Magnetic Minerals in Soils and Paleosols as Recorders of Paleoclimate

NASA Astrophysics Data System (ADS)

Maxbauer, Daniel P.

It is a fundamental challenge for geologists to create quantitative estimates of rainfall and temperature in past climates. Yet, records of past climates are integral for understanding the complexities of earth system dynamics. The research presented in this dissertation begins to establish a framework for reconstructing paleoclimates using the magnetic properties of fossilized soils. Magnetic minerals are ubiquitous in soils, and their composition, grain size, and concentration is often directly related to the ambient climatic conditions that were present during soil formation. Using rock magnetic methods, it is possible to sensitively characterize the magnetic mineral assemblages in natural materials - including soils and paleosols. The fundamentals of rock magnetism and many of the common methods used in rock magnetic applications are presented in chapter 2 and chapter 3, respectively. Chapter 4 reviews the physical, chemical, and biological factors that affect magnetic mineral assemblages in soils, the magnetic methods we use to characterize them, and the known relationships between magnetic minerals in soils and climate. A critical component to developing replicable tools for reconstructing paleoclimate is developing analytical and statistical tools that are accessible to the greater community. Chapter 5 introduces a new model, MAX UnMix, that was developed as an open-source, online tool for rock magnetic data processing that is designed to be user-friendly and accessible. Two case studies, on both fossil (Chapter 7) and modern (Chapter 6) soils, are presented and discuss many issues related to applying magnetic paleoprecipitation proxies in deep time. Chapter 7 discusses difficulties in disentangling the effects of pedogenesis, diagenesis, and recent surficial weathering in Paleocene-Eocene ( 56-55 Ma) paleosols. Chapter 6 explores the relative influence of soil forming factors (vegetation vs. climate) on controlling the pedogenic formation of magnetic

A Taxonomic Reduced-Space Pollen Model for Paleoclimate Reconstruction

NASA Astrophysics Data System (ADS)

Wahl, E. R.; Schoelzel, C.

2010-12-01

Paleoenvironmental reconstruction from fossil pollen often attempts to take advantage of the rich taxonomic diversity in such data. Here, a taxonomically "reduced-space" reconstruction model is explored that would be parsimonious in introducing parameters needing to be estimated within a Bayesian Hierarchical Modeling context. This work involves a refinement of the traditional pollen ratio method. This method is useful when one (or a few) dominant pollen type(s) in a region have a strong positive correlation with a climate variable of interest and another (or a few) dominant pollen type(s) have a strong negative correlation. When, e.g., counts of pollen taxa a and b (r >0) are combined with pollen types c and d (r <0) to form ratios of the form (a + b) / (a + b + c + d), an appropriate estimation form is the binomial logistic generalized linear model (GLM). The GLM can readily model this relationship in the forward form, pollen = g(climate), which is more physically realistic than inverse models often used in paleoclimate reconstruction [climate = f(pollen)]. The specification of the model is: rnum Bin(n,p), where E(r|T) = p = exp(η)/[1+exp(η)], and η = α + β(T); r is the pollen ratio formed as above, rnum is the ratio numerator, n is the ratio denominator (i.e., the sum of pollen counts), the denominator-specific count is (n - rnum), and T is the temperature at each site corresponding to a specific value of r. Ecological and empirical screening identified the model (Spruce+Birch) / (Spruce+Birch+Oak+Hickory) for use in temperate eastern N. America. α and β were estimated using both "traditional" and Bayesian GLM algorithms (in R). Although it includes only four pollen types, the ratio model yields more explained variation ( 80%) in the pollen-temperature relationship of the study region than a 64-taxon modern analog technique (MAT). Thus, the new pollen ratio method represents an information-rich, reduced space data model that can be efficiently employed in

Paleoclimates: Understanding climate change past and present

USGS Publications Warehouse

Cronin, Thomas M.

2010-01-01

The field of paleoclimatology relies on physical, chemical, and biological proxies of past climate changes that have been preserved in natural archives such as glacial ice, tree rings, sediments, corals, and speleothems. Paleoclimate archives obtained through field investigations, ocean sediment coring expeditions, ice sheet coring programs, and other projects allow scientists to reconstruct climate change over much of earth's history. When combined with computer model simulations, paleoclimatic reconstructions are used to test hypotheses about the causes of climatic change, such as greenhouse gases, solar variability, earth's orbital variations, and hydrological, oceanic, and tectonic processes. This book is a comprehensive, state-of-the art synthesis of paleoclimate research covering all geological timescales, emphasizing topics that shed light on modern trends in the earth's climate. Thomas M. Cronin discusses recent discoveries about past periods of global warmth, changes in atmospheric greenhouse gas concentrations, abrupt climate and sea-level change, natural temperature variability, and other topics directly relevant to controversies over the causes and impacts of climate change. This text is geared toward advanced undergraduate and graduate students and researchers in geology, geography, biology, glaciology, oceanography, atmospheric sciences, and climate modeling, fields that contribute to paleoclimatology. This volume can also serve as a reference for those requiring a general background on natural climate variability.

Patterns in leaf morphological traits of Chinese woody plants and the application for paleoclimate reconstruction

NASA Astrophysics Data System (ADS)

Li, Yaoqi; Wang, Zhiheng

2017-04-01

Leaf morphological traits (LMTs) directly influence carbon-uptake and water-loss of plants in different habitats, and hence can be sensitive indicators of plant interaction with climate. The relationships between community-aggregated LMTs and their surrounding climate have been used to reconstruct paleoclimate. However, the uncertainties in its application remain poorly explored. Using distribution maps and LMTs data (leaf margin states, leaf length, leaf width, and length-width product/ratio) of 10480 Chinese woody dicots and dated family-level phylogenies, we demonstrated the variations of LMTs in geographical patterns, and analyzed their relationships with climate across different life-forms (evergreen and deciduous; trees, shrubs and lianas) and species quartiles with different family-ages. Results showed that from southern to northern China, leaves became shorter and narrower, while leaf length-width ratio increased and toothed-margin percentage decreased. Our results revealed great uncertainties in leaf margin-temperature relationships induced by life-form, precipitation and evolutionary history, and suggested that the widely-used method, leaf margin analysis, should be applied cautiously on paleotemperature reconstruction. Differently, mean leaf size responded tightly to spatial variations in annual evapotranspiration (AET) and primary productivity (GPP and NPP), and these relationships remained constant across different life-forms and evolutionary history, suggesting that leaf size could be a useful surrogate for paleo primary productivity.

Multi-proxy Paleoclimate and CO2 Reconstruction from the Latest Middle Eocene Sedimentary Fill of a Subarctic Kimberlitic Maar Crater

NASA Astrophysics Data System (ADS)

Reyes, A. V.; Wolfe, A. P.; Royer, D. L.; Greenwood, D. R.; Tierney, J. E.; Doria, G.; Gagen, M. H.; Siver, P.; Westgate, J.

2016-12-01

Eocene paleoclimate reconstructions are rarely accompanied by parallel estimates of CO2, complicating assessment of the equilibrium climate responses to CO2. We reconstruct temperature, precipitation, and CO2 from latest middle Eocene ( 38 Myrs ago) peats in subarctic Canada, preserved in sediments that record infilling of a kimberlite pipe maar crater. Mutual climatic range analyses of pollen, together with oxygen isotope analyses of a-cellulose from unpermineralized wood and inferenecs from branched glycerol diakyl glycerol tetraethers (GDGTs), reveal a high-latitude humid-temperate forest ecosystem with mean annual temperatures (MATs) >17 °C warmer than present, mean coldest month temperatures above 0 °C, and mean annual precipitation 4x present. Metasequoia stomatal indices and gas-exchange modeling produce median CO2 concentrations of 634 and 432 ppm, respectively, with a consensus median estimate of 494 ppm. Reconstructed MATs are >6 °C warmer than those produced by Eocene climate models forced at 560 ppm CO2, underscoring the capacity for exceptional polar amplification of warming and hydrological intensification under relatively modest CO2 concentrations, once both fast and slow feedbacks become expressed.

Surface Mass Balance of the Greenland Ice Sheet Derived from Paleoclimate Reanalysis

NASA Astrophysics Data System (ADS)

Badgeley, J.; Steig, E. J.; Hakim, G. J.; Anderson, J.; Tardif, R.

2017-12-01

Modeling past ice-sheet behavior requires independent knowledge of past surface mass balance. Though models provide useful insight into ice-sheet response to climate forcing, if past climate is unknown, then ascertaining the rate and extent of past ice-sheet change is limited to geological and geophysical constraints. We use a novel data-assimilation framework developed under the Last Millennium Reanalysis Project (Hakim et al., 2016) to reconstruct past climate over ice sheets with the intent of creating an independent surface mass balance record for paleo ice-sheet modeling. Paleoclimate data assimilation combines the physics of climate models and the time series evidence of proxy records in an offline, ensemble-based approach. This framework allows for the assimilation of numerous proxy records and archive types while maintaining spatial consistency with known climate dynamics and physics captured by the models. In our reconstruction, we use the Community Climate System Model version 4, CMIP5 last millennium simulation (Taylor et al., 2012; Landrum et al., 2013) and a nearly complete database of ice core oxygen isotope records to reconstruct Holocene surface temperature and precipitation over the Greenland Ice Sheet on a decadal timescale. By applying a seasonality to this reconstruction (from the TraCE-21ka simulation; Liu et al., 2009), our reanalysis can be used in seasonally-based surface mass balance models. Here we discuss the methods behind our reanalysis and the performance of our reconstruction through prediction of unassimilated proxy records and comparison to paleoclimate reconstructions and reanalysis products.

Relating Paleoclimate Data and Past Temperature Gradients: Some Suggestive Rules

NASA Technical Reports Server (NTRS)

Rind, David

1999-01-01

Understanding tropical sensitivity is perhaps the major concern confronting researchers, for both past and future climate change issues. Tropical data has been beset by contradictions, and many techniques applicable to the extratropics are either unavailable or fraught with uncertainty when applied at low latitudes. Paleoclimate data, if interpreted within the context of the latitudinal temperature gradient data they imply, can be used to estimate what happened to tropical temperatures in the past, and provide a first guess for what might happen in the future. The approach is made possible by the modeling result that atmospheric dynamical changes, and the climate impacts they produce, respond primarily to temperature gradient changes. Here we review some "rules" obtained from GCM (General Circulation Model) experiments with different sea surface temperature gradients and different forcing, that can be used to relate paleoclimate reconstructions to the likely temperature gradient changes they suggest.

Evaluation of organic geochemical and micropaleontological proxies for Holocene paleoclimate reconstructions in Tampa Bay, Florida

NASA Astrophysics Data System (ADS)

van Soelen, E. E.; Brooks, G.; Lammertsma, E.; Donders, T.; Wagner-Cremer, F.; Sangiorgi, F.; Cremer, H.; Sinninghe Damsté, J. S.; Reichart, G. J.

2009-04-01

The exact consequences of human induced climate change are as yet not known. One of the current debates concerns the relation between rising sea surface temperatures (SST) and enhanced hurricane activity. It has also been suggested that the El Niño Southern Oscillation (ENSO) variability plays a major role in providing favorable circumstances for hurricane development. Paleo-climate reconstructions can help understanding long-term trends in hurricane activity. However, reliable climate reconstructions first require that suitable proxies are developed and tested. For this purpose, a pilot-study was performed using biomarkers, pollen, dinoflagellates and diatoms in a core from Tampa-Bay, Florida, covering the Holocene. The hydrological cycle in this part of Florida is strongly affected by both ENSO [1] and hurricanes. Biomarkers of both terrestrial and marine origin were abundant in the core sediments. High taraxerol concentrations were found which are characteristic for the close proximity of mangrove forests on the bays fringes. Other vascular plant derived biomarkers include friedelanone and β-sitosterol. Marine biomarkers include amongst others dinosterol and long-chain C37 and C38 alkenones, indicative for dinoflagellates and haptophyte algae respectively. These biomarkers are absent in sediments older than 7 kyr BP, indicating a non-marine depositional environment. In sediments younger than 7 kyr BP, increasing amounts of marine biomarkers indicate a transition towards estuarine conditions. SST was reconstructed on the alkenones-based paleothermometer Uk'37 and indicates temperatures of ~ 26°C for the past ~4 kyr. Between 7 and 4 kyr BP, concentrations of alkenones in the sediments are too low for reliable SST reconstructions. The shift towards estuarine conditions is a consequence of rising sea-levels following the last deglaciation and is in agreement with earlier findings by Cronin et al. [2], who recognized a change from lacustrine to marine sediments

Modern and past periglacial features in Central Asia and their implication for paleoclimate reconstructions

NASA Astrophysics Data System (ADS)

Lehmkuhl, Frank

2017-04-01

implication for paleoclimate reconstructions. - Progress in Physical Geography 40: 369-391. DOI: 10.1177/0309133315615778

Monthly paleostreamflow reconstruction from annual tree-ring chronologies

Treesearch

J. H. Stagge; D. E. Rosenberg; R. J. DeRose; T. M. Rittenour

2018-01-01

Paleoclimate reconstructions are increasingly used to characterize annual climate variability prior to the instrumental record, to improve estimates of climate extremes, and to provide a baseline for climate change projections. To date, paleoclimate records have seen limited engineering use to estimate hydrologic risks because water systems models and managers usually...

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

NASA Astrophysics Data System (ADS)

Liu, Yuan; Li, Yu

2017-11-01

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

Paleoclimate of the Neoglacial and Roman Warm Period Reconstructed from Oxygen Isotope Ratios of Limpet Shells (Patella vulgata), Northwest Scotland

NASA Astrophysics Data System (ADS)

Wang, T.; Surge, D. M.; Mithen, S.

2010-12-01

Paleoclimate reconstructions from different regions have reported abrupt climate change around 2800-2700 cal yr B.P. The timing of this abrupt climate change is close to the boundary between the Neoglacial (3300-2500 cal yr B.P.) and Roman Warm Period (2500-1600 cal yr B.P.). However, temporal and spatial variability observed in this climate change event raises controversies about the forcing factors driving it and why it has regional variability. Scotland lies in the North Atlantic Ocean, which responds sensitively to climate change. Therefore, even in the case of subtle climate change, the climate variability of Scotland should be able to capture such change. In this study, we expect that paleoclimate reconstructions of the Neoglacial and Roman Warm Period in Scotland will help improve our knowledge of abrupt climate change at 2800-2700 cal yr B.P. Archaeological shell deposits provide a rich source of climate proxy data preserved as oxygen isotope ratios in shell carbonate. Croig Cave on the Isle of Mull, Scotland, contains a nearly continuous accumulation of shells ranging from 800 BC-500 AD and possibly older. This range represents a broad chronology of human use from the late Bronze to Iron Ages and spans the Neoglacial through Roman Warm Period climate episodes. Here, we present seasonal temperature variability of the two climate episodes based on oxygen isotope ratios of ten limpet shells (Patella vulgata) from Croig Cave. Based on AMS dating (2 sigma calibration), the oldest shell was from 3480-3330 cal yr B.P. and the youngest shell was from 2060-1870 cal yr B.P. Our results indicated that estimated temperatures from the Neoglacial limpets average 6.44±0.56°C for coldest winters and 15.06±0.67°C for warmest summers. For the Roman Warm Period limpets, the average is 5.68±0.36°C for coldest winters and 14.14±0.81°C for warmest summers. We compared our estimated temperatures to the present sea surface temperature (SST) from 1961 to 1990 near our

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

Quantitative ptychographic reconstruction by applying a probe constraint

NASA Astrophysics Data System (ADS)

Reinhardt, J.; Schroer, C. G.

2018-04-01

The coherent scanning technique X-ray ptychography has become a routine tool for high-resolution imaging and nanoanalysis in various fields of research such as chemistry, biology or materials science. Often the ptychographic reconstruction results are analysed in order to yield absolute quantitative values for the object transmission and illuminating probe function. In this work, we address a common ambiguity encountered in scaling the object transmission and probe intensity via the application of an additional constraint to the reconstruction algorithm. A ptychographic measurement of a model sample containing nanoparticles is used as a test data set against which to benchmark in the reconstruction results depending on the type of constraint used. Achieving quantitative absolute values for the reconstructed object transmission is essential for advanced investigation of samples that are changing over time, e.g., during in-situ experiments or in general when different data sets are compared.

Holocene temperature history at the west Greenland Ice Sheet margin reconstructed from lake sediments

NASA Astrophysics Data System (ADS)

Axford, Y.; Losee, S.; Briner, J. P.; Francis, D.; Langdon, P. G.; Walker, I.

2011-12-01

Paleoclimate proxy data can help reduce uncertainties regarding how the Greenland Ice Sheet, and thus global sea level, will respond to future climate change. Studies of terrestrial deposits along Greenland's margins offer opportunities to reconstruct both past temperature changes and the associated changes in Greenland Ice Sheet extent, thus empirically characterizing the ice sheet's response to temperature change. Here we present Holocene paleoclimate reconstructions developed from sediment records of five lakes along the western ice sheet margin, near Jakobshavn Isbræ and Disko Bugt. Insect (Chironomidae, or non-biting midge) remains from North Lake provide quantitative estimates of summer temperatures over the past ca. 7500 years at multi-centennial resolution, and changes in sediment composition at all five lakes offer evidence for glacier fluctuations, changes in lake productivity, and other environmental changes throughout the Holocene. Aims of this study include quantification of warmth in the early to mid Holocene, when summer solar insolation forcing exceeded present-day values at northern latitudes and the local Greenland Ice Sheet margin receded inboard of its present position, and the magnitude of subsequent Neoglacial and Little Ice Age cooling that drove ice sheet expansion. We find that the Jakobshavn Isbrae region experienced the warmest temperatures of the Holocene (with summers 2 to 3.5 degrees C warmer than present) between ~6000 and 4000 years ago. Neoglacial cooling began rather abruptly ~4000 years ago and intensified 3000 years ago. Our proxy data suggest that the coldest summers of the Holocene occurred during the 18th and 19th centuries in the Jakobshavn region. These results agree well with previous glacial geologic studies reconstructing local ice margin positions through the Holocene. Such reconstructions of paleoclimate and past ice sheet extent provide targets for testing and improving ice sheet models.

PaleoClim: new datasets to quantify the impact of past climate changes on modern biodiversity

NASA Astrophysics Data System (ADS)

Hill, D. J.; Brown, J. T.; Carnaval, A. C.; Haywood, A. M.

2017-12-01

Palaeoclimate history is an important driver of modern patterns of biodiversity and many ecological modelling studies have shown the predictive power of palaeoclimate information. However, a major limiting factor to such studies is the availability of global palaeoclimate reconstructions in the relevant bioclim layers. The primary source of such fields is from climate model simulations, which are currently limited to the key PMIP (Paleoclimate Modelling Intercomparison Project) intervals of the mid-Holocene (6ka), the Last Glacial Maximum (21ka) and the Last Interglaciation (130ka). The PaleoClim project will significantly increase the availability of pre-processed palaeoclimate bioclim information and provide a new platform for accessing the information. The first new PaleoClim time period will be the mid-Pliocene Warm Period (3Ma). This is the last period of sustained globally warmer than modern climate in Earth history and represents the last global warmth before the cooling into the Pleistocene ice ages. Being 3 million years ago this represents a significant lengthening of the time range of available bioclim layers and the first time these have been available over evolutionary timescales. PaleoClim will also greatly expand the available Pleistocene time periods, looking to both quantify the differences between the late Pleistocene interglacial periods and understand the role of orbital changes in modulating tropical precipitation and driving modern biodiversity patterns.

Investigating genetic loci that encode plant-derived paleoclimate proxies

NASA Astrophysics Data System (ADS)

Bender, A. L. D.; Suess, M.; Chitwood, D. H.; Bradley, A. S.

2016-12-01

Long chain (>C25) n-alkanes in sediments predominantly derive from terrestrial plant waxes. Hydrogen isotope ratios (δD) of leaf wax hydrocarbons correlate with δDH2O of precipitation and are commonly used as paleoclimate proxies. However, biological variability in the isotopic fractionations between water and plant materials also affects the n-alkane δD values. Correct interpretation of this paleoclimate proxy requires that we resolve genetic and environmental effects. Genetic variability underlying differences in leaf wax structure and isotopic composition can be quantitatively determined through the use of model organisms. Interfertile Solanum sect. Lycopersicon (tomato) species provide an ideal model species complex for this approach. We used a set of 76 precisely defined near-isogenic lines (introgression lines [ILs]) in which small genomic regions from the wild tomato relative Solanum pennellii have been introduced into the genome of the domestic tomato, S. lycopersicum. By characterizing quantitative traits of these ILs (leaf wax structure and isotopic composition), we can resolve the degree to which each trait is regulated by genetic versus environmental factors. We present data from two growth experiments conducted with all 76 ILs. In this study, we quantify leaf wax traits, including δD values, δ13C values, and structural metrics including the methylation index (a variable that describes the ratio of iso­- and anteiso- to n-alkanes). Among ILs, δD values vary by up to 35‰ and 60‰ for C31 and C33 n-alkanes, respectively. Many ILs have methylation indices that are discernably different from the parent domesticated tomato (p < 0.001), which suggests that methylation is a highly polygenic trait. This pattern is similar to the genetics that control leaf shape, another trait commonly used as a paleoclimate proxy. Based on our preliminary analysis, we propose candidate genes that control aspects of plant physiology that affect these quantitative

Impact of reconstruction parameters on quantitative I-131 SPECT

NASA Astrophysics Data System (ADS)

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

2016-07-01

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

A Paleolatitude Calculator for Paleoclimate Studies

PubMed Central

van Hinsbergen, Douwe J. J.; de Groot, Lennart V.; van Schaik, Sebastiaan J.; Spakman, Wim; Bijl, Peter K.; Sluijs, Appy; Langereis, Cor G.; Brinkhuis, Henk

2015-01-01

Realistic appraisal of paleoclimatic information obtained from a particular location requires accurate knowledge of its paleolatitude defined relative to the Earth’s spin-axis. This is crucial to, among others, correctly assess the amount of solar energy received at a location at the moment of sediment deposition. The paleolatitude of an arbitrary location can in principle be reconstructed from tectonic plate reconstructions that (1) restore the relative motions between plates based on (marine) magnetic anomalies, and (2) reconstruct all plates relative to the spin axis using a paleomagnetic reference frame based on a global apparent polar wander path. Whereas many studies do employ high-quality relative plate reconstructions, the necessity of using a paleomagnetic reference frame for climate studies rather than a mantle reference frame appears under-appreciated. In this paper, we briefly summarize the theory of plate tectonic reconstructions and their reference frames tailored towards applications of paleoclimate reconstruction, and show that using a mantle reference frame, which defines plate positions relative to the mantle, instead of a paleomagnetic reference frame may introduce errors in paleolatitude of more than 15° (>1500 km). This is because mantle reference frames cannot constrain, or are specifically corrected for the effects of true polar wander. We used the latest, state-of-the-art plate reconstructions to build a global plate circuit, and developed an online, user-friendly paleolatitude calculator for the last 200 million years by placing this plate circuit in three widely used global apparent polar wander paths. As a novelty, this calculator adds error bars to paleolatitude estimates that can be incorporated in climate modeling. The calculator is available at www.paleolatitude.org. We illustrate the use of the paleolatitude calculator by showing how an apparent wide spread in Eocene sea surface temperatures of southern high latitudes may be in

A Paleolatitude Calculator for Paleoclimate Studies.

PubMed

van Hinsbergen, Douwe J J; de Groot, Lennart V; van Schaik, Sebastiaan J; Spakman, Wim; Bijl, Peter K; Sluijs, Appy; Langereis, Cor G; Brinkhuis, Henk

2015-01-01

Realistic appraisal of paleoclimatic information obtained from a particular location requires accurate knowledge of its paleolatitude defined relative to the Earth's spin-axis. This is crucial to, among others, correctly assess the amount of solar energy received at a location at the moment of sediment deposition. The paleolatitude of an arbitrary location can in principle be reconstructed from tectonic plate reconstructions that (1) restore the relative motions between plates based on (marine) magnetic anomalies, and (2) reconstruct all plates relative to the spin axis using a paleomagnetic reference frame based on a global apparent polar wander path. Whereas many studies do employ high-quality relative plate reconstructions, the necessity of using a paleomagnetic reference frame for climate studies rather than a mantle reference frame appears under-appreciated. In this paper, we briefly summarize the theory of plate tectonic reconstructions and their reference frames tailored towards applications of paleoclimate reconstruction, and show that using a mantle reference frame, which defines plate positions relative to the mantle, instead of a paleomagnetic reference frame may introduce errors in paleolatitude of more than 15° (>1500 km). This is because mantle reference frames cannot constrain, or are specifically corrected for the effects of true polar wander. We used the latest, state-of-the-art plate reconstructions to build a global plate circuit, and developed an online, user-friendly paleolatitude calculator for the last 200 million years by placing this plate circuit in three widely used global apparent polar wander paths. As a novelty, this calculator adds error bars to paleolatitude estimates that can be incorporated in climate modeling. The calculator is available at www.paleolatitude.org. We illustrate the use of the paleolatitude calculator by showing how an apparent wide spread in Eocene sea surface temperatures of southern high latitudes may be in part

Empirical Investigation of Critical Transitions in Paleoclimate

NASA Astrophysics Data System (ADS)

Loskutov, E. M.; Mukhin, D.; Gavrilov, A.; Feigin, A.

2016-12-01

In this work we apply a new empirical method for the analysis of complex spatially distributed systems to the analysis of paleoclimate data. The method consists of two general parts: (i) revealing the optimal phase-space variables and (ii) construction the empirical prognostic model by observed time series. The method of phase space variables construction based on the data decomposition into nonlinear dynamical modes which was successfully applied to global SST field and allowed clearly separate time scales and reveal climate shift in the observed data interval [1]. The second part, the Bayesian approach to optimal evolution operator reconstruction by time series is based on representation of evolution operator in the form of nonlinear stochastic function represented by artificial neural networks [2,3]. In this work we are focused on the investigation of critical transitions - the abrupt changes in climate dynamics - in match longer time scale process. It is well known that there were number of critical transitions on different time scales in the past. In this work, we demonstrate the first results of applying our empirical methods to analysis of paleoclimate variability. In particular, we discuss the possibility of detecting, identifying and prediction such critical transitions by means of nonlinear empirical modeling using the paleoclimate record time series. The study is supported by Government of Russian Federation (agreement #14.Z50.31.0033 with the Institute of Applied Physics of RAS). 1. Mukhin, D., Gavrilov, A., Feigin, A., Loskutov, E., & Kurths, J. (2015). Principal nonlinear dynamical modes of climate variability. Scientific Reports, 5, 15510. http://doi.org/10.1038/srep155102. Ya. I. Molkov, D. N. Mukhin, E. M. Loskutov, A.M. Feigin, (2012) : Random dynamical models from time series. Phys. Rev. E, Vol. 85, n.3.3. Mukhin, D., Kondrashov, D., Loskutov, E., Gavrilov, A., Feigin, A., & Ghil, M. (2015). Predicting Critical Transitions in ENSO models. Part II

Reconstruction of spatio-temporal temperature from sparse historical records using robust probabilistic principal component regression

USGS Publications Warehouse

Tipton, John; Hooten, Mevin B.; Goring, Simon

2017-01-01

Scientific records of temperature and precipitation have been kept for several hundred years, but for many areas, only a shorter record exists. To understand climate change, there is a need for rigorous statistical reconstructions of the paleoclimate using proxy data. Paleoclimate proxy data are often sparse, noisy, indirect measurements of the climate process of interest, making each proxy uniquely challenging to model statistically. We reconstruct spatially explicit temperature surfaces from sparse and noisy measurements recorded at historical United States military forts and other observer stations from 1820 to 1894. One common method for reconstructing the paleoclimate from proxy data is principal component regression (PCR). With PCR, one learns a statistical relationship between the paleoclimate proxy data and a set of climate observations that are used as patterns for potential reconstruction scenarios. We explore PCR in a Bayesian hierarchical framework, extending classical PCR in a variety of ways. First, we model the latent principal components probabilistically, accounting for measurement error in the observational data. Next, we extend our method to better accommodate outliers that occur in the proxy data. Finally, we explore alternatives to the truncation of lower-order principal components using different regularization techniques. One fundamental challenge in paleoclimate reconstruction efforts is the lack of out-of-sample data for predictive validation. Cross-validation is of potential value, but is computationally expensive and potentially sensitive to outliers in sparse data scenarios. To overcome the limitations that a lack of out-of-sample records presents, we test our methods using a simulation study, applying proper scoring rules including a computationally efficient approximation to leave-one-out cross-validation using the log score to validate model performance. The result of our analysis is a spatially explicit reconstruction of spatio

Paleoclimate Reconstruction of Guangxi in SW China during the Past 2000-Year: Stalagmite Records from Two Caves

NASA Astrophysics Data System (ADS)

Lien, W. Y.; Li, H. C.; Mii, H. S.

2017-12-01

Paleoclimate reconstructions help us to understand the role of the East Asian Summer Monsoon (EASM) on local precipitation and controlling factor of EASM variability, and to improve our climatic prediction. This study presents two stalagmite records from Jinlun Cave (23.553oN, 108.265oE) and Yilingyan Cave (23.041oN, 108.297oE) which are only 60 km apart in Guangxi Province, China. The 35-cm long stalagmite JL12 from Jinlun Cave and 10-cm long stalagmite YLY12 from Yilingyan Cave reveal 1500-year and 2000-year continuous growth respectively based on AMS 14C dating. Data points of the AMS 14C dates with the least dead carbon fraction (DCF) are used to build up the age model. Although dead carbons influence the 14C dating results, it is a feasible dating method for the stalagmites as 230Th/U dating on both stalagmites was not successful due to low U contents. A total of 1586 samples from JL12 and 948 samples from YLY12 have been done for stable isotopes analyses to serve as paleoclimate proxies. Comparison of the d18O records with the local rainfall records and the dry-wetness historic records shows the stalagmite d18O records as a rainfall proxy. The JL12 d18O record resembles the YLY12 d18O record in general, though some differences exist, which confirms the d18O records representing the local climate. The relatively lighter (lower) d18O values of the JL12 and YLY12 records during the Medieval Warm Period (MWP, AD900-1200) indicate stronger EASM. In the first phase of Little Ice Age (LIA), from AD1300 to AD1560, the d18O fluctuate drastically and the average during this period was lower, while the d18O was higher in the second phase of Little Ice Age (AD1560-AD1760), exhibiting a drier and stable climate in the second phase. Furthermore, the DCF varies through the stalagmite records, ascending during the LIA, descending during the MWP, which informs dry condition during the LIA and a moist climate in the MWP. Spectral analysis of the high-resolution d18O records

A Reassessment of the Precision of Carbonate Clumped Isotope Measurements: Implications for Calibrations and Paleoclimate Reconstructions

NASA Astrophysics Data System (ADS)

Fernandez, Alvaro; Müller, Inigo A.; Rodríguez-Sanz, Laura; van Dijk, Joep; Looser, Nathan; Bernasconi, Stefano M.

2017-12-01

Carbonate clumped isotopes offer a potentially transformational tool to interpret Earth's history, but the proxy is still limited by poor interlaboratory reproducibility. Here, we focus on the uncertainties that result from the analysis of only a few replicate measurements to understand the extent to which unconstrained errors affect calibration relationships and paleoclimate reconstructions. We find that highly precise data can be routinely obtained with multiple replicate analyses, but this is not always done in many laboratories. For instance, using published estimates of external reproducibilities we find that typical clumped isotope measurements (three replicate analyses) have margins of error at the 95% confidence level (CL) that are too large for many applications. These errors, however, can be systematically reduced with more replicate measurements. Second, using a Monte Carlo-type simulation we demonstrate that the degree of disagreement on published calibration slopes is about what we should expect considering the precision of Δ47 data, the number of samples and replicate analyses, and the temperature range covered in published calibrations. Finally, we show that the way errors are typically reported in clumped isotope data can be problematic and lead to the impression that data are more precise than warranted. We recommend that uncertainties in Δ47 data should no longer be reported as the standard error of a few replicate measurements. Instead, uncertainties should be reported as margins of error at a specified confidence level (e.g., 68% or 95% CL). These error bars are a more realistic indication of the reliability of a measurement.

A quantitative reconstruction software suite for SPECT imaging

NASA Astrophysics Data System (ADS)

Namías, Mauro; Jeraj, Robert

2017-11-01

Quantitative Single Photon Emission Tomography (SPECT) imaging allows for measurement of activity concentrations of a given radiotracer in vivo. Although SPECT has usually been perceived as non-quantitative by the medical community, the introduction of accurate CT based attenuation correction and scatter correction from hybrid SPECT/CT scanners has enabled SPECT systems to be as quantitative as Positron Emission Tomography (PET) systems. We implemented a software suite to reconstruct quantitative SPECT images from hybrid or dedicated SPECT systems with a separate CT scanner. Attenuation, scatter and collimator response corrections were included in an Ordered Subset Expectation Maximization (OSEM) algorithm. A novel scatter fraction estimation technique was introduced. The SPECT/CT system was calibrated with a cylindrical phantom and quantitative accuracy was assessed with an anthropomorphic phantom and a NEMA/IEC image quality phantom. Accurate activity measurements were achieved at an organ level. This software suite helps increasing quantitative accuracy of SPECT scanners.

Rapid regional surface uplift of the northern Altiplano plateau revealed by multiproxy paleoclimate reconstruction

NASA Astrophysics Data System (ADS)

Kar, Nandini; Garzione, Carmala N.; Jaramillo, Carlos; Shanahan, Timothy; Carlotto, Victor; Pullen, Alex; Moreno, Federico; Anderson, Veronica; Moreno, Enrique; Eiler, John

2016-08-01

The central Altiplano is inferred to have experienced ∼ 2.5 ± 1km surface uplift between ∼10 and 6 Ma, while the southern Altiplano experienced a similar magnitude of surface uplift that began earlier, between ∼16 and 9 Ma. To properly constrain the along strike timing of the Altiplano plateau surface uplift, it is necessary to know how and when the northernmost part of the Altiplano plateau evolved. We reconstruct the paleoclimate and infer the corresponding paleoelevation from the Miocene-Pliocene deposits of the Descanso-Yauri basin (14-15°S) in the northernmost part of the Altiplano plateau using 4 different proxies, including carbonate clumped isotope composition (i.e., Δ47 values), carbonate δ18Oc, leaf wax δDwax and pollen assemblages from paleosol, lacustrine and palustrine carbonates and organic-rich sediments. The isotopic signatures reflect past climate conditions of mean annual air temperature (Δ47) and meteoric water isotope values (δ18Oc, δDwax). Our results show that the northernmost plateau remained at low elevation (0.9 ± 0.8 to 2.1 ± 0.9km) until late Miocene time (∼9 Ma) characterized by ∼15 °C warmer than modern temperature (mean annual air temperature of 23 ± 4 °C, 2σ), low elevation vegetation and precipitation signature with reconstructed □ δ18Omw (VSMOW) of - 8.3 ± 2.0 ‰ (2 σ) from carbonate (δ18Oc) and - 8.6 ± 1.8 ‰ (2 σ) from leaf wax (δDwax). Modern elevations of 4 km were not reached until 5.4 ± 1.0Ma, as indicated by a negative shift in δDwax (VSMOW) from - 143.4 ± 12.8 ‰ (2 σ) to - 209.2 ± 21.1 ‰ (2 σ) between 9.1 ± 0.7 and 5.4 ± 1.0Ma. The timing of surface uplift of the northernmost Altiplano is consistent with the evidence for late Miocene surface uplift of the central Altiplano (16-19°S) between 10 and 6 Ma, and indicates that regional scale uplift in the northern-central plateau significantly postdates the onset of surface uplift in the southern Altiplano (19-22°S) between ∼16

Comparison among Reconstruction Algorithms for Quantitative Analysis of 11C-Acetate Cardiac PET Imaging.

PubMed

Shi, Ximin; Li, Nan; Ding, Haiyan; Dang, Yonghong; Hu, Guilan; Liu, Shuai; Cui, Jie; Zhang, Yue; Li, Fang; Zhang, Hui; Huo, Li

2018-01-01

Kinetic modeling of dynamic 11 C-acetate PET imaging provides quantitative information for myocardium assessment. The quality and quantitation of PET images are known to be dependent on PET reconstruction methods. This study aims to investigate the impacts of reconstruction algorithms on the quantitative analysis of dynamic 11 C-acetate cardiac PET imaging. Suspected alcoholic cardiomyopathy patients ( N = 24) underwent 11 C-acetate dynamic PET imaging after low dose CT scan. PET images were reconstructed using four algorithms: filtered backprojection (FBP), ordered subsets expectation maximization (OSEM), OSEM with time-of-flight (TOF), and OSEM with both time-of-flight and point-spread-function (TPSF). Standardized uptake values (SUVs) at different time points were compared among images reconstructed using the four algorithms. Time-activity curves (TACs) in myocardium and blood pools of ventricles were generated from the dynamic image series. Kinetic parameters K 1 and k 2 were derived using a 1-tissue-compartment model for kinetic modeling of cardiac flow from 11 C-acetate PET images. Significant image quality improvement was found in the images reconstructed using iterative OSEM-type algorithms (OSME, TOF, and TPSF) compared with FBP. However, no statistical differences in SUVs were observed among the four reconstruction methods at the selected time points. Kinetic parameters K 1 and k 2 also exhibited no statistical difference among the four reconstruction algorithms in terms of mean value and standard deviation. However, for the correlation analysis, OSEM reconstruction presented relatively higher residual in correlation with FBP reconstruction compared with TOF and TPSF reconstruction, and TOF and TPSF reconstruction were highly correlated with each other. All the tested reconstruction algorithms performed similarly for quantitative analysis of 11 C-acetate cardiac PET imaging. TOF and TPSF yielded highly consistent kinetic parameter results with superior

Pace of glacial retreat and limits on paleoclimate conditions for the Pine Creek Glacier, Montana, during the Pinedale Glaciation

NASA Astrophysics Data System (ADS)

Huss, E.; Laabs, B. J.; Leonard, E. M.; Licciardi, J. M.; Plummer, M. A.; Caffee, M. W.

2012-12-01

The timing of glaciation and the changes in climate that occurred both during and after the Last Glacial Maximum (LGM) in the Rocky Mountains are not well defined. Given the sensitivity of mountain glaciers to factors such as temperature, precipitation, and solar radiation, reconstructions of the history and extent of paleo-glaciers can be used to infer paleoclimate. Pine Creek Valley, located in the Absaroka Mountains in southwestern Montana, is an ideal setting for this type of research because it was occupied by a discrete valley glacier, the extent of which is precisely known during the LGM. To determine the pace and timing of ice retreat in this valley, glacially polished bedrock surfaces along the path of deglaciation were sampled at several points for cosmogenic 10Be surface exposure dating. The ages obtained range from 17.9 ± 0.8 to 13.2 ± 0.5 ka. When combined with the reconstructed ice extent during the LGM and subsequent deglaciation, these ages yield maximum and minimum retreat rates of 3.1 m/yr and 1.1 m/yr, respectively. These values constrain how long it took the glacier to retreat into a well-defined cirque from the terminal moraines. Paleoclimate conditions for the LGM were estimated using a two-dimensional, numerical, combined energy and mass balance and ice flow model. Previous qualitative inferences of paleoclimate in southern Montana indicate climate during the local LGM was colder and drier than modern values. If precipitation values were held constant or reduced for the Pine Creek glacier, the model suggests a temperature depression of at least 8°C.

Tracking variable sedimentation rates in orbitally forced paleoclimate proxy series

NASA Astrophysics Data System (ADS)

Li, M.; Kump, L. R.; Hinnov, L.

2017-12-01

This study addresses two fundamental issues in cyclostratigraphy: quantitative testing of orbital forcing in cyclic sedimentary sequences and tracking variable sedimentation rates. The methodology proposed here addresses these issues as an inverse problem, and estimates the product-moment correlation coefficient between the frequency spectra of orbital solutions and paleoclimate proxy series over a range of "test" sedimentation rates. It is inspired by the ASM method (1). The number of orbital parameters involved in the estimation is also considered. The method relies on the hypothesis that orbital forcing had a significant impact on the paleoclimate proxy variations, and thus is also tested. The null hypothesis of no astronomical forcing is evaluated using the Beta distribution, for which the shape parameters are estimated using a Monte Carlo simulation approach. We introduce a metric to estimate the most likely sedimentation rate using the product-moment correlation coefficient, H0 significance level, and the number of contributing orbital parameters, i.e., the CHO value. The CHO metric is applied with a sliding window to track variable sedimentation rates along the paleoclimate proxy series. Two forward models with uniform and variable sedimentation rates are evaluated to demonstrate the robustness of the method. The CHO method is applied to the classical Late Triassic Newark depth rank series; the estimated sedimentation rates match closely with previously published sedimentation rates and provide a more highly time-resolved estimate (2,3). References: (1) Meyers, S.R., Sageman, B.B., Amer. J. Sci., 307, 773-792, 2007; (2) Kent, D.V., Olsen, P.E., Muttoni, G., Earth-Sci. Rev.166, 153-180, 2017; (3) Li, M., Zhang, Y., Huang, C., Ogg, J., Hinnov, L., Wang, Y., Zou, Z., Li, L., 2017. Earth Plant. Sc. Lett. doi:10.1016/j.epsl.2017.07.015

Petrography and stable isotope geochemistry of Oligocene-Miocene continental carbonates in south Texas: Implications for paleoclimate and paleoenvironment near sea-level

NASA Astrophysics Data System (ADS)

Godfrey, Conan; Fan, Majie; Jesmok, Greg; Upadhyay, Deepshikha; Tripati, Aradhna

2018-05-01

Cenozoic sedimentary rocks in the southern Texas Gulf Coastal Plains contain abundant continental carbonates that are useful for reconstructing terrestrial paleoclimate and paleoenvironment in a region near sea-level. Our field observations and thin section characterizations of the Oligocene and Miocene continental carbonates in south Texas identified three types of pedogenic carbonates, including rhizoliths, carbonate nodules, and platy horizons, and two types of groundwater carbonates, including carbonate-cemented beds and carbonate concretions, with distinctive macromorphologic and micromorphologic features. Based on preservations of authigenic microfabrics and variations of carbon and oxygen isotopic compositions, we suggest these carbonates experienced minimal diagenesis, and their stable isotopic compositions reflect paleoclimate and paleoenvironment in south Texas. Our Oligocene and Miocene carbonate clumped isotope temperatures (T(Δ47)) are 23-28 °C, slightly less than or comparable to the range of modern mean annual and mean warm season air temperature (21-27 °C) in the study area. These T(Δ47) values do not show any dependency on carbonate-type, or trends through time suggesting that groundwater carbonates were formed at shallow depths. These data could indicate that air temperature in south Texas was relatively stable since the early Oligocene. The reconstructed paleo-surface water δ18O values are similar to modern surface water which could indicate that meteoric water δ18O values also remained stable since the early Oligocene. Mean pedogenic carbonate δ13C values increased - 4.6‰ during the late Miocene, most likely reflecting an expansion of C4 grassland in south Texas. This study provides the first mid- and late Cenozoic continental records of paleoclimate and paleoecology in a low-latitude, near sea-level region.

Biomarker signatures in sediment cores of Lake Urmia (NW Iran): Potential implications for paleo-climate and paleo-environment reconstruction

NASA Astrophysics Data System (ADS)

Haghipour, Negar; Eglinton, Timothy Ian; McIntyre, Cameron; Darvishi Khatooni, Javad; Hunziker, Daniela; Mohammadi, Ali

2015-04-01

Lake Urmia, in northwest Iran, is the largest saline lake in the Middle East with a surface area of ~ 5000km2. Historical documents indicate its existence since at least 2000 years BC, and palynological investigation of a 100 m-long core suggest it contains a sedimentary record spanning the last 200 ka. Despite this potential as an archive of paleo-climate and paleo-environmental information, to date there has been no molecular organic geochemical investigation or precise dating of these sediments. As part of an exploratory study, we have analyzed material from 3 recently collected 8 m-long cores from the eastern, western and middle part of the lake, with the aim of gaining insight in to past depositional and environmental conditions from biomarker signatures preserved in Lake Urmia sediments. The main objectives are to 1) constrain major source(s) of organic matter and gain insights into carbon cycle and depositional processes from bulk isotopic (δ13Corg, 14Corg) and molecular information, 2) determine the applicability of molecular proxies (TEX86 index derived from glyceroldialkylglycerol tetraethers, GDGTs, and unsaturation index UK37 based on long chain alkenones) for paleo-temperature reconstruction and 3) reconstruct the paleo- vegetation and hydrology from compound-specific stable isotopes (δ13C and δD of n-alkanes). In select samples examined from the three cores, we find the hydrocarbon fractions are dominated by long-chain n-alkanes, with n-C29 and C31 as the dominant homologues in most of the samples. Based on the n-alkane distribution, we distinguish two main types; Type 1 mainly includes the samples deeper than ca 4 m (CPI= 10.2, ACL= 30), characteristic of a terrestrial higher plant source; Type 2 comprises mainly shallower samples (CPI =1.5, ACL = 27.3) which may suggest an increased contribution of aquatic plants. Preliminary GDGT analyses indicate low BIT values for most samples, which suggest little input of soil-derived branched-GDGTs. The

Quantitative reconstruction of refractive index distribution and imaging of glucose concentration by using diffusing light.

PubMed

Liang, Xiaoping; Zhang, Qizhi; Jiang, Huabei

2006-11-10

We show that a two-step reconstruction method can be adapted to improve the quantitative accuracy of the refractive index reconstruction in phase-contrast diffuse optical tomography (PCDOT). We also describe the possibility of imaging tissue glucose concentration with PCDOT. In this two-step method, we first use our existing finite-element reconstruction algorithm to recover the position and shape of a target. We then use the position and size of the target as a priori information to reconstruct a single value of the refractive index within the target and background regions using a region reconstruction method. Due to the extremely low contrast available in the refractive index reconstruction, we incorporate a data normalization scheme into the two-step reconstruction to combat the associated low signal-to-noise ratio. Through a series of phantom experiments we find that this two-step reconstruction method can considerably improve the quantitative accuracy of the refractive index reconstruction. The results show that the relative error of the reconstructed refractive index is reduced from 20% to within 1.5%. We also demonstrate the possibility of PCDOT for recovering glucose concentration using these phantom experiments.

Paleoclimate reconstruction along the Pole-Equator-Pole transect of the Americas (PEP 1)

USGS Publications Warehouse

Markgraf, Vera; Baumgartner, T.R.; Bradbury, J.P.; Diaz, Henry F.; Dunbar, R.B.; Luckman, B.H.; Seltzer, G.O.; Swetnam, T.W.; Villalba, R.

2000-01-01

Examples are presented of inter-hemispheric comparison of instrumental climate and paleoclimate proxy records from the Americas for different temporal scales. Despite a certain symmetry of seasonal precipitation patterns along the PEP I transect, decadal variability of winter precipitation shows different characteristics in terms of amplitude and frequency in both the last 100 and last 1000 years. Such differences in variability are also seen in a comparison of time series of different El Nino/Southern Oscillation proxy records from North and South America, however, these differences do not appear to affect the spatial correlation with Pacific sea surface temperature patterns. Local and regional differences in response to climate change are even more pronounced for records with lower temporal resolution, and inter-hemispheric synchroneity may or may not be indicative of the same forcing. This aspect is illustrated in an inter-hemispheric comparison of the last 1000 years of glacier variability, and of the full- and lateglacial lake level history.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Use of quantitative SPECT/CT reconstruction in 99mTc-sestamibi imaging of patients with renal masses.

PubMed

Jones, Krystyna M; Solnes, Lilja B; Rowe, Steven P; Gorin, Michael A; Sheikhbahaei, Sara; Fung, George; Frey, Eric C; Allaf, Mohamad E; Du, Yong; Javadi, Mehrbod S

2018-02-01

Technetium-99m ( 99m Tc)-sestamibi single-photon emission computed tomography/computed tomography (SPECT/CT) has previously been shown to allow for the accurate differentiation of benign renal oncocytomas and hybrid oncocytic/chromophobe tumors (HOCTs) apart from other malignant renal tumor histologies, with oncocytomas/HOCTs showing high uptake and renal cell carcinoma (RCC) showing low uptake based on uptake ratios from non-quantitative single-photon emission computed tomography (SPECT) reconstructions. However, in this study, several tumors fell close to the uptake ratio cutoff, likely due to limitations in conventional SPECT/CT reconstruction methods. We hypothesized that application of quantitative SPECT/CT (QSPECT) reconstruction methods developed by our group would provide more robust separation of hot and cold lesions, serving as an imaging framework on which quantitative biomarkers can be validated for evaluation of renal masses with 99m Tc-sestamibi. Single-photon emission computed tomography data were reconstructed using the clinical Flash 3D reconstruction and QSPECT methods. Two blinded readers then characterized each tumor as hot or cold. Semi-quantitative uptake ratios were calculated by dividing lesion activity by background renal activity for both Flash 3D and QSPECT reconstructions. The difference between median (mean) hot and cold tumor uptake ratios measured 0.655 (0.73) with the QSPECT method and 0.624 (0.67) with the conventional method, resulting in increased separation between hot and cold tumors. Sub-analysis of 7 lesions near the separation point showed a higher absolute difference (0.16) between QPSECT and Flash 3D mean uptake ratios compared to the remaining lesions. Our finding of improved separation between uptake ratios of hot and cold lesions using QSPECT reconstruction lays the foundation for additional quantitative SPECT techniques such as SPECT-UV in the setting of renal 99m Tc-sestamibi and other SPECT/CT exams. With robust

Reconstructing pre-instrumental streamflow in Eastern Australia using a water balance approach

NASA Astrophysics Data System (ADS)

Tozer, C. R.; Kiem, A. S.; Vance, T. R.; Roberts, J. L.; Curran, M. A. J.; Moy, A. D.

2018-03-01

Streamflow reconstructions based on paleoclimate proxies provide much longer records than the short instrumental period records on which water resource management plans are currently based. In Australia there is a lack of in-situ high resolution paleoclimate proxy records, but remote proxies with teleconnections to Australian climate have utility in producing streamflow reconstructions. Here we investigate, via a case study for a catchment in eastern Australia, the novel use of an Antarctic ice-core based rainfall reconstruction within a Budyko-framework to reconstruct ∼1000 years of annual streamflow. The resulting streamflow reconstruction captures interannual to decadal variability in the instrumental streamflow, validating both the use of the ice core rainfall proxy record and the Budyko-framework method. In the preinstrumental era the streamflow reconstruction shows longer wet and dry epochs and periods of streamflow variability that are higher than observed in the instrumental era. Importantly, for both the instrumental record and preinstrumental reconstructions, the wet (dry) epochs in the rainfall record are shorter (longer) in the streamflow record and this non-linearity must be considered when inferring hydroclimatic risk or historical water availability directly from rainfall proxy records alone. These insights provide a better understanding of present infrastructure vulnerability in the context of past climate variability for eastern Australia. The streamflow reconstruction presented here also provides a better understanding of the range of hydroclimatic variability possible, and therefore represents a more realistic baseline on which to quantify the potential impacts of anthropogenic climate change on water security.

Monthly paleostreamflow reconstruction from annual tree-ring chronologies

NASA Astrophysics Data System (ADS)

Stagge, J. H.; Rosenberg, D. E.; DeRose, R. J.; Rittenour, T. M.

2018-02-01

Paleoclimate reconstructions are increasingly used to characterize annual climate variability prior to the instrumental record, to improve estimates of climate extremes, and to provide a baseline for climate-change projections. To date, paleoclimate records have seen limited engineering use to estimate hydrologic risks because water systems models and managers usually require streamflow input at the monthly scale. This study explores the hypothesis that monthly streamflows can be adequately modeled by statistically decomposing annual flow reconstructions. To test this hypothesis, a multiple linear regression model for monthly streamflow reconstruction is presented that expands the set of predictors to include annual streamflow reconstructions, reconstructions of global circulation, and potential differences among regional tree-ring chronologies related to tree species and geographic location. This approach is used to reconstruct 600 years of monthly streamflows at two sites on the Bear and Logan rivers in northern Utah. Nash-Sutcliffe Efficiencies remain above zero (0.26-0.60) for all months except April and Pearson's correlation coefficients (R) are 0.94 and 0.88 for the Bear and Logan rivers, respectively, confirming that the model can adequately reproduce monthly flows during the reference period (10/1942 to 9/2015). Incorporating a flexible transition between the previous and concurrent annual reconstructed flows was the most important factor for model skill. Expanding the model to include global climate indices and regional tree-ring chronologies produced smaller, but still significant improvements in model fit. The model presented here is the only approach currently available to reconstruct monthly streamflows directly from tree-ring chronologies and climate reconstructions, rather than using resampling of the observed record. With reasonable estimates of monthly flow that extend back in time many centuries, water managers can challenge systems models with a

Multiproxy biomarker, isotopic and pollen reconstructions of the middle to late Holocene paleoclimate of the Loess Plateau in centre China

NASA Astrophysics Data System (ADS)

Sun, H.; Seki, O.; Zhou, A.; Chen, F.; Schouten, S.; Toney, J. L.; Bendle, J.

2011-12-01

The Asian monsoon is a key component of the earth's climate system that directly affects the livelihood of 50 million people on the loess plateau of central China. At the far edge of monsoonal influence, this region is especially vulnerable to future changes in temperature and evaporation / precipitation. Therefore, paleoclimatic information on the natural sensitivity of the region to changes in monsoon driven aridity are crucial. Despite the need for multiproxy records of Holocene climate from this region, reconstructions are rare, because of the low resolution of loess deposits and the scarcity of other paleoclimate archives (e.g. natural lakes, speleothems). Here we present multiple proxy records from Tianchi lake, one of the few nature lakes on the loess plateau and central China. The chronology is well constrained by a high-resolution (20 AMS 14C dates) radiocarbon age-model, spanning the past 6200 years. Here we present pollen, Glycerol dibiphytanyl glycerol tetraethers (GDGTs), lake macrophyte and higher plant-wax biomarkers to reconstruct regional climate change during the middle to late Holocene. Evidence from pollen data suggest that deciduous trees decreased from 6200 cal yr BP and then more rapidly from 1000 yr BP. Modern and downcore molecular distribution patterns of n-alkanes and n-alkanoic acids, especially n-alkane Paq values, suggest increasing relative abundance of macrophytes over this time, which we interpret (based on lake morphology) as decreasing lake-level. Using the recent Sun et al (2011) regional calibration we derive mean annual GDGT based temperatures (MBT/CBT-MATs) with reasonable ranges. Our temperature reconstruction closely correlates on millennial to centennial timescales with the independent D/H measurements on C28 fatty acid methyl esters (C28 FAMEs), whose signal is assumed to derive primarily from terrestrial plant waxes and the δD values to reflect local changes in relative humidity. Comparisons of our independent GDGT

A fresh look at the Last Glacial Maximum using Paleoclimate Data Assimilation

NASA Astrophysics Data System (ADS)

Malevich, S. B.; Tierney, J. E.; Hakim, G. J.; Tardif, R.

2017-12-01

Quantifying climate conditions during the Last Glacial Maximum ( 21ka) can help us to understand climate responses to forcing and climate states that are poorly represented in the instrumental record. Paleoclimate proxies may be used to estimate these climate conditions, but proxies are sparsely distributed and possess uncertainties from environmental and biogeochemical processes. Alternatively, climate model simulations provide a full-field view, but may predict unrealistic climate states or states not faithful to proxy records. Here, we use data assimilation - combining climate proxy records with a theoretical understanding from climate models - to produce field reconstructions of the LGM that leverage the information from both data and models. To date, data assimilation has mainly been used to produce reconstructions of climate fields through the last millennium. We expand this approach in order to produce a climate fields for the Last Glacial Maximum using an ensemble Kalman filter assimilation. Ensemble samples were formed from output from multiple models including CCSM3, CESM2.1, and HadCM3. These model simulations are combined with marine sediment proxies for upper ocean temperature (TEX86, UK'37, Mg/Ca and δ18O of foraminifera), utilizing forward models based on a newly developed suite of Bayesian proxy system models. We also incorporate age model and radiocarbon reservoir uncertainty into our reconstructions using Bayesian age modeling software. The resulting fields show familiar patterns based on comparison with previous proxy-based reconstructions, but additionally reveal novel patterns of large-scale shifts in ocean-atmosphere dynamics, as the surface temperature data inform upon atmospheric circulation and precipitation patterns.

Branched GDGT-based paleotemperature reconstruction of the last 30,000 years in humid monsoon region of Southeast China

NASA Astrophysics Data System (ADS)

Wang, M.

2017-12-01

The use of bacterial branched glycerol dialkyl glycerol tetraethers (brGDGTs) to reconstruct mean annual air temperatures (MAATs) and environmental pH from soils has sparked significant interest in the terrestrial paleoclimate community. However, the reconstruction of these climate proxies from peat bogs is rare in monsoonal regions of the East Asia. This research was carried out on a core from the Shuizhuyang (SZY) peat bog located in Fujian Province. Branched GDGT (brGDGT) indexes were used for reconstructing the paleoclimate of the last 30 cal ka. The aim was to evaluate quantitatively the MAAT and pH values since the Last Glacial Maximum (LGM) in the subtropical zone of China. Results show that the CBT-MBT'-derived MAAT at MIS 3 is about 15.6 °C on average, which is followed by a significant fall at the LGM (11.7-12.1 °C). The temperature difference between the LGM and the present-day value is as high as 5.8 °C. The synchronous variation of biomarker and pollen proxies indicates that replacement of subtropical evergreen broadleaved forests by coldtolerant, deciduous broadleaved forests was driven by the significant drop in air temperature. Our results also indicate that the Younger Dryas event lasted from about 12.9 to about 11.3 cal ka, and cooling event at 3.2 cal ka in the late Holocene was detected, showing the sensitivity of peat bogs to rapid cooling. Our pH reconstructions indicate that the pH of the bog rose during Heinrich 1 and Bølling-Allerød periods, probably due to low precipitation, and were lowest in the Holocene thermal maximum between 8 ka and 2.5 ka, probably due to higher precipitation. The decoupling of reconstructed MAAT and pH during particularly deglaciation and YD periods supports the hypothesis that the variations in temperature and precipitation are not always synchronous.

Reconstructing Environmental Change Using Lake Varves as a Climate Proxy

ERIC Educational Resources Information Center

Dempsey, Christopher; Bodzin, Alec; Cirucci, Lori; Anastasio, David; Sahagian, Dork

2012-01-01

In this article, the authors describe an investigative activity in which their eighth-grade students reconstructed past environmental change in the New England area using data from lake varves in central Vermont to examine evidence of climate change. The investigation uses an authentic paleoclimate record (Ridge 2011) from the Pleistocene epoch,…

Jurassic-Cretaceous paleogeography, paleoclimate and upwelling of the northern margin of Tethys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Golonka, J.; Krobicki, M.

The Jurassic and Cretaceous global paleogeographic reconstructions illustrate the changing configuration of mountains, land, shallow seas and deep ocean basins. Active plate boundaries, such as spreading centers and subduction zones, are also shown. The Pliensbachian, Toarcian, Bathonian, Oxfordian-Kimmeridgian, Tithonian-Berriasian, Valanginian, Albian, Turonian and Maastrichtian maps were generated The outlines of paleogeography are used as input for paleoclimatic modeling. The PALEOCLIMATE program models global atmospheric pressure, derive paleo-wind directions and estimate the likelihood of coastal upwelling. The program is based on the paleoclimatic methods first developed by Judith Parrish, adopted by C. R. Scotese and modified by M. I. Ross. Themore » maps depict air pressure, wind directions, humid zones and areas favorable for upwelling conditions plotted on the paleogeographic background. Paleoclimate modeling suggests that prevailing Jurassic-Cretaceous wind directions in the northern Tethys area were from north-northeast. These winds were parallel to the axis of Czorsztyn ridge. The ridge was uplifted between Magura and Pieniny basins as the result of extension during Jurassic supercontinent breakup. The upwelling may have been induced at the southeastern margin of the ridge. The model is consistent with rock records, especially from the upper part of ammonitico rosso type Czorsztyn formation. Mass occurrence of Tithonian and Berriasian brachiopods was probably controlled by upwelling-induced trophic relationships which is resulted in the intense growth of benthic organisms on the ridge. This is additionally supported by the presence of phosphorites at localities which corresponded to the continental shelf/slope transition.« less

Evaluation of Sr/Ca-based paleoclimate reconstructions in modern and Medieval Diploria strigosa corals in the northeastern Caribbean

NASA Astrophysics Data System (ADS)

Xu, Y.; Pearson, S. P.; Kilbourne, K.

2013-12-01

period with initial U-series dates near the top of the cores ranging from 1277 × 5 A.D. to 1327 × 5 A.D. Initial Sr/Ca results from the first sub-fossil coral have a seasonal range of 2.65 × 0.27 °C when converted to temperature units with our modern calibration, indicating no significant change from modern times. However, the mean Sr/Ca for this coral is very high (9.388 mmol/mol) compared to the modern corals. We explore the potential causes for this discrepancy in our study. Because reconstructing the mean SST during the Medieval Climate Anomaly may be difficult without temporal overlap with modern corals, our focus is on interannual variability. The coral Sr/Ca based monthly SST anomalies for both modern and sub-fossil corals have larger interannual variances than the instrumental record. One explanation for this is that the SSTs derived from sub-fossil corals are local data for which one expects larger variances than the instrumental data averaged over a 2 x 2 ° grid. This species shows great promise for future paleoclimate reconstructions.

Paleoclimate from fossil plants and application to the early Cenozoic Rocky Mountains

NASA Astrophysics Data System (ADS)

Wing, S. L.

2011-12-01

Wladimir Köppen called vegetation "crystallized, visible climate," and his metaphor encouraged paleobotanists to climb the chain of inference from fossil plants to paleovegetation to paleoclimate. Inferring paleovegetation from fossils has turned out to be very difficult, however, and today most paleobotanical methods for inferring paleoclimate do not try to reconstruct paleovegetation as a first step. Three major approaches are widely use to infer paleoclimate from plant fossils: 1) phylogenetic inferences rely on the climatic distributions of extant relatives of fossils, 2) morphological inferences use present-day correlations of climate with plant morphology (e.g, leaf shape, wood anatomy), and 3) chemical inferences rely on correlations between climate and the stable isotopic composition of plants or organic compounds. Each approach makes assumptions that are hard to verify. Phylogenetic inference depends on accurate identification of fossils, and also assumes that evolution and/or extinction has not shifted the climatic distributions of plant lineages through time. On average this assumption is less valid for older time periods, but probably it is not radically wrong for the early Cenozoic. Morphological approaches don't require taxonomic identification of plant fossils, but do assume that correlations between plant form and climate have been constant over time. This assumption is bolstered if the ecophysiological cause of the morphology-climate correlation is well understood, but often it isn't. Stable isotopic approaches assume that present-day correlations between isotopic composition and climate apply to the past. Commonly the chemical and physiological mechanisms responsible for the correlation are moderately well known, but often the variation among different taxonomic and functional groups of plants is poorly characterized. In spite of limitations and uncertainties on all methods for inferring paleoclimate from fossil plants, broad patterns emerge from

Coupling carbon isotopes with astrochronology and correlation techniques for Late Cretaceous chronostratigraphic refinement and paleoclimate reconstruction

NASA Astrophysics Data System (ADS)

Jones, M. M.; Sageman, B. B.; Meyers, S. R.

2016-12-01

Late Cretaceous carbon isotope ratios (δ13C) recorded in organic matter and marine carbonates preserve an archive of the global carbon cycle in a greenhouse climate state. Due to excellent connectivity among surface carbon reservoirs and the low residence time of carbon in them, excursions in the δ13C that record changes in fluxes serve as widely correlative chronostratigraphic markers. In this study, floating astronomical time scales (ATS) from an organic carbon-rich marine Turonian succession at Demerara Rise (tropical N. Atlantic) are combined with high-resolution δ13C chemostratigraphy to estimate CIE timing and duration for refinement of the geologic time scale. In addition, a Gaussian kernel smoothing technique for objective correlation of astronomically tuned δ13C records is developed. Correlation with three coeval Turonian sections (Western Interior Basin, Texas, & Europe) shows consistency in astronomical and radioisotopic time scale ages for CIEs. In particular, a mid-Turonian sea level fall is demonstrated to be synchronous within 100 ka uncertainty. Spectral analyses of δ13Corg, %TOC, %Carbonate, and C/N time series provide insights into astronomical forcings influencing paleoclimate and paleoceanographic conditions in the tropical proto-North Atlantic upwelling zone. The stable long eccentricity cycle ( 405 ka) is robustly recorded in all geochemical data, and has the highest amplitude in %TOC, %Carbonate, and C/N time series. However, δ13C from Demerara Rise is dominated by a 1 Myr cycle resembling long obliquity, suggesting a dynamic organic carbon reservoir and/or climate feedback originating in high-latitudes was prominent during the Turonian greenhouse carbon cycle. This investigation emphasizes δ13C chemostratigraphy and astrochronology are useful chronostratigraphic methods for importing high-resolution time control into disparate basins to answer questions regarding sea level records, paleoclimate, and mass extinction on a global scale

The Influence of Reconstruction Kernel on Bone Mineral and Strength Estimates Using Quantitative Computed Tomography and Finite Element Analysis.

PubMed

Michalski, Andrew S; Edwards, W Brent; Boyd, Steven K

2017-10-17

Quantitative computed tomography has been posed as an alternative imaging modality to investigate osteoporosis. We examined the influence of computed tomography convolution back-projection reconstruction kernels on the analysis of bone quantity and estimated mechanical properties in the proximal femur. Eighteen computed tomography scans of the proximal femur were reconstructed using both a standard smoothing reconstruction kernel and a bone-sharpening reconstruction kernel. Following phantom-based density calibration, we calculated typical bone quantity outcomes of integral volumetric bone mineral density, bone volume, and bone mineral content. Additionally, we performed finite element analysis in a standard sideways fall on the hip loading configuration. Significant differences for all outcome measures, except integral bone volume, were observed between the 2 reconstruction kernels. Volumetric bone mineral density measured using images reconstructed by the standard kernel was significantly lower (6.7%, p < 0.001) when compared with images reconstructed using the bone-sharpening kernel. Furthermore, the whole-bone stiffness and the failure load measured in images reconstructed by the standard kernel were significantly lower (16.5%, p < 0.001, and 18.2%, p < 0.001, respectively) when compared with the image reconstructed by the bone-sharpening kernel. These data suggest that for future quantitative computed tomography studies, a standardized reconstruction kernel will maximize reproducibility, independent of the use of a quantitative calibration phantom. Copyright © 2017 The International Society for Clinical Densitometry. Published by Elsevier Inc. All rights reserved.

A pseudoproxy assessment of data assimilation for reconstructing the atmosphere-ocean dynamics of hydroclimate extremes

NASA Astrophysics Data System (ADS)

Steiger, Nathan J.; Smerdon, Jason E.

2017-10-01

Because of the relatively brief observational record, the climate dynamics that drive multiyear to centennial hydroclimate variability are not adequately characterized and understood. Paleoclimate reconstructions based on data assimilation (DA) optimally fuse paleoclimate proxies with the dynamical constraints of climate models, thus providing a coherent dynamical picture of the past. DA is therefore an important new tool for elucidating the mechanisms of hydroclimate variability over the last several millennia. But DA has so far remained untested for global hydroclimate reconstructions. Here we explore whether or not DA can be used to skillfully reconstruct global hydroclimate variability along with the driving climate dynamics. Through a set of idealized pseudoproxy experiments, we find that an established DA reconstruction approach can in principle be used to reconstruct hydroclimate at both annual and seasonal timescales. We find that the skill of such reconstructions is generally highest near the proxy sites. This set of reconstruction experiments is specifically designed to estimate a realistic upper bound for the skill of this DA approach. Importantly, this experimental framework allows us to see where and for what variables the reconstruction approach may never achieve high skill. In particular for tree rings, we find that hydroclimate reconstructions depend critically on moisture-sensitive trees, while temperature reconstructions depend critically on temperature-sensitive trees. Real-world DA-based reconstructions will therefore likely require a spatial mixture of temperature- and moisture-sensitive trees to reconstruct both temperature and hydroclimate variables. Additionally, we illustrate how DA can be used to elucidate the dynamical mechanisms of drought with two examples: tropical drivers of multiyear droughts in the North American Southwest and in equatorial East Africa. This work thus provides a foundation for future DA-based hydroclimate

A national perspective on paleoclimate streamflow and water storage infrastructure in the conterminous United States

NASA Astrophysics Data System (ADS)

Ho, Michelle; Lall, Upmanu; Sun, Xun; Cook, Edward

2017-04-01

Large-scale water storage infrastructure in the Conterminous United States (CONUS) provides a means of regulating the temporal variability in water supply with storage capacities ranging from seasonal storage in the wetter east to multi-annual and decadal-scale storage in the drier west. Regional differences in water availability across the CONUS provides opportunities for optimizing water dependent economic activities, such as food and energy production, through storage and transportation. However, the ability to sufficiently regulate water supplies into the future is compromised by inadequate monitoring of non-federally-owned dams that make up around 97% of all dams. Furthermore, many of these dams are reaching or have exceeded their economic design life. Understanding the role of dams in the current and future landscape of water requirements in the CONUS is needed to prioritize dam safety remediation or identify where redundant dams may be removed. A national water assessment and planning process is needed for addressing water requirements, accounting for regional differences in water supply and demand, and the role of dams in such a landscape. Most dams in the CONUS were designed without knowledge of devastating floods and prolonged droughts detected in multi-centennial paleoclimate records, consideration of projected climate change, nor consideration of optimal operation across large-scale regions. As a step towards informing water supply across the CONUS we present a paleoclimate reconstruction of annual streamflow across the CONUS over the past 555 years using a spatially and temporally complete paleoclimate record of summer drought across the CONUS targeting a set of US Geological Survey streamflow sites. The spatial and temporal structures of national streamflow variability are analyzed using hierarchical clustering, principal component analysis, and wavelet analyses. The reconstructions show signals of contemporary droughts such as the Dust Bowl (1930s

Comparing Planning Hydrologic Ensembles associated with Paleoclimate, Projected Climate, and blended Climate Information Sets

NASA Astrophysics Data System (ADS)

Brekke, L. D.; Prairie, J.; Pruitt, T.; Rajagopalan, B.; Woodhouse, C.

2008-12-01

Water resources adaptation planning under climate change involves making assumptions about probabilistic water supply conditions, which are linked to a given climate context (e.g., instrument records, paleoclimate indicators, projected climate data, or blend of these). Methods have been demonstrated to associate water supply assumptions with any of these climate information types. Additionally, demonstrations have been offered that represent these information types in a scenario-rich (ensemble) planning framework, either via ensembles (e.g., survey of many climate projections) or stochastic modeling (e.g., based on instrument records or paleoclimate indicators). If the planning goal involves using a hydrologic ensemble that jointly reflects paleoclimate (e.g., lower- frequency variations) and projected climate information (e.g., monthly to annual trends), methods are required to guide how these information types might be translated into water supply assumptions. However, even if such a method exists, there is lack of understanding on how such a hydrologic ensemble might differ from ensembles developed relative to paleoclimate or projected climate information alone. This research explores two questions: (1) how might paleoclimate and projected climate information be blended into an planning hydrologic ensemble, and (2) how does a planning hydrologic ensemble differ when associated with the individual climate information types (i.e. instrumental records, paleoclimate, projected climate, or blend of the latter two). Case study basins include the Gunnison River Basin in Colorado and the Missouri River Basin above Toston in Montana. Presentation will highlight ensemble development methods by information type, and comparison of ensemble results.

The Power of Cooperation in International Paleoclimate Science: Examples from the PAGES 2k Network and the Ocean2k Working Group

NASA Astrophysics Data System (ADS)

Addison, J. A.

2015-12-01

The Past Global Changes (PAGES) project of IGBP and Future Earth supports research to understand the Earth's past environment to improve future climate predictions and inform strategies for sustainability. Within this framework, the PAGES 2k Network was established to provide a focus on the past 2000 years, a period that encompasses Medieval Climate Anomaly warming, Little Ice Age cooling, and recent anthropogenically-forced climate change. The results of these studies are used for testing earth system models, and for understanding decadal- to centennial-scale variability, which is needed for long-term planning. International coordination and cooperation among the nine regional Working Groups that make up the 2k Network has been critical to the success of PAGES 2k. The collaborative approach is moving toward scientific achievements across the regional groups, including: (i) the development of a community-driven open-access proxy climate database; (ii) integration of multi-resolution proxy records; (iii) development of multivariate climate reconstructions; and (iv) a leap forward in the spatial resolution of paleoclimate reconstructions. The last addition to the 2k Network, the Ocean2k Working Group has further innovated the collaborative approach by: (1) creating an open, receptive environment to discuss ideas exclusively in the virtual space; (2) employing an array of real-time collaborative software tools to enable communication, group document writing, and data analysis; (3) consolidating executive leadership teams to oversee project development and manage grassroots-style volunteer pools; and (4) embracing the value-added role that international and interdisciplinary science can play in advancing paleoclimate hypotheses critical to understanding future change. Ongoing efforts for the PAGES 2k Network are focused on developing new standards for data quality control and archiving. These tasks will provide the foundation for new and continuing "trans-regional" 2k

What We Talk About When We Talk About Drought: Tree-ring Perspectives on Model-Data Comparisons in Hydroclimate Research

NASA Astrophysics Data System (ADS)

Cook, B.; Anchukaitis, K. J.

