Sample records for mapping scans identify
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Cunliffe, Alexandra R.; Armato, Samuel G.; White, Bradley
2015-01-15
Purpose: To characterize the effects of deformable image registration of serial computed tomography (CT) scans on the radiation dose calculated from a treatment planning scan. Methods: Eighteen patients who received curative doses (≥60 Gy, 2 Gy/fraction) of photon radiation therapy for lung cancer treatment were retrospectively identified. For each patient, a diagnostic-quality pretherapy (4–75 days) CT scan and a treatment planning scan with an associated dose map were collected. To establish correspondence between scan pairs, a researcher manually identified anatomically corresponding landmark point pairs between the two scans. Pretherapy scans then were coregistered with planning scans (and associated dose maps)more » using the demons deformable registration algorithm and two variants of the Fraunhofer MEVIS algorithm (“Fast” and “EMPIRE10”). Landmark points in each pretherapy scan were automatically mapped to the planning scan using the displacement vector field output from each of the three algorithms. The Euclidean distance between manually and automatically mapped landmark points (d{sub E}) and the absolute difference in planned dose (|ΔD|) were calculated. Using regression modeling, |ΔD| was modeled as a function of d{sub E}, dose (D), dose standard deviation (SD{sub dose}) in an eight-pixel neighborhood, and the registration algorithm used. Results: Over 1400 landmark point pairs were identified, with 58–93 (median: 84) points identified per patient. Average |ΔD| across patients was 3.5 Gy (range: 0.9–10.6 Gy). Registration accuracy was highest using the Fraunhofer MEVIS EMPIRE10 algorithm, with an average d{sub E} across patients of 5.2 mm (compared with >7 mm for the other two algorithms). Consequently, average |ΔD| was also lowest using the Fraunhofer MEVIS EMPIRE10 algorithm. |ΔD| increased significantly as a function of d{sub E} (0.42 Gy/mm), D (0.05 Gy/Gy), SD{sub dose} (1.4 Gy/Gy), and the algorithm used (≤1 Gy). Conclusions: An average error of <4 Gy in radiation dose was introduced when points were mapped between CT scan pairs using deformable registration, with the majority of points yielding dose-mapping error <2 Gy (approximately 3% of the total prescribed dose). Registration accuracy was highest using the Fraunhofer MEVIS EMPIRE10 algorithm, resulting in the smallest errors in mapped dose. Dose differences following registration increased significantly with increasing spatial registration errors, dose, and dose gradient (i.e., SD{sub dose}). This model provides a measurement of the uncertainty in the radiation dose when points are mapped between serial CT scans through deformable registration.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Cunliffe, A; Contee, C; White, B
Purpose: To characterize the effect of deformable registration of serial computed tomography (CT) scans on the radiation dose calculated from a treatment planning scan. Methods: Eighteen patients who received curative doses (≥60Gy, 2Gy/fraction) of photon radiation therapy for lung cancer treatment were retrospectively identified. For each patient, a diagnostic-quality pre-therapy (4–75 days) CT scan and a treatment planning scan with an associated dose map calculated in Pinnacle were collected. To establish baseline correspondence between scan pairs, a researcher manually identified anatomically corresponding landmark point pairs between the two scans. Pre-therapy scans were co-registered with planning scans (and associated dose maps)more » using the Plastimatch demons and Fraunhofer MEVIS deformable registration algorithms. Landmark points in each pretherapy scan were automatically mapped to the planning scan using the displacement vector field output from both registration algorithms. The absolute difference in planned dose (|ΔD|) between manually and automatically mapped landmark points was calculated. Using regression modeling, |ΔD| was modeled as a function of the distance between manually and automatically matched points (registration error, E), the dose standard deviation (SD-dose) in the eight-pixel neighborhood, and the registration algorithm used. Results: 52–92 landmark point pairs (median: 82) were identified in each patient's scans. Average |ΔD| across patients was 3.66Gy (range: 1.2–7.2Gy). |ΔD| was significantly reduced by 0.53Gy using Plastimatch demons compared with Fraunhofer MEVIS. |ΔD| increased significantly as a function of E (0.39Gy/mm) and SD-dose (2.23Gy/Gy). Conclusion: An average error of <4Gy in radiation dose was introduced when points were mapped between CT scan pairs using deformable registration. Dose differences following registration were significantly increased when the Fraunhofer MEVIS registration algorithm was used, spatial registration errors were larger, and dose gradient was higher (i.e., higher SD-dose). To our knowledge, this is the first study to directly compute dose errors following deformable registration of lung CT scans.« less
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Aiyetan, Paul; Zhang, Bai; Zhang, Zhen; Zhang, Hui
2014-01-01
Mass spectrometry based glycoproteomics has become a major means of identifying and characterizing previously N-linked glycan attached loci (glycosites). In the bottom-up approach, several factors which include but not limited to sample preparation, mass spectrometry analyses, and protein sequence database searches result in previously N-linked peptide spectrum matches (PSMs) of varying lengths. Given that multiple PSM scan map to a glycosite, we reason that identified PSMs are varying length peptide species of a unique set of glycosites. Because associated spectra of these PSMs are typically summed separately, true glycosite associated spectra counts are lost or complicated. Also, these varying length peptide species complicate protein inference as smaller sized peptide sequences are more likely to map to more proteins than larger sized peptides or actual glycosite sequences. Here, we present XGlycScan. XGlycScan maps varying length peptide species to glycosites to facilitate an accurate quantification of glycosite associated spectra counts. We observed that this reduced the variability in reported identifications of mass spectrometry technical replicates of our sample dataset. We also observed that mapping identified peptides to glycosites provided an assessment of search-engine identification. Inherently, XGlycScan reported glycosites reduce the complexity in protein inference. We implemented XGlycScan in the platform independent Java programing language and have made it available as open source. XGlycScan's source code is freely available at https://bitbucket.org/paiyetan/xglycscan/src and its compiled binaries and documentation can be freely downloaded at https://bitbucket.org/paiyetan/xglycscan/downloads. The graphical user interface version can also be found at https://bitbucket.org/paiyetan/xglycscangui/src and https://bitbucket.org/paiyetan/xglycscangui/downloads respectively.
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A scanning defect mapping system for semiconductor characterization
NASA Technical Reports Server (NTRS)
Sopori, Bushnan L.
1994-01-01
We have developed an optical scanning system that generates maps of the spatial distributions of defects in single and polycrystalline silicon wafers. This instrument, called Scanning Defect Mapping System, utilizes differences in the scattering characteristics of dislocation etch pits and grain boundaries from a defect-etched sample to identify and count them. This system simultaneously operates in the dislocation mode and the grain boundary (GB) mode. In the 'dislocation mode,' the optical scattering from the etch pits is used to statistically count dislocations, while ignoring the GB's. Likewise, in the 'grain boundary mode' the system only recognizes the local scattering from the GB's to generate grain boundary distributions. The information generated by this instrument is valuable for material quality control, identifying mechanisms of defect generation and the nature of thermal stresses during the crystal growth, and the solar cell process design.
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Holder, Jourdan T; Kessler, David M; Noble, Jack H; Gifford, René H; Labadie, Robert F
2018-06-01
To quantify and compare the number of cochlear implant (CI) electrodes found to be extracochlear on postoperative computerized tomography (CT) scans, the number of basal electrodes deactivated during standard CI mapping (without knowledge of the postoperative CT scan), and the extent of electrode insertion noted by the surgeon. Retrospective. Academic Medical Center. Two hundred sixty-two patients underwent standard cochlear implantation and postoperative temporal bone CT scanning. Scans were analyzed to determine the number of extracochlear electrodes. Standard CI programming had been completed without knowledge of the extracochlear electrodes identified on the CT. These standard CI maps were reviewed to record the number of deactivated basal electrodes. Lastly, each operative report was reviewed to record the extent of reported electrode insertion. 13.4% (n = 35) of CIs were found to have at least one electrode outside of the cochlea on the CT scan. Review of CI mapping indicated that audiologists had deactivated extracochlear electrodes in 60% (21) of these cases. Review of operative reports revealed that surgeons correctly indicated the number of extracochlear electrodes in 6% (2) of these cases. