Prospective multi-centre Voxel Based Morphometry study employing scanner specific segmentations: Procedure development using CaliBrain structural MRI data

PubMed Central

2009-01-01

Background Structural Magnetic Resonance Imaging (sMRI) of the brain is employed in the assessment of a wide range of neuropsychiatric disorders. In order to improve statistical power in such studies it is desirable to pool scanning resources from multiple centres. The CaliBrain project was designed to provide for an assessment of scanner differences at three centres in Scotland, and to assess the practicality of pooling scans from multiple-centres. Methods We scanned healthy subjects twice on each of the 3 scanners in the CaliBrain project with T1-weighted sequences. The tissue classifier supplied within the Statistical Parametric Mapping (SPM5) application was used to map the grey and white tissue for each scan. We were thus able to assess within scanner variability and between scanner differences. We have sought to correct for between scanner differences by adjusting the probability mappings of tissue occupancy (tissue priors) used in SPM5 for tissue classification. The adjustment procedure resulted in separate sets of tissue priors being developed for each scanner and we refer to these as scanner specific priors. Results Voxel Based Morphometry (VBM) analyses and metric tests indicated that the use of scanner specific priors reduced tissue classification differences between scanners. However, the metric results also demonstrated that the between scanner differences were not reduced to the level of within scanner variability, the ideal for scanner harmonisation. Conclusion Our results indicate the development of scanner specific priors for SPM can assist in pooling of scan resources from different research centres. This can facilitate improvements in the statistical power of quantitative brain imaging studies. PMID:19445668

Methodology and apparatus for diffuse photon imaging

DOEpatents

Feng, S.C.; Zeng, F.; Zhao, H.L.

1997-12-09

Non-invasive near infrared optical medical imaging devices for both hematoma detection in the brain and early tumor detection in the breast is achieved using image reconstruction which allows a mapping of the position dependent contrast diffusive propagation constants, which are related to the optical absorption coefficient and scattering coefficient in the tissue, at near infrared wavelengths. Spatial resolutions in the range of 5 mm for adult brain sizes and breast sizes can be achieved. The image reconstruction utilizes WKB approximation on most probable diffusion paths which has as lowest order approximation the straight line-of-sight between the plurality of sources and the plurality of detectors. The WKB approximation yields a set of linear equations in which the contrast optical absorption coefficients are the unknowns and for which signals can be generated to produce a pixel map of the contrast optical resolution of the scanned tissue. 58 figs.

Methodology and apparatus for diffuse photon mimaging

DOEpatents

Feng, Shechao C.; Zeng, Fanan; Zhao, Hui-Lin

1997-12-09

Non-invasive near infrared optical medical imaging devices for both hematoma detection in the brain and early tumor detection in the breast is achieved using image reconstruction which allows a mapping of the position dependent contrast diffusive propagation constants, which are related to the optical absorption coefficient and scattering coefficient in the tissue, at near infrared wavelengths. Spatial resolutions in the range of 5 mm for adult brain sizes and breast sizes can be achieved. The image reconstruction utilizes WKB approximation on most probable diffusion paths which has as lowest order approximation the straight line-of-sight between the plurality of sources and the plurality of detectors. The WKB approximation yields a set of linear equations in which the contrast optical absorption coefficients are the unknowns and for which signals can be generated to produce a pixel map of the contrast optical resolution of the scanned tissue.

Probabilistic atlas-based segmentation of combined T1-weighted and DUTE MRI for calculation of head attenuation maps in integrated PET/MRI scanners.

PubMed

Poynton, Clare B; Chen, Kevin T; Chonde, Daniel B; Izquierdo-Garcia, David; Gollub, Randy L; Gerstner, Elizabeth R; Batchelor, Tracy T; Catana, Ciprian

2014-01-01

We present a new MRI-based attenuation correction (AC) approach for integrated PET/MRI systems that combines both segmentation- and atlas-based methods by incorporating dual-echo ultra-short echo-time (DUTE) and T1-weighted (T1w) MRI data and a probabilistic atlas. Segmented atlases were constructed from CT training data using a leave-one-out framework and combined with T1w, DUTE, and CT data to train a classifier that computes the probability of air/soft tissue/bone at each voxel. This classifier was applied to segment the MRI of the subject of interest and attenuation maps (μ-maps) were generated by assigning specific linear attenuation coefficients (LACs) to each tissue class. The μ-maps generated with this "Atlas-T1w-DUTE" approach were compared to those obtained from DUTE data using a previously proposed method. For validation of the segmentation results, segmented CT μ-maps were considered to the "silver standard"; the segmentation accuracy was assessed qualitatively and quantitatively through calculation of the Dice similarity coefficient (DSC). Relative change (RC) maps between the CT and MRI-based attenuation corrected PET volumes were also calculated for a global voxel-wise assessment of the reconstruction results. The μ-maps obtained using the Atlas-T1w-DUTE classifier agreed well with those derived from CT; the mean DSCs for the Atlas-T1w-DUTE-based μ-maps across all subjects were higher than those for DUTE-based μ-maps; the atlas-based μ-maps also showed a lower percentage of misclassified voxels across all subjects. RC maps from the atlas-based technique also demonstrated improvement in the PET data compared to the DUTE method, both globally as well as regionally.

Quantification of mammographic masking risk with volumetric breast density maps: how to select women for supplemental screening

NASA Astrophysics Data System (ADS)

Holland, Katharina; van Gils, Carla H.; Wanders, Johanna OP; Mann, Ritse M.; Karssemeijer, Nico

2016-03-01

The sensitivity of mammograms is low for women with dense breasts, since cancers may be masked by dense tissue. In this study, we investigated methods to identify women with density patterns associated with a high masking risk. Risk measures are derived from volumetric breast density maps. We used the last negative screening mammograms of 93 women who subsequently presented with an interval cancer (IC), and, as controls, 930 randomly selected normal screening exams from women without cancer. Volumetric breast density maps were computed from the mammograms, which provide the dense tissue thickness at each location. These were used to compute absolute and percentage glandular tissue volume. We modeled the masking risk for each pixel location using the absolute and percentage dense tissue thickness and we investigated the effect of taking the cancer location probability distribution (CLPD) into account. For each method, we selected cases with the highest masking measure (by thresholding) and computed the fraction of ICs as a function of the fraction of controls selected. The latter can be interpreted as the negative supplemental screening rate (NSSR). Between the models, when incorporating CLPD, no significant differences were found. In general, the methods performed better when CLPD was included. At higher NSSRs some of the investigated masking measures had a significantly higher performance than volumetric breast density. These measures may therefore serve as an alternative to identify women with a high risk for a masked cancer.

Preprocessed Consortium for Neuropsychiatric Phenomics dataset.

PubMed

Gorgolewski, Krzysztof J; Durnez, Joke; Poldrack, Russell A

2017-01-01

Here we present preprocessed MRI data of 265 participants from the Consortium for Neuropsychiatric Phenomics (CNP) dataset. The preprocessed dataset includes minimally preprocessed data in the native, MNI and surface spaces accompanied with potential confound regressors, tissue probability masks, brain masks and transformations. In addition the preprocessed dataset includes unthresholded group level and single subject statistical maps from all tasks included in the original dataset. We hope that availability of this dataset will greatly accelerate research.

On Probability Domains IV

NASA Astrophysics Data System (ADS)

Frič, Roman; Papčo, Martin

2017-12-01

Stressing a categorical approach, we continue our study of fuzzified domains of probability, in which classical random events are replaced by measurable fuzzy random events. In operational probability theory (S. Bugajski) classical random variables are replaced by statistical maps (generalized distribution maps induced by random variables) and in fuzzy probability theory (S. Gudder) the central role is played by observables (maps between probability domains). We show that to each of the two generalized probability theories there corresponds a suitable category and the two resulting categories are dually equivalent. Statistical maps and observables become morphisms. A statistical map can send a degenerated (pure) state to a non-degenerated one —a quantum phenomenon and, dually, an observable can map a crisp random event to a genuine fuzzy random event —a fuzzy phenomenon. The dual equivalence means that the operational probability theory and the fuzzy probability theory coincide and the resulting generalized probability theory has two dual aspects: quantum and fuzzy. We close with some notes on products and coproducts in the dual categories.

Speech processing using conditional observable maximum likelihood continuity mapping

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

Hogden, John; Nix, David

A computer implemented method enables the recognition of speech and speech characteristics. Parameters are initialized of first probability density functions that map between the symbols in the vocabulary of one or more sequences of speech codes that represent speech sounds and a continuity map. Parameters are also initialized of second probability density functions that map between the elements in the vocabulary of one or more desired sequences of speech transcription symbols and the continuity map. The parameters of the probability density functions are then trained to maximize the probabilities of the desired sequences of speech-transcription symbols. A new sequence ofmore » speech codes is then input to the continuity map having the trained first and second probability function parameters. A smooth path is identified on the continuity map that has the maximum probability for the new sequence of speech codes. The probability of each speech transcription symbol for each input speech code can then be output.« less

Can Probability Maps of Swept-Source Optical Coherence Tomography Predict Visual Field Changes in Preperimetric Glaucoma?

PubMed

Lee, Won June; Kim, Young Kook; Jeoung, Jin Wook; Park, Ki Ho

2017-12-01

To determine the usefulness of swept-source optical coherence tomography (SS-OCT) probability maps in detecting locations with significant reduction in visual field (VF) sensitivity or predicting future VF changes, in patients with classically defined preperimetric glaucoma (PPG). Of 43 PPG patients, 43 eyes were followed-up on every 6 months for at least 2 years were analyzed in this longitudinal study. The patients underwent wide-field SS-OCT scanning and standard automated perimetry (SAP) at the time of enrollment. With this wide-scan protocol, probability maps originating from the corresponding thickness map and overlapped with SAP VF test points could be generated. We evaluated the vulnerable VF points with SS-OCT probability maps as well as the prevalence of locations with significant VF reduction or subsequent VF changes observed in the corresponding damaged areas of the probability maps. The vulnerable VF points were shown in superior and inferior arcuate patterns near the central fixation. In 19 of 43 PPG eyes (44.2%), significant reduction in baseline VF was detected within the areas of structural change on the SS-OCT probability maps. In 16 of 43 PPG eyes (37.2%), subsequent VF changes within the areas of SS-OCT probability map change were observed over the course of the follow-up. Structural changes on SS-OCT probability maps could detect or predict VF changes using SAP, in a considerable number of PPG eyes. Careful comparison of probability maps with SAP results could be useful in diagnosing and monitoring PPG patients in the clinical setting.

Fully automatized renal parenchyma volumetry using a support vector machine based recognition system for subject-specific probability map generation in native MR volume data

NASA Astrophysics Data System (ADS)

Gloger, Oliver; Tönnies, Klaus; Mensel, Birger; Völzke, Henry

2015-11-01

In epidemiological studies as well as in clinical practice the amount of produced medical image data strongly increased in the last decade. In this context organ segmentation in MR volume data gained increasing attention for medical applications. Especially in large-scale population-based studies organ volumetry is highly relevant requiring exact organ segmentation. Since manual segmentation is time-consuming and prone to reader variability, large-scale studies need automatized methods to perform organ segmentation. Fully automatic organ segmentation in native MR image data has proven to be a very challenging task. Imaging artifacts as well as inter- and intrasubject MR-intensity differences complicate the application of supervised learning strategies. Thus, we propose a modularized framework of a two-stepped probabilistic approach that generates subject-specific probability maps for renal parenchyma tissue, which are refined subsequently by using several, extended segmentation strategies. We present a three class-based support vector machine recognition system that incorporates Fourier descriptors as shape features to recognize and segment characteristic parenchyma parts. Probabilistic methods use the segmented characteristic parenchyma parts to generate high quality subject-specific parenchyma probability maps. Several refinement strategies including a final shape-based 3D level set segmentation technique are used in subsequent processing modules to segment renal parenchyma. Furthermore, our framework recognizes and excludes renal cysts from parenchymal volume, which is important to analyze renal functions. Volume errors and Dice coefficients show that our presented framework outperforms existing approaches.

Fully automatized renal parenchyma volumetry using a support vector machine based recognition system for subject-specific probability map generation in native MR volume data.

PubMed

Gloger, Oliver; Tönnies, Klaus; Mensel, Birger; Völzke, Henry

2015-11-21

In epidemiological studies as well as in clinical practice the amount of produced medical image data strongly increased in the last decade. In this context organ segmentation in MR volume data gained increasing attention for medical applications. Especially in large-scale population-based studies organ volumetry is highly relevant requiring exact organ segmentation. Since manual segmentation is time-consuming and prone to reader variability, large-scale studies need automatized methods to perform organ segmentation. Fully automatic organ segmentation in native MR image data has proven to be a very challenging task. Imaging artifacts as well as inter- and intrasubject MR-intensity differences complicate the application of supervised learning strategies. Thus, we propose a modularized framework of a two-stepped probabilistic approach that generates subject-specific probability maps for renal parenchyma tissue, which are refined subsequently by using several, extended segmentation strategies. We present a three class-based support vector machine recognition system that incorporates Fourier descriptors as shape features to recognize and segment characteristic parenchyma parts. Probabilistic methods use the segmented characteristic parenchyma parts to generate high quality subject-specific parenchyma probability maps. Several refinement strategies including a final shape-based 3D level set segmentation technique are used in subsequent processing modules to segment renal parenchyma. Furthermore, our framework recognizes and excludes renal cysts from parenchymal volume, which is important to analyze renal functions. Volume errors and Dice coefficients show that our presented framework outperforms existing approaches.

Probabilistic atlas-based segmentation of combined T1-weighted and DUTE MRI for calculation of head attenuation maps in integrated PET/MRI scanners

PubMed Central

Poynton, Clare B; Chen, Kevin T; Chonde, Daniel B; Izquierdo-Garcia, David; Gollub, Randy L; Gerstner, Elizabeth R; Batchelor, Tracy T; Catana, Ciprian

2014-01-01

We present a new MRI-based attenuation correction (AC) approach for integrated PET/MRI systems that combines both segmentation- and atlas-based methods by incorporating dual-echo ultra-short echo-time (DUTE) and T1-weighted (T1w) MRI data and a probabilistic atlas. Segmented atlases were constructed from CT training data using a leave-one-out framework and combined with T1w, DUTE, and CT data to train a classifier that computes the probability of air/soft tissue/bone at each voxel. This classifier was applied to segment the MRI of the subject of interest and attenuation maps (μ-maps) were generated by assigning specific linear attenuation coefficients (LACs) to each tissue class. The μ-maps generated with this “Atlas-T1w-DUTE” approach were compared to those obtained from DUTE data using a previously proposed method. For validation of the segmentation results, segmented CT μ-maps were considered to the “silver standard”; the segmentation accuracy was assessed qualitatively and quantitatively through calculation of the Dice similarity coefficient (DSC). Relative change (RC) maps between the CT and MRI-based attenuation corrected PET volumes were also calculated for a global voxel-wise assessment of the reconstruction results. The μ-maps obtained using the Atlas-T1w-DUTE classifier agreed well with those derived from CT; the mean DSCs for the Atlas-T1w-DUTE-based μ-maps across all subjects were higher than those for DUTE-based μ-maps; the atlas-based μ-maps also showed a lower percentage of misclassified voxels across all subjects. RC maps from the atlas-based technique also demonstrated improvement in the PET data compared to the DUTE method, both globally as well as regionally. PMID:24753982

The Statistical Value of Raw Fluorescence Signal in Luminex xMAP Based Multiplex Immunoassays

PubMed Central

Breen, Edmond J.; Tan, Woei; Khan, Alamgir

2016-01-01

Tissue samples (plasma, saliva, serum or urine) from 169 patients classified as either normal or having one of seven possible diseases are analysed across three 96-well plates for the presences of 37 analytes using cytokine inflammation multiplexed immunoassay panels. Censoring for concentration data caused problems for analysis of the low abundant analytes. Using fluorescence analysis over concentration based analysis allowed analysis of these low abundant analytes. Mixed-effects analysis on the resulting fluorescence and concentration responses reveals a combination of censoring and mapping the fluorescence responses to concentration values, through a 5PL curve, changed observed analyte concentrations. Simulation verifies this, by showing a dependence on the mean florescence response and its distribution on the observed analyte concentration levels. Differences from normality, in the fluorescence responses, can lead to differences in concentration estimates and unreliable probabilities for treatment effects. It is seen that when fluorescence responses are normally distributed, probabilities of treatment effects for fluorescence based t-tests has greater statistical power than the same probabilities from concentration based t-tests. We add evidence that the fluorescence response, unlike concentration values, doesn’t require censoring and we show with respect to differential analysis on the fluorescence responses that background correction is not required. PMID:27243383

Modeling the Insertion Mechanics of Flexible Neural Probes Coated with Sacrificial Polymers for Optimizing Probe Design

PubMed Central

Singh, Sagar; Lo, Meng-Chen; Damodaran, Vinod B.; Kaplan, Hilton M.; Kohn, Joachim; Zahn, Jeffrey D.; Shreiber, David I.

2016-01-01

Single-unit recording neural probes have significant advantages towards improving signal-to-noise ratio and specificity for signal acquisition in brain-to-computer interface devices. Long-term effectiveness is unfortunately limited by the chronic injury response, which has been linked to the mechanical mismatch between rigid probes and compliant brain tissue. Small, flexible microelectrodes may overcome this limitation, but insertion of these probes without buckling requires supporting elements such as a stiff coating with a biodegradable polymer. For these coated probes, there is a design trade-off between the potential for successful insertion into brain tissue and the degree of trauma generated by the insertion. The objective of this study was to develop and validate a finite element model (FEM) to simulate insertion of coated neural probes of varying dimensions and material properties into brain tissue. Simulations were performed to predict the buckling and insertion forces during insertion of coated probes into a tissue phantom with material properties of brain. The simulations were validated with parallel experimental studies where probes were inserted into agarose tissue phantom, ex vivo chick embryonic brain tissue, and ex vivo rat brain tissue. Experiments were performed with uncoated copper wire and both uncoated and coated SU-8 photoresist and Parylene C probes. Model predictions were found to strongly agree with experimental results (<10% error). The ratio of the predicted buckling force-to-predicted insertion force, where a value greater than one would ideally be expected to result in successful insertion, was plotted against the actual success rate from experiments. A sigmoidal relationship was observed, with a ratio of 1.35 corresponding to equal probability of insertion and failure, and a ratio of 3.5 corresponding to a 100% success rate. This ratio was dubbed the “safety factor”, as it indicated the degree to which the coating should be over-designed to ensure successful insertion. Probability color maps were generated to visually compare the influence of design parameters. Statistical metrics derived from the color maps and multi-variable regression analysis confirmed that coating thickness and probe length were the most important features in influencing insertion potential. The model also revealed the effects of manufacturing flaws on insertion potential. PMID:26959021

Compositional cokriging for mapping the probability risk of groundwater contamination by nitrates.

PubMed

Pardo-Igúzquiza, Eulogio; Chica-Olmo, Mario; Luque-Espinar, Juan A; Rodríguez-Galiano, Víctor

2015-11-01

Contamination by nitrates is an important cause of groundwater pollution and represents a potential risk to human health. Management decisions must be made using probability maps that assess the nitrate concentration potential of exceeding regulatory thresholds. However these maps are obtained with only a small number of sparse monitoring locations where the nitrate concentrations have been measured. It is therefore of great interest to have an efficient methodology for obtaining those probability maps. In this paper, we make use of the fact that the discrete probability density function is a compositional variable. The spatial discrete probability density function is estimated by compositional cokriging. There are several advantages in using this approach: (i) problems of classical indicator cokriging, like estimates outside the interval (0,1) and order relations, are avoided; (ii) secondary variables (e.g. aquifer parameters) can be included in the estimation of the probability maps; (iii) uncertainty maps of the probability maps can be obtained; (iv) finally there are modelling advantages because the variograms and cross-variograms of real variables that do not have the restrictions of indicator variograms and indicator cross-variograms. The methodology was applied to the Vega de Granada aquifer in Southern Spain and the advantages of the compositional cokriging approach were demonstrated. Copyright © 2015 Elsevier B.V. All rights reserved.

Automatized spleen segmentation in non-contrast-enhanced MR volume data using subject-specific shape priors

NASA Astrophysics Data System (ADS)

Gloger, Oliver; Tönnies, Klaus; Bülow, Robin; Völzke, Henry

2017-07-01

To develop the first fully automated 3D spleen segmentation framework derived from T1-weighted magnetic resonance (MR) imaging data and to verify its performance for spleen delineation and volumetry. This approach considers the issue of low contrast between spleen and adjacent tissue in non-contrast-enhanced MR images. Native T1-weighted MR volume data was performed on a 1.5 T MR system in an epidemiological study. We analyzed random subsamples of MR examinations without pathologies to develop and verify the spleen segmentation framework. The framework is modularized to include different kinds of prior knowledge into the segmentation pipeline. Classification by support vector machines differentiates between five different shape types in computed foreground probability maps and recognizes characteristic spleen regions in axial slices of MR volume data. A spleen-shape space generated by training produces subject-specific prior shape knowledge that is then incorporated into a final 3D level set segmentation method. Individually adapted shape-driven forces as well as image-driven forces resulting from refined foreground probability maps steer the level set successfully to the segment the spleen. The framework achieves promising segmentation results with mean Dice coefficients of nearly 0.91 and low volumetric mean errors of 6.3%. The presented spleen segmentation approach can delineate spleen tissue in native MR volume data. Several kinds of prior shape knowledge including subject-specific 3D prior shape knowledge can be used to guide segmentation processes achieving promising results.

Infrared mapping resolves soft tissue preservation in 50 million year-old reptile skin.

PubMed

Edwards, N P; Barden, H E; van Dongen, B E; Manning, P L; Larson, P L; Bergmann, U; Sellers, W I; Wogelius, R A

2011-11-07

Non-destructive Fourier Transform InfraRed (FTIR) mapping of Eocene aged fossil reptile skin shows that biological control on the distribution of endogenous organic components within fossilized soft tissue can be resolved. Mapped organic functional units within this approximately 50 Myr old specimen from the Green River Formation (USA) include amide and sulphur compounds. These compounds are most probably derived from the original beta keratin present in the skin because fossil leaf- and other non-skin-derived organic matter from the same geological formation do not show intense amide or thiol absorption bands. Maps and spectra from the fossil are directly comparable to extant reptile skin. Furthermore, infrared results are corroborated by several additional quantitative methods including Synchrotron Rapid Scanning X-Ray Fluorescence (SRS-XRF) and Pyrolysis-Gas Chromatography/Mass Spectrometry (Py-GC/MS). All results combine to clearly show that the organic compound inventory of the fossil skin is different from the embedding sedimentary matrix and fossil plant material. A new taphonomic model involving ternary complexation between keratin-derived organic molecules, divalent trace metals and silicate surfaces is presented to explain the survival of the observed compounds. X-ray diffraction shows that suitable minerals for complex formation are present. Previously, this study would only have been possible with major destructive sampling. Non-destructive FTIR imaging methods are thus shown to be a valuable tool for understanding the taphonomy of high-fidelity preservation, and furthermore, may provide insight into the biochemistry of extinct organisms.

Infrared mapping resolves soft tissue preservation in 50 million year-old reptile skin

PubMed Central

Edwards, N. P.; Barden, H. E.; van Dongen, B. E.; Manning, P. L.; Larson, P. L.; Bergmann, U.; Sellers, W. I.; Wogelius, R. A.

2011-01-01

Non-destructive Fourier Transform InfraRed (FTIR) mapping of Eocene aged fossil reptile skin shows that biological control on the distribution of endogenous organic components within fossilized soft tissue can be resolved. Mapped organic functional units within this approximately 50 Myr old specimen from the Green River Formation (USA) include amide and sulphur compounds. These compounds are most probably derived from the original beta keratin present in the skin because fossil leaf- and other non-skin-derived organic matter from the same geological formation do not show intense amide or thiol absorption bands. Maps and spectra from the fossil are directly comparable to extant reptile skin. Furthermore, infrared results are corroborated by several additional quantitative methods including Synchrotron Rapid Scanning X-Ray Fluorescence (SRS-XRF) and Pyrolysis-Gas Chromatography/Mass Spectrometry (Py-GC/MS). All results combine to clearly show that the organic compound inventory of the fossil skin is different from the embedding sedimentary matrix and fossil plant material. A new taphonomic model involving ternary complexation between keratin-derived organic molecules, divalent trace metals and silicate surfaces is presented to explain the survival of the observed compounds. X-ray diffraction shows that suitable minerals for complex formation are present. Previously, this study would only have been possible with major destructive sampling. Non-destructive FTIR imaging methods are thus shown to be a valuable tool for understanding the taphonomy of high-fidelity preservation, and furthermore, may provide insight into the biochemistry of extinct organisms. PMID:21429928

Studying the effects of fuel treatment based on burn probability on a boreal forest landscape.

PubMed

Liu, Zhihua; Yang, Jian; He, Hong S

2013-01-30

Fuel treatment is assumed to be a primary tactic to mitigate intense and damaging wildfires. However, how to place treatment units across a landscape and assess its effectiveness is difficult for landscape-scale fuel management planning. In this study, we used a spatially explicit simulation model (LANDIS) to conduct wildfire risk assessments and optimize the placement of fuel treatments at the landscape scale. We first calculated a baseline burn probability map from empirical data (fuel, topography, weather, and fire ignition and size data) to assess fire risk. We then prioritized landscape-scale fuel treatment based on maps of burn probability and fuel loads (calculated from the interactions among tree composition, stand age, and disturbance history), and compared their effects on reducing fire risk. The burn probability map described the likelihood of burning on a given location; the fuel load map described the probability that a high fuel load will accumulate on a given location. Fuel treatment based on the burn probability map specified that stands with high burn probability be treated first, while fuel treatment based on the fuel load map specified that stands with high fuel loads be treated first. Our results indicated that fuel treatment based on burn probability greatly reduced the burned area and number of fires of different intensities. Fuel treatment based on burn probability also produced more dispersed and smaller high-risk fire patches and therefore can improve efficiency of subsequent fire suppression. The strength of our approach is that more model components (e.g., succession, fuel, and harvest) can be linked into LANDIS to map the spatially explicit wildfire risk and its dynamics to fuel management, vegetation dynamics, and harvesting. Copyright © 2012 Elsevier Ltd. All rights reserved.

Time-dependent landslide probability mapping

USGS Publications Warehouse

Campbell, Russell H.; Bernknopf, Richard L.; ,

1993-01-01

Case studies where time of failure is known for rainfall-triggered debris flows can be used to estimate the parameters of a hazard model in which the probability of failure is a function of time. As an example, a time-dependent function for the conditional probability of a soil slip is estimated from independent variables representing hillside morphology, approximations of material properties, and the duration and rate of rainfall. If probabilities are calculated in a GIS (geomorphic information system ) environment, the spatial distribution of the result for any given hour can be displayed on a map. Although the probability levels in this example are uncalibrated, the method offers a potential for evaluating different physical models and different earth-science variables by comparing the map distribution of predicted probabilities with inventory maps for different areas and different storms. If linked with spatial and temporal socio-economic variables, this method could be used for short-term risk assessment.

Oregon Cascades Play Fairway Analysis: Faults and Heat Flow maps

DOE Data Explorer

Adam Brandt

2015-11-15

This submission includes a fault map of the Oregon Cascades and backarc, a probability map of heat flow, and a fault density probability layer. More extensive metadata can be found within each zip file.

The Influence of Phonotactic Probability on Nonword Repetition and Fast Mapping in 3-Year-Olds With a History of Expressive Language Delay.

PubMed

MacRoy-Higgins, Michelle; Dalton, Kevin Patrick

2015-12-01

The purpose of this study was to examine the influence of phonotactic probability on sublexical (phonological) and lexical representations in 3-year-olds who had a history of being late talkers in comparison with their peers with typical language development. Ten 3-year-olds who were late talkers and 10 age-matched typically developing controls completed nonword repetition and fast mapping tasks; stimuli for both experimental procedures differed in phonotactic probability. Both participant groups repeated nonwords containing high phonotactic probability sequences more accurately than nonwords containing low phonotactic probability sequences. Participants with typical language showed an early advantage for fast mapping high phonotactic probability words; children who were late talkers required more exposures to the novel words to show the same advantage for fast mapping high phonotactic probability words. Children who were late talkers showed similar sensitivities to phonotactic probability in nonword repetition and word learning when compared with their peers with no history of language delay. However, word learning in children who were late talkers appeared to be slower when compared with their peers.

Revision of Time-Independent Probabilistic Seismic Hazard Maps for Alaska

USGS Publications Warehouse

Wesson, Robert L.; Boyd, Oliver S.; Mueller, Charles S.; Bufe, Charles G.; Frankel, Arthur D.; Petersen, Mark D.

2007-01-01

We present here time-independent probabilistic seismic hazard maps of Alaska and the Aleutians for peak ground acceleration (PGA) and 0.1, 0.2, 0.3, 0.5, 1.0 and 2.0 second spectral acceleration at probability levels of 2 percent in 50 years (annual probability of 0.000404), 5 percent in 50 years (annual probability of 0.001026) and 10 percent in 50 years (annual probability of 0.0021). These maps represent a revision of existing maps based on newly obtained data and assumptions reflecting best current judgments about methodology and approach. These maps have been prepared following the procedures and assumptions made in the preparation of the 2002 National Seismic Hazard Maps for the lower 48 States. A significant improvement relative to the 2002 methodology is the ability to include variable slip rate along a fault where appropriate. These maps incorporate new data, the responses to comments received at workshops held in Fairbanks and Anchorage, Alaska, in May, 2005, and comments received after draft maps were posted on the National Seismic Hazard Mapping Web Site. These maps will be proposed for adoption in future revisions to the International Building Code. In this documentation we describe the maps and in particular explain and justify changes that have been made relative to the 1999 maps. We are also preparing a series of experimental maps of time-dependent hazard that will be described in future documents.

MAP3K8 (TPL2/COT) affects obesity-induced adipose tissue inflammation without systemic effects in humans and in mice.

PubMed

Ballak, Dov B; van Essen, Peter; van Diepen, Janna A; Jansen, Henry; Hijmans, Anneke; Matsuguchi, Tetsuya; Sparrer, Helmut; Tack, Cees J; Netea, Mihai G; Joosten, Leo A B; Stienstra, Rinke

2014-01-01

Chronic low-grade inflammation in adipose tissue often accompanies obesity, leading to insulin resistance and increasing the risk for metabolic diseases. MAP3K8 (TPL2/COT) is an important signal transductor and activator of pro-inflammatory pathways that has been linked to obesity-induced adipose tissue inflammation. We used human adipose tissue biopsies to study the relationship of MAP3K8 expression with markers of obesity and expression of pro-inflammatory cytokines (IL-1β, IL-6 and IL-8). Moreover, we evaluated obesity-induced adipose tissue inflammation and insulin resistance in mice lacking MAP3K8 and WT mice on a high-fat diet (HFD) for 16 weeks. Individuals with a BMI >30 displayed a higher mRNA expression of MAP3K8 in adipose tissue compared to individuals with a normal BMI. Additionally, high mRNA expression levels of IL-1β, IL-6 and IL-8, but not TNF -α, in human adipose tissue were associated with higher expression of MAP3K8. Moreover, high plasma SAA and CRP did not associate with increased MAP3K8 expression in adipose tissue. Similarly, no association was found for MAP3K8 expression with plasma insulin or glucose levels. Mice lacking MAP3K8 had similar bodyweight gain as WT mice, yet displayed lower mRNA expression levels of IL-1β, IL-6 and CXCL1 in adipose tissue in response to the HFD as compared to WT animals. However, MAP3K8 deficient mice were not protected against HFD-induced adipose tissue macrophage infiltration or the development of insulin resistance. Together, the data in both human and mouse show that MAP3K8 is involved in local adipose tissue inflammation, specifically for IL-1β and its responsive cytokines IL-6 and IL-8, but does not seem to have systemic effects on insulin resistance.

LncRNA and mRNA expression profiles of glioblastoma multiforme (GBM) reveal the potential roles of lncRNAs in GBM pathogenesis.

PubMed

Li, Qi; Jia, Hongmei; Li, Haowen; Dong, Chengya; Wang, Yajie; Zou, Zhongmei

2016-11-01

Glioblastoma multiforme (GBM) is the most common brain malignancy. Long non-coding RNAs (lncRNAs) are aberrantly expressed in many cancers and are involved in their cell proliferation, apoptosis, angiogenesis, and invasion. The functional roles of lncRNAs in GBM are less known. We analyzed a cohort of exon microarray datasets from The Cancer Genome Atlas. The differently expressed lncRNAs and mRNA were subjected to construct lncRNA-mRNA co-expression network. Probable functions for lncRNAs were predicted according to lncRNA-mRNA network and genomic adjacency by GO and pathway analysis. The expression of lncRNAs and mRNAs in GBM tissues versus normal brain tissues was examined by quantitative reverse transcription polymerase chain reaction. The 398 lncRNAs and 1995 mRNAs were identified as distinctively expressed in GBM. Probable functional roles for 98 lncRNAs were involved in 30 pathways and 32 gene functions related to tumorigenesis, development, and metastasis. The identified sets of key lncRNAs specific to GBM were subsequently verified by experiment in GBM tissues. Our reports predict the biological functions of a multitude of lncRNAs in GBM that could be potential diagnostic and prognostic biomarkers as well as therapeutic targets. Moreover, our research provides a road map for the identification and analysis of lncRNAs in tumors.

Probabilistic brain tissue segmentation in neonatal magnetic resonance imaging.

PubMed

Anbeek, Petronella; Vincken, Koen L; Groenendaal, Floris; Koeman, Annemieke; van Osch, Matthias J P; van der Grond, Jeroen

2008-02-01

A fully automated method has been developed for segmentation of four different structures in the neonatal brain: white matter (WM), central gray matter (CEGM), cortical gray matter (COGM), and cerebrospinal fluid (CSF). The segmentation algorithm is based on information from T2-weighted (T2-w) and inversion recovery (IR) scans. The method uses a K nearest neighbor (KNN) classification technique with features derived from spatial information and voxel intensities. Probabilistic segmentations of each tissue type were generated. By applying thresholds on these probability maps, binary segmentations were obtained. These final segmentations were evaluated by comparison with a gold standard. The sensitivity, specificity, and Dice similarity index (SI) were calculated for quantitative validation of the results. High sensitivity and specificity with respect to the gold standard were reached: sensitivity >0.82 and specificity >0.9 for all tissue types. Tissue volumes were calculated from the binary and probabilistic segmentations. The probabilistic segmentation volumes of all tissue types accurately estimated the gold standard volumes. The KNN approach offers valuable ways for neonatal brain segmentation. The probabilistic outcomes provide a useful tool for accurate volume measurements. The described method is based on routine diagnostic magnetic resonance imaging (MRI) and is suitable for large population studies.

A Hybrid Hierarchical Approach for Brain Tissue Segmentation by Combining Brain Atlas and Least Square Support Vector Machine

PubMed Central

Kasiri, Keyvan; Kazemi, Kamran; Dehghani, Mohammad Javad; Helfroush, Mohammad Sadegh

2013-01-01

In this paper, we present a new semi-automatic brain tissue segmentation method based on a hybrid hierarchical approach that combines a brain atlas as a priori information and a least-square support vector machine (LS-SVM). The method consists of three steps. In the first two steps, the skull is removed and the cerebrospinal fluid (CSF) is extracted. These two steps are performed using the toolbox FMRIB's automated segmentation tool integrated in the FSL software (FSL-FAST) developed in Oxford Centre for functional MRI of the brain (FMRIB). Then, in the third step, the LS-SVM is used to segment grey matter (GM) and white matter (WM). The training samples for LS-SVM are selected from the registered brain atlas. The voxel intensities and spatial positions are selected as the two feature groups for training and test. SVM as a powerful discriminator is able to handle nonlinear classification problems; however, it cannot provide posterior probability. Thus, we use a sigmoid function to map the SVM output into probabilities. The proposed method is used to segment CSF, GM and WM from the simulated magnetic resonance imaging (MRI) using Brainweb MRI simulator and real data provided by Internet Brain Segmentation Repository. The semi-automatically segmented brain tissues were evaluated by comparing to the corresponding ground truth. The Dice and Jaccard similarity coefficients, sensitivity and specificity were calculated for the quantitative validation of the results. The quantitative results show that the proposed method segments brain tissues accurately with respect to corresponding ground truth. PMID:24696800

Substitute CT generation from a single ultra short time echo MRI sequence: preliminary study

NASA Astrophysics Data System (ADS)

Ghose, Soumya; Dowling, Jason A.; Rai, Robba; Liney, Gary P.

2017-04-01

In MR guided radiation therapy planning both MR and CT images for a patient are acquired and co-registered to obtain a tissue specific HU map. Generation of the HU map directly from the MRI would eliminate the CT acquisition and may improve radiation therapy planning. In this preliminary study of substitute CT (sCT) generation, two porcine leg phantoms were scanned using a 3D ultrashort echo time (PETRA) sequence and co-registered to corresponding CT images to build tissue specific regression models. The model was created from one co-registered CT-PETRA pair to generate the sCT for the other PETRA image. An expectation maximization based clustering was performed on the co-registered PETRA image to identify the soft tissues, dense bone and air class membership probabilities. A tissue specific non linear regression model was built from one registered CT-PETRA pair dataset to predict the sCT of the second PETRA image in a two-fold cross validation schema. A complete substitute CT is generated in 3 min. The mean absolute HU error for air was 0.3 HU, bone was 95 HU, fat was 30 HU and for muscle it was 10 HU. The mean surface reconstruction error for the bone was 1.3 mm. The PETRA sequence enabled a low mean absolute surface distance for the bone and a low HU error for other classes. The sCT generated from a single PETRA sequence shows promise for the generation of fast sCT for MRI based radiation therapy planning.

Rational Variety Mapping for Contrast-Enhanced Nonlinear Unsupervised Segmentation of Multispectral Images of Unstained Specimen

PubMed Central

Kopriva, Ivica; Hadžija, Mirko; Popović Hadžija, Marijana; Korolija, Marina; Cichocki, Andrzej

2011-01-01

A methodology is proposed for nonlinear contrast-enhanced unsupervised segmentation of multispectral (color) microscopy images of principally unstained specimens. The methodology exploits spectral diversity and spatial sparseness to find anatomical differences between materials (cells, nuclei, and background) present in the image. It consists of rth-order rational variety mapping (RVM) followed by matrix/tensor factorization. Sparseness constraint implies duality between nonlinear unsupervised segmentation and multiclass pattern assignment problems. Classes not linearly separable in the original input space become separable with high probability in the higher-dimensional mapped space. Hence, RVM mapping has two advantages: it takes implicitly into account nonlinearities present in the image (ie, they are not required to be known) and it increases spectral diversity (ie, contrast) between materials, due to increased dimensionality of the mapped space. This is expected to improve performance of systems for automated classification and analysis of microscopic histopathological images. The methodology was validated using RVM of the second and third orders of the experimental multispectral microscopy images of unstained sciatic nerve fibers (nervus ischiadicus) and of unstained white pulp in the spleen tissue, compared with a manually defined ground truth labeled by two trained pathophysiologists. The methodology can also be useful for additional contrast enhancement of images of stained specimens. PMID:21708116

Assessing future vent opening locations at the Somma-Vesuvio volcanic complex: 2. Probability maps of the caldera for a future Plinian/sub-Plinian event with uncertainty quantification

NASA Astrophysics Data System (ADS)

Tadini, A.; Bevilacqua, A.; Neri, A.; Cioni, R.; Aspinall, W. P.; Bisson, M.; Isaia, R.; Mazzarini, F.; Valentine, G. A.; Vitale, S.; Baxter, P. J.; Bertagnini, A.; Cerminara, M.; de Michieli Vitturi, M.; Di Roberto, A.; Engwell, S.; Esposti Ongaro, T.; Flandoli, F.; Pistolesi, M.

2017-06-01

In this study, we combine reconstructions of volcanological data sets and inputs from a structured expert judgment to produce a first long-term probability map for vent opening location for the next Plinian or sub-Plinian eruption of Somma-Vesuvio. In the past, the volcano has exhibited significant spatial variability in vent location; this can exert a significant control on where hazards materialize (particularly of pyroclastic density currents). The new vent opening probability mapping has been performed through (i) development of spatial probability density maps with Gaussian kernel functions for different data sets and (ii) weighted linear combination of these spatial density maps. The epistemic uncertainties affecting these data sets were quantified explicitly with expert judgments and implemented following a doubly stochastic approach. Various elicitation pooling metrics and subgroupings of experts and target questions were tested to evaluate the robustness of outcomes. Our findings indicate that (a) Somma-Vesuvio vent opening probabilities are distributed inside the whole caldera, with a peak corresponding to the area of the present crater, but with more than 50% probability that the next vent could open elsewhere within the caldera; (b) there is a mean probability of about 30% that the next vent will open west of the present edifice; (c) there is a mean probability of about 9.5% that the next medium-large eruption will enlarge the present Somma-Vesuvio caldera, and (d) there is a nonnegligible probability (mean value of 6-10%) that the next Plinian or sub-Plinian eruption will have its initial vent opening outside the present Somma-Vesuvio caldera.

United States Geological Survey fire science: fire danger monitoring and forecasting

USGS Publications Warehouse

Eidenshink, Jeff C.; Howard, Stephen M.

2012-01-01

Each day, the U.S. Geological Survey produces 7-day forecasts for all Federal lands of the distributions of number of ignitions, number of fires above a given size, and conditional probabilities of fires growing larger than a specified size. The large fire probability map is an estimate of the likelihood that ignitions will become large fires. The large fire forecast map is a probability estimate of the number of fires on federal lands exceeding 100 acres in the forthcoming week. The ignition forecast map is a probability estimate of the number of fires on Federal land greater than 1 acre in the forthcoming week. The extreme event forecast is the probability estimate of the number of fires on Federal land that may exceed 5,000 acres in the forthcoming week.

Tsunami probability in the Caribbean Region

USGS Publications Warehouse

Parsons, T.; Geist, E.L.

2008-01-01

We calculated tsunami runup probability (in excess of 0.5 m) at coastal sites throughout the Caribbean region. We applied a Poissonian probability model because of the variety of uncorrelated tsunami sources in the region. Coastlines were discretized into 20 km by 20 km cells, and the mean tsunami runup rate was determined for each cell. The remarkable ???500-year empirical record compiled by O'Loughlin and Lander (2003) was used to calculate an empirical tsunami probability map, the first of three constructed for this study. However, it is unclear whether the 500-year record is complete, so we conducted a seismic moment-balance exercise using a finite-element model of the Caribbean-North American plate boundaries and the earthquake catalog, and found that moment could be balanced if the seismic coupling coefficient is c = 0.32. Modeled moment release was therefore used to generate synthetic earthquake sequences to calculate 50 tsunami runup scenarios for 500-year periods. We made a second probability map from numerically-calculated runup rates in each cell. Differences between the first two probability maps based on empirical and numerical-modeled rates suggest that each captured different aspects of tsunami generation; the empirical model may be deficient in primary plate-boundary events, whereas numerical model rates lack backarc fault and landslide sources. We thus prepared a third probability map using Bayesian likelihood functions derived from the empirical and numerical rate models and their attendant uncertainty to weight a range of rates at each 20 km by 20 km coastal cell. Our best-estimate map gives a range of 30-year runup probability from 0 - 30% regionally. ?? irkhaueser 2008.

Probability of detecting atrazine/desethyl-atrazine and elevated concentrations of nitrate plus nitrate as nitrogen in ground water in the Idaho part of the western Snake River Plain

USGS Publications Warehouse

Donato, Mary M.

2000-01-01

As ground water continues to provide an ever-growing proportion of Idaho?s drinking water, concerns about the quality of that resource are increasing. Pesticides (most commonly, atrazine/desethyl-atrazine, hereafter referred to as atrazine) and nitrite plus nitrate as nitrogen (hereafter referred to as nitrate) have been detected in many aquifers in the State. To provide a sound hydrogeologic basis for atrazine and nitrate management in southern Idaho—the largest region of land and water use in the State—the U.S. Geological Survey produced maps showing the probability of detecting these contaminants in ground water in the upper Snake River Basin (published in a 1998 report) and the western Snake River Plain (published in this report). The atrazine probability map for the western Snake River Plain was constructed by overlaying ground-water quality data with hydrogeologic and anthropogenic data in a geographic information system (GIS). A data set was produced in which each well had corresponding information on land use, geology, precipitation, soil characteristics, regional depth to ground water, well depth, water level, and atrazine use. These data were analyzed by logistic regression using a statistical software package. Several preliminary multivariate models were developed and those that best predicted the detection of atrazine were selected. The multivariate models then were entered into a GIS and the probability maps were produced. Land use, precipitation, soil hydrologic group, and well depth were significantly correlated with atrazine detections in the western Snake River Plain. These variables also were important in the 1998 probability study of the upper Snake River Basin. The effectiveness of the probability models for atrazine might be improved if more detailed data were available for atrazine application. A preliminary atrazine probability map for the entire Snake River Plain in Idaho, based on a data set representing that region, also was produced. In areas where this map overlaps the 1998 map of the upper Snake River Basin, the two maps show broadly similar probabilities of detecting atrazine. Logistic regression also was used to develop a preliminary statistical model that predicts the probability of detecting elevated nitrate in the western Snake River Plain. A nitrate probability map was produced from this model. Results showed that elevated nitrate concentrations were correlated with land use, soil organic content, well depth, and water level. Detailed information on nitrate input, specifically fertilizer application, might have improved the effectiveness of this model.

Stereotactic probability and variability of speech arrest and anomia sites during stimulation mapping of the language dominant hemisphere.

PubMed

Chang, Edward F; Breshears, Jonathan D; Raygor, Kunal P; Lau, Darryl; Molinaro, Annette M; Berger, Mitchel S

2017-01-01

OBJECTIVE Functional mapping using direct cortical stimulation is the gold standard for the prevention of postoperative morbidity during resective surgery in dominant-hemisphere perisylvian regions. Its role is necessitated by the significant interindividual variability that has been observed for essential language sites. The aim in this study was to determine the statistical probability distribution of eliciting aphasic errors for any given stereotactically based cortical position in a patient cohort and to quantify the variability at each cortical site. METHODS Patients undergoing awake craniotomy for dominant-hemisphere primary brain tumor resection between 1999 and 2014 at the authors' institution were included in this study, which included counting and picture-naming tasks during dense speech mapping via cortical stimulation. Positive and negative stimulation sites were collected using an intraoperative frameless stereotactic neuronavigation system and were converted to Montreal Neurological Institute coordinates. Data were iteratively resampled to create mean and standard deviation probability maps for speech arrest and anomia. Patients were divided into groups with a "classic" or an "atypical" location of speech function, based on the resultant probability maps. Patient and clinical factors were then assessed for their association with an atypical location of speech sites by univariate and multivariate analysis. RESULTS Across 102 patients undergoing speech mapping, the overall probabilities of speech arrest and anomia were 0.51 and 0.33, respectively. Speech arrest was most likely to occur with stimulation of the posterior inferior frontal gyrus (maximum probability from individual bin = 0.025), and variance was highest in the dorsal premotor cortex and the posterior superior temporal gyrus. In contrast, stimulation within the posterior perisylvian cortex resulted in the maximum mean probability of anomia (maximum probability = 0.012), with large variance in the regions surrounding the posterior superior temporal gyrus, including the posterior middle temporal, angular, and supramarginal gyri. Patients with atypical speech localization were far more likely to have tumors in canonical Broca's or Wernicke's areas (OR 7.21, 95% CI 1.67-31.09, p < 0.01) or to have multilobar tumors (OR 12.58, 95% CI 2.22-71.42, p < 0.01), than were patients with classic speech localization. CONCLUSIONS This study provides statistical probability distribution maps for aphasic errors during cortical stimulation mapping in a patient cohort. Thus, the authors provide an expected probability of inducing speech arrest and anomia from specific 10-mm 2 cortical bins in an individual patient. In addition, they highlight key regions of interindividual mapping variability that should be considered preoperatively. They believe these results will aid surgeons in their preoperative planning of eloquent cortex resection.

Functional mapping of the primate auditory system.

PubMed

Poremba, Amy; Saunders, Richard C; Crane, Alison M; Cook, Michelle; Sokoloff, Louis; Mishkin, Mortimer

2003-01-24

Cerebral auditory areas were delineated in the awake, passively listening, rhesus monkey by comparing the rates of glucose utilization in an intact hemisphere and in an acoustically isolated contralateral hemisphere of the same animal. The auditory system defined in this way occupied large portions of cerebral tissue, an extent probably second only to that of the visual system. Cortically, the activated areas included the entire superior temporal gyrus and large portions of the parietal, prefrontal, and limbic lobes. Several auditory areas overlapped with previously identified visual areas, suggesting that the auditory system, like the visual system, contains separate pathways for processing stimulus quality, location, and motion.

Differential deposition of H2A.Z in rice seedling tissue during the day-night cycle.

PubMed

Zhang, Kang; Xu, Wenying; Wang, Chunchao; Yi, Xin; Su, Zhen

2017-03-04

Chromatin structure has an important role in modulating gene expression. The incorporation of histone variants into the nucleosome leads to important changes in the chromatin structure. The histone variant H2A.Z is highly conserved between different species of fungi, animals, and plants. However, dynamic changes to H2A.Z in rice have not been reported during the day-night cycle. In this study, we generated genome wide maps of H2A.Z for day and night time in harvested seedling tissues by combining chromatin immunoprecipitation and high-throughput sequencing. The analysis results for the H2A.Z data sets detected 7099 genes with higher depositions of H2A.Z in seedling tissues harvested at night compared with seedling tissues harvested during the day, whereas 4597 genes had higher H2A.Z depositions in seedlings harvested during the day. The gene expression profiles data suggested that H2A.Z probably negatively regulated gene expression during the day-night cycle and was involved in many important biologic processes. In general, our results indicated that H2A.Z may play an important role in plant responses to the diurnal oscillation process.

Calibration of the DRASTIC ground water vulnerability mapping method

USGS Publications Warehouse

Rupert, M.G.

2001-01-01

Ground water vulnerability maps developed using the DRASTIC method have been produced in many parts of the world. Comparisons of those maps with actual ground water quality data have shown that the DRASTIC method is typically a poor predictor of ground water contamination. This study significantly improved the effectiveness of a modified DRASTIC ground water vulnerability map by calibrating the point rating schemes to actual ground water quality data by using nonparametric statistical techniques and a geographic information system. Calibration was performed by comparing data on nitrite plus nitrate as nitrogen (NO2 + NO3-N) concentrations in ground water to land-use, soils, and depth to first-encountered ground water data. These comparisons showed clear statistical differences between NO2 + NO3-N concentrations and the various categories. Ground water probability point ratings for NO2 + NO3-N contamination were developed from the results of these comparisons, and a probability map was produced. This ground water probability map was then correlated with an independent set of NO2 + NO3-N data to demonstrate its effectiveness in predicting elevated NO2 + NO3-N concentrations in ground water. This correlation demonstrated that the probability map was effective, but a vulnerability map produced with the uncalibrated DRASTIC method in the same area and using the same data layers was not effective. Considerable time and expense have been outlaid to develop ground water vulnerability maps with the DRASTIC method. This study demonstrates a cost-effective method to improve and verify the effectiveness of ground water vulnerability maps.

Raman molecular imaging of brain frozen tissue sections.

PubMed

Kast, Rachel E; Auner, Gregory W; Rosenblum, Mark L; Mikkelsen, Tom; Yurgelevic, Sally M; Raghunathan, Aditya; Poisson, Laila M; Kalkanis, Steven N

2014-10-01

Raman spectroscopy provides a molecular signature of the region being studied. It is ideal for neurosurgical applications because it is non-destructive, label-free, not impacted by water concentration, and can map an entire region of tissue. The objective of this paper is to demonstrate the meaningful spatial molecular information provided by Raman spectroscopy for identification of regions of normal brain, necrosis, diffusely infiltrating glioma and solid glioblastoma (GBM). Five frozen section tissues (1 normal, 1 necrotic, 1 GBM, and 2 infiltrating glioma) were mapped in their entirety using a 300-µm-square step size. Smaller regions of interest were also mapped using a 25-µm step size. The relative concentrations of relevant biomolecules were mapped across all tissues and compared with adjacent hematoxylin and eosin-stained sections, allowing identification of normal, GBM, and necrotic regions. Raman peaks and peak ratios mapped included 1003, 1313, 1431, 1585, and 1659 cm(-1). Tissue maps identified boundaries of grey and white matter, necrosis, GBM, and infiltrating tumor. Complementary information, including relative concentration of lipids, protein, nucleic acid, and hemoglobin, was presented in a manner which can be easily adapted for in vivo tissue mapping. Raman spectroscopy can successfully provide label-free imaging of tissue characteristics with high accuracy. It can be translated to a surgical or laboratory tool for rapid, non-destructive imaging of tumor margins.

Three-dimensional mapping and regulation of action potential propagation in nanoelectronics-innervated tissues.

PubMed

Dai, Xiaochuan; Zhou, Wei; Gao, Teng; Liu, Jia; Lieber, Charles M

2016-09-01

Real-time mapping and manipulation of electrophysiology in three-dimensional (3D) tissues could have important impacts on fundamental scientific and clinical studies, yet realization is hampered by a lack of effective methods. Here we introduce tissue-scaffold-mimicking 3D nanoelectronic arrays consisting of 64 addressable devices with subcellular dimensions and a submillisecond temporal resolution. Real-time extracellular action potential (AP) recordings reveal quantitative maps of AP propagation in 3D cardiac tissues, enable in situ tracing of the evolving topology of 3D conducting pathways in developing cardiac tissues and probe the dynamics of AP conduction characteristics in a transient arrhythmia disease model and subsequent tissue self-adaptation. We further demonstrate simultaneous multisite stimulation and mapping to actively manipulate the frequency and direction of AP propagation. These results establish new methodologies for 3D spatiotemporal tissue recording and control, and demonstrate the potential to impact regenerative medicine, pharmacology and electronic therapeutics.

Three-dimensional mapping and regulation of action potential propagation in nanoelectronics innervated tissues

PubMed Central

Dai, Xiaochuan; Zhou, Wei; Gao, Teng; Liu, Jia; Lieber, Charles M.

2016-01-01

Real-time mapping and manipulation of electrophysiology in three-dimensional (3D) tissues could impact broadly fundamental scientific and clinical studies, yet realization lacks effective methods. Here we introduce tissue-scaffold-mimicking 3D nanoelectronic arrays consisting of 64 addressable devices with subcellular dimensions and sub-millisecond time-resolution. Real-time extracellular action potential (AP) recordings reveal quantitative maps of AP propagation in 3D cardiac tissues, enable in situ tracing of the evolving topology of 3D conducting pathways in developing cardiac tissues, and probe the dynamics of AP conduction characteristics in a transient arrhythmia disease model and subsequent tissue self-adaptation. We further demonstrate simultaneous multi-site stimulation and mapping to manipulate actively the frequency and direction of AP propagation. These results establish new methodologies for 3D spatiotemporal tissue recording and control, and demonstrate the potential to impact regenerative medicine, pharmacology and electronic therapeutics. PMID:27347837

A stereotaxic, population-averaged T1w ovine brain atlas including cerebral morphology and tissue volumes

PubMed Central

Nitzsche, Björn; Frey, Stephen; Collins, Louis D.; Seeger, Johannes; Lobsien, Donald; Dreyer, Antje; Kirsten, Holger; Stoffel, Michael H.; Fonov, Vladimir S.; Boltze, Johannes

2015-01-01

Standard stereotaxic reference systems play a key role in human brain studies. Stereotaxic coordinate systems have also been developed for experimental animals including non-human primates, dogs, and rodents. However, they are lacking for other species being relevant in experimental neuroscience including sheep. Here, we present a spatial, unbiased ovine brain template with tissue probability maps (TPM) that offer a detailed stereotaxic reference frame for anatomical features and localization of brain areas, thereby enabling inter-individual and cross-study comparability. Three-dimensional data sets from healthy adult Merino sheep (Ovis orientalis aries, 12 ewes and 26 neutered rams) were acquired on a 1.5 T Philips MRI using a T1w sequence. Data were averaged by linear and non-linear registration algorithms. Moreover, animals were subjected to detailed brain volume analysis including examinations with respect to body weight (BW), age, and sex. The created T1w brain template provides an appropriate population-averaged ovine brain anatomy in a spatial standard coordinate system. Additionally, TPM for gray (GM) and white (WM) matter as well as cerebrospinal fluid (CSF) classification enabled automatic prior-based tissue segmentation using statistical parametric mapping (SPM). Overall, a positive correlation of GM volume and BW explained about 15% of the variance of GM while a positive correlation between WM and age was found. Absolute tissue volume differences were not detected, indeed ewes showed significantly more GM per bodyweight as compared to neutered rams. The created framework including spatial brain template and TPM represent a useful tool for unbiased automatic image preprocessing and morphological characterization in sheep. Therefore, the reported results may serve as a starting point for further experimental and/or translational research aiming at in vivo analysis in this species. PMID:26089780

Increasing the Accuracy of Volume and ADC Delineation for Heterogeneous Tumor on Diffusion-Weighted MRI: Correlation with PET/CT

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

Gong, Nan-Jie; Wong, Chun-Sing, E-mail: drcswong@gmail.com; Chu, Yiu-Ching

2013-10-01

Purpose: To improve the accuracy of volume and apparent diffusion coefficient (ADC) measurements in diffusion-weighted magnetic resonance imaging (MRI), we proposed a method based on thresholding both the b0 images and the ADC maps. Methods and Materials: In 21 heterogeneous lesions from patients with metastatic gastrointestinal stromal tumors (GIST), gross lesion were manually contoured, and corresponding volumes and ADCs were denoted as gross tumor volume (GTV) and gross ADC (ADC{sub g}), respectively. Using a k-means clustering algorithm, the probable high-cellularity tumor tissues were selected based on b0 images and ADC maps. ADC and volume of the tissues selected using themore » proposed method were denoted as thresholded ADC (ADC{sub thr}) and high-cellularity tumor volume (HCTV), respectively. The metabolic tumor volume (MTV) in positron emission tomography (PET)/computed tomography (CT) was measured using 40% maximum standard uptake value (SUV{sub max}) as the lower threshold, and corresponding mean SUV (SUV{sub mean}) was also measured. Results: HCTV had excellent concordance with MTV according to Pearson's correlation (r=0.984, P<.001) and linear regression (slope = 1.085, intercept = −4.731). In contrast, GTV overestimated the volume and differed significantly from MTV (P=.005). ADC{sub thr} correlated significantly and strongly with SUV{sub mean} (r=−0.807, P<.001) and SUV{sub max} (r=−0.843, P<.001); both were stronger than those of ADC{sub g}. Conclusions: The proposed lesion-adaptive semiautomatic method can help segment high-cellularity tissues that match hypermetabolic tissues in PET/CT and enables more accurate volume and ADC delineation on diffusion-weighted MR images of GIST.« less

Recursive recovery of Markov transition probabilities from boundary value data

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

Patch, Sarah Kathyrn

1994-04-01

In an effort to mathematically describe the anisotropic diffusion of infrared radiation in biological tissue Gruenbaum posed an anisotropic diffusion boundary value problem in 1989. In order to accommodate anisotropy, he discretized the temporal as well as the spatial domain. The probabilistic interpretation of the diffusion equation is retained; radiation is assumed to travel according to a random walk (of sorts). In this random walk the probabilities with which photons change direction depend upon their previous as well as present location. The forward problem gives boundary value data as a function of the Markov transition probabilities. The inverse problem requiresmore » finding the transition probabilities from boundary value data. Problems in the plane are studied carefully in this thesis. Consistency conditions amongst the data are derived. These conditions have two effects: they prohibit inversion of the forward map but permit smoothing of noisy data. Next, a recursive algorithm which yields a family of solutions to the inverse problem is detailed. This algorithm takes advantage of all independent data and generates a system of highly nonlinear algebraic equations. Pluecker-Grassmann relations are instrumental in simplifying the equations. The algorithm is used to solve the 4 x 4 problem. Finally, the smallest nontrivial problem in three dimensions, the 2 x 2 x 2 problem, is solved.« less

Creating and validating cis-regulatory maps of tissue-specific gene expression regulation

PubMed Central

O'Connor, Timothy R.; Bailey, Timothy L.

2014-01-01

Predicting which genomic regions control the transcription of a given gene is a challenge. We present a novel computational approach for creating and validating maps that associate genomic regions (cis-regulatory modules–CRMs) with genes. The method infers regulatory relationships that explain gene expression observed in a test tissue using widely available genomic data for ‘other’ tissues. To predict the regulatory targets of a CRM, we use cross-tissue correlation between histone modifications present at the CRM and expression at genes within 1 Mbp of it. To validate cis-regulatory maps, we show that they yield more accurate models of gene expression than carefully constructed control maps. These gene expression models predict observed gene expression from transcription factor binding in the CRMs linked to that gene. We show that our maps are able to identify long-range regulatory interactions and improve substantially over maps linking genes and CRMs based on either the control maps or a ‘nearest neighbor’ heuristic. Our results also show that it is essential to include CRMs predicted in multiple tissues during map-building, that H3K27ac is the most informative histone modification, and that CAGE is the most informative measure of gene expression for creating cis-regulatory maps. PMID:25200088

Quantitative Susceptibility Mapping: Contrast Mechanisms and Clinical Applications

PubMed Central

Liu, Chunlei; Wei, Hongjiang; Gong, Nan-Jie; Cronin, Matthew; Dibb, Russel; Decker, Kyle

2016-01-01

Quantitative susceptibility mapping (QSM) is a recently developed MRI technique for quantifying the spatial distribution of magnetic susceptibility within biological tissues. It first uses the frequency shift in the MRI signal to map the magnetic field profile within the tissue. The resulting field map is then used to determine the spatial distribution of the underlying magnetic susceptibility by solving an inverse problem. The solution is achieved by deconvolving the field map with a dipole field, under the assumption that the magnetic field is a result of the superposition of the dipole fields generated by all voxels and that each voxel has its unique magnetic susceptibility. QSM provides improved contrast to noise ratio for certain tissues and structures compared to its magnitude counterpart. More importantly, magnetic susceptibility is a direct reflection of the molecular composition and cellular architecture of the tissue. Consequently, by quantifying magnetic susceptibility, QSM is becoming a quantitative imaging approach for characterizing normal and pathological tissue properties. This article reviews the mechanism generating susceptibility contrast within tissues and some associated applications. PMID:26844301

Probabilistic atlas and geometric variability estimation to drive tissue segmentation.

PubMed

Xu, Hao; Thirion, Bertrand; Allassonnière, Stéphanie

2014-09-10

Computerized anatomical atlases play an important role in medical image analysis. While an atlas usually refers to a standard or mean image also called template, which presumably represents well a given population, it is not enough to characterize the observed population in detail. A template image should be learned jointly with the geometric variability of the shapes represented in the observations. These two quantities will in the sequel form the atlas of the corresponding population. The geometric variability is modeled as deformations of the template image so that it fits the observations. In this paper, we provide a detailed analysis of a new generative statistical model based on dense deformable templates that represents several tissue types observed in medical images. Our atlas contains both an estimation of probability maps of each tissue (called class) and the deformation metric. We use a stochastic algorithm for the estimation of the probabilistic atlas given a dataset. This atlas is then used for atlas-based segmentation method to segment the new images. Experiments are shown on brain T1 MRI datasets. Copyright © 2014 John Wiley & Sons, Ltd.

SE Great Basin Play Fairway Analysis

DOE Data Explorer

Adam Brandt

2015-11-15

This submission includes a Na/K geothermometer probability greater than 200 deg C map, as well as two play fairway analysis (PFA) models. The probability map acts as a composite risk segment for the PFA models. The PFA models differ in their application of magnetotelluric conductors as composite risk segments. These PFA models map out the geothermal potential in the region of SE Great Basin, Utah.

Effect of Non-speckle Echo Signals on Tissue Characteristics for Liver Fibrosis using Probability Density Function of Ultrasonic B-mode image

NASA Astrophysics Data System (ADS)

Mori, Shohei; Hirata, Shinnosuke; Yamaguchi, Tadashi; Hachiya, Hiroyuki

To develop a quantitative diagnostic method for liver fibrosis using an ultrasound B-mode image, a probability imaging method of tissue characteristics based on a multi-Rayleigh model, which expresses a probability density function of echo signals from liver fibrosis, has been proposed. In this paper, an effect of non-speckle echo signals on tissue characteristics estimated from the multi-Rayleigh model was evaluated. Non-speckle signals were determined and removed using the modeling error of the multi-Rayleigh model. The correct tissue characteristics of fibrotic tissue could be estimated with the removal of non-speckle signals.

Rational variety mapping for contrast-enhanced nonlinear unsupervised segmentation of multispectral images of unstained specimen.

PubMed

Kopriva, Ivica; Hadžija, Mirko; Popović Hadžija, Marijana; Korolija, Marina; Cichocki, Andrzej

2011-08-01

A methodology is proposed for nonlinear contrast-enhanced unsupervised segmentation of multispectral (color) microscopy images of principally unstained specimens. The methodology exploits spectral diversity and spatial sparseness to find anatomical differences between materials (cells, nuclei, and background) present in the image. It consists of rth-order rational variety mapping (RVM) followed by matrix/tensor factorization. Sparseness constraint implies duality between nonlinear unsupervised segmentation and multiclass pattern assignment problems. Classes not linearly separable in the original input space become separable with high probability in the higher-dimensional mapped space. Hence, RVM mapping has two advantages: it takes implicitly into account nonlinearities present in the image (ie, they are not required to be known) and it increases spectral diversity (ie, contrast) between materials, due to increased dimensionality of the mapped space. This is expected to improve performance of systems for automated classification and analysis of microscopic histopathological images. The methodology was validated using RVM of the second and third orders of the experimental multispectral microscopy images of unstained sciatic nerve fibers (nervus ischiadicus) and of unstained white pulp in the spleen tissue, compared with a manually defined ground truth labeled by two trained pathophysiologists. The methodology can also be useful for additional contrast enhancement of images of stained specimens. Copyright © 2011 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

OCT-based in vivo tissue injury mapping

NASA Astrophysics Data System (ADS)

Baran, Utku; Li, Yuandong; Wang, Ruikang K.

2016-03-01

Tissue injury mapping (TIM) is developed by using a non-invasive in vivo optical coherence tomography to generate optical attenuation coefficient and microvascular map of the injured tissue. Using TIM, the infarct region development in mouse cerebral cortex during stroke is visualized. Moreover, we demonstrate the in vivo human facial skin structure and microvasculature during an acne lesion development. The results indicate that TIM may help in the study and the treatment of various diseases by providing high resolution images of tissue structural and microvascular changes.

Level set segmentation of medical images based on local region statistics and maximum a posteriori probability.

PubMed

Cui, Wenchao; Wang, Yi; Lei, Tao; Fan, Yangyu; Feng, Yan

2013-01-01

This paper presents a variational level set method for simultaneous segmentation and bias field estimation of medical images with intensity inhomogeneity. In our model, the statistics of image intensities belonging to each different tissue in local regions are characterized by Gaussian distributions with different means and variances. According to maximum a posteriori probability (MAP) and Bayes' rule, we first derive a local objective function for image intensities in a neighborhood around each pixel. Then this local objective function is integrated with respect to the neighborhood center over the entire image domain to give a global criterion. In level set framework, this global criterion defines an energy in terms of the level set functions that represent a partition of the image domain and a bias field that accounts for the intensity inhomogeneity of the image. Therefore, image segmentation and bias field estimation are simultaneously achieved via a level set evolution process. Experimental results for synthetic and real images show desirable performances of our method.

Evaluation of bioreactor-cultivated bone by magnetic resonance microscopy and FTIR microspectroscopy.

PubMed

Chesnick, Ingrid E; Avallone, Francis A; Leapman, Richard D; Landis, William J; Eidelman, Naomi; Potter, Kimberlee

2007-04-01

We present a three-dimensional mineralizing model based on a hollow fiber bioreactor (HFBR) inoculated with primary osteoblasts isolated from embryonic chick calvaria. Using non-invasive magnetic resonance microscopy (MRM), the growth and development of the mineralized tissue around the individual fibers were monitored over a period of 9 weeks. Spatial maps of the water proton MRM properties of the intact tissue, with 78 microm resolution, were used to determine changes in tissue composition with development. Unique changes in the mineral and collagen content of the tissue were detected with high specificity by proton density (PD) and magnetization transfer ratio (MTR) maps, respectively. At the end of the growth period, the presence of a bone-like tissue was verified by histology and the formation of poorly crystalline apatite was verified by selected area electron diffraction and electron probe X-ray microanalysis. FTIR microspectroscopy confirmed the heterogeneous nature of the bone-like tissue formed. FTIR-derived phosphate maps confirmed that those locations with the lowest PD values contained the most mineral, and FTIR-derived collagen maps confirmed that bright pixels on MTR maps corresponded to regions of high collagen content. In conclusion, the spatial mapping of tissue constituents by FTIR microspectroscopy corroborated the findings of non-invasive MRM measurements and supported the role of MRM in monitoring the bone formation process in vitro.

Evaluation of Bioreactor-Cultivated Bone by Magnetic Resonance Microscopy and FTIR Microspectroscopy

PubMed Central

Chesnick, Ingrid E.; Avallone, Frank; Leapman, Richard D.; Landis, William J.; Eidelman, Naomi; Potter, Kimberlee

2007-01-01

We present a three-dimensional mineralizing model based on a hollow fiber bioreactor (HFBR) inoculated with primary osteoblasts isolated from embryonic chick calvaria. Using non-invasive magnetic resonance microscopy (MRM), the growth and development of the mineralized tissue around the individual fibers were monitored over a period of nine weeks. Spatial maps of the water proton MRM properties of the intact tissue, with 78 μm resolution, were used to determine changes in tissue composition with development. Unique changes in the mineral and collagen content of the tissue were detected with high specificity by proton density (PD) and magnetization transfer ratio (MTR) maps, respectively. At the end of the growth period, the presence of a bone-like tissue was verified by histology and the formation of poorly crystalline apatite was verified by selected area electron diffraction and electron probe X-ray microanalysis. FTIR microspectroscopy confirmed the heterogeneous nature of the bone-like tissue formed. FTIR-derived phosphate maps confirmed that those locations with the lowest PD values contained the most mineral, and FTIR-derived collagen maps confirmed that bright pixels on MTR maps corresponded to regions of high collagen content. In conclusion, the spatial mapping of tissue constituents by FTIR microspectroscopy corroborated the findings of non-invasive MRM measurements and supported the role of MRM in monitoring the bone formation process in vitro. PMID:17174620

Spatial context learning approach to automatic segmentation of pleural effusion in chest computed tomography images

NASA Astrophysics Data System (ADS)

Mansoor, Awais; Casas, Rafael; Linguraru, Marius G.

2016-03-01

Pleural effusion is an abnormal collection of fluid within the pleural cavity. Excessive accumulation of pleural fluid is an important bio-marker for various illnesses, including congestive heart failure, pneumonia, metastatic cancer, and pulmonary embolism. Quantification of pleural effusion can be indicative of the progression of disease as well as the effectiveness of any treatment being administered. Quantification, however, is challenging due to unpredictable amounts and density of fluid, complex topology of the pleural cavity, and the similarity in texture and intensity of pleural fluid to the surrounding tissues in computed tomography (CT) scans. Herein, we present an automated method for the segmentation of pleural effusion in CT scans based on spatial context information. The method consists of two stages: first, a probabilistic pleural effusion map is created using multi-atlas segmentation. The probabilistic map assigns a priori probabilities to the presence of pleural uid at every location in the CT scan. Second, a statistical pattern classification approach is designed to annotate pleural regions using local descriptors based on a priori probabilities, geometrical, and spatial features. Thirty seven CT scans from a diverse patient population containing confirmed cases of minimal to severe amounts of pleural effusion were used to validate the proposed segmentation method. An average Dice coefficient of 0.82685 and Hausdorff distance of 16.2155 mm was obtained.

Adaptations to terrestrial overwintering of hatchling northern map turtles, Graptemys geographica.

PubMed

Baker, P J; Costanzo, J P; Iverson, J B; Lee, R E

2003-11-01

We conducted a 3-year field and laboratory study of winter biology in hatchlings of the northern map turtle ( Graptemys geographica). At our study area in northern Indiana, hatchlings routinely overwintered in their natal nests, emerging after the weather warmed in spring. Winter survival was excellent despite the fact that hatchlings were exposed frequently to subfreezing temperatures (to -5.4 degrees C). In the laboratory, cold-acclimated hatchlings exhibited low rates of evaporative water loss (mean=2.0 mg g(-1) day(-1)), which would enable them to conserve body water during winter. Laboratory-reared hatchlings were intolerant of freezing at -2.5 degrees C for 24 h, conditions that are readily survived by freeze-tolerant species of turtles. Winter survival of hatchling G. geographica probably depended on their extensive capacity for supercooling (to -14.8 degrees C) and their well-developed resistance to inoculative freezing, which may occur when hatchlings contact ice and ice-nucleating agents present in nesting soil. Supercooled hatchlings survived a brief exposure to -8 degrees C. Others, held at -6 degrees C for 5 days, maintained ATP concentrations at control levels, although they did accumulate lactate and glucose, probably in response to tissue hypoxia. Therefore, anoxia tolerance, as evidenced by the viability of hatchlings exposed to N(2) gas for 8 days, may promote survival during exposure to subfreezing temperatures.

Automatic detection of anomalies in screening mammograms

PubMed Central

2013-01-01

Background Diagnostic performance in breast screening programs may be influenced by the prior probability of disease. Since breast cancer incidence is roughly half a percent in the general population there is a large probability that the screening exam will be normal. That factor may contribute to false negatives. Screening programs typically exhibit about 83% sensitivity and 91% specificity. This investigation was undertaken to determine if a system could be developed to pre-sort screening-images into normal and suspicious bins based on their likelihood to contain disease. Wavelets were investigated as a method to parse the image data, potentially removing confounding information. The development of a classification system based on features extracted from wavelet transformed mammograms is reported. Methods In the multi-step procedure images were processed using 2D discrete wavelet transforms to create a set of maps at different size scales. Next, statistical features were computed from each map, and a subset of these features was the input for a concerted-effort set of naïve Bayesian classifiers. The classifier network was constructed to calculate the probability that the parent mammography image contained an abnormality. The abnormalities were not identified, nor were they regionalized. The algorithm was tested on two publicly available databases: the Digital Database for Screening Mammography (DDSM) and the Mammographic Images Analysis Society’s database (MIAS). These databases contain radiologist-verified images and feature common abnormalities including: spiculations, masses, geometric deformations and fibroid tissues. Results The classifier-network designs tested achieved sensitivities and specificities sufficient to be potentially useful in a clinical setting. This first series of tests identified networks with 100% sensitivity and up to 79% specificity for abnormalities. This performance significantly exceeds the mean sensitivity reported in literature for the unaided human expert. Conclusions Classifiers based on wavelet-derived features proved to be highly sensitive to a range of pathologies, as a result Type II errors were nearly eliminated. Pre-sorting the images changed the prior probability in the sorted database from 37% to 74%. PMID:24330643

Probability of viremia with HBV, HCV, HIV, and HTLV among tissue donors in the United States.

PubMed

Zou, Shimian; Dodd, Roger Y; Stramer, Susan L; Strong, D Michael

2004-08-19

Tissue-banking organizations in the United States have introduced various review and testing procedures to reduce the risk of the transmission of viral infections from tissue grafts. We estimated the current probability of undetected viremia with hepatitis B virus (HBV), hepatitis C virus (HCV), human immunodeficiency virus (HIV), and human T-lymphotropic virus (HTLV) among tissue donors. Rates of prevalence of hepatitis B surface antigen (HBsAg) and antibodies against HIV (anti-HIV), HCV (anti-HCV), and HTLV (anti-HTLV) were determined among 11,391 donors to five tissue banks in the United States. The data were compared with those of first-time blood donors in order to generate estimated incidence rates among tissue donors. The probability of viremia undetected by screening at the time of tissue donation was estimated on the basis of the incidence estimates and the window periods for these infections. The prevalence of confirmed positive tests among tissue donors was 0.093 percent for anti-HIV, 0.229 percent for HBsAg, 1.091 percent for anti-HCV, and 0.068 percent for anti-HTLV. The incidence rates were estimated to be 30.118, 18.325, 12.380, and 5.586 per 100,000 person-years, respectively. The estimated probability of viremia at the time of donation was 1 in 55,000, 1 in 34,000, 1 in 42,000, and 1 in 128,000, respectively. The prevalence rates of HBV, HCV, HIV, and HTLV infections are lower among tissue donors than in the general population. However, the estimated probability of undetected viremia at the time of tissue donation is higher among tissue donors than among first-time blood donors. The addition of nucleic acid-amplification testing to the screening of tissue donors should reduce the risk of these infections among recipients of donated tissues. Copyright 2004 Massachusetts Medical Society

A Probabilistic Model of Illegal Drug Trafficking Operations in the Eastern Pacific and Caribbean Sea

DTIC Science & Technology

2013-09-01

partner agencies and nations, detects, tracks, and interdicts illegal drug-trafficking in this region. In this thesis, we develop a probability model based...trafficking in this region. In this thesis, we develop a probability model based on intelligence inputs to generate a spatial temporal heat map specifying the...complement and vet such complicated simulation by developing more analytically tractable models. We develop probability models to generate a heat map

Evaluation of carrier collection probability in bifacial interdigitated-back-contact crystalline silicon solar cells by the internal quantum efficiency mapping method

NASA Astrophysics Data System (ADS)

Tachibana, Tomihisa; Tanahashi, Katsuto; Mochizuki, Toshimitsu; Shirasawa, Katsuhiko; Takato, Hidetaka

2018-04-01

Bifacial interdigitated-back-contact (IBC) silicon solar cells with a high bifaciality of 0.91 were fabricated. Screen printing and firing technology were used to reduce the production cost. For the first time, the relationship between the rear side structure and carrier collection probability was evaluated using internal quantum efficiency (IQE) mapping. The measurement results showed that the screen-printed electrode and back surface field (BSF) area led to low IQE. The low carrier collection probability by BSF area can be explained by electrical shading effects. Thus, it is clear that the IQE mapping system is useful to evaluate the IBC cell.

Culture-Independent Identification of Mycobacterium avium Subspecies paratuberculosis in Ovine Tissues: Comparison with Bacterial Culture and Histopathological Lesions

PubMed Central

Acharya, Kamal R.; Dhand, Navneet K.; Whittington, Richard J.; Plain, Karren M.

2017-01-01

Johne’s disease is a chronic debilitating enteropathy of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Current abattoir surveillance programs detect disease via examination of gross lesions and confirmation by histopathological and/or tissue culture, which is time-consuming and has relatively low sensitivity. This study aimed to investigate whether a high-throughput quantitative PCR (qPCR) test is a viable alternative for tissue testing. Intestine and mesenteric lymph nodes were sourced from sheep experimentally infected with MAP and the DNA extracted using a protocol developed for tissues, comprised enzymatic digestion of the tissue homogenate, chemical and mechanical lysis, and magnetic bead-based DNA purification. The extracted DNA was tested by adapting a previously validated qPCR for fecal samples, and the results were compared with culture and histopathology results of the corresponding tissues. The MAP tissue qPCR confirmed infection in the majority of sheep with gross lesions on postmortem (37/38). Likewise, almost all tissue culture (61/64) or histopathology (52/58) positives were detected with good to moderate agreement (Cohen’s kappa statistic) and no significant difference to the reference tests (McNemar’s Chi-square test). Higher MAP DNA quantities corresponded to animals with more severe histopathology (odds ratio: 1.82; 95% confidence interval: 1.60, 2.07). Culture-independent strain typing on tissue DNA was successfully performed. This MAP tissue qPCR method had a sensitivity equivalent to the reference tests and is thus a viable replacement for gross- and histopathological examination of tissue samples in abattoirs. In addition, the test could be validated for testing tissue samples intended for human consumption. PMID:29312970

Culture-Independent Identification of Mycobacterium avium Subspecies paratuberculosis in Ovine Tissues: Comparison with Bacterial Culture and Histopathological Lesions.

PubMed

Acharya, Kamal R; Dhand, Navneet K; Whittington, Richard J; Plain, Karren M

2017-01-01

Johne's disease is a chronic debilitating enteropathy of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Current abattoir surveillance programs detect disease via examination of gross lesions and confirmation by histopathological and/or tissue culture, which is time-consuming and has relatively low sensitivity. This study aimed to investigate whether a high-throughput quantitative PCR (qPCR) test is a viable alternative for tissue testing. Intestine and mesenteric lymph nodes were sourced from sheep experimentally infected with MAP and the DNA extracted using a protocol developed for tissues, comprised enzymatic digestion of the tissue homogenate, chemical and mechanical lysis, and magnetic bead-based DNA purification. The extracted DNA was tested by adapting a previously validated qPCR for fecal samples, and the results were compared with culture and histopathology results of the corresponding tissues. The MAP tissue qPCR confirmed infection in the majority of sheep with gross lesions on postmortem (37/38). Likewise, almost all tissue culture (61/64) or histopathology (52/58) positives were detected with good to moderate agreement (Cohen's kappa statistic) and no significant difference to the reference tests (McNemar's Chi-square test). Higher MAP DNA quantities corresponded to animals with more severe histopathology (odds ratio: 1.82; 95% confidence interval: 1.60, 2.07). Culture-independent strain typing on tissue DNA was successfully performed. This MAP tissue qPCR method had a sensitivity equivalent to the reference tests and is thus a viable replacement for gross- and histopathological examination of tissue samples in abattoirs. In addition, the test could be validated for testing tissue samples intended for human consumption.

Generative diffeomorphic modelling of large MRI data sets for probabilistic template construction.

PubMed

Blaiotta, Claudia; Freund, Patrick; Cardoso, M Jorge; Ashburner, John

2018-02-01

In this paper we present a hierarchical generative model of medical image data, which can capture simultaneously the variability of both signal intensity and anatomical shapes across large populations. Such a model has a direct application for learning average-shaped probabilistic tissue templates in a fully automated manner. While in principle the generality of the proposed Bayesian approach makes it suitable to address a wide range of medical image computing problems, our work focuses primarily on neuroimaging applications. In particular we validate the proposed method on both real and synthetic brain MR scans including the cervical cord and demonstrate that it yields accurate alignment of brain and spinal cord structures, as compared to state-of-the-art tools for medical image registration. At the same time we illustrate how the resulting tissue probability maps can readily be used to segment, bias correct and spatially normalise unseen data, which are all crucial pre-processing steps for MR imaging studies. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Investigation of Thermal Effects of Photocoagulation on Retinal Tissue Using Fine-Motion-Sensitive Dynamic Optical Coherence Tomography.

PubMed

Kurokawa, Kazuhiro; Makita, Shuichi; Yasuno, Yoshiaki

2016-01-01

To enable an objective evaluation of photocoagulation, we characterize thermal tissue changes induced by laser irradiation with different laser parameters using optical coherence tomography (OCT). Spectral-domain OCT with a newly developed image processing method was used to monitor the thermal changes of ex vivo porcine retina. A sequence of OCT B-scans was obtained at the same retinal position simultaneously with the photocoagulation. Cross-sectional tissue displacement maps with respect to an OCT image taken before laser irradiation were computed for images taken before, during, and after laser irradiation, by using a correlation-based custom algorithm. Cross-sectional correlation maps (OCT correlation maps) were also computed from an OCT image taken before laser irradiation as a base-line to visualize alterations of tissue microstructure induced by laser irradiation. By systematically controlling laser power and exposure times, tissue displacements and structural changes of 200 retinal regions of 10 porcine eyes were characterized. Thermal tissue changes were characterized by B-scan images, OCT correlation maps, and tissue displacement maps. Larger tissue deformation was induced with higher laser power and shorter exposure time, while the same total laser energy (10 mJ) was applied. The measured tissue displacements revealed the complicated dynamics of tissue displacements. Three types of dynamics were observed; lateral expansion, lateral constriction, and a type showing more complicated dynamics. The results demonstrated the ability of this OCT-based method to evaluate retinal changes induced by laser irradiation. This evaluation could lead to further understanding of thermal effects, and increasing reproducibility of photocoagulation therapy.

Comparing fuel reduction treatments for reducing wildfire size and intensity in a boreal forest landscape of northeastern China.

PubMed

Wu, Zhiwei; He, Hong S; Liu, Zhihua; Liang, Yu

2013-06-01

Fuel load is often used to prioritize stands for fuel reduction treatments. However, wildfire size and intensity are not only related to fuel loads but also to a wide range of other spatially related factors such as topography, weather and human activity. In prioritizing fuel reduction treatments, we propose using burn probability to account for the effects of spatially related factors that can affect wildfire size and intensity. Our burn probability incorporated fuel load, ignition probability, and spread probability (spatial controls to wildfire) at a particular location across a landscape. Our goal was to assess differences in reducing wildfire size and intensity using fuel-load and burn-probability based treatment prioritization approaches. Our study was conducted in a boreal forest in northeastern China. We derived a fuel load map from a stand map and a burn probability map based on historical fire records and potential wildfire spread pattern. The burn probability map was validated using historical records of burned patches. We then simulated 100 ignitions and six fuel reduction treatments to compare fire size and intensity under two approaches of fuel treatment prioritization. We calibrated and validated simulated wildfires against historical wildfire data. Our results showed that fuel reduction treatments based on burn probability were more effective at reducing simulated wildfire size, mean and maximum rate of spread, and mean fire intensity, but less effective at reducing maximum fire intensity across the burned landscape than treatments based on fuel load. Thus, contributions from both fuels and spatially related factors should be considered for each fuel reduction treatment. Published by Elsevier B.V.

Nitrate probability mapping in the northern aquifer alluvial system of the river Tagus (Portugal) using Disjunctive Kriging.

PubMed

Mendes, Maria Paula; Ribeiro, Luís

2010-02-01

The Water Framework Directive and its daughter directives recognize the urgent need to adopt specific measures against the contamination of water by individual pollutants or a group of pollutants that present a significant risk to the quality of water. Probability maps showing that the nitrate concentrations exceed a legal threshold value in any location of the aquifer are used to assess risk of groundwater quality degradation from intensive agricultural activity in aquifers. In this paper we use Disjunctive Kriging to map the probability that the Nitrates Directive limit (91/676/EEC) is exceeded for the Nitrate Vulnerable Zone of the River Tagus alluvium aquifer. The Tagus alluvial aquifer system belongs to one of the most productive hydrogeological unit of continental Portugal and it is used to irrigate crops. Several groundwater monitoring campaigns were carried out from 2004 to 2006 according to the summer crops cycle. The study reveals more areas on the west bank with higher probabilities of contamination by nitrates (nitrate concentration values above 50mg/L) than on the east bank. The analysis of synthetic temporal probability map shows the areas where there is an increase of nitrates concentration during the summers. Copyright 2009 Elsevier B.V. All rights reserved.

Modeling Dynamic Contrast-Enhanced MRI Data with a Constrained Local AIF.

PubMed

Duan, Chong; Kallehauge, Jesper F; Pérez-Torres, Carlos J; Bretthorst, G Larry; Beeman, Scott C; Tanderup, Kari; Ackerman, Joseph J H; Garbow, Joel R

2018-02-01

This study aims to develop a constrained local arterial input function (cL-AIF) to improve quantitative analysis of dynamic contrast-enhanced (DCE)-magnetic resonance imaging (MRI) data by accounting for the contrast-agent bolus amplitude error in the voxel-specific AIF. Bayesian probability theory-based parameter estimation and model selection were used to compare tracer kinetic modeling employing either the measured remote-AIF (R-AIF, i.e., the traditional approach) or an inferred cL-AIF against both in silico DCE-MRI data and clinical, cervical cancer DCE-MRI data. When the data model included the cL-AIF, tracer kinetic parameters were correctly estimated from in silico data under contrast-to-noise conditions typical of clinical DCE-MRI experiments. Considering the clinical cervical cancer data, Bayesian model selection was performed for all tumor voxels of the 16 patients (35,602 voxels in total). Among those voxels, a tracer kinetic model that employed the voxel-specific cL-AIF was preferred (i.e., had a higher posterior probability) in 80 % of the voxels compared to the direct use of a single R-AIF. Maps of spatial variation in voxel-specific AIF bolus amplitude and arrival time for heterogeneous tissues, such as cervical cancer, are accessible with the cL-AIF approach. The cL-AIF method, which estimates unique local-AIF amplitude and arrival time for each voxel within the tissue of interest, provides better modeling of DCE-MRI data than the use of a single, measured R-AIF. The Bayesian-based data analysis described herein affords estimates of uncertainties for each model parameter, via posterior probability density functions, and voxel-wise comparison across methods/models, via model selection in data modeling.

Normal tissue complication probability modelling of tissue fibrosis following breast radiotherapy

NASA Astrophysics Data System (ADS)

Alexander, M. A. R.; Brooks, W. A.; Blake, S. W.

2007-04-01

Cosmetic late effects of radiotherapy such as tissue fibrosis are increasingly regarded as being of importance. It is generally considered that the complication probability of a radiotherapy plan is dependent on the dose uniformity, and can be reduced by using better compensation to remove dose hotspots. This work aimed to model the effects of improved dose homogeneity on complication probability. The Lyman and relative seriality NTCP models were fitted to clinical fibrosis data for the breast collated from the literature. Breast outlines were obtained from a commercially available Rando phantom using the Osiris system. Multislice breast treatment plans were produced using a variety of compensation methods. Dose-volume histograms (DVHs) obtained for each treatment plan were reduced to simple numerical parameters using the equivalent uniform dose and effective volume DVH reduction methods. These parameters were input into the models to obtain complication probability predictions. The fitted model parameters were consistent with a parallel tissue architecture. Conventional clinical plans generally showed reducing complication probabilities with increasing compensation sophistication. Extremely homogenous plans representing idealized IMRT treatments showed increased complication probabilities compared to conventional planning methods, as a result of increased dose to areas receiving sub-prescription doses using conventional techniques.

Differences in Clinical Features of Methamphetamine Users with Persistent Psychosis and Patients with Schizophrenia.

PubMed

Wang, Liang-Jen; Lin, Shih-Ku; Chen, Yi-Chih; Huang, Ming-Chyi; Chen, Tzu-Ting; Ree, Shao-Chun; Chen, Chih-Ken

Methamphetamine exerts neurotoxic effects and elicits psychotic symptoms. This study attempted to compare clinical differences between methamphetamine users with persistent psychosis (MAP) and patients with schizophrenia. In addition, we examined the discrimination validity by using symptom clusters to differentiate between MAP and schizophrenia. We enrolled 53 MAP patients and 53 patients with schizophrenia. The psychopathology of participants was assessed using the Chinese version of the Diagnostic Interview for Genetic Studies and the 18-item Brief Psychiatric Rating Scale. Logistic regression was used to examine the predicted probability scores of different symptom combinations on discriminating between MAP and schizophrenia. The receiver operating characteristic (ROC) analyses and area under the curve (AUC) were further applied to examine the discrimination validity of the predicted probability scores on differentiating between MAP and schizophrenia. We found that MAP and schizophrenia demonstrated similar patterns of delusions. Compared to patients with schizophrenia, MAP experienced significantly higher proportions of visual hallucinations and of somatic or tactile hallucinations. However, MAP exhibited significantly lower severity in conceptual disorganization, mannerism/posturing, blunted affect, emotional withdrawal, and motor retardation compared to patients with schizophrenia. The ROC analysis showed that a predicted probability score combining the aforementioned 7 items of symptoms could significantly differentiate between MAP and schizophrenia (AUC = 0.77). Findings in the current study suggest that nuanced differences might exist in the clinical presentation of secondary psychosis (MAP) and primary psychosis (schizophrenia). Combining the symptoms as a whole may help with differential diagnosis for MAP and schizophrenia. © 2016 S. Karger AG, Basel.

Parametric mapping of [18F]fluoromisonidazole positron emission tomography using basis functions.

PubMed

Hong, Young T; Beech, John S; Smith, Rob; Baron, Jean-Claude; Fryer, Tim D

2011-02-01

In this study, we show a basis function method (BAFPIC) for voxelwise calculation of kinetic parameters (K(1), k(2), k(3), K(i)) and blood volume using an irreversible two-tissue compartment model. BAFPIC was applied to rat ischaemic stroke micro-positron emission tomography data acquired with the hypoxia tracer [(18)F]fluoromisonidazole because irreversible two-tissue compartmental modelling provided good fits to data from both hypoxic and normoxic tissues. Simulated data show that BAFPIC produces kinetic parameters with significantly lower variability and bias than nonlinear least squares (NLLS) modelling in hypoxic tissue. The advantage of BAFPIC over NLLS is less pronounced in normoxic tissue. K(i) determined from BAFPIC has lower variability than that from the Patlak-Gjedde graphical analysis (PGA) by up to 40% and lower bias, except for normoxic tissue at mid-high noise levels. Consistent with the simulation results, BAFPIC parametric maps of real data suffer less noise-induced variability than do NLLS and PGA. Delineation of hypoxia on BAFPIC k(3) maps is aided by low variability in normoxic tissue, which matches that in K(i) maps. BAFPIC produces K(i) values that correlate well with those from PGA (r(2)=0.93 to 0.97; slope 0.99 to 1.05, absolute intercept <0.00002 mL/g per min). BAFPIC is a computationally efficient method of determining parametric maps with low bias and variance.

Eulerian Mapping Closure Approach for Probability Density Function of Concentration in Shear Flows

NASA Technical Reports Server (NTRS)

He, Guowei; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

The Eulerian mapping closure approach is developed for uncertainty propagation in computational fluid mechanics. The approach is used to study the Probability Density Function (PDF) for the concentration of species advected by a random shear flow. An analytical argument shows that fluctuation of the concentration field at one point in space is non-Gaussian and exhibits stretched exponential form. An Eulerian mapping approach provides an appropriate approximation to both convection and diffusion terms and leads to a closed mapping equation. The results obtained describe the evolution of the initial Gaussian field, which is in agreement with direct numerical simulations.

Collapse susceptibility mapping in karstified gypsum terrain (Sivas basin - Turkey) by conditional probability, logistic regression, artificial neural network models

NASA Astrophysics Data System (ADS)

Yilmaz, Isik; Keskin, Inan; Marschalko, Marian; Bednarik, Martin

2010-05-01

This study compares the GIS based collapse susceptibility mapping methods such as; conditional probability (CP), logistic regression (LR) and artificial neural networks (ANN) applied in gypsum rock masses in Sivas basin (Turkey). Digital Elevation Model (DEM) was first constructed using GIS software. Collapse-related factors, directly or indirectly related to the causes of collapse occurrence, such as distance from faults, slope angle and aspect, topographical elevation, distance from drainage, topographic wetness index- TWI, stream power index- SPI, Normalized Difference Vegetation Index (NDVI) by means of vegetation cover, distance from roads and settlements were used in the collapse susceptibility analyses. In the last stage of the analyses, collapse susceptibility maps were produced from CP, LR and ANN models, and they were then compared by means of their validations. Area Under Curve (AUC) values obtained from all three methodologies showed that the map obtained from ANN model looks like more accurate than the other models, and the results also showed that the artificial neural networks is a usefull tool in preparation of collapse susceptibility map and highly compatible with GIS operating features. Key words: Collapse; doline; susceptibility map; gypsum; GIS; conditional probability; logistic regression; artificial neural networks.

Probabilistic mapping of flood-induced backscatter changes in SAR time series

NASA Astrophysics Data System (ADS)

Schlaffer, Stefan; Chini, Marco; Giustarini, Laura; Matgen, Patrick

2017-04-01

The information content of flood extent maps can be increased considerably by including information on the uncertainty of the flood area delineation. This additional information can be of benefit in flood forecasting and monitoring. Furthermore, flood probability maps can be converted to binary maps showing flooded and non-flooded areas by applying a threshold probability value pF = 0.5. In this study, a probabilistic change detection approach for flood mapping based on synthetic aperture radar (SAR) time series is proposed. For this purpose, conditional probability density functions (PDFs) for land and open water surfaces were estimated from ENVISAT ASAR Wide Swath (WS) time series containing >600 images using a reference mask of permanent water bodies. A pixel-wise harmonic model was used to account for seasonality in backscatter from land areas caused by soil moisture and vegetation dynamics. The approach was evaluated for a large-scale flood event along the River Severn, United Kingdom. The retrieved flood probability maps were compared to a reference flood mask derived from high-resolution aerial imagery by means of reliability diagrams. The obtained performance measures indicate both high reliability and confidence although there was a slight under-estimation of the flood extent, which may in part be attributed to topographically induced radar shadows along the edges of the floodplain. Furthermore, the results highlight the importance of local incidence angle for the separability between flooded and non-flooded areas as specular reflection properties of open water surfaces increase with a more oblique viewing geometry.

Using known map category marginal frequencies to improve estimates of thematic map accuracy

NASA Technical Reports Server (NTRS)

Card, D. H.

1982-01-01

By means of two simple sampling plans suggested in the accuracy-assessment literature, it is shown how one can use knowledge of map-category relative sizes to improve estimates of various probabilities. The fact that maximum likelihood estimates of cell probabilities for the simple random sampling and map category-stratified sampling were identical has permitted a unified treatment of the contingency-table analysis. A rigorous analysis of the effect of sampling independently within map categories is made possible by results for the stratified case. It is noted that such matters as optimal sample size selection for the achievement of a desired level of precision in various estimators are irrelevant, since the estimators derived are valid irrespective of how sample sizes are chosen.

Challenges in making a seismic hazard map for Alaska and the Aleutians

USGS Publications Warehouse

Wesson, R.L.; Boyd, O.S.; Mueller, C.S.; Frankel, A.D.; Freymueller, J.T.

2008-01-01

We present a summary of the data and analyses leading to the revision of the time-independent probabilistic seismic hazard maps of Alaska and the Aleutians. These maps represent a revision of existing maps based on newly obtained data, and reflect best current judgments about methodology and approach. They have been prepared following the procedures and assumptions made in the preparation of the 2002 National Seismic Hazard Maps for the lower 48 States, and will be proposed for adoption in future revisions to the International Building Code. We present example maps for peak ground acceleration, 0.2 s spectral amplitude (SA), and 1.0 s SA at a probability level of 2% in 50 years (annual probability of 0.000404). In this summary, we emphasize issues encountered in preparation of the maps that motivate or require future investigation and research.

Technique for handling wave propagation specific effects in biological tissue: mapping of the photon transport equation to Maxwell's equations.

PubMed

Handapangoda, Chintha C; Premaratne, Malin; Paganin, David M; Hendahewa, Priyantha R D S

2008-10-27

A novel algorithm for mapping the photon transport equation (PTE) to Maxwell's equations is presented. Owing to its accuracy, wave propagation through biological tissue is modeled using the PTE. The mapping of the PTE to Maxwell's equations is required to model wave propagation through foreign structures implanted in biological tissue for sensing and characterization of tissue properties. The PTE solves for only the magnitude of the intensity but Maxwell's equations require the phase information as well. However, it is possible to construct the phase information approximately by solving the transport of intensity equation (TIE) using the full multigrid algorithm.

Self-organized energetic model for collective activity on animal tissue

NASA Astrophysics Data System (ADS)

Dos Santos, Michelle C. Varela; Macedo-Filho, Antonio; Dos Santos Lima, Gustavo Zampier; Corso, Gilberto

We construct a self-organized critical (SOC) model to explain spontaneous collective activity in animal tissue without the necessity of a muscular or a central control nervous system. Our prototype model is an epithelial cuboid tissue formed by a single layer of cells as the internal digestive cavity of primitive animals. The tissue is composed by cells that absorb nutrients and store energy, with probability p, to participate in a collective tissue activity. Each cell can be in two states: at high energy and able to became active or at low metabolic energy and remain at rest. Any cell can spontaneously, with a very low probability, spark a collective activity across its neighbors that share a minimal energy. Cells participating in tissue activity consume all their energy. A power-law relation P(s)∝sγ for the probability of having a collective activity with s cells is observed. By construction this model is analogue to the forest fire SOC model. Our approach produces naturally a critical state for the activity in animal tissue, besides it explains self-sustained activity in a living animal tissue without feedback control.

3D resolved mapping of optical aberrations in thick tissues

PubMed Central

Zeng, Jun; Mahou, Pierre; Schanne-Klein, Marie-Claire; Beaurepaire, Emmanuel; Débarre, Delphine

2012-01-01

We demonstrate a simple method for mapping optical aberrations with 3D resolution within thick samples. The method relies on the local measurement of the variation in image quality with externally applied aberrations. We discuss the accuracy of the method as a function of the signal strength and of the aberration amplitude and we derive the achievable resolution for the resulting measurements. We then report on measured 3D aberration maps in human skin biopsies and mouse brain slices. From these data, we analyse the consequences of tissue structure and refractive index distribution on aberrations and imaging depth in normal and cleared tissue samples. The aberration maps allow the estimation of the typical aplanetism region size over which aberrations can be uniformly corrected. This method and data pave the way towards efficient correction strategies for tissue imaging applications. PMID:22876353

Identification of QTLs Associated with Callogenesis and Embryogenesis in Oil Palm Using Genetic Linkage Maps Improved with SSR Markers

PubMed Central

Ting, Ngoot-Chin; Jansen, Johannes; Nagappan, Jayanthi; Ishak, Zamzuri; Chin, Cheuk-Weng; Tan, Soon-Guan; Cheah, Suan-Choo; Singh, Rajinder

2013-01-01

Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR) markers were developed for dura (ENL48) and pisifera (ML161), the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs) in 23 linkage groups (LGs), covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs) in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs) associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm. PMID:23382832

Optimal Symmetric Multimodal Templates and Concatenated Random Forests for Supervised Brain Tumor Segmentation (Simplified) with ANTsR.

PubMed

Tustison, Nicholas J; Shrinidhi, K L; Wintermark, Max; Durst, Christopher R; Kandel, Benjamin M; Gee, James C; Grossman, Murray C; Avants, Brian B

2015-04-01

Segmenting and quantifying gliomas from MRI is an important task for diagnosis, planning intervention, and for tracking tumor changes over time. However, this task is complicated by the lack of prior knowledge concerning tumor location, spatial extent, shape, possible displacement of normal tissue, and intensity signature. To accommodate such complications, we introduce a framework for supervised segmentation based on multiple modality intensity, geometry, and asymmetry feature sets. These features drive a supervised whole-brain and tumor segmentation approach based on random forest-derived probabilities. The asymmetry-related features (based on optimal symmetric multimodal templates) demonstrate excellent discriminative properties within this framework. We also gain performance by generating probability maps from random forest models and using these maps for a refining Markov random field regularized probabilistic segmentation. This strategy allows us to interface the supervised learning capabilities of the random forest model with regularized probabilistic segmentation using the recently developed ANTsR package--a comprehensive statistical and visualization interface between the popular Advanced Normalization Tools (ANTs) and the R statistical project. The reported algorithmic framework was the top-performing entry in the MICCAI 2013 Multimodal Brain Tumor Segmentation challenge. The challenge data were widely varying consisting of both high-grade and low-grade glioma tumor four-modality MRI from five different institutions. Average Dice overlap measures for the final algorithmic assessment were 0.87, 0.78, and 0.74 for "complete", "core", and "enhanced" tumor components, respectively.

A prostate CAD system based on multiparametric analysis of DCE T1-w, and DW automatically registered images

NASA Astrophysics Data System (ADS)

Giannini, Valentina; Vignati, Anna; Mazzetti, Simone; De Luca, Massimo; Bracco, Christian; Stasi, Michele; Russo, Filippo; Armando, Enrico; Regge, Daniele

2013-02-01

Prostate specific antigen (PSA)-based screening reduces the rate of death from prostate cancer (PCa) by 31%, but this benefit is associated with a high risk of overdiagnosis and overtreatment. As prostate transrectal ultrasound-guided biopsy, the standard procedure for prostate histological sampling, has a sensitivity of 77% with a considerable false-negative rate, more accurate methods need to be found to detect or rule out significant disease. Prostate magnetic resonance imaging has the potential to improve the specificity of PSA-based screening scenarios as a non-invasive detection tool, in particular exploiting the combination of anatomical and functional information in a multiparametric framework. The purpose of this study was to describe a computer aided diagnosis (CAD) method that automatically produces a malignancy likelihood map by combining information from dynamic contrast enhanced MR images and diffusion weighted images. The CAD system consists of multiple sequential stages, from a preliminary registration of images of different sequences, in order to correct for susceptibility deformation and/or movement artifacts, to a Bayesian classifier, which fused all the extracted features into a probability map. The promising results (AUROC=0.87) should be validated on a larger dataset, but they suggest that the discrimination on a voxel basis between benign and malignant tissues is feasible with good performances. This method can be of benefit to improve the diagnostic accuracy of the radiologist, reduce reader variability and speed up the reading time, automatically highlighting probably cancer suspicious regions.

Experimental colitis is exacerbated by concomitant infection with Mycobacterium avium ssp. paratuberculosis.

PubMed

Suwandi, Abdulhadi; Bargen, Imke; Roy, Bishnudeo; Pils, Marina C; Krey, Martina; Zur Lage, Susanne; Basler, Tina; Rohde, Manfred; Falk, Christine S; Hornef, Mathias W; Goethe, Ralph; Weiss, Siegfried

2014-11-01

Crohn's disease (CD) is a chronic inflammatory disorder of the human gastrointestinal tract. Although genetic, immunological, environmental, and bacterial factors have been implicated, the pathogenesis is incompletely understood. The histopathological appearance of CD strikingly resembles Johne's disease, a ruminant inflammatory bowel disease, caused by Mycobacterium avium ssp. paratuberculosis (MAP), but a causative role of MAP in CD has not been established. In this work, we hypothesized that MAP might exacerbate an already existing intestinal disease. We combined dextran sulfate sodium (DSS)-induced colitis with MAP infection in mice and monitored the immune response and bacterial count in different organs. An increased size of liver and spleen was observed in DSS-treated and MAP-infected animals (DSS + MAP) as compared with DSS-treated uninfected (DSS + PBS) mice. Similarly, DSS treatment increased the number and size of MAP-induced liver granulomas and enhanced the MAP counts in enteric tissue. MAP infection in turn delayed the mucosal healing of DSS-induced tissue damage. Finally, high numbers of MAP were found in mesenteric fat tissue causing large granuloma and necrotic regions. Taken together, we present an in vivo model to study the role of MAP infection in CD. Our results confirm the hypothesis that MAP is able to exacerbate existing intestinal inflammation.

A method for producing digital probabilistic seismic landslide hazard maps

USGS Publications Warehouse

Jibson, R.W.; Harp, E.L.; Michael, J.A.

2000-01-01

The 1994 Northridge, California, earthquake is the first earthquake for which we have all of the data sets needed to conduct a rigorous regional analysis of seismic slope instability. These data sets include: (1) a comprehensive inventory of triggered landslides, (2) about 200 strong-motion records of the mainshock, (3) 1:24 000-scale geologic mapping of the region, (4) extensive data on engineering properties of geologic units, and (5) high-resolution digital elevation models of the topography. All of these data sets have been digitized and rasterized at 10 m grid spacing using ARC/INFO GIS software on a UNIX computer. Combining these data sets in a dynamic model based on Newmark's permanent-deformation (sliding-block) analysis yields estimates of coseismic landslide displacement in each grid cell from the Northridge earthquake. The modeled displacements are then compared with the digital inventory of landslides triggered by the Northridge earthquake to construct a probability curve relating predicted displacement to probability of failure. This probability function can be applied to predict and map the spatial variability in failure probability in any ground-shaking conditions of interest. We anticipate that this mapping procedure will be used to construct seismic landslide hazard maps that will assist in emergency preparedness planning and in making rational decisions regarding development and construction in areas susceptible to seismic slope failure. ?? 2000 Elsevier Science B.V. All rights reserved.

A method for producing digital probabilistic seismic landslide hazard maps; an example from the Los Angeles, California, area

USGS Publications Warehouse

Jibson, Randall W.; Harp, Edwin L.; Michael, John A.

1998-01-01

The 1994 Northridge, California, earthquake is the first earthquake for which we have all of the data sets needed to conduct a rigorous regional analysis of seismic slope instability. These data sets include (1) a comprehensive inventory of triggered landslides, (2) about 200 strong-motion records of the mainshock, (3) 1:24,000-scale geologic mapping of the region, (4) extensive data on engineering properties of geologic units, and (5) high-resolution digital elevation models of the topography. All of these data sets have been digitized and rasterized at 10-m grid spacing in the ARC/INFO GIS platform. Combining these data sets in a dynamic model based on Newmark's permanent-deformation (sliding-block) analysis yields estimates of coseismic landslide displacement in each grid cell from the Northridge earthquake. The modeled displacements are then compared with the digital inventory of landslides triggered by the Northridge earthquake to construct a probability curve relating predicted displacement to probability of failure. This probability function can be applied to predict and map the spatial variability in failure probability in any ground-shaking conditions of interest. We anticipate that this mapping procedure will be used to construct seismic landslide hazard maps that will assist in emergency preparedness planning and in making rational decisions regarding development and construction in areas susceptible to seismic slope failure.

Determine precipitation rates from visible and infrared satellite images of clouds by pattern recognition technique. Progress Report, 1 Jul. 1985 - 31 Mar. 1987 Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Weinman, James A.; Garan, Louis

1987-01-01

A more advanced cloud pattern analysis algorithm was subsequently developed to take the shape and brightness of the various clouds into account in a manner that is more consistent with the human analyst's perception of GOES cloud imagery. The results of that classification scheme were compared with precipitation probabilities observed from ships of opportunity off the U.S. east coast to derive empirical regressions between cloud types and precipitation probability. The cloud morphology was then quantitatively and objectively used to map precipitation probabilities during two winter months during which severe cold air outbreaks were observed over the northwest Atlantic. Precipitation probabilities associated with various cloud types are summarized. Maps of precipitation probability derived from the cloud morphology analysis program for two months and the precipitation probability derived from thirty years of ship observation were observed.

Oil spill contamination probability in the southeastern Levantine basin.

PubMed

Goldman, Ron; Biton, Eli; Brokovich, Eran; Kark, Salit; Levin, Noam

2015-02-15

Recent gas discoveries in the eastern Mediterranean Sea led to multiple operations with substantial economic interest, and with them there is a risk of oil spills and their potential environmental impacts. To examine the potential spatial distribution of this threat, we created seasonal maps of the probability of oil spill pollution reaching an area in the Israeli coastal and exclusive economic zones, given knowledge of its initial sources. We performed simulations of virtual oil spills using realistic atmospheric and oceanic conditions. The resulting maps show dominance of the alongshore northerly current, which causes the high probability areas to be stretched parallel to the coast, increasing contamination probability downstream of source points. The seasonal westerly wind forcing determines how wide the high probability areas are, and may also restrict these to a small coastal region near source points. Seasonal variability in probability distribution, oil state, and pollution time is also discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Trellises and Trellis-Based Decoding Algorithms for Linear Block Codes. Part 3; The Map and Related Decoding Algirithms

NASA Technical Reports Server (NTRS)

Lin, Shu; Fossorier, Marc

1998-01-01

In a coded communication system with equiprobable signaling, MLD minimizes the word error probability and delivers the most likely codeword associated with the corresponding received sequence. This decoding has two drawbacks. First, minimization of the word error probability is not equivalent to minimization of the bit error probability. Therefore, MLD becomes suboptimum with respect to the bit error probability. Second, MLD delivers a hard-decision estimate of the received sequence, so that information is lost between the input and output of the ML decoder. This information is important in coded schemes where the decoded sequence is further processed, such as concatenated coding schemes, multi-stage and iterative decoding schemes. In this chapter, we first present a decoding algorithm which both minimizes bit error probability, and provides the corresponding soft information at the output of the decoder. This algorithm is referred to as the MAP (maximum aposteriori probability) decoding algorithm.

Detection of the nipple in automated 3D breast ultrasound using coronal slab-average-projection and cumulative probability map

NASA Astrophysics Data System (ADS)

Kim, Hannah; Hong, Helen

2014-03-01

We propose an automatic method for nipple detection on 3D automated breast ultrasound (3D ABUS) images using coronal slab-average-projection and cumulative probability map. First, to identify coronal images that appeared remarkable distinction between nipple-areola region and skin, skewness of each coronal image is measured and the negatively skewed images are selected. Then, coronal slab-average-projection image is reformatted from selected images. Second, to localize nipple-areola region, elliptical ROI covering nipple-areola region is detected using Hough ellipse transform in coronal slab-average-projection image. Finally, to separate the nipple from areola region, 3D Otsu's thresholding is applied to the elliptical ROI and cumulative probability map in the elliptical ROI is generated by assigning high probability to low intensity region. False detected small components are eliminated using morphological opening and the center point of detected nipple region is calculated. Experimental results show that our method provides 94.4% nipple detection rate.

Probability of Elevated Volatile Organic Compound (VOC) Concentrations in Groundwater in the Eagle River Watershed Valley-Fill Aquifer, Eagle County, North-Central Colorado, 2006-2007

USGS Publications Warehouse

Rupert, Michael G.; Plummer, Niel

2009-01-01

This raster data set delineates the predicted probability of elevated volatile organic compound (VOC) concentrations in groundwater in the Eagle River watershed valley-fill aquifer, Eagle County, North-Central Colorado, 2006-2007. This data set was developed by a cooperative project between the U.S. Geological Survey, Eagle County, the Eagle River Water and Sanitation District, the Town of Eagle, the Town of Gypsum, and the Upper Eagle Regional Water Authority. This project was designed to evaluate potential land-development effects on groundwater and surface-water resources so that informed land-use and water management decisions can be made. This groundwater probability map and its associated probability maps was developed as follows: (1) A point data set of wells with groundwater quality and groundwater age data was overlaid with thematic layers of anthropogenic (related to human activities) and hydrogeologic data by using a geographic information system to assign each well values for depth to groundwater, distance to major streams and canals, distance to gypsum beds, precipitation, soils, and well depth. These data then were downloaded to a statistical software package for analysis by logistic regression. (2) Statistical models predicting the probability of elevated nitrate concentrations, the probability of unmixed young water (using chlorofluorocarbon-11 concentrations and tritium activities), and the probability of elevated volatile organic compound concentrations were developed using logistic regression techniques. (3) The statistical models were entered into a GIS and the probability map was constructed.

Probability of Elevated Nitrate Concentrations in Groundwater in the Eagle River Watershed Valley-Fill Aquifer, Eagle County, North-Central Colorado, 2006-2007

USGS Publications Warehouse

Rupert, Michael G.; Plummer, Niel

2009-01-01

This raster data set delineates the predicted probability of elevated nitrate concentrations in groundwater in the Eagle River watershed valley-fill aquifer, Eagle County, North-Central Colorado, 2006-2007. This data set was developed by a cooperative project between the U.S. Geological Survey, Eagle County, the Eagle River Water and Sanitation District, the Town of Eagle, the Town of Gypsum, and the Upper Eagle Regional Water Authority. This project was designed to evaluate potential land-development effects on groundwater and surface-water resources so that informed land-use and water management decisions can be made. This groundwater probability map and its associated probability maps was developed as follows: (1) A point data set of wells with groundwater quality and groundwater age data was overlaid with thematic layers of anthropogenic (related to human activities) and hydrogeologic data by using a geographic information system to assign each well values for depth to groundwater, distance to major streams and canals, distance to gypsum beds, precipitation, soils, and well depth. These data then were downloaded to a statistical software package for analysis by logistic regression. (2) Statistical models predicting the probability of elevated nitrate concentrations, the probability of unmixed young water (using chlorofluorocarbon-11 concentrations and tritium activities), and the probability of elevated volatile organic compound concentrations were developed using logistic regression techniques. (3) The statistical models were entered into a GIS and the probability map was constructed.

Point-of-care instrument for monitoring tissue health during skin graft repair

NASA Astrophysics Data System (ADS)

Gurjar, R. S.; Seetamraju, M.; Zhang, J.; Feinberg, S. E.; Wolf, D. E.

2011-06-01

We have developed the necessary theoretical framework and the basic instrumental design parameters to enable mapping of subsurface blood dynamics and tissue oxygenation for patients undergoing skin graft procedures. This analysis forms the basis for developing a simple patch geometry, which can be used to map by diffuse optical techniques blood flow velocity and tissue oxygenation as a function of depth in subsurface tissue.skin graft, diffuse correlation analysis, oxygen saturation.

Intraluminal mapping of tissue viscoelastic properties using laser speckle rheology catheter (Conference Presentation)

NASA Astrophysics Data System (ADS)

Wang, Jing; Hosoda, Masaki; Tshikudi, Diane M.; Nadkarni, Seemantini K.

2016-03-01

A number of disease conditions including coronary atherosclerosis, peripheral artery disease and gastro-intestinal malignancies are associated with alterations in tissue mechanical properties. Laser speckle rheology (LSR) has been demonstrated to provide important information on tissue mechanical properties by analyzing the time scale of temporal speckle intensity fluctuations, which serves as an index of tissue viscoelasticity. In order to measure the mechanical properties of luminal organs in vivo, LSR must be conducted via a miniature endoscope or catheter. Here we demonstrate the capability of an omni-directional LSR catheter to quantify tissue mechanical properties over the entire luminal circumference without the need for rotational motion. Retracting the catheter using a motor-drive assembly enables the reconstruction of cylindrical maps of tissue mechanical properties. The performance of the LSR catheter is tested using a luminal phantom with mechanical moduli that vary in both circumferential and longitudinal directions. 2D cylindrical maps of phantom viscoelastic properties are reconstructed over four quadrants of the coronary circumference simultaneously during catheter pullback. The reconstructed cylindrical maps of the decorrelation time constants easily distinguish the different gel components of the phantom with different viscoelastic moduli. The average values of decorrelation times calculated for each gel component of the phantom show a strong correspondence with the viscoelastic moduli measured via standard mechanical rheometry. These results highlight the capability for cylindrical mapping of tissue viscoelastic properties using LSR in luminal organs using a miniature catheter, thus opening the opportunity for improved diagnosis of several disease conditions.

Automatic mapping of event landslides at basin scale in Taiwan using a Montecarlo approach and synthetic land cover fingerprints

NASA Astrophysics Data System (ADS)

Mondini, Alessandro C.; Chang, Kang-Tsung; Chiang, Shou-Hao; Schlögel, Romy; Notarnicola, Claudia; Saito, Hitoshi

2017-12-01

We propose a framework to systematically generate event landslide inventory maps from satellite images in southern Taiwan, where landslides are frequent and abundant. The spectral information is used to assess the pixel land cover class membership probability through a Maximum Likelihood classifier trained with randomly generated synthetic land cover spectral fingerprints, which are obtained from an independent training images dataset. Pixels are classified as landslides when the calculated landslide class membership probability, weighted by a susceptibility model, is higher than membership probabilities of other classes. We generated synthetic fingerprints from two FORMOSAT-2 images acquired in 2009 and tested the procedure on two other images, one in 2005 and the other in 2009. We also obtained two landslide maps through manual interpretation. The agreement between the two sets of inventories is given by the Cohen's k coefficients of 0.62 and 0.64, respectively. This procedure can now classify a new FORMOSAT-2 image automatically facilitating the production of landslide inventory maps.

Magnetic mapping of iron in rodent spleen

PubMed Central

Blissett, Angela R.; Ollander, Brooke; Penn, Brittany; McTigue, Dana M.; Agarwal, Gunjan

2016-01-01

Evaluation of iron distribution and density in biological tissues is important to understand the pathogenesis of a variety of diseases and the fate of exogenously administered iron-based carriers and contrast agents. Iron distribution in tissues is typically characterized via histochemical (Perl’s) stains or immunohistochemistry for ferritin, the major iron storage protein. A more accurate mapping of iron can be achieved via ultrastructural transmission electron microscopy (TEM) based techniques, which involve stringent sample preparation conditions. In this study, we elucidate the capability of magnetic force microscopy (MFM) as a label-free technique to map iron at the nanoscale level in rodent spleen tissue. We complemented and compared our MFM results with those obtained using Perl’s staining and TEM. Our results show how MFM mapping corresponded to sizes of iron-rich lysosomes at a resolution comparable to that of TEM. In addition MFM is compatible with tissue sections commonly prepared for routine histology. PMID:27890658

Method for removing atomic-model bias in macromolecular crystallography

DOEpatents

Terwilliger, Thomas C [Santa Fe, NM

2006-08-01

Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.

Anatomy-guided joint tissue segmentation and topological correction for 6-month infant brain MRI with risk of autism.

PubMed

Wang, Li; Li, Gang; Adeli, Ehsan; Liu, Mingxia; Wu, Zhengwang; Meng, Yu; Lin, Weili; Shen, Dinggang

2018-06-01

Tissue segmentation of infant brain MRIs with risk of autism is critically important for characterizing early brain development and identifying biomarkers. However, it is challenging due to low tissue contrast caused by inherent ongoing myelination and maturation. In particular, at around 6 months of age, the voxel intensities in both gray matter and white matter are within similar ranges, thus leading to the lowest image contrast in the first postnatal year. Previous studies typically employed intensity images and tentatively estimated tissue probabilities to train a sequence of classifiers for tissue segmentation. However, the important prior knowledge of brain anatomy is largely ignored during the segmentation. Consequently, the segmentation accuracy is still limited and topological errors frequently exist, which will significantly degrade the performance of subsequent analyses. Although topological errors could be partially handled by retrospective topological correction methods, their results may still be anatomically incorrect. To address these challenges, in this article, we propose an anatomy-guided joint tissue segmentation and topological correction framework for isointense infant MRI. Particularly, we adopt a signed distance map with respect to the outer cortical surface as anatomical prior knowledge, and incorporate such prior information into the proposed framework to guide segmentation in ambiguous regions. Experimental results on the subjects acquired from National Database for Autism Research demonstrate the effectiveness to topological errors and also some levels of robustness to motion. Comparisons with the state-of-the-art methods further demonstrate the advantages of the proposed method in terms of both segmentation accuracy and topological correctness. © 2018 Wiley Periodicals, Inc.

Spatial vent opening probability map of El Hierro Island (Canary Islands, Spain)

NASA Astrophysics Data System (ADS)

Becerril, Laura; Cappello, Annalisa; Galindo, Inés; Neri, Marco; Del Negro, Ciro

2013-04-01

The assessment of the probable spatial distribution of new eruptions is useful to manage and reduce the volcanic risk. It can be achieved in different ways, but it becomes especially hard when dealing with volcanic areas less studied, poorly monitored and characterized by a low frequent activity, as El Hierro. Even though it is the youngest of the Canary Islands, before the 2011 eruption in the "Las Calmas Sea", El Hierro had been the least studied volcanic Island of the Canaries, with more historically devoted attention to La Palma, Tenerife and Lanzarote. We propose a probabilistic method to build the susceptibility map of El Hierro, i.e. the spatial distribution of vent opening for future eruptions, based on the mathematical analysis of the volcano-structural data collected mostly on the Island and, secondly, on the submerged part of the volcano, up to a distance of ~10-20 km from the coast. The volcano-structural data were collected through new fieldwork measurements, bathymetric information, and analysis of geological maps, orthophotos and aerial photographs. They have been divided in different datasets and converted into separate and weighted probability density functions, which were then included in a non-homogeneous Poisson process to produce the volcanic susceptibility map. Future eruptive events on El Hierro is mainly concentrated on the rifts zones, extending also beyond the shoreline. The major probabilities to host new eruptions are located on the distal parts of the South and West rifts, with the highest probability reached in the south-western area of the West rift. High probabilities are also observed in the Northeast and South rifts, and the submarine parts of the rifts. This map represents the first effort to deal with the volcanic hazard at El Hierro and can be a support tool for decision makers in land planning, emergency plans and civil defence actions.

Streamflow distribution maps for the Cannon River drainage basin, southeast Minnesota, and the St. Louis River drainage basin, northeast Minnesota

USGS Publications Warehouse

Smith, Erik A.; Sanocki, Chris A.; Lorenz, David L.; Jacobsen, Katrin E.

2017-12-27

Streamflow distribution maps for the Cannon River and St. Louis River drainage basins were developed by the U.S. Geological Survey, in cooperation with the Legislative-Citizen Commission on Minnesota Resources, to illustrate relative and cumulative streamflow distributions. The Cannon River was selected to provide baseline data to assess the effects of potential surficial sand mining, and the St. Louis River was selected to determine the effects of ongoing Mesabi Iron Range mining. Each drainage basin (Cannon, St. Louis) was subdivided into nested drainage basins: the Cannon River was subdivided into 152 nested drainage basins, and the St. Louis River was subdivided into 353 nested drainage basins. For each smaller drainage basin, the estimated volumes of groundwater discharge (as base flow) and surface runoff flowing into all surface-water features were displayed under the following conditions: (1) extreme low-flow conditions, comparable to an exceedance-probability quantile of 0.95; (2) low-flow conditions, comparable to an exceedance-probability quantile of 0.90; (3) a median condition, comparable to an exceedance-probability quantile of 0.50; and (4) a high-flow condition, comparable to an exceedance-probability quantile of 0.02.Streamflow distribution maps were developed using flow-duration curve exceedance-probability quantiles in conjunction with Soil-Water-Balance model outputs; both the flow-duration curve and Soil-Water-Balance models were built upon previously published U.S. Geological Survey reports. The selected streamflow distribution maps provide a proactive water management tool for State cooperators by illustrating flow rates during a range of hydraulic conditions. Furthermore, after the nested drainage basins are highlighted in terms of surface-water flows, the streamflows can be evaluated in the context of meeting specific ecological flows under different flow regimes and potentially assist with decisions regarding groundwater and surface-water appropriations. Presented streamflow distribution maps are foundational work intended to support the development of additional streamflow distribution maps that include statistical constraints on the selected flow conditions.

Three-Dimensional Optical Mapping of Nanoparticle Distribution in Intact Tissues.

PubMed

Sindhwani, Shrey; Syed, Abdullah Muhammad; Wilhelm, Stefan; Glancy, Dylan R; Chen, Yih Yang; Dobosz, Michael; Chan, Warren C W

2016-05-24

The role of tissue architecture in mediating nanoparticle transport, targeting, and biological effects is unknown due to the lack of tools for imaging nanomaterials in whole organs. Here, we developed a rapid optical mapping technique to image nanomaterials in intact organs ex vivo and in three-dimensions (3D). We engineered a high-throughput electrophoretic flow device to simultaneously transform up to 48 tissues into optically transparent structures, allowing subcellular imaging of nanomaterials more than 1 mm deep into tissues which is 25-fold greater than current techniques. A key finding is that nanomaterials can be retained in the processed tissue by chemical cross-linking of surface adsorbed serum proteins to the tissue matrix, which enables nanomaterials to be imaged with respect to cells, blood vessels, and other structures. We developed a computational algorithm to analyze and quantitatively map nanomaterial distribution. This method can be universally applied to visualize the distribution and interactions of materials in whole tissues and animals including such applications as the imaging of nanomaterials, tissue engineered constructs, and biosensors within their intact biological environment.

Investigation of an Optimum Detection Scheme for a Star-Field Mapping System

NASA Technical Reports Server (NTRS)

Aldridge, M. D.; Credeur, L.

1970-01-01

An investigation was made to determine the optimum detection scheme for a star-field mapping system that uses coded detection resulting from starlight shining through specially arranged multiple slits of a reticle. The computer solution of equations derived from a theoretical model showed that the greatest probability of detection for a given star and background intensity occurred with the use of a single transparent slit. However, use of multiple slits improved the system's ability to reject the detection of undesirable lower intensity stars, but only by decreasing the probability of detection for lower intensity stars to be mapped. Also, it was found that the coding arrangement affected the root-mean-square star-position error and that detection is possible with error in the system's detected spin rate, though at a reduced probability.

Higher-dimensional attractors with absolutely continuous invariant probability

NASA Astrophysics Data System (ADS)

Bocker, Carlos; Bortolotti, Ricardo

2018-05-01

Consider a dynamical system given by , where E is a linear expanding map of , C is a linear contracting map of and f is in . We provide sufficient conditions for E that imply the existence of an open set of pairs for which the corresponding dynamic T admits a unique absolutely continuous invariant probability. A geometrical characteristic of transversality between self-intersections of images of is present in the dynamic of the maps in . In addition, we give a condition between E and C under which it is possible to perturb f to obtain a pair in .

Mapping fire probability and severity in a Mediterranean area using different weather and fuel moisture scenarios

NASA Astrophysics Data System (ADS)

Arca, B.; Salis, M.; Bacciu, V.; Duce, P.; Pellizzaro, G.; Ventura, A.; Spano, D.

2009-04-01

Although in many countries lightning is the main cause of ignition, in the Mediterranean Basin the forest fires are predominantly ignited by arson, or by human negligence. The fire season peaks coincide with extreme weather conditions (mainly strong winds, hot temperatures, low atmospheric water vapour content) and high tourist presence. Many works reported that in the Mediterranean Basin the projected impacts of climate change will cause greater weather variability and extreme weather conditions, with drier and hotter summers and heat waves. At long-term scale, climate changes could affect the fuel load and the dead/live fuel ratio, and therefore could change the vegetation flammability. At short-time scale, the increase of extreme weather events could directly affect fuel water status, and it could increase large fire occurrence. In this context, detecting the areas characterized by both high probability of large fire occurrence and high fire severity could represent an important component of the fire management planning. In this work we compared several fire probability and severity maps (fire occurrence, rate of spread, fireline intensity, flame length) obtained for a study area located in North Sardinia, Italy, using FlamMap simulator (USDA Forest Service, Missoula). FlamMap computes the potential fire behaviour characteristics over a defined landscape for given weather, wind and fuel moisture data. Different weather and fuel moisture scenarios were tested to predict the potential impact of climate changes on fire parameters. The study area, characterized by a mosaic of urban areas, protected areas, and other areas subject to anthropogenic disturbances, is mainly composed by fire-prone Mediterranean maquis. The input themes needed to run FlamMap were input as grid of 10 meters; the wind data, obtained using a computational fluid-dynamic model, were inserted as gridded file, with a resolution of 50 m. The analysis revealed high fire probability and severity in most of the areas, and therefore a high potential danger. The FlamMap outputs and the derived fire probability maps can be used in decision support systems for fire spread and behaviour and for fire danger assessment with actual and future fire regimes.

Using widely spaced observations of land use, forest attributes, and intrusions to map resource potential and human impact probability

Treesearch

Victor A. Rudis

2000-01-01

Scant information exists about the spatial extent of human impact on forest resource supplies, i.e., depreciative and nonforest uses. I used observations of ground-sampled land use and intrusions on forest land to map the probability of resource use and human impact for broad areas. Data came from a seven-state survey region (Alabama, Arkansas, Louisiana, Mississippi,...

Using widely spaced observations of land use, forest attributes, and intrusions to map resource potential and human impact probability

Treesearch

Victor A. Rudis

2000-01-01

Scant information exists about the spatial extent of human impact on forest resource supplies, i.e., depreciative and nonforest uses. I used observations of ground-sampled land use and intrusions on forest land to map the probability of resource use and human impact for broad areas. Data came from a seven State survey region (Alabama, Arkansas, Louisiana, Mississippi,...

Incorporating Functional Annotations for Fine-Mapping Causal Variants in a Bayesian Framework Using Summary Statistics.

PubMed

Chen, Wenan; McDonnell, Shannon K; Thibodeau, Stephen N; Tillmans, Lori S; Schaid, Daniel J

2016-11-01

Functional annotations have been shown to improve both the discovery power and fine-mapping accuracy in genome-wide association studies. However, the optimal strategy to incorporate the large number of existing annotations is still not clear. In this study, we propose a Bayesian framework to incorporate functional annotations in a systematic manner. We compute the maximum a posteriori solution and use cross validation to find the optimal penalty parameters. By extending our previous fine-mapping method CAVIARBF into this framework, we require only summary statistics as input. We also derived an exact calculation of Bayes factors using summary statistics for quantitative traits, which is necessary when a large proportion of trait variance is explained by the variants of interest, such as in fine mapping expression quantitative trait loci (eQTL). We compared the proposed method with PAINTOR using different strategies to combine annotations. Simulation results show that the proposed method achieves the best accuracy in identifying causal variants among the different strategies and methods compared. We also find that for annotations with moderate effects from a large annotation pool, screening annotations individually and then combining the top annotations can produce overly optimistic results. We applied these methods on two real data sets: a meta-analysis result of lipid traits and a cis-eQTL study of normal prostate tissues. For the eQTL data, incorporating annotations significantly increased the number of potential causal variants with high probabilities. Copyright © 2016 by the Genetics Society of America.

Deep-tissue temperature mapping by multi-illumination photoacoustic tomography aided by a diffusion optical model: a numerical study

NASA Astrophysics Data System (ADS)

Zhou, Yuan; Tang, Eric; Luo, Jianwen; Yao, Junjie

2018-01-01

Temperature mapping during thermotherapy can help precisely control the heating process, both temporally and spatially, to efficiently kill the tumor cells and prevent the healthy tissues from heating damage. Photoacoustic tomography (PAT) has been used for noninvasive temperature mapping with high sensitivity, based on the linear correlation between the tissue's Grüneisen parameter and temperature. However, limited by the tissue's unknown optical properties and thus the optical fluence at depths beyond the optical diffusion limit, the reported PAT thermometry usually takes a ratiometric measurement at different temperatures and thus cannot provide absolute measurements. Moreover, ratiometric measurement over time at different temperatures has to assume that the tissue's optical properties do not change with temperatures, which is usually not valid due to the temperature-induced hemodynamic changes. We propose an optical-diffusion-model-enhanced PAT temperature mapping that can obtain the absolute temperature distribution in deep tissue, without the need of multiple measurements at different temperatures. Based on the initial acoustic pressure reconstructed from multi-illumination photoacoustic signals, both the local optical fluence and the optical parameters including absorption and scattering coefficients are first estimated by the optical-diffusion model, then the temperature distribution is obtained from the reconstructed Grüneisen parameters. We have developed a mathematic model for the multi-illumination PAT of absolute temperatures, and our two-dimensional numerical simulations have shown the feasibility of this new method. The proposed absolute temperature mapping method may set the technical foundation for better temperature control in deep tissue in thermotherapy.

Probability of Unmixed Young Groundwater (defined using chlorofluorocarbon-11 concentrations and tritium activities) in the Eagle River Watershed Valley-Fill Aquifer, Eagle County, North-Central Colorado, 2006-2007

USGS Publications Warehouse

Rupert, Michael G.; Plummer, Niel

2009-01-01

This raster data set delineates the predicted probability of unmixed young groundwater (defined using chlorofluorocarbon-11 concentrations and tritium activities) in groundwater in the Eagle River watershed valley-fill aquifer, Eagle County, North-Central Colorado, 2006-2007. This data set was developed by a cooperative project between the U.S. Geological Survey, Eagle County, the Eagle River Water and Sanitation District, the Town of Eagle, the Town of Gypsum, and the Upper Eagle Regional Water Authority. This project was designed to evaluate potential land-development effects on groundwater and surface-water resources so that informed land-use and water management decisions can be made. This groundwater probability map and its associated probability maps were developed as follows: (1) A point data set of wells with groundwater quality and groundwater age data was overlaid with thematic layers of anthropogenic (related to human activities) and hydrogeologic data by using a geographic information system to assign each well values for depth to groundwater, distance to major streams and canals, distance to gypsum beds, precipitation, soils, and well depth. These data then were downloaded to a statistical software package for analysis by logistic regression. (2) Statistical models predicting the probability of elevated nitrate concentrations, the probability of unmixed young water (using chlorofluorocarbon-11 concentrations and tritium activities), and the probability of elevated volatile organic compound concentrations were developed using logistic regression techniques. (3) The statistical models were entered into a GIS and the probability map was constructed.

Is there more valuable information in PWI datasets for a voxel-wise acute ischemic stroke tissue outcome prediction than what is represented by typical perfusion maps?

NASA Astrophysics Data System (ADS)

Forkert, Nils Daniel; Siemonsen, Susanne; Dalski, Michael; Verleger, Tobias; Kemmling, Andre; Fiehler, Jens

2014-03-01

The acute ischemic stroke is a leading cause for death and disability in the industry nations. In case of a present acute ischemic stroke, the prediction of the future tissue outcome is of high interest for the clinicians as it can be used to support therapy decision making. Within this context, it has already been shown that the voxel-wise multi-parametric tissue outcome prediction leads to more promising results compared to single channel perfusion map thresholding. Most previously published multi-parametric predictions employ information from perfusion maps derived from perfusion-weighted MRI together with other image sequences such as diffusion-weighted MRI. However, it remains unclear if the typically calculated perfusion maps used for this purpose really include all valuable information from the PWI dataset for an optimal tissue outcome prediction. To investigate this problem in more detail, two different methods to predict tissue outcome using a k-nearest-neighbor approach were developed in this work and evaluated based on 18 datasets of acute stroke patients with known tissue outcome. The first method integrates apparent diffusion coefficient and perfusion parameter (Tmax, MTT, CBV, CBF) information for the voxel-wise prediction, while the second method employs also apparent diffusion coefficient information but the complete perfusion information in terms of the voxel-wise residue functions instead of the perfusion parameter maps for the voxel-wise prediction. Overall, the comparison of the results of the two prediction methods for the 18 patients using a leave-one-out cross validation revealed no considerable differences. Quantitatively, the parameter-based prediction of tissue outcome led to a mean Dice coefficient of 0.474, while the prediction using the residue functions led to a mean Dice coefficient of 0.461. Thus, it may be concluded from the results of this study that the perfusion parameter maps typically derived from PWI datasets include all valuable perfusion information required for a voxel-based tissue outcome prediction, while the complete analysis of the residue functions does not add further benefits for the voxel-wise tissue outcome prediction and is also computationally more expensive.

Quantitative Susceptibility Mapping of Human Brain Reflects Spatial Variation in Tissue Composition

PubMed Central

Li, Wei; Wu, Bing; Liu, Chunlei

2011-01-01

Image phase from gradient echo MRI provides a unique contrast that reflects brain tissue composition variations, such as iron and myelin distribution. Phase imaging is emerging as a powerful tool for the investigation of functional brain anatomy and disease diagnosis. However, the quantitative value of phase is compromised by its nonlocal and orientation dependent properties. There is an increasing need for reliable quantification of magnetic susceptibility, the intrinsic property of tissue. In this study, we developed a novel and accurate susceptibility mapping method that is also phase-wrap insensitive. The proposed susceptibility mapping method utilized two complementary equations: (1) the Fourier relationship of phase and magnetic susceptibility; and (2) the first-order partial derivative of the first equation in the spatial frequency domain. In numerical simulation, this method reconstructed the susceptibility map almost free of streaking artifact. Further, the iterative implementation of this method allowed for high quality reconstruction of susceptibility maps of human brain in vivo. The reconstructed susceptibility map provided excellent contrast of iron-rich deep nuclei and white matter bundles from surrounding tissues. Further, it also revealed anisotropic magnetic susceptibility in brain white matter. Hence, the proposed susceptibility mapping method may provide a powerful tool for the study of brain physiology and pathophysiology. Further elucidation of anisotropic magnetic susceptibility in vivo may allow us to gain more insight into the white matter microarchitectures. PMID:21224002

Emergency Assessment of Debris-Flow Hazards from Basins Burned by the Piru, Simi, and Verdale Fires of 2003, Southern California

USGS Publications Warehouse

Cannon, Susan H.; Gartner, Joseph E.; Rupert, Michael G.; Michael, John A.

2003-01-01

These maps present preliminary assessments of the probability of debris-flow activity and estimates of peak discharges that can potentially be generated by debris-flows issuing from basins burned by the Piru, Simi and Verdale Fires of October 2003 in southern California in response to the 25-year, 10-year, and 2-year 1-hour rain storms. The probability maps are based on the application of a logistic multiple regression model that describes the percent chance of debris-flow production from an individual basin as a function of burned extent, soil properties, basin gradients and storm rainfall. The peak discharge maps are based on application of a multiple-regression model that can be used to estimate debris-flow peak discharge at a basin outlet as a function of basin gradient, burn extent, and storm rainfall. Probabilities of debris-flow occurrence for the Piru Fire range between 2 and 94% and estimates of debris flow peak discharges range between 1,200 and 6,640 ft3/s (34 to 188 m3/s). Basins burned by the Simi Fire show probabilities for debris-flow occurrence between 1 and 98%, and peak discharge estimates between 1,130 and 6,180 ft3/s (32 and 175 m3/s). The probabilities for debris-flow activity calculated for the Verdale Fire range from negligible values to 13%. Peak discharges were not estimated for this fire because of these low probabilities. These maps are intended to identify those basins that are most prone to the largest debris-flow events and provide information for the preliminary design of mitigation measures and for the planning of evacuation timing and routes.

Common spectrum of polypeptides occurs in secretion granule membranes of different exocrine glands

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

Cameron, R.S.; Cameron, P.L.; Castle, J.D.

1986-10-01

A highly purified membrane preparation from rat parotid secretion granules has been used as a comparative probe to examine the extent of compositional overlap in granule membranes of three other exocrine secretory tissues - pancreatic, lacrimal, and submandibular - from several standpoints. First, indirect immunofluorescent studies using a polyclonal polyspecific anti-parotid granule membrane antiserum has indicated a selective staining of granule membrane profiles in all acinar cells of all tissues. Second, highly purified granule membrane subfractions have been isolated from each exocrine tissue; comparative two-dimensional (isoelectric focusing; SDS) PAGE of radioiodinated granule membranes has identified 10-15 polypeptides of identical pImore » and apparent molecular mass. These species are likely to be integral membrane components since they are not extracted by either saponin-sodium sulfate or sodium carbonate (pH 11.5) treatments, and they do not have counterparts in the granule content. Finally, the identity among selected parotid and pancreatic radioiodinated granule membrane polypeptides has been documented using two-dimensional peptide mapping of chymotryptic and tryptic digests. These findings clearly indicate that exocrine secretory granules, irrespective of the nature of stored secretion, comprise a type of vesicular carrier with a common (and probably refined) membrane composition. Conceivably, the polypeptides identified carry out general functions related to exocrine secretion.« less

NIH scientists map gene changes driving tumors in common pediatric soft-tissue cancer

Cancer.gov

Scientists have mapped the genetic changes that drive tumors in rhabdomyosarcoma, a pediatric soft-tissue cancer, and found that the disease is characterized by two distinct genotypes. The genetic alterations identified in this malignancy could be useful

Mapping tissue oxygen in vivo by photoacoustic lifetime imaging

NASA Astrophysics Data System (ADS)

Shao, Qi; Morgounova, Ekaterina; Choi, Jeung-Hwan; Jiang, Chunlan; Bischof, John; Ashkenazi, Shai

2013-03-01

Oxygen plays a key role in the energy metabolism of living organisms. Any imbalance in the oxygen levels will affect the metabolic homeostasis and lead to pathophysiological diseases. Hypoxia, a status of low tissue oxygen, is a key factor in tumor biology as it is highly prominent in tumor tissues. However, clinical tools for assessing tissue oxygenation are limited. The gold standard is polarographic needle electrode which is invasive and not capable of mapping (imaging) the oxygen content in tissue. We applied the method of photoacoustic lifetime imaging (PALI) of oxygen-sensitive dye to small animal tissue hypoxia research. PALI is new technology for direct, non-invasive imaging of oxygen. The technique is based on mapping the oxygen-dependent transient optical absorption of Methylene Blue (MB) by pump-probe photoacoustic imaging. Our studies show the feasibility of imaging of dissolved oxygen distribution in phantoms. In vivo experiments demonstrate that the hypoxia region is consistent with the site of subcutaneously xenografted prostate tumor in mice with adequate spatial resolution and penetration depth.

Spatial mapping of metals in tissue-sections using combination of mass-spectrometry and histology through image registration

NASA Astrophysics Data System (ADS)

Anyz, Jiri; Vyslouzilova, Lenka; Vaculovic, Tomas; Tvrdonova, Michaela; Kanicky, Viktor; Haase, Hajo; Horak, Vratislav; Stepankova, Olga; Heger, Zbynek; Adam, Vojtech

2017-01-01

We describe a new procedure for the parallel mapping of selected metals in histologically characterized tissue samples. Mapping is achieved via image registration of digital data obtained from two neighbouring cryosections by scanning the first as a histological sample and subjecting the second to laser ablation inductively coupled plasma mass spectrometry. This computer supported procedure enables determination of the distribution and content of metals of interest directly in the chosen histological zones and represents a substantial improvement over the standard approach, which determines these values in tissue homogenates or whole tissue sections. The potential of the described procedure was demonstrated in a pilot study that analysed Zn and Cu levels in successive development stages of pig melanoma tissue using MeLiM (Melanoma-bearing-Libechov-Minipig) model. We anticipate that the procedure could be useful for a complex understanding of the role that the spatial distribution of metals plays within tissues affected by pathological states including cancer.

Spatial mapping of metals in tissue-sections using combination of mass-spectrometry and histology through image registration

PubMed Central

Anyz, Jiri; Vyslouzilova, Lenka; Vaculovic, Tomas; Tvrdonova, Michaela; Kanicky, Viktor; Haase, Hajo; Horak, Vratislav; Stepankova, Olga; Heger, Zbynek; Adam, Vojtech

2017-01-01

We describe a new procedure for the parallel mapping of selected metals in histologically characterized tissue samples. Mapping is achieved via image registration of digital data obtained from two neighbouring cryosections by scanning the first as a histological sample and subjecting the second to laser ablation inductively coupled plasma mass spectrometry. This computer supported procedure enables determination of the distribution and content of metals of interest directly in the chosen histological zones and represents a substantial improvement over the standard approach, which determines these values in tissue homogenates or whole tissue sections. The potential of the described procedure was demonstrated in a pilot study that analysed Zn and Cu levels in successive development stages of pig melanoma tissue using MeLiM (Melanoma-bearing-Libechov-Minipig) model. We anticipate that the procedure could be useful for a complex understanding of the role that the spatial distribution of metals plays within tissues affected by pathological states including cancer. PMID:28071735

Distribution and probable physiological role of esterases in reproductive, digestive, and fat-body tissues of the adult cotton boll weevil, Anthonomus grandis Boh.

PubMed

Jones, B R; Bancroft, H R

1986-06-01

Polyacrylamide gel electrophoresis was used to examine gut, Malpighian tube, fat-body, testes, and ovarioles tissues of the adult cotton boll weevil, Anthonomus grandis Boh. Esterases for which the inheritance has been reported previously by Terranova using whole-body homogenates were detected in dissected tissues and the probable physiological function of each allozyme is suggested. EST-1 occurs most frequently in ovarioles and female fat bodies. EST-2 is most often found in fat bodies and may be important in lipid turnover. No sex difference was observed. EST-3S is found in fat bodies and reproductive tissue, while EST-3F is always located in gut tissues, indicating that EST-3 is not controlled by a single autosomal locus with two codominant alleles as previously reported. EST-4, the most abundant esterase, can be detected in gut tissue at any age and is probably involved in digestion. EST-5 contains four allozymes which appear most frequently in testes and may be important during reproduction.

Spatial analysis of land use and shallow groundwater vulnerability in the watershed adjacent to Assateague Island National Seashore, Maryland and Virginia, USA

USGS Publications Warehouse

LaMotte, A.E.; Greene, E.A.

2007-01-01

Spatial relations between land use and groundwater quality in the watershed adjacent to Assateague Island National Seashore, Maryland and Virginia, USA were analyzed by the use of two spatial models. One model used a logit analysis and the other was based on geostatistics. The models were developed and compared on the basis of existing concentrations of nitrate as nitrogen in samples from 529 domestic wells. The models were applied to produce spatial probability maps that show areas in the watershed where concentrations of nitrate in groundwater are likely to exceed a predetermined management threshold value. Maps of the watershed generated by logistic regression and probability kriging analysis showing where the probability of nitrate concentrations would exceed 3 mg/L (>0.50) compared favorably. Logistic regression was less dependent on the spatial distribution of sampled wells, and identified an additional high probability area within the watershed that was missed by probability kriging. The spatial probability maps could be used to determine the natural or anthropogenic factors that best explain the occurrence and distribution of elevated concentrations of nitrate (or other constituents) in shallow groundwater. This information can be used by local land-use planners, ecologists, and managers to protect water supplies and identify land-use planning solutions and monitoring programs in vulnerable areas. ?? 2006 Springer-Verlag.

Evaluation of specimen preparation techniques for micro-PIXE localisation of elements in hyperaccumulating plants

NASA Astrophysics Data System (ADS)

Kachenko, Anthony G.; Siegele, Rainer; Bhatia, Naveen P.; Singh, Balwant; Ionescu, Mihail

2008-04-01

Hybanthus floribundus subsp. floribundus, a rare Australian Ni-hyperaccumulating shrub and Pityrogramma calomelanos var. austroamericana, an Australian naturalized As-hyperaccumulating fern are promising species for use in phytoremediation of contaminated sites. Micro-proton-induced X-ray emission (μ-PIXE) spectroscopy was used to map the elemental distribution of the accumulated metal(loid)s, Ca and K in leaf or pinnule tissues of the two plant species. Samples were prepared by two contrasting specimen preparation techniques: freeze-substitution in tetrahydrofuran (THF) and freeze-drying. The specimens were analysed to compare the suitability of each technique in preserving (i) the spatial elemental distribution and (ii) the tissue structure of the specimens. Further, the μ-PIXE results were compared with concentration of elements in the bulk tissue obtained by ICP-AES analysis. In H. floribundus subsp. floribundus, μ-PIXE analysis revealed Ni, Ca and K concentrations in freeze-dried leaf tissues were at par with bulk tissue concentrations. Elemental distribution maps illustrated that Ni was preferentially localised in the adaxial epidermal tissues (1% DW) and least concentration was found in spongy mesophyll tissues (0.53% DW). Conversely, elemental distribution maps of THF freeze-substituted tissues indicated significantly lower Ni, Ca and K concentrations than freeze-dried specimens and bulk tissue concentrations. Moreover, Ni concentrations were uniform across the whole specimen and no localisation was observed. In P. calomelanos var. austroamericana freeze-dried pinnule tissues, μ-PIXE revealed statistically similar As, Ca and K concentrations as compared to bulk tissue concentrations. Elemental distribution maps showed that As localisation was relatively uniform across the whole specimen. Once again, THF freeze-substituted tissues revealed a significant loss of As compared to freeze-dried specimens and the concentrations obtained by bulk tissue analysis. The results demonstrate that freeze-drying is a suitable sample preparation technique to study elemental distribution of ions in H. floribundus and P. calomelanos plant tissues using μ-PIXE spectroscopy. Furthermore, cellular structure was preserved in samples prepared using this technique.

Comparative evaluation of diagnostic tests for the detection of Mycobacterium avium subsp. paratuberculosis in the tissues of sheep affected with distinct pathology of paratuberculosis.

PubMed

Sonawane, Ganesh G; Tripathi, Bhupendra N

2016-12-01

Paratuberculosis or Johne's disease is a chronic infectious granulomatous enteritis, mainly of cattle, sheep, goats, and other domestic and wild animals caused by Mycobacterium avium subsp. paratuberculosis (MAP). Currently, MAP has been recognized as an important animal pathogen with significant zoonotic and public health concerns. The early detection of infected animals using suitable diagnostic methods helps in developing control and preventive strategies for the herd. Therefore, the present study was aimed to determine the comparative efficacy of certain diagnostic methods used in the identification and confirmation of MAP in the ovine tissues with distinct pathology of paratuberculosis. The ileum and mesenteric lymph node (MLN) tissues were collected from 38 sheep infected with paratuberculosis from organized farms of Rajasthan. These animals were further classified as paucibacillary (PB; n=15) or multibacillary (MB; n=23) on the basis of histopathological findings and mycobacterial loads. The ileum and MLN tissues of these animals were subjected to IS900 and 251 gene polymerase chain reaction (PCR) and bacterial culture. The tissue sections from MB, PB, and uninfected control sheep groups were stained using indirect immunoperoxidase technique (IPT) and Ziehl-Neelsen (ZN) method. On bacterial culture examination of the ileum and MLN tissues using Herrold's egg yolk medium, MAP was isolated in 14 (60.9%) MB and 5 (33.3%) PB sheep. Of 38 sheep, IS900 PCR detected 21 (55.2%) positive for MAP, of which 19 (82.6%) were MB and 2 (13.3%) were PB sheep. Similarly, 251 gene PCR detected 25 (65.7%) sheep positive for MAP infection, of which 21 (91.3%) were MB and 4 (27%) were PB sheep. Thus, 251 gene PCR was found superior to IS900 PCR in the detection of MAP from the tissues. In PB sheep, IPT and ZN tests were positive in 87.5% and 50% of ileum sections and 70% and 37.5% in MLN sections, respectively. In MB sheep, IPT and ZN tests detected all animals as positive for MAP organisms or antigen and had equal sensitivity in the detection of MAP. The overall sensitivity of IPT was found superior (95%) to ZN staining (80%) in the demonstration of acid-fast bacteria or its antigen in the tissues. The sensitivity of all the tests in the detection of MAP was lower in PB sheep than in MB sheep. Bacterial culture detected MAP in only 50% of sheep and was found less sensitive than other tests used in the present study. Comparing the overall sensitivity of both the PCR assays, 251 gene PCR was found superior to IS900 gene PCR. The sensitivity of IPT was found superior (95%) to the ZN staining (80%) in the demonstration of acid-fast bacteria in the tissues. In the present study, IPT was found superior in the detection of MAP in PB and MB form of ovine paratuberculosis. This test can be used in the confirmation of post mortem diagnosis and research of paratuberculosis along with histopathology. However, 251 gene PCR assay was found easier to perform than IPT and could be used as paratuberculosis screening test in endemic sheep farms for blood and fecal samples. Copyright © 2016.

Probabilistic, Seismically-Induced Landslide Hazard Mapping of Western Oregon

NASA Astrophysics Data System (ADS)

Olsen, M. J.; Sharifi Mood, M.; Gillins, D. T.; Mahalingam, R.

2015-12-01

Earthquake-induced landslides can generate significant damage within urban communities by damaging structures, obstructing lifeline connection routes and utilities, generating various environmental impacts, and possibly resulting in loss of life. Reliable hazard and risk maps are important to assist agencies in efficiently allocating and managing limited resources to prepare for such events. This research presents a new methodology in order to communicate site-specific landslide hazard assessments in a large-scale, regional map. Implementation of the proposed methodology results in seismic-induced landslide hazard maps that depict the probabilities of exceeding landslide displacement thresholds (e.g. 0.1, 0.3, 1.0 and 10 meters). These maps integrate a variety of data sources including: recent landslide inventories, LIDAR and photogrammetric topographic data, geology map, mapped NEHRP site classifications based on available shear wave velocity data in each geologic unit, and USGS probabilistic seismic hazard curves. Soil strength estimates were obtained by evaluating slopes present along landslide scarps and deposits for major geologic units. Code was then developed to integrate these layers to perform a rigid, sliding block analysis to determine the amount and associated probabilities of displacement based on each bin of peak ground acceleration in the seismic hazard curve at each pixel. The methodology was applied to western Oregon, which contains weak, weathered, and often wet soils at steep slopes. Such conditions have a high landslide hazard even without seismic events. A series of landslide hazard maps highlighting the probabilities of exceeding the aforementioned thresholds were generated for the study area. These output maps were then utilized in a performance based design framework enabling them to be analyzed in conjunction with other hazards for fully probabilistic-based hazard evaluation and risk assessment. a) School of Civil and Construction Engineering, Oregon State University, Corvallis, OR 97331, USA

Regional Mapping of Gas Uptake by Blood and Tissue in the Human Lung using Hyperpolarized Xenon-129 MRI

PubMed Central

Qing, Kun; Ruppert, Kai; Jiang, Yun; Mata, Jaime F.; Miller, G. Wilson; Shim, Y. Michael; Wang, Chengbo; Ruset, Iulian C.; Hersman, F. William; Altes, Talissa A.; Mugler, John P.

2013-01-01

Purpose To develop a breath-hold acquisition for regional mapping of ventilation and the fractions of hyperpolarized xenon-129 (Xe129) dissolved in tissue (lung parenchyma and plasma) and red blood cells (RBCs), and to perform an exploratory study to characterize data obtained in human subjects. Materials and Methods A three-dimensional, multi-echo, radial-trajectory pulse sequence was developed to obtain ventilation (gaseous Xe129), tissue and RBC images in healthy subjects, smokers and asthmatics. Signal ratios (total dissolved Xe129 to gas, tissue-to-gas, RBC-to-gas and RBC-to-tissue) were calculated from the images for quantitative comparison. Results Healthy subjects demonstrated generally uniform values within coronal slices, and a gradient in values along the anterior-to-posterior direction. In contrast, images and associated ratio maps in smokers and asthmatics were generally heterogeneous and exhibited values mostly lower than those in healthy subjects. Whole-lung values of total dissolved Xe129 to gas, tissue-to-gas, and RBC-to-gas ratios in healthy subjects were significantly larger than those in diseased subjects. Conclusion Regional maps of tissue and RBC fractions of dissolved Xe129 were obtained from a short breath-hold acquisition, well tolerated by healthy volunteers and subjects with obstructive lung disease. Marked differences were observed in spatial distributions and overall amounts of Xe129 dissolved in tissue and RBCs among healthy subjects, smokers and asthmatics. PMID:23681559

User’s guide for MapMark4—An R package for the probability calculations in three-part mineral resource assessments

USGS Publications Warehouse

Ellefsen, Karl J.

2017-06-27

MapMark4 is a software package that implements the probability calculations in three-part mineral resource assessments. Functions within the software package are written in the R statistical programming language. These functions, their documentation, and a copy of this user’s guide are bundled together in R’s unit of shareable code, which is called a “package.” This user’s guide includes step-by-step instructions showing how the functions are used to carry out the probability calculations. The calculations are demonstrated using test data, which are included in the package.

Assessment of the prevalence of Mycobacterium avium subsp. paratuberculosis in commercially pasteurized milk.

PubMed

Cerf, O; Griffiths, M; Aziza, F

2007-01-01

Conflicting laboratory-acquired data have been published about the heat resistance of Mycobacterium avium subsp. paratuberculosis (MAP), the cause of the deadly paratuberculosis (Johne's disease) of ruminants. Results of surveys of the presence of MAP in industrially pasteurized milk from several countries are conflicting also. This paper critically reviews the available data on the heat resistance of MAP and, based on these studies, a quantitative model describing the probability of finding MAP in pasteurized milk under the conditions prevailing in industrialized countries was derived using Monte Carlo simulation. The simulation assesses the probability of detecting MAP in 50-mL samples of pasteurized milk as lower than 1%. Hypotheses are presented to explain why higher frequencies were found by some authors; these included improper pasteurization and cross-contamination in the analytical laboratory. Hypotheses implicating a high rate of inter- and intraherd prevalence of paratuberculosis or heavy contamination of raw milk by feces were rejected.

Mapping Wildfire Ignition Probability Using Sentinel 2 and LiDAR (Jerte Valley, Cáceres, Spain)

PubMed Central

Sánchez Sánchez, Yolanda; Mateos Picado, Marina

2018-01-01

Wildfire is a major threat to the environment, and this threat is aggravated by different climatic and socioeconomic factors. The availability of detailed, reliable mapping and periodic and immediate updates makes wildfire prevention and extinction work more effective. An analyst protocol has been generated that allows the precise updating of high-resolution thematic maps. For this protocol, images obtained through the Sentinel 2A satellite, with a return time of five days, have been merged with Light Detection and Ranging (LiDAR) data with a density of 0.5 points/m2 in order to obtain vegetation mapping with an accuracy of 88% (kappa = 0.86), which is then extrapolated to fuel model mapping through a decision tree. This process, which is fast and reliable, serves as a cartographic base for the later calculation of ignition-probability mapping. The generated cartography is a fundamental tool to be used in the decision making involved in the planning of preventive silvicultural treatments, extinguishing media distribution, infrastructure construction, etc. PMID:29522460

Mapping Wildfire Ignition Probability Using Sentinel 2 and LiDAR (Jerte Valley, Cáceres, Spain).

PubMed

Sánchez Sánchez, Yolanda; Martínez-Graña, Antonio; Santos Francés, Fernando; Mateos Picado, Marina

2018-03-09

Wildfire is a major threat to the environment, and this threat is aggravated by different climatic and socioeconomic factors. The availability of detailed, reliable mapping and periodic and immediate updates makes wildfire prevention and extinction work more effective. An analyst protocol has been generated that allows the precise updating of high-resolution thematic maps. For this protocol, images obtained through the Sentinel 2A satellite, with a return time of five days, have been merged with Light Detection and Ranging (LiDAR) data with a density of 0.5 points/m² in order to obtain vegetation mapping with an accuracy of 88% (kappa = 0.86), which is then extrapolated to fuel model mapping through a decision tree. This process, which is fast and reliable, serves as a cartographic base for the later calculation of ignition-probability mapping. The generated cartography is a fundamental tool to be used in the decision making involved in the planning of preventive silvicultural treatments, extinguishing media distribution, infrastructure construction, etc.

Verification of the WFAS Lightning Efficiency Map

Treesearch

Paul Sopko; Don Latham; Isaac Grenfell

2007-01-01

A Lightning Ignition Efficiency map was added to the suite of daily maps offered by the Wildland Fire Assessment System (WFAS) in 1999. This map computes a lightning probability of ignition (POI) based on the estimated fuel type, fuel depth, and 100-hour fuel moisture interpolated from the Remote Automated Weather Station (RAWS) network. An attempt to verify the...

Detection, mapping, and quantification of single walled carbon nanotubes in histological specimens with photoacoustic microscopy.

PubMed

Avti, Pramod K; Hu, Song; Favazza, Christopher; Mikos, Antonios G; Jansen, John A; Shroyer, Kenneth R; Wang, Lihong V; Sitharaman, Balaji

2012-01-01

In the present study, the efficacy of multi-scale photoacoustic microscopy (PAM) was investigated to detect, map, and quantify trace amounts [nanograms (ng) to micrograms (µg)] of SWCNTs in a variety of histological tissue specimens consisting of cancer and benign tissue biopsies (histological specimens from implanted tissue engineering scaffolds). Optical-resolution (OR) and acoustic-resolution (AR)--Photoacoustic microscopy (PAM) was employed to detect, map and quantify the SWCNTs in a variety of tissue histological specimens and compared with other optical techniques (bright-field optical microscopy, Raman microscopy, near infrared (NIR) fluorescence microscopy). Both optical-resolution and acoustic-resolution PAM, allow the detection and quantification of SWCNTs in histological specimens with scalable spatial resolution and depth penetration. The noise-equivalent detection sensitivity to SWCNTs in the specimens was calculated to be as low as ∼7 pg. Image processing analysis further allowed the mapping, distribution, and quantification of the SWCNTs in the histological sections. The results demonstrate the potential of PAM as a promising imaging technique to detect, map, and quantify SWCNTs in histological specimens, and could complement the capabilities of current optical and electron microscopy techniques in the analysis of histological specimens containing SWCNTs.

Automated prediction of tissue outcome after acute ischemic stroke in computed tomography perfusion images

NASA Astrophysics Data System (ADS)

Vos, Pieter C.; Bennink, Edwin; de Jong, Hugo; Velthuis, Birgitta K.; Viergever, Max A.; Dankbaar, Jan Willem

2015-03-01

Assessment of the extent of cerebral damage on admission in patients with acute ischemic stroke could play an important role in treatment decision making. Computed tomography perfusion (CTP) imaging can be used to determine the extent of damage. However, clinical application is hindered by differences among vendors and used methodology. As a result, threshold based methods and visual assessment of CTP images has not yet shown to be useful in treatment decision making and predicting clinical outcome. Preliminary results in MR studies have shown the benefit of using supervised classifiers for predicting tissue outcome, but this has not been demonstrated for CTP. We present a novel method for the automatic prediction of tissue outcome by combining multi-parametric CTP images into a tissue outcome probability map. A supervised classification scheme was developed to extract absolute and relative perfusion values from processed CTP images that are summarized by a trained classifier into a likelihood of infarction. Training was performed using follow-up CT scans of 20 acute stroke patients with complete recanalization of the vessel that was occluded on admission. Infarcted regions were annotated by expert neuroradiologists. Multiple classifiers were evaluated in a leave-one-patient-out strategy for their discriminating performance using receiver operating characteristic (ROC) statistics. Results showed that a RandomForest classifier performed optimally with an area under the ROC of 0.90 for discriminating infarct tissue. The obtained results are an improvement over existing thresholding methods and are in line with results found in literature where MR perfusion was used.

Sampling probability distributions of lesions in mammograms

NASA Astrophysics Data System (ADS)

Looney, P.; Warren, L. M.; Dance, D. R.; Young, K. C.

2015-03-01

One approach to image perception studies in mammography using virtual clinical trials involves the insertion of simulated lesions into normal mammograms. To facilitate this, a method has been developed that allows for sampling of lesion positions across the cranio-caudal and medio-lateral radiographic projections in accordance with measured distributions of real lesion locations. 6825 mammograms from our mammography image database were segmented to find the breast outline. The outlines were averaged and smoothed to produce an average outline for each laterality and radiographic projection. Lesions in 3304 mammograms with malignant findings were mapped on to a standardised breast image corresponding to the average breast outline using piecewise affine transforms. A four dimensional probability distribution function was found from the lesion locations in the cranio-caudal and medio-lateral radiographic projections for calcification and noncalcification lesions. Lesion locations sampled from this probability distribution function were mapped on to individual mammograms using a piecewise affine transform which transforms the average outline to the outline of the breast in the mammogram. The four dimensional probability distribution function was validated by comparing it to the two dimensional distributions found by considering each radiographic projection and laterality independently. The correlation of the location of the lesions sampled from the four dimensional probability distribution function across radiographic projections was shown to match the correlation of the locations of the original mapped lesion locations. The current system has been implemented as a web-service on a server using the Python Django framework. The server performs the sampling, performs the mapping and returns the results in a javascript object notation format.

Detection of infarct lesions from single MRI modality using inconsistency between voxel intensity and spatial location--a 3-D automatic approach.

PubMed

Shen, Shan; Szameitat, André J; Sterr, Annette

2008-07-01

Detection of infarct lesions using traditional segmentation methods is always problematic due to intensity similarity between lesions and normal tissues, so that multispectral MRI modalities were often employed for this purpose. However, the high costs of MRI scan and the severity of patient conditions restrict the collection of multiple images. Therefore, in this paper, a new 3-D automatic lesion detection approach was proposed, which required only a single type of anatomical MRI scan. It was developed on a theory that, when lesions were present, the voxel-intensity-based segmentation and the spatial-location-based tissue distribution should be inconsistent in the regions of lesions. The degree of this inconsistency was calculated, which indicated the likelihood of tissue abnormality. Lesions were identified when the inconsistency exceeded a defined threshold. In this approach, the intensity-based segmentation was implemented by the conventional fuzzy c-mean (FCM) algorithm, while the spatial location of tissues was provided by prior tissue probability maps. The use of simulated MRI lesions allowed us to quantitatively evaluate the performance of the proposed method, as the size and location of lesions were prespecified. The results showed that our method effectively detected lesions with 40-80% signal reduction compared to normal tissues (similarity index > 0.7). The capability of the proposed method in practice was also demonstrated on real infarct lesions from 15 stroke patients, where the lesions detected were in broad agreement with true lesions. Furthermore, a comparison to a statistical segmentation approach presented in the literature suggested that our 3-D lesion detection approach was more reliable. Future work will focus on adapting the current method to multiple sclerosis lesion detection.

Mapping absolute tissue endogenous fluorophore concentrations with chemometric wide-field fluorescence microscopy

NASA Astrophysics Data System (ADS)

Xu, Zhang; Reilley, Michael; Li, Run; Xu, Min

2017-06-01

We report chemometric wide-field fluorescence microscopy for imaging the spatial distribution and concentration of endogenous fluorophores in thin tissue sections. Nonnegative factorization aided by spatial diversity is used to learn both the spectral signature and the spatial distribution of endogenous fluorophores from microscopic fluorescence color images obtained under broadband excitation and detection. The absolute concentration map of individual fluorophores is derived by comparing the fluorescence from "pure" fluorophores under the identical imaging condition following the identification of the fluorescence species by its spectral signature. This method is then demonstrated by characterizing the concentration map of endogenous fluorophores (including tryptophan, elastin, nicotinamide adenine dinucleotide, and flavin adenine dinucleotide) for lung tissue specimens. The absolute concentrations of these fluorophores are all found to decrease significantly from normal, perilesional, to cancerous (squamous cell carcinoma) tissue. Discriminating tissue types using the absolute fluorophore concentration is found to be significantly more accurate than that achievable with the relative fluorescence strength. Quantification of fluorophores in terms of the absolute concentration map is also advantageous in eliminating the uncertainties due to system responses or measurement details, yielding more biologically relevant data, and simplifying the assessment of competing imaging approaches.

In vivo mapping of current density distribution in brain tissues during deep brain stimulation (DBS)

NASA Astrophysics Data System (ADS)

Sajib, Saurav Z. K.; Oh, Tong In; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

2017-01-01

New methods for in vivo mapping of brain responses during deep brain stimulation (DBS) are indispensable to secure clinical applications. Assessment of current density distribution, induced by internally injected currents, may provide an alternative method for understanding the therapeutic effects of electrical stimulation. The current flow and pathway are affected by internal conductivity, and can be imaged using magnetic resonance-based conductivity imaging methods. Magnetic resonance electrical impedance tomography (MREIT) is an imaging method that can enable highly resolved mapping of electromagnetic tissue properties such as current density and conductivity of living tissues. In the current study, we experimentally imaged current density distribution of in vivo canine brains by applying MREIT to electrical stimulation. The current density maps of three canine brains were calculated from the measured magnetic flux density data. The absolute current density values of brain tissues, including gray matter, white matter, and cerebrospinal fluid were compared to assess the active regions during DBS. The resulting current density in different tissue types may provide useful information about current pathways and volume activation for adjusting surgical planning and understanding the therapeutic effects of DBS.

Material Properties of Human Ocular Tissue at 7-µm Resolution.

PubMed

Rohrbach, Daniel; Ito, Kazuyo; Lloyd, Harriet O; Silverman, Ronald H; Yoshida, Kenji; Yamaguchi, Tadashi; Mamou, Jonathan

2017-09-01

Quantitative assessment of the material properties of ocular tissues can provide valuable information for investigating several ophthalmic diseases. Quantitative acoustic microscopy (QAM) offers a means of obtaining such information, but few QAM investigations have been conducted on human ocular tissue. We imaged the optic nerve (ON) and iridocorneal angle in 12-µm deparaffinized sections of the human eye using a custom-built acoustic microscope with a 250-MHz transducer (7-µm lateral resolution). The two-dimensional QAM maps of ultrasound attenuation (α), speed of sound ( c), acoustic impedance ( Z), bulk modulus ( K), and mass density (ρ) were generated. Scanned samples were then stained and imaged by light microscopy for comparison with QAM maps. The spatial resolution and contrast of scanning acoustic microscopy (SAM) maps were sufficient to resolve anatomic layers of the retina (Re); anatomic features in SAM maps corresponded to those seen by light microscopy. Significant variations of the acoustic parameters were found. For example, the sclera was 220 MPa stiffer than Re, choroid, and ON tissue. To the authors' knowledge, this is the first systematic study to assess c, Z, K, ρ, and α of human ocular tissue at the high ultrasound frequencies used in this study.

Esophagus segmentation in CT via 3D fully convolutional neural network and random walk.

PubMed

Fechter, Tobias; Adebahr, Sonja; Baltas, Dimos; Ben Ayed, Ismail; Desrosiers, Christian; Dolz, Jose

2017-12-01

Precise delineation of organs at risk is a crucial task in radiotherapy treatment planning for delivering high doses to the tumor while sparing healthy tissues. In recent years, automated segmentation methods have shown an increasingly high performance for the delineation of various anatomical structures. However, this task remains challenging for organs like the esophagus, which have a versatile shape and poor contrast to neighboring tissues. For human experts, segmenting the esophagus from CT images is a time-consuming and error-prone process. To tackle these issues, we propose a random walker approach driven by a 3D fully convolutional neural network (CNN) to automatically segment the esophagus from CT images. First, a soft probability map is generated by the CNN. Then, an active contour model (ACM) is fitted to the CNN soft probability map to get a first estimation of the esophagus location. The outputs of the CNN and ACM are then used in conjunction with a probability model based on CT Hounsfield (HU) values to drive the random walker. Training and evaluation were done on 50 CTs from two different datasets, with clinically used peer-reviewed esophagus contours. Results were assessed regarding spatial overlap and shape similarity. The esophagus contours generated by the proposed algorithm showed a mean Dice coefficient of 0.76 ± 0.11, an average symmetric square distance of 1.36 ± 0.90 mm, and an average Hausdorff distance of 11.68 ± 6.80, compared to the reference contours. These results translate to a very good agreement with reference contours and an increase in accuracy compared to existing methods. Furthermore, when considering the results reported in the literature for the publicly available Synapse dataset, our method outperformed all existing approaches, which suggests that the proposed method represents the current state-of-the-art for automatic esophagus segmentation. We show that a CNN can yield accurate estimations of esophagus location, and that the results of this model can be refined by a random walk step taking pixel intensities and neighborhood relationships into account. One of the main advantages of our network over previous methods is that it performs 3D convolutions, thus fully exploiting the 3D spatial context and performing an efficient volume-wise prediction. The whole segmentation process is fully automatic and yields esophagus delineations in very good agreement with the gold standard, showing that it can compete with previously published methods. © 2017 American Association of Physicists in Medicine.

Risk-targeted maps for Romania

NASA Astrophysics Data System (ADS)

Vacareanu, Radu; Pavel, Florin; Craciun, Ionut; Coliba, Veronica; Arion, Cristian; Aldea, Alexandru; Neagu, Cristian

2018-03-01

Romania has one of the highest seismic hazard levels in Europe. The seismic hazard is due to a combination of local crustal seismic sources, situated mainly in the western part of the country and the Vrancea intermediate-depth seismic source, which can be found at the bend of the Carpathian Mountains. Recent seismic hazard studies have shown that there are consistent differences between the slopes of the seismic hazard curves for sites situated in the fore-arc and back-arc of the Carpathian Mountains. Consequently, in this study we extend this finding to the evaluation of the probability of collapse of buildings and finally to the development of uniform risk-targeted maps. The main advantage of uniform risk approach is that the target probability of collapse will be uniform throughout the country. Finally, the results obtained are discussed in the light of a recent study with the same focus performed at European level using the hazard data from SHARE project. The analyses performed in this study have pointed out to a dominant influence of the quantile of peak ground acceleration used for anchoring the fragility function. This parameter basically alters the shape of the risk-targeted maps shifting the areas which have higher collapse probabilities from eastern Romania to western Romania, as its exceedance probability increases. Consequently, a uniform procedure for deriving risk-targeted maps appears as more than necessary.

Poster - Thurs Eve-43: Verification of dose calculation with tissue inhomogeneity using MapCHECK.

PubMed

Korol, R; Chen, J; Mosalaei, H; Karnas, S

2008-07-01

MapCHECK (Sun Nuclear, Melbourne, FL) with 445 diode detectors has been used widely for routine IMRT quality assurance (QA) 1 . However, routine IMRT QA has not included the verification of inhomogeneity effects. The objective of this study is to use MapCHECK and a phantom to verify dose calculation and IMRT delivery with tissue inhomogeneity. A phantom with tissue inhomogeneities was placed on top of MapCHECK to measure the planar dose for an anterior beam with photon energy 6 MV or 18 MV. The phantom was composed of a 3.5 cm thick block of lung equivalent material and solid water arranged side by side with a 0.5 cm slab of solid water on the top of the phantom. The phantom setup including MapCHECK was CT scanned and imported into Pinnacle 8.0d for dose calculation. Absolute dose distributions were compared with gamma criteria 3% for dose difference and 3 mm for distance-to-agreement. The results are in good agreement between the measured and calculated planar dose with 88% pass rate based on the gamma analysis. The major dose difference was at the lung-water interface. Further investigation will be performed on a custom designed inhomogeneity phantom with inserts of varying densities and effective depth to create various dose gradients at the interface for dose calculation and delivery verification. In conclusion, a phantom with tissue inhomogeneities can be used with MapCHECK for verification of dose calculation and delivery with tissue inhomogeneity. © 2008 American Association of Physicists in Medicine.

Quantitative Susceptibility Mapping after Sports-Related Concussion.

PubMed

Koch, K M; Meier, T B; Karr, R; Nencka, A S; Muftuler, L T; McCrea, M

2018-06-07

Quantitative susceptibility mapping using MR imaging can assess changes in brain tissue structure and composition. This report presents preliminary results demonstrating changes in tissue magnetic susceptibility after sports-related concussion. Longitudinal quantitative susceptibility mapping metrics were produced from imaging data acquired from cohorts of concussed and control football athletes. One hundred thirty-six quantitative susceptibility mapping datasets were analyzed across 3 separate visits (24 hours after injury, 8 days postinjury, and 6 months postinjury). Longitudinal quantitative susceptibility mapping group analyses were performed on stability-thresholded brain tissue compartments and selected subregions. Clinical concussion metrics were also measured longitudinally in both cohorts and compared with the measured quantitative susceptibility mapping. Statistically significant increases in white matter susceptibility were identified in the concussed athlete group during the acute (24 hour) and subacute (day 8) period. These effects were most prominent at the 8-day visit but recovered and showed no significant difference from controls at the 6-month visit. The subcortical gray matter showed no statistically significant group differences. Observed susceptibility changes after concussion appeared to outlast self-reported clinical recovery metrics at a group level. At an individual subject level, susceptibility increases within the white matter showed statistically significant correlations with return-to-play durations. The results of this preliminary investigation suggest that sports-related concussion can induce physiologic changes to brain tissue that can be detected using MR imaging-based magnetic susceptibility estimates. In group analyses, the observed tissue changes appear to persist beyond those detected on clinical outcome assessments and were associated with return-to-play duration after sports-related concussion. © 2018 by American Journal of Neuroradiology.

Brain tissue segmentation based on DTI data

PubMed Central

Liu, Tianming; Li, Hai; Wong, Kelvin; Tarokh, Ashley; Guo, Lei; Wong, Stephen T.C.

2008-01-01

We present a method for automated brain tissue segmentation based on the multi-channel fusion of diffusion tensor imaging (DTI) data. The method is motivated by the evidence that independent tissue segmentation based on DTI parametric images provides complementary information of tissue contrast to the tissue segmentation based on structural MRI data. This has important applications in defining accurate tissue maps when fusing structural data with diffusion data. In the absence of structural data, tissue segmentation based on DTI data provides an alternative means to obtain brain tissue segmentation. Our approach to the tissue segmentation based on DTI data is to classify the brain into two compartments by utilizing the tissue contrast existing in a single channel. Specifically, because the apparent diffusion coefficient (ADC) values in the cerebrospinal fluid (CSF) are more than twice that of gray matter (GM) and white matter (WM), we use ADC images to distinguish CSF and non-CSF tissues. Additionally, fractional anisotropy (FA) images are used to separate WM from non-WM tissues, as highly directional white matter structures have much larger fractional anisotropy values. Moreover, other channels to separate tissue are explored, such as eigenvalues of the tensor, relative anisotropy (RA), and volume ratio (VR). We developed an approach based on the Simultaneous Truth and Performance Level Estimation (STAPLE) algorithm that combines these two-class maps to obtain a complete tissue segmentation map of CSF, GM, and WM. Evaluations are provided to demonstrate the performance of our approach. Experimental results of applying this approach to brain tissue segmentation and deformable registration of DTI data and spoiled gradient-echo (SPGR) data are also provided. PMID:17804258

BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data

PubMed Central

Ji, Yuan; Xu, Yanxun; Zhang, Qiong; Tsui, Kam-Wah; Yuan, Yuan; Norris, Clift; Liang, Shoudan; Liang, Han

2011-01-01

Summary Next-generation sequencing (NGS) technology generates millions of short reads, which provide valuable information for various aspects of cellular activities and biological functions. A key step in NGS applications (e.g., RNA-Seq) is to map short reads to correct genomic locations within the source genome. While most reads are mapped to a unique location, a significant proportion of reads align to multiple genomic locations with equal or similar numbers of mismatches; these are called multireads. The ambiguity in mapping the multireads may lead to bias in downstream analyses. Currently, most practitioners discard the multireads in their analysis, resulting in a loss of valuable information, especially for the genes with similar sequences. To refine the read mapping, we develop a Bayesian model that computes the posterior probability of mapping a multiread to each competing location. The probabilities are used for downstream analyses, such as the quantification of gene expression. We show through simulation studies and RNA-Seq analysis of real life data that the Bayesian method yields better mapping than the current leading methods. We provide a C++ program for downloading that is being packaged into a user-friendly software. PMID:21517792

Myocardial Tissue Characterization by Magnetic Resonance Imaging

PubMed Central

Ferreira, Vanessa M.; Piechnik, Stefan K.; Robson, Matthew D.; Neubauer, Stefan

2014-01-01

Cardiac magnetic resonance (CMR) imaging is a well-established noninvasive imaging modality in clinical cardiology. Its unsurpassed accuracy in defining cardiac morphology and function and its ability to provide tissue characterization make it well suited for the study of patients with cardiac diseases. Late gadolinium enhancement was a major advancement in the development of tissue characterization techniques, allowing the unique ability of CMR to differentiate ischemic heart disease from nonischemic cardiomyopathies. Using T2-weighted techniques, areas of edema and inflammation can be identified in the myocardium. A new generation of myocardial mapping techniques are emerging, enabling direct quantitative assessment of myocardial tissue properties in absolute terms. This review will summarize recent developments involving T1-mapping and T2-mapping techniques and focus on the clinical applications and future potential of these evolving CMR methodologies. PMID:24576837

A multi-part matching strategy for mapping LOINC with laboratory terminologies

PubMed Central

Lee, Li-Hui; Groß, Anika; Hartung, Michael; Liou, Der-Ming; Rahm, Erhard

2014-01-01

Objective To address the problem of mapping local laboratory terminologies to Logical Observation Identifiers Names and Codes (LOINC). To study different ontology matching algorithms and investigate how the probability of term combinations in LOINC helps to increase match quality and reduce manual effort. Materials and methods We proposed two matching strategies: full name and multi-part. The multi-part approach also considers the occurrence probability of combined concept parts. It can further recommend possible combinations of concept parts to allow more local terms to be mapped. Three real-world laboratory databases from Taiwanese hospitals were used to validate the proposed strategies with respect to different quality measures and execution run time. A comparison with the commonly used tool, Regenstrief LOINC Mapping Assistant (RELMA) Lab Auto Mapper (LAM), was also carried out. Results The new multi-part strategy yields the best match quality, with F-measure values between 89% and 96%. It can automatically match 70–85% of the laboratory terminologies to LOINC. The recommendation step can further propose mapping to (proposed) LOINC concepts for 9–20% of the local terminology concepts. On average, 91% of the local terminology concepts can be correctly mapped to existing or newly proposed LOINC concepts. Conclusions The mapping quality of the multi-part strategy is significantly better than that of LAM. It enables domain experts to perform LOINC matching with little manual work. The probability of term combinations proved to be a valuable strategy for increasing the quality of match results, providing recommendations for proposed LOINC conepts, and decreasing the run time for match processing. PMID:24363318

Automated segmentation of dental CBCT image with prior-guided sequential random forests

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

Wang, Li; Gao, Yaozong; Shi, Feng

Purpose: Cone-beam computed tomography (CBCT) is an increasingly utilized imaging modality for the diagnosis and treatment planning of the patients with craniomaxillofacial (CMF) deformities. Accurate segmentation of CBCT image is an essential step to generate 3D models for the diagnosis and treatment planning of the patients with CMF deformities. However, due to the image artifacts caused by beam hardening, imaging noise, inhomogeneity, truncation, and maximal intercuspation, it is difficult to segment the CBCT. Methods: In this paper, the authors present a new automatic segmentation method to address these problems. Specifically, the authors first employ a majority voting method to estimatemore » the initial segmentation probability maps of both mandible and maxilla based on multiple aligned expert-segmented CBCT images. These probability maps provide an important prior guidance for CBCT segmentation. The authors then extract both the appearance features from CBCTs and the context features from the initial probability maps to train the first-layer of random forest classifier that can select discriminative features for segmentation. Based on the first-layer of trained classifier, the probability maps are updated, which will be employed to further train the next layer of random forest classifier. By iteratively training the subsequent random forest classifier using both the original CBCT features and the updated segmentation probability maps, a sequence of classifiers can be derived for accurate segmentation of CBCT images. Results: Segmentation results on CBCTs of 30 subjects were both quantitatively and qualitatively validated based on manually labeled ground truth. The average Dice ratios of mandible and maxilla by the authors’ method were 0.94 and 0.91, respectively, which are significantly better than the state-of-the-art method based on sparse representation (p-value < 0.001). Conclusions: The authors have developed and validated a novel fully automated method for CBCT segmentation.« less

Liquefaction Hazard Maps for Three Earthquake Scenarios for the Communities of San Jose, Campbell, Cupertino, Los Altos, Los Gatos, Milpitas, Mountain View, Palo Alto, Santa Clara, Saratoga, and Sunnyvale, Northern Santa Clara County, California

USGS Publications Warehouse

Holzer, Thomas L.; Noce, Thomas E.; Bennett, Michael J.

2008-01-01

Maps showing the probability of surface manifestations of liquefaction in the northern Santa Clara Valley were prepared with liquefaction probability curves. The area includes the communities of San Jose, Campbell, Cupertino, Los Altos, Los Gatos Milpitas, Mountain View, Palo Alto, Santa Clara, Saratoga, and Sunnyvale. The probability curves were based on complementary cumulative frequency distributions of the liquefaction potential index (LPI) for surficial geologic units in the study area. LPI values were computed with extensive cone penetration test soundings. Maps were developed for three earthquake scenarios, an M7.8 on the San Andreas Fault comparable to the 1906 event, an M6.7 on the Hayward Fault comparable to the 1868 event, and an M6.9 on the Calaveras Fault. Ground motions were estimated with the Boore and Atkinson (2008) attenuation relation. Liquefaction is predicted for all three events in young Holocene levee deposits along the major creeks. Liquefaction probabilities are highest for the M7.8 earthquake, ranging from 0.33 to 0.37 if a 1.5-m deep water table is assumed, and 0.10 to 0.14 if a 5-m deep water table is assumed. Liquefaction probabilities of the other surficial geologic units are less than 0.05. Probabilities for the scenario earthquakes are generally consistent with observations during historical earthquakes.

Novel Passive Clearing Methods for the Rapid Production of Optical Transparency in Whole CNS Tissue.

PubMed

Woo, Jiwon; Lee, Eunice Yoojin; Park, Hyo-Suk; Park, Jeong Yoon; Cho, Yong Eun

2018-05-08

Since the development of CLARITY, a bioelectrochemical clearing technique that allows for three-dimensional phenotype mapping within transparent tissues, a multitude of novel clearing methodologies including CUBIC (clear, unobstructed brain imaging cocktails and computational analysis), SWITCH (system-wide control of interaction time and kinetics of chemicals), MAP (magnified analysis of the proteome), and PACT (passive clarity technique), have been established to further expand the existing toolkit for the microscopic analysis of biological tissues. The present study aims to improve upon and optimize the original PACT procedure for an array of intact rodent tissues, including the whole central nervous system (CNS), kidneys, spleen, and whole mouse embryos. Termed psPACT (process-separate PACT) and mPACT (modified PACT), these novel techniques provide highly efficacious means of mapping cell circuitry and visualizing subcellular structures in intact normal and pathological tissues. In the following protocol, we provide a detailed, step-by-step outline on how to achieve maximal tissue clearance with minimal invasion of their structural integrity via psPACT and mPACT.

Stiffness mapping prostate biopsy samples using a tactile sensor.

PubMed

Peng, Qiyu; Omata, Sadao; Peehl, Donna M; Constantinou, Chris E

2011-01-01

Previous studies have demonstrated that the stiffness of cancerous cells reflects their pathological stage and progression rates, with increased cancerous cell stiffness associated with increased aggressiveness. Therefore, the elasticity of the cancerous cells has the potential to be used as an indicator of the cancer's aggressiveness. However, the sensitivity and resolution of current palpation and imaging techniques are not sufficient to detect small cancerous tissues. In previous studies, we developed a tactile-based device to map with high resolution the stiffness of a tissue section. The purpose of this study is to evaluate this device using different tissues (BPH, Cancer and PZ) collected from human prostates. The preliminary results show that the tactile device is sensitive enough to tell the differences of the stiffness of different tissues. The results also disclosed the factors (humidity, temperature and tissue degradation) which could dramatically affect the results of stiffness mapping. The tactile technology described in this paper has the potential to help disclose the underlying mechanical mechanisms that lead to increased stiffness in prostate tumors.

Real-Time Vision-Based Stiffness Mapping †.

PubMed

Faragasso, Angela; Bimbo, João; Stilli, Agostino; Wurdemann, Helge Arne; Althoefer, Kaspar; Asama, Hajime

2018-04-26

This paper presents new findings concerning a hand-held stiffness probe for the medical diagnosis of abnormalities during palpation of soft-tissue. Palpation is recognized by the medical community as an essential and low-cost method to detect and diagnose disease in soft-tissue. However, differences are often subtle and clinicians need to train for many years before they can conduct a reliable diagnosis. The probe presented here fills this gap providing a means to easily obtain stiffness values of soft tissue during a palpation procedure. Our stiffness sensor is equipped with a multi degree of freedom (DoF) Aurora magnetic tracker, allowing us to track and record the 3D position of the probe whilst examining a tissue area, and generate a 3D stiffness map in real-time. The stiffness probe was integrated in a robotic arm and tested in an artificial environment representing a good model of soft tissue organs; the results show that the sensor can accurately measure and map the stiffness of a silicon phantom embedded with areas of varying stiffness.

Taxonomic classification of world map units in crop producing areas of Argentina and Brazil with representative US soil series and major land resource areas in which they occur

NASA Technical Reports Server (NTRS)

Huckle, H. F. (Principal Investigator)

1980-01-01

The most probable current U.S. taxonomic classification of the soils estimated to dominate world soil map units (WSM)) in selected crop producing states of Argentina and Brazil are presented. Representative U.S. soil series the units are given. The map units occurring in each state are listed with areal extent and major U.S. land resource areas in which similar soils most probably occur. Soil series sampled in LARS Technical Report 111579 and major land resource areas in which they occur with corresponding similar WSM units at the taxonomic subgroup levels are given.

On Voxel based Iso-Tumor Control Probabilty and Iso-Complication Maps for Selective Boosting and Selective Avoidance Intensity Modulated Radiotherapy.

PubMed

Kim, Yusung; Tomé, Wolfgang A

2008-01-01

Voxel based iso-Tumor Control Probability (TCP) maps and iso-Complication maps are proposed as a plan-review tool especially for functional image-guided intensity-modulated radiotherapy (IMRT) strategies such as selective boosting (dose painting) and conformal avoidance IMRT. The maps employ voxel-based phenomenological biological dose-response models for target volumes and normal organs. Two IMRT strategies for prostate cancer, namely conventional uniform IMRT delivering an EUD = 84 Gy (equivalent uniform dose) to the entire PTV and selective boosting delivering an EUD = 82 Gy to the entire PTV, are investigated, to illustrate the advantages of this approach over iso-dose maps. Conventional uniform IMRT did yield a more uniform isodose map to the entire PTV while selective boosting did result in a nonuniform isodose map. However, when employing voxel based iso-TCP maps selective boosting exhibited a more uniform tumor control probability map compared to what could be achieved using conventional uniform IMRT, which showed TCP cold spots in high-risk tumor subvolumes despite delivering a higher EUD to the entire PTV. Voxel based iso-Complication maps are presented for rectum and bladder, and their utilization for selective avoidance IMRT strategies are discussed. We believe as the need for functional image guided treatment planning grows, voxel based iso-TCP and iso-Complication maps will become an important tool to assess the integrity of such treatment plans.

Fisher statistics for analysis of diffusion tensor directional information.

PubMed

Hutchinson, Elizabeth B; Rutecki, Paul A; Alexander, Andrew L; Sutula, Thomas P

2012-04-30

A statistical approach is presented for the quantitative analysis of diffusion tensor imaging (DTI) directional information using Fisher statistics, which were originally developed for the analysis of vectors in the field of paleomagnetism. In this framework, descriptive and inferential statistics have been formulated based on the Fisher probability density function, a spherical analogue of the normal distribution. The Fisher approach was evaluated for investigation of rat brain DTI maps to characterize tissue orientation in the corpus callosum, fornix, and hilus of the dorsal hippocampal dentate gyrus, and to compare directional properties in these regions following status epilepticus (SE) or traumatic brain injury (TBI) with values in healthy brains. Direction vectors were determined for each region of interest (ROI) for each brain sample and Fisher statistics were applied to calculate the mean direction vector and variance parameters in the corpus callosum, fornix, and dentate gyrus of normal rats and rats that experienced TBI or SE. Hypothesis testing was performed by calculation of Watson's F-statistic and associated p-value giving the likelihood that grouped observations were from the same directional distribution. In the fornix and midline corpus callosum, no directional differences were detected between groups, however in the hilus, significant (p<0.0005) differences were found that robustly confirmed observations that were suggested by visual inspection of directionally encoded color DTI maps. The Fisher approach is a potentially useful analysis tool that may extend the current capabilities of DTI investigation by providing a means of statistical comparison of tissue structural orientation. Copyright © 2012 Elsevier B.V. All rights reserved.

Comparing the Performance of Japan's Earthquake Hazard Maps to Uniform and Randomized Maps

NASA Astrophysics Data System (ADS)

Brooks, E. M.; Stein, S. A.; Spencer, B. D.

2015-12-01

The devastating 2011 magnitude 9.1 Tohoku earthquake and the resulting shaking and tsunami were much larger than anticipated in earthquake hazard maps. Because this and all other earthquakes that caused ten or more fatalities in Japan since 1979 occurred in places assigned a relatively low hazard, Geller (2011) argued that "all of Japan is at risk from earthquakes, and the present state of seismological science does not allow us to reliably differentiate the risk level in particular geographic areas," so a map showing uniform hazard would be preferable to the existing map. Defenders of the maps countered by arguing that these earthquakes are low-probability events allowed by the maps, which predict the levels of shaking that should expected with a certain probability over a given time. Although such maps are used worldwide in making costly policy decisions for earthquake-resistant construction, how well these maps actually perform is unknown. We explore this hotly-contested issue by comparing how well a 510-year-long record of earthquake shaking in Japan is described by the Japanese national hazard (JNH) maps, uniform maps, and randomized maps. Surprisingly, as measured by the metric implicit in the JNH maps, i.e. that during the chosen time interval the predicted ground motion should be exceeded only at a specific fraction of the sites, both uniform and randomized maps do better than the actual maps. However, using as a metric the squared misfit between maximum observed shaking and that predicted, the JNH maps do better than uniform or randomized maps. These results indicate that the JNH maps are not performing as well as expected, that what factors control map performance is complicated, and that learning more about how maps perform and why would be valuable in making more effective policy.

Will it Blend? Visualization and Accuracy Evaluation of High-Resolution Fuzzy Vegetation Maps

NASA Astrophysics Data System (ADS)

Zlinszky, A.; Kania, A.

2016-06-01

Instead of assigning every map pixel to a single class, fuzzy classification includes information on the class assigned to each pixel but also the certainty of this class and the alternative possible classes based on fuzzy set theory. The advantages of fuzzy classification for vegetation mapping are well recognized, but the accuracy and uncertainty of fuzzy maps cannot be directly quantified with indices developed for hard-boundary categorizations. The rich information in such a map is impossible to convey with a single map product or accuracy figure. Here we introduce a suite of evaluation indices and visualization products for fuzzy maps generated with ensemble classifiers. We also propose a way of evaluating classwise prediction certainty with "dominance profiles" visualizing the number of pixels in bins according to the probability of the dominant class, also showing the probability of all the other classes. Together, these data products allow a quantitative understanding of the rich information in a fuzzy raster map both for individual classes and in terms of variability in space, and also establish the connection between spatially explicit class certainty and traditional accuracy metrics. These map products are directly comparable to widely used hard boundary evaluation procedures, support active learning-based iterative classification and can be applied for operational use.

High-resolution x-ray absorption spectroscopy studies of metal compounds in neurodegenerative brain tissue

NASA Astrophysics Data System (ADS)

Collingwood, J. F.; Mikhaylova, A.; Davidson, M. R.; Batich, C.; Streit, W. J.; Eskin, T.; Terry, J.; Barrea, R.; Underhill, R. S.; Dobson, J.

2005-01-01

Fluorescence mapping and microfocus X-ray absorption spectroscopy are used to detect, locate and identify iron biominerals and other inorganic metal accumulations in neurodegenerative brain tissue at sub-cellular resolution (<5 microns). Recent progress in developing the technique is reviewed. Synchrotron X-rays are used to map tissue sections for metals of interest, and XANES and XAFS are used to characterise anomalous concentrations of the metals in-situ so that they can be correlated with tissue structures and disease pathology. Iron anomalies associated with biogenic magnetite, ferritin and haemoglobin are located and identified in an avian tissue model with a pixel resolution ~5 microns. Subsequent studies include brain tissue sections from transgenic Huntington's mice, and the first high-resolution mapping and identification of iron biominerals in human Alzheimer's and control autopsy brain tissue. Technical developments include use of microfocus diffraction to obtain structural information about biominerals in-situ, and depositing sample location grids by lithography for the location of anomalies by conventional microscopy. The combined techniques provide a breakthrough in the study of both intra- and extra-cellular iron compounds and related metals in tissue. The information to be gained from this approach has implications for future diagnosis and treatment of neurodegeneration, and for our understanding of the mechanisms involved.

Association between increased epicardial adipose tissue volume and coronary plaque composition.

PubMed

Yamashita, Kennosuke; Yamamoto, Myong Hwa; Ebara, Seitarou; Okabe, Toshitaka; Saito, Shigeo; Hoshimoto, Koichi; Yakushiji, Tadayuki; Isomura, Naoei; Araki, Hiroshi; Obara, Chiaki; Ochiai, Masahiko

2014-09-01

To assess the relationship between epicardial adipose tissue volume (EATV) and plaque vulnerability in significant coronary stenosis using a 40-MHz intravascular ultrasound (IVUS) imaging system (iMap-IVUS), we analyzed 130 consecutive patients with coronary stenosis who underwent dual-source computed tomography (CT) and cardiac catheterization. Culprit lesions were imaged by iMap-IVUS before stenting. The iMAP-IVUS system classified coronary plaque components as fibrous, lipid, necrotic, or calcified tissue, based on the radiofrequency spectrum. Epicardial adipose tissue was measured as the tissue ranging from -190 to -30 Hounsfield units. EATV, calculated as the sum of the fat areas on short-axis images, was 85.0 ± 34.0 cm(3). There was a positive correlation between EATV and the percentage of necrotic plaque tissue (R (2) = 0.34, P < 0.01), while there was a negative correlation between EATV and the percentage of fibrous tissue (R (2) = 0.24, P < 0.01). Multivariate analysis revealed that an increased low-density lipoprotein cholesterol level (β = 0.15, P = 0.03) and EATV (β = 0.14, P = 0.02) were independently associated with the percentage of necrotic plaque tissue. An increase in EATV was associated with the development of coronary atherosclerosis and, potentially, with the most dangerous type of plaque.

Probabilistic assessment of precipitation-triggered landslides using historical records of landslide occurence, Seattle, Washington

USGS Publications Warehouse

Coe, J.A.; Michael, J.A.; Crovelli, R.A.; Savage, W.Z.; Laprade, W.T.; Nashem, W.D.

2004-01-01

Ninety years of historical landslide records were used as input to the Poisson and binomial probability models. Results from these models show that, for precipitation-triggered landslides, approximately 9 percent of the area of Seattle has annual exceedance probabilities of 1 percent or greater. Application of the Poisson model for estimating the future occurrence of individual landslides results in a worst-case scenario map, with a maximum annual exceedance probability of 25 percent on a hillslope near Duwamish Head in West Seattle. Application of the binomial model for estimating the future occurrence of a year with one or more landslides results in a map with a maximum annual exceedance probability of 17 percent (also near Duwamish Head). Slope and geology both play a role in localizing the occurrence of landslides in Seattle. A positive correlation exists between slope and mean exceedance probability, with probability tending to increase as slope increases. Sixty-four percent of all historical landslide locations are within 150 m (500 ft, horizontal distance) of the Esperance Sand/Lawton Clay contact, but within this zone, no positive or negative correlation exists between exceedance probability and distance to the contact.

Automated tissue classification of pediatric brains from magnetic resonance images using age-specific atlases

NASA Astrophysics Data System (ADS)

Metzger, Andrew; Benavides, Amanda; Nopoulos, Peg; Magnotta, Vincent

2016-03-01

The goal of this project was to develop two age appropriate atlases (neonatal and one year old) that account for the rapid growth and maturational changes that occur during early development. Tissue maps from this age group were initially created by manually correcting the resulting tissue maps after applying an expectation maximization (EM) algorithm and an adult atlas to pediatric subjects. The EM algorithm classified each voxel into one of ten possible tissue types including several subcortical structures. This was followed by a novel level set segmentation designed to improve differentiation between distal cortical gray matter and white matter. To minimize the req uired manual corrections, the adult atlas was registered to the pediatric scans using high -dimensional, symmetric image normalization (SyN) registration. The subject images were then mapped to an age specific atlas space, again using SyN registration, and the resulting transformation applied to the manually corrected tissue maps. The individual maps were averaged in the age specific atlas space and blurred to generate the age appropriate anatomical priors. The resulting anatomical priors were then used by the EM algorithm to re-segment the initial training set as well as an independent testing set. The results from the adult and age-specific anatomical priors were compared to the manually corrected results. The age appropriate atlas provided superior results as compared to the adult atlas. The image analysis pipeline used in this work was built using the open source software package BRAINSTools.

Detection, Mapping, and Quantification of Single Walled Carbon Nanotubes in Histological Specimens with Photoacoustic Microscopy

PubMed Central

Mikos, Antonios G.; Jansen, John A.; Shroyer, Kenneth R.; Wang, Lihong V.; Sitharaman, Balaji

2012-01-01

Aims In the present study, the efficacy of multi-scale photoacoustic microscopy (PAM) was investigated to detect, map, and quantify trace amounts [nanograms (ng) to micrograms (µg)] of SWCNTs in a variety of histological tissue specimens consisting of cancer and benign tissue biopsies (histological specimens from implanted tissue engineering scaffolds). Materials and Methods Optical-resolution (OR) and acoustic-resolution (AR) - Photoacoustic microscopy (PAM) was employed to detect, map and quantify the SWCNTs in a variety of tissue histological specimens and compared with other optical techniques (bright-field optical microscopy, Raman microscopy, near infrared (NIR) fluorescence microscopy). Results Both optical-resolution and acoustic-resolution PAM, allow the detection and quantification of SWCNTs in histological specimens with scalable spatial resolution and depth penetration. The noise-equivalent detection sensitivity to SWCNTs in the specimens was calculated to be as low as ∼7 pg. Image processing analysis further allowed the mapping, distribution, and quantification of the SWCNTs in the histological sections. Conclusions The results demonstrate the potential of PAM as a promising imaging technique to detect, map, and quantify SWCNTs in histological specimens, and could complement the capabilities of current optical and electron microscopy techniques in the analysis of histological specimens containing SWCNTs. PMID:22496892

Quantitative evaluation of ischemic myocardial scar tissue by unenhanced T1 mapping using 3.0 Tesla MR scanner

PubMed Central

Okur, Aylin; Kantarcı, Mecit; Kızrak, Yeşim; Yıldız, Sema; Pirimoğlu, Berhan; Karaca, Leyla; Oğul, Hayri; Sevimli, Serdar

2014-01-01

PURPOSE We aimed to use a noninvasive method for quantifying T1 values of chronic myocardial infarction scar by cardiac magnetic resonance imaging (MRI), and determine its diagnostic performance. MATERIALS AND METHODS We performed cardiac MRI on 29 consecutive patients with known coronary artery disease (CAD) on 3.0 Tesla MRI scanner. An unenhanced T1 mapping technique was used to calculate T1 relaxation time of myocardial scar tissue, and its diagnostic performance was evaluated. Chronic scar tissue was identified by delayed contrast-enhancement (DE) MRI and T2-weighted images. Sensitivity, specificity, and accuracy values were calculated for T1 mapping using DE images as the gold standard. RESULTS Four hundred and forty-two segments were analyzed in 26 patients. While myocardial chronic scar was demonstrated in 45 segments on DE images, T1 mapping MRI showed a chronic scar area in 54 segments. T1 relaxation time was higher in chronic scar tissue, compared with remote areas (1314±98 ms vs. 1099±90 ms, P < 0.001). Therefore, increased T1 values were shown in areas of myocardium colocalized with areas of DE and normal signal on T2-weighted images. There was a significant correlation between T1 mapping and DE images in evaluation of myocardial wall injury extent (P < 0.05). We calculated sensitivity, specificity, and accuracy as 95.5%, 97%, and 96%, respectively. CONCLUSION The results of the present study reveal that T1 mapping MRI combined with T2-weighted images might be a feasible imaging modality for detecting chronic myocardial infarction scar tissue. PMID:25010366

Lung Motion Model Validation Experiments, Free-Breathing Tissue Densitometry, and Ventilation Mapping using Fast Helical CT Imaging

NASA Astrophysics Data System (ADS)

Dou, Hsiang-Tai

The uncertainties due to respiratory motion present significant challenges to accurate characterization of cancerous tissues both in terms of imaging and treatment. Currently available clinical lung imaging techniques are subject to inferior image quality and incorrect motion estimation, with consequences that can systematically impact the downstream treatment delivery and outcome. The main objective of this thesis is the development of the techniques of fast helical computed tomography (CT) imaging and deformable image registration for the radiotherapy applications in accurate breathing motion modeling, lung tissue density modeling and ventilation imaging. Fast helical CT scanning was performed on 64-slice CT scanner using the shortest available gantry rotation time and largest pitch value such that scanning of the thorax region amounts to just two seconds, which is less than typical breathing cycle in humans. The scanning was conducted under free breathing condition. Any portion of the lung anatomy undergoing such scanning protocol would be irradiated for only a quarter second, effectively removing any motion induced image artifacts. The resulting CT data were pristine volumetric images that record the lung tissue position and density in a fraction of the breathing cycle. Following our developed protocol, multiple fast helical CT scans were acquired to sample the tissue positions in different breathing states. To measure the tissue displacement, deformable image registration was performed that registers the non-reference images to the reference one. In modeling breathing motion, external breathing surrogate signal was recorded synchronously with the CT image slices. This allowed for the tissue-specific displacement to be modeled as parametrization of the recorded breathing signal using the 5D lung motion model. To assess the accuracy of the motion model in describing tissue position change, the model was used to simulate the original high-pitch helical CT scan geometries, employed as ground truth data. Image similarity between the simulated and ground truth scans was evaluated. The model validation experiments were conducted in a patient cohort of seventeen patients to assess the model robustness and inter-patient variation. The model error averaged over multiple tracked positions from several breathing cycles was found to be on the order of one millimeter. In modeling the density change under free breathing condition, the determinant of Jacobian matrix from the registration-derived deformation vector field yielded volume change information of the lung tissues. Correlation of the Jacobian values to the corresponding voxel Housfield units (HU) reveals that the density variation for the majority of lung tissues can be very well described by mass conservation relationship. Different tissue types were identified and separately modeled. Large trials of validation experiments were performed. The averaged deviation between the modeled and the reference lung density was 30 HU, which was estimated to be the background CT noise level. In characterizing the lung ventilation function, a novel method was developed to determine the extent of lung tissue volume change. Information on volume change was derived from the deformable image registration of the fast helical CT images in terms of Jacobian values with respect to a reference image. Assuming the multiple volume change measurements are independently and identically distributed, statistical formulation was derived to model ventilation distribution of each lung voxels and empirical minimum and maximum probability distribution of the Jacobian values was computed. Ventilation characteristic was evaluated as the difference of the expectation value from these extremal distributions. The resulting ventilation map was compared with an independently obtained ventilation image derived directly from the lung intensities and good correlation was found using statistical test. In addition, dynamic ventilation characterization was investigated by estimating the voxel-specific ventilation distribution. Ventilation maps were generated at different percentile levels using the tissue volume expansion metrics.

Multi-Agent Cooperative Target Search

PubMed Central

Hu, Jinwen; Xie, Lihua; Xu, Jun; Xu, Zhao

2014-01-01

This paper addresses a vision-based cooperative search for multiple mobile ground targets by a group of unmanned aerial vehicles (UAVs) with limited sensing and communication capabilities. The airborne camera on each UAV has a limited field of view and its target discriminability varies as a function of altitude. First, by dividing the whole surveillance region into cells, a probability map can be formed for each UAV indicating the probability of target existence within each cell. Then, we propose a distributed probability map updating model which includes the fusion of measurement information, information sharing among neighboring agents, information decay and transmission due to environmental changes such as the target movement. Furthermore, we formulate the target search problem as a multi-agent cooperative coverage control problem by optimizing the collective coverage area and the detection performance. The proposed map updating model and the cooperative control scheme are distributed, i.e., assuming that each agent only communicates with its neighbors within its communication range. Finally, the effectiveness of the proposed algorithms is illustrated by simulation. PMID:24865884

Probing the statistics of transport in the Hénon Map

NASA Astrophysics Data System (ADS)

Alus, O.; Fishman, S.; Meiss, J. D.

2016-09-01

The phase space of an area-preserving map typically contains infinitely many elliptic islands embedded in a chaotic sea. Orbits near the boundary of a chaotic region have been observed to stick for long times, strongly influencing their transport properties. The boundary is composed of invariant "boundary circles." We briefly report recent results of the distribution of rotation numbers of boundary circles for the Hénon quadratic map and show that the probability of occurrence of small integer entries of their continued fraction expansions is larger than would be expected for a number chosen at random. However, large integer entries occur with probabilities distributed proportionally to the random case. The probability distributions of ratios of fluxes through island chains is reported as well. These island chains are neighbours in the sense of the Meiss-Ott Markov-tree model. Two distinct universality families are found. The distributions of the ratio between the flux and orbital period are also presented. All of these results have implications for models of transport in mixed phase space.

Improved UTE-based attenuation correction for cranial PET-MR using dynamic magnetic field monitoring

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

Aitken, A. P.; Giese, D.; Tsoumpas, C.

2014-01-15

Purpose: Ultrashort echo time (UTE) MRI has been proposed as a way to produce segmented attenuation maps for PET, as it provides contrast between bone, air, and soft tissue. However, UTE sequences require samples to be acquired during rapidly changing gradient fields, which makes the resulting images prone to eddy current artifacts. In this work it is demonstrated that this can lead to misclassification of tissues in segmented attenuation maps (AC maps) and that these effects can be corrected for by measuring the true k-space trajectories using a magnetic field camera. Methods: The k-space trajectories during a dual echo UTEmore » sequence were measured using a dynamic magnetic field camera. UTE images were reconstructed using nominal trajectories and again using the measured trajectories. A numerical phantom was used to demonstrate the effect of reconstructing with incorrect trajectories. Images of an ovine leg phantom were reconstructed and segmented and the resulting attenuation maps were compared to a segmented map derived from a CT scan of the same phantom, using the Dice similarity measure. The feasibility of the proposed method was demonstrated inin vivo cranial imaging in five healthy volunteers. Simulated PET data were generated for one volunteer to show the impact of misclassifications on the PET reconstruction. Results: Images of the numerical phantom exhibited blurring and edge artifacts on the bone–tissue and air–tissue interfaces when nominal k-space trajectories were used, leading to misclassification of soft tissue as bone and misclassification of bone as air. Images of the tissue phantom and thein vivo cranial images exhibited the same artifacts. The artifacts were greatly reduced when the measured trajectories were used. For the tissue phantom, the Dice coefficient for bone in MR relative to CT was 0.616 using the nominal trajectories and 0.814 using the measured trajectories. The Dice coefficients for soft tissue were 0.933 and 0.934 for the nominal and measured cases, respectively. For air the corresponding figures were 0.991 and 0.993. Compared to an unattenuated reference image, the mean error in simulated PET uptake in the brain was 9.16% when AC maps derived from nominal trajectories was used, with errors in the SUV{sub max} for simulated lesions in the range of 7.17%–12.19%. Corresponding figures when AC maps derived from measured trajectories were used were 0.34% (mean error) and −0.21% to +1.81% (lesions). Conclusions: Eddy current artifacts in UTE imaging can be corrected for by measuring the true k-space trajectories during a calibration scan and using them in subsequent image reconstructions. This improves the accuracy of segmented PET attenuation maps derived from UTE sequences and subsequent PET reconstruction.« less

Distribution of submerged aquatic vegetation in the St. Louis River estuary: Maps and models

EPA Science Inventory

In late summer of 2011 and 2012 we used echo-sounding gear to map the distribution of submerged aquatic vegetation (SAV) in the St. Louis River Estuary (SLRE). From these data we produced maps of SAV distribution and we created logistic models to predict the probability of occurr...

Models for loosely linked gene duplicates suggest lengthy persistence of both copies.

PubMed

O'Hely, Martin; Wockner, Leesa

2007-06-21

Consider the appearance of a duplicate copy of a gene at a locus linked loosely, if at all, to the locus at which the gene is usually found. If all copies of the gene are subject to non-functionalizing mutations, then two fates are possible: loss of functional copies at the duplicate locus (loss of duplicate expression), or loss of functional copies at the original locus (map change). This paper proposes a simple model to address the probability of map change, the time taken for a map change and/or loss of duplicate expression, and considers where in the spectrum between loss of duplicate expression and map change such a duplicate complex is likely to be found. The findings are: the probability of map change is always half the reciprocal of the population size N, the time for a map change to occur is order NlogN generations, and that there is a marked tendency for duplicates to remain near equi-frequency with the gene at the original locus for a large portion of that time. This is in excellent agreement with simulations.

Near-infrared voltage-sensitive fluorescent dyes optimized for optical mapping in blood-perfused myocardium.

PubMed

Matiukas, Arvydas; Mitrea, Bogdan G; Qin, Maochun; Pertsov, Arkady M; Shvedko, Alexander G; Warren, Mark D; Zaitsev, Alexey V; Wuskell, Joseph P; Wei, Mei-de; Watras, James; Loew, Leslie M

2007-11-01

Styryl voltage-sensitive dyes (e.g., di-4-ANEPPS) have been used successfully for optical mapping in cardiac cells and tissues. However, their utility for probing electrical activity deep inside the myocardial wall and in blood-perfused myocardium has been limited because of light scattering and high absorption by endogenous chromophores and hemoglobin at blue-green excitation wavelengths. The purpose of this study was to characterize two new styryl dyes--di-4-ANBDQPQ (JPW-6003) and di-4-ANBDQBS (JPW-6033)--optimized for blood-perfused tissue and intramural optical mapping. Voltage-dependent spectra were recorded in a model lipid bilayer. Optical mapping experiments were conducted in four species (mouse, rat, guinea pig, and pig). Hearts were Langendorff perfused using Tyrode's solution and blood (pig). Dyes were loaded via bolus injection into perfusate. Transillumination experiments were conducted in isolated coronary-perfused pig right ventricular wall preparations. The optimal excitation wavelength in cardiac tissues (650 nm) was >70 nm beyond the absorption maximum of hemoglobin. Voltage sensitivity of both dyes was approximately 10% to 20%. Signal decay half-life due to dye internalization was 80 to 210 minutes, which is 5 to 7 times slower than for di-4-ANEPPS. In transillumination mode, DeltaF/F was as high as 20%. In blood-perfused tissues, DeltaF/F reached 5.5% (1.8 times higher than for di-4-ANEPPS). We have synthesized and characterized two new near-infrared dyes with excitation/emission wavelengths shifted >100 nm to the red. They provide both high voltage sensitivity and 5 to 7 times slower internalization rate compared to conventional dyes. The dyes are optimized for deeper tissue probing and optical mapping of blood-perfused tissue, but they also can be used for conventional applications.

Vehicle Detection for RCTA/ANS (Autonomous Navigation System)

NASA Technical Reports Server (NTRS)

Brennan, Shane; Bajracharya, Max; Matthies, Larry H.; Howard, Andrew B.

2012-01-01

Using a stereo camera pair, imagery is acquired and processed through the JPLV stereo processing pipeline. From this stereo data, large 3D blobs are found. These blobs are then described and classified by their shape to determine which are vehicles and which are not. Prior vehicle detection algorithms are either targeted to specific domains, such as following lead cars, or are intensity- based methods that involve learning typical vehicle appearances from a large corpus of training data. In order to detect vehicles, the JPL Vehicle Detection (JVD) algorithm goes through the following steps: 1. Take as input a left disparity image and left rectified image from JPLV stereo. 2. Project the disparity data onto a two-dimensional Cartesian map. 3. Perform some post-processing of the map built in the previous step in order to clean it up. 4. Take the processed map and find peaks. For each peak, grow it out into a map blob. These map blobs represent large, roughly vehicle-sized objects in the scene. 5. Take these map blobs and reject those that do not meet certain criteria. Build descriptors for the ones that remain. Pass these descriptors onto a classifier, which determines if the blob is a vehicle or not. The probability of detection is the probability that if a vehicle is present in the image, is visible, and un-occluded, then it will be detected by the JVD algorithm. In order to estimate this probability, eight sequences were ground-truthed from the RCTA (Robotics Collaborative Technology Alliances) program, totaling over 4,000 frames with 15 unique vehicles. Since these vehicles were observed at varying ranges, one is able to find the probability of detection as a function of range. At the time of this reporting, the JVD algorithm was tuned to perform best at cars seen from the front, rear, or either side, and perform poorly on vehicles seen from oblique angles.

A tool for the estimation of the distribution of landslide area in R

NASA Astrophysics Data System (ADS)

Rossi, M.; Cardinali, M.; Fiorucci, F.; Marchesini, I.; Mondini, A. C.; Santangelo, M.; Ghosh, S.; Riguer, D. E. L.; Lahousse, T.; Chang, K. T.; Guzzetti, F.

2012-04-01

We have developed a tool in R (the free software environment for statistical computing, http://www.r-project.org/) to estimate the probability density and the frequency density of landslide area. The tool implements parametric and non-parametric approaches to the estimation of the probability density and the frequency density of landslide area, including: (i) Histogram Density Estimation (HDE), (ii) Kernel Density Estimation (KDE), and (iii) Maximum Likelihood Estimation (MLE). The tool is available as a standard Open Geospatial Consortium (OGC) Web Processing Service (WPS), and is accessible through the web using different GIS software clients. We tested the tool to compare Double Pareto and Inverse Gamma models for the probability density of landslide area in different geological, morphological and climatological settings, and to compare landslides shown in inventory maps prepared using different mapping techniques, including (i) field mapping, (ii) visual interpretation of monoscopic and stereoscopic aerial photographs, (iii) visual interpretation of monoscopic and stereoscopic VHR satellite images and (iv) semi-automatic detection and mapping from VHR satellite images. Results show that both models are applicable in different geomorphological settings. In most cases the two models provided very similar results. Non-parametric estimation methods (i.e., HDE and KDE) provided reasonable results for all the tested landslide datasets. For some of the datasets, MLE failed to provide a result, for convergence problems. The two tested models (Double Pareto and Inverse Gamma) resulted in very similar results for large and very large datasets (> 150 samples). Differences in the modeling results were observed for small datasets affected by systematic biases. A distinct rollover was observed in all analyzed landslide datasets, except for a few datasets obtained from landslide inventories prepared through field mapping or by semi-automatic mapping from VHR satellite imagery. The tool can also be used to evaluate the probability density and the frequency density of landslide volume.

'Real angiosome' assessment from peripheral tissue perfusion using tissue oxygen saturation foot-mapping in patients with critical limb ischemia.

PubMed

Kagaya, Y; Ohura, N; Suga, H; Eto, H; Takushima, A; Harii, K

2014-04-01

The "tissue oxygen saturation (StO2) foot-mapping" method was developed using a non-invasive near-infrared tissue oximeter monitor to classify the foot regions as ischemic and non-ischemic areas. The purpose of this study was to evaluate StO2 foot-mapping as a reliable method to detect ischemic areas in the feet of patients with critical limb ischemia (CLI), and to compare the results with assessments from the angiosome model. The foot areas of 20 CLI patients and 20 healthy controls were classified into four regions: (1) 0 ≤ StO2 < 30%, (2) 30 ≤ StO2 < 50%, (3) 50 ≤ StO2 < 70%, and (4) 70 ≤ StO2 ≤ 100% to perform StO2 foot-mapping. Each area occupancy rate was compared between the two groups, and the threshold StO2 value for detecting ischemia was set. Next, the locations of ulcers (in 16 patients) were compared to the predicted ischemic regions by the StO2 foot-mapping and by the angiosome model and angiography. In regions (1) and (2) (StO2 < 50%), the area occupancy rate was significantly higher in the CLI group and almost zero in the control group, so that the threshold StO2 value for detecting ischemia was set at 50%. The locations of ulcers were compatible with StO2 foot-mapping in 87.5% of the cases (14/16), while they were compatible with the assessment from the angiosome model in 68.8% of the cases (11/16). This study suggests that StO2 foot-mapping can successfully and non-invasively detect ischemic areas in the peripheral tissue of the foot, and also more appropriately than the assessment provided by the angiosome model. StO2 foot-mapping can be used to evaluate the real angiosome: the real distribution of the peripheral tissue perfusion in the CLI patient's foot, which is determined by the peripheral microvascular blood flow, rather than the main arterial blood flow. Copyright © 2013 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.

A direct approach to estimating the number of potential fatalities from an eruption: Application to the Central Volcanic Complex of Tenerife Island

NASA Astrophysics Data System (ADS)

Marrero, J. M.; García, A.; Llinares, A.; Rodriguez-Losada, J. A.; Ortiz, R.

2012-03-01

One of the critical issues in managing volcanic crises is making the decision to evacuate a densely-populated region. In order to take a decision of such importance it is essential to estimate the cost in lives for each of the expected eruptive scenarios. One of the tools that assist in estimating the number of potential fatalities for such decision-making is the calculation of the FN-curves. In this case the FN-curve is a graphical representation that relates the frequency of the different hazards to be expected for a particular volcano or volcanic area, and the number of potential fatalities expected for each event if the zone of impact is not evacuated. In this study we propose a method for assessing the impact that a possible eruption from the Tenerife Central Volcanic Complex (CVC) would have on the population at risk. Factors taken into account include the spatial probability of the eruptive scenarios (susceptibility) and the temporal probability of the magnitudes of the eruptive scenarios. For each point or cell of the susceptibility map with greater probability, a series of probability-scaled hazard maps is constructed for the whole range of magnitudes expected. The number of potential fatalities is obtained from the intersection of the hazard maps with the spatial map of population distribution. The results show that the Emergency Plan for Tenerife must provide for the evacuation of more than 100,000 persons.

Application of the FINDER system to the search for epithermal vein gold-silver deposits : Kushikino, Japan, a case study

USGS Publications Warehouse

Singer, Donald A.; Kouda, Ryoichi

1991-01-01

The FINDER system employs geometric probability, Bayesian statistics, and the normal probability density function to integrate spatial and frequency information to produce a map of probabilities of target centers. Target centers can be mineral deposits, alteration associated with mineral deposits, or any other target that can be represented by a regular shape on a two dimensional map. The size, shape, mean, and standard deviation for each variable are characterized in a control area and the results applied by means of FINDER to the study area. The Kushikino deposit consists of groups of quartz-calcite-adularia veins that produced 55 tonnes of gold and 456 tonnes of silver since 1660. Part of a 6 by 10 km area near Kushikino served as a control area. Within the control area, data plotting, contouring, and cluster analysis were used to identify the barren and mineralized populations. Sodium was found to be depleted in an elliptically shaped area 3.1 by 1.6 km, potassium was both depleted and enriched locally in an elliptically shaped area 3.0 by 1.3 km, and sulfur was enriched in an elliptically shaped area 5.8 by 1.6 km. The potassium, sodium, and sulfur content from 233 surface rock samples were each used in FINDER to produce probability maps for the 12 by 30 km study area which includes Kushikino. High probability areas for each of the individual variables are over and offset up to 4 km eastward from the main Kushikino veins. In general, high probability areas identified by FINDER are displaced from the main veins and cover not only the host andesite and the dacite-andesite that is about the same age as the Kushikino mineralization, but also younger sedimentary rocks, andesite, and tuff units east and northeast of Kushikino. The maps also display the same patterns observed near Kushikino, but with somewhat lower probabilities, about 1.5 km east of the old gold prospect, Hajima, and in a broad zone 2.5 km east-west and 1 km north-south, centered 2 km west of the old gold prospect, Yaeyama.

Structure changes of human brain gray matter neurons and astrocytes in acute local ischemic injury.

PubMed

Sergeeva, S P; Shishkina, L V; Litvitskiy, P F; Breslavich, I D; Vinogradov, E V

2016-01-01

The purpose to identify key morphological features of the Astrocytes and Neurons in the acute local cerebral ischemia human cortex. Left middle cerebral artery ischemic stroke died persons (n = 9) brain tissue samples from 3 zones: 1st - contiguous to the tissue necrotic damage site zone, 2nd - 5-10 cm distant from the previous one, 3rd - the damage site symmetrical zone of the contralateral hemisphere. For GFAP, MAP-2, NSE, p53 detection indirect immunoperoxidase immunohistochemical staining method has been used. Also, the samples were Nissl and Hematoxylin-Eosin stained. The most pronounced changes in the quantity and morphological structure of astrocytes and neurons are found in directly adjacent to the necrotic core region of theleft middle cerebral artery ischemic stroke brain. This indicates the prevalence of the inflammation processes around the area of nerve tissueischemic destruction. Morphological changes of neurons and astrocytes, apoptosis, enhanced neuron-astrocyte interaction found in the area bordering on necrotic core (5-10 cm from it), as well as ischemic hearth symmetrical sites of the contralateral hemisphere. This interaction is essential for the neuroplasticityrealization in the local ischemic brain injury. The results obtained were shown the nerve tissue morphological characteristics changes occur in local cerebral cortex ischemic injury not only in the lesion, but also in the contralateral hemisphere. These changes are probably related to the implementation of neuroplasticity.

Quantitative analysis of tissue deformation dynamics reveals three characteristic growth modes and globally aligned anisotropic tissue deformation during chick limb development.

PubMed

Morishita, Yoshihiro; Kuroiwa, Atsushi; Suzuki, Takayuki

2015-05-01

Tissue-level characterization of deformation dynamics is crucial for understanding organ morphogenetic mechanisms, especially the interhierarchical links among molecular activities, cellular behaviors and tissue/organ morphogenetic processes. Limb development is a well-studied topic in vertebrate organogenesis. Nevertheless, there is still little understanding of tissue-level deformation relative to molecular and cellular dynamics. This is mainly because live recording of detailed cell behaviors in whole tissues is technically difficult. To overcome this limitation, by applying a recently developed Bayesian approach, we here constructed tissue deformation maps for chick limb development with high precision, based on snapshot lineage tracing using dye injection. The precision of the constructed maps was validated with a clear statistical criterion. From the geometrical analysis of the map, we identified three characteristic tissue growth modes in the limb and showed that they are consistent with local growth factor activity and cell cycle length. In particular, we report that SHH signaling activity changes dynamically with developmental stage and strongly correlates with the dynamic shift in the tissue growth mode. We also found anisotropic tissue deformation along the proximal-distal axis. Morphogenetic simulation and experimental studies suggested that this directional tissue elongation, and not local growth, has the greatest impact on limb shaping. This result was supported by the novel finding that anisotropic tissue elongation along the proximal-distal axis occurs independently of cell proliferation. Our study marks a pivotal point for multi-scale system understanding in vertebrate development. © 2015. Published by The Company of Biologists Ltd.

Tactile mapping system: a novel imaging technology for surface topography and elasticity of tissues or organs.

PubMed

Oie, Tomonori; Suzuki, Hisato; Fukuda, Toru; Murayama, Yoshinobu; Omata, Sadao; Kanda, Keiichi; Nakayama, Yasuhide

2009-11-01

: We demonstrated that the tactile mapping system (TMS) has a high degree of spatial precision in the distribution mapping of surface elasticity of tissues or organs. : Samples used were a circumferential section of a small-caliber porcine artery (diameter: ∼3 mm) and an elasticity test pattern with a line and space configuration for the distribution mapping of elasticity, prepared by regional micropatterning of a 14-μm thick gelatin hydrogel coating on a polyurethane sheet. Surface topography and elasticity in normal saline were simultaneously investigated by TMS using a probe with a diameter of 5 or 12 μm, a spatial interval of 1 to 5 μm, and an indentation depth of 4 μm. : In the test pattern, a spatial resolution in TMS of <5 μm was acquired under water with a minimal probe diameter and spatial interval of the probe movement. TMS was used for the distribution mapping of surface elasticity in a flat, circumferential section (thickness: ∼0.5 mm) of a porcine artery, and the concentric layers of the vascular wall, including the collagen-rich and elastin-rich layers, could be clearly differentiated in terms of surface elasticity at the spatial resolution of <2 μm. : TMS is a simple and inexpensive technique for the distribution mapping of the surface elasticity in vascular tissues at the spatial resolution <2 μm. TMS has the ability to analyze a complex structure of the tissue samples under normal saline.

Pyroclastic density current hazard maps at Campi Flegrei caldera (Italy): the effects of event scale, vent location and time forecasts.

NASA Astrophysics Data System (ADS)

Bevilacqua, Andrea; Neri, Augusto; Esposti Ongaro, Tomaso; Isaia, Roberto; Flandoli, Franco; Bisson, Marina

2016-04-01

Today hundreds of thousands people live inside the Campi Flegrei caldera (Italy) and in the adjacent part of the city of Naples making a future eruption of such volcano an event with huge consequences. Very high risks are associated with the occurrence of pyroclastic density currents (PDCs). Mapping of background or long-term PDC hazard in the area is a great challenge due to the unknown eruption time, scale and vent location of the next event as well as the complex dynamics of the flow over the caldera topography. This is additionally complicated by the remarkable epistemic uncertainty on the eruptive record, affecting the time of past events, the location of vents as well as the PDCs areal extent estimates. First probability maps of PDC invasion were produced combining a vent-opening probability map, statistical estimates concerning the eruptive scales and a Cox-type temporal model including self-excitement effects, based on the eruptive record of the last 15 kyr. Maps were produced by using a Monte Carlo approach and adopting a simplified inundation model based on the "box model" integral approximation tested with 2D transient numerical simulations of flow dynamics. In this presentation we illustrate the independent effects of eruption scale, vent location and time of forecast of the next event. Specific focus was given to the remarkable differences between the eastern and western sectors of the caldera and their effects on the hazard maps. The analysis allowed to identify areas with elevated probabilities of flow invasion as a function of the diverse assumptions made. With the quantification of some sources of uncertainty in relation to the system, we were also able to provide mean and percentile maps of PDC hazard levels.

Probabilistic self-organizing maps for continuous data.

PubMed

Lopez-Rubio, Ezequiel

2010-10-01

The original self-organizing feature map did not define any probability distribution on the input space. However, the advantages of introducing probabilistic methodologies into self-organizing map models were soon evident. This has led to a wide range of proposals which reflect the current emergence of probabilistic approaches to computational intelligence. The underlying estimation theories behind them derive from two main lines of thought: the expectation maximization methodology and stochastic approximation methods. Here, we present a comprehensive view of the state of the art, with a unifying perspective of the involved theoretical frameworks. In particular, we examine the most commonly used continuous probability distributions, self-organization mechanisms, and learning schemes. Special emphasis is given to the connections among them and their relative advantages depending on the characteristics of the problem at hand. Furthermore, we evaluate their performance in two typical applications of self-organizing maps: classification and visualization.

Porcine MAP3K5 analysis: molecular cloning, characterization, tissue expression pattern, and copy number variations associated with residual feed intake.

PubMed

Pu, L; Zhang, L C; Zhang, J S; Song, X; Wang, L G; Liang, J; Zhang, Y B; Liu, X; Yan, H; Zhang, T; Yue, J W; Li, N; Wu, Q Q; Wang, L X

2016-08-12

Mitogen-activated protein kinase kinase kinase 5 (MAP3K5) is essential for apoptosis, proliferation, differentiation, and immune responses, and is a candidate marker for residual feed intake (RFI) in pig. We cloned the full-length cDNA sequence of porcine MAP3K5 by rapid-amplification of cDNA ends. The 5451-bp gene contains a 5'-untranslated region (UTR) (718 bp), a coding region (3738 bp), and a 3'-UTR (995 bp), and encodes a peptide of 1245 amino acids, which shares 97, 99, 97, 93, 91, and 84% sequence identity with cattle, sheep, human, mouse, chicken, and zebrafish MAP3K5, respectively. The deduced MAP3K5 protein sequence contains two conserved domains: a DUF4071 domain and a protein kinase domain. Phylogenetic analysis showed that porcine MAP3K5 forms a separate branch to vicugna and camel MAP3K5. Tissue expression analysis using real-time quantitative polymerase chain reaction (qRT-PCR) revealed that MAP3K5 was expressed in the heart, liver, spleen, lung, kidney, muscle, fat, pancrea, ileum, and stomach tissues. Copy number variation was detected for porcine MAP3K5 and validated by qRT-PCR. Furthermore, a significant increase in average copy number was detected in the low RFI group when compared to the high RFI group in a Duroc pig population. These results provide useful information regarding the influence of MAP3K5 on RFI in pigs.

Coupling between arterial pressure, cerebral blood velocity, and cerebral tissue oxygenation with spontaneous and forced oscillations.

PubMed

Rickards, Caroline A; Sprick, Justin D; Colby, Hannah B; Kay, Victoria L; Tzeng, Yu-Chieh

2015-04-01

We tested the hypothesis that transmission of arterial pressure to brain tissue oxygenation is low under conditions of arterial pressure instability. Two experimental models of hemodynamic instability were used in healthy human volunteers; (1) oscillatory lower body negative pressure (OLBNP) (N = 8; 5 male, 3 female), and; (2) maximal LBNP to presyncope (N = 21; 13 male, 8 female). Mean arterial pressure (MAP), middle cerebral artery velocity (MCAv), and cerebral tissue oxygen saturation (ScO2) were measured non-invasively. For the OLBNP protocol, between 0 and -60 mmHg negative pressure was applied for 20 cycles at 0.05 Hz, then 20 cycles at 0.1 Hz. For the maximal LBNP protocol, progressive 5 min stages of chamber decompression were applied until the onset of presyncope. Spectral power of MAP, mean MCAv, and ScO2 were calculated within the VLF (0.04-0.07 Hz), and LF (0.07-0.2 Hz) ranges, and cross-spectral coherence was calculated for MAP-mean MCAv, MAP-ScO2, and mean MCAv-ScO2 at baseline, during each OLBNP protocol, and at the level prior to pre-syncope during maximal LBNP (sub-max). The key findings are (1) both 0.1 Hz OLBNP and sub-max LBNP elicited increases in LF power for MAP, mean MCAv, and ScO2 (p ≤ 0.08); (2) 0.05 Hz OLBNP increased VLF power in MAP and ScO2 only (p ≤ 0.06); (3) coherence between MAP-mean MCAv was consistently higher (≥0.71) compared with MAP-ScO2, and mean MCAv-ScO2 (≤0.43) during both OLBNP protocols, and sub-max LBNP (p ≤ 0.04). These data indicate high linearity between pressure and cerebral blood flow variations, but reduced linearity between cerebral tissue oxygenation and both arterial pressure and cerebral blood flow. Measuring arterial pressure variability may not always provide adequate information about the downstream effects on cerebral tissue oxygenation, the key end-point of interest for neuronal viability.

Notochordal cells in the adult intervertebral disc: new perspective on an old question.

PubMed

Risbud, Makarand V; Shapiro, Irving M

2011-01-01

The intervertebral disc is a tissue positioned between each of the vertebrae that accommodates applied biomechanical forces to the spine. The central compartment of the disc contains the nucleus pulposus (NP) which is enclosed by the annulus fibrosus and the endplate cartilage.The NP is derived from the notochord, a rod-like structure of mesodermal origin. Development of the notochord is tightly regulated by interactive transcription factors and target genes. Since a number of these molecules are unique they have be used for cell lineage and fate mapping studies of tissues of the intervertebral disc. These studies have shown that in a number of species including human, NP tissue retains notochordal cells throughout life. In the adult NP, there are present both large and small notochordal cells, as well as a progenitor cell population which can differentiate along the mesengenic pathway. Since tissue renewal in the intervertebral disc is dependent on the ability of these cells to commit to the NP lineage and undergo terminal differentiation, studies have been performed to assess which signaling pathways may regulate these activities. The notch signaling pathway is active in the intervertebral disc and is responsive to hypoxia, probably through HIF-1a. From a disease viewpoint, it is hypothesized that an oxemic shift, possibly mediated by alterations in the vascular supply to the tissues of the disc would be expected to lead to a failure in notochordal progenitor cell activation and a decrease in the number of differentiated cells. In turn, this would lead to decrements in function and enhancement of the effect of agents that are known to promote disc degeneration.

An electrical impedance tomography (EIT) multi-electrode needle-probe device for local assessment of heterogeneous tissue impeditivity.

PubMed

Meroni, Davide; Maglioli, Camilla Carpano; Bovio, Dario; Greco, Francesco G; Aliverti, Andrea

2017-07-01

Electrical Impedance Tomography (EIT) is an image reconstruction technique applied in medicine for the electrical imaging of living tissues. In literature there is the evidence that a large resistivity variation related to the differences of the human tissues exists. As a result of this interest for the electrical characterization of the biological samples, recently the attention is also focused on the identification and characterization of the human tissue, by studying the homogeneity of its structure. An 8 electrodes needle-probe device has been developed with the intent of identifying the structural inhomogeneities under the surface layers. Ex-vivo impeditivity measurements, by placing the needle-probe in 5 different patterns of fat and lean porcine tissue, were performed, and impeditivity maps were obtained by EIDORS open source software for image reconstruction in electrical impedance. The values composing the maps have been analyzed, pointing out a good tissue discrimination, and the conformity with the real images. We conclude that this device is able to perform impeditivity maps matching to reality for position and orientation. In all the five patterns presented is possible to identify and replicate correctly the heterogeneous tissue under test. This new procedure can be helpful to the medical staff to completely characterize the biological sample, in different unclear situations.

On Voxel based Iso-Tumor Control Probabilty and Iso-Complication Maps for Selective Boosting and Selective Avoidance Intensity Modulated Radiotherapy

PubMed Central

Kim, Yusung; Tomé, Wolfgang A.

2010-01-01

Summary Voxel based iso-Tumor Control Probability (TCP) maps and iso-Complication maps are proposed as a plan-review tool especially for functional image-guided intensity-modulated radiotherapy (IMRT) strategies such as selective boosting (dose painting) and conformal avoidance IMRT. The maps employ voxel-based phenomenological biological dose-response models for target volumes and normal organs. Two IMRT strategies for prostate cancer, namely conventional uniform IMRT delivering an EUD = 84 Gy (equivalent uniform dose) to the entire PTV and selective boosting delivering an EUD = 82 Gy to the entire PTV, are investigated, to illustrate the advantages of this approach over iso-dose maps. Conventional uniform IMRT did yield a more uniform isodose map to the entire PTV while selective boosting did result in a nonuniform isodose map. However, when employing voxel based iso-TCP maps selective boosting exhibited a more uniform tumor control probability map compared to what could be achieved using conventional uniform IMRT, which showed TCP cold spots in high-risk tumor subvolumes despite delivering a higher EUD to the entire PTV. Voxel based iso-Complication maps are presented for rectum and bladder, and their utilization for selective avoidance IMRT strategies are discussed. We believe as the need for functional image guided treatment planning grows, voxel based iso-TCP and iso-Complication maps will become an important tool to assess the integrity of such treatment plans. PMID:21151734

Mapping of thermal injury in biologic tissues using quantitative pathologic techniques

NASA Astrophysics Data System (ADS)

Thomsen, Sharon L.

1999-05-01

Qualitative and quantitative pathologic techniques can be used for (1) mapping of thermal injury, (2) comparisons lesion sizes and configurations for different instruments or heating sources and (3) comparisons of treatment effects. Concentric zones of thermal damage form around a single volume heat source. The boundaries between some of these zones are distinct and measurable. Depending on the energy deposition, heating times and tissue type, the zones can include the following beginning at the hotter center and progressing to the cooler periphery: (1) tissue ablation, (2) carbonization, (3) tissue water vaporization, (4) structural protein denaturation (thermal coagulation), (5) vital enzyme protein denaturation, (6) cell membrane disruption, (7) hemorrhage, hemostasis and hyperhemia, (8) tissue necrosis and (9) wound organization and healing.

Effect of Cisplatin on Parotid Gland Function in Concomitant Radiochemotherapy

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

Hey, Jeremias; Setz, Juergen; Gerlach, Reinhard

2009-12-01

Purpose: To determine the influence of concomitant radiochemotherapy with cisplatin on parotid gland tissue complication probability. Methods and Materials: Patients treated with either radiotherapy (n = 61) or concomitant radiochemotherapy with cisplatin (n = 36) for head-and-neck cancer were prospectively evaluated. The dose and volume distributions of the parotid glands were noted in dose-volume histograms. Stimulated salivary flow rates were measured before, during the 2nd and 6th weeks and at 4 weeks and 6 months after the treatment. The data were fit using the normal tissue complication probability model of Lyman. Complication was defined as a reduction of the salivarymore » flow rate to less than 25% of the pretreatment flow rate. Results: The normal tissue complication probability model parameter TD{sub 50} (the dose leading to a complication probability of 50%) was found to be 32.2 Gy at 4 weeks and 32.1 Gy at 6 months for concomitant radiochemotherapy and 41.1 Gy at 4 weeks and 39.6 Gy at 6 months for radiotherapy. The tolerated dose for concomitant radiochemotherapy was at least 7 to 8 Gy lower than for radiotherapy alone at TD{sub 50}. Conclusions: In this study, the concomitant radiochemotherapy tended to cause a higher probability of parotid gland tissue damage. Advanced radiotherapy planning approaches such as intensity-modulated radiotherapy may be partiticularly important for parotid sparing in radiochemotherapy because of cisplatin-related increased radiosensitivity of glands.« less

Spatial cluster analysis of nanoscopically mapped serotonin receptors for classification of fixed brain tissue

NASA Astrophysics Data System (ADS)

Sams, Michael; Silye, Rene; Göhring, Janett; Muresan, Leila; Schilcher, Kurt; Jacak, Jaroslaw

2014-01-01

We present a cluster spatial analysis method using nanoscopic dSTORM images to determine changes in protein cluster distributions within brain tissue. Such methods are suitable to investigate human brain tissue and will help to achieve a deeper understanding of brain disease along with aiding drug development. Human brain tissue samples are usually treated postmortem via standard fixation protocols, which are established in clinical laboratories. Therefore, our localization microscopy-based method was adapted to characterize protein density and protein cluster localization in samples fixed using different protocols followed by common fluorescent immunohistochemistry techniques. The localization microscopy allows nanoscopic mapping of serotonin 5-HT1A receptor groups within a two-dimensional image of a brain tissue slice. These nanoscopically mapped proteins can be confined to clusters by applying the proposed statistical spatial analysis. Selected features of such clusters were subsequently used to characterize and classify the tissue. Samples were obtained from different types of patients, fixed with different preparation methods, and finally stored in a human tissue bank. To verify the proposed method, samples of a cryopreserved healthy brain have been compared with epitope-retrieved and paraffin-fixed tissues. Furthermore, samples of healthy brain tissues were compared with data obtained from patients suffering from mental illnesses (e.g., major depressive disorder). Our work demonstrates the applicability of localization microscopy and image analysis methods for comparison and classification of human brain tissues at a nanoscopic level. Furthermore, the presented workflow marks a unique technological advance in the characterization of protein distributions in brain tissue sections.

Simulation of ultrasonic pulse propagation, distortion, and attenuation in the human chest wall.

PubMed

Mast, T D; Hinkelman, L M; Metlay, L A; Orr, M J; Waag, R C

1999-12-01

A finite-difference time-domain model for ultrasonic pulse propagation through soft tissue has been extended to incorporate absorption effects as well as longitudinal-wave propagation in cartilage and bone. This extended model has been used to simulate ultrasonic propagation through anatomically detailed representations of chest wall structure. The inhomogeneous chest wall tissue is represented by two-dimensional maps determined by staining chest wall cross sections to distinguish between tissue types, digitally scanning the stained cross sections, and mapping each pixel of the scanned images to fat, muscle, connective tissue, cartilage, or bone. Each pixel of the tissue map is then assigned a sound speed, density, and absorption value determined from published measurements and assumed to be representative of the local tissue type. Computational results for energy level fluctuations and arrival time fluctuations show qualitative agreement with measurements performed on the same specimens, but show significantly less waveform distortion than measurements. Visualization of simulated tissue-ultrasound interactions in the chest wall shows possible mechanisms for image aberration in echocardiography, including effects associated with reflection and diffraction caused by rib structures. A comparison of distortion effects for varying pulse center frequencies shows that, for soft tissue paths through the chest wall, energy level and waveform distortion increase markedly with rising ultrasonic frequency and that arrival-time fluctuations increase to a lesser degree.

Spatially resolved proteome mapping of laser capture microdissected tissue with automated sample transfer to nanodroplets.

PubMed

Zhu, Ying; Dou, Maowei; Piehowski, Paul D; Liang, Yiran; Wang, Fangjun; Chu, Rosalie K; Chrisler, Will; Smith, Jordan N; Schwarz, Kaitlynn C; Shen, Yufeng; Shukla, Anil K; Moore, Ronald J; Smith, Richard D; Qian, Wei-Jun; Kelly, Ryan T

2018-06-24

Current mass spectrometry (MS)-based proteomics approaches are ineffective for mapping protein expression in tissue sections with high spatial resolution due to the limited overall sensitivity of conventional workflows. Here we report an integrated and automated method to advance spatially resolved proteomics by seamlessly coupling laser capture microdissection (LCM) with a recently developed nanoliter-scale sample preparation system termed nanoPOTS (Nanodroplet Processing in One pot for Trace Samples). The workflow is enabled by prepopulating nanowells with DMSO, which serves as a sacrificial capture liquid for microdissected tissues. The DMSO droplets efficiently collect laser-pressure catapulted LCM tissues as small as 20 µm in diameter with success rates >87%. We also demonstrate that tissue treatment with DMSO can significantly improve proteome coverage, likely due to its ability to dissolve lipids from tissue and enhance protein extraction efficiency. The LCM-nanoPOTS platform was able to identify 180, 695, and 1827 protein groups on average from 12-µm-thick rat brain cortex tissue sections with diameters of 50, 100, and 200 µm, respectively. We also analyzed 100-µm-diameter sections corresponding to 10-18 cells from three different regions of rat brain and comparatively quantified ~1000 proteins, demonstrating the potential utility for high-resolution spatially resolved mapping of protein expression in tissues. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

A systematical analysis of in vivo contact forces on virtual catheter tip/tissue surface contact during cardiac mapping and intervention.

PubMed

Okumura, Yasuo; Johnson, Susan B; Bunch, T Jared; Henz, Benhur D; O'Brien, Christine J; Packer, Douglas L

2008-06-01

While catheter tip/tissue contact has been shown to be an important determinant of ablative lesions in in vitro studies, the impact of contact on the outcomes of mapping and ablation in the intact heart has not been evaluated. Twelve dogs underwent atrial ablation guided by the Senesitrade mark robotic catheter remote control system. After intracardiac ultrasound (ICE) validation of contact force measured by an in-line mechanical sensor, the relationship between contact force and individual lesion formation was established during irrigated-tipped ablation (flow 17 mL/sec) at 15 watts for 30 seconds. Minimal contact by ICE correlated with force of 4.7 +/- 5.8 grams, consistent contact 9.9 +/- 8.6 grams and tissue tenting produced 25.0 +/- 14.0 grams. Conversely, catheter tip/tissue contact by ICE was predicted by contact force. A contact force of 10-20 and > or =20 grams generated full-thickness, larger volume ablative lesions than that created with <10 grams (98 +/- 69 and 89 +/- 70 mm(3) vs 40 +/- 42 mm(3), P < 0.05). Moderate (10 grams) and marked contact (15-20 grams) application produced 1.5 X greater electroanatomic map volumes that were seen with minimal contact (5 grams) (26 +/- 3 cm(3) vs 33 +/- 6, 39 +/- 3 cm(3), P < 0.05). The electroanatomic map/CT merge process was also more distorted when mapping was generated at moderate to marked contact force. This study shows that mapping and ablation using a robotic sheath guidance system are critically dependent on generated force. These findings suggest that ablative lesion size is optimized by the application of 10-20 grams of contact force, although mapping requires lower-force application to avoid image distortions.

A Monte Carlo study of fluorescence generation probability in a two-layered tissue model

NASA Astrophysics Data System (ADS)

Milej, Daniel; Gerega, Anna; Wabnitz, Heidrun; Liebert, Adam

2014-03-01

It was recently reported that the time-resolved measurement of diffuse reflectance and/or fluorescence during injection of an optical contrast agent may constitute a basis for a technique to assess cerebral perfusion. In this paper, we present results of Monte Carlo simulations of the propagation of excitation photons and tracking of fluorescence photons in a two-layered tissue model mimicking intra- and extracerebral tissue compartments. Spatial 3D distributions of the probability that the photons were converted from excitation to emission wavelength in a defined voxel of the medium (generation probability) during their travel between source and detector were obtained for different optical properties in intra- and extracerebral tissue compartments. It was noted that the spatial distribution of the generation probability depends on the distribution of the fluorophore in the medium and is influenced by the absorption of the medium and of the fluorophore at excitation and emission wavelengths. Simulations were also carried out for realistic time courses of the dye concentration in both layers. The results of the study show that the knowledge of the absorption properties of the medium at excitation and emission wavelengths is essential for the interpretation of the time-resolved fluorescence signals measured on the surface of the head.

Real-Time Vision-Based Stiffness Mapping †

PubMed Central

Althoefer, Kaspar; Asama, Hajime

2018-01-01

This paper presents new findings concerning a hand-held stiffness probe for the medical diagnosis of abnormalities during palpation of soft-tissue. Palpation is recognized by the medical community as an essential and low-cost method to detect and diagnose disease in soft-tissue. However, differences are often subtle and clinicians need to train for many years before they can conduct a reliable diagnosis. The probe presented here fills this gap providing a means to easily obtain stiffness values of soft tissue during a palpation procedure. Our stiffness sensor is equipped with a multi degree of freedom (DoF) Aurora magnetic tracker, allowing us to track and record the 3D position of the probe whilst examining a tissue area, and generate a 3D stiffness map in real-time. The stiffness probe was integrated in a robotic arm and tested in an artificial environment representing a good model of soft tissue organs; the results show that the sensor can accurately measure and map the stiffness of a silicon phantom embedded with areas of varying stiffness. PMID:29701704

Probabilistic storm surge inundation maps for Metro Manila based on Philippine public storm warning signals

NASA Astrophysics Data System (ADS)

Tablazon, J.; Caro, C. V.; Lagmay, A. M. F.; Briones, J. B. L.; Dasallas, L.; Lapidez, J. P.; Santiago, J.; Suarez, J. K.; Ladiero, C.; Gonzalo, L. A.; Mungcal, M. T. F.; Malano, V.

2015-03-01

A storm surge is the sudden rise of sea water over the astronomical tides, generated by an approaching storm. This event poses a major threat to the Philippine coastal areas, as manifested by Typhoon Haiyan on 8 November 2013. This hydro-meteorological hazard is one of the main reasons for the high number of casualties due to the typhoon, with 6300 deaths. It became evident that the need to develop a storm surge inundation map is of utmost importance. To develop these maps, the Nationwide Operational Assessment of Hazards under the Department of Science and Technology (DOST-Project NOAH) simulated historical tropical cyclones that entered the Philippine Area of Responsibility. The Japan Meteorological Agency storm surge model was used to simulate storm surge heights. The frequency distribution of the maximum storm surge heights was calculated using simulation results of tropical cyclones under a specific public storm warning signal (PSWS) that passed through a particular coastal area. This determines the storm surge height corresponding to a given probability of occurrence. The storm surge heights from the model were added to the maximum astronomical tide data from WXTide software. The team then created maps of inundation for a specific PSWS using the probability of exceedance derived from the frequency distribution. Buildings and other structures were assigned a probability of exceedance depending on their occupancy category, i.e., 1% probability of exceedance for critical facilities, 10% probability of exceedance for special occupancy structures, and 25% for standard occupancy and miscellaneous structures. The maps produced show the storm-surge-vulnerable areas in Metro Manila, illustrated by the flood depth of up to 4 m and extent of up to 6.5 km from the coastline. This information can help local government units in developing early warning systems, disaster preparedness and mitigation plans, vulnerability assessments, risk-sensitive land use plans, shoreline defense efforts, and coastal protection measures. These maps can also determine the best areas to build critical structures, or at least determine the level of protection of these structures should they be built in hazard areas. Moreover, these will support the local government units' mandate to raise public awareness, disseminate information about storm surge hazards, and implement appropriate countermeasures for a given PSWS.

STOCHASTIC DUELS WITH HOMING,

DTIC Science & Technology

Duels where both marksmen ’home’ or ’zero in’ on one another are here considered, and the effect of this on the win probability is determined. It is...leads to win probabilities that can be straightforwardly evaluated. Maximum-likelihood estimation of the hit probability and homing from field data is outlined. The solutions of the duels are displayed as contour maps. (Author)

Expression of SNCG, MAP2, SDF-1 and CXCR4 in gastric adenocarcinoma and their clinical significance

PubMed Central

Zheng, Shufang; Shi, Lifang; Zhang, Yi; He, Tao

2014-01-01

Objectives: The purpose of the study was to detect the expression of SNCG, MAP2, SDF-1 and CXCR4 in gastric adenocarcinoma, and to evaluate their roles in the carcinogenesis of gastric adenocarcinoma, development, invasion and metastasis as well as their clinical significance. Methods: The expression of SNCG, MAP2, SDF-1 and CXCR4 was detected by SP immunohistochemical method in 225 cases of gastric adenocarcinoma and 105 cases of nonneoplastic adjacent gastric tissue. The expression of SNCG, MAP2, SDF-1 and CXCR4 mRNA was also detected by RT-PCR method in 50 cases of gastric adenocarcinoma and 30 cases of nonneoplastic adjacent gastric tissue. Results: The expression of SNCG, MAP2, SDF-1 and CXCR4 in the gastric adenocarcinoma was remarkably higher than those in the nonneoplastic adjacent gastric tissue (P < 0.01); The positive expression of SNCG and MAP2 was correlated with the depth of tumor invasion and the metastasis of lymph nodes (P < 0.05), and that of SDF-1 and CXCR4 was correlated with the metastasis of lymph nodes (P < 0.05). Conclusions: SNCG, MAP2, SDF-1 and CXCR4 may play an important role in the carcinogenesis, progression, invasion and metastasis of gastric adenocarcinoma. However, it still needs more exploration whether they can serve as promising therapeutic targets of gastric adenocarcinoma. PMID:25400739

Complex Geometric Models of Diffusion and Relaxation in Healthy and Damaged White Matter

PubMed Central

Farrell, Jonathan A.D.; Smith, Seth A.; Reich, Daniel S.; Calabresi, Peter A.; van Zijl, Peter C.M.

2010-01-01

Which aspects of tissue microstructure affect diffusion weighted MRI signals? Prior models, many of which use Monte-Carlo simulations, have focused on relatively simple models of the cellular microenvironment and have not considered important anatomic details. With the advent of higher-order analysis models for diffusion imaging, such as high-angular-resolution diffusion imaging (HARDI), more realistic models are necessary. This paper presents and evaluates the reproducibility of simulations of diffusion in complex geometries. Our framework is quantitative, does not require specialized hardware, is easily implemented with little programming experience, and is freely available as open-source software. Models may include compartments with different diffusivities, permeabilities, and T2 time constants using both parametric (e.g., spheres and cylinders) and arbitrary (e.g., mesh-based) geometries. Three-dimensional diffusion displacement-probability functions are mapped with high reproducibility, and thus can be readily used to assess reproducibility of diffusion-derived contrasts. PMID:19739233

Mapping Irrigated Areas in the Tunisian Semi-Arid Context with Landsat Thermal and VNIR Data Imagery

NASA Astrophysics Data System (ADS)

Rivalland, Vincent; Drissi, Hsan; Simonneaux, Vincent; Tardy, Benjamin; Boulet, Gilles

2016-04-01

Our study area is the Merguellil semi-arid irrigated plain in Tunisia, where the water resource management is an important stake for governmental institutions, farmer communities and more generally for the environment. Indeed, groundwater abstraction for irrigation is the primary cause of aquifer depletion. Moreover, unregistered pumping practices are widespread and very difficult to survey by authorities. Thus, the identification of areas actually irrigated in the whole plain is of major interest. In order to map the irrigated areas, we tried out a methodology based on the use of Landsat 7 and 8 Land Surface Temperature (LST) data issued from atmospherically corrected thermal band using the LANDARTs Tool jointly with the NDVI vegetation indices obtained from visible ane near infrared (VNIR) bands. For each Landsat acquisition during the years 2012 to 2014, we computed a probability of irrigation based on the location of the pixel in the NDVI - LST space. Basically for a given NDVI value, the cooler the pixel the higher its probability to be irrigated is. For each date, pixels were classified in seven bins of irrigation probability ranges. Pixel probabilities for each date were then summed over the study period resulting in a probability map of irrigation. Comparison with ground data shows a consistent identification of irrigated plots and supports the potential operational interest of the method. However, results were hampered by the low Landsat LST data availability due to clouds and the inadequate revisit frequency of the sensor.

Effects of surrounding land use and water depth on seagrass dynamics relative to a catastrophic algal bloom.

PubMed

Breininger, David R; Breininger, Robert D; Hall, Carlton R

2017-02-01

Seagrasses are the foundation of many coastal ecosystems and are in global decline because of anthropogenic impacts. For the Indian River Lagoon (Florida, U.S.A.), we developed competing multistate statistical models to quantify how environmental factors (surrounding land use, water depth, and time [year]) influenced the variability of seagrass state dynamics from 2003 to 2014 while accounting for time-specific detection probabilities that quantified our ability to determine seagrass state at particular locations and times. We classified seagrass states (presence or absence) at 764 points with geographic information system maps for years when seagrass maps were available and with aerial photographs when seagrass maps were not available. We used 4 categories (all conservation, mostly conservation, mostly urban, urban) to describe surrounding land use within sections of lagoonal waters, usually demarcated by land features that constricted these waters. The best models predicted that surrounding land use, depth, and year would affect transition and detection probabilities. Sections of the lagoon bordered by urban areas had the least stable seagrass beds and lowest detection probabilities, especially after a catastrophic seagrass die-off linked to an algal bloom. Sections of the lagoon bordered by conservation lands had the most stable seagrass beds, which supports watershed conservation efforts. Our results show that a multistate approach can empirically estimate state-transition probabilities as functions of environmental factors while accounting for state-dependent differences in seagrass detection probabilities as part of the overall statistical inference procedure. © 2016 Society for Conservation Biology.

Source-receptor probability of atmospheric long-distance dispersal of viruses to Israel from the eastern Mediterranean area.

PubMed

Klausner, Z; Klement, E; Fattal, E

2018-02-01

Viruses that affect the health of humans and farm animals can spread over long distances via atmospheric mechanisms. The phenomenon of atmospheric long-distance dispersal (LDD) is associated with severe consequences because it may introduce pathogens into new areas. The introduction of new pathogens to Israel was attributed to LDD events numerous times. This provided the motivation for this study which is aimed to identify all the locations in the eastern Mediterranean that may serve as sources for pathogen incursion into Israel via LDD. This aim was achieved by calculating source-receptor relationship probability maps. These maps describe the probability that an infected vector or viral aerosol, once airborne, will have an atmospheric route that can transport it to a distant location. The resultant probability maps demonstrate a seasonal tendency in the probability of specific areas to serve as sources for pathogen LDD into Israel. Specifically, Cyprus' season is the summer; southern Turkey and the Greek islands of Crete, Karpathos and Rhodes are associated with spring and summer; lower Egypt and Jordan may serve as sources all year round, except the summer months. The method used in this study can easily be implemented to any other geographic region. The importance of this study is the ability to provide a climatologically valid and accurate risk assessment tool to support long-term decisions regarding preparatory actions for future outbreaks long before a specific outbreak occurs. © 2017 Blackwell Verlag GmbH.

In-vitro Thermal Maps to Characterize Human Dental Enamel and Dentin.

PubMed

Lancaster, Paula; Brettle, David; Carmichael, Fiona; Clerehugh, Val

2017-01-01

The crown of a human tooth has an outer layer of highly-mineralized tissue called enamel, beneath which is dentin, a less-mineralized tissue which forms the bulk of the tooth-crown and root. The composition and structure of enamel and dentin are different, resulting in different thermal properties. This gives an opportunity to characterize enamel and dentin from their thermal properties and to visually present the findings as a thermal map. The thermal properties of demineralized enamel and dentin may also be sufficiently different from sound tissue to be seen on a thermal map, underpinning future thermal assessment of caries. The primary aim of this novel study was to produce a thermal map of a sound, human tooth-slice to visually characterize enamel and dentin. The secondary aim was to map a human tooth-slice with demineralized enamel and dentin to consider future diagnostic potential of thermal maps for caries-detection. Two human slices of teeth, one sound and one demineralized from a natural carious lesion, were cooled on ice, then transferred to a hotplate at 30°C where the rewarming-sequence was captured by an infra-red thermal camera. Calculation of thermal diffusivity and thermal conductivity was undertaken, and two methods of data-processing used customized software to produce thermal maps from the thermal characteristic-time-to-relaxation and heat-exchange. The two types of thermal maps characterized enamel and dentin. In addition, sound and demineralized enamel and dentin were distinguishable within both maps. This supports thermal assessment of caries and requires further investigation on a whole tooth.

The monophasic action potential upstroke: a means of characterizing local conduction.

PubMed

Levine, J H; Moore, E N; Kadish, A H; Guarnieri, T; Spear, J F

1986-11-01

The upstrokes of monophasic action potentials (MAPs) recorded with an extracellular pressure electrode were characterized in isolated canine tissue preparations in vitro. The characteristics of the MAP upstroke were compared with those of the local action potential foot as well as with the characteristics of approaching electrical activation during uniform and asynchronous conduction. The upstroke of the MAP was exponential during uniform conduction. The time constant of rise of the MAP upstroke (TMAP) correlated with that of the action potential foot (Tfoot): TMAP + 1.01 Tfoot + 0.50; r2 = .80. Furthermore, changes in Tfoot with alterations in cycle length were associated with similar changes in TMAP: Tfoot = 1.06 TMAP - 0.11; r2 = .78. In addition, TMAP and Tfoot both deviated from exponential during asynchronous activation; the inflections that developed in the MAP upstroke correlated in time with intracellular action potential upstrokes that were asynchronous in onset in these tissues. Finally, the field of view of the MAP was determined and was found to be dependent in part on tissue architecture and the space constant. Specifically, the field of view of the MAP was found to be greater parallel compared with transverse to fiber orientation (6.02 +/- 1.74 vs 3.03 +/- 1.10 mm; p less than .01). These data suggest that the MAP upstroke may be used to define and characterize local electrical activation. The relatively large field of view of the MAP suggests that this technique may be a sensitive means to record focal membrane phenomena in vivo.

Using an ultrasound elasticity microscope to map three-dimensional strain in a porcine cornea.

PubMed

Hollman, Kyle W; Shtein, Roni M; Tripathy, Sakya; Kim, Kang

2013-08-01

An ultrasound elasticity microscope was used to map 3-D strain volume in an ex vivo porcine cornea to illustrate its ability to measure the mechanical properties of this tissue. Mechanical properties of the cornea play an important role in its function and, therefore, also in ophthalmic diseases such as kerataconus and corneal ectasia. The ultrasound elasticity microscope combines a tightly focused high-frequency transducer with confocal scanning to produce high-quality speckle over the entire volume of tissue. This system and the analysis were able to generate volume maps of compressional strain in all three directions for porcine corneal tissue, more information than any previous study has reported. Strain volume maps indicated features of the cornea and mechanical behavior as expected. These results constitute a step toward better understanding of corneal mechanics and better treatment of corneal diseases. Copyright © 2013 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Evansville Area Earthquake Hazards Mapping Project (EAEHMP) - Progress Report, 2008

USGS Publications Warehouse

Boyd, Oliver S.; Haase, Jennifer L.; Moore, David W.

2009-01-01

Maps of surficial geology, deterministic and probabilistic seismic hazard, and liquefaction potential index have been prepared by various members of the Evansville Area Earthquake Hazard Mapping Project for seven quadrangles in the Evansville, Indiana, and Henderson, Kentucky, metropolitan areas. The surficial geologic maps feature 23 types of surficial geologic deposits, artificial fill, and undifferentiated bedrock outcrop and include alluvial and lake deposits of the Ohio River valley. Probabilistic and deterministic seismic hazard and liquefaction hazard mapping is made possible by drawing on a wealth of information including surficial geologic maps, water well logs, and in-situ testing profiles using the cone penetration test, standard penetration test, down-hole shear wave velocity tests, and seismic refraction tests. These data were compiled and collected with contributions from the Indiana Geological Survey, Kentucky Geological Survey, Illinois State Geological Survey, United States Geological Survey, and Purdue University. Hazard map products are in progress and are expected to be completed by the end of 2009, with a public roll out in early 2010. Preliminary results suggest that there is a 2 percent probability that peak ground accelerations of about 0.3 g will be exceeded in much of the study area within 50 years, which is similar to the 2002 USGS National Seismic Hazard Maps for a firm rock site value. Accelerations as high as 0.4-0.5 g may be exceeded along the edge of the Ohio River basin. Most of the region outside of the river basin has a low liquefaction potential index (LPI), where the probability that LPI is greater than 5 (that is, there is a high potential for liquefaction) for a M7.7 New Madrid type event is only 20-30 percent. Within the river basin, most of the region has high LPI, where the probability that LPI is greater than 5 for a New Madrid type event is 80-100 percent.

Probability of detecting atrazine/desethyl-atrazine and elevated concentrations of nitrate in ground water in Colorado

USGS Publications Warehouse

Rupert, Michael G.

2003-01-01

Draft Federal regulations may require that each State develop a State Pesticide Management Plan for the herbicides atrazine, alachlor, metolachlor, and simazine. Maps were developed that the State of Colorado could use to predict the probability of detecting atrazine and desethyl-atrazine (a breakdown product of atrazine) in ground water in Colorado. These maps can be incorporated into the State Pesticide Management Plan and can help provide a sound hydrogeologic basis for atrazine management in Colorado. Maps showing the probability of detecting elevated nitrite plus nitrate as nitrogen (nitrate) concentrations in ground water in Colorado also were developed because nitrate is a contaminant of concern in many areas of Colorado. Maps showing the probability of detecting atrazine and(or) desethyl-atrazine (atrazine/DEA) at or greater than concentrations of 0.1 microgram per liter and nitrate concentrations in ground water greater than 5 milligrams per liter were developed as follows: (1) Ground-water quality data were overlaid with anthropogenic and hydrogeologic data using a geographic information system to produce a data set in which each well had corresponding data on atrazine use, fertilizer use, geology, hydrogeomorphic regions, land cover, precipitation, soils, and well construction. These data then were downloaded to a statistical software package for analysis by logistic regression. (2) Relations were observed between ground-water quality and the percentage of land-cover categories within circular regions (buffers) around wells. Several buffer sizes were evaluated; the buffer size that provided the strongest relation was selected for use in the logistic regression models. (3) Relations between concentrations of atrazine/DEA and nitrate in ground water and atrazine use, fertilizer use, geology, hydrogeomorphic regions, land cover, precipitation, soils, and well-construction data were evaluated, and several preliminary multivariate models with various combinations of independent variables were constructed. (4) The multivariate models that best predicted the presence of atrazine/DEA and elevated concentrations of nitrate in ground water were selected. (5) The accuracy of the multivariate models was confirmed by validating the models with an independent set of ground-water quality data. (6) The multivariate models were entered into a geographic information system and the probability maps were constructed.

Comparison of prevalence estimation of Mycobacterium avium subsp. paratuberculosis infection by sampling slaughtered cattle with macroscopic lesions vs. systematic sampling.

PubMed

Elze, J; Liebler-Tenorio, E; Ziller, M; Köhler, H

2013-07-01

The objective of this study was to identify the most reliable approach for prevalence estimation of Mycobacterium avium ssp. paratuberculosis (MAP) infection in clinically healthy slaughtered cattle. Sampling of macroscopically suspect tissue was compared to systematic sampling. Specimens of ileum, jejunum, mesenteric and caecal lymph nodes were examined for MAP infection using bacterial microscopy, culture, histopathology and immunohistochemistry. MAP was found most frequently in caecal lymph nodes, but sampling more tissues optimized the detection rate. Examination by culture was most efficient while combination with histopathology increased the detection rate slightly. MAP was detected in 49/50 animals with macroscopic lesions representing 1.35% of the slaughtered cattle examined. Of 150 systematically sampled macroscopically non-suspect cows, 28.7% were infected with MAP. This indicates that the majority of MAP-positive cattle are slaughtered without evidence of macroscopic lesions and before clinical signs occur. For reliable prevalence estimation of MAP infection in slaughtered cattle, systematic random sampling is essential.

A framework to analyze cerebral mean diffusivity using surface guided diffusion mapping in diffusion tensor imaging

PubMed Central

Kwon, Oh-Hun; Park, Hyunjin; Seo, Sang-Won; Na, Duk L.; Lee, Jong-Min

2015-01-01

The mean diffusivity (MD) value has been used to describe microstructural properties in Diffusion Tensor Imaging (DTI) in cortical gray matter (GM). Recently, researchers have applied a cortical surface generated from the T1-weighted volume. When the DTI data are analyzed using the cortical surface, it is important to assign an accurate MD value from the volume space to the vertex of the cortical surface, considering the anatomical correspondence between the DTI and the T1-weighted image. Previous studies usually sampled the MD value using the nearest-neighbor (NN) method or Linear method, even though there are geometric distortions in diffusion-weighted volumes. Here we introduce a Surface Guided Diffusion Mapping (SGDM) method to compensate for such geometric distortions. We compared our SGDM method with results using NN and Linear methods by investigating differences in the sampled MD value. We also projected the tissue classification results of non-diffusion-weighted volumes to the cortical midsurface. The CSF probability values provided by the SGDM method were lower than those produced by the NN and Linear methods. The MD values provided by the NN and Linear methods were significantly greater than those of the SGDM method in regions suffering from geometric distortion. These results indicate that the NN and Linear methods assigned the MD value in the CSF region to the cortical midsurface (GM region). Our results suggest that the SGDM method is an effective way to correct such mapping errors. PMID:26236180

Absolute continuity for operator valued completely positive maps on C∗-algebras

NASA Astrophysics Data System (ADS)

Gheondea, Aurelian; Kavruk, Ali Şamil

2009-02-01

Motivated by applicability to quantum operations, quantum information, and quantum probability, we investigate the notion of absolute continuity for operator valued completely positive maps on C∗-algebras, previously introduced by Parthasarathy [in Athens Conference on Applied Probability and Time Series Analysis I (Springer-Verlag, Berlin, 1996), pp. 34-54]. We obtain an intrinsic definition of absolute continuity, we show that the Lebesgue decomposition defined by Parthasarathy is the maximal one among all other Lebesgue-type decompositions and that this maximal Lebesgue decomposition does not depend on the jointly dominating completely positive map, we obtain more flexible formulas for calculating the maximal Lebesgue decomposition, and we point out the nonuniqueness of the Lebesgue decomposition as well as a sufficient condition for uniqueness. In addition, we consider Radon-Nikodym derivatives for absolutely continuous completely positive maps that, in general, are unbounded positive self-adjoint operators affiliated to a certain von Neumann algebra, and we obtain a spectral approximation by bounded Radon-Nikodym derivatives. An application to the existence of the infimum of two completely positive maps is indicated, and formulas in terms of Choi's matrices for the Lebesgue decomposition of completely positive maps in matrix algebras are obtained.

Probability of detecting atrazine/desethyl-atrazine and elevated concentrations of nitrate (NO2+NO3-N) in ground water in the Idaho part of the upper Snake River basin

USGS Publications Warehouse

Rupert, Michael G.

1998-01-01

Draft Federal regulations may require that each State develop a State Pesticide Management Plan for the herbicides atrazine, alachlor, cyanazine, metolachlor, and simazine. This study developed maps that the Idaho State Department of Agriculture might use to predict the probability of detecting atrazine and desethyl-atrazine (a breakdown product of atrazine) in ground water in the Idaho part of the upper Snake River Basin. These maps can be incorporated in the State Pesticide Management Plan and help provide a sound hydrogeologic basis for atrazine management in the study area. Maps showing the probability of detecting atrazine/desethyl-atrazine in ground water were developed as follows: (1) Ground-water monitoring data were overlaid with hydrogeologic and anthropogenic data using a geographic information system to produce a data set in which each well had corresponding data on atrazine use, depth to ground water, geology, land use, precipitation, soils, and well depth. These data then were downloaded to a statistical software package for analysis by logistic regression. (2) Individual (univariate) relations between atrazine/desethyl-atrazine in ground water and atrazine use, depth to ground water, geology, land use, precipitation, soils, and well depth data were evaluated to identify those independent variables significantly related to atrazine/ desethyl-atrazine detections. (3) Several preliminary multivariate models with various combinations of independent variables were constructed. (4) The multivariate models which best predicted the presence of atrazine/desethyl-atrazine in ground water were selected. (5) The multivariate models were entered into the geographic information system and the probability maps were constructed. Two models which best predicted the presence of atrazine/desethyl-atrazine in ground water were selected; one with and one without atrazine use. Correlations of the predicted probabilities of atrazine/desethyl-atrazine in ground water with the percent of actual detections were good; r-squared values were 0.91 and 0.96, respectively. Models were verified using a second set of groundwater quality data. Verification showed that wells with water containing atrazine/desethyl-atrazine had significantly higher probability ratings than wells with water containing no atrazine/desethylatrazine (p <0.002). Logistic regression also was used to develop a preliminary model to predict the probability of nitrite plus nitrate as nitrogen concentrations greater than background levels of 2 milligrams per liter. A direct comparison between the atrazine/ desethyl-atrazine and nitrite plus nitrate as nitrogen probability maps was possible because the same ground-water monitoring, hydrogeologic, and anthropogenic data were used to develop both maps. Land use, precipitation, soil hydrologic group, and well depth were significantly related with atrazine/desethyl-atrazine detections. Depth to water, land use, and soil drainage were signifi- cantly related with elevated nitrite plus nitrate as nitrogen concentrations. The differences between atrazine/desethyl-atrazine and nitrite plus nitrate as nitrogen relations were attributed to differences in chemical behavior of these compounds in the environment and possibly to differences in the extent of use and rates of their application.

Fluorescence spectroscopy using indocyanine green for lymph node mapping

NASA Astrophysics Data System (ADS)

Haj-Hosseini, Neda; Behm, Pascal; Shabo, Ivan; Wârdell, Karin

2014-02-01

The principles of cancer treatment has for years been radical resection of the primary tumor. In the oncologic surgeries where the affected cancer site is close to the lymphatic system, it is as important to detect the draining lymph nodes for metastasis (lymph node mapping). As a replacement for conventional radioactive labeling, indocyanine green (ICG) has shown successful results in lymph node mapping; however, most of the ICG fluorescence detection techniques developed are based on camera imaging. In this work, fluorescence spectroscopy using a fiber-optical probe was evaluated on a tissue-like ICG phantom with ICG concentrations of 6-64 μM and on breast tissue from five patients. Fiber-optical based spectroscopy was able to detect ICG fluorescence at low intensities; therefore, it is expected to increase the detection threshold of the conventional imaging systems when used intraoperatively. The probe allows spectral characterization of the fluorescence and navigation in the tissue as opposed to camera imaging which is limited to the view on the surface of the tissue.

Mapping cardiogenic oscillations using synchrotron-based phase contrast CT imaging

NASA Astrophysics Data System (ADS)

Thurgood, Jordan; Dubsky, Stephen; Siu, Karen K. W.; Wallace, Megan; Siew, Melissa; Hooper, Stuart; Fouras, Andreas

2012-10-01

In many animals, including humans, the lungs encase the majority of the heart thus the motion of each organ affects the other. The effects of the motion of the heart on the lungs potentially provides information with regards to both lung and heart health. We present a novel technique that is capable of measuring the effect of the heart on the surrounding lung tissue through the use of advanced synchrotron imaging techniques and recently developed X-ray velocimetry methods. This technique generates 2D frequency response maps of the lung tissue motion at multiple projection angles from projection X-ray images. These frequency response maps are subsequently used to generate 3D reconstructions of the lung tissue exhibiting motion at the frequency of ventilation and the lung tissue exhibiting motion at the frequency of the heart. This technique has a combined spatial and temporal resolution sufficient to observe the dynamic and complex 3D nature of lung-heart interactions.

Distinguishability notion based on Wootters statistical distance: Application to discrete maps

NASA Astrophysics Data System (ADS)

Gomez, Ignacio S.; Portesi, M.; Lamberti, P. W.

2017-08-01

We study the distinguishability notion given by Wootters for states represented by probability density functions. This presents the particularity that it can also be used for defining a statistical distance in chaotic unidimensional maps. Based on that definition, we provide a metric d ¯ for an arbitrary discrete map. Moreover, from d ¯ , we associate a metric space with each invariant density of a given map, which results to be the set of all distinguished points when the number of iterations of the map tends to infinity. Also, we give a characterization of the wandering set of a map in terms of the metric d ¯ , which allows us to identify the dissipative regions in the phase space. We illustrate the results in the case of the logistic and the circle maps numerically and analytically, and we obtain d ¯ and the wandering set for some characteristic values of their parameters. Finally, an extension of the metric space associated for arbitrary probability distributions (not necessarily invariant densities) is given along with some consequences. The statistical properties of distributions given by histograms are characterized in terms of the cardinal of the associated metric space. For two conjugate variables, the uncertainty principle is expressed in terms of the diameters of the associated metric space with those variables.

Towards a minimally invasive sampling tool for high resolution tissue analytical mapping

NASA Astrophysics Data System (ADS)

Gottardi, R.

2015-09-01

Multiple spatial mapping techniques of biological tissues have been proposed over the years, but all present limitations either in terms of resolution, analytical capacity or invasiveness. Ren et al (2015 Nanotechnology 26 284001) propose in their most recent work the use of a picosecond infrared laser (PIRL) under conditions of ultrafast desorption by impulsive vibrational excitation (DIVE) to extract small amounts of cellular and molecular components, conserving their viability, structure and activity. The PIRL DIVE technique would then work as a nanobiopsy with minimal damage to the surrounding tissues, which could potentially be applied for high resolution local structural characterization of tissues in health and disease with the spatial limit determined by the laser focus.

First Volcanological-Probabilistic Pyroclastic Density Current and Fallout Hazard Map for Campi Flegrei and Somma Vesuvius Volcanoes.

NASA Astrophysics Data System (ADS)

Mastrolorenzo, G.; Pappalardo, L.; Troise, C.; Panizza, A.; de Natale, G.

2005-05-01

Integrated volcanological-probabilistic approaches has been used in order to simulate pyroclastic density currents and fallout and produce hazard maps for Campi Flegrei and Somma Vesuvius areas. On the basis of the analyses of all types of pyroclastic flows, surges, secondary pyroclastic density currents and fallout events occurred in the volcanological history of the two volcanic areas and the evaluation of probability for each type of events, matrixs of input parameters for a numerical simulation have been performed. The multi-dimensional input matrixs include the main controlling parameters of the pyroclasts transport and deposition dispersion, as well as the set of possible eruptive vents used in the simulation program. Probabilistic hazard maps provide of each points of campanian area, the yearly probability to be interested by a given event with a given intensity and resulting demage. Probability of a few events in one thousand years are typical of most areas around the volcanoes whitin a range of ca 10 km, including Neaples. Results provide constrains for the emergency plans in Neapolitan area.

Collective odor source estimation and search in time-variant airflow environments using mobile robots.

PubMed

Meng, Qing-Hao; Yang, Wei-Xing; Wang, Yang; Zeng, Ming

2011-01-01

This paper addresses the collective odor source localization (OSL) problem in a time-varying airflow environment using mobile robots. A novel OSL methodology which combines odor-source probability estimation and multiple robots' search is proposed. The estimation phase consists of two steps: firstly, the separate probability-distribution map of odor source is estimated via Bayesian rules and fuzzy inference based on a single robot's detection events; secondly, the separate maps estimated by different robots at different times are fused into a combined map by way of distance based superposition. The multi-robot search behaviors are coordinated via a particle swarm optimization algorithm, where the estimated odor-source probability distribution is used to express the fitness functions. In the process of OSL, the estimation phase provides the prior knowledge for the searching while the searching verifies the estimation results, and both phases are implemented iteratively. The results of simulations for large-scale advection-diffusion plume environments and experiments using real robots in an indoor airflow environment validate the feasibility and robustness of the proposed OSL method.

Collective Odor Source Estimation and Search in Time-Variant Airflow Environments Using Mobile Robots

PubMed Central

Meng, Qing-Hao; Yang, Wei-Xing; Wang, Yang; Zeng, Ming

2011-01-01

This paper addresses the collective odor source localization (OSL) problem in a time-varying airflow environment using mobile robots. A novel OSL methodology which combines odor-source probability estimation and multiple robots’ search is proposed. The estimation phase consists of two steps: firstly, the separate probability-distribution map of odor source is estimated via Bayesian rules and fuzzy inference based on a single robot’s detection events; secondly, the separate maps estimated by different robots at different times are fused into a combined map by way of distance based superposition. The multi-robot search behaviors are coordinated via a particle swarm optimization algorithm, where the estimated odor-source probability distribution is used to express the fitness functions. In the process of OSL, the estimation phase provides the prior knowledge for the searching while the searching verifies the estimation results, and both phases are implemented iteratively. The results of simulations for large-scale advection–diffusion plume environments and experiments using real robots in an indoor airflow environment validate the feasibility and robustness of the proposed OSL method. PMID:22346650

GPU-Based Interactive Exploration and Online Probability Maps Calculation for Visualizing Assimilated Ocean Ensembles Data

NASA Astrophysics Data System (ADS)

Hoteit, I.; Hollt, T.; Hadwiger, M.; Knio, O. M.; Gopalakrishnan, G.; Zhan, P.

2016-02-01

Ocean reanalyses and forecasts are nowadays generated by combining ensemble simulations with data assimilation techniques. Most of these techniques resample the ensemble members after each assimilation cycle. Tracking behavior over time, such as all possible paths of a particle in an ensemble vector field, becomes very difficult, as the number of combinations rises exponentially with the number of assimilation cycles. In general a single possible path is not of interest but only the probabilities that any point in space might be reached by a particle at some point in time. We present an approach using probability-weighted piecewise particle trajectories to allow for interactive probability mapping. This is achieved by binning the domain and splitting up the tracing process into the individual assimilation cycles, so that particles that fall into the same bin after a cycle can be treated as a single particle with a larger probability as input for the next cycle. As a result we loose the possibility to track individual particles, but can create probability maps for any desired seed at interactive rates. The technique is integrated in an interactive visualization system that enables the visual analysis of the particle traces side by side with other forecast variables, such as the sea surface height, and their corresponding behavior over time. By harnessing the power of modern graphics processing units (GPUs) for visualization as well as computation, our system allows the user to browse through the simulation ensembles in real-time, view specific parameter settings or simulation models and move between different spatial or temporal regions without delay. In addition our system provides advanced visualizations to highlight the uncertainty, or show the complete distribution of the simulations at user-defined positions over the complete time series of the domain.

Predicting the spatial extent of liquefaction from geospatial and earthquake specific parameters

USGS Publications Warehouse

Zhu, Jing; Baise, Laurie G.; Thompson, Eric M.; Wald, David J.; Knudsen, Keith L.; Deodatis, George; Ellingwood, Bruce R.; Frangopol, Dan M.

2014-01-01

The spatially extensive damage from the 2010-2011 Christchurch, New Zealand earthquake events are a reminder of the need for liquefaction hazard maps for anticipating damage from future earthquakes. Liquefaction hazard mapping as traditionally relied on detailed geologic mapping and expensive site studies. These traditional techniques are difficult to apply globally for rapid response or loss estimation. We have developed a logistic regression model to predict the probability of liquefaction occurrence in coastal sedimentary areas as a function of simple and globally available geospatial features (e.g., derived from digital elevation models) and standard earthquake-specific intensity data (e.g., peak ground acceleration). Some of the geospatial explanatory variables that we consider are taken from the hydrology community, which has a long tradition of using remotely sensed data as proxies for subsurface parameters. As a result of using high resolution, remotely-sensed, and spatially continuous data as a proxy for important subsurface parameters such as soil density and soil saturation, and by using a probabilistic modeling framework, our liquefaction model inherently includes the natural spatial variability of liquefaction occurrence and provides an estimate of spatial extent of liquefaction for a given earthquake. To provide a quantitative check on how the predicted probabilities relate to spatial extent of liquefaction, we report the frequency of observed liquefaction features within a range of predicted probabilities. The percentage of liquefaction is the areal extent of observed liquefaction within a given probability contour. The regional model and the results show that there is a strong relationship between the predicted probability and the observed percentage of liquefaction. Visual inspection of the probability contours for each event also indicates that the pattern of liquefaction is well represented by the model.

Shear Wave Imaging of Breast Tissue by Color Doppler Shear Wave Elastography.

PubMed

Yamakoshi, Yoshiki; Nakajima, Takahito; Kasahara, Toshihiro; Yamazaki, Mayuko; Koda, Ren; Sunaguchi, Naoki

2017-02-01

Shear wave elastography is a distinctive method to access the viscoelastic characteristic of the soft tissue that is difficult to obtain by other imaging modalities. This paper proposes a novel shear wave elastography [color Doppler shear wave imaging (CD SWI)] for breast tissue. Continuous shear wave is produced by a small lightweight actuator, which is attached to the tissue surface. Shear wave wavefront that propagates in tissue is reconstructed as a binary pattern that consists of zero and the maximum flow velocities on color flow image (CFI). Neither any modifications of the ultrasound color flow imaging instrument nor a high frame rate ultrasound imaging instrument is required to obtain the shear wave wavefront map. However, two conditions of shear wave displacement amplitude and shear wave frequency are needed to obtain the map. However, these conditions are not severe restrictions in breast imaging. This is because the minimum displacement amplitude is [Formula: see text] for an ultrasonic wave frequency of 12 MHz and the shear wave frequency is available from several frequencies suited for breast imaging. Fourier analysis along time axis suppresses clutter noise in CFI. A directional filter extracts shear wave, which propagates in the forward direction. Several maps, such as shear wave phase, velocity, and propagation maps, are reconstructed by CD SWI. The accuracy of shear wave velocity measurement is evaluated for homogeneous agar gel phantom by comparing with the acoustic radiation force impulse method. The experimental results for breast tissue are shown for a shear wave frequency of 296.6 Hz.

Automated MRI segmentation for individualized modeling of current flow in the human head.

PubMed

Huang, Yu; Dmochowski, Jacek P; Su, Yuzhuo; Datta, Abhishek; Rorden, Christopher; Parra, Lucas C

2013-12-01

High-definition transcranial direct current stimulation (HD-tDCS) and high-density electroencephalography require accurate models of current flow for precise targeting and current source reconstruction. At a minimum, such modeling must capture the idiosyncratic anatomy of the brain, cerebrospinal fluid (CSF) and skull for each individual subject. Currently, the process to build such high-resolution individualized models from structural magnetic resonance images requires labor-intensive manual segmentation, even when utilizing available automated segmentation tools. Also, accurate placement of many high-density electrodes on an individual scalp is a tedious procedure. The goal was to develop fully automated techniques to reduce the manual effort in such a modeling process. A fully automated segmentation technique based on Statical Parametric Mapping 8, including an improved tissue probability map and an automated correction routine for segmentation errors, was developed, along with an automated electrode placement tool for high-density arrays. The performance of these automated routines was evaluated against results from manual segmentation on four healthy subjects and seven stroke patients. The criteria include segmentation accuracy, the difference of current flow distributions in resulting HD-tDCS models and the optimized current flow intensities on cortical targets. The segmentation tool can segment out not just the brain but also provide accurate results for CSF, skull and other soft tissues with a field of view extending to the neck. Compared to manual results, automated segmentation deviates by only 7% and 18% for normal and stroke subjects, respectively. The predicted electric fields in the brain deviate by 12% and 29% respectively, which is well within the variability observed for various modeling choices. Finally, optimized current flow intensities on cortical targets do not differ significantly. Fully automated individualized modeling may now be feasible for large-sample EEG research studies and tDCS clinical trials.

Whole-body diffusion kurtosis imaging: initial experience on non-Gaussian diffusion in various organs.

PubMed

Filli, Lukas; Wurnig, Moritz; Nanz, Daniel; Luechinger, Roger; Kenkel, David; Boss, Andreas

2014-12-01

Diffusion kurtosis imaging (DKI) is based on a non-Gaussian diffusion model that should inherently better account for restricted water diffusion within the complex microstructure of most tissues than the conventional diffusion-weighted imaging (DWI), which presumes Gaussian distributed water molecule displacement probability. The aim of this investigation was to test the technical feasibility of in vivo whole-body DKI, probe for organ-specific differences, and compare whole-body DKI and DWI results. Eight healthy subjects underwent whole-body DWI on a clinical 3.0 T magnetic resonance imaging system. Echo-planar images in the axial orientation were acquired at b-values of 0, 150, 300, 500, and 800 mm²/s. Parametrical whole-body maps of the diffusion coefficient (D), the kurtosis (K), and the traditional apparent diffusion coefficient (ADC) were generated. Goodness of fit was compared between DKI and DWI fits using the sums of squared residuals. Data groups were tested for significant differences of the mean by paired Student t tests. Good-quality parametrical whole-body maps of D, K, and ADC could be computed. Compared with ADC values, D values were significantly higher in the cerebral gray matter (by 30%) and white matter (27%), renal cortex (23%) and medulla (21%), spleen (101%), as well as erector spinae muscle (34%) (each P value <0.001). No significant differences between D and ADC were found in the cerebrospinal fluid (P = 0.08) and in the liver (P = 0.13). Curves of DKI fitted the measurement points significantly better than DWI curves did in most organs. Whole-body DKI is technically feasible and may reflect tissue microstructure more meaningfully than whole-body DWI.

Seismic-hazard maps and time histories for the commonwealth of Kentucky.

DOT National Transportation Integrated Search

2008-06-01

The ground-motion hazard maps and time histories for three earthquake scenarios, expected earthquakes, probable earthquakes, and maximum credible earthquakes on the free surface in hard rock (shear-wave velocity >1,500 m/s), were derived using the de...

The Probabilities of Unique Events

DTIC Science & Technology

2012-08-30

social justice and also participated in antinuclear demonstrations. The participants ranked the probability that Linda is a feminist bank teller as...investigated them. We propose a new theory (implemented in a computer program) in which such estimates depend on an intuitive non-numerical system capable only...of simple procedures, and a deliberative system that maps intuitions into numbers. The theory predicts that estimates of the probabilities of

Radiofrequency Ablation, MR Thermometry, and High-Spatial-Resolution MR Parametric Imaging with a Single, Minimally Invasive Device.

PubMed

Ertürk, M Arcan; Sathyanarayana Hegde, Shashank; Bottomley, Paul A

2016-12-01

Purpose To develop and demonstrate in vitro and in vivo a single interventional magnetic resonance (MR)-active device that integrates the functions of precise identification of a tissue site with the delivery of radiofrequency (RF) energy for ablation, high-spatial-resolution thermal mapping to monitor thermal dose, and quantitative MR imaging relaxometry to document ablation-induced tissue changes for characterizing ablated tissue. Materials and Methods All animal studies were approved by the institutional animal care and use committee. A loopless MR imaging antenna composed of a tuned microcable either 0.8 or 2.2 mm in diameter with an extended central conductor was switched between a 3-T MR imaging unit and an RF power source to monitor and perform RF ablation in bovine muscle and human artery samples in vitro and in rabbits in vivo. High-spatial-resolution (250-300-μm) proton resonance frequency shift MR thermometry was interleaved with ablations. Quantitative spin-lattice (T1) and spin-spin (T2) relaxation time MR imaging mapping was performed before and after ablation. These maps were compared with findings from gross tissue examination of the region of ablated tissue after MR imaging. Results High-spatial-resolution MR imaging afforded temperature mapping in less than 8 seconds for monitoring ablation temperatures in excess of 85°C delivered by the same device. This produced irreversible thermal injury and necrosis. Quantitative MR imaging relaxation time maps demonstrated up to a twofold variation in mean regional T1 and T2 after ablation versus before ablation. Conclusion A simple, integrated, minimally invasive interventional probe that provides image-guided therapy delivery, thermal mapping of dose, and detection of ablation-associated MR imaging parametric changes was developed and demonstrated. With this single-device approach, coupling-related safety concerns associated with multiple conductor approaches were avoided. © RSNA, 2016 Online supplemental material is available for this article.

Structure-Preserving Color Normalization and Sparse Stain Separation for Histological Images.

PubMed

Vahadane, Abhishek; Peng, Tingying; Sethi, Amit; Albarqouni, Shadi; Wang, Lichao; Baust, Maximilian; Steiger, Katja; Schlitter, Anna Melissa; Esposito, Irene; Navab, Nassir

2016-08-01

Staining and scanning of tissue samples for microscopic examination is fraught with undesirable color variations arising from differences in raw materials and manufacturing techniques of stain vendors, staining protocols of labs, and color responses of digital scanners. When comparing tissue samples, color normalization and stain separation of the tissue images can be helpful for both pathologists and software. Techniques that are used for natural images fail to utilize structural properties of stained tissue samples and produce undesirable color distortions. The stain concentration cannot be negative. Tissue samples are stained with only a few stains and most tissue regions are characterized by at most one effective stain. We model these physical phenomena that define the tissue structure by first decomposing images in an unsupervised manner into stain density maps that are sparse and non-negative. For a given image, we combine its stain density maps with stain color basis of a pathologist-preferred target image, thus altering only its color while preserving its structure described by the maps. Stain density correlation with ground truth and preference by pathologists were higher for images normalized using our method when compared to other alternatives. We also propose a computationally faster extension of this technique for large whole-slide images that selects an appropriate patch sample instead of using the entire image to compute the stain color basis.

18F-FLT uptake kinetics in head and neck squamous cell carcinoma: a PET imaging study.

PubMed

Liu, Dan; Chalkidou, Anastasia; Landau, David B; Marsden, Paul K; Fenwick, John D

2014-04-01

To analyze the kinetics of 3(')-deoxy-3(')-[F-18]-fluorothymidine (18F-FLT) uptake by head and neck squamous cell carcinomas and involved nodes imaged using positron emission tomography (PET). Two- and three-tissue compartment models were fitted to 12 tumor time-activity-curves (TACs) obtained for 6 structures (tumors or involved nodes) imaged in ten dynamic PET studies of 1 h duration, carried out for five patients. The ability of the models to describe the data was assessed using a runs test, the Akaike information criterion (AIC) and leave-one-out cross-validation. To generate parametric maps the models were also fitted to TACs of individual voxels. Correlations between maps of different parameters were characterized using Pearson'sr coefficient; in particular the phosphorylation rate-constants k3-2tiss and k5 of the two- and three-tissue models were studied alongside the flux parameters KFLT- 2tiss and KFLT of these models, and standardized uptake values (SUV). A methodology based on expectation-maximization clustering and the Bayesian information criterion ("EM-BIC clustering") was used to distil the information from noisy parametric images. Fits of two-tissue models 2C3K and 2C4K and three-tissue models 3C5K and 3C6K comprising three, four, five, and six rate-constants, respectively, pass the runs test for 4, 8, 10, and 11 of 12 tumor TACs. The three-tissue models have lower AIC and cross-validation scores for nine of the 12 tumors. Overall the 3C6K model has the lowest AIC and cross-validation scores and its fitted parameter values are of the same orders of magnitude as literature estimates. Maps of KFLT and KFLT- 2tiss are strongly correlated (r = 0.85) and also correlate closely with SUV maps (r = 0.72 for KFLT- 2tiss, 0.64 for KFLT). Phosphorylation rate-constant maps are moderately correlated with flux maps (r = 0.48 for k3-2tiss vs KFLT- 2tiss and r = 0.68 for k5 vs KFLT); however, neither phosphorylation rate-constant correlates significantly with SUV. EM-BIC clustering reduces the parametric maps to a small number of levels--on average 5.8, 3.5, 3.4, and 1.4 for KFLT- 2tiss, KFLT, k3-2tiss, and k5. This large simplification is potentially useful for radiotherapy dose-painting, but demonstrates the high noise in some maps. Statistical simulations show that voxel level noise degrades TACs generated from the 3C6K model sufficiently that the average AIC score, parameter bias, and total uncertainty of 2C4K model fits are similar to those of 3C6K fits, whereas at the whole tumor level the scores are lower for 3C6K fits. For the patients studied here, whole tumor FLT uptake time-courses are represented better overall by a three-tissue than by a two-tissue model. EM-BIC clustering simplifies noisy parametric maps, providing the best description of the underlying information they contain and is potentially useful for radiotherapy dose-painting. However, the clustering highlights the large degree of noise present in maps of the phosphorylation rate-constantsk5 and k3-2tiss, which are conceptually tightly linked to cellular proliferation. Methods must be found to make these maps more robust-either by constraining other model parameters or modifying dynamic imaging protocols. © 2014 American Association of Physicists in Medicine.

Elasticity mapping of murine abdominal organs in vivo using harmonic motion imaging (HMI)

NASA Astrophysics Data System (ADS)

Payen, Thomas; Palermo, Carmine F.; Sastra, Stephen A.; Chen, Hong; Han, Yang; Olive, Kenneth P.; Konofagou, Elisa E.

2016-08-01

Recently, ultrasonic imaging of soft tissue mechanics has been increasingly studied to image otherwise undetectable pathologies. However, many underlying mechanisms of tissue stiffening remain unknown, requiring small animal studies and adapted elasticity mapping techniques. Harmonic motion imaging (HMI) assesses tissue viscoelasticity by inducing localized oscillation from a periodic acoustic radiation force. The objective of this study was to evaluate the feasibility of HMI for in vivo elasticity mapping of abdominal organs in small animals. Pathological cases, i.e. chronic pancreatitis and pancreatic cancer, were also studied in vivo to assess the capability of HMI for detection of the change in mechanical properties. A 4.5 MHz focused ultrasound transducer (FUS) generated an amplitude-modulated beam resulting in 50 Hz harmonic tissue oscillations at its focus. Axial tissue displacement was estimated using 1D-cross-correlation of RF signals acquired with a 7.8 MHz diagnostic transducer confocally aligned with the FUS. In vitro results in canine liver and kidney showed the correlation between HMI displacement and Young’s moduli measured by rheometry compression testing. HMI was capable of providing reproducible elasticity maps of the mouse abdominal region in vivo allowing the identification of, from stiffest to softest, the murine kidney, pancreas, liver, and spleen. Finally, pancreata affected by pancreatitis and pancreatic cancer showed HMI displacements 1.7 and 2.2 times lower than in the control case, respectively, indicating higher stiffness. The HMI displacement amplitude was correlated with the extent of fibrosis as well as detecting the very onset of stiffening even before fibrosis could be detected on H&E. This work shows that HMI can produce reliable elasticity maps of mouse abdominal region in vivo, thus providing a potentially critical tool to assess pathologies affecting organ elasticity.

Towards optical spectroscopic anatomical mapping (OSAM) for lesion validation in cardiac tissue (Conference Presentation)

NASA Astrophysics Data System (ADS)

Singh-Moon, Rajinder P.; Zaryab, Mohammad; Hendon, Christine P.

2017-02-01

Electroanatomical mapping (EAM) is an invaluable tool for guiding cardiac radiofrequency ablation (RFA) therapy. The principle roles of EAM is the identification of candidate ablation sites by detecting regions of abnormal electrogram activity and lesion validation subsequent to RF energy delivery. However, incomplete lesions may present interim electrical inactivity similar to effective treatment in the acute setting, despite efforts to reveal them with pacing or drugs, such as adenosine. Studies report that the misidentification and recovery of such lesions is a leading cause of arrhythmia recurrence and repeat procedures. In previous work, we demonstrated spectroscopic characterization of cardiac tissues using a fiber optic-integrated RF ablation catheter. In this work, we introduce OSAM (optical spectroscopic anatomical mapping), the application of this spectroscopic technique to obtain 2-dimensional biodistribution maps. We demonstrate its diagnostic potential as an auxiliary method for lesion validation in treated swine preparations. Endocardial lesion sets were created on fresh swine cardiac samples using a commercial RFA system. An optically-integrated catheter console fabricated in-house was used for measurement of tissue optical spectra between 600-1000nm. Three dimensional, Spatio-spectral datasets were generated by raster scanning of the optical catheter across the treated sample surface in the presence of whole blood. Tissue optical parameters were recovered at each spatial position using an inverse Monte Carlo method. OSAM biodistribution maps showed stark correspondence with gross examination of tetrazolium chloride stained tissue specimens. Specifically, we demonstrate the ability of OSAM to readily distinguish between shallow and deeper lesions, a limitation faced by current EAM techniques. These results showcase the OSAMs potential for lesion validation strategies for the treatment of cardiac arrhythmias.

Elasticity mapping of murine abdominal organs in vivo using Harmonic Motion Imaging (HMI)

PubMed Central

Payen, Thomas; Palermo, Carmine F.; Sastra, Steve; Chen, Hong; Han, Yang; Olive, Kenneth P.; Konofagou, Elisa E.

2016-01-01

Recently, ultrasonic imaging of soft tissue mechanics has been increasingly studied to image otherwise undetectable pathologies. However, many underlying mechanisms of tissue stiffening remain unknown, requiring small animal studies and adapted elasticity mapping techniques. Harmonic motion imaging (HMI) assesses tissue viscoelasticity by inducing localized oscillation from a periodic acoustic radiation force. The objective of this study was to evaluate the feasibility of HMI for in vivo elasticity mapping of abdominal organs in small animals. Pathological cases, i.e. chronic pancreatitis and pancreatic cancer, were also studied in vivo to assess the capability of HMI for detection of the change in mechanical properties. A 4.5-MHz focused ultrasound transducer (FUS) generated an amplitude-modulated beam resulting in 50-Hz harmonic tissue oscillations at its focus. Axial tissue displacement was estimated using 1D-cross-correlation of RF signals acquired with a 7.8-MHz diagnostic transducer confocally aligned with the FUS. In vitro results in canine liver and kidney showed the correlation between HMI displacement and Young’s moduli measured by rheometry compression tests. HMI was able to provide reproducible elasticity maps of the mouse abdominal region in vivo allowing the identification of, from stiffest to softest, the murine kidney, pancreas, liver, and spleen. Finally, pancreata affected by pancreatitis and pancreatic cancer showed HMI displacements 1.7 and 2.2 times lower than in the control case, respectively, indicating higher stiffness. HMI displacement was correlated with the extent of fibrosis as well as detecting the very onset of stiffening even before fibrosis could be detected on H&E. This work shows that HMI can produce reliable elasticity maps of mouse abdominal region in vivo providing a crucial tool to understand pathologies affecting organ elasticity. PMID:27401609

Elasticity mapping of murine abdominal organs in vivo using harmonic motion imaging (HMI).

PubMed

Payen, Thomas; Palermo, Carmine F; Sastra, Stephen A; Chen, Hong; Han, Yang; Olive, Kenneth P; Konofagou, Elisa E

2016-08-07

Recently, ultrasonic imaging of soft tissue mechanics has been increasingly studied to image otherwise undetectable pathologies. However, many underlying mechanisms of tissue stiffening remain unknown, requiring small animal studies and adapted elasticity mapping techniques. Harmonic motion imaging (HMI) assesses tissue viscoelasticity by inducing localized oscillation from a periodic acoustic radiation force. The objective of this study was to evaluate the feasibility of HMI for in vivo elasticity mapping of abdominal organs in small animals. Pathological cases, i.e. chronic pancreatitis and pancreatic cancer, were also studied in vivo to assess the capability of HMI for detection of the change in mechanical properties. A 4.5 MHz focused ultrasound transducer (FUS) generated an amplitude-modulated beam resulting in 50 Hz harmonic tissue oscillations at its focus. Axial tissue displacement was estimated using 1D-cross-correlation of RF signals acquired with a 7.8 MHz diagnostic transducer confocally aligned with the FUS. In vitro results in canine liver and kidney showed the correlation between HMI displacement and Young's moduli measured by rheometry compression testing. HMI was capable of providing reproducible elasticity maps of the mouse abdominal region in vivo allowing the identification of, from stiffest to softest, the murine kidney, pancreas, liver, and spleen. Finally, pancreata affected by pancreatitis and pancreatic cancer showed HMI displacements 1.7 and 2.2 times lower than in the control case, respectively, indicating higher stiffness. The HMI displacement amplitude was correlated with the extent of fibrosis as well as detecting the very onset of stiffening even before fibrosis could be detected on H&E. This work shows that HMI can produce reliable elasticity maps of mouse abdominal region in vivo, thus providing a potentially critical tool to assess pathologies affecting organ elasticity.

The maximum entropy method of moments and Bayesian probability theory

NASA Astrophysics Data System (ADS)

Bretthorst, G. Larry

2013-08-01

The problem of density estimation occurs in many disciplines. For example, in MRI it is often necessary to classify the types of tissues in an image. To perform this classification one must first identify the characteristics of the tissues to be classified. These characteristics might be the intensity of a T1 weighted image and in MRI many other types of characteristic weightings (classifiers) may be generated. In a given tissue type there is no single intensity that characterizes the tissue, rather there is a distribution of intensities. Often this distributions can be characterized by a Gaussian, but just as often it is much more complicated. Either way, estimating the distribution of intensities is an inference problem. In the case of a Gaussian distribution, one must estimate the mean and standard deviation. However, in the Non-Gaussian case the shape of the density function itself must be inferred. Three common techniques for estimating density functions are binned histograms [1, 2], kernel density estimation [3, 4], and the maximum entropy method of moments [5, 6]. In the introduction, the maximum entropy method of moments will be reviewed. Some of its problems and conditions under which it fails will be discussed. Then in later sections, the functional form of the maximum entropy method of moments probability distribution will be incorporated into Bayesian probability theory. It will be shown that Bayesian probability theory solves all of the problems with the maximum entropy method of moments. One gets posterior probabilities for the Lagrange multipliers, and, finally, one can put error bars on the resulting estimated density function.

Understanding map projections: Chapter 15

USGS Publications Warehouse

Usery, E. Lynn; Kent, Alexander J.; Vujakovic, Peter

2018-01-01

It has probably never been more important in the history of cartography than now that people understand how maps work. With increasing globalization, for example, world maps provide a key format for the transmission of information, but are often poorly used. Examples of poor understanding and use of projections and the resultant maps are many; for instance, the use of rectangular world maps in the United Kingdom press to show Chinese and Korean missile ranges as circles, something which can only be achieved on equidistant projections and then only from one launch point (Vujakovic, 2014).

Concomitant administration of nitrous oxide and remifentanil reduces oral tissue blood flow without decreasing blood pressure during sevoflurane anesthesia in rabbits.

PubMed

Kasahara, Masataka; Ichinohe, Tatsuya; Okamoto, Sota; Okada, Reina; Kanbe, Hiroaki; Matsuura, Nobuyuki

2015-06-01

To determine whether continuous administration of nitrous oxide and remifentanil—either alone or together—alters blood flow in oral tissues during sevoflurane anesthesia. Eight male tracheotomized Japanese white rabbits were anesthetized with sevoflurane under mechanical ventilation. Heart rate (HR), systolic blood pressure (SBP), diastolic blood pressure (DBP), mean arterial pressure (MAP), common carotid arterial blood flow (CCBF), tongue mucosal blood flow (TMBF), mandibular bone marrow blood flow (BBF), masseter muscle blood flow (MBF), upper alveolar tissue blood flow (UBF), and lower alveolar tissue blood flow (LBF) were recorded in the absence of all test agents and after administration of the test agents (50 % nitrous oxide, 0.4 μg/kg/min remifentanil, and their combination) for 20 min. Nitrous oxide increased SBP, DBP, MAP, CCBF, BBF, MBF, UBF, and LBF relative to baseline values but did not affect HR or TMBF. Remifentanil decreased all hemodynamic variables except DBP. Combined administration of nitrous oxide and remifentanil recovered SBP, DBP, MAP, and CCBF to baseline levels, but HR and oral tissue blood flow remained lower than control values. Our findings suggest that concomitant administration of nitrous oxide and remifentanil reduces blood flow in oral tissues without decreasing blood pressure during sevoflurane anesthesia in rabbits.

Automated detection of submerged navigational obstructions in freshwater impoundments with hull mounted sidescan sonar

NASA Astrophysics Data System (ADS)

Morris, Phillip A.

The prevalence of low-cost side scanning sonar systems mounted on small recreational vessels has created improved opportunities to identify and map submerged navigational hazards in freshwater impoundments. However, these economical sensors also present unique challenges for automated techniques. This research explores related literature in automated sonar imagery processing and mapping technology, proposes and implements a framework derived from these sources, and evaluates the approach with video collected from a recreational grade sonar system. Image analysis techniques including optical character recognition and an unsupervised computer automated detection (CAD) algorithm are employed to extract the transducer GPS coordinates and slant range distance of objects protruding from the lake bottom. The retrieved information is formatted for inclusion into a spatial mapping model. Specific attributes of the sonar sensors are modeled such that probability profiles may be projected onto a three dimensional gridded map. These profiles are computed from multiple points of view as sonar traces crisscross or come near each other. As lake levels fluctuate over time so do the elevation points of view. With each sonar record, the probability of a hazard existing at certain elevations at the respective grid points is updated with Bayesian mechanics. As reinforcing data is collected, the confidence of the map improves. Given a lake's current elevation and a vessel draft, a final generated map can identify areas of the lake that have a high probability of containing hazards that threaten navigation. The approach is implemented in C/C++ utilizing OpenCV, Tesseract OCR, and QGIS open source software and evaluated in a designated test area at Lake Lavon, Collin County, Texas.

Determining Optimal Evacuation Decision Policies for Disasters

DTIC Science & Technology

2012-03-01

18 3.3 Calculating the Hit Probability ( Phit ) . . . . . . . . . . . . . . . . . . 20 3.4 Phit versus Vertical...23 Figure 3.13 Large Probability Matrix (Map) . . . . . . . . . . . . . . . . . . . . . 24 Figure 3.14 Particle Trajectory with Phit data...26 Figure 3.15 Phit versus Vertical Volatility . . . . . . . . . . . . . . . . . . . . . . 27 Figure 4.1 Cost-To

Characterization of multifocal T2*-weighted MRI hypointensities in the basal ganglia of elderly, community-dwelling subjects☆

PubMed Central

Glatz, Andreas; Valdés Hernández, Maria C.; Kiker, Alexander J.; Bastin, Mark E.; Deary, Ian J.; Wardlaw, Joanna M.

2013-01-01

Multifocal T2*-weighted (T2*w) hypointensities in the basal ganglia, which are believed to arise predominantly from mineralized small vessels and perivascular spaces, have been proposed as a biomarker for cerebral small vessel disease. This study provides baseline data on their appearance on conventional structural MRI for improving and automating current manual segmentation methods. Using a published thresholding method, multifocal T2*w hypointensities were manually segmented from whole brain T2*w volumes acquired from 98 community-dwelling subjects in their early 70s. Connected component analysis was used to derive the average T2*w hypointensity count and load per basal ganglia nucleus, as well as the morphology of their connected components, while nonlinear spatial probability mapping yielded their spatial distribution. T1-weighted (T1w), T2-weighted (T2w) and T2*w intensity distributions of basal ganglia T2*w hypointensities and their appearance on T1w and T2w MRI were investigated to gain further insights into the underlying tissue composition. In 75/98 subjects, on average, 3 T2*w hypointensities with a median total volume per intracranial volume of 50.3 ppm were located in and around the globus pallidus. Individual hypointensities appeared smooth and spherical with a median volume of 12 mm3 and median in-plane area of 4 mm2. Spatial probability maps suggested an association between T2*w hypointensities and the point of entry of lenticulostriate arterioles into the brain parenchyma. T1w and T2w and especially the T2*w intensity distributions of these hypointensities, which were negatively skewed, were generally not normally distributed indicating an underlying inhomogeneous tissue structure. Globus pallidus T2*w hypointensities tended to appear hypo- and isointense on T1w and T2w MRI, whereas those from other structures appeared iso- and hypointense. This pattern could be explained by an increased mineralization of the globus pallidus. In conclusion, the characteristic spatial distribution and appearance of multifocal basal ganglia T2*w hypointensities in our elderly cohort on structural MRI appear to support the suggested association with mineralized proximal lenticulostriate arterioles and perivascular spaces. PMID:23769704

Scalable Joint Segmentation and Registration Framework for Infant Brain Images.

PubMed

Dong, Pei; Wang, Li; Lin, Weili; Shen, Dinggang; Wu, Guorong

2017-03-15

The first year of life is the most dynamic and perhaps the most critical phase of postnatal brain development. The ability to accurately measure structure changes is critical in early brain development study, which highly relies on the performances of image segmentation and registration techniques. However, either infant image segmentation or registration, if deployed independently, encounters much more challenges than segmentation/registration of adult brains due to dynamic appearance change with rapid brain development. In fact, image segmentation and registration of infant images can assists each other to overcome the above challenges by using the growth trajectories (i.e., temporal correspondences) learned from a large set of training subjects with complete longitudinal data. Specifically, a one-year-old image with ground-truth tissue segmentation can be first set as the reference domain. Then, to register the infant image of a new subject at earlier age, we can estimate its tissue probability maps, i.e., with sparse patch-based multi-atlas label fusion technique, where only the training images at the respective age are considered as atlases since they have similar image appearance. Next, these probability maps can be fused as a good initialization to guide the level set segmentation. Thus, image registration between the new infant image and the reference image is free of difficulty of appearance changes, by establishing correspondences upon the reasonably segmented images. Importantly, the segmentation of new infant image can be further enhanced by propagating the much more reliable label fusion heuristics at the reference domain to the corresponding location of the new infant image via the learned growth trajectories, which brings image segmentation and registration to assist each other. It is worth noting that our joint segmentation and registration framework is also flexible to handle the registration of any two infant images even with significant age gap in the first year of life, by linking their joint segmentation and registration through the reference domain. Thus, our proposed joint segmentation and registration method is scalable to various registration tasks in early brain development studies. Promising segmentation and registration results have been achieved for infant brain MR images aged from 2-week-old to 1-year-old, indicating the applicability of our method in early brain development study.

Spatial and Temporal Analysis of Eruption Locations, Compositions, and Styles in Northern Harrat Rahat, Kingdom of Saudi Arabia

NASA Astrophysics Data System (ADS)

Dietterich, H. R.; Stelten, M. E.; Downs, D. T.; Champion, D. E.

2017-12-01

Harrat Rahat is a predominantly mafic, 20,000 km2 volcanic field in western Saudi Arabia with an elongate volcanic axis extending 310 km north-south. Prior mapping suggests that the youngest eruptions were concentrated in northernmost Harrat Rahat, where our new geologic mapping and geochronology reveal >300 eruptive vents with ages ranging from 1.2 Ma to a historic eruption in 1256 CE. Eruption compositions and styles vary spatially and temporally within the volcanic field, where extensive alkali basaltic lavas dominate, but more evolved compositions erupted episodically as clusters of trachytic domes and small-volume pyroclastic flows. Analysis of vent locations, compositions, and eruption styles shows the evolution of the volcanic field and allows assessment of the spatio-temporal probabilities of vent opening and eruption styles. We link individual vents and fissures to eruptions and their deposits using field relations, petrography, geochemistry, paleomagnetism, and 40Ar/39Ar and 36Cl geochronology. Eruption volumes and deposit extents are derived from geologic mapping and topographic analysis. Spatial density analysis with kernel density estimation captures vent densities of up to 0.2 %/km2 along the north-south running volcanic axis, decaying quickly away to the east but reaching a second, lower high along a secondary axis to the west. Temporal trends show slight younging of mafic eruption ages to the north in the past 300 ka, as well as clustered eruptions of trachytes over the past 150 ka. Vent locations, timing, and composition are integrated through spatial probability weighted by eruption age for each compositional range to produce spatio-temporal models of vent opening probability. These show that the next mafic eruption is most probable within the north end of the main (eastern) volcanic axis, whereas more evolved compositions are most likely to erupt within the trachytic centers further to the south. These vent opening probabilities, combined with corresponding eruption properties, can be used as the basis for lava flow and tephra fall hazard maps.

Markov Chain Monte Carlo estimation of species distributions: a case study of the swift fox in western Kansas

USGS Publications Warehouse

Sargeant, Glen A.; Sovada, Marsha A.; Slivinski, Christiane C.; Johnson, Douglas H.

2005-01-01

Accurate maps of species distributions are essential tools for wildlife research and conservation. Unfortunately, biologists often are forced to rely on maps derived from observed occurrences recorded opportunistically during observation periods of variable length. Spurious inferences are likely to result because such maps are profoundly affected by the duration and intensity of observation and by methods used to delineate distributions, especially when detection is uncertain. We conducted a systematic survey of swift fox (Vulpes velox) distribution in western Kansas, USA, and used Markov chain Monte Carlo (MCMC) image restoration to rectify these problems. During 1997–1999, we searched 355 townships (ca. 93 km) 1–3 times each for an average cost of $7,315 per year and achieved a detection rate (probability of detecting swift foxes, if present, during a single search) of = 0.69 (95% Bayesian confidence interval [BCI] = [0.60, 0.77]). Our analysis produced an estimate of the underlying distribution, rather than a map of observed occurrences, that reflected the uncertainty associated with estimates of model parameters. To evaluate our results, we analyzed simulated data with similar properties. Results of our simulations suggest negligible bias and good precision when probabilities of detection on ≥1 survey occasions (cumulative probabilities of detection) exceed 0.65. Although the use of MCMC image restoration has been limited by theoretical and computational complexities, alternatives do not possess the same advantages. Image models accommodate uncertain detection, do not require spatially independent data or a census of map units, and can be used to estimate species distributions directly from observations without relying on habitat covariates or parameters that must be estimated subjectively. These features facilitate economical surveys of large regions, the detection of temporal trends in distribution, and assessments of landscape-level relations between species and habitats. Requirements for the use of MCMC image restoration include study areas that can be partitioned into regular grids of mapping units, spatially contagious species distributions, reliable methods for identifying target species, and cumulative probabilities of detection ≥0.65.

Markov chain Monte Carlo estimation of species distributions: A case study of the swift fox in western Kansas

USGS Publications Warehouse

Sargeant, G.A.; Sovada, M.A.; Slivinski, C.C.; Johnson, D.H.

2005-01-01

Accurate maps of species distributions are essential tools for wildlife research and conservation. Unfortunately, biologists often are forced to rely on maps derived from observed occurrences recorded opportunistically during observation periods of variable length. Spurious inferences are likely to result because such maps are profoundly affected by the duration and intensity of observation and by methods used to delineate distributions, especially when detection is uncertain. We conducted a systematic survey of swift fox (Vulpes velox) distribution in western Kansas, USA, and used Markov chain Monte Carlo (MCMC) image restoration to rectify these problems. During 1997-1999, we searched 355 townships (ca. 93 km2) 1-3 times each for an average cost of $7,315 per year and achieved a detection rate (probability of detecting swift foxes, if present, during a single search) of ?? = 0.69 (95% Bayesian confidence interval [BCI] = [0.60, 0.77]). Our analysis produced an estimate of the underlying distribution, rather than a map of observed occurrences, that reflected the uncertainty associated with estimates of model parameters. To evaluate our results, we analyzed simulated data with similar properties. Results of our simulations suggest negligible bias and good precision when probabilities of detection on ???1 survey occasions (cumulative probabilities of detection) exceed 0.65. Although the use of MCMC image restoration has been limited by theoretical and computational complexities, alternatives do not possess the same advantages. Image models accommodate uncertain detection, do not require spatially independent data or a census of map units, and can be used to estimate species distributions directly from observations without relying on habitat covariates or parameters that must be estimated subjectively. These features facilitate economical surveys of large regions, the detection of temporal trends in distribution, and assessments of landscape-level relations between species and habitats. Requirements for the use of MCMC image restoration include study areas that can be partitioned into regular grids of mapping units, spatially contagious species distributions, reliable methods for identifying target species, and cumulative probabilities of detection ???0.65.

Wildfire risk in the wildland-urban interface: A simulation study in northwestern Wisconsin

USGS Publications Warehouse

Massada, Avi Bar; Radeloff, Volker C.; Stewart, Susan I.; Hawbaker, Todd J.

2009-01-01

The rapid growth of housing in and near the wildland–urban interface (WUI) increases wildfirerisk to lives and structures. To reduce fire risk, it is necessary to identify WUI housing areas that are more susceptible to wildfire. This is challenging, because wildfire patterns depend on fire behavior and spread, which in turn depend on ignition locations, weather conditions, the spatial arrangement of fuels, and topography. The goal of our study was to assess wildfirerisk to a 60,000 ha WUI area in northwesternWisconsin while accounting for all of these factors. We conducted 6000 simulations with two dynamic fire models: Fire Area Simulator (FARSITE) and Minimum Travel Time (MTT) in order to map the spatial pattern of burn probabilities. Simulations were run under normal and extreme weather conditions to assess the effect of weather on fire spread, burn probability, and risk to structures. The resulting burn probability maps were intersected with maps of structure locations and land cover types. The simulations revealed clear hotspots of wildfire activity and a large range of wildfirerisk to structures in the study area. As expected, the extreme weather conditions yielded higher burn probabilities over the entire landscape, as well as to different land cover classes and individual structures. Moreover, the spatial pattern of risk was significantly different between extreme and normal weather conditions. The results highlight the fact that extreme weather conditions not only produce higher fire risk than normal weather conditions, but also change the fine-scale locations of high risk areas in the landscape, which is of great importance for fire management in WUI areas. In addition, the choice of weather data may limit the potential for comparisons of risk maps for different areas and for extrapolating risk maps to future scenarios where weather conditions are unknown. Our approach to modeling wildfirerisk to structures can aid fire risk reduction management activities by identifying areas with elevated wildfirerisk and those most vulnerable under extreme weather conditions.

VizieR Online Data Catalog: X-ray sources in the AKARI NEP deep field (Krumpe+, 2015)

NASA Astrophysics Data System (ADS)

Krumpe, M.; Miyaji, T.; Brunner, H.; Hanami, H.; Ishigaki, T.; Takagi, T.; Markowitz, A. G.; Goto, T.; Malkan, M. A.; Matsuhara, H.; Pearson, C.; Ueda, Y.; Wada, T.

2015-06-01

The fits images labelled SeMap* are the sensitivity maps in which we give the minimum flux that would have caused a detection at each position. This flux depends on the maximum likelihood threshold chosen in the source detection run, the point spread function, and the background level at the chosen position. We create sensitivity maps in different energy bands (0.5-2, 0.5-7, 2-4, 2-7, and 4-7keV) by searching for the flux to reject the null-hypothesis that the flux at a given position is only caused by a background fluctuation. In a chosen energy band, we determine for each position in the survey the flux required to obtain a certain Poisson probability above the background counts. Since ML=-ln(P), we know from our ML=12 threshold the probability we are aiming for. In practice, we search for a value of -ln P_total that falls within Delta ML=+/-0.2 of our targeted ML threshold. This tolerance range corresponds to having one spurious source more or less in the whole survey. Note, that outside the deep Subaru/Suprime-Cam imaging the sensitivity maps should be used with caution since we assume for their generation a ML=12 over the whole area covered by Chandra. More details on the procedure of producing the sensitivity maps, including the PSF-summed background map and PSF-weighted averaged exposure maps are given in the paper, section 5.3. The fits images labelled u90* are the upper limit maps, where the upper 90 per cent confidence flux limit is given at each position. We take a Bayesian approach following Kraft, Burrows & Nousek, 1991ApJ...374..344K. Consequently, we obtain the upper 90~per cent confidence flux limit by searching for the flux such that given the observed counts the Bayesian probability of having this flux or larger is 10~per cent. More details on the procedure of producing the upper 90 per cent flux limit maps are given in the paper, section 5.4. (6 data files).

Qualitative and quantitative mass spectrometry imaging of drugs and metabolites in tissue at therapeutic levels.

PubMed

Sun, Na; Walch, Axel

2013-08-01

Mass spectrometry imaging (MSI) is a rapidly evolving technology that yields qualitative and quantitative distribution maps of small pharmaceutical-active molecules and their metabolites in tissue sections in situ. The simplicity, high sensitivity and ability to provide comprehensive spatial distribution maps of different classes of biomolecules make MSI a valuable tool to complement histopathology for diagnostics and biomarker discovery. In this review, qualitative and quantitative MSI of drugs and metabolites in tissue at therapeutic levels are discussed and the impact of this technique in drug discovery and clinical research is highlighted.

Prostate tissue ablation with MRI guided transurethral therapeutic ultrasound and intraoperative assessment of the integrity of the neurovascular bundle

NASA Astrophysics Data System (ADS)

Sammet, Steffen; Partanen, Ari; Yousuf, Ambereen; Wardrip, Craig; Niekrasz, Marek; Antic, Tatjana; Razmaria, Aria; Sokka, Sham; Karczmar, Gregory; Oto, Aytekin

2017-03-01

OBJECTIVES: Evaluation of the precision of prostate tissue ablation with MRI guided therapeuticultrasound by intraoperative objective assessment of the neurovascular bundle in canines in-vivo. METHODS: In this ongoing IACUC approved study, eight male canines were scanned in a clinical 3T Achieva MRI scanner (Philips) before, during, and after ultrasound therapy with a prototype MR-guided ultrasound therapy system (Philips). The system includes a therapy console to plan treatment, to calculate real-time temperature maps, and to control ultrasound exposures with temperature feedback. Atransurethral ultrasound applicator with eight transducer elements was used to ablate canine prostate tissue in-vivo. Ablated prostate tissue volumes were compared to the prescribed target volumes to evaluate technical effectiveness. The ablated volumes determined by MRI (T1, T2, diffusion, dynamic contrast enhanced and 240 CEM43 thermal dose maps) were compared to H&E stained histological slides afterprostatectomy. Potential nerve damage of the neurovascular bundle was objectively assessed intraoperativelyduring prostatectomy with a CaverMap Surgical Aid nerve stimulator (Blue Torch Medical Technologies). RESULTS: Transurethral MRI -guided ultrasound therapy can effectively ablate canine prostate tissue invivo. Coronal MR-imaging confirmed the correct placement of the HIFU transducer. MRI temperature maps were acquired during HIFU treatment, and subsequently used for calculating thermal dose. Prescribed target volumes corresponded to the 240 CEM43 thermal dose maps during HIFU treatment in all canines. Ablated volumes on high resolution anatomical, diffusion weighted, and contrast enhanced MR images matched corresponding histological slides after prostatectomy. MRI guidance with realtime temperature monitoring showed no damage to surrounding tissues, especially to the neurovascular bundle (assessed intra-operatively with a nerve stimulator) or to the rectum wall. CONCLUSIONS: Our study demonstrates the effectiveness and precision of transurethral ultrasound ablation of prostatic tissue in canines with MRI monitoring and guidance. The canine prostate is an excellent model for the human prostate with similar anatomical characteristics and diseases. MRI guidance with real-time, intraoperative temperature monitoring reduces the risk of damaging critical surrounding anatomical structures in ultrasound therapy of the prostate.

Tissue Cancellation in Dual Energy Mammography Using a Calibration Phantom Customized for Direct Mapping.

PubMed

Han, Seokmin; Kang, Dong-Goo

2014-01-01

An easily implementable tissue cancellation method for dual energy mammography is proposed to reduce anatomical noise and enhance lesion visibility. For dual energy calibration, the images of an imaging object are directly mapped onto the images of a customized calibration phantom. Each pixel pair of the low and high energy images of the imaging object was compared to pixel pairs of the low and high energy images of the calibration phantom. The correspondence was measured by absolute difference between the pixel values of imaged object and those of the calibration phantom. Then the closest pixel pair of the calibration phantom images is marked and selected. After the calibration using direct mapping, the regions with lesion yielded different thickness from the background tissues. Taking advantage of the different thickness, the visibility of cancerous lesions was enhanced with increased contrast-to-noise ratio, depending on the size of lesion and breast thickness. However, some tissues near the edge of imaged object still remained after tissue cancellation. These remaining residuals seem to occur due to the heel effect, scattering, nonparallel X-ray beam geometry and Poisson distribution of photons. To improve its performance further, scattering and the heel effect should be compensated.

Mapping the vascular anatomy of free transplanted soft tissue flaps with computed tomographic angiography.

PubMed

Rozen, Warren M; Chubb, Daniel; Ashton, Mark W; Webster, Howard R

2012-05-01

The use of advanced imaging technologies such as computed tomographic angiography (CTA) has opened the door to the analysis of microvascular anatomy not previously demonstrable with prior imaging techniques. While CTA has been used to evaluate the vascular anatomy of donor body regions in the planning of harvest of tissue for free flap transfer, the use of CTA to evaluate tissues after tissue transplantation has not been demonstrated. The current study aimed to explore whether vascular anatomy was able to highlight CTA within transferred flaps. The arterial and venous anatomy of a transferred deep inferior epigastric artery (DIEA) perforator (DIEP) flap was explored postoperatively with the use of CTA. Intra-flap vasculature was mapped and recorded qualitatively. Postoperative CTA is able to highlight the vascular pedicle of a transferred free flap, highlight the course of individual perforators supplying the flap, and map the zones of lesser perfusion by the source pedicle. The current study has demonstrated that CTA may be of value in identifying vascular anatomy within transferred tissue, as a guide to evaluate flap perfusion and planning further surgery involving the flap. © Springer-Verlag 2011

MAP3K19 Is a Novel Regulator of TGF-β Signaling That Impacts Bleomycin-Induced Lung Injury and Pulmonary Fibrosis

PubMed Central

Franz-Bacon, Karin; DiTirro, Danielle N.; Ly, Tai Wei; Bacon, Kevin B.

2016-01-01

Idiopathic pulmonary fibrosis (IPF) is a progressive, debilitating disease for which two medications, pirfenidone and nintedanib, have only recently been approved for treatment. The cytokine TGF-β has been shown to be a central mediator in the disease process. We investigated the role of a novel kinase, MAP3K19, upregulated in IPF tissue, in TGF-β-induced signal transduction and in bleomycin-induced pulmonary fibrosis. MAP3K19 has a very limited tissue expression, restricted primarily to the lungs and trachea. In pulmonary tissue, expression was predominantly localized to alveolar and interstitial macrophages, bronchial epithelial cells and type II pneumocytes of the epithelium. MAP3K19 was also found to be overexpressed in bronchoalveolar lavage macrophages from IPF patients compared to normal patients. Treatment of A549 or THP-1 cells with either MAP3K19 siRNA or a highly potent and specific inhibitor reduced phospho-Smad2 & 3 nuclear translocation following TGF-β stimulation. TGF-β-induced gene transcription was also strongly inhibited by both the MAP3K19 inhibitor and nintedanib, whereas pirfenidone had a much less pronounced effect. In combination, the MAP3K19 inhibitor appeared to act synergistically with either pirfenidone or nintedanib, at the level of target gene transcription or protein production. Finally, in an animal model of IPF, inhibition of MAP3K19 strongly attenuated bleomycin-induced pulmonary fibrosis when administered either prophylactically ortherapeutically. In summary, these results strongly suggest that inhibition of MAP3K19 may have a beneficial therapeutic effect in the treatment of IPF and represents a novel strategy to target this disease. PMID:27144281

MAP3K19 Is a Novel Regulator of TGF-β Signaling That Impacts Bleomycin-Induced Lung Injury and Pulmonary Fibrosis.

PubMed

Boehme, Stefen A; Franz-Bacon, Karin; DiTirro, Danielle N; Ly, Tai Wei; Bacon, Kevin B

2016-01-01

Idiopathic pulmonary fibrosis (IPF) is a progressive, debilitating disease for which two medications, pirfenidone and nintedanib, have only recently been approved for treatment. The cytokine TGF-β has been shown to be a central mediator in the disease process. We investigated the role of a novel kinase, MAP3K19, upregulated in IPF tissue, in TGF-β-induced signal transduction and in bleomycin-induced pulmonary fibrosis. MAP3K19 has a very limited tissue expression, restricted primarily to the lungs and trachea. In pulmonary tissue, expression was predominantly localized to alveolar and interstitial macrophages, bronchial epithelial cells and type II pneumocytes of the epithelium. MAP3K19 was also found to be overexpressed in bronchoalveolar lavage macrophages from IPF patients compared to normal patients. Treatment of A549 or THP-1 cells with either MAP3K19 siRNA or a highly potent and specific inhibitor reduced phospho-Smad2 & 3 nuclear translocation following TGF-β stimulation. TGF-β-induced gene transcription was also strongly inhibited by both the MAP3K19 inhibitor and nintedanib, whereas pirfenidone had a much less pronounced effect. In combination, the MAP3K19 inhibitor appeared to act synergistically with either pirfenidone or nintedanib, at the level of target gene transcription or protein production. Finally, in an animal model of IPF, inhibition of MAP3K19 strongly attenuated bleomycin-induced pulmonary fibrosis when administered either prophylactically ortherapeutically. In summary, these results strongly suggest that inhibition of MAP3K19 may have a beneficial therapeutic effect in the treatment of IPF and represents a novel strategy to target this disease.

Laboratory Workflow Analysis of Culture of Periprosthetic Tissues in Blood Culture Bottles.

PubMed

Peel, Trisha N; Sedarski, John A; Dylla, Brenda L; Shannon, Samantha K; Amirahmadi, Fazlollaah; Hughes, John G; Cheng, Allen C; Patel, Robin

2017-09-01

Culture of periprosthetic tissue specimens in blood culture bottles is more sensitive than conventional techniques, but the impact on laboratory workflow has yet to be addressed. Herein, we examined the impact of culture of periprosthetic tissues in blood culture bottles on laboratory workflow and cost. The workflow was process mapped, decision tree models were constructed using probabilities of positive and negative cultures drawn from our published study (T. N. Peel, B. L. Dylla, J. G. Hughes, D. T. Lynch, K. E. Greenwood-Quaintance, A. C. Cheng, J. N. Mandrekar, and R. Patel, mBio 7:e01776-15, 2016, https://doi.org/10.1128/mBio.01776-15), and the processing times and resource costs from the laboratory staff time viewpoint were used to compare periprosthetic tissues culture processes using conventional techniques with culture in blood culture bottles. Sensitivity analysis was performed using various rates of positive cultures. Annualized labor savings were estimated based on salary costs from the U.S. Labor Bureau for Laboratory staff. The model demonstrated a 60.1% reduction in mean total staff time with the adoption of tissue inoculation into blood culture bottles compared to conventional techniques (mean ± standard deviation, 30.7 ± 27.6 versus 77.0 ± 35.3 h per month, respectively; P < 0.001). The estimated annualized labor cost savings of culture using blood culture bottles was $10,876.83 (±$337.16). Sensitivity analysis was performed using various rates of culture positivity (5 to 50%). Culture in blood culture bottles was cost-effective, based on the estimated labor cost savings of $2,132.71 for each percent increase in test accuracy. In conclusion, culture of periprosthetic tissue in blood culture bottles is not only more accurate than but is also cost-saving compared to conventional culture methods. Copyright © 2017 American Society for Microbiology.

Mechanical perturbation control of cardiac alternans

NASA Astrophysics Data System (ADS)

Hazim, Azzam; Belhamadia, Youssef; Dubljevic, Stevan

2018-05-01

Cardiac alternans is a disturbance in heart rhythm that is linked to the onset of lethal cardiac arrhythmias. Mechanical perturbation control has been recently used to suppress alternans in cardiac tissue of relevant size. In this control strategy, cardiac tissue mechanics are perturbed via active tension generated by the heart's electrical activity, which alters the tissue's electric wave profile through mechanoelectric coupling. We analyze the effects of mechanical perturbation on the dynamics of a map model that couples the membrane voltage and active tension systems at the cellular level. Therefore, a two-dimensional iterative map of the heart beat-to-beat dynamics is introduced, and a stability analysis of the system of coupled maps is performed in the presence of a mechanical perturbation algorithm. To this end, a bidirectional coupling between the membrane voltage and active tension systems in a single cardiac cell is provided, and a discrete form of the proposed control algorithm, that can be incorporated in the coupled maps, is derived. In addition, a realistic electromechanical model of cardiac tissue is employed to explore the feasibility of suppressing alternans at cellular and tissue levels. Electrical activity is represented in two detailed ionic models, the Luo-Rudy 1 and the Fox models, while two active contractile tension models, namely a smooth variant of the Nash-Panfilov model and the Niederer-Hunter-Smith model, are used to represent mechanical activity in the heart. The Mooney-Rivlin passive elasticity model is employed to describe passive mechanical behavior of the myocardium.

An algorithm to predict the connectome of neural microcircuits

PubMed Central

Reimann, Michael W.; King, James G.; Muller, Eilif B.; Ramaswamy, Srikanth; Markram, Henry

2015-01-01

Experimentally mapping synaptic connections, in terms of the numbers and locations of their synapses and estimating connection probabilities, is still not a tractable task, even for small volumes of tissue. In fact, the six layers of the neocortex contain thousands of unique types of synaptic connections between the many different types of neurons, of which only a handful have been characterized experimentally. Here we present a theoretical framework and a data-driven algorithmic strategy to digitally reconstruct the complete synaptic connectivity between the different types of neurons in a small well-defined volume of tissue—the micro-scale connectome of a neural microcircuit. By enforcing a set of established principles of synaptic connectivity, and leveraging interdependencies between fundamental properties of neural microcircuits to constrain the reconstructed connectivity, the algorithm yields three parameters per connection type that predict the anatomy of all types of biologically viable synaptic connections. The predictions reproduce a spectrum of experimental data on synaptic connectivity not used by the algorithm. We conclude that an algorithmic approach to the connectome can serve as a tool to accelerate experimental mapping, indicating the minimal dataset required to make useful predictions, identifying the datasets required to improve their accuracy, testing the feasibility of experimental measurements, and making it possible to test hypotheses of synaptic connectivity. PMID:26500529

A multi-source probabilistic hazard assessment of tephra dispersal in the Neapolitan area

NASA Astrophysics Data System (ADS)

Sandri, Laura; Costa, Antonio; Selva, Jacopo; Folch, Arnau; Macedonio, Giovanni; Tonini, Roberto

2015-04-01

In this study we present the results obtained from a long-term Probabilistic Hazard Assessment (PHA) of tephra dispersal in the Neapolitan area. Usual PHA for tephra dispersal needs the definition of eruptive scenarios (usually by grouping eruption sizes and possible vent positions in a limited number of classes) with associated probabilities, a meteorological dataset covering a representative time period, and a tephra dispersal model. PHA then results from combining simulations considering different volcanological and meteorological conditions through weights associated to their specific probability of occurrence. However, volcanological parameters (i.e., erupted mass, eruption column height, eruption duration, bulk granulometry, fraction of aggregates) typically encompass a wide range of values. Because of such a natural variability, single representative scenarios or size classes cannot be adequately defined using single values for the volcanological inputs. In the present study, we use a method that accounts for this within-size-class variability in the framework of Event Trees. The variability of each parameter is modeled with specific Probability Density Functions, and meteorological and volcanological input values are chosen by using a stratified sampling method. This procedure allows for quantifying hazard without relying on the definition of scenarios, thus avoiding potential biases introduced by selecting single representative scenarios. Embedding this procedure into the Bayesian Event Tree scheme enables the tephra fall PHA and its epistemic uncertainties. We have appied this scheme to analyze long-term tephra fall PHA from Vesuvius and Campi Flegrei, in a multi-source paradigm. We integrate two tephra dispersal models (the analytical HAZMAP and the numerical FALL3D) into BET_VH. The ECMWF reanalysis dataset are used for exploring different meteorological conditions. The results obtained show that PHA accounting for the whole natural variability are consistent with previous probabilities maps elaborated for Vesuvius and Campi Flegrei on the basis of single representative scenarios, but show significant differences. In particular, the area characterized by a 300 kg/m2-load exceedance probability larger than 5%, accounting for the whole range of variability (that is, from small violent strombolian to plinian eruptions), is similar to that displayed in the maps based on the medium magnitude reference eruption, but it is of a smaller extent. This is due to the relatively higher weight of the small magnitude eruptions considered in this study, but neglected in the reference scenario maps. On the other hand, in our new maps the area characterized by a 300 kg/m2-load exceedance probability larger than 1% is much larger than that of the medium magnitude reference eruption, due to the contribution of plinian eruptions at lower probabilities, again neglected in the reference scenario maps.

A Brownian Bridge Movement Model to Track Mobile Targets

DTIC Science & Technology

2016-09-01

breakout of Chinese forces in the South China Sea. Probability heat maps, depicting the probability of a target location at discrete times, are...achieve a higher probability of detection, it is more effective to have sensors cover a wider area at fewer discrete points in time than to have a...greater number of discrete looks using sensors covering smaller areas. 14. SUBJECT TERMS Brownian bridge movement models, unmanned sensors

What is the correct cost functional for variational data assimilation?

NASA Astrophysics Data System (ADS)

Bröcker, Jochen

2018-03-01

Variational approaches to data assimilation, and weakly constrained four dimensional variation (WC-4DVar) in particular, are important in the geosciences but also in other communities (often under different names). The cost functions and the resulting optimal trajectories may have a probabilistic interpretation, for instance by linking data assimilation with maximum aposteriori (MAP) estimation. This is possible in particular if the unknown trajectory is modelled as the solution of a stochastic differential equation (SDE), as is increasingly the case in weather forecasting and climate modelling. In this situation, the MAP estimator (or "most probable path" of the SDE) is obtained by minimising the Onsager-Machlup functional. Although this fact is well known, there seems to be some confusion in the literature, with the energy (or "least squares") functional sometimes been claimed to yield the most probable path. The first aim of this paper is to address this confusion and show that the energy functional does not, in general, provide the most probable path. The second aim is to discuss the implications in practice. Although the mentioned results pertain to stochastic models in continuous time, they do have consequences in practice where SDE's are approximated by discrete time schemes. It turns out that using an approximation to the SDE and calculating its most probable path does not necessarily yield a good approximation to the most probable path of the SDE proper. This suggest that even in discrete time, a version of the Onsager-Machlup functional should be used, rather than the energy functional, at least if the solution is to be interpreted as a MAP estimator.

Brain tumor segmentation from multimodal magnetic resonance images via sparse representation.

PubMed

Li, Yuhong; Jia, Fucang; Qin, Jing

2016-10-01

Accurately segmenting and quantifying brain gliomas from magnetic resonance (MR) images remains a challenging task because of the large spatial and structural variability among brain tumors. To develop a fully automatic and accurate brain tumor segmentation algorithm, we present a probabilistic model of multimodal MR brain tumor segmentation. This model combines sparse representation and the Markov random field (MRF) to solve the spatial and structural variability problem. We formulate the tumor segmentation problem as a multi-classification task by labeling each voxel as the maximum posterior probability. We estimate the maximum a posteriori (MAP) probability by introducing the sparse representation into a likelihood probability and a MRF into the prior probability. Considering the MAP as an NP-hard problem, we convert the maximum posterior probability estimation into a minimum energy optimization problem and employ graph cuts to find the solution to the MAP estimation. Our method is evaluated using the Brain Tumor Segmentation Challenge 2013 database (BRATS 2013) and obtained Dice coefficient metric values of 0.85, 0.75, and 0.69 on the high-grade Challenge data set, 0.73, 0.56, and 0.54 on the high-grade Challenge LeaderBoard data set, and 0.84, 0.54, and 0.57 on the low-grade Challenge data set for the complete, core, and enhancing regions. The experimental results show that the proposed algorithm is valid and ranks 2nd compared with the state-of-the-art tumor segmentation algorithms in the MICCAI BRATS 2013 challenge. Copyright © 2016 Elsevier B.V. All rights reserved.

Machine learning based brain tumour segmentation on limited data using local texture and abnormality.

PubMed

Bonte, Stijn; Goethals, Ingeborg; Van Holen, Roel

2018-05-07

Brain tumour segmentation in medical images is a very challenging task due to the large variety in tumour shape, position, appearance, scanning modalities and scanning parameters. Most existing segmentation algorithms use information from four different MRI-sequences, but since this is often not available, there is need for a method able to delineate the different tumour tissues based on a minimal amount of data. We present a novel approach using a Random Forests model combining voxelwise texture and abnormality features on a contrast-enhanced T1 and FLAIR MRI. We transform the two scans into 275 feature maps. A random forest model next calculates the probability to belong to 4 tumour classes or 5 normal classes. Afterwards, a dedicated voxel clustering algorithm provides the final tumour segmentation. We trained our method on the BraTS 2013 database and validated it on the larger BraTS 2017 dataset. We achieve median Dice scores of 40.9% (low-grade glioma) and 75.0% (high-grade glioma) to delineate the active tumour, and 68.4%/80.1% for the total abnormal region including edema. Our fully automated brain tumour segmentation algorithm is able to delineate contrast enhancing tissue and oedema with high accuracy based only on post-contrast T1-weighted and FLAIR MRI, whereas for non-enhancing tumour tissue and necrosis only moderate results are obtained. This makes the method especially suitable for high-grade glioma. Copyright © 2018 Elsevier Ltd. All rights reserved.

Atlas Based Segmentation and Mapping of Organs at Risk from Planning CT for the Development of Voxel-Wise Predictive Models of Toxicity in Prostate Radiotherapy

NASA Astrophysics Data System (ADS)

Acosta, Oscar; Dowling, Jason; Cazoulat, Guillaume; Simon, Antoine; Salvado, Olivier; de Crevoisier, Renaud; Haigron, Pascal

The prediction of toxicity is crucial to managing prostate cancer radiotherapy (RT). This prediction is classically organ wise and based on the dose volume histograms (DVH) computed during the planning step, and using for example the mathematical Lyman Normal Tissue Complication Probability (NTCP) model. However, these models lack spatial accuracy, do not take into account deformations and may be inappropiate to explain toxicity events related with the distribution of the delivered dose. Producing voxel wise statistical models of toxicity might help to explain the risks linked to the dose spatial distribution but is challenging due to the difficulties lying on the mapping of organs and dose in a common template. In this paper we investigate the use of atlas based methods to perform the non-rigid mapping and segmentation of the individuals' organs at risk (OAR) from CT scans. To build a labeled atlas, 19 CT scans were selected from a population of patients treated for prostate cancer by radiotherapy. The prostate and the OAR (Rectum, Bladder, Bones) were then manually delineated by an expert and constituted the training data. After a number of affine and non rigid registration iterations, an average image (template) representing the whole population was obtained. The amount of consensus between labels was used to generate probabilistic maps for each organ. We validated the accuracy of the approach by segmenting the organs using the training data in a leave one out scheme. The agreement between the volumes after deformable registration and the manually segmented organs was on average above 60% for the organs at risk. The proposed methodology provides a way to map the organs from a whole population on a single template and sets the stage to perform further voxel wise analysis. With this method new and accurate predictive models of toxicity will be built.

Identification of phreatophytic groundwater dependent ecosystems using geospatial technologies

NASA Astrophysics Data System (ADS)

Perez Hoyos, Isabel Cristina

The protection of groundwater dependent ecosystems (GDEs) is increasingly being recognized as an essential aspect for the sustainable management and allocation of water resources. Ecosystem services are crucial for human well-being and for a variety of flora and fauna. However, the conservation of GDEs is only possible if knowledge about their location and extent is available. Several studies have focused on the identification of GDEs at specific locations using ground-based measurements. However, recent progress in technologies such as remote sensing and their integration with geographic information systems (GIS) has provided alternative ways to map GDEs at much larger spatial extents. This study is concerned with the discovery of patterns in geospatial data sets using data mining techniques for mapping phreatophytic GDEs in the United States at 1 km spatial resolution. A methodology to identify the probability of an ecosystem to be groundwater dependent is developed. Probabilities are obtained by modeling the relationship between the known locations of GDEs and main factors influencing groundwater dependency, namely water table depth (WTD) and aridity index (AI). A methodology is proposed to predict WTD at 1 km spatial resolution using relevant geospatial data sets calibrated with WTD observations. An ensemble learning algorithm called random forest (RF) is used in order to model the distribution of groundwater in three study areas: Nevada, California, and Washington, as well as in the entire United States. RF regression performance is compared with a single regression tree (RT). The comparison is based on contrasting training error, true prediction error, and variable importance estimates of both methods. Additionally, remote sensing variables are omitted from the process of fitting the RF model to the data to evaluate the deterioration in the model performance when these variables are not used as an input. Research results suggest that although the prediction accuracy of a single RT is reduced in comparison with RFs, single trees can still be used to understand the interactions that might be taking place between predictor variables and the response variable. Regarding RF, there is a great potential in using the power of an ensemble of trees for prediction of WTD. The superior capability of RF to accurately map water table position in Nevada, California, and Washington demonstrate that this technique can be applied at scales larger than regional levels. It is also shown that the removal of remote sensing variables from the RF training process degrades the performance of the model. Using the predicted WTD, the probability of an ecosystem to be groundwater dependent (GDE probability) is estimated at 1 km spatial resolution. The modeling technique is evaluated in the state of Nevada, USA to develop a systematic approach for the identification of GDEs and it is then applied in the United States. The modeling approach selected for the development of the GDE probability map results from a comparison of the performance of classification trees (CT) and classification forests (CF). Predictive performance evaluation for the selection of the most accurate model is achieved using a threshold independent technique, and the prediction accuracy of both models is assessed in greater detail using threshold-dependent measures. The resulting GDE probability map can potentially be used for the definition of conservation areas since it can be translated into a binary classification map with two classes: GDE and NON-GDE. These maps are created by selecting a probability threshold. It is demonstrated that the choice of this threshold has dramatic effects on deterministic model performance measures.

Probabilistic mapping of descriptive health status responses onto health state utilities using Bayesian networks: an empirical analysis converting SF-12 into EQ-5D utility index in a national US sample.

PubMed

Le, Quang A; Doctor, Jason N

2011-05-01

As quality-adjusted life years have become the standard metric in health economic evaluations, mapping health-profile or disease-specific measures onto preference-based measures to obtain quality-adjusted life years has become a solution when health utilities are not directly available. However, current mapping methods are limited due to their predictive validity, reliability, and/or other methodological issues. We employ probability theory together with a graphical model, called a Bayesian network, to convert health-profile measures into preference-based measures and to compare the results to those estimated with current mapping methods. A sample of 19,678 adults who completed both the 12-item Short Form Health Survey (SF-12v2) and EuroQoL 5D (EQ-5D) questionnaires from the 2003 Medical Expenditure Panel Survey was split into training and validation sets. Bayesian networks were constructed to explore the probabilistic relationships between each EQ-5D domain and 12 items of the SF-12v2. The EQ-5D utility scores were estimated on the basis of the predicted probability of each response level of the 5 EQ-5D domains obtained from the Bayesian inference process using the following methods: Monte Carlo simulation, expected utility, and most-likely probability. Results were then compared with current mapping methods including multinomial logistic regression, ordinary least squares, and censored least absolute deviations. The Bayesian networks consistently outperformed other mapping models in the overall sample (mean absolute error=0.077, mean square error=0.013, and R overall=0.802), in different age groups, number of chronic conditions, and ranges of the EQ-5D index. Bayesian networks provide a new robust and natural approach to map health status responses into health utility measures for health economic evaluations.

Influence of Intramyocardial Adipose Tissue on the Accuracy of Endocardial Contact Mapping of the Chronic Myocardial Infarction Substrate.

PubMed

Samanta, Rahul; Kumar, Saurabh; Chik, William; Qian, Pierre; Barry, Michael A; Al Raisi, Sara; Bhaskaran, Abhishek; Farraha, Melad; Nadri, Fazlur; Kizana, Eddy; Thiagalingam, Aravinda; Kovoor, Pramesh; Pouliopoulos, Jim

2017-10-01

Recent studies have demonstrated that intramyocardial adipose tissue (IMAT) may contribute to ventricular electrophysiological remodeling in patients with chronic myocardial infarction. Using an ovine model of myocardial infarction, we aimed to determine the influence of IMAT on scar tissue identification during endocardial contact mapping and optimal voltage-based mapping criteria for defining IMAT dense regions. In 7 sheep, left ventricular endocardial and transmural mapping was performed 84 weeks (15-111 weeks) post-myocardial infarction. Spearman rank correlation coefficient was used to assess the relationship between endocardial contact electrogram amplitude and histological composition of myocardium. Receiver operator characteristic curves were used to derive optimal electrogram thresholds for IMAT delineation during endocardial mapping and to describe the use of endocardial mapping for delineation of IMAT dense regions within scar. Endocardial electrogram amplitude correlated significantly with IMAT (unipolar r =-0.48±0.12, P <0.001; bipolar r =-0.45±0.22, P =0.04) but not collagen (unipolar r =-0.36±0.24, P =0.13; bipolar r =-0.43±0.31, P =0.16). IMAT dense regions of myocardium reliably identified using endocardial mapping with thresholds of <3.7 and <0.6 mV, respectively, for unipolar, bipolar, and combined modalities (single modality area under the curve=0.80, P <0.001; combined modality area under the curve=0.84, P <0.001). Unipolar mapping using optimal thresholding remained significantly reliable (area under the curve=0.76, P <0.001) during mapping of IMAT, confined to putative scar border zones (bipolar amplitude, 0.5-1.5 mV). These novel findings enhance our understanding of the confounding influence of IMAT on endocardial scar mapping. Combined bipolar and unipolar voltage mapping using optimal thresholds may be useful for delineating IMAT dense regions of myocardium, in postinfarct cardiomyopathy. © 2017 American Heart Association, Inc.

Subject-specific bone attenuation correction for brain PET/MR: can ZTE-MRI substitute CT scan accurately?

PubMed

Khalifé, Maya; Fernandez, Brice; Jaubert, Olivier; Soussan, Michael; Brulon, Vincent; Buvat, Irène; Comtat, Claude

2017-09-21

In brain PET/MR applications, accurate attenuation maps are required for accurate PET image quantification. An implemented attenuation correction (AC) method for brain imaging is the single-atlas approach that estimates an AC map from an averaged CT template. As an alternative, we propose to use a zero echo time (ZTE) pulse sequence to segment bone, air and soft tissue. A linear relationship between histogram normalized ZTE intensity and measured CT density in Hounsfield units ([Formula: see text]) in bone has been established thanks to a CT-MR database of 16 patients. Continuous AC maps were computed based on the segmented ZTE by setting a fixed linear attenuation coefficient (LAC) to air and soft tissue and by using the linear relationship to generate continuous μ values for the bone. Additionally, for the purpose of comparison, four other AC maps were generated: a ZTE derived AC map with a fixed LAC for the bone, an AC map based on the single-atlas approach as provided by the PET/MR manufacturer, a soft-tissue only AC map and, finally, the CT derived attenuation map used as the gold standard (CTAC). All these AC maps were used with different levels of smoothing for PET image reconstruction with and without time-of-flight (TOF). The subject-specific AC map generated by combining ZTE-based segmentation and linear scaling of the normalized ZTE signal into [Formula: see text] was found to be a good substitute for the measured CTAC map in brain PET/MR when used with a Gaussian smoothing kernel of [Formula: see text] corresponding to the PET scanner intrinsic resolution. As expected TOF reduces AC error regardless of the AC method. The continuous ZTE-AC performed better than the other alternative MR derived AC methods, reducing the quantification error between the MRAC corrected PET image and the reference CTAC corrected PET image.

Subject-specific bone attenuation correction for brain PET/MR: can ZTE-MRI substitute CT scan accurately?

NASA Astrophysics Data System (ADS)

Khalifé, Maya; Fernandez, Brice; Jaubert, Olivier; Soussan, Michael; Brulon, Vincent; Buvat, Irène; Comtat, Claude

2017-10-01

In brain PET/MR applications, accurate attenuation maps are required for accurate PET image quantification. An implemented attenuation correction (AC) method for brain imaging is the single-atlas approach that estimates an AC map from an averaged CT template. As an alternative, we propose to use a zero echo time (ZTE) pulse sequence to segment bone, air and soft tissue. A linear relationship between histogram normalized ZTE intensity and measured CT density in Hounsfield units (HU ) in bone has been established thanks to a CT-MR database of 16 patients. Continuous AC maps were computed based on the segmented ZTE by setting a fixed linear attenuation coefficient (LAC) to air and soft tissue and by using the linear relationship to generate continuous μ values for the bone. Additionally, for the purpose of comparison, four other AC maps were generated: a ZTE derived AC map with a fixed LAC for the bone, an AC map based on the single-atlas approach as provided by the PET/MR manufacturer, a soft-tissue only AC map and, finally, the CT derived attenuation map used as the gold standard (CTAC). All these AC maps were used with different levels of smoothing for PET image reconstruction with and without time-of-flight (TOF). The subject-specific AC map generated by combining ZTE-based segmentation and linear scaling of the normalized ZTE signal into HU was found to be a good substitute for the measured CTAC map in brain PET/MR when used with a Gaussian smoothing kernel of 4~mm corresponding to the PET scanner intrinsic resolution. As expected TOF reduces AC error regardless of the AC method. The continuous ZTE-AC performed better than the other alternative MR derived AC methods, reducing the quantification error between the MRAC corrected PET image and the reference CTAC corrected PET image.

Mapping the biological condition of USA rivers and streams

EPA Science Inventory

We predicted the probable (pr) biological condition (BC) of ~5.4 million km of stream within the conterminous USA (CONUS). National maps of prBC could provide an important tool for prioritizing monitoring and restoration of streams. The USEPA uses a spatially balanced survey desi...

The effects of vent location, event scale and time forecasts on pyroclastic density current hazard maps at Campi Flegrei caldera (Italy)

NASA Astrophysics Data System (ADS)

Bevilacqua, Andrea; Neri, Augusto; Bisson, Marina; Esposti Ongaro, Tomaso; Flandoli, Franco; Isaia, Roberto; Rosi, Mauro; Vitale, Stefano

2017-09-01

This study presents a new method for producing long-term hazard maps for pyroclastic density currents (PDC) originating at Campi Flegrei caldera. Such method is based on a doubly stochastic approach and is able to combine the uncertainty assessments on the spatial location of the volcanic vent, the size of the flow and the expected time of such an event. The results are obtained by using a Monte Carlo approach and adopting a simplified invasion model based on the box model integral approximation. Temporal assessments are modelled through a Cox-type process including self-excitement effects, based on the eruptive record of the last 15 kyr. Mean and percentile maps of PDC invasion probability are produced, exploring their sensitivity to some sources of uncertainty and to the effects of the dependence between PDC scales and the caldera sector where they originated. Conditional maps representative of PDC originating inside limited zones of the caldera, or of PDC with a limited range of scales are also produced. Finally, the effect of assuming different time windows for the hazard estimates is explored, also including the potential occurrence of a sequence of multiple events. Assuming that the last eruption of Monte Nuovo (A.D. 1538) marked the beginning of a new epoch of activity similar to the previous ones, results of the statistical analysis indicate a mean probability of PDC invasion above 5% in the next 50 years on almost the entire caldera (with a probability peak of 25% in the central part of the caldera). In contrast, probability values reduce by a factor of about 3 if the entire eruptive record is considered over the last 15 kyr, i.e. including both eruptive epochs and quiescent periods.

Toward uniform probabilistic seismic hazard assessments for Southeast Asia

NASA Astrophysics Data System (ADS)

Chan, C. H.; Wang, Y.; Shi, X.; Ornthammarath, T.; Warnitchai, P.; Kosuwan, S.; Thant, M.; Nguyen, P. H.; Nguyen, L. M.; Solidum, R., Jr.; Irsyam, M.; Hidayati, S.; Sieh, K.

2017-12-01

Although most Southeast Asian countries have seismic hazard maps, various methodologies and quality result in appreciable mismatches at national boundaries. We aim to conduct a uniform assessment across the region by through standardized earthquake and fault databases, ground-shaking scenarios, and regional hazard maps. Our earthquake database contains earthquake parameters obtained from global and national seismic networks, harmonized by removal of duplicate events and the use of moment magnitude. Our active-fault database includes fault parameters from previous studies and from the databases implemented for national seismic hazard maps. Another crucial input for seismic hazard assessment is proper evaluation of ground-shaking attenuation. Since few ground-motion prediction equations (GMPEs) have used local observations from this region, we evaluated attenuation by comparison of instrumental observations and felt intensities for recent earthquakes with predicted ground shaking from published GMPEs. We then utilize the best-fitting GMPEs and site conditions into our seismic hazard assessments. Based on the database and proper GMPEs, we have constructed regional probabilistic seismic hazard maps. The assessment shows highest seismic hazard levels near those faults with high slip rates, including the Sagaing Fault in central Myanmar, the Sumatran Fault in Sumatra, the Palu-Koro, Matano and Lawanopo Faults in Sulawesi, and the Philippine Fault across several islands of the Philippines. In addition, our assessment demonstrates the important fact that regions with low earthquake probability may well have a higher aggregate probability of future earthquakes, since they encompass much larger areas than the areas of high probability. The significant irony then is that in areas of low to moderate probability, where building codes are usually to provide less seismic resilience, seismic risk is likely to be greater. Infrastructural damage in East Malaysia during the 2015 Sabah earthquake offers a case in point.

Risk-targeted versus current seismic design maps for the conterminous United States

USGS Publications Warehouse

Luco, Nicolas; Ellingwood, Bruce R.; Hamburger, Ronald O.; Hooper, John D.; Kimball, Jeffrey K.; Kircher, Charles A.

2007-01-01

The probabilistic portions of the seismic design maps in the NEHRP Provisions (FEMA, 2003/2000/1997), and in the International Building Code (ICC, 2006/2003/2000) and ASCE Standard 7-05 (ASCE, 2005a), provide ground motion values from the USGS that have a 2% probability of being exceeded in 50 years. Under the assumption that the capacity against collapse of structures designed for these "uniformhazard" ground motions is equal to, without uncertainty, the corresponding mapped value at the location of the structure, the probability of its collapse in 50 years is also uniform. This is not the case however, when it is recognized that there is, in fact, uncertainty in the structural capacity. In that case, siteto-site variability in the shape of ground motion hazard curves results in a lack of uniformity. This paper explains the basis for proposed adjustments to the uniform-hazard portions of the seismic design maps currently in the NEHRP Provisions that result in uniform estimated collapse probability. For seismic design of nuclear facilities, analogous but specialized adjustments have recently been defined in ASCE Standard 43-05 (ASCE, 2005b). In support of the 2009 update of the NEHRP Provisions currently being conducted by the Building Seismic Safety Council (BSSC), herein we provide examples of the adjusted ground motions for a selected target collapse probability (or target risk). Relative to the probabilistic MCE ground motions currently in the NEHRP Provisions, the risk-targeted ground motions for design are smaller (by as much as about 30%) in the New Madrid Seismic Zone, near Charleston, South Carolina, and in the coastal region of Oregon, with relatively little (<15%) change almost everywhere else in the conterminous U.S.

Fire-probability maps for the Brazilian Amazonia

NASA Astrophysics Data System (ADS)

Cardoso, M.; Nobre, C.; Obregon, G.; Sampaio, G.

2009-04-01

Most fires in Amazonia result from the combination between climate and land-use factors. They occur mainly in the dry season and are used as an inexpensive tool for land clearing and management. However, their unintended consequences are of important concern. Fire emissions are the most important sources of greenhouse gases and aerosols in the region, accidental fires are a major threat to protected areas, and frequent fires may lead to permanent conversion of forest areas into savannas. Fire-activity models have thus become important tools for environmental analyses in Amazonia. They are used, for example, in warning systems for monitoring the risk of burnings in protected areas, to improve the description of biogeochemical cycles and vegetation composition in ecosystem models, and to help estimate the long-term potential for savannas in biome models. Previous modeling studies for the whole region were produced in units of satellite fire pixels, which complicate their direct use for environmental applications. By reinterpreting remote-sensing based data using a statistical approach, we were able to calibrate models for the whole region in units of probability, or chance of fires to occur. The application of these models for years 2005 and 2006 provided maps of fire potential at 3-month and 0.25-deg resolution as a function of precipitation and distance from main roads. In both years, the performance of the resulting maps was better for the period July-September. During these months, most of satellite-based fire observations were located in areas with relatively high chance of fire, as determined by the modeled probability maps. In addition to reproduce reasonably well the areas presenting maximum fire activity as detected by remote sensing, the new results in units of probability are easier to apply than previous estimates from fire-pixel models.

Fire-probability maps for the Brazilian Amazonia

NASA Astrophysics Data System (ADS)

Cardoso, Manoel; Sampaio, Gilvan; Obregon, Guillermo; Nobre, Carlos

2010-05-01

Most fires in Amazonia result from the combination between climate and land-use factors. They occur mainly in the dry season and are used as an inexpensive tool for land clearing and management. However, their unintended consequences are of important concern. Fire emissions are the most important sources of greenhouse gases and aerosols in the region, accidental fires are a major threat to protected areas, and frequent fires may lead to permanent conversion of forest areas into savannas. Fire-activity models have thus become important tools for environmental analyses in Amazonia. They are used, for example, in warning systems for monitoring the risk of burnings in protected areas, to improve the description of biogeochemical cycles and vegetation composition in ecosystem models, and to help estimate the long-term potential for savannas in biome models. Previous modeling studies for the whole region were produced in units of satellite fire pixels, which complicate their direct use for environmental applications. By reinterpreting remote-sensing based data using a statistical approach, we were able to calibrate models for the whole region in units of probability, or chance of fires to occur. The application of these models for years 2005 and 2006 provided maps of fire potential at 3-month and 0.25-deg resolution as a function of precipitation and distance from main roads. In both years, the performance of the resulting maps was better for the period July-September. During these months, most of satellite-based fire observations were located in areas with relatively high chance of fire, as determined by the modeled probability maps. In addition to reproduce reasonably well the areas presenting maximum fire activity as detected by remote sensing, the new results in units of probability are easier to apply than previous estimates from fire-pixel models.

Identification of Stochastically Perturbed Autonomous Systems from Temporal Sequences of Probability Density Functions

NASA Astrophysics Data System (ADS)

Nie, Xiaokai; Luo, Jingjing; Coca, Daniel; Birkin, Mark; Chen, Jing

2018-03-01

The paper introduces a method for reconstructing one-dimensional iterated maps that are driven by an external control input and subjected to an additive stochastic perturbation, from sequences of probability density functions that are generated by the stochastic dynamical systems and observed experimentally.

Planetary Geology and Geophysics Program

NASA Technical Reports Server (NTRS)

McGill, George E.

2004-01-01

Geological mapping and topical studies, primarily in the southern Acidalia Planitia/Cydonia Mensae region of Mars is presented. The overall objective was to understand geologic processes and crustal history in the northern lowland in order to assess the probability that an ocean once existed in this region. The major deliverable is a block of 6 1:500,000 scale geologic maps that will be published in 2004 as a single map at 1:1,000,000 scale along with extensive descriptive and interpretive text. A major issue addressed by the mapping was the relative ages of the extensive plains of Acidalia Planitia and the knobs and mesas of Cydonia Mensae. The mapping results clearly favor a younger age for the plains. Topical studies included a preliminary analysis of the very abundant small domes and cones to assess the possibility that their origins could be determined by detailed mapping and remote-sensing analysis. We also tested the validity of putative shorelines by using GIs to co-register full-resolution MOLA altimetry data and Viking images with these shorelines plotted on them. Of the 3 proposed shorelines in this area, one is probably valid, one is definitely not valid, and the third is apparently 2 shorelines closely spaced in elevation. Publications supported entirely or in part by this grant are included.

Noninvasive Spatially Offset and Transmission Raman Mapping of Breast Tissue: A Multimodal Approach Towards the In Vivo Assessment of Tissue Pathology

DTIC Science & Technology

2013-06-01

spectroscopy on tissue biopsies to correlate spectral bands with healthy and diseased breast tissue. Observed spectral changes are compared to infrared...capabilities and performance. Additionally, we conduct spectroscopy on tissue biopsies to correlate spectral bands with healthy and diseased ... disease states, ie hyperplasia, dysplasia, malignant, benign. The instrumentation has been built and characterized using archived tissue that was

Mapping local anisotropy axis for scattering media using backscattering Mueller matrix imaging

NASA Astrophysics Data System (ADS)

He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Guo, Yihong; He, Yonghong; Ma, Hui

2014-03-01

Mueller matrix imaging techniques can be used to detect the micro-structure variations of superficial biological tissues, including the sizes and shapes of cells, the structures in cells, and the densities of the organelles. Many tissues contain anisotropic fibrous micro-structures, such as collagen fibers, elastin fibers, and muscle fibers. Changes of these fibrous structures are potentially good indicators for some pathological variations. In this paper, we propose a quantitative analysis technique based on Mueller matrix for mapping local anisotropy axis of scattering media. By conducting both experiments on silk sample and Monte Carlo simulation based on the sphere-cylinder scattering model (SCSM), we extract anisotropy axis parameters from different backscattering Mueller matrix elements. Moreover, we testify the possible applications of these parameters for biological tissues. The preliminary experimental results of human cancerous samples show that, these parameters are capable to map the local axis of fibers. Since many pathological changes including early stage cancers affect the well aligned structures for tissues, the experimental results indicate that these parameters can be used as potential tools in clinical applications for biomedical diagnosis purposes.

Automated adipose study for assessing cancerous human breast tissue using optical coherence tomography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gan, Yu; Yao, Xinwen; Chang, Ernest W.; Bin Amir, Syed A.; Hibshoosh, Hanina; Feldman, Sheldon; Hendon, Christine P.

2017-02-01

Breast cancer is the third leading cause of death in women in the United States. In human breast tissue, adipose cells are infiltrated or replaced by cancer cells during the development of breast tumor. Therefore, an adipose map can be an indicator of identifying cancerous region. We developed an automated classification method to generate adipose map within human breast. To facilitate the automated classification, we first mask the B-scans from OCT volumes by comparing the signal noise ratio with a threshold. Then, the image was divided into multiple blocks with a size of 30 pixels by 30 pixels. In each block, we extracted texture features such as local standard deviation, entropy, homogeneity, and coarseness. The features of each block were input to a probabilistic model, relevance vector machine (RVM), which was trained prior to the experiment, to classify tissue types. For each block within the B-scan, RVM identified the region with adipose tissue. We calculated the adipose ratio as the number of blocks identified as adipose over the total number of blocks within the B-scan. We obtained OCT images from patients (n = 19) in Columbia medical center. We automatically generated the adipose maps from 24 B-scans including normal samples (n = 16) and cancerous samples (n = 8). We found the adipose regions show an isolated pattern that in cancerous tissue while a clustered pattern in normal tissue. Moreover, the adipose ratio (52.30 ± 29.42%) in normal tissue was higher than the that in cancerous tissue (12.41 ± 10.07%).

SU-D-18C-05: Variable Bolus Arterial Spin Labeling MRI for Accurate Cerebral Blood Flow and Arterial Transit Time Mapping

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

Johnston, M; Jung, Y

2014-06-01

Purpose: Arterial spin labeling (ASL) is an MRI perfusion imaging method from which quantitative cerebral blood flow (CBF) maps can be calculated. Acquisition with variable post-labeling delays (PLD) and variable TRs allows for arterial transit time (ATT) mapping and leads to more accurate CBF quantification with a scan time saving of 48%. In addition, T1 and M0 maps can be obtained without a separate scan. In order to accurately estimate ATT and T1 of brain tissue from the ASL data, variable labeling durations were invented, entitled variable-bolus ASL. Methods: All images were collected on a healthy subject with a 3Tmore » Siemens Skyra scanner. Variable-bolus Psuedo-continuous ASL (PCASL) images were collected with 7 TI times ranging 100-4300ms in increments of 700ms with TR ranging 1000-5200ms. All boluses were 1600ms when the TI allowed, otherwise the bolus duration was 100ms shorter than the TI. All TI times were interleaved to reduce sensitivity to motion. Voxel-wise T1 and M0 maps were estimated using a linear least squares fitting routine from the average singal from each TI time. Then pairwise subtraction of each label/control pair and averaging for each TI time was performed. CBF and ATT maps were created using the standard model by Buxton et al. with a nonlinear fitting routine using the T1 tissue map. Results: CBF maps insensitive to ATT were produced along with ATT maps. Both maps show patterns and averages consistent with literature. The T1 map also shows typical T1 contrast. Conclusion: It has been demonstrated that variablebolus ASL produces CBF maps free from the errors due to ATT and tissue T1 variations and provides M0, T1, and ATT maps which have potential utility. This is accomplished with a single scan in a feasible scan time (under 6 minutes) with low sensivity to motion.« less

LINKS: learning-based multi-source IntegratioN frameworK for Segmentation of infant brain images.

PubMed

Wang, Li; Gao, Yaozong; Shi, Feng; Li, Gang; Gilmore, John H; Lin, Weili; Shen, Dinggang

2015-03-01

Segmentation of infant brain MR images is challenging due to insufficient image quality, severe partial volume effect, and ongoing maturation and myelination processes. In the first year of life, the image contrast between white and gray matters of the infant brain undergoes dramatic changes. In particular, the image contrast is inverted around 6-8months of age, and the white and gray matter tissues are isointense in both T1- and T2-weighted MR images and thus exhibit the extremely low tissue contrast, which poses significant challenges for automated segmentation. Most previous studies used multi-atlas label fusion strategy, which has the limitation of equally treating the different available image modalities and is often computationally expensive. To cope with these limitations, in this paper, we propose a novel learning-based multi-source integration framework for segmentation of infant brain images. Specifically, we employ the random forest technique to effectively integrate features from multi-source images together for tissue segmentation. Here, the multi-source images include initially only the multi-modality (T1, T2 and FA) images and later also the iteratively estimated and refined tissue probability maps of gray matter, white matter, and cerebrospinal fluid. Experimental results on 119 infants show that the proposed method achieves better performance than other state-of-the-art automated segmentation methods. Further validation was performed on the MICCAI grand challenge and the proposed method was ranked top among all competing methods. Moreover, to alleviate the possible anatomical errors, our method can also be combined with an anatomically-constrained multi-atlas labeling approach for further improving the segmentation accuracy. Copyright © 2014 Elsevier Inc. All rights reserved.

LINKS: Learning-based multi-source IntegratioN frameworK for Segmentation of infant brain images

PubMed Central

Wang, Li; Gao, Yaozong; Shi, Feng; Li, Gang; Gilmore, John H.; Lin, Weili; Shen, Dinggang

2014-01-01

Segmentation of infant brain MR images is challenging due to insufficient image quality, severe partial volume effect, and ongoing maturation and myelination processes. In the first year of life, the image contrast between white and gray matters of the infant brain undergoes dramatic changes. In particular, the image contrast is inverted around 6-8 months of age, and the white and gray matter tissues are isointense in both T1- and T2-weighted MR images and thus exhibit the extremely low tissue contrast, which poses significant challenges for automated segmentation. Most previous studies used multi-atlas label fusion strategy, which has the limitation of equally treating the different available image modalities and is often computationally expensive. To cope with these limitations, in this paper, we propose a novel learning-based multi-source integration framework for segmentation of infant brain images. Specifically, we employ the random forest technique to effectively integrate features from multi-source images together for tissue segmentation. Here, the multi-source images include initially only the multi-modality (T1, T2 and FA) images and later also the iteratively estimated and refined tissue probability maps of gray matter, white matter, and cerebrospinal fluid. Experimental results on 119 infants show that the proposed method achieves better performance than other state-of-the-art automated segmentation methods. Further validation was performed on the MICCAI grand challenge and the proposed method was ranked top among all competing methods. Moreover, to alleviate the possible anatomical errors, our method can also be combined with an anatomically-constrained multi-atlas labeling approach for further improving the segmentation accuracy. PMID:25541188

High-spatial-resolution mapping of the oxygen concentration in cortical tissue (Conference Presentation)

NASA Astrophysics Data System (ADS)

Jaswal, Rajeshwer S.; Yaseen, Mohammad A.; Fu, Buyin; Boas, David A.; Sakadžic, Sava

2016-03-01

Due to a lack of imaging tools for high-resolution imaging of cortical tissue oxygenation, the detailed maps of the oxygen partial pressure (PO2) around arterioles, venules, and capillaries remain largely unknown. Therefore, we have limited knowledge about the mechanisms that secure sufficient oxygen delivery in microvascular domains during brain activation, and provide some metabolic reserve capacity in diseases that affect either microvascular networks or the regulation of cerebral blood flow (CBF). To address this challenge, we applied a Two-Photon PO2 Microscopy to map PO2 at different depths in mice cortices. Measurements were performed through the cranial window in the anesthetized healthy mice as well as in the mouse models of microvascular dysfunctions. In addition, microvascular morphology was recorded by the two-photon microscopy at the end of each experiment and subsequently segmented. Co-registration of the PO2 measurements and exact microvascular morphology enabled quantification of the tissue PO2 dependence on distance from the arterioles, capillaries, and venules at various depths. Our measurements reveal significant spatial heterogeneity of the cortical tissue PO2 distribution that is dominated by the high oxygenation in periarteriolar spaces. In cases of impaired oxygen delivery due to microvascular dysfunction, significant reduction in tissue oxygenation away from the arterioles was observed. These tissue domains may be the initial sites of cortical injury that can further exacerbate the progression of the disease.

Simultaneous Nonrigid Registration, Segmentation, and Tumor Detection in MRI Guided Cervical Cancer Radiation Therapy

PubMed Central

Lu, Chao; Chelikani, Sudhakar; Jaffray, David A.; Milosevic, Michael F.; Staib, Lawrence H.; Duncan, James S.

2013-01-01

External beam radiation therapy (EBRT) for the treatment of cancer enables accurate placement of radiation dose on the cancerous region. However, the deformation of soft tissue during the course of treatment, such as in cervical cancer, presents significant challenges for the delineation of the target volume and other structures of interest. Furthermore, the presence and regression of pathologies such as tumors may violate registration constraints and cause registration errors. In this paper, automatic segmentation, nonrigid registration and tumor detection in cervical magnetic resonance (MR) data are addressed simultaneously using a unified Bayesian framework. The proposed novel method can generate a tumor probability map while progressively identifying the boundary of an organ of interest based on the achieved nonrigid transformation. The method is able to handle the challenges of significant tumor regression and its effect on surrounding tissues. The new method was compared to various currently existing algorithms on a set of 36 MR data from six patients, each patient has six T2-weighted MR cervical images. The results show that the proposed approach achieves an accuracy comparable to manual segmentation and it significantly outperforms the existing registration algorithms. In addition, the tumor detection result generated by the proposed method has a high agreement with manual delineation by a qualified clinician. PMID:22328178

QDMR: a quantitative method for identification of differentially methylated regions by entropy

PubMed Central

Zhang, Yan; Liu, Hongbo; Lv, Jie; Xiao, Xue; Zhu, Jiang; Liu, Xiaojuan; Su, Jianzhong; Li, Xia; Wu, Qiong; Wang, Fang; Cui, Ying

2011-01-01

DNA methylation plays critical roles in transcriptional regulation and chromatin remodeling. Differentially methylated regions (DMRs) have important implications for development, aging and diseases. Therefore, genome-wide mapping of DMRs across various temporal and spatial methylomes is important in revealing the impact of epigenetic modifications on heritable phenotypic variation. We present a quantitative approach, quantitative differentially methylated regions (QDMRs), to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy. QDMR was applied to synthetic methylation patterns and methylation profiles detected by methylated DNA immunoprecipitation microarray (MeDIP-chip) in human tissues/cells. This approach can give a reasonable quantitative measure of methylation difference across multiple samples. Then DMR threshold was determined from methylation probability model. Using this threshold, QDMR identified 10 651 tissue DMRs which are related to the genes enriched for cell differentiation, including 4740 DMRs not identified by the method developed by Rakyan et al. QDMR can also measure the sample specificity of each DMR. Finally, the application to methylation profiles detected by reduced representation bisulphite sequencing (RRBS) in mouse showed the platform-free and species-free nature of QDMR. This approach provides an effective tool for the high-throughput identification of potential functional regions involved in epigenetic regulation. PMID:21306990

Development of spatial-temporal ventilation heterogeneity and probability analysis tools for hyperpolarized 3He magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Choy, S.; Ahmed, H.; Wheatley, A.; McCormack, D. G.; Parraga, G.

2010-03-01

We developed image analysis tools to evaluate spatial and temporal 3He magnetic resonance imaging (MRI) ventilation in asthma and cystic fibrosis. We also developed temporal ventilation probability maps to provide a way to describe and quantify ventilation heterogeneity over time, as a way to test respiratory exacerbations or treatment predictions and to provide a discrete probability measurement of 3He ventilation defect persistence.

Arsenic concentrations, related environmental factors, and the predicted probability of elevated arsenic in groundwater in Pennsylvania

USGS Publications Warehouse

Gross, Eliza L.; Low, Dennis J.

2013-01-01

Logistic regression models were created to predict and map the probability of elevated arsenic concentrations in groundwater statewide in Pennsylvania and in three intrastate regions to further improve predictions for those three regions (glacial aquifer system, Gettysburg Basin, Newark Basin). Although the Pennsylvania and regional predictive models retained some different variables, they have common characteristics that can be grouped by (1) geologic and soils variables describing arsenic sources and mobilizers, (2) geochemical variables describing the geochemical environment of the groundwater, and (3) locally specific variables that are unique to each of the three regions studied and not applicable to statewide analysis. Maps of Pennsylvania and the three intrastate regions were produced that illustrate that areas most at risk are those with geology and soils capable of functioning as an arsenic source or mobilizer and geochemical groundwater conditions able to facilitate redox reactions. The models have limitations because they may not characterize areas that have localized controls on arsenic mobility. The probability maps associated with this report are intended for regional-scale use and may not be accurate for use at the field scale or when considering individual wells.

Linking sounds to meanings: infant statistical learning in a natural language.

PubMed

Hay, Jessica F; Pelucchi, Bruna; Graf Estes, Katharine; Saffran, Jenny R

2011-09-01

The processes of infant word segmentation and infant word learning have largely been studied separately. However, the ease with which potential word forms are segmented from fluent speech seems likely to influence subsequent mappings between words and their referents. To explore this process, we tested the link between the statistical coherence of sequences presented in fluent speech and infants' subsequent use of those sequences as labels for novel objects. Notably, the materials were drawn from a natural language unfamiliar to the infants (Italian). The results of three experiments suggest that there is a close relationship between the statistics of the speech stream and subsequent mapping of labels to referents. Mapping was facilitated when the labels contained high transitional probabilities in the forward and/or backward direction (Experiment 1). When no transitional probability information was available (Experiment 2), or when the internal transitional probabilities of the labels were low in both directions (Experiment 3), infants failed to link the labels to their referents. Word learning appears to be strongly influenced by infants' prior experience with the distribution of sounds that make up words in natural languages. Copyright © 2011 Elsevier Inc. All rights reserved.

CD4 T Cell Dependent Colitis Exacerbation Following Re-Exposure of Mycobacterium avium ssp. paratuberculosis.

PubMed

Suwandi, Abdulhadi; Bargen, Imke; Pils, Marina C; Krey, Martina; Zur Lage, Susanne; Singh, Anurag K; Basler, Tina; Falk, Christine S; Seidler, Ursula; Hornef, Mathias W; Goethe, Ralph; Weiss, Siegfried

2017-01-01

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of Johne's disease (JD), a chronic inflammatory bowel disease of cattle characterized by intermittent to chronic diarrhea. In addition, MAP has been isolated from Crohn's disease (CD) patients. The impact of MAP on severity of clinical symptoms in JD as well as its role in CD are yet unknown. We have previously shown that MAP is able to colonize inflamed enteric tissue and to exacerbate the inflammatory tissue response (Suwandi et al., 2014). In the present study, we analyzed how repeated MAP administration influences the course of dextran sulfate sodium (DSS)-induced colitis. In comparison to mice exposed to DSS or MAP only, repeated exposure of DSS-treated mice to MAP (DSS/MAP) revealed a significantly enhanced clinical score, reduction of colon length as well as severe CD4 + T cell infiltration into the colonic lamina propria . Functional analysis identified a critical role of CD4 + T cells in the MAP-induced disease exacerbation. Additionally, altered immune responses were observed when closely related mycobacteria species such as M. avium ssp. avium and M. avium ssp. hominissuis were administered. These data reveal the specific ability of MAP to aggravate intestinal inflammation and clinical symptoms. Overall, this phenotype is compatible with similar disease promoting capabilites of MAP in JD and CD.

CD4 T Cell Dependent Colitis Exacerbation Following Re-Exposure of Mycobacterium avium ssp. paratuberculosis

PubMed Central

Suwandi, Abdulhadi; Bargen, Imke; Pils, Marina C.; Krey, Martina; Zur Lage, Susanne; Singh, Anurag K.; Basler, Tina; Falk, Christine S.; Seidler, Ursula; Hornef, Mathias W.; Goethe, Ralph; Weiss, Siegfried

2017-01-01

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of Johne's disease (JD), a chronic inflammatory bowel disease of cattle characterized by intermittent to chronic diarrhea. In addition, MAP has been isolated from Crohn's disease (CD) patients. The impact of MAP on severity of clinical symptoms in JD as well as its role in CD are yet unknown. We have previously shown that MAP is able to colonize inflamed enteric tissue and to exacerbate the inflammatory tissue response (Suwandi et al., 2014). In the present study, we analyzed how repeated MAP administration influences the course of dextran sulfate sodium (DSS)-induced colitis. In comparison to mice exposed to DSS or MAP only, repeated exposure of DSS-treated mice to MAP (DSS/MAP) revealed a significantly enhanced clinical score, reduction of colon length as well as severe CD4+ T cell infiltration into the colonic lamina propria. Functional analysis identified a critical role of CD4+ T cells in the MAP-induced disease exacerbation. Additionally, altered immune responses were observed when closely related mycobacteria species such as M. avium ssp. avium and M. avium ssp. hominissuis were administered. These data reveal the specific ability of MAP to aggravate intestinal inflammation and clinical symptoms. Overall, this phenotype is compatible with similar disease promoting capabilites of MAP in JD and CD. PMID:28361039

Measuring novices' field mapping abilities using an in-class exercise based on expert task analysis

NASA Astrophysics Data System (ADS)

Caulkins, J. L.

2010-12-01

We are interested in developing a model of expert-like behavior for improving the teaching methods of undergraduate field geology. Our aim is to assist students in mastering the process of field mapping more efficiently and effectively and to improve their ability to think creatively in the field. To examine expert-mapping behavior, a cognitive task analysis was conducted with expert geologic mappers in an attempt to define the process of geologic mapping (i.e. to understand how experts carry out geological mapping). The task analysis indicates that expert mappers have a wealth of geologic scenarios at their disposal that they compare against examples seen in the field, experiences that most undergraduate mappers will not have had. While presenting students with many geological examples in class may increase their understanding of geologic processes, novices still struggle when presented with a novel field situation. Based on the task analysis, a short (45-minute) paper-map-based exercise was designed and tested with 14 pairs of 3rd year geology students. The exercise asks students to generate probable geologic models based on a series of four (4) data sets. Each data set represents a day’s worth of data; after the first “day,” new sheets simply include current and previously collected data (e.g. “Day 2” data set includes data from “Day 1” plus the new “Day 2” data). As the geologic complexity increases, students must adapt, reject or generate new geologic models in order to fit the growing data set. Preliminary results of the exercise indicate that students who produced more probable geologic models, and produced higher ratios of probable to improbable models, tended to go on to do better on the mapping exercises at the 3rd year field school. These results suggest that those students with more cognitively available geologic models may be more able to use these models in field settings than those who are unable to draw on these models for whatever reason. Giving students practice at generating geologic models to explain data may be useful in preparing our students for field mapping exercises.

Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues.

PubMed

Ku, Taeyun; Swaney, Justin; Park, Jeong-Yoon; Albanese, Alexandre; Murray, Evan; Cho, Jae Hun; Park, Young-Gyun; Mangena, Vamsi; Chen, Jiapei; Chung, Kwanghun

2016-09-01

The biology of multicellular organisms is coordinated across multiple size scales, from the subnanoscale of molecules to the macroscale, tissue-wide interconnectivity of cell populations. Here we introduce a method for super-resolution imaging of the multiscale organization of intact tissues. The method, called magnified analysis of the proteome (MAP), linearly expands entire organs fourfold while preserving their overall architecture and three-dimensional proteome organization. MAP is based on the observation that preventing crosslinking within and between endogenous proteins during hydrogel-tissue hybridization allows for natural expansion upon protein denaturation and dissociation. The expanded tissue preserves its protein content, its fine subcellular details, and its organ-scale intercellular connectivity. We use off-the-shelf antibodies for multiple rounds of immunolabeling and imaging of a tissue's magnified proteome, and our experiments demonstrate a success rate of 82% (100/122 antibodies tested). We show that specimen size can be reversibly modulated to image both inter-regional connections and fine synaptic architectures in the mouse brain.

Neural correlates of the divergence of instrumental probability distributions.

PubMed

Liljeholm, Mimi; Wang, Shuo; Zhang, June; O'Doherty, John P

2013-07-24

Flexible action selection requires knowledge about how alternative actions impact the environment: a "cognitive map" of instrumental contingencies. Reinforcement learning theories formalize this map as a set of stochastic relationships between actions and states, such that for any given action considered in a current state, a probability distribution is specified over possible outcome states. Here, we show that activity in the human inferior parietal lobule correlates with the divergence of such outcome distributions-a measure that reflects whether discrimination between alternative actions increases the controllability of the future-and, further, that this effect is dissociable from those of other information theoretic and motivational variables, such as outcome entropy, action values, and outcome utilities. Our results suggest that, although ultimately combined with reward estimates to generate action values, outcome probability distributions associated with alternative actions may be contrasted independently of valence computations, to narrow the scope of the action selection problem.

Statistical Inference in Hidden Markov Models Using k-Segment Constraints

PubMed Central

Titsias, Michalis K.; Holmes, Christopher C.; Yau, Christopher

2016-01-01

Hidden Markov models (HMMs) are one of the most widely used statistical methods for analyzing sequence data. However, the reporting of output from HMMs has largely been restricted to the presentation of the most-probable (MAP) hidden state sequence, found via the Viterbi algorithm, or the sequence of most probable marginals using the forward–backward algorithm. In this article, we expand the amount of information we could obtain from the posterior distribution of an HMM by introducing linear-time dynamic programming recursions that, conditional on a user-specified constraint in the number of segments, allow us to (i) find MAP sequences, (ii) compute posterior probabilities, and (iii) simulate sample paths. We collectively call these recursions k-segment algorithms and illustrate their utility using simulated and real examples. We also highlight the prospective and retrospective use of k-segment constraints for fitting HMMs or exploring existing model fits. Supplementary materials for this article are available online. PMID:27226674

Imaging Electric Properties of Biological Tissues by RF Field Mapping in MRI

PubMed Central

Zhang, Xiaotong; Zhu, Shanan; He, Bin

2010-01-01

The electric properties (EPs) of biological tissue, i.e., the electric conductivity and permittivity, can provide important information in the diagnosis of various diseases. The EPs also play an important role in specific absorption rate (SAR) calculation, a major concern in high-field Magnetic Resonance Imaging (MRI), as well as in non-medical areas such as wireless-telecommunications. The high-field MRI system is accompanied by significant wave propagation effects, and the radio frequency (RF) radiation is dependent on the EPs of biological tissue. Based on the measurement of the active transverse magnetic component of the applied RF field (known as B1-mapping technique), we propose a dual-excitation algorithm, which uses two sets of measured B1 data to noninvasively reconstruct the electric properties of biological tissues. The Finite Element Method (FEM) was utilized in three-dimensional (3D) modeling and B1 field calculation. A series of computer simulations were conducted to evaluate the feasibility and performance of the proposed method on a 3D head model within a transverse electromagnetic (TEM) coil and a birdcage (BC) coil. Using a TEM coil, when noise free, the reconstructed EP distribution of tissues in the brain has relative errors of 12% ∼ 28% and correlated coefficients of greater than 0.91. Compared with other B1-mapping based reconstruction algorithms, our approach provides superior performance without the need for iterative computations. The present simulation results suggest that good reconstruction of electric properties from B1 mapping can be achieved. PMID:20129847

Analysis of neoplastic lesions in magnetic resonance imaging using self-organizing maps.

PubMed

Mei, Paulo Afonso; de Carvalho Carneiro, Cleyton; Fraser, Stephen J; Min, Li Li; Reis, Fabiano

2015-12-15

To provide an improved method for the identification and analysis of brain tumors in MRI scans using a semi-automated computational approach, that has the potential to provide a more objective, precise and quantitatively rigorous analysis, compared to human visual analysis. Self-Organizing Maps (SOM) is an unsupervised, exploratory data analysis tool, which can automatically domain an image into selfsimilar regions or clusters, based on measures of similarity. It can be used to perform image-domain of brain tissue on MR images, without prior knowledge. We used SOM to analyze T1, T2 and FLAIR acquisitions from two MRI machines in our service from 14 patients with brain tumors confirmed by biopsies--three lymphomas, six glioblastomas, one meningioma, one ganglioglioma, two oligoastrocytomas and one astrocytoma. The SOM software was used to analyze the data from the three image acquisitions from each patient and generated a self-organized map for each containing 25 clusters. Damaged tissue was separated from the normal tissue using the SOM technique. Furthermore, in some cases it allowed to separate different areas from within the tumor--like edema/peritumoral infiltration and necrosis. In lesions with less precise boundaries in FLAIR, the estimated damaged tissue area in the resulting map appears bigger. Our results showed that SOM has the potential to be a powerful MR imaging analysis technique for the assessment of brain tumors. Copyright © 2015. Published by Elsevier B.V.

The lipid-reactive oxygen species phenotype of breast cancer. Raman spectroscopy and mapping, PCA and PLSDA for invasive ductal carcinoma and invasive lobular carcinoma. Molecular tumorigenic mechanisms beyond Warburg effect.

PubMed

Surmacki, Jakub; Brozek-Pluska, Beata; Kordek, Radzislaw; Abramczyk, Halina

2015-04-07

Vibrational signatures of human breast tissue (invasive ductal carcinoma and invasive lobular carcinoma) were used to identify, characterize and discriminate structures in normal (noncancerous) and cancerous tissues by confocal Raman imaging, Raman spectroscopy and IR spectroscopy. The most important differences between normal and cancerous tissues were found in regions characteristic for vibrations of carotenoids, fatty acids, proteins, and interfacial water. Particular attention was paid to the role played by unsaturated fatty acids and their derivatives. K-means clustering and basis analysis followed by PCA and PLSDA is employed to analyze Raman spectroscopic maps of human breast tissue and for a statistical analysis of the samples (82 patients, 164 samples). Raman maps successfully identify regions of carotenoids, fatty acids, and proteins. The intensities, frequencies and profiles of the average Raman spectra differentiate the biochemical composition of normal and cancerous tissues. The paper demonstrates that Raman imaging has reached a clinically relevant level in regard to breast cancer diagnosis applications. The sensitivity and specificity obtained directly from PLSLD and cross validation are equal to 90.5% and 84.8% for calibration and 84.7% and 71.9% for cross-validation respectively.

The response analysis of fractional-order stochastic system via generalized cell mapping method.

PubMed

Wang, Liang; Xue, Lili; Sun, Chunyan; Yue, Xiaole; Xu, Wei

2018-01-01

This paper is concerned with the response of a fractional-order stochastic system. The short memory principle is introduced to ensure that the response of the system is a Markov process. The generalized cell mapping method is applied to display the global dynamics of the noise-free system, such as attractors, basins of attraction, basin boundary, saddle, and invariant manifolds. The stochastic generalized cell mapping method is employed to obtain the evolutionary process of probability density functions of the response. The fractional-order ϕ 6 oscillator and the fractional-order smooth and discontinuous oscillator are taken as examples to give the implementations of our strategies. Studies have shown that the evolutionary direction of the probability density function of the fractional-order stochastic system is consistent with the unstable manifold. The effectiveness of the method is confirmed using Monte Carlo results.

Classification criteria and probability risk maps: limitations and perspectives.

PubMed

Saisana, Michaela; Dubois, Gregoire; Chaloulakou, Archontoula; Spyrellis, Nikolas

2004-03-01

Delineation of polluted zones with respect to regulatory standards, accounting at the same time for the uncertainty of the estimated concentrations, relies on classification criteria that can lead to significantly different pollution risk maps, which, in turn, can depend on the regulatory standard itself. This paper reviews four popular classification criteria related to the violation of a probability threshold or a physical threshold, using annual (1996-2000) nitrogen dioxide concentrations from 40 air monitoring stations in Milan. The relative advantages and practical limitations of each criterion are discussed, and it is shown that some of the criteria are more appropriate for the problem at hand and that the choice of the criterion can be supported by the statistical distribution of the data and/or the regulatory standard. Finally, the polluted area is estimated over the different years and concentration thresholds using the appropriate risk maps as an additional source of uncertainty.

Improving deep convolutional neural networks with mixed maxout units.

PubMed

Zhao, Hui-Zhen; Liu, Fu-Xian; Li, Long-Yue

2017-01-01

Motivated by insights from the maxout-units-based deep Convolutional Neural Network (CNN) that "non-maximal features are unable to deliver" and "feature mapping subspace pooling is insufficient," we present a novel mixed variant of the recently introduced maxout unit called a mixout unit. Specifically, we do so by calculating the exponential probabilities of feature mappings gained by applying different convolutional transformations over the same input and then calculating the expected values according to their exponential probabilities. Moreover, we introduce the Bernoulli distribution to balance the maximum values with the expected values of the feature mappings subspace. Finally, we design a simple model to verify the pooling ability of mixout units and a Mixout-units-based Network-in-Network (NiN) model to analyze the feature learning ability of the mixout models. We argue that our proposed units improve the pooling ability and that mixout models can achieve better feature learning and classification performance.

Landing Site Dispersion Analysis and Statistical Assessment for the Mars Phoenix Lander

NASA Technical Reports Server (NTRS)

Bonfiglio, Eugene P.; Adams, Douglas; Craig, Lynn; Spencer, David A.; Strauss, William; Seelos, Frank P.; Seelos, Kimberly D.; Arvidson, Ray; Heet, Tabatha

2008-01-01

The Mars Phoenix Lander launched on August 4, 2007 and successfully landed on Mars 10 months later on May 25, 2008. Landing ellipse predicts and hazard maps were key in selecting safe surface targets for Phoenix. Hazard maps were based on terrain slopes, geomorphology maps and automated rock counts of MRO's High Resolution Imaging Science Experiment (HiRISE) images. The expected landing dispersion which led to the selection of Phoenix's surface target is discussed as well as the actual landing dispersion predicts determined during operations in the weeks, days, and hours before landing. A statistical assessment of these dispersions is performed, comparing the actual landing-safety probabilities to criteria levied by the project. Also discussed are applications for this statistical analysis which were used by the Phoenix project. These include using the statistical analysis used to verify the effectiveness of a pre-planned maneuver menu and calculating the probability of future maneuvers.

Probability of cavitation for single ultrasound pulses applied to tissues and tissue-mimicking materials

PubMed Central

Maxwell, Adam D.; Cain, Charles A.; Hall, Timothy L.; Fowlkes, J. Brian; Xu, Zhen

2012-01-01

In this article, the negative pressure values at which inertial cavitation consistently occurs in response to a single, 2-cycle, focused ultrasound pulse were measured in several media relevant to cavitation-based ultrasound therapy. The pulse was focused into a chamber containing one of the media, which included liquids, tissue-mimicking materials, and ex-vivo canine tissue. Focal waveforms were measured by two separate techniques using a fiber-optic hydrophone. Inertial cavitation was identified by high-speed photography in optically transparent media and an acoustic passive cavitation detector. The probability of cavitation (Pcav) for a single pulse as a function of peak negative pressure (p−) followed a sigmoid curve, with the probability approaching 1 when the pressure amplitude was sufficient. The statistical threshold (defined as Pcav = 0.5) was between p− = 26.0–30.0 MPa in all samples with a high water content, but varied between p− = 13.7 to > 36 MPa for other media. A model for radial cavitation bubble dynamics was employed to evaluate the behavior of cavitation nuclei at these pressure levels. A single bubble nucleus with an inertial cavitation threshold of p− = 28.2 MPa was estimated to have a 2.5 nm radius in distilled water. These data may be valuable for cavitation-based ultrasound therapy to predict the likelihood of cavitation at different pressure levels and dimensions of cavitation-induced lesions in tissue. PMID:23380152

Validation Workshop of the DRDC Concept Map Knowledge Model: Issues in Intelligence Analysis

DTIC Science & Technology

2010-06-29

group noted problems with grammar , and a more standard approach to the grammar of the linking term (e.g. use only active tense ) would certainly have...Knowledge Model is distinct from a Concept Map. A Concept Map is a single map, probably presented in one view, while a Knowledge Model is a set of...Agenda The workshop followed the agenda presented in Table 2-3. Table 2-3: Workshop Agenda Time Title 13:00 – 13:15 Registration 13:15 – 13:45

Incorporating Functional Genomic Information in Genetic Association Studies Using an Empirical Bayes Approach.

PubMed

Spencer, Amy V; Cox, Angela; Lin, Wei-Yu; Easton, Douglas F; Michailidou, Kyriaki; Walters, Kevin

2016-04-01

There is a large amount of functional genetic data available, which can be used to inform fine-mapping association studies (in diseases with well-characterised disease pathways). Single nucleotide polymorphism (SNP) prioritization via Bayes factors is attractive because prior information can inform the effect size or the prior probability of causal association. This approach requires the specification of the effect size. If the information needed to estimate a priori the probability density for the effect sizes for causal SNPs in a genomic region isn't consistent or isn't available, then specifying a prior variance for the effect sizes is challenging. We propose both an empirical method to estimate this prior variance, and a coherent approach to using SNP-level functional data, to inform the prior probability of causal association. Through simulation we show that when ranking SNPs by our empirical Bayes factor in a fine-mapping study, the causal SNP rank is generally as high or higher than the rank using Bayes factors with other plausible values of the prior variance. Importantly, we also show that assigning SNP-specific prior probabilities of association based on expert prior functional knowledge of the disease mechanism can lead to improved causal SNPs ranks compared to ranking with identical prior probabilities of association. We demonstrate the use of our methods by applying the methods to the fine mapping of the CASP8 region of chromosome 2 using genotype data from the Collaborative Oncological Gene-Environment Study (COGS) Consortium. The data we analysed included approximately 46,000 breast cancer case and 43,000 healthy control samples. © 2016 The Authors. *Genetic Epidemiology published by Wiley Periodicals, Inc.

Probability-based nitrate contamination map of groundwater in Kinmen.

PubMed

Liu, Chen-Wuing; Wang, Yeuh-Bin; Jang, Cheng-Shin

2013-12-01

Groundwater supplies over 50% of drinking water in Kinmen. Approximately 16.8% of groundwater samples in Kinmen exceed the drinking water quality standard (DWQS) of NO3 (-)-N (10 mg/L). The residents drinking high nitrate-polluted groundwater pose a potential risk to health. To formulate effective water quality management plan and assure a safe drinking water in Kinmen, the detailed spatial distribution of nitrate-N in groundwater is a prerequisite. The aim of this study is to develop an efficient scheme for evaluating spatial distribution of nitrate-N in residential well water using logistic regression (LR) model. A probability-based nitrate-N contamination map in Kinmen is constructed. The LR model predicted the binary occurrence probability of groundwater nitrate-N concentrations exceeding DWQS by simple measurement variables as independent variables, including sampling season, soil type, water table depth, pH, EC, DO, and Eh. The analyzed results reveal that three statistically significant explanatory variables, soil type, pH, and EC, are selected for the forward stepwise LR analysis. The total ratio of correct classification reaches 92.7%. The highest probability of nitrate-N contamination map presents in the central zone, indicating that groundwater in the central zone should not be used for drinking purposes. Furthermore, a handy EC-pH-probability curve of nitrate-N exceeding the threshold of DWQS was developed. This curve can be used for preliminary screening of nitrate-N contamination in Kinmen groundwater. This study recommended that the local agency should implement the best management practice strategies to control nonpoint nitrogen sources and carry out a systematic monitoring of groundwater quality in residential wells of the high nitrate-N contamination zones.

Statistical Significance of Optical Map Alignments

PubMed Central

Sarkar, Deepayan; Goldstein, Steve; Schwartz, David C.

2012-01-01

Abstract The Optical Mapping System constructs ordered restriction maps spanning entire genomes through the assembly and analysis of large datasets comprising individually analyzed genomic DNA molecules. Such restriction maps uniquely reveal mammalian genome structure and variation, but also raise computational and statistical questions beyond those that have been solved in the analysis of smaller, microbial genomes. We address the problem of how to filter maps that align poorly to a reference genome. We obtain map-specific thresholds that control errors and improve iterative assembly. We also show how an optimal self-alignment score provides an accurate approximation to the probability of alignment, which is useful in applications seeking to identify structural genomic abnormalities. PMID:22506568

Probabilistic Surface Characterization for Safe Landing Hazard Detection and Avoidance (HDA)

NASA Technical Reports Server (NTRS)

Johnson, Andrew E. (Inventor); Ivanov, Tonislav I. (Inventor); Huertas, Andres (Inventor)

2015-01-01

Apparatuses, systems, computer programs and methods for performing hazard detection and avoidance for landing vehicles are provided. Hazard assessment takes into consideration the geometry of the lander. Safety probabilities are computed for a plurality of pixels in a digital elevation map. The safety probabilities are combined for pixels associated with one or more aim points and orientations. A worst case probability value is assigned to each of the one or more aim points and orientations.

Transcriptome-wide N 6 -methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern.

PubMed

Tao, Xuelian; Chen, Jianning; Jiang, Yanzhi; Wei, Yingying; Chen, Yan; Xu, Huaming; Zhu, Li; Tang, Guoqing; Li, Mingzhou; Jiang, Anan; Shuai, Surong; Bai, Lin; Liu, Haifeng; Ma, Jideng; Jin, Long; Wen, Anxiang; Wang, Qin; Zhu, Guangxiang; Xie, Meng; Wu, Jiayun; He, Tao; Huang, Chunyu; Gao, Xiang; Li, Xuewei

2017-04-28

N 6 -methyladenosine (m 6 A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and potential regulatory functions of reversible m 6 A methylation on mRNA have been revealed by mapping of m 6 A methylomes in several species. m 6 A modification in active gene regulation manifests itself as altered methylation profiles in a tissue-specific manner or in response to changing cellular or species living environment. However, up to date, there has no data on m 6 A porcine transcriptome-wide map and its potential biological roles in adipose deposition and muscle growth. In this work, we used methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq) technique to acquire the first ever m 6 A porcine transcriptome-wide map. Transcriptomes of muscle and adipose tissues from three different pig breeds, the wild boar, Landrace, and Rongchang pig, were used to generate these maps. Our findings show that there were 5,872 and 2,826 m 6 A peaks respectively, in the porcine muscle and adipose tissue transcriptomes. Stop codons, 3'-untranslated regions, and coding regions were found to be mainly enriched for m 6 A peaks. Gene ontology analysis revealed that common m 6 A peaks in nuclear genes are associated with transcriptional factors, suggestive of a relationship between m 6 A mRNA methylation and nuclear genome transcription. Some genes showed tissue- and breed-differential methylation, and have novel biological functions. We also found a relationship between the m 6 A methylation extent and the transcript level, suggesting a regulatory role for m 6 A in gene expression. This comprehensive map provides a solid basis for the determination of potential functional roles for RNA m 6 A modification in adipose deposition and muscle growth.

Factors That Influence Fast Mapping in Children Exposed to Spanish and English

PubMed Central

Alt, Mary; Meyers, Christina; Figueroa, Cecilia

2015-01-01

Purpose The purpose of this study was to determine if children exposed to two languages would benefit from the phonotactic probability cues of a single language in the same way as monolingual peers and to determine if cross-linguistic influence would be present in a fast mapping task. Method Two groups of typically-developing children (monolingual English and bilingual Spanish-English) took part in a computer-based fast mapping task which manipulated phonotactic probability. Children were preschool-aged (N = 50) or school-aged (N = 34). Fast mapping was assessed through name identification and naming tasks. Data were analyzed using mixed ANOVAs with post-hoc testing and simple regression. Results Bilingual and monolingual preschoolers showed sensitivity to English phonotactic cues in both tasks, but bilingual preschoolers were less accurate than monolingual peers in the naming task. School-aged bilingual children had nearly identical performance to monolingual peers. Conclusions Knowing that children exposed to two languages can benefit from the statistical cues of a single language can help inform ideas about instruction and assessment for bilingual learners. PMID:23816663

Mapping aerial metal deposition in metropolitan areas from tree bark: a case study in Sheffield, England.

PubMed

Schelle, E; Rawlins, B G; Lark, R M; Webster, R; Staton, I; McLeod, C W

2008-09-01

We investigated the use of metals accumulated on tree bark for mapping their deposition across metropolitan Sheffield by sampling 642 trees of three common species. Mean concentrations of metals were generally an order of magnitude greater than in samples from a remote uncontaminated site. We found trivially small differences among tree species with respect to metal concentrations on bark, and in subsequent statistical analyses did not discriminate between them. We mapped the concentrations of As, Cd and Ni by lognormal universal kriging using parameters estimated by residual maximum likelihood (REML). The concentrations of Ni and Cd were greatest close to a large steel works, their probable source, and declined markedly within 500 m of it and from there more gradually over several kilometres. Arsenic was much more evenly distributed, probably as a result of locally mined coal burned in domestic fires for many years. Tree bark seems to integrate airborne pollution over time, and our findings show that sampling and analysing it are cost-effective means of mapping and identifying sources.

Labeling single cell for in-vivo study of cell fate mapping and lineage tracing

NASA Astrophysics Data System (ADS)

He, Sicong; Xu, Jin; Wu, Yi; Tian, Ye; Sun, Qiqi; Wen, Zilong; Qu, Jianan Y.

2018-02-01

Cell fate mapping and lineage tracing are significant ways to understanding the developmental origins of biological tissues. It requires labeling individual cells and tracing the development of their progeny. We develop an infrared laser-evoked gene operator heat-shock microscope system to achieve single-cell labeling in zebrafish. With a fluorescent thermometry technique, we measure the temperature increase in zebrafish tissues induced by infrared laser and identify the optimal heat shock conditions for single-cell gene induction in different types of zebrafish cells. We use this technique to study the fate mapping of T lymphocytes and discover the distinct waves of lymphopoiesis during the zebrafish development.

Positive contraction mappings for classical and quantum Schrödinger systems

NASA Astrophysics Data System (ADS)

Georgiou, Tryphon T.; Pavon, Michele

2015-03-01

The classical Schrödinger bridge seeks the most likely probability law for a diffusion process, in path space, that matches marginals at two end points in time; the likelihood is quantified by the relative entropy between the sought law and a prior. Jamison proved that the new law is obtained through a multiplicative functional transformation of the prior. This transformation is characterised by an automorphism on the space of endpoints probability measures, which has been studied by Fortet, Beurling, and others. A similar question can be raised for processes evolving in a discrete time and space as well as for processes defined over non-commutative probability spaces. The present paper builds on earlier work by Pavon and Ticozzi and begins by establishing solutions to Schrödinger systems for Markov chains. Our approach is based on the Hilbert metric and shows that the solution to the Schrödinger bridge is provided by the fixed point of a contractive map. We approach, in a similar manner, the steering of a quantum system across a quantum channel. We are able to establish existence of quantum transitions that are multiplicative functional transformations of a given Kraus map for the cases where the marginals are either uniform or pure states. As in the Markov chain case, and for uniform density matrices, the solution of the quantum bridge can be constructed from the fixed point of a certain contractive map. For arbitrary marginal densities, extensive numerical simulations indicate that iteration of a similar map leads to fixed points from which we can construct a quantum bridge. For this general case, however, a proof of convergence remains elusive.

Video attention deviation estimation using inter-frame visual saliency map analysis

NASA Astrophysics Data System (ADS)

Feng, Yunlong; Cheung, Gene; Le Callet, Patrick; Ji, Yusheng

2012-01-01

A viewer's visual attention during video playback is the matching of his eye gaze movement to the changing video content over time. If the gaze movement matches the video content (e.g., follow a rolling soccer ball), then the viewer keeps his visual attention. If the gaze location moves from one video object to another, then the viewer shifts his visual attention. A video that causes a viewer to shift his attention often is a "busy" video. Determination of which video content is busy is an important practical problem; a busy video is difficult for encoder to deploy region of interest (ROI)-based bit allocation, and hard for content provider to insert additional overlays like advertisements, making the video even busier. One way to determine the busyness of video content is to conduct eye gaze experiments with a sizable group of test subjects, but this is time-consuming and costineffective. In this paper, we propose an alternative method to determine the busyness of video-formally called video attention deviation (VAD): analyze the spatial visual saliency maps of the video frames across time. We first derive transition probabilities of a Markov model for eye gaze using saliency maps of a number of consecutive frames. We then compute steady state probability of the saccade state in the model-our estimate of VAD. We demonstrate that the computed steady state probability for saccade using saliency map analysis matches that computed using actual gaze traces for a range of videos with different degrees of busyness. Further, our analysis can also be used to segment video into shorter clips of different degrees of busyness by computing the Kullback-Leibler divergence using consecutive motion compensated saliency maps.

[Obesity and heart].

PubMed

Svačina, Štěpán

2014-12-01

Cardiovascular complications of obesity are traditionally considered an important complication of obesity. Obesity itself is probably not direct cause of atherosclerosis or coronary heart disease. This may occur indirectly in metabolic complications of obesity, especially diabetes and metabolic syndrome. However, thrombogenicity potential of obesity contributes to embolism and atherosclerosis development. In cardiology is well-known a phenomenon of obesity paradox when obese patients have better prognosis than thin. This is the case of heart failure and some other cardiovascular diseases. Recently, a new concept has emerged of myokines - hormones from muscle tissue that have extensive protective effects on organism and probably on heart. Whether heart is a source of myokines is uncertain. However, undoubted importance has epicardial and pericardial fatty tissue. The epicardial fatty tissue has mainly protective effects on myocardium. This fatty tissue may produce factors of inflammation affecting the myocardium. Relationship between amount of epicardial fatty tissue and coronary heart disease is rather pathogenic. Currently, it is certain that obesity brings more metabolic and cancer complications than cardiovascular and accurate contribution to pathogenic or protective character of fatty tissue in cardiology requires further research. Nevertheless, the conclusion is that adipose tissue of organism and around the heart may be in some circumstances beneficial.

Quantitative micro-elastography: imaging of tissue elasticity using compression optical coherence elastography

PubMed Central

Kennedy, Kelsey M.; Chin, Lixin; McLaughlin, Robert A.; Latham, Bruce; Saunders, Christobel M.; Sampson, David D.; Kennedy, Brendan F.

2015-01-01

Probing the mechanical properties of tissue on the microscale could aid in the identification of diseased tissues that are inadequately detected using palpation or current clinical imaging modalities, with potential to guide medical procedures such as the excision of breast tumours. Compression optical coherence elastography (OCE) maps tissue strain with microscale spatial resolution and can delineate microstructural features within breast tissues. However, without a measure of the locally applied stress, strain provides only a qualitative indication of mechanical properties. To overcome this limitation, we present quantitative micro-elastography, which combines compression OCE with a compliant stress sensor to image tissue elasticity. The sensor consists of a layer of translucent silicone with well-characterized stress-strain behaviour. The measured strain in the sensor is used to estimate the two-dimensional stress distribution applied to the sample surface. Elasticity is determined by dividing the stress by the strain in the sample. We show that quantification of elasticity can improve the ability of compression OCE to distinguish between tissues, thereby extending the potential for inter-sample comparison and longitudinal studies of tissue elasticity. We validate the technique using tissue-mimicking phantoms and demonstrate the ability to map elasticity of freshly excised malignant and benign human breast tissues. PMID:26503225

MAPS of Cancer

NASA Technical Reports Server (NTRS)

Gray, Lincoln

1998-01-01

Our goal was to produce an interactive visualization from a mathematical model that successfully predicts metastases from head and neck cancer. We met this goal early in the project. The visualization is available for the public to view. Our work appears to fill a need for more information about this deadly disease. The idea of this project was to make an easily interpretable visualization based on what we call "functional maps" of disease. A functional map is a graphic summary of medical data, where distances between parts of the body are determined by the probability of disease, not by anatomical distances. Functional maps often beat little resemblance to anatomical maps, but they can be used to predict the spread of disease. The idea of modeling the spread of disease in an abstract multidimensional space is difficult for many people. Our goal was to make the important predictions easy to see. NASA must face this problem frequently: how to help laypersons and professionals see important trends in abstract, complex data. We took advantage of concepts perfected in NASA's graphics libraries. As an analogy, consider a functional map of early America. Suppose we choose travel times, rather than miles, as our measures of inter-city distances. For Abraham Lincoln, travel times would have been the more meaningful measure of separation between cities. In such a map New Orleans would be close to Memphis because of the Mississippi River. St. Louis would be close to Portland because of the Oregon Trail. Oklahoma City would be far from Little Rock because of the Cheyenne. Such a map would look puzzling to those of us who have always seen physical maps, but the functional map would be more useful in predicting the probabilities of inter-site transit. Continuing the analogy, we could predict the spread of social diseases such as gambling along the rivers and cattle rustling along the trails. We could simply print the functional map of America, but it would be more interesting to show meaningful patterns of dispersal. We had previously published the functional map of the head and neck, but it was difficult to explain to either patients or surgeons because that view of our body did not resemble anatomy. This discrepancy between functional and physical maps is just a mathematical restatement of the well-known fact that some diseases, such as head and neck cancer, spread in complex patterns, not always to the next nearest site. We had discovered that a computer could re-arrange anatomy so that this particular disease spreads to the next nearest site. The functional map explains over 95% of the metastases in 1400 patients. In a sense, we had graphed what our body "looks like" to a tumor. The tumor readily travels between adjacent areas in the functional map. The functional map is a succinct visual display of trends that are not easily appreciated in tables of probabilities.

Evaluation of normal lung tissue complication probability in gated and conventional radiotherapy using the 4D XCAT digital phantom.

PubMed

Shahzadeh, Sara; Gholami, Somayeh; Aghamiri, Seyed Mahmood Reza; Mahani, Hojjat; Nabavi, Mansoure; Kalantari, Faraz

2018-06-01

The present study was conducted to investigate normal lung tissue complication probability in gated and conventional radiotherapy (RT) as a function of diaphragm motion, lesion size, and its location using 4D-XCAT digital phantom in a simulation study. Different time series of 3D-CT images were generated using the 4D-XCAT digital phantom. The binary data obtained from this phantom were then converted to the digital imaging and communication in medicine (DICOM) format using an in-house MATLAB-based program to be compatible with our treatment planning system (TPS). The 3D-TPS with superposition computational algorithm was used to generate conventional and gated plans. Treatment plans were generated for 36 different XCAT phantom configurations. These included four diaphragm motions of 20, 25, 30 and 35 mm, three lesion sizes of 3, 4, and 5 cm in diameter and each tumor was placed in four different lung locations (right lower lobe, right upper lobe, left lower lobe and left upper lobe). The complication of normal lung tissue was assessed in terms of mean lung dose (MLD), the lung volume receiving ≥20 Gy (V20), and normal tissue complication probability (NTCP). The results showed that the gated RT yields superior outcomes in terms of normal tissue complication compared to the conventional RT. For all cases, the gated radiation therapy technique reduced the mean dose, V20, and NTCP of lung tissue by up to 5.53 Gy, 13.38%, and 23.89%, respectively. The results of this study showed that the gated RT provides significant advantages in terms of the normal lung tissue complication, compared to the conventional RT, especially for the lesions near the diaphragm. Copyright © 2018 Elsevier Ltd. All rights reserved.

Y-90 SPECT ML image reconstruction with a new model for tissue-dependent bremsstrahlung production using CT information: a proof-of-concept study

NASA Astrophysics Data System (ADS)

Lim, Hongki; Fessler, Jeffrey A.; Wilderman, Scott J.; Brooks, Allen F.; Dewaraja, Yuni K.

2018-06-01

While the yield of positrons used in Y-90 PET is independent of tissue media, Y-90 SPECT imaging is complicated by the tissue dependence of bremsstrahlung photon generation. The probability of bremsstrahlung production is proportional to the square of the atomic number of the medium. Hence, the same amount of activity in different tissue regions of the body will produce different numbers of bremsstrahlung photons. Existing reconstruction methods disregard this tissue-dependency, potentially impacting both qualitative and quantitative imaging of heterogeneous regions of the body such as bone with marrow cavities. In this proof-of-concept study, we propose a new maximum-likelihood method that incorporates bremsstrahlung generation probabilities into the system matrix, enabling images of the desired Y-90 distribution to be reconstructed instead of the ‘bremsstrahlung distribution’ that is obtained with existing methods. The tissue-dependent probabilities are generated by Monte Carlo simulation while bone volume fractions for each SPECT voxel are obtained from co-registered CT. First, we demonstrate the tissue dependency in a SPECT/CT imaging experiment with Y-90 in bone equivalent solution and water. Visually, the proposed reconstruction approach better matched the true image and the Y-90 PET image than the standard bremsstrahlung reconstruction approach. An XCAT phantom simulation including bone and marrow regions also demonstrated better agreement with the true image using the proposed reconstruction method. Quantitatively, compared with the standard reconstruction, the new method improved estimation of the liquid bone:water activity concentration ratio by 40% in the SPECT measurement and the cortical bone:marrow activity concentration ratio by 58% in the XCAT simulation.

Identification, prediction, and mitigation of sinkhole hazards in evaporite karst areas

USGS Publications Warehouse

Gutierrez, F.; Cooper, A.H.; Johnson, K.S.

2008-01-01

Sinkholes usually have a higher probability of occurrence and a greater genetic diversity in evaporite terrains than in carbonate karst areas. This is because evaporites have a higher solubility and, commonly, a lower mechanical strength. Subsidence damage resulting from evaporite dissolution generates substantial losses throughout the world, but the causes are only well understood in a few areas. To deal with these hazards, a phased approach is needed for sinkhole identification, investigation, prediction, and mitigation. Identification techniques include field surveys and geomorphological mapping combined with accounts from local people and historical sources. Detailed sinkhole maps can be constructed from sequential historical maps, recent topographical maps, and digital elevation models (DEMs) complemented with building-damage surveying, remote sensing, and high-resolution geodetic surveys. On a more detailed level, information from exposed paleosubsidence features (paleokarst), speleological explorations, geophysical investigations, trenching, dating techniques, and boreholes may help in investigating dissolution and subsidence features. Information on the hydrogeological pathways including caves, springs, and swallow holes are particularly important especially when corroborated by tracer tests. These diverse data sources make a valuable database-the karst inventory. From this dataset, sinkhole susceptibility zonations (relative probability) may be produced based on the spatial distribution of the features and good knowledge of the local geology. Sinkhole distribution can be investigated by spatial distribution analysis techniques including studies of preferential elongation, alignment, and nearest neighbor analysis. More objective susceptibility models may be obtained by analyzing the statistical relationships between the known sinkholes and the conditioning factors. Chronological information on sinkhole formation is required to estimate the probability of occurrence of sinkholes (number of sinkholes/km2 year). Such spatial and temporal predictions, frequently derived from limited records and based on the assumption that past sinkhole activity may be extrapolated to the future, are non-corroborated hypotheses. Validation methods allow us to assess the predictive capability of the susceptibility maps and to transform them into probability maps. Avoiding the most hazardous areas by preventive planning is the safest strategy for development in sinkhole-prone areas. Corrective measures could be applied to reduce the dissolution activity and subsidence processes. A more practical solution for safe development is to reduce the vulnerability of the structures by using subsidence-proof designs. ?? 2007 Springer-Verlag.

Novel cardiac magnetic resonance biomarkers: native T1 and extracellular volume myocardial mapping.

PubMed

Cannaò, Paola Maria; Altabella, Luisa; Petrini, Marcello; Alì, Marco; Secchi, Francesco; Sardanelli, Francesco

2016-04-28

Cardiac magnetic resonance (CMR) is a non-invasive diagnostic tool playing a key role in the assessment of cardiac morphology and function as well as in tissue characterization. Late gadolinium enhancement is a fundamental CMR technique for detecting focal or regional abnormalities such as scar tissue, replacement fibrosis, or inflammation using qualitative, semi-quantitative, or quantitative methods, but not allowing for evaluating the whole myocardium in the presence of diffuse disease. The novel T1 mapping approach permits a quantitative assessment of the entire myocardium providing a voxel-by-voxel map of native T1 relaxation time, obtained before the intravenous administration of gadolinium-based contrast material. Combining T1 data obtained before and after contrast injection, it is also possible to calculate the voxel-by-voxel extracellular volume (ECV), resulting in another myocardial parametric map. This article describes technical challenges and clinical perspectives of these two novel CMR biomarkers: myocardial native T1 and ECV mapping.

An automated method for mapping human tissue permittivities by MRI in hyperthermia treatment planning.

PubMed

Farace, P; Pontalti, R; Cristoforetti, L; Antolini, R; Scarpa, M

1997-11-01

This paper presents an automatic method to obtain tissue complex permittivity values to be used as input data in the computer modelling for hyperthermia treatment planning. Magnetic resonance (MR) images were acquired and the tissue water content was calculated from the signal intensity of the image pixels. The tissue water content was converted into complex permittivity values by monotonic functions based on mixture theory. To obtain a water content map by MR imaging a gradient-echo pulse sequence was used and an experimental procedure was set up to correct for relaxation and radiofrequency field inhomogeneity effects on signal intensity. Two approaches were followed to assign the permittivity values to fat-rich tissues: (i) fat-rich tissue localization by a segmentation procedure followed by assignment of tabulated permittivity values; (ii) water content evaluation by chemical shift imaging followed by permittivity calculation. Tests were performed on phantoms of known water content to establish the reliability of the proposed method. MRI data were acquired and processed pixel-by-pixel according to the outlined procedure. The signal intensity in the phantom images correlated well with water content. Experiments were performed on volunteers' healthy tissue. In particular two anatomical structures were chosen to calculate permittivity maps: the head and the thigh. The water content and electric permittivity values were obtained from the MRI data and compared to others in the literature. A good agreement was found for muscle, cerebrospinal fluid (CSF) and white and grey matter. The advantages of the reported method are discussed in the light of possible application in hyperthermia treatment planning.

A new statistical methodology predicting chip failure probability considering electromigration

NASA Astrophysics Data System (ADS)

Sun, Ted

In this research thesis, we present a new approach to analyze chip reliability subject to electromigration (EM) whose fundamental causes and EM phenomenon happened in different materials are presented in this thesis. This new approach utilizes the statistical nature of EM failure in order to assess overall EM risk. It includes within-die temperature variations from the chip's temperature map extracted by an Electronic Design Automation (EDA) tool to estimate the failure probability of a design. Both the power estimation and thermal analysis are performed in the EDA flow. We first used the traditional EM approach to analyze the design with a single temperature across the entire chip that involves 6 metal and 5 via layers. Next, we used the same traditional approach but with a realistic temperature map. The traditional EM analysis approach and that coupled with a temperature map and the comparison between the results of considering and not considering temperature map are presented in in this research. A comparison between these two results confirms that using a temperature map yields a less pessimistic estimation of the chip's EM risk. Finally, we employed the statistical methodology we developed considering a temperature map and different use-condition voltages and frequencies to estimate the overall failure probability of the chip. The statistical model established considers the scaling work with the usage of traditional Black equation and four major conditions. The statistical result comparisons are within our expectations. The results of this statistical analysis confirm that the chip level failure probability is higher i) at higher use-condition frequencies for all use-condition voltages, and ii) when a single temperature instead of a temperature map across the chip is considered. In this thesis, I start with an overall review on current design types, common flows, and necessary verifications and reliability checking steps used in this IC design industry. Furthermore, the important concepts about "Scripting Automation" which is used in all the integration of using diversified EDA tools in this research work are also described in detail with several examples and my completed coding works are also put in the appendix for your reference. Hopefully, this construction of my thesis will give readers a thorough understanding about my research work from the automation of EDA tools to the statistical data generation, from the nature of EM to the statistical model construction, and the comparisons among the traditional EM analysis and the statistical EM analysis approaches.

{sup 18}F-FLT uptake kinetics in head and neck squamous cell carcinoma: A PET imaging study

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

Liu, Dan, E-mail: dan.liu@oncology.ox.ac.uk; Fenwick, John D.; Chalkidou, Anastasia

2014-04-15

Purpose: To analyze the kinetics of 3{sup ′}-deoxy-3{sup ′}-[F-18]-fluorothymidine (18F-FLT) uptake by head and neck squamous cell carcinomas and involved nodes imaged using positron emission tomography (PET). Methods: Two- and three-tissue compartment models were fitted to 12 tumor time-activity-curves (TACs) obtained for 6 structures (tumors or involved nodes) imaged in ten dynamic PET studies of 1 h duration, carried out for five patients. The ability of the models to describe the data was assessed using a runs test, the Akaike information criterion (AIC) and leave-one-out cross-validation. To generate parametric maps the models were also fitted to TACs of individual voxels.more » Correlations between maps of different parameters were characterized using Pearson'sr coefficient; in particular the phosphorylation rate-constants k{sub 3-2tiss} and k{sub 5} of the two- and three-tissue models were studied alongside the flux parameters K{sub FLT-2tiss} and K{sub FLT} of these models, and standardized uptake values (SUV). A methodology based on expectation-maximization clustering and the Bayesian information criterion (“EM-BIC clustering”) was used to distil the information from noisy parametric images. Results: Fits of two-tissue models 2C3K and 2C4K and three-tissue models 3C5K and 3C6K comprising three, four, five, and six rate-constants, respectively, pass the runs test for 4, 8, 10, and 11 of 12 tumor TACs. The three-tissue models have lower AIC and cross-validation scores for nine of the 12 tumors. Overall the 3C6K model has the lowest AIC and cross-validation scores and its fitted parameter values are of the same orders of magnitude as literature estimates. Maps ofK{sub FLT} and K{sub FLT-2tiss} are strongly correlated (r = 0.85) and also correlate closely with SUV maps (r = 0.72 for K{sub FLT-2tiss}, 0.64 for K{sub FLT}). Phosphorylation rate-constant maps are moderately correlated with flux maps (r = 0.48 for k{sub 3-2tiss} vs K{sub FLT-2tiss} and r = 0.68 for k{sub 5} vs K{sub FLT}); however, neither phosphorylation rate-constant correlates significantly with SUV. EM-BIC clustering reduces the parametric maps to a small number of levels—on average 5.8, 3.5, 3.4, and 1.4 for K{sub FLT-2tiss}, K{sub FLT}, k{sub 3-2tiss}, and k{sub 5.} This large simplification is potentially useful for radiotherapy dose-painting, but demonstrates the high noise in some maps. Statistical simulations show that voxel level noise degrades TACs generated from the 3C6K model sufficiently that the average AIC score, parameter bias, and total uncertainty of 2C4K model fits are similar to those of 3C6K fits, whereas at the whole tumor level the scores are lower for 3C6K fits. Conclusions: For the patients studied here, whole tumor FLT uptake time-courses are represented better overall by a three-tissue than by a two-tissue model. EM-BIC clustering simplifies noisy parametric maps, providing the best description of the underlying information they contain and is potentially useful for radiotherapy dose-painting. However, the clustering highlights the large degree of noise present in maps of the phosphorylation rate-constantsk{sub 5} and k{sub 3-2tiss}, which are conceptually tightly linked to cellular proliferation. Methods must be found to make these maps more robust—either by constraining other model parameters or modifying dynamic imaging protocols.« less

A fully traits-based approach to modeling global vegetation distribution.

PubMed

van Bodegom, Peter M; Douma, Jacob C; Verheijen, Lieneke M

2014-09-23

Dynamic Global Vegetation Models (DGVMs) are indispensable for our understanding of climate change impacts. The application of traits in DGVMs is increasingly refined. However, a comprehensive analysis of the direct impacts of trait variation on global vegetation distribution does not yet exist. Here, we present such analysis as proof of principle. We run regressions of trait observations for leaf mass per area, stem-specific density, and seed mass from a global database against multiple environmental drivers, making use of findings of global trait convergence. This analysis explained up to 52% of the global variation of traits. Global trait maps, generated by coupling the regression equations to gridded soil and climate maps, showed up to orders of magnitude variation in trait values. Subsequently, nine vegetation types were characterized by the trait combinations that they possess using Gaussian mixture density functions. The trait maps were input to these functions to determine global occurrence probabilities for each vegetation type. We prepared vegetation maps, assuming that the most probable (and thus, most suited) vegetation type at each location will be realized. This fully traits-based vegetation map predicted 42% of the observed vegetation distribution correctly. Our results indicate that a major proportion of the predictive ability of DGVMs with respect to vegetation distribution can be attained by three traits alone if traits like stem-specific density and seed mass are included. We envision that our traits-based approach, our observation-driven trait maps, and our vegetation maps may inspire a new generation of powerful traits-based DGVMs.

A Cooperative Search and Coverage Algorithm with Controllable Revisit and Connectivity Maintenance for Multiple Unmanned Aerial Vehicles.

PubMed

Liu, Zhong; Gao, Xiaoguang; Fu, Xiaowei

2018-05-08

In this paper, we mainly study a cooperative search and coverage algorithm for a given bounded rectangle region, which contains several unknown stationary targets, by a team of unmanned aerial vehicles (UAVs) with non-ideal sensors and limited communication ranges. Our goal is to minimize the search time, while gathering more information about the environment and finding more targets. For this purpose, a novel cooperative search and coverage algorithm with controllable revisit mechanism is presented. Firstly, as the representation of the environment, the cognitive maps that included the target probability map (TPM), the uncertain map (UM), and the digital pheromone map (DPM) are constituted. We also design a distributed update and fusion scheme for the cognitive map. This update and fusion scheme can guarantee that each one of the cognitive maps converges to the same one, which reflects the targets’ true existence or absence in each cell of the search region. Secondly, we develop a controllable revisit mechanism based on the DPM. This mechanism can concentrate the UAVs to revisit sub-areas that have a large target probability or high uncertainty. Thirdly, in the frame of distributed receding horizon optimizing, a path planning algorithm for the multi-UAVs cooperative search and coverage is designed. In the path planning algorithm, the movement of the UAVs is restricted by the potential fields to meet the requirements of avoiding collision and maintaining connectivity constraints. Moreover, using the minimum spanning tree (MST) topology optimization strategy, we can obtain a tradeoff between the search coverage enhancement and the connectivity maintenance. The feasibility of the proposed algorithm is demonstrated by comparison simulations by way of analyzing the effects of the controllable revisit mechanism and the connectivity maintenance scheme. The Monte Carlo method is employed to validate the influence of the number of UAVs, the sensing radius, the detection and false alarm probabilities, and the communication range on the proposed algorithm.

Fast algorithm for probabilistic bone edge detection (FAPBED)

NASA Astrophysics Data System (ADS)

Scepanovic, Danilo; Kirshtein, Joshua; Jain, Ameet K.; Taylor, Russell H.

2005-04-01

The registration of preoperative CT to intra-operative reality systems is a crucial step in Computer Assisted Orthopedic Surgery (CAOS). The intra-operative sensors include 3D digitizers, fiducials, X-rays and Ultrasound (US). FAPBED is designed to process CT volumes for registration to tracked US data. Tracked US is advantageous because it is real time, noninvasive, and non-ionizing, but it is also known to have inherent inaccuracies which create the need to develop a framework that is robust to various uncertainties, and can be useful in US-CT registration. Furthermore, conventional registration methods depend on accurate and absolute segmentation. Our proposed probabilistic framework addresses the segmentation-registration duality, wherein exact segmentation is not a prerequisite to achieve accurate registration. In this paper, we develop a method for fast and automatic probabilistic bone surface (edge) detection in CT images. Various features that influence the likelihood of the surface at each spatial coordinate are combined using a simple probabilistic framework, which strikes a fair balance between a high-level understanding of features in an image and the low-level number crunching of standard image processing techniques. The algorithm evaluates different features for detecting the probability of a bone surface at each voxel, and compounds the results of these methods to yield a final, low-noise, probability map of bone surfaces in the volume. Such a probability map can then be used in conjunction with a similar map from tracked intra-operative US to achieve accurate registration. Eight sample pelvic CT scans were used to extract feature parameters and validate the final probability maps. An un-optimized fully automatic Matlab code runs in five minutes per CT volume on average, and was validated by comparison against hand-segmented gold standards. The mean probability assigned to nonzero surface points was 0.8, while nonzero non-surface points had a mean value of 0.38 indicating clear identification of surface points on average. The segmentation was also sufficiently crisp, with a full width at half maximum (FWHM) value of 1.51 voxels.

Improving experimental phases for strong reflections prior to density modification

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

Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.

Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005), Acta Cryst. D 61, 899–902], the impact of identifying optimized phases for a small numbermore » of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. Lastly, a computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.« less

Improving experimental phases for strong reflections prior to density modification

DOE PAGES

Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.; ...

2013-09-20

Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005), Acta Cryst. D 61, 899–902], the impact of identifying optimized phases for a small numbermore » of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. Lastly, a computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.« less

Evaluation of seismic design spectrum based on UHS implementing fourth-generation seismic hazard maps of Canada

NASA Astrophysics Data System (ADS)

Ahmed, Ali; Hasan, Rafiq; Pekau, Oscar A.

2016-12-01

Two recent developments have come into the forefront with reference to updating the seismic design provisions for codes: (1) publication of new seismic hazard maps for Canada by the Geological Survey of Canada, and (2) emergence of the concept of new spectral format outdating the conventional standardized spectral format. The fourth -generation seismic hazard maps are based on enriched seismic data, enhanced knowledge of regional seismicity and improved seismic hazard modeling techniques. Therefore, the new maps are more accurate and need to incorporate into the Canadian Highway Bridge Design Code (CHBDC) for its next edition similar to its building counterpart National Building Code of Canada (NBCC). In fact, the code writers expressed similar intentions with comments in the commentary of CHBCD 2006. During the process of updating codes, NBCC, and AASHTO Guide Specifications for LRFD Seismic Bridge Design, American Association of State Highway and Transportation Officials, Washington (2009) lowered the probability level from 10 to 2% and 10 to 5%, respectively. This study has brought five sets of hazard maps corresponding to 2%, 5% and 10% probability of exceedance in 50 years developed by the GSC under investigation. To have a sound statistical inference, 389 Canadian cities are selected. This study shows the implications of the changes of new hazard maps on the design process (i.e., extent of magnification or reduction of the design forces).

Implementation of fast macromolecular proton fraction mapping on 1.5 and 3 Tesla clinical MRI scanners: preliminary experience

NASA Astrophysics Data System (ADS)

Yarnykh, V.; Korostyshevskaya, A.

2017-08-01

Macromolecular proton fraction (MPF) is a biophysical parameter describing the amount of macromolecular protons involved into magnetization exchange with water protons in tissues. MPF represents a significant interest as a magnetic resonance imaging (MRI) biomarker of myelin for clinical applications. A recent fast MPF mapping method enabled clinical translation of MPF measurements due to time-efficient acquisition based on the single-point constrained fit algorithm. However, previous MPF mapping applications utilized only 3 Tesla MRI scanners and modified pulse sequences, which are not commonly available. This study aimed to test the feasibility of MPF mapping implementation on a 1.5 Tesla clinical scanner using standard manufacturer’s sequences and compare the performance of this method between 1.5 and 3 Tesla scanners. MPF mapping was implemented on 1.5 and 3 Tesla MRI units of one manufacturer with either optimized custom-written or standard product pulse sequences. Whole-brain three-dimensional MPF maps obtained from a single volunteer were compared between field strengths and implementation options. MPF maps demonstrated similar quality at both field strengths. MPF values in segmented brain tissues and specific anatomic regions appeared in close agreement. This experiment demonstrates the feasibility of fast MPF mapping using standard sequences on 1.5 T and 3 T clinical scanners.

The planetary spatial data infrastructure for the OSIRIS-REx mission

NASA Astrophysics Data System (ADS)

DellaGiustina, D. N.; Selznick, S.; Nolan, M. C.; Enos, H. L.; Lauretta, D. S.

2017-12-01

The primary objective of the Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer (OSIRIS-REx) mission is to return a pristine sample of carbonaceous material from primitive asteroid (101955) Bennu. Understanding the geospatial context of Bennu is critical to choosing a sample-site and also linking the nature of the sample to the global properties of Bennu and the broader asteroid population. We established a planetary spatial data infrastructure (PSDI) support the primary objective of OSIRIS-REx. OSIRIS-REx is unique among planetary missions in that all remote sensing is performed to support the sample return objective. Prior to sampling, OSIRIS-REx will survey Bennu for nearly two years to select and document the most valuable primary and backup sample sites. During this period, the mission will combine coordinated observations from five science instruments into four thematic maps: deliverability, safety, sampleability, and scientific value. The deliverability map assesses the probability that the flight dynamics team can deliver the spacecraft to the desired location. The safety map indicates the probability that physical hazards are present at the sample-site. The sampleability map quantifies the probability that a sample can be successfully collected from the surface. Finally, the scientific value map shows the probability that the collected sample contains organics and volatiles and also places the sample site in a definitive geological context relative to Bennu's history. The OSIRIS-REx Science Processing and Operations Center (SPOC) serves as the operational PSDI for the mission. The SPOC is tasked with intake of all data from the spacecraft and other ground sources and assimilating these data into a single comprehensive system for processing and presentation. The SPOC centralizes all geographic data of Bennu in a relational database and ensures that standardization and provenance are maintained throughout proximity operations.The SPOC is a live system that handles inputs from spacecraft and science instrument telemetry, and science data producers. It includes multiple levels of validation, both automated and manual to process all data in a robust and reliable manner and eventually deliver it to the NASA Planetary Data System for archive.

Wildfire risk in the wildland-urban interface: A simulation study in northwestern Wisconsin

USGS Publications Warehouse

Bar-Massada, A.; Radeloff, V.C.; Stewart, S.I.; Hawbaker, T.J.

2009-01-01

The rapid growth of housing in and near the wildland-urban interface (WUI) increases wildfire risk to lives and structures. To reduce fire risk, it is necessary to identify WUI housing areas that are more susceptible to wildfire. This is challenging, because wildfire patterns depend on fire behavior and spread, which in turn depend on ignition locations, weather conditions, the spatial arrangement of fuels, and topography. The goal of our study was to assess wildfire risk to a 60,000 ha WUI area in northwestern Wisconsin while accounting for all of these factors. We conducted 6000 simulations with two dynamic fire models: Fire Area Simulator (FARSITE) and Minimum Travel Time (MTT) in order to map the spatial pattern of burn probabilities. Simulations were run under normal and extreme weather conditions to assess the effect of weather on fire spread, burn probability, and risk to structures. The resulting burn probability maps were intersected with maps of structure locations and land cover types. The simulations revealed clear hotspots of wildfire activity and a large range of wildfire risk to structures in the study area. As expected, the extreme weather conditions yielded higher burn probabilities over the entire landscape, as well as to different land cover classes and individual structures. Moreover, the spatial pattern of risk was significantly different between extreme and normal weather conditions. The results highlight the fact that extreme weather conditions not only produce higher fire risk than normal weather conditions, but also change the fine-scale locations of high risk areas in the landscape, which is of great importance for fire management in WUI areas. In addition, the choice of weather data may limit the potential for comparisons of risk maps for different areas and for extrapolating risk maps to future scenarios where weather conditions are unknown. Our approach to modeling wildfire risk to structures can aid fire risk reduction management activities by identifying areas with elevated wildfire risk and those most vulnerable under extreme weather conditions. ?? 2009 Elsevier B.V.

Real-time three-dimensional temperature mapping in photothermal therapy with optoacoustic tomography

NASA Astrophysics Data System (ADS)

Oyaga Landa, Francisco Javier; Deán-Ben, Xosé Luís.; Sroka, Ronald; Razansky, Daniel

2017-07-01

Ablation and photothermal therapy are widely employed medical protocols where the selective destruction of tissue is a necessity as in cancerous tissue removal or vascular and brain abnormalities. Tissue denaturation takes place when the temperature reaches a threshold value while the time of exposure determines the lesion size. Therefore, the spatio-temporal distribution of temperature plays a crucial role in the outcome of these clinical interventions. We demonstrate fast volumetric temperature mapping with optoacoustic tomography based on real-time optoacoustic readings from the treated region. The performance of the method was investigated in tissue-mimicking phantom experiments. The new ability to non-invasively measure temperature volumetrically in an entire treated region with high spatial and temporal resolutions holds potential for improving safety and efficacy of thermal ablation and to advance the general applicability of laser-based therapy.

Hyperspectral Stimulated Raman Scattering Microscopy Unravels Aberrant Accumulation of Saturated Fat in Human Liver Cancer.

PubMed

Yan, Shuai; Cui, Sishan; Ke, Kun; Zhao, Bixing; Liu, Xiaolong; Yue, Shuhua; Wang, Ping

2018-06-05

Lipid metabolism is dysregulated in human cancers. The analytical tools that could identify and quantitatively map metabolites in unprocessed human tissues with submicrometer resolution are highly desired. Here, we implemented analytical hyperspectral stimulated Raman scattering microscopy to map the lipid metabolites in situ in normal and cancerous liver tissues from 24 patients. In contrast to the conventional wisdom that unsaturated lipid accumulation enhances tumor cell survival and proliferation, we unexpectedly visualized substantial amount of saturated fat accumulated in cancerous liver tissues, which was not seen in majority of their adjacent normal tissues. Further analysis by mass spectrometry confirmed significant high levels of glyceryl tripalmitate specifically in cancerous liver. These findings suggest that the aberrantly accumulated saturated fat may have great potential to be a metabolic biomarker for liver cancer.

On Schrödinger's bridge problem

NASA Astrophysics Data System (ADS)

Friedland, S.

2017-11-01

In the first part of this paper we generalize Georgiou-Pavon's result that a positive square matrix can be scaled uniquely to a column stochastic matrix which maps a given positive probability vector to another given positive probability vector. In the second part we prove that a positive quantum channel can be scaled to another positive quantum channel which maps a given positive definite density matrix to another given positive definite density matrix using Brouwer's fixed point theorem. This result proves the Georgiou-Pavon conjecture for two positive definite density matrices, made in their recent paper. We show that the fixed points are unique for certain pairs of positive definite density matrices. Bibliography: 15 titles.

Using remote sensing in support of environmental management: A framework for selecting products, algorithms and methods.

PubMed

de Klerk, Helen M; Gilbertson, Jason; Lück-Vogel, Melanie; Kemp, Jaco; Munch, Zahn

2016-11-01

Traditionally, to map environmental features using remote sensing, practitioners will use training data to develop models on various satellite data sets using a number of classification approaches and use test data to select a single 'best performer' from which the final map is made. We use a combination of an omission/commission plot to evaluate various results and compile a probability map based on consistently strong performing models across a range of standard accuracy measures. We suggest that this easy-to-use approach can be applied in any study using remote sensing to map natural features for management action. We demonstrate this approach using optical remote sensing products of different spatial and spectral resolution to map the endemic and threatened flora of quartz patches in the Knersvlakte, South Africa. Quartz patches can be mapped using either SPOT 5 (used due to its relatively fine spatial resolution) or Landsat8 imagery (used because it is freely accessible and has higher spectral resolution). Of the variety of classification algorithms available, we tested maximum likelihood and support vector machine, and applied these to raw spectral data, the first three PCA summaries of the data, and the standard normalised difference vegetation index. We found that there is no 'one size fits all' solution to the choice of a 'best fit' model (i.e. combination of classification algorithm or data sets), which is in agreement with the literature that classifier performance will vary with data properties. We feel this lends support to our suggestion that rather than the identification of a 'single best' model and a map based on this result alone, a probability map based on the range of consistently top performing models provides a rigorous solution to environmental mapping. Copyright © 2016 Elsevier Ltd. All rights reserved.

Serial analysis of gene expression (SAGE) in normal human trabecular meshwork.

PubMed

Liu, Yutao; Munro, Drew; Layfield, David; Dellinger, Andrew; Walter, Jeffrey; Peterson, Katherine; Rickman, Catherine Bowes; Allingham, R Rand; Hauser, Michael A

2011-04-08

To identify the genes expressed in normal human trabecular meshwork tissue, a tissue critical to the pathogenesis of glaucoma. Total RNA was extracted from human trabecular meshwork (HTM) harvested from 3 different donors. Extracted RNA was used to synthesize individual SAGE (serial analysis of gene expression) libraries using the I-SAGE Long kit from Invitrogen. Libraries were analyzed using SAGE 2000 software to extract the 17 base pair sequence tags. The extracted sequence tags were mapped to the genome using SAGE Genie map. A total of 298,834 SAGE tags were identified from all HTM libraries (96,842, 88,126, and 113,866 tags, respectively). Collectively, there were 107,325 unique tags. There were 10,329 unique tags with a minimum of 2 counts from a single library. These tags were mapped to known unique Unigene clusters. Approximately 29% of the tags (orphan tags) did not map to a known Unigene cluster. Thirteen percent of the tags mapped to at least 2 Unigene clusters. Sequence tags from many glaucoma-related genes, including myocilin, optineurin, and WD repeat domain 36, were identified. This is the first time SAGE analysis has been used to characterize the gene expression profile in normal HTM. SAGE analysis provides an unbiased sampling of gene expression of the target tissue. These data will provide new and valuable information to improve understanding of the biology of human aqueous outflow.

Dual-energy CT iodine maps as an alternative quantitative imaging biomarker to abdominal CT perfusion: determination of appropriate trigger delays for acquisition using bolus tracking.

PubMed

Skornitzke, Stephan; Fritz, Franziska; Mayer, Philipp; Koell, Marco; Hansen, Jens; Pahn, Gregor; Hackert, Thilo; Kauczor, Hans-Ulrich; Stiller, Wolfram

2018-05-01

Quantitative evaluation of different bolus tracking trigger delays for acquisition of dual energy (DE) CT iodine maps as an alternative to CT perfusion. Prior to this retrospective analysis of prospectively acquired data, DECT perfusion sequences were dynamically acquired in 22 patients with pancreatic carcinoma using dual source CT at 80/140 kV p with tin filtration. After deformable motion-correction, perfusion maps of blood flow (BF) were calculated from 80 kV p image series of DECT, and iodine maps were calculated for each of the 34 DECT acquisitions per patient. BF and iodine concentrations were measured in healthy pancreatic tissue and carcinoma. To evaluate potential DECT acquisition triggered by bolus tracking, measured iodine concentrations from the 34 DECT acquisitions per patient corresponding to different trigger delays were assessed for correlation to BF and intergroup differences between tissue types depending on acquisition time. Average BF measured in healthy pancreatic tissue and carcinoma was 87.6 ± 28.4 and 38.6 ± 22.2 ml/100 ml min -1 , respectively. Correlation between iodine concentrations and BF was statistically significant for bolus tracking with trigger delay greater than 0 s (r max = 0.89; p < 0.05). Differences in iodine concentrations between healthy pancreatic tissue and carcinoma were statistically significant for DECT acquisitions corresponding to trigger delays of 15-21 s (p < 0.05). An acquisition window between 15 and 21 s after exceeding bolus tracking threshold shows promising results for acquisition of DECT iodine maps as an alternative to CT perfusion measurements of BF. Advances in knowledge: After clinical validation, DECT iodine maps of pancreas acquired using bolus tracking with appropriate trigger delay as determined in this study could offer an alternative quantitative imaging biomarker providing functional information for tumor assessment at reduced patient radiation exposure compared to CT perfusion measurements of BF.

Comparison of Content Structure and Cognitive Structure in the Learning of Probability.

ERIC Educational Resources Information Center

Geeslin, William E.

Digraphs, graphs, and task analysis were used to map out the content structure of a programed text (SMSG) in elementary probability. Mathematical structure was defined as the relationship between concepts within a set of abstract systems. The word association technique was used to measure the existing relations (cognitive structure) in S's memory…

Predicting the temporal and spatial probability of orographic cloud cover in the Luquillo Experimental Forest in Puerto Rico using generalized linear (mixed) models.

Treesearch

Wei Wu; Charlesb Hall; Lianjun Zhang

2006-01-01

We predicted the spatial pattern of hourly probability of cloud cover in the Luquillo Experimental Forest (LEF) in North-Eastern Puerto Rico using four different models. The probability of cloud cover (defined as “the percentage of the area covered by clouds in each pixel on the map” in this paper) at any hour and any place is a function of three topographic variables...

Work probability distribution and tossing a biased coin

NASA Astrophysics Data System (ADS)

Saha, Arnab; Bhattacharjee, Jayanta K.; Chakraborty, Sagar

2011-01-01

We show that the rare events present in dissipated work that enters Jarzynski equality, when mapped appropriately to the phenomenon of large deviations found in a biased coin toss, are enough to yield a quantitative work probability distribution for the Jarzynski equality. This allows us to propose a recipe for constructing work probability distribution independent of the details of any relevant system. The underlying framework, developed herein, is expected to be of use in modeling other physical phenomena where rare events play an important role.

Using NIR spatial illumination for detection and mapping chromophore changes during cerebral edema

NASA Astrophysics Data System (ADS)

Abookasis, David; Mathews, Marlon S.; Owen, Christopher M.; Binder, Devin K.; Linskey, Mark E.; Frostig, Ron D.; Tromberg, Bruce J.

2008-02-01

We used spatially modulated near-infrared (NIR) light to detect and map chromophore changes during cerebral edema in the rat neocortex. Cerebral edema was induced by intraperitoneal injections of free water (35% of body weight). Intracranial pressure (ICP) was measured with an optical fiber based Fabry-Perot interferometer sensor inserted into the parenchyma of the right frontal lobe during water administration. Increase in ICP from a baseline value of 10 cm-water to 145 cm-water was observed. Following induction of cerebral edema, there was a 26+/-1.7% increase in tissue concentration of deoxyhemoglobin and a 47+/-4.7%, 17+/-3% and 37+/-3.7% decrease in oxyhemoglobin, total hemoglobin concentration and cerebral tissue oxygen saturation levels, respectively. To the best of our knowledge, this is the first report describing the use of NIR spatial modulation of light for detecting and mapping changes in tissue concentrations of physiologic chromophores over time in response to cerebral edema.

CT Perfusion in Acute Stroke: "Black Holes" on Time-to-Peak Image Maps Indicate Unsalvageable Brain.

PubMed

Meagher, Ruairi; Shankar, Jai Jai Shiva

2016-11-01

CT perfusion is becoming important in acute stroke imaging to determine optimal patient-management strategies. The purpose of this study was to examine the predictive value of time-to-peak image maps and, specifically, a phenomenon coined a "black hole" for assessing infarcted brain tissue at the time of scan. Acute stroke patients were screened for the presence of black holes and their follow-up imaging (noncontrast CT or MR) was reviewed to assess for infarcted brain tissue. Of the 23 patients with signs of acute ischemia on CT perfusion, all had black holes. The black holes corresponded with areas of infarcted brain on follow-up imaging (specificity 100%). Black holes demonstrated significantly lower cerebral blood volumes (P < .001) and cerebral blood flow (P < .001) compared to immediately adjacent tissue. Black holes on time-to-peak image maps represent areas of unsalvageable brain. Copyright © 2016 by the American Society of Neuroimaging.

Automated cell-type classification in intact tissues by single-cell molecular profiling

PubMed Central

2018-01-01

A major challenge in biology is identifying distinct cell classes and mapping their interactions in vivo. Tissue-dissociative technologies enable deep single cell molecular profiling but do not provide spatial information. We developed a proximity ligation in situ hybridization technology (PLISH) with exceptional signal strength, specificity, and sensitivity in tissue. Multiplexed data sets can be acquired using barcoded probes and rapid label-image-erase cycles, with automated calculation of single cell profiles, enabling clustering and anatomical re-mapping of cells. We apply PLISH to expression profile ~2900 cells in intact mouse lung, which identifies and localizes known cell types, including rare ones. Unsupervised classification of the cells indicates differential expression of ‘housekeeping’ genes between cell types, and re-mapping of two sub-classes of Club cells highlights their segregated spatial domains in terminal airways. By enabling single cell profiling of various RNA species in situ, PLISH can impact many areas of basic and medical research. PMID:29319504

Association of intraoperative tissue oxygenation with suspected risk factors for tissue hypoxia.

PubMed

Spruit, R J; Schwarte, L A; Hakenberg, O W; Scheeren, T W L

2013-10-01

Tissue hypoxia may cause organ dysfunction, but not much is known about tissue oxygenation in the intraoperative setting. We studied microcirculatory tissue oxygen saturation (StO₂) to determine representative values for anesthetized patients undergoing urological surgery and to test the hypothesis that StO₂ is associated with known perioperative risk factors for morbidity and mortality, conventionally monitored variables, and hypotension requiring norepinephrine. Using near-infrared spectroscopy, we measured StO₂ on the thenar eminence in 160 patients undergoing open urological surgery under general anesthesia (FiO2 0.35-0.4), and calculated its correlations with age, risk level for general perioperative complications and mortality (high if age ≥70 and procedure is radical cystectomy), mean arterial pressure (MAP), hemoglobin concentration (Hb), central venous oxygen saturation (ScvO₂), and norepinephrine use. The time averaged StO₂ was 86 ± 6 % (mean ± SD). In the multivariate analysis, Hb [standardized coefficient (SC) 0.21, p = 0.003], ScvO₂ (SC 0.53, p < 0.001) and high risk level (SC 0.06, p = 0.03) were significant independent variables correlated with StO₂. SStO₂ was partly dependent on MAP only when this was below 65 mmHg (lowest MAP SC 0.20, p = 0.006, MAP area under the curve <65 mmHg SC 0.03, p = 0.02). Finally, StO₂ was slightly lower in patients requiring norepinephrine (85 ± 6 vs. 89 ± 6 %, p = 0.001). Intraoperative StO₂ in urological patients was comparable to that of healthy volunteers breathing room air as reported in the literature and correlated with known perioperative risk factors. Further research should investigate its association with outcome and the effect of interventions aimed at optimizing StO₂.

Evaluation of linear discriminant analysis for automated Raman histological mapping of esophageal high-grade dysplasia

NASA Astrophysics Data System (ADS)

Hutchings, Joanne; Kendall, Catherine; Shepherd, Neil; Barr, Hugh; Stone, Nicholas

2010-11-01

Rapid Raman mapping has the potential to be used for automated histopathology diagnosis, providing an adjunct technique to histology diagnosis. The aim of this work is to evaluate the feasibility of automated and objective pathology classification of Raman maps using linear discriminant analysis. Raman maps of esophageal tissue sections are acquired. Principal component (PC)-fed linear discriminant analysis (LDA) is carried out using subsets of the Raman map data (6483 spectra). An overall (validated) training classification model performance of 97.7% (sensitivity 95.0 to 100% and specificity 98.6 to 100%) is obtained. The remainder of the map spectra (131,672 spectra) are projected onto the classification model resulting in Raman images, demonstrating good correlation with contiguous hematoxylin and eosin (HE) sections. Initial results suggest that LDA has the potential to automate pathology diagnosis of esophageal Raman images, but since the classification of test spectra is forced into existing training groups, further work is required to optimize the training model. A small pixel size is advantageous for developing the training datasets using mapping data, despite lengthy mapping times, due to additional morphological information gained, and could facilitate differentiation of further tissue groups, such as the basal cells/lamina propria, in the future, but larger pixels sizes (and faster mapping) may be more feasible for clinical application.

Spatial reconstruction of single-cell gene expression data.

PubMed

Satija, Rahul; Farrell, Jeffrey A; Gennert, David; Schier, Alexander F; Regev, Aviv

2015-05-01

Spatial localization is a key determinant of cellular fate and behavior, but methods for spatially resolved, transcriptome-wide gene expression profiling across complex tissues are lacking. RNA staining methods assay only a small number of transcripts, whereas single-cell RNA-seq, which measures global gene expression, separates cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos and generated a transcriptome-wide map of spatial patterning. We confirmed Seurat's accuracy using several experimental approaches, then used the strategy to identify a set of archetypal expression patterns and spatial markers. Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems.

Radiobiological Impact of Reduced Margins and Treatment Technique for Prostate Cancer in Terms of Tumor Control Probability (TCP) and Normal Tissue Complication Probability (NTCP)

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

Jensen, Ingelise, E-mail: inje@rn.d; Carl, Jesper; Lund, Bente

2011-07-01

Dose escalation in prostate radiotherapy is limited by normal tissue toxicities. The aim of this study was to assess the impact of margin size on tumor control and side effects for intensity-modulated radiation therapy (IMRT) and 3D conformal radiotherapy (3DCRT) treatment plans with increased dose. Eighteen patients with localized prostate cancer were enrolled. 3DCRT and IMRT plans were compared for a variety of margin sizes. A marker detectable on daily portal images was presupposed for narrow margins. Prescribed dose was 82 Gy within 41 fractions to the prostate clinical target volume (CTV). Tumor control probability (TCP) calculations based on themore » Poisson model including the linear quadratic approach were performed. Normal tissue complication probability (NTCP) was calculated for bladder, rectum and femoral heads according to the Lyman-Kutcher-Burman method. All plan types presented essentially identical TCP values and very low NTCP for bladder and femoral heads. Mean doses for these critical structures reached a minimum for IMRT with reduced margins. Two endpoints for rectal complications were analyzed. A marked decrease in NTCP for IMRT plans with narrow margins was seen for mild RTOG grade 2/3 as well as for proctitis/necrosis/stenosis/fistula, for which NTCP <7% was obtained. For equivalent TCP values, sparing of normal tissue was demonstrated with the narrow margin approach. The effect was more pronounced for IMRT than 3DCRT, with respect to NTCP for mild, as well as severe, rectal complications.« less

Recurrent pregnancy loss evaluation combined with 24-chromosome microarray of miscarriage tissue provides a probable or definite cause of pregnancy loss in over 90% of patients.

PubMed

Popescu, F; Jaslow, C R; Kutteh, W H

2018-04-01

Will the addition of 24-chromosome microarray analysis on miscarriage tissue combined with the standard American Society for Reproductive Medicine (ASRM) evaluation for recurrent miscarriage explain most losses? Over 90% of patients with recurrent pregnancy loss (RPL) will have a probable or definitive cause identified when combining genetic testing on miscarriage tissue with the standard ASRM evaluation for recurrent miscarriage. RPL is estimated to occur in 2-4% of reproductive age couples. A probable cause can be identified in approximately 50% of patients after an ASRM recommended workup including an evaluation for parental chromosomal abnormalities, congenital and acquired uterine anomalies, endocrine imbalances and autoimmune factors including antiphospholipid syndrome. Single-center, prospective cohort study that included 100 patients seen in a private RPL clinic from 2014 to 2017. All 100 women had two or more pregnancy losses, a complete evaluation for RPL as defined by the ASRM, and miscarriage tissue evaluated by 24-chromosome microarray analysis after their second or subsequent miscarriage. Frequencies of abnormal results for evidence-based diagnostic tests considered definite or probable causes of RPL (karyotyping for parental chromosomal abnormalities, and 24-chromosome microarray evaluation for products of conception (POC); pelvic sonohysterography, hysterosalpingogram, or hysteroscopy for uterine anomalies; immunological tests for lupus anticoagulant and anticardiolipin antibodies; and blood tests for thyroid stimulating hormone (TSH), prolactin and hemoglobin A1c) were evaluated. We excluded cases where there was maternal cell contamination of the miscarriage tissue or if the ASRM evaluation was incomplete. A cost analysis for the evaluation of RPL was conducted to determine whether a proposed procedure of 24-chromome microarray evaluation followed by an ASRM RPL workup (for those RPL patients who had a normal 24-chromosome microarray evaluation) was more cost-efficient than conducting ASRM RPL workups on RPL patients followed by 24-chromosome microarray analysis (for those RPL patients who had a normal RPL workup). A definite or probable cause of pregnancy loss was identified in the vast majority (95/100; 95%) of RPL patients when a 24-chromosome pair microarray evaluation of POC testing is combined with the standard ASRM RPL workup evaluation at the time of the second or subsequent loss. The ASRM RPL workup identified an abnormality and a probable explanation for pregnancy loss in only 45/100 or 45% of all patients. A definite abnormality was identified in 67/100 patients or 67% when initial testing was performed using 24-chromosome microarray analyses on the miscarriage tissue. Only 5/100 (5%) patients, who had a euploid loss and a normal ASRM RPL workup, had a pregnancy loss without a probable or definitive cause identified. All other losses were explained by an abnormal 24-chromosome microarray analysis of the miscarriage tissue, an abnormal finding of the RPL workup, or a combination of both. Results from the cost analysis indicated that an initial approach of using a 24-chromosome microarray analysis on miscarriage tissue resulted in a 50% savings in cost to the health care system and to the patient. This is a single-center study on a small group of well-characterized women with RPL. There was an incomplete follow-up on subsequent pregnancy outcomes after evaluation, however this should not affect our principal results. The maternal age of patients varied from 26 to 45 years old. More aneuploid pregnancy losses would be expected in older women, particularly over the age of 35 years old. Evaluation of POC using 24-chromosome microarray analysis adds significantly to the ASRM recommended evaluation of RPL. Genetic evaluation on miscarriage tissue obtained at the time of the second and subsequent pregnancy losses should be offered to all couples with two or more consecutive pregnancy losses. The combination of a genetic evaluation on miscarriage tissue with an evidence-based evaluation for RPL will identify a probable or definitive cause in over 90% of miscarriages. No funding was received for this study and there are no conflicts of interest to declare. Not applicable.

Detection of Head and Neck Cancer in Surgical Specimens Using Quantitative Hyperspectral Imaging.

PubMed

Lu, Guolan; Little, James V; Wang, Xu; Zhang, Hongzheng; Patel, Mihir R; Griffith, Christopher C; El-Deiry, Mark W; Chen, Amy Y; Fei, Baowei

2017-09-15

Purpose: This study intends to investigate the feasibility of using hyperspectral imaging (HSI) to detect and delineate cancers in fresh, surgical specimens of patients with head and neck cancers. Experimental Design: A clinical study was conducted in order to collect and image fresh, surgical specimens from patients ( N = 36) with head and neck cancers undergoing surgical resection. A set of machine-learning tools were developed to quantify hyperspectral images of the resected tissue in order to detect and delineate cancerous regions which were validated by histopathologic diagnosis. More than two million reflectance spectral signatures were obtained by HSI and analyzed using machine-learning methods. The detection results of HSI were compared with autofluorescence imaging and fluorescence imaging of two vital-dyes of the same specimens. Results: Quantitative HSI differentiated cancerous tissue from normal tissue in ex vivo surgical specimens with a sensitivity and specificity of 91% and 91%, respectively, and which was more accurate than autofluorescence imaging ( P < 0.05) or fluorescence imaging of 2-NBDG ( P < 0.05) and proflavine ( P < 0.05). The proposed quantification tools also generated cancer probability maps with the tumor border demarcated and which could provide real-time guidance for surgeons regarding optimal tumor resection. Conclusions: This study highlights the feasibility of using quantitative HSI as a diagnostic tool to delineate the cancer boundaries in surgical specimens, and which could be translated into the clinic application with the hope of improving clinical outcomes in the future. Clin Cancer Res; 23(18); 5426-36. ©2017 AACR . ©2017 American Association for Cancer Research.

User’s guide for MapMark4GUI—A graphical user interface for the MapMark4 R package

USGS Publications Warehouse

Shapiro, Jason

2018-05-29

MapMark4GUI is an R graphical user interface (GUI) developed by the U.S. Geological Survey to support user implementation of the MapMark4 R statistical software package. MapMark4 was developed by the U.S. Geological Survey to implement probability calculations for simulating undiscovered mineral resources in quantitative mineral resource assessments. The GUI provides an easy-to-use tool to input data, run simulations, and format output results for the MapMark4 package. The GUI is written and accessed in the R statistical programming language. This user’s guide includes instructions on installing and running MapMark4GUI and descriptions of the statistical output processes, output files, and test data files.

THEMATIC ACCURACY OF THE 1992 NATIONAL LAND-COVER DATA (NLCD) FOR THE EASTERN UNITED STATES: STATISTICAL METHODOLOGY AND REGIONAL RESULTS

EPA Science Inventory

The accuracy of the National Land Cover Data (NLCD) map is assessed via a probability sampling design incorporating three levels of stratification and two stages of selection. Agreement between the map and reference land-cover labels is defined as a match between the primary or a...

Factors that Influence Fast Mapping in Children Exposed to Spanish and English

ERIC Educational Resources Information Center

Alt, Mary; Meyers, Christina; Figueroa, Cecilia

2013-01-01

Purpose: The purpose of this study was to determine whether children exposed to 2 languages would benefit from the phonotactic probability cues of a single language in the same way as monolingual peers and to determine whether crosslinguistic influence would be present in a fast-mapping task. Method: Two groups of typically developing children…

MRI-guided attenuation correction in whole-body PET/MR: assessment of the effect of bone attenuation.

PubMed

Akbarzadeh, A; Ay, M R; Ahmadian, A; Alam, N Riahi; Zaidi, H

2013-02-01

Hybrid PET/MRI presents many advantages in comparison with its counterpart PET/CT in terms of improved soft-tissue contrast, decrease in radiation exposure, and truly simultaneous and multi-parametric imaging capabilities. However, the lack of well-established methodology for MR-based attenuation correction is hampering further development and wider acceptance of this technology. We assess the impact of ignoring bone attenuation and using different tissue classes for generation of the attenuation map on the accuracy of attenuation correction of PET data. This work was performed using simulation studies based on the XCAT phantom and clinical input data. For the latter, PET and CT images of patients were used as input for the analytic simulation model using realistic activity distributions where CT-based attenuation correction was utilized as reference for comparison. For both phantom and clinical studies, the reference attenuation map was classified into various numbers of tissue classes to produce three (air, soft tissue and lung), four (air, lungs, soft tissue and cortical bones) and five (air, lungs, soft tissue, cortical bones and spongeous bones) class attenuation maps. The phantom studies demonstrated that ignoring bone increases the relative error by up to 6.8% in the body and up to 31.0% for bony regions. Likewise, the simulated clinical studies showed that the mean relative error reached 15% for lesions located in the body and 30.7% for lesions located in bones, when neglecting bones. These results demonstrate an underestimation of about 30% of tracer uptake when neglecting bone, which in turn imposes substantial loss of quantitative accuracy for PET images produced by hybrid PET/MRI systems. Considering bones in the attenuation map will considerably improve the accuracy of MR-guided attenuation correction in hybrid PET/MR to enable quantitative PET imaging on hybrid PET/MR technologies.

PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities.

PubMed

Malekpour, Seyed Amir; Pezeshk, Hamid; Sadeghi, Mehdi

2016-11-03

Copy Number Variation (CNV) is envisaged to be a major source of large structural variations in the human genome. In recent years, many studies apply Next Generation Sequencing (NGS) data for the CNV detection. However, still there is a necessity to invent more accurate computational tools. In this study, mate pair NGS data are used for the CNV detection in a Hidden Markov Model (HMM). The proposed HMM has position specific emission probabilities, i.e. a Gaussian mixture distribution. Each component in the Gaussian mixture distribution captures a different type of aberration that is observed in the mate pairs, after being mapped to the reference genome. These aberrations may include any increase (decrease) in the insertion size or change in the direction of mate pairs that are mapped to the reference genome. This HMM with Position-Specific Emission probabilities (PSE-HMM) is utilized for the genome-wide detection of deletions and tandem duplications. The performance of PSE-HMM is evaluated on a simulated dataset and also on a real data of a Yoruban HapMap individual, NA18507. PSE-HMM is effective in taking observation dependencies into account and reaches a high accuracy in detecting genome-wide CNVs. MATLAB programs are available at http://bs.ipm.ir/softwares/PSE-HMM/ .

Correction to “New maps of California to improve tsunami preparedness”

NASA Astrophysics Data System (ADS)

Barberopoulou, Aggeliki; Borrero, Jose C.; Uslu, Burak; Kalligeris, Nikos; Goltz, James D.; Wilson, Rick I.; Synolakis, Costas E.

2009-05-01

In the 21 April issue (Eos, 90(16), 2009), the article titled “New maps of California to improve tsunami preparedness” contained an error in its Figure 2 caption. Figure 2 is a map of Goleta, a city in Santa Barbara County. Thus, the first sentence of the caption should read, “Newly created tsunami inundation maps for Goleta, a city in Santa Barbara County, Calif., show the city's ‘wet line’ in black, representing the highest probable tsunami runup modeled for the region added to average water levels at high tide.” Eos deeply regrets this error.

Probabilistic-driven oriented Speckle reducing anisotropic diffusion with application to cardiac ultrasonic images.

PubMed

Vegas-Sanchez-Ferrero, G; Aja-Fernandez, S; Martin-Fernandez, M; Frangi, A F; Palencia, C

2010-01-01

A novel anisotropic diffusion filter is proposed in this work with application to cardiac ultrasonic images. It includes probabilistic models which describe the probability density function (PDF) of tissues and adapts the diffusion tensor to the image iteratively. For this purpose, a preliminary study is performed in order to select the probability models that best fit the stastitical behavior of each tissue class in cardiac ultrasonic images. Then, the parameters of the diffusion tensor are defined taking into account the statistical properties of the image at each voxel. When the structure tensor of the probability of belonging to each tissue is included in the diffusion tensor definition, a better boundaries estimates can be obtained instead of calculating directly the boundaries from the image. This is the main contribution of this work. Additionally, the proposed method follows the statistical properties of the image in each iteration. This is considered as a second contribution since state-of-the-art methods suppose that noise or statistical properties of the image do not change during the filter process.

Radiotherapy of soft tissue sarcomas in dogs.

PubMed

McChesney, S L; Withrow, S J; Gillette, E L; Powers, B E; Dewhirst, M W

1989-01-01

Megavoltage radiotherapy was administered to 42 dogs with soft tissue sarcoma. Acceptable local control of these aggressive tumors was achieved after one year of treatment. Control rates of 48 and 67% were obtained at doses of 45 and 50 gray (Gy), respectively. At 2 years, control rates decreased to 33% at the dose of 50 Gy. Serious complications developed in 4 of 42 dogs at doses of 40 to 50 Gy. The estimated dose with a 50% probability for causing serious complications was 54 Gy, given in 10 fractions. We believe that the large doses per fraction used in this study probably led to an increased probability for necrosis. Hemangiopericytomas seemed to be more responsive than fibrosarcomas. Only 2 of 11 recurrent tumors were controlled with surgery. Good local control was achieved with radiation alone for one year at doses with a low probability for serious complications; however, higher total radiation doses or combined modalities, such as surgery and radiation or radiation and hyperthermia, may be needed for longer-term control.

Mapping local orientation of aligned fibrous scatterers for cancerous tissues using backscattering Mueller matrix imaging

NASA Astrophysics Data System (ADS)

He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Liu, Shaoxiong; Guo, Yihong; Wu, Jian; He, Yonghong; Ma, Hui

2014-10-01

Polarization measurements are sensitive to the microstructure of tissues and can be used to detect pathological changes. Many tissues contain anisotropic fibrous structures. We obtain the local orientation of aligned fibrous scatterers using different groups of the backscattering Mueller matrix elements. Experiments on concentrically well-aligned silk fibers and unstained human papillary thyroid carcinoma tissues show that the m22, m33, m23, and m32 elements have better contrast but higher degeneracy for the extraction of orientation angles. The m12 and m13 elements show lower contrast, but allow us to determine the orientation angle for the fibrous scatterers along all directions. Moreover, Monte Carlo simulations based on the sphere-cylinder scattering model indicate that the oblique incidence of the illumination beam introduces some errors in the orientation angles obtained by both methods. Mapping the local orientation of anisotropic tissues may not only provide information on pathological changes, but can also give new leads to reduce the orientation dependence of polarization measurements.

Lesion registration for longitudinal disease tracking in an imaging informatics-based multiple sclerosis eFolder

NASA Astrophysics Data System (ADS)

Ma, Kevin; Liu, Joseph; Zhang, Xuejun; Lerner, Alex; Shiroishi, Mark; Amezcua, Lilyana; Liu, Brent

2016-03-01

We have designed and developed a multiple sclerosis eFolder system for patient data storage, image viewing, and automatic lesion quantification results stored in DICOM-SR format. The web-based system aims to be integrated in DICOM-compliant clinical and research environments to aid clinicians in patient treatments and data analysis. The system needs to quantify lesion volumes, identify and register lesion locations to track shifts in volume and quantity of lesions in a longitudinal study. In order to perform lesion registration, we have developed a brain warping and normalizing methodology using Statistical Parametric Mapping (SPM) MATLAB toolkit for brain MRI. Patients' brain MR images are processed via SPM's normalization processes, and the brain images are analyzed and warped according to the tissue probability map. Lesion identification and contouring are completed by neuroradiologists, and lesion volume quantification is completed by the eFolder's CAD program. Lesion comparison results in longitudinal studies show key growth and active regions. The results display successful lesion registration and tracking over a longitudinal study. Lesion change results are graphically represented in the web-based user interface, and users are able to correlate patient progress and changes in the MRI images. The completed lesion and disease tracking tool would enable the eFolder to provide complete patient profiles, improve the efficiency of patient care, and perform comprehensive data analysis through an integrated imaging informatics system.

High-speed multislice T1 mapping using inversion-recovery echo-planar imaging.

PubMed

Ordidge, R J; Gibbs, P; Chapman, B; Stehling, M K; Mansfield, P

1990-11-01

Tissue contrast in MR images is a strong function of spin-lattice (T1) and spin-spin (T2) relaxation times. However, the T1 relaxation time is rarely quantified because of the long scan time required to produce an accurate T1 map of the subject. In a standard 2D FT technique, this procedure may take up to 30 min. Modifications of the echo-planar imaging (EPI) technique which incorporate the principle of inversion recovery (IR) enable multislice T1 maps to be produced in total scan times varying from a few seconds up to a minute. Using IR-EPI, rapid quantification of T1 values may thus lead to better discrimination between tissue types in an acceptable scan time.

Four-dimensional optoacoustic temperature mapping in laser-induced thermotherapy

NASA Astrophysics Data System (ADS)

Oyaga Landa, Francisco Javier; Deán-Ben, Xosé Luís.; Sroka, Ronald; Razansky, Daniel

2018-02-01

Photoablative laser therapy is in common use for selective destruction of malignant masses, vascular and brain abnormalities. Tissue ablation and coagulation are irreversible processes occurring shortly after crossing a certain thermal exposure threshold. As a result, accurate mapping of the temperature field is essential for optimizing the outcome of these clinical interventions. Here we demonstrate four-dimensional optoacoustic temperature mapping of the entire photoablated region. Accuracy of the method is investigated in tissue-mimicking phantom experiments. Deviations of the volumetric optoacoustic temperature readings provided at 40ms intervals remained below 10% for temperature elevations above 3°C, as validated by simultaneous thermocouple measurements. The excellent spatio-temporal resolution of the new temperature monitoring approach aims at improving safety and efficacy of laser-based photothermal procedures.

Choice of surrogate tissue influences neonatal EWAS findings.

PubMed

Lin, Xinyi; Teh, Ai Ling; Chen, Li; Lim, Ives Yubin; Tan, Pei Fang; MacIsaac, Julia L; Morin, Alexander M; Yap, Fabian; Tan, Kok Hian; Saw, Seang Mei; Lee, Yung Seng; Holbrook, Joanna D; Godfrey, Keith M; Meaney, Michael J; Kobor, Michael S; Chong, Yap Seng; Gluckman, Peter D; Karnani, Neerja

2017-12-05

Epigenomes are tissue specific and thus the choice of surrogate tissue can play a critical role in interpreting neonatal epigenome-wide association studies (EWAS) and in their extrapolation to target tissue. To develop a better understanding of the link between tissue specificity and neonatal EWAS, and the contributions of genotype and prenatal factors, we compared genome-wide DNA methylation of cord tissue and cord blood, two of the most accessible surrogate tissues at birth. In 295 neonates, DNA methylation was profiled using Infinium HumanMethylation450 beadchip arrays. Sites of inter-individual variability in DNA methylation were mapped and compared across the two surrogate tissues at birth, i.e., cord tissue and cord blood. To ascertain the similarity to target tissues, DNA methylation profiles of surrogate tissues were compared to 25 primary tissues/cell types mapped under the Epigenome Roadmap project. Tissue-specific influences of genotype on the variable CpGs were also analyzed. Finally, to interrogate the impact of the in utero environment, EWAS on 45 prenatal factors were performed and compared across the surrogate tissues. Neonatal EWAS results were tissue specific. In comparison to cord blood, cord tissue showed higher inter-individual variability in the epigenome, with a lower proportion of CpGs influenced by genotype. Both neonatal tissues were good surrogates for target tissues of mesodermal origin. They also showed distinct phenotypic associations, with effect sizes of the overlapping CpGs being in the same order of magnitude. The inter-relationship between genetics, prenatal factors and epigenetics is tissue specific, and requires careful consideration in designing and interpreting future neonatal EWAS. This birth cohort is a prospective observational study, designed to study the developmental origins of health and disease, and was retrospectively registered on 1 July 2010 under the identifier NCT01174875 .

Effects of Ultrasound Frequency and Tissue Stiffness on the Histotripsy Intrinsic Threshold for Cavitation

PubMed Central

Vlaisavljevich, Eli; Lin, Kuang-Wei; Maxwell, Adam; Warnez, Matthew; Mancia, Lauren; Singh, Rahul; Putnam, Andrew J.; Fowlkes, Brian; Johnsen, Eric; Cain, Charles; Xu, Zhen

2015-01-01

Histotripsy is an ultrasound ablation method that depends on the initiation of a cavitation bubble cloud to fractionate soft tissue. Previous work has demonstrated a cavitation cloud can be formed by a single pulse with one high amplitude negative cycle, when the negative pressure amplitude directly exceeds a pressure threshold intrinsic to the medium. We hypothesize that the intrinsic threshold in water-based tissues is determined by the properties of the water inside the tissue and changes in tissue stiffness or ultrasound frequency will have a minimal impact on the histotripsy intrinsic threshold. To test this hypothesis, the histotripsy intrinsic threshold was investigated both experimentally and theoretically. The probability of cavitation was measured by subjecting tissue phantoms with adjustable mechanical properties and ex vivo tissues to a histotripsy pulse of 1–2 cycles produced by 345 kHz, 500 kHz, 1.5 MHz, and 3 MHz histotripsy transducers. Cavitation was detected and characterized by passive cavitation detection and high-speed photography, from which the probability of cavitation was measured vs. pressure amplitude. The results demonstrated that the intrinsic threshold (the negative pressure at which probability=0.5) is independent of stiffness for Young’s moduli (E) < 1 MPa with only a small increase (~2–3 MPa) in the intrinsic threshold for tendon (E=380 MPa). Additionally, results for all samples showed only a small increase of ~2–3 MPa when the frequency was increased from 345 kHz to 3 MHz. The intrinsic threshold was measured to be between 24.7–30.6 MPa for all samples and frequencies tested in this study. Overall, the results of this study indicate that the intrinsic threshold to initiate a histotripsy bubble cloud is not significantly impacted by tissue stiffness or ultrasound frequency in hundreds of kHz to MHz range. PMID:25766571

Effects of ultrasound frequency and tissue stiffness on the histotripsy intrinsic threshold for cavitation.

PubMed

Vlaisavljevich, Eli; Lin, Kuang-Wei; Maxwell, Adam; Warnez, Matthew T; Mancia, Lauren; Singh, Rahul; Putnam, Andrew J; Fowlkes, Brian; Johnsen, Eric; Cain, Charles; Xu, Zhen

2015-06-01

Histotripsy is an ultrasound ablation method that depends on the initiation of a cavitation bubble cloud to fractionate soft tissue. Previous work has indicated that a cavitation cloud can be formed by a single pulse with one high-amplitude negative cycle, when the negative pressure amplitude directly exceeds a pressure threshold intrinsic to the medium. We hypothesize that the intrinsic threshold in water-based tissues is determined by the properties of the water inside the tissue, and changes in tissue stiffness or ultrasound frequency will have a minimal impact on the histotripsy intrinsic threshold. To test this hypothesis, the histotripsy intrinsic threshold was investigated both experimentally and theoretically. The probability of cavitation was measured by subjecting tissue phantoms with adjustable mechanical properties and ex vivo tissues to a histotripsy pulse of 1-2 cycles produced by 345-kHz, 500-kHz, 1.5-MHz and 3-MHz histotripsy transducers. Cavitation was detected and characterized by passive cavitation detection and high-speed photography, from which the probability of cavitation was measured versus pressure amplitude. The results revealed that the intrinsic threshold (the negative pressure at which probability = 0.5) is independent of stiffness for Young's moduli (E) <1 MPa, with only a small increase (∼2-3 MPa) in the intrinsic threshold for tendon (E = 380 MPa). Additionally, results for all samples revealed only a small increase of ∼2-3 MPa when the frequency was increased from 345 kHz to 3 MHz. The intrinsic threshold was measured to be between 24.7 and 30.6 MPa for all samples and frequencies tested in this study. Overall, the results of this study indicate that the intrinsic threshold to initiate a histotripsy bubble cloud is not significantly affected by tissue stiffness or ultrasound frequency in the hundreds of kilohertz to megahertz range. Copyright © 2015 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Quantitative Evaluation of Segmentation- and Atlas-Based Attenuation Correction for PET/MR on Pediatric Patients.

PubMed

Bezrukov, Ilja; Schmidt, Holger; Gatidis, Sergios; Mantlik, Frédéric; Schäfer, Jürgen F; Schwenzer, Nina; Pichler, Bernd J

2015-07-01

Pediatric imaging is regarded as a key application for combined PET/MR imaging systems. Because existing MR-based attenuation-correction methods were not designed specifically for pediatric patients, we assessed the impact of 2 potentially influential factors: inter- and intrapatient variability of attenuation coefficients and anatomic variability. Furthermore, we evaluated the quantification accuracy of 3 methods for MR-based attenuation correction without (SEGbase) and with bone prediction using an adult and a pediatric atlas (SEGwBONEad and SEGwBONEpe, respectively) on PET data of pediatric patients. The variability of attenuation coefficients between and within pediatric (5-17 y, n = 17) and adult (27-66 y, n = 16) patient collectives was assessed on volumes of interest (VOIs) in CT datasets for different tissue types. Anatomic variability was assessed on SEGwBONEad/pe attenuation maps by computing mean differences to CT-based attenuation maps for regions of bone tissue, lungs, and soft tissue. PET quantification was evaluated on VOIs with physiologic uptake and on 80% isocontour VOIs with elevated uptake in the thorax and abdomen/pelvis. Inter- and intrapatient variability of the bias was assessed for each VOI group and method. Statistically significant differences in mean VOI Hounsfield unit values and linear attenuation coefficients between adult and pediatric collectives were found in the lungs and femur. The prediction of attenuation maps using the pediatric atlas showed a reduced error in bone tissue and better delineation of bone structure. Evaluation of PET quantification accuracy showed statistically significant mean errors in mean standardized uptake values of -14% ± 5% and -23% ± 6% in bone marrow and femur-adjacent VOIs with physiologic uptake for SEGbase, which could be reduced to 0% ± 4% and -1% ± 5% using SEGwBONEpe attenuation maps. Bias in soft-tissue VOIs was less than 5% for all methods. Lung VOIs showed high SDs in the range of 15% for all methods. For VOIs with elevated uptake, mean and SD were less than 5% except in the thorax. The use of a dedicated atlas for the pediatric patient collective resulted in improved attenuation map prediction in osseous regions and reduced interpatient bias variation in femur-adjacent VOIs. For the lungs, in which intrapatient variation was higher for the pediatric collective, a patient- or group-specific attenuation coefficient might improve attenuation map accuracy. Mean errors of -14% and -23% in bone marrow and femur-adjacent VOIs can affect PET quantification in these regions when bone tissue is ignored. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Imaging Odor-Evoked Activities in the Mouse Olfactory Bulb using Optical Reflectance and Autofluorescence Signals

PubMed Central

Chery, Romain; L'Heureux, Barbara; Bendahmane, Mounir; Renaud, Rémi; Martin, Claire; Pain, Frédéric; Gurden, Hirac

2011-01-01

In the brain, sensory stimulation activates distributed populations of neurons among functional modules which participate to the coding of the stimulus. Functional optical imaging techniques are advantageous to visualize the activation of these modules in sensory cortices with high spatial resolution. In this context, endogenous optical signals that arise from molecular mechanisms linked to neuroenergetics are valuable sources of contrast to record spatial maps of sensory stimuli over wide fields in the rodent brain. Here, we present two techniques based on changes of endogenous optical properties of the brain tissue during activation. First the intrinsic optical signals (IOS) are produced by a local alteration in red light reflectance due to: (i) absorption by changes in blood oxygenation level and blood volume (ii) photon scattering. The use of in vivo IOS to record spatial maps started in the mid 1980's with the observation of optical maps of whisker barrels in the rat and the orientation columns in the cat visual cortex1. IOS imaging of the surface of the rodent main olfactory bulb (OB) in response to odorants was later demonstrated by Larry Katz's group2. The second approach relies on flavoprotein autofluorescence signals (FAS) due to changes in the redox state of these mitochondrial metabolic intermediates. More precisely, the technique is based on the green fluorescence due to oxidized state of flavoproteins when the tissue is excited with blue light. Although such signals were probably among the first fluorescent molecules recorded for the study of brain activity by the pioneer studies of Britton Chances and colleagues3, it was not until recently that they have been used for mapping of brain activation in vivo. FAS imaging was first applied to the somatosensory cortex in rodents in response to hindpaw stimulation by Katsuei Shibuki's group4. The olfactory system is of central importance for the survival of the vast majority of living species because it allows efficient detection and identification of chemical substances in the environment (food, predators). The OB is the first relay of olfactory information processing in the brain. It receives afferent projections from the olfactory primary sensory neurons that detect volatile odorant molecules. Each sensory neuron expresses only one type of odorant receptor and neurons carrying the same type of receptor send their nerve processes to the same well-defined microregions of ˜100μm3 constituted of discrete neuropil, the olfactory glomerulus (Fig. 1). In the last decade, IOS imaging has fostered the functional exploration of the OB5, 6, 7 which has become one of the most studied sensory structures. The mapping of OB activity with FAS imaging has not been performed yet. Here, we show the successive steps of an efficient protocol for IOS and FAS imaging to map odor-evoked activities in the mouse OB. PMID:22064685

Comparison of rapid diagnostic tests to detect Mycobacterium avium subsp. paratuberculosis disseminated infection in bovine liver.

PubMed

Zarei, Mehdi; Ghorbanpour, Masoud; Tajbakhsh, Samaneh; Mosavari, Nader

2017-08-01

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, a chronic enteritis in cattle and other domestic and wild ruminants. The presence of MAP in tissues other than intestines and associated lymph nodes, such as meat and liver, is a potential public health concern. In the present study, the relationship between the results of rapid diagnostic tests of the Johne's disease, such as serum ELISA, rectal scraping PCR, and acid-fast staining, and the presence of MAP in liver was evaluated. Blood, liver, and rectal scraping samples were collected from 200 slaughtered cattle with unknown Johne's disease status. ELISA was performed to determine the MAP antibody activity in the serum. Acid-fast staining was performed on rectal scraping samples, and PCR was performed on rectal scraping and liver samples. PCR-positive liver samples were used for mycobacterial culture. Overall, the results of this study demonstrated that MAP can be detected and cultured from liver of slaughtered cattle and rapid diagnostic tests of Johne's disease have limited value in detecting cattle with MAP infection in liver. These findings show that the presence of MAP in liver tissue may occur in cows with negative results for rapid diagnostic tests and vice versa. Hence, liver might represent another possible risk of human exposure to MAP. Given concerns about a potential zoonotic role for MAP, these results show the necessity to find new methods for detecting cattle with MAP disseminated infection.

Probability density function formalism for optical coherence tomography signal analysis: a controlled phantom study.

PubMed

Weatherbee, Andrew; Sugita, Mitsuro; Bizheva, Kostadinka; Popov, Ivan; Vitkin, Alex

2016-06-15

The distribution of backscattered intensities as described by the probability density function (PDF) of tissue-scattered light contains information that may be useful for tissue assessment and diagnosis, including characterization of its pathology. In this Letter, we examine the PDF description of the light scattering statistics in a well characterized tissue-like particulate medium using optical coherence tomography (OCT). It is shown that for low scatterer density, the governing statistics depart considerably from a Gaussian description and follow the K distribution for both OCT amplitude and intensity. The PDF formalism is shown to be independent of the scatterer flow conditions; this is expected from theory, and suggests robustness and motion independence of the OCT amplitude (and OCT intensity) PDF metrics in the context of potential biomedical applications.

Systematic variations in multi-spectral lidar representations of canopy height profiles and gap probability

NASA Astrophysics Data System (ADS)

Chasmer, L.; Hopkinson, C.; Gynan, C.; Mahoney, C.; Sitar, M.

2015-12-01

Airborne and terrestrial lidar are increasingly used in forest attribute modeling for carbon, ecosystem and resource monitoring. The near infra-red wavelength at 1064nm has been utilised most in airborne applications due to, for example, diode manufacture costs, surface reflectance and eye safety. Foliage reflects well at 1064nm and most of the literature on airborne lidar forest structure is based on data from this wavelength. However, lidar systems also operate at wavelengths further from the visible spectrum (e.g. 1550nm) for eye safety reasons. This corresponds to a water absorption band and can be sensitive to attenuation if surfaces contain moisture. Alternatively, some systems operate in the visible range (e.g. 532nm) for specialised applications requiring simultaneous mapping of terrestrial and bathymetric surfaces. All these wavelengths provide analogous 3D canopy structure reconstructions and thus offer the potential to be combined for spatial comparisons or temporal monitoring. However, a systematic comparison of wavelength-dependent foliage profile and gap probability (index of transmittance) is needed. Here we report on two multispectral lidar missions carried out in 2013 and 2015 over conifer, deciduous and mixed stands in Ontario, Canada. The first used separate lidar sensors acquiring comparable data at three wavelengths, while the second used a single sensor with 3 integrated laser systems. In both cases, wavelenegths sampled were 532nm, 1064nm and 1550nm. The experiment revealed significant differences in proportions of returns at ground level, the vertical foliage distribution and gap probability across wavelengths. Canopy attenuation was greatest at 532nm due to photosynthetic plant tissue absorption. Relative to 1064nm, foliage was systematically undersampled at the 10% to 60% height percentiles at both 1550nm and 532nm (this was confirmed with coincident terrestrial lidar data). When using all returns to calculate gap probability, all wavelengths were within 6% but when using first returns only, gap probability was overestimated by 67% at 532nm and 11% by 1550nm. These results demonstrate that each wavelength contains distinct information about canopy attributes and models must account for variations in wavelength if applied to data for monitoring purposes.

WE-AB-202-01: Evaluating the Toxicity Reduction with CT-Ventilation Functional Avoidance Radiation Therapy

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

Vinogradskiy, Y; Miyasaka, Y; Kadoya, N

Purpose: CT-ventilation is an exciting new imaging modality that uses 4DCTs to calculate lung ventilation. Studies have proposed to use 4DCT-ventilation imaging for functional avoidance radiotherapy which implies designing treatment plans to spare functional portions of the lung. Although retrospective studies have been performed to evaluate the dosimetric gains to functional lung; no work has been done to translate the dosimetric gains to an improvement in pulmonary toxicity. The purpose of our work was to evaluate the potential reduction in toxicity for 4DCT-ventilation based functional avoidance. Methods: 70 lung cancer patients with 4DCT imaging were used for the study. CT-ventilationmore » maps were calculated using the patient’s 4DCT, deformable image registrations, and a density-change-based algorithm. Radiation pneumonitis was graded using imaging and clinical information. Log-likelihood methods were used to fit a normal-tissue-complication-probability (NTCP) model predicting grade 2+ radiation pneumonitis as a function of doses (mean and V20) to functional lung (>15% ventilation). For 20 patients a functional plan was generated that reduced dose to functional lung while meeting RTOG 0617-based constraints. The NTCP model was applied to the functional plan to determine the reduction in toxicity with functional planning Results: The mean dose to functional lung was 16.8 and 17.7 Gy with the functional and clinical plans respectively. The corresponding grade 2+ pneumonitis probability was 26.9% with the clinically-used plan and 24.6% with the functional plan (8.5% reduction). The V20-based grade 2+ pneumonitis probability was 23.7% with the clinically-used plan and reduced to 19.6% with the functional plan (20.9% reduction). Conclusion: Our results revealed a reduction of 9–20% in complication probability with functional planning. To our knowledge this is the first study to apply complication probability to convert dosimetric results to toxicity improvement. The results presented in the current work provide seminal data for prospective clinical trials in functional avoidance. YV discloses funding from State of Colorado. TY discloses National Lung Cancer Partnership; Young Investigator Research grant.« less

Azimuthally invariant Mueller-matrix mapping of biological optically anisotropic network

NASA Astrophysics Data System (ADS)

Ushenko, Yu. O.; Vanchuliak, O.; Bodnar, G. B.; Ushenko, V. O.; Grytsyuk, M.; Pavlyukovich, N.; Pavlyukovich, O. V.; Antonyuk, O.

2017-09-01

A new technique of Mueller-matrix mapping of polycrystalline structure of histological sections of biological tissues is suggested. The algorithms of reconstruction of distribution of parameters of linear and circular dichroism of histological sections liver tissue of mice with different degrees of severity of diabetes are found. The interconnections between such distributions and parameters of linear and circular dichroism of liver of mice tissue histological sections are defined. The comparative investigations of coordinate distributions of parameters of amplitude anisotropy formed by Liver tissue with varying severity of diabetes (10 days and 24 days) are performed. The values and ranges of change of the statistical (moments of the 1st - 4th order) parameters of coordinate distributions of the value of linear and circular dichroism are defined. The objective criteria of cause of the degree of severity of the diabetes differentiation are determined.

Geostatistical applications in environmental remediation

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

Stewart, R.N.; Purucker, S.T.; Lyon, B.F.

1995-02-01

Geostatistical analysis refers to a collection of statistical methods for addressing data that vary in space. By incorporating spatial information into the analysis, geostatistics has advantages over traditional statistical analysis for problems with a spatial context. Geostatistics has a history of success in earth science applications, and its popularity is increasing in other areas, including environmental remediation. Due to recent advances in computer technology, geostatistical algorithms can be executed at a speed comparable to many standard statistical software packages. When used responsibly, geostatistics is a systematic and defensible tool can be used in various decision frameworks, such as the Datamore » Quality Objectives (DQO) process. At every point in the site, geostatistics can estimate both the concentration level and the probability or risk of exceeding a given value. Using these probability maps can assist in identifying clean-up zones. Given any decision threshold and an acceptable level of risk, the probability maps identify those areas that are estimated to be above or below the acceptable risk. Those areas that are above the threshold are of the most concern with regard to remediation. In addition to estimating clean-up zones, geostatistics can assist in designing cost-effective secondary sampling schemes. Those areas of the probability map with high levels of estimated uncertainty are areas where more secondary sampling should occur. In addition, geostatistics has the ability to incorporate soft data directly into the analysis. These data include historical records, a highly correlated secondary contaminant, or expert judgment. The role of geostatistics in environmental remediation is a tool that in conjunction with other methods can provide a common forum for building consensus.« less

Variation of mutational burden in healthy human tissues suggests non-random strand segregation and allows measuring somatic mutation rates.

PubMed

Werner, Benjamin; Sottoriva, Andrea

2018-06-01

The immortal strand hypothesis poses that stem cells could produce differentiated progeny while conserving the original template strand, thus avoiding accumulating somatic mutations. However, quantitating the extent of non-random DNA strand segregation in human stem cells remains difficult in vivo. Here we show that the change of the mean and variance of the mutational burden with age in healthy human tissues allows estimating strand segregation probabilities and somatic mutation rates. We analysed deep sequencing data from healthy human colon, small intestine, liver, skin and brain. We found highly effective non-random DNA strand segregation in all adult tissues (mean strand segregation probability: 0.98, standard error bounds (0.97,0.99)). In contrast, non-random strand segregation efficiency is reduced to 0.87 (0.78,0.88) in neural tissue during early development, suggesting stem cell pool expansions due to symmetric self-renewal. Healthy somatic mutation rates differed across tissue types, ranging from 3.5 × 10-9/bp/division in small intestine to 1.6 × 10-7/bp/division in skin.

Influence of contact force on voltage mapping: A combined magnetic resonance imaging and electroanatomic mapping study in patients with tetralogy of Fallot.

PubMed

Teijeira-Fernandez, Elvis; Cochet, Hubert; Bourier, Felix; Takigawa, Masateru; Cheniti, Ghassen; Thompson, Nathaniel; Frontera, Antonio; Camaioni, Claudia; Massouille, Gregoire; Jalal, Zakaria; Derval, Nicolas; Iriart, Xavier; Denis, Arnaud; Hocini, Meleze; Haissaguerre, Michel; Jais, Pierre; Thambo, Jean-Benoit; Sacher, Frederic

2018-03-20

Voltage criteria for ventricular mapping have been obtained from small series of patients and prioritizing high specificity. The purpose of this study was to analyse the potential influence of contact force (CF) on voltage mapping and to define voltage cutoff values for right ventricular (RV) scar using the tetralogy of Fallot as a model of transmural RV scar and magnetic resonance imaging (MRI) as reference. Fourteen patients (age 32.6 ± 14.3 years; 5 female) with repaired tetralogy of Fallot underwent high-resolution cardiac MRI (1.25 × 1.25 × 2.5 mm). Scar, defined as pixels with intensity >50% maximum, was mapped over the RV geometry and merged within the CARTO system to RV endocardial voltage maps acquired using a 3.5-mm ablation catheter with CF technology (SmartTouch, Biosense Webster). In total, 2446 points were analyzed, 915 within scars and 1531 in healthy tissue according to MRI. CF correlated to unipolar (ρ = 0.186; P <.001) and bipolar voltage in healthy tissue (ρ = 0.245; P <.001) and in scar tissue. Receiver operating characteristic curve analysis excluding points with very low CF (<5g) identified optimal voltage cutoffs of 5.19 mV for unipolar voltage and 1.76 mV for bipolar voltage, yielding sensitivity/specificity of 0.89/0.85 and 0.9/0.9, respectively. CF is an important factor to be taken into account for voltage mapping. If good CF is applied, unipolar and bipolar voltage cutoffs of 5.19 mV and 1.76 mV are optimal for identifying RV scar on endocardial mapping with the SmartTouch catheter. Data on the diagnostic accuracy of different voltage cutoff values are provided. Copyright © 2018 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Polarization-interference mapping of biological fluids polycrystalline films in differentiation of weak changes of optical anisotropy

NASA Astrophysics Data System (ADS)

Ushenko, V. O.; Vanchuliak, O.; Sakhnovskiy, M. Y.; Dubolazov, O. V.; Grygoryshyn, P.; Soltys, I. V.; Olar, O. V.; Antoniv, A.

2017-09-01

The theoretical background of the azimuthally stable method of polarization-interference mapping of the histological sections of the biopsy of the prostate tissue on the basis of the spatial frequency selection of the mechanisms of linear and circular birefringence is presented. The diagnostic application of a new correlation parameter - complex degree of mutual anisotropy - is analytically substantiated. The method of measuring coordinate distributions of complex degree of mutual anisotropy with further spatial filtration of their high- and low-frequency components is developed. The interconnections of such distributions with parameters of linear and circular birefringence of prostate tissue histological sections are found. The objective criteria of differentiation of benign and malignant conditions of prostate tissue are determined.

Southern pine beetle infestation probability mapping using weights of evidence analysis

Treesearch

Jason B. Grogan; David L. Kulhavy; James C. Kroll

2010-01-01

Weights of Evidence (WofE) spatial analysis was used to predict probability of southern pine beetle (Dendroctonus frontalis) (SPB) infestation in Angelina, Nacogdoches, San Augustine and Shelby Co., TX. Thematic data derived from Landsat imagery (1974–2002 Landsat 1–7) were used. Data layers included: forest covertype, forest age, forest patch size...

Extinction time of a stochastic predator-prey model by the generalized cell mapping method

NASA Astrophysics Data System (ADS)

Han, Qun; Xu, Wei; Hu, Bing; Huang, Dongmei; Sun, Jian-Qiao

2018-03-01

The stochastic response and extinction time of a predator-prey model with Gaussian white noise excitations are studied by the generalized cell mapping (GCM) method based on the short-time Gaussian approximation (STGA). The methods for stochastic response probability density functions (PDFs) and extinction time statistics are developed. The Taylor expansion is used to deal with non-polynomial nonlinear terms of the model for deriving the moment equations with Gaussian closure, which are needed for the STGA in order to compute the one-step transition probabilities. The work is validated with direct Monte Carlo simulations. We have presented the transient responses showing the evolution from a Gaussian initial distribution to a non-Gaussian steady-state one. The effects of the model parameter and noise intensities on the steady-state PDFs are discussed. It is also found that the effects of noise intensities on the extinction time statistics are opposite to the effects on the limit probability distributions of the survival species.

A geometrical shift results in erroneous appearance of low frequency tissue eddy current induced phase maps.

PubMed

Mandija, Stefano; van Lier, Astrid L H M W; Katscher, Ulrich; Petrov, Petar I; Neggers, Sebastian F W; Luijten, Peter R; van den Berg, Cornelis A T

2016-09-01

Knowledge on low frequency (LF) tissue conductivity is relevant for various biomedical purposes. To obtain this information, LF phase maps arising from time-varying imaging gradients have been demonstrated to create a LF conductivity contrast. Essential in this methodology is the subtraction of phase images acquired with opposite gradient polarities to separate LF and RF phase effects. Here we demonstrate how sensitive these subtractions are with respect to geometrical distortions. The effect of geometrical distortions on LF phase maps is mathematically defined. After quantifying typical geometrical distortions, their effects on LF phase maps are evaluated using conductive phantoms. For validation, electromagnetic simulations of LF phase maps were performed. Even sub-voxel distortions of 10% of the voxel size, measured for a typical LF MR sequence, cause leakage of RF phase into LF phase of several milli-radians, leading to a misleading pattern of LF phase maps. This leakage is mathematically confirmed, while simulations indicate that the expected LF phase should be in order of micro-radians. The conductivity scaling of LF phase maps is attributable to the RF phase leakage, thus dependent on the RF conductivity. In fact, simulations show that the LF phase is not measurable. Magn Reson Med 76:905-912, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Assignment of functional activations to probabilistic cytoarchitectonic areas revisited.

PubMed

Eickhoff, Simon B; Paus, Tomas; Caspers, Svenja; Grosbras, Marie-Helene; Evans, Alan C; Zilles, Karl; Amunts, Katrin

2007-07-01

Probabilistic cytoarchitectonic maps in standard reference space provide a powerful tool for the analysis of structure-function relationships in the human brain. While these microstructurally defined maps have already been successfully used in the analysis of somatosensory, motor or language functions, several conceptual issues in the analysis of structure-function relationships still demand further clarification. In this paper, we demonstrate the principle approaches for anatomical localisation of functional activations based on probabilistic cytoarchitectonic maps by exemplary analysis of an anterior parietal activation evoked by visual presentation of hand gestures. After consideration of the conceptual basis and implementation of volume or local maxima labelling, we comment on some potential interpretational difficulties, limitations and caveats that could be encountered. Extending and supplementing these methods, we then propose a supplementary approach for quantification of structure-function correspondences based on distribution analysis. This approach relates the cytoarchitectonic probabilities observed at a particular functionally defined location to the areal specific null distribution of probabilities across the whole brain (i.e., the full probability map). Importantly, this method avoids the need for a unique classification of voxels to a single cortical area and may increase the comparability between results obtained for different areas. Moreover, as distribution-based labelling quantifies the "central tendency" of an activation with respect to anatomical areas, it will, in combination with the established methods, allow an advanced characterisation of the anatomical substrates of functional activations. Finally, the advantages and disadvantages of the various methods are discussed, focussing on the question of which approach is most appropriate for a particular situation.

Flood-inundation maps for a 15-mile reach of the Kalamazoo River from Marshall to Battle Creek, Michigan, 2010

USGS Publications Warehouse

Hoard, C.J.; Fowler, K.K.; Kim, M.H.; Menke, C.D.; Morlock, S.E.; Peppler, M.C.; Rachol, C.M.; Whitehead, M.T.

2010-01-01

Digital flood-inundation maps for a 15-mile reach of the Kalamazoo River from Marshall to Battle Creek, Michigan, were created by the U.S. Geological Survey (USGS) in cooperation with the U.S. Environmental Protection Agency to help guide remediation efforts following a crude-oil spill on July 25, 2010. The spill happened on Talmadge Creek, a tributary of the Kalamazoo River near Marshall, during a flood. The floodwaters transported the spilled oil down the Kalamazoo River and deposited oil in impoundments and on the surfaces of islands and flood plains. Six flood-inundation maps were constructed corresponding to the flood stage (884.09 feet) coincident with the oil spill on July 25, 2010, as well as for floods with annual exceedance probabilities of 0.2, 1, 2, 4, and 10 percent. Streamflow at the USGS streamgage at Marshall, Michigan (USGS site ID 04103500), was used to calculate the flood probabilities. From August 13 to 18, 2010, 35 channel cross sections, 17 bridges and 1 dam were surveyed. These data were used to construct a water-surface profile for the July 25, 2010, flood by use of a one-dimensional step-backwater model. The calibrated model was used to estimate water-surface profiles for other flood probabilities. The resulting six flood-inundation maps were created with a geographic information system by combining flood profiles with a 1.2-foot vertical and 10-foot horizontal resolution digital elevation model derived from Light Detection and Ranging data.

Quantifying volcanic hazard at Campi Flegrei caldera (Italy) with uncertainty assessment: 2. Pyroclastic density current invasion maps

NASA Astrophysics Data System (ADS)

Neri, Augusto; Bevilacqua, Andrea; Esposti Ongaro, Tomaso; Isaia, Roberto; Aspinall, Willy P.; Bisson, Marina; Flandoli, Franco; Baxter, Peter J.; Bertagnini, Antonella; Iannuzzi, Enrico; Orsucci, Simone; Pistolesi, Marco; Rosi, Mauro; Vitale, Stefano

2015-04-01

Campi Flegrei (CF) is an example of an active caldera containing densely populated settlements at very high risk of pyroclastic density currents (PDCs). We present here an innovative method for assessing background spatial PDC hazard in a caldera setting with probabilistic invasion maps conditional on the occurrence of an explosive event. The method encompasses the probabilistic assessment of potential vent opening positions, derived in the companion paper, combined with inferences about the spatial density distribution of PDC invasion areas from a simplified flow model, informed by reconstruction of deposits from eruptions in the last 15 ka. The flow model describes the PDC kinematics and accounts for main effects of topography on flow propagation. Structured expert elicitation is used to incorporate certain sources of epistemic uncertainty, and a Monte Carlo approach is adopted to produce a set of probabilistic hazard maps for the whole CF area. Our findings show that, in case of eruption, almost the entire caldera is exposed to invasion with a mean probability of at least 5%, with peaks greater than 50% in some central areas. Some areas outside the caldera are also exposed to this danger, with mean probabilities of invasion of the order of 5-10%. Our analysis suggests that these probability estimates have location-specific uncertainties which can be substantial. The results prove to be robust with respect to alternative elicitation models and allow the influence on hazard mapping of different sources of uncertainty, and of theoretical and numerical assumptions, to be quantified.

The "Clinton" sands in Canton, Dover, Massillon, and Navarre quadrangles, Ohio

USGS Publications Warehouse

Pepper, James Franklin; De Witt, Wallace; Everhart, Gail M.

1953-01-01

The Canton, Dover, Massillon, and Navarre quadrangles cover about 880 square miles in eastern Ohio. Canton is the largest city in the mapped area. In these four quadrangles, the well drillers generally recognize three "Clinton" sands - in descending order, the "stray Clinton", the "red Clinton", and the "white Clinton". The Clinton sands of Ohio are of early Silurian age and probably correlate with the middle and upper part of the Albion sandstone in the Niagara gorge section in western New York.The study of drillers' logs and examination of well samples show that of the three so-called Clinton sands, the red is most readily recognized. The "Packer shell", a probable equivalent of the Clinton formation of New York, and the Queenston shale - the drillers' "red Medina" - are also good units for short distance correlations.Each of the Clinton sands consists of a thin layer that contains long narrow lenses of thicker sand. Although the pattern of the trend of the lenses varies for each of the Clinton sands, the trend generally is westward across the mapped area. It is thought that these lenses represent deposition in channels, probably offshore from a large delta.Production of gas and oil from the so-called Clinton apparently is closely related to the sorting, porosity, and permeability of the sand. Stratigraphic traps contain the oil or gas, and structure appears to be relatively unimportant in localizing the accumulation of the petroleum.East of the mapped area, the Clinton sands have not produced oil or gas in commercial quantities. Several parts of the mapped area may hold additional amounts of gas.

Three-Dimensional Gene Map of Cancer Cell Types: Structural Entropy Minimisation Principle for Defining Tumour Subtypes

PubMed Central

Li, Angsheng; Yin, Xianchen; Pan, Yicheng

2016-01-01

In this study, we propose a method for constructing cell sample networks from gene expression profiles, and a structural entropy minimisation principle for detecting natural structure of networks and for identifying cancer cell subtypes. Our method establishes a three-dimensional gene map of cancer cell types and subtypes. The identified subtypes are defined by a unique gene expression pattern, and a three-dimensional gene map is established by defining the unique gene expression pattern for each identified subtype for cancers, including acute leukaemia, lymphoma, multi-tissue, lung cancer and healthy tissue. Our three-dimensional gene map demonstrates that a true tumour type may be divided into subtypes, each defined by a unique gene expression pattern. Clinical data analyses demonstrate that most cell samples of an identified subtype share similar survival times, survival indicators and International Prognostic Index (IPI) scores and indicate that distinct subtypes identified by our algorithms exhibit different overall survival times, survival ratios and IPI scores. Our three-dimensional gene map establishes a high-definition, one-to-one map between the biologically and medically meaningful tumour subtypes and the gene expression patterns, and identifies remarkable cells that form singleton submodules. PMID:26842724

Accurate and quantitative polarization-sensitive OCT by unbiased birefringence estimator with noise-stochastic correction

NASA Astrophysics Data System (ADS)

Kasaragod, Deepa; Sugiyama, Satoshi; Ikuno, Yasushi; Alonso-Caneiro, David; Yamanari, Masahiro; Fukuda, Shinichi; Oshika, Tetsuro; Hong, Young-Joo; Li, En; Makita, Shuichi; Miura, Masahiro; Yasuno, Yoshiaki

2016-03-01

Polarization sensitive optical coherence tomography (PS-OCT) is a functional extension of OCT that contrasts the polarization properties of tissues. It has been applied to ophthalmology, cardiology, etc. Proper quantitative imaging is required for a widespread clinical utility. However, the conventional method of averaging to improve the signal to noise ratio (SNR) and the contrast of the phase retardation (or birefringence) images introduce a noise bias offset from the true value. This bias reduces the effectiveness of birefringence contrast for a quantitative study. Although coherent averaging of Jones matrix tomography has been widely utilized and has improved the image quality, the fundamental limitation of nonlinear dependency of phase retardation and birefringence to the SNR was not overcome. So the birefringence obtained by PS-OCT was still not accurate for a quantitative imaging. The nonlinear effect of SNR to phase retardation and birefringence measurement was previously formulated in detail for a Jones matrix OCT (JM-OCT) [1]. Based on this, we had developed a maximum a-posteriori (MAP) estimator and quantitative birefringence imaging was demonstrated [2]. However, this first version of estimator had a theoretical shortcoming. It did not take into account the stochastic nature of SNR of OCT signal. In this paper, we present an improved version of the MAP estimator which takes into account the stochastic property of SNR. This estimator uses a probability distribution function (PDF) of true local retardation, which is proportional to birefringence, under a specific set of measurements of the birefringence and SNR. The PDF was pre-computed by a Monte-Carlo (MC) simulation based on the mathematical model of JM-OCT before the measurement. A comparison between this new MAP estimator, our previous MAP estimator [2], and the standard mean estimator is presented. The comparisons are performed both by numerical simulation and in vivo measurements of anterior and posterior eye segment as well as in skin imaging. The new estimator shows superior performance and also shows clearer image contrast.

Automatic bladder segmentation from CT images using deep CNN and 3D fully connected CRF-RNN.

PubMed

Xu, Xuanang; Zhou, Fugen; Liu, Bo

2018-03-19

Automatic approach for bladder segmentation from computed tomography (CT) images is highly desirable in clinical practice. It is a challenging task since the bladder usually suffers large variations of appearance and low soft-tissue contrast in CT images. In this study, we present a deep learning-based approach which involves a convolutional neural network (CNN) and a 3D fully connected conditional random fields recurrent neural network (CRF-RNN) to perform accurate bladder segmentation. We also propose a novel preprocessing method, called dual-channel preprocessing, to further advance the segmentation performance of our approach. The presented approach works as following: first, we apply our proposed preprocessing method on the input CT image and obtain a dual-channel image which consists of the CT image and an enhanced bladder density map. Second, we exploit a CNN to predict a coarse voxel-wise bladder score map on this dual-channel image. Finally, a 3D fully connected CRF-RNN refines the coarse bladder score map and produce final fine-localized segmentation result. We compare our approach to the state-of-the-art V-net on a clinical dataset. Results show that our approach achieves superior segmentation accuracy, outperforming the V-net by a significant margin. The Dice Similarity Coefficient of our approach (92.24%) is 8.12% higher than that of the V-net. Moreover, the bladder probability maps performed by our approach present sharper boundaries and more accurate localizations compared with that of the V-net. Our approach achieves higher segmentation accuracy than the state-of-the-art method on clinical data. Both the dual-channel processing and the 3D fully connected CRF-RNN contribute to this improvement. The united deep network composed of the CNN and 3D CRF-RNN also outperforms a system where the CRF model acts as a post-processing method disconnected from the CNN.

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

Engstroem, K; Casares-Magaz, O; Muren, L

Purpose: Multi-parametric MRI (mp-MRI) is being introduced in radiotherapy (RT) of prostate cancer, including for tumour delineation in focal boosting strategies. We recently developed an image-based tumour control probability model, based on cell density distributions derived from apparent diffusion coefficient (ADC) maps. Beyond tumour volume and cell densities, tumour hypoxia is also an important determinant of RT response. Since tissue perfusion from mp-MRI has been related to hypoxia we have explored the patterns of ADC and perfusion maps, and the relations between them, inside and outside prostate index lesions. Methods: ADC and perfusion maps from 20 prostate cancer patients weremore » used, with the prostate and index lesion delineated by a dedicated uro-radiologist. To reduce noise, the maps were averaged over a 3×3×3 voxel cube. Associations between different ADC and perfusion histogram parameters within the prostate, inside and outside the index lesion, were evaluated with the Pearson’s correlation coefficient. In the voxel-wise analysis, scatter plots of ADC vs perfusion were analysed for voxels in the prostate, inside and outside of the index lesion, again with the associations quantified with the Pearson’s correlation coefficient. Results: Overall ADC was lower inside the index lesion than in the normal prostate as opposed to ktrans that was higher inside the index lesion than outside. In the histogram analysis, the minimum ktrans was significantly correlated with the maximum ADC (Pearson=0.47; p=0.03). At the voxel level, 15 of the 20 cases had a statistically significant inverse correlation between ADC and perfusion inside the index lesion; ten of the cases had a Pearson < −0.4. Conclusion: The minimum value of ktrans across the tumour was correlated to the maximum ADC. However, on the voxel level, the ‘local’ ktrans in the index lesion is inversely (i.e. negatively) correlated to the ‘local’ ADC in most patients. Research agreement with Varian Medical Systems, not related to the work presented in this abstract.« less

Digital tissue and what it may reveal about the brain.

PubMed

Morgan, Josh L; Lichtman, Jeff W

2017-10-30

Imaging as a means of scientific data storage has evolved rapidly over the past century from hand drawings, to photography, to digital images. Only recently can sufficiently large datasets be acquired, stored, and processed such that tissue digitization can actually reveal more than direct observation of tissue. One field where this transformation is occurring is connectomics: the mapping of neural connections in large volumes of digitized brain tissue.

Maps Showing Seismic Landslide Hazards in Anchorage, Alaska

USGS Publications Warehouse

Jibson, Randall W.; Michael, John A.

2009-01-01

The devastating landslides that accompanied the great 1964 Alaska earthquake showed that seismically triggered landslides are one of the greatest geologic hazards in Anchorage. Maps quantifying seismic landslide hazards are therefore important for planning, zoning, and emergency-response preparation. The accompanying maps portray seismic landslide hazards for the following conditions: (1) deep, translational landslides, which occur only during great subduction-zone earthquakes that have return periods of =~300-900 yr; (2) shallow landslides for a peak ground acceleration (PGA) of 0.69 g, which has a return period of 2,475 yr, or a 2 percent probability of exceedance in 50 yr; and (3) shallow landslides for a PGA of 0.43 g, which has a return period of 475 yr, or a 10 percent probability of exceedance in 50 yr. Deep, translational landslide hazard zones were delineated based on previous studies of such landslides, with some modifications based on field observations of locations of deep landslides. Shallow-landslide hazards were delineated using a Newmark-type displacement analysis for the two probabilistic ground motions modeled.

Maps showing seismic landslide hazards in Anchorage, Alaska

USGS Publications Warehouse

Jibson, Randall W.

2014-01-01

The devastating landslides that accompanied the great 1964 Alaska earthquake showed that seismically triggered landslides are one of the greatest geologic hazards in Anchorage. Maps quantifying seismic landslide hazards are therefore important for planning, zoning, and emergency-response preparation. The accompanying maps portray seismic landslide hazards for the following conditions: (1) deep, translational landslides, which occur only during great subduction-zone earthquakes that have return periods of =300-900 yr; (2) shallow landslides for a peak ground acceleration (PGA) of 0.69 g, which has a return period of 2,475 yr, or a 2 percent probability of exceedance in 50 yr; and (3) shallow landslides for a PGA of 0.43 g, which has a return period of 475 yr, or a 10 percent probability of exceedance in 50 yr. Deep, translational landslide hazards were delineated based on previous studies of such landslides, with some modifications based on field observations of locations of deep landslides. Shallow-landslide hazards were delineated using a Newmark-type displacement analysis for the two probabilistic ground motions modeled.

Improving deep convolutional neural networks with mixed maxout units

PubMed Central

Liu, Fu-xian; Li, Long-yue

2017-01-01

Motivated by insights from the maxout-units-based deep Convolutional Neural Network (CNN) that “non-maximal features are unable to deliver” and “feature mapping subspace pooling is insufficient,” we present a novel mixed variant of the recently introduced maxout unit called a mixout unit. Specifically, we do so by calculating the exponential probabilities of feature mappings gained by applying different convolutional transformations over the same input and then calculating the expected values according to their exponential probabilities. Moreover, we introduce the Bernoulli distribution to balance the maximum values with the expected values of the feature mappings subspace. Finally, we design a simple model to verify the pooling ability of mixout units and a Mixout-units-based Network-in-Network (NiN) model to analyze the feature learning ability of the mixout models. We argue that our proposed units improve the pooling ability and that mixout models can achieve better feature learning and classification performance. PMID:28727737

SU-E-J-233: Effect of Brachytherapy Seed Artifacts in T2 and Proton Density Maps in MR Images

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

Mashouf, S; University of Toronto, Dept of Radiation Oncology, Toronto, Ontario; Fatemi-Ardekani, A

Purpose: This study aims at investigating the influence of brachytherapy seeds on T2 and proton density (PD) maps generated from MR images. Proton density maps can be used to extract water content. Since dose absorbed in tissue surrounding low energy brachytherapy seeds are highly influenced by tissue composition, knowing the water content is a first step towards implementing a heterogeneity correction algorithm using MR images. Methods: An LDR brachytherapy (IsoAid Advantage Pd-103) seed was placed in the middle of an agar-based gel phantom and imaged using a 3T Philips MR scanner with a 168-channel head coil. A multiple echo sequencemore » with TE=20, 40, 60, 80, 100 (ms) with large repetition time (TR=6259ms) was used to extract T2 and PD maps. Results: Seed artifacts were considerably reduced on T2 maps compared to PD maps. The variation of PD around the mean was obtained as −97% to 125% (±1%) while for T2 it was recorded as −71% to 24% (±1%). Conclusion: PD maps which are required for heterogeneity corrections are susceptible to artifacts from seeds. Seed artifacts on T2 maps, however, are significantly reduced due to not being sensitive to B0 field variation.« less

Cardiac tissue slices: preparation, handling, and successful optical mapping.

PubMed

Wang, Ken; Lee, Peter; Mirams, Gary R; Sarathchandra, Padmini; Borg, Thomas K; Gavaghan, David J; Kohl, Peter; Bollensdorff, Christian

2015-05-01

Cardiac tissue slices are becoming increasingly popular as a model system for cardiac electrophysiology and pharmacology research and development. Here, we describe in detail the preparation, handling, and optical mapping of transmembrane potential and intracellular free calcium concentration transients (CaT) in ventricular tissue slices from guinea pigs and rabbits. Slices cut in the epicardium-tangential plane contained well-aligned in-slice myocardial cell strands ("fibers") in subepicardial and midmyocardial sections. Cut with a high-precision slow-advancing microtome at a thickness of 350 to 400 μm, tissue slices preserved essential action potential (AP) properties of the precutting Langendorff-perfused heart. We identified the need for a postcutting recovery period of 36 min (guinea pig) and 63 min (rabbit) to reach 97.5% of final steady-state values for AP duration (APD) (identified by exponential fitting). There was no significant difference between the postcutting recovery dynamics in slices obtained using 2,3-butanedione 2-monoxime or blebistatin as electromechanical uncouplers during the cutting process. A rapid increase in APD, seen after cutting, was caused by exposure to ice-cold solution during the slicing procedure, not by tissue injury, differences in uncouplers, or pH-buffers (bicarbonate; HEPES). To characterize intrinsic patterns of CaT, AP, and conduction, a combination of multipoint and field stimulation should be used to avoid misinterpretation based on source-sink effects. In summary, we describe in detail the preparation, mapping, and data analysis approaches for reproducible cardiac tissue slice-based investigations into AP and CaT dynamics. Copyright © 2015 the American Physiological Society.

Cardiac tissue slices: preparation, handling, and successful optical mapping

PubMed Central

Wang, Ken; Lee, Peter; Mirams, Gary R.; Sarathchandra, Padmini; Borg, Thomas K.; Gavaghan, David J.; Kohl, Peter

2015-01-01

Cardiac tissue slices are becoming increasingly popular as a model system for cardiac electrophysiology and pharmacology research and development. Here, we describe in detail the preparation, handling, and optical mapping of transmembrane potential and intracellular free calcium concentration transients (CaT) in ventricular tissue slices from guinea pigs and rabbits. Slices cut in the epicardium-tangential plane contained well-aligned in-slice myocardial cell strands (“fibers”) in subepicardial and midmyocardial sections. Cut with a high-precision slow-advancing microtome at a thickness of 350 to 400 μm, tissue slices preserved essential action potential (AP) properties of the precutting Langendorff-perfused heart. We identified the need for a postcutting recovery period of 36 min (guinea pig) and 63 min (rabbit) to reach 97.5% of final steady-state values for AP duration (APD) (identified by exponential fitting). There was no significant difference between the postcutting recovery dynamics in slices obtained using 2,3-butanedione 2-monoxime or blebistatin as electromechanical uncouplers during the cutting process. A rapid increase in APD, seen after cutting, was caused by exposure to ice-cold solution during the slicing procedure, not by tissue injury, differences in uncouplers, or pH-buffers (bicarbonate; HEPES). To characterize intrinsic patterns of CaT, AP, and conduction, a combination of multipoint and field stimulation should be used to avoid misinterpretation based on source-sink effects. In summary, we describe in detail the preparation, mapping, and data analysis approaches for reproducible cardiac tissue slice-based investigations into AP and CaT dynamics. PMID:25595366

The challenge of modelling and mapping the future distribution and impact of invasive alien species

Treesearch

Robert C. Venette

2015-01-01

Invasions from alien species can jeopardize the economic, environmental or social benefits derived from biological systems. Biosecurity measures seek to protect those systems from accidental or intentional introductions of species that might become injurious. Pest risk maps convey how the probability of invasion by an alien species or the potential consequences of that...

Functional Reorganization in the Developing Lexicon: Separable and Changing Influences of Lexical and Phonological Variables on Children's Fast-Mapping

ERIC Educational Resources Information Center

McKean, Cristina; Letts, Carolyn; Howard, David

2013-01-01

Neighbourhood Density (ND) and Phonotactic Probability (PP) influence word learning in children. This influence appears to change over development but the separate developmental trajectories of influence of PP and ND on word learning have not previously been mapped. This study examined the cross-sectional developmental trajectories of influence of…

Mapping the Distribution and Biomass of Emergent Aquatic Plants in the Sacramento-San Joaquin River Delta of California Using Landsat Imagery Analysis

NASA Technical Reports Server (NTRS)

Potter, Christopher

2015-01-01

This study evaluated the cost-effective and timely use of Landsat imagery to map and monitor emergent aquatic plant biomass and to filter satellite image products for the most probable locations of water hyacinth coverage in the Delta based on field observations collected immediately after satellite image acquisition.

A Violation of the Conditional Independence Assumption in the Two-High-Threshold Model of Recognition Memory

ERIC Educational Resources Information Center

Chen, Tina; Starns, Jeffrey J.; Rotello, Caren M.

2015-01-01

The 2-high-threshold (2HT) model of recognition memory assumes that test items result in distinct internal states: they are either detected or not, and the probability of responding at a particular confidence level that an item is "old" or "new" depends on the state-response mapping parameters. The mapping parameters are…

Brain Injury Lesion Imaging Using Preconditioned Quantitative Susceptibility Mapping without Skull Stripping.

PubMed

Soman, S; Liu, Z; Kim, G; Nemec, U; Holdsworth, S J; Main, K; Lee, B; Kolakowsky-Hayner, S; Selim, M; Furst, A J; Massaband, P; Yesavage, J; Adamson, M M; Spincemallie, P; Moseley, M; Wang, Y

2018-04-01

Identifying cerebral microhemorrhage burden can aid in the diagnosis and management of traumatic brain injury, stroke, hypertension, and cerebral amyloid angiopathy. MR imaging susceptibility-based methods are more sensitive than CT for detecting cerebral microhemorrhage, but methods other than quantitative susceptibility mapping provide results that vary with field strength and TE, require additional phase maps to distinguish blood from calcification, and depict cerebral microhemorrhages as bloom artifacts. Quantitative susceptibility mapping provides universal quantification of tissue magnetic property without these constraints but traditionally requires a mask generated by skull-stripping, which can pose challenges at tissue interphases. We evaluated the preconditioned quantitative susceptibility mapping MR imaging method, which does not require skull-stripping, for improved depiction of brain parenchyma and pathology. Fifty-six subjects underwent brain MR imaging with a 3D multiecho gradient recalled echo acquisition. Mask-based quantitative susceptibility mapping images were created using a commonly used mask-based quantitative susceptibility mapping method, and preconditioned quantitative susceptibility images were made using precondition-based total field inversion. All images were reviewed by a neuroradiologist and a radiology resident. Ten subjects (18%), all with traumatic brain injury, demonstrated blood products on 3D gradient recalled echo imaging. All lesions were visible on preconditioned quantitative susceptibility mapping, while 6 were not visible on mask-based quantitative susceptibility mapping. Thirty-one subjects (55%) demonstrated brain parenchyma and/or lesions that were visible on preconditioned quantitative susceptibility mapping but not on mask-based quantitative susceptibility mapping. Six subjects (11%) demonstrated pons artifacts on preconditioned quantitative susceptibility mapping and mask-based quantitative susceptibility mapping; they were worse on preconditioned quantitative susceptibility mapping. Preconditioned quantitative susceptibility mapping MR imaging can bring the benefits of quantitative susceptibility mapping imaging to clinical practice without the limitations of mask-based quantitative susceptibility mapping, especially for evaluating cerebral microhemorrhage-associated pathologies, such as traumatic brain injury. © 2018 by American Journal of Neuroradiology.

Minimal entropy approximation for cellular automata

NASA Astrophysics Data System (ADS)

Fukś, Henryk

2014-02-01

We present a method for the construction of approximate orbits of measures under the action of cellular automata which is complementary to the local structure theory. The local structure theory is based on the idea of Bayesian extension, that is, construction of a probability measure consistent with given block probabilities and maximizing entropy. If instead of maximizing entropy one minimizes it, one can develop another method for the construction of approximate orbits, at the heart of which is the iteration of finite-dimensional maps, called minimal entropy maps. We present numerical evidence that the minimal entropy approximation sometimes outperforms the local structure theory in characterizing the properties of cellular automata. The density response curve for elementary CA rule 26 is used to illustrate this claim.

Identification of land degradation evidences in an organic farm using probability maps (Croatia)

NASA Astrophysics Data System (ADS)

Pereira, Paulo; Bogunovic, Igor; Estebaranz, Ferran

2017-04-01

Land degradation is a biophysical process with important impacts on society, economy and policy. Areas affected by land degradation do not provide services in quality and with capacity to full-field the communities that depends on them (Amaya-Romero et al., 2015; Beyene, 2015; Lanckriet et al., 2015). Agricultural activities are one of the main causes of land degradation (Kraaijvanger and Veldkamp, 2015), especially when they decrease soil organic matter (SOM), a crucial element for soil fertility. In temperate areas, the critical level of SOM concentration in agricultural soils is 3.4%. Below this level there is a potential decrease of soil quality (Loveland and Weeb, 2003). However, no previous work was carried out in other environments, such as the Mediterranean. The spatial distribution of potential degraded land is important to be identified and mapped, in order to identify the areas that need restoration (Brevik et al., 2016; Pereira et al., 2017). The aim of this work is to assess the spatial distribution of areas with evidences of land degradation (SOM bellow 3.4%) using probability maps in an organic farm located in Croatia. In order to find the best method, we compared several probability methods, such as Ordinary Kriging (OK), Simple Kriging (SK), Universal Kriging (UK), Indicator Kriging (IK), Probability Kriging (PK) and Disjunctive Kriging (DK). The study area is located on the Istria peninsula (45°3' N; 14°2' E), with a total area of 182 ha. One hundred eighty-two soil samples (0-30 cm) were collected during July of 2015 and SOM was assessed using wet combustion procedure. The assessment of the best probability method was carried out using leave one out cross validation method. The probability method with the lowest Root Mean Squared Error (RMSE) was the most accurate. The results showed that the best method to predict the probability of potential land degradation was SK with an RMSE of 0.635, followed by DK (RMSE=0.636), UK (RMSE=0.660), OK (RMSE=0.660), IK (RMSE=0.722) and PK (RMSE=1.661). According to the most accurate method, it is observed that the majority of the area studied has a high probability to be degraded. Measures are needed to restore this area. References Amaya-Romero, M., Abd-Elmabod, S., Munoz-Rojas, M., Castellano, G., Ceacero, C., Alvarez, S., Mendez, M., De la Rosa, D. (2015) Evaluating soil threats under climate change scenarios in the Andalusia region, Southern Spain. Land Degradation and Development, 26, 441-449. Beyene, F. (2015) Incentives and challenges in community based rangeland management: Evidence from Eastern Ethiopia. Land Degradation and Development, 26, 502-509. Brevik, E., Calzolari, C., Miller, B., Pereira, P., Kabala, C., Baumgarten, A., Jordán, A. (2016) Historical perspectives and future needs in soil mapping, classification and pedological modelling, Geoderma, 264, Part B, 256-274. Kraaijvanger, R., Veldkamp, T. (2015) Grain productivity, fertilizer response and nutrient balance of farming systems in Tigray, Ethiopia: A Multiprespective view in relation do soil fertility degradation. Land Degradation and Development, 26, 701-710. Lanckriet, S., Derudder, B., Naudts, J., Bauer, H., Deckers, J., Haile, M., Nyssen, J. (2015) A political ecology perspective of land degradation in the North Ethiopian Highlands. Land Degradation and Development, 26, 521-530. Loveland, P., Weeb, J. (2003) Is there a critical level of organic matter in the agricultural soils of temperate regions: a review. Soil & Tillage Research, 70, 1-18. Pereira, P., Brevik, E., Munoz-Rojas, M., Miller, B., Smetanova, A., Depellegrin, D., Misiune, I., Novara, A., Cerda, A. Soil mapping and process modelling for sustainable land management. In: Pereira, P., Brevik, E., Munoz-Rojas, M., Miller, B. (Eds.) Soil mapping and process modelling for sustainable land use management (Elsevier Publishing House) ISBN: 9780128052006

Direct Evaluation of MR-Derived Attenuation Correction Maps for PET/MR of the Mouse Myocardium

NASA Astrophysics Data System (ADS)

Evans, Eleanor; Buonincontri, Guido; Hawkes, Rob C.; Ansorge, Richard E.; Carpenter, T. Adrian; Sawiak, Stephen J.

2016-02-01

Attenuation correction (AC) must be applied to provide accurate measurements of PET tracer activity concentrations. Due to the limited space available in PET/MR scanners, MR-derived AC (MRAC) is used as a substitute for transmission source scanning. In preclinical PET/MR, there has been limited exploration of MRAC, as the magnitude of AC in murine imaging is much smaller than that required in clinical scans. We investigated if a simple 2 class (air and tissue) segmentation-based MRAC approach could provide adequate AC for mouse PET imaging. To construct the default MRAC μ maps, MR images were thresholded and segmented using ASIPRO software (Siemens Molecular Imaging), which defined the mouse body region as tissue with a uniform linear attenuation coefficient ( μ) of 0.095 cm - 1, and the background and lungs as air, with a μ value of 0 cm - 1. To correct for the misassignment of the lungs as air, two further MRAC μ maps were tested: 1) MRAC (tissue) approach, which changed the lung region designation from air to tissue ( μ = 0.095 cm - 1) and 2) MRAC (lung) approach, which treated the lungs as an additional tissue class, with a μ value of 0.032 cm - 1. All μ maps were then forward projected to create attenuation sinograms for image reconstruction. Standard uptake value (SUV) maps of the myocardium were derived for 10 mice with and without AC applied using gold standard transmission scans (TXAC), the 3 MRAC methods and PET emission scans (EmAC). All AC methods produced significantly different myocardial SUVs to those produced without AC when compared across the mouse group ( ). Similar ( ) SUV were derived with all AC methods, with the best agreement to TXAC achieved using the MRAC (tissue) method, giving a mean difference of 0.9±2.4% in myocardial SUV when compared across all mice. SUV differences of up to 40%, however, were seen in areas adjacent to the RF coil in images produced using all AC methods, except for TXAC. A 2 class MRAC approach can therefore provide acceptable AC for myocardial imaging in mice, although additional CT templates of coils and animals beds would be recommended to further improve image quantification.

Correction of Gradient Nonlinearity Bias in Quantitative Diffusion Parameters of Renal Tissue with Intra Voxel Incoherent Motion.

PubMed

Malyarenko, Dariya I; Pang, Yuxi; Senegas, Julien; Ivancevic, Marko K; Ross, Brian D; Chenevert, Thomas L

2015-12-01

Spatially non-uniform diffusion weighting bias due to gradient nonlinearity (GNL) causes substantial errors in apparent diffusion coefficient (ADC) maps for anatomical regions imaged distant from magnet isocenter. Our previously-described approach allowed effective removal of spatial ADC bias from three orthogonal DWI measurements for mono-exponential media of arbitrary anisotropy. The present work evaluates correction feasibility and performance for quantitative diffusion parameters of the two-component IVIM model for well-perfused and nearly isotropic renal tissue. Sagittal kidney DWI scans of a volunteer were performed on a clinical 3T MRI scanner near isocenter and offset superiorly. Spatially non-uniform diffusion weighting due to GNL resulted both in shift and broadening of perfusion-suppressed ADC histograms for off-center DWI relative to unbiased measurements close to isocenter. Direction-average DW-bias correctors were computed based on the known gradient design provided by vendor. The computed bias maps were empirically confirmed by coronal DWI measurements for an isotropic gel-flood phantom. Both phantom and renal tissue ADC bias for off-center measurements was effectively removed by applying pre-computed 3D correction maps. Comparable ADC accuracy was achieved for corrections of both b -maps and DWI intensities in presence of IVIM perfusion. No significant bias impact was observed for IVIM perfusion fraction.

Correction of Gradient Nonlinearity Bias in Quantitative Diffusion Parameters of Renal Tissue with Intra Voxel Incoherent Motion

PubMed Central

Malyarenko, Dariya I.; Pang, Yuxi; Senegas, Julien; Ivancevic, Marko K.; Ross, Brian D.; Chenevert, Thomas L.

2015-01-01

Spatially non-uniform diffusion weighting bias due to gradient nonlinearity (GNL) causes substantial errors in apparent diffusion coefficient (ADC) maps for anatomical regions imaged distant from magnet isocenter. Our previously-described approach allowed effective removal of spatial ADC bias from three orthogonal DWI measurements for mono-exponential media of arbitrary anisotropy. The present work evaluates correction feasibility and performance for quantitative diffusion parameters of the two-component IVIM model for well-perfused and nearly isotropic renal tissue. Sagittal kidney DWI scans of a volunteer were performed on a clinical 3T MRI scanner near isocenter and offset superiorly. Spatially non-uniform diffusion weighting due to GNL resulted both in shift and broadening of perfusion-suppressed ADC histograms for off-center DWI relative to unbiased measurements close to isocenter. Direction-average DW-bias correctors were computed based on the known gradient design provided by vendor. The computed bias maps were empirically confirmed by coronal DWI measurements for an isotropic gel-flood phantom. Both phantom and renal tissue ADC bias for off-center measurements was effectively removed by applying pre-computed 3D correction maps. Comparable ADC accuracy was achieved for corrections of both b-maps and DWI intensities in presence of IVIM perfusion. No significant bias impact was observed for IVIM perfusion fraction. PMID:26811845

Analysis and inundation mapping of the April-May 2011 flood at selected locations in northern and eastern Arkansas and southern Missouri

USGS Publications Warehouse

Westerman, Drew A.; Merriman, Katherine R.; De Lanois, Jeanne L.; Berenbrock, Charles

2013-01-01

Precipitation that fell from April 19 through May 3, 2011, resulted in widespread flooding across northern and eastern Arkansas and southern Missouri. The first storm produced a total of approximately 16 inches of precipitation over an 8-day period, and the following storms produced as much as 12 inches of precipitation over a 2-day period. Moderate to major flooding occurred quickly along many streams within Arkansas and Missouri (including the Black, Cache, Illinois, St. Francis, and White Rivers) at levels that had not been seen since the historic 1927 floods. The 2011 flood claimed an estimated 21 lives in Arkansas and Missouri, and damage caused by the flooding resulted in a Federal Disaster Declaration for 59 Arkansas counties that received Federal or State assistance. To further the goal of documenting and understanding floods, the U.S. Geological Survey, in cooperation with the Federal Emergency Management Agency, the U.S. Army Corps of Engineers–Little Rock and Memphis Districts, and Arkansas Natural Resources Commission, conducted a study to summarize meteorological and hydrological conditions before the flood; computed flood-peak magnitudes for 39 streamgages; estimated annual exceedance probabilities for 37 of those streamgages; determined the joint probabilities for 11 streamgages paired to the Mississippi River at Helena, Arkansas, which refers to the probability that locations on two paired streams simultaneously experience floods of a magnitude greater than or equal to a given annual exceedance probability; collected high-water marks; constructed flood-peak inundation maps showing maximum flood extent and water depths; and summarized flood damages and effects. For the period of record used in this report, peak-of-record stage occurred at 24 of the 39 streamgages, and peak-of-record streamflow occurred at 13 of the 30 streamgages where streamflow was determined. Annual exceedance probabilities were estimated to be less than 0.5 percent at three streamgages. The joint probability values for streamgages paired with the Mississippi River at Helena, Ark., streamgage indicate a low probability of concurrent flooding with the paired streamgages. The inundation maps show the flood-peak extent and water depth of flooding for two stream reaches on the White River and two on the Black River; the vicinities of the communities of Holly Grove and Cotton Plant, Ark.; a reach of the White River that includes the crossing of Interstate 40 north of De Valls Bluff, Ark.; and the Tailwaters of Beaver Dam near Eureka Springs, Ark., Table Rock Dam near Branson, Mo., and Bull Shoals Dam near Flippin, Ark. The data and inundation maps can be used for flood response, recovery, and planning efforts by Federal, State, and local agencies.

Mercury Amalgam Diffusion in Human Teeth Probed Using Femtosecond LIBS.

PubMed

Bello, Liciane Toledo; da Ana, Patricia Aparecida; Santos, Dário; Krug, Francisco José; Zezell, Denise Maria; Vieira, Nilson Dias; Samad, Ricardo Elgul

2017-04-01

In this work the diffusion of mercury and other elements from amalgam tooth restorations through the surrounding dental tissue (dentin) was evaluated using femtosecond laser-induced breakdown spectroscopy (fs-LIBS). To achieve this, seven deciduous and eight permanent extracted human molar teeth with occlusal amalgam restorations were half-sectioned and analyzed using pulses from a femtosecond laser. The measurements were performed from the amalgam restoration along the amalgam/dentin interface to the apical direction. It was possible to observe the presence of metallic elements (silver, mercury, copper and tin) emission lines, as well as dental constituent ones, providing fingerprints of each material and comparable data for checking the consistence of the results. It was also shown that the elements penetration depth values in each tooth are usually similar and consistent, for both deciduous and permanent teeth, indicating that all the metals diffuse into the dentin by the same mechanism. We propose that this diffusion mechanism is mainly through liquid dragging inside the dentin tubules. The mercury diffused further in permanent teeth than in deciduous teeth, probably due to the longer diffusion times due to the age of the restorations. It was possible to conclude that the proposed femtosecond-LIBS system can detect the presence of metals in the dental tissue, among the tooth constituent elements, and map the distribution of endogenous and exogenous chemical elements, with a spatial resolution that can be brought under 100 µm.

Automated MRI Segmentation for Individualized Modeling of Current Flow in the Human Head

PubMed Central

Huang, Yu; Dmochowski, Jacek P.; Su, Yuzhuo; Datta, Abhishek; Rorden, Christopher; Parra, Lucas C.

2013-01-01

Objective High-definition transcranial direct current stimulation (HD-tDCS) and high-density electroencephalography (HD-EEG) require accurate models of current flow for precise targeting and current source reconstruction. At a minimum, such modeling must capture the idiosyncratic anatomy of brain, cerebrospinal fluid (CSF) and skull for each individual subject. Currently, the process to build such high-resolution individualized models from structural magnetic resonance images (MRI) requires labor-intensive manual segmentation, even when leveraging available automated segmentation tools. Also, accurate placement of many high-density electrodes on individual scalp is a tedious procedure. The goal was to develop fully automated techniques to reduce the manual effort in such a modeling process. Approach A fully automated segmentation technique based on Statical Parametric Mapping 8 (SPM8), including an improved tissue probability map (TPM) and an automated correction routine for segmentation errors, was developed, along with an automated electrode placement tool for high-density arrays. The performance of these automated routines was evaluated against results from manual segmentation on 4 healthy subjects and 7 stroke patients. The criteria include segmentation accuracy, the difference of current flow distributions in resulting HD-tDCS models and the optimized current flow intensities on cortical targets. Main results The segmentation tool can segment out not just the brain but also provide accurate results for CSF, skull and other soft tissues with a field of view (FOV) extending to the neck. Compared to manual results, automated segmentation deviates by only 7% and 18% for normal and stroke subjects, respectively. The predicted electric fields in the brain deviate by 12% and 29% respectively, which is well within the variability observed for various modeling choices. Finally, optimized current flow intensities on cortical targets do not differ significantly. Significance Fully automated individualized modeling may now be feasible for large-sample EEG research studies and tDCS clinical trials. PMID:24099977

Automated MRI segmentation for individualized modeling of current flow in the human head

NASA Astrophysics Data System (ADS)

Huang, Yu; Dmochowski, Jacek P.; Su, Yuzhuo; Datta, Abhishek; Rorden, Christopher; Parra, Lucas C.

2013-12-01

Objective. High-definition transcranial direct current stimulation (HD-tDCS) and high-density electroencephalography require accurate models of current flow for precise targeting and current source reconstruction. At a minimum, such modeling must capture the idiosyncratic anatomy of the brain, cerebrospinal fluid (CSF) and skull for each individual subject. Currently, the process to build such high-resolution individualized models from structural magnetic resonance images requires labor-intensive manual segmentation, even when utilizing available automated segmentation tools. Also, accurate placement of many high-density electrodes on an individual scalp is a tedious procedure. The goal was to develop fully automated techniques to reduce the manual effort in such a modeling process. Approach. A fully automated segmentation technique based on Statical Parametric Mapping 8, including an improved tissue probability map and an automated correction routine for segmentation errors, was developed, along with an automated electrode placement tool for high-density arrays. The performance of these automated routines was evaluated against results from manual segmentation on four healthy subjects and seven stroke patients. The criteria include segmentation accuracy, the difference of current flow distributions in resulting HD-tDCS models and the optimized current flow intensities on cortical targets.Main results. The segmentation tool can segment out not just the brain but also provide accurate results for CSF, skull and other soft tissues with a field of view extending to the neck. Compared to manual results, automated segmentation deviates by only 7% and 18% for normal and stroke subjects, respectively. The predicted electric fields in the brain deviate by 12% and 29% respectively, which is well within the variability observed for various modeling choices. Finally, optimized current flow intensities on cortical targets do not differ significantly.Significance. Fully automated individualized modeling may now be feasible for large-sample EEG research studies and tDCS clinical trials.

Contaminants in fish tissue from US lakes and reservoirs: A national probabilistic study

EPA Science Inventory

An unequal probability design was used to develop national estimates for 268 persistent, bioaccumulative, and toxic chemicals in fish tissue from lakes and reservoirs of the conterminous United States (excluding the Laurentian Great Lakes and Great Salt Lake). Predator (fillet) ...

Correlation of quantitative dual-energy computed tomography iodine maps and abdominal computed tomography perfusion measurements: are single-acquisition dual-energy computed tomography iodine maps more than a reduced-dose surrogate of conventional computed tomography perfusion?

PubMed

Stiller, Wolfram; Skornitzke, Stephan; Fritz, Franziska; Klauss, Miriam; Hansen, Jens; Pahn, Gregor; Grenacher, Lars; Kauczor, Hans-Ulrich

2015-10-01

Study objectives were the quantitative evaluation of whether conventional abdominal computed tomography (CT) perfusion measurements mathematically correlate with quantitative single-acquisition dual-energy CT (DECT) iodine concentration maps, the determination of the optimum time of acquisition for achieving maximum correlation, and the estimation of the potential for radiation exposure reduction when replacing conventional CT perfusion by single-acquisition DECT iodine concentration maps. Dual-energy CT perfusion sequences were dynamically acquired over 51 seconds (34 acquisitions every 1.5 seconds) in 24 patients with histologically verified pancreatic carcinoma using dual-source DECT at tube potentials of 80 kVp and 140 kVp. Using software developed in-house, perfusion maps were calculated from 80-kVp image series using the maximum slope model after deformable motion correction. In addition, quantitative iodine maps were calculated for each of the 34 DECT acquisitions per patient. Within a manual segmentation of the pancreas, voxel-by-voxel correlation between the perfusion map and each of the iodine maps was calculated for each patient to determine the optimum time of acquisition topt defined as the acquisition time of the iodine map with the highest correlation coefficient. Subsequently, regions of interest were placed inside the tumor and inside healthy pancreatic tissue, and correlation between mean perfusion values and mean iodine concentrations within these regions of interest at topt was calculated for the patient sample. The mean (SD) topt was 31.7 (5.4) seconds after the start of contrast agent injection. The mean (SD) perfusion values for healthy pancreatic and tumor tissues were 67.8 (26.7) mL per 100 mL/min and 43.7 (32.2) mL per 100 mL/min, respectively. At topt, the mean (SD) iodine concentrations were 2.07 (0.71) mg/mL in healthy pancreatic and 1.69 (0.98) mg/mL in tumor tissue, respectively. Overall, the correlation between perfusion values and iodine concentrations was high (0.77), with correlation of 0.89 in tumor and of 0.56 in healthy pancreatic tissue at topt. Comparing radiation exposure associated with a single DECT acquisition at topt (0.18 mSv) to that of an 80 kVp CT perfusion sequence (2.96 mSv) indicates that an average reduction of Deff by 94% could be achieved by replacing conventional CT perfusion with a single-acquisition DECT iodine concentration map. Quantitative iodine concentration maps obtained with DECT correlate well with conventional abdominal CT perfusion measurements, suggesting that quantitative iodine maps calculated from a single DECT acquisition at an organ-specific and patient-specific optimum time of acquisition might be able to replace conventional abdominal CT perfusion measurements if the time of acquisition is carefully calibrated. This could lead to large reductions of radiation exposure to the patients while offering quantitative perfusion data for diagnosis.

Derivation of the expressions for γ50 and D50 for different individual TCP and NTCP models

NASA Astrophysics Data System (ADS)

Stavreva, N.; Stavrev, P.; Warkentin, B.; Fallone, B. G.

2002-10-01

This paper presents a complete set of formulae for the position (D50) and the normalized slope (γ50) of the dose-response relationship based on the most commonly used radiobiological models for tumours as well as for normal tissues. The functional subunit response models (critical element and critical volume) are used in the derivation of the formulae for the normal tissue. Binomial statistics are used to describe the tumour control probability, the functional subunit response as well as the normal tissue complication probability. The formulae are derived for the single hit and linear quadratic models of cell kill in terms of the number of fractions and dose per fraction. It is shown that the functional subunit models predict very steep, almost step-like, normal tissue individual dose-response relationships. Furthermore, the formulae for the normalized gradient depend on the cellular parameters α and β when written in terms of number of fractions, but not when written in terms of dose per fraction.

Maps on statistical manifolds exactly reduced from the Perron-Frobenius equations for solvable chaotic maps

NASA Astrophysics Data System (ADS)

Goto, Shin-itiro; Umeno, Ken

2018-03-01

Maps on a parameter space for expressing distribution functions are exactly derived from the Perron-Frobenius equations for a generalized Boole transform family. Here the generalized Boole transform family is a one-parameter family of maps, where it is defined on a subset of the real line and its probability distribution function is the Cauchy distribution with some parameters. With this reduction, some relations between the statistical picture and the orbital one are shown. From the viewpoint of information geometry, the parameter space can be identified with a statistical manifold, and then it is shown that the derived maps can be characterized. Also, with an induced symplectic structure from a statistical structure, symplectic and information geometric aspects of the derived maps are discussed.

Towards a Global Land Subsidence Map

NASA Astrophysics Data System (ADS)

Erkens, G.; Kooi, H.; Sutanudjaja, E.

2017-12-01

Land subsidence is a global problem, but a global land subsidence map is not available yet. Such map is crucial to raise global awareness of land subsidence, as land subsidence causes extensive damage (probably in the order of billions of dollars annually). Insights in the rates of subsidence are particularly relevant for low lying deltas and coastal zones, for which any further loss in elevation is unwanted. With the global land subsidence map relative sea level rise predictions may be improved, contributing to global flood risk calculations. In this contribution, we discuss the approach and progress we have made so far in making a global land subsidence map. The first results will be presented and discussed, and we give an outlook on the work needed to derive a global land subsidence map.

Map and Database of Probable and Possible Quaternary Faults in Afghanistan

USGS Publications Warehouse

Ruleman, C.A.; Crone, A.J.; Machette, M.N.; Haller, K.M.; Rukstales, K.S.

2007-01-01

The U.S. Geological Survey (USGS) with support from the U.S. Agency for International Development (USAID) mission in Afghanistan, has prepared a digital map showing the distribution of probable and suspected Quaternary faults in Afghanistan. This map is a key component of a broader effort to assess and map the country's seismic hazards. Our analyses of remote-sensing imagery reveal a complex array of tectonic features that we interpret to be probable and possible active faults within the country and in the surrounding border region. In our compilation, we have mapped previously recognized active faults in greater detail, and have categorized individual features based on their geomorphic expression. We assigned mapped features to eight newly defined domains, each of which contains features that appear to have similar styles of deformation. The styles of deformation associated with each domain provide insight into the kinematics of the modern tectonism, and define a tectonic framework that helps constrain deformational models of the Alpine-Himalayan orogenic belt. The modern fault movements, deformation, and earthquakes in Afghanistan are driven by the collision between the northward-moving Indian subcontinent and Eurasia. The patterns of probable and possible Quaternary faults generally show that much of the modern tectonic activity is related to transfer of plate-boundary deformation across the country. The left-lateral, strike-slip Chaman fault in southeastern Afghanistan probably has the highest slip rate of any fault in the country; to the north, this slip is distributed onto several fault systems. At the southern margin of the Kabul block, the style of faulting changes from mainly strike-slip motion associated with the boundary between the Indian and Eurasian plates, to transpressional and transtensional faulting. North and northeast of the Kabul block, we recognized a complex pattern of potentially active strike-slip, thrust, and normal faults that form a conjugate shear system in a transpressional region of the Trans-Himalayan orogenic belt. The general patterns and orientations of faults and the styles of deformation that we interpret from the imagery are consistent with the styles of faulting determined from focal mechanisms of historical earthquakes. Northwest-trending strike-slip fault zones are cut and displaced by younger, southeast-verging thrust faults; these relations define the interaction between northwest-southeast-oriented contraction and northwest-directed extrusion in the western Himalaya, Pamir, and Hindu Kush regions. Transpression extends into north-central Afghanistan where north-verging contraction along the east-west-trending Alburz-Marmul fault system interacts with northwest-trending strike-slip faults. Pressure ridges related to thrust faulting and extensional basins bounded by normal faults are located at major stepovers in these northwest-trending strike-slip systems. In contrast, young faulting in central and western Afghanistan indicates that the deformation is dominated by extension where strike-slip fault zones transition into regions of normal faults. In addition to these initial observations, our digital map and database provide a foundation that can be expanded, complemented, and modified as future investigations provide more detailed information about the location, characteristics, and history of movement on Quaternary faults in Afghanistan.

Averaged kick maps: less noise, more signal…and probably less bias

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

Pražnikar, Jure; Afonine, Pavel V.; Gunčar, Gregor

2009-09-01

Averaged kick maps are the sum of a series of individual kick maps, where each map is calculated from atomic coordinates modified by random shifts. These maps offer the possibility of an improved and less model-biased map interpretation. Use of reliable density maps is crucial for rapid and successful crystal structure determination. Here, the averaged kick (AK) map approach is investigated, its application is generalized and it is compared with other map-calculation methods. AK maps are the sum of a series of kick maps, where each kick map is calculated from atomic coordinates modified by random shifts. As such, theymore » are a numerical analogue of maximum-likelihood maps. AK maps can be unweighted or maximum-likelihood (σ{sub A}) weighted. Analysis shows that they are comparable and correspond better to the final model than σ{sub A} and simulated-annealing maps. The AK maps were challenged by a difficult structure-validation case, in which they were able to clarify the problematic region in the density without the need for model rebuilding. The conclusion is that AK maps can be useful throughout the entire progress of crystal structure determination, offering the possibility of improved map interpretation.« less

Radiobiological impact of reduced margins and treatment technique for prostate cancer in terms of tumor control probability (TCP) and normal tissue complication probability (NTCP).

PubMed

Jensen, Ingelise; Carl, Jesper; Lund, Bente; Larsen, Erik H; Nielsen, Jane

2011-01-01

Dose escalation in prostate radiotherapy is limited by normal tissue toxicities. The aim of this study was to assess the impact of margin size on tumor control and side effects for intensity-modulated radiation therapy (IMRT) and 3D conformal radiotherapy (3DCRT) treatment plans with increased dose. Eighteen patients with localized prostate cancer were enrolled. 3DCRT and IMRT plans were compared for a variety of margin sizes. A marker detectable on daily portal images was presupposed for narrow margins. Prescribed dose was 82 Gy within 41 fractions to the prostate clinical target volume (CTV). Tumor control probability (TCP) calculations based on the Poisson model including the linear quadratic approach were performed. Normal tissue complication probability (NTCP) was calculated for bladder, rectum and femoral heads according to the Lyman-Kutcher-Burman method. All plan types presented essentially identical TCP values and very low NTCP for bladder and femoral heads. Mean doses for these critical structures reached a minimum for IMRT with reduced margins. Two endpoints for rectal complications were analyzed. A marked decrease in NTCP for IMRT plans with narrow margins was seen for mild RTOG grade 2/3 as well as for proctitis/necrosis/stenosis/fistula, for which NTCP <7% was obtained. For equivalent TCP values, sparing of normal tissue was demonstrated with the narrow margin approach. The effect was more pronounced for IMRT than 3DCRT, with respect to NTCP for mild, as well as severe, rectal complications. Copyright © 2011 American Association of Medical Dosimetrists. Published by Elsevier Inc. All rights reserved.

A finite element model of remote palpation of breast lesions using radiation force: factors affecting tissue displacement.

PubMed

Nightingale, K R; Nightingale, R W; Palmeri, M L; Trahey, G E

2000-01-01

The early detection of breast cancer reduces patient mortality. The most common method of breast cancer detection is palpation. However, lesions that lie deep within the breast are difficult to palpate when they are small. Thus, a method of remote palpation, which may allow the detection of small lesions lying deep within the breast, is currently under investigation. In this method, acoustic radiation force is used to apply localized forces within tissue (to tissue volumes on the order of 2 mm3) and the resulting tissue displacements are mapped using ultrasonic correlation based methods. A volume of tissue that is stiffer than the surrounding medium (i.e., a lesion) distributes the force throughout the tissue beneath it, resulting in larger regions of displacement, and smaller maximum displacements. The resulting displacement maps may be used to image tissue stiffness. A finite-element-model (FEM) of acoustic remote palpation is presented in this paper. Using this model, a parametric analysis of the affect of varying tissue and acoustic beam characteristics on radiation force induced tissue displacements is performed. The results are used to evaluate the potential of acoustic remote palpation to provide useful diagnostic information in a clinical setting. The potential for using a single diagnostic transducer to both generate radiation force and track the resulting displacements is investigated.

Sub-diffusive scattering parameter maps recovered using wide-field high-frequency structured light imaging.

PubMed

Kanick, Stephen Chad; McClatchy, David M; Krishnaswamy, Venkataramanan; Elliott, Jonathan T; Paulsen, Keith D; Pogue, Brian W

2014-10-01

This study investigates the hypothesis that structured light reflectance imaging with high spatial frequency patterns [Formula: see text] can be used to quantitatively map the anisotropic scattering phase function distribution [Formula: see text] in turbid media. Monte Carlo simulations were used in part to establish a semi-empirical model of demodulated reflectance ([Formula: see text]) in terms of dimensionless scattering [Formula: see text] and [Formula: see text], a metric of the first two moments of the [Formula: see text] distribution. Experiments completed in tissue-simulating phantoms showed that simultaneous analysis of [Formula: see text] spectra sampled at multiple [Formula: see text] in the frequency range [0.05-0.5] [Formula: see text] allowed accurate estimation of both [Formula: see text] in the relevant tissue range [0.4-1.8] [Formula: see text], and [Formula: see text] in the range [1.4-1.75]. Pilot measurements of a healthy volunteer exhibited [Formula: see text]-based contrast between scar tissue and surrounding normal skin, which was not as apparent in wide field diffuse imaging. These results represent the first wide-field maps to quantify sub-diffuse scattering parameters, which are sensitive to sub-microscopic tissue structures and composition, and therefore, offer potential for fast diagnostic imaging of ultrastructure on a size scale that is relevant to surgical applications.

Micro-PIXE mapping of mineral distribution in mature grain of two pearl millet cultivars

NASA Astrophysics Data System (ADS)

Minnis-Ndimba, R.; Kruger, J.; Taylor, J. R. N.; Mtshali, C.; Pineda-Vargas, C. A.

2015-11-01

Micro-proton-induced X-ray emission (micro-PIXE) was used to map the distribution of several nutritionally important minerals found in the grain tissue of two cultivars of pearl millet (Pennisetum glaucum (L.) R. Br.). The distribution maps revealed that the predominant localisation of minerals was within the germ (consisting of the scutellum and embryo) and the outer grain layers (specifically the pericarp and aleurone); whilst the bulk of the endosperm tissue featured relatively low concentrations of the surveyed minerals. Within the germ, the scutellum was revealed as a major storage tissue for P and K, whilst Ca, Mn and Zn were more prominent within the embryo. Fe was revealed to have a distinctive distribution pattern, confined to the dorsal end of the scutellum; but was also highly concentrated in the outer grain layers. Interestingly, the hilar region was also revealed as a site of high accumulation of minerals, particularly for S, Ca, Mn, Fe and Zn, which may be part of a defensive strategy against infection or damage. Differences between the two cultivars, in terms of the bulk Fe and P content obtained via inductively coupled plasma optical emission spectrometry (ICP-OES), concurred with the average concentration data determined from the analysis of micro-PIXE spectra specifically extracted from the endosperm tissue.

Color mapping of one specific velocity of a biological fluid flows with complex geometry using optical coherence tomography

NASA Astrophysics Data System (ADS)

Potlov, A. Yu.; Frolov, S. V.; Proskurin, S. G.

2018-04-01

The method of Doppler color mapping of one specific (previously chosen) velocity in a turbulent flow inside biological tissues using optical coherence tomography is described. The key features of the presented method are: the raw data are separated into three parts, corresponding to the unmoving biological tissue, the positively and negatively directed biological fluid flows; the further independent signal processing procedure yields the structure image and two images of the chosen velocity, which are then normalised, encoded and joined. The described method can be used to obtain in real time the anatomical maps of the chosen velocities in normal and pathological states. The described method can be applied not only in optical coherence tomography, but also in endoscopic and Doppler ultrasonic medical imaging systems.

Comparison of Probabilistic Coastal Inundation Maps Based on Historical Storms and Statistically Modeled Storm Ensemble

NASA Astrophysics Data System (ADS)

Feng, X.; Sheng, Y.; Condon, A. J.; Paramygin, V. A.; Hall, T.

2012-12-01

A cost effective method, JPM-OS (Joint Probability Method with Optimal Sampling), for determining storm response and inundation return frequencies was developed and applied to quantify the hazard of hurricane storm surges and inundation along the Southwest FL,US coast (Condon and Sheng 2012). The JPM-OS uses piecewise multivariate regression splines coupled with dimension adaptive sparse grids to enable the generation of a base flood elevation (BFE) map. Storms are characterized by their landfall characteristics (pressure deficit, radius to maximum winds, forward speed, heading, and landfall location) and a sparse grid algorithm determines the optimal set of storm parameter combinations so that the inundation from any other storm parameter combination can be determined. The end result is a sample of a few hundred (197 for SW FL) optimal storms which are simulated using a dynamically coupled storm surge / wave modeling system CH3D-SSMS (Sheng et al. 2010). The limited historical climatology (1940 - 2009) is explored to develop probabilistic characterizations of the five storm parameters. The probability distributions are discretized and the inundation response of all parameter combinations is determined by the interpolation in five-dimensional space of the optimal storms. The surge response and the associated joint probability of the parameter combination is used to determine the flood elevation with a 1% annual probability of occurrence. The limited historical data constrains the accuracy of the PDFs of the hurricane characteristics, which in turn affect the accuracy of the BFE maps calculated. To offset the deficiency of limited historical dataset, this study presents a different method for producing coastal inundation maps. Instead of using the historical storm data, here we adopt 33,731 tracks that can represent the storm climatology in North Atlantic basin and SW Florida coasts. This large quantity of hurricane tracks is generated from a new statistical model which had been used for Western North Pacific (WNP) tropical cyclone (TC) genesis (Hall 2011) as well as North Atlantic tropical cyclone genesis (Hall and Jewson 2007). The introduction of these tracks complements the shortage of the historical samples and allows for more reliable PDFs required for implementation of JPM-OS. Using the 33,731 tracks and JPM-OS, an optimal storm ensemble is determined. This approach results in different storms/winds for storm surge and inundation modeling, and produces different Base Flood Elevation maps for coastal regions. Coastal inundation maps produced by the two different methods will be discussed in detail in the poster paper.

Improving diagnostic accuracy of prostate carcinoma by systematic random map-biopsy.

PubMed

Szabó, J; Hegedûs, G; Bartók, K; Kerényi, T; Végh, A; Romics, I; Szende, B

2000-01-01

Systematic random rectal ultrasound directed map-biopsy of the prostate was performed in 77 RDE (rectal digital examination) positive and 25 RDE negative cases, if applicable. Hypoechoic areas were found in 30% of RDE positive and in 16% of RDE negative cases. The score for carcinoma in the hypoechoic areas was 6.5% in RDE positive and 0% in RDE negative cases, whereas systematic map biopsy detected 62% carcinomas in RDE positive, and 16% carcinomas in RDE negative patients. The probability of positive diagnosis of prostate carcinoma increased in parallel with the number of biopsy samples/case. The importance of systematic map biopsy is emphasized.

Landsat for practical forest type mapping - A test case

NASA Technical Reports Server (NTRS)

Bryant, E.; Dodge, A. G., Jr.; Warren, S. D.

1980-01-01

Computer classified Landsat maps are compared with a recent conventional inventory of forest lands in northern Maine. Over the 196,000 hectare area mapped, estimates of the areas of softwood, mixed wood and hardwood forest obtained by a supervised classification of the Landsat data and a standard inventory based on aerial photointerpretation, probability proportional to prediction, field sampling and a standard forest measurement program are found to agree to within 5%. The cost of the Landsat maps is estimated to be $0.065/hectare. It is concluded that satellite techniques are worth developing for forest inventories, although they are not yet refined enough to be incorporated into current practical inventories.

Alternative Polyadenylation Directs Tissue-Specific miRNA Targeting in Caenorhabditis elegans Somatic Tissues

PubMed Central

Blazie, Stephen M.; Geissel, Heather C.; Wilky, Henry; Joshi, Rajan; Newbern, Jason; Mangone, Marco

2017-01-01

mRNA expression dynamics promote and maintain the identity of somatic tissues in living organisms; however, their impact in post-transcriptional gene regulation in these processes is not fully understood. Here, we applied the PAT-Seq approach to systematically isolate, sequence, and map tissue-specific mRNA from five highly studied Caenorhabditis elegans somatic tissues: GABAergic and NMDA neurons, arcade and intestinal valve cells, seam cells, and hypodermal tissues, and studied their mRNA expression dynamics. The integration of these datasets with previously profiled transcriptomes of intestine, pharynx, and body muscle tissues, precisely assigns tissue-specific expression dynamics for 60% of all annotated C. elegans protein-coding genes, providing an important resource for the scientific community. The mapping of 15,956 unique high-quality tissue-specific polyA sites in all eight somatic tissues reveals extensive tissue-specific 3′untranslated region (3′UTR) isoform switching through alternative polyadenylation (APA) . Almost all ubiquitously transcribed genes use APA and harbor miRNA targets in their 3′UTRs, which are commonly lost in a tissue-specific manner, suggesting widespread usage of post-transcriptional gene regulation modulated through APA to fine tune tissue-specific protein expression. Within this pool, the human disease gene C. elegans orthologs rack-1 and tct-1 use APA to switch to shorter 3′UTR isoforms in order to evade miRNA regulation in the body muscle tissue, resulting in increased protein expression needed for proper body muscle function. Our results highlight a major positive regulatory role for APA, allowing genes to counteract miRNA regulation on a tissue-specific basis. PMID:28348061

Alternative Polyadenylation Directs Tissue-Specific miRNA Targeting in Caenorhabditis elegans Somatic Tissues.

PubMed

Blazie, Stephen M; Geissel, Heather C; Wilky, Henry; Joshi, Rajan; Newbern, Jason; Mangone, Marco

2017-06-01

mRNA expression dynamics promote and maintain the identity of somatic tissues in living organisms; however, their impact in post-transcriptional gene regulation in these processes is not fully understood. Here, we applied the PAT-Seq approach to systematically isolate, sequence, and map tissue-specific mRNA from five highly studied Caenorhabditis elegans somatic tissues: GABAergic and NMDA neurons, arcade and intestinal valve cells, seam cells, and hypodermal tissues, and studied their mRNA expression dynamics. The integration of these datasets with previously profiled transcriptomes of intestine, pharynx, and body muscle tissues, precisely assigns tissue-specific expression dynamics for 60% of all annotated C. elegans protein-coding genes, providing an important resource for the scientific community. The mapping of 15,956 unique high-quality tissue-specific polyA sites in all eight somatic tissues reveals extensive tissue-specific 3'untranslated region (3'UTR) isoform switching through alternative polyadenylation (APA) . Almost all ubiquitously transcribed genes use APA and harbor miRNA targets in their 3'UTRs, which are commonly lost in a tissue-specific manner, suggesting widespread usage of post-transcriptional gene regulation modulated through APA to fine tune tissue-specific protein expression. Within this pool, the human disease gene C. elegans orthologs rack-1 and tct-1 use APA to switch to shorter 3'UTR isoforms in order to evade miRNA regulation in the body muscle tissue, resulting in increased protein expression needed for proper body muscle function. Our results highlight a major positive regulatory role for APA, allowing genes to counteract miRNA regulation on a tissue-specific basis. Copyright © 2017 Blazie et al.

Colorectal carcinoma: Ex vivo evaluation using 3-T high-spatial-resolution quantitative T2 mapping and its correlation with histopathologic findings.

PubMed

Yamada, Ichiro; Yoshino, Norio; Hikishima, Keigo; Miyasaka, Naoyuki; Yamauchi, Shinichi; Uetake, Hiroyuki; Yasuno, Masamichi; Saida, Yukihisa; Tateishi, Ukihide; Kobayashi, Daisuke; Eishi, Yoshinobu

2017-05-01

In this study, we aimed to evaluate the feasibility of determining the mural invasion depths of colorectal carcinomas using high-spatial-resolution (HSR) quantitative T2 mapping on a 3-T magnetic resonance (MR) scanner. Twenty colorectal specimens containing adenocarcinomas were imaged on a 3-T MR system equipped with a 4-channel phased-array surface coil. HSR quantitative T2 maps were acquired using a spin-echo sequence with a repetition time/echo time of 7650/22.6-361.6ms (16 echoes), 87×43.5-mm field of view, 2-mm section thickness, 448×224 matrix, and average of 1. HSR fast-spin-echo T2-weighted images were also acquired. Differences between the T2 values (ms) of the tumor tissue, colorectal wall layers, and fibrosis were measured, and the MR images and histopathologic findings were compared. In all specimens (20/20, 100%), the HSR quantitative T2 maps clearly depicted an 8-layer normal colorectal wall in which the T2 values of each layer differed from those of the adjacent layer(s) (P<0.001). Using this technique, fibrosis (73.6±9.4ms) and tumor tissue (104.2±6.4ms) could also be clearly differentiated (P<0.001). In 19 samples (95%), the HSR quantitative T2 maps and histopathologic data yielded the same findings regarding the tumor invasion depth. Our results indicate that 3-T HSR quantitative T2 mapping is useful for distinguishing colorectal wall layers and differentiating tumor and fibrotic tissues. Accordingly, this technique could be used to determine mural invasion by colorectal carcinomas with a high level of accuracy. Copyright © 2017 Elsevier Inc. All rights reserved.

Allocating Fire Mitigation Funds on the Basis of the Predicted Probabilities of Forest Wildfire

Treesearch

Ronald E. McRoberts; Greg C. Liknes; Mark D. Nelson; Krista M. Gebert; R. James Barbour; Susan L. Odell; Steven C. Yaddof

2005-01-01

A logistic regression model was used with map-based information to predict the probability of forest fire for forested areas of the United States. Model parameters were estimated using a digital layer depicting the locations of wildfires and satellite imagery depicting thermal hotspots. The area of the United States in the upper 50th percentile with respect to...

Using Landscape-Based Decision Rules to Prioritize Locations of Fuel Treatments in the Boreal Mixedwood of Western Canada

Treesearch

Marc-André Parisien; Dave R. Junor; Victor G. Kafka

2006-01-01

This study used a rule-based approach to prioritize locations of fuel treatments in the boreal mixedwood forest of western Canada. The burn probability (BP) in and around Prince Albert National Park in Saskatchewan was mapped using the Burn-P3 (Probability, Prediction, and Planning) model. Fuel treatment locations were determined according to three scenarios and five...

The Sparta Fault, Southern Greece: From segmentation and tectonic geomorphology to seismic hazard mapping and time dependent probabilities

NASA Astrophysics Data System (ADS)

Papanikolaοu, Ioannis D.; Roberts, Gerald P.; Deligiannakis, Georgios; Sakellariou, Athina; Vassilakis, Emmanuel

2013-06-01

The Sparta Fault system is a major structure approximately 64 km long that bounds the eastern flank of the Taygetos Mountain front (2407 m) and shapes the present-day Sparta basin. It was activated in 464 B.C., devastating the city of Sparta. This fault is examined and described in terms of its geometry, segmentation, drainage pattern and post-glacial throw, emphasising how these parameters vary along strike. Qualitative analysis of long profile catchments shows a significant difference in longitudinal convexity between the central and both the south and north parts of the fault system, leading to the conclusion of varying uplift rate along strike. Catchments are sensitive in differential uplift as it is observed by the calculated differences of the steepness index ksn between the outer (ksn < 83) and central parts (121 < ksn < 138) of the Sparta Fault along strike the fault system. Based on fault throw-rates and the bedrock geology a seismic hazard map has been constructed that extracts a locality specific long-term earthquake recurrence record. Based on this map the town of Sparta would experience a destructive event similar to that in 464 B.C. approximately every 1792 ± 458 years. Since no other major earthquake M ~ 7.0 has been generated by this system since 464 B.C., a future event could be imminent. As a result, not only time-independent but also time-dependent probabilities, which incorporate the concept of the seismic cycle, have been calculated for the town of Sparta, showing a considerably higher time-dependent probability of 3.0 ± 1.5% over the next 30 years compared to the time-independent probability of 1.66%. Half of the hanging wall area of the Sparta Fault can experience intensities ≥ IX, but belongs to the lowest category of seismic risk of the national seismic building code. On view of these relatively high calculated probabilities, a reassessment of the building code might be necessary.

The Sparta Fault, Southern Greece: From Segmentation and Tectonic Geomorphology to Seismic Hazard Mapping and Time Dependent Probabilities

NASA Astrophysics Data System (ADS)

Papanikolaou, Ioannis; Roberts, Gerald; Deligiannakis, Georgios; Sakellariou, Athina; Vassilakis, Emmanuel

2013-04-01

The Sparta Fault system is a major structure approximately 64 km long that bounds the eastern flank of the Taygetos Mountain front (2.407 m) and shapes the present-day Sparta basin. It was activated in 464 B.C., devastating the city of Sparta. This fault is examined and described in terms of its geometry, segmentation, drainage pattern and postglacial throw, emphasizing how these parameters vary along strike. Qualitative analysis of long profile catchments shows a significant difference in longitudinal convexity between the central and both the south and north parts of the fault system, leading to the conclusion of varying uplift rate along strike. Catchments are sensitive in differential uplift as it is observed by the calculated differences of the steepness index ksn between the outer (ksn<83) and central parts (121

Probability of cavitation for single ultrasound pulses applied to tissues and tissue-mimicking materials.

PubMed

Maxwell, Adam D; Cain, Charles A; Hall, Timothy L; Fowlkes, J Brian; Xu, Zhen

2013-03-01

In this study, the negative pressure values at which inertial cavitation consistently occurs in response to a single, two-cycle, focused ultrasound pulse were measured in several media relevant to cavitation-based ultrasound therapy. The pulse was focused into a chamber containing one of the media, which included liquids, tissue-mimicking materials, and ex vivo canine tissue. Focal waveforms were measured by two separate techniques using a fiber-optic hydrophone. Inertial cavitation was identified by high-speed photography in optically transparent media and an acoustic passive cavitation detector. The probability of cavitation (P(cav)) for a single pulse as a function of peak negative pressure (p(-)) followed a sigmoid curve, with the probability approaching one when the pressure amplitude was sufficient. The statistical threshold (defined as P(cav) = 0.5) was between p(-) = 26 and 30 MPa in all samples with high water content but varied between p(-) = 13.7 and >36 MPa in other media. A model for radial cavitation bubble dynamics was employed to evaluate the behavior of cavitation nuclei at these pressure levels. A single bubble nucleus with an inertial cavitation threshold of p(-) = 28.2 megapascals was estimated to have a 2.5 nm radius in distilled water. These data may be valuable for cavitation-based ultrasound therapy to predict the likelihood of cavitation at various pressure levels and dimensions of cavitation-induced lesions in tissue. Copyright © 2013 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Quantified elasticity mapping of ocular tissue using acoustic radiation force optical coherence elastography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Qu, Yueqiao; He, Youmin; Zhang, Yi; Ma, Teng; Zhu, Jiang; Miao, Yusi; Dai, Cuixia; Silverman, Ronald; Humayun, Mark S.; Zhou, Qifa; Chen, Zhongping

2017-02-01

Age-related macular degeneration and keratoconus are two ocular diseases occurring in the posterior and anterior eye, respectively. In both conditions, the mechanical elasticity of the respective tissues changes during the early onset of disease. It is necessary to detect these differences and treat the diseases in their early stages to provide proper treatment. Acoustic radiation force optical coherence elastography is a method of elasticity mapping using confocal ultrasound waves for excitation and Doppler optical coherence tomography for detection. We report on an ARF-OCE system that uses modulated compression wave based excitation signals, and detects the spatial and frequency responses of the tissue. First, all components of the system is synchronized and triggered such that the signal is consistent between frames. Next, phantom studies are performed to validate and calibrate the relationship between the resonance frequency and the Young's modulus. Then the frequency responses of the anterior and posterior eye are detected for porcine and rabbit eyes, and the results correlated to the elasticity. Finally, spatial elastograms are obtained for a porcine retina. Layer segmentation and analysis is performed and correlated to the histology of the retina, where five distinct layers are recognized. The elasticities of the tissue layers will be quantified according to the mean thickness and displacement response for the locations on the retina. This study is a stepping stone to future in-vivo animal studies, where the elastic modulus of the ocular tissue can be quantified and mapped out accordingly.

Probabilistic flood inundation mapping at ungauged streams due to roughness coefficient uncertainty in hydraulic modelling

NASA Astrophysics Data System (ADS)

Papaioannou, George; Vasiliades, Lampros; Loukas, Athanasios; Aronica, Giuseppe T.

2017-04-01

Probabilistic flood inundation mapping is performed and analysed at the ungauged Xerias stream reach, Volos, Greece. The study evaluates the uncertainty introduced by the roughness coefficient values on hydraulic models in flood inundation modelling and mapping. The well-established one-dimensional (1-D) hydraulic model, HEC-RAS is selected and linked to Monte-Carlo simulations of hydraulic roughness. Terrestrial Laser Scanner data have been used to produce a high quality DEM for input data uncertainty minimisation and to improve determination accuracy on stream channel topography required by the hydraulic model. Initial Manning's n roughness coefficient values are based on pebble count field surveys and empirical formulas. Various theoretical probability distributions are fitted and evaluated on their accuracy to represent the estimated roughness values. Finally, Latin Hypercube Sampling has been used for generation of different sets of Manning roughness values and flood inundation probability maps have been created with the use of Monte Carlo simulations. Historical flood extent data, from an extreme historical flash flood event, are used for validation of the method. The calibration process is based on a binary wet-dry reasoning with the use of Median Absolute Percentage Error evaluation metric. The results show that the proposed procedure supports probabilistic flood hazard mapping at ungauged rivers and provides water resources managers with valuable information for planning and implementing flood risk mitigation strategies.

A Probabilistic Strategy for Understanding Action Selection

PubMed Central

Kim, Byounghoon; Basso, Michele A.

2010-01-01

Brain regions involved in transforming sensory signals into movement commands are the likely sites where decisions are formed. Once formed, a decision must be read-out from the activity of populations of neurons to produce a choice of action. How this occurs remains unresolved. We recorded from four superior colliculus (SC) neurons simultaneously while monkeys performed a target selection task. We implemented three models to gain insight into the computational principles underlying population coding of action selection. We compared the population vector average (PVA), winner-takes-all (WTA) and a Bayesian model, maximum a posteriori estimate (MAP) to determine which predicted choices most often. The probabilistic model predicted more trials correctly than both the WTA and the PVA. The MAP model predicted 81.88% whereas WTA predicted 71.11% and PVA/OLE predicted the least number of trials at 55.71 and 69.47%. Recovering MAP estimates using simulated, non-uniform priors that correlated with monkeys’ choice performance, improved the accuracy of the model by 2.88%. A dynamic analysis revealed that the MAP estimate evolved over time and the posterior probability of the saccade choice reached a maximum at the time of the saccade. MAP estimates also scaled with choice performance accuracy. Although there was overlap in the prediction abilities of all the models, we conclude that movement choice from populations of neurons may be best understood by considering frameworks based on probability. PMID:20147560

Molecular imaging of cannabis leaf tissue with MeV-SIMS method

NASA Astrophysics Data System (ADS)

Jenčič, Boštjan; Jeromel, Luka; Ogrinc Potočnik, Nina; Vogel-Mikuš, Katarina; Kovačec, Eva; Regvar, Marjana; Siketić, Zdravko; Vavpetič, Primož; Rupnik, Zdravko; Bučar, Klemen; Kelemen, Mitja; Kovač, Janez; Pelicon, Primož

2016-03-01

To broaden our analytical capabilities with molecular imaging in addition to the existing elemental imaging with micro-PIXE, a linear Time-Of-Flight mass spectrometer for MeV Secondary Ion Mass Spectrometry (MeV-SIMS) was constructed and added to the existing nuclear microprobe at the Jožef Stefan Institute. We measured absolute molecular yields and damage cross-section of reference materials, without significant alteration of the fragile biological samples during the duration of measurements in the mapping mode. We explored the analytical capability of the MeV-SIMS technique for chemical mapping of the plant tissue of medicinal cannabis leaves. A series of hand-cut plant tissue slices were prepared by standard shock-freezing and freeze-drying protocol and deposited on the Si wafer. We show the measured MeV-SIMS spectra showing a series of peaks in the mass area of cannabinoids, as well as their corresponding maps. The indicated molecular distributions at masses of 345.5 u and 359.4 u may be attributed to the protonated THCA and THCA-C4 acids, and show enhancement in the areas with opened trichome morphology.

Atlas of depth-duration frequency of precipitation annual maxima for Texas

USGS Publications Warehouse

Asquith, William H.; Roussel, Meghan C.

2004-01-01

Ninety-six maps depicting the spatial variation of the depth-duration frequency of precipitation annual maxima for Texas are presented. The recurrence intervals represented are 2, 5, 10, 25, 50, 100, 250, and 500 years. The storm durations represented are 15 and 30 minutes; 1, 2, 3, 6, and 12 hours; and 1, 2, 3, 5, and 7 days. The maps were derived using geographically referenced parameter maps of probability distributions used in previously published research by the U.S. Geological Survey to model the magnitude and frequency of precipitation annual maxima for Texas. The maps in this report apply that research and update depth-duration frequency of precipitation maps available in earlier studies done by the National Weather Service.

A probable risk factor of female breast cancer: study on benign and malignant breast tissue samples.

PubMed

Rehman, Sohaila; Husnain, Syed M

2014-01-01

The study reports enhanced Fe, Cu, and Zn contents in breast tissues, a probable risk factor of breast cancer in females. Forty-one formalin-fixed breast tissues were analyzed using atomic absorption spectrophotometry. Twenty malignant, six adjacent to malignant and 15 benign tissues samples were investigated. The malignant tissues samples were of grade 11 and type invasive ductal carcinoma. The quantitative comparison between the elemental levels measured in the two types of specimen (benign and malignant) tissues (removed after surgery) suggests significant elevation of these metals (Fe, Cu, and Zn) in the malignant tissue. The specimens were collected just after mastectomy of women aged 19 to 59 years from the hospitals of Islamabad and Rawalpindi, Pakistan. Most of the patients belong to urban areas of Pakistan. Findings of study depict that these elements have a promising role in the initiation and development of carcinoma as consistent pattern of elevation for Fe, Cu, and Zn was observed. The results showed the excessive accumulation of Fe (229 ± 121 mg/L) in malignant breast tissue samples of patients (p < 0.05) to that in benign tissues samples (49.1 ± 11.4 mg/L). Findings indicated that excess accumulation of iron in malignant tissues can be a risk factor of breast cancer. In order to validate our method of analysis, certified reference material muscle tissue lyophilized (IAEA) MA-M-2/TM was analyzed for metal studied. Determined concentrations were quite in good agreement with certified levels. Asymmetric concentration distribution for Fe, Cu, and Zn was observed in both malignant and benign tissue samples.

Long-term multi-hazard assessment for El Misti volcano (Peru)

NASA Astrophysics Data System (ADS)

Sandri, Laura; Thouret, Jean-Claude; Constantinescu, Robert; Biass, Sébastien; Tonini, Roberto

2014-02-01

We propose a long-term probabilistic multi-hazard assessment for El Misti Volcano, a composite cone located <20 km from Arequipa. The second largest Peruvian city is a rapidly expanding economic centre and is classified by UNESCO as World Heritage. We apply the Bayesian Event Tree code for Volcanic Hazard (BET_VH) to produce probabilistic hazard maps for the predominant volcanic phenomena that may affect c.900,000 people living around the volcano. The methodology accounts for the natural variability displayed by volcanoes in their eruptive behaviour, such as different types/sizes of eruptions and possible vent locations. For this purpose, we treat probabilistically several model runs for some of the main hazardous phenomena (lahars, pyroclastic density currents (PDCs), tephra fall and ballistic ejecta) and data from past eruptions at El Misti (tephra fall, PDCs and lahars) and at other volcanoes (PDCs). The hazard maps, although neglecting possible interactions among phenomena or cascade effects, have been produced with a homogeneous method and refer to a common time window of 1 year. The probability maps reveal that only the north and east suburbs of Arequipa are exposed to all volcanic threats except for ballistic ejecta, which are limited to the uninhabited but touristic summit cone. The probability for pyroclastic density currents reaching recently expanding urban areas and the city along ravines is around 0.05 %/year, similar to the probability obtained for roof-critical tephra loading during the rainy season. Lahars represent by far the most probable threat (around 10 %/year) because at least four radial drainage channels can convey them approximately 20 km away from the volcano across the entire city area in heavy rain episodes, even without eruption. The Río Chili Valley represents the major concern to city safety owing to the probable cascading effect of combined threats: PDCs and rockslides, dammed lake break-outs and subsequent lahars or floods. Although this study does not intend to replace the current El Misti hazard map, the quantitative results of this probabilistic multi-hazard assessment can be incorporated into a multi-risk analysis, to support decision makers in any future improvement of the current hazard evaluation, such as further land-use planning and possible emergency management.

Molecular mechanisms underlying variations in lung function: a systems genetics analysis

PubMed Central

Obeidat, Ma’en; Hao, Ke; Bossé, Yohan; Nickle, David C; Nie, Yunlong; Postma, Dirkje S; Laviolette, Michel; Sandford, Andrew J; Daley, Denise D; Hogg, James C; Elliott, W Mark; Fishbane, Nick; Timens, Wim; Hysi, Pirro G; Kaprio, Jaakko; Wilson, James F; Hui, Jennie; Rawal, Rajesh; Schulz, Holger; Stubbe, Beate; Hayward, Caroline; Polasek, Ozren; Järvelin, Marjo-Riitta; Zhao, Jing Hua; Jarvis, Deborah; Kähönen, Mika; Franceschini, Nora; North, Kari E; Loth, Daan W; Brusselle, Guy G; Smith, Albert Vernon; Gudnason, Vilmundur; Bartz, Traci M; Wilk, Jemma B; O’Connor, George T; Cassano, Patricia A; Tang, Wenbo; Wain, Louise V; Artigas, María Soler; Gharib, Sina A; Strachan, David P; Sin, Don D; Tobin, Martin D; London, Stephanie J; Hall, Ian P; Paré, Peter D

2016-01-01

Summary Background Lung function measures reflect the physiological state of the lung, and are essential to the diagnosis of chronic obstructive pulmonary disease (COPD). The SpiroMeta-CHARGE consortium undertook the largest genome-wide association study (GWAS) so far (n=48 201) for forced expiratory volume in 1 s (FEV1) and the ratio of FEV1 to forced vital capacity (FEV1/FVC) in the general population. The lung expression quantitative trait loci (eQTLs) study mapped the genetic architecture of gene expression in lung tissue from 1111 individuals. We used a systems genetics approach to identify single nucleotide polymorphisms (SNPs) associated with lung function that act as eQTLs and change the level of expression of their target genes in lung tissue; termed eSNPs. Methods The SpiroMeta-CHARGE GWAS results were integrated with lung eQTLs to map eSNPs and the genes and pathways underlying the associations in lung tissue. For comparison, a similar analysis was done in peripheral blood. The lung mRNA expression levels of the eSNP-regulated genes were tested for associations with lung function measures in 727 individuals. Additional analyses identified the pleiotropic effects of eSNPs from the published GWAS catalogue, and mapped enrichment in regulatory regions from the ENCODE project. Finally, the Connectivity Map database was used to identify potential therapeutics in silico that could reverse the COPD lung tissue gene signature. Findings SNPs associated with lung function measures were more likely to be eQTLs and vice versa. The integration mapped the specific genes underlying the GWAS signals in lung tissue. The eSNP-regulated genes were enriched for developmental and inflammatory pathways; by comparison, SNPs associated with lung function that were eQTLs in blood, but not in lung, were only involved in inflammatory pathways. Lung function eSNPs were enriched for regulatory elements and were over-represented among genes showing differential expression during fetal lung development. An mRNA gene expression signature for COPD was identified in lung tissue and compared with the Connectivity Map. This in-silico drug repurposing approach suggested several compounds that reverse the COPD gene expression signature, including a nicotine receptor antagonist. These findings represent novel therapeutic pathways for COPD. Interpretation The system genetics approach identified lung tissue genes driving the variation in lung function and susceptibility to COPD. The identification of these genes and the pathways in which they are enriched is essential to understand the pathophysiology of airway obstruction and to identify novel therapeutic targets and biomarkers for COPD, including drugs that reverse the COPD gene signature in silico. Funding The research reported in this article was not specifically funded by any agency. See Acknowledgments for a full list of funders of the lung eQTL study and the Spiro-Meta CHARGE GWAS. PMID:26404118

Acoustic methods for cavitation mapping in biomedical applications

NASA Astrophysics Data System (ADS)

Wan, M.; Xu, S.; Ding, T.; Hu, H.; Liu, R.; Bai, C.; Lu, S.

2015-12-01

In recent years, cavitation is increasingly utilized in a wide range of applications in biomedical field. Monitoring the spatial-temporal evolution of cavitation bubbles is of great significance for efficiency and safety in biomedical applications. In this paper, several acoustic methods for cavitation mapping proposed or modified on the basis of existing work will be presented. The proposed novel ultrasound line-by-line/plane-by-plane method can depict cavitation bubbles distribution with high spatial and temporal resolution and may be developed as a potential standard 2D/3D cavitation field mapping method. The modified ultrafast active cavitation mapping based upon plane wave transmission and reception as well as bubble wavelet and pulse inversion technique can apparently enhance the cavitation to tissue ratio in tissue and further assist in monitoring the cavitation mediated therapy with good spatial and temporal resolution. The methods presented in this paper will be a foundation to promote the research and development of cavitation imaging in non-transparent medium.

Tumor tissue characterization using polarization-sensitive second harmonic generation microscopy

NASA Astrophysics Data System (ADS)

Tokarz, Danielle; Cisek, Richard; Golaraei, Ahmad; Krouglov, Serguei; Navab, Roya; Niu, Carolyn; Sakashita, Shingo; Yasufuku, Kazuhiro; Tsao, Ming-Sound; Asa, Sylvia L.; Barzda, Virginijus; Wilson, Brian C.

2015-06-01

Changes in the ultrastructure of collagen in various tumor and non-tumor human tissues including lung, pancreas and thyroid were investigated ex vivo by a polarization-sensitive second harmonic generation (SHG) microscopy technique referred to as polarization-in, polarization-out (PIPO) SHG. This involves measuring the orientation of the linear polarization of outgoing SHG as a function of the linear polarization orientation of incident laser radiation. From the PIPO SHG data, the second-order nonlinear optical susceptibility tensor component ratio, χ(2) ZZZ'/χ(2) ZXX', for each pixel of the SHG image was obtained and presented as color-coded maps. Further, the orientation of collagen fibers in the tissue was deduced. Since the χ(2) ZZZ'/χ(2) ZXX' values represent the organization of collagen in the tissue, theses maps revealed areas of altered collagen structure (not simply concentration) within tissue sections. Statistically-significant differences in χ(2) ZZZ'/χ(2) ZXX' were found between tumor and non-tumor tissues, which varied from organ to organ. Hence, PIPO SHG microscopy could potentially be used to aid pathologists in diagnosing cancer. Additionally, PIPO SHG microscopy could aid in characterizing the structure of collagen in other collagen-related biological processes such as wound repair.

An empirical probability density distribution of planetary ionosphere storms with geomagnetic precursors

NASA Astrophysics Data System (ADS)

Gulyaeva, Tamara; Stanislawska, Iwona; Arikan, Feza; Arikan, Orhan

The probability of occurrence of the positive and negative planetary ionosphere storms is evaluated using the W index maps produced from Global Ionospheric Maps of Total Electron Content, GIM-TEC, provided by Jet Propulsion Laboratory, and transformed from geographic coordinates to magnetic coordinates frame. The auroral electrojet AE index and the equatorial disturbance storm time Dst index are investigated as precursors of the global ionosphere storm. The superposed epoch analysis is performed for 77 intense storms (Dst≤-100 nT) and 227 moderate storms (-100

Shape Classification Using Wasserstein Distance for Brain Morphometry Analysis.

PubMed

Su, Zhengyu; Zeng, Wei; Wang, Yalin; Lu, Zhong-Lin; Gu, Xianfeng

2015-01-01

Brain morphometry study plays a fundamental role in medical imaging analysis and diagnosis. This work proposes a novel framework for brain cortical surface classification using Wasserstein distance, based on uniformization theory and Riemannian optimal mass transport theory. By Poincare uniformization theorem, all shapes can be conformally deformed to one of the three canonical spaces: the unit sphere, the Euclidean plane or the hyperbolic plane. The uniformization map will distort the surface area elements. The area-distortion factor gives a probability measure on the canonical uniformization space. All the probability measures on a Riemannian manifold form the Wasserstein space. Given any 2 probability measures, there is a unique optimal mass transport map between them, the transportation cost defines the Wasserstein distance between them. Wasserstein distance gives a Riemannian metric for the Wasserstein space. It intrinsically measures the dissimilarities between shapes and thus has the potential for shape classification. To the best of our knowledge, this is the first. work to introduce the optimal mass transport map to general Riemannian manifolds. The method is based on geodesic power Voronoi diagram. Comparing to the conventional methods, our approach solely depends on Riemannian metrics and is invariant under rigid motions and scalings, thus it intrinsically measures shape distance. Experimental results on classifying brain cortical surfaces with different intelligence quotients demonstrated the efficiency and efficacy of our method.

Emergency Assessment of Debris-Flow Hazards from Basins Burned by the Padua Fire of 2003, Southern California

USGS Publications Warehouse

Cannon, Susan H.; Gartner, Joseph E.; Rupert, Michael G.; Michael, John A.

2004-01-01

Results of a present preliminary assessment of the probability of debris-flow activity and estimates of peak discharges that can potentially be generated by debris flows issuing from basins burned by the Padua Fire of October 2003 in southern California in response to 25-year, 10-year, and 2-year recurrence, 1-hour duration rain storms are presented. The resulting probability maps are based on the application of a logistic multiple-regression model (Cannon and others, 2004) that describes the percent chance of debris-flow production from an individual basin as a function of burned extent, soil properties, basin gradients, and storm rainfall. The resulting peak discharge maps are based on application of a multiple-regression model (Cannon and others, 2004) that can be used to estimate debris-flow peak discharge at a basin outlet as a function of basin gradient, burn extent, and storm rainfall. Probabilities of debris-flow occurrence for the Padua Fire range between 0 and 99% and estimates of debris-flow peak discharges range between 1211 and 6,096 ft3/s (34 to 173 m3/s). These maps are intended to identify those basins that are most prone to the largest debris-flow events and provide information for the preliminary design of mitigation measures and for the planning of evacuation timing and routes.

Shape Classification Using Wasserstein Distance for Brain Morphometry Analysis

PubMed Central

Su, Zhengyu; Zeng, Wei; Wang, Yalin; Lu, Zhong-Lin; Gu, Xianfeng

2015-01-01

Brain morphometry study plays a fundamental role in medical imaging analysis and diagnosis. This work proposes a novel framework for brain cortical surface classification using Wasserstein distance, based on uniformization theory and Riemannian optimal mass transport theory. By Poincare uniformization theorem, all shapes can be conformally deformed to one of the three canonical spaces: the unit sphere, the Euclidean plane or the hyperbolic plane. The uniformization map will distort the surface area elements. The area-distortion factor gives a probability measure on the canonical uniformization space. All the probability measures on a Riemannian manifold form the Wasserstein space. Given any 2 probability measures, there is a unique optimal mass transport map between them, the transportation cost defines the Wasserstein distance between them. Wasserstein distance gives a Riemannian metric for the Wasserstein space. It intrinsically measures the dissimilarities between shapes and thus has the potential for shape classification. To the best of our knowledge, this is the first work to introduce the optimal mass transport map to general Riemannian manifolds. The method is based on geodesic power Voronoi diagram. Comparing to the conventional methods, our approach solely depends on Riemannian metrics and is invariant under rigid motions and scalings, thus it intrinsically measures shape distance. Experimental results on classifying brain cortical surfaces with different intelligence quotients demonstrated the efficiency and efficacy of our method. PMID:26221691

Automated reference-free detection of motion artifacts in magnetic resonance images.

PubMed

Küstner, Thomas; Liebgott, Annika; Mauch, Lukas; Martirosian, Petros; Bamberg, Fabian; Nikolaou, Konstantin; Yang, Bin; Schick, Fritz; Gatidis, Sergios

2018-04-01

Our objectives were to provide an automated method for spatially resolved detection and quantification of motion artifacts in MR images of the head and abdomen as well as a quality control of the trained architecture. T1-weighted MR images of the head and the upper abdomen were acquired in 16 healthy volunteers under rest and under motion. Images were divided into overlapping patches of different sizes achieving spatial separation. Using these patches as input data, a convolutional neural network (CNN) was trained to derive probability maps for the presence of motion artifacts. A deep visualization offers a human-interpretable quality control of the trained CNN. Results were visually assessed on probability maps and as classification accuracy on a per-patch, per-slice and per-volunteer basis. On visual assessment, a clear difference of probability maps was observed between data sets with and without motion. The overall accuracy of motion detection on a per-patch/per-volunteer basis reached 97%/100% in the head and 75%/100% in the abdomen, respectively. Automated detection of motion artifacts in MRI is feasible with good accuracy in the head and abdomen. The proposed method provides quantification and localization of artifacts as well as a visualization of the learned content. It may be extended to other anatomic areas and used for quality assurance of MR images.

New machine learning tools for predictive vegetation mapping after climate change: Bagging and Random Forest perform better than Regression Tree Analysis

Treesearch

L.R. Iverson; A.M. Prasad; A. Liaw

2004-01-01

More and better machine learning tools are becoming available for landscape ecologists to aid in understanding species-environment relationships and to map probable species occurrence now and potentially into the future. To thal end, we evaluated three statistical models: Regression Tree Analybib (RTA), Bagging Trees (BT) and Random Forest (RF) for their utility in...

Artificial Intelligence-Based Student Learning Evaluation: A Concept Map-Based Approach for Analyzing a Student's Understanding of a Topic

ERIC Educational Resources Information Center

Jain, G. Panka; Gurupur, Varadraj P.; Schroeder, Jennifer L.; Faulkenberry, Eileen D.

2014-01-01

In this paper, we describe a tool coined as artificial intelligence-based student learning evaluation tool (AISLE). The main purpose of this tool is to improve the use of artificial intelligence techniques in evaluating a student's understanding of a particular topic of study using concept maps. Here, we calculate the probability distribution of…

Towards noninvasive method for the detection of pathological tissue variations by mapping different blood parameters

NASA Astrophysics Data System (ADS)

Abdallah, Omar; Qananwah, Qasem; Abo Alam, Kawther; Bolz, Armin

2010-04-01

This paper describes the development of an early detection method for probing pathological tissue variations. The method could be used for classifying various tissue alteration namely tumors tissue or skin disorders. The used approach is based on light scattering and absorption spectroscopy. Spectral content of the scattered light provides diagnostic information about the tissue contents. The importance of this method is using a safe light that has less power than the used in the imaging methods that will enable the frequent examination of tissue, while the exiting modalities have drawbacks like ionization, high cost, time-consuming, and agents' usage. A modality for mapping the oxygen saturation distribution in tissues noninvasively is new in this area of research, since this study focuses on the oxygen molecule in the tissue which supposed to be homogenously distributed through the tissues. Cancers may cause greater vascularization and greater oxygen consumption than in normal tissue. Therefore, oxygen existence and homogeneity will be alternated depending on the tissue state. In the proposed system, the signal was extracted after illuminating the tissue by light emitting diodes (LED's) that emits light in two wavelengths, red (660 nm) and infrared (880 nm). The absorption in these wavelengths is mainly due to oxyhemoglobin (HbO2) and deoxyhemoglobin (Hb) while other blood and tissue contents nearly have low effect on the signal. The backscattered signal which is received by a photodiodes array (128 PDs) was measured and processed using LabVIEW. Photoplethysmogram (PPG) signals have been measured at different locations. These signals will be used to differentiate between the normal and the pathological tissues. Variations in hemoglobin concentration and blood perfusion will also be used as an important indication feature for this purpose.

A new plan-scoring method using normal tissue complication probability for personalized treatment plan decisions in prostate cancer

NASA Astrophysics Data System (ADS)

Kim, Kwang Hyeon; Lee, Suk; Shim, Jang Bo; Yang, Dae Sik; Yoon, Won Sup; Park, Young Je; Kim, Chul Yong; Cao, Yuan Jie; Chang, Kyung Hwan

2018-01-01

The aim of this study was to derive a new plan-scoring index using normal tissue complication probabilities to verify different plans in the selection of personalized treatment. Plans for 12 patients treated with tomotherapy were used to compare scoring for ranking. Dosimetric and biological indexes were analyzed for the plans for a clearly distinguishable group ( n = 7) and a similar group ( n = 12), using treatment plan verification software that we developed. The quality factor ( QF) of our support software for treatment decisions was consistent with the final treatment plan for the clearly distinguishable group (average QF = 1.202, 100% match rate, n = 7) and the similar group (average QF = 1.058, 33% match rate, n = 12). Therefore, we propose a normal tissue complication probability (NTCP) based on the plan scoring index for verification of different plans for personalized treatment-plan selection. Scoring using the new QF showed a 100% match rate (average NTCP QF = 1.0420). The NTCP-based new QF scoring method was adequate for obtaining biological verification quality and organ risk saving using the treatment-planning decision-support software we developed for prostate cancer.

Characterizing optical properties and spatial heterogeneity of human ovarian tissue using spatial frequency domain imaging

NASA Astrophysics Data System (ADS)

Nandy, Sreyankar; Mostafa, Atahar; Kumavor, Patrick D.; Sanders, Melinda; Brewer, Molly; Zhu, Quing

2016-10-01

A spatial frequency domain imaging (SFDI) system was developed for characterizing ex vivo human ovarian tissue using wide-field absorption and scattering properties and their spatial heterogeneities. Based on the observed differences between absorption and scattering images of different ovarian tissue groups, six parameters were quantitatively extracted. These are the mean absorption and scattering, spatial heterogeneities of both absorption and scattering maps measured by a standard deviation, and a fitting error of a Gaussian model fitted to normalized mean Radon transform of the absorption and scattering maps. A logistic regression model was used for classification of malignant and normal ovarian tissues. A sensitivity of 95%, specificity of 100%, and area under the curve of 0.98 were obtained using six parameters extracted from the SFDI images. The preliminary results demonstrate the diagnostic potential of the SFDI method for quantitative characterization of wide-field optical properties and the spatial distribution heterogeneity of human ovarian tissue. SFDI could be an extremely robust and valuable tool for evaluation of the ovary and detection of neoplastic changes of ovarian cancer.

Quantitative real-time optical imaging of the tissue metabolic rate of oxygen consumption

NASA Astrophysics Data System (ADS)

Ghijsen, Michael; Lentsch, Griffin R.; Gioux, Sylvain; Brenner, Matthew; Durkin, Anthony J.; Choi, Bernard; Tromberg, Bruce J.

2018-03-01

The tissue metabolic rate of oxygen consumption (tMRO2) is a clinically relevant marker for a number of pathologies including cancer and arterial occlusive disease. We present and validate a noncontact method for quantitatively mapping tMRO2 over a wide, scalable field of view at 16 frames / s. We achieve this by developing a dual-wavelength, near-infrared coherent spatial frequency-domain imaging (cSFDI) system to calculate tissue optical properties (i.e., absorption, μa, and reduced scattering, μs‧, parameters) as well as the speckle flow index (SFI) at every pixel. Images of tissue oxy- and deoxyhemoglobin concentration ( [ HbO2 ] and [HHb]) are calculated from optical properties and combined with SFI to calculate tMRO2. We validate the system using a series of yeast-hemoglobin tissue-simulating phantoms and conduct in vivo tests in humans using arterial occlusions that demonstrate sensitivity to tissue metabolic oxygen debt and its repayment. Finally, we image the impact of cyanide exposure and toxicity reversal in an in vivo rabbit model showing clear instances of mitochondrial uncoupling and significantly diminished tMRO2. We conclude that dual-wavelength cSFDI provides rapid, quantitative, wide-field mapping of tMRO2 that can reveal unique spatial and temporal dynamics relevant to tissue pathology and viability.

Overexpression of peptide deformylase in breast, colon, and lung cancers.

PubMed

Randhawa, Harsharan; Chikara, Shireen; Gehring, Drew; Yildirim, Tuba; Menon, Jyotsana; Reindl, Katie M

2013-07-01

Human mitochondrial peptide deformylase (PDF) has been proposed as a novel cancer therapeutic target. However, very little is known about its expression and regulation in human tissues. The purpose of this study was to characterize the expression pattern of PDF in cancerous tissues and to identify mechanisms that regulate its expression. The mRNA expression levels of PDF and methionine aminopeptidase 1D (MAP1D), an enzyme involved in a related pathway with PDF, were determined using tissue panels containing cDNA from patients with various types of cancer (breast, colon, kidney, liver, lung, ovarian, prostate, or thyroid) and human cell lines. Protein levels of PDF were also determined in 2 colon cancer patients via western blotting. Colon cancer cells were treated with inhibitors of ERK, Akt, and mTOR signaling pathways and the resulting effects on PDF and MAP1D mRNA levels were determined by qPCR for colon and lung cancer cell lines. Finally, the effects of a PDF inhibitor, actinonin, on the proliferation of breast, colon, and prostate cell lines were determined using the CyQUANT assay. PDF and MAP1D mRNA levels were elevated in cancer cell lines compared to non-cancer lines. PDF mRNA levels were significantly increased in breast, colon, and lung cancer samples while MAP1D mRNA levels were increased in just colon cancers. The expression of PDF and MAP1D varied with stage in these cancers. Further, PDF protein expression was elevated in colon cancer tissue samples. Inhibition of the MEK/ERK, but not PI3K or mTOR, pathway reduced the expression of PDF and MAP1D in both colon and lung cancer cell lines. Further, inhibition of PDF with actinonin resulted in greater reduction of breast, colon, and prostate cancer cell proliferation than non-cancer cell lines. This is the first report showing that PDF is over-expressed in breast, colon, and lung cancers, and the first evidence that the MEK/ERK pathway plays a role in regulating the expression of PDF and MAP1D. The over-expression of PDF in several cancers and the inhibition of cancer cell growth by a PDF inhibitor suggest this enzyme may act as an oncogene to promote cancer cell proliferation.

Overexpression of peptide deformylase in breast, colon, and lung cancers

PubMed Central

2013-01-01

Background Human mitochondrial peptide deformylase (PDF) has been proposed as a novel cancer therapeutic target. However, very little is known about its expression and regulation in human tissues. The purpose of this study was to characterize the expression pattern of PDF in cancerous tissues and to identify mechanisms that regulate its expression. Methods The mRNA expression levels of PDF and methionine aminopeptidase 1D (MAP1D), an enzyme involved in a related pathway with PDF, were determined using tissue panels containing cDNA from patients with various types of cancer (breast, colon, kidney, liver, lung, ovarian, prostate, or thyroid) and human cell lines. Protein levels of PDF were also determined in 2 colon cancer patients via western blotting. Colon cancer cells were treated with inhibitors of ERK, Akt, and mTOR signaling pathways and the resulting effects on PDF and MAP1D mRNA levels were determined by qPCR for colon and lung cancer cell lines. Finally, the effects of a PDF inhibitor, actinonin, on the proliferation of breast, colon, and prostate cell lines were determined using the CyQUANT assay. Results PDF and MAP1D mRNA levels were elevated in cancer cell lines compared to non-cancer lines. PDF mRNA levels were significantly increased in breast, colon, and lung cancer samples while MAP1D mRNA levels were increased in just colon cancers. The expression of PDF and MAP1D varied with stage in these cancers. Further, PDF protein expression was elevated in colon cancer tissue samples. Inhibition of the MEK/ERK, but not PI3K or mTOR, pathway reduced the expression of PDF and MAP1D in both colon and lung cancer cell lines. Further, inhibition of PDF with actinonin resulted in greater reduction of breast, colon, and prostate cancer cell proliferation than non-cancer cell lines. Conclusions This is the first report showing that PDF is over-expressed in breast, colon, and lung cancers, and the first evidence that the MEK/ERK pathway plays a role in regulating the expression of PDF and MAP1D. The over-expression of PDF in several cancers and the inhibition of cancer cell growth by a PDF inhibitor suggest this enzyme may act as an oncogene to promote cancer cell proliferation. PMID:23815882

PERFORMANCE, RELIABILITY, AND IMPROVEMENT OF A TISSUE-SPECIFIC METABOLIC SIMULATOR

EPA Science Inventory

A methodology is described that has been used to build and enhance a simulator for rat liver metabolism providing reliable predictions within a large chemical domain. The tissue metabolism simulator (TIMES) utilizes a heuristic algorithm to generate plausible metabolic maps using...

Validity of T2 mapping in characterization of the regeneration tissue by bone marrow derived cell transplantation in osteochondral lesions of the ankle.

PubMed

Battaglia, M; Rimondi, E; Monti, C; Guaraldi, F; Sant'Andrea, A; Buda, R; Cavallo, M; Giannini, S; Vannini, F

2011-11-01

Bone marrow derived cell transplantation (BMDCT) has been recently suggested as a possible surgical technique to repair osteochondral lesions. To date, no qualitative MRI studies have evaluated its efficacy. The aim of our study is to investigate the validity of MRI T2-mapping sequence in characterizing the reparative tissue obtained and its ability to correlate with clinical results. 20 patients with an osteochondral lesion of the talus underwent BMDCT and were evaluated at 2 years follow up using MRI T2-mapping sequence. 20 healthy volunteers were recruited as controls. MRI images were acquired using a protocol suggested by the International Cartilage Repair Society, MOCART scoring system and T2 mapping. Results were then correlated with AOFAS clinical score. AOFAS score increased from 66.8±14.5 pre-operatively to 91.2±8.3 (p<0.0005) at 2 years follow-up. T2-relaxation time value of 35-45 ms was derived from healthy ankles evaluation and assumed as normal hyaline cartilage value and used as a control. Regenerated tissue with a T2-relaxation time value comparable to hyaline cartilage was found in all the cases treated, covering a mean of 78% of the repaired lesion area. A high clinical score was related directly to isointense signal in DPFSE fat sat (p=0.05), and percentage of regenerated hyaline cartilage (p=0.05), inversely to the percentage of regenerated fibrocartilage. Lesion's depth negatively related to the integrity of the repaired tissue's surface (tau=-0.523, p=0.007), and to the percentage of regenerated hyaline cartilage (rho=-0.546, p=0.013). Because of its ability to detect cartilage's quality and to correlate to the clinical score, MRI T2-mapping sequence integrated with Mocart score represent a valid, non-invasive technique for qualitative cartilage assessment after regenerative surgical procedures. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Survey design for lakes and reservoirs in the United States to assess contaminants in fish tissue

EPA Science Inventory

The National Lake Fish Tissue Study (NLFTS) was the first survey of fish contamination in lakes and reservoirs in the 48 conterminous states based on probability survey design. This study included the largest set (268) of persistent, bioaccumulative, and toxic (PBT) chemicals ev...

Rooting of conifer propagules

Treesearch

R.L. Mott

1977-01-01

An outline of the general problems involved with the propagation of elite conifer clones by rooted cuttings is drawn from published reports. New approaches for resolving these problems can come from studies of clone production through tissue culture methods. Probable extension of tissue culture techniques will permit the establishment of clones from adult, proven trees...

Factorization of Observables

NASA Astrophysics Data System (ADS)

Eliaš, Peter; Frič, Roman

2017-12-01

Categorical approach to probability leads to better understanding of basic notions and constructions in generalized (fuzzy, operational, quantum) probability, where observables—dual notions to generalized random variables (statistical maps)—play a major role. First, to avoid inconsistencies, we introduce three categories L, S, and P, the objects and morphisms of which correspond to basic notions of fuzzy probability theory and operational probability theory, and describe their relationships. To illustrate the advantages of categorical approach, we show that two categorical constructions involving observables (related to the representation of generalized random variables via products, or smearing of sharp observables, respectively) can be described as factorizing a morphism into composition of two morphisms having desired properties. We close with a remark concerning products.

Heavy Metal Content in Chilean Fish Related to Habitat Use, Tissue Type and River of Origin.

PubMed

Copaja, S V; Pérez, C A; Vega-Retter, C; Véliz, D

2017-12-01

In this study, we analyze the concentration of ten metals in two freshwater fish-the benthic catfish Trichomycterus areolatus and the limnetic silverside Basilichthys microlepidotus-in order to detect possible accumulation differences related to fish habitat (benthic or pelagic), tissue type (gill, liver and muscle), and the river of origin (four different rivers) in central Chile. The MANOVA performed with all variables and metals, revealed independent effects of fish, tissue and river. In the case of the fish factor, Cu, Cr, Mo and Zn showed statistically higher concentrations in catfish compared with silverside for all tissues and in all rivers (p < 0.05). In the case of the tissue factor, Al, Cr, Fe and Mn had statistically higher concentrations in liver and gills than in muscle (p  < 0.05). For the river effect, the analysis showed higher concentrations of Cr, Mn and Pb in the Cogoti river and the lower concentrations in the Recoleta river. These results suggest that not all metals have the same pattern of accumulation; however, some metals tend to accumulate more in readily catfish, probably due to their benthic habit, and in liver and gill tissue, probably as a result of accumulation from food sources and respiration.

The Probabilities of Unique Events

PubMed Central

Khemlani, Sangeet S.; Lotstein, Max; Johnson-Laird, Phil

2012-01-01

Many theorists argue that the probabilities of unique events, even real possibilities such as President Obama's re-election, are meaningless. As a consequence, psychologists have seldom investigated them. We propose a new theory (implemented in a computer program) in which such estimates depend on an intuitive non-numerical system capable only of simple procedures, and a deliberative system that maps intuitions into numbers. The theory predicts that estimates of the probabilities of conjunctions should often tend to split the difference between the probabilities of the two conjuncts. We report two experiments showing that individuals commit such violations of the probability calculus, and corroborating other predictions of the theory, e.g., individuals err in the same way even when they make non-numerical verbal estimates, such as that an event is highly improbable. PMID:23056224

Spatial patterns of high Aedes aegypti oviposition activity in northwestern Argentina.

PubMed

Estallo, Elizabet Lilia; Más, Guillermo; Vergara-Cid, Carolina; Lanfri, Mario Alberto; Ludueña-Almeida, Francisco; Scavuzzo, Carlos Marcelo; Introini, María Virginia; Zaidenberg, Mario; Almirón, Walter Ricardo

2013-01-01

In Argentina, dengue has affected mainly the Northern provinces, including Salta. The objective of this study was to analyze the spatial patterns of high Aedes aegypti oviposition activity in San Ramón de la Nueva Orán, northwestern Argentina. The location of clusters as hot spot areas should help control programs to identify priority areas and allocate their resources more effectively. Oviposition activity was detected in Orán City (Salta province) using ovitraps, weekly replaced (October 2005-2007). Spatial autocorrelation was measured with Moran's Index and depicted through cluster maps to identify hot spots. Total egg numbers were spatially interpolated and a classified map with Ae. aegypti high oviposition activity areas was performed. Potential breeding and resting (PBR) sites were geo-referenced. A logistic regression analysis of interpolated egg numbers and PBR location was performed to generate a predictive mapping of mosquito oviposition activity. Both cluster maps and predictive map were consistent, identifying in central and southern areas of the city high Ae. aegypti oviposition activity. A logistic regression model was successfully developed to predict Ae. aegypti oviposition activity based on distance to PBR sites, with tire dumps having the strongest association with mosquito oviposition activity. A predictive map reflecting probability of oviposition activity was produced. The predictive map delimitated an area of maximum probability of Ae. aegypti oviposition activity in the south of Orán city where tire dumps predominate. The overall fit of the model was acceptable (ROC=0.77), obtaining 99% of sensitivity and 75.29% of specificity. Distance to tire dumps is inversely associated with high mosquito activity, allowing us to identify hot spots. These methodologies are useful for prevention, surveillance, and control of tropical vector borne diseases and might assist National Health Ministry to focus resources more effectively.

Seismic hazard assessment of Syria using seismicity, DEM, slope, active tectonic and GIS

NASA Astrophysics Data System (ADS)

Ahmad, Raed; Adris, Ahmad; Singh, Ramesh

2016-07-01

In the present work, we discuss the use of an integrated remote sensing and Geographical Information System (GIS) techniques for evaluation of seismic hazard areas in Syria. The present study is the first time effort to create seismic hazard map with the help of GIS. In the proposed approach, we have used Aster satellite data, digital elevation data (30 m resolution), earthquake data, and active tectonic maps. Many important factors for evaluation of seismic hazard were identified and corresponding thematic data layers (past earthquake epicenters, active faults, digital elevation model, and slope) were generated. A numerical rating scheme has been developed for spatial data analysis using GIS to identify ranking of parameters to be included in the evaluation of seismic hazard. The resulting earthquake potential map delineates the area into different relative susceptibility classes: high, moderate, low and very low. The potential earthquake map was validated by correlating the obtained different classes with the local probability that produced using conventional analysis of observed earthquakes. Using earthquake data of Syria and the peak ground acceleration (PGA) data is introduced to the model to develop final seismic hazard map based on Gutenberg-Richter (a and b values) parameters and using the concepts of local probability and recurrence time. The application of the proposed technique in Syrian region indicates that this method provides good estimate of seismic hazard map compared to those developed from traditional techniques (Deterministic (DSHA) and probabilistic seismic hazard (PSHA). For the first time we have used numerous parameters using remote sensing and GIS in preparation of seismic hazard map which is found to be very realistic.

Spiral waves characterization: Implications for an automated cardiodynamic tissue characterization.

PubMed

Alagoz, Celal; Cohen, Andrew R; Frisch, Daniel R; Tunç, Birkan; Phatharodom, Saran; Guez, Allon

2018-07-01

Spiral waves are phenomena observed in cardiac tissue especially during fibrillatory activities. Spiral waves are revealed through in-vivo and in-vitro studies using high density mapping that requires special experimental setup. Also, in-silico spiral wave analysis and classification is performed using membrane potentials from entire tissue. In this study, we report a characterization approach that identifies spiral wave behaviors using intracardiac electrogram (EGM) readings obtained with commonly used multipolar diagnostic catheters that perform localized but high-resolution readings. Specifically, the algorithm is designed to distinguish between stationary, meandering, and break-up rotors. The clustering and classification algorithms are tested on simulated data produced using a phenomenological 2D model of cardiac propagation. For EGM measurements, unipolar-bipolar EGM readings from various locations on tissue using two catheter types are modeled. The distance measure between spiral behaviors are assessed using normalized compression distance (NCD), an information theoretical distance. NCD is a universal metric in the sense it is solely based on compressibility of dataset and not requiring feature extraction. We also introduce normalized FFT distance (NFFTD) where compressibility is replaced with a FFT parameter. Overall, outstanding clustering performance was achieved across varying EGM reading configurations. We found that effectiveness in distinguishing was superior in case of NCD than NFFTD. We demonstrated that distinct spiral activity identification on a behaviorally heterogeneous tissue is also possible. This report demonstrates a theoretical validation of clustering and classification approaches that provide an automated mapping from EGM signals to assessment of spiral wave behaviors and hence offers a potential mapping and analysis framework for cardiac tissue wavefront propagation patterns. Copyright © 2018 Elsevier B.V. All rights reserved.

Local breast density assessment using reacquired mammographic images.

PubMed

García, Eloy; Diaz, Oliver; Martí, Robert; Diez, Yago; Gubern-Mérida, Albert; Sentís, Melcior; Martí, Joan; Oliver, Arnau

2017-08-01

The aim of this paper is to evaluate the spatial glandular volumetric tissue distribution as well as the density measures provided by Volpara™ using a dataset composed of repeated pairs of mammograms, where each pair was acquired in a short time frame and in a slightly changed position of the breast. We conducted a retrospective analysis of 99 pairs of repeatedly acquired full-field digital mammograms from 99 different patients. The commercial software Volpara™ Density Maps (Volpara Solutions, Wellington, New Zealand) is used to estimate both the global and the local glandular tissue distribution in each image. The global measures provided by Volpara™, such as breast volume, volume of glandular tissue, and volumetric breast density are compared between the two acquisitions. The evaluation of the local glandular information is performed using histogram similarity metrics, such as intersection and correlation, and local measures, such as statistics from the difference image and local gradient correlation measures. Global measures showed a high correlation (breast volume R=0.99, volume of glandular tissue R=0.94, and volumetric breast density R=0.96) regardless the anode/filter material. Similarly, histogram intersection and correlation metric showed that, for each pair, the images share a high degree of information. Regarding the local distribution of glandular tissue, small changes in the angle of view do not yield significant differences in the glandular pattern, whilst changes in the breast thickness between both acquisition affect the spatial parenchymal distribution. This study indicates that Volpara™ Density Maps is reliable in estimating the local glandular tissue distribution and can be used for its assessment and follow-up. Volpara™ Density Maps is robust to small variations of the acquisition angle and to the beam energy, although divergences arise due to different breast compression conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

HELP: XID+, the probabilistic de-blender for Herschel SPIRE maps

NASA Astrophysics Data System (ADS)

Hurley, P. D.; Oliver, S.; Betancourt, M.; Clarke, C.; Cowley, W. I.; Duivenvoorden, S.; Farrah, D.; Griffin, M.; Lacey, C.; Le Floc'h, E.; Papadopoulos, A.; Sargent, M.; Scudder, J. M.; Vaccari, M.; Valtchanov, I.; Wang, L.

2017-01-01

We have developed a new prior-based source extraction tool, XID+, to carry out photometry in the Herschel SPIRE (Spectral and Photometric Imaging Receiver) maps at the positions of known sources. XID+ is developed using a probabilistic Bayesian framework that provides a natural framework in which to include prior information, and uses the Bayesian inference tool Stan to obtain the full posterior probability distribution on flux estimates. In this paper, we discuss the details of XID+ and demonstrate the basic capabilities and performance by running it on simulated SPIRE maps resembling the COSMOS field, and comparing to the current prior-based source extraction tool DESPHOT. Not only we show that XID+ performs better on metrics such as flux accuracy and flux uncertainty accuracy, but we also illustrate how obtaining the posterior probability distribution can help overcome some of the issues inherent with maximum-likelihood-based source extraction routines. We run XID+ on the COSMOS SPIRE maps from Herschel Multi-Tiered Extragalactic Survey using a 24-μm catalogue as a positional prior, and a uniform flux prior ranging from 0.01 to 1000 mJy. We show the marginalized SPIRE colour-colour plot and marginalized contribution to the cosmic infrared background at the SPIRE wavelengths. XID+ is a core tool arising from the Herschel Extragalactic Legacy Project (HELP) and we discuss how additional work within HELP providing prior information on fluxes can and will be utilized. The software is available at https://github.com/H-E-L-P/XID_plus. We also provide the data product for COSMOS. We believe this is the first time that the full posterior probability of galaxy photometry has been provided as a data product.

Accounting for geophysical information in geostatistical characterization of unexploded ordnance (UXO) sites.

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

Saito, Hirotaka; Goovaerts, Pierre; McKenna, Sean Andrew

2003-06-01

Efficient and reliable unexploded ordnance (UXO) site characterization is needed for decisions regarding future land use. There are several types of data available at UXO sites and geophysical signal maps are one of the most valuable sources of information. Incorporation of such information into site characterization requires a flexible and reliable methodology. Geostatistics allows one to account for exhaustive secondary information (i.e.,, known at every location within the field) in many different ways. Kriging and logistic regression were combined to map the probability of occurrence of at least one geophysical anomaly of interest, such as UXO, from a limited numbermore » of indicator data. Logistic regression is used to derive the trend from a geophysical signal map, and kriged residuals are added to the trend to estimate the probabilities of the presence of UXO at unsampled locations (simple kriging with varying local means or SKlm). Each location is identified for further remedial action if the estimated probability is greater than a given threshold. The technique is illustrated using a hypothetical UXO site generated by a UXO simulator, and a corresponding geophysical signal map. Indicator data are collected along two transects located within the site. Classification performances are then assessed by computing proportions of correct classification, false positive, false negative, and Kappa statistics. Two common approaches, one of which does not take any secondary information into account (ordinary indicator kriging) and a variant of common cokriging (collocated cokriging), were used for comparison purposes. Results indicate that accounting for exhaustive secondary information improves the overall characterization of UXO sites if an appropriate methodology, SKlm in this case, is used.« less

Corticostriatal connectivity fingerprints: Probability maps based on resting-state functional connectivity.

PubMed

Jaspers, Ellen; Balsters, Joshua H; Kassraian Fard, Pegah; Mantini, Dante; Wenderoth, Nicole

2017-03-01

Over the last decade, structure-function relationships have begun to encompass networks of brain areas rather than individual structures. For example, corticostriatal circuits have been associated with sensorimotor, limbic, and cognitive information processing, and damage to these circuits has been shown to produce unique behavioral outcomes in Autism, Parkinson's Disease, Schizophrenia and healthy ageing. However, it remains an open question how abnormal or absent connectivity can be detected at the individual level. Here, we provide a method for clustering gross morphological structures into subregions with unique functional connectivity fingerprints, and generate network probability maps usable as a baseline to compare individual cases against. We used connectivity metrics derived from resting-state fMRI (N = 100), in conjunction with hierarchical clustering methods, to parcellate the striatum into functionally distinct clusters. We identified three highly reproducible striatal subregions, across both hemispheres and in an independent replication dataset (N = 100) (dice-similarity values 0.40-1.00). Each striatal seed region resulted in a highly reproducible distinct connectivity fingerprint: the putamen showed predominant connectivity with cortical and cerebellar sensorimotor and language processing areas; the ventromedial striatum cluster had a distinct limbic connectivity pattern; the caudate showed predominant connectivity with the thalamus, frontal and occipital areas, and the cerebellum. Our corticostriatal probability maps agree with existing connectivity data in humans and non-human primates, and showed a high degree of replication. We believe that these maps offer an efficient tool to further advance hypothesis driven research and provide important guidance when investigating deviant connectivity in neurological patient populations suffering from e.g., stroke or cerebral palsy. Hum Brain Mapp 38:1478-1491, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Conductive carbon tape used for support and mounting of both whole animal and fragile heat-treated tissue sections for MALDI MS imaging and quantitation.

PubMed

Goodwin, Richard J A; Nilsson, Anna; Borg, Daniel; Langridge-Smith, Pat R R; Harrison, David J; Mackay, C Logan; Iverson, Suzanne L; Andrén, Per E

2012-08-30

Analysis of whole animal tissue sections by MALDI MS imaging (MSI) requires effective sample collection and transfer methods to allow the highest quality of in situ analysis of small or hard to dissect tissues. We report on the use of double-sided adhesive conductive carbon tape during whole adult rat tissue sectioning of carboxymethyl cellulose (CMC) embedded animals, with samples mounted onto large format conductive glass and conductive plastic MALDI targets, enabling MSI analysis to be performed on both TOF and FT-ICR MALDI mass spectrometers. We show that mounting does not unduly affect small molecule MSI detection by analyzing tiotropium abundance and distribution in rat lung tissues, with direct on-tissue quantitation achieved. Significantly, we use the adhesive tape to provide support to embedded delicate heat-stabilized tissues, enabling sectioning and mounting to be performed that maintained tissue integrity on samples that had previously been impossible to adequately prepare section for MSI analysis. The mapping of larger peptidomic molecules was not hindered by tape mounting samples and we demonstrate this by mapping the distribution of PEP-19 in both native and heat-stabilized rat brains. Furthermore, we show that without heat stabilization PEP-19 degradation fragments can detected and identified directly by MALDI MSI analysis. Copyright © 2012 Elsevier B.V. All rights reserved.

In vivo microvascular imaging of human oral and nasal cavities using swept-source optical coherence tomography with a single forward/side viewing probe

NASA Astrophysics Data System (ADS)

Choi, Woo June; Wang, Ruikang K.

2015-03-01

We report three-dimensional (3D) imaging of microcirculation within human cavity tissues in vivo using a high-speed swept-source optical coherence tomography (SS-OCT) at 1.3 μm with a modified probe interface. Volumetric structural OCT images of the inner tissues of oral and nasal cavities are acquired with a field of view of 2 mm x 2 mm. Two types of disposable and detachable probe attachments are devised and applied to the port of the imaging probe of OCT system, enabling forward and side imaging scans for selective and easy access to specific cavity tissue sites. Blood perfusion is mapped with OCT-based microangiography from 3D structural OCT images, in which a novel vessel extraction algorithm is used to decouple dynamic light scattering signals, due to moving blood cells, from the background scattering signals due to static tissue elements. Characteristic tissue anatomy and microvessel architectures of various cavity tissue regions of a healthy human volunteer are identified with the 3D OCT images and the corresponding 3D vascular perfusion maps at a level approaching capillary resolution. The initial finding suggests that the proposed method may be engineered into a promising tool for evaluating and monitoring tissue microcirculation and its alteration within a wide-range of cavity tissues in the patients with various pathological conditions.

Simulation study of amplitude-modulated (AM) harmonic motion imaging (HMI) for stiffness contrast quantification with experimental validation.

PubMed

Maleke, Caroline; Luo, Jianwen; Gamarnik, Viktor; Lu, Xin L; Konofagou, Elisa E

2010-07-01

The objective of this study is to show that Harmonic Motion Imaging (HMI) can be used as a reliable tumor-mapping technique based on the tumor's distinct stiffness at the early onset of disease. HMI is a radiation-force-based imaging method that generates a localized vibration deep inside the tissue to estimate the relative tissue stiffness based on the resulting displacement amplitude. In this paper, a finite-element model (FEM) study is presented, followed by an experimental validation in tissue-mimicking polyacrylamide gels and excised human breast tumors ex vivo. This study compares the resulting tissue motion in simulations and experiments at four different gel stiffnesses and three distinct spherical inclusion diameters. The elastic moduli of the gels were separately measured using mechanical testing. Identical transducer parameters were used in both the FEM and experimental studies, i.e., a 4.5-MHz single-element focused ultrasound (FUS) and a 7.5-MHz diagnostic (pulse-echo) transducer. In the simulation, an acoustic pressure field was used as the input stimulus to generate a localized vibration inside the target. Radiofrequency (rf) signals were then simulated using a 2D convolution model. A one-dimensional cross-correlation technique was performed on the simulated and experimental rf signals to estimate the axial displacement resulting from the harmonic radiation force. In order to measure the reliability of the displacement profiles in estimating the tissue stiffness distribution, the contrast-transfer efficiency (CTE) was calculated. For tumor mapping ex vivo, a harmonic radiation force was applied using a 2D raster-scan technique. The 2D HMI images of the breast tumor ex vivo could detect a malignant tumor (20 x 10 mm2) surrounded by glandular and fat tissues. The FEM and experimental results from both gels and breast tumors ex vivo demonstrated that HMI was capable of detecting and mapping the tumor or stiff inclusion with various diameters or stiffnesses. HMI may thus constitute a promising technique in tumor detection (>3 mm in diameter) and mapping based on its distinct stiffness.

Limitations of metallothioneins in common cockles (Cerastoderma edule) and sponges (Haliclona oculata) as biomarkers of metal contamination in a semi-enclosed coastal area.

PubMed

Aly, W; Williams, I D; Hudson, M D

2014-03-01

Poole Harbour is typical of many heavily anthropologically impacted semi-enclosed estuarine coastal areas under pressure from metal pollution across the world. This study examined the physiological significance of metal burdens within that sensitive area, and assessed the potential use of metallothionein (MT) concentrations in two organisms: the common cockle (Cerastoderma edule) and the Mermaid's glove sponge (Haliclona oculata) for mapping the spatial extent of the biological response to metal contamination. A spectrophotometric method was applied for detection of MT in the bivalve, and for the first time to detect MT in sponges. The results show that while some metal concentrations in cockle and sponge tissues and in their surrounding environment (water and sediment) could be related to sources of metal contamination, MT values in the soft tissue of cockles and whole tissue of sponges are not. No relation could be found between MT in both cockles and sponges, and any of the tested metals (As, Cd, Cr, Cu, Pb, Hg, Ni, Ag, Sn, Zn). Furthermore, some of the lowest MT concentrations were detected in heavily polluted areas, indicating that MT concentrations in tested organisms are not exclusively associated with metal concentrations, as other environmental factors could affect induction of this protein. Organisms probably have a high tolerance to metal contamination and chronic exposure to a high level of contamination resulted in developing a variety of detoxification mechanisms. Results indicate that further study of metal stress in this type of ecosystem may need to examine other indicator species and/or apply a different biomonitoring technique. Copyright © 2013 Elsevier B.V. All rights reserved.

Imaging the spectral reflectance properties of bipolar radiofrequency-fused bowel tissue

NASA Astrophysics Data System (ADS)

Clancy, Neil T.; Arya, Shobhit; Stoyanov, Danail; Du, Xiaofei; Hanna, George B.; Elson, Daniel S.

2015-07-01

Delivery of radiofrequency (RF) electrical energy is used during surgery to heat and seal tissue, such as vessels, allowing resection without blood loss. Recent work has suggested that this approach may be extended to allow surgical attachment of larger tissue segments for applications such as bowel anastomosis. In a large series of porcine surgical procedures bipolar RF energy was used to resect and re-seal the small bowel in vivo with a commercial tissue fusion device (Ligasure; Covidien PLC, USA). The tissue was then imaged with a multispectral imaging laparoscope to obtain a spectral datacube comprising both fused and healthy tissue. Maps of blood volume, oxygen saturation and scattering power were derived from the measured reflectance spectra using an optimised light-tissue interaction model. A 60% increase in reflectance of visible light (460-700 nm) was observed after fusion, with the tissue taking on a white appearance. Despite this the distinctive shape of the haemoglobin absorption spectrum was still noticeable in the 460-600 nm wavelength range. Scattering power increased in the fused region in comparison to normal serosa, while blood volume and oxygen saturation decreased. Observed fusion-induced changes in the reflectance spectrum are consistent with the biophysical changes induced through tissue denaturation and increased collagen cross-linking. The multispectral imager allows mapping of the spatial extent of these changes and classification of the zone of damaged tissue. Further analysis of the spectral data in parallel with histopathological examination of excised specimens will allow correlation of the optical property changes with microscopic alterations in tissue structure.

Prevalence of developmental dental hard-tissue anomalies and association with caries and oral hygiene status of children in Southwestern, Nigeria.

PubMed

Popoola, Bamidele O; Onyejaka, Nneka; Folayan, Morenike O

2016-07-07

Developmental dental hard tissue anomalies are often associated with oral health problems. This study determined the clinical prevalence of developmental dental hard tissue anomalies in the permanent dentition of children resident in southwestern Nigeria and its association with dental caries and poor oral hygiene status. This was a cross-sectional study recruiting 1565 school children, 12 to 15 year old attending schools in Ibadan, Oyo State and Ile-Ife, Osun State. All eligible study participants had oral examinations conducted to determine presence of developmental hard dental tissue anomalies, caries and oral hygiene status. The prevalence of developmental dental hard tissue anomalies was determined. Logistic Poisson regression was used to determine the association of between developmental dental hard tissue anomalies, caries and oral hygiene status. Only 65 (4.2 %) children had clinically diagnosed developmental dental hard tissue anomalies. The most prevalent anomaly was enamel hypoplasia (2.2 %). More females (p = 0.003) and more children with middle socioeconomic class (p = 0.001) had enamel hypoplasia. The probability of having poor oral hygiene was significantly increased for children with developmental dental anomalies (APR: 0.07; 95 % CI: 0.03 - 0.12; p = 0.002). The probability of having caries was insignificantly increased for children with developmental dental hard tissue anomalies (APR: 0.005; 95 % CI: -0.03 - 0.04; p = 0.08). The most prevalence clinically detectable developmental dental hard tissue anomalies for the study population was enamel hypoplasia. The presence of developmental dental hard tissue anomalies significantly increased the chances of having poor oral hygiene but not caries. Further studies are required to understand if poor oral hygiene is associated with dental caries in children with developmental dental hard tissue anomalies.

Parametric methods for characterizing myocardial tissue by magnetic resonance imaging (part 2): T2 mapping.

PubMed

Perea Palazón, R J; Solé Arqués, M; Prat González, S; de Caralt Robira, T M; Cibeira López, M T; Ortiz Pérez, J T

2015-01-01

Cardiac magnetic resonance imaging is considered the reference technique for characterizing myocardial tissue; for example, T2-weighted sequences make it possible to evaluate areas of edema or myocardial inflammation. However, traditional sequences have many limitations and provide only qualitative information. Moreover, traditional sequences depend on the reference to remote myocardium or skeletal muscle, which limits their ability to detect and quantify diffuse myocardial damage. Recently developed magnetic resonance myocardial mapping techniques enable quantitative assessment of parameters indicative of edema. These techniques have proven better than traditional sequences both in acute cardiomyopathy and in acute ischemic heart disease. This article synthesizes current developments in T2 mapping as well as their clinical applications and limitations. Copyright © 2014 SERAM. Published by Elsevier España, S.L.U. All rights reserved.

The Influence of Phonotactic Probability on Nonword Repetition and Fast Mapping in 3-Year-Olds with a History of Expressive Language Delay

ERIC Educational Resources Information Center

MacRoy-Higgins, Michelle; Dalton, Kevin Patrick

2015-01-01

Purpose: The purpose of this study was to examine the influence of phonotactic probability on sublexical (phonological) and lexical representations in 3-year-olds who had a history of being late talkers in comparison with their peers with typical language development. Method: Ten 3-year-olds who were late talkers and 10 age-matched typically…

Correlation between the Temperature Dependence of Intrsinsic Mr Parameters and Thermal Dose Measured by a Rapid Chemical Shift Imaging Technique

PubMed Central

Taylor, Brian A.; Elliott, Andrew M.; Hwang, Ken-Pin; Hazle, John D.; Stafford, R. Jason

2011-01-01

In order to investigate simultaneous MR temperature imaging and direct validation of tissue damage during thermal therapy, temperature-dependent signal changes in proton resonance frequency (PRF) shifts, R2* values, and T1-weighted amplitudes are measured from one technique in ex vivo tissue heated with a 980-nm laser at 1.5T and 3.0T. Using a multi-gradient echo acquisition and signal modeling with the Stieglitz-McBride algorithm, the temperature sensitivity coefficient (TSC) values of these parameters are measured in each tissue at high spatiotemporal resolutions (1.6×1.6×4mm3,≤5sec) at the range of 25-61 °C. Non-linear changes in MR parameters are examined and correlated with an Arrhenius rate dose model of thermal damage. Using logistic regression, the probability of changes in these parameters is calculated as a function of thermal dose to determine if changes correspond to thermal damage. Temperature calibrations demonstrate TSC values which are consistent with previous studies. Temperature sensitivity of R2* and, in some cases, T1-weighted amplitudes are statistically different before and after thermal damage occurred. Significant changes in the slopes of R2* as a function of temperature are observed. Logistic regression analysis shows that these changes could be accurately predicted using the Arrhenius rate dose model (Ω=1.01±0.03), thereby showing that the changes in R2* could be direct markers of protein denaturation. Overall, by using a chemical shift imaging technique with simultaneous temperature estimation, R2* mapping and T1-W imaging, it is shown that changes in the sensitivity of R2* and, to a lesser degree, T1-W amplitudes are measured in ex vivo tissue when thermal damage is expected to occur according to Arrhenius rate dose models. These changes could possibly be used for direct validation of thermal damage in contrast to model-based predictions. PMID:21721063

Genome-wide identification and analysis of A-to-I RNA editing events in bovine by transcriptome sequencing

PubMed Central

Salehi, Abdolreza; Rivera, Rocío Melissa

2018-01-01

RNA editing increases the diversity of the transcriptome and proteome. Adenosine-to-inosine (A-to-I) editing is the predominant type of RNA editing in mammals and it is catalyzed by the adenosine deaminases acting on RNA (ADARs) family. Here, we used a largescale computational analysis of transcriptomic data from brain, heart, colon, lung, spleen, kidney, testes, skeletal muscle and liver, from three adult animals in order to identify RNA editing sites in bovine. We developed a computational pipeline and used a rigorous strategy to identify novel editing sites from RNA-Seq data in the absence of corresponding DNA sequence information. Our methods take into account sequencing errors, mapping bias, as well as biological replication to reduce the probability of obtaining a false-positive result. We conducted a detailed characterization of sequence and structural features related to novel candidate sites and found 1,600 novel canonical A-to-I editing sites in the nine bovine tissues analyzed. Results show that these sites 1) occur frequently in clusters and short interspersed nuclear elements (SINE) repeats, 2) have a preference for guanines depletion/enrichment in the flanking 5′/3′ nucleotide, 3) occur less often in coding sequences than other regions of the genome, and 4) have low evolutionary conservation. Further, we found that a positive correlation exists between expression of ADAR family members and tissue-specific RNA editing. Most of the genes with predicted A-to-I editing in each tissue were significantly enriched in biological terms relevant to the function of the corresponding tissue. Lastly, the results highlight the importance of the RNA editome in nervous system regulation. The present study extends the list of RNA editing sites in bovine and provides pipelines that may be used to investigate the editome in other organisms. PMID:29470549

Organization of the spinal trigeminal nucleus in star-nosed moles.

PubMed

Sawyer, Eva K; Leitch, Duncan B; Catania, Kenneth C

2014-10-01

Somatosensory inputs from the face project to multiple regions of the trigeminal nuclear complex in the brainstem. In mice and rats, three subdivisions contain visible representations of the mystacial vibrissae, the principal sensory nucleus, spinal trigeminal subnucleus interpolaris, and subnucleus caudalis. These regions are considered important for touch with high spatial acuity, active touch, and pain and temperature sensation, respectively. Like mice and rats, the star-nosed mole (Condylura cristata) is a somatosensory specialist. Given the visible star pattern in preparations of the star-nosed mole cortex and the principal sensory nucleus, we hypothesized there were star patterns in the spinal trigeminal nucleus subnuclei interpolaris and caudalis. In sections processed for cytochrome oxidase, we found star-like segmentation consisting of lightly stained septa separating darkly stained patches in subnucleus interpolaris (juvenile tissue) and subnucleus caudalis (juvenile and adult tissue). Subnucleus caudalis represented the face in a three-dimensional map, with the most anterior part of the face represented more rostrally than posterior parts of the face. Multiunit electrophysiological mapping was used to map the ipsilateral face. Ray-specific receptive fields in adults matched the CO segmentation. The mean areas of multiunit receptive fields in subnucleus interpolaris and caudalis were larger than previously mapped receptive fields in the mole's principal sensory nucleus. The proportion of tissue devoted to each ray's representation differed between the subnucleus interpolaris and the principal sensory nucleus. Our finding that different trigeminal brainstem maps can exaggerate different parts of the face could provide new insights for the roles of these different somatosensory stations. © 2014 Wiley Periodicals, Inc.

Organization of the spinal trigeminal nucleus in Star-Nosed Moles

PubMed Central

Sawyer, Eva K.; Leitch, Duncan B.; Catania, Kenneth C.

2014-01-01

Somatosensory inputs from the face project to multiple regions of the trigeminal nuclear complex in the brainstem. In mice and rats three subdivisions contain visible representations of the mystacial vibrissae: the principal sensory nucleus, the spinal trigeminal subnucleus interpolaris and subnucleus caudalis. These regions are considered important for touch with high spatial acuity, active touch, and pain and temperature sensation, respectively. Like mice and rats, the star-nosed mole (Condylura cristata) is a somatosensory specialist. Given the visible star pattern in preparations of the star-nosed mole cortex and the principal sensory nucleus, we hypothesized there were star patterns in the spinal trigeminal nucleus subnuclei interpolaris and caudalis. In sections processed for cytochrome oxidase we found star-like segmentation consisting of lightly stained septa separating darkly stained patches in subnucleus interpolaris (juvenile tissue) and subnucleus caudalis (juvenile and adult tissue). Subnucleus caudalis represented the face in a three-dimensional map with the most anterior part of the face represented more rostrally than posterior parts of the face. Multi-unit electrophysiological mapping was used to map the ipsilateral face. Ray-specific receptive fields in adults matched the CO-segmentation. The mean areas of multiunit receptive fields in subnucleus interpolaris and caudalis were larger than previously mapped receptive fields in the mole's principal sensory nucleus. The proportion of tissue devoted to each ray's representation differed between subnucleus interpolaris and the principal sensory nucleus. Our finding that different trigeminal brainstem maps can exaggerate different parts of the face could provide new insights for the roles of these different somatosensory stations. PMID:24715542

Comb-push Ultrasound Shear Elastography (CUSE): A Novel Method for Two-dimensional Shear Elasticity Imaging of Soft Tissues

PubMed Central

Song, Pengfei; Zhao, Heng; Manduca, Armando; Urban, Matthew W.; Greenleaf, James F.; Chen, Shigao

2012-01-01

Fast and accurate tissue elasticity imaging is essential in studying dynamic tissue mechanical properties. Various ultrasound shear elasticity imaging techniques have been developed in the last two decades. However, to reconstruct a full field-of-view 2D shear elasticity map, multiple data acquisitions are typically required. In this paper, a novel shear elasticity imaging technique, comb-push ultrasound shear elastography (CUSE), is introduced in which only one rapid data acquisition (less than 35 ms) is needed to reconstruct a full field-of-view 2D shear wave speed map (40 mm × 38 mm). Multiple unfocused ultrasound beams arranged in a comb pattern (comb-push) are used to generate shear waves. A directional filter is then applied upon the shear wave field to extract the left-to-right (LR) and right-to-left (RL) propagating shear waves. Local shear wave speed is recovered using a time-of-flight method based on both LR and RL waves. Finally a 2D shear wave speed map is reconstructed by combining the LR and RL speed maps. Smooth and accurate shear wave speed maps are reconstructed using the proposed CUSE method in two calibrated homogeneous phantoms with different moduli. Inclusion phantom experiments demonstrate that CUSE is capable of providing good contrast (contrast-to-noise-ratio ≥ 25 dB) between the inclusion and background without artifacts and is insensitive to inclusion positions. Safety measurements demonstrate that all regulated parameters of the ultrasound output level used in CUSE sequence are well below the FDA limits for diagnostic ultrasound. PMID:22736690

Saliency Detection via Absorbing Markov Chain With Learnt Transition Probability.

PubMed

Lihe Zhang; Jianwu Ai; Bowen Jiang; Huchuan Lu; Xiukui Li

2018-02-01

In this paper, we propose a bottom-up saliency model based on absorbing Markov chain (AMC). First, a sparsely connected graph is constructed to capture the local context information of each node. All image boundary nodes and other nodes are, respectively, treated as the absorbing nodes and transient nodes in the absorbing Markov chain. Then, the expected number of times from each transient node to all other transient nodes can be used to represent the saliency value of this node. The absorbed time depends on the weights on the path and their spatial coordinates, which are completely encoded in the transition probability matrix. Considering the importance of this matrix, we adopt different hierarchies of deep features extracted from fully convolutional networks and learn a transition probability matrix, which is called learnt transition probability matrix. Although the performance is significantly promoted, salient objects are not uniformly highlighted very well. To solve this problem, an angular embedding technique is investigated to refine the saliency results. Based on pairwise local orderings, which are produced by the saliency maps of AMC and boundary maps, we rearrange the global orderings (saliency value) of all nodes. Extensive experiments demonstrate that the proposed algorithm outperforms the state-of-the-art methods on six publicly available benchmark data sets.

Mars Exploration Rovers Landing Dispersion Analysis

NASA Technical Reports Server (NTRS)

Knocke, Philip C.; Wawrzyniak, Geoffrey G.; Kennedy, Brian M.; Desai, Prasun N.; Parker, TImothy J.; Golombek, Matthew P.; Duxbury, Thomas C.; Kass, David M.

2004-01-01

Landing dispersion estimates for the Mars Exploration Rover missions were key elements in the site targeting process and in the evaluation of landing risk. This paper addresses the process and results of the landing dispersion analyses performed for both Spirit and Opportunity. The several contributors to landing dispersions (navigation and atmospheric uncertainties, spacecraft modeling, winds, and margins) are discussed, as are the analysis tools used. JPL's MarsLS program, a MATLAB-based landing dispersion visualization and statistical analysis tool, was used to calculate the probability of landing within hazardous areas. By convolving this with the probability of landing within flight system limits (in-spec landing) for each hazard area, a single overall measure of landing risk was calculated for each landing ellipse. In-spec probability contours were also generated, allowing a more synoptic view of site risks, illustrating the sensitivity to changes in landing location, and quantifying the possible consequences of anomalies such as incomplete maneuvers. Data and products required to support these analyses are described, including the landing footprints calculated by NASA Langley's POST program and JPL's AEPL program, cartographically registered base maps and hazard maps, and flight system estimates of in-spec landing probabilities for each hazard terrain type. Various factors encountered during operations, including evolving navigation estimates and changing atmospheric models, are discussed and final landing points are compared with approach estimates.

Integrating statistical and process-based models to produce probabilistic landslide hazard at regional scale

NASA Astrophysics Data System (ADS)

Strauch, R. L.; Istanbulluoglu, E.

2017-12-01

We develop a landslide hazard modeling approach that integrates a data-driven statistical model and a probabilistic process-based shallow landslide model for mapping probability of landslide initiation, transport, and deposition at regional scales. The empirical model integrates the influence of seven site attribute (SA) classes: elevation, slope, curvature, aspect, land use-land cover, lithology, and topographic wetness index, on over 1,600 observed landslides using a frequency ratio (FR) approach. A susceptibility index is calculated by adding FRs for each SA on a grid-cell basis. Using landslide observations we relate susceptibility index to an empirically-derived probability of landslide impact. This probability is combined with results from a physically-based model to produce an integrated probabilistic map. Slope was key in landslide initiation while deposition was linked to lithology and elevation. Vegetation transition from forest to alpine vegetation and barren land cover with lower root cohesion leads to higher frequency of initiation. Aspect effects are likely linked to differences in root cohesion and moisture controlled by solar insulation and snow. We demonstrate the model in the North Cascades of Washington, USA and identify locations of high and low probability of landslide impacts that can be used by land managers in their design, planning, and maintenance.

An atlas of DNA methylation in diverse bovine tissues

USDA-ARS?s Scientific Manuscript database

We launched an effort to produce a reference cattle DNA methylation resource to improve animal production. We will employ experimental pipelines built around next generation sequencing technologies to map DNA methylation in cultured cells and primary tissues systems frequently involved in animal pro...

Introducing ShakeMap to potential users in Puerto Rico using scenarios of damaging historical and probable earthquakes

NASA Astrophysics Data System (ADS)

Huerfano, V. A.; Cua, G.; von Hillebrandt, C.; Saffar, A.

2007-12-01

The island of Puerto Rico has a long history of damaging earthquakes. Major earthquakes from off-shore sources have affected Puerto Rico in 1520, 1615, 1670, 1751, 1787, 1867, and 1918 (Mueller et al, 2003; PRSN Catalogue). Recent trenching has also yielded evidence of possible M7.0 events inland (Prentice, 2000). The high seismic hazard, large population, high tsunami potential and relatively poor construction practice can result in a potentially devastating combination. Efficient emergency response in event of a large earthquake will be crucial to minimizing the loss of life and disruption of lifeline systems in Puerto Rico. The ShakeMap system (Wald et al, 2004) developed by the USGS to rapidly display and disseminate information about the geographical distribution of ground shaking (and hence potential damage) following a large earthquake has proven to be a vital tool for post earthquake emergency response efforts, and is being adopted/emulated in various seismically active regions worldwide. Implementing a robust ShakeMap system is among the top priorities of the Puerto Rico Seismic Network. However, the ultimate effectiveness of ShakeMap in post- earthquake response depends not only on its rapid availability, but also on the effective use of the information it provides. We developed ShakeMap scenarios of a suite of damaging historical and probable earthquakes that severely impact San Juan, Ponce, and Mayagüez, the 3 largest cities in Puerto Rico. Earthquake source parameters were obtained from McCann and Mercado (1998); and Huérfano (2004). For historical earthquakes that generated tsunamis, tsunami inundation maps were generated using the TIME method (Shuto, 1991). The ShakeMap ground shaking maps were presented to local and regional governmental and emergency response agencies at the 2007 Annual conference of the Puerto Rico Emergency Management and Disaster Administration in San Juan, PR, and at numerous other emergency management talks and training sessions. Economic losses are estimated using the ShakeMap scenario ground motions (Saffar, 2007). The calibration tasks necessary in generating these scenarios (developing Vs30 maps, attenuation relationships) complement the on-going efforts of the Puerto Rico Seismic Network to generate ShakeMaps in real-time.

Mapping cis- and trans-regulatory effects across multiple tissues in twins

PubMed Central

Grundberg, Elin; Small, Kerrin S.; Hedman, Åsa K.; Nica, Alexandra C.; Buil, Alfonso; Keildson, Sarah; Bell, Jordana T.; Yang, Tsun-Po; Meduri, Eshwar; Barrett, Amy; Nisbett, James; Sekowska, Magdalena; Wilk, Alicja; Shin, So-Youn; Glass, Daniel; Travers, Mary; Min, Josine L.; Ring, Sue; Ho, Karen; Thorleifsson, Gudmar; Kong, Augustine; Thorsteindottir, Unnur; Ainali, Chrysanthi; Dimas, Antigone S.; Hassanali, Neelam; Ingle, Catherine; Knowles, David; Krestyaninova, Maria; Lowe, Christopher E.; Di Meglio, Paola; Montgomery, Stephen B.; Parts, Leopold; Potter, Simon; Surdulescu, Gabriela; Tsaprouni, Loukia; Tsoka, Sophia; Bataille, Veronique; Durbin, Richard; Nestle, Frank O.; O’Rahilly, Stephen; Soranzo, Nicole; Lindgren, Cecilia M.; Zondervan, Krina T.; Ahmadi, Kourosh R.; Schadt, Eric E.; Stefansson, Kari; Smith, George Davey; McCarthy, Mark I.; Deloukas, Panos; Dermitzakis, Emmanouil T.; Spector, Tim D.

2013-01-01

Sequence-based variation in gene expression is a key driver of disease risk. Common variants regulating expression in cis have been mapped in many eQTL studies typically in single tissues from unrelated individuals. Here, we present a comprehensive analysis of gene expression across multiple tissues conducted in a large set of mono- and dizygotic twins that allows systematic dissection of genetic (cis and trans) and non-genetic effects on gene expression. Using identity-by-descent estimates, we show that at least 40% of the total heritable cis-effect on expression cannot be accounted for by common cis-variants, a finding which exposes the contribution of low frequency and rare regulatory variants with respect to both transcriptional regulation and complex trait susceptibility. We show that a substantial proportion of gene expression heritability is trans to the structural gene and identify several replicating trans-variants which act predominantly in a tissue-restricted manner and may regulate the transcription of many genes. PMID:22941192

Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA.

PubMed

Guo, Shicheng; Diep, Dinh; Plongthongkum, Nongluk; Fung, Ho-Lim; Zhang, Kang; Zhang, Kun

2017-04-01

Adjacent CpG sites in mammalian genomes can be co-methylated owing to the processivity of methyltransferases or demethylases, yet discordant methylation patterns have also been observed, which are related to stochastic or uncoordinated molecular processes. We focused on a systematic search and investigation of regions in the full human genome that show highly coordinated methylation. We defined 147,888 blocks of tightly coupled CpG sites, called methylation haplotype blocks, after analysis of 61 whole-genome bisulfite sequencing data sets and validation with 101 reduced-representation bisulfite sequencing data sets and 637 methylation array data sets. Using a metric called methylation haplotype load, we performed tissue-specific methylation analysis at the block level. Subsets of informative blocks were further identified for deconvolution of heterogeneous samples. Finally, using methylation haplotypes we demonstrated quantitative estimation of tumor load and tissue-of-origin mapping in the circulating cell-free DNA of 59 patients with lung or colorectal cancer.

Tomographic image reconstruction using x-ray phase information

NASA Astrophysics Data System (ADS)

Momose, Atsushi; Takeda, Tohoru; Itai, Yuji; Hirano, Keiichi

1996-04-01

We have been developing phase-contrast x-ray computed tomography (CT) to make possible the observation of biological soft tissues without contrast enhancement. Phase-contrast x-ray CT requires for its input data the x-ray phase-shift distributions or phase-mapping images caused by an object. These were measured with newly developed fringe-scanning x-ray interferometry. Phase-mapping images at different projection directions were obtained by rotating the object in an x-ray interferometer, and were processed with a standard CT algorithm. A phase-contrast x-ray CT image of a nonstained cancerous tissue was obtained using 17.7 keV synchrotron x rays with 12 micrometer voxel size, although the size of the observation area was at most 5 mm. The cancerous lesions were readily distinguishable from normal tissues. Moreover, fine structures corresponding to cancerous degeneration and fibrous tissues were clearly depicted. It is estimated that the present system is sensitive down to a density deviation of 4 mg/cm3.

Preliminary geologic map of the Black Mountain area northeast of Victorville, San Bernardino County, California

USGS Publications Warehouse

Stone, Paul

2006-01-01

The Black Mountain area is in the Mojave Desert about 20 km northeast of Victorville, California. The geology of this area is of interest primarily for its excellent exposures of the early Mesozoic Fairview Valley Formation, a sequence of weakly metamorphosed sedimentary rocks including a thick, commercially important unit of limestone conglomerate that has been mined for cement at Black Mountain Quarry for several decades. Recent geochronologic work has shown that the Fairview Valley Formation is probably of Early Jurassic age. This preliminary geologic map of the Black Mountain area depicts the stratigraphic and structural relations of the Fairview Valley Formation and the associated rocks, most notably the overlying Sidewinder Volcanics of Early(?), Middle, and Late(?) Jurassic age. The map is based on new field studies by the author designed to clarify details of the stratigraphy and structure unresolved by previous investigations. The map is considered preliminary because the ages of some geologic units critical for a satisfactory understanding of the stratigraphic and structural framework remain unknown. The map area also includes a segment of the Helendale Fault, one of several faults of known or inferred late Cenozoic right-lateral displacement that make up the Eastern California Shear Zone. The fault is marked by aligned northeast-facing scarps in Pleistocene or older alluvial deposits and the underlying bedrock units. Relations in the map area suggest that right-lateral displacement on the Helendale Fault probably does not exceed 2 km, a conclusion compatible with previous estimates of displacement on this fault based on relations both within and outside the Black Mountain area.

Mapping the dynamics of brain perfusion using functional ultrasound in a rat model of transient middle cerebral artery occlusion

PubMed Central

Brunner, Clément; Isabel, Clothilde; Martin, Abraham; Dussaux, Clara; Savoye, Anne; Emmrich, Julius; Montaldo, Gabriel; Mas, Jean-Louis; Urban, Alan

2015-01-01

Following middle cerebral artery occlusion, tissue outcome ranges from normal to infarcted depending on depth and duration of hypoperfusion as well as occurrence and efficiency of reperfusion. However, the precise time course of these changes in relation to tissue and behavioral outcome remains unsettled. To address these issues, a three-dimensional wide field-of-view and real-time quantitative functional imaging technique able to map perfusion in the rodent brain would be desirable. Here, we applied functional ultrasound imaging, a novel approach to map relative cerebral blood volume without contrast agent, in a rat model of brief proximal transient middle cerebral artery occlusion to assess perfusion in penetrating arterioles and venules acutely and over six days thanks to a thinned-skull preparation. Functional ultrasound imaging efficiently mapped the acute changes in relative cerebral blood volume during occlusion and following reperfusion with high spatial resolution (100 µm), notably documenting marked focal decreases during occlusion, and was able to chart the fine dynamics of tissue reperfusion (rate: one frame/5 s) in the individual rat. No behavioral and only mild post-mortem immunofluorescence changes were observed. Our study suggests functional ultrasound is a particularly well-adapted imaging technique to study cerebral perfusion in acute experimental stroke longitudinally from the hyper-acute up to the chronic stage in the same subject. PMID:26721392

Improved magnetic resonance fingerprinting reconstruction with low-rank and subspace modeling.

PubMed

Zhao, Bo; Setsompop, Kawin; Adalsteinsson, Elfar; Gagoski, Borjan; Ye, Huihui; Ma, Dan; Jiang, Yun; Ellen Grant, P; Griswold, Mark A; Wald, Lawrence L

2018-02-01

This article introduces a constrained imaging method based on low-rank and subspace modeling to improve the accuracy and speed of MR fingerprinting (MRF). A new model-based imaging method is developed for MRF to reconstruct high-quality time-series images and accurate tissue parameter maps (e.g., T 1 , T 2 , and spin density maps). Specifically, the proposed method exploits low-rank approximations of MRF time-series images, and further enforces temporal subspace constraints to capture magnetization dynamics. This allows the time-series image reconstruction problem to be formulated as a simple linear least-squares problem, which enables efficient computation. After image reconstruction, tissue parameter maps are estimated via dictionary-based pattern matching, as in the conventional approach. The effectiveness of the proposed method was evaluated with in vivo experiments. Compared with the conventional MRF reconstruction, the proposed method reconstructs time-series images with significantly reduced aliasing artifacts and noise contamination. Although the conventional approach exhibits some robustness to these corruptions, the improved time-series image reconstruction in turn provides more accurate tissue parameter maps. The improvement is pronounced especially when the acquisition time becomes short. The proposed method significantly improves the accuracy of MRF, and also reduces data acquisition time. Magn Reson Med 79:933-942, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Master Amino acid Pattern as sole and total substitute for dietary proteins during a weight-loss diet to achieve the body's nitrogen balance equilibrium.

PubMed

Lucà-Moretti, M; Grandi, A; Lucà, E; Muratori, G; Nofroni, M G; Mucci, M P; Gambetta, P; Stimolo, R; Drago, P; Giudice, G; Tamburlin, N; Karbalai, M; Valente, C; Moras, G

2003-01-01

Results of this multicentric study have shown that by giving Master Amino acid Pattern (MAP) as a sole and total substitute of dietary proteins to 500 overweight participants undergoing the American Nutrition Clinics/Overweight Management Program (ANC/OMP), the participants' body nitrogen balance could be maintained in equilibrium with essentially no calories (MAP 1 g=0.04 kcal), thereby preserving the body's structural and functional proteins, eliminating excessive water retention from the interstitial compartment, and preventing the sudden weight increase after study conclusion commonly known as the yo-yo effect. Study results have shown that the use of MAP, in conjunction with the ANC/OMP regimen, has proven to be safe and effective by preventing those adverse effects associated with a negative nitrogen balance, such as oversized or flabby tissue, stretch marks, the sagging of breast tissue, increased hair loss, faded hair color, and fragile or brittle nails. Also prevented were those anomalies commonly associated with weight-loss diets, such as hunger, weakness, headache caused by ketosis, constipation, and decreased libido. The use of MAP in conjunction with the ANC/OMP also allowed for mean weight loss of 2.5 kg (5.5 lb) per week, achieved through reduction of excessive fat tissue and elimination of excessive water retention from the interstitial compartment.