2017-12-01

Comparative analyses of paleoclimate reconstructions and climate model simulations can provide valuable insights into past and future climate events. Conducting meaningful and quantitative comparisons, however, can be difficult for a variety of reasons. Here, we use tree-ring based hydroclimate reconstructions to discuss some best practices for paleoclimate-model comparisons, highlighting recent studies that have successfully used this approach. These analyses have improved our understanding of the Medieval-era megadroughts, ocean forcing of large scale drought patterns, and even climate change contributions to future drought risk. Additional work is needed, however, to better reconcile and formalize uncertainties across observed, modeled, and reconstructed variables. In this regard, process based forward models of proxy-systems will likely be a critical tool moving forward.

Paleoclimate and Amerindians: Evidence from stable isotopes and atmospheric circulation

USGS Publications Warehouse

Lovvorn, M.B.; Frison, G.C.; Tieszen, L.L.

2001-01-01

Two Amerindian demographic shifts are attributed to climate change in the northwest plains of North America: at ???11,000 calendar years before present (yr BP), Amerindian culture apparently split into foothills-mountains vs. plains biomes; and from 8,000-5,000 yr BP, scarce archaeological sites on the open plains suggest emigration during xeric "Altithermal" conditions. We reconstructed paleoclimates from stable isotopes in prehistoric bison bone and relations between weather and fractions of C4 plants in forage. Further, we developed a climate-change model that synthesized stable isotope, existing qualitative evidence (e.g., palynological, erosional), and global climate mechanisms affecting this midlatitude region. Our isotope data indicate significant warming from ???12,400 to 11,900 yr BP, supporting climate-driven cultural separation. However, isotope evidence of apparently wet, warm conditions at 7,300 yr BP refutes emigration to avoid xeric conditions. Scarcity of archaeological sites is best explained by rapid climate fluctuations after catastrophic draining of the Laurentide Lakes, which disrupted North Atlantic Deep Water production and subsequently altered monsoonal inputs to the open plains.

Phosphate mineral formation in Lake Baikal sediments and implications for paleoclimate

NASA Astrophysics Data System (ADS)

Fagel, N.; Alleman, L. Y.; André, L.; Cloots, R.; Hatert, F.; Juvigné, E.; Renson, V.

2003-04-01

The more than 20 million years old Lake Baikal sedimentary record provides a good climate archive. While most paleoclimate reconstructions are mainly based on biotic proxies, we tested in this study other minerogenic tracers. In particular, it was suggested that the formation of authigenic and/or diagenetic phosphate minerals in Baïkal sediments underlines transitions from glacial to interglacial periods (Deike et al., 1997). The phosphate mineral formation previously evidenced (Müller et al., 2002) may be sensitive to suspended sediment concentrations: glacial periods are characterised by high detrital discharge, interglacial intervals are marked by low detrital supply but high biogenic sedimentation. Phosphate minerals were observed in Baïkal sediments from recent to 65 kyr BP. Their abundance was related to the sedimentation rate, the phosphate enrichment layers being particularly common on low sedimentation site, i.e., the Academician Ridge. Major and trace elements have been analysed by ICP-AES and ICP-MS on four cores drilled on topographic hills, in the southern basin (Posolsky bank, CON01-604), in the central part (Academician Ridge, VER98-1-3 and VER98-1-14) and in the northern basin (Continent Ridge, CON01-603). The geochemical signature is consistent with the occurrence of Mn-Fe-phosphate minerals. For instance P2O5 reaches up to 3% wt. relative to a mean value of 0.3 in the background sediment, MnO2 presents an enrichment factor up to 6. There is no associated enrichment in any of the trace elements measured at the same levels. In the sediments, those P-Mn-Fe rich levels are related either to sparse millimetric dark concretions or to a layer (or a group of layers) defined by an alignment of numerous concretions but there is no so-called crusts. The concretions, isolated by >63 mm sieving, present a lamellar morphology. They are identified as Fe-phosphate phases with a variable proportion of Mn. The powder diffraction diagram is consistent with

Joint reconstruction of activity and attenuation in Time-of-Flight PET: A Quantitative Analysis.

PubMed

Rezaei, Ahmadreza; Deroose, Christophe M; Vahle, Thomas; Boada, Fernando; Nuyts, Johan

2018-03-01

Joint activity and attenuation reconstruction methods from time of flight (TOF) positron emission tomography (PET) data provide an effective solution to attenuation correction when no (or incomplete/inaccurate) information on the attenuation is available. One of the main barriers limiting their use in clinical practice is the lack of validation of these methods on a relatively large patient database. In this contribution, we aim at validating the activity reconstructions of the maximum likelihood activity reconstruction and attenuation registration (MLRR) algorithm on a whole-body patient data set. Furthermore, a partial validation (since the scale problem of the algorithm is avoided for now) of the maximum likelihood activity and attenuation reconstruction (MLAA) algorithm is also provided. We present a quantitative comparison of the joint reconstructions to the current clinical gold-standard maximum likelihood expectation maximization (MLEM) reconstruction with CT-based attenuation correction. Methods: The whole-body TOF-PET emission data of each patient data set is processed as a whole to reconstruct an activity volume covering all the acquired bed positions, which helps to reduce the problem of a scale per bed position in MLAA to a global scale for the entire activity volume. Three reconstruction algorithms are used: MLEM, MLRR and MLAA. A maximum likelihood (ML) scaling of the single scatter simulation (SSS) estimate to the emission data is used for scatter correction. The reconstruction results are then analyzed in different regions of interest. Results: The joint reconstructions of the whole-body patient data set provide better quantification in case of PET and CT misalignments caused by patient and organ motion. Our quantitative analysis shows a difference of -4.2% (±2.3%) and -7.5% (±4.6%) between the joint reconstructions of MLRR and MLAA compared to MLEM, averaged over all regions of interest, respectively. Conclusion: Joint activity and attenuation

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

PubMed

Hein, L R

2001-10-01

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

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.

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.

Using Paleo-climate Comparisons to Constrain Future Projections in CMIP5

NASA Technical Reports Server (NTRS)

Schmidt, G. A.; Annan, J D.; Bartlein, P. J.; Cook, B. I.; Guilyardi, E.; Hargreaves, J. C.; Harrison, S. P.; Kageyama, M.; LeGrande, A. N..; Konecky, B.;

3D quantitative photoacoustic image reconstruction using Monte Carlo method and linearization

NASA Astrophysics Data System (ADS)

Okawa, Shinpei; Hirasawa, Takeshi; Tsujita, Kazuhiro; Kushibiki, Toshihiro; Ishihara, Miya

2018-02-01

To quantify the functional and structural information of peripheral blood vessels for diagnoses of diseases which affects peripheral blood vessels such as diabetes and peripheral vascular disease, a 3D quantitative photoacoustic tomography (QPAT) reconstructing the optical properties such as the absorption coefficient reflecting microvascular structures and hemoglobin concentration and oxygenation saturation is studied. QPAT image reconstruction algorithms based on radiative transfer equation (RTE) and photon diffusion equation (PDE) have been proposed. However, it is not easy to use RTE in the clinical practice because of the huge computational load and long calculation time. On the other hand, it is always considered problematic to use PDE, because it does not approximate RTE well near the illuminating position. In this study, we developed the 3D QPAT image reconstruction using Monte Carlo (MC) method which approximates RTE better than PDE to reconstruct the optical properties in the region near the illuminating surface. To reduce the calculation time, we applied linearization. The QPAT image reconstruction algorithm with MC method and linearization was examined in numerical simulations and phantom experiment by use of a scanning system with a single probe consisting of P(VDF-TrFE) piezo electric film and optical fiber.

Reconstructing Climate Change: The Model-Data Ping-Pong

NASA Astrophysics Data System (ADS)

Stocker, T. F.

2017-12-01

When Cesare Emiliani, the father of paleoceanography, made the first attempts at a quantitative reconstruction of Pleistocene climate change in the early 1950s, climate models were not yet conceived. The understanding of paleoceanographic records was therefore limited, and scientists had to resort to plausibility arguments to interpret their data. With the advent of coupled climate models in the early 1970s, for the first time hypotheses about climate processes and climate change could be tested in a dynamically consistent framework. However, only a model hierarchy can cope with the long time scales and the multi-component physical-biogeochemical Earth System. There are many examples how climate models have inspired the interpretation of paleoclimate data on the one hand, and conversely, how data have questioned long-held concepts and models. In this lecture I critically revisit a few examples of this model-data ping-pong, such as the bipolar seesaw, the mid-Holocene greenhouse gas increase, millennial and rapid CO2 changes reconstructed from polar ice cores, and the interpretation of novel paleoceanographic tracers. These examples also highlight many of the still unsolved questions and provide guidance for future research. The combination of high-resolution paleoceanographic data and modeling has never been more relevant than today. It will be the key for an appropriate risk assessment of impacts on the Earth System that are already underway in the Anthropocene.

A multi-proxy paleolimnological reconstruction of Holocene climate conditions in the Great Basin, United States

NASA Astrophysics Data System (ADS)

Reinemann, Scott A.; Porinchu, David F.; Bloom, Amy M.; Mark, Bryan G.; Box, Jason E.

2009-11-01

A sediment core spanning ˜ 7000 cal yr BP recovered from Stella Lake, a small sub-alpine lake located in Great Basin National Park, Nevada, was analyzed for subfossil chironomids (non-biting midges), diatoms, and organic content (estimated by loss-on-ignition (LOI)). Subfossil chironomid analysis indicates that Stella Lake was characterized by a warm, middle Holocene, followed by a cool "Neoglacial" period, with the last two millennia characterized by a return to warmer conditions. Throughout the majority of the core the Stella Lake diatom-community composition is dominated by small, periphytic taxa which are suggestive of shallow, cool, alkaline, oligotrophic waters with extensive seasonal ice cover. A reconstruction of mean July air temperature (MJAT) was developed by applying a midge-based inference model for MJAT (two-component WA-PLS) consisting of 79 lakes and 54 midge taxa ( rjack2 = 0.55, RMSEP = 0.9°C). Comparison of the chironomid-inferred temperature record to existing regional paleoclimate reconstructions suggests that the midge-inferred temperatures correspond well to regional patterns. This multi-proxy record provides valuable insight into regional Holocene climate and environmental conditions by providing a quantitative reconstruction of peak Holocene warmth and aquatic ecosystem response to these changes in the Great Basin, a region projected to experience increased aridity and higher temperatures.

Recent eolian activity and paleoclimate fluctuations in the Ferris Lost Soldier Area, South-Central Wyoming

NASA Astrophysics Data System (ADS)

Gaylord, D. R.

1983-09-01

The Ferris Dune Fields were examined. Sand dunes are especially valuable in paleoclimate reconstructions because they: (1) bury and preserve datable materials and artifacts; (2) respond to even subtle changes in wind velocity and direction as reflected both in external morphology and internal structures; and (3) remain unconsolidated, making them amenable to easy textural and compositional examination. The valley of Clear Creek in the Ferris Dunes reveals a relatively continuous Holocene section of interbedded dune and interdunal pond deposits. Radiocarbon dates from the interdunal pond strata at Clear Creek, theoretical sand dune migration rates, compositional analysis of periglacial sand wedges, and relative dating of actively migrating parabolic dunes reveals a general sequence of geologic-climatic events that affected the Ferris-Lost Soldier area. The most recent major reactivaton of dunes occurred approximately 290 years ago.

Quantitative cardiac SPECT reconstruction with reduced image degradation due to patient anatomy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsui, B.M.W.; Zhao, X.D.; Gregoriou, G.K.

1994-12-01

Patient anatomy has complicated effects on cardiac SPECT images. The authors investigated reconstruction methods which substantially reduced these effects for improved image quality. A 3D mathematical cardiac-torso (MCAT) phantom which models the anatomical structures in the thorax region were used in the study. The phantom was modified to simulate variations in patient anatomy including regions of natural thinning along the myocardium, body size, diaphragmatic shape, gender, and size and shape of breasts for female patients. Distributions of attenuation coefficients and Tl-201 uptake in different organs in a normal patient were also simulated. Emission projection data were generated from the phantomsmore » including effects of attenuation and detector response. The authors have observed the attenuation-induced artifacts caused by patient anatomy in the conventional FBP reconstructed images. Accurate attenuation compensation using iterative reconstruction algorithms and attenuation maps substantially reduced the image artifacts and improved quantitative accuracy. They conclude that reconstruction methods which accurately compensate for non-uniform attenuation can substantially reduce image degradation caused by variations in patient anatomy in cardiac SPECT.« less

Ocean-atmosphere forcing of South American tropical paleoclimate, LGM to present

NASA Astrophysics Data System (ADS)

Baker, P. A.; Fritz, S. C.; Dwyer, G. S.; Rigsby, C. A.; Silva, C. G.; Burns, S. J.

2012-12-01

Because of many recent terrestrial paleoclimatic and marine paleoceanographic records, late Quaternary South American tropical paleoclimate is as well understood as that anywhere in the world. While lessons learned from the recent instrumental record of climate are informative, this record is too short to capture much of the lower frequency variability encountered in the paleoclimate records and much of the observed paleoclimate is without modern analogue. This paleoclimate is known to be regionally variable with significant differences both north and south of the equator and between the western high Andes and eastern lowlands of the Amazon and Nordeste Brazil. Various extrinsic forcing mechanisms affected climate throughout the period, including global concentrations of GHGs, Northern Hemisphere ice sheet forcing, seasonal insolation forcing of the South American summer monsoon (SASM), millennial-scale Atlantic forcing, and Pacific forcing of the large-scale Walker circulation. The magnitude of the climate response to these forcings varied temporally, largely because of the varying amplitude of the forcing itself. For example, during the last glacial, large-amplitude north Atlantic forcing during Heinrich 1 and the LGM itself, led to wet (dry) conditions south (north) of the equator. During the Holocene, Atlantic forcing was lower amplitude, thus seasonal insolation forcing generally predominated with a weaker-than-normal SASM during the early Holocene resulting in dry conditions in the south-western tropics and wet conditions in the eastern lowlands and Nordeste; in the late Holocene seasonal insolation reached a maximum in the southern tropics and climate conditions reversed.

Late Cretaceous paleosols as paleoclimate proxies of high-latitude Southern Hemisphere: Mata Amarilla Formation, Patagonia, Argentina

NASA Astrophysics Data System (ADS)

Varela, Augusto N.; Raigemborn, M. Sol; Richiano, Sebastián; White, Tim; Poiré, Daniel G.; Lizzoli, Sabrina

2018-01-01

Although there is general consensus that a global greenhouse climate characterized the mid-Cretaceous, details of the climate state of the mid-Cretaceous Southern Hemisphere are less clearly understood. In particular, continental paleoclimate reconstructions are scarce and exclusively derived from paleontological records. Using paleosol-derived climofunction studies of the mid- to Upper Cretaceous Mata Amarilla Formation, southern Patagonia, Argentina, we present a reconstruction of the mid-Cretaceous climate of southern South America. Our results indicate that at 60° south paleolatitude during the Cenomanian-Santonian stages, the climate was subtropical temperate-warm (12 °C ± 2.1 °C) and humid (1404 ± 108 mm/yr) with marked rainfall seasonality. These results are consistent with both previous estimations from the fossil floras of the Mata Amarilla Formation and other units of the Southern Hemisphere, and with the previous observations of the displacement of tropical and subtropical floras towards the poles in both hemispheres. The data presented here show a more marked seasonality and slightly lower mean annual precipitation and mean annual temperature values than those recorded at the same paleolatitudes in the Northern Hemisphere.

Preservation of carbonate clumped isotopes in sedimentary paleoclimate archives

NASA Astrophysics Data System (ADS)

Henkes, G. A.; Passey, B. H.; Grossman, E. L.; Shenton, B.; Perez-Huerta, A.

2014-12-01

Carbonate clumped isotope thermometry is increasingly used to reconstruct paleotemperatures of ancient terrestrial environments. One promising application is elucidating paleoelevation from carbonate archives such as paleosols, lacustrine marls, and fossil freshwater shells. Unlike conventional stable isotope approaches (e.g., mineral δ18O or δD), clumped isotope thermometry is independent of the isotopic composition of the precipitating waters and can therefore be used to reconstruct elevation by both the temperature-altitude relationship and the rainfall δ18O-altitude relationship. However, interpretation of clumped isotope data is not without its own complications. Like conventional stable isotopes, clumped isotope paleotemperatures can be effectively reset to warmer values by dissolution/reprecipitation-type diagenesis during sedimentary burial. It is also known that carbonate clumped isotope bonds (i.e., 13C-18O) are susceptible to 'reordering' in the solid mineral lattice at warmer burial temperatures, with laboratory studies of natural carbonates indicating activation of this phenomenon at temperatures as low as 100 °C over geologic timescales. A challenge in applying carbonate clumped isotope thermometry to natural samples is now evaluating terrestrial archives with respect to both types of alteration: 'open-system' alteration and 'closed-system' bond reordering. In this talk we will review our experimental efforts to constrain the kinetics of clumped isotope reordering, with relevance to low-temperature carbonates like fossil shells and early diagenetic minerals, and present new laboratory data that further inform our theoretical framework for the mechanism(s) of 13C-18O bond reordering. Together with traditional analytical and petrographic screening for recrystallization, empirical and laboratory studies of carbonate clumped isotope reordering represent the next steps in evaluating isotopic records of paleoclimate, paleobiology, and paleoelevation

A calibrated iterative reconstruction for quantitative photoacoustic tomography using multi-angle light-sheet illuminations

NASA Astrophysics Data System (ADS)

Wang, Yihan; Lu, Tong; Zhang, Songhe; Song, Shaoze; Wang, Bingyuan; Li, Jiao; Zhao, Huijuan; Gao, Feng

2018-02-01

Quantitative photoacoustic tomography (q-PAT) is a nontrivial technique can be used to reconstruct the absorption image with a high spatial resolution. Several attempts have been investigated by setting point sources or fixed-angle illuminations. However, in practical applications, these schemes normally suffer from low signal-to-noise ratio (SNR) or poor quantification especially for large-size domains, due to the limitation of the ANSI-safety incidence and incompleteness in the data acquisition. We herein present a q-PAT implementation that uses multi-angle light-sheet illuminations and a calibrated iterative multi-angle reconstruction. The approach can acquire more complete information on the intrinsic absorption and SNR-boosted photoacoustic signals at selected planes from the multi-angle wide-field excitations of light-sheet. Therefore, the sliced absorption maps over whole body can be recovered in a measurementflexible, noise-robust and computation-economic way. The proposed approach is validated by the phantom experiment, exhibiting promising performances in image fidelity and quantitative accuracy.

Late Pliocene Depositional History and Paleoclimate Reconstructions of the Southwest Pacific

NASA Astrophysics Data System (ADS)

Royce, B.; Patterson, M. O.; Pietras, J.

2017-12-01

Drift deposits off the eastern margin of New Zealand are important archives for the paleoclimate and paleoceanographic history of the southwest Pacific. Ocean Drilling Program (ODP) Site 1123 is located on the North Chatham rise drift just North of the westerly wind driven Subtropical Front (STF) and provides a record of near continuous sediment deposition since the Miocene along the southwest Pacific deep western boundary current (DWBC). While the Miocene and Late Pleistocene portion of this record have been well studied, the Late Pliocene record is less well developed. Southern Ocean geological records demonstrate that Late Pliocene cooling is the transient time bracketing the warmer than present Early Pliocene and bipolar glaciation at 2.7 Ma. A newly developed, robust, and astronomically tuned long-term record of benthic δ13C from ODP Site 1123 spanning the Early to Late Pliocene implies a reduction in Southern Ocean ventilation and lowering of preformed values from waters sourced along the Antarctic margin during the Late Pliocene. Thus, Late Pliocene Southern Hemisphere cooling and sea ice expansion may have drastically reduced outgassing and increased the burial of heat into the deep ocean. South Atlantic records off the west coast of Africa demonstrate an increase in the flux of iron to the open ocean during this time potentially enhancing surface ocean productivity and providing an additional cooling mechanism. Currently, atmospheric transport of dust to the Southern Ocean is dominated by persistent mid-latitude circumpolar westerly winds; this is particularly relevant for dust sourced from New Zealand. The Late Pliocene to Early Pleistocene uplift of the North Island axial ranges and South Island southern alps potentially provided a greater amount of not only sediment to the deep ocean, but also wind blow dust to the Pacific sector of the Southern Ocean. We will present a detailed high-resolution sedimentological study on the development of the Chatham

Climate Forcing Reconstructions for Use in PMIP Simulations of the Last Millennium (v1.0)

NASA Technical Reports Server (NTRS)

Schmidt, Gavin A.; Jungclaus, J.H.; Steinhilber, F.; Vieira, L. E. A.; Ammann, C. M.; Bard, E.; Braconnot, P.; Crowley, T. J.; Delayque, G.; Joos, F.;

Promote quantitative ischemia imaging via myocardial perfusion CT iterative reconstruction with tensor total generalized variation regularization

NASA Astrophysics Data System (ADS)

Gu, Chengwei; Zeng, Dong; Lin, Jiahui; Li, Sui; He, Ji; Zhang, Hao; Bian, Zhaoying; Niu, Shanzhou; Zhang, Zhang; Huang, Jing; Chen, Bo; Zhao, Dazhe; Chen, Wufan; Ma, Jianhua

2018-06-01

Myocardial perfusion computed tomography (MPCT) imaging is commonly used to detect myocardial ischemia quantitatively. A limitation in MPCT is that an additional radiation dose is required compared to unenhanced CT due to its repeated dynamic data acquisition. Meanwhile, noise and streak artifacts in low-dose cases are the main factors that degrade the accuracy of quantifying myocardial ischemia and hamper the diagnostic utility of the filtered backprojection reconstructed MPCT images. Moreover, it is noted that the MPCT images are composed of a series of 2/3D images, which can be naturally regarded as a 3/4-order tensor, and the MPCT images are globally correlated along time and are sparse across space. To obtain higher fidelity ischemia from low-dose MPCT acquisitions quantitatively, we propose a robust statistical iterative MPCT image reconstruction algorithm by incorporating tensor total generalized variation (TTGV) regularization into a penalized weighted least-squares framework. Specifically, the TTGV regularization fuses the spatial correlation of the myocardial structure and the temporal continuation of the contrast agent intake during the perfusion. Then, an efficient iterative strategy is developed for the objective function optimization. Comprehensive evaluations have been conducted on a digital XCAT phantom and a preclinical porcine dataset regarding the accuracy of the reconstructed MPCT images, the quantitative differentiation of ischemia and the algorithm’s robustness and efficiency.

Coupling of oceanic carbon and nitrogen: A window to spatially resolved quantitative reconstruction of nitrate inventories

NASA Astrophysics Data System (ADS)

Glock, N.; Liebetrau, V.; Gorb, S.; Wallmann, K. J. G.; Erdem, Z.; Schönfeld, J.; Eisenhauer, A.

2017-12-01

Anthropogenic impact has led to a severe acceleration of the global nitrogen cycle. Every second nitrogen atom in the biosphere may now originate from anthropogenic sources such as chemical fertilizers and the burning of fossil fuels. A quantitative reconstruction of past reactive nitrogen inventories is invaluable to facilitate projections for future scenarios and calibrations for such paleoproxies should be done as long the natural signature is still visible. Here we present a first quantitative reconstruction of nitrate concentrations in intermediate water depths of the Peruvian oxygen minimum zone over the last deglaciation using the pore density in the benthic foraminiferal species Bolivina spissa. A comparison of the nitrate reconstruction to the stable carbon isotope (δ13C) record reveals a strong coupling between the carbon and nitrogen cycles. The linear correlation between δ13C and nitrate availability remained stable over the last 22,000 years, facilitating the use of δ13C records as a quantitative nitrate proxy. The combination of the pore density record with δ13C records shows an elevated oceanic nitrate inventory during the Last Glacial Maximum as compared to the Holocene. Our novel proxy approach is consistent with the results of previous δ15N-based biogeochemical modeling studies, and thus provides sound estimates of the nitrate inventory in the glacial and deglacial ocean.

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

Rapid Late Holocene glacier fluctuations reconstructed from South Georgia lake sediments using novel analytical and numerical techniques

NASA Astrophysics Data System (ADS)

van der Bilt, Willem; Bakke, Jostein; Werner, Johannes; Paasche, Øyvind; Rosqvist, Gunhild

2016-04-01

The collapse of ice shelves, rapidly retreating glaciers and a dramatic recent temperature increase show that Southern Ocean climate is rapidly shifting. Also, instrumental and modelling data demonstrate transient interactions between oceanic and atmospheric forcings as well as climatic teleconnections with lower-latitude regions. Yet beyond the instrumental period, a lack of proxy climate timeseries impedes our understanding of Southern Ocean climate. Also, available records often lack the resolution and chronological control required to resolve rapid climate shifts like those observed at present. Alpine glaciers are found on most Southern Ocean islands and quickly respond to shifts in climate through changes in mass balance. Attendant changes in glacier size drive variations in the production of rock flour, the suspended product of glacial erosion. This climate response may be captured by downstream distal glacier-fed lakes, continuously recording glacier history. Sediment records from such lakes are considered prime sources for paleoclimate reconstructions. Here, we present the first reconstruction of Late Holocene glacier variability from the island of South Georgia. Using a toolbox of advanced physical, geochemical (XRF) and magnetic proxies, in combination with state-of-the-art numerical techniques, we fingerprinted a glacier signal from glacier-fed lake sediments. This lacustrine sediment signal was subsequently calibrated against mapped glacier extent with the help of geomorphological moraine evidence and remote sensing techniques. The outlined approach enabled us to robustly resolve variations of a complex glacier at sub-centennial timescales, while constraining the sedimentological imprint of other geomorphic catchment processes. From a paleoclimate perspective, our reconstruction reveals a dynamic Late Holocene climate, modulated by long-term shifts in regional circulation patterns. We also find evidence for rapid medieval glacier retreat as well as a

Evaluation of dynamic row-action maximum likelihood algorithm reconstruction for quantitative 15O brain PET.

PubMed

Ibaraki, Masanobu; Sato, Kaoru; Mizuta, Tetsuro; Kitamura, Keishi; Miura, Shuichi; Sugawara, Shigeki; Shinohara, Yuki; Kinoshita, Toshibumi

2009-09-01

A modified version of row-action maximum likelihood algorithm (RAMLA) using a 'subset-dependent' relaxation parameter for noise suppression, or dynamic RAMLA (DRAMA), has been proposed. The aim of this study was to assess the capability of DRAMA reconstruction for quantitative (15)O brain positron emission tomography (PET). Seventeen healthy volunteers were studied using a 3D PET scanner. The PET study included 3 sequential PET scans for C(15)O, (15)O(2) and H (2) (15) O. First, the number of main iterations (N (it)) in DRAMA was optimized in relation to image convergence and statistical image noise. To estimate the statistical variance of reconstructed images on a pixel-by-pixel basis, a sinogram bootstrap method was applied using list-mode PET data. Once the optimal N (it) was determined, statistical image noise and quantitative parameters, i.e., cerebral blood flow (CBF), cerebral blood volume (CBV), cerebral metabolic rate of oxygen (CMRO(2)) and oxygen extraction fraction (OEF) were compared between DRAMA and conventional FBP. DRAMA images were post-filtered so that their spatial resolutions were matched with FBP images with a 6-mm FWHM Gaussian filter. Based on the count recovery data, N (it) = 3 was determined as an optimal parameter for (15)O PET data. The sinogram bootstrap analysis revealed that DRAMA reconstruction resulted in less statistical noise, especially in a low-activity region compared to FBP. Agreement of quantitative values between FBP and DRAMA was excellent. For DRAMA images, average gray matter values of CBF, CBV, CMRO(2) and OEF were 46.1 +/- 4.5 (mL/100 mL/min), 3.35 +/- 0.40 (mL/100 mL), 3.42 +/- 0.35 (mL/100 mL/min) and 42.1 +/- 3.8 (%), respectively. These values were comparable to corresponding values with FBP images: 46.6 +/- 4.6 (mL/100 mL/min), 3.34 +/- 0.39 (mL/100 mL), 3.48 +/- 0.34 (mL/100 mL/min) and 42.4 +/- 3.8 (%), respectively. DRAMA reconstruction is applicable to quantitative (15)O PET study and is superior to

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 tomore » 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.« less

Quantitative phase imaging and complex field reconstruction by pupil modulation differential phase contrast

PubMed Central

Lu, Hangwen; Chung, Jaebum; Ou, Xiaoze; Yang, Changhuei

2016-01-01

Differential phase contrast (DPC) is a non-interferometric quantitative phase imaging method achieved by using an asymmetric imaging procedure. We report a pupil modulation differential phase contrast (PMDPC) imaging method by filtering a sample’s Fourier domain with half-circle pupils. A phase gradient image is captured with each half-circle pupil, and a quantitative high resolution phase image is obtained after a deconvolution process with a minimum of two phase gradient images. Here, we introduce PMDPC quantitative phase image reconstruction algorithm and realize it experimentally in a 4f system with an SLM placed at the pupil plane. In our current experimental setup with the numerical aperture of 0.36, we obtain a quantitative phase image with a resolution of 1.73μm after computationally removing system aberrations and refocusing. We also extend the depth of field digitally by 20 times to ±50μm with a resolution of 1.76μm. PMID:27828473

Optimized coral reconstructions of the Indian Ocean Dipole: An assessment of location and length considerations

NASA Astrophysics Data System (ADS)

Abram, Nerilie J.; Dixon, Bronwyn C.; Rosevear, Madelaine G.; Plunkett, Benjamin; Gagan, Michael K.; Hantoro, Wahyoe S.; Phipps, Steven J.

2015-10-01

The Indian Ocean Dipole (IOD; or Indian Ocean Zonal Mode) is a coupled ocean-atmosphere climate oscillation that has profound impacts on rainfall distribution across the Indian Ocean region. Instrumental records provide a reliable representation of IOD behavior since 1958, while coral reconstructions currently extend the IOD history back to 1846. Large fluctuations in the number and intensity of positive IOD events over time are evident in these records, but it is unclear to what extent this represents multidecadal modulation of the IOD or an anthropogenically forced change in IOD behavior. In this study we explore the suitability of coral records from single-site locations in the equatorial Indian Ocean for capturing information about the occurrence and magnitude of positive IOD (pIOD) events. We find that the optimum location for coral reconstructions of the IOD occurs in the southeastern equatorial Indian Ocean, along the coast of Java and Sumatra between ~3 and 7°S. Here the strong ocean cooling and atmospheric drying during pIOD events are unambiguously recorded in coral oxygen isotope records, which capture up to 50% of IOD variance. Unforced experiments with coupled climate models suggest that potential biases in coral estimates of pIOD frequency are skewed toward overestimating pIOD recurrence intervals and become larger with shorter reconstruction windows and longer pIOD recurrence times. Model output also supports the assumption of stationarity in sea surface temperature relationships in the optimum IOD location that is necessary for paleoclimate reconstructions. This study provides a targeted framework for the future generation of paleoclimate records, including optimized coral reconstructions of past IOD variability.

Quantitative reconstructions in multi-modal photoacoustic and optical coherence tomography imaging

NASA Astrophysics Data System (ADS)

Elbau, P.; Mindrinos, L.; Scherzer, O.

2018-01-01

In this paper we perform quantitative reconstruction of the electric susceptibility and the Grüneisen parameter of a non-magnetic linear dielectric medium using measurement of a multi-modal photoacoustic and optical coherence tomography system. We consider the mathematical model presented in Elbau et al (2015 Handbook of Mathematical Methods in Imaging ed O Scherzer (New York: Springer) pp 1169-204), where a Fredholm integral equation of the first kind for the Grüneisen parameter was derived. For the numerical solution of the integral equation we consider a Galerkin type method.

Photoacoustic image reconstruction: a quantitative analysis

NASA Astrophysics Data System (ADS)

Sperl, Jonathan I.; Zell, Karin; Menzenbach, Peter; Haisch, Christoph; Ketzer, Stephan; Marquart, Markus; Koenig, Hartmut; Vogel, Mika W.

2007-07-01

Photoacoustic imaging is a promising new way to generate unprecedented contrast in ultrasound diagnostic imaging. It differs from other medical imaging approaches, in that it provides spatially resolved information about optical absorption of targeted tissue structures. Because the data acquisition process deviates from standard clinical ultrasound, choice of the proper image reconstruction method is crucial for successful application of the technique. In the literature, multiple approaches have been advocated, and the purpose of this paper is to compare four reconstruction techniques. Thereby, we focused on resolution limits, stability, reconstruction speed, and SNR. We generated experimental and simulated data and reconstructed images of the pressure distribution using four different methods: delay-and-sum (DnS), circular backprojection (CBP), generalized 2D Hough transform (HTA), and Fourier transform (FTA). All methods were able to depict the point sources properly. DnS and CBP produce blurred images containing typical superposition artifacts. The HTA provides excellent SNR and allows a good point source separation. The FTA is the fastest and shows the best FWHM. In our study, we found the FTA to show the best overall performance. It allows a very fast and theoretically exact reconstruction. Only a hardware-implemented DnS might be faster and enable real-time imaging. A commercial system may also perform several methods to fully utilize the new contrast mechanism and guarantee optimal resolution and fidelity.

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

PubMed

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

2015-04-13

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

Winter temperature conditions (1670-2010) reconstructed from varved sediments, western Canadian High Arctic

NASA Astrophysics Data System (ADS)

Amann, Benjamin; Lamoureux, Scott F.; Boreux, Maxime P.

2017-09-01

Advances in paleoclimatology from the Arctic have provided insights into long-term climate conditions. However, while past annual and summer temperature have received considerable research attention, comparatively little is known about winter paleoclimate. Arctic winter is of special interest as it is the season with the highest sensitivity to climate change, and because it differs substantially from summer and annual measures. Therefore, information about past changes in winter climate is key to improve our knowledge of past forced climate variability and to reduce uncertainty in climate projections. In this context, Arctic lakes with snowmelt-fed catchments are excellent potential winter climate archives. They respond strongly to snowmelt-induced runoff, and indirectly to winter temperature and snowfall conditions. To date, only a few well-calibrated lake sediment records exist, which appear to reflect site-specific responses with differing reconstructions. This limits the possibility to resolve large-scale winter climate change prior the instrumental period. Here, we present a well-calibrated quantitative temperature and snowfall record for the extended winter season (November through March; NDJFM) from Chevalier Bay (Melville Island, NWT, Canadian Arctic) back to CE 1670. The coastal embayment has a large catchment influenced by nival terrestrial processes, which leads to high sedimentation rates and annual sedimentary structures (varves). Using detailed microstratigraphic analysis from two sediment cores and supported by μ-XRF data, we separated the nival sedimentary units (spring snowmelt) from the rainfall units (summer) and identified subaqueous slumps. Statistical correlation analysis between the proxy data and monthly climate variables reveals that the thickness of the nival units can be used to predict winter temperature (r = 0.71, pc < 0.01, 5-yr filter) and snowfall (r = 0.65, pc < 0.01, 5-yr filter) for the western Canadian High Arctic over the last

Triple Oxygen and Clumped Isotopes in Synthetic and Natural Carbonates: Implications for Paleoclimate and Paleohydrology Studies

NASA Astrophysics Data System (ADS)

Laskar, A. H.; Rangarajan, R.; Liang, M. C.

2016-12-01

Conventional oxygen isotope (δ18O) has widely been used for paleoclimate studies. However, multiple influencing factors such as temperature, precipitation and kinetic effects during carbonate precipitation complicate the interpretation of δ18O data sometimes. Triple oxygen isotope (Δ17O) in carbonates could be sensitive to kinetic effect occur during its precipitation in water. Carbonates may also record the Δ17O signature of the parent waters, providing a basis in the natural carbonates for identifying kinetic processes such as rapid degassing at lower relative humidity inside a cave during speleothem deposition. Clumped isotopes (Δ47) in carbonates give the formation temperatures of the carbonates if precipitated under isotopic equilibrium. The first goal of the study is to explore the applicability of Δ17O for paleohydrolocial studies. The second is to reconstruct paleotemperature with suitable natural carbonates using Δ47values. This is a rare paleoclimate study utilizing two sophisticated new tools. CO2 produced from carbonates by acid digestion was used for both Δ47 and Δ17O analysis. Purified CO2 samples were directly introduced into the Mass spectrometer (MAT 253) for clumped isotope analysis [1] and CO2-O2 exchange method in presence of platinum for Δ17O analysis [2,3]. We measured Δ47 and Δ17O values in synthetic carbonates precipitated at different temperatures (10-90 oC) and Δ17O values in the water from which the carbonate precipitated. We observed consistent Δ47 values in the carbonates while Δ17O were found to vary. Probably a proper slope (between δ18O and δ17O) selection for carbonates would give consistent results. We also measured Δ47 and Δ17O in modern and well dated speleothems from Chinese and Indian caves to study the paleohydrology and paleotemperature. Δ47 and Δ17O were also measured in modern natural carbonate depositions such as corals, foraminifer and marbles to explore their potentials for paleoclimate studies

The impact of using different modern climate data sets in pollen-based paleoclimate reconstructions of North America

NASA Astrophysics Data System (ADS)

Ladd, M.; Way, R. G.; Viau, A. E.

2015-03-01

The use of different modern climate data sets is shown to impact a continental-scale pollen-based reconstruction of mean July temperature (TJUL) over the last 2000 years for North America. Data from climate stations, physically modeled from climate stations and reanalysis products are used to calibrate the reconstructions. Results show that the use of reanalysis products produces warmer and/or smoother reconstructions as compared to the use of station based data sets. The reconstructions during the period of 1050-1550 CE are shown to be more variable because of a high latitude cold-bias in the modern TJUL data. The ultra-high resolution WorldClim gridded data may only useful if the modern pollen sites have at least the same spatial precision as the gridded dataset. Hence we justify the use of the lapse-rate corrected University of East Anglia Climate Research Unit (CRU) based Whitmore modern climate data set for North American pollen-based climate reconstructions.

Querying Provenance Information: Basic Notions and an Example from Paleoclimate Reconstruction

NASA Astrophysics Data System (ADS)

Stodden, V.; Ludaescher, B.; Bocinsky, K.; Kintigh, K.; Kohler, T.; McPhillips, T.; Rush, J.

2016-12-01

Computational models are used to reconstruct and explain past environments and to predict likely future environments. For example, Bocinsky and Kohler have performed a 2,000-year reconstruction of the rain-fed maize agricultural niche in the US Southwest. The resulting academic publications not only contain traditional method descriptions, figures, etc. but also links to code and data for basic transparency and reproducibility. Examples include ResearchCompendia.org and the new project "Merging Science and Cyberinfrastructure Pathways: The Whole Tale." Provenance information provides a further critical element to understand a published study and to possibly extend or challenge the findings of the original authors. We present different notions and uses of provenance information using a computational archaeology example, e.g., the common use of "provenance for others" (for transparency and reproducibility), but also the more elusive but equally important use of "provenance for self". To this end, we distinguish prospective provenance (a.k.a. workflow) from retrospective provenance (a.k.a. data lineage) and show how combinations of both forms of provenance can be used to answer different kinds of important questions about a workflow and its execution. Since many workflows are developed using scripting or special purpose languages such as Python and R, we employ an approach and toolkit called YesWorkflow that brings provenance modeling, capture, and querying into the realm of scripting. YesWorkflow employs the basic W3C PROV standard, as well as the ProvONE extension for sharing and exchanging retrospective and prospective provenance information, respectively. Finally, we argue that the utility of provenance information should be maximized by developing different kinds provenance questions and queries during the early phases of computational workflow design and implementation.

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

Quantitative Susceptibility Mapping using Structural Feature based Collaborative Reconstruction (SFCR) in the Human Brain

PubMed Central

Cai, Congbo; Chen, Zhong; van Zijl, Peter C.M.

2017-01-01

The reconstruction of MR quantitative susceptibility mapping (QSM) from local phase measurements is an ill posed inverse problem and different regularization strategies incorporating a priori information extracted from magnitude and phase images have been proposed. However, the anatomy observed in magnitude and phase images does not always coincide spatially with that in susceptibility maps, which could give erroneous estimation in the reconstructed susceptibility map. In this paper, we develop a structural feature based collaborative reconstruction (SFCR) method for QSM including both magnitude and susceptibility based information. The SFCR algorithm is composed of two consecutive steps corresponding to complementary reconstruction models, each with a structural feature based l1 norm constraint and a voxel fidelity based l2 norm constraint, which allows both the structure edges and tiny features to be recovered, whereas the noise and artifacts could be reduced. In the M-step, the initial susceptibility map is reconstructed by employing a k-space based compressed sensing model incorporating magnitude prior. In the S-step, the susceptibility map is fitted in spatial domain using weighted constraints derived from the initial susceptibility map from the M-step. Simulations and in vivo human experiments at 7T MRI show that the SFCR method provides high quality susceptibility maps with improved RMSE and MSSIM. Finally, the susceptibility values of deep gray matter are analyzed in multiple head positions, with the supine position most approximate to the gold standard COSMOS result. PMID:27019480

Assessing the risk persistent drought using climate model simulations and paleoclimate data

USGS Publications Warehouse

Ault, Toby R.; Cole, Julia E.; Overpeck, Jonathan T.; Pederson, Gregory T.; Meko, David M.

2014-01-01

Projected changes in global rainfall patterns will likely alter water supplies and ecosystems in semiarid regions during the coming century. Instrumental and paleoclimate data indicate that natural hydroclimate fluctuations tend to be more energetic at low (multidecadal to multicentury) than at high (interannual) frequencies. State-of-the-art global climate models do not capture this characteristic of hydroclimate variability, suggesting that the models underestimate the risk of future persistent droughts. Methods are developed here for assessing the risk of such events in the coming century using climate model projections as well as observational (paleoclimate) information. Where instrumental and paleoclimate data are reliable, these methods may provide a more complete view of prolonged drought risk. In the U.S. Southwest, for instance, state-of-the-art climate model projections suggest the risk of a decade-scale megadrought in the coming century is less than 50%; the analysis herein suggests that the risk is at least 80%, and may be higher than 90% in certain areas. The likelihood of longer-lived events (>35 yr) is between 20% and 50%, and the risk of an unprecedented 50-yr megadrought is nonnegligible under the most severe warming scenario (5%–10%). These findings are important to consider as adaptation and mitigation strategies are developed to cope with regional impacts of climate change, where population growth is high and multidecadal megadrought—worse than anything seen during the last 2000 years—would pose unprecedented challenges to water resources in the region.

Constraining Lipid Biomarker Paleoclimate Proxies in a Small Arctic Watershed

NASA Astrophysics Data System (ADS)

Dion-Kirschner, H.; McFarlin, J. M.; Axford, Y.; Osburn, M. R.

2017-12-01

Arctic amplification of climate change renders high-latitude environments unusually sensitive to changes in climatic conditions (Serreze and Barry, 2011). Lipid biomarkers, and their hydrogen and carbon isotopic compositions, can yield valuable paleoclimatic and paleoecological information. However, many variables affect the production and preservation of lipids and their constituent isotopes, including precipitation, plant growth conditions, biosynthesis mechanisms, and sediment depositional processes (Sachse et al., 2012). These variables are particularly poorly constrained for high-latitude environments, where trees are sparse or not present, and plants grow under continuous summer light and cool temperatures during a short growing season. Here we present a source-to-sink study of a single watershed from the Kangerlussuaq region of southwest Greenland. Our analytes from in and around `Little Sugarloaf Lake' (LSL) include terrestrial and aquatic plants, plankton, modern lake water, surface sediments, and a sediment core. This diverse sample set allows us to fulfill three goals: 1) We evaluate the production of lipids and isotopic signatures in the modern watershed in comparison to modern climate. Our data exhibit genus-level trends in leaf wax production and isotopic composition, and help clarify the difference between terrestrial and aquatic signals. 2) We evaluate the surface sediment of LSL to determine how lipid biomarkers from the watershed are incorporated into sediments. We constrain the relative contributions of terrestrial plants, aquatic plants, and other aquatic organisms to the sediment in this watershed. 3) We apply this modern source-to-sink calibration to the analysis of a 65 cm sediment core record. Our core is organic-rich, and relatively high deposition rates allow us to reconstruct paleoenvironmental changes with high resolution. Our work will help determine the veracity of these common paleoclimate proxies, specifically for research in

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

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

PubMed

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

2015-07-14

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

PRISM 8 degrees X 10 degrees North Hemisphere paleoclimate reconstruction; digital data

USGS Publications Warehouse

Barron, John A.; Cronin, Thomas M.; Dowsett, Harry J.; Fleming, Farley R.; Holtz, Thomas R.; Ishman, Scott E.; Poore, Richard Z.; Thompson, Robert S.; Willard, Debra A.

1994-01-01

The PRISM 8?x10? data set represents several years of investigation by PRISM (Pliocene Research, Interpretation, and Synoptic Mapping) Project members. One of the goals of PRISM is to produce time-slice reconstructions of intervals of warmer than modern climate within the Pliocene Epoch. The first of these was chosen to be at 3.0 Ma (time scale of Berggren et al., 1985) and is published in Global and Planetary Change (Dowsett et al., 1994). This document contains the actual data sets and a brief explanation of how they were constructed. For paleoenvironmental interpretations and discussion of each data set, see Dowsett et al., in press. The data sets includes sea level, land ice distribution, vegetation or land cover, sea surface temperature and sea-ice cover matrices. This reconstruction of Middle Pliocene climate is organized as a series of datasets representing different environmental attributes. The data sets are designed for use with the GISS Model II atmospheric general circulation model (GCM) using an 8?x10? resolution (Hansen et al., 1983). The first step in documenting the Pliocene climate involves assigning an appropriate fraction of land versus ocean to each grid box. Following grid cell by grid cell, land versus ocean allocations, winter and summer sea ice coverage of ocean areas are assigned and then winter and summer sea surface temperatures are assigned to open ocean areas. Average land ice cover is recorded for land areas and then land areas not covered by ice are assigned proportions of six vegetation or land cover categories modified from Hansen et al. (1983).

A Millennial-length Reconstruction of the Western Pacific Pattern with Associated Paleoclimate

NASA Astrophysics Data System (ADS)

Wright, W. E.; Guan, B. T.; Wei, K.

2010-12-01

The Western Pacific Pattern (WP) is a lesser known 500 hPa pressure pattern similar to the NAO or PNA. As defined, the poles of the WP index are centered on 60°N over the Kamchatka peninsula and the neighboring Pacific and on 32.5°N over the western north Pacific. However, the area of influence for the southern half of the dipole includes a wide swath from East Asia, across Taiwan, through the Philippine Sea, to the western north Pacific. Tree rings of Taiwanese Chamaecyparis obtusa var. formosana in this extended region show significant correlation with the WP, and with local temperature. The WP is also significantly correlated with atmospheric temperatures over Taiwan, especially at 850hPa and 700 hPa, pressure levels that bracket the tree site. Spectral analysis indicates that variations in the WP occur at relatively high frequency, with most power at less than 5 years. Simple linear regression against high frequency variants of the tree-ring chronology yielded the most significant correlation coefficients. Two reconstructions are presented. The first uses a tree-ring time series produced as the first intrinsic mode function (IMF) from an Ensemble Empirical Mode Decomposition (EEMD), based on the Hilbert-Huang Transform. The significance of the regression using the EEMD-derived time series was much more significant than time series produced using traditional high pass filtering. The second also uses the first IMF of a tree-ring time series, but the dataset was first sorted and partitioned at a specified quantile prior to EEMD decomposition, with the mean of the partitioned data forming the input to the EEMD. The partitioning was done to filter out the less climatically sensitive tree rings, a common problem with shade tolerant trees. Time series statistics indicate that the first reconstruction is reliable to 1241 of the Common Era. Reliability of the second reconstruction is dependent on the development of statistics related to the quantile partitioning, and

A reconstruction of global hydroclimate and dynamical variables over the Common Era.

PubMed

Steiger, Nathan J; Smerdon, Jason E; Cook, Edward R; Cook, Benjamin I

2018-05-22

Hydroclimate extremes critically affect human and natural systems, but there remain many unanswered questions about their causes and how to interpret their dynamics in the past and in climate change projections. These uncertainties are due, in part, to the lack of long-term, spatially resolved hydroclimate reconstructions and information on the underlying physical drivers for many regions. Here we present the first global reconstructions of hydroclimate and associated climate dynamical variables over the past two thousand years. We use a data assimilation approach tailored to reconstruct hydroclimate that optimally combines 2,978 paleoclimate proxy-data time series with the physical constraints of an atmosphere-ocean climate model. The global reconstructions are annually or seasonally resolved and include two spatiotemporal drought indices, near-surface air temperature, an index of North Atlantic variability, the location of the intertropical convergence zone, and monthly Niño indices. This database, called the Paleo Hydrodynamics Data Assimilation product (PHYDA), will provide a critical new platform for investigating the causes of past climate variability and extremes, while informing interpretations of future hydroclimate projections.

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

PubMed

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

2016-08-01

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

A modern pollen-climate dataset from the Darjeeling area, eastern Himalaya: Assessing its potential for past climate reconstruction

NASA Astrophysics Data System (ADS)

Ghosh, Ruby; Bruch, Angela A.; Portmann, Felix; Bera, Subir; Paruya, Dipak Kumar; Morthekai, P.; Ali, Sheikh Nawaz

2017-10-01

Relying on the ability of pollen assemblages to differentiate among elevationally stratified vegetation zones, we assess the potential of a modern pollen-climate dataset from the Darjeeling area, eastern Himalaya, in past climate reconstructions. The dataset includes 73 surface samples from 25 sites collected from a c. 130-3600 m a.s.l. elevation gradient along a horizontal distance of c. 150 km and 124 terrestrial pollen taxa, which are analysed with respect to various climatic and environmental variables such as mean annual temperature (MAT), mean annual precipitation (MAP), mean temperature of coldest quarter (MTCQ), mean temperature of warmest quarter (MTWQ), mean precipitation of driest quarter (MPDQ), mean precipitation of wettest quarter (MPWQ), AET (actual evapotranspiration) and MI (moisture index). To check the reliability of the modern pollen-climate relationships different ordination methods are employed and subsequently tested with Huisman-Olff-Fresco (HOF) models. A series of pollen-climate parameter transfer functions using weighted-averaging regression and calibration partial least squares (WA-PLS) models are developed to reconstruct past climate changes from modern pollen data, and have been cross-validated. Results indicate that three of the environmental variables i.e., MTCQ, MPDQ and MI have strong potential for past climate reconstruction based on the available surface pollen dataset. The potential of the present modern pollen-climate relationship for regional quantitative paleoclimate reconstruction is further tested on a Late Quaternary fossil pollen profile from the Darjeeling foothill region with previously reconstructed and quantified climate. The good agreement with existing data allows for new insights in the hydroclimatic conditions during the Last glacial maxima (LGM) with (winter) temperature being the dominant controlling factor for glacial changes during the LGM in the eastern Himalaya.

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

An 8700 year paleoclimate reconstruction from the southern Maya lowlands

USGS Publications Warehouse

Wahl, David B.; Byrne, Roger; Anderson, Lysanna

2014-01-01

Analysis of a sediment core from Lago Puerto Arturo, a closed basin lake in northern Peten, Guatemala, has provided an ∼8700 cal year record of climate change and human activity in the southern Maya lowlands. Stable isotope, magnetic susceptibility, and pollen analyses were used to reconstruct environmental change in the region. Results indicate a relatively wet early to middle Holocene followed by a drier late Holocene, which we interpret as reflecting long-term changes in insolation (precession). Higher frequency variability is more likely attributable to changes in ocean/atmosphere circulation in both the North Atlantic and the Pacific Oceans. Pollen and isotope data show that most of the period of prehispanic agricultural settlement, i.e. ∼5000–1000 cal yr BP, was characterized by drier conditions than previous or subsequent periods. The presence ofZea (corn) pollen through peak aridity during the Terminal Classic period (∼1250–1130 cal yr BP) suggests that drought may not have had as negative an impact as previously proposed. A dramatic negative shift in isotope values indicates an increase in precipitation after ∼950 cal yr BP (hereafter BP).

500-year Reconstructions of Circulation in the Northeastern Pacific and Western North America: Relation to Precipitation and Fire Conditions in California and Precipitation in Hawai'i

NASA Astrophysics Data System (ADS)

Wahl, E. R.; Zorita, E.; Trouet, V.; Diaz, H. F.

2015-12-01

A reconstruction of the position of the North Pacific Jet Stream (NPJ) over the past 500 years is evaluated in relation to dry and wet extremes in California and extremes of Sierra Nevada fire activity. This work represents a unique combination of independent annually-resolved paleoclimate and paleoecological reconstructions in the region. Results indicate that fire and precipitation extremes are both closely linked with NPJ winter position, with characteristic wet/low fire and dry/high fire NPJ spatial features in the Pacific adjacent to western North America. These features are in turn evaluated in 21st century climate model scenarios using transient integrations over the past millennium, the instrumental period, and the 21st century. The reconstruction of NPJ position is driven by an analog process that employs independent paleoclimate field reconstructions to select model states closest to the reconstructions; it is thus logically and scientifically most consistent to use comparable models to evaluate the future in relation to the past. Initial results indicate that relatively wet/low fire regional conditions are reasonably possible in the later 21st century under a high greenhouse gas forcing regime (RCP 8.5), even though temperatures rise significantly. Related hydroclimate research reconstructs a precipitation index for the Hawai'ian Islands (HI-precip) over the past 500 years. A northeastern Pacific sea level pressure index reconstructed using the analog process is employed as the driving variable in a calibration against HI-precip. Initial reconstruction results indicate significant bicentennial spectral power, which includes a long-term drying trend that began around 1850 and continues into the first decades of the 21st century. Related statistical downscaling of climate model output for HI-precip to the end of the 21st century suggests the possibility of continued drying under RCP 8.5.

Reconstruction of early Holocene paleoclimate and environment in the SW Kola region, Russian Arctic

NASA Astrophysics Data System (ADS)

Grekov, Ivan; Kolka, Vasiliy; Syrykh, Liudmila; Nazarova, Larisa

2016-04-01

In the current period of the global climate change it becomes necessary to have a clear understanding of not only the changes taking place in the components of the natural environment, but also to understand development of all interactions between those components. Quaternary terrigenic sediments and lakes of the Kola Peninsula store information about the development of the region in the Late Glacial and Holocene: movements of the glacier, neotectonic activity, post-glacial rebound, formation and development of natural environments after deglaciation. Multi-proxy study of landscapes evolution of the Kola Peninsula in the Late Quaternary will help to establish a detailed reconstruction of climatic and environmental changes of this poor studied sector of the Arctic. Quaternary history on the Kola Peninsula is represented mainly by Late Pleistocene and Holocene sediments covering the Baltic Shield (Lavrova, 1960; Evzerov, 2015). Several palaeolimnological investigations in the Baltic Shield area have been performed earlier (Donner et al., 1977; Anundsen, 1985; Berglund, 2004). Studies of the southern coast of the Kola Peninsula have shown that marine transgression took place in the Late Pleistocene that was then replaced by a regression with variable speed. The slowdown of the uplift of the area took place between 8800 - 6800 BP (cal. years) and corresponded to the time of the Tapes transgression of the Arctic Ocean (Evzerov et al. 2010; Kolka, et al., 2013). Palaeoclimatic studies based on micro-paleontological analyzes indicate uneven development of the Kola Peninsula landscapes in the Late Glacial and Early Holocene. The northern coast of the Peninsula became free of ice first. In this area tundra-steppe vegetation was established for a short time and was later replaced by tundra (Snyder et al, 2000). Southern part of the Kola Peninsula was dependent on the conditions of deglaciation of the White Sea basin and cleared of ice much later (Evzerov et al., 2010; Kolka

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duan, X; Arbique, G; Guild, J

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

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

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

PubMed

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

2016-04-01

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

Examining bias in pollen-based quantitative climate reconstructions induced by human impact on vegetation in China

NASA Astrophysics Data System (ADS)

Ding, Wei; Xu, Qinghai; Tarasov, Pavel E.

2017-09-01

Human impact is a well-known confounder in pollen-based quantitative climate reconstructions as most terrestrial ecosystems have been artificially affected to varying degrees. In this paper, we use a human-induced pollen dataset (H-set) and a corresponding natural pollen dataset (N-set) to establish pollen-climate calibration sets for temperate eastern China (TEC). The two calibration sets, taking a weighted averaging partial least squares (WA-PLS) approach, are used to reconstruct past climate variables from a fossil record, which is located at the margin of the East Asian summer monsoon in north-central China and covers the late glacial Holocene from 14.7 ka BP (thousands of years before AD 1950). Ordination results suggest that mean annual precipitation (Pann) is the main explanatory variable of both pollen composition and percentage distributions in both datasets. The Pann reconstructions, based on the two calibration sets, demonstrate consistently similar patterns and general trends, suggesting a relatively strong climate impact on the regional vegetation and pollen spectra. However, our results also indicate that the human impact may obscure climate signals derived from fossil pollen assemblages. In a test with modern climate and pollen data, the Pann influence on pollen distribution decreases in the H-set, while the human influence index (HII) rises. Moreover, the relatively strong human impact reduces woody pollen taxa abundances, particularly in the subhumid forested areas. Consequently, this shifts their model-inferred Pann optima to the arid end of the gradient compared to Pann tolerances in the natural dataset and further produces distinct deviations when the total tree pollen percentages are high (i.e. about 40 % for the Gonghai area) in the fossil sequence. In summary, the calibration set with human impact used in our experiment can produce a reliable general pattern of past climate, but the human impact on vegetation affects the pollen

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Paleoclimate and Paleoecology of Central Utah during the Past ≈200,000 Years from Soil Carbonate Pendants

NASA Astrophysics Data System (ADS)

Huth, T.; Cerling, T. E.; Fernandez, D. P.; Mackey, G. N., III; Bowling, D. R.; Marchetti, D. W.; Passey, B. H.

2016-12-01

Understanding the magnitude and duration of past climate events is essential to make accurate predictions about how global climate will vary over the next century. Quantitative paleoclimate records from arid regions are difficult to obtain, often present complex growth histories, and have poor chronologic dating relative to marine sediment archives. Pendants, which are several centimeter thick coatings of soil carbonate formed on the bottoms of boulders, represent a novel source for soil and climate records in arid areas. We developed two high resolution stable isotope paleorecords (C and O) from pendants collected in Utah at Torrey and the University of Utah Rio Mesa research station ≈200 km east of Torrey. The pendants are dense, finely laminated, and formed at >20 cm depth. They were dated by the cosmogenic 3He, U/Th, and radiocarbon methodologies. The pendants have nearly identical C isotope records with a roughly sinusoidal shape. The most negative values (-4‰ VPDB) occur during what we tentatively identify through radiocarbon dates as the Younger Dryas. Plants using the C4 photosynthetic pathway dominate through both records, as demonstrated by δ13C values of -4 to -1‰ (≈70-100% C4 plants). The consistency between these two records meets theoretical expectations that the sites, which sit at similar latitudes, should show similar changes in paleoecology and paleoclimate through time. The oxygen isotope record at Rio Mesa is dynamic and does not match the Torrey record. It ranges from -7 to -13‰ (VPDB) and shows a consistent increase towards the present. At 11 cal yr BP there is a 1.5‰ spike in the record. These patterns are in strong contrast to the Torrey record, which stays between -8 and -9‰ for the entirety of the record. The Torrey record can be reasonably explained through isotopic effects caused by factors like ocean temperature, glaciation extent, and temperature of calcite formation. However, these factors are inadequate to explain the

Genetic Diversity of Globally Dispersed Lacustrine Group I Haptophytes: Implications for Quantitative Temperature Reconstructions

NASA Astrophysics Data System (ADS)

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

2017-12-01

There are significant uncertainties surrounding the forcings that drive terrestrial temperature changes on local and regional scales. Quantitative temperature reconstructions from terrestrial sites, such as lakes, help to unravel the fundamental processes that drive changes in temperature on different temporal and spatial scales. Recent studies at Brown University show that distinct alkenones, long chain ketones produced by haptophytes, are found in many freshwater, alkaline lakes in the Northern Hemisphere, highlighting these systems as targets for quantitative continental temperature reconstructions. These freshwater alkenones are produced by the Group I haptophyte phylotype and are characterized by a distinct signature: the presence of isomeric tri-unsaturated ketones and absence of alkenoates. There are currently no cultured representatives of the "Group I" haptophytes, hence they are only known based on their rRNA gene signatures. Here we present robust evidence that Northern Hemispheric freshwater, alkaline lakes with the characteristic "Group I" alkenone signature all host the same clade of Isochrysidales haptophytes. We employed next generation DNA amplicon sequencing to target haptophyte specific hypervariable regions of the large and small-subunit ribosomal RNA gene from 13 different lakes from three continents (i.e., North America, Europe, and Asia). Combined with previously published sequences, our genetic data show that the Group I haptophyte is genetically diverse on a regional and global scale, and even within the same lake. We present two case studies from a suite of five lakes in Alaska and three in Iceland to assess the impact of various environmental factors affecting Group I diversity and alkenone production. Despite the genetic diversity in this group, the overall ketone signature is conserved. Based on global surface sediment samples and in situ Alaskan lake calibrations, alkenones produced by different operational taxonomic units of the Group

Late Quaternary Slip Rate Along the Selaha Fault, Central Segment of the Xianshuihe Fault System, Eastern Tibet, and Regional Paleoclimate Reconstruction

NASA Astrophysics Data System (ADS)

Chevalier, M. L.; Bai, M.; Pan, J.; Replumaz, A.; Leloup, P. H.; Li, H.

2017-12-01

The left-slip Xianshuihe fault system in E Tibet is considered as one of the most tectonically active fault system in China. Studying its activity, especially its slip rate at different time scales, is essential to evaluate regional earthquake hazards. Here, we focus on the central segment, where the Xianshuihe fault splays into three branches: the Selaha, Yalahe and Zheduotang faults. We use 10Be cosmogenic dating at 3 sites where the active Selaha fault cuts and left-laterally offsets moraine crests and levees. By matching their emplacement ages with their offsets, we obtain a conservative late Quaternary horizontal slip-rate of 5.7-12 mm/yr at TG levees and SLH moraine, or 9.6-9.9 mm/yr assuming that the slip rate should be constant between the two nearby sites. At YJG moraine, we obtain a lower slip rate of 4.4±0.5 mm/yr, most likely because the parallel Zheduotang fault shares the slip rate at this longitude, therefore suggesting a 5 mm/yr slip rate along the Zheduotang fault. A higher slip rate along the short ( 60 km) and discontinuous Selaha fault compared to that along the long ( 300 km) and linear Ganzi fault (7 mm/yr) suggests a high earthquake hazard in the densely populated city of Kangding. Using the moraine ages that we determined here in addition to our previous studies in the same region allows us to study the timing and extent of past glaciations in the Himalayan-Tibetan orogen. This is essential to reconstruct regional paleoclimate and to understand variations in the atmospheric circulation due to the high-altitude low latitude Tibetan Plateau, in order to possibly predict future climate changes. We dated 6 glacial deposits from SE Tibet using 10Be cosmogenic dating on 68 boulders and only found advances during the Last Glacial Maximum (limited) and Marine Isotope Stage-6 (extensive), with no signal in between. That the two coldest periods are LGM and MIS-6 is in agreement with the Northern hemisphere cooling cycles, suggesting that in SE Tibet

A 2,000-year reconstruction of the rain-fed maize agricultural niche in the US Southwest.

PubMed

Bocinsky, R Kyle; Kohler, Timothy A

2014-12-04

Humans experience, adapt to and influence climate at local scales. Paleoclimate research, however, tends to focus on continental, hemispheric or global scales, making it difficult for archaeologists and paleoecologists to study local effects. Here we introduce a method for high-frequency, local climate-field reconstruction from tree-rings. We reconstruct the rain-fed maize agricultural niche in two regions of the southwestern United States with dense populations of prehispanic farmers. Niche size and stability are highly variable within and between the regions. Prehispanic rain-fed maize farmers tended to live in agricultural refugia--areas most reliably in the niche. The timing and trajectory of the famous thirteenth century Pueblo migration can be understood in terms of relative niche size and stability. Local reconstructions like these illuminate the spectrum of strategies past humans used to adapt to climate change by recasting climate into the distributions of resources on which they depended.

The bivalve Glycymeris planicostalis as a high-resolution paleoclimate archive for the Rupelian (Early Oligocene) of central Europe

NASA Astrophysics Data System (ADS)

Walliser, E. O.; Schöne, B. R.; Tütken, T.; Zirkel, J.; Grimm, K. I.; Pross, J.

2015-04-01

Current global warming is likely to result in a unipolar glaciated world with unpredictable repercussions on atmospheric and oceanic circulation patterns. These changes are expected to affect seasonal extremes and the year-to-year variability of seasonality. To better constrain the mode and tempo of the anticipated changes, climatologists require ultra-high-resolution proxy data of time intervals in the past, e.g., the Oligocene, during which boundary conditions were similar to those predicted for the near future. In the present paper, we assess whether such information can be obtained from shells of the long-lived bivalve mollusk Glycymeris planicostalis from the late Rupelian of the Mainz Basin, Germany. Our results indicate that the studied shells are pristinely preserved and provide an excellent archive for reconstructing changes of sea surface temperature on seasonal to interannual timescales. Shells of G. planicostalis grew uninterruptedly during winter and summer and therefore recorded the full seasonal temperature amplitude that prevailed in the Mainz Basin ~ 30 Ma. Absolute sea surface temperature data were reconstructed from δ18Oshell values assuming a δ18Owater signature that was extrapolated from coeval sirenian tooth enamel. Reconstructed values range between 12.3 and 22.0 °C and agree well with previous estimates based on planktonic foraminifera and shark teeth. However, temperatures during seasonal extremes vary greatly on interannual timescales. Mathematically re-sampled (i.e., corrected for uneven number of samples per annual increment) winter and summer temperatures averaged over 40 annual increments of three specimens equal 13.6 ± 0.8 and 17.3 ± 1.2 °C, respectively. Such high-resolution paleoclimate information can be highly relevant for numerical climate studies aiming to predict possible future climates in a unipolar glaciated or, ultimately, polar-ice-free world.

High-resolution paleoclimate records of Holocene hydroclimatic variability in the Eastern Colombian Andes from Lago de Tota

NASA Astrophysics Data System (ADS)

Ahmed, M. N.; Bird, B. W.; Escobar, J.; Polissar, P. J.

2017-12-01

The Northern Hemisphere (NH) South American Monsoon (SAM) is a significant source of precipitation for the North Andes (north of 0˚) and has major control over regional hydroclimate variability. Holocene-length histories of NH SAM variability are few compared to the Southern Hemisphere (SH), limiting understanding of how these systems are connected on orbital and shorter timescales. Here, we present multi-proxy lake-sediment-based paleoclimate and paleohydrologic reconstructions from Lago de Tota, Colombia, using sedimentological, geochemical and leaf-wax hydrogen isotopic indicators from radiometically dated cores. The results indicate periods of wet and dry climate phases during the past 9000 BP with an average Holocene sedimentation rate 33cm/kyr. An increase in total organic matter (TOM) content and finer grain-size distributions was observed from 8000 to 3200 BP, suggesting a period of high lake level. This was followed by lower TOM and coarser grain sizes, suggesting lower lake levels from 3200 BP to the present. Although Tota's lake level pattern is antiphased with other lake level reconstructions from the NH and SH Andes, it is consistent with hypothesized changes in atmospheric convection over the Andes during the Holocene and the way in which they would be modified by the so-called dry island effect in the Colombian Andes. This suggests that a common forcing mechanism can be invoked to explain differing millennial-scale Andean hydroclimate changes, namely atmospheric convection. Orbital and Pacific atmosphere-forcing are therefore likely to have played a significant role in driving pan-Andean hydroclimate variability based on their inter-hemispheric influence on Andean convection.

Patterns and timing of loess-paleosol transitions in Eurasia: Constraints for paleoclimate studies

NASA Astrophysics Data System (ADS)

Zeeden, Christian; Hambach, Ulrich; Obreht, Igor; Hao, Qingzhen; Abels, Hemmo A.; Veres, Daniel; Lehmkuhl, Frank; Gavrilov, Milivoj B.; Marković, Slobodan B.

2018-03-01

Loess-paleosol sequences are the most extensive terrestrial paleoclimate records in Europe and Asia documenting atmospheric circulation patterns, vegetation, and sedimentary dynamics in response to glacial-interglacial cyclicity. Between the two sides of the Eurasian continent, differences may exist in response and response times to glacial changes and finding these is essential to understand the climate systems of the northern hemisphere. Therefore, assessment of common patterns and regional differences in loess-paleosol sequences (LPS) is vital, but remains, however, uncertain. Another key to interpret these records is to constrain the mechanisms responsible for the formation and preservation of paleosols and loess layers in these paleoclimate archives. This study therefore compares LPS magnetic susceptibility records as proxies for paleosol formation intensity for selected sites from the central Chinese Loess Plateau and the Carpathian Basin in Europe over the last 440 kyr. Inconsistencies and crucial issues concerning the timing, correlation and paleoclimate potential of selected Eurasian LPS are outlined. Our comparison of Eurasian LPS shows generally similar patterns of paleosol formation, while highlighting several crucial differences. Especially for paleosols developed around 200 and 300 ka, the reported timing of soil formation differs by up to 30 ka. In addition, a drying and cooling trend over the last 300 ka has been documented in Europe, with no such evidence in the Asian records. The comparison shows that there is still uncertainty in defining the chronostratigraphic framework for these records on glacial-interglacial time scales in the order of 5-30 kyr for the last 440 ka. We argue that the baseline of the magnetic susceptibility proxy in loess from the Carpathian Basin is the most striking difference between European LPS and the Chinese Loess Plateau. In our opinion, many of the current timing/age differences may be overcome once a comparable

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

Holocene climate variability in Texas, USA: An integration of existing paleoclimate data and modeling with a new, high-resolution speleothem record

USGS Publications Warehouse

Wong, Corinne I.; Banner, Jay L.; Musgrove, MaryLynn

2015-01-01

Delineating the climate processes governing precipitation variability in drought-prone Texas is critical for predicting and mitigating climate change effects, and requires the reconstruction of past climate beyond the instrumental record. We synthesize existing paleoclimate proxy data and climate simulations to provide an overview of climate variability in Texas during the Holocene. Conditions became progressively warmer and drier transitioning from the early to mid Holocene, culminating between 7 and 3 ka (thousand years ago), and were more variable during the late Holocene. The timing and relative magnitude of Holocene climate variability, however, is poorly constrained owing to considerable variability among the different records. To help address this, we present a new speleothem (NBJ) reconstruction from a central Texas cave that comprises the highest resolution proxy record to date, spanning the mid to late Holocene. NBJ trace-element concentrations indicate variable moisture conditions with no clear temporal trend. There is a decoupling between NBJ growth rate, trace-element concentrations, and δ18O values, which indicate that (i) the often direct relation between speleothem growth rate and moisture availability is likely complicated by changes in the overlying ecosystem that affect subsurface CO2 production, and (ii) speleothem δ18O variations likely reflect changes in moisture source (i.e., proportion of Pacific-vs. Gulf of Mexico-derived moisture) that appear not to be linked to moisture amount.

Holocene climate variability in Texas, USA: An integration of existing paleoclimate data and modeling with a new, high-resolution speleothem record

NASA Astrophysics Data System (ADS)

Wong, Corinne I.; Banner, Jay L.; Musgrove, MaryLynn

2015-11-01

Delineating the climate processes governing precipitation variability in drought-prone Texas is critical for predicting and mitigating climate change effects, and requires the reconstruction of past climate beyond the instrumental record. We synthesize existing paleoclimate proxy data and climate simulations to provide an overview of climate variability in Texas during the Holocene. Conditions became progressively warmer and drier transitioning from the early to mid Holocene, culminating between 7 and 3 ka (thousand years ago), and were more variable during the late Holocene. The timing and relative magnitude of Holocene climate variability, however, is poorly constrained owing to considerable variability among the different records. To help address this, we present a new speleothem (NBJ) reconstruction from a central Texas cave that comprises the highest resolution proxy record to date, spanning the mid to late Holocene. NBJ trace-element concentrations indicate variable moisture conditions with no clear temporal trend. There is a decoupling between NBJ growth rate, trace-element concentrations, and δ18O values, which indicate that (i) the often direct relation between speleothem growth rate and moisture availability is likely complicated by changes in the overlying ecosystem that affect subsurface CO2 production, and (ii) speleothem δ18O variations likely reflect changes in moisture source (i.e., proportion of Pacific-vs. Gulf of Mexico-derived moisture) that appear not to be linked to moisture amount.

Accelerated Brain DCE-MRI Using Iterative Reconstruction With Total Generalized Variation Penalty for Quantitative Pharmacokinetic Analysis: A Feasibility Study.

PubMed

Wang, Chunhao; Yin, Fang-Fang; Kirkpatrick, John P; Chang, Zheng

2017-08-01

To investigate the feasibility of using undersampled k-space data and an iterative image reconstruction method with total generalized variation penalty in the quantitative pharmacokinetic analysis for clinical brain dynamic contrast-enhanced magnetic resonance imaging. Eight brain dynamic contrast-enhanced magnetic resonance imaging scans were retrospectively studied. Two k-space sparse sampling strategies were designed to achieve a simulated image acquisition acceleration factor of 4. They are (1) a golden ratio-optimized 32-ray radial sampling profile and (2) a Cartesian-based random sampling profile with spatiotemporal-regularized sampling density constraints. The undersampled data were reconstructed to yield images using the investigated reconstruction technique. In quantitative pharmacokinetic analysis on a voxel-by-voxel basis, the rate constant K trans in the extended Tofts model and blood flow F B and blood volume V B from the 2-compartment exchange model were analyzed. Finally, the quantitative pharmacokinetic parameters calculated from the undersampled data were compared with the corresponding calculated values from the fully sampled data. To quantify each parameter's accuracy calculated using the undersampled data, error in volume mean, total relative error, and cross-correlation were calculated. The pharmacokinetic parameter maps generated from the undersampled data appeared comparable to the ones generated from the original full sampling data. Within the region of interest, most derived error in volume mean values in the region of interest was about 5% or lower, and the average error in volume mean of all parameter maps generated through either sampling strategy was about 3.54%. The average total relative error value of all parameter maps in region of interest was about 0.115, and the average cross-correlation of all parameter maps in region of interest was about 0.962. All investigated pharmacokinetic parameters had no significant differences between

Role of Seasonal Transitions and Westerly Jets in East Asian Paleoclimate

NASA Astrophysics Data System (ADS)

Chiang, J. C. H.; Fung, I. Y.; Wu, C. H.; Cai, Y.; Edman, J. P.; Liu, Y.; Day, J. A.; Bhattacharya, T.; Mondal, Y.; Labrousse, C.

2015-12-01

The summer rainfall climate of East Asia underwent large and abrupt changes during past climates. However, current interpretations of said changes are typically formulated in terms of modulation of summer monsoon intensity, and do not account for the known complexity in the seasonal evolution of East Asian rainfall, which exhibits sharp transition from the Spring regime to the Meiyu, and then again from the Meiyu to the Summer regime. We explore the interpretation that East Asian rainfall climate undergoes a modulation of its seasonality during said paleoclimate changes. Following previous suggestions we focus on role of the westerlies over Asia, that its latitude relative to Tibet is critical in determining the stepwise transitions in East Asian rainfall seasons. In support of this linkage, we show from observational data that the interannual co-variation of June (July-August) rainfall and upper tropospheric zonal winds show properties consistent with an altered timing of the transition to the Meiyu (Summer), and with more northward-shifted westerlies for earlier transitions. We similarly suggest that East Asian paleoclimate changes resulted from an altered timing in the northward evolution of the jet and hence the seasonal transitions, in particular the transition of the jet from south of the Plateau to the north. In an extreme scenario - which we speculate the climate system tended towards during stadial (cold) phases of D/O stadials and periods of low Northern Hemisphere summer insolation - the jet does not jump north of the Plateau, essentially keeping East Asia in prolonged Spring conditions. We argue that this hypothesis provides a viable explanation for a key paleoproxy signature of D/O stadials over East Asia, namely the heavier mean d18O of precipitation as recorded in speleothem records. The southward jet position prevents the low-level monsoonal flow - which is isotopically light - from penetrating into the interior of East Asia; as such, precipitation

Role of Seasonal Transitions and Westerly Jets in East Asian Paleoclimate

NASA Astrophysics Data System (ADS)

Chiang, J. C. H.; Fung, I. Y.; Wu, C. H.; Cai, Y.; Edman, J. P.; Liu, Y.; Day, J. A.; Bhattacharya, T.; Mondal, Y.; Labrousse, C.

2014-12-01

The summer rainfall climate of East Asia underwent large and abrupt changes in response to precessional forcing, glacial-interglacial cycles as well as abrupt changes to the North Atlantic during the last glacial. Current interpretations of said changes are typically formulated in terms of modulation of summer monsoon intensity, and do not account for the known complexity in the seasonal evolution of East Asian rainfall, which exhibits sharp transition from the Spring regime to the Meiyu, and then again from the Meiyu to the summertime. We explore the interpretation that East Asian rainfall climate undergoes a modulation of its seasonality during said paleoclimate changes. Following previous suggestions, we focus on role of the westerly jet: namely that the latitude of this westerly jet relative to Tibet is critical in determining the stepwise transitions in East Asian rainfall seasons. In support of this linkage, we show evidence from observational data for such a linkage in the timing of the Meiyu and Summer transitions, with more northward-shifted westerlies associated with earlier transitions. We similarly suggest that East Asian paleoclimate changes resulted from an altered timing in the northward evolution of the jet and hence the seasonal transitions, in particular the transition of the jet from south of the Plateau to the north that determines the seasonal transition from Spring rains to the Meiyu. In an extreme scenario - which we speculate the climate system tended towards during stadial (cold) phases of D/O stadials and periods of low Northern Hemisphere summer insolation - the jet does not jump north of the Plateau, essentially keeping East Asia in prolonged Spring conditions. We show that this hypothesis can explain a key paleoproxy signature of D/O stadials over East Asia, namely the heavier mean δ18O of precipitation as recorded in speleothem records. The southward jet position prevents the low-level monsoonal flow - which is isotopically light

Quantitative underwater 3D motion analysis using submerged video cameras: accuracy analysis and trajectory reconstruction.

PubMed

Silvatti, Amanda P; Cerveri, Pietro; Telles, Thiago; Dias, Fábio A S; Baroni, Guido; Barros, Ricardo M L

2013-01-01

In this study we aim at investigating the applicability of underwater 3D motion capture based on submerged video cameras in terms of 3D accuracy analysis and trajectory reconstruction. Static points with classical direct linear transform (DLT) solution, a moving wand with bundle adjustment and a moving 2D plate with Zhang's method were considered for camera calibration. As an example of the final application, we reconstructed the hand motion trajectories in different swimming styles and qualitatively compared this with Maglischo's model. Four highly trained male swimmers performed butterfly, breaststroke and freestyle tasks. The middle fingertip trajectories of both hands in the underwater phase were considered. The accuracy (mean absolute error) of the two calibration approaches (wand: 0.96 mm - 2D plate: 0.73 mm) was comparable to out of water results and highly superior to the classical DLT results (9.74 mm). Among all the swimmers, the hands' trajectories of the expert swimmer in the style were almost symmetric and in good agreement with Maglischo's model. The kinematic results highlight symmetry or asymmetry between the two hand sides, intra- and inter-subject variability in terms of the motion patterns and agreement or disagreement with the model. The two outcomes, calibration results and trajectory reconstruction, both move towards the quantitative 3D underwater motion analysis.

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

PubMed

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

2012-05-01

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

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

NASA Astrophysics Data System (ADS)

Zhao, C.; Feng, X.

2017-12-01

BrGDGTs have been proposed as a proxy for quantitative paleotemperature reconstructions in terrestrial environment, and numerous transfer functions have been framed based on modern soils and lake sediments. However, these spatial-based functions have been seldom successful for paleotemperature reconstructions in lake sediments. In this study, we report a quantitative temperature record over the past 2000 years, using a temporal-based transfer function inferred from branched GDGTs from a sediment core collected at a small alpine lake (Tiancai lake, 26°38'E, 99°43'N, 3898 m asl) in a remote location in subtropical southwestern China. The chronology is established by both 210Pb and AMS-14C dating methods. We find a significant correlation between brGDGT distributions and instrumental mean annual air temperature (MAAT) (R2=0.902, p<0.0001) over the past 60 years. We then establish a local instrumental calibration and apply it to the entire core for MAAT reconstruction over the past 2000 years. Our preliminary results show the reconstructed MAAT varies between -0.77 and 4.13° over the past 2000 years. Our data indicate four warm intervals at 20-142AD, 321-578AD, 796-1215AD and after 1940AD, and four cold intervals at 158-321AD, 550-657AD, 1500-1727AD, 1810-1912AD. The warm period at 796-1215AD and the cold period at 1500-1727AD are likely corresponding with the Medieval Climate Anomaly (MCA) and the Little Ice Age (LIA), respectively, which is consistent with published data in northern China and the northern Hemisphere. Our preliminary result indicates that this temporal-based calibration could be more practical in some environmental-stable open lakes, and also suggests coherent temperature changes in the subtropical and high-latitude northern hemisphere over the past 2000 years.

Objectively combining AR5 instrumental period and paleoclimate climate sensitivity evidence

NASA Astrophysics Data System (ADS)

Lewis, Nicholas; Grünwald, Peter

2018-03-01

Combining instrumental period evidence regarding equilibrium climate sensitivity with largely independent paleoclimate proxy evidence should enable a more constrained sensitivity estimate to be obtained. Previous, subjective Bayesian approaches involved selection of a prior probability distribution reflecting the investigators' beliefs about climate sensitivity. Here a recently developed approach employing two different statistical methods—objective Bayesian and frequentist likelihood-ratio—is used to combine instrumental period and paleoclimate evidence based on data presented and assessments made in the IPCC Fifth Assessment Report. Probabilistic estimates from each source of evidence are represented by posterior probability density functions (PDFs) of physically-appropriate form that can be uniquely factored into a likelihood function and a noninformative prior distribution. The three-parameter form is shown accurately to fit a wide range of estimated climate sensitivity PDFs. The likelihood functions relating to the probabilistic estimates from the two sources are multiplicatively combined and a prior is derived that is noninformative for inference from the combined evidence. A posterior PDF that incorporates the evidence from both sources is produced using a single-step approach, which avoids the order-dependency that would arise if Bayesian updating were used. Results are compared with an alternative approach using the frequentist signed root likelihood ratio method. Results from these two methods are effectively identical, and provide a 5-95% range for climate sensitivity of 1.1-4.05 K (median 1.87 K).

Sequence stratigraphy, paleoclimate, and tectonics of coal-bearing strata

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jack C. Pashin; Robert A. Gastaldo

2004-07-15

The origin of coal-bearing strata has been debated vigorously for more than a century, and with the emergence of coalbed methane as a major energy resource and the possibility of sequestering greenhouse gas in coal, this debate has never been more relevant. This volume contains 10 chapters on coal-bearing strata of Carboniferous through Tertiary age and is based on a special session that was held at an AAPG Annual Meeting in New Orleans. Contributors have employed a multitude of approaches ranging from basin analysis to plant taphonomy to support a variety of views on the sequence stratigraphy, paleoclimate, and tectonicsmore » of coal-bearing strata.« less

Reconstruction of Middle Eocene - Late Oligocene Southern Ocean paleoclimate through calcareous nannofossils and stable isotopes

NASA Astrophysics Data System (ADS)

Villa, Giuliana; Fioroni, Chiara; Persico, Davide; Pea, Laura; Bohaty, Steve

2010-05-01

The transition from the ice free early Paleogene world to the glaciated conditions of the early Oligocene has been matter of discussion in the last years. This transition has not been monotonic but punctuated by numerous transient cooling and warming events. Here we present a summary of recent studies based on Nannofossil response to climatic changes during the Eocene and Oligocene. Collected data issue from high latitudes ODP Sites 748, 738, 744, 689 and 690. Based on a detailed revision of the biostratigraphy carried out through quantitative analysis, we conducted paleoecological studies on calcareous nannofossils through the late middle Eocene to the - late Oligocene interval to identify abundance variations of selected taxa in response to changes in sea surface temperature (SST) and trophic conditions. The nannofossil-based interpretation has been compared with detailed oxygen and carbon stable isotope stratigraphy confirming the climate variability in the Southern Ocean for this time interval. We identify the Middle Eocene Climatic optimum (MECO) event, related with the regional exclusion of Paleogenic warm-water taxa from the Southern Ocean, followed by the progressive cooling trend particularly emphasized during the cooling events at about 39 Ma, 37 Ma and 35.5 Ma. In the earliest Oligocene, marked changes in calcareous nannofossil assemblages are strikingly associated with the Oi-1 event recorded in perfect accordance with the oxygen isotope records. For most of the Oligocene we recorded a cold phase, while a warming trend is detected in the late Oligocene. In addiction, a marked increase of taxa thriving in eutrophic conditions coupled with a decrease in oligotrophic taxa, suggests the presence of a time interval (from about 36 Ma to about 26 Ma) with prevailing eutrophic conditions that correspond to an increase of the carbon stable isotope curve. This interval well corresponds with the clay mineral concentration that shows at Site 738 a higher

Improved spectral comparisons of paleoclimate models and observations via proxy system modeling: Implications for multi-decadal variability

NASA Astrophysics Data System (ADS)

Dee, S. G.; Parsons, L. A.; Loope, G. R.; Overpeck, J. T.; Ault, T. R.; Emile-Geay, J.

2017-10-01

The spectral characteristics of paleoclimate observations spanning the last millennium suggest the presence of significant low-frequency (multi-decadal to centennial scale) variability in the climate system. Since this low-frequency climate variability is critical for climate predictions on societally-relevant scales, it is essential to establish whether General Circulation models (GCMs) are able to simulate it faithfully. Recent studies find large discrepancies between models and paleoclimate data at low frequencies, prompting concerns surrounding the ability of GCMs to predict long-term, high-magnitude variability under greenhouse forcing (Laepple and Huybers, 2014a, 2014b). However, efforts to ground climate model simulations directly in paleoclimate observations are impeded by fundamental differences between models and the proxy data: proxy systems often record a multivariate and/or nonlinear response to climate, precluding a direct comparison to GCM output. In this paper we bridge this gap via a forward proxy modeling approach, coupled to an isotope-enabled GCM. This allows us to disentangle the various contributions to signals embedded in ice cores, speleothem calcite, coral aragonite, tree-ring width, and tree-ring cellulose. The paper addresses the following questions: (1) do forward-modeled ;pseudoproxies; exhibit variability comparable to proxy data? (2) if not, which processes alter the shape of the spectrum of simulated climate variability, and are these processes broadly distinguishable from climate? We apply our method to representative case studies, and broaden these insights with an analysis of the PAGES2k database (PAGES2K Consortium, 2013). We find that current proxy system models (PSMs) can help resolve model-data discrepancies on interannual to decadal timescales, but cannot account for the mismatch in variance on multi-decadal to centennial timescales. We conclude that, specific to this set of PSMs and isotope-enabled model, the paleoclimate

A Record of Holocene Paleoclimate Evolution from Robertson Bay, Victoria Land, Antarctica

NASA Astrophysics Data System (ADS)

Riesselman, C. R.; Truax, O.; Wilson, G. S.; Parker, R. L.; Yoo, K. C.; Lee, J. I.; Levy, R. H.; Mckay, R. M.

2017-12-01

Regionally representative records of how Antarctica responded to the transition from the Last Glacial Maximum into the Holocene are an essential component of understanding the processes by which the Antarctic cryosphere responds to a changing climate. Here, we present a high-resolution record of Holocene Antarctic paleoclimate evolution from a previously unstudied section of the Victoria Land margin. In 2015 the Korea Polar Research Institute collected a 571 cm sediment core, GC57, from Robertson Bay, a protected embayment west of Cape Adare and adjacent to the outlet glaciers of the Transantarctic Mountains. Using diatom assemblages, bulk sediment geochemistry, and the magnetic properties of GC57, we aim to reconstruct the response of the East Antarctic Ice Sheet to warming associated with deglaciation and the Holocene climatic optima at the interface between the Ross Sea and the Southern Ocean. Our multiproxy approach allows us to study sea ice extent, seasonality, ocean stratification and circulation, and primary productivity from the mid-Holocene (7,400 14C year BP) to the present. A sea-ice associated diatom assemblage indicative of summer sea surface temperatures below 0˚C dominates the basal section of GC57. Although diatoms are well preserved, the unit is characterized by low wt% biogenic silica (average 9%) and a high concentration of magnetic minerals, indicating that biogenic production persisted despite substantial terrigenous input into the bay. A rapid transition at 4708 14C yr BP is identified by a steep increase in wt% BSi (average 13%), a decrease in magnetic minerals, and a subtle assemblage change towards sea-ice associated diatoms with slightly warmer temperature tolerances. The novel ramped pyrolosis 14C dating methodology allows us to date the carbon fixed concurrent with deposition and generate a robust age model for GC57 with an accuracy previously difficult to achieve given the uncertainties associated with dating bulk acid insoluble

Human eyeball model reconstruction and quantitative analysis.

PubMed

Xing, Qi; Wei, Qi

2014-01-01

Determining shape of the eyeball is important to diagnose eyeball disease like myopia. In this paper, we present an automatic approach to precisely reconstruct three dimensional geometric shape of eyeball from MR Images. The model development pipeline involved image segmentation, registration, B-Spline surface fitting and subdivision surface fitting, neither of which required manual interaction. From the high resolution resultant models, geometric characteristics of the eyeball can be accurately quantified and analyzed. In addition to the eight metrics commonly used by existing studies, we proposed two novel metrics, Gaussian Curvature Analysis and Sphere Distance Deviation, to quantify the cornea shape and the whole eyeball surface respectively. The experiment results showed that the reconstructed eyeball models accurately represent the complex morphology of the eye. The ten metrics parameterize the eyeball among different subjects, which can potentially be used for eye disease diagnosis.

Alkenone-based reconstructions show four-phase Holocene temperature history for Arctic Svalbard

NASA Astrophysics Data System (ADS)

van der Bilt, W. G. M.; D'Andrea, W. J.; Bakke, J.; Balascio, N.; Werner, J.; Bradley, R. S.

2016-12-01

Situated at the crossroads of global oceanic and atmospheric circulation patterns, the Arctic is a key component of Earth`s climate system. Amplified by sea-ice feedbacks, even modest shifts in regional heat budget drive large climate responses. This is highlighted by the dramatic response of the Arctic to global warming. Assessing the signature of underlying forcings require paleoclimate records, allowing us to expand our knowledge beyond the short instrumental period and contextualize ongoing warming. However, such data are scarce and sparse in the Arctic, limiting our ability to address these issues. We present two quantitative Holocene-length summer temperature reconstructions from the Arctic Svalbard archipelago. Temperature estimates are based on alkenone unsaturation ratios measured on sediment cores from two lakes. Our data reveal a dynamic Holocene temperature history, with reconstructed lake water temperatures spanning a range of 6-8 °C, and characterized by four phases. The Early Holocene was marked by an early ( 10.5 ka cal. BP) onset of insolation-driven Hypsithermal conditions, likely compounded by strengthening oceanic heat transport. This warm interval was interrupted by cooling between 10.5-8.3 ka cal. BP that we attribute to cooling effects from the melting Northern Hemisphere ice sheets. Temperatures declined throughout the Middle Holocene, following a gradual trend that was accentuated by two cooling steps between 7.8-7 ka cal. BP and 4.4-3.5 ka cal. BP. These transitions coincide with a strengthening influence of Arctic water and sea-ice in the adjacent eastern Fram Strait. During the Late Holocene (past 4 ka), temperature change decoupled from the still-declining insolation, and fluctuated around cold mean conditions. This study improves our understanding of Arctic climate dynamics by demonstrating that Holocene Svalbard temperatures were governed by an alternation of forcing mechanism.

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

Quantitative Image Reconstruction for Total-Body PET Imaging Using the 2-meter Long EXPLORER Scanner

PubMed Central

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

2017-01-01

The EXPLORER project aims to build a 2-meter long total-body PET scanner, which will provide extremely high sensitivity for imaging the entire human body. It will possess a range of capabilities currently unavailable to state-of-the-art clinical PET scanners with a limited axial field-of-view. The huge number of lines-of-response (LORs) of the EXPLORER poses a challenge to the data handling and image reconstruction. The objective of this study is to develop a quantitative image reconstruction method for the EXPLORER and compare its performance with current whole-body scanners. Fully 3D image reconstruction was performed using time-of-flight list-mode data with parallel computation. To recover the resolution loss caused by the parallax error between crystal pairs at a large axial ring difference or transaxial radial offset, we applied an image domain resolution model estimated from point source data. To evaluate the image quality, we conducted computer simulations using the SimSET Monte-Carlo toolkit and XCAT 2.0 anthropomorphic phantom to mimic a 20-minute whole-body PET scan with an injection of 25 MBq 18F-FDG. We compare the performance of the EXPLORER with a current clinical scanner that has an axial FOV of 22 cm. The comparison results demonstrated superior image quality from the EXPLORER with a 6.9-fold reduction in noise standard deviation comparing with multi-bed imaging using the clinical scanner. PMID:28240215

Quantitative susceptibility mapping: Report from the 2016 reconstruction challenge.

PubMed

Langkammer, Christian; Schweser, Ferdinand; Shmueli, Karin; Kames, Christian; Li, Xu; Guo, Li; Milovic, Carlos; Kim, Jinsuh; Wei, Hongjiang; Bredies, Kristian; Buch, Sagar; Guo, Yihao; Liu, Zhe; Meineke, Jakob; Rauscher, Alexander; Marques, José P; Bilgic, Berkin

2018-03-01

The aim of the 2016 quantitative susceptibility mapping (QSM) reconstruction challenge was to test the ability of various QSM algorithms to recover the underlying susceptibility from phase data faithfully. Gradient-echo images of a healthy volunteer acquired at 3T in a single orientation with 1.06 mm isotropic resolution. A reference susceptibility map was provided, which was computed using the susceptibility tensor imaging algorithm on data acquired at 12 head orientations. Susceptibility maps calculated from the single orientation data were compared against the reference susceptibility map. Deviations were quantified using the following metrics: root mean squared error (RMSE), structure similarity index (SSIM), high-frequency error norm (HFEN), and the error in selected white and gray matter regions. Twenty-seven submissions were evaluated. Most of the best scoring approaches estimated the spatial frequency content in the ill-conditioned domain of the dipole kernel using compressed sensing strategies. The top 10 maps in each category had similar error metrics but substantially different visual appearance. Because QSM algorithms were optimized to minimize error metrics, the resulting susceptibility maps suffered from over-smoothing and conspicuity loss in fine features such as vessels. As such, the challenge highlighted the need for better numerical image quality criteria. Magn Reson Med 79:1661-1673, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Why Study Paleoclimate?

USGS Publications Warehouse

Robinson, Marci; Dowsett, Harry

2010-01-01

U.S. Geological Survey (USGS) researchers are at the forefront of paleoclimate research, the study of past climates. With their unique skills and perspective, only geologists have the tools necessary to delve into the distant past (long before instrumental records were collected) in order to better understand global environmental conditions that were very different from today's conditions. Paleoclimatologists are geologists who study past climates to answer questions about what the Earth was like in the past and to enable projections, plans, and preparations for the future. The Intergovernmental Panel on Climate Change (IPCC) has projected a future warmer climate that has the potential to affect every person on Earth. Extreme weather events, rising sea level, and migrating ecosystems and resources could result in worldwide socio-economic stresses if not met with prudent and proactive action plans based on quality scientific research. Still, the most dangerous aspect of our changing climate is the uncertainty in the exact nature and rate of projected climate change. To reduce the uncertainties, USGS paleoclimatologists are studying a possible analog to a future warmer climate. The middle part of the Piacenzian Stage of the Pliocene Epoch, about 3.3 to 3.0 million years ago, is the most recent period in Earth's history in which global warmth reached and remained at temperatures similar to those projected for the end of this century, about 2 degrees C to 3 degrees C warmer on average than today over the entire globe. This past warmer time interval preceded the ice ages but was recent enough, geologically, to be very similar to today in terms of ocean circulation and the position of the continents. Also, the populations of plants and animals were much like those of today, and so geologists can use their fossils to estimate past environmental conditions such as temperature and sea level.

Development and Application of Otoliths as Paleoclimate Proxies.

NASA Astrophysics Data System (ADS)

Andrus, C. T.; Crowe, D. E.; Sandweiss, D. H.

2001-12-01

Otoliths are small (<20 mm) accretionary aragonite ear structures in teleost fish. Otolith aragonite is precipitated in oxygen isotope equilibrium with ambient water, thus otolith δ 18O values are proxies for temperature. Otolith growth is marked by concentric bands that reflect, in most species, daily to annual growth periods. New techniques of high-resolution CO2 extraction from aragonite, such as laser microprobe and micromill, permit measurement of δ 18O at temporal resolutions fine enough to discern seasonal climate variation. Otoliths are abundant in most maritime archaeological sites and are also found as fossils as old as the Jurassic. Gross otolith morphology is taxon-specific, often permitting identification to the species level. Depending on the behavior and natural history of each species, conditions within different environments and habitats may be recorded in the isotope chemistry. These environments range from abyssal oceanic depths to mid-continental rivers and lakes, but the most abundant archaeological otoliths are from fish that inhabit shallow coastal waters. Unlike most proxies that are sessile, fish are pelagic and thus record a paleoclimate record indicative of the range of habitats in which the individual grew. In fish with well-understood life histories, such as most economically significant species, this permits evaluation of multiple habitat climates through ontogeny as recorded in the incremental growth. In species with a defined home range (i.e. non-migratory), an integrated temperature history of region can be reconstructed from the δ 18O values, thus avoiding micro-environmental biases sometimes associated with sessile proxies. An example of such use of otoliths is our recent analyses of δ 18O profiles from mid-Holocene archaeological sites in coastal Peru that reflect sea surface temperature (SST) histories. This is an area of coast that lacks more traditional proxies, such as coral, yet is central to the understanding of a

Multi-centennial upper-ocean heat content reconstruction using online data assimilation

NASA Astrophysics Data System (ADS)

Perkins, W. A.; Hakim, G. J.

2017-12-01

The Last Millennium Reanalysis (LMR) provides an advanced paleoclimate ensemble data assimilation framework for multi-variate climate field reconstructions over the Common Era. Although reconstructions in this framework with full Earth system models remain prohibitively expensive, recent work has shown improved ensemble reconstruction validation using computationally inexpensive linear inverse models (LIMs). Here we leverage these techniques in pursuit of a new multi-centennial field reconstruction of upper-ocean heat content (OHC), synthesizing model dynamics with observational constraints from proxy records. OHC is an important indicator of internal climate variability and responds to planetary energy imbalances. Therefore, a consistent extension of the OHC record in time will help inform aspects of low-frequency climate variability. We use the Community Climate System Model version 4 (CCSM4) and Max Planck Institute (MPI) last millennium simulations to derive the LIMs, and the PAGES2K v.2.0 proxy database to perform annually resolved reconstructions of upper-OHC, surface air temperature, and wind stress over the last 500 years. Annual OHC reconstructions and uncertainties for both the global mean and regional basins are compared against observational and reanalysis data. We then investigate differences in dynamical behavior at decadal and longer time scales between the reconstruction and simulations in the last-millennium Coupled Model Intercomparison Project version 5 (CMIP5). Preliminary investigation of 1-year forecast skill for an OHC-only LIM shows largely positive spatial grid point local anomaly correlations (LAC) with a global average LAC of 0.37. Compared to 1-year OHC persistence forecast LAC (global average LAC of 0.30), the LIM outperforms the persistence forecasts in the tropical Indo-Pacific region, the equatorial Atlantic, and in certain regions near the Antarctic Circumpolar Current. In other regions, the forecast correlations are less than the

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.

Quantitative reconstruction of the nonvolatile sensometabolome of a red wine.

PubMed

Hufnagel, Jan Carlos; Hofmann, Thomas

2008-10-08

The first comprehensive quantitative determination of 82 putative taste-active metabolites and mineral salts, the ranking of these compounds in their sensory impact based on dose-over-threshold (DoT) factors, followed by the confirmation of their sensory relevance by taste reconstruction and omission experiments enabled the decoding of the nonvolatile sensometabolome of a red wine. For the first time, the bitterness of the red wine could be demonstrated to be induced by subthreshold concentrations of phenolic acid ethyl esters and flavan-3-ols. Whereas the velvety astringent onset was imparted by three flavon-3-ol glucosides and dihydroflavon-3-ol rhamnosides, the puckering astringent offset was caused by a polymeric fraction exhibiting molecular masses above >5 kDa and was found to be amplified by the organic acids. The perceived sourness was imparted by l-tartaric acid, d-galacturonic acid, acetic acid, succinic acid, l-malic acid, and l-lactic acid and was slightly suppressed by the chlorides of potassium, magnesium, and ammonium, respectively. In addition, d-fructose and glycerol as well as subthreshold concentrations of glucose, 1,2-propandiol, and myo-inositol were found to be responsible for the sweetness, whereas the mouthfulness and body of the red wine were induced only by glycerol, 1,2-propandiol, and myo-inositol.

Sclerochronological analysis of Saxidomus gigantea: Implications for reconstructing past seasonality and sea ice extent in the Northern Pacific Ocean

NASA Astrophysics Data System (ADS)

Bassett, C.; Andrus, C. F. T.

2015-12-01

Sclerochronological analysis of biogenic carbonates provides valuable paleoenvironmental information. Oxygen isotope analysis of bivalve shell yields information on the temperature of the water in which the organism grew. However, in coastal environments, variations in δ18Owater may complicate the interpretation of shell isotope profiles. Measuring and comparing the length of seasonal shell growth in select species of bivalves may complement isotopic analysis, together providing a more precise paleoclimate reconstruction. This project aims to determine the reliability of sclerochronological analysis of bivalves in reconstructing seasonality along the Northwest Coast of North America. To compare bivalves growing at different seasonal temperature conditions, samples of Saxidomus gigantea were collected from southern Alaska and northern British Columbia. Winter cessation lines were identified using oxygen isotope (δ18O) peaks from a profile of variation over the life of the clam, which was sampled sequentially from a section of its shell. Shell growth stops below ~4-5°C and so each winter cessation indicates temperatures lower than this threshold. Lunar-daily growth lines were counted between these winter growth cessation breaks, which quantitatively measure the length of the growing season. The resulting data were compared between habitats to assess if this is a useful method of determining the length of the growing season. If this method of assessing seasonality appears valid, it can be applied to ancient shells abundant in archaeological shell middens to make inferences about past seawater conditions and potentially indicate the presence or absence of the conditions necessary for sea ice accumulation.

Quantitative risk assessment using empirical vulnerability functions from debris flow event reconstruction

NASA Astrophysics Data System (ADS)

Luna, Byron Quan; Blahut, Jan; Camera, Corrado; van Westen, Cees; Sterlacchini, Simone; Apuani, Tiziana; Akbas, Sami

2010-05-01

For a quantitative risk assessment framework it is essential to assess not only the hazardous process itself but to perform an analysis of their consequences. This quantitative assessment should include the expected monetary losses as the product of the probability of occurrence of a hazard with a given magnitude and its vulnerability. A quantifiable integrated approach of both hazard and risk is becoming a required practice in risk reduction management. Dynamic run-out models for debris flows are able to calculate physical outputs (extension, depths, velocities, impact pressures) and to determine the zones where the elements at risk could suffer an impact. These results are then applied for vulnerability and risk calculations. The risk assessment has been conducted in the Valtellina Valley, a typical Italian alpine valley lying in northern Italy (Lombardy Region). On 13th July 2008, after more than two days of intense rainfall, several debris and mud flows were released in the central part of valley between Morbegno and Berbenno. One of the largest debris flows occurred in Selvetta. The debris flow event was reconstructed after extensive field work and interviews with local inhabitants and civil protection teams. Also inside the Valtellina valley, between the 22nd and the 23rd of May 1983, two debris flows happened in Tresenda (Teglio municipality), causing casualties and considerable economic damages. On the same location, during the 26th of November 2002, another debris flow occurred that caused significant damage. For the quantification of a new scenario, the outcome results obtained from the event of Selvetta were applied in Tresenda. The Selvetta and Tresenda event were modelled with the FLO2D program. FLO2D is an Eulerian formulation with a finite differences numerical scheme that requires the specification of an input hydrograph. The internal stresses are isotropic and the basal shear stresses are calculated using a quadratic model. The significance of

Holocene temperature and hydrological changes reconstructed by bacterial 3-hydroxy fatty acids in a stalagmite from central China

NASA Astrophysics Data System (ADS)

Wang, Canfa; Bendle, James A.; Zhang, Hongbin; Yang, Yi; Liu, Deng; Huang, Junhua; Cui, Jingwei; Xie, Shucheng

2018-07-01

To achieve a sufficient understanding of the spatial dynamics of terrestrial climate variability, new proxies and networks of data that cover thousands of years and run up to the present day are needed. Here we show the first Gram-negative bacterial 3-hydroxy fatty acid (3-OH-FA) based temperature and hydrological records from any paleoclimate archive globally. The data, covering the last 9 ka before present (BP), are generated from an individual stalagmite, collected from Heshang Cave, located on a tributary of the Yangtze River, central China (30°27‧N, 110°25‧E; 294 m). Our results indicate a clear early-to-middle Holocene Climatic Optimum (8.0-6.0 ka BP) followed by a long-term monotonic cooling and increasing variability over the last 0.9 ka BP. The hydrological record shows two relatively long wet periods (8.8-5.9 ka BP and 3.0-0 ka BP) and one relatively dry period (5.9-3.0 ka BP) in central China. We show that 3-OH-FA biomarkers hold promise as independent tools for paleoclimate reconstruction, with the potential to deconvolve temperature and hydrological signals from an individual stalagmite.

Paleoclimate Reconstruction at Lamanai, Belize Using Oxygen-Isotope Tropical Dendrochronology

NASA Astrophysics Data System (ADS)

Prentice, A.; Webb, E. A.; White, C. D.; Graham, E.

2009-05-01

Tropical dendrochronology can be complicated because many trees growing in these areas lack distinct visible annual rings. However, the oxygen-isotope composition of wood growing in tropical regions can provide a record of seasonal fluctuations in the amount of precipitation even when visible rings are absent. Variations in the oxygen-isotope compositions of cellulose as the trees grow can be related to the relative timing of wet and dry seasons and used to identify periods of drought. In this study, the oxygen-isotope composition was determined for cellulose extracted from living trees at the site of Lamanai, Belize to assess the variation in oxygen-isotope values that result from heterogeneity within individual tree rings and seasonal fluctuations in amount of precipitation. In temperate regions, the latewood rings that form during periods of reduced growth are traditionally selected for oxygen-isotope analysis of cellulose because their oxygen-isotope compositions are more directly influenced by climate and precipitation during the growing season. However, in tropical isotope dendrochronology, when visible rings are present, detailed sampling of both the light coloured earlywood and the denser latewood is required. At Lamanai, a seasonal signal was evident in the oxygen- isotope composition of the cellulose when tree rings were sectioned in very small increments (approximately every mm), sub-sampling both earlywood and latewood. However, the visible rings did not always correspond with minimum or maximum oxygen-isotope values. As a result, the amplitude of the oxygen-isotope signal obtained by considering only latewood samples is smaller than that obtained from fine-increment sampling. Hence, the oxygen-isotope values of latewood samples alone did not provide accurate data for climate reconstruction. Multiple series of latewood samples extracted from different cross-sections of the same tree did not consistently show the same trends in oxygen isotope values

Holocene temperature shifts around Greenland: Paleolimnological approaches to quantifying past warmth and documenting its consequences

NASA Astrophysics Data System (ADS)

Axford, Y.; Lasher, G. E.; McFarlin, J. M.; Francis, D. R.; Kelly, M. A.; Langdon, P. G.; Levy, L.; Osburn, M. R.; Osterberg, E. C.

2015-12-01

Insolation-driven warmth across the Arctic during the early to middle Holocene (the Holocene Thermal Maximum, or HTM) represents a geologically accessible analog for future warming and its impacts. Improved constraints on the magnitude and seasonality of HTM warmth around Greenland's margins can advance the use of paleoclimate data to test and improve climate and ice sheet models. Here we present an overview of our recent efforts to reconstruct climate through the Holocene around the margins of the Greenland Ice Sheet using multiple proxies in lake sediments. We use insect (chironomid) assemblages to derive quantitative estimates of Holocene temperatures at sites with minimal soil and vegetation development near the eastern, northwestern and western margins of the ice sheet. Our chironomid-based temperature reconstructions consistently imply HTM July air temperatures 3 to 4.5 °C warmer than the pre-industrial late Holocene in these sectors of Greenland. The timing of reconstructed peak warmth differs between sites, with onset varying from ~10 ka to ~6.5 ka, but in good agreement with glacial geology and other evidence from each region. Our reconstructed temperature anomalies are larger than those typically inferred from annually-integrated indicators from the ice sheet itself, but comparable to the few other quantitative summer temperature estimates available from beyond the ice sheet on Greenland. Additional records are needed to confirm the magnitude of HTM warmth and to better define its seasonality and spatial pattern. To provide independent constraints on paleotemperatures and to elucidate additional aspects of Holocene paleoclimate, we are also employing oxygen isotopes of chironomid remains and other aquatic organic materials, and molecular organic proxies, in parallel (see Lasher et al. and McFarlin et al., this meeting). Combined with glacial geologic evidence, these multi-proxy records elucidate diverse aspects of HTM climate around Greenland - including

Towards community-driven paleogeographic reconstructions: integrating open-access paleogeographic and paleobiology data with plate tectonics

NASA Astrophysics Data System (ADS)

Wright, N.; Zahirovic, S.; Müller, R. D.; Seton, M.

2013-03-01

A variety of paleogeographic reconstructions have been published, with applications ranging from paleoclimate, ocean circulation and faunal radiation models to resource exploration; yet their uncertainties remain difficult to assess as they are generally presented as low-resolution static maps. We present a methodology for ground-truthing the digital Palaeogeographic Atlas of Australia by linking the GPlates plate reconstruction tool to the global Paleobiology Database and a Phanerozoic plate motion model. We develop a spatio-temporal data mining workflow to validate the Phanerozoic Palaeogeographic Atlas of Australia with paleoenvironments derived from fossil data. While there is general agreement between fossil data and the paleogeographic model, the methodology highlights key inconsistencies. The Early Devonian paleogeographic model of southeastern Australia insufficiently describes the Emsian inundation that may be refined using biofacies distributions. Additionally, the paleogeographic model and fossil data can be used to strengthen numerical models, such as the dynamic topography and the associated inundation of eastern Australia during the Cretaceous. Although paleobiology data provide constraints only for paleoenvironments with high preservation potential of organisms, our approach enables the use of additional proxy data to generate improved paleogeographic reconstructions.

Towards adaptable, interactive and quantitative paleogeographic maps

NASA Astrophysics Data System (ADS)

Wright, N.; Zahirovic, S.; Müller, R. D.; Seton, M.

2012-07-01

A variety of paleogeographic atlases have been constructed, with applications from paleoclimate, ocean circulation and faunal radiation models to resource exploration; yet their uncertainties remain difficult to assess, as they are generally presented as low-resolution static maps. We present a methodology for ground-truthing paleogeographic maps, by linking the GPlates plate reconstruction tool to the global Paleobiology Database and a Phanerozoic plate motion model. We develop a spatio-temporal data mining workflow to compare a Phanerozoic Paleogeographic Atlas of Australia with biogeographic indicators. The agreement between fossil data and paleogeographic maps is quite good, but the methodology also highlights key inconsistencies. The Early Devonian paleogeography of southeastern Australia insufficiently describes the Emsian inundation that is supported by biogeography. Additionally, the Cretaceous inundation of eastern Australia retreats by 110 Ma according to the paleogeography, but the biogeography indicates that inundation prevailed until at least 100 Ma. Paleobiogeography can also be used to refine Gondwana breakup and the extent of pre-breakup Greater India can be inferred from the southward limit of inundation along western Australia. Although paleobiology data provide constraints only for paleoenvironments with high preservation potential of organisms, our approach enables the use of additional proxy data to generate improved paleogeographic reconstructions.

The Martian paleoclimate and enhanced atmospheric carbon dioxide

NASA Technical Reports Server (NTRS)

Cess, R. D.; Owen, T.; Ramanathan, V.

1980-01-01

Current evidence indicates that the Martian surface is abundant with water presently in the form of ice, while the atmosphere was at one time more massive with a past surface pressure of as much as 1 atm of CO2. In an attempt to understand the Martian paleoclimate, a past CO2-H2O greenhouse was modeled and global temperatures which are consistent with an earlier presence of liquid surface water are found in agreement with the extensive evidence for past fluvial erosion. An important aspect of the CO2-H2O greenhouse model is the detailed inclusion of CO2 hot bands. For a surface pressure of 1 atm of CO2, the present greenhouse model predicts a global mean surface temperature of 294 K, but if the hot bands are excluded, a surface temperature of only 250 K is achieved.

AMS applications to the paleoclimate changing study in China

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, K.; Chen, T.M.; Yuan, D.X.

1995-12-01

To study the paleoclimates changing in China, a high-resolution AMS radio-carbon dating of a loess profile at Weinan, Shaanxi Province, has been carried out and an age of 10,300 BP has been assigned to be the beginning of the HOLOCENE in the studied areas. In the south of China, a stalagmite of 1.2-m high taken from Panlong-dong cave, Guilin, Guangxi Province, has also been studied. The dating with micro-stratification sampling shows that the climate in HOLOCENE was generally damp and warm, but there was a short cola period during 10-11 Ka BP. The resolution of AMS carbon dating of stalagmitemore » is 100 years for the warm and damp period and 500 years for the dry and cold period.« less

Reconstruction of late Holocene climate based on tree growth and mechanistic hierarchical models

USGS Publications Warehouse

Tipton, John; Hooten, Mevin B.; Pederson, Neil; Tingley, Martin; Bishop, Daniel

2016-01-01

Reconstruction of pre-instrumental, late Holocene climate is important for understanding how climate has changed in the past and how climate might change in the future. Statistical prediction of paleoclimate from tree ring widths is challenging because tree ring widths are a one-dimensional summary of annual growth that represents a multi-dimensional set of climatic and biotic influences. We develop a Bayesian hierarchical framework using a nonlinear, biologically motivated tree ring growth model to jointly reconstruct temperature and precipitation in the Hudson Valley, New York. Using a common growth function to describe the response of a tree to climate, we allow for species-specific parameterizations of the growth response. To enable predictive backcasts, we model the climate variables with a vector autoregressive process on an annual timescale coupled with a multivariate conditional autoregressive process that accounts for temporal correlation and cross-correlation between temperature and precipitation on a monthly scale. Our multi-scale temporal model allows for flexibility in the climate response through time at different temporal scales and predicts reasonable climate scenarios given tree ring width data.

Prior-knowledge Fitting of Accelerated Five-dimensional Echo Planar J-resolved Spectroscopic Imaging: Effect of Nonlinear Reconstruction on Quantitation.

PubMed

Iqbal, Zohaib; Wilson, Neil E; Thomas, M Albert

2017-07-24

1 H Magnetic Resonance Spectroscopic imaging (SI) is a powerful tool capable of investigating metabolism in vivo from mul- tiple regions. However, SI techniques are time consuming, and are therefore difficult to implement clinically. By applying non-uniform sampling (NUS) and compressed sensing (CS) reconstruction, it is possible to accelerate these scans while re- taining key spectral information. One recently developed method that utilizes this type of acceleration is the five-dimensional echo planar J-resolved spectroscopic imaging (5D EP-JRESI) sequence, which is capable of obtaining two-dimensional (2D) spectra from three spatial dimensions. The prior-knowledge fitting (ProFit) algorithm is typically used to quantify 2D spectra in vivo, however the effects of NUS and CS reconstruction on the quantitation results are unknown. This study utilized a simulated brain phantom to investigate the errors introduced through the acceleration methods. Errors (normalized root mean square error >15%) were found between metabolite concentrations after twelve-fold acceleration for several low concentra- tion (<2 mM) metabolites. The Cramér Rao lower bound% (CRLB%) values, which are typically used for quality control, were not reflective of the increased quantitation error arising from acceleration. Finally, occipital white (OWM) and gray (OGM) human brain matter were quantified in vivo using the 5D EP-JRESI sequence with eight-fold acceleration.

1,500 year quantitative reconstruction of winter precipitation in the Pacific Northwest

PubMed Central

Steinman, Byron A.; Abbott, Mark B.; Mann, Michael E.; Stansell, Nathan D.; Finney, Bruce P.

2012-01-01

Multiple paleoclimate proxies are required for robust assessment of past hydroclimatic conditions. Currently, estimates of drought variability over the past several thousand years are based largely on tree-ring records. We produced a 1,500-y record of winter precipitation in the Pacific Northwest using a physical model-based analysis of lake sediment oxygen isotope data. Our results indicate that during the Medieval Climate Anomaly (MCA) (900–1300 AD) the Pacific Northwest experienced exceptional wetness in winter and that during the Little Ice Age (LIA) (1450–1850 AD) conditions were drier, contrasting with hydroclimatic anomalies in the desert Southwest and consistent with climate dynamics related to the El Niño Southern Oscillation (ENSO) and the Pacific Decadal Oscillation (PDO). These findings are somewhat discordant with drought records from tree rings, suggesting that differences in seasonal sensitivity between the two proxies allow a more compete understanding of the climate system and likely explain disparities in inferred climate trends over centennial timescales. PMID:22753510

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

PubMed

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

2015-10-01

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

North Pacific atmospheric rivers and their influence on western North America at the Last Glacial Maximum

NASA Astrophysics Data System (ADS)

Lora, Juan M.; Mitchell, Jonathan L.; Risi, Camille; Tripati, Aradhna E.

2017-01-01

Southwestern North America was wetter than present during the Last Glacial Maximum. The causes of increased water availability have been recently debated, and quantitative precipitation reconstructions have been underutilized in model-data comparisons. We investigate the climatological response of North Pacific atmospheric rivers to the glacial climate using model simulations and paleoclimate reconstructions. Atmospheric moisture transport due to these features shifted toward the southeast relative to modern. Enhanced southwesterly moisture delivery between Hawaii and California increased precipitation in the southwest while decreasing it in the Pacific Northwest, in agreement with reconstructions. Coupled climate models that are best able to reproduce reconstructed precipitation changes simulate decreases in sea level pressure across the eastern North Pacific and show the strongest southeastward shifts of moisture transport relative to a modern climate. Precipitation increases of ˜1 mm d-1, due largely to atmospheric rivers, are of the right magnitude to account for reconstructed pluvial conditions in parts of southwestern North America during the Last Glacial Maximum.

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

NASA Astrophysics Data System (ADS)

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

2012-03-01

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

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

Postglacial paleoclimates of the Foxe Basin and surrounding regions (Nunavut, Canada): a multiproxy lake sediment archive study

NASA Astrophysics Data System (ADS)

Pienitz, Reinhard; Beaudoin, Anne; Narancic, Biljana; Rolland, Nicolas; Wagner, Anne-Marie; Zimmermann, Claudia

2013-04-01

decadal-millennial scale records of quantitative variations in water quality parameters (e.g., temperature, dissolved organic carbon, alkalinity) to explore fundamental questions concerning postglacial ecosystem succession and water quality trends in northern landscapes. Regional comparisons with ice core data from the Penny Ice Cap and the Greenland Ice Sheet, as well as with paleoceanographic data from surrounding marine environments should also allow us refine regional paleoclimate models.

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

PubMed

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

2017-05-15

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

Studies of Cave Sediments: Physical and Chemical Records of Paleoclimate (Revised Edition)

NASA Astrophysics Data System (ADS)

Baker, Andy

2007-10-01

Caves have long fascinated humankind, from prehistory to present-day tourism. Caves are also a subject for a range of scientific investigations, including cave biology, archaeology, paleoclimatology, geology, hydrology, and geomorphology. One of the benefits caves provide is their role as a repository of material that might not otherwise survive on the Earth's surface, due to caves' interiors being protected from physical erosion by nature of their underground locations. Studies of Cave Sediments focuses on this role as a repository, in particular on Quaternary (historic to 1.8 million years old) paleoclimate information preserved in cave sediments.

Using paleoclimate data to improve models of the Antarctic Ice Sheet

NASA Astrophysics Data System (ADS)

King, M. A.; Phipps, S. J.; Roberts, J. L.; White, D.

2016-12-01

Ice sheet models are the most descriptive tools available to simulate the future evolution of the Antarctic Ice Sheet (AIS), including its contribution towards changes in global sea level. However, our knowledge of the dynamics of the coupled ice-ocean-lithosphere system is inevitably limited, in part due to a lack of observations. Furthemore, to build computationally efficient models that can be run for multiple millennia, it is necessary to use simplified descriptions of ice dynamics. Ice sheet modeling is therefore an inherently uncertain exercise. The past evolution of the AIS provides an opportunity to constrain the description of physical processes within ice sheet models and, therefore, to constrain our understanding of the role of the AIS in driving changes in global sea level. We use the Parallel Ice Sheet Model (PISM) to demonstrate how paleoclimate data can improve our ability to predict the future evolution of the AIS. A large, perturbed-physics ensemble is generated, spanning uncertainty in the parameterizations of four key physical processes within ice sheet models: ice rheology, ice shelf calving, and the stress balances within ice sheets and ice shelves. A Latin hypercube approach is used to optimally sample the range of uncertainty in parameter values. This perturbed-physics ensemble is used to simulate the evolution of the AIS from the Last Glacial Maximum ( 21,000 years ago) to present. Paleoclimate records are then used to determine which ensemble members are the most realistic. This allows us to use data on past climates to directly constrain our understanding of the past contribution of the AIS towards changes in global sea level. Critically, it also allows us to determine which ensemble members are likely to generate the most realistic projections of the future evolution of the AIS.

A simple conceptual model to interpret the 100 000 years dynamics of paleo-climate records

NASA Astrophysics Data System (ADS)

Quiroga Lombard, C. S.; Balenzuela, P.; Braun, H.; Chialvo, D. R.

2010-10-01

Spectral analyses performed on records of cosmogenic nuclides reveal a group of dominant spectral components during the Holocene period. Only a few of them are related to known solar cycles, i.e., the De Vries/Suess, Gleissberg and Hallstatt cycles. The origin of the others remains uncertain. On the other hand, time series of North Atlantic atmospheric/sea surface temperatures during the last ice age display the existence of repeated large-scale warming events, called Dansgaard-Oeschger (DO) events, spaced around multiples of 1470 years. The De Vries/Suess and Gleissberg cycles with periods close to 1470/7 (~210) and 1470/17 (~86.5) years have been proposed to explain these observations. In this work we found that a conceptual bistable model forced with the De Vries/Suess and Gleissberg cycles plus noise displays a group of dominant frequencies similar to those obtained in the Fourier spectra from paleo-climate during the Holocene. Moreover, we show that simply changing the noise amplitude in the model we obtain similar power spectra to those corresponding to GISP2 δ18O (Greenland Ice Sheet Project 2) during the last ice age. These results give a general dynamical framework which allows us to interpret the main characteristic of paleoclimate records from the last 100 000 years.

Using modern analogues to reconstruct past landcover

NASA Astrophysics Data System (ADS)

Brewer, Simon

2016-04-01

The physical cover of the earth plays an important role in the earth system. It affects the climate through feedbacks such as albedo and surface roughness, forms part of the carbon cycle as both sink and source and is both affected by and can affect human societies. Reconstructing past changes in land use and land cover helps to understand how these interactions may have changed over time, and provides important boundary conditions for paleoclimate models. Pollen assemblages, extracted from sedimentary sequences, provide one of the most abundant sources of information about past changes in land cover over the Holocene period. However, the relationship between plant cover and sedimentary pollen abundance is complex and non-linear, being affected by differential dispersal, production and taxonomic resolution. One method to correct for this and provide quantified estimates of past land cover is to calibrate modern pollen assemblages against contemporary remotely sensed estimates of land cover. Results will be presented from developing such a calibration for a set of European modern pollen samples and AVHRR-based tree cover estimates. An emphasis will be placed on the output of validation tests of the calibration, and what this indicates for the predictive skill of this approach. The calibration will then be applied to a set of pollen sequences for the European continent for the past 11,000 years, and the patterns of reconstructed land cover will be discussed.

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.

The investigation of terrestrial analogs for the paleoclimate of Mars

NASA Astrophysics Data System (ADS)

Thorpe, M.; Hurowitz, J.; Dehouck, E.

2016-12-01

The paleoclimate of Mars is recorded in sedimentary rocks and deposits, with geochemical and mineralogical lines of evidence illustrating an active hydrologic cycle and aqueous weathering environment. The nature of this paleoclimate remains a debatable subject, with several competing hypothesis existing from warm and wet to cold and icy. However, sedimentary processes in basaltic terrains are understudied, leading to an inadequate reference frame for the sedimentary record of Mars. Therefore, investigating the effects of climate on basaltic terrestrial analogs will help in establishing a context for understanding the ancient conditions of Mars. The Columbia River Basalts in Idaho, USA will serve as conditions in a warm and wet climate, while the weathering of Icelandic Basalts in southwestern Iceland will provide a cold and wet climate scenario. In the warm and wet conditions of Idaho, Miocene basaltic source rock is broken down by physical and chemical weathering, transported by streams and deposited locally as small deltas. The sediment that accumulates preserves the basaltic provenance mineralogy in grain sizes as small as silt. The major elemental geochemistry displays chemical weathering trends that are consistent with decreasing grain size, and interpreted as mafic mineral dissolution (i.e., olivine and pyroxenes). Clay mineral phases are separated into the finest grain size fraction during the sedimentation process and are identified as smectite clays. A similar story of preserving basaltic mineralogy is illustrated by Icelandic deposits, except mechanical breakdown of the sediment appears to have a larger impact. Primary mafic minerals are identified in even the clay size fraction of the Icelandic fluvial delta deposits. Additionally, there are limited abundances of clay mineral phases, with more obvious contributions of poorly crystalline phases in the less than 2 micron fraction. The preservation of basaltic provenance in the mineralogy of sediments

Late Pleistocene-Holocene paleoclimate in southwestern Brazilian Amazonia with basis on floristic changes interpreted from isotope data

NASA Astrophysics Data System (ADS)

Rossetti, D. F.; Cohen, M. C. L.; Pessenda, L. C. R.

2015-12-01

Previous late Quaternary paleoclimatic interpretations in Amazonia have considered fluctuating dry to wet episodes with changes from savanna to forest, a view that concurs with other proposals of undisturbed rainforest despite global oscillations. Most of this debate is based on pollen data, but such elements are scarce in Amazonian sedimentary records. This work interprets vegetation in the Late Pleistocene and Holocene in a southwestern Amazonia lowland using δ13C, δ15N, C/N integrated with geomorphology, sedimentology and radiocarbon dating. The goal was to reconstruct vegetation changes through time and analyze their relation to climate and sedimentary dynamics. Fluvial channel and floodplain deposits with phytoplankton, as well as C3 and C4 land plants, were recorded. Between 42,033-43,168 cal yr BP and 34,804-35,584 cal yr BP, C4 land plants increased as a result of a climate drier than todaýs. However, wet climate prevailed from this time-frame until the onset of the Last Glaciation Maximum. In the Pleistocene/Holocene transition, there was an increased contribution of C4 land plants potentially related to dry episodes. However, the increased contribution of this type of land plant is not synchronous with Holocene dry episodes previously documented for the Amazonian lowland. On the other hand, it is remarkable that the record of this plant type was verified only in sites with modern grassland confined to fluvial paleo-landforms. Thus, rather than due to a dry climatic episode, the recorded grassland expansion and its maintenance up to the present time in the studied sites is more likely associated with the evolution of depositional environments, being coincidental with the progressive abandonment of fluvial systems. An important conclusion derived from the present work is that great care must be placed when reconstructing late Quaternary paleoclimate in Amazonia based on changes in floristic patterns, as they may be also a response to sedimentary dynamics.

Coupling of oceanic carbon and nitrogen facilitates spatially resolved quantitative reconstruction of nitrate inventories.

PubMed

Glock, Nicolaas; Erdem, Zeynep; Wallmann, Klaus; Somes, Christopher J; Liebetrau, Volker; Schönfeld, Joachim; Gorb, Stanislav; Eisenhauer, Anton

2018-03-23

Anthropogenic impacts are perturbing the global nitrogen cycle via warming effects and pollutant sources such as chemical fertilizers and burning of fossil fuels. Understanding controls on past nitrogen inventories might improve predictions for future global biogeochemical cycling. Here we show the quantitative reconstruction of deglacial bottom water nitrate concentrations from intermediate depths of the Peruvian upwelling region, using foraminiferal pore density. Deglacial nitrate concentrations correlate strongly with downcore δ 13 C, consistent with modern water column observations in the intermediate Pacific, facilitating the use of δ 13 C records as a paleo-nitrate-proxy at intermediate depths and suggesting that the carbon and nitrogen cycles were closely coupled throughout the last deglaciation in the Peruvian upwelling region. Combining the pore density and intermediate Pacific δ 13 C records shows an elevated nitrate inventory of >10% during the Last Glacial Maximum relative to the Holocene, consistent with a δ 13 C-based and δ 15 N-based 3D ocean biogeochemical model and previous box modeling studies.

A quantitative evaluation of the three dimensional reconstruction of patients' coronary arteries.

PubMed

Klein, J L; Hoff, J G; Peifer, J W; Folks, R; Cooke, C D; King, S B; Garcia, E V

1998-04-01

Through extensive training and experience angiographers learn to mentally reconstruct the three dimensional (3D) relationships of the coronary arterial branches. Graphic computer technology can assist angiographers to more quickly visualize the coronary 3D structure from limited initial views and then help to determine additional helpful views by predicting subsequent angiograms before they are obtained. A new computer method for facilitating 3D reconstruction and visualization of human coronary arteries was evaluated by reconstructing biplane left coronary angiograms from 30 patients. The accuracy of the reconstruction was assessed in two ways: 1) by comparing the vessel's centerlines of the actual angiograms with the centerlines of a 2D projection of the 3D model projected into the exact angle of the actual angiogram; and 2) by comparing two 3D models generated by different simultaneous pairs on angiograms. The inter- and intraobserver variability of reconstruction were evaluated by mathematically comparing the 3D model centerlines of repeated reconstructions. The average absolute corrected displacement of 14,662 vessel centerline points in 2D from 30 patients was 1.64 +/- 2.26 mm. The average corrected absolute displacement of 3D models generated from different biplane pairs was 7.08 +/- 3.21 mm. The intraobserver variability of absolute 3D corrected displacement was 5.22 +/- 3.39 mm. The interobserver variability was 6.6 +/- 3.1 mm. The centerline analyses show that the reconstruction algorithm is mathematically accurate and reproducible. The figures presented in this report put these measurement errors into clinical perspective showing that they yield an accurate representation of the clinically relevant information seen on the actual angiograms. These data show that this technique can be clinically useful by accurately displaying in three dimensions the complex relationships of the branches of the coronary arterial tree.

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

PubMed

Carroll, Linda J; Rothe, J Peter

2010-09-01

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

Water Table Depth Reconstruction in Ombrotrophic Peatlands Using Biomarker Abundance Ratios and Compound-Specific Hydrogen Isotope Composition

NASA Astrophysics Data System (ADS)

Nichols, J. E.; Jackson, S. T.; Booth, R. K.; Pendall, E. G.; Huang, Y.

2005-12-01

Sediment cores from ombrotrophic peat bogs provide sensitive records of changes in precipitation/evaporation (P/E) balance. Various proxies have been developed to reconstruct surface moisture conditions in peat bogs, including testate amoebae, plant macrofossils, and peat humification. Studying species composition of testate amoeba assemblages is time consuming and requires specialized training. Humification index can be influenced by environmental factors other than moisture balance. The plant macrofossil proxy is less quantitative and cannot be performed on highly decomposed samples. We demonstrate that the ratio of C23 alkane to C29 alkane abundance may provide a simple alternative or complementary means of tracking peatland water-table depth. Data for this proxy can be collected quickly using a small sample (100 mg dry). Water-table depth decreases during drought, and abundance of Sphagnum, the dominant peat-forming genus, decreases as vascular plants increase. Sphagnum moss produces mainly medium chain-length alkanes (C21-C25) while vascular plants (grasses and shrubs) produce primarily longer chain-length alkanes (C27-C31). Therefore, C23:C29 n-alkane ratios quantitatively track the water table depth fluctuations in peat bogs. We compared C23:C29 n-alkane ratios in a core from Minden Bog (southeastern Michigan) with water table depth reconstructions based on testate-amoeba assemblages and humification. The 184-cm core spans the past ~3kyr of continuous peat deposition in the bog. Our results indicate that the alkane ratios closely track the water table depth variations, with C29 most abundant during droughts. We also explored the use of D/H ratios in Sphagnum biomarkers as a water-table depth proxy. Compound-specific hydrogen isotope ratio analyses were performed on Sphagnum biomarkers: C23 and C25 alkane and C24 acid. Dry periods are represented in these records by an enrichment of deuterium in these Sphagnum-specific compounds. These events also correlate

Acropora interbranch skeleton Sr/Ca ratios: Evaluation of a potential new high-resolution paleothermometer

NASA Astrophysics Data System (ADS)

Sadler, James; Nguyen, Ai D.; Leonard, Nicole D.; Webb, Gregory E.; Nothdurft, Luke D.

2016-04-01

The majority of coral geochemistry-based paleoclimate reconstructions in the Indo-Pacific are conducted on selectively cored colonies of massive Porites. This restriction to a single genus may make it difficult to amass the required paleoclimate data for studies that require deep reef coring techniques. Acropora, however, is a highly abundant coral genus in both modern and fossil reef systems and displays potential as a novel climate archive. Here we present a calibration study for Sr/Ca ratios recovered from interbranch skeleton in corymbose Acropora colonies from Heron Reef, southern Great Barrier Reef. Significant intercolony differences in absolute Sr/Ca ratios were normalized by producing anomaly plots of both coral geochemistry and instrumental water temperature records. Weighted linear regression of these anomalies from the lagoon and fore-reef slope provide a sensitivity of -0.05 mmol/mol °C-1, with a correlation coefficient (r2 = 0.65) comparable to those of genera currently used in paleoclimate reconstructions. Reconstructions of lagoon and reef slope mean seasonality in water temperature accurately identify the greater seasonal amplitude observed in the lagoon of Heron Reef. A longer calibration period is, however, required for reliable reconstructions of annual mean water temperatures.

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

42 CFR 82.26 - How will NIOSH report dose reconstruction results?

Code of Federal Regulations, 2014 CFR

2014-10-01

... OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED ACTIVITIES METHODS FOR CONDUCTING DOSE RECONSTRUCTION UNDER... dose reconstruction, justification for the decision, and if possible, a quantitative estimate of the...

42 CFR 82.26 - How will NIOSH report dose reconstruction results?

Code of Federal Regulations, 2010 CFR

2010-10-01

... OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED ACTIVITIES METHODS FOR CONDUCTING DOSE RECONSTRUCTION UNDER... dose reconstruction, justification for the decision, and if possible, a quantitative estimate of the...

42 CFR 82.26 - How will NIOSH report dose reconstruction results?

Code of Federal Regulations, 2012 CFR

2012-10-01

... OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED ACTIVITIES METHODS FOR CONDUCTING DOSE RECONSTRUCTION UNDER... dose reconstruction, justification for the decision, and if possible, a quantitative estimate of the...

42 CFR 82.26 - How will NIOSH report dose reconstruction results?

Code of Federal Regulations, 2013 CFR

2013-10-01

... OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED ACTIVITIES METHODS FOR CONDUCTING DOSE RECONSTRUCTION UNDER... dose reconstruction, justification for the decision, and if possible, a quantitative estimate of the...

42 CFR 82.26 - How will NIOSH report dose reconstruction results?

Code of Federal Regulations, 2011 CFR

2011-10-01

... OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED ACTIVITIES METHODS FOR CONDUCTING DOSE RECONSTRUCTION UNDER... dose reconstruction, justification for the decision, and if possible, a quantitative estimate of the...

High Resolution Spatiotemporal Climate Reconstruction and Variability in East Asia during Little Ice Age

NASA Astrophysics Data System (ADS)

Lin, K. H. E.; Wang, P. K.; Lee, S. Y.; Liao, Y. C.; Fan, I. C.; Liao, H. M.

2017-12-01

The Little ice Age (LIA) is one of the most prominent epochs in paleoclimate reconstruction of the Common Era. While the signals of LIA were generally discovered across hemispheres, wide arrays of regional variability were found, and the reconstructed anomalies were sometimes inconsistent across studies by using various proxy data or historical records. This inconsistency is mainly attributed to limited data coverage at fine resolution that can assist high-resolution climate reconstruction in the continuous spatiotemporal trends. Qing dynasty (1644-1911 CE) of China existed in the coldest period of LIA. Owing to a long-standing tradition that acquired local officials to record odds and social or meteorological events, thousands of local chronicles were left. Zhang eds. (2004) took two decades to compile all these meteorological records in a compendium, for which we then digitized and coded all records into our REACHS database system for reconstructing climate. There were in total 1,435 points (sites) in our database for over 80,000 events in the period of time. After implementing two-rounds coding check for data quality control (accuracy rate 87.2%), multiple indexes were retrieved for reconstructing annually and seasonally resolved temperature and precipitation series for North, Central, and South China. The reconstruction methods include frequency count and grading, with usage of multiple regression models to test sensitivity and to calculate correlations among several reconstructed series. Validation was also conducted through comparison with instrumental data and with other reconstructed series in previous studies. Major research results reveal interannual (3-5 years), decadal (8-12 years), and interdecadal (≈30 years) variabilities with strong regional expressions across East China. Cooling effect was not homogenously distributed in space and time. Flood and drought conditions frequently repeated but the spatiotemporal pattern was variant, indicating likely

A comparison of high-resolution pollen-inferred climate data from central Minnesota, USA, to 19th century US military fort climate data and tree-ring inferred climate reconstructions

NASA Astrophysics Data System (ADS)

St Jacques, J.; Cumming, B. F.; Sauchyn, D.; Vanstone, J. R.; Dickenson, J.; Smol, J. P.

2013-12-01

A vital component of paleoclimatology is the validation of paleoclimatological reconstructions. Unfortunately, there is scant instrumental data prior to the 20th century available for this. Hence, typically, we can only do long-term validation using other proxy-inferred climate reconstructions. Minnesota, USA, with its long military fort climate records beginning in 1820 and early dense network of climate stations, offers a rare opportunity for proxy validation. We compare a high-resolution (4-year), millennium-scale, pollen-inferred paleoclimate record derived from varved Lake Mina in central Minnesota to early military fort records and dendroclimatological records. When inferring a paleoclimate record from a pollen record, we rely upon the pollen-climate relationship being constant in time. However, massive human impacts have significantly altered vegetation; and the relationship between modern instrumental climate data and the modern pollen rain becomes altered from what it was in the past. In the Midwest, selective logging, fire suppression, deforestation and agriculture have strongly influenced the modern pollen rain since Euro-American settlement in the mid-1800s. We assess the signal distortion introduced by using the conventional method of modern post-settlement pollen and climate calibration sets to infer climate at Lake Mina from pre-settlement pollen data. Our first February and May temperature reconstructions are based on a pollen dataset contemporaneous with early settlement to which corresponding climate data from the earliest instrumental records has been added to produce a 'pre-settlement' calibration set. The second February and May temperature reconstructions are based on a conventional 'modern' pollen-climate dataset from core-top pollen samples and modern climate normals. The temperature reconstructions are then compared to the earliest instrumental records from Fort Snelling, Minnesota, and it is shown that the reconstructions based on the pre

First experiences with model based iterative reconstructions influence on quantitative plaque volume and intensity measurements in coronary computed tomography angiography.

PubMed

Precht, H; Kitslaar, P H; Broersen, A; Gerke, O; Dijkstra, J; Thygesen, J; Egstrup, K; Lambrechtsen, J

2017-02-01

Investigate the influence of adaptive statistical iterative reconstruction (ASIR) and the model-based IR (Veo) reconstruction algorithm in coronary computed tomography angiography (CCTA) images on quantitative measurements in coronary arteries for plaque volumes and intensities. Three patients had three independent dose reduced CCTA performed and reconstructed with 30% ASIR (CTDI vol at 6.7 mGy), 60% ASIR (CTDI vol 4.3 mGy) and Veo (CTDI vol at 1.9 mGy). Coronary plaque analysis was performed for each measured CCTA volumes, plaque burden and intensities. Plaque volume and plaque burden show a decreasing tendency from ASIR to Veo as median volume for ASIR is 314 mm 3 and 337 mm 3 -252 mm 3 for Veo and plaque burden is 42% and 44% for ASIR to 39% for Veo. The lumen and vessel volume decrease slightly from 30% ASIR to 60% ASIR with 498 mm 3 -391 mm 3 for lumen volume and vessel volume from 939 mm 3 to 830 mm 3 . The intensities did not change overall between the different reconstructions for either lumen or plaque. We found a tendency of decreasing plaque volumes and plaque burden but no change in intensities with the use of low dose Veo CCTA (1.9 mGy) compared to dose reduced ASIR CCTA (6.7 mGy & 4.3 mGy), although more studies are warranted. Copyright © 2016 The College of Radiographers. Published by Elsevier Ltd. All rights reserved.

Anatomical reconstructions of pediatric airways from endoscopic images: a pilot study of the accuracy of quantitative endoscopy.

PubMed

Meisner, Eric M; Hager, Gregory D; Ishman, Stacey L; Brown, David; Tunkel, David E; Ishii, Masaru

2013-11-01

To evaluate the accuracy of three-dimensional (3D) airway reconstructions obtained using quantitative endoscopy (QE). We developed this novel technique to reconstruct precise 3D representations of airway geometries from endoscopic video streams. This method, based on machine vision methodologies, uses a post-processing step of the standard videos obtained during routine laryngoscopy and bronchoscopy. We hypothesize that this method is precise and will generate assessment of airway size and shape similar to those obtained using computed tomography (CT). This study was approved by the institutional review board (IRB). We analyzed video sequences from pediatric patients receiving rigid bronchoscopy. We generated 3D scaled airway models of the subglottis, trachea, and carina using QE. These models were compared to 3D airway models generated from CT. We used the CT data as the gold standard measure of airway size, and used a mixed linear model to estimate the average error in cross-sectional area and effective diameter for QE. The average error in cross sectional area (area sliced perpendicular to the long axis of the airway) was 7.7 mm(2) (variance 33.447 mm(4)). The average error in effective diameter was 0.38775 mm (variance 2.45 mm(2)), approximately 9% error. Our pilot study suggests that QE can be used to generate precise 3D reconstructions of airways. This technique is atraumatic, does not require ionizing radiation, and integrates easily into standard airway assessment protocols. We conjecture that this technology will be useful for staging airway disease and assessing surgical outcomes. Copyright © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

A lacustrine record from Lop Nur, Xinjiang, China: Implications for paleoclimate change during Late Pleistocene

USGS Publications Warehouse

Chao, L.; Zicheng, P.; Dong, Y.; Weiguo, L.; Zhaofeng, Z.; Jianfeng, H.; Chenlin, C.

2009-01-01

Climate variability during the Late Pleistocene is studied from the proxies in core CK-2 drilled from the Luobei Depression (91??03???E, 40??47???N), Lop Nur in the eastern Tarim Basin, Xinjiang, China. Geophysical and geochemical properties, including magnetic susceptibility, granularity, chroma, carbonate content, loss on ignition and trace elements, have been determined to reconstruct the environmental evolution of the area during 32-9 ka BP. The chronology is established by uranium-thorium disequilibrium dating techniques. Our data suggest four paleoclimate stages, indicating glacial variations between cold-humid and warm-arid environments. A period of extreme humidity occurred during 31,900-19,200 yr BP is attributed the last glacial maximum (LGM). The period was followed by a warm-arid episode during 19,200-13,500 yr BP. Then a cold-humid interval during 13,500-12,700 yr BP may correspond to another cooling phases at high latitudes of the Northern Hemisphere. The last stage from 12,700 to 9000 yr BP has a trend that the climate turned warm and arid. The Lop Nur region is characterized by particularly humid stadials and arid interstadials. The climate variability in Lop Nur was constrained by global climate change because it is correlated with Dansgaard-Oeschger and Heinrich events, which were observed at the northern high latitudes. The synchroneity of the palaeoclimatic events suggested that cold air activity at the northern high latitudes was the most important factor that influenced the climate evolution in the Lop Nur region. A probable mechanism that involves the migration of westerly winds is proposed to interpret this synchroneity. ?? 2008 Elsevier Ltd.

A quantitative history of precipitation and hydrologic variability for the last 45 ka: Lake Titicaca, Salar de Coipasa and Salar de Uyuni, Peru and Bolivia

NASA Astrophysics Data System (ADS)

Nunnery, A.; Baker, P. A.; Coe, M. T.; Fritz, S. C.; Rigsby, C. A.

