei; Babich, Valery; Li, Hong-Chun; Shilov, Pavel

    2016-06-01

    We report the first high-resolution (20-50 years) mid- to late Holocene pollen records from Lake Teletskoye, the largest lake in the Altai Mountains, in south-eastern West Siberia. Generally, the mid- to late Holocene (the last 4250 years) vegetation of the north-eastern Altai, as recorded in two studied sediment cores, is characterised by Siberian pine-spruce-fir forests that are similar to those of the present day. A relatively cool and dry interval with July temperatures lower than those of today occurred between 3.9 and 3.6 ka BP. The widespread distribution of open, steppe-like communities with Artemisia, Chenopodiaceae and Cyperaceae reflects maximum deforestation during this interval. After ca. 3.5 ka BP, the coniferous mountain taiga spread significantly, with maximum woody coverage and taiga biome scores between ca. 2.7 and 1.6 ka BP. This coincides well with the highest July temperature (approximately 1 °C higher than today) intervals. A short period of cooling about 1.3-1.4 ka BP could have been triggered by the increased volcanic activity recorded across the Northern Hemisphere. A new period of cooling started around 1100-1150 CE, with the minimum July temperatures occurring between 1450 and 1800 CE.

  18. Parameterisation of Biome BGC to assess forest ecosystems in Africa

    NASA Astrophysics Data System (ADS)

    Gautam, Sishir; Pietsch, Stephan A.

    2010-05-01

    African forest ecosystems are an important environmental and economic resource. Several studies show that tropical forests are critical to society as economic, environmental and societal resources. Tropical forests are carbon dense and thus play a key role in climate change mitigation. Unfortunately, the response of tropical forests to environmental change is largely unknown owing to insufficient spatially extensive observations. Developing regions like Africa where records of forest management for long periods are unavailable the process-based ecosystem simulation model - BIOME BGC could be a suitable tool to explain forest ecosystem dynamics. This ecosystem simulation model uses descriptive input parameters to establish the physiology, biochemistry, structure, and allocation patterns within vegetation functional types, or biomes. Undocumented parameters for larger-resolution simulations are currently the major limitations to regional modelling in African forest ecosystems. This study was conducted to document input parameters for BIOME-BGC for major natural tropical forests in the Congo basin. Based on available literature and field measurements updated values for turnover and mortality, allometry, carbon to nitrogen ratios, allocation of plant material to labile, cellulose, and lignin pools, tree morphology and other relevant factors were assigned. Daily climate input data for the model applications were generated using the statistical weather generator MarkSim. The forest was inventoried at various sites and soil samples of corresponding stands across Gabon were collected. Carbon and nitrogen in the collected soil samples were determined from soil analysis. The observed tree volume, soil carbon and soil nitrogen were then compared with the simulated model outputs to evaluate the model performance. Furthermore, the simulation using Congo Basin specific parameters and generalised BIOME BGC parameters for tropical evergreen broadleaved tree species were also

  19. Extreme precipitation patterns reduced terrestrial ecosystem production across biomes

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Moran, S. M.; Nearing, M.; Ponce Campos, G. E.; Huete, A. R.; Buda, A. R.; Bosch, D. D.; Gunter, S. A.; Kitchen, S. G.; McNab, W.; Morgan, J. A.; McClaran, M. P.; Montoya, D. S.; Peters, D. P.; Starks, P. J.

    2012-12-01

    Precipitation regimes are predicted to shift to more extreme patterns that are characterized by more intense rainfall events and longer dry intervals, yet their ecological impacts on vegetation production remain uncertain across biomes in natural climatic conditions. This in situ study investigated the effects of novel climatic conditions on aboveground net primary production (ANPP) by combining a greenness index from satellite measurements and climatic records during 2000 to 2009 from 11 long-term experimental sites in multiple biomes and climates. Results showed that extreme precipitation patterns decreased the sensitivity of ANPP to total annual precipitation (PT), at the regional and decadal scales, leading to a mean 20% decrease in rain-use efficiency across biomes. Relative decreases in ANPP were greatest for arid grassland (16%) and Mediterranean forest (20%), and less for mesic grassland and temperate forest (3%). The co-occurrence of more heavy rainfall events and longer dry intervals caused greater water stress that resulted in reduced vegetation production. A new generalized model was developed to improve predictions of the ANPP response to changes in extreme precipitation patterns by using a function of both PT and an index of precipitation extremes. These findings suggest that extreme precipitation patterns have more substantial and complex effects on vegetation production across biomes, and are as important as total annual precipitation in understanding vegetation processes. With predictions of more extreme weather events, forecasts of ecosystem production should consider these non-linear responses to altered precipitation patterns associated with climate change. Figure. Relation of production across precipitation gradients for 11 sites for two groups (Low: R95p% < 20%, High: R95p% ≥ 20%). See Table 2 for R95p% definitions. The relations were significantly different for the two groups (F2, 106 = 18.51, P < 0.0001).

  20. Evaluation of the resolving potency of a novel reconstruction filter on periodontal ligament space with dental cone-beam CT: a quantitative phantom study

    NASA Astrophysics Data System (ADS)

    Houno, Yuuki; Hishikawa, Toshimitsu; Gotoh, Ken-ichi; Naitoh, Munetaka; Ariji, Eiichiro; Kodera, Yoshie

    2014-03-01

    Diagnosis of the alveolar bone condition is important for the treatment planning of periodontal disease. Especially the determination of periodontal ligament space is the most important remark because it represents the periodontal tissue support for tooth retention. However, owing to the image blur of the current cone-beam CT (CBCT) imaging technique, the periodontal ligament space is difficult to visualize. In this study, we developed an original periodontal ligament phantom (PLP) and evaluated the image quality of simulated periodontal ligament space using a novel reconstruction filter for CBCT that emphasized high frequency component. PLP was composed from two resin blocks of different materials, the bone equivalent block and the dentine equivalent block. They were assembled to make continuously changing space from 0.0 to 1.0 millimeter that mimics periodontal ligament space. PLP was placed in water and the image was obtained by using Alphard-3030 dental cone-beam CT (Asahi Roentgen Industry Co., Ltd.). Then we reconstructed the projection data with a novel reconstruction filter. The axial images were compared with conventional reconstructed images. In novel filter reconstruction images, 0.4 millimeter of the space width was steadily detected by calculation of pixel value, on the other hand 0.6 millimeter was in conventional images. With our method, the resolving potency of conebeam CT images was improved.

  1. Deforestation changes land-atmosphere interactions across South American biomes

    NASA Astrophysics Data System (ADS)

    Salazar, Alvaro; Katzfey, Jack; Thatcher, Marcus; Syktus, Jozef; Wong, Kenneth; McAlpine, Clive

    2016-04-01

    South American biomes are increasingly affected by land use/land cover change. However, the climatic impacts of this phenomenon are still not well understood. In this paper, we model vegetation-climate interactions with a focus on four main biomes distributed in four key regions: The Atlantic Forest, the Cerrado, the Dry Chaco, and the Chilean Matorral ecosystems. We applied a three member ensemble climate model simulation for the period 1981-2010 (30 years) at 25 km resolution over the focus regions to quantify the changes in the regional climate resulting from historical deforestation. The results of computed modelling experiments show significant changes in surface fluxes, temperature and moisture in all regions. For instance, simulated temperature changes were stronger in the Cerrado and the Chilean Matorral with an increase of between 0.7 and 1.4 °C. Changes in the hydrological cycle revealed high regional variability. The results showed consistent significant decreases in relative humidity and soil moisture, and increases in potential evapotranspiration across biomes, yet without conclusive changes in precipitation. These impacts were more significant during the dry season, which resulted to be drier and warmer after deforestation.

  2. Constrained variability of modeled T:ET ratio across biomes

    NASA Astrophysics Data System (ADS)

    Fatichi, Simone; Pappas, Christoforos

    2017-07-01

    A large variability (35-90%) in the ratio of transpiration to total evapotranspiration (referred here as T:ET) across biomes or even at the global scale has been documented by a number of studies carried out with different methodologies. Previous empirical results also suggest that T:ET does not covary with mean precipitation and has a positive dependence on leaf area index (LAI). Here we use a mechanistic ecohydrological model, with a refined process-based description of evaporation from the soil surface, to investigate the variability of T:ET across biomes. Numerical results reveal a more constrained range and higher mean of T:ET (70 ± 9%, mean ± standard deviation) when compared to observation-based estimates. T:ET is confirmed to be independent from mean precipitation, while it is found to be correlated with LAI seasonally but uncorrelated across multiple sites. Larger LAI increases evaporation from interception but diminishes ground evaporation with the two effects largely compensating each other. These results offer mechanistic model-based evidence to the ongoing research about the patterns of T:ET and the factors influencing its magnitude across biomes.

  3. FIFE data analysis: Testing BIOME-BGC predictions for grasslands

    NASA Technical Reports Server (NTRS)

    Hunt, E. Raymond, Jr.

    1994-01-01

    The First International Satellite Land Surface Climatology Project (ISLSCP) Field Experiment (FIFE) was conducted in a 15 km by 15 km research area located 8 km south of Manhattan, Kansas. The site consists primarily of native tallgrass prairie mixed with gallery oak forests and croplands. The objectives of FIFE are to better understand the role of biology in controlling the interactions between the land and the atmosphere, and to determine the value of remotely sensed data for estimating climatological parameters. The goals of FIFE are twofold: the upscale integration of models, and algorithm development for satellite remote sensing. The specific objectives of the field campaigns carried out in 1987 and 1989 were the simultaneous acquisition of satellite, atmospheric, and surface data; and the understanding of the processes controlling surface energy and mass exchange. Collected data were used to study the dynamics of various ecosystem processes (photosynthesis, evaporation and transpiration, autotrophic and heterotrophic respiration, etc.). Modelling terrestrial ecosystems at scales larger than that of a homogeneous plot led to the development of simple, generalized models of biogeochemical cycles that can be accurately applied to different biomes through the use of remotely sensed data. A model was developed called BIOME-BGC (for BioGeochemical Cycles) from a coniferous forest ecosystem model, FOREST-BGC, where a biome is considered a combination of a life forms in a specified climate. A predominately C4-photosynthetic grassland is probably the most different from a coniferous forest possible, hence the FIFE site was an excellent study area for testing BIOME-BGC. The transition from an essentially one-dimensional calculation to three-dimensional, landscape scale simulations requires the introduction of such factors as meteorology, climatology, and geomorphology. By using remotely sensed geographic information data for important model inputs, process

  4. Quantitative evaluation of anterior tibial translation during isokinetic motion in knees with anterior cruciate ligament reconstruction using either patellar or hamstring tendon grafts

    PubMed Central

    Sato, N.; Terauchi, M.; Kimura, M.; Takagishi, K.

    2005-01-01

    We studied 79 patients with unilateral injury to the anterior cruciate ligament (ACL). The patients were randomly allocated to reconstruction with autologous patellar bone-tendon-bone (BTB) grafts (49 knees) or hamstring tendon (ST) grafts (30 knees). We measured anterior tibial translation (ATT) during isokinetic concentric contraction exercise 18–20 months after surgery using a computerized electrogoniometer. In both groups the highest ATT during exercise was observed at a knee flexion of about 20° and was 13.5±3.0 mm in the BTB group and 13.9±3.4 mm in the ST group. There was no difference in the ATT between the reconstructed and healthy knees. For a range of knee flexion between 30 and 50° the ATT in the ST group was significantly higher on the reconstructed side than on the healthy side. In the BTB group, the mean ATT in the reconstructed group was similar to that on the healthy side at a knee flexion angle between 0 and 90°. PMID:16075231

  5. General patterns of acclimation of leaf respiration to elevated temperatures across biomes and plant types.

    PubMed

    Slot, Martijn; Kitajima, Kaoru

    2015-03-01

    Respiration is instrumental for survival and growth of plants, but increasing costs of maintenance processes with warming have the potential to change the balance between photosynthetic carbon uptake and respiratory carbon release from leaves. Climate warming may cause substantial increases of leaf respiratory carbon fluxes, which would further impact the carbon balance of terrestrial vegetation. However, downregulation of respiratory physiology via thermal acclimation may mitigate this impact. We have conducted a meta-analysis with data collected from 43 independent studies to assess quantitatively the thermal acclimation capacity of leaf dark respiration to warming of terrestrial plant species from across the globe. In total, 282 temperature contrasts were included in the meta-analysis, representing 103 species of forbs, graminoids, shrubs, trees and lianas native to arctic, boreal, temperate and tropical ecosystems. Acclimation to warming was found to decrease respiration at a set temperature in the majority of the observations, regardless of the biome of origin and growth form, but respiration was not completely homeostatic across temperatures in the majority of cases. Leaves that developed at a new temperature had a greater capacity for acclimation than those transferred to a new temperature. We conclude that leaf respiration of most terrestrial plants can acclimate to gradual warming, potentially reducing the magnitude of the positive feedback between climate and the carbon cycle in a warming world. More empirical data are, however, needed to improve our understanding of interspecific variation in thermal acclimation capacity, and to better predict patterns in respiratory carbon fluxes both within and across biomes in the face of ongoing global warming.

  6. Role of fire in biome-boundary shifts in Europe

    NASA Astrophysics Data System (ADS)

    Thonicke, Kirsten; Rolinski, Susanne; von Bloh, Werner; Walz, Ariane; Rammig, Anja

    2013-04-01

    Recent studies have shown that climatic fire risk is projected to increase with future climate change due to increases in droughts and heat waves. In many fire regimes this trend translates into increasing area burnt, but recent analyses of fire statistics and other fire-related data have shown that climate fire risk is not always linearly related to area burnt or fire severity. This means that vegetation productivity, i.e. fuel production, or landscape fragmentation, e.g. through land-use and transportation routes, influence fire spread. Drier climate negatively impacts vegetation productivity, thus leading to less fuel load which further limits fire spread despite similar fire risk. The sensitivity of the affected vegetation also influences fire effects and post-fire mortality. Climate variability additionally contributes to the non-linearity of these processes, which is likely to change under future climate conditions. All these factors point to important feedbacks between vegetation and fire, which can be investigated using dynamic process-based vegetation-fire models such as LPJmL-SPITFIRE. We investigate the role of climate variability on European fire regimes, and if the interaction between climate variability and fire can be responsible for biome shifts under climate change conditions. We apply LPJmL-SPITFIRE to future climate change scenario, 1) the WATCH-ERAI-REMO climate scenario which was run for the SRES A1B emission scenario to Europe and 2) the same climate scenario but with reduced climate variability. Here, we investigate the effects of climate variability and CO2-fertilization on future fire regimes, vegetation dynamics and associated biome shifts. It is hypothesized that climate variability influences vegetation-fire interactions along biome borders, especially in Eastern Europe. Mediterranean countries are most likely to face fuel limitation, leading to a reduction in fire towards the end of the century. Transitions in vegetation composition

  7. Evaluation of image reconstruction algorithms encompassing Time-Of-Flight and Point Spread Function modelling for quantitative cardiac PET: phantom studies.

    PubMed

    Presotto, L; Gianolli, L; Gilardi, M C; Bettinardi, V

    2015-04-01

    To perform kinetic modelling quantification, PET dynamic data must be acquired in short frames, where different critical conditions are met. The accuracy of reconstructed images influences quantification. The added value of Time-Of-Flight (TOF) and Point Spread Function (PSF) in cardiac image reconstruction was assessed. A static phantom was used to simulate two extreme conditions: (i) the bolus passage and (ii) the steady uptake. Various count statistics and independent noise realisations were considered. A moving phantom filled with two different radionuclides was used to simulate: (i) a great range of contrasts and (ii) the cardio/respiratory motion. Analytical and iterative reconstruction (IR) algorithms also encompassing TOF and PSF modelling were evaluated. Both analytic and IR algorithms provided good results in all the evaluated conditions. The amount of bias introduced by IR was found to be limited. TOF allowed faster convergence and lower noise levels. PSF achieved near full myocardial activity recovery in static conditions. Motion degraded performances, but the addition of both TOF and PSF maintained the best overall behaviour. IR accounting for TOF and PSF can be recommended for the quantification of dynamic cardiac PET studies as they improve the results compared to analytic and standard IR.

  8. Quantitative and qualitative comparison of standard-dose and low-dose pediatric head computed tomography: a retrospective study assessing the effect of adaptive statistical iterative reconstruction.

    PubMed

    Kilic, Koray; Erbas, Gonca; Guryildirim, Melike; Konus, Oznur Leman; Arac, Mehmet; Ilgit, Erhan; Isik, Sedat

    2013-01-01

    Our aim was to assess the effect of adaptive statistical iterative reconstruction (ASIR) on pediatric head computed tomography (CT) examinations. We retrospectively reviewed 305 pediatric head CT examinations. The study population consisted of standard dose (STD, n = 152) examinations reconstructed with filtered back projection and low dose (LD, n = 153) examinations reconstructed with 30% (LD30) and 0% (LD0) ASIR. We compared groups by means of radiation dose, noise measures, and visual grading. Student t test, 1-way analysis of variance test, and Mann-Whitney U test were used for statistical analysis. The dose in the LD30 group was significantly lower (29%) than that in the STD group (P < 0.001). The noise in the white matter (P < 0.001), SNR (P < 0.001), and subjective image noise (P = 0.044) was significantly better in the STD group than those in the LD30 group. There was no significant difference between LD30 and STD groups in the sharpness (P = 0.141), diagnostic acceptability (P = 0.079), and artifacts (P = 0.750) and contrast-to-noise ratio (P = 0.718). In conclusion, we found that a blend of 30% ASIR in a 16-slice multidetector CT produces diagnostically acceptable pediatric head CT examinations with a 29% less dose.

  9. USGS: providing scientific understanding of the sagebrush biome

    USGS Publications Warehouse

    ,

    2005-01-01

    Early explorers wrote about the vast sea of sagebrush that stretched in front of them. Today, the consequences of land-use practices, invasion by exotic plants, and altered disturbance regimes have touched virtually all of these seemingly endless expanses. Increasing human populations in the western United States, the infrastructure necessary to support these populations, and a growing demand for natural resources exert a large influence. Changes within the biome have resulted in its designation as one of the most endangered ecosystems in North America.

  10. Evaluating fire danger in Brazilian biomes: present and future patterns

    NASA Astrophysics Data System (ADS)

    Silva, Patrícia; Bastos, Ana; DaCamara, Carlos; Libonati, Renata

    2017-04-01

    Climate change is expected to have a significant impact on fire occurrence and activity, particularly in Brazil, a region known to be fire-prone [1]. The Brazilian savanna, commonly referred to as cerrado, is a fire-adapted biome covering more than 20% of the country's total area. It presents the highest numbers of fire events, making it particularly susceptible to changes in climate. It is thus essential to understand the present fire regimes in Brazilian biomes, in order to better evaluate future patterns. The CPTEC/INPE, the Brazilian Center for Weather Forecasting and Climate Research at the Brazilian National Institute of Space Research developed a fire danger index based on the occurrence of hundreds of thousands of fire events in the main Brazilian biomes [2]: the Meteorological Fire Danger Index (MFDI). This index indicates the predisposition of vegetation to be burned on a given day, for given climate conditions preceding that day. It relies on daily values of air temperature, relative humidity, accumulated precipitation and vegetation cover. In this study we aim to access the capability of the MFDI to accurately replicate present fire conditions for different biomes, with a special focus on cerrado. To this end, we assess the link between the MFDI as calculated by three different reanalysis (ERA-Interim, NCEP/DOE Reanalysis 2 and MERRA-2) and the observed burned area. We further calculate the validated MFDI using a regional climate model, the RCA4 as forced by EC-Earth from CORDEX, to understand the ability of the model to characterize present fire danger. Finally, the need to calibrate the model to better characterize future fire danger was also evaluated. This work was developed within the framework of the Brazilian Fire-Land-Atmosphere System (BrFLAS) Project financed by the Portuguese and Brazilian science foundations, FCT and FAPESP (project references FAPESP/1389/2014 and 2014/20042-2). [1] KRAWCHUK, M.A.; MORITZ, M.A.; PARISIEN, M.A.; VAN DORN, J

  11. Reconstruction of Metabolic Pathways, Protein Expression, and Homeostasis Machineries across Maize Bundle Sheath and Mesophyll Chloroplasts: Large-Scale Quantitative Proteomics Using the First Maize Genome Assembly1[W][OA

    PubMed Central

    Friso, Giulia; Majeran, Wojciech; Huang, Mingshu; Sun, Qi; van Wijk, Klaas J.

    2010-01-01

    Chloroplasts in differentiated bundle sheath (BS) and mesophyll (M) cells of maize (Zea mays) leaves are specialized to accommodate C4 photosynthesis. This study provides a reconstruction of how metabolic pathways, protein expression, and homeostasis functions are quantitatively distributed across BS and M chloroplasts. This yielded new insights into cellular specialization. The experimental analysis was based on high-accuracy mass spectrometry, protein quantification by spectral counting, and the first maize genome assembly. A bioinformatics workflow was developed to deal with gene models, protein families, and gene duplications related to the polyploidy of maize; this avoided overidentification of proteins and resulted in more accurate protein quantification. A total of 1,105 proteins were assigned as potential chloroplast proteins, annotated for function, and quantified. Nearly complete coverage of primary carbon, starch, and tetrapyrole metabolism, as well as excellent coverage for fatty acid synthesis, isoprenoid, sulfur, nitrogen, and amino acid metabolism, was obtained. This showed, for example, quantitative and qualitative cell type-specific specialization in starch biosynthesis, arginine synthesis, nitrogen assimilation, and initial steps in sulfur assimilation. An extensive overview of BS and M chloroplast protein expression and homeostasis machineries (more than 200 proteins) demonstrated qualitative and quantitative differences between M and BS chloroplasts and BS-enhanced levels of the specialized chaperones ClpB3 and HSP90 that suggest active remodeling of the BS proteome. The reconstructed pathways are presented as detailed flow diagrams including annotation, relative protein abundance, and cell-specific expression pattern. Protein annotation and identification data, and projection of matched peptides on the protein models, are available online through the Plant Proteome Database. PMID:20089766

  12. Plant functional traits and soil carbon sequestration in contrasting biomes.

    PubMed

    De Deyn, Gerlinde B; Cornelissen, Johannes H C; Bardgett, Richard D

    2008-05-01

    Plant functional traits control a variety of terrestrial ecosystem processes, including soil carbon storage which is a key component of the global carbon cycle. Plant traits regulate net soil carbon storage by controlling carbon assimilation, its transfer and storage in belowground biomass, and its release from soil through respiration, fire and leaching. However, our mechanistic understanding of these processes is incomplete. Here, we present a mechanistic framework, based on the plant traits that drive soil carbon inputs and outputs, for understanding how alteration of vegetation composition will affect soil carbon sequestration under global changes. First, we show direct and indirect plant trait effects on soil carbon input and output through autotrophs and heterotrophs, and through modification of abiotic conditions, which need to be considered to determine the local carbon sequestration potential. Second, we explore how the composition of key plant traits and soil biota related to carbon input, release and storage prevail in different biomes across the globe, and address the biome-specific mechanisms by which plant trait composition may impact on soil carbon sequestration. We propose that a trait-based approach will help to develop strategies to preserve and promote carbon sequestration.

  13. Comparison of North and South American biomes from AVHRR observations

    NASA Technical Reports Server (NTRS)

    Goward, Samuel N.; Dye, Dennis; Kerber, Arlene; Kalb, Virginia

    1987-01-01

    Previous analysis of the North American continent with AVHRR-derived vegetation index measurements showed a strong relation between known patterns of vegetation seasonality, productivity and the spectral vegetation index measurements. This study extends that analysis to South America to evaluate the degree to which these findings extend to tropical regions. The results show that the spectral vegetation index measurements provide a general indicator of vegetation activity across the major biomes of the Western Hemisphere of the earth, including tropical regions. The satellite-observed patterns are strongly related to the known climatology of the continents and may offer a means to improve understanding of global bioclimatology. For example, South America is shown to have a longer growing season with much earlier spring green-up than North America. The time integral of the measurements, computed from 12 composited monthly values, produces a value that is related to published net primary productivity data. However, limited net primary production data does not allow complete evaluation of satellite-observed contrasts between North and South American biomes. These results suggest that satellite-derived spectral vegetation index measurements are of great potential value in improving knowledge of the earth's biosphere.

  14. Comparison of North and South American biomes from AVHRR observations

    NASA Technical Reports Server (NTRS)

    Goward, Samuel N.; Dye, Dennis; Kerber, Arlene; Kalb, Virginia

    1987-01-01

    Previous analysis of the North American continent with AVHRR-derived vegetation index measurements showed a strong relation between known patterns of vegetation seasonality, productivity and the spectral vegetation index measurements. This study extends that analysis to South America to evaluate the degree to which these findings extend to tropical regions. The results show that the spectral vegetation index measurements provide a general indicator of vegetation activity across the major biomes of the Western Hemisphere of the earth, including tropical regions. The satellite-observed patterns are strongly related to the known climatology of the continents and may offer a means to improve understanding of global bioclimatology. For example, South America is shown to have a longer growing season with much earlier spring green-up than North America. The time integral of the measurements, computed from 12 composited monthly values, produces a value that is related to published net primary productivity data. However, limited net primary production data does not allow complete evaluation of satellite-observed contrasts between North and South American biomes. These results suggest that satellite-derived spectral vegetation index measurements are of great potential value in improving knowledge of the earth's biosphere.

  15. Ticks parasitizing bats (Mammalia: Chiroptera) in the Caatinga Biome, Brazil.

    PubMed

    Luz, Hermes Ribeiro; Muñoz-Leal, Sebastián; Almeida, Juliana Cardoso de; Faccini, João Luiz Horacio; Labruna, Marcelo Bahia

    2016-01-01

    In this paper, the authors report ticks parasitizing bats from the Serra das Almas Natural Reserve (RPPN) located in the municipality of Crateús, state of Ceará, in the semiarid Caatinga biome of northeastern Brazil. The study was carried out during nine nights in the dry season (July 2012) and 10 nights in the rainy season (February 2013). Only bats of the Phyllostomidae and Mormoopidae families were parasitized by ticks. The species Artibeus planirostris and Carolia perspicillata were the most parasitized. A total of 409 larvae were collected and classified into three genera: Antricola (n = 1), Nothoaspis (n = 1) and Ornithodoros (n = 407). Four species were morphologically identified as Nothoaspis amazoniensis, Ornithodoros cavernicolous, Ornithodoros fonsecai, Ornithodoros hasei, and Ornithodoros marinkellei. Ornithodoros hasei was the most common tick associated with bats in the current study. The present study expand the distributional ranges of at least three soft ticks into the Caatinga biome, and highlight an unexpected richness of argasid ticks inhabiting this arid ecosystem.

  16. Climate sensitivity of shrub growth across the tundra biome

    NASA Astrophysics Data System (ADS)

    Myers-Smith, Isla H.; Elmendorf, Sarah C.; Beck, Pieter S. A.; Wilmking, Martin; Hallinger, Martin; Blok, Daan; Tape, Ken D.; Rayback, Shelly A.; Macias-Fauria, Marc; Forbes, Bruce C.; Speed, James D. M.; Boulanger-Lapointe, Noémie; Rixen, Christian; Lévesque, Esther; Schmidt, Niels Martin; Baittinger, Claudia; Trant, Andrew J.; Hermanutz, Luise; Collier, Laura Siegwart; Dawes, Melissa A.; Lantz, Trevor C.; Weijers, Stef; Jørgensen, Rasmus Halfdan; Buchwal, Agata; Buras, Allan; Naito, Adam T.; Ravolainen, Virve; Schaepman-Strub, Gabriela; Wheeler, Julia A.; Wipf, Sonja; Guay, Kevin C.; Hik, David S.; Vellend, Mark

    2015-09-01

    Rapid climate warming in the tundra biome has been linked to increasing shrub dominance. Shrub expansion can modify climate by altering surface albedo, energy and water balance, and permafrost, yet the drivers of shrub growth remain poorly understood. Dendroecological data consisting of multi-decadal time series of annual shrub growth provide an underused resource to explore climate-growth relationships. Here, we analyse circumpolar data from 37 Arctic and alpine sites in 9 countries, including 25 species, and ~42,000 annual growth records from 1,821 individuals. Our analyses demonstrate that the sensitivity of shrub growth to climate was: (1) heterogeneous, with European sites showing greater summer temperature sensitivity than North American sites, and (2) higher at sites with greater soil moisture and for taller shrubs (for example, alders and willows) growing at their northern or upper elevational range edges. Across latitude, climate sensitivity of growth was greatest at the boundary between the Low and High Arctic, where permafrost is thawing and most of the global permafrost soil carbon pool is stored. The observed variation in climate-shrub growth relationships should be incorporated into Earth system models to improve future projections of climate change impacts across the tundra biome.

  17. Pollen-based biomes for Beringia 18,000, 6000 and 0 14C yr BP

    USGS Publications Warehouse

    Edwards, M.E.; Anderson, P.M.; Brubaker, L.B.; Ager, T.A.; Andreev, A.A.; Bigelow, N.H.; Cwynar, L.C.; Eisner, Wendy R.; Harrison, S.P.; Hu, F.-S.; Jolly, D.; Lozhkin, A.V.; MacDonald, G.M.; Mock, C.J.; Ritchie, J.C.; Sher, A.V.; Spear, R.W.; Williams, J.W.; Yu, G.

    2000-01-01

    The objective biomization method developed by Prentice et al. (1996) for Europe was extended using modern pollen samples from Beringia and then applied to fossil pollen data to reconstruct palaeovegetation patterns at 6000 and 18,000 14C yr BP. The predicted modern distribution of tundra, taiga and cool conifer forests in Alaska and north-western Canada generally corresponds well to actual vegetation patterns, although sites in regions characterized today by a mosaic of forest and tundra vegetation tend to be preferentially assigned to tundra. Siberian larch forests are delimited less well, probably due to the extreme under-representation of Larix in pollen spectra. The biome distribution across Beringia at 6000 14C yr BP was broadly similar to today, with little change in the northern forest limit, except for a possible northward-advance in the Mackenzie delta region. The western forest limit in Alaska was probably east of its modern position. At 18,000 14C yr BP the whole of Beringia was covered by tundra. However, the importance of the various plant functional types varied from site to site, supporting the idea that the vegetation cover was a mosaic of different tundra types.

  18. The past is a guide to the future? Comparing Middle Pliocene vegetation with predicted biome distributions for the twenty-first century.

    PubMed

    Salzmann, U; Haywood, A M; Lunt, D J

    2009-01-13

    During the Middle Pliocene, the Earth experienced greater global warmth compared with today, coupled with higher atmospheric CO2 concentrations. To determine the extent to which the Middle Pliocene can be used as a 'test bed' for future warming, we compare data and model-based Middle Pliocene vegetation with simulated global biome distributions for the mid- and late twenty-first century. The best agreement is found when a Middle Pliocene biome reconstruction is compared with a future scenario using 560 ppmv atmospheric CO2. In accordance with palaeobotanical data, all model simulations indicate a generally warmer and wetter climate, resulting in a northward shift of the taiga-tundra boundary and a spread of tropical savannah and woodland in Africa and Australia at the expense of deserts. Our data-model comparison reveals differences in the distribution of polar vegetation, which indicate that the high latitudes during the Middle Pliocene were still warmer than its predicted modern analogue by several degrees. However, our future scenarios do not consider multipliers associated with 'long-term' climate sensitivity. Changes in global temperature, and thus biome distributions, at higher atmospheric CO2 levels will not have reached an equilibrium state (as is the case for the Middle Pliocene) by the end of this century.

  19. The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition.

    PubMed

    Heitlinger, Emanuel; Ferreira, Susana C M; Thierer, Dagmar; Hofer, Heribert; East, Marion L

    2017-01-01

    In mammals, two factors likely to affect the diversity and composition of intestinal bacteria (bacterial microbiome) and eukaryotes (eukaryome) are social status and age. In species in which social status determines access to resources, socially dominant animals maintain better immune processes and health status than subordinates. As high species diversity is an index of ecosystem health, the intestinal biome of healthier, socially dominant animals should be more diverse than those of subordinates. Gradual colonization of the juvenile intestine after birth predicts lower intestinal biome diversity in juveniles than adults. We tested these predictions on the effect of: (1) age (juvenile/adult) and (2) social status (low/high) on bacterial microbiome and eukaryome diversity and composition in the spotted hyena (Crocuta crocuta), a highly social, female-dominated carnivore in which social status determines access to resources. We comprehensively screened feces from 35 individually known adult females and 7 juveniles in the Serengeti ecosystem for bacteria and eukaryotes, using a set of 48 different amplicons (4 for bacterial 16S, 44 for eukaryote 18S) in a multi-amplicon sequencing approach. We compared sequence abundances to classical coprological egg or oocyst counts. For all parasite taxa detected in more than six samples, the number of sequence reads significantly predicted the number of eggs or oocysts counted, underscoring the value of an amplicon sequencing approach for quantitative measurements of parasite load. In line with our predictions, our results revealed a significantly less diverse microbiome in juveniles than adults and a significantly higher diversity of eukaryotes in high-ranking than low-ranking animals. We propose that free-ranging wildlife can provide an intriguing model system to assess the adaptive value of intestinal biome diversity for both bacteria and eukaryotes.

  20. The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition

    PubMed Central

    Heitlinger, Emanuel; Ferreira, Susana C. M.; Thierer, Dagmar; Hofer, Heribert; East, Marion L.

    2017-01-01

    In mammals, two factors likely to affect the diversity and composition of intestinal bacteria (bacterial microbiome) and eukaryotes (eukaryome) are social status and age. In species in which social status determines access to resources, socially dominant animals maintain better immune processes and health status than subordinates. As high species diversity is an index of ecosystem health, the intestinal biome of healthier, socially dominant animals should be more diverse than those of subordinates. Gradual colonization of the juvenile intestine after birth predicts lower intestinal biome diversity in juveniles than adults. We tested these predictions on the effect of: (1) age (juvenile/adult) and (2) social status (low/high) on bacterial microbiome and eukaryome diversity and composition in the spotted hyena (Crocuta crocuta), a highly social, female-dominated carnivore in which social status determines access to resources. We comprehensively screened feces from 35 individually known adult females and 7 juveniles in the Serengeti ecosystem for bacteria and eukaryotes, using a set of 48 different amplicons (4 for bacterial 16S, 44 for eukaryote 18S) in a multi-amplicon sequencing approach. We compared sequence abundances to classical coprological egg or oocyst counts. For all parasite taxa detected in more than six samples, the number of sequence reads significantly predicted the number of eggs or oocysts counted, underscoring the value of an amplicon sequencing approach for quantitative measurements of parasite load. In line with our predictions, our results revealed a significantly less diverse microbiome in juveniles than adults and a significantly higher diversity of eukaryotes in high-ranking than low-ranking animals. We propose that free-ranging wildlife can provide an intriguing model system to assess the adaptive value of intestinal biome diversity for both bacteria and eukaryotes. PMID:28670573

  1. Factors affecting ammonium uptake in streams - an inter-biome perspective

    Treesearch

    Jackson R Webster; Partick J. Mulholland; Jennifer L. Tanks; H. Maurice Valett; Walter K. Dodds; Bruce J. Peterson; William B. Bowden; Clifford N. Dahm; Stuart Findlay; Stanley V. Gregory; Nancy B. Grimm; Stephen K. Hamilton; Sherri L. Johnson; Eugenia Marti; William H. McDowell; Judy L. Meyer; Donna D. Morrall; Steven A. Thomas; Wilfred M. Wollhem

    2003-01-01

    1. The Lotic Intersite Nitrogen experiment (LINX) was a coordinated study of the relationships between North American biomes and factors governing ammonium uptake in streams. Our objective was to relate inter-biome variability of ammonium uptake to physical, chemical and biological processes. 2. Data were collected from 11 streams ranging from arctic to tropical and...

  2. Increasing atmospheric CO2 overrides the historical legacy of multiple stable biome states in Africa.

    PubMed

    Moncrieff, Glenn R; Scheiter, Simon; Bond, William J; Higgins, Steven I

    2014-02-01

    The dominant vegetation over much of the global land surface is not predetermined by contemporary climate, but also influenced by past environmental conditions. This confounds attempts to predict current and future biome distributions, because even a perfect model would project multiple possible biomes without knowledge of the historical vegetation state. Here we compare the distribution of tree- and grass-dominated biomes across Africa simulated using a dynamic global vegetation model (DGVM). We explicitly evaluate where and under what conditions multiple stable biome states are possible for current and projected future climates. Our simulation results show that multiple stable biomes states are possible for vast areas of tropical and subtropical Africa under current conditions. Widespread loss of the potential for multiple stable biomes states is projected in the 21st Century, driven by increasing atmospheric CO2 . Many sites where currently both tree-dominated and grass-dominated biomes are possible become deterministically tree-dominated. Regions with multiple stable biome states are widespread and require consideration when attempting to predict future vegetation changes. Testing for behaviour characteristic of systems with multiple stable equilibria, such as hysteresis and dependence on historical conditions, and the resulting uncertainty in simulated vegetation, will lead to improved projections of global change impacts.

  3. Climate and litter quality differently modulate the effects of soil fauna on litter decomposition across biomes.

    PubMed

    García-Palacios, Pablo; Maestre, Fernando T; Kattge, Jens; Wall, Diana H

    2013-08-01

    Climate and litter quality have been identified as major drivers of litter decomposition at large spatial scales. However, the role played by soil fauna remains largely unknown, despite its importance for litter fragmentation and microbial activity. We synthesised litterbag studies to quantify the effect sizes of soil fauna on litter decomposition rates at the global and biome scales, and to assess how climate, litter quality and soil fauna interact to determine such rates. Soil fauna consistently enhanced litter decomposition at both global and biome scales (average increment ~ 37%). [corrected]. However, climate and litter quality differently modulated the effects of soil fauna on decomposition rates between biomes, from climate-driven biomes to those where climate effects were mediated by changes in litter quality. Our results advocate for the inclusion of biome-specific soil fauna effects on litter decomposition as a mean to reduce the unexplained variation in large-scale decomposition models. © 2013 John Wiley & Sons Ltd/CNRS.

  4. Flammable biomes dominated by eucalypts originated at the Cretaceous-Palaeogene boundary.

    PubMed

    Crisp, Michael D; Burrows, Geoffrey E; Cook, Lyn G; Thornhill, Andrew H; Bowman, David M J S

    2011-02-15

    Fire is a major modifier of communities, but the evolutionary origins of its prevalent role in shaping current biomes are uncertain. Australia is among the most fire-prone continents, with most of the landmass occupied by the fire-dependent sclerophyll and savanna biomes. In contrast to biomes with similar climates in other continents, Australia has a tree flora dominated by a single genus, Eucalyptus, and related Myrtaceae. A unique mechanism in Myrtaceae for enduring and recovering from fire damage likely resulted in this dominance. Here, we find a conserved phylogenetic relationship between post-fire resprouting (epicormic) anatomy and biome evolution, dating from 60 to 62 Ma, in the earliest Palaeogene. Thus, fire-dependent communities likely existed 50 million years earlier than previously thought. We predict that epicormic resprouting could make eucalypt forests and woodlands an excellent long-term carbon bank for reducing atmospheric CO(2) compared with biomes with similar fire regimes in other continents.

  5. Climate and litter quality differently modulate the effects of soil fauna on litter decomposition across biomes

    PubMed Central

    García-Palacios, Pablo; Maestre, Fernando T.; Kattge, Jens; Wall, Diana H.

    2015-01-01

    Climate and litter quality have been identified as major drivers of litter decomposition at large spatial scales. However, the role played by soil fauna remains largely unknown, despite its importance for litter fragmentation and microbial activity. We synthesized litterbag studies to quantify the effect sizes of soil fauna on litter decomposition rates at the global and biome scales, and to assess how climate, litter quality and soil fauna interact to determine such rates. Soil fauna consistently enhanced litter decomposition at both global and biome scales (average increment ~27%). However, climate and litter quality differently modulated the effects of soil fauna on decomposition rates between biomes, from climate-driven biomes to those where climate effects were mediated by changes in litter quality. Our results advocate for the inclusion of biome-specific soil fauna effects on litter decomposition as a mean to reduce the unexplained variation in large-scale decomposition models. PMID:23763716

  6. A quantitative comparison of psychological and emotional health measures in 360 plastic surgery candidates: is there a difference between aesthetic and reconstructive patients?

    PubMed

    Cordeiro, Christina N; Clarke, Alex; White, Paul; Sivakumar, Bran; Ong, Juling; Butler, Peter E M

    2010-09-01

    This study examines the utility of the aesthetic and reconstructive categorization for making treatment decisions in patients seeking facial surgery. A total of 360 patients with aesthetic or combined functional aesthetic deficits were included. Validated psychological scales were used as outcome measures. All subjects showed clinically significant levels of appearance-related distress, with highest levels in the aesthetic and lowest levels in the functionally impaired group. Significant gender differences were not found on any psychological measures. A small negative correlation was found between age and distress. These findings challenge the validity of restricting treatment on the basis of an aesthetic distinction, since this is the group demonstrating the highest level of need. Neither age nor gender is a reliable discriminator. Subjective assessment of noticeability of disfigurement and associated psychological distress may be more useful in prioritizing treatment in systems with limited resources.

  7. Benchmarking carbon fluxes of the ISIMIP2a biome models

    NASA Astrophysics Data System (ADS)

    Chang, Jinfeng; Ciais, Philippe; Wang, Xuhui; Piao, Shilong; Asrar, Ghassem; Betts, Richard; Chevallier, Frédéric; Dury, Marie; François, Louis; Frieler, Katja; García Cantú Ros, Anselmo; Henrot, Alexandra-Jane; Hickler, Thomas; Ito, Akihiko; Morfopoulos, Catherine; Munhoven, Guy; Nishina, Kazuya; Ostberg, Sebastian; Pan, Shufen; Peng, Shushi; Rafique, Rashid; Reyer, Christopher; Rödenbeck, Christian; Schaphoff, Sibyll; Steinkamp, Jörg; Tian, Hanqin; Viovy, Nicolas; Yang, Jia; Zeng, Ning; Zhao, Fang

    2017-04-01

    The purpose of this study is to evaluate the eight ISIMIP2a biome models against independent estimates of long-term net carbon fluxes (i.e. Net Biome Productivity, NBP) over terrestrial ecosystems for the recent four decades (1971-2010). We evaluate modeled global NBP against 1) the updated global residual land sink (RLS) plus land use emissions (E LUC) from the Global Carbon Project (GCP), presented as R + L in this study by Le Quéré et al (2015), and 2) the land CO2 fluxes from two atmospheric inversion systems: Jena CarboScope s81_v3.8 and CAMS v15r2, referred to as F Jena and F CAMS respectively. The model ensemble-mean NBP (that includes seven models with land-use change) is higher than but within the uncertainty of R + L, while the simulated positive NBP trend over the last 30 yr is lower than that from R + L and from the two inversion systems. ISIMIP2a biome models well capture the interannual variation of global net terrestrial ecosystem carbon fluxes. Tropical NBP represents 31 ± 17% of global total NBP during the past decades, and the year-to-year variation of tropical NBP contributes most of the interannual variation of global NBP. According to the models, increasing Net Primary Productivity (NPP) was the main cause for the generally increasing NBP. Significant global NBP anomalies from the long-term mean between the two phases of El Niño Southern Oscillation (ENSO) events are simulated by all models (p < 0.05), which is consistent with the R + L estimate (p = 0.06), also mainly attributed to NPP anomalies, rather than to changes in heterotrophic respiration (Rh). The global NPP and NBP anomalies during ENSO events are dominated by their anomalies in tropical regions impacted by tropical climate variability. Multiple regressions between R + L, F Jena and F CAMS interannual variations and tropical climate variations reveal a significant negative response of global net terrestrial ecosystem carbon fluxes to tropical mean annual temperature variation

  8. Benchmarking carbon fluxes of the ISIMIP2a biome models

    DOE PAGES

    Chang, Jinfeng; Ciais, Philippe; Wang, Xuhui; ...

    2017-03-28

    The purpose of this study is to evaluate the eight ISIMIP2a biome models against independent estimates of long-term net carbon fluxes (i.e. Net Biome Productivity, NBP) over terrestrial ecosystems for the recent four decades (1971–2010). Here, we evaluate modeled global NBP against 1) the updated global residual land sink (RLS) plus land use emissions (ELUC) from the Global Carbon Project (GCP), presented as R + L in this study by Le Quéré et al (2015), and 2) the land CO2 fluxes from two atmospheric inversion systems: Jena CarboScope s81_v3.8 and CAMS v15r2, referred to as FJena and FCAMS respectively. Themore » model ensemble-mean NBP (that includes seven models with land-use change) is higher than but within the uncertainty of R + L, while the simulated positive NBP trend over the last 30 yr is lower than that from R + L and from the two inversion systems. ISIMIP2a biome models well capture the interannual variation of global net terrestrial ecosystem carbon fluxes. Tropical NBP represents 31 ± 17% of global total NBP during the past decades, and the year-to-year variation of tropical NBP contributes most of the interannual variation of global NBP. According to the models, increasing Net Primary Productivity (NPP) was the main cause for the generally increasing NBP. Significant global NBP anomalies from the long-term mean between the two phases of El Niño Southern Oscillation (ENSO) events are simulated by all models (p < 0.05), which is consistent with the R + L estimate (p = 0.06), also mainly attributed to NPP anomalies, rather than to changes in heterotrophic respiration (Rh). The global NPP and NBP anomalies during ENSO events are dominated by their anomalies in tropical regions impacted by tropical climate variability. Multiple regressions between R + L, FJena and FCAMS interannual variations and tropical climate variations reveal a significant negative response of global net terrestrial ecosystem carbon fluxes to tropical mean annual temperature

  9. Response of vegetation to drought time-scales across global land biomes.

    PubMed

    Vicente-Serrano, Sergio M; Gouveia, Célia; Camarero, Jesús Julio; Beguería, Santiago; Trigo, Ricardo; López-Moreno, Juan I; Azorín-Molina, César; Pasho, Edmond; Lorenzo-Lacruz, Jorge; Revuelto, Jesús; Morán-Tejeda, Enrique; Sanchez-Lorenzo, Arturo

    2013-01-02

    We evaluated the response of the Earth land biomes to drought by correlating a drought index with three global indicators of vegetation activity and growth: vegetation indices from satellite imagery, tree-ring growth series, and Aboveground Net Primary Production (ANPP) records. Arid and humid biomes are both affected by drought, and we suggest that the persistence of the water deficit (i.e., the drought time-scale) could be playing a key role in determining the sensitivity of land biomes to drought. We found that arid biomes respond to drought at short time-scales; that is, there is a rapid vegetation reaction as soon as water deficits below normal conditions occur. This may be due to the fact that plant species of arid regions have mechanisms allowing them to rapidly adapt to changing water availability. Humid biomes also respond to drought at short time-scales, but in this case the physiological mechanisms likely differ from those operating in arid biomes, as plants usually have a poor adaptability to water shortage. On the contrary, semiarid and subhumid biomes respond to drought at long time-scales, probably because plants are able to withstand water deficits, but they lack the rapid response of arid biomes to drought. These results are consistent among three vegetation parameters analyzed and across different land biomes, showing that the response of vegetation to drought depends on characteristic drought time-scales for each biome. Understanding the dominant time-scales at which drought most influences vegetation might help assessing the resistance and resilience of vegetation and improving our knowledge of vegetation vulnerability to climate change.

  10. Response of vegetation to drought time-scales across global land biomes

    NASA Astrophysics Data System (ADS)

    Vicente-Serrano, Sergio M.; Gouveia, Célia; Julio Camarero, Jesús; Beguería, Santiago; Trigo, Ricardo; López-Moreno, Juan I.; Azorín-Molina, César; Pasho, Edmond; Lorenzo-Lacruz, Jorge; Revuelto, Jesús; Morán-Tejeda, Enrique; Sanchez-Lorenzo, Arturo

    2013-01-01

    We evaluated the response of the Earth land biomes to drought by correlating a drought index with three global indicators of vegetation activity and growth: vegetation indices from satellite imagery, tree-ring growth series, and Aboveground Net Primary Production (ANPP) records. Arid and humid biomes are both affected by drought, and we suggest that the persistence of the water deficit (i.e., the drought time-scale) could be playing a key role in determining the sensitivity of land biomes to drought. We found that arid biomes respond to drought at short time-scales; that is, there is a rapid vegetation reaction as soon as water deficits below normal conditions occur. This may be due to the fact that plant species of arid regions have mechanisms allowing them to rapidly adapt to changing water availability. Humid biomes also respond to drought at short time-scales, but in this case the physiological mechanisms likely differ from those operating in arid biomes, as plants usually have a poor adaptability to water shortage. On the contrary, semiarid and subhumid biomes respond to drought at long time-scales, probably because plants are able to withstand water deficits, but they lack the rapid response of arid biomes to drought. These results are consistent among three vegetation parameters analyzed and across different land biomes, showing that the response of vegetation to drought depends on characteristic drought time-scales for each biome. Understanding the dominant time-scales at which drought most influences vegetation might help assessing the resistance and resilience of vegetation and improving our knowledge of vegetation vulnerability to climate change.

  11. Response of vegetation to drought time-scales across global land biomes

    PubMed Central

    Vicente-Serrano, Sergio M.; Gouveia, Célia; Camarero, Jesús Julio; Beguería, Santiago; Trigo, Ricardo; López-Moreno, Juan I.; Azorín-Molina, César; Pasho, Edmond; Lorenzo-Lacruz, Jorge; Revuelto, Jesús; Morán-Tejeda, Enrique; Sanchez-Lorenzo, Arturo

    2013-01-01

    We evaluated the response of the Earth land biomes to drought by correlating a drought index with three global indicators of vegetation activity and growth: vegetation indices from satellite imagery, tree-ring growth series, and Aboveground Net Primary Production (ANPP) records. Arid and humid biomes are both affected by drought, and we suggest that the persistence of the water deficit (i.e., the drought time-scale) could be playing a key role in determining the sensitivity of land biomes to drought. We found that arid biomes respond to drought at short time-scales; that is, there is a rapid vegetation reaction as soon as water deficits below normal conditions occur. This may be due to the fact that plant species of arid regions have mechanisms allowing them to rapidly adapt to changing water availability. Humid biomes also respond to drought at short time-scales, but in this case the physiological mechanisms likely differ from those operating in arid biomes, as plants usually have a poor adaptability to water shortage. On the contrary, semiarid and subhumid biomes respond to drought at long time-scales, probably because plants are able to withstand water deficits, but they lack the rapid response of arid biomes to drought. These results are consistent among three vegetation parameters analyzed and across different land biomes, showing that the response of vegetation to drought depends on characteristic drought time-scales for each biome. Understanding the dominant time-scales at which drought most influences vegetation might help assessing the resistance and resilience of vegetation and improving our knowledge of vegetation vulnerability to climate change. PMID:23248309

  12. In vivo bone tunnel evaluation of nanoparticle-grafts using an ACL reconstruction rabbit model.

    PubMed

    Grant, Sheila A; Smith, Sarah E; Schmidt, Hilary; Pfeiffer, Ferris; Kuroki, Kei; Sherman, Seth; White, Richard; Grant, David A

    2017-04-01

    Acellular human gracilis tendons conjugated with gold nanoparticles (AuNP) and hydroxyapatite nanoparticles (nano-HAp) were used as a graft in an anterior cruciate ligament (ACL) reconstruction rabbit model. The ACLs of 11 New Zealand rabbits were reconstructed using grafts conjugated without nanoparticles, with AuNP only, and with both AuNP and nano-HAp. Semi-quantitative histological scoring of bone tunnel portion of grafts was performed after 14 weeks. Bone tunnels were scored for graft degeneration, graft remodeling, percentage of new host fibrous connective, collateral connection, head-to-head connection, graft collagen fiber organization, new host fibrous connective tissue organization, and graft and interface vascularity. All grafts were intact at 14 weeks. Results of bone tunnel scoring indicate remodeling in all graft types with new organized host fibrous connective tissue, head-to-head connection to bone and mild inflammation associated with remodeling. Components of the 20 nm AuNP grafts have significantly more graft degeneration, more new host fibrous connective tissue, and more vascularity compared to crosslinked grafts. Comparison between femoral and tibial tunnel scores indicate more degeneration in femoral tunnels compared to tibial tunnels. Overall results indicated potentially enhanced remodeling from the use of 20 nm AuNP grafts. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1071-1082, 2017.

  13. Softball Games Bring NCI and Leidos Biomed Employees Together | Poster

    Cancer.gov

    NCI and Leidos Biomed employees took to the fields at Nallin Pond for the third annual slow-pitch softball games on August 26. The series attracted 54 employees who were divided into four teams, Red, Blue, Gray, and White, and they were cheered on by about 40 enthusiastic spectators. In the first set of games, the Gray team defeated the Blue team, 15–8, and the White team pulled out a win against the Red team, 17–15. After a brief rest, the two winning teams and the two losing teams faced each other in a second set of games. On Field 1, the “winners” match-up of the Gray and White teams was a nail biter, with a close score throughout the game. Daylight was a factor, however, and the team captains decided to call the game for safety reasons. With a lead of 15 to 13, the Gray team was declared the overall winner.

  14. Softball Games Bring NCI and Leidos Biomed Employees Together | Poster

    Cancer.gov

    NCI and Leidos Biomed employees took to the fields at Nallin Pond for the third annual slow-pitch softball games on August 26. The series attracted 54 employees who were divided into four teams, Red, Blue, Gray, and White, and they were cheered on by about 40 enthusiastic spectators. In the first set of games, the Gray team defeated the Blue team, 15–8, and the White team pulled out a win against the Red team, 17–15. After a brief rest, the two winning teams and the two losing teams faced each other in a second set of games. On Field 1, the “winners” match-up of the Gray and White teams was a nail biter, with a close score throughout the game. Daylight was a factor, however, and the team captains decided to call the game for safety reasons. With a lead of 15 to 13, the Gray team was declared the overall winner.

  15. Biogeography of photoautotrophs in the high polar biome

    PubMed Central

    Pointing, Stephen B.; Burkhard Büdel; Convey, Peter; Gillman, Len N.; Körner, Christian; Leuzinger, Sebastian; Vincent, Warwick F.

    2015-01-01

    The global latitudinal gradient in biodiversity weakens in the high polar biome and so an alternative explanation for distribution of Arctic and Antarctic photoautotrophs is required. Here we identify how temporal, microclimate and evolutionary drivers of biogeography are important, rather than the macroclimate features that drive plant diversity patterns elsewhere. High polar ecosystems are biologically unique, with a more central role for bryophytes, lichens and microbial photoautotrophs over that of vascular plants. Constraints on vascular plants arise mainly due to stature and ontogenetic barriers. Conversely non-vascular plant and microbial photoautotroph distribution is correlated with favorable microclimates and the capacity for poikilohydric dormancy. Contemporary distribution also depends on evolutionary history, with adaptive and dispersal traits as well as legacy influencing biogeography. We highlight the relevance of these findings to predicting future impacts on diversity of polar photoautotrophs and to the current status of plants in Arctic and Antarctic conservation policy frameworks. PMID:26442009

  16. Comparative patterns of plant invasions in the Mediterranean biome.

    PubMed

    Arianoutsou, Margarita; Delipetrou, Pinelopi; Vilà, Montserrat; Dimitrakopoulos, Panayiotis G; Celesti-Grapow, Laura; Wardell-Johnson, Grant; Henderson, Lesley; Fuentes, Nicol; Ugarte-Mendes, Eduardo; Rundel, Philip W

    2013-01-01

    The objective of this work was to compare and contrast the patterns of alien plant invasions in the world's five mediterranean-climate regions (MCRs). We expected landscape age and disturbance history to have bearing on levels of invasion. We assembled a database on naturalized alien plant taxa occurring in natural and semi-natural terrestrial habitats of all five regions (specifically Spain, Italy, Greece and Cyprus from the Mediterranean Basin, California, central Chile, the Cape Region of South Africa and Southwestern - SW Australia). We used multivariate (hierarchical clustering and NMDS ordination) trait and habitat analysis to compare characteristics of regions, taxa and habitats across the mediterranean biome. Our database included 1627 naturalized species with an overall low taxonomic similarity among the five MCRs. Herbaceous perennials were the most frequent taxa, with SW Australia exhibiting both the highest numbers of naturalized species and the highest taxonomic similarity (homogenization) among habitats, and the Mediterranean Basin the lowest. Low stress and highly disturbed habitats had the highest frequency of invasion and homogenization in all regions, and high natural stress habitats the lowest, while taxonomic similarity was higher among different habitats in each region than among regions. Our analysis is the first to describe patterns of species characteristics and habitat vulnerability for a single biome. We have shown that a broad niche (i.e. more than one habitat) is typical of naturalized plant species, regardless of their geographical area of origin, leading to potential for high homogenization within each region. Habitats of the Mediterranean Basin are apparently the most resistant to plant invasion, possibly because their landscapes are generally of relatively recent origin, but with a more gradual exposure to human intervention over a longer period.

  17. Improved simulation of poorly drained forests using Biome-BGC.

    PubMed

    Bond-Lamberty, Ben; Gower, Stith T; Ahl, Douglas E

    2007-05-01

    Forested wetlands and peatlands are important in boreal and terrestrial biogeochemical cycling, but most general-purpose forest process models are designed and parameterized for upland systems. We describe changes made to Biome-BGC, an ecophysiological process model, that improve its ability to simulate poorly drained forests. Model changes allowed for: (1) lateral water inflow from a surrounding watershed, and variable surface and subsurface drainage; (2) adverse effects of anoxic soil on decomposition and nutrient mineralization; (3) closure of leaf stomata in flooded soils; and (4) growth of nonvascular plants (i.e., bryophytes). Bryophytes were treated as ectohydric broadleaf evergreen plants with zero stomatal conductance, whose cuticular conductance to CO(2) was dependent on plant water content. Individual model changes were parameterized with published data, and ecosystem-level model performance was assessed by comparing simulated output to field data from the northern BOREAS site in Manitoba, Canada. The simulation of the poorly drained forest model exhibited reduced decomposition and vascular plant growth (-90%) compared with that of the well-drained forest model; the integrated bryophyte photosynthetic response accorded well with published data. Simulated net primary production, biomass and soil carbon accumulation broadly agreed with field measurements, although simulated net primary production was higher than observed data in well-drained stands. Simulated net primary production in the poorly drained forest was most sensitive to oxygen restriction on soil processes, and secondarily to stomatal closure in flooded conditions. The modified Biome-BGC remains unable to simulate true wetlands that are subject to prolonged flooding, because it does not track organic soil formation, water table changes, soil redox potential or anaerobic processes.

  18. Varying influence of environmental gradients on vegetation patterns across biomes

    NASA Astrophysics Data System (ADS)

    Dahlin, K.; Asner, G. P.; Mascaro, J.; Taylor, P.

    2016-12-01

    Environmental gradients, like elevation, slope, aspect, and soil properties, filter vegetation types at the local scale. These `environmental filters' create conditions that are conducive to the success or failure of different plant types, influencing landscape-scale heterogeneity in taxonomic diversity, functional diversity, biomass accumulation, greenness, and more. Niche-based models implicitly assume that environmental filtering is the dominant process controlling plant distributions. While environmental filtering is a well understood process, its importance relative to other drivers of heterogeneity, like disturbance, human impacts, and plant-animal interactions, remains unknown and likely varies between biomes. Here we synthesize results from several studies using data from the Carnegie Airborne Observatory - a fused LiDAR and imaging spectroscopy system - that mapped a vegetation patterns in multiple biomes and associated these with environmental gradients. The study sites range from Panama to California, and the patterns range from aboveground carbon to foliar chemistry. We show that at fine spatial scales environmental filtering is a strong predictor of aboveground biomass in a dry system (Jasper Ridge Biological Preserve, California - Dahlin et al 2012) but a weak predictor of plant functional traits in that same system (Dahlin et al 2014), a weak predictor of aboveground carbon in the tropics (Barro Colorado Island, Panama - Mascaro et al 2011; Osa Peninsula, Costa Rica - Taylor et al 2015), and a weak predictor of greenness (NDVI) in a disturbed dry system (Santa Cruz Island, California - Dahlin et al 2014). Collectively, these results suggest that while environmental filtering is an important driver of landscape-scale heterogeneity, it is not the only, or often even the most important, driver for many of these systems and patterns.

  19. Comparative Patterns of Plant Invasions in the Mediterranean Biome

    PubMed Central

    Arianoutsou, Margarita; Delipetrou, Pinelopi; Vilà, Montserrat; Dimitrakopoulos, Panayiotis G.; Celesti-Grapow, Laura; Wardell-Johnson, Grant; Henderson, Lesley; Fuentes, Nicol; Ugarte-Mendes, Eduardo; Rundel, Philip W.

    2013-01-01

    The objective of this work was to compare and contrast the patterns of alien plant invasions in the world’s five mediterranean-climate regions (MCRs). We expected landscape age and disturbance history to have bearing on levels of invasion. We assembled a database on naturalized alien plant taxa occurring in natural and semi-natural terrestrial habitats of all five regions (specifically Spain, Italy, Greece and Cyprus from the Mediterranean Basin, California, central Chile, the Cape Region of South Africa and Southwestern - SW Australia). We used multivariate (hierarchical clustering and NMDS ordination) trait and habitat analysis to compare characteristics of regions, taxa and habitats across the mediterranean biome. Our database included 1627 naturalized species with an overall low taxonomic similarity among the five MCRs. Herbaceous perennials were the most frequent taxa, with SW Australia exhibiting both the highest numbers of naturalized species and the highest taxonomic similarity (homogenization) among habitats, and the Mediterranean Basin the lowest. Low stress and highly disturbed habitats had the highest frequency of invasion and homogenization in all regions, and high natural stress habitats the lowest, while taxonomic similarity was higher among different habitats in each region than among regions. Our analysis is the first to describe patterns of species characteristics and habitat vulnerability for a single biome. We have shown that a broad niche (i.e. more than one habitat) is typical of naturalized plant species, regardless of their geographical area of origin, leading to potential for high homogenization within each region. Habitats of the Mediterranean Basin are apparently the most resistant to plant invasion, possibly because their landscapes are generally of relatively recent origin, but with a more gradual exposure to human intervention over a longer period. PMID:24244443

  20. Carbon dioxide measurements in tropical East African biomes

    NASA Astrophysics Data System (ADS)

    Schnell, R. C.; Odh, S.-A.; Njau, L. N.

    1981-06-01

    From January 1977 through May 1978 atmospheric CO2 concentrations were measured hourly and/or continuously at bimonthly intervals over periods varying from 5 to 8 days at 10 different locations in Kenya, East Africa. During each of these periods, at least two, and in some cases five, vertical profile measurements of CO2 concentrations were conducted above different biomes. A large diurnal CO2 periodicity was observed over land, with daytime drawdowns to 322 ppm and nighttime buildups to more than 400 ppm observed in savannah regions. In and around tropical rain forests, drawdowns to 310 ppm and buildups to more than 400 ppm were regularly observed. On the higher reaches of Mount Kenya, the diurnal CO2 cycle was considerably reduced in amplitude, with variations in the range of 2-6 ppm throughout the 16-month study period. On sunny days, the drawdown of CO2 was measurable to heights of at least 4000 m above ground level. Other CO2 concentration measurements in air over the Indian Ocean (to distances of up to 450 km upwind of the coast) produced fairly consistent concentrations of about 328.5 ppm which did not fluctuate diurnally. The weekly mean CO2 concentrations over Kenya appear to have a bimodal structure, with minima occurring in July and January. On the basis of the data collected during the study it appears likely that regular observations at a high-altitude station on Mount Kenya, either with flask sampling or continuous analyzer measurements, are likely to yield data useful for estimates of CO2 concentration backgrounds and trends. Also, there is strong evidence that Mount Kenya would be a good location to measure large-scale interhemispheric CO2 exchanges and provide a unique base from which to study the effects of the tropical biome on biogeochemical phenomena.

  1. Carbon dioxide measurements in tropical east African biomes

    SciTech Connect

    Schnell, R.C.; Odh, S.A.; Njau, L.N.

    1981-06-20

    From January 1977 through May 1978 atmospheric CO/sub 2/ concentrations were measured hourly and/or continuously at bimonthly intervals over periods varying from 5 to 8 days at 10 different locations in Kenya, East Africa. During each of these periods, at least two, and in some cases five, vertical profile measurements of CO/sub 2/ concentrations were conducted above different biomes. A large diurnal CO/sub 2/ periodicity was observed over land, with daytime drawdowns to 322 ppm and nighttime buildups to more than 400 ppm observed in savannah regions. In and around tropical rain forests, drawdowns to 310 ppm and buildups to more than 400 ppm were regularly observed. On the higher reaches of Mount Kenya, the diurnal CO/sub 2/ cycle was considerably reduced in amplitude, with variations in the range of 2-6 ppm throughout the 16-month study period. On sunny days, the drawdown of CO/sub 2/ was measurable to heights of at least 4000 m above ground level. Other CO/sub 2/ measurements in air over the Indian Ocean (to distances of up to 450 km upwind of the coast) produced fairly consistent concentrations of about 328.5 ppm which did not fluctuate diurnally. The weekly mean CO/sub 2/ concentrations over Kenya appear to have a bimodal structure, with minima occurring in July and January. On the basis of the data collected during the study it appears likely that regular observations at a high-altitude station on Mount Kenya, either with flask sampling or continuous analyzer measurements, are likely to yield data useful for estimates of CO/sub 2/ concentration backgrounds and trends. Also, there is strong evidence that Mount Kenya would be a good location to measure large-scale interhemispheric CO/sub 2/ exchanges and provide a unique base from which to study the effects of the tropical biome on biogeochemical phenomena. 20 references, 12 figures, 2 tables.

  2. A quantitative comparison of noise reduction across five commercial (hybrid and model-based) iterative reconstruction techniques: an anthropomorphic phantom study.

    PubMed

    Patino, Manuel; Fuentes, Jorge M; Hayano, Koichi; Kambadakone, Avinash R; Uyeda, Jennifer W; Sahani, Dushyant V

    2015-02-01

    OBJECTIVE. The objective of our study was to compare the performance of three hybrid iterative reconstruction techniques (IRTs) (ASiR, iDose4, SAFIRE) and their respective strengths for image noise reduction on low-dose CT examinations using filtered back projection (FBP) as the standard reference. Also, we compared the performance of these three hybrid IRTs with two model-based IRTs (Veo and IMR) for image noise reduction on low-dose examinations. MATERIALS AND METHODS. An anthropomorphic abdomen phantom was scanned at 100 and 120 kVp and different tube current-exposure time products (25-100 mAs) on three CT systems (for ASiR and Veo, Discovery CT750 HD; for iDose4 and IMR, Brilliance iCT; and for SAFIRE, Somatom Definition Flash). Images were reconstructed using FBP and using IRTs at various strengths. Nine noise measurements (mean ROI size, 423 mm(2)) on extracolonic fat for the different strengths of IRTs were recorded and compared with FBP using ANOVA. Radiation dose, which was measured as the volume CT dose index and dose-length product, was also compared. RESULTS. There were no significant differences in radiation dose and image noise among the scanners when FBP was used (p > 0.05). Gradual image noise reduction was observed with each increasing increment of hybrid IRT strength, with a maximum noise suppression of approximately 50% (48.2-53.9%). Similar noise reduction was achieved on the scanners by applying specific hybrid IRT strengths. Maximum noise reduction was higher on model-based IRTs (68.3-81.1%) than hybrid IRTs (48.2-53.9%) (p < 0.05). CONCLUSION. When constant scanning parameters are used, radiation dose and image noise on FBP are similar for CT scanners made by different manufacturers. Significant image noise reduction is achieved on low-dose CT examinations rendered with IRTs. The image noise on various scanners can be matched by applying specific hybrid IRT strengths. Model-based IRTs attain substantially higher noise reduction than hybrid

  3. Breast Reconstruction

    MedlinePlus

    ... rebuild the shape of the breast. Instead of breast reconstruction, you could choose to wear a breast form ... one woman may not be right for another. Breast reconstruction may be done at the same time as ...

  4. A postoperative analysis of perfusion dynamics in deep inferior epigastric perforator flap breast reconstruction: a noninvasive quantitative measurement of flap oxygen saturation and blood flow.

    PubMed

    Rahmanian-Schwarz, Afshin; Rothenberger, Jens; Amr, Amro; Jaminet, Patrick; Schaller, Hans-Eberhard

    2012-11-01

    The blood supply of microvascular free flaps is rated as very critical, particularly in the first postoperative days. Only a timely recognition of a complication and its treatment can ensure the survival of the flap. To quantify the postoperative perfusion dynamics, we measured the oxygen supply and blood flow of the deep inferior epigastric perforator (DIEP) flaps. A total of 23 patients undergoing DIEP flap breast reconstruction were involved in this study. Noninvasive measurements were performed with the O2C-device, which combines the determination of hemoglobin oxygenation and blood flow using white light and laser light. The first measurement was performed immediately after the flap anastomosis. Further measurements were carried out on the first, third, fifth, and seventh postoperative days. The preoperative value represents our baseline. With the exception of the third day, all postoperative measurements were above the baseline. On the third postoperative day, there was a decrease in the cutaneous oxygen saturation of 22% and a decrease in blood flow of 18% on average, regardless of the individual fluctuations of patient's blood pressure. The postoperative perfusion characteristics of the DIEP flap showed a critical drop in the cutaneous oxygen supply and blood flow on the third postoperative day. This represents a potential risk and should be considered in the postoperative management of the DIEP flap.

  5. Holocene vegetation and climate change in southern New Zealand: linkages between forest composition and quantitative surface moisture reconstructions from an ombrogenous bog

    NASA Astrophysics Data System (ADS)

    Wilmshurst, Janet M.; McGlone, Matt S.; Charman, Dan J.

    2002-10-01

    This paper presents a Holocene pollen record from an ombrotrophic bog in Southland, New Zealand, together with multiproxy data (testate amoebae, peat humification and plant macrofossils) from the same core to establish an independent semiquantitative record of peatland surface moisture. Linkages between reconstructed peatland surface moisture and regional forest composition are investigated using redundancy analysis of the forest pollen data constrained with predicted bog water-table depths. Over 32% of the pollen data variance can be explained by surface moisture changes in the bog, suggesting a common cause of water-table and regional vegetation change. Water tables were higher during the early to mid-Holocene when the forest was dominated by podocarp taxa. Water tables lowered after about 3300 cal. yr BP coevally with the expansion of Nothofagus species, culminating with the dominance of Nothofagus subgenus Fuscospora in the past 1200 cal. yr BP. This is in apparent opposition to the warm/dry to cool/wet trend suggested by subjective interpretation of pollen data alone, from this and other studies. We suggest that during the late Holocene, drier summers associated with shifts in solar insolation caused reduced surface wetness and summer humidity, which together with a trend to cooler winters, apparently favoured the regeneration of Nothofagus species.

  6. The diversification of eastern South American open vegetation biomes: Historical biogeography and perspectives

    NASA Astrophysics Data System (ADS)

    Werneck, Fernanda P.

    2011-06-01

    The eastern-central South American open vegetation biomes occur across an extensive range of environmental conditions and are organized diagonally including three complexly interacting tropical/sub-tropical biomes. Seasonally Dry Tropical Forests (SDTFs), Cerrado, and Chaco biomes are seasonally stressed by drought, characterized by significant plant and animal endemism, high levels of diversity, and highly endangered. However, these open biomes have been overlooked in biogeographic studies and conservation projects in South America, especially regarding fauna studies. Here I compile and evaluate the biogeographic hypotheses previously proposed for the diversification of these three major open biomes, specifically their distributions located eastern and southern of Andes. My goal is to generate predictions and provide a background for testable hypotheses. I begin by investigating both continental (inter-biome) and regional (within-biome) levels, and I then provide a biogeographical summary for these regions. I also suggest how novel molecular-based historical biogeographic/phylogeographic approaches could contribute to the resolution of long-standing questions, identify potential target fauna groups for development of these lines of study, and describe fertile future research agendas.

  7. Model prediction of biome-specific global soil respiration from 1960 to 2012

    NASA Astrophysics Data System (ADS)

    Zhao, Zhengyong; Peng, Changhui; Yang, Qi; Meng, Fan-Rui; Song, Xinzhang; Chen, Shutao; Epule, Terence Epule; Li, Peng; Zhu, Qiuan

    2017-07-01

    Biome-specific soil respiration (Rs) has important yet different roles in both the carbon cycle and climate change from regional to global scales. To date, no comparable studies related to global biome-specific Rs have been conducted applying comprehensive global Rs databases. The goal of this study was to develop artificial neural network (ANN) models capable of spatially estimating global Rs and to evaluate the effects of interannual climate variations on 10 major biomes. We used 1976 annual Rs field records extracted from global Rs literature to train and test the ANN models. We determined that the best ANN model for predicting biome-specific global annual Rs was the one that applied mean annual temperature (MAT), mean annual precipitation (MAP), and biome type as inputs (r2 = 0.60). The ANN models reported an average global Rs of 93.3 ± 6.1 Pg C yr-1 from 1960 to 2012 and an increasing trend in average global annual Rs of 0.04 Pg C yr-1. Estimated annual Rs increased with increases in MAT and MAP in cropland, boreal forest, grassland, shrubland, and wetland biomes. Additionally, estimated annual Rs decreased with increases in MAT and increased with increases in MAP in desert and tundra biomes, and only significantly decreased with increases in MAT (r2 = 0.87) in the savannah biome. The developed biome-specific global Rs database for global land and soil carbon models will aid in understanding the mechanisms underlying variations in soil carbon dynamics and in quantifying uncertainty in the global soil carbon cycle.

  8. Quantitative Comparison of the in situ Microbial Communities in Different Biomes

    DTIC Science & Technology

    1995-09-01

    without written permission from the Publisher. Copies of this book can be purchase from: Sociedade Brasileira de Microbiologia Av. Prof. Lineu Prestes...Boston, H.L. and White, D.C. (1991) Periphyton response along an industrial effluent gradient: Lipid-based physiological stress analysis and pattern

  9. Robust patella motion tracking using intensity-based 2D-3D registration on dynamic bi-plane fluoroscopy: towards quantitative assessment in MPFL reconstruction surgery

    NASA Astrophysics Data System (ADS)

    Otake, Yoshito; Esnault, Matthieu; Grupp, Robert; Kosugi, Shinichi; Sato, Yoshinobu

    2016-03-01

    The determination of in vivo motion of multiple-bones using dynamic fluoroscopic images and computed tomography (CT) is useful for post-operative assessment of orthopaedic surgeries such as medial patellofemoral ligament reconstruction. We propose a robust method to measure the 3D motion of multiple rigid objects with high accuracy using a series of bi-plane fluoroscopic images and a multi-resolution, intensity-based, 2D-3D registration. A Covariance Matrix Adaptation Evolution Strategy (CMA-ES) optimizer was used with a gradient correlation similarity metric. Four approaches to register three rigid objects (femur, tibia-fibula and patella) were implemented: 1) an individual bone approach registering one bone at a time, each with optimization of a six degrees of freedom (6DOF) parameter, 2) a sequential approach registering one bone at a time but using the previous bone results as the background in DRR generation, 3) a simultaneous approach registering all the bones together (18DOF) and 4) a combination of the sequential and the simultaneous approaches. These approaches were compared in experiments using simulated images generated from the CT of a healthy volunteer and measured fluoroscopic images. Over the 120 simulated frames of motion, the simultaneous approach showed improved registration accuracy compared to the individual approach: with less than 0.68mm root-mean-square error (RMSE) for translation and less than 1.12° RMSE for rotation. A robustness evaluation was conducted with 45 trials of a randomly perturbed initialization showed that the sequential approach improved robustness significantly (74% success rate) compared to the individual bone approach (34% success) for patella registration (femur and tibia-fibula registration had a 100% success rate with each approach).

  10. 42 CFR 82.26 - How will NIOSH report dose reconstruction results?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED ACTIVITIES METHODS FOR CONDUCTING DOSE RECONSTRUCTION UNDER... dose reconstruction, justification for the decision, and if possible, a quantitative estimate of...

  11. 42 CFR 82.26 - How will NIOSH report dose reconstruction results?

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED ACTIVITIES METHODS FOR CONDUCTING DOSE RECONSTRUCTION UNDER... dose reconstruction, justification for the decision, and if possible, a quantitative estimate of...

  12. 42 CFR 82.26 - How will NIOSH report dose reconstruction results?

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED ACTIVITIES METHODS FOR CONDUCTING DOSE RECONSTRUCTION UNDER... dose reconstruction, justification for the decision, and if possible, a quantitative estimate of...

  13. 42 CFR 82.26 - How will NIOSH report dose reconstruction results?

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED ACTIVITIES METHODS FOR CONDUCTING DOSE RECONSTRUCTION UNDER... dose reconstruction, justification for the decision, and if possible, a quantitative estimate of...

  14. Survival and growth of under-planted trees: a meta-analysis across four biomes.

    PubMed

    Paquette, Alain; Bouchard, André; Cogliastro, Alain

    2006-08-01

    The transformation of natural forest regeneration processes by human activities has created the need to develop and implement new models of forest management. Alternative silvicultural systems such as variable retention harvest, partial and patch cuts, and older forest management practices such as under-planting, are used in many forests around the world, particularly in North American oak stands, the boreal and coastal temperate rain forests of Canada and the United States, and in many degraded tropical regions of Asia and the Americas. Specific objectives are pursued in each of these biomes, but some are common to most regions, such as preservation of cover and structure and their associated benefits for natural or artificial regeneration due to moderation of the microclimate, development of optimal light and competition conditions, and reduced predation by herbivores. Shelterwoods are often presented as an alternative to clear-cutting to improve the survival of planted trees. A meta-analysis of published results with randomization tests was performed to test the relationship between overstory density and planted seedling growth and survival. Multiple comparisons were also used to reveal optimal levels of overstory density, if they exist. A majority of studies show that survival and growth improve as stand density decreases to an intermediate level, below which they either drop or stabilize. This level seems optimal in most conditions, as it is also more apt to fulfill other objectives imposed on today's forest activities, such as the conservation of forest processes and structures, and the reconstruction of degraded stands through the accelerated return of mid- to late-successional species.

  15. Simulating economics and environmental impacts of beef and soybean systems in Brazil's Pamas and Amozon Biomes

    USDA-ARS?s Scientific Manuscript database

    Recent reductions in the deforestation of the Amazon biome have highlighted the need for the sustainable intensification of beef and commodity crop production in Brazil to increase agricultural productivity without accelerating adverse environmental impacts related to greenhouse gas emissions, eutro...

  16. BIOME: A scientific data archive search-and-order system using browser-aware, dynamic pages

    NASA Technical Reports Server (NTRS)

    Jennings, S. V.; Yow, T. G.; Ng, V. W.

    1997-01-01

    The Oak Ridge National Laboratory's (ORNL) Distributed Active Archive Center (DAAC) is a data archive and distribution center for the National Air and Space Administration's (NASA) Earth Observing System Data and Information System (EOSDIS). Both the Earth Observing System (EOS) and EOSDIS are components of NASA's contribution to the US Global Change Research Program through its Mission to Planet Earth Program. The ORNL DAAC provides access to data used in ecological and environmental research such as global change, global warming, and terrestrial ecology. Because of its large and diverse data holdings, the challenge for the ORNL DAAC is to help users find data of interest from the hundreds of thousands of files available at the DAAC without overwhelming them. Therefore, the ORNL DAAC has developed the Biogeochemical Information Ordering Management Environment (BIOME), a customized search and order system for the World Wide Web (WWW). BIOME is a public system located at http://www-eosdis. ornl.gov/BIOME/biome.html.

  17. Carbon sources and sinks in forest biomes of the former Soviet Union

    SciTech Connect

    Kolchugina, T.P.; Vinson, T.S.

    1993-06-01

    Net primary productivity (NPP) of Soviet forest biomes has been estimated from an equilibrium analysis at seven percent of the global terrestrial NPP, 20 percent of the world's total forest NPP, and half of boreal and temperate forest NPP. However, an equilibrium analysis does not allow the assessment of the role of forest biomes in carbon sequestration because it is based on the assumption that the annual carbon increment in forest biomes equals the amount of carbon released to the atmosphere through respiration. A non-equilibrium analysis accounts for carbon sequestration during specific stages of forest ecosystem development. Sources and sinks of carbon and the sequestration potential of forest biomes in the former Soviet Union are assessed in the present study under non-equilibrium conditions by considering (1) net ecosystem productivity of different age forest stands and their actual coverage, (2) carbon flux related to forest fires, (3) the rate of peat accumulation, and (4) anthropogenic influences.

  18. A binocular indirect ophthalmomicroscope (BIOM) for non-contact wide-angle vitreous surgery.

    PubMed

    Spitznas, M

    1987-01-01

    The binocular indirect ophthalmomicroscope (BIOM) incorporates the principles of indirect ophthalmoscopy in the operating microscope. When used with an image inverting system, it enables noncontact 70 degrees-90 degrees wide-angle observation of the fundus during vitreous microsurgery.

  19. BIOME: A scientific data archive search-and-order system using browser-aware, dynamic pages

    NASA Technical Reports Server (NTRS)

    Jennings, S. V.; Yow, T. G.; Ng, V. W.

    1997-01-01

    The Oak Ridge National Laboratory's (ORNL) Distributed Active Archive Center (DAAC) is a data archive and distribution center for the National Air and Space Administration's (NASA) Earth Observing System Data and Information System (EOSDIS). Both the Earth Observing System (EOS) and EOSDIS are components of NASA's contribution to the US Global Change Research Program through its Mission to Planet Earth Program. The ORNL DAAC provides access to data used in ecological and environmental research such as global change, global warming, and terrestrial ecology. Because of its large and diverse data holdings, the challenge for the ORNL DAAC is to help users find data of interest from the hundreds of thousands of files available at the DAAC without overwhelming them. Therefore, the ORNL DAAC has developed the Biogeochemical Information Ordering Management Environment (BIOME), a customized search and order system for the World Wide Web (WWW). BIOME is a public system located at http://www-eosdis. ornl.gov/BIOME/biome.html.

  20. Biomass Allocation Patterns across China’s Terrestrial Biomes

    PubMed Central

    Wang, Limei; Li, Longhui; Chen, Xi; Tian, Xin; Wang, Xiaoke; Luo, Geping

    2014-01-01

    Root to shoot ratio (RS) is commonly used to describe the biomass allocation between below- and aboveground parts of plants. Determining the key factors influencing RS and interpreting the relationship between RS and environmental factors is important for biological and ecological research. In this study, we compiled 2088 pairs of root and shoot biomass data across China’s terrestrial biomes to examine variations in the RS and its responses to biotic and abiotic factors including vegetation type, soil texture, climatic variables, and stand age. The median value of RS (RSm) for grasslands, shrublands, and forests was 6.0, 0.73, and 0.23, respectively. The range of RS was considerably wide for each vegetation type. RS values for all three major vegetation types were found to be significantly correlated to mean annual precipitation (MAP) and potential water deficit index (PWDI). Mean annual temperature (MAT) also significantly affect the RS for forests and grasslands. Soil texture and forest origin altered the response of RS to climatic factors as well. An allometric formula could be used to well quantify the relationship between aboveground and belowground biomass, although each vegetation type had its own inherent allometric relationship. PMID:24710503

  1. Climate control of terrestrial carbon exchange across biomes and continents

    SciTech Connect

    Ricciuto, Daniel M; Gu, Lianhong

    2010-07-01

    Understanding the relationships between climate and carbon exchange by terrestrial ecosystems is critical to predict future levels of atmospheric carbon dioxide because of the potential accelerating effects of positive climate carbon cycle feedbacks. However, directly observed relationships between climate and terrestrial CO2 exchange with the atmosphere across biomes and continents are lacking. Here we present data describing the relationships between net ecosystem exchange of carbon (NEE) and climate factors as measured using the eddy covariance method at 125 unique sites in various ecosystems over six continents with a total of 559 site-years. We find that NEE observed at eddy covariance sites is (1) a strong function of mean annual temperature at mid- and high-latitudes, (2) a strong function of dryness at mid- and low-latitudes, and (3) a function of both temperature and dryness around the mid-latitudinal belt (45 N). The sensitivity of NEE to mean annual temperature breaks down at ~ 16 C (a threshold value of mean annual temperature), above which no further increase of CO2 uptake with temperature was observed and dryness influence overrules temperature influence.

  2. Cross-biome comparison of microbial association networks

    PubMed Central

    Faust, Karoline; Lima-Mendez, Gipsi; Lerat, Jean-Sébastien; Sathirapongsasuti, Jarupon F.; Knight, Rob; Huttenhower, Curtis; Lenaerts, Tom; Raes, Jeroen

    2015-01-01

    Clinical and environmental meta-omics studies are accumulating an ever-growing amount of microbial abundance data over a wide range of ecosystems. With a sufficiently large sample number, these microbial communities can be explored by constructing and analyzing co-occurrence networks, which detect taxon associations from abundance data and can give insights into community structure. Here, we investigate how co-occurrence networks differ across biomes and which other factors influence their properties. For this, we inferred microbial association networks from 20 different 16S rDNA sequencing data sets and observed that soil microbial networks harbor proportionally fewer positive associations and are less densely interconnected than host-associated networks. After excluding sample number, sequencing depth and beta-diversity as possible drivers, we found a negative correlation between community evenness and positive edge percentage. This correlation likely results from a skewed distribution of negative interactions, which take place preferentially between less prevalent taxa. Overall, our results suggest an under-appreciated role of evenness in shaping microbial association networks. PMID:26579106

  3. Plant community responses to experimental warming across the tundra biome

    PubMed Central

    Walker, Marilyn D.; Wahren, C. Henrik; Hollister, Robert D.; Henry, Greg H. R.; Ahlquist, Lorraine E.; Alatalo, Juha M.; Bret-Harte, M. Syndonia; Calef, Monika P.; Callaghan, Terry V.; Carroll, Amy B.; Epstein, Howard E.; Jónsdóttir, Ingibjörg S.; Klein, Julia A.; Magnússon, Borgþór; Molau, Ulf; Oberbauer, Steven F.; Rewa, Steven P.; Robinson, Clare H.; Shaver, Gaius R.; Suding, Katharine N.; Thompson, Catharine C.; Tolvanen, Anne; Totland, Ørjan; Turner, P. Lee; Tweedie, Craig E.; Webber, Patrick J.; Wookey, Philip A.

    2006-01-01

    Recent observations of changes in some tundra ecosystems appear to be responses to a warming climate. Several experimental studies have shown that tundra plants and ecosystems can respond strongly to environmental change, including warming; however, most studies were limited to a single location and were of short duration and based on a variety of experimental designs. In addition, comparisons among studies are difficult because a variety of techniques have been used to achieve experimental warming and different measurements have been used to assess responses. We used metaanalysis on plant community measurements from standardized warming experiments at 11 locations across the tundra biome involved in the International Tundra Experiment. The passive warming treatment increased plant-level air temperature by 1-3°C, which is in the range of predicted and observed warming for tundra regions. Responses were rapid and detected in whole plant communities after only two growing seasons. Overall, warming increased height and cover of deciduous shrubs and graminoids, decreased cover of mosses and lichens, and decreased species diversity and evenness. These results predict that warming will cause a decline in biodiversity across a wide variety of tundra, at least in the short term. They also provide rigorous experimental evidence that recently observed increases in shrub cover in many tundra regions are in response to climate warming. These changes have important implications for processes and interactions within tundra ecosystems and between tundra and the atmosphere. PMID:16428292

  4. Plant community responses to experimental warming across the tundra biome.

    PubMed

    Walker, Marilyn D; Wahren, C Henrik; Hollister, Robert D; Henry, Greg H R; Ahlquist, Lorraine E; Alatalo, Juha M; Bret-Harte, M Syndonia; Calef, Monika P; Callaghan, Terry V; Carroll, Amy B; Epstein, Howard E; Jónsdóttir, Ingibjörg S; Klein, Julia A; Magnússon, Borgthór; Molau, Ulf; Oberbauer, Steven F; Rewa, Steven P; Robinson, Clare H; Shaver, Gaius R; Suding, Katharine N; Thompson, Catharine C; Tolvanen, Anne; Totland, Ørjan; Turner, P Lee; Tweedie, Craig E; Webber, Patrick J; Wookey, Philip A

    2006-01-31

    Recent observations of changes in some tundra ecosystems appear to be responses to a warming climate. Several experimental studies have shown that tundra plants and ecosystems can respond strongly to environmental change, including warming; however, most studies were limited to a single location and were of short duration and based on a variety of experimental designs. In addition, comparisons among studies are difficult because a variety of techniques have been used to achieve experimental warming and different measurements have been used to assess responses. We used metaanalysis on plant community measurements from standardized warming experiments at 11 locations across the tundra biome involved in the International Tundra Experiment. The passive warming treatment increased plant-level air temperature by 1-3 degrees C, which is in the range of predicted and observed warming for tundra regions. Responses were rapid and detected in whole plant communities after only two growing seasons. Overall, warming increased height and cover of deciduous shrubs and graminoids, decreased cover of mosses and lichens, and decreased species diversity and evenness. These results predict that warming will cause a decline in biodiversity across a wide variety of tundra, at least in the short term. They also provide rigorous experimental evidence that recently observed increases in shrub cover in many tundra regions are in response to climate warming. These changes have important implications for processes and interactions within tundra ecosystems and between tundra and the atmosphere.

  5. [A convex-concave contact lens for vitreoretinal operations with the BIOM].

    PubMed

    Eckardt, C; Wiechens, B

    1991-01-01

    A new convex-concave contact lens for wide-angle vitreoretinal surgery with the BIOM was developed. Placed on an eye, in which silicone oil is injected, it prevents the formation of an optically disturbing oil-water-film on the surface of the cornea. Thus the new contact lens leads to an essential improvement of the fundus view intraoperatively without affecting the optical properties of the BIOM.

  6. Penile Reconstruction

    PubMed Central

    Salgado, Christopher J.; Chim, Harvey; Tang, Jennifer C.; Monstrey, Stan J.; Mardini, Samir

    2011-01-01

    A variety of surgical options exists for penile reconstruction. The key to success of therapy is holistic management of the patient, with attention to the psychological aspects of treatment. In this article, we review reconstructive modalities for various types of penile defects inclusive of partial and total defects as well as the buried penis, and also describe recent basic science advances, which may promise new options for penile reconstruction. PMID:22851914

  7. Calibration and application of lipid hydrogen isotopic ratios for quantitative reconstruction of new england climate variability over the past 15 kyr

    NASA Astrophysics Data System (ADS)

    Hou, Juzhi

    2009-11-01

    precipitation deltaD variations, with particularly high fidelity in dry regions, although more studies in other regions will be important to further test this proxy. In Chapter 4, I present a centennial-scale record of climate change during the transition based on D/H ratios of C22 n-alkanoic acid (deltaDBA) from a sediment core in Blood Pond, Massachusetts. The abrupt climate events observed in Blood Pond records show remarkable similarity with Greenland ice core delta18O records during the Pleistocene. During the early Holocene, the northeastern North America deltaDBA record was more variable than Greenland, possibly due to the close proximity of the Laurentide ice sheet, and impact of freshwater outbursts as the ice sheet rapidly retreated. In Chapter 5, I present decadal-scale temperature records from Blood Pond, Massachusetts during the early Holocene which revealed two abrupt climate reversals. The isotopic records infer a cooling of 3˜4°C between 9.3 and 9.1 ka against the millennial scale climate background, mainly induced by changes in precipitation seasonality. In comparison, the 8.2 ka event displays smaller amplitude of temperature cooling of 1˜2°C at our southern New England site. The observed climatic reversal at ˜ 9.2 ka as representing increased proportion of winter precipitation in conjunction with a drier and cooler summer, triggered by slowdown in thermohaline circulation as a result of freshwater release from the proglacial lakes. The results suggest that the seasonality of the precipitation at the southern New England was highly sensitive to meltwater releases, especially prior to the final collapse of the LIS. In Chapter 6, I present decadal to centennial resolution temperature records from two lakes in the northeastern North America to investigate the relationship between solar activity and temperature changes during the late Pleistocene to early Holocene. The temperature reconstructions from the two lakes of 100 km apart in New England are highly

  8. North American paleoclimate reconstructions for the Last Glacial Maximum using an inverse modeling through iterative forward modeling approach applied to pollen data

    NASA Astrophysics Data System (ADS)

    Izumi, Kenji; Bartlein, Patrick J.

    2016-10-01

    The inverse modeling through iterative forward modeling (IMIFM) approach was used to reconstruct Last Glacial Maximum (LGM) climates from North American fossil pollen data. The approach was validated using modern pollen data and observed climate data. While the large-scale LGM temperature IMIFM reconstructions are similar to those calculated using conventional statistical approaches, the reconstructions of moisture variables differ between the two approaches. We used two vegetation models, BIOME4 and BIOME5-beta, with the IMIFM approach to evaluate the effects on the LGM climate reconstruction of differences in water use efficiency, carbon use efficiency, and atmospheric CO2 concentrations. Although lower atmospheric CO2 concentrations influence pollen-based LGM moisture reconstructions, they do not significantly affect temperature reconstructions over most of North America. This study implies that the LGM climate was very cold but not very much drier than present over North America, which is inconsistent with previous studies.

  9. Penile reconstruction

    PubMed Central

    Garaffa, Giulio; Sansalone, Salvatore; Ralph, David J

    2013-01-01

    During the most recent years, a variety of new techniques of penile reconstruction have been described in the literature. This paper focuses on the most recent advances in male genital reconstruction after trauma, excision of benign and malignant disease, in gender reassignment surgery and aphallia with emphasis on surgical technique, cosmetic and functional outcome. PMID:22426595

  10. Biogeochemical cycling in terrestrial ecosystems of the Caatinga Biome.

    PubMed

    Menezes, R S C; Sampaio, E V S B; Giongo, V; Pérez-Marin, A M

    2012-08-01

    The biogeochemical cycles of C, N, P and water, the impacts of land use in the stocks and flows of these elements and how they can affect the structure and functioning of Caatinga were reviewed. About half of this biome is still covered by native secondary vegetation. Soils are deficient in nutrients, especially N and P. Average concentrations of total soil P and C in the top layer (0-20 cm) are 196 mg kg(-1) and 9.3 g kg(-1), corresponding to C stocks around 23 Mg ha(-1). Aboveground biomass of native vegetation varies from 30 to 50 Mg ha(-1), and average root biomass from 3 to 12 Mg ha(-1). Average annual productivities and biomass accumulation in different land use systems vary from 1 to 7 Mg ha(-1) year(-1). Biological atmospheric N2 fixation is estimated to vary from 3 to 11 kg N ha(-1) year-1 and 21 to 26 kg N ha(-1) year(-1) in mature and secondary Caatinga, respectively. The main processes responsible for nutrient and water losses are fire, soil erosion, runoff and harvest of crops and animal products. Projected climate changes in the future point to higher temperatures and rainfall decreases. In face of the high intrinsic variability, actions to increase sustainability should improve resilience and stability of the ecosystems. Land use systems based on perennial species, as opposed to annual species, may be more stable and resilient, thus more adequate to face future potential increases in climate variability. Long-term studies to investigate the potential of the native biodiversity or adapted exotic species to design sustainable land use systems should be encouraged.

  11. Ligament reconstruction.

    PubMed

    Glickel, Steven Z; Gupta, Salil

    2006-05-01

    Volar ligament reconstruction is an effective technique for treating symptomatic laxity of the CMC joint of the thumb. The laxity may bea manifestation of generalized ligament laxity,post-traumatic, or metabolic (Ehler-Danlos). There construction reduces the shear forces on the joint that contribute to the development and persistence of inflammation. Although there have been only a few reports of the results of volar ligament reconstruction, the use of the procedure to treat Stage I and Stage II disease gives good to excellent results consistently. More advanced stages of disease are best treated by trapeziectomy, with or without ligament reconstruction.

  12. Expanding the global network of protected areas to save the imperiled mediterranean biome.

    PubMed

    Underwood, Emma C; Klausmeyer, Kirk R; Cox, Robin L; Busby, Sylvia M; Morrison, Scott A; Shaw, M Rebecca

    2009-02-01

    : Global goals established by the Convention on Biological Diversity stipulate that 10% of the world's ecological regions must be effectively conserved by 2010. To meet that goal for the mediterranean biome, at least 5% more land must be formally protected over the next few years. Although global assessments identify the mediterranean biome as a priority, without biologically meaningful analysis units, finer-resolution data, and corresponding prioritization analysis, future conservation investments could lead to more area being protected without increasing the representation of unique mediterranean ecosystems. We used standardized analysis units and six potential natural vegetation types stratified by 3 elevation zones in a global gap analysis that systematically explored conservation priorities across the mediterranean biome. The highest levels of protection were in Australia, South Africa, and California-Baja California (from 9-11%), and the lowest levels of protection were in Chile and the mediterranean Basin (<1%). Protection was skewed to montane elevations in three out of five regions. Across the biome only one of the six vegetation types--mediterranean shrubland--exceeded 10% protection. The remaining vegetation types--grassland, scrub, succulent dominated, woodland, and forest--each had <3% protection. To guard against biases in future protection efforts and ensure the protection of species characteristic of the mediterranean biome, we identified biodiversity assemblages with <10% protection and subject to >30% conversion and suggest that these assemblages be elevated to high-priority status in future conservation efforts.

  13. An intercomparison of biogenic emissions estimates from BEIS2 and BIOME: Reconciling the differences

    SciTech Connect

    Wilkinson, J.G.; Emigh, R.A.; Pierce, T.E.

    1996-12-31

    Biogenic emissions play a critical role in urban and regional air quality. For instance, biogenic emissions contribute upwards of 76% of the daily hydrocarbon emissions in the Atlanta, Georgia airshed. The Biogenic Emissions Inventory System-Version 2.0 (BEIS2) and the Biogenic Model for Emissions (BIOME) are two models that compute biogenic emissions estimates. BEIS2 is a FORTRAN-based system, and BIOME is an ARC/INFO{reg_sign} - and SAS{reg_sign}-based system. Although the technical formulations of the models are similar, the models produce different biogenic emissions estimates for what appear to be essentially the same inputs. The goals of our study are the following: (1) Determine why BIOME and BEIS2 produce different emissions estimates; (2) Attempt to understand the impacts that the differences have on the emissions estimates; (3) Reconcile the differences where possible; and (4) Present a framework for the use of BEIS2 and BIOME. In this study, we used the Coastal Oxidant Assessment for Southeast Texas (COAST) biogenics data which were supplied to us courtesy of the Texas Natural Resource Conservation Commission (TNRCC), and we extracted the BEIS2 data for the same domain. We compared the emissions estimates of the two models using their respective data sets BIOME Using TNRCC data and BEIS2 using BEIS2 data.

  14. Evolutionary biology and anthropology suggest biome reconstitution as a necessary approach toward dealing with immune disorders.

    PubMed

    Parker, William; Ollerton, Jeff

    2013-01-01

    Industrialized society currently faces a wide range of non-infectious, immune-related pandemics. These pandemics include a variety of autoimmune, inflammatory and allergic diseases that are often associated with common environmental triggers and with genetic predisposition, but that do not occur in developing societies. In this review, we briefly present the idea that these pandemics are due to a limited number of evolutionary mismatches, the most damaging being 'biome depletion'. This particular mismatch involves the loss of species from the ecosystem of the human body, the human biome, many of which have traditionally been classified as parasites, although some may actually be commensal or even mutualistic. This view, evolved from the 'hygiene hypothesis', encompasses a broad ecological and evolutionary perspective that considers host-symbiont relations as plastic, changing through ecological space and evolutionary time. Fortunately, this perspective provides a blueprint, termed 'biome reconstitution', for disease treatment and especially for disease prevention. Biome reconstitution includes the controlled and population-wide reintroduction (i.e. domestication) of selected species that have been all but eradicated from the human biome in industrialized society and holds great promise for the elimination of pandemics of allergic, inflammatory and autoimmune diseases.

  15. Evolutionary biology and anthropology suggest biome reconstitution as a necessary approach toward dealing with immune disorders

    PubMed Central

    Parker, William; Ollerton, Jeff

    2013-01-01

    Industrialized society currently faces a wide range of non-infectious, immune-related pandemics. These pandemics include a variety of autoimmune, inflammatory and allergic diseases that are often associated with common environmental triggers and with genetic predisposition, but that do not occur in developing societies. In this review, we briefly present the idea that these pandemics are due to a limited number of evolutionary mismatches, the most damaging being ‘biome depletion’. This particular mismatch involves the loss of species from the ecosystem of the human body, the human biome, many of which have traditionally been classified as parasites, although some may actually be commensal or even mutualistic. This view, evolved from the ‘hygiene hypothesis’, encompasses a broad ecological and evolutionary perspective that considers host-symbiont relations as plastic, changing through ecological space and evolutionary time. Fortunately, this perspective provides a blueprint, termed ‘biome reconstitution’, for disease treatment and especially for disease prevention. Biome reconstitution includes the controlled and population-wide reintroduction (i.e. domestication) of selected species that have been all but eradicated from the human biome in industrialized society and holds great promise for the elimination of pandemics of allergic, inflammatory and autoimmune diseases. PMID:24481190

  16. ACL reconstruction

    MedlinePlus

    ... This increases the chance you may have a meniscus tear. ACL reconstruction may be used for these ... When other ligaments are also injured When your meniscus is torn Before surgery, talk to your health ...

  17. Breast Reconstruction

    MedlinePlus

    ... senos Preguntas Para el Médico Datos Para la Vida Komen El cuidado de sus senos:Consejos útiles ... can help . Cost Federal law requires most insurance plans cover the cost of breast reconstruction. Learn more ...

  18. Site-specific seasonal models of carbon fluxes in terrestrial biomes

    SciTech Connect

    King, A.W.; DeAngelis, D.L.

    1986-01-01

    A set of site-specific computer simulation models of seasonal terrestrial carbon exchange has been assembled from open-literature sources. This collection is designed to facilitate the development of biome-level models for each of the principal terrestrial vegetation biomes on earth, for their integration into a global model of seasonal CO/sub 2/ variation in the atmosphere. The models are described in sufficient detail that their underlying assumptions can be compared. Descriptions include the following aspects of each model: (1) the compartments; (2) the carbon fluxes between compartments; and (3) the climatic variables that drive the carbon fluxes. In particular, the functional forms of the dependencies of respiration and photosynthesis on the driving variables are described. The methods by which these models will be extrapolated to biome-level models are also discussed.

  19. Drivers of greening trend across vertically distributed biomes in temperate arid Asia

    NASA Astrophysics Data System (ADS)

    Ren, Ji; Liu, Hongyan; Yin, Yi; He, Siyuan

    2007-04-01

    This study investigates vegetation responses to climate changes by analyzing 19 years (1982-2000) of both climatic data and growing season Normalized Difference Vegetation Index (NDVI) for vertically distributed desert, steppe, forest and meadow, in the middle part of the northern slope of Tianshan Mountains. Vegetation activity exhibited greening trend in all biomes, owing mainly to reduction of water stress caused by increasing precipitation, although warming trend negated that effect because of temperature-induced drought. Precipitation acted as a remarkable driving force of plant growth in each biome through the whole growing season (spring, summer, autumn), its effect could always persist into the next season, however, the sensitivity decreased across biomes with increasing precipitation. Warming-induced snow melt played a positive role in boosting plant growth during spring in steppe, forest and meadow. Except that, warming produced negative effects.

  20. Concluding remarks: overall impacts on biodiversity and future perspectives for conservation in the Pantanal biome.

    PubMed

    Alho, C J R

    2011-04-01

    The Pantanal biome is characterised by seasonal flooding which determines specific ecosystem processes, with the occurrence of adapted plants and animals to the annual shrinking and expansion of habitats due to the seasonal hydrological regime. Biodiversity abundance varies during the dry and wet seasons. The Pantanal's biodiversity is a fundamental component of ecosystem services for human society, including nutrient cycling, fish production, ecotourism, carbon storage, flood control, among others, which are relevant to regional and global environmental consequences. The biome has been impacted by the conversion of natural vegetation into agricultural fields and pasture for cattle raising, with alteration and loss of natural habitats and biodiversity. Major negative impacts occur in uplands, with drastic deforestation of savanna vegetation, where main rivers feeding the Pantanal have their springs. This article discusses future needs and priorities for ecological research, in order to better understand the biome's natural system, to achieve conservation and sustainable use.

  1. Combining climatic and soil properties better predicts covers of Brazilian biomes.

    PubMed

    Arruda, Daniel M; Fernandes-Filho, Elpídio I; Solar, Ricardo R C; Schaefer, Carlos E G R

    2017-04-01

    Several techniques have been used to model the area covered by biomes or species. However, most models allow little freedom of choice of response variables and are conditioned to the use of climate predictors. This major restriction of the models has generated distributions of low accuracy or inconsistent with the actual cover. Our objective was to characterize the environmental space of the most representative biomes of Brazil and predict their cover, using climate and soil-related predictors. As sample units, we used 500 cells of 100 km(2) for ten biomes, derived from the official vegetation map of Brazil (IBGE 2004). With a total of 38 (climatic and soil-related) predictors, an a priori model was run with the random forest classifier. Each biome was calibrated with 75% of the samples. The final model was based on four climate and six soil-related predictors, the most important variables for the a priori model, without collinearity. The model reached a kappa value of 0.82, generating a highly consistent prediction with the actual cover of the country. We showed here that the richness of biomes should not be underestimated, and that in spite of the complex relationship, highly accurate modeling based on climatic and soil-related predictors is possible. These predictors are complementary, for covering different parts of the multidimensional niche. Thus, a single biome can cover a wide range of climatic space, versus a narrow range of soil types, so that its prediction is best adjusted by soil-related variables, or vice versa.

  2. Observing and Quantifying Ecological Disturbance Impacts on Semi-arid Biomes in the Southwestern US.

    NASA Astrophysics Data System (ADS)

    Litvak, M. E.; Krofcheck, D. J.; Morillas, L.; Fox, A. M.

    2014-12-01

    The magnitude of carbon fluxes through arid and semi-arid ecosystems is considered modest, but integrated over the ~40% of the global land surface covered by these ecosystems, the total carbon stored is almost twice that in temperate forest ecosystems. In the semi-arid Southwestern U.S., drought and rising temperatures have triggered insect outbreaks, fire and widespread mortality in the past 5 years, all of which are predicted to increase in the next century. Understanding how resilient carbon pools and fluxes in these biomes are to these disturbances constitutes a large uncertainty in our ability to understand both carbon and energy flux dynamics in this region. We use an 8 year record (2007-2014) of continuous measurements of net ecosystem exchange of carbon (NEE) and its components (gross primary productivity (GPP) and ecosystem respiration (Re), and evapotranspiration (ET) made over the New Mexico Elevation Gradient (NMEG) network of flux tower sites (desert grassland, creosote shrubland, juniper savanna, piñon-juniper woodland, ponderosa pine and subalpine mixed conifer) to quantify the biome-specific responses of carbon and water dynamics to these disturbances. In particular, we focus on biome-specific responses across the NMEG biomes to the extended drought in this region from 2011-2014, and to the widespread mortality observed in piñon-juniper woodlands following the turn of the century drought (1999-2002) and multi-year recent drought. Finally, we compare functional responses of land-surface fluxes to recent catastrophic fires (grassland, subalpine conifer biomes), and insect outbreaks (subalpine conifer and piñon-juniper woodland biomes). We discuss the results in terms of which disturbances have contributed to and are likely to trigger the largest changes in carbon sequestration in this region in response to predicted climate change scenarios.

  3. Combining climatic and soil properties better predicts covers of Brazilian biomes

    NASA Astrophysics Data System (ADS)

    Arruda, Daniel M.; Fernandes-Filho, Elpídio I.; Solar, Ricardo R. C.; Schaefer, Carlos E. G. R.

    2017-04-01

    Several techniques have been used to model the area covered by biomes or species. However, most models allow little freedom of choice of response variables and are conditioned to the use of climate predictors. This major restriction of the models has generated distributions of low accuracy or inconsistent with the actual cover. Our objective was to characterize the environmental space of the most representative biomes of Brazil and predict their cover, using climate and soil-related predictors. As sample units, we used 500 cells of 100 km2 for ten biomes, derived from the official vegetation map of Brazil (IBGE 2004). With a total of 38 (climatic and soil-related) predictors, an a priori model was run with the random forest classifier. Each biome was calibrated with 75% of the samples. The final model was based on four climate and six soil-related predictors, the most important variables for the a priori model, without collinearity. The model reached a kappa value of 0.82, generating a highly consistent prediction with the actual cover of the country. We showed here that the richness of biomes should not be underestimated, and that in spite of the complex relationship, highly accurate modeling based on climatic and soil-related predictors is possible. These predictors are complementary, for covering different parts of the multidimensional niche. Thus, a single biome can cover a wide range of climatic space, versus a narrow range of soil types, so that its prediction is best adjusted by soil-related variables, or vice versa.

  4. BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities

    PubMed Central

    Chipman, Hugh; Gu, Hong; Bielawski, Joseph P.

    2014-01-01

    Metagenomics yields enormous numbers of microbial sequences that can be assigned a metabolic function. Using such data to infer community-level metabolic divergence is hindered by the lack of a suitable statistical framework. Here, we describe a novel hierarchical Bayesian model, called BiomeNet (Bayesian inference of metabolic networks), for inferring differential prevalence of metabolic subnetworks among microbial communities. To infer the structure of community-level metabolic interactions, BiomeNet applies a mixed-membership modelling framework to enzyme abundance information. The basic idea is that the mixture components of the model (metabolic reactions, subnetworks, and networks) are shared across all groups (microbiome samples), but the mixture proportions vary from group to group. Through this framework, the model can capture nested structures within the data. BiomeNet is unique in modeling each metagenome sample as a mixture of complex metabolic systems (metabosystems). The metabosystems are composed of mixtures of tightly connected metabolic subnetworks. BiomeNet differs from other unsupervised methods by allowing researchers to discriminate groups of samples through the metabolic patterns it discovers in the data, and by providing a framework for interpreting them. We describe a collapsed Gibbs sampler for inference of the mixture weights under BiomeNet, and we use simulation to validate the inference algorithm. Application of BiomeNet to human gut metagenomes revealed a metabosystem with greater prevalence among inflammatory bowel disease (IBD) patients. Based on the discriminatory subnetworks for this metabosystem, we inferred that the community is likely to be closely associated with the human gut epithelium, resistant to dietary interventions, and interfere with human uptake of an antioxidant connected to IBD. Because this metabosystem has a greater capacity to exploit host-associated glycans, we speculate that IBD-associated communities might arise

  5. BOREAS RSS-8 BIOME-BGC Model Simulations at Tower Flux Sites in 1994

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G. (Editor); Nickeson, Jaime (Editor); Kimball, John

    2000-01-01

    BIOME-BGC is a general ecosystem process model designed to simulate biogeochemical and hydrologic processes across multiple scales (Running and Hunt, 1993). In this investigation, BIOME-BGC was used to estimate daily water and carbon budgets for the BOREAS tower flux sites for 1994. Carbon variables estimated by the model include gross primary production (i.e., net photosynthesis), maintenance and heterotrophic respiration, net primary production, and net ecosystem carbon exchange. Hydrologic variables estimated by the model include snowcover, evaporation, transpiration, evapotranspiration, soil moisture, and outflow. The information provided by the investigation includes input initialization and model output files for various sites in tabular ASCII format.

  6. Where do the treeless tundra areas of northern highlands fit in the global biome system: toward an ecologically natural subdivision of the tundra biome.

    PubMed

    Virtanen, Risto; Oksanen, Lauri; Oksanen, Tarja; Cohen, Juval; Forbes, Bruce C; Johansen, Bernt; Käyhkö, Jukka; Olofsson, Johan; Pulliainen, Jouni; Tømmervik, Hans

    2016-01-01

    According to some treatises, arctic and alpine sub-biomes are ecologically similar, whereas others find them highly dissimilar. Most peculiarly, large areas of northern tundra highlands fall outside of the two recent subdivisions of the tundra biome. We seek an ecologically natural resolution to this long-standing and far-reaching problem. We studied broad-scale patterns in climate and vegetation along the gradient from Siberian tundra via northernmost Fennoscandia to the alpine habitats of European middle-latitude mountains, as well as explored those patterns within Fennoscandian tundra based on climate-vegetation patterns obtained from a fine-scale vegetation map. Our analyses reveal that ecologically meaningful January-February snow and thermal conditions differ between different types of tundra. High precipitation and mild winter temperatures prevail on middle-latitude mountains, low precipitation and usually cold winters prevail on high-latitude tundra, and Scandinavian mountains show intermediate conditions. Similarly, heath-like plant communities differ clearly between middle latitude mountains (alpine) and high-latitude tundra vegetation, including its altitudinal extension on Scandinavian mountains. Conversely, high abundance of snowbeds and large differences in the composition of dwarf shrub heaths distinguish the Scandinavian mountain tundra from its counterparts in Russia and the north Fennoscandian inland. The European tundra areas fall into three ecologically rather homogeneous categories: the arctic tundra, the oroarctic tundra of northern heights and mountains, and the genuinely alpine tundra of middle-latitude mountains. Attempts to divide the tundra into two sub-biomes have resulted in major discrepancies and confusions, as the oroarctic areas are included in the arctic tundra in some biogeographic maps and in the alpine tundra in others. Our analyses based on climate and vegetation criteria thus seem to resolve the long-standing biome

  7. The Theory of Variances in Equilibrium Reconstruction

    SciTech Connect

    Zakharov, Leonid E.; Lewandowski, Jerome; Foley, Elizabeth L.; Levinton, Fred M.; Yuh, Howard Y.; Drozdov, Vladimir; McDonald, Darren

    2008-01-14

    The theory of variances of equilibrium reconstruction is presented. It complements existing practices with information regarding what kind of plasma profiles can be reconstructed, how accurately, and what remains beyond the abilities of diagnostic systems. The σ-curves, introduced by the present theory, give a quantitative assessment of quality of effectiveness of diagnostic systems in constraining equilibrium reconstructions. The theory also suggests a method for aligning the accuracy of measurements of different physical nature.

  8. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.

    PubMed

    McDonald, Daniel; Clemente, Jose C; Kuczynski, Justin; Rideout, Jai Ram; Stombaugh, Jesse; Wendel, Doug; Wilke, Andreas; Huse, Susan; Hufnagle, John; Meyer, Folker; Knight, Rob; Caporaso, J Gregory

    2012-07-12

    We present the Biological Observation Matrix (BIOM, pronounced "biome") format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observation metadata. As the number of categories of comparative omics data types (collectively, the "ome-ome") grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses. The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages. The BIOM file format and the biom-format project are steps toward reducing the "bioinformatics bottleneck" that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium.

  9. Climate change in Inner Mongolia from 1955 to 2005—trends at regional, biome and local scales

    NASA Astrophysics Data System (ADS)

    Lu, N.; Wilske, B.; Ni, J.; John, R.; Chen, J.

    2009-10-01

    This study investigated the climate change in Inner Mongolia based on 51 meteorological stations from 1955 to 2005. The climate data was analyzed at the regional, biome (i.e. forest, grassland and desert) and station scales, with the biome scale as our primary focus. The climate records showed trends of warmer and drier conditions in the region. The annual daily mean, maximum and minimum temperature increased whereas the diurnal temperature range (DTR) decreased. The decreasing trend of annual precipitation was not significant. However, the vapor pressure deficit (VPD) increased significantly. On the decadal scale, the warming and drying trends were more significant in the last 30 years than the preceding 20 years. The climate change varied among biomes, with more pronounced changes in the grassland and the desert biomes than in the forest biome. DTR and VPD showed the clearest inter-biome gradient from the lowest rate of change in the forest biome to the highest rate of change in the desert biome. The rates of change also showed large variations among the individual stations. Our findings correspond with the IPCC predictions that the future climate will vary significantly by location and through time, suggesting that adaptation strategies also need to be spatially viable.

  10. Carbon storage in permafrost and soils of the mammoth tundra-steppe biome: role in the global carbon budget

    Treesearch

    N.S. Zimov; S.A. Zimov; A.E. Zimova; G.M. Zimova; V.I. Chuprynin; F.S. Chapin

    2009-01-01

    During the Last Glacial Maximum (LGM), atmospheric CO2 concentration was 80-100 ppmv lower than in preindustrial times. At that time steppe-tundra was the most extensive biome on Earth. Some authors assume that C storage in that biome was very small, similar to today's deserts, and that the terrestrial carbon (C) reservoir increased at the...

  11. 50-kyr vegetation history in the western Verkhoyansk Mountains region (NE Asia) reconstructed from fossil pollen data

    NASA Astrophysics Data System (ADS)

    Müller, Stefanie; Tarasov, Pavel E.; Andreev, Andrei A.; Tütken, Thomas; Gartz, Steffi; Diekmann, Bernhard

    2010-05-01

    A detailed radiocarbon-dated pollen record from Lake Billyakh (65°17'N, 126°47'E; 340 m a.s.l.) situated in the western part of the Verkhoyansk Mountains, about 140 km south of the Arctic Circle is presented. A set of 53 surface pollen samples representing tundra, cold-deciduous forest and taiga was collected in northern and central Yakutia communities to verify the accuracy of the quantitative biome reconstruction method and to obtain a more precise attribution of the identified pollen taxa to the main regional biomes. The adjusted method is then applied to the pollen record from Lake Billyakh to gain an objective reconstruction of vegetation and environments since about 50.7 kyr BP. The results of the pollen analysis and pollen-based biome reconstruction suggest that herbaceous tundra and steppe communities dominated the area from 50.7 to 13.5 kyr BP. The lowest pollen percentages of woody taxa and the highest values of Artemisia pollen attest that the 31-15 kyr BP period as the driest and coldest interval of the entire record. A relative high content of taxa representing shrub tundra communities and the presence of larch pollen recorded prior to 31 kyr and after 13.5 kyr BP likely indicate interstadial climate amelioration associated with the middle and latest parts of the last glacial. An increase in pollen percentages of herbaceous taxa around 12 kyr BP suggests broader distribution of drier communities in response to the colder and drier than present climate of the Younger Dryas. The onset of the Holocene is marked by the highest values of shrub taxa, mainly Betula sect. Nanae/Fruticosae. Pollen percentages of arboreal taxa increase gradually and reach maximum values after 7 kyr BP. The latter maximum mainly reflects the spread of Pinus sylvestris in central Yakutia as a response to the mid-Holocene climatic optimum. The quasi-continuous presence of larch, shrubby birch and alder pollen throughout the whole record is the most striking feature of the pollen

  12. Project Reconstruct.

    ERIC Educational Resources Information Center

    Helisek, Harriet; Pratt, Donald

    1994-01-01

    Presents a project in which students monitor their use of trash, input and analyze information via a database and computerized graphs, and "reconstruct" extinct or endangered animals from recyclable materials. The activity was done with second-grade students over a period of three to four weeks. (PR)

  13. Project Reconstruct.

    ERIC Educational Resources Information Center

    Helisek, Harriet; Pratt, Donald

    1994-01-01

    Presents a project in which students monitor their use of trash, input and analyze information via a database and computerized graphs, and "reconstruct" extinct or endangered animals from recyclable materials. The activity was done with second-grade students over a period of three to four weeks. (PR)

  14. Hantavirus pulmonary syndrome and rodent reservoirs in the savanna-like biome of Brazil's southeastern region.

    PubMed

    Limongi, J E; Oliveira, R C; Guterres, A; Costa Neto, S F; Fernandes, J; Vicente, L H B; Coelho, M G; Ramos, V N; Ferreira, M S; Bonvicino, C R; D'Andrea, P S; Lemos, E R S

    2016-04-01

    This paper describes the diversity of rodent fauna in an area endemic for hantavirus cardiopulmonary syndrome (HCPS) in Brazil, the population dynamics and the relationship of rodents with hantavirus in the Cerrado (savanna-like) biome. Additionally, an analysis is made of the partial S segment sequences of the hantaviruses obtained from serologically confirmed human HCPS cases and from rodent specimens. Rodents were collected during four campaigns. Human serum samples were collected from suspected cases of HCPS at hospitals in the state of Minas Gerais. The samples antibody-reactive by ELISA were processed by RT-PCR. The PCR product was amplified and sequenced. Hantavirus was detected only in Necromys lasiurus, the wild rodent species most prevalent in the Cerrado biome (min-max: 50-83·7%). All the six human serum samples were hantavirus seropositive and five showed amplified PCR products. The analysis of the nucleotide sequences showed the circulation of a single genotype, the Araraquara hantavirus. The environmental changes that have occurred in the Cerrado biome in recent decades have favoured N. lasiurus in interspecific competition of habitats, thus increasing the risk of contact between humans and rodent species infected with hantavirus. Our data corroborate the definition of N. lasiurus as the main hantavirus reservoir in the Cerrado biome.

  15. Long term biosustainability in a high energy, low diversity crustal biome

    SciTech Connect

    Lin, L-H.; Wang, P-L.; Rumble, D.; Lippmann-Pipke, J.; SherwoodLollar, B.; Boice, E.; Pratt, L.; Brodie, E.; Hazen, T.C.; Andersen,G.L.; DeSantis, T.; Moser, D.P.; Kershaw, D.; Onstott, T.

    2006-10-01

    Geochemical, microbiological, and molecular analyses of alkaline saline groundwater at 2.8 kilometers depth in Archaean metabasalt revealed a microbial biome dominated by a single phylotype affiliated with thermophilic sulfate reducers belonging to Firmicutes. These sulfate reducers were sustained by geologically produced sulfate and hydrogen at concentrations sufficient to maintain activities for millions of years with no apparent reliance on photosynthetically derived substrates.

  16. Isolation and phylogenetic relationships of bat trypanosomes from different biomes in Mato Grosso, Brazil.

    PubMed

    Marcili, Arlei; da Costa, Andrea P; Soares, Herbert S; Acosta, Igor da C L; de Lima, Julia T R; Minervino, Antonio H H; Melo, Andréia T L; Aguiar, Daniel M; Pacheco, Richard C; Gennari, Solange M

    2013-12-01

    In the order Chiroptera, more than 30 trypanosome species belonging to the subgenera Herpetosoma, Schizotrypanum, Megatrypanum, and Trypanozoon have been described. The species Trypanosoma cruzi , Trypanosoma cruzi marinkellei, and Trypanosoma dionisii are the most common in bats and belong to the Schizotrypanum subgenus. Bats from 2 different biomes, Pantanal and Amazonia/Cerrado in the state of Mato Grosso, Brazil, were evaluated according to the presence of trypanosome parasites by means of hemoculture and PCR in primary samples (blood samples). A total of 211 bats from 20 different species were caught and the trypanosome prevalence, evaluated through hemoculture, was 9.0% (19), 15.5% (13), and 4.8% (6) in the municipalities of Confresa (Amazonia/Cerrado biome) and Poconé (Pantanal biome). Among the 123 primary samples obtained from the bats, only 3 (2.4%) were positive. Phylogenetic analysis using trypanosomatid barcoding (V7V8 region of SSU rDNA) identified all the isolates and primary samples as T. c. marinkellei. The sequences of the isolates were segregated according to the bat host genus or species and suggest that co-evolutionary patterns exist between hosts and parasites. Further studies in different Brazilian regions and biomes need to be conducted in order to gain real understanding of the diversity of trypanosomes in bats.

  17. Environmental Literacy through Relationships: Connecting Biomes and Society in a Sustainable City

    ERIC Educational Resources Information Center

    Haverkos, Kimberly; Bautista, Nazan

    2011-01-01

    In this article, the authors share a project developed and implemented in an eighth-grade science classroom in which students apply what they have learned about biomes to create sustainable cities. This project promotes environmental literacy through helping students understand the interrelated elements of sustainable environmental systems and how…

  18. The Biome Project: Developing a Legitimate Parallel Curriculum for Physical Education and Life Sciences

    ERIC Educational Resources Information Center

    Hastie, Peter Andrew

    2013-01-01

    The purpose of this article is to describe the outcomes of a parallel curriculum project between life sciences and physical education. Throughout a 6-week period, students in grades two through five became members of teams that represented different animal species and biomes, and concurrently participated in a season of gymnastics skills and…

  19. Vegetation productivity responds to sub-annual climate conditions across semiarid biomes

    USDA-ARS?s Scientific Manuscript database

    In the Southwestern United States (SW), the current prolonged warm drought is similar to the predicted future climate change scenarios for the region. This study aimed to determine patterns in vegetation response to the early 21st century drought across multiple biomes. We hypothesized that differen...

  20. Water balance in paired watersheds with eucalyptus and degraded grassland in Pampa biome

    USDA-ARS?s Scientific Manuscript database

    Rangelands of the Pampa biome, which cover regions of Argentina, Uruguay and Brazil (176,496 km2 – 2.07% of Brazilian territory and 63% of Rio Grande do Sul State territory, southern region of Brazil) in South America (total area of 750,000 km2), are being substituted by crops and commercial eucalyp...

  1. The Biome Project: Developing a Legitimate Parallel Curriculum for Physical Education and Life Sciences

    ERIC Educational Resources Information Center

    Hastie, Peter Andrew

    2013-01-01

    The purpose of this article is to describe the outcomes of a parallel curriculum project between life sciences and physical education. Throughout a 6-week period, students in grades two through five became members of teams that represented different animal species and biomes, and concurrently participated in a season of gymnastics skills and…

  2. Leaf carbon contents vary with the plant life forms and biomes

    NASA Astrophysics Data System (ADS)

    Ma, S.; He, F.; Tian, D.; Fang, J.

    2016-12-01

    Leaf carbon content per dry mass (LCC) is an important plant trait and also a very key factor influencing our estimations of regional and global carbon sequestration in plants. Compared with the nitrogen and phosphorus, Carbon content of plants change slight, and most studies have accepted the value of 50%, however, the variations of LCC among different biomes and life forms remain unclear. By a meta-analysis, we collected 18,338 data of plants LCC from literatures and TRY database. Our result showed that the geometric mean for plant LCC was 46.82%, but varied greatly among plant life forms. Specifically, higher LCC appeared in trees and shrubs with average values of 47.64% and 46.32%, respectively. Herbaceous plants showed a lower LCC of 44.88%, while crops and aquatic plants both exhibited the lowest LCC values of 41.93% and 41.20%, respectively. Moreover, deciduous and evergreen trees had similar LCC, while coniferous trees showed higher LCC than broadleaved trees. Remarkably, the LCC of perennial herbs demonstrated the highest with an average of 45.11% among all the herbaceous plants. In summary, the LCC showed an increase with the following order of biomes: cropland, grassland, shrubland and forest. Our results indicated that the LCC of plants was lower that 50%, and could be a perfect factor to distinguish the plant life forms and biomes. Key words: leaf carbon content, plant traits, biome, life form.

  3. Biome-specific scaling of ocean productivity, temperature, and carbon export efficiency

    NASA Astrophysics Data System (ADS)

    Britten, Gregory L.; Primeau, François W.

    2016-05-01

    Mass conservation and metabolic theory place constraints on how marine export production (EP) scales with net primary productivity (NPP) and sea surface temperature (SST); however, little is empirically known about how these relationships vary across ecologically distinct ocean biomes. Here we compiled in situ observations of EP, NPP, and SST and used statistical model selection theory to demonstrate significant biome-specific scaling relationships among these variables. Multiple statistically similar models yield a threefold variation in the globally integrated carbon flux (~4-12 Pg C yr-1) when applied to climatological satellite-derived NPP and SST. Simulated NPP and SST input variables from a 4×CO2 climate model experiment further show that biome-specific scaling alters the predicted response of EP to simulated increases of atmospheric CO2. These results highlight the need to better understand distinct pathways of carbon export across unique ecological biomes and may help guide proposed efforts for in situ observations of the ocean carbon cycle.

  4. Environmental Literacy through Relationships: Connecting Biomes and Society in a Sustainable City

    ERIC Educational Resources Information Center

    Haverkos, Kimberly; Bautista, Nazan

    2011-01-01

    In this article, the authors share a project developed and implemented in an eighth-grade science classroom in which students apply what they have learned about biomes to create sustainable cities. This project promotes environmental literacy through helping students understand the interrelated elements of sustainable environmental systems and how…

  5. Carbon storage in frozen loess and soils of the mammoth tundra-steppe biome

    NASA Astrophysics Data System (ADS)

    Zimov, N.; Zimov, S.; Zimova, A.; Zimova, G.; Chuprynin, V.; Chapin, S. F.

    2008-12-01

    During the Last Glacial Maximum (LGM), atmospheric CO2 concentration was 80-100 ppmv lower than in pre- industrial times. At the time of LGM steppe-tundra was the most extensive biome on Earth. Some estimates of the C storage in that biome assume that it was similar to cold desert and that the terrestrial carbon (C) reservoir increased at the Pleistocene-Holocene transition by 400-1300 Gt, requiring that the world oceans be a large C source. To estimate C storage in the entire steppe-tundra biome we used data of C storage in soils of this biome that persisted in permafrost of Siberia and Alaska and developed a model that describes C accumulation in soil profiles and in permafrost. The model shows a slow but consistent C increase in soil when permafrost appears. At the Pleistocene-Holocene boundary tundra-steppe soils became a C source of greater than 1000 Gt to the atmosphere. The implications of these model results are that the ocean was not a source of carbon but absorbed several hundreds of gigatons of C at that time. The model results also show that restoring the tundra-steppe ecosystem in northern Siberia would enhance soil C storage.

  6. BIOME: A scientific data archive search-and-order system using browser-aware, dynamic pages.

    SciTech Connect

    Jennings, S.V.; Yow, T.G.; Ng, V.W.

    1997-08-01

    The Oak Ridge National Laboratory`s (ORNL) Distributed Active Archive Center (DAAC) is a data archive and distribution center for the National Air and Space Administration`s (NASA) Earth Observing System Data and Information System (EOSDIS). Both the Earth Observing System (EOS) and EOSDIS are components of NASA`s contribution to the US Global Change Research Program through its Mission to Planet Earth Program. The ORNL DAAC provides access to data used in ecological and environmental research such as global change, global warming, and terrestrial ecology. Because of its large and diverse data holdings, the challenge for the ORNL DAAC is to help users find data of interest from the hundreds of thousands of files available at the DAAC without overwhelming them. Therefore, the ORNL DAAC has developed the Biogeochemical Information Ordering Management Environment (BIOME), a customized search and order system for the World Wide Web (WWW). BIOME is a public system located at http://www-eosdis.ornl.gov/BIOME/biome.html.

  7. Response of Cross-biome Productivity to the Early 21st Century Drought

    NASA Astrophysics Data System (ADS)

    Ponce-Campos, G. E.; Moran, S. M.; Huete, A. R.; Zhang, Y.; Bresloff, C. J.; Huxman, T. E.; Bosch, D. D.; Buda, A. R.; Gunter, S. A.; Kitchen, S. G.; McNab, W.; McClaran, M. P.; Morgan, J. A.; Peters, D. P.; Sadler, E.; Seyfried, M. S.; Starks, P. J.; Montoya, D. S.; Heartsill, T.; Eamus, D.

    2012-12-01

    The response of ecosystem productivity to contemporary drought coupled with record warming presents important challenges to predictive ecological modeling. In this study, we investigated the response of annual above-ground net primary production (ANPP) to precipitation variability during the early 21st century drought (2000-2009). The analysis combined satellite estimates of vegetation greenness with meteorological data from in situ climate network stations at experimental sites across a range of biomes from grassland to forest in Northern and Southern Hemispheres. We found that despite enduring prolonged warm drought conditions, all biomes retained their ANPP sensitivities to mean annual precipitation. Rain use efficiencies (RUE = ANPP/precipitation) were highest for the grassland and decreased with higher precipitation over the humid forest sites. For the most extreme drought conditions in the driest years, cross-biome RUE converged to a common, maximum rain use efficiency (RUEmax) that exceeded values previously reported. These results have implications for predicting productivity responses to potential climate change across a range of terrestrial biomes. The satellite-based approach demonstrated here may provide a means of monitoring productivity at experimental sites to better understand the consequences of predicted climate change on food security and resource management.

  8. Extreme precipitation patterns and reductions of terrestrial ecosystem production across biomes

    NASA Astrophysics Data System (ADS)

    Zhang, Yongguang; Susan Moran, M.; Nearing, Mark A.; Ponce Campos, Guillermo E.; Huete, Alfredo R.; Buda, Anthony R.; Bosch, David D.; Gunter, Stacey A.; Kitchen, Stanley G.; Henry McNab, W.; Morgan, Jack A.; McClaran, Mitchel P.; Montoya, Diane S.; Peters, Debra P. C.; Starks, Patrick J.

    2013-03-01

    Precipitation regimes are predicted to shift to more extreme patterns that are characterized by more heavy rainfall events and longer dry intervals, yet their ecological impacts on vegetation production remain uncertain across biomes in natural climatic conditions. This in situ study investigated the effects of these climatic conditions on aboveground net primary production (ANPP) by combining a greenness index from satellite measurements and climatic records during 2000-2009 from 11 long-term experimental sites in multiple biomes and climates. Results showed that extreme precipitation patterns decreased the sensitivity of ANPP to total annual precipitation (PT) at the regional and decadal scales, leading to decreased rain use efficiency (RUE; by 20% on average) across biomes. Relative decreases in ANPP were greatest for arid grassland (16%) and Mediterranean forest (20%) and less for mesic grassland and temperate forest (3%). The cooccurrence of heavy rainfall events and longer dry intervals caused greater water stress conditions that resulted in reduced vegetation production. A new generalized model was developed using a function of both PT and an index of precipitation extremes and improved predictions of the sensitivity of ANPP to changes in precipitation patterns. Our results suggest that extreme precipitation patterns have substantially negative effects on vegetation production across biomes and are as important as PT. With predictions of more extreme weather events, forecasts of ecosystem production should consider these nonlinear responses to altered extreme precipitation patterns associated with climate change.

  9. Seasonal Biophysical Dynamics of Biomes from Space Using MODIS Vegetation Indices

    NASA Astrophysics Data System (ADS)

    Huete, A. R.; Didan, K.; Ratana, P.; Miura, T.

    2002-12-01

    We utilized two years of Terra- Moderate Resolution Imaging Spectroradiometer (MODIS) Vegetation Index (VI) products to analyze the seasonal and spatial patterns of photosynthetic vegetation activity over a global range of biomes, from hyperarid surfaces to per-humid tropical rainforests. This was done in support of a global-based MODIS VI validation analysis. Using global land cover classification schemes and climatic data, we analyzed the seasonality patterns of major biome types and climatic regions. Both the normalized difference vegetation index (NDVI) and the enhanced vegetation index (EVI) at 250-m, 500-m, and 1-km were used to extract seasonal profile curves. The quality assurance (QA) information of the output products was used in noise removal and data filtering prior to the generation of the seasonal profiles. Histogram analyses were also performed for each biome type and climatic region as well as over site-intensive, core validation sites with flux towers. The seasonal patterns of the semiarid and savannah regions were very pronounced with distinct dry and wet seasonal trends. Forested regions exhibited less pronounced trends, with the exception of some of the deciduous broadleaf forests. The NDVI and EVI responded differently to canopy photosynthetic activity and canopy structural variations and complemented each other in the global analysis of seasonality patterns. Lastly, we compared the seasonal trends of some of the biomes with those obtained with the AVHRR-NDVI product and found the MODIS VI products to respond with greater sensitivity.

  10. Animal Movement and Establishment of Vaccinia Virus Cantagalo Strain in Amazon Biome, Brazil

    PubMed Central

    Quixabeira-Santos, Jociane Cristina; Medaglia, Maria Luiza G.; Pescador, Caroline A.

    2011-01-01

    To understand the emergence of vaccinia virus Cantagalo strain in the Amazon biome of Brazil, during 2008–2010 we conducted a molecular and epidemiologic survey of poxvirus outbreaks. Data indicate that animal movement was the major cause of virus dissemination within Rondônia State, leading to the establishment and spread of this pathogen. PMID:21470472

  11. Assessing the Urban Heat Island Effect Across Biomes in the Continental USA Using Landsat and MODIS

    NASA Technical Reports Server (NTRS)

    Imhoff, Marc L.; Bounoua, L.; Zhang, Ping; Wolfe, Robert

    2011-01-01

    Impervious surface area (ISA) from the Landsat TM and land surface temperature (LST) from MODIS averaged over three annual cycles (2003-2005) are used in a spatial analysis to assess the urban heat island (UHI) skin temperature amplitude and its relationship to development intensity, size, and ecological setting for 38 of the most populous cities in the continental United States. Development intensity zones based on %ISA are defined across urban gradients and used to stratify sampling of LST and NDVI. We find that ecological context significantly influences the amplitude of summer daytime UHI (urban - rural temperature difference) with the largest 8 C (average) for cities built in mixed forest biomes. For all cities ISA is the primary driver for increase in temperature explaining 70% of the total variance. Annually, urban areas are warmer than the non-urban fringe by 2.9 C, except in biomes with arid and semiarid climates. The average amplitude of the UHI is asymmetric with a 4.3 C difference in summer and 1.3 C in winter. In desert environments, UHI's point to a possible heat sink effect. Results show that the urban heat island amplitude increases with city size and is seasonally asymmetric for a large number of cities across most biomes. The implications are that for urban areas developed within forested ecosystems the summertime UHI can be quite high relative to the wintertime UHI suggesting that the residential energy consumption required for summer cooling is likely to increase with urban growth within those biomes.

  12. Nitrate uptake across biomes and the influence of elemental stoichiometry: A new look at LINX II

    NASA Astrophysics Data System (ADS)

    Wymore, Adam S.; Coble, Ashley A.; Rodríguez-Cardona, Bianca; McDowell, William H.

    2016-08-01

    Considering recent increases in anthropogenic N loading, it is essential to identify the controls on N removal and retention in aquatic ecosystems because the fate of N has consequences for water quality in streams and downstream ecosystems. Biological uptake of nitrate (NO3-) is a major pathway by which N is removed from these ecosystems. Here we used data from the second Lotic Intersite Nitrogen eXperiment (LINX II) in a multivariate analysis to identify the primary drivers of variation in NO3- uptake velocity among biomes. Across 69 study watersheds in North America, dissolved organic carbon:NO3- ratios and photosynthetically active radiation were identified as the two most important predictor variables in explaining NO3- uptake velocity. However, within a specific biome the predictor variables of NO3- uptake velocity varied and included various physical, chemical, and biological attributes. Our analysis demonstrates the broad control of elemental stoichiometry on NO3- uptake velocity as well as the importance of biome-specific predictors. Understanding this spatial variation has important implications for biome-specific watershed management and the downstream export of NO3-, as well as for development of spatially explicit global models that describe N dynamics in streams and rivers.

  13. Explicit Not Implicit Preferences Predict Conservation Intentions for Endangered Species and Biomes.

    PubMed

    Echeverri, Alejandra; Callahan, Megan M; Chan, Kai M A; Satterfield, Terre; Zhao, Jiaying

    2017-01-01

    Conservation of biodiversity is determined in part by human preferences. Preferences relevant to conservation have been examined largely via explicit measures (e.g., a self-reported degree of liking), with implicit measures (e.g., preconscious, automatic evaluations) receiving relatively less attention. This is the case despite psychological evidence from other contexts that implicit preferences are more informative of behavior. Thus, the type of measure that predicts conservation intentions for biodiversity is unknown. We conducted three studies to examine conservation intentions in light of people's explicit and implicit preferences toward four endangered species (sea otter, American badger, caribou, yellow-breasted chat) and four biomes (forest, ocean, grassland, tundra). In Study 1 (n = 55), we found that people implicitly preferred caribou most, but explicitly preferred sea otter most, with a significant multiple regression where participants' explicit preferences dictated their stated intended donations for conservation of each species. In Study 2 (n = 57) we found that people implicitly and explicitly preferred forest and ocean over grassland and tundra. Explicit rather than implicit preferences predicted the intended donation for conservation of the ocean biome. Study 3 involved a broader online sample of participants (n = 463) and also found that explicit preferences dictated the intended donations for conservation of biomes and species. Our findings reveal discrepancies between implicit and explicit preferences toward species, but not toward biomes. Importantly, the results demonstrate that explicit rather than implicit preferences predict conservation intentions for biodiversity. The current findings have several implications for conservation and the communication of biodiversity initiatives.

  14. Extreme precipitation patterns and reductions of terrestrial ecosystem production across biomes

    Treesearch

    Yongguang Zhang; M. Susan Moran; Mark A. Nearing; Guillermo E. Ponce Campos; Alfredo R. Huete; Anthony R. Buda; David D. Bosch; Stacey A. Gunter; Stanley G. Kitchen; W. Henry McNab; Jack A. Morgan; Mitchel P. McClaran; Diane S. Montoya; Debra P.C. Peters; Patrick J. Starks

    2013-01-01

    Precipitation regimes are predicted to shift to more extreme patterns that are characterized by more heavy rainfall events and longer dry intervals, yet their ecological impacts on vegetation production remain uncertain across biomes in natural climatic conditions. This in situ study investigated the effects of these climatic conditions on aboveground net primary...

  15. Himalayan uplift shaped biomes in Miocene temperate Asia: evidence from leguminous Caragana

    Treesearch

    Ming-Li Zhang; Xiao-Guo Xiang; Juan-Juan Xue; Stewart C. Sanderson; Peter W. Fritsch

    2016-01-01

    Caragana, with distinctive variation in leaf and rachis characters, exhibits three centers of geographic distribution, i.e., Central Asia, the Qinghai-Tibetan Plateau (QTP), and East Asia, corresponding to distinct biomes. Because Caragana species are often ecologically dominant components of the vegetation in these regions, it is regarded as a key taxon for...

  16. New Coupled Model Used Inversely for Reconstructing Past Terrestrial Carbon Storage from Pollen Data: Validation of Model Using Modern Data

    NASA Astrophysics Data System (ADS)

    Wu, H.; Guiot, J.; Peng, C.; Guo, Z.

    2010-12-01

    The knowledge of potential impacts of climate change on terrestrial vegetation is crucial for understanding long-term global carbon cycles. Discrepancy in data has long existed between past carbon storage reconstructions since the Last Glacial Maximum by means of pollen, carbon isotope, and general circulation model (GCM) analysis. This may be due to the fact that these methods do not synthetically take into account significant differences in climate distribution between modern and past conditions as well as the effects of atmospheric CO2 concentration on vegetation. In this study, a new estimate of past biospheric carbon stocks is reported utilizing a new integrated ecosystem model (PCM) built on a physiological process vegetation model (BIOME4) coupled with a process-based biospheric carbon model (DEMETER). The PCM was constrained to fit pollen data to obtain realistic estimates. It was estimated that the probability distribution of climatic parameters, as simulated by BIOME4 in an inverse process, was compatible with pollen data while DEMETER successfully simulated the carbon storage values with the corresponding outputs of BIOME4. The carbon model was validated with observable global vegetation biomass and soil carbon, and the inversion scheme was tested against 1491 surface pollen spectra sample sites procured in Africa and Eurasia. Results show that this method can successfully simulate most biomes at selected pollen sites as well as demonstrate that the coefficient of determination (R) calculated between the observed and reconstructed modern climates vary from 0.83 to 0.97. Comparisons between the simulated biome-average terrestrial carbon variables with available observations also indicate a consensus: R variability of 0.96 for vegetation carbon density and 0.90 for soil carbon density. These results demonstrate the reliability and feasibility of this climate reconstruction method and its efficiency in reconstructing past terrestrial carbon storage.

  17. Comparing projections of future changes in runoff from hydrological and biome models in ISI-MIP

    NASA Astrophysics Data System (ADS)

    Davie, J. C. S.; Falloon, P. D.; Kahana, R.; Dankers, R.; Betts, R.; Portmann, F. T.; Wisser, D.; Clark, D. B.; Ito, A.; Masaki, Y.; Nishina, K.; Fekete, B.; Tessler, Z.; Wada, Y.; Liu, X.; Tang, Q.; Hagemann, S.; Stacke, T.; Pavlick, R.; Schaphoff, S.; Gosling, S. N.; Franssen, W.; Arnell, N.

    2013-10-01

    Future changes in runoff can have important implications for water resources and flooding. In this study, runoff projections from ISI-MIP (Inter-sectoral Impact Model Intercomparison Project) simulations forced with HadGEM2-ES bias-corrected climate data under the Representative Concentration Pathway 8.5 have been analysed for differences between impact models. Projections of change from a baseline period (1981-2010) to the future (2070-2099) from 12 impacts models which contributed to the hydrological and biomes sectors of ISI-MIP were studied. The biome models differed from the hydrological models by the inclusion of CO2 impacts and most also included a dynamic vegetation distribution. The biome and hydrological models agreed on the sign of runoff change for most regions of the world. However, in West Africa, the hydrological models projected drying, and the biome models a moistening. The biome models tended to produce larger increases and smaller decreases in regionally averaged runoff than the hydrological models, although there is large inter-model spread. The timing of runoff change was similar, but there were differences in magnitude, particularly at peak runoff. The impact of vegetation distribution change was much smaller than the projected change over time, while elevated CO2 had an effect as large as the magnitude of change over time projected by some models in some regions. The effect of CO2 on runoff was not consistent across the models, with two models showing increases and two decreases. There was also more spread in projections from the runs with elevated CO2 than with constant CO2. The biome models which gave increased runoff from elevated CO2 were also those which differed most from the hydrological models. Spatially, regions with most difference between model types tended to be projected to have most effect from elevated CO2, and seasonal differences were also similar, so elevated CO2 can partly explain the differences between hydrological and

  18. Forgotten forests - issues and prospects in biome mapping using Seasonally Dry Tropical Forests as a case study

    PubMed Central

    2011-01-01

    Background South America is one of the most species diverse continents in the world. Within South America diversity is not distributed evenly at both local and continental scales and this has led to the recognition of various areas with unique species assemblages. Several schemes currently exist which divide the continental-level diversity into large species assemblages referred to as biomes. Here we review five currently available biome maps for South America, including the WWF Ecoregions, the Americas basemap, the Land Cover Map of South America, Morrone's Biogeographic regions of Latin America, and the Ecological Systems Map. The comparison is performed through a case study on the Seasonally Dry Tropical Forest (SDTF) biome using herbarium data of habitat specialist species. Results Current biome maps of South America perform poorly in depicting SDTF distribution. The poor performance of the maps can be attributed to two main factors: (1) poor spatial resolution, and (2) poor biome delimitation. Poor spatial resolution strongly limits the use of some of the maps in GIS applications, especially for areas with heterogeneous landscape such as the Andes. Whilst the Land Cover Map did not suffer from poor spatial resolution, it showed poor delimitation of biomes. The results highlight that delimiting structurally heterogeneous vegetation is difficult based on remote sensed data alone. A new refined working map of South American SDTF biome is proposed, derived using the Biome Distribution Modelling (BDM) approach where georeferenced herbarium data is used in conjunction with bioclimatic data. Conclusions Georeferenced specimen data play potentially an important role in biome mapping. Our study shows that herbarium data could be used as a way of ground-truthing biome maps in silico. The results also illustrate that herbarium data can be used to model vegetation maps through predictive modelling. The BDM approach is a promising new method in biome mapping, and could be

  19. Estimating 40 years of nitrogen deposition in global biomes using the SCIAMACHY NO2 column

    USGS Publications Warehouse

    Lu, Xuehe; Zhang, Xiuying; Liu, Jinxun; Jin, Jiaxin

    2016-01-01

    Owing to human activity, global nitrogen (N) cycles have been altered. In the past 100 years, global N deposition has increased. Currently, the monitoring and estimating of N deposition and the evaluation of its effects on global carbon budgets are the focus of many researchers. NO2 columns retrieved by space-borne sensors provide us with a new way of exploring global N cycles and these have the ability to estimate N deposition. However, the time range limitation of NO2 columns makes the estimation of long timescale N deposition difficult. In this study we used ground-based NOx emission data to expand the density of NO2columns, and 40 years of N deposition (1970–2009) was inverted using the multivariate linear model with expanded NO2 columns. The dynamic of N deposition was examined in both global and biome scales. The results show that the average N deposition was 0.34 g N m–2 year–1 in the 2000s, which was an increase of 38.4% compared with the 1970s’. The total N deposition in different biomes is unbalanced. N deposition is only 38.0% of the global total in forest biomes; this is made up of 25.9%, 11.3, and 0.7% in tropical, temperate, and boreal forests, respectively. As N-limited biomes, there was little increase of N deposition in boreal forests. However, N deposition has increased by a total of 59.6% in tropical forests and croplands, which are N-rich biomes. Such characteristics may influence the effects on global carbon budgets.

  20. Aura-biomes are present in the water layer above coral reef benthic macro-organisms.

    PubMed

    Walsh, Kevin; Haggerty, J Matthew; Doane, Michael P; Hansen, John J; Morris, Megan M; Moreira, Ana Paula B; de Oliveira, Louisi; Leomil, Luciana; Garcia, Gizele D; Thompson, Fabiano; Dinsdale, Elizabeth A

    2017-01-01

    As coral reef habitats decline worldwide, some reefs are transitioning from coral- to algal-dominated benthos with the exact cause for this shift remaining elusive. Increases in the abundance of microbes in the water column has been correlated with an increase in coral disease and reduction in coral cover. Here we investigated how multiple reef organisms influence microbial communities in the surrounding water column. Our study consisted of a field assessment of microbial communities above replicate patches dominated by a single macro-organism. Metagenomes were constructed from 20 L of water above distinct macro-organisms, including (1) the coral Mussismilia braziliensis, (2) fleshy macroalgae (Stypopodium, Dictota and Canistrocarpus), (3) turf algae, and (4) the zoanthid Palythoa caribaeorum and were compared to the water microbes collected 3 m above the reef. Microbial genera and functional potential were annotated using MG-RAST and showed that the dominant benthic macro-organisms influence the taxa and functions of microbes in the water column surrounding them, developing a specific "aura-biome". The coral aura-biome reflected the open water column, and was associated with Synechococcus and functions suggesting oligotrophic growth, while the fleshy macroalgae aura-biome was associated with Ruegeria, Pseudomonas, and microbial functions suggesting low oxygen conditions. The turf algae aura-biome was associated with Vibrio, Flavobacterium, and functions suggesting pathogenic activity, while zoanthids were associated with Alteromonas and functions suggesting a stressful environment. Because each benthic organism has a distinct aura-biome, a change in benthic cover will change the microbial community of the water, which may lead to either the stimulation or suppression of the recruitment of benthic organisms.

  1. Forest carbon emissions from cropland expansion in the Brazilian Cerrado biome

    NASA Astrophysics Data System (ADS)

    Noojipady, Praveen; Morton, C. Douglas; Macedo, N. Marcia; Victoria, C. Daniel; Huang, Chengquan; Gibbs, K. Holly; Edson Bolfe, L.

    2017-02-01

    Land use, land use change, and forestry accounted for two-thirds of Brazil’s greenhouse gas emissions profile in 2005. Amazon deforestation has declined by more than 80% over the past decade, yet Brazil’s forests extend beyond the Amazon biome. Rapid expansion of cropland in the neighboring Cerrado biome has the potential to undermine climate mitigation efforts if emissions from dry forest and woodland conversion negate some of the benefits of avoided Amazon deforestation. Here, we used satellite data on cropland expansion, forest cover, and vegetation carbon stocks to estimate annual gross forest carbon emissions from cropland expansion in the Cerrado biome. Nearly half of the Cerrado met Brazil’s definition of forest cover in 2000 (≥0.5 ha with ≥10% canopy cover). In areas of established crop production, conversion of both forest and non-forest Cerrado formations for cropland declined during 2003–2013. However, forest carbon emissions from cropland expansion increased over the past decade in Matopiba, a new frontier of agricultural production that includes portions of Maranhão, Tocantins, Piauí, and Bahia states. Gross carbon emissions from cropland expansion in the Cerrado averaged 16.28 Tg C yr‑1 between 2003 and 2013, with forest-to-cropland conversion accounting for 29% of emissions. The fraction of forest carbon emissions from Matopiba was much higher; between 2010–2013, large-scale cropland conversion in Matopiba contributed 45% of total Cerrado forest carbon emissions. Carbon emissions from Cerrado-to-cropland transitions offset 5%–7% of the avoided emissions from reduced Amazon deforestation rates during 2011–2013. Comprehensive national estimates of forest carbon fluxes, including all biomes, are critical to detect cross-biome leakage within countries and achieve climate mitigation targets to reduce emissions from land use, land use change, and forestry.

  2. The theory of variances in equilibrium reconstruction

    SciTech Connect

    Zakharov, Leonid E.; Lewandowski, Jerome; Foley, Elizabeth L.; Levinton, Fred M.; Yuh, Howard Y.; Drozdov, Vladimir; McDonald, D. C.

    2008-09-15

    The theory of variances of equilibrium reconstruction is presented. It complements existing practices with information regarding what kind of plasma characteristics can be reconstructed, how accurately, and what remains beyond the abilities of diagnostic systems. The {sigma}-curves, introduced by the present theory, give a quantitative assessment of quality of effectiveness of diagnostic systems in constraining equilibrium reconstructions. The theory also suggests a method for aligning the accuracy of measurements of different physical nature and for improvements of numerical algorithms used in reconstruction.

  3. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

    PubMed Central

    2012-01-01

    Background We present the Biological Observation Matrix (BIOM, pronounced “biome”) format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observation metadata. As the number of categories of comparative omics data types (collectively, the “ome-ome”) grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses. Findings The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages. Conclusions The BIOM file format and the biom-format project are steps toward reducing the “bioinformatics bottleneck” that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium. PMID:23587224

  4. Future changes in South American biomass distributions, biome distributions and plant trait spectra is dependent on applied atmospheric forcings.

    NASA Astrophysics Data System (ADS)

    Langan, Liam; Scheiter, Simon; Higgins, Steven

    2017-04-01

    It remains poorly understood why the position of the forest-savanna biome boundary, in a domain defined by precipitation and temperature, differs in South America, Africa and Australia. Process based Dynamic Global Vegetation Models (DGVMs) are a valuable tool to investigate the determinants of vegetation distributions, however, many DGVMs fail to predict the spatial distribution or indeed presence of the South American savanna biome. Evidence suggests fire plays a significant role in mediating forest-savanna biome boundaries, however, fire alone appear to be insufficient to predict these boundaries in South America. We hypothesize that interactions between precipitation, constraints on tree rooting depth and fire, affect the probability of savanna occurrence and the position of the savanna-forest boundary. We tested our hypotheses at tropical forest and savanna sites in Brazil and Venezuela using a novel DGVM, aDGVM2, which allows plant trait spectra, constrained by trade-offs between traits, to evolve in response to abiotic and biotic conditions. Plant hydraulics is represented by the cohesion-tension theory, this allowed us to explore how soil and plant hydraulics control biome distributions and plant traits. The resulting community trait distributions are emergent properties of model dynamics. We showed that across much of South America the biome state is not determined by climate alone. Interactions between tree rooting depth, fire and precipitation affected the probability of observing a given biome state and the emergent traits of plant communities. Simulations where plant rooting depth varied in space provided the best match to satellite derived biomass estimates and generated biome distributions that reproduced contemporary biome maps well. Future projections showed that biomass distributions, biome distributions and plant trait spectra will change, however, the magnitude of these changes are highly dependent on the applied atmospheric forcings.

  5. Quantitative precipitation estimates for the northeastern Qinghai-Tibetan Plateau over the last 18,000 years

    NASA Astrophysics Data System (ADS)

    Li, Jianyong; Dodson, John; Yan, Hong; Cheng, Bo; Zhang, Xiaojian; Xu, Qinghai; Ni, Jian; Lu, Fengyan

    2017-05-01

    Quantitative information regarding the long-term variability of precipitation and vegetation during the period covering both the Late Glacial and the Holocene on the Qinghai-Tibetan Plateau (QTP) is scarce. Herein, we provide new and numerical reconstructions for annual mean precipitation (PANN) and vegetation history over the last 18,000 years using high-resolution pollen data from Lakes Dalianhai and Qinghai on the northeastern QTP. Hitherto, five calibration techniques including weighted averaging, weighted average-partial least squares regression, modern analogue technique, locally weighted weighted averaging regression, and maximum likelihood were first employed to construct robust inference models and to produce reliable PANN estimates on the QTP. The biomization method was applied for reconstructing the vegetation dynamics. The study area was dominated by steppe and characterized with a highly variable, relatively dry climate at 18,000-11,000 cal years B.P. PANN increased since the early Holocene, obtained a maximum at 8000-3000 cal years B.P. with coniferous-temperate mixed forest as the dominant biome, and thereafter declined to present. The PANN reconstructions are broadly consistent with other proxy-based paleoclimatic records from the northeastern QTP and the northern region of monsoonal China. The possible mechanisms behind the precipitation changes may be tentatively attributed to the internal feedback processes of higher latitude (e.g., North Atlantic) and lower latitude (e.g., subtropical monsoon) competing climatic regimes, which are primarily modulated by solar energy output as the external driving force. These findings may provide important insights into understanding the future Asian precipitation dynamics under the projected global warming.

  6. Defining global syndromes of fire and the relationship of these to biomes, climate and human activity

    NASA Astrophysics Data System (ADS)

    Lehmann, C.; Archibald, S.; Gomez-Dans, J.; Bradstock, R.

    2012-12-01

    Fire is a ubiquitous component of the Earth system that remains poorly understood. To date, global scale understanding of fire is limited largely to the annual extent of burning as detected by satellites. This is problematic because fire is multi-dimensional, and focus on individual metrics belies both the complexity and importance of fire within the Earth system. In an applied sense, the lack of a unified understanding of fire impedes estimation of GHG emissions or prediction of future fire regimes as a consequence of changing patterns of climate and land use. To address this we identified five key characteristics of fire regimes: size, frequency, intensity, season and extent. We combined new global datasets with existing datasets to examine cross-correlations among characteristics. We demonstrate that only certain combinations of fire characteristics are possible and this likely reflects fundamental energetic constraints derived from interactions between under-lying fuel types, climate and rates of re-growth post-fire. For example, very intense fires can only occur infrequently because a system requires a lengthy period to develop sufficient fuel to burn. Further, very cool fires only occur infrequently because fuels are not available to burn. Following, we applied a clustering algorithm to these data to determine whether we could identify syndromes of fire regimes. Pyromes, as global syndromes of fire are conceptually analogous to biomes (global syndromes of vegetation) where the extent of each pyrome is determined solely as a product of the fire characteristics themselves. A point of difference to biomes being that no one has previously attempted to quantify the global range of fire syndromes. We identified five pyromes, four of which we believe represent distinctions between crown, litter and grass-fuelled fires. The relationship of pyromes to biomes and climate are not deterministic as different biomes and climates may be represented within a single pyrome

  7. Remote Sensing of the Urban Heat Island Effect Across Biomes in the Continental USA

    NASA Technical Reports Server (NTRS)

    Imhoff, Marc L.; Zhang, Ping; Wolfe, Robert E.; Bounoua, Lahouari

    2010-01-01

    Impervious surface area (ISA) from the Landsat TM-based NLCD 2001 dataset and land surface temperature (LST) from MODIS averaged over three annual cycles (2003-2005) are used in a spatial analysis to assess the urban heat island (UHI) skin temperature amplitude and its relationship to development intensity, size, and ecological setting for 38 of the most populous cities in the continental United States. Development intensity zones based on %ISA are defined for each urban area emanating outward from the urban core to the nonurban rural areas nearby and used to stratify sampling for land surface temperatures and NDVI. Sampling is further constrained by biome and elevation to insure objective intercomparisons between zones and between cities in different biomes permitting the definition of hierarchically ordered zones that are consistent across urban areas in different ecological setting and across scales. We find that ecological context significantly influences the amplitude of summer daytime UHI (urban-rural temperature difference) the largest (8 C average) observed for cities built in biomes dominated by temperate broadleaf and mixed forest. For all cities combined, ISA is the primary driver for increase in temperature explaining 70% of the total variance in LST. On a yearly average, urban areas are substantially warmer than the non-urban fringe by 2.9 C, except for urban areas in biomes with arid and semiarid climates. The average amplitude of the UHI is remarkably asymmetric with a 4.3 C temperature difference in summer and only 1.3 C in winter. In desert environments, the LST's response to ISA presents an uncharacteristic "U-shaped" horizontal gradient decreasing from the urban core to the outskirts of the city and then increasing again in the suburban to the rural zones. UHI's calculated for these cities point to a possible heat sink effect. These observational results show that the urban heat island amplitude both increases with city size and is seasonally

  8. Estimation of Carbon Flux of Forest Ecosystem over Qilian Mountains by BIOME-BGC Model

    NASA Astrophysics Data System (ADS)

    Yan, Min; Tian, Xin; Li, Zengyuan; Chen, Erxue; Li, Chunmei

    2014-11-01

    The gross primary production (GPP) and net ecosystem exchange (NEE) are important indicators for carbon fluxes. This study aims at evaluating the forest GPP and NEE over the Qilian Mountains using meteorological, remotely sensed and other ancillary data at large scale. To realize this, the widely used ecological-process-based model, Biome-BGC, and remote-sensing-based model, MODIS GPP algorithm, were selected for the simulation of the forest carbon fluxes. The combination of these two models was based on calibrating the Biome-BGC by the optimized MODIS GPP algorithm. The simulated GPP and NEE values were evaluated against the eddy covariance observed GPPs and NEEs, and the well agreements have been reached, with R2=0.76, 0.67 respectively.

  9. Estimation of Carbon Flux of Forest Ecosystem over Qilian Mountains by BIOME-BGC Model

    NASA Astrophysics Data System (ADS)

    Yan, Min; Tian, Xin; Li, Zengyuan; Chen, Erxue; Li, Chunmei

    2014-11-01

    The gross primary production (GPP) and net ecosystem exchange (NEE) are important indicators for carbon fluxes. This study aims at evaluating the forest GPP and NEE over the Qilian Mountains using meteorological, remotely sensed and other ancillary data at large scale. To realize this, the widely used ecological-process- based model, Biome-BGC, and remote-sensing-based model, MODIS GPP algorithm, were selected for the simulation of the forest carbon fluxes. The combination of these two models was based on calibrating the Biome-BGC by the optimized MODIS GPP algorithm. The simulated GPP and NEE values were evaluated against the eddy covariance observed GPPs and NEEs, and the well agreements have been reached, with R2=0.76, 0.67 respectively.

  10. Candidatus Rickettsia andeanae, a spotted fever group agent infecting Amblyomma parvum ticks in two Brazilian biomes.

    PubMed

    Nieri-Bastos, Fernanda Aparecida; Lopes, Marcos Gomes; Cançado, Paulo Henrique Duarte; Rossa, Giselle Ayres Razera; Faccini, João Luiz Horácio; Gennari, Solange Maria; Labruna, Marcelo Bahia

    2014-04-01

    Adult ticks of the species Amblyomma parvum were collected from the vegetation in the Pantanal biome (state of Mato Grosso do Sul) and from horses in the Cerrado biome (state of Piauí) in Brazil. The ticks were individually tested for rickettsial infection via polymerase chain reaction (PCR) targeting three rickettsial genes, gltA, ompA and ompB. Overall, 63.5% (40/63) and 66.7% (2/3) of A. parvum ticks from Pantanal and Cerrado, respectively, contained rickettsial DNA, which were all confirmed by DNA sequencing to be 100% identical to the corresponding fragments of the gltA, ompA and ompB genes of Candidatus Rickettsia andeanae. This report is the first to describe Ca. R. andeanae in Brazil.

  11. [The application of biomed-informatics in cardiovascular research--data and knowledge].

    PubMed

    Zhang, Qi-Peng; Sun, Dong-Yong; Lu, Ming; Qin, Pu; Shang, Tong

    2005-04-01

    With the development of biotechnology, especially the projects which lead to high throughout experimental results, lots of data have been jammed in every related fields, and broke the balance between data and knowledge in these fields. It is urgent to refine these data, and let them be more productive. To avoid these data being decaying into rubbish, technology and theory such as database, statistics, data mining, knowledge management, and artificial intelligence had been applied into biologic and medical study fields. So, a new standalone research subject--biomed-informatics has been formed. This paper reviewed the application of biomed-informatics in cardiovascular research, and gave the view for the future development of this subject.

  12. Candidatus Rickettsia andeanae, a spotted fever group agent infecting Amblyomma parvum ticks in two Brazilian biomes

    PubMed Central

    Nieri-Bastos, Fernanda Aparecida; Lopes, Marcos Gomes; Cançado, Paulo Henrique Duarte; Rossa, Giselle Ayres Razera; Faccini, João Luiz Horácio; Gennari, Solange Maria; Labruna, Marcelo Bahia

    2014-01-01

    Adult ticks of the species Amblyomma parvum were collected from the vegetation in the Pantanal biome (state of Mato Grosso do Sul) and from horses in the Cerrado biome (state of Piauí) in Brazil. The ticks were individually tested for rickettsial infection via polymerase chain reaction (PCR) targeting three rickettsial genes, gltA, ompA and ompB. Overall, 63.5% (40/63) and 66.7% (2/3) of A. parvum ticks from Pantanal and Cerrado, respectively, contained rickettsial DNA, which were all confirmed by DNA sequencing to be 100% identical to the corresponding fragments of the gltA, ompA and ompB genes of Candidatus Rickettsia andeanae. This report is the first to describe Ca. R. andeanae in Brazil. PMID:24714968

  13. Equilibrium analysis of carbon pools and fluxes of forest biomes in the former Soviet Union

    SciTech Connect

    Kolchugina, T.P.; Vinson, T.S.

    1993-01-01

    Forests are an important component of the biosphere and sequestration of carbon in boreal forests may represent one of the few realistic alternatives to ameliorate changes in atmospheric chemistry. The former Soviet Union has the greatest expanse of boreal forests in the world; however, the role of these forests in the terrestrial carbon cycle is not fully understood because the carbon budget of the Soviet forest sector has not been established. In recognition of the need to determine the role of these forests in the global carbon cycle, the carbon budget of forest biomes in the former Soviet Union was assessed based on an equilibrium analysis of carbon cycle pools and fluxes. Net primary productivity was used to identify the rate of carbon turnover in the forest biomes.

  14. Developing Land Surface Type Map with Biome Classification Scheme Using Suomi NPP/JPSS VIIRS Data

    NASA Astrophysics Data System (ADS)

    Zhang, Rui; Huang, Chengquan; Zhan, Xiwu; Jin, Huiran

    2016-08-01

    Accurate representation of actual terrestrial surface types at regional to global scales is an important element for a wide range of applications, such as land surface parameterization, modeling of biogeochemical cycles, and carbon cycle studies. In this study, in order to meet the requirement of the retrieval of global leaf area index (LAI) and fraction of photosynthetically active radiation absorbed by the vegetation (fPAR) and other studies, a global map generated from Suomi National Polar- orbiting Partnership (S-NPP) Visible Infrared Imaging Radiometer Suite (VIIRS) surface reflectance data in six major biome classes based on their canopy structures, which include: Grass/Cereal Crops, Shrubs, Broadleaf Crops, Savannas, Broadleaf Forests, and Needleleaf Forests, was created. The primary biome classes were converted from an International Geosphere-Biosphere Program (IGBP) legend global surface type data that was created in previous study, and the separation of two crop types are based on a secondary classification.

  15. Aridity, not fire, favors nitrogen-fixing plants across tropical savanna and forest biomes.

    PubMed

    Pellegrini, Adam F A; Staver, A Carla; Hedin, Lars O; Charles-Dominique, Tristan; Tourgee, Amy

    2016-09-01

    Tropical savannas are hypothesized to be hot spots of nitrogen-fixer diversity and activity because of the high disturbance and low nitrogen characteristic of savanna landscapes. Here we compare the abundances of nitrogen-fixing and non-fixing trees in both tropical savannas and tropical forests under climatically equivalent conditions, using plant inventory studies across 566 plots in South America and Africa. A single factor, aridity, explained 19-54% of the variance in fixer abundance, and unexpectedly was more important than fire frequency, biome, and continent. Nitrogen fixers were more abundant in arid environments; as a result, African savannas, which tend to be drier, were richer in nitrogen fixers than South American savannas. Fixer abundance converged on similar levels in forests in both continents. We conclude that climate plays a greater role than fire in determining the distribution of nitrogen fixers across tropical savanna and forest biomes.

  16. Shifting Environmental Ranges and Biome Potential According to the Whittaker Relationship

    NASA Astrophysics Data System (ADS)

    de Jong, R.; Garonna, I.; Schaepman, M. E.

    2015-12-01

    Robert H. Whittaker classified biome types mainly as a function of Mean Annual Temperature (MAT) and Mean Annual Precipitation (MAP), resulting in the well-known Whittaker plot1. This relationship is still being used to map biomes globally2. The same inputs (MAT and MAP), augmented with a radiation proxy, are used in the resource-balance perspective for modeling large-scale vegetation productivity as a function of abiotic factors3. These two approaches, used in a temporally dynamic manner, provided us indicators of shifts in growth-limiting factors4 and associated environmental ranges of vegetation, which, in turn, are key indicators for the study of global change and biodiversity5. We present a study in which we used the Whittaker relationship and CRU TS 3.22 climatic data to map regions that showed variable biome potential. These regions are likely to indicate ecotones - i.e. interactions zones between biomes - that have been subject to abiotic change and where a change in the vegetation system can be anticipated. At the same time, we used remotely sensed data (GIMMS v3g 1982-2012) to study gradients in vegetation dynamics in these zones. Preliminary results show strongest environmental shifts in northern ecotones, e.g. on the tundra - boreal boundary, and associated changes in climatic growth-limiting factors4. [1] Whittaker RH (1975) Communities and Ecosystems, Macmillan, 385p.[2] Ricklefs RE (2008) The Economy of Nature, W. H. Freeman, 620p.[3] Field CB, Randerson JT, Malmström CM (1995) Global net primary production: Combining ecology and remote sensing. Remote Sensing of Environment, 51, 74-88.[4] Schenkel D, Garonna I, De Jong R, Schaepman ME (this conference) Linking Land Surface Phenology and Growth Limiting Factor Shifts over the Past 30 Years.[5] University of Zurich Research Priority Program on Global Change and Biodiversity, http://www.gcb.uzh.ch

  17. Explicit Not Implicit Preferences Predict Conservation Intentions for Endangered Species and Biomes

    PubMed Central

    Chan, Kai M. A.; Satterfield, Terre; Zhao, Jiaying

    2017-01-01

    Conservation of biodiversity is determined in part by human preferences. Preferences relevant to conservation have been examined largely via explicit measures (e.g., a self-reported degree of liking), with implicit measures (e.g., preconscious, automatic evaluations) receiving relatively less attention. This is the case despite psychological evidence from other contexts that implicit preferences are more informative of behavior. Thus, the type of measure that predicts conservation intentions for biodiversity is unknown. We conducted three studies to examine conservation intentions in light of people’s explicit and implicit preferences toward four endangered species (sea otter, American badger, caribou, yellow-breasted chat) and four biomes (forest, ocean, grassland, tundra). In Study 1 (n = 55), we found that people implicitly preferred caribou most, but explicitly preferred sea otter most, with a significant multiple regression where participants’ explicit preferences dictated their stated intended donations for conservation of each species. In Study 2 (n = 57) we found that people implicitly and explicitly preferred forest and ocean over grassland and tundra. Explicit rather than implicit preferences predicted the intended donation for conservation of the ocean biome. Study 3 involved a broader online sample of participants (n = 463) and also found that explicit preferences dictated the intended donations for conservation of biomes and species. Our findings reveal discrepancies between implicit and explicit preferences toward species, but not toward biomes. Importantly, the results demonstrate that explicit rather than implicit preferences predict conservation intentions for biodiversity. The current findings have several implications for conservation and the communication of biodiversity initiatives. PMID:28135298

  18. Ecological consequences of the expansion of N2-fixing plants in cold biomes

    USGS Publications Warehouse

    Hiltbrunner, Erika; Aerts, Rien; Bühlmann, Tobias; Huss-Danell, Kerstin; Magnusson, Borgthor; Myrold, David D.; Reed, Sasha C.; Sigurdsson, Bjarni D.; Körner, Christian

    2014-01-01

    Research in warm-climate biomes has shown that invasion by symbiotic dinitrogen (N2)-fixing plants can transform ecosystems in ways analogous to the transformations observed as a consequence of anthropogenic, atmospheric nitrogen (N) deposition: declines in biodiversity, soil acidification, and alterations to carbon and nutrient cycling, including increased N losses through nitrate leaching and emissions of the powerful greenhouse gas nitrous oxide (N2O). Here, we used literature review and case study approaches to assess the evidence for similar transformations in cold-climate ecosystems of the boreal, subarctic and upper montane-temperate life zones. Our assessment focuses on the plant genera Lupinus and Alnus, which have become invasive largely as a consequence of deliberate introductions and/or reduced land management. These cold biomes are commonly located in remote areas with low anthropogenic N inputs, and the environmental impacts of N2-fixer invasion appear to be as severe as those from anthropogenic N deposition in highly N polluted areas. Hence, inputs of N from N2 fixation can affect ecosystems as dramatically or even more strongly than N inputs from atmospheric deposition, and biomes in cold climates represent no exception with regard to the risk of being invaded by N2-fixing species. In particular, the cold biomes studied here show both a strong potential to be transformed by N2-fixing plants and a rapid subsequent saturation in the ecosystem’s capacity to retain N. Therefore, analogous to increases in N deposition, N2-fixing plant invasions must be deemed significant threats to biodiversity and to environmental quality.

  19. Aura-biomes are present in the water layer above coral reef benthic macro-organisms

    PubMed Central

    Haggerty, J. Matthew; Doane, Michael P.; Hansen, John J.; Morris, Megan M.; Moreira, Ana Paula B.; de Oliveira, Louisi; Leomil, Luciana; Garcia, Gizele D.; Thompson, Fabiano; Dinsdale, Elizabeth A.

    2017-01-01

    As coral reef habitats decline worldwide, some reefs are transitioning from coral- to algal-dominated benthos with the exact cause for this shift remaining elusive. Increases in the abundance of microbes in the water column has been correlated with an increase in coral disease and reduction in coral cover. Here we investigated how multiple reef organisms influence microbial communities in the surrounding water column. Our study consisted of a field assessment of microbial communities above replicate patches dominated by a single macro-organism. Metagenomes were constructed from 20 L of water above distinct macro-organisms, including (1) the coral Mussismilia braziliensis, (2) fleshy macroalgae (Stypopodium, Dictota and Canistrocarpus), (3) turf algae, and (4) the zoanthid Palythoa caribaeorum and were compared to the water microbes collected 3 m above the reef. Microbial genera and functional potential were annotated using MG-RAST and showed that the dominant benthic macro-organisms influence the taxa and functions of microbes in the water column surrounding them, developing a specific “aura-biome”. The coral aura-biome reflected the open water column, and was associated with Synechococcus and functions suggesting oligotrophic growth, while the fleshy macroalgae aura-biome was associated with Ruegeria, Pseudomonas, and microbial functions suggesting low oxygen conditions. The turf algae aura-biome was associated with Vibrio, Flavobacterium, and functions suggesting pathogenic activity, while zoanthids were associated with Alteromonas and functions suggesting a stressful environment. Because each benthic organism has a distinct aura-biome, a change in benthic cover will change the microbial community of the water, which may lead to either the stimulation or suppression of the recruitment of benthic organisms. PMID:28828261

  20. Ecological consequences of the expansion of N₂-fixing plants in cold biomes.

    PubMed

    Hiltbrunner, Erika; Aerts, Rien; Bühlmann, Tobias; Huss-Danell, Kerstin; Magnusson, Borgthor; Myrold, David D; Reed, Sasha C; Sigurdsson, Bjarni D; Körner, Christian

    2014-09-01

    Research in warm-climate biomes has shown that invasion by symbiotic dinitrogen (N2)-fixing plants can transform ecosystems in ways analogous to the transformations observed as a consequence of anthropogenic, atmospheric nitrogen (N) deposition: declines in biodiversity, soil acidification, and alterations to carbon and nutrient cycling, including increased N losses through nitrate leaching and emissions of the powerful greenhouse gas nitrous oxide (N2O). Here, we used literature review and case study approaches to assess the evidence for similar transformations in cold-climate ecosystems of the boreal, subarctic and upper montane-temperate life zones. Our assessment focuses on the plant genera Lupinus and Alnus, which have become invasive largely as a consequence of deliberate introductions and/or reduced land management. These cold biomes are commonly located in remote areas with low anthropogenic N inputs, and the environmental impacts of N2-fixer invasion appear to be as severe as those from anthropogenic N deposition in highly N polluted areas. Hence, inputs of N from N2 fixation can affect ecosystems as dramatically or even more strongly than N inputs from atmospheric deposition, and biomes in cold climates represent no exception with regard to the risk of being invaded by N2-fixing species. In particular, the cold biomes studied here show both a strong potential to be transformed by N2-fixing plants and a rapid subsequent saturation in the ecosystem's capacity to retain N. Therefore, analogous to increases in N deposition, N2-fixing plant invasions must be deemed significant threats to biodiversity and to environmental quality.

  1. A hierarchical analysis of terrestrial ecosystem model Biome-BGC: Equilibrium analysis and model calibration

    SciTech Connect

    Thornton, Peter E; Wang, Weile; Law, Beverly E.; Nemani, Ramakrishna R

    2009-01-01

    The increasing complexity of ecosystem models represents a major difficulty in tuning model parameters and analyzing simulated results. To address this problem, this study develops a hierarchical scheme that simplifies the Biome-BGC model into three functionally cascaded tiers and analyzes them sequentially. The first-tier model focuses on leaf-level ecophysiological processes; it simulates evapotranspiration and photosynthesis with prescribed leaf area index (LAI). The restriction on LAI is then lifted in the following two model tiers, which analyze how carbon and nitrogen is cycled at the whole-plant level (the second tier) and in all litter/soil pools (the third tier) to dynamically support the prescribed canopy. In particular, this study analyzes the steady state of these two model tiers by a set of equilibrium equations that are derived from Biome-BGC algorithms and are based on the principle of mass balance. Instead of spinning-up the model for thousands of climate years, these equations are able to estimate carbon/nitrogen stocks and fluxes of the target (steady-state) ecosystem directly from the results obtained by the first-tier model. The model hierarchy is examined with model experiments at four AmeriFlux sites. The results indicate that the proposed scheme can effectively calibrate Biome-BGC to simulate observed fluxes of evapotranspiration and photosynthesis; and the carbon/nitrogen stocks estimated by the equilibrium analysis approach are highly consistent with the results of model simulations. Therefore, the scheme developed in this study may serve as a practical guide to calibrate/analyze Biome-BGC; it also provides an efficient way to solve the problem of model spin-up, especially for applications over large regions. The same methodology may help analyze other similar ecosystem models as well.

  2. Genetic diversity of bats coronaviruses in the Atlantic Forest hotspot biome, Brazil.

    PubMed

    Góes, Luiz Gustavo Bentim; Campos, Angélica Cristine de Almeida; Carvalho, Cristiano de; Ambar, Guilherme; Queiroz, Luzia Helena; Cruz-Neto, Ariovaldo Pereira; Munir, Muhammad; Durigon, Edison Luiz

    2016-10-01

    Bats are notorious reservoirs of genetically-diverse and high-profile pathogens, and are playing crucial roles in the emergence and re-emergence of viruses, both in human and in animals. In this report, we identified and characterized previously unknown and diverse genetic clusters of bat coronaviruses in the Atlantic Forest Biome, Brazil. These results highlight the virus richness of bats and their possible roles in the public health. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. [Practical experiences in conversion to the wide angle observation systems for vitreous surgery BIOM, SDI, VPF].

    PubMed

    Senn, P

    1991-05-01

    The wide-angle observation system for vitreous surgery introduced by Spitznas und Reiner has the following advantages: Wide angle of view. Large depth of field. Good view to the periphery even with narrow pupil. Easy gas fluid exchange in a phacic eye. Free mobility of the eye when working in the periphery. Changing from the conventional vitrectomy lens system to the BIOM an experienced surgeon is familiar with the new system in a very short time.

  4. Software quality assurance and software safety in the Biomed Control System

    SciTech Connect

    Singh, R.P.; Chu, W.T.; Ludewigt, B.A.; Marks, K.M.; Nyman, M.A.; Renner, T.R.; Stradtner, R.

    1989-10-31

    The Biomed Control System is a hardware/software system used for the delivery, measurement and monitoring of heavy-ion beams in the patient treatment and biology experiment rooms in the Bevalac at the Lawrence Berkeley Laboratory (LBL). This paper describes some aspects of this system including historical background philosophy, configuration management, hardware features that facilitate software testing, software testing procedures, the release of new software quality assurance, safety and operator monitoring. 3 refs.

  5. The 13th Annual Aurora Biomed Ion Channel Retreat: Three Days of Research, Technology, and Networking.

    PubMed

    Magee, Kaylee E A; Stanwood, Shawna R

    2016-03-01

    The 13th Annual Ion Channel Retreat was held by Aurora Biomed in Vancouver, Canada from July 7 to 9, 2015. The meeting showcased prominent current research including cardiac safety and pharmacology; ion channel structure, function and engineering; transporters and ion pumps; screening technologies; ion channels as disease targets; alcohol, tobacco, and ion channels; and ion channels as pain targets. This report summarizes the work presented at the retreat.

  6. Localized and efficient cardiac CT reconstruction

    NASA Astrophysics Data System (ADS)

    Clark, D. P.; Badea, C. T.

    2017-03-01

    The superiority of iterative reconstruction techniques over classic analytical ones is well documented in a variety of CT imaging applications where radiation dose and sampling time are limiting factors. However, by definition, the iterative nature of advanced reconstruction techniques is accompanied by a substantial increase in data processing time. This problem is further exacerbated in temporal and spectral CT reconstruction problems where the gap between the amount of data acquired and the amount of data to be reconstructed is exaggerated within the framework of compressive sensing. Two keys to overcoming this barrier include (1) advancements in parallel-computing technology and (2) advancements in data-efficient reconstruction. In this work, we propose a novel, two-stage strategy for 4D cardiac CT reconstruction which leverages these two keys by (1) exploiting GPU computing hardware and by (2) reconstructing temporal contrast on a limited spatial domain. Following a review of the proposed algorithm, we demonstrate its application in retrospectively gated cardiac CT reconstruction using the 4D MOBY mouse phantom. Quantitatively, reconstructing the temporal contrast on a limited domain reduces the overall reconstruction error by 20% and the reconstruction error within the dynamic portion of the phantom by 15% (root-mean-square error metric). A complementary in vivo mouse experiment demonstrates a suitable reconstruction fidelity to allow the measurement of cardiac functional metrics while reducing computation time by 75% relative to direct reconstruction of ten phases of the cardiac cycle. We believe that the proposed algorithm will serve as the basis for novel, data-efficient, multi-dimensional CT reconstruction techniques.

  7. Quantifying the resilience of carbon dynamics in semi-arid biomes in the Southwestern U.S. to drought

    NASA Astrophysics Data System (ADS)

    Litvak, M. E.; Krofcheck, D. J.; Maurer, G.

    2015-12-01

    Semi-arid biomes in many parts of the Southwestern U.S. have experienced a range of precipitation over the last decade, ranging from wetter than average years 2006-2010 (relative to the 40-year PRISM mean), extreme drought years (2010-2011) and slightly dry-average precipitation years (2013-2015). While annual carbon uptake in semi-arid biomes of the Southwestern US is relatively low, compared to more temperate ecosystems, collectively these biomes store a significant amount of carbon on a regional scale. It is therefore of great interest to understand what impact this range in precipitation variability has on inter- and intra- annual variability in regional carbon dynamics. We use an 9 year record from 2007-2015 of continuous measurements of net ecosystem exchange of carbon (NEE) and its components (gross primary productivity (GPP) and ecosystem respiration (Re), made across a network of flux towers along an elevation/aridity gradient in New Mexico, the New Mexico Elevation Gradient (NMEG), to quantify biome-specific responses of carbon dynamics to climate variability over this time period. Biomes include a desert grassland, creosote shrubland, juniper savanna, piño