Science.gov

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. Reconstructed Arctic biome and soil distributions: implications for the late Quaternary permafrost subsystem

    NASA Astrophysics Data System (ADS)

    Hendricks, A.; Saito, K.; Bigelow, N. H.; Walsh, J. E.

    2013-12-01

    As part of a larger project exploring permafrost distribution in the Arctic and Beringia region, we are updating BIOME4 model outputs and pollen maps for 21ka (ka = thousand years ago), 6ka, and 0ka time periods. Vegetation is a key control for permafrost distribution as it can affect the surface conditions controlling permafrost in high latitudes. BIOME4 is a coupled biogeography and biogeochemical model that simulates the global equilibrium distribution of biomes. BIOME4 was initially run with two historical climatologies for the 20th century, one of which is a more current climatology not used in previous BIOME4 runs, to obtain a general 'present day' view of the biome distributions. The updated climatology shows advances in the tree line in northern Alaska, but both climatologies generally agree on evergreen and deciduous taiga/montane forest locations. Using PMIP3/CMIP5 global circulation model climate and soil data as well as prescribed carbon dioxide concentrations, we ran the BIOME4 model for each time period. 21ka reconstructions based on the BIOME4 model output show various types of tundra widespread across the region, as far south as 40°N. This differs from present day where modeled tundra is generally limited to northern areas poleward of 70°N, the southernmost extent being ~60°N. However, when compared to real-world data provided by the updated BIOME 6000 global palaeovegetation map, preliminary 21ka tundra biomes differ in coverage. The model places shrub tundras in the focus region where we know graminoid or steppe type tundra existed. The discrepancy appears to arise from soil moisture content that was not changed in the BIOME4 runs for the different time periods, implying that soil water content may be very important in obtaining correct biome distributions in the Arctic. In particular, the modeling results suggest that moisture may be a critical feature determining the distribution of shrubby vs. herbaceous tundra. We know from lake level

  4. 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

  5. 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

  6. A reconstruction of Atlantic Central African biomes and forest succession stages derived from modern pollen data and plant functional types

    NASA Astrophysics Data System (ADS)

    Lebamba, J.; Ngomanda, A.; Vincens, A.; Jolly, D.; Favier, C.; Elenga, H.; Bentaleb, I.

    2009-01-01

    New detailed vegetation reconstructions are proposed in Atlantic Central Africa from a modern pollen data set derived from 199 sites (Cameroon, Gabon and Congo) including 131 new sites. In this study, the concept of plant functional classification is improved with new and more detailed plant functional types (PFTs) and new aggregations of pollen taxa. Using the biomisation method, we reconstructed (1) modern potential biomes and (2) potential succession stages of forest regeneration, a new approach in Atlantic Central African vegetation dynamics and ecosystem functioning reconstruction. When compared to local vegetation, potential biomes are correctly reconstructed (97.5% of the sites) and tropical evergreen to semi-evergreen forest (TRFO biome) is well identified from semi-deciduous forest (TSFO biome). When the potential biomes are superimposed on the White's vegetation map, only 76.4% of the sites are correctly reconstructed. But using botanical data, correspondence and cluster analyses, the 43 sites from Congo (Mayombe) evidence more affinities with those of central Gabon and so they can also be considered as correctly reconstructed as TRFO biome and White's map must be revised. In terms of potential succession stages of forest regeneration, the mature forest (TMFO) is well differentiated from the secondary forest (TSFE), but inside this latter group, the young and the pioneer stages are not clearly identified due probably to their low sampling representation. Moreover, linked to their progressive and mosaic character, the boundaries between two forest biomes or two forest stages are not clearly detected and need also a more intensive sampling in such transitions.

  7. 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

  8. 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

  9. 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

  10. 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/

  11. 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.

  12. 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

  13. 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

  14. Bayesian Image Reconstruction in Quantitative Photoacoustic Tomography.

    PubMed

    Tarvainen, Tanja; Pulkkinen, Aki; Cox, Ben; Kaipio, Jari; Arridge, Simon

    2013-08-30

    Quantitative photoacoustic tomography is an emerging imaging technique aimed at estimating chromophore concentrations inside tissues from photoacoustic images, which are formed by combining optical information and ultrasonic propagation. This is a hybrid imaging problem in which the solution of one inverse problem acts as the data for another ill-posed inverse problem. In the optical reconstruction of quantitative photoacoustic tomography, the data is obtained as a solution of an acoustic inverse initial value problem. Thus, both the data and the noise are affected by the method applied to solve the acoustic inverse problem. In this paper, the noise of optical data is modelled as Gaussian distributed with mean and covariance approximated by solving several acoustic inverse initial value problems using acoustic noise samples as data. Furthermore, Bayesian approximation error modelling is applied to compensate for the modelling errors in the optical data caused by the acoustic solver. The results show that modelling of the noise statistics and the approximation errors can improve the optical reconstructions. PMID:24001987

  15. Multigrid-based reconstruction algorithm for quantitative photoacoustic tomography.

    PubMed

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

    2015-07-01

    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

  16. 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

  17. APPROXIMATION OF SURFACES IN QUANTITATIVE 3-D RECONSTRUCTIONS

    EPA Science Inventory

    In serial section reconstructions a series of planar profiles are taken representing curves on the surface of the structure to be reconstructed. or a number of quantitative serial section methods, approximation of a surface is done by the formation of tiles between points of adja...

  18. 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.

  19. A pollen-based biome reconstruction over the last 3.562 million years in the Far East Russian Arctic - new insights into climate-vegetation relationships at the regional scale

    NASA Astrophysics Data System (ADS)

    Tarasov, P. E.; Andreev, A. A.; Anderson, P. M.; Lozhkin, A. V.; Leipe, C.; Haltia, E.; Nowaczyk, N. R.; Wennrich, V.; Brigham-Grette, J.; Melles, M.

    2013-12-01

    The recent and fossil pollen data obtained under the frame of the multi-disciplinary international El'gygytgyn Drilling Project represent a unique archive, which allows the testing of a range of pollen-based reconstruction approaches and the deciphering of changes in the regional vegetation and climate. In the current study we provide details of the biome reconstruction method applied to the late Pliocene and Quaternary pollen records from Lake El'gygytgyn. All terrestrial pollen taxa identified in the spectra from Lake El'gygytgyn were assigned to major vegetation types (biomes), which today occur near the lake and in the broader region of eastern and northern Asia and, thus, could be potentially present in this region during the past. When applied to the pollen spectra from the middle Pleistocene to present, the method suggests (1) a predominance of tundra during the Holocene, (2) a short interval during the marine isotope stage (MIS) 5.5 interglacial distinguished by cold deciduous forest, and (3) long phases of taiga dominance during MIS 31 and, particularly, MIS 11.3. These two latter interglacials seem to be some of the longest and warmest intervals in the study region within the past million years. During the late Pliocene-early Pleistocene interval (i.e., ~3.562-2.200 Ma), there is good correspondence between the millennial-scale vegetation changes documented in the Lake El'gygytgyn record and the alternation of cold and warm marine isotope stages, which reflect changes in the global ice volume and sea level. The biome reconstruction demonstrates changes in the regional vegetation from generally warmer/wetter environments of the earlier (i.e., Pliocene) interval towards colder/drier environments of the Pleistocene. The reconstruction indicates that the taxon-rich cool mixed and cool conifer forest biomes are mostly characteristic of the time prior to MIS G16, whereas the tundra biome becomes a prominent feature starting from MIS G6. These results

  20. 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

  1. 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

  2. A comparison of ancestral state reconstruction methods for quantitative characters.

    PubMed

    Royer-Carenzi, Manuela; Didier, Gilles

    2016-09-01

    Choosing an ancestral state reconstruction method among the alternatives available for quantitative characters may be puzzling. We present here a comparison of seven of them, namely the maximum likelihood, restricted maximum likelihood, generalized least squares under Brownian, Brownian-with-trend and Ornstein-Uhlenbeck models, phylogenetic independent contrasts and squared parsimony methods. A review of the relations between these methods shows that the maximum likelihood, the restricted maximum likelihood and the generalized least squares under Brownian model infer the same ancestral states and can only be distinguished by the distributions accounting for the reconstruction uncertainty which they provide. The respective accuracy of the methods is assessed over character evolution simulated under a Brownian motion with (and without) directional or stabilizing selection. We give the general form of ancestral state distributions conditioned on leaf states under the simulation models. Ancestral distributions are used first, to give a theoretical lower bound of the expected reconstruction error, and second, to develop an original evaluation scheme which is more efficient than comparing the reconstructed and the simulated states. Our simulations show that: (i) the distributions of the reconstruction uncertainty provided by the methods generally make sense (some more than others); (ii) it is essential to detect the presence of an evolutionary trend and to choose a reconstruction method accordingly; (iii) all the methods show good performances on characters under stabilizing selection; (iv) without trend or stabilizing selection, the maximum likelihood method is generally the most accurate. PMID:27234644

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Facegram - Objective quantitative analysis in facial reconstructive surgery.

    PubMed

    Gerós, Ana; Horta, Ricardo; Aguiar, Paulo

    2016-06-01

    Evaluation of effectiveness in reconstructive plastic surgery has become an increasingly important asset in comparing and choosing the most suitable medical procedure to handle facial disfigurement. Unfortunately, traditional methods to assess the results of surgical interventions are mostly qualitative and lack information about movement dynamics. Along with this, the few existing methodologies tailored to objectively quantify surgery results are not practical in the medical field due to constraints in terms of cost, complexity and poor suitability to clinical environment. These limitations enforce an urgent need for the creation of a new system to quantify facial movement and allow for an easy interpretation by medical experts. With this in mind, we present here a novel method capable of quantitatively and objectively assess complex facial movements, using a set of morphological, static and dynamic measurements. For this purpose, RGB-D cameras are used to acquire both color and depth images, and a modified block matching algorithm, combining depth and color information, was developed to track the position of anatomical landmarks of interest. The algorithms are integrated into a user-friendly graphical interface and the analysis outcomes are organized into an innovative medical tool, named facegram. This system was developed in close collaboration with plastic surgeons and the methods were validated using control subjects and patients with facial paralysis. The system was shown to provide useful and detailed quantitative information (static and dynamic) making it an appropriate solution for objective quantitative characterization of facial movement in a clinical environment. PMID:26994664

  8. Quantitative Climate Reconstruction Based On Pollen Data From Russian Arctic

    NASA Astrophysics Data System (ADS)

    Tarasov, P. E.; Andreev, A. A.; Hubberten, H.-W.

    Three different statistical approaches have been tested to get quantitative reconstruc- tion of the Late Quaternary climate fluctuations in the Russian Arctic using surface pollen data set from the northern Eurasia. An information-statistical method (Kli- manov, 1984) is based on the statistical correlations between the total pollen and spore abundance, as well as relative values of 14 most common tree and shrub pollen taxa. Over 800 recent pollen spectra from 220 sites across the northern Eurasia were used to worked out the method. It has been applied to the fossil pollen records from the Rus- sian Arctic (e.g. Andreev and Klimanov, 2000). However, we found that it has a clear limitation in reconstruction of climate from spectra with low percentages of arboreal pollen. A plant functional type (PFT) method gives better results in reconstruction of modern climate in the forest-tundra and tundra zone (Tarasov et al., 1999). However, transfer functions between modern PFT scores and climate were also derived from the data set with a limited number of Russian Arctic pollen spectra. A best modern ana- logues method (Guiot, 1990) have been applied to the recently updated modern pollen data set, including over 1100 pollen spectra from the areas of the former USSR and Mongolia. Totally, 77 arboreal and non-arboreal pollen taxa were included in the anal- ysis. Modern climate variables at the pollen sampling sites have been calculated from the climate database with precise topography (W. Cramer, pers. comm.). We found that the mean July temperature and the sum of the mean daily temperatures above 5zC (growing-degree-days) can be reconstructed in the Russian Arctic with high accuracy. However, pollen spectra from Russian Arctic do not show a clear response to changes in the mean January temperature and in moisture index. Among the other tested vari- ables annual precipitation and runoff (annual precipitation minus evaporation) were reconstructed from the modern pollen spectra

  9. 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

  10. Quantitative assessment of healthy and reconstructed cleft lip using ultrasonography

    PubMed Central

    Devadiga, Sumana; Desai, Anil Kumar; Joshi, Shamsunder; Gopalakrishnan, K.

    2016-01-01

    Purpose: This study is conducted to investigate the feasibility of echographic imaging of tissue thickness of healthy and reconstructed cleft lip. Design: Prospective study. Materials and Methods: The study was conducted in SDM Craniofacial Unit, Dharwad and was approved by Local Institutional Review Board. A total of 30 patients, age group ranging from 4 to 25 years, of which 15 postoperative unilateral cleft lip constituted the test group. The remaining 15 with no cleft deformities, no gross facial asymmetry, constituted the control group. The thickness of the mucosa, submucosa, muscle and full thickness of the upper lip were measured with the transversal images using ultrasonography at midpoint of philtrum, right and left side philtral ridges and vermillion border, at 1, 3, 6 months interval. Results: There was an increase in muscle thickness at the vermillion border (mean = 6.9 mm) and philtral ridge (5.9 mm). Equal muscle thickness were found between the normal and test group at 6 months follow-up in a relaxed position, which was statistically significant (P = 0.0404). Conclusion: Quantitative assessment of thickness and echo levels of various lip tissues are done with proper echographic calibration. Diagnostic potentials of this method for noninvasive evaluation of cleft lip reconstructions were achieved by this study. PMID:27134448

  11. 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

  12. 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.

  13. Quantitative reconstruction of the last interglacial vegetation and climate based on the pollen record from Lake Baikal, Russia

    NASA Astrophysics Data System (ADS)

    Tarasov, P.; Granoszewski, W.; Bezrukova, E.; Brewer, S.; Nita, M.; Abzaeva, A.; Oberhänsli, H.

    2005-11-01

    Changes in mean temperature of the coldest ( T c) and warmest month ( T w), annual precipitation ( P ann) and moisture index (α) were reconstructed from a continuous pollen record from Lake Baikal, Russia. The pollen sequence CON01-603-2 (53°57'N, 108°54'E) was recovered from a 386 m water depth in the Continent Ridge and dated to ca. 130 114.8 ky BP. This time interval covers the complete last interglacial (LI), corresponding to MIS 5e. Results of pollen analysis and pollen-based quantitative biome reconstruction show pronounced changes in the regional vegetation throughout the record. Shrubby tundra covered the area at the beginning of MIS 5e (ca. 130 128 ky), consistent with the end of the Middle Pleistocene glaciation. The late glacial climate was characterised by low winter and summer temperatures ( T c ~ -38 to -35°C and T w~11 13°C) and low annual precipitation ( P ann~300 mm). However, the wide spread of tundra vegetation suggests rather moist environments associated with low temperatures and evaporation (reconstructed α~1). Tundra was replaced by boreal conifer forest (taiga) by ca. 128 ky BP, suggesting a transition to the interglacial. Taiga-dominant phase lasted until ca. 117.4 ky BP, e.g. about 10 ky. The most favourable climate conditions occurred during the first half of the LI. P ann reached 500 mm soon after 128 ky BP. However, temperature changed more gradually. Maximum values of T c ~ -20°C and T w~16 17°C are reconstructed from about 126 ky BP. Conditions became gradually colder after ca. 121 ky BP. T c dropped to ~ -27°C and T w to ~15°C by 119.5 ky BP. The reconstructed increase in continentality was accompanied by a decrease in P ann to ~400 420 mm. However, the climate was still humid enough (α~0.9) to support growth of boreal evergreen conifers. A sharp turn towards a dry climate is reconstructed after ca. 118 ky BP, causing retreat of forest and spread of cool grass-shrub communities. Cool steppe dominated the vegetation in the

  14. North American Biome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  15. Reconstruction-classification method for quantitative photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Malone, Emma; Powell, Samuel; Cox, Ben T.; Arridge, Simon

    2015-12-01

    We propose a combined reconstruction-classification method for simultaneously recovering absorption and scattering in turbid media from images of absorbed optical energy. This method exploits knowledge that optical parameters are determined by a limited number of classes to iteratively improve their estimate. Numerical experiments show that the proposed approach allows for accurate recovery of absorption and scattering in two and three dimensions, and delivers superior image quality with respect to traditional reconstruction-only approaches.

  16. Quantitative Photoacoustic Image Reconstruction using Fluence Dependent Chromophores

    PubMed Central

    Cox, B.T.; Laufer, J.G.; Beard, P.C.

    2010-01-01

    In biomedical photoacoustic imaging the images are proportional to the absorbed optical energy density, and not the optical absorption, which makes it difficult to obtain a quantitatively accurate image showing the concentration of a particular absorbing chromophore from photoacoustic measurements alone. Here it is shown that the spatially varying concentration of a chromophore whose absorption becomes zero above a threshold light fluence can be estimated from photoacoustic images obtained at increasing illumination strengths. This technique provides an alternative to model-based multiwavelength approaches to quantitative photoacoustic imaging, and a new approach to photoacoustic molecular and functional imaging. PMID:21258458

  17. 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.

  18. Quantitative reconstruction of leukocyte subsets using DNA methylation

    PubMed Central

    2014-01-01

    Background Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune modulations in virtually any blood sample including archived samples previously precluded from such analysis. Here we assess the performance characteristics and validity of this approach. Results Using Illumina Infinium HumanMethylation27 and VeraCode GoldenGate Methylation Assay microarrays, we measure DNA methylation in leukocyte subsets purified from human whole blood and identify cell lineage-specific DNA methylation signatures that distinguish human T cells, B cells, NK cells, monocytes, eosinophils, basophils and neutrophils. We employ a bioinformatics-based approach to quantify these cell types in complex mixtures, including whole blood, using DNA methylation at as few as 20 CpG loci. A reconstruction experiment confirms that the approach could accurately measure the composition of mixtures of human blood leukocyte subsets. Applying the DNA methylation-based approach to quantify the cellular components of human whole blood, we verify its accuracy by direct comparison to gold standard immune quantification methods that utilize physical, optical and proteomic characteristics of the cells. We also demonstrate that the approach is not affected by storage of blood samples, even under conditions prohibiting the use of gold standard methods. Conclusions Cell mixture distributions within peripheral blood can be assessed accurately and reliably using DNA methylation. Thus, precise immune cell differential estimates can be reconstructed using only DNA rather than whole cells. PMID:24598480

  19. 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

    2016-03-01

    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%. PMID:26837636

  20. Quantitative SPECT reconstruction using CT-derived corrections

    NASA Astrophysics Data System (ADS)

    Willowson, Kathy; Bailey, Dale L.; Baldock, Clive

    2008-06-01

    A method for achieving quantitative single-photon emission computed tomography (SPECT) based upon corrections derived from x-ray computed tomography (CT) data is presented. A CT-derived attenuation map is used to perform transmission-dependent scatter correction (TDSC) in conjunction with non-uniform attenuation correction. The original CT data are also utilized to correct for partial volume effects in small volumes of interest. The accuracy of the quantitative technique has been evaluated with phantom experiments and clinical lung ventilation/perfusion SPECT/CT studies. A comparison of calculated values with the known total activities and concentrations in a mixed-material cylindrical phantom, and in liver and cardiac inserts within an anthropomorphic torso phantom, produced accurate results. The total activity in corrected ventilation-subtracted perfusion images was compared to the calibrated injected dose of [99mTc]-MAA (macro-aggregated albumin). The average difference over 12 studies between the known and calculated activities was found to be -1%, with a range of ±7%.

  1. The quantitative reconstruction of paleoprecipitation from Chinese loess 10Be

    NASA Astrophysics Data System (ADS)

    Zhou, Weijian; Xian, Feng; Du, Yajuan; Kong, Xianghui; Wu, Zhenkun

    2016-04-01

    Cosmogenic 10Be is a promising precipitation index, because its fallout flux in sediments is mainly controlled by wet precipitation after its production in the atmosphere. Here we report on a new study for reconstructing precipitation during the last 130 ka using 10Be measurements from Chinese loess, with multivariable linear regression to remove the geomagnetic field modulation and dust flux dilution effects from the loess 10Be record. The broad similarity between our result and speleothem δ18O indicates that the new precipitation record is robust. It also records an interesting increase in precipitation that occurred during Marine Isotope Stage 3 (MIS 3), exhibiting a similar rainfall amount with that of MIS 5, suggesting that MIS 3 is a special period with strengthened summer Monsoon intensity. By comparison with a stacked marine isotope record and a summer insolation record, our precipitation data clearly show a close correspondence with Northern Hemisphere summer (June, July, and August) solar insolation changes on orbital timescales. During MIS 3, our record follows the insolation differential between 30°N and 30°S, suggesting that rising rainfall changes during MIS 3 are a response to the interhemispheric summer insolation differential forcing.

  2. A comparison of quantitative reconstruction techniques for PIXE-tomography analysis applied to biological samples

    NASA Astrophysics Data System (ADS)

    Beasley, D. G.; Alves, L. C.; Barberet, Ph.; Bourret, S.; Devès, G.; Gordillo, N.; Michelet, C.; Le Trequesser, Q.; Marques, A. C.; Seznec, H.; da Silva, R. C.

    2014-07-01

    The tomographic reconstruction of biological specimens requires robust algorithms, able to deal with low density contrast and low element concentrations. At the IST/ITN microprobe facility new GPU-accelerated reconstruction software, JPIXET, has been developed, which can significantly increase the speed of quantitative reconstruction of Proton Induced X-ray Emission Tomography (PIXE-T) data. It has a user-friendly graphical user interface for pre-processing, data analysis and reconstruction of PIXE-T and Scanning Transmission Ion Microscopy Tomography (STIM-T). The reconstruction of PIXE-T data is performed using either an algorithm based on a GPU-accelerated version of the Maximum Likelihood Expectation Maximisation (MLEM) method or a GPU-accelerated version of the Discrete Image Space Reconstruction Algorithm (DISRA) (Sakellariou (2001) [2]). The original DISRA, its accelerated version, and the MLEM algorithm, were compared for the reconstruction of a biological sample of Caenorhabditis elegans - a small worm. This sample was analysed at the microbeam line of the AIFIRA facility of CENBG, Bordeaux. A qualitative PIXE-T reconstruction was obtained using the CENBG software package TomoRebuild (Habchi et al. (2013) [6]). The effects of pre-processing and experimental conditions on the elemental concentrations are discussed.

  3. Quantitative comparison of FBP, EM, and Bayesian reconstruction algorithms for the IndyPET scanner.

    PubMed

    Frese, Thomas; Rouze, Ned C; Bouman, Charles A; Sauer, Ken; Hutchins, Gary D

    2003-02-01

    We quantitatively compare filtered backprojection (FBP), expectation-maximization (EM), and Bayesian reconstruction algorithms as applied to the IndyPET scanner--a dedicated research scanner which has been developed for small and intermediate field of view imaging applications. In contrast to previous approaches that rely on Monte Carlo simulations, a key feature of our investigation is the use of an empirical system kernel determined from scans of line source phantoms. This kernel is incorporated into the forward model of the EM and Bayesian algorithms to achieve resolution recovery. Three data sets are used, data collected on the IndyPET scanner using a bar phantom and a Hoffman three-dimensional brain phantom, and simulated data containing a hot lesion added to a uniform background. Reconstruction quality is analyzed quantitatively in terms of bias-variance measures (bar phantom) and mean square error (lesion phantom). We observe that without use of the empirical system kernel, the FBP, EM, and Bayesian algorithms give similar performance. However, with the inclusion of the empirical kernel, the iterative algorithms provide superior reconstructions compared with FBP, both in terms of visual quality and quantitative measures. Furthermore, Bayesian methods outperform EM. We conclude that significant improvements in reconstruction quality can be realized by combining accurate models of the system response with Bayesian reconstruction algorithms. PMID:12716002

  4. 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.

  5. 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

  6. A quantitative evaluation study of four-dimensional gated cardiac SPECT reconstruction.

    PubMed

    Jin, Mingwu; Yang, Yongyi; Niu, Xiaofeng; Marin, Thibault; Brankov, Jovan G; Feng, Bing; Pretorius, P Hendrik; King, Michael A; Wernick, Miles N

    2009-09-21

    In practice, gated cardiac SPECT images suffer from a number of degrading factors, including distance-dependent blur, attenuation, scatter and increased noise due to gating. Recently, we proposed a motion-compensated approach for four-dimensional (4D) reconstruction for gated cardiac SPECT and demonstrated that use of motion-compensated temporal smoothing could be effective for suppressing the increased noise due to lowered counts in individual gates. In this work, we further develop this motion-compensated 4D approach by also taking into account attenuation and scatter in the reconstruction process, which are two major degrading factors in SPECT data. In our experiments, we conducted a thorough quantitative evaluation of the proposed 4D method using Monte Carlo simulated SPECT imaging based on the 4D NURBS-based cardiac-torso (NCAT) phantom. In particular, we evaluated the accuracy of the reconstructed left ventricular myocardium using a number of quantitative measures including regional bias-variance analyses and wall intensity uniformity. The quantitative results demonstrate that use of motion-compensated 4D reconstruction can improve the accuracy of the reconstructed myocardium, which in turn can improve the detectability of perfusion defects. Moreover, our results reveal that while traditional spatial smoothing could be beneficial, its merit would become diminished with the use of motion-compensated temporal regularization. As a preliminary demonstration, we also tested our 4D approach on patient data. The reconstructed images from both simulated and patient data demonstrated that our 4D method can improve the definition of the LV wall. PMID:19724094

  7. 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.

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

    PubMed

    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. PMID:26158503

  9. 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.

  10. Central African biomes and forest succession stages derived from modern pollen data and plant functional types

    NASA Astrophysics Data System (ADS)

    Lebamba, J.; Ngomanda, A.; Vincens, A.; Jolly, D.; Favier, C.; Elenga, H.; Bentaleb, I.

    2009-07-01

    New detailed vegetation reconstructions are proposed in Atlantic Central Africa from a modern pollen data set derived from 199 sites (Cameroon, Gabon and Congo) including 131 new sites. In this study, the concept of plant functional classification is improved with new and more detailed plant functional types (PFTs) and new aggregations of pollen taxa. Using the biomisation method, we reconstructed (1) modern potential biomes and (2) potential succession stages of forest regeneration, a new approach in Atlantic Central African vegetation dynamics and ecosystem functioning reconstruction. When compared to local vegetation, potential biomes are correctly reconstructed (97.5% of the sites) and tropical rain forest (TRFO biome) is well identified from tropical seasonal forest (TSFO biome). When the potential biomes are superimposed on the White's vegetation map, only 76.4% of the sites are correctly reconstructed. But using botanical data, correspondence and cluster analyses, the 43 sites from Congo (Mayombe) evidence more affinities with those of central Gabon and so they can also be considered as correctly reconstructed as TRFO biome and White's map should be revised. In terms of potential succession stages of forest regeneration, the mature forest (TMFO) is well differentiated from the secondary forest (TSFE), but inside this latter group, the young and the pioneer stages are not clearly identified due probably to their low sampling representation. Moreover, linked to their progressive and mosaic character, the boundaries between two forest biomes or two forest stages are not clearly detected and need also a more intensive sampling in such transitions.

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

    PubMed Central

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

    2015-01-01

    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 provided accurate ranking of the reconstruction methods. We also demonstrated the application of consistency checks to test the no-gold-standard output. PMID:26430292

  12. 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.

  13. 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.

  14. 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. PMID:26493189

  15. 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. PMID:25770744

  16. 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.

  17. 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.

  18. Quantitative assessment of automatic reconstructions of branching systems obtained from laser scanning

    PubMed Central

    Boudon, Frédéric; Preuksakarn, Chakkrit; Ferraro, Pascal; Diener, Julien; Nacry, Philippe; Nikinmaa, Eero; Godin, Christophe

    2014-01-01

    Background and Aims Automatic acquisition of plant architecture is a major challenge for the construction of quantitative models of plant development. Recently, 3-D laser scanners have made it possible to acquire 3-D images representing a sampling of an object's surface. A number of specific methods have been proposed to reconstruct plausible branching structures from this new type of data, but critical questions remain regarding their suitability and accuracy before they can be fully exploited for use in biological applications. Methods In this paper, an evaluation framework to assess the accuracy of tree reconstructions is presented. The use of this framework is illustrated on a selection of laser scans of trees. Scanned data were manipulated by experienced researchers to produce reference tree reconstructions against which comparisons could be made. The evaluation framework is given two tree structures and compares both their elements and their topological organization. Similar elements are identified based on geometric criteria using an optimization algorithm. The organization of these elements is then compared and their similarity quantified. From these analyses, two indices of geometrical and structural similarities are defined, and the automatic reconstructions can thus be compared with the reference structures in order to assess their accuracy. Key Results The evaluation framework that was developed was successful at capturing the variation in similarities between two structures as different levels of noise were introduced. The framework was used to compare three different reconstruction methods taken from the literature, and allowed sensitive parameters of each one to be determined. The framework was also generalized for the evaluation of root reconstruction from 2-D images and demonstrated its sensitivity to higher architectural complexity of structure which was not detected with a global evaluation criterion. Conclusions The evaluation framework

  19. 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

  20. 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

  1. Quantitative comparison of reconstruction methods for intra-voxel fiber recovery from diffusion MRI.

    PubMed

    Daducci, Alessandro; Canales-Rodríguez, Erick Jorge; Descoteaux, Maxime; Garyfallidis, Eleftherios; Gur, Yaniv; Lin, Ying-Chia; Mani, Merry; Merlet, Sylvain; Paquette, Michael; Ramirez-Manzanares, Alonso; Reisert, Marco; Reis Rodrigues, Paulo; Sepehrband, Farshid; Caruyer, Emmanuel; Choupan, Jeiran; Deriche, Rachid; Jacob, Mathews; Menegaz, Gloria; Prčkovska, Vesna; Rivera, Mariano; Wiaux, Yves; Thiran, Jean-Philippe

    2014-02-01

    Validation is arguably the bottleneck in the diffusion magnetic resonance imaging (MRI) community. This paper evaluates and compares 20 algorithms for recovering the local intra-voxel fiber structure from diffusion MRI data and is based on the results of the "HARDI reconstruction challenge" organized in the context of the "ISBI 2012" conference. Evaluated methods encompass a mixture of classical techniques well known in the literature such as diffusion tensor, Q-Ball and diffusion spectrum imaging, algorithms inspired by the recent theory of compressed sensing and also brand new approaches proposed for the first time at this contest. To quantitatively compare the methods under controlled conditions, two datasets with known ground-truth were synthetically generated and two main criteria were used to evaluate the quality of the reconstructions in every voxel: correct assessment of the number of fiber populations and angular accuracy in their orientation. This comparative study investigates the behavior of every algorithm with varying experimental conditions and highlights strengths and weaknesses of each approach. This information can be useful not only for enhancing current algorithms and develop the next generation of reconstruction methods, but also to assist physicians in the choice of the most adequate technique for their studies. PMID:24132007

  2. 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. PMID:19635691

  3. 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. PMID:24978968

  4. Quantitative accuracy of MAP reconstruction for dynamic PET imaging in small animals

    PubMed Central

    Cheng, Ju-Chieh (Kevin); Shoghi, Kooresh; Laforest, Richard

    2012-01-01

    Purpose: Iterative reconstruction algorithms are becoming more commonly employed in positron emission tomography (PET) imaging; however, the quantitative accuracy of the reconstructed images still requires validation for various levels of contrast and counting statistics. Methods: The authors present an evaluation of the quantitative accuracy of the 3D maximum a posteriori (3D-MAP) image reconstruction algorithm for dynamic PET imaging with comparisons to two of the most widely used reconstruction algorithms: the 2D filtered-backprojection (2D-FBP) and 2D-ordered subsets expectation maximization (2D-OSEM) on the Siemens microPET scanners. The study was performed for various levels of count density encountered in typical dynamic scanning as well as the imaging of cardiac activity concentration in small animal studies on the Focus 120. Specially designed phantoms were used for evaluation of the spatial resolution, image quality, and quantitative accuracy. A normal mouse was employed to evaluate the accuracy of the blood time activity concentration extracted from left ventricle regions of interest (ROIs) within the images as compared to the actual blood activity concentration measured from arterial blood sampling. Results: For MAP reconstructions, the spatial resolution and contrast have been found to reach a stable value after 20 iterations independent of the β values (i.e., hyper parameter which controls the weight of the penalty term) and count density within the frame. The spatial resolution obtained with 3D-MAP reaches values of ∼1.0 mm with a β of 0.01 while the 2D-FBP has value of 1.8 mm and 2D-OSEM has a value of 1.6 mm. It has been observed that the lower the hyper parameter β used in MAP, more iterations are needed to reach the stable noise level (i.e., image roughness). The spatial resolution is improved by using a lower β value at the expense of higher image noise. However, with similar noise level the spatial resolution achieved by 3D-MAP was

  5. 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

  6. An analytical approach to quantitative reconstruction of non-uniform attenuated brain SPECT.

    PubMed

    Liang, Z; Ye, J; Harrington, D P

    1994-11-01

    An analytical approach to quantitative brain SPECT (single-photon-emission computed tomography) with non-uniform attenuation is developed. The approach formulates accurately the projection-transform equation as a summation of primary- and scatter-photon contributions. The scatter contribution can be estimated using the multiple-energy-window samples and removed from the primary-energy-window data by subtraction. The approach models the primary contribution as a convolution of the attenuated source and the detector-response kernel at a constant depth from the detector with the central-ray approximation. The attenuated Radon transform of the source can be efficiently deconvolved using the depth-frequency relation. The approach inverts exactly the attenuated Radon transform by Fourier transforms and series expansions. The performance of the analytical approach was studied for both uniform- and non-uniform-attenuation cases, and compared to the conventional FBP (filtered-backprojection) method by computer simulations. A patient brain X-ray image was acquired by a CT (computed-tomography) scanner and converted to the object-specific attenuation map for 140 keV energy. The mathematical Hoffman brain phantom was used to simulate the emission source and was resized such that it was completely surrounded by the skull of the CT attenuation map. The detector-response kernel was obtained from measurements of a point source at several depths in air from a parallel-hole collimator of a SPECT camera. The projection data were simulated from the object-specific attenuating source including the depth-dependent detector response. Quantitative improvement (>5%) in reconstructing the data was demonstrated with the nonuniform attenuation compensation, as compared to the uniform attenuation correction and the conventional FBP reconstruction. The commuting time was less than 5 min on an HP/730 desktop computer for an image array of 1282*32 from 128 projections of 128*32 size. PMID

  7. 3D reconstruction and quantitative assessment method of mitral eccentric regurgitation from color Doppler echocardiography

    NASA Astrophysics Data System (ADS)

    Liu, Qi; Ge, Yi Nan; Wang, Tian Fu; Zheng, Chang Qiong; Zheng, Yi

    2005-10-01

    Based on the two-dimensional color Doppler image in this article, multilane transesophageal rotational scanning method is used to acquire original Doppler echocardiography while echocardiogram is recorded synchronously. After filtering and interpolation, the surface rendering and volume rendering methods are performed. Through analyzing the color-bar information and the color Doppler flow image's superposition principle, the grayscale mitral anatomical structure and color-coded regurgitation velocity parameter were separated from color Doppler flow images, three-dimensional reconstruction of mitral structure and regurgitation velocity distribution was implemented separately, fusion visualization of the reconstructed regurgitation velocity distribution parameter with its corresponding 3D mitral anatomical structures was realized, which can be used in observing the position, phase, direction and measuring the jet length, area, volume, space distribution and severity level of the mitral regurgitation. In addition, in patients with eccentric mitral regurgitation, this new modality overcomes the inherent limitations of two-dimensional color Doppler flow image by depicting the full extent of the jet trajectory, the area of eccentric regurgitation on three-dimensional image was much larger than that on two-dimensional image, the area variation tendency and volume variation tendency of regurgitation have been shown in figure at different angle and different systolic phase. The study shows that three-dimensional color Doppler provides quantitative measurements of eccentric mitral regurgitation that are more accurate and reproducible than conventional color Doppler.

  8. 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

  9. 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

  10. 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

    2013-06-01

    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

  11. 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

  12. 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. PMID:26086729

  13. 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'. PMID:27502385

  14. Iterative reconstruction for quantitative computed tomography analysis of emphysema: consistent results using different tube currents

    PubMed Central

    Yamashiro, Tsuneo; Miyara, Tetsuhiro; Honda, Osamu; Tomiyama, Noriyuki; Ohno, Yoshiharu; Noma, Satoshi; Murayama, Sadayuki

    2015-01-01

    Purpose To assess the advantages of iterative reconstruction for quantitative computed tomography (CT) analysis of pulmonary emphysema. Materials and methods Twenty-two patients with pulmonary emphysema underwent chest CT imaging using identical scanners with three different tube currents: 240, 120, and 60 mA. Scan data were converted to CT images using Adaptive Iterative Dose Reduction using Three Dimensional Processing (AIDR3D) and a conventional filtered-back projection mode. Thus, six scans with and without AIDR3D were generated per patient. All other scanning and reconstruction settings were fixed. The percent low attenuation area (LAA%; < −950 Hounsfield units) and the lung density 15th percentile were automatically measured using a commercial workstation. Comparisons of LAA% and 15th percentile results between scans with and without using AIDR3D were made by Wilcoxon signed-rank tests. Associations between body weight and measurement errors among these scans were evaluated by Spearman rank correlation analysis. Results Overall, scan series without AIDR3D had higher LAA% and lower 15th percentile values than those with AIDR3D at each tube current (P<0.0001). For scan series without AIDR3D, lower tube currents resulted in higher LAA% values and lower 15th percentiles. The extent of emphysema was significantly different between each pair among scans when not using AIDR3D (LAA%, P<0.0001; 15th percentile, P<0.01), but was not significantly different between each pair among scans when using AIDR3D. On scans without using AIDR3D, measurement errors between different tube current settings were significantly correlated with patients’ body weights (P<0.05), whereas these errors between scans when using AIDR3D were insignificantly or minimally correlated with body weight. Conclusion The extent of emphysema was more consistent across different tube currents when CT scans were converted to CT images using AIDR3D than using a conventional filtered-back projection

  15. TOWARD A RULE-BASED BIOME MODEL

    EPA Science Inventory

    Current projections of the response of the biosphere to global climatic change indicate as much as 50% to 90% spatial displacement of extratropical biomes. he mechanism of spatial shift could be dominated by either 1) competitive displacement of northern biomes by southern biomes...

  16. 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

  17. Particle Size Evidence of Intertidal Elevation: A Basis for Quantitative Sea-level Reconstruction

    NASA Astrophysics Data System (ADS)

    Plater, Andrew; Mills, Hayley; Zhang, Weiguo; Dong, Chenyin

    2014-05-01

    The relationship between particle size distributions and bed elevation within the tidal frame is controlled largely by hydroperiod and proximity to tidal ingress. Here, the upper part of the intertidal zone is characterised by poorly sorted, near symmetrical, platy- to mesokurtic, fine-grained particle size distributions due to particle settling from suspension as the tidal flow velocity decreases to high tide slack water. Indeed, an elevational or spatial gradient in particle size distribution can be observed whereby shorter hydroperiods (higher elevations) are accompanied by slower and more variable flow velocities. However, this gradient may become complicated by creek networks, whereby particle size can be observed to decrease away from creek margins, or extant vegetation that increases bed friction. Unvegetated, planar tidal flats in the Yangtze estuary offer an ideal test bed to explore evidence for a quantitative relationship between particle size distributions and bed elevation within the tidal frame. Such a relationship would then serve as an effective proxy for tidal level preserved within sediment cores, and thus a means for reconstructing past sea level. This principle is based largely on ecological transfer function-based reconstructions of Holocene sea level from foraminifera and diatoms. Surface sediment samples were collected along three transects extending eastwards from Chongming Island in South Branch channel of the Yangtze estuary. Sample positions relative to the high water mark were determined using RTK surveying, and particle size analysis was undertaken using laser granulometry. Unconstrained cluster analysis, based on unweighted Euclidean distance, was undertaken on the particle size classes at 0.25 phi intervals (up to 50 size bins) as well as Udden-Wentworth size classes (6-7 size bins). All three transects demonstrate a good clustering of particle size classes with distance and elevation, i.e. sites that are higher within the tidal frame

  18. 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.

  19. 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.

  20. Influence of cardiac and respiratory motion on tomographic reconstructions of the heart: implications for quantitative nuclear cardiology

    SciTech Connect

    Ter-Pogossian, M.M.; Bergmann, S.R.; Sobel, B.E.

    1982-12-01

    The potential influence of physiological, periodic motions of the heart due to the cardiac cycle, the respiratory cycle, or both on quantitative image reconstruction by positron emission tomography (PET) has been largely neglected. To define their quantitative impact, cardiac PET was performed in 6 dogs after injection of /sup 11/C-palmitate under disparate conditions including: normal cardiac and respiration cycles and cardiac arrest with and without respiration. Although in vitro assay of myocardial samples demonstrated that palmitate uptake was homogeneous (coefficient of variation . 10.1%), analysis of the reconstructed images demonstrated significant heterogeneity of apparent cardiac distribution of radioactivity due to both intrinsic cardiac and respiratory motion. Image degradation due to respiratory motion was demonstrated in a healthy human volunteer as well, in whom cardiac tomography was performed with Super PETT I during breath-holding and during normal breathing. The results indicate that quantitatively significant degradation of reconstructions of true tracer distribution occurs in cardiac PET due to both intrinsic cardiac and respiratory induced motion of the heart. They suggest that avoidance of or minimization of these influences can be accomplished by gating with respect to both the cardiac cycle and respiration or by employing brief scan times during breath-holding.

  1. 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

  2. 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

  3. Quantitative simulation and density reconstruction in high-energy X-ray radiograph

    NASA Astrophysics Data System (ADS)

    Tang, Li; Xu, Haibo

    2014-03-01

    Numerical radiograph using Monte Carlo method is used to study fidelity of density reconstruction in high-energy X-ray radiography. A density reconstruction method for a polyenergetic X-ray source and an object composed of different materials is proposed. The method includes energy spectrum, angular spectrum and spot size of photon source. And it includes mass absorption coefficients explicitly in density reconstruction as well. A constrained conjugate gradient algorithm and variation regularization are applied to determine material edges and density reconstruction of a French test object. It shows that the method is valid for density reconstruction and energy spectrum of imaging photons is important in obtaining accurate material densities in high-energy X-ray radiograph.

  4. Post-Reconstruction Non-Local Means Filtering Methods using CT Side Information for Quantitative SPECT

    PubMed Central

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

    2013-01-01

    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

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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).

  10. 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

  11. Quantitative Targeted Absolute Proteomics of Transporters and Pharmacoproteomics-Based Reconstruction of P-Glycoprotein Function in Mouse Small Intestine.

    PubMed

    Akazawa, Takanori; Uchida, Yasuo; Tachikawa, Masanori; Ohtsuki, Sumio; Terasaki, Tetsuya

    2016-07-01

    The purpose of this study was to investigate whether a pharmacokinetic model integrating in vitro mdr1a efflux activity (which we previously reported) with in vitro/in vivo differences in protein expression level can reconstruct intestinal mdr1a function. In situ intestinal permeability-surface area product ratio between wild-type and mdr1a/1b (-/-) mice is one of the parameters used to describe intestinal mdr1a function. The reconstructed ratios of six mdr1a substrates (dexamethasone, digoxin, loperamide, quinidine, verapamil, vinblastine) and one nonsubstrate (diazepam) were consistent with the observed values reported by Adachi et al. within 2.1-fold difference. Thus, intestinal mdr1a function can be reconstructed by our pharmacoproteomic modeling approach. Furthermore, we evaluated regional differences in protein expression levels of mouse intestinal transporters. Sixteen (mdr1a, mrp4, bcrp, abcg5, abcg8, glut1, 4f2hc, sglt1, lat2, pept1, mct1, slc22a18, ostβ, villin1, Na(+)/K(+)-ATPase, γ-gtp) out of 46 target molecules were detected by employing our established quantitative targeted absolute proteomics technique. The protein expression amounts of mdr1a and bcrp increased progressively from duodenum to ileum. Sglt1, lat2, and 4f2hc were highly expressed in jejunum and ileum. Mct1 and ostβ were highly expressed in ileum. The quantitative expression profiles established here should be helpful to understand and predict intestinal transporter functions. PMID:27276518

  12. 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

  13. 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.

  14. 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.

  15. New Image Reconstruction Methods for Accelerated Quantitative Parameter Mapping and Magnetic Resonance Angiography

    NASA Astrophysics Data System (ADS)

    Velikina, J. V.; Samsonov, A. A.

    2016-02-01

    Advanced MRI techniques often require sampling in additional (non-spatial) dimensions such as time or parametric dimensions, which significantly elongate scan time. Our purpose was to develop novel iterative image reconstruction methods to reduce amount of acquired data in such applications using prior knowledge about signal in the extra dimensions. The efforts have been made to accelerate two applications, namely, time resolved contrast enhanced MR angiography and T1 mapping. Our result demonstrate that significant acceleration (up to 27x times) may be achieved using our proposed iterative reconstruction techniques.

  16. TGS[underscore]FIT: Image reconstruction software for quantitative, low-resolution tomographic assays

    SciTech Connect

    Estep, R J

    1993-01-01

    We developed the computer program TGS[underscore]FIT to aid in researching the tomographic gamma scanner method of nondestructive assay. This software, written in C-programming, language, implements a full Beer's Law attenuation correction in reconstructing low-resolution emission tomograms. The attenuation coefficients for the corrections are obtained by reconstructing a transmission tomogram of the same resolution. The command-driven interface, combined with (crude) simulation capabilities and command file control, allows design studies to be performed in a semi-automated manner.

  17. Quantitative reconstruction for myocardial perfusion SPECT: an efficient approach by depth-dependent deconvolution and matrix rotation.

    PubMed

    Ye, J; Liang, Z; Harrington, D P

    1994-08-01

    An efficient reconstruction method for myocardial perfusion single-photon emission computed tomography (SPECT) has been developed which compensates simultaneously for attenuation, scatter, and resolution variation. The scattered photons in the primary-energy-window measurements are approximately removed by subtracting the weighted scatter-energy-window samples. The resolution variation is corrected by deconvolving the subtracted data with the detector-response kernel in frequency space using the depth-dependent frequency relation. The attenuated photons are compensated by recursively tracing the attenuation factors through the object-specific attenuation map. An experimental chest phantom with defects inside myocardium was used to test the method. The attenuation map of the phantom was reconstructed from transmission scans using a flat external source and a high-resolution parallel-hole collimator of a single-detector system. The detector-response kernel was approximated from measurements of a point source in air at several depths from the collimator surface. The emission data were acquired by the same detector setting. A computer simulation using similar protocols as in the experiment was performed. Both the simulation and experiment showed significant improvement in quantification with the proposed method, as compared to the conventional filtered-backprojection technique. The quantitative gain by the additional deconvolution was demonstrated. The computation time was less than 20 min on a HP/730 desktop computer for reconstruction of a 1282 x 64 array from 128 projections of 128 x 64 samples. PMID:15551566

  18. 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.

  19. 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.

  20. Towards quantitative sea ice reconstructions in the northern North Atlantic: A combined biomarker and numerical modelling approach

    NASA Astrophysics Data System (ADS)

    Müller, Juliane; Wagner, Axel; Fahl, Kirsten; Stein, Ruediger; Prange, Matthias; Lohmann, Gerrit

    2011-06-01

    Organic geochemical analyses of marine surface sediments from the continental margins of East Greenland and West Spitsbergen provide for a biomarker-based estimate of recent sea ice conditions in the northern North Atlantic. By means of the sea ice proxy IP 25 and phytoplankton derived biomarkers (e.g. brassicasterol and dinosterol) we reconstruct sea ice and sea surface conditions, respectively. The combination of IP 25 with a phytoplankton marker (in terms of a phytoplankton marker-IP 25 index; PIP 25) proves highly valuable to properly interpret the sea ice proxy signal as an under- or overestimation of sea ice coverage can be circumvented. A comparison of this biomarker-based assessment of the sea ice distribution in the study area with (1) modern remote sensing data and (2) numerical modelling results reveal a good agreement between organic geochemical, satellite and modelling observations. The reasonable simulation of modern sea ice conditions by means of a regional ocean-sea ice model demonstrates the feasibility to effectively integrate the complex atmospheric and oceanic circulation features as they prevail in the study area. The good correlation between modelled sea ice parameters and the biomarker-based estimate of sea ice coverage substantiates that linking proxy and model data occurs to be a promising concept in terms of a cross-evaluation. This combinatory approach may provide a first step towards quantitative sea ice reconstructions by means of IP 25. Future IP 25 studies on marine surface sediments from the Arctic realm, however, are recommended to extend and validate this new attempt of using IP 25 in combination with a phytoplankton marker as a quantitative measure for sea ice reconstructions.

  1. 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.

  2. 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

  3. 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. PMID:23236159

  4. 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

  5. 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.

  6. CLIMATE CONSTRAINTS AND ISSUES OF SCALE CONTROLLING REGIONAL BIOMES

    EPA Science Inventory

    The prosepct of climate change threatens to cause large changes in regional biomes. hese effects could be in the form of qualitative changes within biomes, as well as spatial changes in the boundaries of biomes. he boundaries, or ecotones, between biomes have been suggested as po...

  7. Accelerated 4D Quantitative Single Point EPR Imaging Using Model-based Reconstruction

    PubMed Central

    Jang, Hyungseok; Matsumoto, Shingo; Devasahayam, Nallathamby; Subramanian, Sankaran; Zhuo, Jiachen; Krishna, Murali C.; McMillan, Alan B

    2014-01-01

    Purpose EPRI has surfaced as a promising non-invasive imaging modality that is capable of imaging tissue oxygenation. Due to extremely short spin-spin relaxation time, EPRI benefits from single point imaging and inherently suffers from limited spatial and temporal resolution, preventing localization of small hypoxic tissues and differentiation of hypoxia dynamics, making accelerated imaging a crucial issue. Method In this study, methods for accelerated single point imaging were developed by combining a bilateral k-space extrapolation technique with model-based reconstruction that benefits from dense sampling in the parameter domain (measurement of the T2* decay of an FID). In bilateral k-space extrapolation, more k-space samples are obtained in a sparsely sampled region by bilaterally extrapolating data from temporally neighboring k-spaces. To improve the accuracy of T2* estimation, a principal component analysis (PCA)-based method was implemented. Result In a computer simulation and a phantom experiment, the proposed methods showed its capability for reliable T2* estimation with high acceleration (8-fold, 15-fold, and 30-fold accelerations for 61×61×61, 95×95×95, and 127×127×127 matrix, respectively). Conclusion By applying bilateral k-space extrapolation and model-based reconstruction, improved scan times with higher spatial resolution can be achieved in the current SP-EPRI modality. PMID:24803382

  8. 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

    2016-04-01

    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.

  9. 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.

  10. 3-D Monte Carlo-Based Scatter Compensation in Quantitative I-131 SPECT Reconstruction

    PubMed Central

    Dewaraja, Yuni K.; Ljungberg, Michael; Fessler, Jeffrey A.

    2010-01-01

    We have implemented highly accurate Monte Carlo based scatter modeling (MCS) with 3-D ordered subsets expectation maximization (OSEM) reconstruction for I-131 single photon emission computed tomography (SPECT). The scatter is included in the statistical model as an additive term and attenuation and detector response are included in the forward/backprojector. In the present implementation of MCS, a simple multiple window-based estimate is used for the initial iterations and in the later iterations the Monte Carlo estimate is used for several iterations before it is updated. For I-131, MCS was evaluated and compared with triple energy window (TEW) scatter compensation using simulation studies of a mathematical phantom and a clinically realistic voxel-phantom. Even after just two Monte Carlo updates, excellent agreement was found between the MCS estimate and the true scatter distribution. Accuracy and noise of the reconstructed images were superior with MCS compared to TEW. However, the improvement was not large, and in some cases may not justify the large computational requirements of MCS. Furthermore, it was shown that the TEW correction could be improved for most of the targets investigated here by applying a suitably chosen scaling factor to the scatter estimate. Finally clinical application of MCS was demonstrated by applying the method to an I-131 radioimmunotherapy (RIT) patient study. PMID:20104252

  11. 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.

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

    PubMed

    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

  13. Quantitative morphochemical characterization of the neurons in substantia nigra of rat brain and its volume reconstruction.

    PubMed

    Khudoerkov, R M; Voronkov, D N; Dikalova, Yu V

    2014-04-01

    Three cell compartments differing by size and proportion of neurons were identified by 3D reconstruction of the substantia nigra pars compacta of the rat brain based on immunohistochemical localization of tyrosine hydroxylase, a marker of dopamine neurons. Dopaminepositive neurons prevailed over dopamine-free neurons (1.45:1) in the most voluminous (75%) dorsal part, and in smaller lateral and ventral parts, inverse cell ratios were observed: 0.54:1 and 0.78:1, respectively. Morphometry characterized the substantia nigra pars compacta as a structure consisting not only of several parts, but of horizons and showed differences between the neurons both in several parts and in several layers within the part. The revealed morphochemical heterogeneity of the substantia nigra pars compacta provides better understanding of the selective damage to its structures in Parkinson's disease. PMID:24824717

  14. 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

  15. 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%. PMID:22256218

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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'. PMID:27502382

  1. 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.

  2. Quantitation of the reconstruction quality of a four-dimensional computed tomography process for lung cancer patients

    SciTech Connect

    Lu Wei; Parikh, Parag J.; El Naqa, Issam M.; Nystrom, Michelle M.; Hubenschmidt, James P.; Wahab, Sasha H.; Mutic, Sasa; Singh, Anurag K.; Christensen, Gary E.; Bradley, Jeffrey D.; Low, Daniel A.

    2005-04-01

    We have developed a four-dimensional computed tomography (4D CT) technique for mapping breathing motion in radiotherapy treatment planning. A multislice CT scanner (1.5 mm slices) operated in cine mode was used to acquire 12 contiguous slices in each couch position for 15 consecutive scans (0.5 s rotation, 0.25 s between scans) while the patient underwent simultaneous quantitative spirometry measurements to provide a sorting metric. The spirometry-sorted scans were used to reconstruct a 4D data set. A critical factor for 4D CT is quantifying the reconstructed data set quality which we measure by correlating the metric used relative to internal-object motion. For this study, the internal air content within the lung was used as a surrogate for internal motion measurements. Thresholding and image morphological operations were applied to delineate the air-containing tissues (lungs, trachea) from each CT slice. The Hounsfield values were converted to the internal air content (V). The relationship between the air content and spirometer-measured tidal volume ({nu}) was found to be quite linear throughout the lungs and was used to estimate the overall accuracy and precision of tidal volume-sorted 4D CT. Inspection of the CT-scan air content as a function of tidal volume showed excellent correlations (typically r>0.99) throughout the lung volume. Because of the discovered linear relationship, the ratio of internal air content to tidal volume was indicative of the fraction of air change in each couch position. Theoretically, due to air density differences within the lung and in room, the sum of these ratios would equal 1.11. For 12 patients, the mean value was 1.08{+-}0.06, indicating the high quality of spirometry-based image sorting. The residual of a first-order fit between {nu} and V was used to estimate the process precision. For all patients, the precision was better than 8%, with a mean value of 5.1%{+-}1.9%. This quantitative analysis highlights the value of using

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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. PMID:25739646

  13. Late Mesozoic- Cenozoic plate boundaries in the North Atlantic – Arctic: Quantitative reconstructions using Hellinger criterion in GPlates

    NASA Astrophysics Data System (ADS)

    Gaina, Carmen; Watson, Robin; Cirbus, Juraj

    2015-04-01

    Cretaceous extension that resulted in the formation of several sedimentary basins along the North American and western and southwestern Greenland margin was followed by seafloor spreading in the Labrador Sea and Baffin Bay. Controversy regarding the timing of the oldest oceanic crust in these basins spanned more than 25 years and it is still not resolved due to the complexity of the margins and non-uniqueness of potential field data interpretation. Here we revisit the geophysical data (in particular the magnetic and gravity data) available for the Labrador Sea and Baffin Bay in order to identify the age of oceanic crust and infer new parameters that can be used for quantitative kinematic reconstructions. We identify chrons 20 to 29 for the central part of the basin. For the crust formed near the extinct spreading ridge we have modelled chrons 19 to 15 assuming an ultraslow spreading rate. Oceanic crust older than chron 29 is uncertain and may be part of a transitional crust that possibly contains other type of crust or exhumed mantle. The new magnetic anomaly identifications were inverted using the Hellinger (1981) criterion of fit. In this method the magnetic data are regarded as points on two conjugate isochrons consisting of great circle segments. This method has been extensively used for kinematic reconstructions since Royer and Chang (1991) first implemented it for quantitative plate tectonics, and is now available as a new interactive tool in the open-source software GPlates (www.gplates.org). The GPlates Hellinger tool lets the user interactively generate a best-fit rotation pole to a series of segmented magnetic picks. The fitting and determination of uncertainties are based on the FORTRAN program hellinger1 (Chang, 1988; Hellinger, 1981; Hanna and Chang, 1990); Royer and Chang, 1991). Input data can be viewed and adjusted both tabularly and graphically, and the best fit can be viewed and tested on the GPlates globe. The new set of rotations and their

  14. 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.

  15. 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

    Purpose 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). Materials and Methods 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. Results 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

  16. 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

  17. 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,…

  18. Assessing The Effects of Within-lake Variability of Fossil Assemblages On Quantitative Chironomid-inferred Temperature Reconstruction

    NASA Astrophysics Data System (ADS)

    Heiri, O.; Birks, H. J. B.; Brooks, S. J.; Velle, G.; Willassen, E.

    An important aspect when applying organism-based palaeolimnological methods to sediment cores is the inherent variability of fossil assemblages within a lake basin. Subfossil chironomids in lake sediments have been used extensively to quantify past summer air and water temperatures. However, little is known on how heterogeneous fossil distribution affects these estimates. In an effort to assess this variability we took a total of 20 surface sediment samples each in three small and shallow (7-9 m wa- ter depth) Norwegian lakes. In every lake two transects of seven samples were taken from the centre of the lake towards the littoral and six samples in the deepest part of the lake basin. Although the fossil assemblages were generally very similar within a lake basin, there was - in all three lakes - a distinct shift in the abundances of chi- ronomid taxa towards the littoral (water depth explaining 10-18% of the total variance in the percentage data as assessed by a Detrended Canonical Correspondence Anal- ysis). When we applied to our data a quantitative chironomid-July air temperature transfer-function based on surface sediments from the deepest parts of 153 Norwegian lakes, the variability of reconstructed temperatures in our three study lakes was only slightly smaller in the 6 deep-water samples (standard deviations (SD) of 0.48, 0.52 and 0.58C) than in all the 20 samples (SD of 0.55, 0.56 and 0.59 C). Our results suggest that within-lake variability of subfossil chironomid assemblages can account for a significant part of the overall prediction error of the chironomid-July air tempera- ture model of 1.03C. Furthermore, the lack of a clear trend in inferred values towards the littoral and the similar standard deviation of the total samples as compared to the deep-water samples suggest that the Norwegian transfer-function, though calibrated on samples from the deepest part of the lake, may also be applicable to sediment cores from closer to the lake shore. It

  19. 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.

  20. 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

  1. 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.

  2. 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.

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

    PubMed

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

    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

  4. 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

  5. Reconstruction and Quantitative Characterization of Multiphase, Multiscale Three-Dimensional Microstructure of a Cast Al-Si Base Alloy

    NASA Astrophysics Data System (ADS)

    Singh, H.; Gokhale, A. M.; Mao, Y.; Tewari, A.; Sachdev, A. K.

    2009-12-01

    The serial sectioning technique is well known for the reconstruction of three-dimensional (3D) microstructures of opaque materials. In recent years, techniques also have been developed for the reconstruction of high-fidelity, large-volume segments of 3D microstructures that use montage serial sections and robot-assisted automated acquisitions of montage serial sections. This article reports the reconstruction of the multiphase, multiscale 3D microstructure of a permanent mold cast unmodified Al-12 wt pct Si-1 wt pct Ni base alloy that contains eutectic Si platelets, coarse primary polyhedral Si particles, Fe-rich script intermetallic particles, and pores. These constituents are segmented, reconstructed, rendered, and characterized in three dimensions. The estimated 3D microstrucutral attributes include the distribution of eutectic platelet thickness; the mean volume, mean surface area, and mean thickness of the eutectic Si platelets; the mean volume and the mean surface area of the polyhedral primary Si particles; and the mean number of faces, edges, and corners on the polyhedral primary Si particles.

  6. 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

  7. 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.

  8. 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. PMID:27037715

  9. A chrysophyte-based quantitative reconstruction of winter severity from varved lake sediments in NE Poland during the past millennium and its relationship to natural climate variability

    NASA Astrophysics Data System (ADS)

    Hernández-Almeida, I.; Grosjean, M.; Przybylak, R.; Tylmann, W.

    2015-08-01

    Chrysophyte cysts are recognized as powerful proxies of cold-season temperatures. In this paper we use the relationship between chrysophyte assemblages and the number of days below 4 °C (DB4 °C) in the epilimnion of a lake in northern Poland to develop a transfer function and to reconstruct winter severity in Poland for the last millennium. DB4 °C is a climate variable related to the length of the winter. Multivariate ordination techniques were used to study the distribution of chrysophytes from sediment traps of 37 low-land lakes distributed along a variety of environmental and climatic gradients in northern Poland. Of all the environmental variables measured, stepwise variable selection and individual Redundancy analyses (RDA) identified DB4 °C as the most important variable for chrysophytes, explaining a portion of variance independent of variables related to water chemistry (conductivity, chlorides, K, sulfates), which were also important. A quantitative transfer function was created to estimate DB4 °C from sedimentary assemblages using partial least square regression (PLS). The two-component model (PLS-2) had a coefficient of determination of Rcross2  = 0.58, with root mean squared error of prediction (RMSEP, based on leave-one-out) of 3.41 days. The resulting transfer function was applied to an annually-varved sediment core from Lake Żabińskie, providing a new sub-decadal quantitative reconstruction of DB4 °C with high chronological accuracy for the period AD 1000-2010. During Medieval Times (AD 1180-1440) winters were generally shorter (warmer) except for a decade with very long and severe winters around AD 1260-1270 (following the AD 1258 volcanic eruption). The 16th and 17th centuries and the beginning of the 19th century experienced very long severe winters. Comparison with other European cold-season reconstructions and atmospheric indices for this region indicates that large parts of the winter variability (reconstructed DB4 °C) is due

  10. 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

  11. Quantitative evaluation of simultaneous reconstruction with model-based crosstalk compensation for 99mTc/123I dual-isotope simultaneous acquisition brain SPECT.

    PubMed

    Du, Yong; Frey, Eric C

    2009-06-01

    A model-based method has been previously developed to estimate and compensate for the crosstalk and downscatter contamination in simultaneous 123I/99mTc dual-isotope SPECT imaging. In this method, photon scatter in the object is modeled using the effective source scatter estimate technique. Photon interactions with the collimator-detector are estimated using precalculated Monte Carlo simulated point response functions. Two different approaches, simultaneous and alternating model-based compensations, have been proposed for iterative reconstruction-based crosstalk and downscatter contamination compensation. In this work, both model-based approaches were evaluated in the context of quantitative accuracy when imaging the dopaminergic system using both Monte Carlo simulated and experimentally acquired data. Results indicate that mddel-based estimates of the crosstalk and downscatter contamination in both energy windows were in good agreement with the truth for the simulated data. The effects of the contamination reduced image contrast and overestimated absolute activity in all structures by up to 66%. Compensation using both model-based approaches improved image contrast. Errors in absolute activity quantitation were also reduced to less than +/-5% for most brain structures. The accuracy of striatal specific binding potentials, calculated as the ratio of activity in various striatal structures to the background, was also greatly improved after model-based compensation. In conclusion, model-based compensation of simultaneously acquired images of 99mTc and 123I labeled brain imaging agents provided image quality and quantitative accuracy that were comparable to the image without crosstalk. Both proposed compensation approaches can potentially be applied clinically, but when reconstruction time is a limiting factor, the alternating model-based compensation may be preferable. PMID:19610291

  12. 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).

  13. 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.

  14. A qualitative and quantitative analysis of radiation dose and image quality of computed tomography images using adaptive statistical iterative reconstruction.

    PubMed

    Hussain, Fahad Ahmed; Mail, Noor; Shamy, Abdulrahman M; Suliman, Alghamdi; Saoudi, Abdelhamid

    2016-01-01

    Image quality is a key issue in radiology, particularly in a clinical setting where it is important to achieve accurate diagnoses while minimizing radiation dose. Some computed tomography (CT) manufacturers have introduced algorithms that claim significant dose reduction. In this study, we assessed CT image quality produced by two reconstruction algorithms provided with GE Healthcare's Discovery 690 Elite positron emission tomography (PET) CT scanner. Image quality was measured for images obtained at various doses with both conventional filtered back-projection (FBP) and adaptive statistical iterative reconstruction (ASIR) algorithms. A stan-dard CT dose index (CTDI) phantom and a pencil ionization chamber were used to measure the CT dose at 120 kVp and an exposure of 260 mAs. Image quality was assessed using two phantoms. CT images of both phantoms were acquired at tube voltage (kV) of 120 with exposures ranging from 25 mAs to 400 mAs. Images were reconstructed using FBP and ASIR ranging from 10% to 100%, then analyzed for noise, low-contrast detectability, contrast-to-noise ratio (CNR), and modulation transfer function (MTF). Noise was 4.6 HU in water phantom images acquired at 260 mAs/FBP 120 kV and 130 mAs/50% ASIR 120 kV. The large objects (fre-quency < 7 lp/cm) retained fairly acceptable image quality at 130 mAs/50% ASIR, compared to 260 mAs/FBP. The application of ASIR for small objects (frequency >7 lp/cm) showed poor visibility compared to FBP at 260 mAs and even worse for images acquired at less than 130 mAs. ASIR blending more than 50% at low dose tends to reduce contrast of small objects (frequency >7 lp/cm). We concluded that dose reduction and ASIR should be applied with close attention if the objects to be detected or diagnosed are small (frequency > 7 lp/cm). Further investigations are required to correlate the small objects (frequency > 7 lp/cm) to patient anatomy and clinical diagnosis. PMID:27167261

  15. 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. PMID:25204435

  16. 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.

  17. 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

  18. 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. PMID:26755692

  19. 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…

  20. 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

  1. Future Biome Projections in Alaska and East Russia

    NASA Astrophysics Data System (ADS)

    Hendricks, A.; Saito, K.; Bigelow, N. H.; Walsh, J. E.

    2014-12-01

    We projected Arctic biomes across a region including Alaska and Eastern Russia using the BIOME4 biogeochemical and biogeography vegetation model. BIOME4, which produces an equilibrium vegetation distribution under a given climate condition, was forced by CMIP5/PMIP3 climate data considered in IPCC AR5. We are exploring vegetation and permafrost distributions during the last 21,000 years and future projections (2100 C.E.) to gain an understanding of the effects of climate shifts on this complex subsystem. When forced with the baseline climatology, compiled from the University of Delaware temperature and precipitation climatology and ERA-40 sunshine data, our biome simulations were generally consistent with current vegetation observations in the study region. The biomes in this region are mostly evergreen and deciduous taiga capped by shrub and graminoid tundras to the north. The more noticeable differences were the tree line simulated north of the Brooks Range in Alaska and evergreen taiga in southwest Alaska where we know these biomes do not exist today. The projected changes in climate conditions in the region under a RCP8.5 climate scenario (significant warming upwards of 10°C by some models, an increase in precipitation by as much as 40%, and carbon dioxide concentration reaching approximately 940 ppm) drive shifts in Arctic biomes. The tree line shifts northward while shrub tundra and graminoid tundra regions decrease significantly. An intrusion of cool mixed, deciduous, and conifer forests above 60° north, especially in southwest Alaska, were marked and were not modeled for present day. Across eastern Russia, deciduous taiga begins to overtake evergreen taiga, except along the coastal regions where evergreen taiga remains the favored biome. The implications of vegetation shifts in the Arctic are vast and include effects on snow cover, soil properties, permafrost distribution, and albedo, not to mention impacts on local fauna and people of the Artic.

  2. 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.

  3. 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

  4. A quantitative and qualitative comparison of aquatic and terrestrial plant lignin phenols: Critical information for paleoecological reconstructions

    NASA Astrophysics Data System (ADS)

    Thomas, E. K.; Gao, L.; Huang, Y.

    2009-12-01

    caution when using lignin phenols in sedimentary archives to reconstruct changes in terrestrial vegetation. We determined the types of lignin phenols in each plant sample and compare the lignin phenol ratios in our samples to the database of lignin phenol ratios for terrestrial plants, with the goal of identifying characteristic differences between terrestrial and aquatic lignin phenols. This is the first report of the lignin phenol composition of freshwater aquatic plants, and is important information for studies that utilize lignin phenols to reconstruct ecological conditions.

  5. 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.

  6. 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.

  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. 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

  9. 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.

  10. 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

  11. Quantitative reconstruction of the Holocene climate in the Mediterranean basin inferred from marine and continental pollen records: model/data comparison

    NASA Astrophysics Data System (ADS)

    Peyron, Odile; Magny, Michel; Combourieu Nebout, Nathalie; Goring, Simon; Brayshaw, David; Joannin, Sebastien; Kouli, Katerina; de Beaulieu, Jacques-Louis; Brugiapaglia, Elisabetta E.; Kotthoff, Ulrich; Pross, Joerg; Sadori, Laura; Fletcher, William; Desprat, Stephanie

    2013-04-01

    The Holocene period is particularly well investigated in the Mediterranean area by a large amount of data (palynologi¬cal, speleothems, or lake-level evidence). All these data show the Holocene to have a complex pat¬tern of climatic change across the Mediterranean region with strong and spatial and temporal variability. Recent studies based on lake-level records from Italy suggest a North-South climatic partition in the central Mediterranean through the Holocene (Magny et al., 2012). If the recent precipitation estimates based on pollen records of these Italian lakes seem support these interpretation (Peyron et al., 2012), given the scarcity of reliable palaeoclimatic records in the north and central-south Mediterranean, new evidence is needed to validate this hypothesis at the scale of the Mediterranean basin, particularly in East and West Mediterranean regions. This study aims to provide robust and precise quantitative estimates of the Holocene climate in the Mediterranean region based on: (1) A multi-method approach to better assess the error of reconstruction inherent in pollen-based climate predictions; (2) Four high-resolution pollen records taken from lakes located along a latitudinal gradient from the northern Italy to the south Italy. Three lakes are from peninsular Italy (Lake Ledro, Lake Accesa, Lake Trifoglietti), and one is from Sicily (Lake Pergusa). In addition, one pollen record is located in Greece (Tenaghi Philippon); (3) Six high-resolution pollen records taken from marine cores located along a longitudinal gradient from the Alboran Sea to the Aegean Sea (cores ODP 976, MD95-2043, MD90-917, MD04-2797, SL152, and NS14). These quantitative estimates of the Holocene climate will be compared to the simulations performed with a regional model (Brayshaw et al., 2010). We investigate climatic trends during the Holocene and test the hypothesis proposed by Magny et al., (2012) of opposite mid-Holocene summer precipitation regimes between the north

  12. Information for seasonal models of carbon fluxes in terrestrial biomes

    SciTech Connect

    King, A.W.; DeAngelis, D.L.

    1985-06-01

    This report is a compilation of information that can be used in developing seasonal carbon flux models for several principal terrestrial biome types. The information includes flux data as well as models made either to simulate such data or to deduce fluxes not directly measurable. The report is divided into three sections that examine (1) photosynthetic production, (2) litterfall, and (3) decomposition during a year. The sections on photosynthetic production and decomposition discuss a large number of models that relate the processes to basic abiotic variables in each of several biome types. The information on litterfall, however, is largely empirical phenology data. A fourth section demonstrates the application of this compiled information to a compartment model of seasonal carbon flux in terrestrial biomes. 14 figs., 12 tabs.

  13. 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

  14. 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.

  15. Climate reconstruction from pollen and δ13C using inverse vegetation modeling. Implication for past and future climates

    NASA Astrophysics Data System (ADS)

    Hatté, C.; Rousseau, D.-D.; Guiot, J.

    2009-01-01

    An improved inverse vegetation model has been designed to better specify both temperature and precipitation estimates from vegetation descriptions. It is based on the BIOME4 vegetation model and uses both vegetation δ13C and biome as constraints. Previous inverse models based on only one of the two proxies were already improvements over standard reconstruction methods such as the modern analog since these did not take into account some external forcings, for example CO2 concentration. This new approach makes it possible to describe a potential "isotopic niche" defined by analogy with the "climatic niche" theory. Boreal and temperate biomes simulated by BIOME4 are considered in this study. We demonstrate the impact of CO2 concentration on biome existence domains by replacing a "most likely biome" with another with increased CO2 concentration. Additionally, the climate imprint on δ13C between and within biomes is shown: the colder the biome, the lighter its potential isotopic niche; and the higher the precipitation, the lighter the δ13C. For paleoclimate purposes, previous inverse models based on either biome or δ13C did not allow informative paleoclimatic reconstructions of both precipitation and temperature. Application of the new approach to the Eemian of La Grande Pile palynological and geochemical records reduces the range in precipitation values by more than 50% reduces the range in temperatures by about 15% compared to previous inverse modeling approaches. This shows evidence of climate instabilities during Eemian period that can be correlated with independent continental and marine records.

  16. Climate reconstruction from pollen and δ13C records using inverse vegetation modeling - Implication for past and future climates

    NASA Astrophysics Data System (ADS)

    Hatté, C.; Rousseau, D.-D.; Guiot, J.

    2009-04-01

    An improved inverse vegetation model has been designed to better specify both temperature and precipitation estimates from vegetation descriptions. It is based on the BIOME4 vegetation model and uses both vegetation δ13C and biome as constraints. Previous inverse models based on only one of the two proxies were already improvements over standard reconstruction methods such as the modern analog since these did not take into account some external forcings, for example CO2 concentration. This new approach makes it possible to describe a potential "isotopic niche" defined by analogy with the "climatic niche" theory. Boreal and temperate biomes simulated by BIOME4 are considered in this study. We demonstrate the impact of CO2 concentration on biome existence domains by replacing a "most likely biome" with another with increased CO2 concentration. Additionally, the climate imprint on δ13C between and within biomes is shown: the colder the biome, the lighter its potential isotopic niche; and the higher the precipitation, the lighter the δ13C. For paleoclimate purposes, previous inverse models based on either biome or δ13C did not allow informative paleoclimatic reconstructions of both precipitation and temperature. Application of the new approach to the Eemian of La Grande Pile palynological and geochemical records reduces the range in precipitation values by more than 50% reduces the range in temperatures by about 15% compared to previous inverse modeling approaches. This shows evidence of climate instabilities during Eemian period that can be correlated with independent continental and marine records.

  17. 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

  18. Hydrogen Isotopic Ratios of Lacustrine Algal and Terrestrial Organic Matter as a Quantitative Proxy for the Reconstruction of Relative Humidity and Source Water Composition in Continental Settings

    NASA Astrophysics Data System (ADS)

    Cross, E.; Hollander, D.; Huang, Y.; Vanvleet, E.

    2004-12-01

    Sedimentary studies have indicated that hydrologic conditions in low latitude continental environments have varied significantly during the late Quaternary and throughout the mid to late Holocene in association with sea level variations and major climatic phenomena such as the migration and mean position of the ITCZ. However, a quantitative approach to understanding hydrologic variability (i.e. variations in source water composition and relative humidity) is needed to accurately reconstruct changes in moisture balance and paleoclimatic conditions. Lake Tulane, located in Central Florida, is a subtropical, groundwater-fed acidic lake with a high sedimentation rate and well-preserved organic matter. This study utilizes the hydrogen isotopic composition (dD) of organic molecules (fatty acids) associated with algal (C16) and terrestrial (C28) materials in a lacustrine system to provide a modern calibration that quantifies the isotopic behavior associated with 1) changes in the chemistry of source waters and 2) variability in relative humidity. Over an annual cycle, the dDC16 of modern algal material shows little variability reflecting a constant dD of lake water coincident with the groundwater-fed nature of the lake and relatively constant dD of precipitation. Terrestrial biomass shows a seasonal variability of ~15% with more enriched values occurring in winter when higher rates of evapotranspiration lead to isotopic enrichment. Seasonal variations in the magnitude of isotopic offset between the algae and terrestrial markers, (DdD(C16-C28) ), removes the variations in the source waters and, is quantitatively related to seasonal changes (~6%) in the relative humidity. Together, dDC16 and dDCc16-c28) from lacustrine archives can serve as proxies for the quantitative reconstruction of source water composition and relative humidity from sedimentary records preserved in continental settings. These newly developed dD molecular-hydrologic proxies are applied to the

  19. CARBON BALANCE OF FOREST BIOMES IN THE FORMER USSR

    EPA Science Inventory

    Sources and sinks of carbon and the sequestration potential of forest biomes in the former Soviet Union (FSU) were assessed under non-equilibrium conditions by considering, 1) net ecosystem productivity (NEP) of different age forest stands and actual forest coverage, 2) carbon fl...

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

    NASA Astrophysics Data System (ADS)

    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.

    2004-06-01

    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 (RUEmax) that is typical of arid ecosystems. RUEmax 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. 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. PMID:15190350

  2. Retrieving Biome Types from Multi-angle Spectral Data

    NASA Astrophysics Data System (ADS)

    Schull, M. A.; Xu, L.; Latorre, P.; Samanta, A.; Myneni, R. B.; Knyazikhin, Y.

    2009-12-01

    Many studies have been conducted to demonstrate the ability of multi-angle spectral data to discriminate plant dominant species. Most have employed the use of empirically based techniques, which are site specific, requires some initial training based on characteristics of known leaf and/or canopy spectra and therefore may not be extendable to operational use or adapted to changing/unknown land cover. An ancillary objective of the MISR LAI/FPAR algorithm is classification of global vegetation into biome types. The algorithm is based on the 3D radiative transfer equation. Its performance suggests that is has valid LAI retrievals and correct biome identification in about 20% of the pixels. However with a probability of about 70%, uncertainties in LAI retrievals due to biome misclassification do not exceed uncertainties in the observations. In this poster we present an approach to improve reliability of the distribution of biomes and dominant species from multi angle spectral data. The radiative transfer theory of canopy spectral invariants underlies the approach, which facilitates parameterization of the canopy bidirectional reflectance factor in terms of the leaf spectrum and two spectrally invariant and structurally varying variables - recollision and directional escape probabilities. Theoretical and empirical analyses of ground and airborne data acquired by AVIRIS, AirMISR over two sites in New England and CHRIS/PROBA over BARAX site in Spain suggest that the canopy spectral invariants convey information about canopy structure at both the macro and micro scales. These properties allow for the natural separation of biome classes based on the location of points on the total escape probability vs the proportional escape ratio log-log plane.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  4. 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…

  5. Soil Acidobacterial 16S rRNA Gene Sequences Reveal Subgroup Level Differences between Savanna-Like Cerrado and Atlantic Forest Brazilian Biomes

    PubMed Central

    Catão, Elisa C. P.; Lopes, Fabyano A. C.; Araújo, Janaína F.; de Castro, Alinne P.; Barreto, Cristine C.; Bustamante, Mercedes M. C.; Quirino, Betania F.; Krüger, Ricardo H.

    2014-01-01

    16S rRNA sequences from the phylum Acidobacteria have been commonly reported from soil microbial communities, including those from the Brazilian Savanna (Cerrado) and the Atlantic Forest biomes, two biomes that present contrasting characteristics of soil and vegetation. Using 16S rRNA sequences, the present work aimed to study acidobacterial diversity and distribution in soils of Cerrado savanna and two Atlantic forest sites. PCA and phylogenetic reconstruction showed that the acidobacterial communities found in “Mata de galeria” forest soil samples from the Cerrado biome have a tendency to separate from the other Cerrado vegetation microbial communities in the direction of those found in the Atlantic Forest, which is correlated with a high abundance of Acidobacteria subgroup 2 (GP2). Environmental conditions seem to promote a negative correlation between GP2 and subgroup 1 (GP1) abundance. Also GP2 is negatively correlated to pH, but positively correlated to high Al3+ concentrations. The Cerrado soil showed the lowest Acidobacteria richness and diversity indexes of OTUs at the species and subgroups levels when compared to Atlantic Forest soils. These results suggest specificity of acidobacterial subgroups to soils of different biomes and are a starting point to understand their ecological roles, a topic that needs to be further explored. PMID:25309599

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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).

  12. 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

  13. 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.

  14. 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

  15. 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

  16. Comparison of volumetric bone mineral density in the operated and contralateral knee after anterior cruciate ligament and reconstruction: A 1-year follow-up study using peripheral quantitative computed tomography.

    PubMed

    Mündermann, Annegret; Payer, Nina; Felmet, Gernot; Riehle, Hartmut

    2015-12-01

    The purpose of this study was to quantify changes in volumetric bone mineral density (vBMD) in the tibial plateau of the operated and contralateral leg measured using peripheral quantitative computed tomography (pQCT) before and 3, 6, and 12 months after anterior cruciate ligament (ACL) reconstruction. The ACL was reconstructed with a hamstring tendon autograft using press-fit fixation. pQCT measurements of the proximal tibia were obtained in 61 patients after ACL reconstruction, and total, cortical, and trabecular vBMD were calculated. vBMD in the operated leg decreased from baseline to 3 months (-12% [total], -11% [cortical], and -12.6% [trabecular]; p<0.001) and remained below baseline for 12 months after surgery (6 months: -9.5%, -9.4%, and -9.6%, p<0.001; 12 months: -8%, -5%, and -11%, p<0.001). vBMD in the contralateral leg was slightly reduced only 6 months after surgery. Including age and sex as covariates into the analysis did not affect the results. ACL reconstruction contributed to loss in bone mineral density within the first year after surgery. The role of factors such as time of weight-bearing, joint mechanics, post-traumatic inflammatory reactions, or genetic predisposition in modulating the development of posttraumatic knee osteoarthritis after ACL injury should be further elucidated. PMID:26123943

  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. 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.

  19. 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. PMID:25481817

  20. USGS: providing scientific understanding of the sagebrush biome

    USGS Publications Warehouse

    U.S. Geological Survey

    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.

  1. 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.

  2. 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.

  3. 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.

  4. 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. PMID:18854302

  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. 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

    2011-01-01

    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. PMID:21326225

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. Reconstruction of the paleo-coastline of Santorini island (Greece), after the 1613 BC volcanic eruption: A GIS-based quantitative methodology

    NASA Astrophysics Data System (ADS)

    Oikonomidis, Dimitrios; Albanakis, Konstantinos; Pavlides, Spyridon; Fytikas, Michael

    2016-02-01

    A catastrophic volcanic explosion took place in Thera/Santorini island around 1613 BC, known as the `Minoan' eruption. Many papers have dealt with the shape of the shoreline of the island before the eruption, but none with the shape of the shoreline exactly after it, assuming that it would be the same with the contemporary one. However, this is not correct due to the wave erosion. In this paper, a new DEM was constructed, covering both land and submarine morphology, then topographic sections were drawn around the island. Using these sections, the `missing parts' (sea-wave erosion) were calculated, the shoreline was reconstructed as it was one day after the eruption and finally the erosion rate was calculated.

  13. 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.

  14. 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

  15. 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.

  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. Parameter Sensitivity of the Arctic BIOME BGC model for Estimating Evapotranspiration

    NASA Astrophysics Data System (ADS)

    Engstrom, R. N.; Hope, A.

    2005-12-01

    Modeling evapotranspiration (ET) in Arctic coastal plain ecosystems is challenging due to the unique environmental conditions, including non-vascular vegetation, permafrost, and a large standing dead vegetation component. In a previous study, the commonly used ecosystem process model, BIOME BGC, was modified to include representations of these unique Arctic conditions. The modifications resulted in a new model, Arctic BIOME BGC that significantly reduced the random and systematic errors when compared to eddy flux tower measurements. However, the modifications made in Arctic BIOME BGC added complexity and a number of new parameters. In this study the generalized sensitivity analysis methodology was used to examine the Arctic BIOME BGC model sensitivity to the thirteen parameters in the application of estimating daily ET over a four year time period in the Arctic coastal plain. The thirteen parameters investigated represented those which most directly impact model ET estimates and include all of the new ones added in the development of Arctic BIOME BGC. Results indicate that the model was highly sensitive to eight of the thirteen parameters. This suggests that the new process representations added in Arctic BIOME BGC were important for modeling ET in these ecosystems. Two parameters, standing dead leaf area index and snow absorptivity, had unique, identifiable values that corresponded well to observed data. Overall, there were many physically realistic parameter sets that were able to produce acceptable model predictions indicating that parameter equifinality is present within the model.

  19. Pollen-inferred quantitative reconstructions of Holocene land-cover in NW Europe for the evaluation of past climate-vegetation feedbacks -Evaluation of the REVEALS-based reconstruction using the Czech Republic database

    NASA Astrophysics Data System (ADS)

    Mazier, Florence; Kuneš, Petr; Sugita, Shinya; Trondman, Anna-Kari; Broström, Anna; Gaillard, Marie-José

    2010-05-01

    Quantitative estimates of land-cover changes during the Holocene have become increasingly important for a better understanding of the earth surface-atmosphere feedbacks, and refining climate models. The LANDCLIM project and research network (sponsored by the Swedish [VR] and Nordic [NordForsk] Research Councils) aim to quantify human-induced changes in regional vegetation and land-cover in NW Europe during the Holocene in order to evaluate the effects of these changes on the regional climate through altered feedbacks (see Gaillard et al. CL 1.22). We use the REVEALS model (Sugita 2007) to estimate the percentage cover of groups of taxa (Plant Functional Types - PFTs) from fossil pollen data at the 1o x 1o scale for selected time windows of the Holocene with contrasting human-induced land-cover (0-100 cal BP, 100-350 cal BP, 350-700 cal BP, 2700-3200 cal BP and 5700-6200 cal BP). The past cover of PFTs will be compared with the outputs of the LPJ-GUESS, a widely-used dynamic vegetation model, and applied as an alternative to the simulated LPG-GUESS vegetation to run the regional climate model RCA3 for the past. Parameters required for REVEALS applications are: raw pollen counts from well-dated pollen sites, pollen productivity estimates (PPEs), fall speed of pollen (FSP), and site size. PPEs and FSP are currently available for 34 taxa in NW Europe (Broström et al, 2008). Large sites (> 100-500 ha) are preferable for estimating regional vegetation composition using REVEALS. However, pollen data from large sites are limited, and bogs and mires have been often used, particularly in mountainous areas. In this study, we use pollen data (Kuneš et al, 2009) from variously-sized sites in each 1°x1° grid cells in the Czech and Slovak Republics. Different methodological alternatives are tested in order to evaluate their impact on the REVEALS-based estimates of the regional vegetation: 1) basin type (lakes or bogs), 2) number of taxa (with or without entomophilous taxa), 3

  20. 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. PMID:23011295

  1. Declines of biomes and biotas and the future of evolution

    PubMed Central

    Woodruff, David S.

    2001-01-01

    Although panel discussants disagreed whether the biodiversity crisis constitutes a mass extinction event, all agreed that current extinction rates are 50–500 times background and are increasing and that the consequences for the future evolution of life are serious. In response to the on-going rapid decline of biomes and homogenization of biotas, the panelists predicted changes in species geographic ranges, genetic risks of extinction, genetic assimilation, natural selection, mutation rates, the shortening of food chains, the increase in nutrient-enriched niches permitting the ascendancy of microbes, and the differential survival of ecological generalists. Rates of evolutionary processes will change in different groups, and speciation in the larger vertebrates is essentially over. Action taken over the next few decades will determine how impoverished the biosphere will be in 1,000 years when many species will suffer reduced evolvability and require interventionist genetic and ecological management. Whether the biota will continue to provide the dependable ecological services humans take for granted is less clear. The discussants offered recommendations, including two of paramount importance (concerning human populations and education), seven identifying specific scientific activities to better equip us for stewardship of the processes of evolution, and one suggesting that such stewardship is now our responsibility. The ultimate test of evolutionary biology as a science is not whether it solves the riddles of the past but rather whether it enables us to manage the future of the biosphere. Our inability to make clearer predictions about the future of evolution has serious consequences for both biodiversity and humanity. PMID:11344296

  2. 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

  3. 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

  4. 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

  5. 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.

  6. A Biome map for Modelling Global Mid-Pliocene Climate Change

    NASA Astrophysics Data System (ADS)

    Salzmann, U.; Haywood, A. M.

    2006-12-01

    The importance of vegetation-climate feedbacks was highlighted by several paleo-climate modelling exercises but their role as a boundary condition in Tertiary modelling has not been fully recognised or explored. Several paleo-vegetation datasets and maps have been produced for specific time slabs or regions for the Tertiary, but the vegetation classifications that have been used differ, thus making meaningful comparisons difficult. In order to facilitate further investigations into Tertiary climate and environmental change we are presently implementing the comprehensive GIS database TEVIS (Tertiary Environment and Vegetation Information System). TEVIS integrates marine and terrestrial vegetation data, taken from fossil pollen, leaf or wood, into an internally consistent classification scheme to produce for different time slabs global Tertiary Biome and Mega- Biome maps (Harrison & Prentice, 2003). In the frame of our ongoing 5-year programme we present a first global vegetation map for the mid-Pliocene time slab, a period of sustained global warmth. Data were synthesised from the PRISM data set (Thompson and Fleming 1996) after translating them to the Biome classification scheme and from new literature. The outcomes of the Biome map are compared with modelling results using an advanced numerical general circulation model (HadAM3) and the BIOME 4 vegetation model. Our combined proxy data and modelling approach will provide new palaeoclimate datasets to test models that are used to predict future climate change, and provide a more rigorous picture of climate and environmental changes during the Neogene.

  7. 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

  8. Image reconstruction

    SciTech Connect

    Defrise, Michel; Gullberg, Grant T.

    2006-04-05

    We give an overview of the role of Physics in Medicine andBiology in development of tomographic reconstruction algorithms. We focuson imaging modalities involving ionizing radiation, CT, PET and SPECT,and cover a wide spectrum of reconstruction problems, starting withclassical 2D tomogra tomography in the 1970s up to 4D and 5D problemsinvolving dynamic imaging of moving organs.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. Breast reconstruction.

    PubMed

    DellaCroce, Frank J; Wolfe, Emily T

    2013-04-01

    As diagnostic technology has progressed and the understanding of the disease process has evolved, the number of mastectomies performed in the United States has increased. Breast reconstructive techniques have commensurately become more sophisticated along the same timeline. The result is that those facing mastectomy have the potential to simultaneously retain physical beauty and wholeness. Only 33% of women who are otherwise candidates for immediate reconstruction at the time of mastectomy choose reconstruction. Patients generally have a high level of satisfaction with the option they choose, contributing to a feeling of overall recovery and physical and emotional wholeness. PMID:23464695

  14. 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.

  15. ACL reconstruction

    MedlinePlus

    ... Tissue taken from a donor is called an allograft. The procedure is usually performed with the help ... This increases the chance you may have a meniscus tear. ACL reconstruction may be used for these ...

  16. [Eyebrow reconstruction].

    PubMed

    Baraër, F; Darsonval, V; Lejeune, F; Bochot-Hermouet, B; Rousseau, P

    2013-10-01

    The eyebrow is an essential anatomical area, from a social point of view, so its reconstruction, in case of skin defect, must be as meticulous as possible, with the less residual sequela. Capillary density extremely varies from one person to another and the different methods of restoration of this area should absolutely take this into consideration. We are going to review the various techniques of reconstruction, according to the sex and the surface to cover. PMID:23896574

  17. 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. PMID:23859496

  18. 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.

  19. CARBON SOURCES AND SINKS IN THE FOREST BIOMES OF THE FORMER SOVIET UNION

    EPA Science Inventory

    Net primary productivity (NPP) of Soviet forest biomes hall 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. owever, an equilibrium analysis does no...

  20. Animal movement and establishment of vaccinia virus Cantagalo strain in Amazon biome, Brazil.

    PubMed

    Quixabeira-Santos, Jociane Cristina; Medaglia, Maria Luiza G; Pescador, Caroline A; Damaso, Clarissa R

    2011-04-01

    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 Rondonia State, leading to the establishment and spread of this pathogen. PMID:21470472

  1. 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.

  2. 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. PMID:26541807

  3. 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.

  4. 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.

  5. 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…

  6. Vegetation productivity responds to sub-annual climate conditions across semiarid biomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  7. 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…

  8. 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

  9. 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.

  10. Space-based observations of fire NOx emission coefficients: a global biome-scale comparison

    NASA Astrophysics Data System (ADS)

    Mebust, A. K.; Cohen, R. C.

    2014-03-01

    Biomass burning represents both a significant and highly variable source of NOx to the atmosphere. This variability stems from both the episodic nature of fires, and from fire conditions such as the modified combustion efficiency of the fire, the nitrogen content of the fuel and possibly other factors that have not been identified or evaluated by comparison with observations. Satellite instruments offer an opportunity to observe emissions from wildfires, providing a large suite of measurements which allow us to study mean behavior and variability on the regional scale in a statistically rigorous manner. Here we use space-based measurements of fire radiative power from the Moderate Resolution Imaging Spectroradiometer in combination with NO2 tropospheric column densities from the Ozone Monitoring Instrument to measure mean emission coefficients (ECs in g NO MJ-1) from fires for global biomes, and across a wide range of smaller-scale ecoregions, defined as spatially-distinct clusters of fires with similar fuel type. Mean ECs for all biomes fall between 0.250-0.362 g NO MJ-1, a range that is smaller than found in previous studies of biome-scale emission factors. The majority of ecoregion ECs fall within or near this range, implying that under most conditions, mean fire emissions of NOx per unit energy are similar between different regions regardless of fuel type or spatial variability. In contrast to these similarities, we find that about 24% of individual ecoregion ECs deviate significantly (with 95% confidence) from the mean EC for the associated biome, and a similar number of ecoregion ECs falls outside the range of all mean biome ECs, implying that there are some regions where fuel type-specific global emission parameterizations fail to capture local fire NOx emissions.