2011-12-01

Precipitation on the Bolivian/Peruvian Altiplano is dominantly controlled by the South American summer Monsoon (SASM). Over long timescales moisture transport to the Altiplano by the SASM fluctuates in intensity due to precessional insolation forcing as well as teleconnections to millennial scale abrupt temperature shifts in the North Atlantic. These long-term changes in moisture transport have been observed in multiple paleoclimate and paleo-lake level records as advances and retreats of large lakes in the terminal basin (the Salar de Uyuni). Several previous studies using energy/water balance models have been applied to paleoclimate records in attempts to provide quantitative constraints on past precipitation and temperature (P and T). For example, Blodgett et al. concluded that high paleolake stands, first dated at ca. 16,000 cal. yr BP, required P 20% higher and T 5°C colder than modern. We expand on this work conducting two experiments. The first uses a latitudinal paleohydrologic profile to reconstruct hydrological history. The second uses a terrestrial hydrology model (THMB) to "predict" lake level given changes in P and T. The profile is constructed using records from Lake Titicaca (LT), Salar de Coipasa (SC) and Salar de Uyuni (SU). LT carbonate and diatom records indicate a deep, overflowing lake for much of the last 100 ka with a distinct dry, closed-basin phase in the early to mid Holocene. A continuous sediment core from SC indicates lake level fluctuations between deep and shallow phases for the last 45 ka. A natural gamma radiation log from SU, where large paleolakes alternated with shallow salt pans characteristic of drier and/or warmer periods, shows alternation between wet and dry phases through time. These three records give evidence to the complex nature of Altiplano hydrology, most notably the ability to sustain lakes in the SC basin while exhibiting dry conditions in SU. For the second experiment, THMB, which estimates water balance and

Pseudoproxy Experiments Using the BARCAST Reconstruction Technique: Effects on Spatiotemporal Persistence Properties

NASA Astrophysics Data System (ADS)

Nilsen, T.; Divine, D.; Rypdal, M.; Werner, J.; Rypdal, K.

2016-12-01

in Earth's Temperature Field: Analysis of Stochastic-Diffusive Energy Balance Models. J. Climate, 28, 8379-8395. Tingley & Huybers, 2010: A Bayesian algorithm for reconstructing climate anomalies in space and time. Part I: Development and applications to paleoclimate reconstruction problems. J. Climate, 23, 2759-2781.

Adaptive Statistical Iterative Reconstruction-V Versus Adaptive Statistical Iterative Reconstruction: Impact on Dose Reduction and Image Quality in Body Computed Tomography.

PubMed

Gatti, Marco; Marchisio, Filippo; Fronda, Marco; Rampado, Osvaldo; Faletti, Riccardo; Bergamasco, Laura; Ropolo, Roberto; Fonio, Paolo

The aim of this study was to evaluate the impact on dose reduction and image quality of the new iterative reconstruction technique: adaptive statistical iterative reconstruction (ASIR-V). Fifty consecutive oncologic patients acted as case controls undergoing during their follow-up a computed tomography scan both with ASIR and ASIR-V. Each study was analyzed in a double-blinded fashion by 2 radiologists. Both quantitative and qualitative analyses of image quality were conducted. Computed tomography scanner radiation output was 38% (29%-45%) lower (P < 0.0001) for the ASIR-V examinations than for the ASIR ones. The quantitative image noise was significantly lower (P < 0.0001) for ASIR-V. Adaptive statistical iterative reconstruction-V had a higher performance for the subjective image noise (P = 0.01 for 5 mm and P = 0.009 for 1.25 mm), the other parameters (image sharpness, diagnostic acceptability, and overall image quality) being similar (P > 0.05). Adaptive statistical iterative reconstruction-V is a new iterative reconstruction technique that has the potential to provide image quality equal to or greater than ASIR, with a dose reduction around 40%.

Variability of East Asian summer monsoon precipitation during the Holocene and possible forcing mechanisms

NASA Astrophysics Data System (ADS)

Lu, Fuzhi; Ma, Chunmei; Zhu, Cheng; Lu, Huayu; Zhang, Xiaojian; Huang, Kangyou; Guo, Tianhong; Li, Kaifeng; Li, Lan; Li, Bing; Zhang, Wenqing

2018-03-01

Projecting how the East Asian summer monsoon (EASM) rainfall will change with global warming is essential for human sustainability. Reconstructing Holocene climate can provide critical insight into its forcing and future variability. However, quantitative reconstructions of Holocene summer precipitation are lacking for tropical and subtropical China, which is the core region of the EASM influence. Here we present high-resolution annual and summer rainfall reconstructions covering the whole Holocene based on the pollen record at Xinjie site from the lower Yangtze region. Summer rainfall was less seasonal and 30% higher than modern values at 10-6 cal kyr BP and gradually declined thereafter, which broadly followed the Northern Hemisphere summer insolation. Over the last two millennia, however, the summer rainfall has deviated from the downward trend of summer insolation. We argue that greenhouse gas forcing might have offset summer insolation forcing and contributed to the late Holocene rainfall anomaly, which is supported by the TraCE-21 ka transient simulation. Besides, tropical sea-surface temperatures could modulate summer rainfall by affecting evaporation of seawater. The rainfall pattern concurs with stalagmite and other proxy records from southern China but differs from mid-Holocene rainfall maximum recorded in arid/semiarid northern China. Summer rainfall in northern China was strongly suppressed by high-northern-latitude ice volume forcing during the early Holocene in spite of high summer insolation. In addition, the El Niño/Southern Oscillation might be responsible for droughts of northern China and floods of southern China during the late Holocene. Furthermore, quantitative rainfall reconstructions indicate that the Paleoclimate Modeling Intercomparison Project (PMIP) simulations underestimate the magnitude of Holocene precipitation changes. Our results highlight the spatial and temporal variability of the Holocene EASM precipitation and potential forcing

High-resolution multiproxy climate reconstruction for southern South America since 1000 AD: LOTRED-SA, a new IGBP-PAGES initiative

NASA Astrophysics Data System (ADS)

Kiefer, T.

2006-12-01

Regional high-resolution multi-proxy climate reconstructions and associated uncertainties for the last ca. 1000 years is a priority area of future research within the Past Global Changes project of the International Geosphere Biosphere Programme (IGBP-PAGES). Considerable progress has been made in the reconstruction techniques, in the handling of a wide range of high- and low-frequency proxy data, and in the quantity and quality of proxy data sets available at continental and northern hemispheric or global scale. Regional reconstructions are particularly important since regional climate change and extremes exhibit much larger amplitudes than hemispherical and global reconstructions. LOTRED-SA (Long-Term climate REconstruction and Dynamics of southern South America is a new collaborative long-term initiative under the umbrella of PAGES and will involve many research groups from different countries. The initiative seeks (i) to collate the large number of disperse already existing and new paleoclimate data sets (documentary data, early instrumental data, data from tree rings, glaciers and ice cores, high resolution marine and lake sediments, pollen data of peat cores etc.) for the last ca. 1000 years available for South America, and (ii) to use the Mann et al. (1998, Nature), Luterbacher et al. (2004, Science) and Moberg et al. (2005, Nature) methodologies to work towards a regional reconstruction at different temporal and spatial resolution with associated uncertainties for southern South America. This contribution reports on the state-of-the-art and the scientific highlights of the first LOTRED-SA science conference (October 2006 in Mendoza, Argentina).

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

PubMed

Veeraraghavan, Rengasayee; Gourdie, Robert G

2016-11-07

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

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Bayesian Models for Streamflow and River Network Reconstruction using Tree Rings

NASA Astrophysics Data System (ADS)

Ravindranath, A.; Devineni, N.

2016-12-01

Water systems face non-stationary, dynamically shifting risks due to shifting societal conditions and systematic long-term variations in climate manifesting as quasi-periodic behavior on multi-decadal time scales. Water systems are thus vulnerable to long periods of wet or dry hydroclimatic conditions. Streamflow is a major component of water systems and a primary means by which water is transported to serve ecosystems' and human needs. Thus, our concern is in understanding streamflow variability. Climate variability and impacts on water resources are crucial factors affecting streamflow, and multi-scale variability increases risk to water sustainability and systems. Dam operations are necessary for collecting water brought by streamflow while maintaining downstream ecological health. Rules governing dam operations are based on streamflow records that are woefully short compared to periods of systematic variation present in the climatic factors driving streamflow variability and non-stationarity. We use hierarchical Bayesian regression methods in order to reconstruct paleo-streamflow records for dams within a basin using paleoclimate proxies (e.g. tree rings) to guide the reconstructions. The riverine flow network for the entire basin is subsequently modeled hierarchically using feeder stream and tributary flows. This is a starting point in analyzing streamflow variability and risks to water systems, and developing a scientifically-informed dynamic risk management framework for formulating dam operations and water policies to best hedge such risks. We will apply this work to the Missouri and Delaware River Basins (DRB). Preliminary results of streamflow reconstructions for eight dams in the upper DRB using standard Gaussian regression with regional tree ring chronologies give streamflow records that now span two to two and a half centuries, and modestly smoothed versions of these reconstructed flows indicate physically-justifiable trends in the time series.

Afghanistan Reconstruction - A Quantitative Analysis of the International Effort

DTIC Science & Technology

2008-03-01

author: Ghost Wars) and Peter Tomsen (U.S. Ambassador to Afghanistan 1989-92) Interviewed by PBS Frontline “Return of the Taliban”. 119 Dobbins... 10062 4123 3453 36881 Table 6. Projects by ANDS sector and Year The table shows that the peak of the reconstruction effort, in terms of number of

Calibration-free quantitative surface topography reconstruction in scanning electron microscopy.

PubMed

Faber, E T; Martinez-Martinez, D; Mansilla, C; Ocelík, V; Hosson, J Th M De

2015-01-01

This work presents a new approach to obtain reliable surface topography reconstructions from 2D Scanning Electron Microscopy (SEM) images. In this method a set of images taken at different tilt angles are compared by means of digital image correlation (DIC). It is argued that the strength of the method lies in the fact that precise knowledge about the nature of the rotation (vector and/or magnitude) is not needed. Therefore, the great advantage is that complex calibrations of the measuring equipment are avoided. The paper presents the necessary equations involved in the methods, including derivations and solutions. The method is illustrated with examples of 3D reconstructions followed by a discussion on the relevant experimental parameters. Copyright © 2014 Elsevier B.V. All rights reserved.

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

PubMed

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

2015-07-01

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

Climate reconstruction analysis using coexistence likelihood estimation (CRACLE): a method for the estimation of climate using vegetation.

PubMed

Harbert, Robert S; Nixon, Kevin C

2015-08-01

• Plant distributions have long been understood to be correlated with the environmental conditions to which species are adapted. Climate is one of the major components driving species distributions. Therefore, it is expected that the plants coexisting in a community are reflective of the local environment, particularly climate.• Presented here is a method for the estimation of climate from local plant species coexistence data. The method, Climate Reconstruction Analysis using Coexistence Likelihood Estimation (CRACLE), is a likelihood-based method that employs specimen collection data at a global scale for the inference of species climate tolerance. CRACLE calculates the maximum joint likelihood of coexistence given individual species climate tolerance characterization to estimate the expected climate.• Plant distribution data for more than 4000 species were used to show that this method accurately infers expected climate profiles for 165 sites with diverse climatic conditions. Estimates differ from the WorldClim global climate model by less than 1.5°C on average for mean annual temperature and less than ∼250 mm for mean annual precipitation. This is a significant improvement upon other plant-based climate-proxy methods.• CRACLE validates long hypothesized interactions between climate and local associations of plant species. Furthermore, CRACLE successfully estimates climate that is consistent with the widely used WorldClim model and therefore may be applied to the quantitative estimation of paleoclimate in future studies. © 2015 Botanical Society of America, Inc.

The affect of tissue depth variation on craniofacial reconstructions.

PubMed

Starbuck, John M; Ward, Richard E

2007-10-25

We examined the affect of tissue depth variation on the reconstruction of facial form, through the application of the American method, utilizing published tissue depth measurements for emaciated, normal, and obese faces. In this preliminary study, three reconstructions were created on reproductions of the same skull for each set of tissue depth measurements. The resulting morphological variation was measured quantitatively using the anthropometric craniofacial variability index (CVI). This method employs 16 standard craniofacial anthropometric measurements and the results reflect "pattern variation" or facial harmony. We report no appreciable variation in the quantitative measure of the pattern facial form obtained from the three different sets of tissue depths. Facial similarity was assessed qualitatively utilizing surveys of photographs of the three reconstructions. Surveys indicated that subjects frequently perceived the reconstructions as representing different individuals. This disagreement indicates that size of the face may blind observers to similarities in facial form. This research is significant because it illustrates the confounding effect that normal human variation contributes in the successful recognition of individuals from a representational three-dimensional facial reconstruction. Research results suggest that successful identification could be increased if multiple reconstructions were created which reflect a wide range of possible outcomes for facial form. The creation of multiple facial images, from a single skull, will be facilitated as computerized versions of facial reconstruction are further developed and refined.

Computed Tomography Image Quality Evaluation of a New Iterative Reconstruction Algorithm in the Abdomen (Adaptive Statistical Iterative Reconstruction-V) a Comparison With Model-Based Iterative Reconstruction, Adaptive Statistical Iterative Reconstruction, and Filtered Back Projection Reconstructions.

PubMed

Goodenberger, Martin H; Wagner-Bartak, Nicolaus A; Gupta, Shiva; Liu, Xinming; Yap, Ramon Q; Sun, Jia; Tamm, Eric P; Jensen, Corey T

The purpose of this study was to compare abdominopelvic computed tomography images reconstructed with adaptive statistical iterative reconstruction-V (ASIR-V) with model-based iterative reconstruction (Veo 3.0), ASIR, and filtered back projection (FBP). Abdominopelvic computed tomography scans for 36 patients (26 males and 10 females) were reconstructed using FBP, ASIR (80%), Veo 3.0, and ASIR-V (30%, 60%, 90%). Mean ± SD patient age was 32 ± 10 years with mean ± SD body mass index of 26.9 ± 4.4 kg/m. Images were reviewed by 2 independent readers in a blinded, randomized fashion. Hounsfield unit, noise, and contrast-to-noise ratio (CNR) values were calculated for each reconstruction algorithm for further comparison. Phantom evaluation of low-contrast detectability (LCD) and high-contrast resolution was performed. Adaptive statistical iterative reconstruction-V 30%, ASIR-V 60%, and ASIR 80% were generally superior qualitatively compared with ASIR-V 90%, Veo 3.0, and FBP (P < 0.05). Adaptive statistical iterative reconstruction-V 90% showed superior LCD and had the highest CNR in the liver, aorta, and, pancreas, measuring 7.32 ± 3.22, 11.60 ± 4.25, and 4.60 ± 2.31, respectively, compared with the next best series of ASIR-V 60% with respective CNR values of 5.54 ± 2.39, 8.78 ± 3.15, and 3.49 ± 1.77 (P <0.0001). Veo 3.0 and ASIR 80% had the best and worst spatial resolution, respectively. Adaptive statistical iterative reconstruction-V 30% and ASIR-V 60% provided the best combination of qualitative and quantitative performance. Adaptive statistical iterative reconstruction 80% was equivalent qualitatively, but demonstrated inferior spatial resolution and LCD.

A new method of morphological comparison for bony reconstructive surgery: maxillary reconstruction using scapular tip bone

NASA Astrophysics Data System (ADS)

Chan, Harley; Gilbert, Ralph W.; Pagedar, Nitin A.; Daly, Michael J.; Irish, Jonathan C.; Siewerdsen, Jeffrey H.

2010-02-01

esthetic appearance is one of the most important factors for reconstructive surgery. The current practice of maxillary reconstruction chooses radial forearm, fibula or iliac rest osteocutaneous to recreate three-dimensional complex structures of the palate and maxilla. However, these bone flaps lack shape similarity to the palate and result in a less satisfactory esthetic. Considering similarity factors and vasculature advantages, reconstructive surgeons recently explored the use of scapular tip myo-osseous free flaps to restore the excised site. We have developed a new method that quantitatively evaluates the morphological similarity of the scapula tip bone and palate based on a diagnostic volumetric computed tomography (CT) image. This quantitative result was further interpreted as a color map that rendered on the surface of a three-dimensional computer model. For surgical planning, this color interpretation could potentially assist the surgeon to maximize the orientation of the bone flaps for best fit of the reconstruction site. With approval from the Research Ethics Board (REB) of the University Health Network, we conducted a retrospective analysis with CT image obtained from 10 patients. Each patient had a CT scans including the maxilla and chest on the same day. Based on this image set, we simulated total, subtotal and hemi palate reconstruction. The procedure of simulation included volume segmentation, conversing the segmented volume to a stereo lithography (STL) model, manual registration, computation of minimum geometric distances and curvature between STL model. Across the 10 patients data, we found the overall root-mean-square (RMS) conformance was 3.71+/- 0.16 mm

The Island of Amsterdamøya: A key site for studying past climate in the Arctic Archipelago of Svalbard

NASA Astrophysics Data System (ADS)

Bakke, Jostein; Balascio, Nicholas; van der Bilt, Willem G. M.; Bradley, Raymond; D'Andrea, William J.; Gjerde, Marthe; Ólafsdóttir, Sædís; Røthe, Torgeir; De Wet, Greg

2018-03-01

This paper introduces a series of articles assembled in a special issue that explore Holocene climate evolution, as recorded in lakes on the Island of Amsterdamøya on the westernmost fringe of the Arctic Svalbard archipelago. Due to its location near the interface of oceanic and atmospheric systems sourced from Arctic and Atlantic regions, Amsterdamøya is a key site for recording the terrestrial response to marine and atmospheric changes. We employed multi-proxy approaches on lake sediments, integrating physical, biogeochemical, and isotopic analyses to infer past changes in temperature, precipitation, and glacier activity. The results comprise a series of quantitative Holocene-length paleoclimate reconstructions that reveal different aspects of past climate change. Each of the four papers addresses various facets of the Holocene climate history of north-western Svalbard, including a reconstruction of the Annabreen glacier based on the sedimentology of the distal glacier-fed lake Gjøavatnet, a reconstruction of changing hydrologic conditions based on sedimentology and stratigraphy in Lake Hakluytvatnet, reconstruction of summer temperature based on alkenone paleothermometry from lakes Hakluytvatnet and Hajeren, and a hydrogen isotope-based hydrological reconstruction from lake Hakluytvatnet. We also present high-resolution paleomagnetic secular variation data from the same lake, which document important regional magnetic field variations and demonstrate the potential for use in synchronizing Holocene sedimentary records in the Arctic. The paleoclimate picture that emerges is one of early Holocene warmth from ca. 10.5 ka BP interrupted by transient cooling ca. 10-8ka BP, and followed by cooling that mostly manifested as two stepwise events ca. 7 and 4 ka BP. The past 4ka were characterized by dynamic glaciers and summer temperature fluctuations decoupled from the declining summer insolation.

Seasonally Distinct Reconstructions of Northern Alaskan Temperature Variability Since the Last Glacial Maximum

NASA Astrophysics Data System (ADS)

Longo, W. M.; Crowther, J.; Daniels, W.; Russell, J. M.; Giblin, A. E.; Morrill, C.; Zhang, X.; Wang, X.; Huang, Y.

2015-12-01

Paleoclimate reconstructions have provided little consensus on how continental temperatures in Eastern Beringia changed from the Last Glacial Maximum (LGM) to the present. Reconstructions show regional differences in LGM severity, the timing of deglacial warming, and Holocene temperature variability. Currently, arctic temperatures are increasing at the fastest rates on the planet, highlighting the need to identify the sensitivities of arctic systems to various climate forcings. This cannot be done without resolving the complex climate history of Eastern Beringia. Here, we present two new organic geochemical temperature reconstructions from Lake E5, north central Alaska that span the LGM, last glacial termination and Holocene. The proxies (alkenones and brGDGTs) record seasonally distinct temperatures, allowing for the attribution of different forcings to each proxy. The alkenone-based UK37 reconstruction records spring/early summer lake temperatures and indicates a 4 oC abrupt warming at 13.1 ka and a relatively warm late Holocene, which peaks at 2.4 ka and exhibits a cooling trend from 2.4 to 0.1 ka. The brGDGT reconstruction is calibrated to mean annual air temperature and interpreted here as exhibiting a strong warm season bias. BrGDGTs show an abrupt 4.5 oC warming at 14 ka, and show evidence for an early Holocene Thermal Maximum (HTM), which cools by 3 oC after 8.4 ka. Because UK37 temperatures do not exhibit an early HTM, we hypothesize that summer insolation had a minimal effect on spring/early summer lake temperatures. Instead, the UK37 reconstruction agrees with sea ice and sea surface temperature reconstructions from the Beaufort and Chukchi Seas and northeast Pacific Ocean. We hypothesize that forcings associated with sea ice concentration and changes in atmospheric circulation had stronger affects on spring/early summer lake temperatures and we present modern observational data in support of this hypothesis. By contrast, the summer-biased br

A Multiproxy Reconstruction of Holocene Southern Westerlies from the Auckland Islands

NASA Astrophysics Data System (ADS)

Nichols, J. E.; Moy, C. M.; Peteet, D. M.; Weiss, A.; Curtin, L. G.

2015-12-01

The strength and position of the Southern Hemisphere Westerly Wind belt plays an important role in our understanding of the global carbon cycle and glacial-interglacial climate change. We present a paleoclimate record that is primarily influenced by the strength and latitudinal position of the Southern Hemisphere Westerly Winds from a late Holocene lake sediment core and a peat core that spans the last 13,000 years, both obtained from New Zealand's subantarctic Auckland Islands (50°S, 166°E). Several proxy indicators contribute to our reconstruction. Hydrogen isotope ratios of specific organic molecules allow us to reconstruct the hydrogen isotope ratios of precipitation. Using macrofossil counts and the abundances of leaf wax biomarkers, we are able to estimate the moisture balance at our sites. Model simulations of the Westerlies and the rate and isotope ratios of precipitation allow us to interpret our proxy data as changes in the strength and position of the Westerly Winds. In our lacustrine sediment, we found that the Westerlies have been shifting southward since the Little Ice Age, consistent with modern observations of a southward shift. In the peatland sediment, we found a multi-millennial northward shift in the Westerlies during the middle Holocene. We will present further ongoing work that strengthens the chronology of Auckland Islands environmental change and integrates these results with vegetation shifts identified in pollen and macrofossil data.

Do Skeletal Density Changes Within the Tissue Layer of Corals Affect Paleoclimate Reconstructions?

NASA Astrophysics Data System (ADS)

Griffiths, J. S.; DeLong, K. L.; Quinn, T.; Taylor, F. W.; Kilbourne, K. H.; Wagner, A. J.

2016-02-01

Sea surface temperature (SST) reconstructions from coral geochemistry provide information on past climate variability; however, not all coral studies agree on a common calibration slope. Therefore, understanding the impacts of coral skeletal growth on strontium-to-calcium ratios (Sr/Ca) and oxygen isotopic ratios (δ18O) is necessary to ensure accurate calibrations. The study of Gagan et al. (2012) suggests that for the Pacific coral genera Porites, SST calibrations for coral Sr/Ca and δ18O need to be adjusted to account for skeletal density changes in the tissue layer, which may attenuate the seasonal cycle in coral geochemistry. We attempt to duplicate those results and density patterns in several Porites lutea colonies from two locations, yet our results do not show an increase in density in the tissue layer. Another study with Montastraea faveolata reveals reduced seasonality in coral Sr/Ca compared to slower-growing Siderastrea siderea in close proximity and same water depth, suggesting the faster growing M. faveolata geochemistry may be attenuated. By measuring skeletal density changes by micromilling a standard volume throughout the tissue layer and immediately below, we find no pattern of skeletal accumulation in the tissue layer of multiple colonies of M. faveolata and S. siderea from different locations. We conclude that these species lay down all of their skeletal material at the skeleton surface, thus skeletal density changes in the tissue layer do not account for reduced seasonality. We propose that time averaging occurs in M. faveolata as a result of the coral polyp's deep calyces mixing time intervals in the adjacent thecal wall in which micromilling for geochemical analysis produces a sample area that contains several growth increments. Our results show that skeletal density growth effects cannot be applied to all coral genera and paves the way for new research on calyx depth as an alternative explanation for differences in coral calibration slopes.

PET Image Reconstruction Incorporating 3D Mean-Median Sinogram Filtering

NASA Astrophysics Data System (ADS)

Mokri, S. S.; Saripan, M. I.; Rahni, A. A. Abd; Nordin, A. J.; Hashim, S.; Marhaban, M. H.

2016-02-01

Positron Emission Tomography (PET) projection data or sinogram contained poor statistics and randomness that produced noisy PET images. In order to improve the PET image, we proposed an implementation of pre-reconstruction sinogram filtering based on 3D mean-median filter. The proposed filter is designed based on three aims; to minimise angular blurring artifacts, to smooth flat region and to preserve the edges in the reconstructed PET image. The performance of the pre-reconstruction sinogram filter prior to three established reconstruction methods namely filtered-backprojection (FBP), Maximum likelihood expectation maximization-Ordered Subset (OSEM) and OSEM with median root prior (OSEM-MRP) is investigated using simulated NCAT phantom PET sinogram as generated by the PET Analytical Simulator (ASIM). The improvement on the quality of the reconstructed images with and without sinogram filtering is assessed according to visual as well as quantitative evaluation based on global signal to noise ratio (SNR), local SNR, contrast to noise ratio (CNR) and edge preservation capability. Further analysis on the achieved improvement is also carried out specific to iterative OSEM and OSEM-MRP reconstruction methods with and without pre-reconstruction filtering in terms of contrast recovery curve (CRC) versus noise trade off, normalised mean square error versus iteration, local CNR versus iteration and lesion detectability. Overall, satisfactory results are obtained from both visual and quantitative evaluations.

Comparison of clinical and physics scoring of PET images when image reconstruction parameters are varied.

PubMed

Walsh, C; Johnston, C; Sheehy, N; O' Reilly, G

2013-02-01

In this study the quantitative and qualitative image quality (IQ) measurements with clinical judgement of IQ in positron emission tomography (PET) were compared. The limitations of IQ metrics and the proposed criteria of acceptability for PET scanners are discussed. Phantom and patient images were reconstructed using seven different iterative reconstruction protocols. For each reconstructed set of images, IQ was scored based both on the visual analysis and on the quantitative metrics. The quantitative physics metrics did not rank the reconstruction protocols in the same order as the clinicians' scoring of perceived IQ (R(s)=-0.54). Better agreement was achieved when comparing the clinical perception of IQ to the physicist's visual assessment of IQ in the phantom images (R(s)=+0.59). The closest agreement was seen between the quantitative physics metrics and the measurement of the standard uptake values (SUVs) in small tumours (R(s)=+0.92). Given the disparity between the clinical perception of IQ and the physics metrics a cautious approach to use of IQ measurements for determining suspension levels is warranted.

Absorption Reconstruction Improves Biodistribution Assessment of Fluorescent Nanoprobes Using Hybrid Fluorescence-mediated Tomography

PubMed Central

Gremse, Felix; Theek, Benjamin; Kunjachan, Sijumon; Lederle, Wiltrud; Pardo, Alessa; Barth, Stefan; Lammers, Twan; Naumann, Uwe; Kiessling, Fabian

2014-01-01

Aim: Fluorescence-mediated tomography (FMT) holds potential for accelerating diagnostic and theranostic drug development. However, for proper quantitative fluorescence reconstruction, knowledge on optical scattering and absorption, which are highly heterogeneous in different (mouse) tissues, is required. We here describe methods to assess these parameters using co-registered micro Computed Tomography (µCT) data and nonlinear whole-animal absorption reconstruction, and evaluate their importance for assessment of the biodistribution and target site accumulation of fluorophore-labeled drug delivery systems. Methods: Besides phantoms with varying degrees of absorption, mice bearing A431 tumors were imaged 15 min and 48 h after i.v. injection of a fluorophore-labeled polymeric drug carrier (pHPMA-Dy750) using µCT-FMT. The outer shape of mice and a scattering map were derived using automated segmentation of the µCT data. Furthermore, a 3D absorption map was reconstructed from the trans-illumination data. We determined the absorption of five interactively segmented regions (heart, liver, kidney, muscle, tumor). Since blood is the main near-infrared absorber in vivo, the absorption was also estimated from the relative blood volume (rBV), determined by contrast-enhanced µCT. We compared the reconstructed absorption with the rBV-based values and analyzed the effect of using the absorption map on the fluorescence reconstruction. Results: Phantom experiments demonstrated that absorption reconstruction is possible and necessary for quantitative fluorescence reconstruction. In vivo, the reconstructed absorption showed high values in strongly blood-perfused organs such as the heart, liver and kidney. The absorption values correlated strongly with the rBV-based absorption values, confirming the accuracy of the absorption reconstruction. Usage of homogenous absorption instead of the reconstructed absorption map resulted in reduced values in the heart, liver and kidney, by

Quantitative neuroanatomy for connectomics in Drosophila

PubMed Central

Schneider-Mizell, Casey M; Gerhard, Stephan; Longair, Mark; Kazimiers, Tom; Li, Feng; Zwart, Maarten F; Champion, Andrew; Midgley, Frank M; Fetter, Richard D; Saalfeld, Stephan; Cardona, Albert

2016-01-01

Neuronal circuit mapping using electron microscopy demands laborious proofreading or reconciliation of multiple independent reconstructions. Here, we describe new methods to apply quantitative arbor and network context to iteratively proofread and reconstruct circuits and create anatomically enriched wiring diagrams. We measured the morphological underpinnings of connectivity in new and existing reconstructions of Drosophila sensorimotor (larva) and visual (adult) systems. Synaptic inputs were preferentially located on numerous small, microtubule-free 'twigs' which branch off a single microtubule-containing 'backbone'. Omission of individual twigs accounted for 96% of errors. However, the synapses of highly connected neurons were distributed across multiple twigs. Thus, the robustness of a strong connection to detailed twig anatomy was associated with robustness to reconstruction error. By comparing iterative reconstruction to the consensus of multiple reconstructions, we show that our method overcomes the need for redundant effort through the discovery and application of relationships between cellular neuroanatomy and synaptic connectivity. DOI: http://dx.doi.org/10.7554/eLife.12059.001 PMID:26990779

Towards quantitative imaging: stability of fully automated nodule segmentation across varied dose levels and reconstruction parameters in a low-dose CT screening patient cohort

NASA Astrophysics Data System (ADS)

Wahi-Anwar, M. Wasil; Emaminejad, Nastaran; Hoffman, John; Kim, Grace H.; Brown, Matthew S.; McNitt-Gray, Michael F.

2018-02-01

Quantitative imaging in lung cancer CT seeks to characterize nodules through quantitative features, usually from a region of interest delineating the nodule. The segmentation, however, can vary depending on segmentation approach and image quality, which can affect the extracted feature values. In this study, we utilize a fully-automated nodule segmentation method - to avoid reader-influenced inconsistencies - to explore the effects of varied dose levels and reconstruction parameters on segmentation. Raw projection CT images from a low-dose screening patient cohort (N=59) were reconstructed at multiple dose levels (100%, 50%, 25%, 10%), two slice thicknesses (1.0mm, 0.6mm), and a medium kernel. Fully-automated nodule detection and segmentation was then applied, from which 12 nodules were selected. Dice similarity coefficient (DSC) was used to assess the similarity of the segmentation ROIs of the same nodule across different reconstruction and dose conditions. Nodules at 1.0mm slice thickness and dose levels of 25% and 50% resulted in DSC values greater than 0.85 when compared to 100% dose, with lower dose leading to a lower average and wider spread of DSC values. At 0.6mm, the increased bias and wider spread of DSC values from lowering dose were more pronounced. The effects of dose reduction on DSC for CAD-segmented nodules were similar in magnitude to reducing the slice thickness from 1.0mm to 0.6mm. In conclusion, variation of dose and slice thickness can result in very different segmentations because of noise and image quality. However, there exists some stability in segmentation overlap, as even at 1mm, an image with 25% of the lowdose scan still results in segmentations similar to that seen in a full-dose scan.

Convergence optimization of parametric MLEM reconstruction for estimation of Patlak plot parameters.

PubMed

Angelis, Georgios I; Thielemans, Kris; Tziortzi, Andri C; Turkheimer, Federico E; Tsoumpas, Charalampos

2011-07-01

In dynamic positron emission tomography data many researchers have attempted to exploit kinetic models within reconstruction such that parametric images are estimated directly from measurements. This work studies a direct parametric maximum likelihood expectation maximization algorithm applied to [(18)F]DOPA data using reference-tissue input function. We use a modified version for direct reconstruction with a gradually descending scheme of subsets (i.e. 18-6-1) initialized with the FBP parametric image for faster convergence and higher accuracy. The results compared with analytic reconstructions show quantitative robustness (i.e. minimal bias) and clinical reproducibility within six human acquisitions in the region of clinical interest. Bland-Altman plots for all the studies showed sufficient quantitative agreement between the direct reconstructed parametric maps and the indirect FBP (--0.035x+0.48E--5). Copyright © 2011 Elsevier Ltd. All rights reserved.

A biomechanical modeling guided simultaneous motion estimation and image reconstruction technique (SMEIR-Bio) for 4D-CBCT reconstruction

NASA Astrophysics Data System (ADS)

Huang, Xiaokun; Zhang, You; Wang, Jing

2017-03-01

Four-dimensional (4D) cone-beam computed tomography (CBCT) enables motion tracking of anatomical structures and removes artifacts introduced by motion. However, the imaging time/dose of 4D-CBCT is substantially longer/higher than traditional 3D-CBCT. We previously developed a simultaneous motion estimation and image reconstruction (SMEIR) algorithm, to reconstruct high-quality 4D-CBCT from limited number of projections to reduce the imaging time/dose. However, the accuracy of SMEIR is limited in reconstructing low-contrast regions with fine structure details. In this study, we incorporate biomechanical modeling into the SMEIR algorithm (SMEIR-Bio), to improve the reconstruction accuracy at low-contrast regions with fine details. The efficacy of SMEIR-Bio is evaluated using 11 lung patient cases and compared to that of the original SMEIR algorithm. Qualitative and quantitative comparisons showed that SMEIR-Bio greatly enhances the accuracy of reconstructed 4D-CBCT volume in low-contrast regions, which can potentially benefit multiple clinical applications including the treatment outcome analysis.

Sparsity-constrained PET image reconstruction with learned dictionaries

NASA Astrophysics Data System (ADS)

Tang, Jing; Yang, Bao; Wang, Yanhua; Ying, Leslie

2016-09-01

PET imaging plays an important role in scientific and clinical measurement of biochemical and physiological processes. Model-based PET image reconstruction such as the iterative expectation maximization algorithm seeking the maximum likelihood solution leads to increased noise. The maximum a posteriori (MAP) estimate removes divergence at higher iterations. However, a conventional smoothing prior or a total-variation (TV) prior in a MAP reconstruction algorithm causes over smoothing or blocky artifacts in the reconstructed images. We propose to use dictionary learning (DL) based sparse signal representation in the formation of the prior for MAP PET image reconstruction. The dictionary to sparsify the PET images in the reconstruction process is learned from various training images including the corresponding MR structural image and a self-created hollow sphere. Using simulated and patient brain PET data with corresponding MR images, we study the performance of the DL-MAP algorithm and compare it quantitatively with a conventional MAP algorithm, a TV-MAP algorithm, and a patch-based algorithm. The DL-MAP algorithm achieves improved bias and contrast (or regional mean values) at comparable noise to what the other MAP algorithms acquire. The dictionary learned from the hollow sphere leads to similar results as the dictionary learned from the corresponding MR image. Achieving robust performance in various noise-level simulation and patient studies, the DL-MAP algorithm with a general dictionary demonstrates its potential in quantitative PET imaging.

Testing the Sun-climate Connection with Paleoclimate Data

NASA Technical Reports Server (NTRS)

Crowley, Thomas J.; Howard, Matthew K.

1990-01-01

If there is a significant sun-climate connection, it should be detectable in high-resolution paleoclimate records. Of particular interest is the last few thousand years, where we have both indices of solar variability (C-14 and Be-10) and climate variations (alpine glaciers, tree rings, ice cores, corals, etc.). Although there are a few exceptions, statistical analyses of solar and climate records generally indicates a flickering relationship between the two -- sometimes it seems to be present, sometimes not. The most repeatable solar climate periods occur at approx. 120 and approx. 56 yrs, although there is also evidence for approx. 420 and approx. 200 yrs. power in some records. However, coherence between solar and climate spectra is usually low, and occurrence of solar spectra in climate records is sometimes dependent on choice of analysis program. These results suggest in general a relatively weak sun-climate link on time scales of decades to centuries. This conclusion is consistent with previous studies and with the observation that inferred climate fluctuations of 1.0 to 1.5 C on this time scale would require solar constant variations of approximately 0.5 to 1.0 percent. This change in forcing is almost an order of magnitude greater than observed changes over the last solar cycle and appears to be on the far-outer limit of acceptable changes for a Maunder Minimum-type event.

Botulinum toxin in preparation of oral cavity for microsurgical reconstruction.

PubMed

Corradino, Bartolo; Di Lorenzo, Sara; Mossuto, Carmela; Costa, Renato Patrizio; Moschella, Francesco

2010-01-01

Infiltration of botulinum toxin in the major salivary glands allows a temporary reduction of salivation that begins 8 days afterwards and returns to normal within 2 months. The inhibition of salivary secretion, carried out before the oral cavity reconstructive surgery, could allow a reduction of the incidence of oro-cutaneous fistulas and local complications. Saliva stagnation is a risk factor for patients who have to undergo reconstructive microsurgery of the oral cavity, because of fistula formation and local complications in the oral cavity. The authors suggest infiltration of botulinum toxin in the major salivary glands to reduce salivation temporarily during the healing stage. During the preoperative stage, 20 patients with oral cavity carcinoma who were candidates for microsurgical reconstruction underwent sialoscintigraphy and a quantitative measurement of the salivary secretion. Injection of botulinum toxin was carried out in the salivary glands 4 days before surgery. The saliva quantitative measurement was repeated 3 and 8 days after infiltration, sialoscintigraphy after 15 days. In all cases, the saliva quantitative measurement revealed a reduction of 50% and 70% of the salivary secretion after 72 h and 8 days, respectively. A lower rate of local complications was observed.

Climatic history of the northeastern United States during the past 3000 years

NASA Astrophysics Data System (ADS)

Marlon, Jennifer R.; Pederson, Neil; Nolan, Connor; Goring, Simon; Shuman, Bryan; Robertson, Ann; Booth, Robert; Bartlein, Patrick J.; Berke, Melissa A.; Clifford, Michael; Cook, Edward; Dieffenbacher-Krall, Ann; Dietze, Michael C.; Hessl, Amy; Hubeny, J. Bradford; Jackson, Stephen T.; Marsicek, Jeremiah; McLachlan, Jason; Mock, Cary J.; Moore, David J. P.; Nichols, Jonathan; Peteet, Dorothy; Schaefer, Kevin; Trouet, Valerie; Umbanhowar, Charles; Williams, John W.; Yu, Zicheng

2017-10-01

Many ecosystem processes that influence Earth system feedbacks - vegetation growth, water and nutrient cycling, disturbance regimes - are strongly influenced by multidecadal- to millennial-scale climate variations that cannot be directly observed. Paleoclimate records provide information about these variations, forming the basis of our understanding and modeling of them. Fossil pollen records are abundant in the NE US, but cannot simultaneously provide information about paleoclimate and past vegetation in a modeling context because this leads to circular logic. If pollen data are used to constrain past vegetation changes, then the remaining paleoclimate archives in the northeastern US (NE US) are quite limited. Nonetheless, a growing number of diverse reconstructions have been developed but have not yet been examined together. Here we conduct a systematic review, assessment, and comparison of paleotemperature and paleohydrological proxies from the NE US for the last 3000 years. Regional temperature reconstructions (primarily summer) show a long-term cooling trend (1000 BCE-1700 CE) consistent with hemispheric-scale reconstructions, while hydroclimate data show gradually wetter conditions through the present day. Multiple proxies suggest that a prolonged, widespread drought occurred between 550 and 750 CE. Dry conditions are also evident during the Medieval Climate Anomaly, which was warmer and drier than the Little Ice Age and drier than today. There is some evidence for an acceleration of the longer-term wetting trend in the NE US during the past century; coupled with an abrupt shift from decreasing to increasing temperatures in the past century, these changes could have wide-ranging implications for species distributions, ecosystem dynamics, and extreme weather events. More work is needed to gather paleoclimate data in the NE US to make inter-proxy comparisons and to improve estimates of uncertainty in reconstructions.

Climatic History of the Northeastern United States During the Past 3000 Years

NASA Technical Reports Server (NTRS)

Marlon, Jennifer R.; Pederson, Neil; Nolan, Connor; Goring, Simon; Shuman, Bryan; Robertson, Ann; Booth, Robert; Bartlein, Patrick J.; Berke, Melissa A.; Clifford, Michael;

Local motion-compensated method for high-quality 3D coronary artery reconstruction

PubMed Central

Liu, Bo; Bai, Xiangzhi; Zhou, Fugen

2016-01-01

The 3D reconstruction of coronary artery from X-ray angiograms rotationally acquired on C-arm has great clinical value. While cardiac-gated reconstruction has shown promising results, it suffers from the problem of residual motion. This work proposed a new local motion-compensated reconstruction method to handle this issue. An initial image was firstly reconstructed using a regularized iterative reconstruction method. Then a 3D/2D registration method was proposed to estimate the residual vessel motion. Finally, the residual motion was compensated in the final reconstruction using the extended iterative reconstruction method. Through quantitative evaluation, it was found that high-quality 3D reconstruction could be obtained and the result was comparable to state-of-the-art method. PMID:28018741

Quantitative Holocene climatic reconstructions for the lower Yangtze region of China

NASA Astrophysics Data System (ADS)

Li, Jianyong; Dodson, John; Yan, Hong; Wang, Weiming; Innes, James B.; Zong, Yongqiang; Zhang, Xiaojian; Xu, Qinghai; Ni, Jian; Lu, Fengyan

2018-02-01

Quantitative proxy-based and high-resolution palaeoclimatic datasets are scarce for the lower reaches of the Yangtze River (LYR) basin. This region is in a transitional vegetation zone which is climatologically sensitive; and as a birthplace for prehistorical civilization in China, it is important to understand how palaeoclimatic dynamics played a role in affecting cultural development in the region. We present a pollen-based and regionally-averaged Holocene climatic twin-dataset for mean total annual precipitation (PANN) and mean annual temperature (TANN) covering the last 10,000 years for the LYR region. This is based on the technique of weighted averaging-partial least squares regression to establish robust calibration models for obtaining reliable climatic inferences. The pollen-based reconstructions generally show an early Holocene climatic optimum with both abundant monsoonal rainfall and warm thermal conditions, and a declining pattern of both PANN and TANN values in the middle to late Holocene. The main driving forces behind the Holocene climatic changes in the LYR area are likely summer solar insolation associated with tropical or subtropical macro-scale climatic circulations such as the Intertropical Convergence Zone (ITCZ), Western Pacific Subtropical High (WPSH), and El Niño/Southern Oscillation (ENSO). Regional multi-proxy comparisons indicate that the Holocene variations in precipitation and temperature for the LYR region display an in-phase relationship with other related proxy records from southern monsoonal China and the Indian monsoon-influenced regions, but are inconsistent with the Holocene moisture or temperature records from northern monsoonal China and the westerly-dominated region in northwestern China. Overall, our comprehensive palaeoclimatic dataset and models may be significant tools for understanding the Holocene Asian monsoonal evolution and for anticipating its future dynamics in eastern Asia.

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

PubMed

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

2015-08-01

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

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

Joint MR-PET reconstruction using a multi-channel image regularizer

PubMed Central

Koesters, Thomas; Otazo, Ricardo; Bredies, Kristian; Sodickson, Daniel K

2016-01-01

While current state of the art MR-PET scanners enable simultaneous MR and PET measurements, the acquired data sets are still usually reconstructed separately. We propose a new multi-modality reconstruction framework using second order Total Generalized Variation (TGV) as a dedicated multi-channel regularization functional that jointly reconstructs images from both modalities. In this way, information about the underlying anatomy is shared during the image reconstruction process while unique differences are preserved. Results from numerical simulations and in-vivo experiments using a range of accelerated MR acquisitions and different MR image contrasts demonstrate improved PET image quality, resolution, and quantitative accuracy. PMID:28055827

Multiscale temporal variability and regional patterns in 555 years of conterminous U.S. streamflow

NASA Astrophysics Data System (ADS)

Ho, Michelle; Lall, Upmanu; Sun, Xun; Cook, Edward R.

2017-04-01

The development of paleoclimate streamflow reconstructions in the conterminous United States (CONUS) has provided water resource managers with improved insights into multidecadal and centennial scale variability that cannot be reliably detected using shorter instrumental records. Paleoclimate streamflow reconstructions have largely focused on individual catchments limiting the ability to quantify variability across the CONUS. The Living Blended Drought Atlas (LBDA), a spatially and temporally complete 555 year long paleoclimate record of summer drought across the CONUS, provides an opportunity to reconstruct and characterize streamflow variability at a continental scale. We explore the validity of the first paleoreconstructions of streamflow that span the CONUS informed by the LBDA targeting a set of U.S. Geological Survey streamflow sites. The reconstructions are skillful under cross validation across most of the country, but the variance explained is generally low. Spatial and temporal structures of streamflow variability are analyzed using hierarchical clustering, principal component analysis, and wavelet analyses. Nine spatially coherent clusters are identified. The reconstructions show signals of contemporary droughts such as the Dust Bowl (1930s) and 1950s droughts. Decadal-scale variability was detected in the late 1900s in the western U.S., however, similar modes of temporal variability were rarely present prior to the 1950s. The twentieth century featured longer wet spells and shorter dry spells compared with the preceding 450 years. Streamflows in the Pacific Northwest and Northeast are negatively correlated with the central U.S. suggesting the potential to mitigate some drought impacts by balancing economic activities and insurance pools across these regions during major droughts.

Sparse reconstruction of liver cirrhosis from monocular mini-laparoscopic sequences

NASA Astrophysics Data System (ADS)

Marcinczak, Jan Marek; Painer, Sven; Grigat, Rolf-Rainer

2015-03-01

Mini-laparoscopy is a technique which is used by clinicians to inspect the liver surface with ultra-thin laparoscopes. However, so far no quantitative measures based on mini-laparoscopic sequences are possible. This paper presents a Structure from Motion (SfM) based methodology to do 3D reconstruction of liver cirrhosis from mini-laparoscopic videos. The approach combines state-of-the-art tracking, pose estimation, outlier rejection and global optimization to obtain a sparse reconstruction of the cirrhotic liver surface. Specular reflection segmentation is included into the reconstruction framework to increase the robustness of the reconstruction. The presented approach is evaluated on 15 endoscopic sequences using three cirrhotic liver phantoms. The median reconstruction accuracy ranges from 0.3 mm to 1 mm.

Experimental Reconstructions of Surface Temperature using the PAGES 2k Network

NASA Astrophysics Data System (ADS)

Wang, Jianghao; Emile-Geay, Julien; Vaccaro, Adam; Guillot, Dominique; Rajaratnam, Bala

2014-05-01

studies (Wang et al., 2014). The updated set of reconstructions, with uncertainties, will provide a broader context for the evaluation of the unusual character of the 20th century warming. The reconstructions will also be used to constrain fingerprinting analyses, which is particularly useful in discriminating between externally forced signals and internal variability. Reference: Guillot, D., B. Rajaratnam, and J. Emile-Geay, Statistical paleoclimate reconstructions via markov random fields, Ann. Appl. Stat., submitted. Mann, M. E., Z. Zhang, S. Rutherford, R. S. Bradley, M. K. Hughes, D. Shindell, C. Ammann, G. Faluvegi, and F. Ni, Global signatures and dynamical origins of the little ice age and medieval climate anomaly, Science, 326 (5957), 1256-1260, 2009. PAGES2K Consortium, Continental-scale temperature variability during the past two millennia, Nature Geosci, 6(5), 339-346, 2013. Smerdon, J. E., A. Kaplan, D. Chang, and M. N. Evans, A pseudoproxy evaluation of the CCA and RegEM methods for reconstructing climate fields of the last millennium*, J. Clim., 23(18), 4856-4880, 2010. Wang, J., J. Emile-Geay, A. D. Vaccaro, and D. Guillot, Fragility of estimated spatial temperature patterns in climate field reconstructions of the Common Era, Abstract PP41B-03 presented at Fall Meeting, AGU, San Francisco, Calif., 2013. Wang, J., J. Emile-Geay, D. Guillot, J. Smerdon, and B. Rajaratnam, Evaluating climate field reconstruction techniques using improved emulations of real-world conditions, Clim.Past, 10(1), 1-19, 2014.

Maximum Likelihood Reconstruction for Magnetic Resonance Fingerprinting

PubMed Central

Zhao, Bo; Setsompop, Kawin; Ye, Huihui; Cauley, Stephen; Wald, Lawrence L.

2017-01-01

This paper introduces a statistical estimation framework for magnetic resonance (MR) fingerprinting, a recently proposed quantitative imaging paradigm. Within this framework, we present a maximum likelihood (ML) formalism to estimate multiple parameter maps directly from highly undersampled, noisy k-space data. A novel algorithm, based on variable splitting, the alternating direction method of multipliers, and the variable projection method, is developed to solve the resulting optimization problem. Representative results from both simulations and in vivo experiments demonstrate that the proposed approach yields significantly improved accuracy in parameter estimation, compared to the conventional MR fingerprinting reconstruction. Moreover, the proposed framework provides new theoretical insights into the conventional approach. We show analytically that the conventional approach is an approximation to the ML reconstruction; more precisely, it is exactly equivalent to the first iteration of the proposed algorithm for the ML reconstruction, provided that a gridding reconstruction is used as an initialization. PMID:26915119

Maximum Likelihood Reconstruction for Magnetic Resonance Fingerprinting.

PubMed

Zhao, Bo; Setsompop, Kawin; Ye, Huihui; Cauley, Stephen F; Wald, Lawrence L

2016-08-01

This paper introduces a statistical estimation framework for magnetic resonance (MR) fingerprinting, a recently proposed quantitative imaging paradigm. Within this framework, we present a maximum likelihood (ML) formalism to estimate multiple MR tissue parameter maps directly from highly undersampled, noisy k-space data. A novel algorithm, based on variable splitting, the alternating direction method of multipliers, and the variable projection method, is developed to solve the resulting optimization problem. Representative results from both simulations and in vivo experiments demonstrate that the proposed approach yields significantly improved accuracy in parameter estimation, compared to the conventional MR fingerprinting reconstruction. Moreover, the proposed framework provides new theoretical insights into the conventional approach. We show analytically that the conventional approach is an approximation to the ML reconstruction; more precisely, it is exactly equivalent to the first iteration of the proposed algorithm for the ML reconstruction, provided that a gridding reconstruction is used as an initialization.

A modified discrete algebraic reconstruction technique for multiple grey image reconstruction for limited angle range tomography.

PubMed

Liang, Zhiting; Guan, Yong; Liu, Gang; Chen, Xiangyu; Li, Fahu; Guo, Pengfei; Tian, Yangchao

2016-03-01

The `missing wedge', which is due to a restricted rotation range, is a major challenge for quantitative analysis of an object using tomography. With prior knowledge of the grey levels, the discrete algebraic reconstruction technique (DART) is able to reconstruct objects accurately with projections in a limited angle range. However, the quality of the reconstructions declines as the number of grey levels increases. In this paper, a modified DART (MDART) was proposed, in which each independent region of homogeneous material was chosen as a research object, instead of the grey values. The grey values of each discrete region were estimated according to the solution of the linear projection equations. The iterative process of boundary pixels updating and correcting the grey values of each region was executed alternately. Simulation experiments of binary phantoms as well as multiple grey phantoms show that MDART is capable of achieving high-quality reconstructions with projections in a limited angle range. The interesting advancement of MDART is that neither prior knowledge of the grey values nor the number of grey levels is necessary.

Reconstruction of a high-resolution late holocene arctic paleoclimate record from Colville River delta sediments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schreiner, Kathryn Melissa; Lowry, Thomas Stephen

2013-10-01

This work was partially supported by the Sandia National Laboratories, Laboratory Directed Research and Development (LDRD) fellowship program in conjunction with Texas A&M University (TAMU). The research described herein is the work of Kathryn M. Schreiner (Katie) and her advisor, Thomas S. Bianchi and represents a concise description of Katies dissertation that was submitted to the TAMU Office of Graduate Studies in May 2013 in partial fulfillment of her doctorate of philosophy degree. High Arctic permafrost soils contain a massive amount of organic carbon, accounting for twice as much carbon as what is currently stored as carbon dioxide in themore » atmosphere. However, with current warming trends this sink is in danger of thawing and potentially releasing large amounts of carbon as both carbon dioxide and methane into the atmosphere. It is difficult to make predictions about the future of this sink without knowing how it has reacted to past temperature and climate changes. This project investigated long term, fine scale particulate organic carbon (POC) delivery by the high-Arctic Colville River into Simpsons Lagoon in the near-shore Beaufort Sea. Modern POC was determined to be a mixture of three sources (riverine soils, coastal erosion, and marine). Downcore POC measurements were performed in a core close to the Colville River output and a core close to intense coastal erosion. Inputs of the three major sources were found to vary throughout the last two millennia, and in the Colville River core covary significantly with Alaskan temperature reconstructions.« less

Correspondence of terrestrial and marine paleoclimates, SW Florida, during Mid-Pliocene periods of global warmth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willard, D.A.; Cronin, T.M.; Litwin, R.J.

Pollen and ostracode samples from shallow-marine strata of the Pinecrest Beds near Sarasota, FL were studied to compare terrestrial and marine paleoclimate records during periods of middle Pliocene global warmth. Pollen assemblages from strata deposited during sea-level highstands from about 3.5--3.0 Ma are dominated by Pinus pollen with subdominant Ouercus and common taxodiaceous pollen, which increases markedly in abundance near about 3.0 Ma. Comparison with modern, shallow-marine pollen assemblages from the east coast of the United States indicates that the 3.5--3.0 Ma vegetation was, overall, similar to vegetation from the southern third Florida. However, near 3.0 Ma, pollen assemblages becomemore » less similar to modern assemblages due to higher percentages of taxodiaceous pollen and lower percentages of herbaceous pollen. Such changes are consistent with warmer climates and, possibly, moister soil conditions. Marine ostracodes also show progressively higher percentages of thermophilic (subtropical/tropical) taxa and decreasing percentages of cryophilic (temperature) taxa between 3.5--3.0 Ma. From about 2.5--2.0 Ma, ostracode assemblages recorded open-bay, sometimes brackish environments similar to those in subtropical eastern North America today. The Pinecrest paleoclimate record shows (1) that during two periods of global warmth and high sea level, subtropical terrestrial and marine climates were not substantially warmer than today; (2) ocean and atmosphere temperatures probably were about the same as today, perhaps slightly higher during peak warmth near 3.0 Ma; (3) changes in pollen assemblages appear to lag behind changes in ostracode assemblages; (4) progressively warmer local climates 3.5--3.0 Ma probably record an increasing influence of warm Gulf Stream water as the Central American Isthmus closed.« less

Beyond annual streamflow reconstructions for the Upper Colorado River Basin: a paleo-water-balance approach

USGS Publications Warehouse

Gangopadhyay, Subhrendu; McCabe, Gregory J.; Woodhouse, Connie A.

2015-01-01

In this paper, we present a methodology to use annual tree-ring chronologies and a monthly water balance model to generate annual reconstructions of water balance variables (e.g., potential evapotrans- piration (PET), actual evapotranspiration (AET), snow water equivalent (SWE), soil moisture storage (SMS), and runoff (R)). The method involves resampling monthly temperature and precipitation from the instrumental record directed by variability indicated by the paleoclimate record. The generated time series of monthly temperature and precipitation are subsequently used as inputs to a monthly water balance model. The methodology is applied to the Upper Colorado River Basin, and results indicate that the methodology reliably simulates water-year runoff, maximum snow water equivalent, and seasonal soil moisture storage for the instrumental period. As a final application, the methodology is used to produce time series of PET, AET, SWE, SMS, and R for the 1404–1905 period for the Upper Colorado River Basin.

Developing Age Models to Utilize High Arctic Coastal Sediments for Paleoclimate Research: Results from the Colville Delta and Simpson Lagoon, Alaska

NASA Astrophysics Data System (ADS)

Miller, A. J.; Allison, M. A.; Bianchi, T. S.; Marcantonio, F.

2012-12-01

Sediment cores collected from Simpson Lagoon on the inner Beaufort Sea shelf adjacent to the Colville River delta, AK are being utilized to develop new, high-resolution (sub-decadal scale) archives of the 0-3,000 year Arctic paleoclimate record necessary to assess natural and anthropogenic climate variability. An imperative first step for developing a new paleoclimate archive is to establish methodologies for constraining the age-depth relationship. Naturally occurring and bomb-produced radioisotopes have been utilized in sediments to constrain downcore variability of accumulation rates on 100-103 y timescales, but this methodology is complicated by low activities of many of these tracers at high latitudes. The present study utilizes the combination of a (1) multi-tracer approach and a (2) tailored measurement strategy to overcome this limitation. 210Pb and 137Cs analyses were conducted on the fine (<32μm) sediment fraction to maximize measurable activity and to minimize radioisotope activity variability resulting from changes in grain size: 137Cs geochronologies proved more reliable in this setting and revealed mm/y sediment accumulation in the lagoon. To corroborate the 137Cs results, 239,240Pu activities were analyzed for selected sites using ICP-MS which has ultra-low detection limits, and yielded accumulation rates that matched the Cs geochronology. Age model development for the remainder of the core lengths (>~100 y in age) were completed using radiocarbon dating of benthic foraminifera tests, which proved the only datable in situ carbon available in this sediment archive. These dates have been used to constrain the ages of acoustic reflectors in CHIRP subbottom seismic records collected from the lagoon. Using this age control, spatial patterns of lagoonal sediment accumulation over the last ~3 ky were derived from the CHIRP data. Two depocenters are identified and validate combining age-dated coring with high-resolution seismic profiling to identify areas

Whole-body PET parametric imaging employing direct 4D nested reconstruction and a generalized non-linear Patlak model

NASA Astrophysics Data System (ADS)

Karakatsanis, Nicolas A.; Rahmim, Arman

2014-03-01

Graphical analysis is employed in the research setting to provide quantitative estimation of PET tracer kinetics from dynamic images at a single bed. Recently, we proposed a multi-bed dynamic acquisition framework enabling clinically feasible whole-body parametric PET imaging by employing post-reconstruction parameter estimation. In addition, by incorporating linear Patlak modeling within the system matrix, we enabled direct 4D reconstruction in order to effectively circumvent noise amplification in dynamic whole-body imaging. However, direct 4D Patlak reconstruction exhibits a relatively slow convergence due to the presence of non-sparse spatial correlations in temporal kinetic analysis. In addition, the standard Patlak model does not account for reversible uptake, thus underestimating the influx rate Ki. We have developed a novel whole-body PET parametric reconstruction framework in the STIR platform, a widely employed open-source reconstruction toolkit, a) enabling accelerated convergence of direct 4D multi-bed reconstruction, by employing a nested algorithm to decouple the temporal parameter estimation from the spatial image update process, and b) enhancing the quantitative performance particularly in regions with reversible uptake, by pursuing a non-linear generalized Patlak 4D nested reconstruction algorithm. A set of published kinetic parameters and the XCAT phantom were employed for the simulation of dynamic multi-bed acquisitions. Quantitative analysis on the Ki images demonstrated considerable acceleration in the convergence of the nested 4D whole-body Patlak algorithm. In addition, our simulated and patient whole-body data in the postreconstruction domain indicated the quantitative benefits of our extended generalized Patlak 4D nested reconstruction for tumor diagnosis and treatment response monitoring.

Implementation of higher-order vertical finite elements in ISSM v4.13 for improved ice sheet flow modeling over paleoclimate timescales

NASA Astrophysics Data System (ADS)

Cuzzone, Joshua K.; Morlighem, Mathieu; Larour, Eric; Schlegel, Nicole; Seroussi, Helene

2018-05-01

Paleoclimate proxies are being used in conjunction with ice sheet modeling experiments to determine how the Greenland ice sheet responded to past changes, particularly during the last deglaciation. Although these comparisons have been a critical component in our understanding of the Greenland ice sheet sensitivity to past warming, they often rely on modeling experiments that favor minimizing computational expense over increased model physics. Over Paleoclimate timescales, simulating the thermal structure of the ice sheet has large implications on the modeled ice viscosity, which can feedback onto the basal sliding and ice flow. To accurately capture the thermal field, models often require a high number of vertical layers. This is not the case for the stress balance computation, however, where a high vertical resolution is not necessary. Consequently, since stress balance and thermal equations are generally performed on the same mesh, more time is spent on the stress balance computation than is otherwise necessary. For these reasons, running a higher-order ice sheet model (e.g., Blatter-Pattyn) over timescales equivalent to the paleoclimate record has not been possible without incurring a large computational expense. To mitigate this issue, we propose a method that can be implemented within ice sheet models, whereby the vertical interpolation along the z axis relies on higher-order polynomials, rather than the traditional linear interpolation. This method is tested within the Ice Sheet System Model (ISSM) using quadratic and cubic finite elements for the vertical interpolation on an idealized case and a realistic Greenland configuration. A transient experiment for the ice thickness evolution of a single-dome ice sheet demonstrates improved accuracy using the higher-order vertical interpolation compared to models using the linear vertical interpolation, despite having fewer degrees of freedom. This method is also shown to improve a model's ability to capture sharp

Quantitative imaging technique using the layer-stripping algorithm

NASA Astrophysics Data System (ADS)

Beilina, L.

2017-07-01

We present the layer-stripping algorithm for the solution of the hyperbolic coefficient inverse problem (CIP). Our numerical examples show quantitative reconstruction of small tumor-like inclusions in two-dimensions.

Recent advances in 3D SEM surface reconstruction.

PubMed

Tafti, Ahmad P; Kirkpatrick, Andrew B; Alavi, Zahrasadat; Owen, Heather A; Yu, Zeyun

2015-11-01

The scanning electron microscope (SEM), as one of the most commonly used instruments in biology and material sciences, employs electrons instead of light to determine the surface properties of specimens. However, the SEM micrographs still remain 2D images. To effectively measure and visualize the surface attributes, we need to restore the 3D shape model from the SEM images. 3D surface reconstruction is a longstanding topic in microscopy vision as it offers quantitative and visual information for a variety of applications consisting medicine, pharmacology, chemistry, and mechanics. In this paper, we attempt to explain the expanding body of the work in this area, including a discussion of recent techniques and algorithms. With the present work, we also enhance the reliability, accuracy, and speed of 3D SEM surface reconstruction by designing and developing an optimized multi-view framework. We then consider several real-world experiments as well as synthetic data to examine the qualitative and quantitative attributes of our proposed framework. Furthermore, we present a taxonomy of 3D SEM surface reconstruction approaches and address several challenging issues as part of our future work. Copyright © 2015 Elsevier Ltd. All rights reserved.

Paleosol Proxies for Low Elevation Paleoclimate East of the Andes, Northwestern Argentina

NASA Astrophysics Data System (ADS)

Rosario, J. J.; Jordan, T. E.; Garzione, C. N.; Higgins, P.; Hernandez, R.; Hernandez, J.

2009-12-01

Paleosols can be used as a proxy for paleoclimate, paleoenvironment, and geomorphological reconstructions. The weathering imprint in the minerals in paleosols can be used as a proxy for moisture conditions, while other environmental information can be obtained from stable isotopes in their minerals such as δ13C and δ18O. The goal of this study is to document changes in paleosol characteristics’ driven by climate change in NW Argentina over the time period between ~14 Ma and 5.1 Ma during a time of significant uplift and climate change in the Altiplano. During this time interval, landscape of the low elevation foreland basin changed as the consequence of the propagation of Andean thrust-fold deformation. Paleosols are interbedded in three stratigraphic sections that are described, sampled, and studied along the Iruya, Peña Colorada, and La Porcelana rivers, distributed from west to east, respectively. Field observations of the paleosols, stratigraphic column construction, thin section petrography and textures, x-ray diffraction (XRD), and stable isotopes together provide climatic proxies. These The stratigraphic columns represent a distributary depositional system, or megafan, whose syn-deformational nature is documented by Echevarría et al. (2003). Argillic-calcic paleosols developed on silty and sandy mudstones in the floodplain environment, with pedogenic calcium carbonate formed as nodules and rizoliths. The Microscopic features show that paleosols on the floodplain contain argillans. Semi-humid to semi-arid conditions are suggested by clay lessivage and calcium carbonate precipitation respectively. The mineralogy reflected by the XRD shows kaolinite, illite, and calcium carbonate in the western stratigraphic column that represents moderate climatic conditions (semi-humid to semi-arid). The coexistence of these minerals suggests seasonal variations in moisture. The eastern columns exhibit wetter soil conditions, including oxide minerals as well as hematite

Autogenic geomorphic processes determine the resolution and fidelity of terrestrial paleoclimate records.

PubMed

Foreman, Brady Z; Straub, Kyle M

2017-09-01

Terrestrial paleoclimate records rely on proxies hosted in alluvial strata whose beds are deposited by unsteady and nonlinear geomorphic processes. It is broadly assumed that this renders the resultant time series of terrestrial paleoclimatic variability noisy and incomplete. We evaluate this assumption using a model of oscillating climate and the precise topographic evolution of an experimental alluvial system. We find that geomorphic stochasticity can create aliasing in the time series and spurious climate signals, but these issues are eliminated when the period of climate oscillation is longer than a key time scale of internal dynamics in the geomorphic system. This emergent autogenic geomorphic behavior imparts regularity to deposition and represents a natural discretization interval of the continuous climate signal. We propose that this time scale in nature could be in excess of 10 4 years but would still allow assessments of the rates of climate change at resolutions finer than the existing age model techniques in isolation.

Autogenic geomorphic processes determine the resolution and fidelity of terrestrial paleoclimate records

PubMed Central

Foreman, Brady Z.; Straub, Kyle M.

2017-01-01

Terrestrial paleoclimate records rely on proxies hosted in alluvial strata whose beds are deposited by unsteady and nonlinear geomorphic processes. It is broadly assumed that this renders the resultant time series of terrestrial paleoclimatic variability noisy and incomplete. We evaluate this assumption using a model of oscillating climate and the precise topographic evolution of an experimental alluvial system. We find that geomorphic stochasticity can create aliasing in the time series and spurious climate signals, but these issues are eliminated when the period of climate oscillation is longer than a key time scale of internal dynamics in the geomorphic system. This emergent autogenic geomorphic behavior imparts regularity to deposition and represents a natural discretization interval of the continuous climate signal. We propose that this time scale in nature could be in excess of 104 years but would still allow assessments of the rates of climate change at resolutions finer than the existing age model techniques in isolation. PMID:28924607

Predicting supramolecular self-assembly on reconstructed metal surfaces

NASA Astrophysics Data System (ADS)

Roussel, Thomas J.; Barrena, Esther; Ocal, Carmen; Faraudo, Jordi

2014-06-01

The prediction of supramolecular self-assembly onto solid surfaces is still challenging in many situations of interest for nanoscience. In particular, no previous simulation approach has been capable to simulate large self-assembly patterns of organic molecules over reconstructed surfaces (which have periodicities over large distances) due to the large number of surface atoms and adsorbing molecules involved. Using a novel simulation technique, we report here large scale simulations of the self-assembly patterns of an organic molecule (DIP) over different reconstructions of the Au(111) surface. We show that on particular reconstructions, the molecule-molecule interactions are enhanced in a way that long-range order is promoted. Also, the presence of a distortion in a reconstructed surface pattern not only induces the presence of long-range order but also is able to drive the organization of DIP into two coexisting homochiral domains, in quantitative agreement with STM experiments. On the other hand, only short range order is obtained in other reconstructions of the Au(111) surface. The simulation strategy opens interesting perspectives to tune the supramolecular structure by simulation design and surface engineering if choosing the right molecular building blocks and stabilising the chosen reconstruction pattern.The prediction of supramolecular self-assembly onto solid surfaces is still challenging in many situations of interest for nanoscience. In particular, no previous simulation approach has been capable to simulate large self-assembly patterns of organic molecules over reconstructed surfaces (which have periodicities over large distances) due to the large number of surface atoms and adsorbing molecules involved. Using a novel simulation technique, we report here large scale simulations of the self-assembly patterns of an organic molecule (DIP) over different reconstructions of the Au(111) surface. We show that on particular reconstructions, the molecule

Computer-assisted midface reconstruction in Treacher Collins syndrome part 1: skeletal reconstruction.

PubMed

Herlin, Christian; Doucet, Jean Charles; Bigorre, Michèle; Khelifa, Hatem Cheikh; Captier, Guillaume

2013-10-01

Treacher Collins syndrome (TCS) is a severe and complex craniofacial malformation affecting the facial skeleton and soft tissues. The palate as well as the external and middle ear are also affected, but his prognosis is mainly related to neonatal airway management. Methods of zygomatico-orbital reconstruction are numerous and currently use primarily autologous bone, lyophilized cartilage, alloplastic implants, or even free flaps. This work developed a reliable "customized" method of zygomatico-orbital bony reconstruction using a generic reference model tailored to each patient. From a standard computed tomography (CT) acquisition, we studied qualitatively and quantitatively the skeleton of four individuals with TCS whose age was between 6 and 20 years. In parallel, we studied 40 controls at the same age to obtain a morphometric database of reference. Surgical simulation was carried out using validated software used in craniofacial surgery. The zygomatic hypoplasia was very important quantitatively and morphologically in all TCS individuals. Orbital involvement was mainly morphological, with volumes comparable to the controls of the same age. The control database was used to create three-dimensional computer models to be used in the manufacture of cutting guides for autologous cranial bone grafts or alloplastic implants perfectly adapted to each patient's morphology. Presurgical simulation was also used to fabricate custom positioning guides permitting a simple and reliable surgical procedure. The use of a virtual database allowed us to design a reliable and reproducible skeletal reconstruction method for this rare and complex syndrome. The use of presurgical simulation tools seem essential in this type of craniofacial malformation to increase the reliability of these uncommon and complex surgical procedures, and to ensure stable results over time. Copyright © 2013 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights

Estimation of 3D reconstruction errors in a stereo-vision system

NASA Astrophysics Data System (ADS)

Belhaoua, A.; Kohler, S.; Hirsch, E.

2009-06-01

The paper presents an approach for error estimation for the various steps of an automated 3D vision-based reconstruction procedure of manufactured workpieces. The process is based on a priori planning of the task and built around a cognitive intelligent sensory system using so-called Situation Graph Trees (SGT) as a planning tool. Such an automated quality control system requires the coordination of a set of complex processes performing sequentially data acquisition, its quantitative evaluation and the comparison with a reference model (e.g., CAD object model) in order to evaluate quantitatively the object. To ensure efficient quality control, the aim is to be able to state if reconstruction results fulfill tolerance rules or not. Thus, the goal is to evaluate independently the error for each step of the stereo-vision based 3D reconstruction (e.g., for calibration, contour segmentation, matching and reconstruction) and then to estimate the error for the whole system. In this contribution, we analyze particularly the segmentation error due to localization errors for extracted edge points supposed to belong to lines and curves composing the outline of the workpiece under evaluation. The fitting parameters describing these geometric features are used as quality measure to determine confidence intervals and finally to estimate the segmentation errors. These errors are then propagated through the whole reconstruction procedure, enabling to evaluate their effect on the final 3D reconstruction result, specifically on position uncertainties. Lastly, analysis of these error estimates enables to evaluate the quality of the 3D reconstruction, as illustrated by the shown experimental results.

Magnetic Resonance-based Motion Correction for Quantitative PET in Simultaneous PET-MR Imaging.

PubMed

Rakvongthai, Yothin; El Fakhri, Georges

2017-07-01

Motion degrades image quality and quantitation of PET images, and is an obstacle to quantitative PET imaging. Simultaneous PET-MR offers a tool that can be used for correcting the motion in PET images by using anatomic information from MR imaging acquired concurrently. Motion correction can be performed by transforming a set of reconstructed PET images into the same frame or by incorporating the transformation into the system model and reconstructing the motion-corrected image. Several phantom and patient studies have validated that MR-based motion correction strategies have great promise for quantitative PET imaging in simultaneous PET-MR. Copyright © 2017 Elsevier Inc. All rights reserved.

Real-time quasi-3D tomographic reconstruction

NASA Astrophysics Data System (ADS)

Buurlage, Jan-Willem; Kohr, Holger; Palenstijn, Willem Jan; Joost Batenburg, K.

2018-06-01

Developments in acquisition technology and a growing need for time-resolved experiments pose great computational challenges in tomography. In addition, access to reconstructions in real time is a highly demanded feature but has so far been out of reach. We show that by exploiting the mathematical properties of filtered backprojection-type methods, having access to real-time reconstructions of arbitrarily oriented slices becomes feasible. Furthermore, we present , software for visualization and on-demand reconstruction of slices. A user of can interactively shift and rotate slices in a GUI, while the software updates the slice in real time. For certain use cases, the possibility to study arbitrarily oriented slices in real time directly from the measured data provides sufficient visual and quantitative insight. Two such applications are discussed in this article.

Major Evolutionary Trends in Hydrogen Isotope Fractionation of Vascular Plant Leaf Waxes

PubMed Central

Gao, Li; Edwards, Erika J.; Zeng, Yongbo; Huang, Yongsong

2014-01-01

Hydrogen isotopic ratios of terrestrial plant leaf waxes (δD) have been widely used for paleoclimate reconstructions. However, underlying controls for the observed large variations in leaf wax δD values in different terrestrial vascular plants are still poorly understood, hampering quantitative paleoclimate interpretation. Here we report plant leaf wax and source water δD values from 102 plant species grown in a common environment (New York Botanic Garden), chosen to represent all the major lineages of terrestrial vascular plants and multiple origins of common plant growth forms. We found that leaf wax hydrogen isotope fractionation relative to plant source water is best explained by membership in particular lineages, rather than by growth forms as previously suggested. Monocots, and in particular one clade of grasses, display consistently greater hydrogen isotopic fractionation than all other vascular plants, whereas lycopods, representing the earlier-diverging vascular plant lineage, display the smallest fractionation. Data from greenhouse experiments and field samples suggest that the changing leaf wax hydrogen isotopic fractionation in different terrestrial vascular plants may be related to different strategies in allocating photosynthetic substrates for metabolic and biosynthetic functions, and potential leaf water isotopic differences. PMID:25402476

Weight Multispectral Reconstruction Strategy for Enhanced Reconstruction Accuracy and Stability With Cerenkov Luminescence Tomography.

PubMed

Hongbo Guo; Xiaowei He; Muhan Liu; Zeyu Zhang; Zhenhua Hu; Jie Tian

2017-06-01

Cerenkov luminescence tomography (CLT) provides a novel technique for 3-D noninvasive detection of radiopharmaceuticals in living subjects. However, because of the severe scattering of Cerenkov light, the reconstruction accuracy and stability of CLT is still unsatisfied. In this paper, a modified weight multispectral CLT (wmCLT) reconstruction strategy was developed which split the Cerenkov radiation spectrum into several sub-spectral bands and weighted the sub-spectral results to obtain the final result. To better evaluate the property of the wmCLT reconstruction strategy in terms of accuracy, stability and practicability, several numerical simulation experiments and in vivo experiments were conducted and the results obtained were compared with the traditional multispectral CLT (mCLT) and hybrid-spectral CLT (hCLT) reconstruction strategies. The numerical simulation results indicated that wmCLT strategy significantly improved the accuracy of Cerenkov source localization and intensity quantitation and exhibited good stability in suppressing noise in numerical simulation experiments. And the comparison of the results achieved from different in vivo experiments further indicated significant improvement of the wmCLT strategy in terms of the shape recovery of the bladder and the spatial resolution of imaging xenograft tumors. Overall the strategy reported here will facilitate the development of nuclear and optical molecular tomography in theoretical study.

Dynamic PET image reconstruction integrating temporal regularization associated with respiratory motion correction for applications in oncology

NASA Astrophysics Data System (ADS)

Merlin, Thibaut; Visvikis, Dimitris; Fernandez, Philippe; Lamare, Frédéric

2018-02-01

Respiratory motion reduces both the qualitative and quantitative accuracy of PET images in oncology. This impact is more significant for quantitative applications based on kinetic modeling, where dynamic acquisitions are associated with limited statistics due to the necessity of enhanced temporal resolution. The aim of this study is to address these drawbacks, by combining a respiratory motion correction approach with temporal regularization in a unique reconstruction algorithm for dynamic PET imaging. Elastic transformation parameters for the motion correction are estimated from the non-attenuation-corrected PET images. The derived displacement matrices are subsequently used in a list-mode based OSEM reconstruction algorithm integrating a temporal regularization between the 3D dynamic PET frames, based on temporal basis functions. These functions are simultaneously estimated at each iteration, along with their relative coefficients for each image voxel. Quantitative evaluation has been performed using dynamic FDG PET/CT acquisitions of lung cancer patients acquired on a GE DRX system. The performance of the proposed method is compared with that of a standard multi-frame OSEM reconstruction algorithm. The proposed method achieved substantial improvements in terms of noise reduction while accounting for loss of contrast due to respiratory motion. Results on simulated data showed that the proposed 4D algorithms led to bias reduction values up to 40% in both tumor and blood regions for similar standard deviation levels, in comparison with a standard 3D reconstruction. Patlak parameter estimations on reconstructed images with the proposed reconstruction methods resulted in 30% and 40% bias reduction in the tumor and lung region respectively for the Patlak slope, and a 30% bias reduction for the intercept in the tumor region (a similar Patlak intercept was achieved in the lung area). Incorporation of the respiratory motion correction using an elastic model along with a

Dynamic PET image reconstruction integrating temporal regularization associated with respiratory motion correction for applications in oncology.

PubMed

Merlin, Thibaut; Visvikis, Dimitris; Fernandez, Philippe; Lamare, Frédéric

2018-02-13

Respiratory motion reduces both the qualitative and quantitative accuracy of PET images in oncology. This impact is more significant for quantitative applications based on kinetic modeling, where dynamic acquisitions are associated with limited statistics due to the necessity of enhanced temporal resolution. The aim of this study is to address these drawbacks, by combining a respiratory motion correction approach with temporal regularization in a unique reconstruction algorithm for dynamic PET imaging. Elastic transformation parameters for the motion correction are estimated from the non-attenuation-corrected PET images. The derived displacement matrices are subsequently used in a list-mode based OSEM reconstruction algorithm integrating a temporal regularization between the 3D dynamic PET frames, based on temporal basis functions. These functions are simultaneously estimated at each iteration, along with their relative coefficients for each image voxel. Quantitative evaluation has been performed using dynamic FDG PET/CT acquisitions of lung cancer patients acquired on a GE DRX system. The performance of the proposed method is compared with that of a standard multi-frame OSEM reconstruction algorithm. The proposed method achieved substantial improvements in terms of noise reduction while accounting for loss of contrast due to respiratory motion. Results on simulated data showed that the proposed 4D algorithms led to bias reduction values up to 40% in both tumor and blood regions for similar standard deviation levels, in comparison with a standard 3D reconstruction. Patlak parameter estimations on reconstructed images with the proposed reconstruction methods resulted in 30% and 40% bias reduction in the tumor and lung region respectively for the Patlak slope, and a 30% bias reduction for the intercept in the tumor region (a similar Patlak intercept was achieved in the lung area). Incorporation of the respiratory motion correction using an elastic model along with a

Global Paleobathymetry Reconstruction with Realistic Shelf-Slope and Sediment Wedge

NASA Astrophysics Data System (ADS)

Goswami, A.; Hinnov, L. A.; Gnanadesikan, A.; Olson, P.

2013-12-01

We present paleo-ocean bathymetry reconstructions in a 0.1°x0.1° resolution, using simple geophysical models (Plate Model Equation for oceanic lithosphere), published ages of the ocean floor (Müller et al. 2008), and modern world sediment thickness data (Divins 2003). The motivation is to create realistic paleobathymetry to understand the effect of ocean floor roughness on tides and heat transport in paleoclimate simulations. The values for the parameters in the Plate Model Equation are deduced from Crosby et al. (2006) and are used together with ocean floor age to model Depth to Basement. On top of the Depth to Basement, we added an isostatically adjusted multilayer sediment layer, as indicated from sediment thickness data of the modern oceans and marginal seas (Divins 2003). We also created another version of the sediment layer from the Müller et al. dataset. The Depth to Basement with the appropriate sediment layer together represent a realistic paleobathymetry. A Sediment Wedge was modeled to complement the reconstructed paleobathymetry by extending it to the coastlines. In this process we added a modeled Continental Shelf and Continental Slope to match the extent of the reconstructed paleobathymetry. The Sediment Wedge was prepared by studying the modern ocean where a complete history of seafloor spreading is preserved (north, south and central Atlantic Ocean, Southern Ocean between Australia-Antarctica, and the Pacific Ocean off the west coast of South America). The model takes into account the modern continental shelf-slope structure (as evident from ETOPO1/ETOPO5), tectonic margin type (active vs. passive margin) and age of the latest tectonic activity (USGS & CGMW). Once the complete ocean bathymetry is modeled, we combine it with PALEOMAP (Scotese, 2011) continental reconstructions to produce global paleoworld elevation-bathymetry maps. Modern time (00 Ma) was assumed as a test case. Using the above-described methodology we reconstructed modern ocean

Multiproxy Holocene paleoclimate records from the southern Peruvian Andes - what new can we learn from the stable carbon isotope composition of high altitude organic matter deposits?

NASA Astrophysics Data System (ADS)

Skrzypek, Grzegorz; Engel, Zbyněk

2015-04-01

Interpretation of the Central Andean paleoclimate over the last millennia still represents a research challenge demanding deeper studies [1,2]. Several high-resolution paleoclimate proxies for the last 10,000 years have been developed for the northern hemisphere. However, similar proxies are very limited for South America, particularly for high altitudes where, for example, tree-ring chronologies are not available and instrumental records are very limited. Consequently, our knowledge of high altitude climate changes in arid regions of the Peruvian Andes mainly relies on ice-core and lake deposit studies. In our study, we used a new alternative proxy for interpretation of palaeoclimate conditions based on a peat core taken from the Carhuasanta Valley at the foot of Nevado Mismi in the southern Peruvian Andes (15° 30'S, 71° 43'W, 4809m a.s.l.). The stable carbon isotope composition (δ13C) of Distichia peat reflects mainly the relative variation of the mean air temperature during subsequent growing seasons [3], and allows reconstructions of palaeotemperature changes. In contrast, peat organic carbon concentration (C % wt) records mainly wetness in the valley, directly corresponding to the changes in runoff in the upper part of the catchment. The most prominent climate changes recorded in the peat over last 4ka occurred between 3040 and 2750 cal. yrs BP. The initial warming turned to a very rapid cooling to temperatures at least 2° C lower than the mean for the Late Holocene. Initially drier conditions within this event turned to a short wet phase after 2780 cal. yrs BP, when the temperature increased again. This event coincides with significant changes in peat and ice core records in the Central Andes that match the timing of the global climate event around 2.8 cal. ka BP. Climatic conditions in the study area became relatively dry and stable after the event for about 800 years. Highly variable temperatures and humidity prevailed during the last 2000 years, when

Climatic and environmental controls on speleothem oxygen-isotope values

NASA Astrophysics Data System (ADS)

Lachniet, Matthew S.

2009-03-01

Variations in speleothem oxygen-isotope values ( δ18O) result from a complicated interplay of environmental controls and processes in the ocean, atmosphere, soil zone, epikarst, and cave system. As such, the controls on speleothem δ18O values are extremely complex. An understanding of the processes that control equilibrium and kinetic fractionation of oxygen isotopes in water and carbonate species is essential for the proper interpretation of speleothem δ18O as paleoclimate and paleoenvironmental proxies, and is best complemented by study of site-specific cave processes such as infiltration, flow routing, drip seasonality and saturation state, and cave microclimate, among others. This review is a process-based summary of the multiple controls on δ18O in the atmosphere, soil, epikarst, and speleothem calcite, illustrated with case studies. Primary controls of δ18O in the atmosphere include temperature and relative humidity through their role in the multiple isotope "effects". Variability and modifications of water δ18O values in the soil and epikarst zones are dominated by evaporation, mixing, and infiltration of source waters. The isotopically effective recharge into a cave system consists of those waters that participate in precipitation of CaCO 3, resulting in calcite deposition rates which may be biased to time periods with optimal dripwater saturation state. Recent modeling, experimental, and observational data yield insight into the significance of kinetic fractionation between dissolved carbonate phases and solid CaCO 3, and have implications for the 'Hendy' test. To assist interpretation of speleothem δ18O time series, quantitative and semi-quantitative δ18O-climate calibrations are discussed with an emphasis on some of the difficulties inherent in using modern spatial and temporal isotope gradients to interpret speleothems as paleoclimate proxy records. Finally, several case studies of globally significant speleothem paleoclimate records are

Quantitative IR microscopy and spectromics open the way to 3D digital pathology.

PubMed

Bobroff, Vladimir; Chen, Hsiang-Hsin; Delugin, Maylis; Javerzat, Sophie; Petibois, Cyril

2017-04-01

Currently, only mass-spectrometry (MS) microscopy brings a quantitative analysis of chemical contents of tissue samples in 3D. Here, the reconstruction of a 3D quantitative chemical images of a biological tissue by FTIR spectro-microscopy is reported. An automated curve-fitting method is developed to extract all intense absorption bands constituting IR spectra. This innovation benefits from three critical features: (1) the correction of raw IR spectra to make them quantitatively comparable; (2) the automated and iterative data treatment allowing to transfer the IR-absorption spectrum into a IR-band spectrum; (3) the reconstruction of an 3D IR-band matrix (x, y, z for voxel position and a 4 th dimension with all IR-band parameters). Spectromics, which is a new method for exploiting spectral data for tissue metadata reconstruction, is proposed to further translate the related chemical information in 3D, as biochemical and anatomical tissue parameters. An example is given with oxidative stress distribution and the reconstruction of blood vessels in tissues. The requirements of IR microscopy instrumentation to propose 3D digital histology as a clinical routine technology is briefly discussed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pollen-Based Inverse Modelling versus Data Assimilation, two Different Ways to Consider Priors in Paleoclimate Reconstruction: Application to the Mediterranean Holocene

NASA Astrophysics Data System (ADS)

Guiot, J.

2017-12-01

In the last decades, climate reconstruction has much evolved. A important step has been passed with inverse modelling approach proposed by Guiot et al (2000). It is based on appropriate algorithms in the frame of the Bayesian statistical theory to estimate the inputs of a vegetation model when the outputs are known. The inputs are the climate variables that we want to reconstruct and the outputs are vegetation characteristics, which can be compared to pollen data. The Bayesian framework consists in defining prior distribution of the wanted climate variables and in using data and a model to estimate posterior probability distribution. The main interest of the method is the possibility to set different values of exogenous variables as the atmospheric CO2 concentration. The fact that the CO2 concentration has an influence on the photosynthesis and that its level is different between the calibration period (the 20th century) and the past, there is an important risk of biases on the reconstructions. After that initial paper, numerous papers have been published showing the interested of the method. In that approach, the prior distribution is fixed by educated guess of by using complementary information on the expected climate (other proxies or other records). In the data assimilation approach, the prior distribution is provided by a climate model. The use of a vegetation model together with proxy data, enable to calculate posterior distributions. Data assimilation consists in constraining climate model to reproduce estimates relatively close to the data, taking into account the respective errors of the data and of the climate model (Dubinkina et al, 2011). We compare both approaches using pollen data for the Holocene from the Mediterranean. Pollen data have been extracted from the European Pollen Database. The earth system model, LOVECLIM, is run to simulate Holocene climate with appropriate boundary conditions and realistic forcing. Simulated climate variables

Ice cores and calcite precipitates from alpine ice caves as useful proxies in paleoclimate reconstructions

NASA Astrophysics Data System (ADS)

Colucci, Renato R.; Barbante, Carlo; Bertò, Michele; Dreossi, Giuliano; Festi, Daniela; Forte, Emanuele; Gabrieli, Jacopo; Guglielmin, Mauro; Lenaz, Davide; Luetscher, Marc; Maggi, Valter; Princivalle, Francesco; Schwikowski, Margit; Stenni, Barbara; Žebre, Manja

2017-04-01

In the last years a growing set of research campaigns have been undertaken in the European southeastern Alps. The aim of such interest is mainly due to the peculiar climatic conditions of this area, allowing the existence of periglacial and glacial evidence at the lowest altitude in the Alps. The reason for such "anomaly" is likely ascribable to very high mean annual precipitation and local topoclimatic amplifications. In the frame of this research, in the fall 2013 a 7.8 m long ice-core has been extracted from a permanent cave ice deposit located in the area of Mt. Canin (2,587 masl) in the Julian Alps. The ice-core has been cut and analysed in terms of: a) oxygen and hydrogen isotope composition; b); black carbon and dust concentrations; c) water conductivity; d) mineralogical analyses via X-ray powder diffraction. In the fall 2016, in the same area, a set of 1.0 m long horizontal ice cores have been extracted in another ice cave deposit, intercepting a preserved layer of coarse cryogenic cave carbonates (CCCcoarse). Such original finding represents the first alpine evidence of in situ CCCcoarse and the first occurrence from the southern side of the Alps. A unique opportunity to better understand the processes associated with the formation of CCCcoarse and the well-preserved status of samples allow planning, besides U/Th datings, several different analyses which may be associated with the precipitation of CCC. Subglacial calcite crusts, widespread in the area, represents a further proxy able to help understanding the evolution of climate during the holocene in this alpine sector. In the light of accelerated climate change we discuss here the potential of this still untapped and fragile cryospheric archives for paleoclimatic reconstructions in high elevated areas of the Alps.

Climate Reconstructions of the Younger Dryas: An ELA Model Investigating Variability in ELA Depressions, Temperature, and Precipitation Changes for the Graubϋnden Alps

NASA Astrophysics Data System (ADS)

Keeler, D. G.; Rupper, S.; Schaefer, J. M.; Finkel, R. C.

2015-12-01

The high sensitivity of mountain glaciers to even small perturbations in climate, combined with a near global distribution, make alpine glaciers an important target for terrestrial paleoclimate reconstructions. The geomorphic remnant of past glaciers can yield important insights into past climate, particularly in regions where other methods of reconstruction are not possible. The quantitative conversion of these changes in geomorphology to a climate signal, however, presents a significant challenge. A particular need exists for a versatile climate reconstruction method applicable to diverse glacierized regions around the globe. Because the glacier equilibrium line altitude (ELA) provides a more explicit comparison of climate than properties such as glacier length or area, ELA methods lend themselves well to such a need, and allow for a more direct investigation of the primary drivers of mountain glaciations during specific events. Here, we present an ELA model for quantifying changes in climate based on changes in glacier extent, while accounting for differences in glacier width, glacier shape, bed topography, ice thickness, and glacier length. The model furthermore provides bounds on the ΔELA using Monte Carlo simulations. These methods are validated using published mass balances and ELA measurements from 4 modern glaciers in the European Alps. We then use this ELA model, combined with a surface mass and energy balance model, to estimate the changes in temperature/precipitation between the Younger Dryas (constrained by 10Be surface exposure ages) and the present day for three glacier systems in the Graubϋnden Alps. Our results indicate an ELA depression in this area of 257 m ±45 m during the Younger Dryas (YD) relative to today. This corresponds to a 1.3 °C ±0.36 °C decrease in temperature or a 156% ±30% increase in precipitation relative to today. These results indicate the likelihood of a predominantly temperature-driven change rather than a strong

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 to the

Reconstruction of multistage massive rock slope failure: Polymethodical approach in Lake Oeschinen (CH)

NASA Astrophysics Data System (ADS)

Knapp, Sibylle; Gilli, Adrian; Anselmetti, Flavio S.; Hajdas, Irka

2016-04-01

Lateglacial and Holocene rock-slope failures occur often as multistage failures where paraglacial adjustment and stress adaptation are hypothesised to control stages of detachment. However, we have only limited datasets to reconstruct detailed stages of large multistage rock-slope failures, and still aim at improving our models in terms of geohazard assessment. Here we use lake sediments, well-established for paleoclimate and paleoseismological reconstruction, with a focus on the reconstruction of rock-slope failures. We present a unique inventory from Lake Oeschinen (Bernese Alps, Switzerland) covering about 2.4 kyrs of rock-slope failure history. The lake sediments have been analysed using sediment-core analysis, radiocarbon dating and seismic-to-core and core-to-core correlations, and these were linked to historical and meteorological records. The results imply that the lake is significantly younger than the ~9 kyrs old Kandersteg rock avalanche (Tinner et al., 2005) and shows multiple rock-slope failures, two of which could be C14-dated. Several events detached from the same area potentially initiated by prehistoric earthquakes (Monecke et al., 2006) and later from stress relaxation processes. The data imply unexpected short recurrence rates that can be related to certain detachment scarps and also help to understand the generation of a historical lake-outburst flood. Here we show how polymethodical analysis of lake sediments can help to decipher massive multistage rock-slope failure. References Monecke, K., Anselmetti, F.S., Becker, A., Schnellmann, M., Sturm, M., Giardini, D., 2006. Earthquake-induced deformation structures in lake deposits: A Late Pleistocene to Holocene paleoseismic record for Central Switzerland. Eclogae Geologicae Helvetiae, 99(3), 343-362. Tinner, W., Kaltenrieder, P., Soom, M., Zwahlen, P., Schmidhalter, M., Boschetti, A., Schlüchter, C., 2005. Der nacheiszeitliche Bergsturz im Kandertal (Schweiz): Alter und Auswirkungen auf die

A biomechanical modeling-guided simultaneous motion estimation and image reconstruction technique (SMEIR-Bio) for 4D-CBCT reconstruction

NASA Astrophysics Data System (ADS)

Huang, Xiaokun; Zhang, You; Wang, Jing

2018-02-01

Reconstructing four-dimensional cone-beam computed tomography (4D-CBCT) images directly from respiratory phase-sorted traditional 3D-CBCT projections can capture target motion trajectory, reduce motion artifacts, and reduce imaging dose and time. However, the limited numbers of projections in each phase after phase-sorting decreases CBCT image quality under traditional reconstruction techniques. To address this problem, we developed a simultaneous motion estimation and image reconstruction (SMEIR) algorithm, an iterative method that can reconstruct higher quality 4D-CBCT images from limited projections using an inter-phase intensity-driven motion model. However, the accuracy of the intensity-driven motion model is limited in regions with fine details whose quality is degraded due to insufficient projection number, which consequently degrades the reconstructed image quality in corresponding regions. In this study, we developed a new 4D-CBCT reconstruction algorithm by introducing biomechanical modeling into SMEIR (SMEIR-Bio) to boost the accuracy of the motion model in regions with small fine structures. The biomechanical modeling uses tetrahedral meshes to model organs of interest and solves internal organ motion using tissue elasticity parameters and mesh boundary conditions. This physics-driven approach enhances the accuracy of solved motion in the organ’s fine structures regions. This study used 11 lung patient cases to evaluate the performance of SMEIR-Bio, making both qualitative and quantitative comparisons between SMEIR-Bio, SMEIR, and the algebraic reconstruction technique with total variation regularization (ART-TV). The reconstruction results suggest that SMEIR-Bio improves the motion model’s accuracy in regions containing small fine details, which consequently enhances the accuracy and quality of the reconstructed 4D-CBCT images.

Analyser-based phase contrast image reconstruction using geometrical optics.

PubMed

Kitchen, M J; Pavlov, K M; Siu, K K W; Menk, R H; Tromba, G; Lewis, R A

2007-07-21

Analyser-based phase contrast imaging can provide radiographs of exceptional contrast at high resolution (<100 microm), whilst quantitative phase and attenuation information can be extracted using just two images when the approximations of geometrical optics are satisfied. Analytical phase retrieval can be performed by fitting the analyser rocking curve with a symmetric Pearson type VII function. The Pearson VII function provided at least a 10% better fit to experimentally measured rocking curves than linear or Gaussian functions. A test phantom, a hollow nylon cylinder, was imaged at 20 keV using a Si(1 1 1) analyser at the ELETTRA synchrotron radiation facility. Our phase retrieval method yielded a more accurate object reconstruction than methods based on a linear fit to the rocking curve. Where reconstructions failed to map expected values, calculations of the Takagi number permitted distinction between the violation of the geometrical optics conditions and the failure of curve fitting procedures. The need for synchronized object/detector translation stages was removed by using a large, divergent beam and imaging the object in segments. Our image acquisition and reconstruction procedure enables quantitative phase retrieval for systems with a divergent source and accounts for imperfections in the analyser.

MR Guided PET Image Reconstruction

PubMed Central

Bai, Bing; Li, Quanzheng; Leahy, Richard M.

2013-01-01

The resolution of PET images is limited by the physics of positron-electron annihilation and instrumentation for photon coincidence detection. Model based methods that incorporate accurate physical and statistical models have produced significant improvements in reconstructed image quality when compared to filtered backprojection reconstruction methods. However, it has often been suggested that by incorporating anatomical information, the resolution and noise properties of PET images could be improved, leading to better quantitation or lesion detection. With the recent development of combined MR-PET scanners, it is possible to collect intrinsically co-registered MR images. It is therefore now possible to routinely make use of anatomical information in PET reconstruction, provided appropriate methods are available. In this paper we review research efforts over the past 20 years to develop these methods. We discuss approaches based on the use of both Markov random field priors and joint information or entropy measures. The general framework for these methods is described and their performance and longer term potential and limitations discussed. PMID:23178087

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

Temperature reconstruction for the Tibetan Plateau in the past 2ka years from ice cores and human documentary record

NASA Astrophysics Data System (ADS)

Yang, X.

2011-12-01

Temperature variation in the past 2000 years on the plateau is reconstructed from Puruogangri ice core d18O, and compared before compositing with other three ice core records as the Dunde ice core (northeast Plateau), Guliya ice core (northwest Plateau) and Dasuopu ice core (south Plateau). The comparison reveals the synchroneity of large-scale climate events, and the composition highlights the warming in the 7th century and 12-13th centuries, and the cold in the 19th century. We searched for historical documentary about Tibet since A.D. 620, extracting record of human activities and social development directly determined or indirectly influenced by climate, and categorizing it into five aspects as basic resources, economic development, military strength, national coherence, and cultural and religious development, to quantify Tibetan development till A.D. 1900. Curve based upon the sum of the five aspects shows Tibetan national strength variation in the past 2000 years. The composited ice core record and Tibetan national strength variation shows consistency, especially during the Songtsen Gampo reign, medieval warm period and the 19th century cold period, thus suggesting the dominative role of climate change in Tibetan civilization before modern ages, as well as proposing the potential application of historical record in paleoclimate reconstruction on the Tibetan Plateau.

Optimization of CT image reconstruction algorithms for the lung tissue research consortium (LTRC)

NASA Astrophysics Data System (ADS)

McCollough, Cynthia; Zhang, Jie; Bruesewitz, Michael; Bartholmai, Brian

2006-03-01

To create a repository of clinical data, CT images and tissue samples and to more clearly understand the pathogenetic features of pulmonary fibrosis and emphysema, the National Heart, Lung, and Blood Institute (NHLBI) launched a cooperative effort known as the Lung Tissue Resource Consortium (LTRC). The CT images for the LTRC effort must contain accurate CT numbers in order to characterize tissues, and must have high-spatial resolution to show fine anatomic structures. This study was performed to optimize the CT image reconstruction algorithms to achieve these criteria. Quantitative analyses of phantom and clinical images were conducted. The ACR CT accreditation phantom containing five regions of distinct CT attenuations (CT numbers of approximately -1000 HU, -80 HU, 0 HU, 130 HU and 900 HU), and a high-contrast spatial resolution test pattern, was scanned using CT systems from two manufacturers (General Electric (GE) Healthcare and Siemens Medical Solutions). Phantom images were reconstructed using all relevant reconstruction algorithms. Mean CT numbers and image noise (standard deviation) were measured and compared for the five materials. Clinical high-resolution chest CT images acquired on a GE CT system for a patient with diffuse lung disease were reconstructed using BONE and STANDARD algorithms and evaluated by a thoracic radiologist in terms of image quality and disease extent. The clinical BONE images were processed with a 3 x 3 x 3 median filter to simulate a thicker slice reconstructed in smoother algorithms, which have traditionally been proven to provide an accurate estimation of emphysema extent in the lungs. Using a threshold technique, the volume of emphysema (defined as the percentage of lung voxels having a CT number lower than -950 HU) was computed for the STANDARD, BONE, and BONE filtered. The CT numbers measured in the ACR CT Phantom images were accurate for all reconstruction kernels for both manufacturers. As expected, visual evaluation of the

Reconstructing Common Era Climate Fields Using Data Assimilation, Proxies, and a Linear Climate Model

NASA Astrophysics Data System (ADS)

Perkins, W. A.; Hakim, G. J.

2016-12-01

In this work, we examine the skill of a new approach to performing climate field reconstructions (CFRs) using a form of online paleoclimate data assimilation (PDA). Many previous studies have foregone climate model forecasts during assimilation due to the computational expense of running coupled global climate models (CGCMs), and the relatively low skill of these forecasts on longer timescales. Here we greatly diminish the computational costs by employing an empirical forecast model (known as a linear inverse model; LIM), which has been shown to have comparable skill to CGCMs. CFRs of annually averaged 2m air temperature anomalies are compared between the Last Millennium Reanalysis framework (no forecasting or "offline"), a persistence forecast, and four LIM forecasting experiments over the instrumental period (1850 - 2000). We test LIM calibrations for observational (Berkeley Earth), reanalysis (20th Century Reanalysis), and CMIP5 climate model (CCSM4 and MPI) data. Generally, we find that the usage of LIM forecasts for online PDA increases reconstruction agreement with the instrumental record for both spatial and global mean temperature (GMT). The detrended GMT skill metrics show the most dramatic increases in skill with coefficient of efficiency (CE) improvements over the no-forecasting benchmark averaging 57%. LIM experiments display a common pattern of spatial field increases in CE skill over northern hemisphere land areas and in the high-latitude North Atlantic - Barents Sea corridor (Figure 1). However, the non-GCM-calibrated LIMs introduce other deficiencies into the spatial skill of these reconstructions, likely due to aspects of the LIM calibration process. Overall, the CMIP5 LIMs have the best performance when considering both spatial fields and GMT. A comparison with the persistence forecast experiment suggests that improvements are associated with the usage of the LIM forecasts, and not simple persistence of temperature anomalies over time. These

A cross-platform freeware tool for digital reconstruction of neuronal arborizations from image stacks.

PubMed

Brown, Kerry M; Donohue, Duncan E; D'Alessandro, Giampaolo; Ascoli, Giorgio A

2005-01-01

Digital reconstruction of neuronal arborizations is an important step in the quantitative investigation of cellular neuroanatomy. In this process, neurites imaged by microscopy are semi-manually traced through the use of specialized computer software and represented as binary trees of branching cylinders (or truncated cones). Such form of the reconstruction files is efficient and parsimonious, and allows extensive morphometric analysis as well as the implementation of biophysical models of electrophysiology. Here, we describe Neuron_ Morpho, a plugin for the popular Java application ImageJ that mediates the digital reconstruction of neurons from image stacks. Both the executable and code of Neuron_ Morpho are freely distributed (www.maths. soton.ac.uk/staff/D'Alessandro/morpho or www.krasnow.gmu.edu/L-Neuron), and are compatible with all major computer platforms (including Windows, Mac, and Linux). We tested Neuron_Morpho by reconstructing two neurons from each of the two preparations representing different brain areas (hippocampus and cerebellum), neuritic type (pyramidal cell dendrites and olivar axonal projection terminals), and labeling method (rapid Golgi impregnation and anterograde dextran amine), and quantitatively comparing the resulting morphologies to those of the same cells reconstructed with the standard commercial system, Neurolucida. None of the numerous morphometric measures that were analyzed displayed any significant or systematic difference between the two reconstructing systems.

Image reconstruction from cone-beam projections with attenuation correction

NASA Astrophysics Data System (ADS)

Weng, Yi

1997-07-01

In single photon emission computered tomography (SPECT) imaging, photon attenuation within the body is a major factor contributing to the quantitative inaccuracy in measuring the distribution of radioactivity. Cone-beam SPECT provides improved sensitivity for imaging small organs. This thesis extends the results for 2D parallel- beam and fan-beam geometry to 3D parallel-beam and cone- beam geometries in order to derive filtered backprojection reconstruction algorithms for the 3D exponential parallel-beam transform and for the exponential cone-beam transform with sampling on a sphere. An exact inversion formula for the 3D exponential parallel-beam transform is obtained and is extended to the 3D exponential cone-beam transform. Sampling on a sphere is not useful clinically and current cone-beam tomography, with the focal point traversing a planar orbit, does not acquire sufficient data to give an accurate reconstruction. Thus a data acquisition method that obtains complete data for cone-beam SPECT by simultaneously rotating the gamma camera and translating the patient bed, so that cone-beam projections can be obtained with the focal point traversing a helix that surrounds the patient was developed. First, an implementation of Grangeat's algorithm for helical cone- beam projections was developed without attenuation correction. A fast new rebinning scheme was developed that uses all of the detected data to reconstruct the image and properly normalizes any multiply scanned data. In the case of attenuation no theorem analogous to Tuy's has been proven. We hypothesized that an artifact-free reconstruction could be obtained even if the cone-beam data are attenuated, provided the imaging orbit satisfies Tuy's condition and the exact attenuation map is known. Cone-beam emission data were acquired by using a circle- and-line and a helix orbit on a clinical SPECT system. An iterative conjugate gradient reconstruction algorithm was used to reconstruct projection data with a

Analytic TOF PET reconstruction algorithm within DIRECT data partitioning framework

PubMed Central

Matej, Samuel; Daube-Witherspoon, Margaret E.; Karp, Joel S.

2016-01-01

Iterative reconstruction algorithms are routinely used for clinical practice; however, analytic algorithms are relevant candidates for quantitative research studies due to their linear behavior. While iterative algorithms also benefit from the inclusion of accurate data and noise models the widespread use of TOF scanners with less sensitivity to noise and data imperfections make analytic algorithms even more promising. In our previous work we have developed a novel iterative reconstruction approach (Direct Image Reconstruction for TOF) providing convenient TOF data partitioning framework and leading to very efficient reconstructions. In this work we have expanded DIRECT to include an analytic TOF algorithm with confidence weighting incorporating models of both TOF and spatial resolution kernels. Feasibility studies using simulated and measured data demonstrate that analytic-DIRECT with appropriate resolution and regularization filters is able to provide matched bias vs. variance performance to iterative TOF reconstruction with a matched resolution model. PMID:27032968

Analytic TOF PET reconstruction algorithm within DIRECT data partitioning framework

NASA Astrophysics Data System (ADS)

Matej, Samuel; Daube-Witherspoon, Margaret E.; Karp, Joel S.

2016-05-01

Iterative reconstruction algorithms are routinely used for clinical practice; however, analytic algorithms are relevant candidates for quantitative research studies due to their linear behavior. While iterative algorithms also benefit from the inclusion of accurate data and noise models the widespread use of time-of-flight (TOF) scanners with less sensitivity to noise and data imperfections make analytic algorithms even more promising. In our previous work we have developed a novel iterative reconstruction approach (DIRECT: direct image reconstruction for TOF) providing convenient TOF data partitioning framework and leading to very efficient reconstructions. In this work we have expanded DIRECT to include an analytic TOF algorithm with confidence weighting incorporating models of both TOF and spatial resolution kernels. Feasibility studies using simulated and measured data demonstrate that analytic-DIRECT with appropriate resolution and regularization filters is able to provide matched bias versus variance performance to iterative TOF reconstruction with a matched resolution model.

Multiproxy Reduced-Dimension Reconstruction of Holocene Tropical Pacific SST Fields and Indian Monsoon Variability

NASA Astrophysics Data System (ADS)

Gill, E.; Rajagopalan, B.; Molnar, P. H.; Marchitto, T. M., Jr.; Kushnir, Y.

2016-12-01

We develop a multiproxy reduced-dimension methodology that blends magnesium calcium (Mg/Ca) and alkenone (UK'37) paleo sea surface temperature (SST) records from the eastern and western equatorial Pacific to recreate snapshots of full field SSTs and zonal wind anomalies from 10 to 2 ka BP in 2000-year increments. In the reconstruction, the zonal SST difference (average west Pacific SST minus average east Pacific SST) is largest at 10 ka (0.26°C), with coldest SST anomalies of -0.9°C in the eastern equatorial Pacific and concurrent easterly maximum zonal wind anomalies of 7 m s-1 throughout the central Pacific. From 10 to 2 ka, the entire equatorial Pacific warms, but at a faster rate in the east than in the west. These patterns are broadly consistent with previous inferences of reduced El Niño-Southern Oscillation variability associated with a cooler and/or "La Niña-like" state during the early to middle Holocene. At present there is a strong negative correlation between tropical pacific SSTs and Indian summer monsoon strength. Assuming ENSO-monsoon teleconnections were the same during early Holocene, we would expect a cooler tropical Pacific to enhance the summer Indian monsoon. To test this idea, we used the same tropical Pacific SST proxy records and a similar reduced-dimension technique to reconstruct fields of Arabian Sea wind-stress curl and Indian summer monsoon precipitation. Reconstructions for 10 ka reveal wind-stress curl anomalies of 30% greater than present day off the coastlines of Oman and Yemen, which suggest greater coastal upwelling and an enhanced monsoon jet during this time. Spatial rainfall reconstructions reveal the greatest difference in precipitation at 10 ka over the core monsoon region ( 20-60% greater than present day). Specifically, reconstructions from 10 ka reveal 40-60% greater rainfall over North West India, a region home to abundant paleo-lake records spanning the Holocene but is at present remarkably dry ( 200-450 mm of annual

Holocene Temperature Reconstructions from Arctic Lakes based on Alkenone Paleothermometry and Non-Destructive Scanning Techniques

NASA Astrophysics Data System (ADS)

D'Andrea, W. J.; Balascio, N. L.; Bradley, R. S.; Bakke, J.; Gjerde, M.; Kaufman, D. S.; Briner, J. P.; von Gunten, L.

2014-12-01

Generating continuous, accurate and quantitative Holocene temperature estimates from the Arctic is an ongoing challenge. In many Arctic regions, tree ring-based approaches cannot be used and lake sediments provide the most valuable repositories for extracting paleotemperature information. Advances in lacustrine alkenone paleothermometry now allow for quantitative reconstruction of lake-water temperature based on the UK37 values of sedimentary alkenones. In addition, a recent study demonstrated the efficacy of non-destructive scanning reflectance spectroscopy in the visible range (VIS-RS) for high-resolution quantitative temperature reconstruction from arctic lake sediments1. In this presentation, I will report a new UK37-based temperature reconstruction and a scanning VIS-RS record (using the RABD660;670 index as a measure of sedimentary chlorin content) from Kulusuk Lake in southeastern Greenland (65.6°N, 37.1°W). The UK37 record reveals a ~3°C increase in summer lake water temperatures between ~10ka and ~7ka followed by sustained warmth until ~4ka and a gradual (~3°C) cooling until ~400 yr BP. The strong correlation between UK37 and RABD660;670 measured in the same sediment core provides further evidence that in arctic lakes where temperature regulates primary productivity, and thereby sedimentary chlorin content, these proxies can be combined to develop high-resolution quantitative temperature records. The Holocene temperature history of Kulusuk Lake determined using this approach corresponds to changes in the size of the glaciers adjacent to the lake, as inferred from sediment minerogenic properties measured with scanning XRF. Glaciers retreated during early Holocene warming, likely disappeared during the period of mid-Holocene warmth, and advanced after 4ka. I will also discuss new UK37 and RABD660;670 reconstructions from northwestern Svalbard and the central Brooks Range of Alaska within the framework of published regional temperature reconstructions and

Dose reconstruction for individuals exposed to ionizing radiation using chromosome painting

NASA Technical Reports Server (NTRS)

Lucas, J. N.; Cox, A. B. (Principal Investigator)

1997-01-01

To be most useful, a biomarker for dose reconstruction should employ an end point that is highly quantitative, stable with time and easily measured. Reciprocal translocations have been shown to be a promising biomarker that is linked to both prior exposure and risk, and they can be measured easily and quantitatively using fluorescence in situ hybridization. In contrast to other biomarkers that are available, the frequency of reciprocal translocations in individuals exposed to whole-body radiation is stable with time after exposure, has rather small interindividual variability and can be measured accurately at low levels of exposure. Results from recent studies demonstrate that measurements of reciprocal translocation frequencies, facilitated by chromosome painting, can be used to reconstruct radiation dose for individuals exposed in the distant past.

Dose reconstruction for individuals exposed to ionizing radiation using chromosome painting.

PubMed

Lucas, J N

1997-11-01

To be most useful, a biomarker for dose reconstruction should employ an end point that is highly quantitative, stable with time and easily measured. Reciprocal translocations have been shown to be a promising biomarker that is linked to both prior exposure and risk, and they can be measured easily and quantitatively using fluorescence in situ hybridization. In contrast to other biomarkers that are available, the frequency of reciprocal translocations in individuals exposed to whole-body radiation is stable with time after exposure, has rather small interindividual variability and can be measured accurately at low levels of exposure. Results from recent studies demonstrate that measurements of reciprocal translocation frequencies, facilitated by chromosome painting, can be used to reconstruct radiation dose for individuals exposed in the distant past.

Quantitative characterization of surface topography using spectral analysis

NASA Astrophysics Data System (ADS)

Jacobs, Tevis D. B.; Junge, Till; Pastewka, Lars

2017-03-01

Roughness determines many functional properties of surfaces, such as adhesion, friction, and (thermal and electrical) contact conductance. Recent analytical models and simulations enable quantitative prediction of these properties from knowledge of the power spectral density (PSD) of the surface topography. The utility of the PSD is that it contains statistical information that is unbiased by the particular scan size and pixel resolution chosen by the researcher. In this article, we first review the mathematical definition of the PSD, including the one- and two-dimensional cases, and common variations of each. We then discuss strategies for reconstructing an accurate PSD of a surface using topography measurements at different size scales. Finally, we discuss detecting and mitigating artifacts at the smallest scales, and computing upper/lower bounds on functional properties obtained from models. We accompany our discussion with virtual measurements on computer-generated surfaces. This discussion summarizes how to analyze topography measurements to reconstruct a reliable PSD. Analytical models demonstrate the potential for tuning functional properties by rationally tailoring surface topography—however, this potential can only be achieved through the accurate, quantitative reconstruction of the PSDs of real-world surfaces.

The impact of system matrix dimension on small FOV SPECT reconstruction with truncated projections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chan, Chung, E-mail: Chung.Chan@yale.edu, E-mail: Chi.Liu@yale.edu; Wu, Jing; Liu, Chi, E-mail: Chung.Chan@yale.edu, E-mail: Chi.Liu@yale.edu

Purpose: A dedicated cardiac hybrid single photon emission computed tomography (SPECT)/CT scanner that uses cadmium zinc telluride detectors and multiple pinhole collimators for stationary acquisition offers many advantages. However, the impact of the reconstruction system matrix (SM) dimension on the reconstructed image quality from truncated projections and 19 angular samples acquired on this scanner has not been extensively investigated. In this study, the authors aimed to investigate the impact of the dimensions of SM and the use of body contour derived from adjunctive CT imaging as an object support in reconstruction on this scanner, in relation to background extracardiac activity.more » Methods: The authors first simulated a generic SPECT/CT system to image four NCAT phantoms with various levels of extracardiac activity and compared the reconstructions using SM in different dimensions and with/without body contour as a support for quantitative evaluations. The authors then compared the reconstructions of 18 patient studies, which were acquired on a GE Discovery NM570c scanner following injection of different radiotracers, including {sup 99m}Tc-Tetrofosmin and {sup 123}I-mIBG, comparing the scanner’s default SM that incompletely covers the body with a large SM that incorporates a patient specific full body contour. Results: The simulation studies showed that the reconstructions using a SM that only partially covers the body yielded artifacts on the edge of the field of view (FOV), overestimation of activity and increased nonuniformity in the blood pool for the phantoms with higher relative levels of extracardiac activity. However, the impact on the quantitative accuracy in the high activity region, such as the myocardium, was subtle. On the other hand, an excessively large SM that enclosed the entire body alleviated the artifacts and reduced overestimation in the blood pool, but yielded slight underestimation in myocardium and defect regions. The

Image reconstruction for PET/CT scanners: past achievements and future challenges

PubMed Central

Tong, Shan; Alessio, Adam M; Kinahan, Paul E

2011-01-01

PET is a medical imaging modality with proven clinical value for disease diagnosis and treatment monitoring. The integration of PET and CT on modern scanners provides a synergy of the two imaging modalities. Through different mathematical algorithms, PET data can be reconstructed into the spatial distribution of the injected radiotracer. With dynamic imaging, kinetic parameters of specific biological processes can also be determined. Numerous efforts have been devoted to the development of PET image reconstruction methods over the last four decades, encompassing analytic and iterative reconstruction methods. This article provides an overview of the commonly used methods. Current challenges in PET image reconstruction include more accurate quantitation, TOF imaging, system modeling, motion correction and dynamic reconstruction. Advances in these aspects could enhance the use of PET/CT imaging in patient care and in clinical research studies of pathophysiology and therapeutic interventions. PMID:21339831

Pleistocene climate, phylogeny, and climate envelope models: an integrative approach to better understand species' response to climate change.

PubMed

Lawing, A Michelle; Polly, P David

2011-01-01

Mean annual temperature reported by the Intergovernmental Panel on Climate Change increases at least 1.1°C to 6.4°C over the next 90 years. In context, a change in climate of 6°C is approximately the difference between the mean annual temperature of the Last Glacial Maximum (LGM) and our current warm interglacial. Species have been responding to changing climate throughout Earth's history and their previous biological responses can inform our expectations for future climate change. Here we synthesize geological evidence in the form of stable oxygen isotopes, general circulation paleoclimate models, species' evolutionary relatedness, and species' geographic distributions. We use the stable oxygen isotope record to develop a series of temporally high-resolution paleoclimate reconstructions spanning the Middle Pleistocene to Recent, which we use to map ancestral climatic envelope reconstructions for North American rattlesnakes. A simple linear interpolation between current climate and a general circulation paleoclimate model of the LGM using stable oxygen isotope ratios provides good estimates of paleoclimate at other time periods. We use geologically informed rates of change derived from these reconstructions to predict magnitudes and rates of change in species' suitable habitat over the next century. Our approach to modeling the past suitable habitat of species is general and can be adopted by others. We use multiple lines of evidence of past climate (isotopes and climate models), phylogenetic topology (to correct the models for long-term changes in the suitable habitat of a species), and the fossil record, however sparse, to cross check the models. Our models indicate the annual rate of displacement in a clade of rattlesnakes over the next century will be 2 to 3 orders of magnitude greater (430-2,420 m/yr) than it has been on average for the past 320 ky (2.3 m/yr).

Pleistocene Climate, Phylogeny, and Climate Envelope Models: An Integrative Approach to Better Understand Species' Response to Climate Change

PubMed Central

Lawing, A. Michelle; Polly, P. David

2011-01-01

Mean annual temperature reported by the Intergovernmental Panel on Climate Change increases at least 1.1°C to 6.4°C over the next 90 years. In context, a change in climate of 6°C is approximately the difference between the mean annual temperature of the Last Glacial Maximum (LGM) and our current warm interglacial. Species have been responding to changing climate throughout Earth's history and their previous biological responses can inform our expectations for future climate change. Here we synthesize geological evidence in the form of stable oxygen isotopes, general circulation paleoclimate models, species' evolutionary relatedness, and species' geographic distributions. We use the stable oxygen isotope record to develop a series of temporally high-resolution paleoclimate reconstructions spanning the Middle Pleistocene to Recent, which we use to map ancestral climatic envelope reconstructions for North American rattlesnakes. A simple linear interpolation between current climate and a general circulation paleoclimate model of the LGM using stable oxygen isotope ratios provides good estimates of paleoclimate at other time periods. We use geologically informed rates of change derived from these reconstructions to predict magnitudes and rates of change in species' suitable habitat over the next century. Our approach to modeling the past suitable habitat of species is general and can be adopted by others. We use multiple lines of evidence of past climate (isotopes and climate models), phylogenetic topology (to correct the models for long-term changes in the suitable habitat of a species), and the fossil record, however sparse, to cross check the models. Our models indicate the annual rate of displacement in a clade of rattlesnakes over the next century will be 2 to 3 orders of magnitude greater (430-2,420 m/yr) than it has been on average for the past 320 ky (2.3 m/yr). PMID:22164305

CT image reconstruction with half precision floating-point values.

PubMed

Maaß, Clemens; Baer, Matthias; Kachelrieß, Marc

2011-07-01

Analytic CT image reconstruction is a computationally demanding task. Currently, the even more demanding iterative reconstruction algorithms find their way into clinical routine because their image quality is superior to analytic image reconstruction. The authors thoroughly analyze a so far unconsidered but valuable tool of tomorrow's reconstruction hardware (CPU and GPU) that allows implementing the forward projection and backprojection steps, which are the computationally most demanding parts of any reconstruction algorithm, much more efficiently. Instead of the standard 32 bit floating-point values (float), a recently standardized floating-point value with 16 bit (half) is adopted for data representation in image domain and in rawdata domain. The reduction in the total data amount reduces the traffic on the memory bus, which is the bottleneck of today's high-performance algorithms, by 50%. In CT simulations and CT measurements, float reconstructions (gold standard) and half reconstructions are visually compared via difference images and by quantitative image quality evaluation. This is done for analytical reconstruction (filtered backprojection) and iterative reconstruction (ordered subset SART). The magnitude of quantization noise, which is caused by a reduction in the data precision of both rawdata and image data during image reconstruction, is negligible. This is clearly shown for filtered backprojection and iterative ordered subset SART reconstruction. In filtered backprojection, the implementation of the backprojection should be optimized for low data precision if the image data are represented in half format. In ordered subset SART image reconstruction, no adaptations are necessary and the convergence speed remains unchanged. Half precision floating-point values allow to speed up CT image reconstruction without compromising image quality.

Improved Reconstruction of Radio Holographic Signal for Forward Scatter Radar Imaging

PubMed Central

Hu, Cheng; Liu, Changjiang; Wang, Rui; Zeng, Tao

2016-01-01

Forward scatter radar (FSR), as a specially configured bistatic radar, is provided with the capabilities of target recognition and classification by the Shadow Inverse Synthetic Aperture Radar (SISAR) imaging technology. This paper mainly discusses the reconstruction of radio holographic signal (RHS), which is an important procedure in the signal processing of FSR SISAR imaging. Based on the analysis of signal characteristics, the method for RHS reconstruction is improved in two parts: the segmental Hilbert transformation and the reconstruction of mainlobe RHS. In addition, a quantitative analysis of the method’s applicability is presented by distinguishing between the near field and far field in forward scattering. Simulation results validated the method’s advantages in improving the accuracy of RHS reconstruction and imaging. PMID:27164114

Quantitative Hydraulic Models Of Early Land Plants Provide Insight Into Middle Paleozoic Terrestrial Paleoenvironmental Conditions

NASA Astrophysics Data System (ADS)

Wilson, J. P.; Fischer, W. W.

2010-12-01

humidity (<20%) combined with elevated temperatures (>25°C) could cause sufficient cavitation to reduce hydraulic conductivity by 50%. This suggests that the Early Devonian environments that supported the earliest vascular plants were not subject to prolonged midseason droughts, or, alternatively, that the growing season was short. This places minimum constraints on water availability (e.g., groundwater hydration, relative humidity) in locations where Asteroxylon fossils are found; these environments must have had high relative humidities, comparable to tropical riparian environments. Given these constraints, biome-scale paleovegetation models that place early vascular plants distal to water sources can be revised to account for reduced drought tolerance. Paleoclimate proxies that treat early terrestrial plants as functionally interchangeable can incorporate physiological differences in a quantitatively meaningful way. Application of hydraulic models to fossil plants provides an additional perspective on the 475 million-year history of terrestrial photosynthetic environments and has potential to corroborate other plant-based paleoclimate proxies.

Late Pliocene - Early Pleistocene paleoenvironmental reconstruction based on stable isotope compositions of Stephanorhinus sp. and Mammut sp. teeth

NASA Astrophysics Data System (ADS)

Szabó, Péter; Kovács, János; Kocsis, László; Gasparik, Mihály; Vennemann, Torsten; Demény, Attila; Virág, Attila

2014-05-01

Stable isotope measurements of skeletal apatite from herbivorous mammals are often used to provide information on the terrestrial paleoenvironment and paleoclimate. In this study fossil teeth of Stephanorhinus Kretzoi 1942 (rhinoceros) and Mammut Blumenbach 1799 (mastodon), amongst others, were investigated from the Carpathian Basin. According to the biostratigraphy, the age of the samples has a range from Late Pliocene to Early Pleistocene. Reconstructing paleoclimate and paleoenvironment of this era is important as it can be an analogue for the future climate. Oxygen and carbon isotopic compositions were measured from the tooth enamel, because it is believed to be the most resistant to diagenetic alteration (e.g., Kohn & Cerling, 2002). The carbon isotopic composition in the carbonate fraction of apatite can be related to the diet of the animal (Kohn & Cerling, 2002). Hence, it can reflect the photosynthetic pathway (C3 or C4) of the plants consumed by these herbivores. The δ18O values were determined in the phosphate fraction of apatite. In the case of large mammals that are obligate drinkers, the δ18O values closely track those of the environmental water (Bryant & Froelich, 1995). Knowing the δ18O values of environmental water and relating it to local precipitation, the mean annual temperature (MAT) of the site can be calculated (Dansgaard, 1964). The δ13C values range from -10 to -15 o (VPDB). The result clearly shows that these animals consumed C3 plants. Most of the δ13C values indicate mixed grassland-open woodland rather than a closed canopy forest. Although there is variation in the δ18O values (mean 14.2 ± 1.0 o VSMOW, n=17), most of the samples would support a MAT range of 8-12 ° C. This is in good agreement with other proxies for the localities and time period (Kovács et al., 2013). Bryant, D.J. & Froelich, P.N. (1995) A model of oxygen-isotope fractionation in bodywater of large-mammals. Geochimica et Cosmochimica Acta 59, 4523

Quantitative Analysis of the Effect of Iterative Reconstruction Using a Phantom: Determining the Appropriate Blending Percentage

PubMed Central

Kim, Hyun Gi; Lee, Young Han; Choi, Jin-Young; Park, Mi-Suk; Kim, Myeong-Jin; Kim, Ki Whang

2015-01-01

Purpose To investigate the optimal blending percentage of adaptive statistical iterative reconstruction (ASIR) in a reduced radiation dose while preserving a degree of image quality and texture that is similar to that of standard-dose computed tomography (CT). Materials and Methods The CT performance phantom was scanned with standard and dose reduction protocols including reduced mAs or kVp. Image quality parameters including noise, spatial, and low-contrast resolution, as well as image texture, were quantitatively evaluated after applying various blending percentages of ASIR. The optimal blending percentage of ASIR that preserved image quality and texture compared to standard dose CT was investigated in each radiation dose reduction protocol. Results As the percentage of ASIR increased, noise and spatial-resolution decreased, whereas low-contrast resolution increased. In the texture analysis, an increasing percentage of ASIR resulted in an increase of angular second moment, inverse difference moment, and correlation and in a decrease of contrast and entropy. The 20% and 40% dose reduction protocols with 20% and 40% ASIR blending, respectively, resulted in an optimal quality of images with preservation of the image texture. Conclusion Blending the 40% ASIR to the 40% reduced tube-current product can maximize radiation dose reduction and preserve adequate image quality and texture. PMID:25510772

Accurate sparse-projection image reconstruction via nonlocal TV regularization.

PubMed

Zhang, Yi; Zhang, Weihua; Zhou, Jiliu

2014-01-01

Sparse-projection image reconstruction is a useful approach to lower the radiation dose; however, the incompleteness of projection data will cause degeneration of imaging quality. As a typical compressive sensing method, total variation has obtained great attention on this problem. Suffering from the theoretical imperfection, total variation will produce blocky effect on smooth regions and blur edges. To overcome this problem, in this paper, we introduce the nonlocal total variation into sparse-projection image reconstruction and formulate the minimization problem with new nonlocal total variation norm. The qualitative and quantitative analyses of numerical as well as clinical results demonstrate the validity of the proposed method. Comparing to other existing methods, our method more efficiently suppresses artifacts caused by low-rank reconstruction and reserves structure information better.

Reconstruction of biofilm images: combining local and global structural parameters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Resat, Haluk; Renslow, Ryan S.; Beyenal, Haluk

2014-10-20

Digitized images can be used for quantitative comparison of biofilms grown under different conditions. Using biofilm image reconstruction, it was previously found that biofilms with a completely different look can have nearly identical structural parameters and that the most commonly utilized global structural parameters were not sufficient to uniquely define these biofilms. Here, additional local and global parameters are introduced to show that these parameters considerably increase the reliability of the image reconstruction process. Assessment using human evaluators indicated that the correct identification rate of the reconstructed images increased from 50% to 72% with the introduction of the new parametersmore » into the reconstruction procedure. An expanded set of parameters especially improved the identification of biofilm structures with internal orientational features and of structures in which colony sizes and spatial locations varied. Hence, the newly introduced structural parameter sets helped to better classify the biofilms by incorporating finer local structural details into the reconstruction process.« less

A Convex Formulation for Magnetic Particle Imaging X-Space Reconstruction.

PubMed

Konkle, Justin J; Goodwill, Patrick W; Hensley, Daniel W; Orendorff, Ryan D; Lustig, Michael; Conolly, Steven M

2015-01-01

Magnetic Particle Imaging (mpi) is an emerging imaging modality with exceptional promise for clinical applications in rapid angiography, cell therapy tracking, cancer imaging, and inflammation imaging. Recent publications have demonstrated quantitative mpi across rat sized fields of view with x-space reconstruction methods. Critical to any medical imaging technology is the reliability and accuracy of image reconstruction. Because the average value of the mpi signal is lost during direct-feedthrough signal filtering, mpi reconstruction algorithms must recover this zero-frequency value. Prior x-space mpi recovery techniques were limited to 1d approaches which could introduce artifacts when reconstructing a 3d image. In this paper, we formulate x-space reconstruction as a 3d convex optimization problem and apply robust a priori knowledge of image smoothness and non-negativity to reduce non-physical banding and haze artifacts. We conclude with a discussion of the powerful extensibility of the presented formulation for future applications.

Two schemes for quantitative photoacoustic tomography based on Monte Carlo simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Yubin; Yuan, Zhen, E-mail: zhenyuan@umac.mo

Purpose: The aim of this study was to develop novel methods for photoacoustically determining the optical absorption coefficient of biological tissues using Monte Carlo (MC) simulation. Methods: In this study, the authors propose two quantitative photoacoustic tomography (PAT) methods for mapping the optical absorption coefficient. The reconstruction methods combine conventional PAT with MC simulation in a novel way to determine the optical absorption coefficient of biological tissues or organs. Specifically, the authors’ two schemes were theoretically and experimentally examined using simulations, tissue-mimicking phantoms, ex vivo, and in vivo tests. In particular, the authors explored these methods using several objects withmore » different absorption contrasts embedded in turbid media and by using high-absorption media when the diffusion approximation was not effective at describing the photon transport. Results: The simulations and experimental tests showed that the reconstructions were quantitatively accurate in terms of the locations, sizes, and optical properties of the targets. The positions of the recovered targets were accessed by the property profiles, where the authors discovered that the off center error was less than 0.1 mm for the circular target. Meanwhile, the sizes and quantitative optical properties of the targets were quantified by estimating the full width half maximum of the optical absorption property. Interestingly, for the reconstructed sizes, the authors discovered that the errors ranged from 0 for relatively small-size targets to 26% for relatively large-size targets whereas for the recovered optical properties, the errors ranged from 0% to 12.5% for different cases. Conclusions: The authors found that their methods can quantitatively reconstruct absorbing objects of different sizes and optical contrasts even when the diffusion approximation is unable to accurately describe the photon propagation in biological tissues. In particular

Compensation of missing wedge effects with sequential statistical reconstruction in electron tomography.

PubMed

Paavolainen, Lassi; Acar, Erman; Tuna, Uygar; Peltonen, Sari; Moriya, Toshio; Soonsawad, Pan; Marjomäki, Varpu; Cheng, R Holland; Ruotsalainen, Ulla

2014-01-01

Electron tomography (ET) of biological samples is used to study the organization and the structure of the whole cell and subcellular complexes in great detail. However, projections cannot be acquired over full tilt angle range with biological samples in electron microscopy. ET image reconstruction can be considered an ill-posed problem because of this missing information. This results in artifacts, seen as the loss of three-dimensional (3D) resolution in the reconstructed images. The goal of this study was to achieve isotropic resolution with a statistical reconstruction method, sequential maximum a posteriori expectation maximization (sMAP-EM), using no prior morphological knowledge about the specimen. The missing wedge effects on sMAP-EM were examined with a synthetic cell phantom to assess the effects of noise. An experimental dataset of a multivesicular body was evaluated with a number of gold particles. An ellipsoid fitting based method was developed to realize the quantitative measures elongation and contrast in an automated, objective, and reliable way. The method statistically evaluates the sub-volumes containing gold particles randomly located in various parts of the whole volume, thus giving information about the robustness of the volume reconstruction. The quantitative results were also compared with reconstructions made with widely-used weighted backprojection and simultaneous iterative reconstruction technique methods. The results showed that the proposed sMAP-EM method significantly suppresses the effects of the missing information producing isotropic resolution. Furthermore, this method improves the contrast ratio, enhancing the applicability of further automatic and semi-automatic analysis. These improvements in ET reconstruction by sMAP-EM enable analysis of subcellular structures with higher three-dimensional resolution and contrast than conventional methods.

Neogene interaction of the westerlies and high topography north of the Plateau: Implications for Central Asia paleoclimate

NASA Astrophysics Data System (ADS)

Caves Rugenstein, J. K.; Bayshashov, B. U.; Zhamangara, A.; Ritch, A. J.; Ibarra, D. E.; Sjostrom, D. J.; Mix, H.; Winnick, M.; Chamberlain, C. P.

2017-12-01

The timing of high surface topography and the corresponding climatic impacts of the many high ranges north of the Tibetan Plateau, such as the Altai and Tian Shan, remain poorly constrained. Most Neogene reconstructions of Central Asia climate come from interior China, where the influences of Altai and Tian Shan uplift are difficult to deconvolve from effects due to Tibetan Plateau uplift and changes in global climate. We present a new pedogenic carbonate oxygen and carbon isotope record from terrestrial Neogene sediments of the Zaysan Basin in eastern Kazakhstan, which lies upwind of the Altai and Tian Shan, in contrast to the numerous paleoclimate records from interior China. The δ18O values of pedogenic carbonate exhibit a robust 4‰ decrease in the late Neogene—a trend that sharply contrasts with nearly all downwind records of δ18O from Central Asia. We attribute this decrease to the establishment of the modern seasonal precipitation regime whereby Kazakhstan receives the majority of its moisture in the spring and fall, which lowers the δ18O of pedogenic carbonates. The dominance of spring and fall precipitation in Kazakhstan results from the interaction of the mid-latitude jet with the high topography of the Altai and Tian Shan during its movement northward in spring and southward in fall. The late Miocene interaction of the jet with these actively uplifting northern Central Asia ranges reorganized Central Asia climate, establishing starkly different seasonal precipitation regimes, further drying interior China, and increasing the incidence of the lee cyclones that deposit dust on the Loess Plateau. To the south of the Zaysan Basin, earlier shifts in δ18O hint at early Neogene changes in climate attributable to a late Oligocene/early Miocene phase of uplift in the Tian Shan. We conclude that paleoclimatic changes in Central Asia in the Neogene are more tightly controlled by the interaction of the mid-latitude westerlies with the bounding ranges of

Tropical North Atlantic Coral-Based Sea Surface Temperature and Salinity Reconstructions From the Little Ice Age and Early Holocene

NASA Astrophysics Data System (ADS)

Saenger, C.; Cohen, A.; Oppo, D.; Hubbard, D.

2006-12-01

Understanding the magnitude and spatial extent of tropical sea surface temperature (SST) cooling during the Little Ice Age (~1400-1850 A.D.; LIA) is important for elucidating low-latitude paleoclimate, but present estimates are poorly constrained. We used Sr/Ca and δ18O variability within the aragonitic skeleton of the coral genus Montastrea to reconstruct SST and sea surface salinity (SSS) during the LIA and early Holocene (EH) in the tropical Atlantic. Four seasonally-resolved coral Sr/Ca records from St. Croix, U.S. Virgin Islands, and Bermuda indicate SST is highly correlated (r2 = 0.94) with modern Montastrea Sr/Ca and mean annual coral extension. A Sr/Ca -SST calibration that combines temperature and growth rate effects on coral Sr/Ca was applied to fossil St. Croix corals to reconstruct Caribbean climate during 5-10 year intervals of the LIA (440 ± 30 yBP) and EH (7200 ± 30; EH). Contrary to previous coral-based LIA proxy reconstructions, we find mean SST during the LIA was similar to today, but approximately 1.2°C cooler during the EH. Both periods exhibited higher amplitude seasonal variability indicating other SST estimates may be seasonally biased. Based on residual coral δ18O, we find the LIA and EH were saltier, which suggests previous cooling estimates of 1-3°C relative to today may be exaggerated by changes in seawater δ18O. Our results are consistent with a southerly migration of the Intertropical Convergence Zone (ITCZ) during the LIA, but their corroboration requires longer, high-resolution proxy reconstructions that place our two brief multi-annual coral records from the LIA and EH, respectively, within the context of multi-decadal variability.

Confidence estimation for quantitative photoacoustic imaging

NASA Astrophysics Data System (ADS)

Gröhl, Janek; Kirchner, Thomas; Maier-Hein, Lena

2018-02-01

Quantification of photoacoustic (PA) images is one of the major challenges currently being addressed in PA research. Tissue properties can be quantified by correcting the recorded PA signal with an estimation of the corresponding fluence. Fluence estimation itself, however, is an ill-posed inverse problem which usually needs simplifying assumptions to be solved with state-of-the-art methods. These simplifications, as well as noise and artifacts in PA images reduce the accuracy of quantitative PA imaging (PAI). This reduction in accuracy is often localized to image regions where the assumptions do not hold true. This impedes the reconstruction of functional parameters when averaging over entire regions of interest (ROI). Averaging over a subset of voxels with a high accuracy would lead to an improved estimation of such parameters. To achieve this, we propose a novel approach to the local estimation of confidence in quantitative reconstructions of PA images. It makes use of conditional probability densities to estimate confidence intervals alongside the actual quantification. It encapsulates an estimation of the errors introduced by fluence estimation as well as signal noise. We validate the approach using Monte Carlo generated data in combination with a recently introduced machine learning-based approach to quantitative PAI. Our experiments show at least a two-fold improvement in quantification accuracy when evaluating on voxels with high confidence instead of thresholding signal intensity.

Toward Quantitative Small Animal Pinhole SPECT: Assessment of Quantitation Accuracy Prior to Image Compensations

PubMed Central

Chen, Chia-Lin; Wang, Yuchuan; Lee, Jason J. S.; Tsui, Benjamin M. W.

2011-01-01

Purpose We assessed the quantitation accuracy of small animal pinhole single photon emission computed tomography (SPECT) under the current preclinical settings, where image compensations are not routinely applied. Procedures The effects of several common image-degrading factors and imaging parameters on quantitation accuracy were evaluated using Monte-Carlo simulation methods. Typical preclinical imaging configurations were modeled, and quantitative analyses were performed based on image reconstructions without compensating for attenuation, scatter, and limited system resolution. Results Using mouse-sized phantom studies as examples, attenuation effects alone degraded quantitation accuracy by up to −18% (Tc-99m or In-111) or −41% (I-125). The inclusion of scatter effects changed the above numbers to −12% (Tc-99m or In-111) and −21% (I-125), respectively, indicating the significance of scatter in quantitative I-125 imaging. Region-of-interest (ROI) definitions have greater impacts on regional quantitation accuracy for small sphere sources as compared to attenuation and scatter effects. For the same ROI, SPECT acquisitions using pinhole apertures of different sizes could significantly affect the outcome, whereas the use of different radii-of-rotation yielded negligible differences in quantitation accuracy for the imaging configurations simulated. Conclusions We have systematically quantified the influence of several factors affecting the quantitation accuracy of small animal pinhole SPECT. In order to consistently achieve accurate quantitation within 5% of the truth, comprehensive image compensation methods are needed. PMID:19048346

MR fingerprinting reconstruction with Kalman filter.

PubMed

Zhang, Xiaodi; Zhou, Zechen; Chen, Shiyang; Chen, Shuo; Li, Rui; Hu, Xiaoping

2017-09-01

Magnetic resonance fingerprinting (MR fingerprinting or MRF) is a newly introduced quantitative magnetic resonance imaging technique, which enables simultaneous multi-parameter mapping in a single acquisition with improved time efficiency. The current MRF reconstruction method is based on dictionary matching, which may be limited by the discrete and finite nature of the dictionary and the computational cost associated with dictionary construction, storage and matching. In this paper, we describe a reconstruction method based on Kalman filter for MRF, which avoids the use of dictionary to obtain continuous MR parameter measurements. With this Kalman filter framework, the Bloch equation of inversion-recovery balanced steady state free-precession (IR-bSSFP) MRF sequence was derived to predict signal evolution, and acquired signal was entered to update the prediction. The algorithm can gradually estimate the accurate MR parameters during the recursive calculation. Single pixel and numeric brain phantom simulation were implemented with Kalman filter and the results were compared with those from dictionary matching reconstruction algorithm to demonstrate the feasibility and assess the performance of Kalman filter algorithm. The results demonstrated that Kalman filter algorithm is applicable for MRF reconstruction, eliminating the need for a pre-define dictionary and obtaining continuous MR parameter in contrast to the dictionary matching algorithm. Copyright © 2017 Elsevier Inc. All rights reserved.

Triple oxygen and hydrogen isotopes of gypsum hydration water for quantitative paleo-humidity reconstruction

NASA Astrophysics Data System (ADS)

Gázquez, Fernando; Morellón, Mario; Bauska, Thomas; Herwartz, Daniel; Surma, Jakub; Moreno, Ana; Staubwasser, Michael; Valero-Garcés, Blas; Delgado-Huertas, Antonio; Hodell, David A.

2018-01-01

Atmospheric relative humidity is an important parameter affecting vegetation yet paleo-humidity proxies are scarce and difficult to calibrate. Here we use triple oxygen (δ17O and δ18O) and hydrogen (δD) isotopes of structurally-bound gypsum hydration water (GHW) extracted from lacustrine gypsum to quantify past changes in atmospheric relative humidity. An evaporation isotope-mass-balance model is used together with Monte Carlo simulations to determine the range of climatological conditions that simultaneously satisfy the stable isotope results of GHW, and with statistically robust estimates of uncertainty. We apply this method to reconstruct the isotopic composition of paleo-waters of Lake Estanya (NE Spain) and changes in normalized atmospheric relative humidity (RHn) over the last glacial termination and Holocene (from ∼15 to 0.6 cal. kyrs BP). The isotopic record indicates the driest conditions occurred during the Younger Dryas (YD; ∼12-13 cal. kyrs BP). We estimate a RHn of ∼40-45% during the YD, which is ∼30-35% lower than today. Because of the southward displacement of the Polar Front to ∼42°N, it was both windier and drier during the YD than the Bølling-Allerød period and Holocene. Mean atmospheric moisture gradually increased from the Preboreal to Early Holocene (∼11 to 8 cal. kyrs BP, 50-60%), reaching 70-75% RHn from ∼7.5 cal. kyrs BP until present-day. We demonstrate that combining hydrogen and triple oxygen isotopes in GHW provides a powerful tool for quantitative estimates of past changes in relative humidity.

Towards Better Calibration of Modern Palynological Data against Climate: A Case Study in Osaka Bay, Japan

NASA Astrophysics Data System (ADS)

Kitaba, I.; Nakagawa, T.; McClymont, E.; Dettman, D. L.; Yamada, K.; Takemura, K.; Hyodo, M.

2014-12-01

Many of the difficulties in the pollen fossil-based paleoclimate reconstruction in coastal regions derive from the complex sedimentary processes of the near-shore environment. In order to examine this problem, we carried out pollen analysis of surface sediments collected from 35 sites in Osaka Bay, Japan. Using the biomisation method, the surrounding vegetation was accurately reconstructed at all sites. Applying the modern analogue technique to the same data, however, led to reconstructed temperatures that were lower by ca. 5 deg. C and precipitation amounts higher by ca. 5000 mm than the current sea level climate of the region. The range of reconstructed values was larger than the reconstruction error associated with the method. The principal component analysis shows that the surface pollen variation in Osaka Bay reflects sedimentary processes. This significant error associated with the quantitative climatic reconstruction using pollen data is attributed to the fact that the pollen assemblage is not determined solely by climate but reflects non-climatic influences. The accuracy and precision of climatic reconstruction can be improved significantly by expanding counts of minor taxa. Given this result, we re-examined the reconstructed climate using Osaka Bay palynological record reported in Kitaba et al. (2013). This new method did not significantly alter the overall variation in the reconstructed climate, and thus we conclude that the reconstruction was generally reliable. However, some intervals were strongly affected by depositional environmental change. In these, a climate signal can be extracted by excluding the patterns that arise from coastal sedimentation.

Penalized maximum likelihood simultaneous longitudinal PET image reconstruction with difference-image priors.

PubMed

Ellis, Sam; Reader, Andrew J

2018-04-26

Many clinical contexts require the acquisition of multiple positron emission tomography (PET) scans of a single subject, for example, to observe and quantitate changes in functional behaviour in tumors after treatment in oncology. Typically, the datasets from each of these scans are reconstructed individually, without exploiting the similarities between them. We have recently shown that sharing information between longitudinal PET datasets by penalizing voxel-wise differences during image reconstruction can improve reconstructed images by reducing background noise and increasing the contrast-to-noise ratio of high-activity lesions. Here, we present two additional novel longitudinal difference-image priors and evaluate their performance using two-dimesional (2D) simulation studies and a three-dimensional (3D) real dataset case study. We have previously proposed a simultaneous difference-image-based penalized maximum likelihood (PML) longitudinal image reconstruction method that encourages sparse difference images (DS-PML), and in this work we propose two further novel prior terms. The priors are designed to encourage longitudinal images with corresponding differences which have (a) low entropy (DE-PML), and (b) high sparsity in their spatial gradients (DTV-PML). These two new priors and the originally proposed longitudinal prior were applied to 2D-simulated treatment response [ 18 F]fluorodeoxyglucose (FDG) brain tumor datasets and compared to standard maximum likelihood expectation-maximization (MLEM) reconstructions. These 2D simulation studies explored the effects of penalty strengths, tumor behaviour, and interscan coupling on reconstructed images. Finally, a real two-scan longitudinal data series acquired from a head and neck cancer patient was reconstructed with the proposed methods and the results compared to standard reconstruction methods. Using any of the three priors with an appropriate penalty strength produced images with noise levels equivalent to

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nyflot, MJ; Yang, F; Byrd, D

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

Development and sustainability of NSF-funded climate change education efforts: lessons learned and strategies used to develop the Reconstructing Earth's Climate History (REaCH) curriculum (Invited)

NASA Astrophysics Data System (ADS)

St John, K. K.; Jones, M. H.; Leckie, R. M.; Pound, K. S.; Krissek, L. A.

2013-12-01

The context for understanding modern global climate change lies in the records of Earth's past. This is demonstrated by decades of paleoclimate research by scientists in organizations such as IODP and ANDRILL, yet making that science accessible to educators has been a long-standing challenge. Furthermore, content transfer is not enough; in science education, addressing how we know is as important as addressing what we know about science. To that end, our initial NSF-CCLI/TUES objective of Teaching Anchor Concepts of Climate Change (NSF #0737335) was to put authentic data and published case studies of past climate change at students' fingertips in a series of 7 multipart inquiry-based exercise modules for undergraduate classroom and lab use. After 4 years of funding (incl. 2 no-cost extensions) we surpassed our project objective and established an avenue for sustainability that is proving successful. The purpose of this presentation is to share (1) the process by which we developed the curriculum and (2) the strategies used to ensure sustainability. The curriculum development process reflected many of the same successful strategies used in scientific research. It drew on the knowledge and skills of the team; it was collaborative, iterative, and primarily distributive, yet at times directive. The team included paleoclimate researchers and educators from a broad range of undergraduate institutions. We evaluated published data from scientific reports and peer-reviewed journal articles, and used these as the foundation for writing curriculum that was data-rich and inquiry-based. In total 14 multipart exercise modules were developed. The feedback from early and frequent meeting presentations, from formative evaluation by students in courses and by faculty in workshops, and from peer-review by paleoclimate scientists and undergraduate educators helped us fine-tune the materials to the needs of the education and paleoclimate science communities. It additionally helped us

High-resolution reconstruction of Arctic paleoclimate derived from 53 million year old kimberlite-hosted Metasequoia wood

NASA Astrophysics Data System (ADS)

Walker, J. J.; Halfar, J.; Schulze, D.; Gedalof, Z.; Moore, G. W. K.

2009-04-01

The recovery of exceptionally well preserved Eocene wood from kimberlite pipes in the Lac de Gras region of the Northwest Territories, Canada, has allowed for the characterization of the local temperature and hydrologic patterns on an annual scale for this arctic ecosystem (present day latitude: 64 deg N). Wood fragments of ancient Metasequoia sp. trees mixed into the crater facies during kimberlite emplacement were recovered from the Ekati and Diavik diamond mines. Wood recovered from the Ekati "Panda" pipe, which has been dated using Rb-Sr age determination at 53.3 +/- 0.6 million years, is unique in that it exhibits extremely low vitrinite reflectance values, comparable to that of modern near-surface peats. The implication is that the wood has undergone minimal thermal or compressional alteration, thus preserving the geochemical signatures originally formed during growth. Ring width measurements representing over 100 years of climate data show congruence between multiple samples, thus enabling the development of a floating master chronology. Patterns contained in this chronology are of particular interest as the early Eocene was characterized by a period of unusual warming that has been compared to modern day climate change. Wood cellulose does not exchange atoms with its surroundings after formation, making it an ideal candidate for stable isotope analysis once it has been separated from associated whole-wood components. A robotic micromilling device was used to collect whole wood samples of latewood from annual tree rings. The α-cellulose in the samples will be isolated and analyzed for δ13C and δ18O, generating a 34-year floating chronology that can be used to reconstruct decadal scale temperature and humidity patterns. Successful application of this technique suggests that a longer Eocene chronology, using additional wood samples recovered from the Panda pipe as well as samples from neighbouring pipes in the Lac de Gras region, can be developed.

Alkenone-based reconstructions reveal four-phase Holocene temperature evolution for High Arctic Svalbard

NASA Astrophysics Data System (ADS)

van der Bilt, Willem G. M.; D'Andrea, William J.; Bakke, Jostein; Balascio, Nicholas L.; Werner, Johannes P.; Gjerde, Marthe; Bradley, Raymond S.

2018-03-01

Situated at the crossroads of major oceanic and atmospheric circulation patterns, the Arctic is a key component of Earth's climate system. Compounded by sea-ice feedbacks, even modest shifts in the region's heat budget drive large climate responses. This is highlighted by the observed amplified response of the Arctic to global warming. Assessing the imprint and signature of underlying forcing mechanisms require paleoclimate records, allowing us to expand our knowledge beyond the short instrumental period and contextualize ongoing warming. However, such datasets are scarce and sparse in the Arctic, limiting our ability to address these issues. Here, we present two quantitative Holocene-length paleotemperature records from the High Arctic Svalbard archipelago, situated in the climatically sensitive Arctic North Atlantic. Temperature estimates are based on U37K unsaturation ratios from sediment cores of two lakes. Our data reveal a dynamic Holocene temperature evolution, with reconstructed summer lake water temperatures spanning a range of ∼6-8 °C, and characterized by four phases. The Early Holocene was marked by an early onset (∼10.5 ka cal. BP) of insolation-driven Hypsithermal conditions, likely compounded by strengthening oceanic heat transport. This warm interval was interrupted by cooling between ∼10.5-8.3 ka cal. BP that we attribute to cooling effects from the melting Northern Hemisphere ice sheets. Temperatures declined throughout the Middle Holocene, following a gradual trend that was accentuated by two cooling steps between ∼7.8-7 ka cal. BP and around ∼4.4-4.3 ka cal. BP. These transitions coincide with a strengthening influence of Arctic water and sea-ice in the adjacent Fram Strait. During the Late Holocene (past 4 ka), temperature change decoupled from the still-declining insolation, and fluctuated around comparatively cold mean conditions. By showing that Holocene Svalbard temperatures were governed by an alternation of forcings, this study

Calibrating Geochemical Proxies in an Aragonite Stalagmite from the West Coast of India

NASA Astrophysics Data System (ADS)

Kaushal, N.; Henderson, G. M.; Yadava, M. G.; Ramesh, R.

2016-12-01

The Indian Monsoon is a major component of the global climatic system. Reconstruction of its past behaviour from stalagmites could be a powerful approach to understand its operation in varied climate states. Such records from the west coast would be valuable for the information they might impart about rainfall intensity and composition as air-masses first move onto the continent from the Arabian Sea, providing important constraints for other sites further inland. Carbonate rocks are sparse on the west coast, however, limiting availability of potential stalagmite sites. Here we report δ18O, δ13C and trace element analyses on the only stalagmite so far reported from the west coast. The sample grew from 1666 to 1997 AD in north Karnataka and is formed of aragonite, rather than calcite which is more commonly used for speleothem paleoclimate reconstruction. We aim to assess the use of aragonite geochemistry for paleoclimate reconstruction in general, and the rainfall at this particular site. Findings include: 1) Carbonate forming in the cave today appears to be in oxygen-isotope equilibrium, but the stalagmite has a kinetic overprint which is influenced by the slope of the growing surface of the sample. This local control on δ18O makes its use for reconstruction challenging. 2) Trace element measurements may provide more robust indicators of local paleoclimate. 3) High resolution sampling of 11 annual growth layers capture a strong seasonal record controlled by prior aragonite precipitation (PAP). PAP, similar to PCP, is a promising proxy for seasonal dryness or seasonal change in the partial pressure of carbon dioxide in this cave.

A new node on the SE Asian paleoclimate map: the alkaline crater lakes of central Myanmar

NASA Astrophysics Data System (ADS)

Smittenberg, Rienk H.; Chabangborn, Akkaneewut; Thu Aung, Lin; Fritz, Sherilyn; Wohlfarth, Barbara

2014-05-01

SE Asia is climatically a key region where the Asian monsoon system connects with the Indo-Pacific warm pool and from where much (latent) heat gets transported to higher latitudes. We recently obtained sediment cores from four crater lakes located in Central Myanmar, with the aim to further colour the still largely white space on the SE Asian paleoclimate map. The chain of volcanic craters extending northeast to southwest in the vicinity of the lower Chindwin River in central Myanmar have been known for a long time. These craters are aligned west of the Sagaing Fault, which is a continental transform fault between the Indian and Sunda continental plates. Four of the craters still contain lakes, while several of the smaller craters are drained and used for agriculture. The region has a tropical Savannah climate, with warm temperatures throughout the year. Precipitation is almost absent during the dry season but increases to an average monthly precipitation of 100-134 mm per month during the monsoon season (May through October). Three of the four lakes, named Twin Ywa (30 m depth), Twin Taung (60 m), and Twin Pyauk (8m), are highly alkaline (pH 10-11), support extensive cyanobacterial blooms and are anoxic below a few meters water depth. Their sediments are composed of highly organic and laminated algae gyttjas. The shallower (2m), oxic and more neutral (pH 7.5) Lake Leshe contains organic-lean clays but with clear variations in colour and bulk density that likely mark changes in humidity though time. The lake levels of the relatively small crater lakes are solely regulated by precipitation and evaporation, and their limnology and water isotope compositions are therefore sensitive to changes in monsoon intensity. We will present limnological data including water isotopic compositions, and initial bulk sedimentary data as well as preliminary age determinations. These will form the basis for more extensive multi-proxy analyses that should result in an improved insight

Investigation of iterative image reconstruction in three-dimensional optoacoustic tomography

PubMed Central

Wang, Kun; Su, Richard; Oraevsky, Alexander A; Anastasio, Mark A

2012-01-01

Iterative image reconstruction algorithms for optoacoustic tomography (OAT), also known as photoacoustic tomography, have the ability to improve image quality over analytic algorithms due to their ability to incorporate accurate models of the imaging physics, instrument response, and measurement noise. However, to date, there have been few reported attempts to employ advanced iterative image reconstruction algorithms for improving image quality in three-dimensional (3D) OAT. In this work, we implement and investigate two iterative image reconstruction methods for use with a 3D OAT small animal imager: namely, a penalized least-squares (PLS) method employing a quadratic smoothness penalty and a PLS method employing a total variation norm penalty. The reconstruction algorithms employ accurate models of the ultrasonic transducer impulse responses. Experimental data sets are employed to compare the performances of the iterative reconstruction algorithms to that of a 3D filtered backprojection (FBP) algorithm. By use of quantitative measures of image quality, we demonstrate that the iterative reconstruction algorithms can mitigate image artifacts and preserve spatial resolution more effectively than FBP algorithms. These features suggest that the use of advanced image reconstruction algorithms can improve the effectiveness of 3D OAT while reducing the amount of data required for biomedical applications. PMID:22864062

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. © 2015 American Academy of Forensic Sciences.

SU-D-210-03: Limited-View Multi-Source Quantitative Photoacoustic Tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, J; Gao, H

2015-06-15

Purpose: This work is to investigate a novel limited-view multi-source acquisition scheme for the direct and simultaneous reconstruction of optical coefficients in quantitative photoacoustic tomography (QPAT), which has potentially improved signal-to-noise ratio and reduced data acquisition time. Methods: Conventional QPAT is often considered in two steps: first to reconstruct the initial acoustic pressure from the full-view ultrasonic data after each optical illumination, and then to quantitatively reconstruct optical coefficients (e.g., absorption and scattering coefficients) from the initial acoustic pressure, using multi-source or multi-wavelength scheme.Based on a novel limited-view multi-source scheme here, We have to consider the direct reconstruction of opticalmore » coefficients from the ultrasonic data, since the initial acoustic pressure can no longer be reconstructed as an intermediate variable due to the incomplete acoustic data in the proposed limited-view scheme. In this work, based on a coupled photo-acoustic forward model combining diffusion approximation and wave equation, we develop a limited-memory Quasi-Newton method (LBFGS) for image reconstruction that utilizes the adjoint forward problem for fast computation of gradients. Furthermore, the tensor framelet sparsity is utilized to improve the image reconstruction which is solved by Alternative Direction Method of Multipliers (ADMM). Results: The simulation was performed on a modified Shepp-Logan phantom to validate the feasibility of the proposed limited-view scheme and its corresponding image reconstruction algorithms. Conclusion: A limited-view multi-source QPAT scheme is proposed, i.e., the partial-view acoustic data acquisition accompanying each optical illumination, and then the simultaneous rotations of both optical sources and ultrasonic detectors for next optical illumination. Moreover, LBFGS and ADMM algorithms are developed for the direct reconstruction of optical coefficients from

Adaptive statistical iterative reconstruction improves image quality without affecting perfusion CT quantitation in primary colorectal cancer.

PubMed

Prezzi, D; Goh, V; Virdi, S; Mallett, S; Grierson, C; Breen, D J

2017-01-01

To determine the effect of Adaptive Statistical Iterative Reconstruction (ASIR) on perfusion CT (pCT) parameter quantitation and image quality in primary colorectal cancer. Prospective observational study. Following institutional review board approval and informed consent, 32 patients with colorectal adenocarcinoma underwent pCT (100 kV, 150 mA, 120 s acquisition, axial mode). Tumour regional blood flow (BF), blood volume (BV), mean transit time (MTT) and permeability surface area product (PS) were determined using identical regions-of-interests for ASIR percentages of 0%, 20%, 40%, 60%, 80% and 100%. Image noise, contrast-to-noise ratio (CNR) and pCT parameters were assessed across ASIR percentages. Coefficients of variation (CV), repeated measures analysis of variance (rANOVA) and Spearman' rank order correlation were performed with statistical significance at 5%. With increasing ASIR percentages, image noise decreased by 33% while CNR increased by 61%; peak tumour CNR was greater than 1.5 with 60% ASIR and above. Mean BF, BV, MTT and PS differed by less than 1.8%, 2.9%, 2.5% and 2.6% across ASIR percentages. CV were 4.9%, 4.2%, 3.3% and 7.9%; rANOVA P values: 0.85, 0.62, 0.02 and 0.81 respectively. ASIR improves image noise and CNR without altering pCT parameters substantially.

Accelerating simultaneous algebraic reconstruction technique with motion compensation using CUDA-enabled GPU.

PubMed

Pang, Wai-Man; Qin, Jing; Lu, Yuqiang; Xie, Yongming; Chui, Chee-Kong; Heng, Pheng-Ann

2011-03-01

To accelerate the simultaneous algebraic reconstruction technique (SART) with motion compensation for speedy and quality computed tomography reconstruction by exploiting CUDA-enabled GPU. Two core techniques are proposed to fit SART into the CUDA architecture: (1) a ray-driven projection along with hardware trilinear interpolation, and (2) a voxel-driven back-projection that can avoid redundant computation by combining CUDA shared memory. We utilize the independence of each ray and voxel on both techniques to design CUDA kernel to represent a ray in the projection and a voxel in the back-projection respectively. Thus, significant parallelization and performance boost can be achieved. For motion compensation, we rectify each ray's direction during the projection and back-projection stages based on a known motion vector field. Extensive experiments demonstrate the proposed techniques can provide faster reconstruction without compromising image quality. The process rate is nearly 100 projections s (-1), and it is about 150 times faster than a CPU-based SART. The reconstructed image is compared against ground truth visually and quantitatively by peak signal-to-noise ratio (PSNR) and line profiles. We further evaluate the reconstruction quality using quantitative metrics such as signal-to-noise ratio (SNR) and mean-square-error (MSE). All these reveal that satisfactory results are achieved. The effects of major parameters such as ray sampling interval and relaxation parameter are also investigated by a series of experiments. A simulated dataset is used for testing the effectiveness of our motion compensation technique. The results demonstrate our reconstructed volume can eliminate undesirable artifacts like blurring. Our proposed method has potential to realize instantaneous presentation of 3D CT volume to physicians once the projection data are acquired.

Using the latest paleoclimate insights to better quantify the risk of low probability, high impact floods and hydrological droughts - how robust are existing water resource management and supply systems in eastern Australia?

NASA Astrophysics Data System (ADS)

Kiem, Anthony; Vance, Tessa; Roberts, Jason; Ho, Michelle

2015-04-01

Floods and droughts always have and always will occur. Both natural climate variability and anthropogenic change influence flood and drought risk but their exact roles, and proportional importance, are not yet properly understood or quantified. To address these challenges, and to move towards a more resilient, well adapted world, a paradigm shift is required that accepts and accounts for the non-linear and non-stationary nature of the processes that drive hydroclimatic risk. This study focuses on recent research from Australia that utilizes several independently derived paleoclimate reconstructions to better understand interannual to multidecadal climate variability and to provide improved quantification of the true risk of low probability, high impact floods and hydrological droughts in the heavily populated eastern Australian region. It is demonstrated that the instrumental hydroclimatic records (which cover only 100 years at best for most parts of Australia) do not capture the full range of flooding and drought that is possible. Also discussed are the implications for water resources management of the realisation that hydroclimatic risk changes over time and that fundamental questions of whether flood and drought risk in Australia will increase or decrease in the future (and where and when and by how much) are as yet unanswered, and how decision makers can robustly deal with such uncertainty.

Impacts of Mega-droughts on Water and Food Security in the Indo-Gangetic Plains: A Paleoclimate Scenario Analysis

NASA Astrophysics Data System (ADS)

Zhu, T.; Pitois, G.; Ringler, C.; Wang, D.; Rosegrant, M. W.

2014-12-01

Spanning over Pakistan, northern India, Nepal, and Bangladesh, the Indo-Gangetic Plains (IGP) is the home of several hundred million people and the "bread basket" for much of South Asia. The flat terrain, fertile soils, and favorable climate of the IGP make it agriculturally productive. However prolonged droughts caused by consecutive monsoon failures can seriously affect crop production and social wellbeing, in particular for the eastern part of the plains where agriculture remains largely rain-fed. Severe droughts were observed in the IGP historically, and recent paleoclimate studies reveal that more severe and long-lasting "mega-droughts" had happened in the distant past. Agricultural losses from major droughts can dramatically affect food systems and increase the vulnerability of resource-poor people given the delicate balance between food supply and demand under growing natural resource scarcity. To estimate the potential impacts of "mega-droughts" on the water and food systems in the IGP, we develop worst-case drought scenarios through inverse modeling of tree-ring-based PDSI reconstruction that covers the period 1300-1899 (A.D.), and analyze these historic mega-drought scenarios using IFPRI's IMPACT global water and food projections model. The base year of the IMPACT model is parameterized using socioeconomic and engineering data that reflect today's water management and infrastructure, agricultural technologies, population, income, and market institutions. The base year simulation is validated against observations to ensure model fidelity. Anticipated changes of the above factors in the future out to 2050 are specified using demographic and economic growth projections and literature data. Model simulation results represent the consequences of mega-droughts in the IGP given technological and socioeconomic conditions of today and in the future. We also explore policy options for increasing the resilience of water and food systems in the IGP, through scenario

Late Quaternary paleoclimate of western Alaska inferred from fossil chironomids and its relation to vegetation histories

USGS Publications Warehouse

Kurek, Joshua; Cwynar, Les C.; Ager, Thomas A.; Abbott, Mark B.; Edwards, Mary E.

2009-01-01

Fossil Chironomidae assemblages (with a few Chaoboridae and Ceratopogonidae) from Zagoskin and Burial Lakes in western Alaska provide quantitative reconstructions of mean July air temperatures for periods of the late-middle Wisconsin (~39,000-34,000 cal yr B.P.) to the present. Inferred temperatures are compared with previously analyzed pollen data from each site summarized here by indirect ordination. Paleotemperature trends reveal substantial differences in the timing of climatic warming following the late Wisconsin at each site, although chronological uncertainty exists. Zagoskin Lake shows early warming beginning at about 21,000 cal yr B.P., whereas warming at Burial Lake begins ~4000 years later. Summer climates during the last glacial maximum (LGM) were on average ~3.5C° below the modern temperatures at each site. Major shifts in vegetation occurred from ~19,000 to 10,000 cal yr B.P. at Zagoskin Lake and from ~17,000 to 10,000 cal yr B.P. at Burial Lake. Vegetation shifts followed climatic warming, when temperatures neared modern values. Both sites provide evidence of an early postglacial thermal maximum at ~12,300 cal yr B.P. These chironomid records, combined with other insect-based climatic reconstructions from Beringia, indicate that during the LGM: (1) greater continentality likely influenced regions adjacent to the Bering Land Bridge and (2) summer climates were, at times, not dominated by severe cold.

Surgical treatment of subacute and chronic valgus instability in multiligament-injured knees with superficial medial collateral ligament reconstruction using Achilles allografts: a quantitative analysis with a minimum 2-year follow-up.

PubMed

Liu, Xin; Feng, Hua; Zhang, Hui; Hong, Lei; Wang, Xue Song; Zhang, Jin; Shen, Jie Wei

2013-05-01

Symptomatic medial collateral ligament (MCL) instability is rare, and it is frequently associated with multiligament injuries. Most clinical investigations have failed to clearly define the specific objective outcome measures assessing the stability of the MCL quantitatively before and after the reconstruction procedure. To quantitatively evaluate the early clinical outcomes of patients with valgus instability of knee joints who had undergone superficial MCL reconstruction using Achilles tendon allografts. Case series; Level of evidence, 4. From August 2005 to December 2010, 19 consecutive patients with MCL injuries were included in this study. The inclusion criteria were (1) a subacute or chronic MCL injury, with a time from initial injury to surgery of longer than 3 weeks, and (2) valgus laxity graded C or D according to the International Knee Documentation Committee (IKDC). All patients underwent superficial MCL reconstruction using Achilles tendon allografts. To evaluate the laxity of the MCL preoperatively and postoperatively, valgus stress radiographs using a Telos device were used. Other assessments included the IKDC subjective functional evaluation and Lysholm score estimation. Sixteen of the 19 patients (12 men and 4 women) were available for final follow-up. The median age of the patients was 37 years (range, 19-53 years); mean body mass index (BMI) was 26.4 (range, 21.7-29.4). The mean time from injury to surgery was 15.9 months (range, 24 days to 84 months), and median follow-up period was 34 months (range, 24-67 months). The mean medial knee laxity (side-to-side difference) was 8.9 ± 3.2 mm (range, 6-15.9 mm) preoperatively and 1.1 ± 0.9 mm (range, -1.1 to 3.2 mm) postoperatively (P < .001). The preoperative mean IKDC subjective knee functional score was 49.8 ± 6.9 (range, 31-57.5), while the postoperative functional score was 84.3 ± 6.0 (range, 71.3-93.1) (P < .001). The mean Lysholm score was 69.3 ± 5.9 (range, 55-78) preoperatively and 88.6 �

Impact of prehistoric cooking practices on paleoenvironmental proxies in shell midden constituents

NASA Astrophysics Data System (ADS)

Müller, Peter; Staudigel, Philip; Murray, Sean T.; Westphal, Hildegard; Swart, Peter K.

2016-04-01

Paleoenvironmental proxy records such as oxygen isotopes of calcareous skeletal structures like fish otoliths or mollusk shells provide highest-resolution information about environmental conditions experienced by the organism. Accumulations of such skeletal structures by ancient coastal populations in so called "shell midden" deposits provide us with sub-seasonally resolved paleoclimate records covering time spans up to several millennia. Given their high temporal resolution, these deposits are increasingly used for paleoclimate reconstructions and complement our understanding of ancient climate changes. However, gathered as comestibles, most of these skeletal remains were subject to prehistoric cooking methods prior to deposition. The associated alteration of the chemical proxy signatures as well as the subsequent error for paleoenvironmental reconstructions remained almost entirely neglected so far. Here, we present clumped isotope, conventional oxygen and carbon isotopes as well as element:Ca ratios measured in modern bivalve shells after exposing them to different prehistoric cooking methods. Our data show that most cooking methods considerably alter commonly used paleoclimate proxy systems which can lead to substantial misinterpretations of ancient climate conditions. Since the magnitude of chemical alteration is not distinguishable from natural temperature variability in most coastal settings, the alteration of shell midden constituents by prehistoric cooking remains likely unnoticed in most cases. Thus, depending on the cooking method, pre-depositional heating might have introduced considerable errors into previous paleoclimate studies. However, our data also show that clumped isotope thermometry represents a suitable diagnostic tool to detect such pre-depositional cooking events and also allows differentiating between the most commonly applied prehistoric cooking methods.

Ranking of tree-ring based temperature reconstructions of the past millennium

NASA Astrophysics Data System (ADS)

Esper, Jan; Krusic, Paul J.; Ljungqvist, Fredrik C.; Luterbacher, Jürg; Carrer, Marco; Cook, Ed; Davi, Nicole K.; Hartl-Meier, Claudia; Kirdyanov, Alexander; Konter, Oliver; Myglan, Vladimir; Timonen, Mauri; Treydte, Kerstin; Trouet, Valerie; Villalba, Ricardo; Yang, Bao; Büntgen, Ulf

2016-08-01

Tree-ring chronologies are widely used to reconstruct high-to low-frequency variations in growing season temperatures over centuries to millennia. The relevance of these timeseries in large-scale climate reconstructions is often determined by the strength of their correlation against instrumental temperature data. However, this single criterion ignores several important quantitative and qualitative characteristics of tree-ring chronologies. Those characteristics are (i) data homogeneity, (ii) sample replication, (iii) growth coherence, (iv) chronology development, and (v) climate signal including the correlation with instrumental data. Based on these 5 characteristics, a reconstruction-scoring scheme is proposed and applied to 39 published, millennial-length temperature reconstructions from Asia, Europe, North America, and the Southern Hemisphere. Results reveal no reconstruction scores highest in every category and each has their own strengths and weaknesses. Reconstructions that perform better overall include N-Scan and Finland from Europe, E-Canada from North America, Yamal and Dzhelo from Asia. Reconstructions performing less well include W-Himalaya and Karakorum from Asia, Tatra and S-Finland from Europe, and Great Basin from North America. By providing a comprehensive set of criteria to evaluate tree-ring chronologies we hope to improve the development of large-scale temperature reconstructions spanning the past millennium. All reconstructions and their corresponding scores are provided at http://www.blogs.uni-mainz.de/fb09climatology.

Evaluation of a 3D point cloud tetrahedral tomographic reconstruction method

PubMed Central

Pereira, N F; Sitek, A

2011-01-01

Tomographic reconstruction on an irregular grid may be superior to reconstruction on a regular grid. This is achieved through an appropriate choice of the image space model, the selection of an optimal set of points and the use of any available prior information during the reconstruction process. Accordingly, a number of reconstruction-related parameters must be optimized for best performance. In this work, a 3D point cloud tetrahedral mesh reconstruction method is evaluated for quantitative tasks. A linear image model is employed to obtain the reconstruction system matrix and five point generation strategies are studied. The evaluation is performed using the recovery coefficient, as well as voxel- and template-based estimates of bias and variance measures, computed over specific regions in the reconstructed image. A similar analysis is performed for regular grid reconstructions that use voxel basis functions. The maximum likelihood expectation maximization reconstruction algorithm is used. For the tetrahedral reconstructions, of the five point generation methods that are evaluated, three use image priors. For evaluation purposes, an object consisting of overlapping spheres with varying activity is simulated. The exact parallel projection data of this object are obtained analytically using a parallel projector, and multiple Poisson noise realizations of these exact data are generated and reconstructed using the different point generation strategies. The unconstrained nature of point placement in some of the irregular mesh-based reconstruction strategies has superior activity recovery for small, low-contrast image regions. The results show that, with an appropriately generated set of mesh points, the irregular grid reconstruction methods can out-perform reconstructions on a regular grid for mathematical phantoms, in terms of the performance measures evaluated. PMID:20736496

Evaluation of a 3D point cloud tetrahedral tomographic reconstruction method

NASA Astrophysics Data System (ADS)

Pereira, N. F.; Sitek, A.

2010-09-01

Tomographic reconstruction on an irregular grid may be superior to reconstruction on a regular grid. This is achieved through an appropriate choice of the image space model, the selection of an optimal set of points and the use of any available prior information during the reconstruction process. Accordingly, a number of reconstruction-related parameters must be optimized for best performance. In this work, a 3D point cloud tetrahedral mesh reconstruction method is evaluated for quantitative tasks. A linear image model is employed to obtain the reconstruction system matrix and five point generation strategies are studied. The evaluation is performed using the recovery coefficient, as well as voxel- and template-based estimates of bias and variance measures, computed over specific regions in the reconstructed image. A similar analysis is performed for regular grid reconstructions that use voxel basis functions. The maximum likelihood expectation maximization reconstruction algorithm is used. For the tetrahedral reconstructions, of the five point generation methods that are evaluated, three use image priors. For evaluation purposes, an object consisting of overlapping spheres with varying activity is simulated. The exact parallel projection data of this object are obtained analytically using a parallel projector, and multiple Poisson noise realizations of these exact data are generated and reconstructed using the different point generation strategies. The unconstrained nature of point placement in some of the irregular mesh-based reconstruction strategies has superior activity recovery for small, low-contrast image regions. The results show that, with an appropriately generated set of mesh points, the irregular grid reconstruction methods can out-perform reconstructions on a regular grid for mathematical phantoms, in terms of the performance measures evaluated.

Robustness of Reconstructed Ancestral Protein Functions to Statistical Uncertainty.

PubMed

Eick, Geeta N; Bridgham, Jamie T; Anderson, Douglas P; Harms, Michael J; Thornton, Joseph W

2017-02-01

Hypotheses about the functions of ancient proteins and the effects of historical mutations on them are often tested using ancestral protein reconstruction (APR)-phylogenetic inference of ancestral sequences followed by synthesis and experimental characterization. Usually, some sequence sites are ambiguously reconstructed, with two or more statistically plausible states. The extent to which the inferred functions and mutational effects are robust to uncertainty about the ancestral sequence has not been studied systematically. To address this issue, we reconstructed ancestral proteins in three domain families that have different functions, architectures, and degrees of uncertainty; we then experimentally characterized the functional robustness of these proteins when uncertainty was incorporated using several approaches, including sampling amino acid states from the posterior distribution at each site and incorporating the alternative amino acid state at every ambiguous site in the sequence into a single "worst plausible case" protein. In every case, qualitative conclusions about the ancestral proteins' functions and the effects of key historical mutations were robust to sequence uncertainty, with similar functions observed even when scores of alternate amino acids were incorporated. There was some variation in quantitative descriptors of function among plausible sequences, suggesting that experimentally characterizing robustness is particularly important when quantitative estimates of ancient biochemical parameters are desired. The worst plausible case method appears to provide an efficient strategy for characterizing the functional robustness of ancestral proteins to large amounts of sequence uncertainty. Sampling from the posterior distribution sometimes produced artifactually nonfunctional proteins for sequences reconstructed with substantial ambiguity. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and

Cochlear implant-related three-dimensional characteristics determined by micro-computed tomography reconstruction.

PubMed

Ni, Yusu; Dai, Peidong; Dai, Chunfu; Li, Huawei

2017-01-01

To explore the structural characteristics of the cochlea in three-dimensional (3D) detail using 3D micro-computed tomography (mCT) image reconstruction of the osseous labyrinth, with the aim of improving the structural design of electrodes, the selection of stimulation sites, and the effectiveness of cochlear implantation. Three temporal bones were selected from among adult donors' temporal bone specimens. A micro-CT apparatus (GE eXplore) was used to scan three specimens with a voxel resolution of 45 μm. We obtained about 460 slices/specimen, which produced abundant data. The osseous labyrinth images of three specimens were reconstructed from mCT. The cochlea and its spiral characteristics were measured precisely using Able Software 3D-DOCTOR. The 3D images of the osseous labyrinth, including the cochlea, vestibule, and semicircular canals, were reconstructed. The 3D models of the cochlea showed the spatial relationships and surface structural characteristics. Quantitative data concerning the cochlea and its spiral structural characteristics were analyzed with regard to cochlear implantation. The 3D reconstruction of mCT images clearly displayed the detailed spiral structural characteristics of the osseous labyrinth. Quantitative data regarding the cochlea and its spiral structural characteristics could help to improve electrode structural design, signal processing, and the effectiveness of cochlear implantation. Clin. Anat. 30:39-43, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The Influence of Sampling Density on Bayesian Age-Depth Models and Paleoclimatic Reconstructions - Lessons Learned from Lake Titicaca - Bolivia/Peru

NASA Astrophysics Data System (ADS)

Salenbien, W.; Baker, P. A.; Fritz, S. C.; Guedron, S.

2014-12-01

Lake Titicaca is one of the most important archives of paleoclimate in tropical South America, and prior studies have elucidated patterns of climate variation at varied temporal scales over the past 0.5 Ma. Yet, slow sediment accumulation rates in the main deeper basin of the lake have precluded analysis of the lake's most recent history at high resolution. To obtain a paleoclimate record of the last few millennia at multi-decadal resolution, we obtained five short cores, ranging from 139 to 181 cm in length, from the shallower Wiñaymarka sub-basin of of Lake Titicaca, where sedimentation rates are higher than in the lake's main basin. Selected cores have been analyzed for their geochemical signature by scanning XRF, diatom stratigraphy, sedimentology, and for 14C age dating. A total of 72 samples were 14C-dated using a Gas Ion Source automated high-throughput method for carbonate samples (mainly Littoridina sp. and Taphius montanus gastropod shells) at NOSAMS (Woods Hole Oceanographic Institute) with an analytical precision higher than 2%. The method has lower analytical precision compared with traditional AMS radiocarbon dating, but the lower cost enables analysis of a larger number of samples, and the error associated with the lower precision is relatively small for younger samples (< ~8,000 years). A 172-cm-long core was divided into centimeter long sections, and 47 14C dates were obtained from 1-cm intervals, averaging one date every 3-4 cm. The other cores were radiocarbon dated with a sparser sampling density that focused on visual unconformities and shell beds. The high-resolution radiocarbon analysis reveals complex sedimentation patterns in visually continuous sections, with abundant indicators of bioturbated or reworked sediments and periods of very rapid sediment accumulation. These features are not evident in the sparser sampling strategy but have significant implications for reconstructing past lake level and paleoclimatic history.

Evaluation of interpolation methods for surface-based motion compensated tomographic reconstruction for cardiac angiographic C-arm data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mueller, Kerstin; Schwemmer, Chris; Hornegger, Joachim

2013-03-15

Purpose: For interventional cardiac procedures, anatomical and functional information about the cardiac chambers is of major interest. With the technology of angiographic C-arm systems it is possible to reconstruct intraprocedural three-dimensional (3D) images from 2D rotational angiographic projection data (C-arm CT). However, 3D reconstruction of a dynamic object is a fundamental problem in C-arm CT reconstruction. The 2D projections are acquired over a scan time of several seconds, thus the projection data show different states of the heart. A standard FDK reconstruction algorithm would use all acquired data for a filtered backprojection and result in a motion-blurred image. In thismore » approach, a motion compensated reconstruction algorithm requiring knowledge of the 3D heart motion is used. The motion is estimated from a previously presented 3D dynamic surface model. This dynamic surface model results in a sparse motion vector field (MVF) defined at control points. In order to perform a motion compensated reconstruction, a dense motion vector field is required. The dense MVF is generated by interpolation of the sparse MVF. Therefore, the influence of different motion interpolation methods on the reconstructed image quality is evaluated. Methods: Four different interpolation methods, thin-plate splines (TPS), Shepard's method, a smoothed weighting function, and a simple averaging, were evaluated. The reconstruction quality was measured on phantom data, a porcine model as well as on in vivo clinical data sets. As a quality index, the 2D overlap of the forward projected motion compensated reconstructed ventricle and the segmented 2D ventricle blood pool was quantitatively measured with the Dice similarity coefficient and the mean deviation between extracted ventricle contours. For the phantom data set, the normalized root mean square error (nRMSE) and the universal quality index (UQI) were also evaluated in 3D image space. Results: The quantitative evaluation

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

Direct 4D reconstruction of parametric images incorporating anato-functional joint entropy.

PubMed

Tang, Jing; Kuwabara, Hiroto; Wong, Dean F; Rahmim, Arman

2010-08-07

We developed an anatomy-guided 4D closed-form algorithm to directly reconstruct parametric images from projection data for (nearly) irreversible tracers. Conventional methods consist of individually reconstructing 2D/3D PET data, followed by graphical analysis on the sequence of reconstructed image frames. The proposed direct reconstruction approach maintains the simplicity and accuracy of the expectation-maximization (EM) algorithm by extending the system matrix to include the relation between the parametric images and the measured data. A closed-form solution was achieved using a different hidden complete-data formulation within the EM framework. Furthermore, the proposed method was extended to maximum a posterior reconstruction via incorporation of MR image information, taking the joint entropy between MR and parametric PET features as the prior. Using realistic simulated noisy [(11)C]-naltrindole PET and MR brain images/data, the quantitative performance of the proposed methods was investigated. Significant improvements in terms of noise versus bias performance were demonstrated when performing direct parametric reconstruction, and additionally upon extending the algorithm to its Bayesian counterpart using the MR-PET joint entropy measure.

Multi-proxy Reconstructions of the Eastern Equatorial Pacific: Measuring Sr/Ca, Ba/Ca, and Li/Mg in Modern Corals Using ICP-OES

NASA Astrophysics Data System (ADS)

Cheung, A. H.; Cole, J. E.; Vetter, L.; Jimenez, G.; Thompson, D. M.; Tudhope, A. W.

2017-12-01

Sea surface temperature (SST) in the Eastern Equatorial Pacific (EEP) exhibits large variability on multiple timescales. These variations are often related to modes of climate variability that exert significant influence on global climate, such as the El Niño Southern Oscillation. However, the short length and sparsity of instrumental data in the EEP limits our ability to discern changes in this region. Geochemical signals in corals can help extend instrumental data further back in time. While δ18O and Sr/Ca are the most commonly analyzed geochemical tracers of SST in corals, they often have site-specific complications. Several alternatives (e.g., Li/Mg) have been proposed to overcome these challenges, but have yet to be applied to long climate records, in part due to the cost and time required to measure these elements. Here, we develop a new method that uses Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES) to analyze Li/Mg, Sr/Ca, and Ba/Ca ratios in coral aragonite. We apply this method to two Porites spp. corals collected from the northern Galapagos archipelago (Wolf and Darwin Islands). We specifically assess the fidelity of Li/Mg and Sr/Ca to reconstruct SST, and Ba/Ca to reconstruct upwelling conditions. Our results confirm that both Li/Mg and Sr/Ca track SST. We show that despite analytical noise, downcore reconstructions of Li/Mg have the potential to provide additional information about SST that is not present in reconstructions generated from Sr/Ca alone. Skeletal Ba/Ca shows little relationship with upwelling, perhaps because of the distance of our sites from the center of upwelling in the southern Galapagos. These results demonstrate the potential for analyzing Sr, Li, Ba, Mg simultaneously in corals with a cost- and time- efficient method, which may be applied to coral paleoclimate sites worldwide.

A heuristic statistical stopping rule for iterative reconstruction in emission tomography.

PubMed

Ben Bouallègue, F; Crouzet, J F; Mariano-Goulart, D

2013-01-01

We propose a statistical stopping criterion for iterative reconstruction in emission tomography based on a heuristic statistical description of the reconstruction process. The method was assessed for MLEM reconstruction. Based on Monte-Carlo numerical simulations and using a perfectly modeled system matrix, our method was compared with classical iterative reconstruction followed by low-pass filtering in terms of Euclidian distance to the exact object, noise, and resolution. The stopping criterion was then evaluated with realistic PET data of a Hoffman brain phantom produced using the GATE platform for different count levels. The numerical experiments showed that compared with the classical method, our technique yielded significant improvement of the noise-resolution tradeoff for a wide range of counting statistics compatible with routine clinical settings. When working with realistic data, the stopping rule allowed a qualitatively and quantitatively efficient determination of the optimal image. Our method appears to give a reliable estimation of the optimal stopping point for iterative reconstruction. It should thus be of practical interest as it produces images with similar or better quality than classical post-filtered iterative reconstruction with a mastered computation time.

The PMIP4 Contribution to CMIP6-Part 4: Scientific Objectives and Experimental Design of the PMIP4-CMIP6 Last Glacial Maximum Experiments and PMIP4 Sensitivity Experiments

NASA Technical Reports Server (NTRS)

Kageyama, Masa; Albani, Samuel; Braconnot, Pascale; Harrison, Sandy P.; Hopcroft, Peter O.; Ivanovic, Ruza F.; Lambert, Fabrice; Marti, Olivier; Peltier, W. Richard; Peterschmitt, Jean-Yves;

The PMIP4 contribution to CMIP6 - Part 4: Scientific objectives and experimental design of the PMIP4-CMIP6 Last Glacial Maximum experiments and PMIP4 sensitivity experiments

NASA Astrophysics Data System (ADS)

Kageyama, Masa; Albani, Samuel; Braconnot, Pascale; Harrison, Sandy P.; Hopcroft, Peter O.; Ivanovic, Ruza F.; Lambert, Fabrice; Marti, Olivier; Peltier, W. Richard; Peterschmitt, Jean-Yves; Roche, Didier M.; Tarasov, Lev; Zhang, Xu; Brady, Esther C.; Haywood, Alan M.; LeGrande, Allegra N.; Lunt, Daniel J.; Mahowald, Natalie M.; Mikolajewicz, Uwe; Nisancioglu, Kerim H.; Otto-Bliesner, Bette L.; Renssen, Hans; Tomas, Robert A.; Zhang, Qiong; Abe-Ouchi, Ayako; Bartlein, Patrick J.; Cao, Jian; Li, Qiang; Lohmann, Gerrit; Ohgaito, Rumi; Shi, Xiaoxu; Volodin, Evgeny; Yoshida, Kohei; Zhang, Xiao; Zheng, Weipeng

2017-11-01

The Last Glacial Maximum (LGM, 21 000 years ago) is one of the suite of paleoclimate simulations included in the current phase of the Coupled Model Intercomparison Project (CMIP6). It is an interval when insolation was similar to the present, but global ice volume was at a maximum, eustatic sea level was at or close to a minimum, greenhouse gas concentrations were lower, atmospheric aerosol loadings were higher than today, and vegetation and land-surface characteristics were different from today. The LGM has been a focus for the Paleoclimate Modelling Intercomparison Project (PMIP) since its inception, and thus many of the problems that might be associated with simulating such a radically different climate are well documented. The LGM state provides an ideal case study for evaluating climate model performance because the changes in forcing and temperature between the LGM and pre-industrial are of the same order of magnitude as those projected for the end of the 21st century. Thus, the CMIP6 LGM experiment could provide additional information that can be used to constrain estimates of climate sensitivity. The design of the Tier 1 LGM experiment (lgm) includes an assessment of uncertainties in boundary conditions, in particular through the use of different reconstructions of the ice sheets and of the change in dust forcing. Additional (Tier 2) sensitivity experiments have been designed to quantify feedbacks associated with land-surface changes and aerosol loadings, and to isolate the role of individual forcings. Model analysis and evaluation will capitalize on the relative abundance of paleoenvironmental observations and quantitative climate reconstructions already available for the LGM.

Clumped isotope calibration data for lacustrine carbonates: A progress report

NASA Astrophysics Data System (ADS)

Tripati, A.

2015-12-01

Our capacity to understand Earth's environmental history is highly dependent on the accuracy of reconstructions of past climates. Lake sediments provide important archives of terrestrial climate change, and represent an important tool for reconstructing paleohydrology, paleoclimate, paleoenvironment, and paleoaltimetry. Unfortunately, while multiple methods for constraining marine temperature exist, quantitative terrestrial proxies are scarcer - tree rings, speleothems, and leaf margin analyses have all been used with varying degrees of accuracy. Clumped isotope thermometry has the potential to be a useful instrument for determining terrestrial climates: multiple studies have shown the fraction of 13C—18O bonds in carbonates is inversely related to the temperature at which the rocks formed. We have been measuring the abundance of 13C18O16O in the CO2 produced by the dissolution of carbonate minerals in phosphoric acid in modern lake samples and comparing results to independently known estimates of lake water temperature. Here we discuss an extensive calibration dataset comprised of 132 analyses of 97 samples from 44 localities, including microbialites, tufas, and micrites endogenic carbonates, freshwater gastropods, bivalves, microbialites, and ooids.

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

PubMed

Zhang, Zhen; Xia, Shumin; Kanchanawong, Pakorn

2017-05-22

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

Reanalysis of the 1893 heat wave in France through offline data assimilation in a downscaled ensemble meteorological reconstruction

NASA Astrophysics Data System (ADS)

Devers, Alexandre; Vidal, Jean-Philippe; Lauvernet, Claire; Graff, Benjamin

2017-04-01

The knowledge of historical French weather has recently been improved through the development of the SCOPE (Spatially COherent Probabilistic Extended) Climate reconstruction, a probabilistic high-resolution daily reconstruction of precipitation and temperature covering the period 1871-2012 and based on the statistical downscaling of the Twentieth Century Reanalysis (Caillouet et al., 2016). However, historical surface observations - even though rather scarce and sparse - do exist from at least the beginning of the period considered, and this information does not currently feed SCOPE Climate reconstructions. The goal of this study is therefore to assimilate these historical observations into SCOPE Climate reconstructions in order to build a 150-year meteorological reanalysis over France. This study considers "offline" data assimilation methods - Kalman filtering methods like the Ensemble Square Root Filter - that have successfully been used in recent paleoclimate studies, i.e. at much larger temporal and spatial scales (see e.g. Bhend et al., 2012). These methods are here applied for reconstructing the 8-24 August 1893 heat wave in France, using all available daily temperature observations from that period. Temperatures reached that summer were indeed compared at the time to those of Senegal (Garnier, 2012). Results show a spatially coherent view of the heat wave at the national scale as well as a reduced uncertainty compared to initial meteorological reconstructions, thus demonstrating the added value of data assimilation. In order to assess the performance of assimilation methods in a more recent context, these methods are also used to reconstruct the well-known 3-14 August 2003 heat wave by using (1) all available stations, and (2) the same station density as in August 1893, the rest of the observations being saved for validation. This analysis allows comparing two heat waves having occurred 100 years apart in France with different associated uncertainties, in

Scattering calculation and image reconstruction using elevation-focused beams

PubMed Central

Duncan, David P.; Astheimer, Jeffrey P.; Waag, Robert C.

2009-01-01

Pressure scattered by cylindrical and spherical objects with elevation-focused illumination and reception has been analytically calculated, and corresponding cross sections have been reconstructed with a two-dimensional algorithm. Elevation focusing was used to elucidate constraints on quantitative imaging of three-dimensional objects with two-dimensional algorithms. Focused illumination and reception are represented by angular spectra of plane waves that were efficiently computed using a Fourier interpolation method to maintain the same angles for all temporal frequencies. Reconstructions were formed using an eigenfunction method with multiple frequencies, phase compensation, and iteration. The results show that the scattered pressure reduces to a two-dimensional expression, and two-dimensional algorithms are applicable when the region of a three-dimensional object within an elevation-focused beam is approximately constant in elevation. The results also show that energy scattered out of the reception aperture by objects contained within the focused beam can result in the reconstructed values of attenuation slope being greater than true values at the boundary of the object. Reconstructed sound speed images, however, appear to be relatively unaffected by the loss in scattered energy. The broad conclusion that can be drawn from these results is that two-dimensional reconstructions require compensation to account for uncaptured three-dimensional scattering. PMID:19425653

Scattering calculation and image reconstruction using elevation-focused beams.

PubMed

Duncan, David P; Astheimer, Jeffrey P; Waag, Robert C

2009-05-01

Pressure scattered by cylindrical and spherical objects with elevation-focused illumination and reception has been analytically calculated, and corresponding cross sections have been reconstructed with a two-dimensional algorithm. Elevation focusing was used to elucidate constraints on quantitative imaging of three-dimensional objects with two-dimensional algorithms. Focused illumination and reception are represented by angular spectra of plane waves that were efficiently computed using a Fourier interpolation method to maintain the same angles for all temporal frequencies. Reconstructions were formed using an eigenfunction method with multiple frequencies, phase compensation, and iteration. The results show that the scattered pressure reduces to a two-dimensional expression, and two-dimensional algorithms are applicable when the region of a three-dimensional object within an elevation-focused beam is approximately constant in elevation. The results also show that energy scattered out of the reception aperture by objects contained within the focused beam can result in the reconstructed values of attenuation slope being greater than true values at the boundary of the object. Reconstructed sound speed images, however, appear to be relatively unaffected by the loss in scattered energy. The broad conclusion that can be drawn from these results is that two-dimensional reconstructions require compensation to account for uncaptured three-dimensional scattering.

MO-FG-204-08: Optimization-Based Image Reconstruction From Unevenly Distributed Sparse Projection Views

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Huiqiao; Yang, Yi; Tang, Xiangyang

2015-06-15

Purpose: Optimization-based reconstruction has been proposed and investigated for reconstructing CT images from sparse views, as such the radiation dose can be substantially reduced while maintaining acceptable image quality. The investigation has so far focused on reconstruction from evenly distributed sparse views. Recognizing the clinical situations wherein only unevenly sparse views are available, e.g., image guided radiation therapy, CT perfusion and multi-cycle cardiovascular imaging, we investigate the performance of optimization-based image reconstruction from unevenly sparse projection views in this work. Methods: The investigation is carried out using the FORBILD and an anthropomorphic head phantoms. In the study, 82 views, whichmore » are evenly sorted out from a full (360°) axial CT scan consisting of 984 views, form sub-scan I. Another 82 views are sorted out in a similar manner to form sub-scan II. As such, a CT scan with sparse (164) views at 1:6 ratio are formed. By shifting the two sub-scans relatively in view angulation, a CT scan with unevenly distributed sparse (164) views at 1:6 ratio are formed. An optimization-based method is implemented to reconstruct images from the unevenly distributed views. By taking the FBP reconstruction from the full scan (984 views) as the reference, the root mean square (RMS) between the reference and the optimization-based reconstruction is used to evaluate the performance quantitatively. Results: In visual inspection, the optimization-based method outperforms the FBP substantially in the reconstruction from unevenly distributed, which are quantitatively verified by the RMS gauged globally and in ROIs in both the FORBILD and anthropomorphic head phantoms. The RMS increases with increasing severity in the uneven angular distribution, especially in the case of anthropomorphic head phantom. Conclusion: The optimization-based image reconstruction can save radiation dose up to 12-fold while providing acceptable image

Ultralow dose computed tomography attenuation correction for pediatric PET CT using adaptive statistical iterative reconstruction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brady, Samuel L., E-mail: samuel.brady@stjude.org; Shulkin, Barry L.

2015-02-15

Purpose: To develop ultralow dose computed tomography (CT) attenuation correction (CTAC) acquisition protocols for pediatric positron emission tomography CT (PET CT). Methods: A GE Discovery 690 PET CT hybrid scanner was used to investigate the change to quantitative PET and CT measurements when operated at ultralow doses (10–35 mA s). CT quantitation: noise, low-contrast resolution, and CT numbers for 11 tissue substitutes were analyzed in-phantom. CT quantitation was analyzed to a reduction of 90% volume computed tomography dose index (0.39/3.64; mGy) from baseline. To minimize noise infiltration, 100% adaptive statistical iterative reconstruction (ASiR) was used for CT reconstruction. PET imagesmore » were reconstructed with the lower-dose CTAC iterations and analyzed for: maximum body weight standardized uptake value (SUV{sub bw}) of various diameter targets (range 8–37 mm), background uniformity, and spatial resolution. Radiation dose and CTAC noise magnitude were compared for 140 patient examinations (76 post-ASiR implementation) to determine relative dose reduction and noise control. Results: CT numbers were constant to within 10% from the nondose reduced CTAC image for 90% dose reduction. No change in SUV{sub bw}, background percent uniformity, or spatial resolution for PET images reconstructed with CTAC protocols was found down to 90% dose reduction. Patient population effective dose analysis demonstrated relative CTAC dose reductions between 62% and 86% (3.2/8.3–0.9/6.2). Noise magnitude in dose-reduced patient images increased but was not statistically different from predose-reduced patient images. Conclusions: Using ASiR allowed for aggressive reduction in CT dose with no change in PET reconstructed images while maintaining sufficient image quality for colocalization of hybrid CT anatomy and PET radioisotope uptake.« less

Late Quaternary paleoclimate of western Alaska inferred from fossil chironomids and its relation to vegetation histories

NASA Astrophysics Data System (ADS)

Kurek, Joshua; Cwynar, Les C.; Ager, Thomas A.; Abbott, Mark B.; Edwards, Mary E.

2009-05-01

Fossil Chironomidae assemblages (with a few Chaoboridae and Ceratopogonidae) from Zagoskin and Burial Lakes in western Alaska provide quantitative reconstructions of mean July air temperatures for periods of the late-middle Wisconsin (˜39,000-34,000 cal yr B.P.) to the present. Inferred temperatures are compared with previously analyzed pollen data from each site summarized here by indirect ordination. Paleotemperature trends reveal substantial differences in the timing of climatic warming following the late Wisconsin at each site, although chronological uncertainty exists. Zagoskin Lake shows early warming beginning at about 21,000 cal yr B.P., whereas warming at Burial Lake begins ˜4000 years later. Summer climates during the last glacial maximum (LGM) were on average ˜3.5 °C below the modern temperatures at each site. Major shifts in vegetation occurred from ˜19,000 to 10,000 cal yr B.P. at Zagoskin Lake and from ˜17,000 to 10,000 cal yr B.P. at Burial Lake. Vegetation shifts followed climatic warming, when temperatures neared modern values. Both sites provide evidence of an early postglacial thermal maximum at ˜12,300 cal yr B.P. These chironomid records, combined with other insect-based climatic reconstructions from Beringia, indicate that during the LGM: (1) greater continentality likely influenced regions adjacent to the Bering Land Bridge and (2) summer climates were, at times, not dominated by severe cold.

Protistan Diversity in the Arctic: A Case of Paleoclimate Shaping Modern Biodiversity?

PubMed Central

Stoeck, Thorsten; Kasper, Jennifer; Bunge, John; Leslin, Chesley; Ilyin, Valya; Epstein, Slava

2007-01-01

Background The impact of climate on biodiversity is indisputable. Climate changes over geological time must have significantly influenced the evolution of biodiversity, ultimately leading to its present pattern. Here we consider the paleoclimate data record, inferring that present-day hot and cold environments should contain, respectively, the largest and the smallest diversity of ancestral lineages of microbial eukaryotes. Methodology/Principal Findings We investigate this hypothesis by analyzing an original dataset of 18S rRNA gene sequences from Western Greenland in the Arctic, and data from the existing literature on 18S rRNA gene diversity in hydrothermal vent, temperate sediments, and anoxic water column communities. Unexpectedly, the community from the cold environment emerged as one of the richest observed to date in protistan species, and most diverse in ancestral lineages. Conclusions/Significance This pattern is consistent with natural selection sweeps on aerobic non-psychrophilic microbial eukaryotes repeatedly caused by low temperatures and global anoxia of snowball Earth conditions. It implies that cold refuges persisted through the periods of greenhouse conditions, which agrees with some, although not all, current views on the extent of the past global cooling and warming events. We therefore identify cold environments as promising targets for microbial discovery. PMID:17710128

Investigating the Influence of Vegetation Type on Modern Leaf Wax Hydrogen Isotopes from a High Latitude Ombrotrophic Bog to Inform Paleoclimate Interpretation

NASA Astrophysics Data System (ADS)

Balascio, N.; D'Andrea, W. J.; Anderson, R. S.

2016-12-01

Leaf wax hydrogen isotopes have been used to track changes in the isotopic composition of meteoric waters in a variety of locations. However, leaf wax compounds preserved in sedimentary environments reflect a mix of plant sources that can have a large range of molecular distributions and biosynthetic fractionation factors potentially complicating paleoclimate interpretations. Here we attempt to constrain the influence of vegetation type on leaf wax hydrogen isotope values at an ombrotrophic bog in northern Norway. We present: (i) δD values of n-alkanes from modern bog vegetation to establish the influence of vegetation type on n-alkane distributions and to provide a site-specific assessment of the biosynthetic isotopic fractionation, and (ii) δD values of n-alkanes from a sediment core spanning the last 10 ka where vegetation changes have been reconstructed based on pollen analysis. We found 14 different vegetation types growing on the bog surface that have average chain lengths from 25 to 30.5 and δD values of n-C25 to n-C33 ranging from -197‰ to -116‰. These samples also have a range of δD values among n-alkane homologues, from 1‰ to 33‰. Based on isotopic measurements of modern bog water, we calculate the average apparent fractionation of n-alkanes to be -108 ± 22‰. Sedimentary δD values of n-C25 to n-C33 over the last 10 ka range from -229 to -158‰ with distinct trends among mid- and long-chain length homologues. Changes in chain lengths and δD values, at times, correspond to vegetation shifts documented by pollen data, but also show unique trends that we interpret to represent variations in local precipitation isotopes related to past hydroclimate change.

Compound Specific δD Values Across a Tropical Precipitation Gradient: Implications for Low-latitude Paleoclimate Reconstructions

NASA Astrophysics Data System (ADS)

Douglas, P. M.; Pagani, M.; Brenner, M.; Curtis, J. H.; Hodell, D. A.

2009-12-01

Hydrogen isotopes (δD) of terrestrial and aquatic plant lipids have been used to reconstruct past continental hydrological change in low-latitude settings. Generally, lipid δD values correlate strongly with the isotopic composition of precipitation, although evapotranspiration and biosynthetic fractionation are important influences on the δD of leaf waxes. Few studies have focused on constraining the controls on δD values of lipids in the tropics, where high evaporation rates impact both leaf and lake water isotopic composition. We measured δD values in surface waters and lipids extracted from leaves, lake sediments and soils along a latitudinal transect across Mexico, Guatemala and Honduras, a region with distinct dry and wet seasons. The δD values of leaf waxes extracted from lake sediments are positively correlated with surface water δD values (r = 0.73). The apparent fractionation between stream waters (inferred to represent plant source water) and leaf waxes (ɛlw) is negatively correlated with mean annual precipitation (r = -0.89), likely due to greater evapotranspiration and D-enriched leaf water in drier climates. δD values of leaf waxes extracted directly from leaves collected during the rainy season (August 2008) are similarly correlated with surface water δD values (r = 0.85). Leaf ɛlw values, however, are not significantly correlated with mean annual precipitation. It is possible that the correlation between ɛlw and mean annual precipitation in lake sediment leaf waxes is related to seasonal variability in evapotranspiration. Specifically, lake sediment leaf waxes could predominantly represent production during the dry season when evapotranspiration effects are strongest and when many tropical tree species shed their leaves. Possible seasonal variability in fractionation between source water and leaf wax lipids should be taken into account when interpreting leaf wax δD records from tropical locations, both in terms of controlling for long

Climatic thresholds for pedogenic iron oxides under aerobic conditions: Processes and their significance in paleoclimate reconstruction

NASA Astrophysics Data System (ADS)

Long, Xiaoyong; Ji, Junfeng; Barrón, Vidal; Torrent, José

2016-10-01

Iron oxides are widely distributed across the surface of the Earth as a result of the aerobic weathering of primary Fe-bearing minerals. Pedogenic iron oxides which consist mainly of hematite (Hm), goethite (Gt), maghemite (Mgh), are often concentrated synchronously in aerobic soils under low to moderate rainfall regimes. Magnetic susceptibility (χ) and redness, which respectively reflect the content of Mgh and Hm in soils, are considered reasonable pedogenic and climatic indicators in soil taxonomy and paleorainfall reconstruction. However, under high rainfall regimes, the grain growth of Mgh and transformation to Hm, combined with the prior formation of Gt under conditions of high relative humidity (RH), can result in magnetic reduction and dramatic yellowing of soils and sediments, which explains the existence of rainfall thresholds for Mgh and Hm at a large scale even before the pedogenic environment turns anaerobic. In order to capture the rainfall thresholds for Mgh and Hm occurring under aerobic conditions, we explored a tropical transect across a granitic region where the soil color turned from red to yellow under a wide rainfall range of 900-2200 mm/yr and a corresponding mean annual RH range of 77%-85%. We observed a lower rainfall threshold of ∼1500 mm/yr and a corresponding RH ∼80% for Mgh and Hm along this transect, as well as a higher rainfall threshold of ∼1700 mm/yr and a corresponding RH of ∼81% for Gt and total pedogenic iron oxides (citrate/bicarbonate/dithionite-extractable Fe, Fed). Cross-referencing with comparable studies in temperate and subtropical regions, we noted that the rainfall or RH thresholds for Fed and Hm or Mgh likewise increase with temperature. Moreover, the different thresholds for total and individual iron oxide phase indicates that a negative correlation between chemical weathering intensity and redness or χ in sediment sequences can occur under the prevalent climate regime just between their thresholds. Finally

Alpha image reconstruction (AIR): A new iterative CT image reconstruction approach using voxel-wise alpha blending

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hofmann, Christian; Sawall, Stefan; Knaup, Michael

2014-06-15

Purpose: Iterative image reconstruction gains more and more interest in clinical routine, as it promises to reduce image noise (and thereby patient dose), to reduce artifacts, or to improve spatial resolution. Among vendors and researchers, however, there is no consensus of how to best achieve these aims. The general approach is to incorporatea priori knowledge into iterative image reconstruction, for example, by adding additional constraints to the cost function, which penalize variations between neighboring voxels. However, this approach to regularization in general poses a resolution noise trade-off because the stronger the regularization, and thus the noise reduction, the stronger themore » loss of spatial resolution and thus loss of anatomical detail. The authors propose a method which tries to improve this trade-off. The proposed reconstruction algorithm is called alpha image reconstruction (AIR). One starts with generating basis images, which emphasize certain desired image properties, like high resolution or low noise. The AIR algorithm reconstructs voxel-specific weighting coefficients that are applied to combine the basis images. By combining the desired properties of each basis image, one can generate an image with lower noise and maintained high contrast resolution thus improving the resolution noise trade-off. Methods: All simulations and reconstructions are performed in native fan-beam geometry. A water phantom with resolution bar patterns and low contrast disks is simulated. A filtered backprojection (FBP) reconstruction with a Ram-Lak kernel is used as a reference reconstruction. The results of AIR are compared against the FBP results and against a penalized weighted least squares reconstruction which uses total variation as regularization. The simulations are based on the geometry of the Siemens Somatom Definition Flash scanner. To quantitatively assess image quality, the authors analyze line profiles through resolution patterns to define a

Quantitative ultrasonic evaluation of concrete structures using one-sided access

NASA Astrophysics Data System (ADS)

Khazanovich, Lev; Hoegh, Kyle

2016-02-01

Nondestructive diagnostics of concrete structures is an important and challenging problem. A recent introduction of array ultrasonic dry point contact transducer systems offers opportunities for quantitative assessment of the subsurface condition of concrete structures, including detection of defects and inclusions. The methods described in this paper are developed for signal interpretation of shear wave impulse response time histories from multiple fixed distance transducer pairs in a self-contained ultrasonic linear array. This included generalizing Kirchoff migration-based synthetic aperture focusing technique (SAFT) reconstruction methods to handle the spatially diverse transducer pair locations, creating expanded virtual arrays with associated reconstruction methods, and creating automated reconstruction interpretation methods for reinforcement detection and stochastic flaw detection. Interpretation of the reconstruction techniques developed in this study were validated using the results of laboratory and field forensic studies. Applicability of the developed methods for solving practical engineering problems was demonstrated.

Paleohydrology Reconstruction of the Tropical South America for the Past 1.6 Million Years.

NASA Astrophysics Data System (ADS)

Oliveira, A. S.; Baker, P. A.; Silva, C. G.; Dwyer, G. S.; Rigsby, C. A.; Chiessi, C. M.

2016-12-01

The western Atlantic equatorial margin has been recognized as an important part of global climate change. It is responsible for the transfer of moisture to South America and, heat and fresh water to the northern hemisphere. It might hold answers to past and present global climate. We reconstructed the last 1.6 million years of the paleoclimatic record of the Tropical South American to assess a long period of oceanic and atmospheric variability, which still remains unknown to science. Paleoclimate reconstructions of the Tropical South American are determined on a sediment core located on the Brazilian continental slope. High-resolution XRF analyses of Fe, Ti, K and Ca are used to define the paleohydrologic evolution. Here we present elemental ratios of Ti/Ca and Fe/K, to determine variability in Tropical South America. Differences in sediment input observed on Fe/K and Ti/Ca ratios suggest periods of increased chemical weathering and precipitation. Comparison of our data with the Cariaco basin Molybdenum (Mo) records, suggests that the Intertropical Convergence Zone (ITCZ) is triggering wet periods on Tropical South America, distinguishing a clear North-South anti-phase over the last 600 ka. Southward displacement of the ITCZ in the Mid-Pleistocene Transition, indicates changes in the variability mode of the ITCZ N-S excursion, modulating the precipitation over Tropical South America. We also show that extensive northward migration of Antarctic Polar Front induces a drastic change in the Tropical South America hydrological system, triggering long periods of drought, potentially driven by cooler sea surface temperature of the South Atlantic. This study is funded by Capes- IODP 38/2014 and the Duke University.

Chronological reconstruction of eolianites and transversal mobile dunes of northwest coast of Ceará State - Brazil, in the last 3000 cal yrs BP

NASA Astrophysics Data System (ADS)

Castro, João Wagner Alencar; Malta, Julia Varella; Miguel, Lucas Lavo Antonio Jimo; Cabral, Caique Lima; Passemilio, Alvaro Balmant

2017-10-01

Dunefields are very common in the northern coastal zone of northeast Brazil. They have the potential to yield important information about paleoclimate, paleo-winds and regional winds and their response to sea-level fluctuations during the Holocene. We reconstructed the coastal dunes geochronological evolution of northwest Ceará State - Brazil, in the last 3000 cal yrs BP, using detailed analyses of lithostratigraphy, microfossil (foraminifera), wind regime, dune monitoring and 8 radiocarbon dates. The chronology was based on 14C dating in eolianites and monitoring transversal mobile dunes movement processes. Radiocarbon date results indicated that the dunes corresponding to eolianites revealed ages between 2760-2480 and 980-750 cal yrs BP, suggesting that the vast transversal mobile dunefields were formed after this period in similar condition to the current sea-level. We considered that the material transportation by the prevailing east winds towards the transversal dunes is estimated in the order of 11.0 m/year, thus the current aeolian system is less than 1000 yrs BP.

Quantitative myocardial blood flow imaging with integrated time-of-flight PET-MR.

PubMed

Kero, Tanja; Nordström, Jonny; Harms, Hendrik J; Sörensen, Jens; Ahlström, Håkan; Lubberink, Mark

2017-12-01

The use of integrated PET-MR offers new opportunities for comprehensive assessment of cardiac morphology and function. However, little is known on the quantitative accuracy of cardiac PET imaging with integrated time-of-flight PET-MR. The aim of the present work was to validate the GE Signa PET-MR scanner for quantitative cardiac PET perfusion imaging. Eleven patients (nine male; mean age 59 years; range 46-74 years) with known or suspected coronary artery disease underwent 15 O-water PET scans at rest and during adenosine-induced hyperaemia on a GE Discovery ST PET-CT and a GE Signa PET-MR scanner. PET-MR images were reconstructed using settings recommended by the manufacturer, including time-of-flight (TOF). Data were analysed semi-automatically using Cardiac VUer software, resulting in both parametric myocardial blood flow (MBF) images and segment-based MBF values. Correlation and agreement between PET-CT-based and PET-MR-based MBF values for all three coronary artery territories were assessed using regression analysis and intra-class correlation coefficients (ICC). In addition to the cardiac PET-MR reconstruction protocol as recommended by the manufacturer, comparisons were made using a PET-CT resolution-matched reconstruction protocol both without and with TOF to assess the effect of time-of-flight and reconstruction parameters on quantitative MBF values. Stress MBF data from one patient was excluded due to movement during the PET-CT scanning. Mean MBF values at rest and stress were (0.92 ± 0.12) and (2.74 ± 1.37) mL/g/min for PET-CT and (0.90 ± 0.23) and (2.65 ± 1.15) mL/g/min for PET-MR (p = 0.33 and p = 0.74). ICC between PET-CT-based and PET-MR-based regional MBF was 0.98. Image quality was improved with PET-MR as compared to PET-CT. ICC between PET-MR-based regional MBF with and without TOF and using different filter and reconstruction settings was 1.00. PET-MR-based MBF values correlated well with PET-CT-based MBF values and

Reconstruction method for fringe projection profilometry based on light beams.

PubMed

Li, Xuexing; Zhang, Zhijiang; Yang, Chen

2016-12-01

A novel reconstruction method for fringe projection profilometry, based on light beams, is proposed and verified by experiments. Commonly used calibration techniques require the parameters of projector calibration or the reference planes placed in many known positions. Obviously, introducing the projector calibration can reduce the accuracy of the reconstruction result, and setting the reference planes to many known positions is a time-consuming process. Therefore, in this paper, a reconstruction method without projector's parameters is proposed and only two reference planes are introduced. A series of light beams determined by the subpixel point-to-point map on the two reference planes combined with their reflected light beams determined by the camera model are used to calculate the 3D coordinates of reconstruction points. Furthermore, the bundle adjustment strategy and the complementary gray-code phase-shifting method are utilized to ensure the accuracy and stability. Qualitative and quantitative comparisons as well as experimental tests demonstrate the performance of our proposed approach, and the measurement accuracy can reach about 0.0454 mm.

Facebook Facts: Breast Reconstruction Patient-Reported Outcomes Using Social Media.

PubMed

Tang, Sherry Y Q; Israel, Jacqueline S; Poore, Samuel O; Afifi, Ahmed M

2018-05-01

Social media are used for information sharing among patients with similar health conditions, and analysis of social media activity could inform clinical decision-making. The aim of this study was to use Facebook to evaluate a cohort of individuals' perceptions of and satisfaction with breast reconstruction. In this observational study, the authors collected and analyzed posts pertaining to autologous and implant-based breast reconstruction from active Facebook groups. Patient satisfaction data were categorized, and a thematic analysis of posts was conducted. Qualitative posts were grouped based on common themes and quantitatively compared using frequency and chi-square analysis. The authors evaluated 500 posts from two Facebook groups. Two hundred sixty-four posts referenced deep inferior epigastric perforator (DIEP) flap reconstruction and 117 were related to implant-based reconstruction. Among individuals referencing DIEP flap reconstruction, 52 percent were satisfied, compared with 20 percent of individuals who referenced satisfaction with implant-based reconstruction (p < 0.0001). Individuals posting about DIEP flaps reported a higher rate of unexpected side effects (p < 0.001) and numbness (p = 0.004). When referencing implant-based reconstruction, individuals reported significantly higher rates of infection, contracture, and implant failure (p < 0.001). Based on the authors' review of social media activity, individuals undergoing DIEP flap breast reconstruction expressed relatively high individual satisfaction despite difficult postoperative recovery. Individuals who referenced implant-based reconstruction mentioned infection and implant failure, leading to high rates of dissatisfaction. Social media appear to provide informational and emotional support to patients. Plastic surgeons can use social media to gather unbiased information of patients' experience to inform clinical conversation and guide clinical practice.

Efficient robust reconstruction of dynamic PET activity maps with radioisotope decay constraints.

PubMed

Gao, Fei; Liu, Huafeng; Shi, Pengcheng

2010-01-01

Dynamic PET imaging performs sequence of data acquisition in order to provide visualization and quantification of physiological changes in specific tissues and organs. The reconstruction of activity maps is generally the first step in dynamic PET. State space Hinfinity approaches have been proved to be a robust method for PET image reconstruction where, however, temporal constraints are not considered during the reconstruction process. In addition, the state space strategies for PET image reconstruction have been computationally prohibitive for practical usage because of the need for matrix inversion. In this paper, we present a minimax formulation of the dynamic PET imaging problem where a radioisotope decay model is employed as physics-based temporal constraints on the photon counts. Furthermore, a robust steady state Hinfinity filter is developed to significantly improve the computational efficiency with minimal loss of accuracy. Experiments are conducted on Monte Carlo simulated image sequences for quantitative analysis and validation.

Quantitative PET/CT scanner performance characterization based upon the society of nuclear medicine and molecular imaging clinical trials network oncology clinical simulator phantom.

PubMed

Sunderland, John J; Christian, Paul E

2015-01-01

The Clinical Trials Network (CTN) of the Society of Nuclear Medicine and Molecular Imaging (SNMMI) operates a PET/CT phantom imaging program using the CTN's oncology clinical simulator phantom, designed to validate scanners at sites that wish to participate in oncology clinical trials. Since its inception in 2008, the CTN has collected 406 well-characterized phantom datasets from 237 scanners at 170 imaging sites covering the spectrum of commercially available PET/CT systems. The combined and collated phantom data describe a global profile of quantitative performance and variability of PET/CT data used in both clinical practice and clinical trials. Individual sites filled and imaged the CTN oncology PET phantom according to detailed instructions. Standard clinical reconstructions were requested and submitted. The phantom itself contains uniform regions suitable for scanner calibration assessment, lung fields, and 6 hot spheric lesions with diameters ranging from 7 to 20 mm at a 4:1 contrast ratio with primary background. The CTN Phantom Imaging Core evaluated the quality of the phantom fill and imaging and measured background standardized uptake values to assess scanner calibration and maximum standardized uptake values of all 6 lesions to review quantitative performance. Scanner make-and-model-specific measurements were pooled and then subdivided by reconstruction to create scanner-specific quantitative profiles. Different makes and models of scanners predictably demonstrated different quantitative performance profiles including, in some cases, small calibration bias. Differences in site-specific reconstruction parameters increased the quantitative variability among similar scanners, with postreconstruction smoothing filters being the most influential parameter. Quantitative assessment of this intrascanner variability over this large collection of phantom data gives, for the first time, estimates of reconstruction variance introduced into trials from allowing

Comparison of tree-ring δ18O and meteorological data from Java island, Indonesia

NASA Astrophysics Data System (ADS)

Watanabe, Y.; Hisamochi, R.; Sano, M.; Nakatsuka, T.; Tazuru, S.; Sugiyama, J.; Tsuda, T.; Tagami, T.

2016-12-01

Tree-ring has been widely recognized as a powerful tool to reconstruct the paleoclimate of terrestrial areas because it has an advantage of exact dating with annual resolution. Paleoclimate reconstruction based on tree-ring is, however, extremely limited in the tropics because it is difficult to acquire long-lived wood samples with annual tree-ring. In this study, as for four teak samples from central Java and six teak samples from western Java, we measured teak δ18O values on annual scale over the last 70 years to evaluate the conformity among oxygen isotopic variations of Javanese teak trees. As a result, oxygen isotopic time series of ten teak trees has significant correlations between each other, suggesting that Javanese teak δ18O values are affected by common climatic factor. In addition, there are significant positive correlations between teak δ18O values and precipitation during the dry season prior to growing season.

Reconstruction of three-dimensional porous media using a single thin section

NASA Astrophysics Data System (ADS)

Tahmasebi, Pejman; Sahimi, Muhammad

2012-06-01

The purpose of any reconstruction method is to generate realizations of two- or multiphase disordered media that honor limited data for them, with the hope that the realizations provide accurate predictions for those properties of the media for which there are no data available, or their measurement is difficult. An important example of such stochastic systems is porous media for which the reconstruction technique must accurately represent their morphology—the connectivity and geometry—as well as their flow and transport properties. Many of the current reconstruction methods are based on low-order statistical descriptors that fail to provide accurate information on the properties of heterogeneous porous media. On the other hand, due to the availability of high resolution two-dimensional (2D) images of thin sections of a porous medium, and at the same time, the high cost, computational difficulties, and even unavailability of complete 3D images, the problem of reconstructing porous media from 2D thin sections remains an outstanding unsolved problem. We present a method based on multiple-point statistics in which a single 2D thin section of a porous medium, represented by a digitized image, is used to reconstruct the 3D porous medium to which the thin section belongs. The method utilizes a 1D raster path for inspecting the digitized image, and combines it with a cross-correlation function, a grid splitting technique for deciding the resolution of the computational grid used in the reconstruction, and the Shannon entropy as a measure of the heterogeneity of the porous sample, in order to reconstruct the 3D medium. It also utilizes an adaptive technique for identifying the locations and optimal number of hard (quantitative) data points that one can use in the reconstruction process. The method is tested on high resolution images for Berea sandstone and a carbonate rock sample, and the results are compared with the data. To make the comparison quantitative, two sets

Region of interest processing for iterative reconstruction in x-ray computed tomography

NASA Astrophysics Data System (ADS)

Kopp, Felix K.; Nasirudin, Radin A.; Mei, Kai; Fehringer, Andreas; Pfeiffer, Franz; Rummeny, Ernst J.; Noël, Peter B.

2015-03-01

The recent advancements in the graphics card technology raised the performance of parallel computing and contributed to the introduction of iterative reconstruction methods for x-ray computed tomography in clinical CT scanners. Iterative maximum likelihood (ML) based reconstruction methods are known to reduce image noise and to improve the diagnostic quality of low-dose CT. However, iterative reconstruction of a region of interest (ROI), especially ML based, is challenging. But for some clinical procedures, like cardiac CT, only a ROI is needed for diagnostics. A high-resolution reconstruction of the full field of view (FOV) consumes unnecessary computation effort that results in a slower reconstruction than clinically acceptable. In this work, we present an extension and evaluation of an existing ROI processing algorithm. Especially improvements for the equalization between regions inside and outside of a ROI are proposed. The evaluation was done on data collected from a clinical CT scanner. The performance of the different algorithms is qualitatively and quantitatively assessed. Our solution to the ROI problem provides an increase in signal-to-noise ratio and leads to visually less noise in the final reconstruction. The reconstruction speed of our technique was observed to be comparable with other previous proposed techniques. The development of ROI processing algorithms in combination with iterative reconstruction will provide higher diagnostic quality in the near future.

Sub-aperture switching based ptychographic iterative engine (sasPIE) method for quantitative imaging

NASA Astrophysics Data System (ADS)

Sun, Aihui; Kong, Yan; Jiang, Zhilong; Yu, Wei; Liu, Fei; Xue, Liang; Wang, Shouyu; Liu, Cheng

2018-03-01

Though ptychographic iterative engine (PIE) has been widely adopted in the quantitative micro-imaging with various illuminations as visible light, X-ray and electron beam, the mechanical inaccuracy in the raster scanning of the sample relative to the illumination always degrades the reconstruction quality seriously and makes the resolution reached much lower than that determined by the numerical aperture of the optical system. To overcome this disadvantage, the sub-aperture switching based PIE method is proposed: the mechanical scanning in the common PIE is replaced by the sub-aperture switching, and the reconstruction error related to the positioning inaccuracy is completely avoided. The proposed technique remarkably improves the reconstruction quality, reduces the complexity of the experimental setup and fundamentally accelerates the data acquisition and reconstruction.

Climate regime shifts in paleoclimate time series from the Yucatán Peninsula: from the Preclassic to Classic period

NASA Astrophysics Data System (ADS)

Polanco Martínez, Josue M.; Medina-Elizalde, Martin; Burns, Stephen J.; Jiang, Xiuyang; Shen, Chuan-Chou

2015-04-01

It has been widely accepted by the paleoclimate and archaeology communities that extreme climate events (especially droughts) and past climate change played an important role in the cultural changes that occurred in at least some parts of the Maya Lowlands, from the Pre-Classic (2000 BC to 250 AD) to Post-Classic periods (1000 to 1521 AD) [1, 2]. In particular, a large number of studies suggest that the decline of the Maya civilization in the Terminal Classic Period was greatly influenced by prolonged severe drought events that probably triggered significant societal disruptions [1, 3, 4, 5]. Going further on these issues, the aim of this work is to detect climate regime shifts in several paleoclimate time series from the Yucatán Peninsula (México) that have been used as rainfall proxies [3, 5, 6, 7]. In order to extract information from the paleoclimate data studied, we have used a change point method [8] as implemented in the R package strucchange, as well as the RAMFIT method [9]. The preliminary results show for all the records analysed a prominent regime shift between 400 to 200 BCE (from a noticeable increase to a remarkable fall in precipitation), which is strongest in the recently obtained stalagmite (Itzamna) delta18-O precipitation record [7]. References [1] Gunn, J. D., Matheny, R. T., Folan, W. J., 2002. Climate-change studies in the Maya area. Ancient Mesoamerica, 13(01), 79-84. [2] Yaeger, J., Hodell, D. A., 2008. The collapse of Maya civilization: assessing the interaction of culture, climate, and environment. El Niño, Catastrophism, and Culture Change in Ancient America, 197-251. [3] Hodell, D. A., Curtis, J. H., Brenner, M., 1995. Possible role of climate in the collapse of Classic Maya civilization. Nature, 375(6530), 391-394. [4] Aimers, J., Hodell, D., 2011. Societal collapse: Drought and the Maya. Nature 479(7371), 44-45 (2011). [5] Medina-Elizalde, M., Rohling, E. J., 2012. Collapse of Classic Maya civilization related to modest reduction

Nonlinear detection of paleoclimate-variability transitions possibly related to human evolution

NASA Astrophysics Data System (ADS)

Donges, J. F.; Donner, R. V.; Trauth, M. H.; Marwan, N.; Schellnhuber, H. J.; Kurths, J.

2012-04-01

Potential paleoclimatic driving mechanisms acting on human evolution present an open problem of cross-disciplinary scientific interest. The analysis of paleoclimate archives encoding the environmental variability in East Africa during the last 5 Ma (million years) has triggered an ongoing debate about possible candidate processes and evolutionary mechanisms. In this work, we apply a novel nonlinear statistical technique, recurrence network analysis, to three distinct marine records of terrigenous dust flux. Our method enables us to identify three epochs with transitions between qualitatively different types of environmental variability in North and East Africa during the (i) Mid-Pliocene (3.35-3.15 Ma BP (before present)), (ii) Early Pleistocene (2.25-1.6 Ma BP), and (iii) Mid-Pleistocene (1.1-0.7 Ma BP). A deeper examination of these transition periods reveals potential climatic drivers, including (i) large-scale changes in ocean currents due to a spatial shift of the Indonesian throughflow in combination with an intensification of Northern Hemisphere glaciation, (ii) a global reorganization of the atmospheric Walker circulation induced in the tropical Pacific and Indian Ocean, and (iii) shifts in the dominating temporal variability pattern of glacial activity during the Mid-Pleistocene, respectively. A reexamination of the available fossil record demonstrates statistically significant coincidences between the detected transition periods and major steps in hominin evolution. This suggests that the observed shifts between more regular and more erratic environmental variability may have acted as a trigger for rapid change in the development of humankind in Africa.

A new space-time characterization of Northern Hemisphere drought in model simulations of the past and future as compared to the paleoclimate record

NASA Astrophysics Data System (ADS)

Coats, S.; Smerdon, J. E.; Stevenson, S.; Fasullo, J.; Otto-Bliesner, B. L.

2017-12-01

The observational record, which provides only limited sampling of past climate variability, has made it difficult to quantitatively analyze the complex spatio-temporal character of drought. To provide a more complete characterization of drought, machine learning based methods that identify drought in three-dimensional space-time are applied to climate model simulations of the last millennium and future, as well as tree-ring based reconstructions of hydroclimate over the Northern Hemisphere extratropics. A focus is given to the most persistent and severe droughts of the past 1000 years. Analyzing reconstructions and simulations in this context allows for a validation of the spatio-temporal character of persistent and severe drought in climate model simulations. Furthermore, the long records provided by the reconstructions and simulations, allows for sufficient sampling to constrain projected changes to the spatio-temporal character of these features using the reconstructions. Along these lines, climate models suggest that there will be large increases in the persistence and severity of droughts over the coming century, but little change in their spatial extent. These models, however, exhibit biases in the spatio-temporal character of persistent and severe drought over parts of the Northern Hemisphere, which may undermine their usefulness for future projections. Despite these limitations, and in contrast to previous claims, there are no systematic changes in the character of persistent and severe droughts in simulations of the historical interval. This suggests that climate models are not systematically overestimating the hydroclimate response to anthropogenic forcing over this period, with critical implications for confidence in hydroclimate projections.

BPF-type region-of-interest reconstruction for parallel translational computed tomography.

PubMed

Wu, Weiwen; Yu, Hengyong; Wang, Shaoyu; Liu, Fenglin

2017-01-01

The objective of this study is to present and test a new ultra-low-cost linear scan based tomography architecture. Similar to linear tomosynthesis, the source and detector are translated in opposite directions and the data acquisition system targets on a region-of-interest (ROI) to acquire data for image reconstruction. This kind of tomographic architecture was named parallel translational computed tomography (PTCT). In previous studies, filtered backprojection (FBP)-type algorithms were developed to reconstruct images from PTCT. However, the reconstructed ROI images from truncated projections have severe truncation artefact. In order to overcome this limitation, we in this study proposed two backprojection filtering (BPF)-type algorithms named MP-BPF and MZ-BPF to reconstruct ROI images from truncated PTCT data. A weight function is constructed to deal with data redundancy for multi-linear translations modes. Extensive numerical simulations are performed to evaluate the proposed MP-BPF and MZ-BPF algorithms for PTCT in fan-beam geometry. Qualitative and quantitative results demonstrate that the proposed BPF-type algorithms cannot only more accurately reconstruct ROI images from truncated projections but also generate high-quality images for the entire image support in some circumstances.

Error analysis and correction in wavefront reconstruction from the transport-of-intensity equation

PubMed Central

Barbero, Sergio; Thibos, Larry N.

2007-01-01

Wavefront reconstruction from the transport-of-intensity equation (TIE) is a well-posed inverse problem given smooth signals and appropriate boundary conditions. However, in practice experimental errors lead to an ill-condition problem. A quantitative analysis of the effects of experimental errors is presented in simulations and experimental tests. The relative importance of numerical, misalignment, quantization, and photodetection errors are shown. It is proved that reduction of photodetection noise by wavelet filtering significantly improves the accuracy of wavefront reconstruction from simulated and experimental data. PMID:20052302

Sensitivity of leaf size and shape to climate: Global patterns and paleoclimatic applications

USGS Publications Warehouse

Peppe, D.J.; Royer, D.L.; Cariglino, B.; Oliver, S.Y.; Newman, S.; Leight, E.; Enikolopov, G.; Fernandez-Burgos, M.; Herrera, F.; Adams, J.M.; Correa, E.; Currano, E.D.; Erickson, J.M.; Hinojosa, L.F.; Hoganson, J.W.; Iglesias, A.; Jaramillo, C.A.; Johnson, K.R.; Jordan, G.J.; Kraft, N.J.B.; Lovelock, E.C.; Lusk, C.H.; Niinemets, U.; Penuelas, J.; Rapson, G.; Wing, S.L.; Wright, I.J.

2011-01-01

Paleobotanists have long used models based on leaf size and shape to reconstruct paleoclimate. However, most models incorporate a single variable or use traits that are not physiologically or functionally linked to climate, limiting their predictive power. Further, they often underestimate paleotemperature relative to other proxies. Here we quantify leaf-climate correlations from 92 globally distributed, climatically diverse sites, and explore potential confounding factors. Multiple linear regression models for mean annual temperature (MAT) and mean annual precipitation (MAP) are developed and applied to nine well-studied fossil floras. We find that leaves in cold climates typically have larger, more numerous teeth, and are more highly dissected. Leaf habit (deciduous vs evergreen), local water availability, and phylogenetic history all affect these relationships. Leaves in wet climates are larger and have fewer, smaller teeth. Our multivariate MAT and MAP models offer moderate improvements in precision over univariate approaches (??4.0 vs 4.8??C for MAT) and strong improvements in accuracy. For example, our provisional MAT estimates for most North American fossil floras are considerably warmer and in better agreement with independent paleoclimate evidence. Our study demonstrates that the inclusion of additional leaf traits that are functionally linked to climate improves paleoclimate reconstructions. This work also illustrates the need for better understanding of the impact of phylogeny and leaf habit on leaf-climate relationships. ?? 2011 The Authors. New Phytologist ?? 2011 New Phytologist Trust.

Quantitative assessment of cancer cell morphology and movement using telecentric digital holographic microscopy

NASA Astrophysics Data System (ADS)

Nguyen, Thanh C.; Nehmetallah, George; Lam, Van; Chung, Byung Min; Raub, Christopher

2017-02-01

Digital holographic microscopy (DHM) provides label-free and real-time quantitative phase information relevant to the analysis of dynamic biological systems. A DHM based on telecentric configuration optically mitigates phase aberrations due to the microscope objective and linear high frequency fringes due to the reference beam thus minimizing digital aberration correction needed for distortion free 3D reconstruction. The purpose of this work is to quantitatively assess growth and migratory behavior of invasive cancer cells using a telecentric DHM system. Together, the height and lateral shape features of individual cells, determined from time-lapse series of phase reconstructions, should reveal aspects of cell migration, cell-matrix adhesion, and cell cycle phase transitions. To test this, MDA-MB-231 breast cancer cells were cultured on collagen-coated or un-coated glass, and 3D holograms were reconstructed over 2 hours. Cells on collagencoated glass had an average 14% larger spread area than cells on uncoated glass (n=18-22 cells/group). The spread area of cells on uncoated glass were 15-21% larger than cells seeded on collagen hydrogels (n=18-22 cells/group). Premitotic cell rounding was observed with average phase height increasing 57% over 10 minutes. Following cell division phase height decreased linearly (R2=0.94) to 58% of the original height pre-division. Phase objects consistent with lamellipodia were apparent from the reconstructions at the leading edge of migrating cells. These data demonstrate the ability to track quantitative phase parameters and relate them to cell morphology during cell migration and division on adherent substrates, using telecentric DHM. The technique enables future studies of cell-matrix interactions relevant to cancer.

Acoustic properties of healthy and reconstructed cleft lip

NASA Astrophysics Data System (ADS)

Thijssen, Johan M.; van Hees, Nancy J.; Weijers, Gert G.; Huyskens, Rinske W.; Nillesen, Maartje; Katsaros, Christos; de Korte, Chris L.

2006-03-01

The feasibility of echographic imaging of the tissues in healthy lip and in reconstructed cleft lip and estimating the dimensions and the normalized echo level of these tissues is investigated. Echographic images of the upper lip were made with commercial medical ultrasound equipment, using a linear array transducer (7-11 MHz bandwidth) and a non-contact gel coupling. Tissue dimensions were measured by means of software calipers. Echo levels were calibrated and corrected for beam characteristics, gel path and tissue attenuation by using a tissue-mimicking phantom. At central position of philtrum, mean thickness (and standard deviation) of lip loose connective tissue layer, orbicularis oris muscle and dense connective layer was 4.0 (sd 0.1) mm, 2.3 (sd 0.7) mm, 2.2 (sd 0.7) mm, respectively, in healthy lip at rest. Mean (sd) echo level of muscle and dense connective tissue layer with respect to echo level of lip loose connective tissue layer was in relaxed condition: - 19.3 (sd 0.6) dB and - 10.7 (sd 4.0) dB, respectively. Echo level of loose connective tissue layer was +25.6 (sd 4.2) dB relative to phantom echo level obtained in the focus of the transducer. Color mode echo images were calculated, after adaptive filtering of the images, which show the tissues in separate colors and highlight the details of healthy lip and reconstructed cleft lip. Quantitative assessment of thickness and echo level of various lip tissues is feasible after proper calibration of the echographic equipment. Diagnostic potentials of the developed quantitative echographic techniques for non-invasive evaluation of the outcome of cleft lip reconstruction are promising.

Quantitative 3D high resolution transmission ultrasound tomography: creating clinically relevant images (Conference Presentation)

NASA Astrophysics Data System (ADS)

Wiskin, James; Klock, John; Iuanow, Elaine; Borup, Dave T.; Terry, Robin; Malik, Bilal H.; Lenox, Mark

2017-03-01

There has been a great deal of research into ultrasound tomography for breast imaging over the past 35 years. Few successful attempts have been made to reconstruct high-resolution images using transmission ultrasound. To this end, advances have been made in 2D and 3D algorithms that utilize either time of arrival or full wave data to reconstruct images with high spatial and contrast resolution suitable for clinical interpretation. The highest resolution and quantitative accuracy result from inverse scattering applied to full wave data in 3D. However, this has been prohibitively computationally expensive, meaning that full inverse scattering ultrasound tomography has not been considered clinically viable. Here we show the results of applying a nonlinear inverse scattering algorithm to 3D data in a clinically useful time frame. This method yields Quantitative Transmission (QT) ultrasound images with high spatial and contrast resolution. We reconstruct sound speeds for various 2D and 3D phantoms and verify these values with independent measurements. The data are fully 3D as is the reconstruction algorithm, with no 2D approximations. We show that 2D reconstruction algorithms can introduce artifacts into the QT breast image which are avoided by using a full 3D algorithm and data. We show high resolution gross and microscopic anatomic correlations comparing cadaveric breast QT images with MRI to establish imaging capability and accuracy. Finally, we show reconstructions of data from volunteers, as well as an objective visual grading analysis to confirm clinical imaging capability and accuracy.

Lake sediment-based Late Holocene glacier reconstruction reveals medieval retreat and two-phase Little Ice Age on subantarctic South Georgia

NASA Astrophysics Data System (ADS)

van der Bilt, W. G. M.; Bakke, J.; Werner, J.; Paasche, O.; Rosqvist, G. N.; Vatle, S. S.

2016-12-01

Southern Ocean climate is rapidly changing. Yet beyond the instrumental period (± 100 years), our comprehension of climate variability in the region is restricted by a lack of high-resolution paleoclimate records. Alpine glaciers, ubiquitous on Southern Ocean islands, may provide such data as they rapidly respond to climate shifts, recording attendant changes in extent by variations in glacial erosion. Rock flour, the fine-grained fraction of this process, is suspended in meltwater streams and transfers this signal to the sediments of downstream lakes, continuously recording glacier history. Here, we use this relationship and present the first reconstruction of the Late Holocene (1250 cal. yr BP - present) glacier history of the Southern Ocean island of South Georgia, using sediments from the glacier-fed Middle Hamberg lake. Variations are resolved on multi-centennial scales due to robust chronological control. To fingerprint a glacial erosion signal, we employed a set of routinely used physical, geochemical and magnetic parameters. Using Titanium counts, validated against changes in sediment density and grain size distribution, we continuously reconstruct glacier variations over the past millennium. Refining local moraine evidence and supporting evidence from other Southern Hemisphere sites, this study shows a progressive diminishing of consecutive Late Holocene advances. These include a two-stage Little Ice Age, in agreement with other Southern Hemisphere glacier evidence. The presented record furthermore captures an unreported retreat phase behind present limits around 500 cal. yr BP.

Vessel wall characterization using quantitative MRI: what's in a number?

PubMed

Coolen, Bram F; Calcagno, Claudia; van Ooij, Pim; Fayad, Zahi A; Strijkers, Gustav J; Nederveen, Aart J

2018-02-01

The past decade has witnessed the rapid development of new MRI technology for vessel wall imaging. Today, with advances in MRI hardware and pulse sequences, quantitative MRI of the vessel wall represents a real alternative to conventional qualitative imaging, which is hindered by significant intra- and inter-observer variability. Quantitative MRI can measure several important morphological and functional characteristics of the vessel wall. This review provides a detailed introduction to novel quantitative MRI methods for measuring vessel wall dimensions, plaque composition and permeability, endothelial shear stress and wall stiffness. Together, these methods show the versatility of non-invasive quantitative MRI for probing vascular disease at several stages. These quantitative MRI biomarkers can play an important role in the context of both treatment response monitoring and risk prediction. Given the rapid developments in scan acceleration techniques and novel image reconstruction, we foresee the possibility of integrating the acquisition of multiple quantitative vessel wall parameters within a single scan session.

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism

PubMed Central

Chang, Roger L; Ghamsari, Lila; Manichaikul, Ani; Hom, Erik F Y; Balaji, Santhanam; Fu, Weiqi; Shen, Yun; Hao, Tong; Palsson, Bernhard Ø; Salehi-Ashtiani, Kourosh; Papin, Jason A

2011-01-01

Metabolic network reconstruction encompasses existing knowledge about an organism's metabolism and genome annotation, providing a platform for omics data analysis and phenotype prediction. The model alga Chlamydomonas reinhardtii is employed to study diverse biological processes from photosynthesis to phototaxis. Recent heightened interest in this species results from an international movement to develop algal biofuels. Integrating biological and optical data, we reconstructed a genome-scale metabolic network for this alga and devised a novel light-modeling approach that enables quantitative growth prediction for a given light source, resolving wavelength and photon flux. We experimentally verified transcripts accounted for in the network and physiologically validated model function through simulation and generation of new experimental growth data, providing high confidence in network contents and predictive applications. The network offers insight into algal metabolism and potential for genetic engineering and efficient light source design, a pioneering resource for studying light-driven metabolism and quantitative systems biology. PMID:21811229

Quantitative tomographic imaging of intermolecular FRET in small animals

PubMed Central

Venugopal, Vivek; Chen, Jin; Barroso, Margarida; Intes, Xavier

2012-01-01

Forster resonance energy transfer (FRET) is a nonradiative transfer of energy between two fluorescent molecules (a donor and an acceptor) in nanometer range proximity. FRET imaging methods have been applied to proteomic studies and drug discovery applications based on intermolecular FRET efficiency measurements and stoichiometric measurements of FRET interaction as quantitative parameters of interest. Importantly, FRET provides information about biomolecular interactions at a molecular level, well beyond the diffraction limits of standard microscopy techniques. The application of FRET to small animal imaging will allow biomedical researchers to investigate physiological processes occurring at nanometer range in vivo as well as in situ. In this work a new method for the quantitative reconstruction of FRET measurements in small animals, incorporating a full-field tomographic acquisition system with a Monte Carlo based hierarchical reconstruction scheme, is described and validated in murine models. Our main objective is to estimate the relative concentration of two forms of donor species, i.e., a donor molecule involved in FRETing to an acceptor close by and a nonFRETing donor molecule. PMID:23243567

Plant taphonomy in incised valleys: Implications for interpreting paleoclimate from fossil plants

USGS Publications Warehouse

Demko, T.M.; Dubiel, R.F.; Parrish, Judith T.

1998-01-01

Paleoclimatic interpretations of the Upper Triassic Chinle Formation (Colorado Plateau) based on plants conflict with those based on the sedimentary rocks. The plants are suggestive of a humid, equable climate, whereas the rocks are more consistent with deposition under highly seasonal precipitation and ground-water conditions. Fossil plant assemblages are limited to the lower members of the Chinle Formation, which were deposited within incised valleys that were cut into underlying Lower to Middle Triassic and older rocks. In contrast, the upper members of the formation, which were deposited across the fluvial plain after the incised valleys were filled, have few preserved fossil plants. The taphonomic characteristics of the plant fossil assemblages, within the stratigraphic and hydrologic context of the incised valley-fill sequence, explain the vertical and lateral distribution of these assemblages. The depositional, hydrological, and near-surface geochemical conditions were more conducive to preservation of the plants. Fossil plant assemblages in fully terrestrial incised-valley fills should be taphonomically biased toward riparian wetland environments. If those assemblages are used to interpret paleoclimate, the paleoclimatic interpretations will also be biased. The bias may be particularly strong in climates such as those during deposition of the Chinle Formation, when the riparian wetlands may reflect local hydrologic conditions rather than regional climate, and should be taken into account when using these types of plant assemblages in paleoclimatic interpretations.

Whole-body direct 4D parametric PET imaging employing nested generalized Patlak expectation-maximization reconstruction

PubMed Central

Karakatsanis, Nicolas A.; Casey, Michael E.; Lodge, Martin A.; Rahmim, Arman; Zaidi, Habib

2016-01-01

Whole-body (WB) dynamic PET has recently demonstrated its potential in translating the quantitative benefits of parametric imaging to the clinic. Post-reconstruction standard Patlak (sPatlak) WB graphical analysis utilizes multi-bed multi-pass PET acquisition to produce quantitative WB images of the tracer influx rate Ki as a complimentary metric to the semi-quantitative standardized uptake value (SUV). The resulting Ki images may suffer from high noise due to the need for short acquisition frames. Meanwhile, a generalized Patlak (gPatlak) WB post-reconstruction method had been suggested to limit Ki bias of sPatlak analysis at regions with non-negligible 18F-FDG uptake reversibility; however, gPatlak analysis is non-linear and thus can further amplify noise. In the present study, we implemented, within the open-source Software for Tomographic Image Reconstruction (STIR) platform, a clinically adoptable 4D WB reconstruction framework enabling efficient estimation of sPatlak and gPatlak images directly from dynamic multi-bed PET raw data with substantial noise reduction. Furthermore, we employed the optimization transfer methodology to accelerate 4D expectation-maximization (EM) convergence by nesting the fast image-based estimation of Patlak parameters within each iteration cycle of the slower projection-based estimation of dynamic PET images. The novel gPatlak 4D method was initialized from an optimized set of sPatlak ML-EM iterations to facilitate EM convergence. Initially, realistic simulations were conducted utilizing published 18F-FDG kinetic parameters coupled with the XCAT phantom. Quantitative analyses illustrated enhanced Ki target-to-background ratio (TBR) and especially contrast-to-noise ratio (CNR) performance for the 4D vs. the indirect methods and static SUV. Furthermore, considerable convergence acceleration was observed for the nested algorithms involving 10–20 sub-iterations. Moreover, systematic reduction in Ki % bias and improved TBR were

Whole-body direct 4D parametric PET imaging employing nested generalized Patlak expectation-maximization reconstruction

NASA Astrophysics Data System (ADS)

Karakatsanis, Nicolas A.; Casey, Michael E.; Lodge, Martin A.; Rahmim, Arman; Zaidi, Habib

2016-08-01

Whole-body (WB) dynamic PET has recently demonstrated its potential in translating the quantitative benefits of parametric imaging to the clinic. Post-reconstruction standard Patlak (sPatlak) WB graphical analysis utilizes multi-bed multi-pass PET acquisition to produce quantitative WB images of the tracer influx rate K i as a complimentary metric to the semi-quantitative standardized uptake value (SUV). The resulting K i images may suffer from high noise due to the need for short acquisition frames. Meanwhile, a generalized Patlak (gPatlak) WB post-reconstruction method had been suggested to limit K i bias of sPatlak analysis at regions with non-negligible 18F-FDG uptake reversibility; however, gPatlak analysis is non-linear and thus can further amplify noise. In the present study, we implemented, within the open-source software for tomographic image reconstruction platform, a clinically adoptable 4D WB reconstruction framework enabling efficient estimation of sPatlak and gPatlak images directly from dynamic multi-bed PET raw data with substantial noise reduction. Furthermore, we employed the optimization transfer methodology to accelerate 4D expectation-maximization (EM) convergence by nesting the fast image-based estimation of Patlak parameters within each iteration cycle of the slower projection-based estimation of dynamic PET images. The novel gPatlak 4D method was initialized from an optimized set of sPatlak ML-EM iterations to facilitate EM convergence. Initially, realistic simulations were conducted utilizing published 18F-FDG kinetic parameters coupled with the XCAT phantom. Quantitative analyses illustrated enhanced K i target-to-background ratio (TBR) and especially contrast-to-noise ratio (CNR) performance for the 4D versus the indirect methods and static SUV. Furthermore, considerable convergence acceleration was observed for the nested algorithms involving 10-20 sub-iterations. Moreover, systematic reduction in K i % bias and improved TBR were

Using Macrofossils to Reconstruct Paleoenvironmental History of Cedar Swamp, High Point NJ

NASA Astrophysics Data System (ADS)

Buhler, K. M.; Peteet, D. M.

2016-12-01

Macrofossils from deep sediment cores taken from bog environments can reveal much about the paleoclimate of a certain site. A research study conducted by Niering in 1953 focused on the pollen records from Cedar Bog that, although are able to indicate which species were present regionally, are not able to establish the specific local vegetation of the site. By identifying and counting macrofossils from the core, we can determine the species growing in Cedar Bog in High Point State Park, NJ and utilize that data to reconstruct a paleoclimatic history at the highest elevation in New Jersey. We took a 6.5m core from Cedar Bog and, from that, used 4cm³ samples taken throughout the entire depth to wash through a 250um sieve and sift through at 60x magnification, identifying the macrofossils using an extensive Lamont Doherty Earth Observatory reference collection. Additionally, we tested for the percentage of organic matter through the core using loss on ignition. We found 5 zones throughout the core depth that indicate altering habitats. Beginning with low organic matter, less than 5%, the deepest part of the core has little vegetation but high rock content. The next zone introduced Chamaecyparis thyoides in the region and a period of changing organic matter. Following this comes a domination of aquatic plants and byrozoan statoblast and, afterwards, a shift towards sedges. The top of the core shows present day vegetation types from Cedar Bog, such as sphagnum moss and Tsuga canadensis, and 96% organic matter content. The lack of vegetation and high rock content, around 6.5m deep, signal erosion that took place after deglaciation. The vegetation types in zone 2 indicate deep lake/open landscape conditions. High aquatic vegetation and bryozoan statoblasts suggest a shallow lake. The site filled in to become a fen wetland as evidenced by the abundance of Scirpus and Cladium. The final zone signifies a bog habitat represented by the domination of sphagnum and Chamaedaphne

Connecting Paleo and Modern Oceanographic Data to Understand Atlantic Meridional Overturning Circulation Over Decades to Centuries

NASA Technical Reports Server (NTRS)

Kilbourne, Hali; Klockmann, Marlene; Moreno-Chamarro, Eduardo; Ortega, Pablo; Romanou, Anastasia; Srokosz, Meric; Szuts, Zoltan; Thirumalai, Kaustubh; Hall, Ian; Heimbach, Patrick;

Hydrodynamic Influences on Multiproxy-based Paleoclimate Reconstructions from Marine Sediments

NASA Astrophysics Data System (ADS)

Ausin Gonzalez, B.; Magill, C.; Wenk, P.; Haugh, G.; McIntyre, C.; Haghipour, N.; Hodell, D. A.; Eglinton, T. I.

2017-12-01

Multiproxy approaches, including those based on the abundance and composition of sedimentary organic matter at both the bulk (total organic carbon; TOC) and molecular (e.g., alkenone-derived Uk'37) level, are increasingly applied in investigations of past climate variability. Constraining of short-term and abrupt climate changes requires the establishment of accurate chronostratigraphies. For the last glacial to the present, a single age-depth model is typically constructed from radiocarbon ages of planktonic foraminifera and then applied to all proxy records derived from the same sediment core. Here, we develop independent, high-resolution 14C chronologies for planktonic foraminifera, TOC, and alkenones for a sediment core retrieved from the so-called "Shackleton sites" in the Northeast Atlantic Ocean. We observe 14C age offsets between these sedimentary components of up to several thousand years within the same sediment layer, with TOC and alkenones exhibiting older ages than corresponding foraminiferal carbonate. This asynchroneity suggests that application of planktic foraminifera-based chronostratigraphies to other proxy carriers (e.g., TOC and alkenones) may lead to spurious interpretation of sedimentary records. In order to further explore the influence of lateral transport processes on organic matter signatures and ages, we performed down-core, grain size-specific OC 14C analyses on selected sediment horizons. Results indicate strong interdependence between 14C age of OC and sediment grain size, underlying strong hydrodynamic controls on OC age. Furthermore, the magnitude of these temporal offsets varies over time in concert with changes in the strength of the Mediterranean Outflow Water (MOW), implying that OC [proxy] signatures are influenced by non-local inputs. Such influences co-vary with ocean and climate changes, such as Heinrinch Event 1, the Younger Dryas, and those corresponding to deposition of Sapropel 1 in the Mediterranean Sea (ca. 8 ka BP). Our findings suggest an interplay between past climate and ocean change, hydrodynamic forcing, and the (a)synchroneity of multiproxy records, and highlight the importance of developing independent, proxy-specific chronostratigraphies to accurately decipher past millennial- and centennial-scale climate variability.

Role of ground water in geomorphology, geology, and paleoclimate of the Southern High Plains, USA.

PubMed

Wood, Warren W

2002-01-01

Study of ground water in the Southern High Plains is central to an understanding of the geomorphology, deposition of economic minerals, and climate change record in the area. Ground water has controlled the course of the Canadian and Pecos rivers that isolated the Southern High Plains from the Great Plains and has contributed significantly to the continuing retreat of the westward escarpment. Evaporative and dissolution processes are responsible for current plateau topography and the development of the signature 20,000 small playa basins and 40 to 50 large saline lake basins in the area. In conjunction with eolian processes, ground water transport controls the mineralogy of commercially valuable mineral deposits and sets up the distribution of fine efflorescent salts that adversely affect water quality. As the water table rises and retreats, lunette and tufa formation provides valuable paleoclimate data for the Southern High Plains. In all these cases, an understanding of ground water processes contributes valuable information to a broad range of geological topics, well beyond traditional interest in water supply and environmental issues.

The Impact of the Geologic History and Paleoclimate on the Diversification of East African Cichlids

PubMed Central

Danley, Patrick D.; Husemann, Martin; Ding, Baoqing; DiPietro, Lyndsay M.; Beverly, Emily J.; Peppe, Daniel J.

2012-01-01

The cichlid fishes of the East African Great Lakes are the largest extant vertebrate radiation identified to date. These lakes and their surrounding waters support over 2,000 species of cichlid fish, many of which are descended from a single common ancestor within the past 10 Ma. The extraordinary East African cichlid diversity is intricately linked to the highly variable geologic and paleoclimatic history of this region. Greater than 10 Ma, the western arm of the East African rift system began to separate, thereby creating a series of rift basins that would come to contain several water bodies, including the extremely deep Lakes Tanganyika and Malawi. Uplifting associated with this rifting backponded many rivers and created the extremely large, but shallow Lake Victoria. Since their creation, the size, shape, and existence of these lakes have changed dramatically which has, in turn, significantly influenced the evolutionary history of the lakes' cichlids. This paper reviews the geologic history and paleoclimate of the East African Great Lakes and the impact of these forces on the region's endemic cichlid flocks. PMID:22888465

3D SAPIV particle field reconstruction method based on adaptive threshold.

PubMed

Qu, Xiangju; Song, Yang; Jin, Ying; Li, Zhenhua; Wang, Xuezhen; Guo, ZhenYan; Ji, Yunjing; He, Anzhi

2018-03-01

Particle image velocimetry (PIV) is a necessary flow field diagnostic technique that provides instantaneous velocimetry information non-intrusively. Three-dimensional (3D) PIV methods can supply the full understanding of a 3D structure, the complete stress tensor, and the vorticity vector in the complex flows. In synthetic aperture particle image velocimetry (SAPIV), the flow field can be measured with large particle intensities from the same direction by different cameras. During SAPIV particle reconstruction, particles are commonly reconstructed by manually setting a threshold to filter out unfocused particles in the refocused images. In this paper, the particle intensity distribution in refocused images is analyzed, and a SAPIV particle field reconstruction method based on an adaptive threshold is presented. By using the adaptive threshold to filter the 3D measurement volume integrally, the three-dimensional location information of the focused particles can be reconstructed. The cross correlations between images captured from cameras and images projected by the reconstructed particle field are calculated for different threshold values. The optimal threshold is determined by cubic curve fitting and is defined as the threshold value that causes the correlation coefficient to reach its maximum. The numerical simulation of a 16-camera array and a particle field at two adjacent time events quantitatively evaluates the performance of the proposed method. An experimental system consisting of a camera array of 16 cameras was used to reconstruct the four adjacent frames in a vortex flow field. The results show that the proposed reconstruction method can effectively reconstruct the 3D particle fields.

Ultra-low dose quantitative CT myocardial perfusion imaging with sparse-view dynamic acquisition and image reconstruction: A feasibility study.

PubMed

Enjilela, Esmaeil; Lee, Ting-Yim; Hsieh, Jiang; Wisenberg, Gerald; Teefy, Patrick; Yadegari, Andrew; Bagur, Rodrigo; Islam, Ali; Branch, Kelley; So, Aaron

2018-03-01

We implemented and validated a compressed sensing (CS) based algorithm for reconstructing dynamic contrast-enhanced (DCE) CT images of the heart from sparsely sampled X-ray projections. DCE CT imaging of the heart was performed on five normal and ischemic pigs after contrast injection. DCE images were reconstructed with filtered backprojection (FBP) and CS from all projections (984-view) and 1/3 of all projections (328-view), and with CS from 1/4 of all projections (246-view). Myocardial perfusion (MP) measurements with each protocol were compared to those with the reference 984-view FBP protocol. Both the 984-view CS and 328-view CS protocols were in good agreements with the reference protocol. The Pearson correlation coefficients of 984-view CS and 328-view CS determined from linear regression analyses were 0.98 and 0.99 respectively. The corresponding mean biases of MP measurement determined from Bland-Altman analyses were 2.7 and 1.2ml/min/100g. When only 328 projections were used for image reconstruction, CS was more accurate than FBP for MP measurement with respect to 984-view FBP. However, CS failed to generate MP maps comparable to those with 984-view FBP when only 246 projections were used for image reconstruction. DCE heart images reconstructed from one-third of a full projection set with CS were minimally affected by aliasing artifacts, leading to accurate MP measurements with the effective dose reduced to just 33% of conventional full-view FBP method. The proposed CS sparse-view image reconstruction method could facilitate the implementation of sparse-view dynamic acquisition for ultra-low dose CT MP imaging. Copyright © 2017 Elsevier B.V. All rights reserved.

Correlation between surface reconstruction and polytypism in InAs nanowire selective area epitaxy

NASA Astrophysics Data System (ADS)

Liu, Ziyang; Merckling, Clement; Rooyackers, Rita; Richard, Olivier; Bender, Hugo; Mols, Yves; Vila, María; Rubio-Zuazo, Juan; Castro, Germán R.; Collaert, Nadine; Thean, Aaron; Vandervorst, Wilfried; Heyns, Marc

2017-12-01

The mechanism of widely observed intermixing of wurtzite and zinc-blende crystal structures in InAs nanowire (NW) grown by selective area epitaxy (SAE) is studied. We demonstrate that the crystal structure in InAs NW grown by SAE can be controlled using basic growth parameters, and wurtzitelike InAs NWs are achieved. We link the polytypic InAs NWs SAE to the reconstruction of the growth front (111)B surface. Surface reconstruction study of InAs (111) substrate and the following homoepitaxy experiment suggest that (111) planar defect nucleation is related to the (1 × 1) reconstruction of InAs (111)B surface. In order to reveal it more clearly, a model is presented to correlate growth temperature and arsenic partial pressure with InAs NW crystal structure. This model considers the transition between (1 × 1) and (2 × 2) surface reconstructions in the frame of adatom atoms adsorption/desorption, and the polytypism is thus linked to reconstruction quantitatively. The experimental data fit well with the model, which highly suggests that surface reconstruction plays an important role in the polytypism phenomenon in InAs NWs SAE.

TH-AB-207A-05: A Fully-Automated Pipeline for Generating CT Images Across a Range of Doses and Reconstruction Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, S; Lo, P; Hoffman, J

Purpose: To evaluate the robustness of CAD or Quantitative Imaging methods, they should be tested on a variety of cases and under a variety of image acquisition and reconstruction conditions that represent the heterogeneity encountered in clinical practice. The purpose of this work was to develop a fully-automated pipeline for generating CT images that represent a wide range of dose and reconstruction conditions. Methods: The pipeline consists of three main modules: reduced-dose simulation, image reconstruction, and quantitative analysis. The first two modules of the pipeline can be operated in a completely automated fashion, using configuration files and running the modulesmore » in a batch queue. The input to the pipeline is raw projection CT data; this data is used to simulate different levels of dose reduction using a previously-published algorithm. Filtered-backprojection reconstructions are then performed using FreeCT-wFBP, a freely-available reconstruction software for helical CT. We also added support for an in-house, model-based iterative reconstruction algorithm using iterative coordinate-descent optimization, which may be run in tandem with the more conventional recon methods. The reduced-dose simulations and image reconstructions are controlled automatically by a single script, and they can be run in parallel on our research cluster. The pipeline was tested on phantom and lung screening datasets from a clinical scanner (Definition AS, Siemens Healthcare). Results: The images generated from our test datasets appeared to represent a realistic range of acquisition and reconstruction conditions that we would expect to find clinically. The time to generate images was approximately 30 minutes per dose/reconstruction combination on a hybrid CPU/GPU architecture. Conclusion: The automated research pipeline promises to be a useful tool for either training or evaluating performance of quantitative imaging software such as classifiers and CAD algorithms across

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.

Theory and algorithms for image reconstruction on chords and within regions of interest

NASA Astrophysics Data System (ADS)

Zou, Yu; Pan, Xiaochuan; Sidky, Emilâ Y.

2005-11-01

We introduce a formula for image reconstruction on a chord of a general source trajectory. We subsequently develop three algorithms for exact image reconstruction on a chord from data acquired with the general trajectory. Interestingly, two of the developed algorithms can accommodate data containing transverse truncations. The widely used helical trajectory and other trajectories discussed in literature can be interpreted as special cases of the general trajectory, and the developed theory and algorithms are thus directly applicable to reconstructing images exactly from data acquired with these trajectories. For instance, chords on a helical trajectory are equivalent to the n-PI-line segments. In this situation, the proposed algorithms become the algorithms that we proposed previously for image reconstruction on PI-line segments. We have performed preliminary numerical studies, which include the study on image reconstruction on chords of two-circle trajectory, which is nonsmooth, and on n-PI lines of a helical trajectory, which is smooth. Quantitative results of these studies verify and demonstrate the proposed theory and algorithms.

Including Fossils in Phylogenetic Climate Reconstructions: A Deep Time Perspective on the Climatic Niche Evolution and Diversification of Spiny Lizards (Sceloporus).

PubMed

Lawing, A Michelle; Polly, P David; Hews, Diana K; Martins, Emília P

2016-08-01

Fossils and other paleontological information can improve phylogenetic comparative method estimates of phenotypic evolution and generate hypotheses related to species diversification. Here, we use fossil information to calibrate ancestral reconstructions of suitable climate for Sceloporus lizards in North America. Integrating data from the fossil record, general circulation models of paleoclimate during the Miocene, climate envelope modeling, and phylogenetic comparative methods provides a geographically and temporally explicit species distribution model of Sceloporus-suitable habitat through time. We provide evidence to support the historic biogeographic hypothesis of Sceloporus diversification in warm North American deserts and suggest a relatively recent Sceloporus invasion into Mexico around 6 Ma. We use a physiological model to map extinction risk. We suggest that the number of hours of restriction to a thermal refuge limited Sceloporus from inhabiting Mexico until the climate cooled enough to provide suitable habitat at approximately 6 Ma. If the future climate returns to the hotter climates of the past, Mexico, the place of highest modern Sceloporus richness, will no longer provide suitable habitats for Sceloporus to survive and reproduce.

In vivo quantitative bioluminescence tomography using heterogeneous and homogeneous mouse models.

PubMed

Liu, Junting; Wang, Yabin; Qu, Xiaochao; Li, Xiangsi; Ma, Xiaopeng; Han, Runqiang; Hu, Zhenhua; Chen, Xueli; Sun, Dongdong; Zhang, Rongqing; Chen, Duofang; Chen, Dan; Chen, Xiaoyuan; Liang, Jimin; Cao, Feng; Tian, Jie

2010-06-07

Bioluminescence tomography (BLT) is a new optical molecular imaging modality, which can monitor both physiological and pathological processes by using bioluminescent light-emitting probes in small living animal. Especially, this technology possesses great potential in drug development, early detection, and therapy monitoring in preclinical settings. In the present study, we developed a dual modality BLT prototype system with Micro-computed tomography (MicroCT) registration approach, and improved the quantitative reconstruction algorithm based on adaptive hp finite element method (hp-FEM). Detailed comparisons of source reconstruction between the heterogeneous and homogeneous mouse models were performed. The models include mice with implanted luminescence source and tumor-bearing mice with firefly luciferase report gene. Our data suggest that the reconstruction based on heterogeneous mouse model is more accurate in localization and quantification than the homogeneous mouse model with appropriate optical parameters and that BLT allows super-early tumor detection in vivo based on tomographic reconstruction of heterogeneous mouse model signal.

A new method for separating the climatic and biological trend components from tree ring series, with implications for paleoclimate reconstructions

NASA Astrophysics Data System (ADS)

Bouldin, J.

2010-12-01

In the reconstruction of past climates from tree rings multi-decadal to multi-centennial periods, one longstanding problem is the confounding of the natural biological growth trend of the tree with any existing long term trends in the climate. No existing analytical method is capable of resolving these two change components, so it remains unclear how accurate existing ring series standardizations are, and by implication, climate reconstructions based upon them. For example, dendrochronological at the ITRDB are typically standardized by detrending, at each site, each individual tree core, using a relatively stiff deterministic function such as a negative exponential curve or smoothing spline. Another approach, referred to as RCS (Regional Curve Standardization) attempts to solve some problems of the individual series detrending, by constructing a single growth curve from the aggregated cambial ages of the rings of the cores at a site (or collection of sites). This curve is presumed to represent the “ideal” or expected growth of the trees from which it is derived. Although an improvement in some respects, this method will be degraded in direct proportion to the lack of a mixture of tree sizes or ages throughout the span of the chronology. I present a new method of removing the biological curve from tree ring series, such that temporal changes better represent the environmental variation captured by the tree rings. The method institutes several new approaches, such as the correction for the estimated number of missed rings near the pith, and the use of tree size and ring area relationships instead of the traditional tree ages and ring widths. The most important innovation is a careful extraction of the existing information on the relationship between tree size (basal area) and ring area that exists within each single year of the chronology. This information is, by definition, not contaminated by temporal climatic changes, and so when removed, leaves the

3800 Years of Quantitative Precipitation Reconstruction from the Northwest Yucatan Peninsula

PubMed Central

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

2013-01-01

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

Coupled hydromechanical paleoclimate analyses of density-dependant groundwater flow in discretely fractured crystalline rock settings

NASA Astrophysics Data System (ADS)

Normani, S. D.; Sykes, J. F.; Jensen, M. R.

2009-04-01

A high resolution sub-regional scale (84 km2) density-dependent, fracture zone network groundwater flow model with hydromechanical coupling and pseudo-permafrost, was developed from a larger 5734 km2 regional scale groundwater flow model of a Canadian Shield setting in fractured crystalline rock. The objective of the work is to illustrate aspects of regional and sub-regional groundwater flow that are relevant to the long-term performance of a hypothetical nuclear fuel repository. The discrete fracture dual continuum numerical model FRAC3DVS-OPG was used for all simulations. A discrete fracture zone network model delineated from surface features was superimposed onto an 789887 element flow domain mesh. Orthogonal fracture faces (between adjacent finite element grid blocks) were used to best represent the irregular discrete fracture zone network. The crystalline rock between these structural discontinuities was assigned properties characteristic of those reported for the Canadian Shield at the Underground Research Laboratory at Pinawa, Manitoba. Interconnectivity of permeable fracture features is an important pathway for the possibly relatively rapid migration of average water particles and subsequent reduction in residence times. The multiple 121000 year North American continental scale paleoclimate simulations are provided by W.R. Peltier using the University of Toronto Glacial Systems Model (UofT GSM). Values of ice sheet normal stress, and proglacial lake depth from the UofT GSM are applied to the sub-regional model as surface boundary conditions, using a freshwater head equivalent to the normal stress imposed by the ice sheet at its base. Permafrost depth is applied as a permeability reduction to both three-dimensional grid blocks and fractures that lie within the time varying permafrost zone. Two different paleoclimate simulations are applied to the sub-regional model to investigate the effect on the depth of glacial meltwater migration into the subsurface. In

Resolution Enhancement in PET Reconstruction Using Collimation

NASA Astrophysics Data System (ADS)

Metzler, Scott D.; Matej, Samuel; Karp, Joel S.

2013-02-01

Collimation can improve both the spatial resolution and sampling properties compared to the same scanner without collimation. Spatial resolution improves because each original crystal can be conceptually split into two (i.e., doubling the number of in-plane crystals) by masking half the crystal with a high-density attenuator (e.g., tungsten); this reduces coincidence efficiency by 4× since both crystals comprising the line of response (LOR) are masked, but yields 4× as many resolution-enhanced (RE) LORs. All the new RE LORs can be measured by scanning with the collimator in different configurations.In this simulation study, the collimator was assumed to be ideal, neither allowing gamma penetration nor truncating the field of view. Comparisons were made in 2D between an uncollimated small-animal system with 2-mm crystals that were assumed to be perfectly absorbing and the same system with collimation that narrowed the effective crystal size to 1 mm. Digital phantoms included a hot-rod and a single-hot-spot, both in a uniform background with activity ratio of 4:1. In addition to the collimated and uncollimated configurations, angular and spatial wobbling acquisitions of the 2-mm case were also simulated. Similarly, configurations with different combinations of the RE LORs were considered including (i) all LORs, (ii) only those parallel to the 2-mm LORs; and (iii) only cross pairs that are not parallel to the 2-mm LORs. Lastly, quantitative studies were conducted for collimated and uncollimated data using contrast recovery coefficient and mean-squared error (MSE) as metrics. The reconstructions show that for most noise levels there is a substantial improvement in image quality (i.e., visual quality, resolution, and a reduction in artifacts) by using collimation even when there are 4 fewer counts or-in some cases-comparing with the noiseless uncollimated reconstruction. By comparing various configurations of sampling, the results show that it is the matched

Assimilating the ICE-6G_C Reconstruction of the Latest Quaternary Ice Age Cycle Into Numerical Simulations of the Laurentide and Fennoscandian Ice Sheets

NASA Astrophysics Data System (ADS)

Stuhne, G. R.; Peltier, W. R.

2017-12-01

We analyze the effects of nudging 100 kyr numerical simulations of the Laurentide and Fennoscandian ice sheets toward the glacial isostatic adjustment-based (GIA-based) ICE-6G_C reconstruction of the most recent ice age cycle. Starting with the ice physics approximations of the PISM ice sheet model and the SeaRISE simulation protocols, we incorporate nudging at characteristic time scales, τf, through anomalous mass balance terms in the ice mass conservation equation. As should be expected, these mass balances exhibit physically unrealistic details arising from pure GIA-based reconstruction geometry when nudging is very strong (τf=20 years for North America), while weakly nudged (τf=1,000 years) solutions deviate from ICE-6G_C sufficiently to degrade its observational fit quality. For reasonable intermediate time scales (τf=100 years and 200 years), we perturbatively analyze nudged ice dynamics as a superposition of "leading-order smoothing" that diffuses ICE-6G_C in a physically and observationally consistent manner and "higher-order" deviations arising, for instance, from biases in the time dependence of surface climate boundary conditions. Based upon the relative deviations between respective nudged simulations in which these biases follow surface temperature from ice cores and eustatic sea level from marine sediment cores, we compute "ice core climate adjustments" that suggest how local paleoclimate observations may be applied to the systematic refinement of ICE-6G_C. Our results are consistent with a growing body of evidence suggesting that the geographical origins of Meltwater Pulse 1B (MWP1b) may lie primarily in North America as opposed to Antarctica (as reconstructed in ICE-6G_C).

Accelerating image reconstruction in dual-head PET system by GPU and symmetry properties.

PubMed

Chou, Cheng-Ying; Dong, Yun; Hung, Yukai; Kao, Yu-Jiun; Wang, Weichung; Kao, Chien-Min; Chen, Chin-Tu

2012-01-01

Positron emission tomography (PET) is an important imaging modality in both clinical usage and research studies. We have developed a compact high-sensitivity PET system that consisted of two large-area panel PET detector heads, which produce more than 224 million lines of response and thus request dramatic computational demands. In this work, we employed a state-of-the-art graphics processing unit (GPU), NVIDIA Tesla C2070, to yield an efficient reconstruction process. Our approaches ingeniously integrate the distinguished features of the symmetry properties of the imaging system and GPU architectures, including block/warp/thread assignments and effective memory usage, to accelerate the computations for ordered subset expectation maximization (OSEM) image reconstruction. The OSEM reconstruction algorithms were implemented employing both CPU-based and GPU-based codes, and their computational performance was quantitatively analyzed and compared. The results showed that the GPU-accelerated scheme can drastically reduce the reconstruction time and thus can largely expand the applicability of the dual-head PET system.

Reconstructing ancient river dynamics from the stratigraphic record: can lessons from the past inform our future?

NASA Astrophysics Data System (ADS)

Hajek, E. A.; Chamberlin, E.; Baisden, T.

2014-12-01

The richness of the deep-time record and its potential for revealing important characteristics of ancient fluvial landscapes has been demonstrated time and again, including compelling examples of rivers altering their behavior in response to changes in vegetation patterns or abrupt shifts in water and sediment discharge. At present, reconstructions of ancient river and floodplain dynamics are commonly qualitative, and when quantitative metrics are used, it is often for comparison among ancient deposits. Without being able to reconstruct, more comprehensively, important aspects of ancient river and floodplains dynamics, this information has only anecdotal relevance for evaluating and managing present-day landscapes. While methods for reconstructing hydrodynamic and morphodynamic aspects of ancient rivers and floodplains are useful, uncertainties associated with these snapshots complicate the ability to translate observations from geologic to engineering scales, thereby limiting the utility of insight from Earth's past in decision-making and development of sustainable landscape-management practices for modern fluvial landscapes. Here, we explore the degree to which paleomorphodynamic reconstructions from ancient channel and floodplain deposits can be used to make specific, quantitative inferences about ancient river dynamics. We compare a suite of paleoenvironmental measurements from a variety of ancient fluvial deposits (including reconstructions of paleoflow depth, paleoslope, paleo-channel mobility, the caliber of paleo-sediment load, and paleo-floodplain heterogeneity) in an effort to evaluate sampling and empirical uncertainties associated with these methods and identify promising avenues for developing more detailed landscape reconstructions. This work is aimed at helping to develop strategies for extracting practicable information from the stratigraphic record that is relevant for sustainably managing and predicting changes in today's environments.

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.

Quantitative proton imaging from multiple physics processes: a proof of concept

NASA Astrophysics Data System (ADS)

Bopp, C.; Rescigno, R.; Rousseau, M.; Brasse, D.

2015-07-01

Proton imaging is developed in order to improve the accuracy of charged particle therapy treatment planning. It makes it possible to directly map the relative stopping powers of the materials using the information on the energy loss of the protons. In order to reach a satisfactory spatial resolution in the reconstructed images, the position and direction of each particle is recorded upstream and downstream from the patient. As a consequence of individual proton detection, information on the transmission rate and scattering of the protons is available. Image reconstruction processes are proposed to make use of this information. A proton tomographic acquisition of an anthropomorphic head phantom was simulated. The transmission rate of the particles was used to reconstruct a map of the macroscopic cross section for nuclear interactions of the materials. A two-step iterative reconstruction process was implemented to reconstruct a map of the inverse scattering length of the materials using the scattering of the protons. Results indicate that, while the reconstruction processes should be optimized, it is possible to extract quantitative information from the transmission rate and scattering of the protons. This suggests that proton imaging could provide additional knowledge on the materials that may be of use to further improve treatment planning.

Quantitative proton imaging from multiple physics processes: a proof of concept.

PubMed

Bopp, C; Rescigno, R; Rousseau, M; Brasse, D

2015-07-07

Proton imaging is developed in order to improve the accuracy of charged particle therapy treatment planning. It makes it possible to directly map the relative stopping powers of the materials using the information on the energy loss of the protons. In order to reach a satisfactory spatial resolution in the reconstructed images, the position and direction of each particle is recorded upstream and downstream from the patient. As a consequence of individual proton detection, information on the transmission rate and scattering of the protons is available. Image reconstruction processes are proposed to make use of this information. A proton tomographic acquisition of an anthropomorphic head phantom was simulated. The transmission rate of the particles was used to reconstruct a map of the macroscopic cross section for nuclear interactions of the materials. A two-step iterative reconstruction process was implemented to reconstruct a map of the inverse scattering length of the materials using the scattering of the protons. Results indicate that, while the reconstruction processes should be optimized, it is possible to extract quantitative information from the transmission rate and scattering of the protons. This suggests that proton imaging could provide additional knowledge on the materials that may be of use to further improve treatment planning.

A GATE evaluation of the sources of error in quantitative {sup 90}Y PET

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strydhorst, Jared, E-mail: jared.strydhorst@gmail.

Purpose: Accurate reconstruction of the dose delivered by {sup 90}Y microspheres using a postembolization PET scan would permit the establishment of more accurate dose–response relationships for treatment of hepatocellular carcinoma with {sup 90}Y. However, the quality of the PET data obtained is compromised by several factors, including poor count statistics and a very high random fraction. This work uses Monte Carlo simulations to investigate what impact factors other than low count statistics have on the quantification of {sup 90}Y PET. Methods: PET acquisitions of two phantoms—a NEMA PET phantom and the NEMA IEC PET body phantom-containing either {sup 90}Y ormore » {sup 18}F were simulated using GATE. Simulated projections were created with subsets of the simulation data allowing the contributions of random, scatter, and LSO background to be independently evaluated. The simulated projections were reconstructed using the commercial software for the simulated scanner, and the quantitative accuracy of the reconstruction and the contrast recovery of the reconstructed images were evaluated. Results: The quantitative accuracy of the {sup 90}Y reconstructions were not strongly influenced by the high random fraction present in the projection data, and the activity concentration was recovered to within 5% of the known value. The contrast recovery measured for simulated {sup 90}Y data was slightly poorer than that for simulated {sup 18}F data with similar count statistics. However, the degradation was not strongly linked to any particular factor. Using a more restricted energy range to reduce the random fraction in the projections had no significant effect. Conclusions: Simulations of {sup 90}Y PET confirm that quantitative {sup 90}Y is achievable with the same approach as that used for {sup 18}F, and that there is likely very little margin for improvement by attempting to model aspects unique to {sup 90}Y, such as the much higher random fraction or the presence of

Mastectomy Skin Necrosis After Breast Reconstruction: A Comparative Analysis Between Autologous Reconstruction and Implant-Based Reconstruction.

PubMed

Sue, Gloria R; Lee, Gordon K

2018-05-01

Mastectomy skin necrosis is a significant problem after breast reconstruction. We sought to perform a comparative analysis on this complication between patients undergoing autologous breast reconstruction and patients undergoing 2-stage expander implant breast reconstruction. A retrospective review was performed on consecutive patients undergoing autologous breast reconstruction or 2-stage expander implant breast reconstruction by the senior author from 2006 through 2015. Patient demographic factors including age, body mass index, history of diabetes, history of smoking, and history of radiation to the breast were collected. Our primary outcome measure was mastectomy skin necrosis. Fisher exact test was used for statistical analysis between the 2 patient cohorts. The treatment patterns of mastectomy skin necrosis were then analyzed. We identified 204 patients who underwent autologous breast reconstruction and 293 patients who underwent 2-stage expander implant breast reconstruction. Patients undergoing autologous breast reconstruction were older, heavier, more likely to have diabetes, and more likely to have had prior radiation to the breast compared with patients undergoing implant-based reconstruction. The incidence of mastectomy skin necrosis was 30.4% of patients in the autologous group compared with only 10.6% of patients in the tissue expander group (P < 0.001). The treatment of this complication differed between these 2 patient groups. In general, those with autologous reconstructions were treated with more conservative means. Although 37.1% of patients were treated successfully with local wound care in the autologous group, only 3.2% were treated with local wound care in the tissue expander group (P < 0.001). Less than half (29.0%) of patients in the autologous group were treated with an operative intervention for this complication compared with 41.9% in the implant-based group (P = 0.25). Mastectomy skin necrosis is significantly more likely to occur after

Geomorphic evidence for former lobate debris aprons at low latitudes on Mars: Indicators of the Martian paleoclimate

USGS Publications Warehouse

Hauber, E.; Van Gasselt, S.; Chapman, M.G.; Neukum, G.

2008-01-01

Circumferential depressions enclosing mesas and plateaus in the northern Kasei Valles and in the Tartarus Colles regions of Mars are interpreted as indicators of the former extent of lobate debris aprons, thought to be mixtures of ice and elastic particles. These former lobate debris aprons existed about 1 Ga ago and were embayed by lavas or other flow deposits. After the lobate debris aprons had been removed by sublimation and deflation, topographic depressions with a depth of 50 m and a width of several kilometers were left behind between the mesa or plateau scarp and the solidified flow materials. These depressions or moats are located equatorward of ??30?? at significantly lower latitudes than generally observed for occurrences of modem, intact lobate debris aprons. This observation provides evidence that the paleoclimate at that time was different than today, probably due to a higher averaged obliquity of the planet's rotational axis. Copyright 2008 by the American Geophysical Union.

Documentary reconstruction of monsoon rainfall variability over western India, 1781-1860

NASA Astrophysics Data System (ADS)

Adamson, George C. D.; Nash, David J.

2014-02-01

Investigations into the climatic forcings that affect the long-term variability of the Indian summer monsoon are constrained by a lack of reliable rainfall data prior to the late nineteenth century. Extensive qualitative and quantitative meteorological information for the pre-instrumental period exists within historical documents, although these materials have been largely unexplored. This paper presents the first reconstruction of monsoon variability using documentary sources, focussing on western India for the period 1781-1860. Three separate reconstructions are generated, for (1) Mumbai, (2) Pune and (3) the area of Gujarat bordering the Gulf of Khambat. A composite chronology is then produced from the three reconstructions, termed the Western India Monsoon Rainfall reconstruction (WIMR). The WIMR exhibits four periods of generally deficient monsoon rainfall (1780-1785, 1799-1806, 1830-1838 and 1845-1857) and three of above-normal rainfall (1788-1794, 1813-1828 and 1839-1844). The WIMR shows good correspondence with a dendroclimatic drought reconstruction for Kerala, although agreement with the western Indian portion of the tree-ring derived Monsoon Asia Drought Atlas is less strong. The reconstruction is used to examine the long-term relationship between the El Nino-Southern Oscillation (ENSO) and monsoon rainfall over western India. This exhibits peaks and troughs in correlation over time, suggesting a regular long-term fluctuation. This may be an internal oscillation in the ENSO-monsoon system or may be related to volcanic aerosol forcings. Further reconstructions of monsoon rainfall are necessary to validate this. The study highlights uncertainties in existing published rainfall records for 1817-1846 for western India.

Geometric reconstruction using tracked ultrasound strain imaging

NASA Astrophysics Data System (ADS)

Pheiffer, Thomas S.; Simpson, Amber L.; Ondrake, Janet E.; Miga, Michael I.

2013-03-01

The accurate identification of tumor margins during neurosurgery is a primary concern for the surgeon in order to maximize resection of malignant tissue while preserving normal function. The use of preoperative imaging for guidance is standard of care, but tumor margins are not always clear even when contrast agents are used, and so margins are often determined intraoperatively by visual and tactile feedback. Ultrasound strain imaging creates a quantitative representation of tissue stiffness which can be used in real-time. The information offered by strain imaging can be placed within a conventional image-guidance workflow by tracking the ultrasound probe and calibrating the image plane, which facilitates interpretation of the data by placing it within a common coordinate space with preoperative imaging. Tumor geometry in strain imaging is then directly comparable to the geometry in preoperative imaging. This paper presents a tracked ultrasound strain imaging system capable of co-registering with preoperative tomograms and also of reconstructing a 3D surface using the border of the strain lesion. In a preliminary study using four phantoms with subsurface tumors, tracked strain imaging was registered to preoperative image volumes and then tumor surfaces were reconstructed using contours extracted from strain image slices. The volumes of the phantom tumors reconstructed from tracked strain imaging were approximately between 1.5 to 2.4 cm3, which was similar to the CT volumes of 1.0 to 2.3 cm3. Future work will be done to robustly characterize the reconstruction accuracy of the system.

Image reconstruction from few-view CT data by gradient-domain dictionary learning.

PubMed

Hu, Zhanli; Liu, Qiegen; Zhang, Na; Zhang, Yunwan; Peng, Xi; Wu, Peter Z; Zheng, Hairong; Liang, Dong

2016-05-21

Decreasing the number of projections is an effective way to reduce the radiation dose exposed to patients in medical computed tomography (CT) imaging. However, incomplete projection data for CT reconstruction will result in artifacts and distortions. In this paper, a novel dictionary learning algorithm operating in the gradient-domain (Grad-DL) is proposed for few-view CT reconstruction. Specifically, the dictionaries are trained from the horizontal and vertical gradient images, respectively and the desired image is reconstructed subsequently from the sparse representations of both gradients by solving the least-square method. Since the gradient images are sparser than the image itself, the proposed approach could lead to sparser representations than conventional DL methods in the image-domain, and thus a better reconstruction quality is achieved. To evaluate the proposed Grad-DL algorithm, both qualitative and quantitative studies were employed through computer simulations as well as real data experiments on fan-beam and cone-beam geometry. The results show that the proposed algorithm can yield better images than the existing algorithms.

Image Reconstruction Under Contact Impedance Effect in Micro Electrical Impedance Tomography Sensors.

PubMed

Liu, Xiayi; Yao, Jiafeng; Zhao, Tong; Obara, Hiromichi; Cui, Yahui; Takei, Masahiro

2018-06-01

Contact impedance has an important effect on micro electrical impedance tomography (EIT) sensors compared to conventional macro sensors. In the present work, a complex contact impedance effect ratio ξ is defined to quantitatively evaluate the effect of the contact impedance on the accuracy of the reconstructed images by micro EIT. Quality of the reconstructed image under various ξ is estimated by the phantom simulation to find the optimum algorithm. The generalized vector sampled pattern matching (GVSPM) method reveals the best image quality and the best tolerance to ξ. Moreover, the images of yeast cells sedimentary distribution in a multilayered microchannel are reconstructed by the GVSPM method under various mean magnitudes of contact impedance effect ratio |ξ|. The result shows that the best image quality that has the smallest voltage error U E = 0.581 is achieved with measurement frequency f = 1 MHz and mean magnitude |ξ| = 26. In addition, the reconstructed images of cells distribution become improper while f < 10 kHz and mean value of |ξ| > 2400.

Comparison analysis between filtered back projection and algebraic reconstruction technique on microwave imaging

NASA Astrophysics Data System (ADS)

Ramadhan, Rifqi; Prabowo, Rian Gilang; Aprilliyani, Ria; Basari

2018-02-01

Victims of acute cancer and tumor are growing each year and cancer becomes one of the causes of human deaths in the world. Cancers or tumor tissue cells are cells that grow abnormally and turn to take over and damage the surrounding tissues. At the beginning, cancers or tumors do not have definite symptoms in its early stages, and can even attack the tissues inside of the body. This phenomena is not identifiable under visual human observation. Therefore, an early detection system which is cheap, quick, simple, and portable is essensially required to anticipate the further development of cancer or tumor. Among all of the modalities, microwave imaging is considered to be a cheaper, simple, and portable system method. There are at least two simple image reconstruction algorithms i.e. Filtered Back Projection (FBP) and Algebraic Reconstruction Technique (ART), which have been adopted in some common modalities. In this paper, both algorithms will be compared by reconstructing the image from an artificial tissue model (i.e. phantom), which has two different dielectric distributions. We addressed two performance comparisons, namely quantitative and qualitative analysis. Qualitative analysis includes the smoothness of the image and also the success in distinguishing dielectric differences by observing the image with human eyesight. In addition, quantitative analysis includes Histogram, Structural Similarity Index (SSIM), Mean Squared Error (MSE), and Peak Signal-to-Noise Ratio (PSNR) calculation were also performed. As a result, quantitative parameters of FBP might show better values than the ART. However, ART is likely more capable to distinguish two different dielectric value than FBP, due to higher contrast in ART and wide distribution grayscale level.

Water content, speciation and isotopic composition in volcanic glass: an open window on magma degassing processes or paleoclimate?

NASA Astrophysics Data System (ADS)

Martin, Erwan; Bindeman, Ilya; Balan, Etienne; Palandri, Jim; Seligman, Angela; Villemant, Benoit

2016-04-01

The content, speciation and isotopic composition of water in volcanic glass have been used for decades as recorder of magma degassing or late glass rehydration processes. Magmatic or paleoclimate information are derived depending on the primary (magmatic) or meteoric (secondary) origin of water. In this study, we attempt to discriminate residual magmatic from secondary meteoric water in volcanic glass. Using samples from different geological settings and different climatic conditions, we show that the H-isotope composition and water content measured via a TC/EA-MAT253 system in volcanic glass alone are not always sufficient to provide clear distinction between magmatic and meteoric origin. However, it is quite easy to resolve δD evolution during post-deposit rehydration by meteoric water from magma degassing when volcanic glass have a δD <-100‰ or >-50‰ and [H2O]tot >1.5-2wt.%. Water speciation inferred from near-infrared spectroscopy also provides valuable information complementary to isotopic and total water measurements. During magma degassing (typically with [H2O]tot decreasing from 6wt.% to ~0wt.% water) H2O/OH is expected to decrease from 2 to close to 0. However, our dataset shows the opposite trend with an increase of H2O/OH from 2 to ~5. We interpret it as post deposit rehydration of the volcanic glass. Overall our results show that the discrimination of the water origin is essential to discuss magma degassing processes or paleoclimatic reconstitutions. The present study of hydrous glass supports the use of H-isotopes of volcanic glass to discuss paleoclimate reconstitution in a specific region. To this purpose, the volcanic glass has to be almost fully rehydrated in order to fingerprint the isotopic composition of the rehydration water. A sharp time constrain can be obtained if the full rehydration occurs quickly after the eruption. This is most likely to occur in meters thick volcanic pyroclast deposits that undergo slow cooling rates and thus can

Denoised ordered subset statistically penalized algebraic reconstruction technique (DOS-SPART) in digital breast tomosynthesis

NASA Astrophysics Data System (ADS)

Garrett, John; Li, Yinsheng; Li, Ke; Chen, Guang-Hong

2017-03-01

Digital breast tomosynthesis (DBT) is a three dimensional (3D) breast imaging modality in which projections are acquired over a limited angular span around the compressed breast and reconstructed into image slices parallel to the detector. DBT has been shown to help alleviate the breast tissue overlapping issues of two dimensional (2D) mammography. Since the overlapping tissues may simulate cancer masses or obscure true cancers, this improvement is critically important for improved breast cancer screening and diagnosis. In this work, a model-based image reconstruction method is presented to show that spatial resolution in DBT volumes can be maintained while dose is reduced using the presented method when compared to that of a state-of-the-art commercial reconstruction technique. Spatial resolution was measured in phantom images and subjectively in a clinical dataset. Noise characteristics were explored in a cadaver study. In both the quantitative and subjective results the image sharpness was maintained and overall image quality was maintained at reduced doses when the model-based iterative reconstruction was used to reconstruct the volumes.

The importance of metadata to assess information content in digital reconstructions of neuronal morphology.

PubMed

Parekh, Ruchi; Armañanzas, Rubén; Ascoli, Giorgio A

2015-04-01

Digital reconstructions of axonal and dendritic arbors provide a powerful representation of neuronal morphology in formats amenable to quantitative analysis, computational modeling, and data mining. Reconstructed files, however, require adequate metadata to identify the appropriate animal species, developmental stage, brain region, and neuron type. Moreover, experimental details about tissue processing, neurite visualization and microscopic imaging are essential to assess the information content of digital morphologies. Typical morphological reconstructions only partially capture the underlying biological reality. Tracings are often limited to certain domains (e.g., dendrites and not axons), may be incomplete due to tissue sectioning, imperfect staining, and limited imaging resolution, or can disregard aspects irrelevant to their specific scientific focus (such as branch thickness or depth). Gauging these factors is critical in subsequent data reuse and comparison. NeuroMorpho.Org is a central repository of reconstructions from many laboratories and experimental conditions. Here, we introduce substantial additions to the existing metadata annotation aimed to describe the completeness of the reconstructed neurons in NeuroMorpho.Org. These expanded metadata form a suitable basis for effective description of neuromorphological data.

Climatic history of the northeastern United States during the past 3000 years

USGS Publications Warehouse

Marlon, Jennifer R.; Pederson, Neil; Nolan, Connor; Goring, Simon; Shuman, Bryan; Robertson, Ann; Booth, Robert K.; Bartlein, Patrick J.; Berke, Melissa A.; Clifford, Michael; Cook, Edward; Dieffenbacher-Krall, Ann; Dietze, Michael C.; Hessl, Amy; Hubeny, J. Bradford; Jackson, Stephen T.; Marsicek, Jeremiah; McLachlan, Jason S.; Mock, Cary J.; Moore, David J. P.; Nichols, Jonathan M.; Peteet, Dorothy M.; Schaefer, Kevin; Trouet, Valerie; Umbanhowar, Charles; Williams, John W.; Yu, Zicheng

2017-01-01

Many ecosystem processes that influence Earth system feedbacks, including vegetation growth, water and nutrient cycling, and disturbance regimes, are strongly influenced by multi-decadal to millennial-scale variations in climate that cannot be captured by instrumental climate observations. Paleoclimate information is therefore essential for understanding contemporary ecosystems and their potential trajectories under a variety of future climate conditions. With the exception of fossil pollen records, there are a limited number of northeastern US (NE US) paleoclimate archives that can provide constraints on its temperature and hydroclimate history. Moreover, the records that do exist have not been considered together. Tree-ring data indicate that the 20th century was one of the wettest of the past 500 years in the eastern US (Pederson et al., 2014), and lake-level records suggest it was one of the wettest in the Holocene (Newby et al., 2014); how such results compare with other available data remains unclear, however. Here we conduct a systematic review, assessment, and comparison of paleotemperature and paleohydrological proxies from the NE US for the last 3000 years. Regional temperature reconstructions are consistent with the long-term cooling trend (1000 BCE–1700 CE) evident in hemispheric-scale reconstructions, but hydroclimate reconstructions reveal new information, including an abrupt transition from wet to dry conditions around 550–750 CE. NE US paleo data suggest that conditions during the Medieval Climate Anomaly were warmer and drier than during the Little Ice Age, and drier than today. There is some evidence for an acceleration over the past century of a longer-term wetting trend in the NE US, and coupled with the abrupt shift from a cooling trend to a warming trend from increased greenhouse gases, may have wide-ranging implications for species distributions, ecosystem dynamics, and extreme weather events. More work is needed to gather paleoclimate

Effects of the approximations of light propagation on quantitative photoacoustic tomography using two-dimensional photon diffusion equation and linearization

NASA Astrophysics Data System (ADS)

Okawa, Shinpei; Hirasawa, Takeshi; Kushibiki, Toshihiro; Ishihara, Miya

2017-12-01

Quantitative photoacoustic tomography (QPAT) employing a light propagation model will play an important role in medical diagnoses by quantifying the concentration of hemoglobin or a contrast agent. However, QPAT by the light propagation model with the three-dimensional (3D) radiative transfer equation (RTE) requires a huge computational load in the iterative forward calculations involved in the updating process to reconstruct the absorption coefficient. The approximations of the light propagation improve the efficiency of the image reconstruction for the QPAT. In this study, we compared the 3D/two-dimensional (2D) photon diffusion equation (PDE) approximating 3D RTE with the Monte Carlo simulation based on 3D RTE. Then, the errors in a 2D PDE-based linearized image reconstruction caused by the approximations were quantitatively demonstrated and discussed in the numerical simulations. It was clearly observed that the approximations affected the reconstructed absorption coefficient. The 2D PDE-based linearized algorithm succeeded in the image reconstruction of the region with a large absorption coefficient in the 3D phantom. The value reconstructed in the phantom experiment agreed with that in the numerical simulation, so that it was validated that the numerical simulation of the image reconstruction predicted the relationship between the true absorption coefficient of the target in the 3D medium and the reconstructed value with the 2D PDE-based linearized algorithm. Moreover, the the true absorption coefficient in 3D medium was estimated from the 2D reconstructed image on the basis of the prediction by the numerical simulation. The estimation was successful in the phantom experiment, although some limitations were revealed.

Quantitative Image Quality and Histogram-Based Evaluations of an Iterative Reconstruction Algorithm at Low-to-Ultralow Radiation Dose Levels: A Phantom Study in Chest CT

PubMed Central

Lee, Ki Baek

2018-01-01

Objective To describe the quantitative image quality and histogram-based evaluation of an iterative reconstruction (IR) algorithm in chest computed tomography (CT) scans at low-to-ultralow CT radiation dose levels. Materials and Methods In an adult anthropomorphic phantom, chest CT scans were performed with 128-section dual-source CT at 70, 80, 100, 120, and 140 kVp, and the reference (3.4 mGy in volume CT Dose Index [CTDIvol]), 30%-, 60%-, and 90%-reduced radiation dose levels (2.4, 1.4, and 0.3 mGy). The CT images were reconstructed by using filtered back projection (FBP) algorithms and IR algorithm with strengths 1, 3, and 5. Image noise, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR) were statistically compared between different dose levels, tube voltages, and reconstruction algorithms. Moreover, histograms of subtraction images before and after standardization in x- and y-axes were visually compared. Results Compared with FBP images, IR images with strengths 1, 3, and 5 demonstrated image noise reduction up to 49.1%, SNR increase up to 100.7%, and CNR increase up to 67.3%. Noteworthy image quality degradations on IR images including a 184.9% increase in image noise, 63.0% decrease in SNR, and 51.3% decrease in CNR, and were shown between 60% and 90% reduced levels of radiation dose (p < 0.0001). Subtraction histograms between FBP and IR images showed progressively increased dispersion with increased IR strength and increased dose reduction. After standardization, the histograms appeared deviated and ragged between FBP images and IR images with strength 3 or 5, but almost normally-distributed between FBP images and IR images with strength 1. Conclusion The IR algorithm may be used to save radiation doses without substantial image quality degradation in chest CT scanning of the adult anthropomorphic phantom, down to approximately 1.4 mGy in CTDIvol (60% reduced dose). PMID:29354008

Optical Ptychographic Microscope for Quantitative Bio-Mechanical Imaging

NASA Astrophysics Data System (ADS)

Anthony, Nicholas; Cadenazzi, Guido; Nugent, Keith; Abbey, Brian

The role that mechanical forces play in biological processes such as cell movement and death is becoming of significant interest to further develop our understanding of the inner workings of cells. The most common method used to obtain stress information is photoelasticity which maps a samples birefringence, or its direction dependent refractive indices, using polarized light. However this method only provides qualitative data and for stress information to be useful quantitative data is required. Ptychography is a method for quantitatively determining the phase of a samples complex transmission function. The technique relies upon the collection of multiple overlapping coherent diffraction patterns from laterally displaced points on the sample. The overlap of measurement points provides complementary information that significantly aids in the reconstruction of the complex wavefield exiting the sample and allows for quantitative imaging of weakly interacting specimens. Here we describe recent advances at La Trobe University Melbourne on achieving quantitative birefringence mapping using polarized light ptychography with applications in cell mechanics. Australian Synchrotron, ARC Centre of Excellence for Advanced Molecular Imaging.

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

NASA Astrophysics Data System (ADS)

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

2008-04-01

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

Research on assessment and improvement method of remote sensing image reconstruction

NASA Astrophysics Data System (ADS)

Sun, Li; Hua, Nian; Yu, Yanbo; Zhao, Zhanping

2018-01-01

Remote sensing image quality assessment and improvement is an important part of image processing. Generally, the use of compressive sampling theory in remote sensing imaging system can compress images while sampling which can improve efficiency. A method of two-dimensional principal component analysis (2DPCA) is proposed to reconstruct the remote sensing image to improve the quality of the compressed image in this paper, which contain the useful information of image and can restrain the noise. Then, remote sensing image quality influence factors are analyzed, and the evaluation parameters for quantitative evaluation are introduced. On this basis, the quality of the reconstructed images is evaluated and the different factors influence on the reconstruction is analyzed, providing meaningful referential data for enhancing the quality of remote sensing images. The experiment results show that evaluation results fit human visual feature, and the method proposed have good application value in the field of remote sensing image processing.

Noise spatial nonuniformity and the impact of statistical image reconstruction in CT myocardial perfusion imaging.

PubMed

Lauzier, Pascal Theriault; Tang, Jie; Speidel, Michael A; Chen, Guang-Hong

2012-07-01

To achieve high temporal resolution in CT myocardial perfusion imaging (MPI), images are often reconstructed using filtered backprojection (FBP) algorithms from data acquired within a short-scan angular range. However, the variation in the central angle from one time frame to the next in gated short scans has been shown to create detrimental partial scan artifacts when performing quantitative MPI measurements. This study has two main purposes. (1) To demonstrate the existence of a distinct detrimental effect in short-scan FBP, i.e., the introduction of a nonuniform spatial image noise distribution; this nonuniformity can lead to unexpectedly high image noise and streaking artifacts, which may affect CT MPI quantification. (2) To demonstrate that statistical image reconstruction (SIR) algorithms can be a potential solution to address the nonuniform spatial noise distribution problem and can also lead to radiation dose reduction in the context of CT MPI. Projection datasets from a numerically simulated perfusion phantom and an in vivo animal myocardial perfusion CT scan were used in this study. In the numerical phantom, multiple realizations of Poisson noise were added to projection data at each time frame to investigate the spatial distribution of noise. Images from all datasets were reconstructed using both FBP and SIR reconstruction algorithms. To quantify the spatial distribution of noise, the mean and standard deviation were measured in several regions of interest (ROIs) and analyzed across time frames. In the in vivo study, two low-dose scans at tube currents of 25 and 50 mA were reconstructed using FBP and SIR. Quantitative perfusion metrics, namely, the normalized upslope (NUS), myocardial blood volume (MBV), and first moment transit time (FMT), were measured for two ROIs and compared to reference values obtained from a high-dose scan performed at 500 mA. Images reconstructed using FBP showed a highly nonuniform spatial distribution of noise. This spatial

Noise spatial nonuniformity and the impact of statistical image reconstruction in CT myocardial perfusion imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lauzier, Pascal Theriault; Tang Jie; Speidel, Michael A.

Purpose: To achieve high temporal resolution in CT myocardial perfusion imaging (MPI), images are often reconstructed using filtered backprojection (FBP) algorithms from data acquired within a short-scan angular range. However, the variation in the central angle from one time frame to the next in gated short scans has been shown to create detrimental partial scan artifacts when performing quantitative MPI measurements. This study has two main purposes. (1) To demonstrate the existence of a distinct detrimental effect in short-scan FBP, i.e., the introduction of a nonuniform spatial image noise distribution; this nonuniformity can lead to unexpectedly high image noise andmore » streaking artifacts, which may affect CT MPI quantification. (2) To demonstrate that statistical image reconstruction (SIR) algorithms can be a potential solution to address the nonuniform spatial noise distribution problem and can also lead to radiation dose reduction in the context of CT MPI. Methods: Projection datasets from a numerically simulated perfusion phantom and an in vivo animal myocardial perfusion CT scan were used in this study. In the numerical phantom, multiple realizations of Poisson noise were added to projection data at each time frame to investigate the spatial distribution of noise. Images from all datasets were reconstructed using both FBP and SIR reconstruction algorithms. To quantify the spatial distribution of noise, the mean and standard deviation were measured in several regions of interest (ROIs) and analyzed across time frames. In the in vivo study, two low-dose scans at tube currents of 25 and 50 mA were reconstructed using FBP and SIR. Quantitative perfusion metrics, namely, the normalized upslope (NUS), myocardial blood volume (MBV), and first moment transit time (FMT), were measured for two ROIs and compared to reference values obtained from a high-dose scan performed at 500 mA. Results: Images reconstructed using FBP showed a highly nonuniform spatial

Noise spatial nonuniformity and the impact of statistical image reconstruction in CT myocardial perfusion imaging

PubMed Central

Lauzier, Pascal Thériault; Tang, Jie; Speidel, Michael A.; Chen, Guang-Hong

2012-01-01

Purpose: To achieve high temporal resolution in CT myocardial perfusion imaging (MPI), images are often reconstructed using filtered backprojection (FBP) algorithms from data acquired within a short-scan angular range. However, the variation in the central angle from one time frame to the next in gated short scans has been shown to create detrimental partial scan artifacts when performing quantitative MPI measurements. This study has two main purposes. (1) To demonstrate the existence of a distinct detrimental effect in short-scan FBP, i.e., the introduction of a nonuniform spatial image noise distribution; this nonuniformity can lead to unexpectedly high image noise and streaking artifacts, which may affect CT MPI quantification. (2) To demonstrate that statistical image reconstruction (SIR) algorithms can be a potential solution to address the nonuniform spatial noise distribution problem and can also lead to radiation dose reduction in the context of CT MPI. Methods: Projection datasets from a numerically simulated perfusion phantom and an in vivo animal myocardial perfusion CT scan were used in this study. In the numerical phantom, multiple realizations of Poisson noise were added to projection data at each time frame to investigate the spatial distribution of noise. Images from all datasets were reconstructed using both FBP and SIR reconstruction algorithms. To quantify the spatial distribution of noise, the mean and standard deviation were measured in several regions of interest (ROIs) and analyzed across time frames. In the in vivo study, two low-dose scans at tube currents of 25 and 50 mA were reconstructed using FBP and SIR. Quantitative perfusion metrics, namely, the normalized upslope (NUS), myocardial blood volume (MBV), and first moment transit time (FMT), were measured for two ROIs and compared to reference values obtained from a high-dose scan performed at 500 mA. Results: Images reconstructed using FBP showed a highly nonuniform spatial distribution

Influence of the limited detector size on spatial variations of the reconstruction accuracy in holographic tomography

NASA Astrophysics Data System (ADS)

Kostencka, Julianna; Kozacki, Tomasz; Hennelly, Bryan; Sheridan, John T.

2017-06-01

Holographic tomography (HT) allows noninvasive, quantitative, 3D imaging of transparent microobjects, such as living biological cells and fiber optics elements. The technique is based on acquisition of multiple scattered fields for various sample perspectives using digital holographic microscopy. Then, the captured data is processed with one of the tomographic reconstruction algorithms, which enables 3D reconstruction of refractive index distribution. In our recent works we addressed the issue of spatially variant accuracy of the HT reconstructions, which results from the insufficient model of diffraction that is applied in the widely-used tomographic reconstruction algorithms basing on the Rytov approximation. In the present study, we continue investigating the spatially variant properties of the HT imaging, however, we are now focusing on the limited spatial size of holograms as a source of this problem. Using the Wigner distribution representation and the Ewald sphere approach, we show that the limited size of the holograms results in a decreased quality of tomographic imaging in off-center regions of the HT reconstructions. This is because the finite detector extent becomes a limiting aperture that prohibits acquisition of full information about diffracted fields coming from the out-of-focus structures of a sample. The incompleteness of the data results in an effective truncation of the tomographic transfer function for the out-of-center regions of the tomographic image. In this paper, the described effect is quantitatively characterized for three types of the tomographic systems: the configuration with 1) object rotation, 2) scanning of the illumination direction, 3) the hybrid HT solution combing both previous approaches.

Evidence for early postglacial warming in Mount Field National Park, Tasmania

NASA Astrophysics Data System (ADS)

Rees, Andrew B. H.; Cwynar, Les C.

2010-02-01

Situated between the Western Pacific Warm Pool to the north and Antarctica to the south, Tasmania is an ideal location to study both postglacial and Holocene paleoclimates. Few well-dated, quantitative temperature reconstructions exist for the region so that important questions about the occurrence and magnitude of events, such as the Antarctic Cold Reversal and Younger Dryas, in Tasmania remain unanswered. Here, we provide chironomid-based reconstructions of temperature of the warmest quarter (TWARM) for two small subalpine lakes, Eagle and Platypus Tarns, Mount Field National Park. Shortly after deglaciation, TWARM reached modern values by approximately 15 000 cal a BP and remained high until 13 000 cal a BP after which temperatures began to cool steadily, reaching a minimum by 11 100-10 000 cal a BP. These results are consistent with sea surface temperature (SST) reconstructions from south of Tasmania but are in stark contrast to temperature inferences drawn from vegetation reconstructions based on pollen data that indicate cool initial temperatures followed by a broad warm period between 11 600-6800 cal a BP (10 000-6000 14C a BP). The chironomid record broadly matches the summer insolation curve whereas the vegetation record and associated climate inferences mirror winter insolation. The Antarctic Cold Reversal and Younger Dryas cold events are not evident in the chironomid-inferred temperatures, but the Antarctic Cold Reversal is evident in the loss-on-ignition curves.

The Role of Arctic Sea Ice in Last Millennium Climate Variability: Model-Proxy Comparisons Using Ensemble Members and Novel Model Experiments.

NASA Astrophysics Data System (ADS)

Gertler, C. G.; Monier, E.; Prinn, R. G.

2016-12-01

Variability in sea ice extent is a prominent feature of forced simulations of the last millennium and reconstructions of paleoclimate using proxy records. The rapid 20th century decline in sea ice extent is most likely due to greenhouse gas forcing, but the accuracy of future projections depend on the characterization of natural variability. Declining sea ice extent affects regional climate and society, but also plays a large role in Arctic amplification, with implications for mid-latitude circulation and even large-scale climate oscillations. To characterize the effects of natural and anthropogenic climate forcing on sea ice and the related changes in large-scale atmospheric circulation, a combination of instrumental record, paleoclimate reconstructions, and general circulation models can be employed to recreate sea ice extents and the corresponding atmosphere-ocean states. Model output from the last millennium ensemble (LME) is compared to a proxy-based sea ice reconstruction and a global proxy network using a variety of statistical and data assimilation techniques. Further model runs using the Community Earth Systems Model (CESM) are performed with the same inputs as LME but forced with experimental sea ice extents, and results are contextualized within the larger ensemble by a variety of metrics.

A modern plant-climate research dataset for modelling eastern North American plant taxa.

NASA Astrophysics Data System (ADS)

Gonzales, L. M.; Grimm, E. C.; Williams, J. W.; Nordheim, E. V.

2008-12-01

Continental-scale modern pollen-climate data repositories are a primary data source for paleoclimate reconstructions. However, these repositories can contain artifacts, such as records from different depositional environment and replicate records, that can influence the observed pollen-climate relationships as well as the paleoclimate reconstructions derived from these relationships. In this paper, we address the issues related to these artifacts as we define the methods used to create a research dataset from the North American Modern Pollen Database (Whitmore et al., 2005). Additionally, we define the methods used to select the environmental variables that are best for modeling regional pollen-climate relationships from the research dataset. Because the depositional environment determines the relative strengths of the local and regional pollen signals, combining data from different depositional environments results in pollen abundances that can be influenced by the local pollen signal. Replicate records in pollen-climate datasets can skew pollen-climate relationships by causing an over- or under- representation of pollen abundances in climate space. When these two artifacts are combined, the errors introduced into pollen-climate relationship modeling are compounded. The research dataset we present consists of 2,613 records in eastern North America, of which 70.9% are lacustrine sites. We demonstrate that this new research database improves upon the modeling of regional pollen-climate relationships for eastern North American taxa. The research dataset encompasses the majority of the temperature and mean summer precipitation ranges of the NAMPD's climatic range and 40% of its mean winter precipitation range. NAMPD sites with higher winter precipitation are located along the northwestern coast of North America where a rainshadow effect produces abundant winter precipitation. We present our analysis of the research dataset for use in paleoclimate reconstructions, and

Factors informing fear of reinjury after anterior cruciate ligament reconstruction.

PubMed

Ross, Cheryl A; Clifford, Amanda; Louw, Quinette A

2017-02-01

Fear of reinjury is associated with cessation of sport after anterior cruciate ligament (ACL) reconstruction despite normal postoperative knee function. The objective of this study is to describe factors informing athletes' experience of fear of reinjury post ACL reconstruction, in athletes who cited fear as the sole reason for not returning to their pre-injury level of sport. Mixed-methods study design of qualitative and a preliminary quantitative component. A conveniently selected private hospital. Ten male and two female athletes, aged between 19 and 45 years, were eligible for the interview from 68 male and 32 female potential participants (age range 17-50) who underwent an ACL reconstruction using any graft type, excluding revision or multi-ligament surgery. To explore factors informing fear of reinjury in participants citing fear of reinjury as the sole reason for not returning to sport, albeit normal knee function. From the participant interview, four themes emerged: undergoing the surgery and recovery again, nature of the pre-injury sport imposing risk of reinjury, personality traits, and social priorities. Clinicians should be aware of factors informing fear of reinjury post ACL reconstruction. Modifiable fears including pain, mode and length of rehabilitation and psychological factors should be considered during rehabilitation to potentially improve the return to sport rate.

Errors and Uncertainties in Dose Reconstruction for Radiation Effects Research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strom, Daniel J.

Dose reconstruction for studies of the health effects of ionizing radiation have been carried out for many decades. Major studies have included Japanese bomb survivors, atomic veterans, downwinders of the Nevada Test Site and Hanford, underground uranium miners, and populations of nuclear workers. For such studies to be credible, significant effort must be put into applying the best science to reconstructing unbiased absorbed doses to tissues and organs as a function of time. In many cases, more and more sophisticated dose reconstruction methods have been developed as studies progressed. For the example of the Japanese bomb survivors, the dose surrogatemore » “distance from the hypocenter” was replaced by slant range, and then by TD65 doses, DS86 doses, and more recently DS02 doses. Over the years, it has become increasingly clear that an equal level of effort must be expended on the quantitative assessment of uncertainty in such doses, and to reducing and managing uncertainty. In this context, this paper reviews difficulties in terminology, explores the nature of Berkson and classical uncertainties in dose reconstruction through examples, and proposes a path forward for Joint Coordinating Committee for Radiation Effects Research (JCCRER) Project 2.4 that requires a reasonably small level of effort for DOSES-2008.« less

Accurate Construction of Photoactivated Localization Microscopy (PALM) Images for Quantitative Measurements

PubMed Central

Coltharp, Carla; Kessler, Rene P.; Xiao, Jie

2012-01-01

Localization-based superresolution microscopy techniques such as Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) have allowed investigations of cellular structures with unprecedented optical resolutions. One major obstacle to interpreting superresolution images, however, is the overcounting of molecule numbers caused by fluorophore photoblinking. Using both experimental and simulated images, we determined the effects of photoblinking on the accurate reconstruction of superresolution images and on quantitative measurements of structural dimension and molecule density made from those images. We found that structural dimension and relative density measurements can be made reliably from images that contain photoblinking-related overcounting, but accurate absolute density measurements, and consequently faithful representations of molecule counts and positions in cellular structures, require the application of a clustering algorithm to group localizations that originate from the same molecule. We analyzed how applying a simple algorithm with different clustering thresholds (tThresh and dThresh) affects the accuracy of reconstructed images, and developed an easy method to select optimal thresholds. We also identified an empirical criterion to evaluate whether an imaging condition is appropriate for accurate superresolution image reconstruction with the clustering algorithm. Both the threshold selection method and imaging condition criterion are easy to implement within existing PALM clustering algorithms and experimental conditions. The main advantage of our method is that it generates a superresolution image and molecule position list that faithfully represents molecule counts and positions within a cellular structure, rather than only summarizing structural properties into ensemble parameters. This feature makes it particularly useful for cellular structures of heterogeneous densities and irregular geometries, and

[Differential diagnosis of papillary carcinomas of the thyroid, using image analysis and three dimensional reconstruction from serial sections].

PubMed

Holschbach, A; Kriete, A; Schäffer, R

1990-01-01

Papillae with fibrovascular cores are characteristic of papillary carcinoma of the thyroid. Papillae may be found in diffuse hyperplasia, nodular hyperplasia, Hashimoto's disease and follicular adenoma. Tissues from ten benign hyperplasias and ten papillary carcinomas were reconstructed from serial sections with three dimensional reconstruction programs. Significant qualitative and quantitative differences were found between the hyperplasia and the carcinoma. The principal differences between papillae of papillary carcinoma and hyperplasia were more clearly seen in the three dimensional reconstruction, than by means of morphometric methods. Certain criteria, e.g. the volume of papillae, were useful only with regard to the third dimension. Nevertheless, three dimensional reconstruction of biological tissue is a time consuming procedure which is not yet suitable for routine examination.

Reconstruction of multiple-pinhole micro-SPECT data using origin ensembles.

PubMed

Lyon, Morgan C; Sitek, Arkadiusz; Metzler, Scott D; Moore, Stephen C

2016-10-01

methods showed decreased reconstruction time and no loss of performance when compared to conventional OE alone. OE-reconstructed images were found to be quantitatively and qualitatively similar to MLEM, yet OE also provided estimates of image uncertainty. Some acceleration of the reconstruction can be gained through the use of parallel computing. The OE algorithm is useful for reconstructing multiple-pinhole SPECT data and can be easily modified for real-time reconstruction.

Paleoenvironmental reconstruction of the Oligocene-Miocene deposits of the Tethyan Seaway, Qom Formation, Central Iran

NASA Astrophysics Data System (ADS)

Dabaghi Sadr, Fatemeh; Schmiedl, Gerhard

2017-04-01

The Cenozoic climate transition from greenhouse to icehouse conditions was associated with major paleogeographic changes in the Tethyan realm. The closure of the Tethyan Seaway and its Iranian gateways during the terminal Paleogene and early Neogene, between approximately 28 and 18 million years, influenced the latitudinal exchange of water masses and energy and is documented in sediment successions of the Qom formation in central Iran. Little is known on the spatial expression and the exact depositional histories of the Qom Formation on orbital time-scales, including a lack of quantitative sea-level reconstructions and studies on the impact of climatic and tectonic changes on marine ecosystems and sedimentation processes. The PhD project focuses on the investigation of lithostratigraphy, biostratigraphy, paleoecology and paleoenvironmental evolution of the Iranian gateways based on late Oligocene to early Miocene foraminiferal faunas and carbonate facies from selected sediment sections of the Qom Basin. The Qom Formation was deposited in the Central Iranian back-arc basin during the Oligocene-Miocene. In this study foraminiferal faunas and carbonate microfacies were studied based on total 191 samples of two section of Qom Formation. One of them is Molkabad section, which is located northwest of Molkabad mountains, southeast of Garmsar. The section mainly consists of limestones, calcareous marls, marls, and gypsum-bearing marls with a total thickness of 760 meters. The Qom Formation at Molkabad section overlies Eocene rocks with an unconformity and consists of the following lithostratigraphic units (from the lower to upper part): Lithothamnium Limestone, Lower Marl Limestone, Bryozoa Limestone, and Upper Marl Group. The Molkabad fault separates the Qom Formation from the overlying Upper Red Formation. The other section is located at Navab anticline in Qom Formation .The section mainly consist of limestone, marl, and gypsum with a total thickness of 318 meters Navab

Optshrink LR + S: accelerated fMRI reconstruction using non-convex optimal singular value shrinkage.

PubMed

Aggarwal, Priya; Shrivastava, Parth; Kabra, Tanay; Gupta, Anubha

2017-03-01

This paper presents a new accelerated fMRI reconstruction method, namely, OptShrink LR + S method that reconstructs undersampled fMRI data using a linear combination of low-rank and sparse components. The low-rank component has been estimated using non-convex optimal singular value shrinkage algorithm, while the sparse component has been estimated using convex l 1 minimization. The performance of the proposed method is compared with the existing state-of-the-art algorithms on real fMRI dataset. The proposed OptShrink LR + S method yields good qualitative and quantitative results.

Quantitative phase-contrast digital holographic microscopy for cell dynamic evaluation

NASA Astrophysics Data System (ADS)

Yu, Lingfeng; Mohanty, Samarendra; Berns, Michael W.; Chen, Zhongping

2009-02-01

The laser microbeam uses lasers to alter and/or to ablate intracellular organelles and cellular and tissue samples, and, today, has become an important tool for cell biologists to study the molecular mechanism of complex biological systems by removing individual cells or sub-cellular organelles. However, absolute quantitation of the localized alteration/damage to transparent phase objects, such as the cell membrane or chromosomes, was not possible using conventional phase-contrast or differential interference contrast microscopy. We report the development of phase-contrast digital holographic microscopy for quantitative evaluation of cell dynamic changes in real time during laser microsurgery. Quantitative phase images are recorded during the process of laser microsurgery and thus, the dynamic change in phase can be continuously evaluated. Out-of-focus organelles are re-focused by numerical reconstruction algorithms.

The adaptive statistical iterative reconstruction-V technique for radiation dose reduction in abdominal CT: comparison with the adaptive statistical iterative reconstruction technique.

PubMed

Kwon, Heejin; Cho, Jinhan; Oh, Jongyeong; Kim, Dongwon; Cho, Junghyun; Kim, Sanghyun; Lee, Sangyun; Lee, Jihyun

2015-10-01

To investigate whether reduced radiation dose abdominal CT images reconstructed with adaptive statistical iterative reconstruction V (ASIR-V) compromise the depiction of clinically competent features when compared with the currently used routine radiation dose CT images reconstructed with ASIR. 27 consecutive patients (mean body mass index: 23.55 kg m(-2) underwent CT of the abdomen at two time points. At the first time point, abdominal CT was scanned at 21.45 noise index levels of automatic current modulation at 120 kV. Images were reconstructed with 40% ASIR, the routine protocol of Dong-A University Hospital. At the second time point, follow-up scans were performed at 30 noise index levels. Images were reconstructed with filtered back projection (FBP), 40% ASIR, 30% ASIR-V, 50% ASIR-V and 70% ASIR-V for the reduced radiation dose. Both quantitative and qualitative analyses of image quality were conducted. The CT dose index was also recorded. At the follow-up study, the mean dose reduction relative to the currently used common radiation dose was 35.37% (range: 19-49%). The overall subjective image quality and diagnostic acceptability of the 50% ASIR-V scores at the reduced radiation dose were nearly identical to those recorded when using the initial routine-dose CT with 40% ASIR. Subjective ratings of the qualitative analysis revealed that of all reduced radiation dose CT series reconstructed, 30% ASIR-V and 50% ASIR-V were associated with higher image quality with lower noise and artefacts as well as good sharpness when compared with 40% ASIR and FBP. However, the sharpness score at 70% ASIR-V was considered to be worse than that at 40% ASIR. Objective image noise for 50% ASIR-V was 34.24% and 46.34% which was lower than 40% ASIR and FBP. Abdominal CT images reconstructed with ASIR-V facilitate radiation dose reductions of to 35% when compared with the ASIR. This study represents the first clinical research experiment to use ASIR-V, the newest version of

Sensitivity after bilateral prophylactic mastectomy and immediate reconstruction.

PubMed

Gahm, Jessica; Jurell, Göran; Wickman, Marie; Hansson, Per

2007-01-01

The purpose of this retrospective study was to evaluate the cutaneous somatosensory function and patients' subjective experience after bilateral prophylactic mastectomy and immediate reconstruction with implants. Twenty-four patients treated during an eight-year period were included. Somatosensory examination was made at least two years after the latest surgery to study perception thresholds to touch, warmth, cold, and heat pain, using quantitative techniques. Patients also completed a questionnaire about subjective sensitivity. Sixteen women who had had no previous breast surgery were used as a control group. Most patients reported decreased sensitivity in the breasts, which was confirmed by the results from the quantitative somatosensory examination. The results also showed that the ability to experience sexual feelings in the breast is usually lost after this type of operation, and as many as 14 patients reported spontaneous or stimulus-evoked discomfort in the breasts.

Late-Holocene climate evolution at the WAIS Divide site, West Antarctica: Bubble number-density estimates

USGS Publications Warehouse

Fegyveresi, John M.; Alley, R.B.; Spencer, M.K.; Fitzpatrick, J.J.; Steig, E.J.; White, J.W.C.; McConnell, J.R.; Taylor, K.C.

2011-01-01

A surface cooling of ???1.7??C occurred over the ???two millennia prior to ???1700 CE at the West Antarctic ice sheet (WAIS) Divide site, based on trends in observed bubble number-density of samples from the WDC06A ice core, and on an independently constructed accumulation-rate history using annual-layer dating corrected for density variations and thinning from ice flow. Density increase and grain growth in polar firn are both controlled by temperature and accumulation rate, and the integrated effects are recorded in the number-density of bubbles as the firn changes to ice. Numberdensity is conserved in bubbly ice following pore close-off, allowing reconstruction of either paleotemperature or paleo-accumulation rate if the other is known. A quantitative late-Holocene paleoclimate reconstruction is presented for West Antarctica using data obtained from the WAIS Divide WDC06A ice core and a steady-state bubble number-density model. The resultant temperature history agrees closely with independent reconstructions based on stable-isotopic ratios of ice. The ???1.7??C cooling trend observed is consistent with a decrease in Antarctic summer duration from changing orbital obliquity, although it remains possible that elevation change at the site contributed part of the signal. Accumulation rate and temperature dropped together, broadly consistent with control by saturation vapor pressure.

Holocene glacier activity reconstructed from proglacial lake Gjøavatnet on Amsterdamøya, NW Svalbard

NASA Astrophysics Data System (ADS)

de Wet, Gregory A.; Balascio, Nicholas L.; D'Andrea, William J.; Bakke, Jostein; Bradley, Raymond S.; Perren, Bianca

2018-03-01

Well-dated and highly resolved paleoclimate records from high latitudes allow for a better understanding of past climate change. Lake sediments are excellent archives of environmental change, and can record processes occurring within the catchment, such as the growth or demise of an upstream glacier. Here we present a Holocene-length, multi-proxy lake sediment record from proglacial lake Gjøavatnet on the island of Amsterdamøya, northwest Svalbard. Today, Gjøavatnet receives meltwater from the Annabreen glacier and contains a record of changes in glacier activity linked to regional climate conditions. We measured changes in organic matter content, dry bulk density, bulk carbon isotopes, elemental concentrations via Itrax core-scanning, and diatom community composition to reconstruct variability in glacier extent back through time. Our reconstruction indicates that glacially derived sedimentation in the lake decreased markedly at ∼11.1 cal kyr BP, although a glacier likely persisted in the catchment until ∼8.4 cal kyr BP. During the mid-Holocene (∼8.4-1.0 cal kyr BP) there was significantly limited glacial influence in the catchment and enhanced deposition of organic-rich sediment in the lake. The deposition of organic rich sediments during this time was interrupted by at least three multi-centennial intervals of reduced organic matter accumulation (∼5.9-5.0, 2.7-2.0, and 1.7-1.5 cal kyr BP). Considering our chronological information and a sedimentological comparison with intervals of enhanced glacier input, we interpret these intervals not as glacial advances, but rather as cold/dry episodes that inhibited organic matter production in the lake and surrounding catchment. At ∼1.0 cal kyr BP, input of glacially derived sediment to Gjøavatnet abruptly increased, representing the rapid expansion of the Annabreen glacier.

Effects of Piecewise Spatial Smoothing in 4-D SPECT Reconstruction

NASA Astrophysics Data System (ADS)

Qi, Wenyuan; Yang, Yongyi; King, Michael A.

2014-02-01

In nuclear medicine, cardiac gated SPECT images are known to suffer from significantly increased noise owing to limited data counts. Consequently, spatial (and temporal) smoothing has been indispensable for suppressing the noise artifacts in SPECT reconstruction. However, recently we demonstrated that the benefit of spatial processing in motion-compensated reconstruction of gated SPECT (aka 4-D) could be outweighed by its adverse effects on the myocardium, which included degraded wall motion and perfusion defect detectability. In this work, we investigate whether we can alleviate these adverse effects by exploiting an alternative spatial smoothing prior in 4-D based on image total variation (TV). TV based prior is known to induce piecewise smoothing which can preserve edge features (such as boundaries of the heart wall) in reconstruction. However, it is not clear whether such a property would necessarily be beneficial for improving the accuracy of the myocardium in 4-D reconstruction. In particular, it is unknown whether it would adversely affect the detectability of perfusion defects that are small in size or low in contrast. In our evaluation study, we first use Monte Carlo simulated imaging with 4-D NURBS-based cardiac-torso (NCAT) phantom wherein the ground truth is known for quantitative comparison. We evaluated the accuracy of the reconstructed myocardium using a number of metrics, including regional and overall accuracy of the myocardium, accuracy of the phase activity curve (PAC) of the LV wall for wall motion, uniformity and spatial resolution of the LV wall, and detectability of perfusion defects using a channelized Hotelling observer (CHO). For lesion detection, we simulated perfusion defects with different sizes and contrast levels with the focus being on perfusion defects that are subtle. As a preliminary demonstration, we also tested on three sets of clinical acquisitions. From the quantitative results, it was demonstrated that TV smoothing could

Reconstructing lake ice cover in subarctic lakes using a diatom-based inference model

NASA Astrophysics Data System (ADS)

Weckström, Jan; Hanhijärvi, Sami; Forsström, Laura; Kuusisto, Esko; Korhola, Atte

2014-03-01

A new quantitative diatom-based lake ice cover inference model was developed to reconstruct past ice cover histories and applied to four subarctic lakes. The used ice cover model is based on a calculated melting degree day value of +130 and a freezing degree day value of -30 for each lake. The reconstructed Holocene ice cover duration histories show similar trends to the independently reconstructed regional air temperature history. The ice cover duration was around 7 days shorter than the average ice cover duration during the warmer early Holocene (approximately 10 to 6.5 calibrated kyr B.P.) and around 3-5 days longer during the cool Little Ice Age (approximately 500 to 100 calibrated yr B.P.). Although the recent climate warming is represented by only 2-3 samples in the sediment series, these show a rising trend in the prolonged ice-free periods of up to 2 days. Diatom-based ice cover inference models can provide a powerful tool to reconstruct past ice cover histories in remote and sensitive areas where no measured data are available.

Direct Parametric Reconstruction With Joint Motion Estimation/Correction for Dynamic Brain PET Data.

PubMed

Jiao, Jieqing; Bousse, Alexandre; Thielemans, Kris; Burgos, Ninon; Weston, Philip S J; Schott, Jonathan M; Atkinson, David; Arridge, Simon R; Hutton, Brian F; Markiewicz, Pawel; Ourselin, Sebastien

2017-01-01

Direct reconstruction of parametric images from raw photon counts has been shown to improve the quantitative analysis of dynamic positron emission tomography (PET) data. However it suffers from subject motion which is inevitable during the typical acquisition time of 1-2 hours. In this work we propose a framework to jointly estimate subject head motion and reconstruct the motion-corrected parametric images directly from raw PET data, so that the effects of distorted tissue-to-voxel mapping due to subject motion can be reduced in reconstructing the parametric images with motion-compensated attenuation correction and spatially aligned temporal PET data. The proposed approach is formulated within the maximum likelihood framework, and efficient solutions are derived for estimating subject motion and kinetic parameters from raw PET photon count data. Results from evaluations on simulated [ 11 C]raclopride data using the Zubal brain phantom and real clinical [ 18 F]florbetapir data of a patient with Alzheimer's disease show that the proposed joint direct parametric reconstruction motion correction approach can improve the accuracy of quantifying dynamic PET data with large subject motion.

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

Paleoecology and high-resolution paleohydrology of a kettle peatland in upper Michigan

NASA Astrophysics Data System (ADS)

Booth, Robert K.; Jackson, Stephen T.; Gray, Catherine E. D.

2004-01-01

We investigated the developmental and hydrological history of a Sphagnum-dominated, kettle peatland in Upper Michigan using testate amoebae, plant macrofossils, and pollen. Our primary objective was to determine if the paleohydrological record of the peatland represents a record of past climate variability at subcentennial to millennial time scales. To assess the role of millennial-scale climate variability on peatland paleohydrology, we compared the timing of peatland and upland vegetation changes. To investigate the role of higher-frequency climate variability on peatland paleohydrology, we used testate amoebae to reconstruct a high-resolution, hydrologic history of the peatland for the past 5100 years, and compared this record to other regional records of paleoclimate and vegetation. Comparisons revealed coherent patterns of hydrological, vegetational, and climatic changes, suggesting that peatland paleohydrology responded to climate variability at millennial to sub-centennial time scales. Although ombrotrophic peatlands have been the focus of most high-resolution peatland paleoclimate research, paleohydrological records from Sphagnum-dominated, closed-basin peatlands record high-frequency and low-magnitude climatic changes and thus represent a significant source of unexplored paleoclimate data.

Facial asymmetry quantitative evaluation in oculoauriculovertebral spectrum.

PubMed

Manara, Renzo; Schifano, Giovanni; Brotto, Davide; Mardari, Rodica; Ghiselli, Sara; Gerunda, Antonio; Ghirotto, Cristina; Fusetti, Stefano; Piacentile, Katherine; Scienza, Renato; Ermani, Mario; Martini, Alessandro

2016-03-01

Facial asymmetries in oculoauriculovertebral spectrum (OAVS) patients might require surgical corrections that are mostly based on qualitative approach and surgeon's experience. The present study aimed to develop a quantitative 3D CT imaging-based procedure suitable for maxillo-facial surgery planning in OAVS patients. Thirteen OAVS patients (mean age 3.5 ± 4.0 years; range 0.2-14.2, 6 females) and 13 controls (mean age 7.1 ± 5.3 years; range 0.6-15.7, 5 females) who underwent head CT examination were retrospectively enrolled. Eight bilateral anatomical facial landmarks were defined on 3D CT images (porion, orbitale, most anterior point of frontozygomatic suture, most superior point of temporozygomatic suture, most posterior-lateral point of the maxilla, gonion, condylion, mental foramen) and distance from orthogonal planes (in millimeters) was used to evaluate the asymmetry on each axis and to calculate a global asymmetry index of each anatomical landmark. Mean asymmetry values and relative confidence intervals were obtained from the control group. OAVS patients showed 2.5 ± 1.8 landmarks above the confidence interval while considering the global asymmetry values; 12 patients (92%) showed at least one pathologically asymmetric landmark. Considering each axis, the mean number of pathologically asymmetric landmarks increased to 5.5 ± 2.6 (p = 0.002) and all patients presented at least one significant landmark asymmetry. Modern CT-based 3D reconstructions allow accurate assessment of facial bone asymmetries in patients affected by OAVS. The evaluation as a global score and in different orthogonal axes provides precise quantitative data suitable for maxillo-facial surgical planning. CT-based 3D reconstruction might allow a quantitative approach for planning and following-up maxillo-facial surgery in OAVS patients.

Investigation of practical initial attenuation image estimates in TOF-MLAA reconstruction for PET/MR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Ju-Chieh, E-mail: chengjuchieh@gmail.com; Y

Purpose: Time-of-flight joint attenuation and activity positron emission tomography reconstruction requires additional calibration (scale factors) or constraints during or post-reconstruction to produce a quantitative μ-map. In this work, the impact of various initializations of the joint reconstruction was investigated, and the initial average mu-value (IAM) method was introduced such that the forward-projection of the initial μ-map is already very close to that of the reference μ-map, thus reducing/minimizing the offset (scale factor) during the early iterations of the joint reconstruction. Consequently, the accuracy and efficiency of unconstrained joint reconstruction such as time-of-flight maximum likelihood estimation of attenuation and activity (TOF-MLAA)more » can be improved by the proposed IAM method. Methods: 2D simulations of brain and chest were used to evaluate TOF-MLAA with various initial estimates which include the object filled with water uniformly (conventional initial estimate), bone uniformly, the average μ-value uniformly (IAM magnitude initialization method), and the perfect spatial μ-distribution but with a wrong magnitude (initialization in terms of distribution). 3D GATE simulation was also performed for the chest phantom under a typical clinical scanning condition, and the simulated data were reconstructed with a fully corrected list-mode TOF-MLAA algorithm with various initial estimates. The accuracy of the average μ-values within the brain, chest, and abdomen regions obtained from the MR derived μ-maps was also evaluated using computed tomography μ-maps as the gold-standard. Results: The estimated μ-map with the initialization in terms of magnitude (i.e., average μ-value) was observed to reach the reference more quickly and naturally as compared to all other cases. Both 2D and 3D GATE simulations produced similar results, and it was observed that the proposed IAM approach can produce quantitative μ-map/emission when the

ANALOG: a program for estimating paleoclimate parameters using the method of modern analogs

USGS Publications Warehouse

Schweitzer, Peter N.

1994-01-01

Beginning in the 1970s with CLIMAP, paleoclimatologists have been trying to derive quantitative estimates of climatic parameters from the sedimentary record. In general the procedure is to observe the modern distribution of some component of surface sediment that depends on climate, find an empirical relationship between climate and the character of sediments, then extrapolate past climate by studying older sediments in the same way. Initially the empirical relationship between climate and components of the sediment was determined using a multiple regression technique (Imbrie and Kipp, 1971). In these studies sea-floor sediments were examined to determine the percentage of various species of planktonic foraminifera present in them. Supposing that the distribution of foraminiferal assemblages depended strongly on the extremes of annual sea-surface temperature (SST), the foraminiferal assemblages (refined through use of varimax factor analysis) were regressed against the average SST during the coolest and warmest months of the year. The result was a set of transfer functions, equations that could be used to estimate cool and warm SST from the faunal composition of a sediment sample. Assuming that the ecological preference of the species had remained constant throughout the last several hundred thousand years, these transfer functions could be used to estimate SSTs during much of the late Pleistocene. Hutson (1980) and Overpeck, Webb, and Prentice (1985) proposed an alternative approach to estimating paleoclimatic parameters. Their 'method of modern analogs' revolved not around the existence of a few climatically-sensitive faunal assemblages but rather on the expectation that similar climatic regimes should foster similar faunal and floral assemblages. From a large pool of modern samples, those few are selected whose faunal compositions are most similar to a given fossil sample. Paleoclimate estimates are derived using the climatic character of only the most similar

MR-guided dynamic PET reconstruction with the kernel method and spectral temporal basis functions

NASA Astrophysics Data System (ADS)

Novosad, Philip; Reader, Andrew J.

2016-06-01

Recent advances in dynamic positron emission tomography (PET) reconstruction have demonstrated that it is possible to achieve markedly improved end-point kinetic parameter maps by incorporating a temporal model of the radiotracer directly into the reconstruction algorithm. In this work we have developed a highly constrained, fully dynamic PET reconstruction algorithm incorporating both spectral analysis temporal basis functions and spatial basis functions derived from the kernel method applied to a co-registered T1-weighted magnetic resonance (MR) image. The dynamic PET image is modelled as a linear combination of spatial and temporal basis functions, and a maximum likelihood estimate for the coefficients can be found using the expectation-maximization (EM) algorithm. Following reconstruction, kinetic fitting using any temporal model of interest can be applied. Based on a BrainWeb T1-weighted MR phantom, we performed a realistic dynamic [18F]FDG simulation study with two noise levels, and investigated the quantitative performance of the proposed reconstruction algorithm, comparing it with reconstructions incorporating either spectral analysis temporal basis functions alone or kernel spatial basis functions alone, as well as with conventional frame-independent reconstruction. Compared to the other reconstruction algorithms, the proposed algorithm achieved superior performance, offering a decrease in spatially averaged pixel-level root-mean-square-error on post-reconstruction kinetic parametric maps in the grey/white matter, as well as in the tumours when they were present on the co-registered MR image. When the tumours were not visible in the MR image, reconstruction with the proposed algorithm performed similarly to reconstruction with spectral temporal basis functions and was superior to both conventional frame-independent reconstruction and frame-independent reconstruction with kernel spatial basis functions. Furthermore, we demonstrate that a joint spectral

MR-guided dynamic PET reconstruction with the kernel method and spectral temporal basis functions.

PubMed

Novosad, Philip; Reader, Andrew J

2016-06-21

Recent advances in dynamic positron emission tomography (PET) reconstruction have demonstrated that it is possible to achieve markedly improved end-point kinetic parameter maps by incorporating a temporal model of the radiotracer directly into the reconstruction algorithm. In this work we have developed a highly constrained, fully dynamic PET reconstruction algorithm incorporating both spectral analysis temporal basis functions and spatial basis functions derived from the kernel method applied to a co-registered T1-weighted magnetic resonance (MR) image. The dynamic PET image is modelled as a linear combination of spatial and temporal basis functions, and a maximum likelihood estimate for the coefficients can be found using the expectation-maximization (EM) algorithm. Following reconstruction, kinetic fitting using any temporal model of interest can be applied. Based on a BrainWeb T1-weighted MR phantom, we performed a realistic dynamic [(18)F]FDG simulation study with two noise levels, and investigated the quantitative performance of the proposed reconstruction algorithm, comparing it with reconstructions incorporating either spectral analysis temporal basis functions alone or kernel spatial basis functions alone, as well as with conventional frame-independent reconstruction. Compared to the other reconstruction algorithms, the proposed algorithm achieved superior performance, offering a decrease in spatially averaged pixel-level root-mean-square-error on post-reconstruction kinetic parametric maps in the grey/white matter, as well as in the tumours when they were present on the co-registered MR image. When the tumours were not visible in the MR image, reconstruction with the proposed algorithm performed similarly to reconstruction with spectral temporal basis functions and was superior to both conventional frame-independent reconstruction and frame-independent reconstruction with kernel spatial basis functions. Furthermore, we demonstrate that a joint spectral

SU-E-J-218: Evaluation of CT Images Created Using a New Metal Artifact Reduction Reconstruction Algorithm for Radiation Therapy Treatment Planning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niemkiewicz, J; Palmiotti, A; Miner, M

2014-06-01

Purpose: Metal in patients creates streak artifacts in CT images. When used for radiation treatment planning, these artifacts make it difficult to identify internal structures and affects radiation dose calculations, which depend on HU numbers for inhomogeneity correction. This work quantitatively evaluates a new metal artifact reduction (MAR) CT image reconstruction algorithm (GE Healthcare CT-0521-04.13-EN-US DOC1381483) when metal is present. Methods: A Gammex Model 467 Tissue Characterization phantom was used. CT images were taken of this phantom on a GE Optima580RT CT scanner with and without steel and titanium plugs using both the standard and MAR reconstruction algorithms. HU valuesmore » were compared pixel by pixel to determine if the MAR algorithm altered the HUs of normal tissues when no metal is present, and to evaluate the effect of using the MAR algorithm when metal is present. Also, CT images of patients with internal metal objects using standard and MAR reconstruction algorithms were compared. Results: Comparing the standard and MAR reconstructed images of the phantom without metal, 95.0% of pixels were within ±35 HU and 98.0% of pixels were within ±85 HU. Also, the MAR reconstruction algorithm showed significant improvement in maintaining HUs of non-metallic regions in the images taken of the phantom with metal. HU Gamma analysis (2%, 2mm) of metal vs. non-metal phantom imaging using standard reconstruction resulted in an 84.8% pass rate compared to 96.6% for the MAR reconstructed images. CT images of patients with metal show significant artifact reduction when reconstructed with the MAR algorithm. Conclusion: CT imaging using the MAR reconstruction algorithm provides improved visualization of internal anatomy and more accurate HUs when metal is present compared to the standard reconstruction algorithm. MAR reconstructed CT images provide qualitative and quantitative improvements over current reconstruction algorithms, thus improving radiation

Quantitative 3D reconstruction of airway and pulmonary vascular trees using HRCT

NASA Astrophysics Data System (ADS)

Wood, Susan A.; Hoford, John D.; Hoffman, Eric A.; Zerhouni, Elias A.; Mitzner, Wayne A.

1993-07-01

Accurate quantitative measurements of airway and vascular dimensions are essential to evaluate function in the normal and diseased lung. In this report, a novel method is described for three-dimensional extraction and analysis of pulmonary tree structures using data from High Resolution Computed Tomography (HRCT). Serially scanned two-dimensional slices of the lower left lobe of isolated dog lungs were stacked to create a volume of data. Airway and vascular trees were three-dimensionally extracted using a three dimensional seeded region growing algorithm based on difference in CT number between wall and lumen. To obtain quantitative data, we reduced each tree to its central axis. From the central axis, branch length is measured as the distance between two successive branch points, branch angle is measured as the angle produced by two daughter branches, and cross sectional area is measured from a plane perpendicular to the central axis point. Data derived from these methods can be used to localize and quantify structural differences both during changing physiologic conditions and in pathologic lungs.

Initial phantom study comparing image quality in computed tomography using adaptive statistical iterative reconstruction and new adaptive statistical iterative reconstruction v.

PubMed

Lim, Kyungjae; Kwon, Heejin; Cho, Jinhan; Oh, Jongyoung; Yoon, Seongkuk; Kang, Myungjin; Ha, Dongho; Lee, Jinhwa; Kang, Eunju

2015-01-01

The purpose of this study was to assess the image quality of a novel advanced iterative reconstruction (IR) method called as "adaptive statistical IR V" (ASIR-V) by comparing the image noise, contrast-to-noise ratio (CNR), and spatial resolution from those of filtered back projection (FBP) and adaptive statistical IR (ASIR) on computed tomography (CT) phantom image. We performed CT scans at 5 different tube currents (50, 70, 100, 150, and 200 mA) using 3 types of CT phantoms. Scanned images were subsequently reconstructed in 7 different scan settings, such as FBP, and 3 levels of ASIR and ASIR-V (30%, 50%, and 70%). The image noise was measured in the first study using body phantom. The CNR was measured in the second study using contrast phantom and the spatial resolutions were measured in the third study using a high-resolution phantom. We compared the image noise, CNR, and spatial resolution among the 7 reconstructed image scan settings to determine whether noise reduction, high CNR, and high spatial resolution could be achieved at ASIR-V. At quantitative analysis of the first and second studies, it showed that the images reconstructed using ASIR-V had reduced image noise and improved CNR compared with those of FBP and ASIR (P < 0.001). At qualitative analysis of the third study, it also showed that the images reconstructed using ASIR-V had significantly improved spatial resolution than those of FBP and ASIR (P < 0.001). Our phantom studies showed that ASIR-V provides a significant reduction in image noise and a significant improvement in CNR as well as spatial resolution. Therefore, this technique has the potential to reduce the radiation dose further without compromising image quality.

A new OH5 reconstruction with an assessment of its uncertainty.

PubMed

Benazzi, Stefano; Bookstein, Fred L; Strait, David S; Weber, Gerhard W

2011-07-01

The OH5 cranium, holotype of Paranthropus boisei consists of two main portions that do not fit together: the extensively reconstructed face and a portion of the neurocranium. A physical reconstruction of the cranium was carried out by Tobias in 1967, who did not discuss problems related to deformation, although he noted a slight functional asymmetry. Nevertheless, the reconstructed cranium shows some anomalies, mainly due to the right skewed position of the upper calvariofacial fragment and uncertainty of the relative position of the neurocranium to the face, which hamper further quantitative analysis of OH5's cranial geometry. Here, we present a complete virtual reconstruction of OH5, using three-dimensional (3D) digital data, geometric morphometric (GM) methods and computer-aided design (CAD) techniques. Starting from a CT scan of Tobias's reconstruction, a semi-automatic segmentation method was used to remove Tobias's plaster. The upper calvariofacial fragment was separated from the lower facial fragment and re-aligned using superposition of their independent midsagittal planes in a range of feasible positions. The missing parts of the right hemiface were reconstructed using non-uniform rational basis-spline (NURBS) surface and subsequently mirrored using the midsagittal plane to arrive at a symmetrical facial reconstruction. A symmetric neurocranium was obtained as the average of the original shape and its mirrored version. The alignment between the two symmetric shapes (face and neurocranium) used their independent midsagittal plane and a reference shape (KNM-ER 406) to highly reduce their degrees of freedom. From the series of alternative reconstructions, we selected the middle of this rather small feasible range. When reconstructed as a range in this way, the whole cranial form of this unique specimen can be further quantified by comparative coordinate-based methods such as GM or can be used for finite element modeling (FEM) explorations of hypotheses about

Computed Tomography Imaging of a Hip Prosthesis Using Iterative Model-Based Reconstruction and Orthopaedic Metal Artefact Reduction: A Quantitative Analysis.

PubMed

Wellenberg, Ruud H H; Boomsma, Martijn F; van Osch, Jochen A C; Vlassenbroek, Alain; Milles, Julien; Edens, Mireille A; Streekstra, Geert J; Slump, Cornelis H; Maas, Mario

To quantify the combined use of iterative model-based reconstruction (IMR) and orthopaedic metal artefact reduction (O-MAR) in reducing metal artefacts and improving image quality in a total hip arthroplasty phantom. Scans acquired at several dose levels and kVps were reconstructed with filtered back-projection (FBP), iterative reconstruction (iDose) and IMR, with and without O-MAR. Computed tomography (CT) numbers, noise levels, signal-to-noise-ratios and contrast-to-noise-ratios were analysed. Iterative model-based reconstruction results in overall improved image quality compared to iDose and FBP (P < 0.001). Orthopaedic metal artefact reduction is most effective in reducing severe metal artefacts improving CT number accuracy by 50%, 60%, and 63% (P < 0.05) and reducing noise by 1%, 62%, and 85% (P < 0.001) whereas improving signal-to-noise-ratios by 27%, 47%, and 46% (P < 0.001) and contrast-to-noise-ratios by 16%, 25%, and 19% (P < 0.001) with FBP, iDose, and IMR, respectively. The combined use of IMR and O-MAR strongly improves overall image quality and strongly reduces metal artefacts in the CT imaging of a total hip arthroplasty phantom.

3D spine reconstruction of postoperative patients from multi-level manifold ensembles.

PubMed

Kadoury, Samuel; Labelle, Hubert; Parent, Stefan

2014-01-01

The quantitative assessment of surgical outcomes using personalized anatomical models is an essential task for the treatment of spinal deformities such as adolescent idiopathic scoliosis. However an accurate 3D reconstruction of the spine from postoperative X-ray images remains challenging due to presence of instrumentation (metallic rods and screws) occluding vertebrae on the spine. In this paper, we formulate the reconstruction problem as an optimization over a manifold of articulated spine shapes learned from pathological training data. The manifold itself is represented using a novel data structure, a multi-level manifold ensemble, which contains links between nodes in a single hierarchical structure, as well as links between different hierarchies, representing overlapping partitions. We show that this data structure allows both efficient localization and navigation on the manifold, for on-the-fly building of local nonlinear models (manifold charting). Our reconstruction framework was tested on pre- and postoperative X-ray datasets from patients who underwent spinal surgery. Compared to manual ground-truth, our method achieves a 3D reconstruction accuracy of 2.37 +/- 0.85 mm for postoperative spine models and can deal with severe cases of scoliosis.

Reconstructing past sea ice cover of the Northern Hemisphere from dinocyst assemblages: status of the approach

NASA Astrophysics Data System (ADS)

de Vernal, Anne; Rochon, André; Fréchette, Bianca; Henry, Maryse; Radi, Taoufik; Solignac, Sandrine

2013-11-01

Dinocysts occur in a wide range of environmental conditions, including polar areas. We review here their use for the reconstruction of paleo sea ice cover in such environments. In the Arctic Ocean and subarctic seas characterized by dense sea ice cover, Islandinium minutum, Islandinium? cezare, Echinidinium karaense, Polykrikos sp. var. Arctic, Spiniferites elongatus-frigidus and Impagidinium pallidum are common and often occur with more cosmopolitan taxa such as Operculodinium centrocarpum sensu Wall & Dale, cyst of Pentapharsodinium dalei and Brigantedinium spp. Canonical correspondence analyses conducted on dinocyst assemblages illustrate relationships with sea surface parameters such as salinity, temperature, and sea ice cover. The application of the modern analogue technique permits quantitative reconstruction of past sea ice cover, which is expressed in terms of seasonal extent of sea ice cover (months per year with more than 50% of sea ice concentration) or mean annual sea ice concentration (in tenths). The accuracy of reconstructions or root mean square error of prediction (RMSEP) is ±1.1 over 10, which corresponds to perennial sea ice. Such an error is close to the interannual variability (standard deviation) of observed sea ice cover. Mismatch between the time interval of instrumental data used as reference (1953-2000) and the time interval represented by dinocyst populations in surface sediment samples, which may cover decades if not centuries, is another source of error. Despite uncertainties, dinocyst assemblages are useful for making quantitative reconstruction of seasonal sea ice cover.

Aragonite-Calcite Inversion During Biogenic Carbonate Sampling: Considerations for Interpreting Isotopic Measurements in Paleoclimate Studies

NASA Astrophysics Data System (ADS)

Waite, A. J.; Swart, P. K.

2011-12-01

As aragonite is the metastable polymorph of calcium carbonate, it lends itself to monotropic inversion to the more stable polymorph, calcite. This inversion is possible through an increase in the temperature and pressure conditions to which the sample is exposed and, although first noted nearly a century ago, has been primarily discussed in the context of sample roasting prior to analyses in paleoclimatological studies. Over the last several decades, however, researchers have found evidence to suggest that the friction associated with the sampling of biogenic carbonates via milling/drilling also induces inversion. Furthermore, this inversion may be associated with a shift in measured oxygen isotopic values and ultimately have significant implications for the interpretation of paleoclimatic reconstructions. Despite this, the isotopic heterogeneity of biogenic aragonite skeletons makes the effects of inversion challenging to test and the subject remains underrepresented in the literature. Here we present a first order study into the effects of milling on both the mineralogy and isotopic compositions measured in sclerosponges, corals, and molluscs. X-Ray diffraction analysis of samples hand ground with a mortar and pestle reveal 100% aragonitic skeletons. Conversely, samples milled with a computerized micromill show measurable inversion to calcite. On average, percent inversion of aragonite to calcite for individual specimens was 15% for sclerosponges, 16% for corals, and 9% for molluscs. Isotopic data from these specimens show that the higher the percentage of aragonite inverted to calcite, the more depleted the measured oxygen isotopic values. In the largest of the datasets (sclerosponges), it is evident that the range of oxygen isotope values from milled samples (-0.02 to +0.84%) exceeds the range in values for those samples which were hand ground and showed no inversion (+0.53 to +0.90%). This, coupled with the strong correlation between the two variables

Quantitative damage imaging using Lamb wave diffraction tomography

NASA Astrophysics Data System (ADS)

Zhang, Hai-Yan; Ruan, Min; Zhu, Wen-Fa; Chai, Xiao-Dong

2016-12-01

In this paper, we investigate the diffraction tomography for quantitative imaging damages of partly through-thickness holes with various shapes in isotropic plates by using converted and non-converted scattered Lamb waves generated numerically. Finite element simulations are carried out to provide the scattered wave data. The validity of the finite element model is confirmed by the comparison of scattering directivity pattern (SDP) of circle blind hole damage between the finite element simulations and the analytical results. The imaging method is based on a theoretical relation between the one-dimensional (1D) Fourier transform of the scattered projection and two-dimensional (2D) spatial Fourier transform of the scattering object. A quantitative image of the damage is obtained by carrying out the 2D inverse Fourier transform of the scattering object. The proposed approach employs a circle transducer network containing forward and backward projections, which lead to so-called transmission mode (TMDT) and reflection mode diffraction tomography (RMDT), respectively. The reconstructed results of the two projections for a non-converted S0 scattered mode are investigated to illuminate the influence of the scattering field data. The results show that Lamb wave diffraction tomography using the combination of TMDT and RMDT improves the imaging effect compared with by using only the TMDT or RMDT. The scattered data of the converted A0 mode are also used to assess the performance of the diffraction tomography method. It is found that the circle and elliptical shaped damages can still be reasonably identified from the reconstructed images while the reconstructed results of other complex shaped damages like crisscross rectangles and racecourse are relatively poor. Project supported by the National Natural Science Foundation of China (Grant Nos. 11474195, 11274226, 11674214, and 51478258).

MO-DE-207A-07: Filtered Iterative Reconstruction (FIR) Via Proximal Forward-Backward Splitting: A Synergy of Analytical and Iterative Reconstruction Method for CT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, H

Purpose: This work is to develop a general framework, namely filtered iterative reconstruction (FIR) method, to incorporate analytical reconstruction (AR) method into iterative reconstruction (IR) method, for enhanced CT image quality. Methods: FIR is formulated as a combination of filtered data fidelity and sparsity regularization, and then solved by proximal forward-backward splitting (PFBS) algorithm. As a result, the image reconstruction decouples data fidelity and image regularization with a two-step iterative scheme, during which an AR-projection step updates the filtered data fidelity term, while a denoising solver updates the sparsity regularization term. During the AR-projection step, the image is projected tomore » the data domain to form the data residual, and then reconstructed by certain AR to a residual image which is in turn weighted together with previous image iterate to form next image iterate. Since the eigenvalues of AR-projection operator are close to the unity, PFBS based FIR has a fast convergence. Results: The proposed FIR method is validated in the setting of circular cone-beam CT with AR being FDK and total-variation sparsity regularization, and has improved image quality from both AR and IR. For example, AIR has improved visual assessment and quantitative measurement in terms of both contrast and resolution, and reduced axial and half-fan artifacts. Conclusion: FIR is proposed to incorporate AR into IR, with an efficient image reconstruction algorithm based on PFBS. The CBCT results suggest that FIR synergizes AR and IR with improved image quality and reduced axial and half-fan artifacts. The authors was partially supported by the NSFC (#11405105), the 973 Program (#2015CB856000), and the Shanghai Pujiang Talent Program (#14PJ1404500).« less

Variability in Bias of Gridded Sea Surface Temperature Data Products: Implications for Seasonally Resolved Marine Proxy Reconstructions

NASA Astrophysics Data System (ADS)

Ouellette, G., Jr.; DeLong, K. L.

2016-12-01

Seasonally resolved reconstructions of sea surface temperature (SST) are commonly produced using isotopic ratios and trace elemental ratios within the skeletal material of marine organisms such as corals, coralline algae, and mollusks. Using these geochemical proxies to produce paleoclimate reconstructions requires using regression methods to calibrate the proxy to observed SST, ideally with in situ SST records that span many years. Unfortunately, the few locations with in situ SST records rarely coincide with the time span of the marine proxy archive. Therefore, SST data products are often used for calibration and they are based on MOHSST or ICOADS SST observations as their main SST source but use different algorithms to produce globally gridded data products. These products include the Hadley Center's HADSST (5º) and interpolated HADISST (1º), NOAA's extended reconstructed SST (ERSST; 2º), optimum interpolation SST (OISST; 1º), and the Kaplan SST (5º). This study assessed the potential bias in these data products at marine archive sites throughout the tropical Atlantic using in situ SST where it was available, and a high-resolution (4 km) satellite-based SST data product from NOAA Pathfinder that has been shown to closely reflect in situ SST for our locations. Bias was assessed at each site, and then within each data product across the region for spatial homogeneity. Our results reveal seasonal biases in all data products, but not for all locations and not of a uniform magnitude or season among products. We found the largest differences in mean SST on the order of 1-3°C for single sites in the Gulf of Mexico, and differences for regional mean SST bias were 0.5-1°C when sites in the Gulf of Mexico were compared to sites in the Caribbean Sea within the same data product. No one SST data product outperformed the others and no systematic bias was found. This analysis illustrates regional strengths and weaknesses of these data products, and serves as a

3D Reconstruction of the Retinal Arterial Tree Using Subject-Specific Fundus Images

NASA Astrophysics Data System (ADS)

Liu, D.; Wood, N. B.; Xu, X. Y.; Witt, N.; Hughes, A. D.; Samcg, Thom

Systemic diseases, such as hypertension and diabetes, are associated with changes in the retinal microvasculature. Although a number of studies have been performed on the quantitative assessment of the geometrical patterns of the retinal vasculature, previous work has been confined to 2 dimensional (2D) analyses. In this paper, we present an approach to obtain a 3D reconstruction of the retinal arteries from a pair of 2D retinal images acquired in vivo. A simple essential matrix based self-calibration approach was employed for the "fundus camera-eye" system. Vessel segmentation was performed using a semi-automatic approach and correspondence between points from different images was calculated. The results of 3D reconstruction show the centreline of retinal vessels and their 3D curvature clearly. Three-dimensional reconstruction of the retinal vessels is feasible and may be useful in future studies of the retinal vasculature in disease.

Inverse transport problems in quantitative PAT for molecular imaging

NASA Astrophysics Data System (ADS)

Ren, Kui; Zhang, Rongting; Zhong, Yimin

2015-12-01

Fluorescence photoacoustic tomography (fPAT) is a molecular imaging modality that combines photoacoustic tomography with fluorescence imaging to obtain high-resolution imaging of fluorescence distributions inside heterogeneous media. The objective of this work is to study inverse problems in the quantitative step of fPAT where we intend to reconstruct physical coefficients in a coupled system of radiative transport equations using internal data recovered from ultrasound measurements. We derive uniqueness and stability results on the inverse problems and develop some efficient algorithms for image reconstructions. Numerical simulations based on synthetic data are presented to validate the theoretical analysis. The results we present here complement these in Ren K and Zhao H (2013 SIAM J. Imaging Sci. 6 2024-49) on the same problem but in the diffusive regime.

Modelled vs. reconstructed past fire dynamics - how can we compare?

NASA Astrophysics Data System (ADS)

Brücher, Tim; Brovkin, Victor; Kloster, Silvia; Marlon, Jennifer R.; Power, Mitch J.

2015-04-01

Fire is an important process that affects climate through changes in CO2 emissions, albedo, and aerosols (Ward et al. 2012). Fire-history reconstructions from charcoal accumulations in sediment indicate that biomass burning has increased since the Last Glacial Maximum (Power et al. 2008; Marlon et al. 2013). Recent comparisons with transient climate model output suggest that this increase in global ?re activity is linked primarily to variations in temperature and secondarily to variations in precipitation (Daniau et al. 2012). In this study, we discuss the best way to compare global ?re model output with charcoal records. Fire models generate quantitative output for burned area and fire-related emissions of CO2, whereas charcoal data indicate relative changes in biomass burning for specific regions and time periods only. However, models can be used to relate trends in charcoal data to trends in quantitative changes in burned area or fire carbon emissions. Charcoal records are often reported as Z-scores (Power et al. 2008). Since Z-scores are non-linear power transformations of charcoal influxes, we must evaluate if, for example, a two-fold increase in the standardized charcoal reconstruction corresponds to a 2- or 200-fold increase in the area burned. In our study we apply the Z-score metric to the model output. This allows us to test how well the model can quantitatively reproduce the charcoal-based reconstructions and how Z-score metrics affect the statistics of model output. The Global Charcoal Database (GCD version 2.5; www.gpwg.org/gpwgdb.html) is used to determine regional and global paleofire trends from 218 sedimentary charcoal records covering part or all of the last 8 ka BP. To retrieve regional and global composites of changes in fire activity over the Holocene the time series of Z-scores are linearly averaged to achieve regional composites. A coupled climate-carbon cycle model, CLIMBA (Brücher et al. 2014), is used for this study. It consists of the

Pollen-based continental climate reconstructions at 6 and 21 ka: a global synthesis

USGS Publications Warehouse

Bartlein, P.J.; Harrison, S.P.; Brewer, Sandra; Connor, S.; Davis, B.A.S.; Gajewski, K.; Guiot, J.; Harrison-Prentice, T. I.; Henderson, A.; Peyron, O.; Prentice, I.C.; Scholze, M.; Seppa, H.; Shuman, B.; Sugita, S.; Thompson, R.S.; Viau, A.E.; Williams, J.; Wu, H.

2010-01-01

Subfossil pollen and plant macrofossil data derived from 14C-dated sediment profiles can provide quantitative information on glacial and interglacial climates. The data allow climate variables related to growing-season warmth, winter cold, and plant-available moisture to be reconstructed. Continental-scale reconstructions have been made for the mid-Holocene (MH, around 6 ka) and Last Glacial Maximum (LGM, around 21 ka), allowing comparison with palaeoclimate simulations currently being carried out as part of the fifth Assessment Report (AR5) of the Intergovernmental Panel on Climate Change. The synthesis of the available MH and LGM climate reconstructions and their uncertainties, obtained using modern-analogue, regression and model-inversion techniques, is presented for four temperature variables and two moisture variables. Reconstructions of the same variables based on surface-pollen assemblages are shown to be accurate and unbiased. Reconstructed LGM and MH climate anomaly patterns are coherent, consistent between variables, and robust with respect to the choice of technique. They support a conceptual model of the controls of Late Quaternary climate change whereby the first-order effects of orbital variations and greenhouse forcing on the seasonal cycle of temperature are predictably modified by responses of the atmospheric circulation and surface energy balance.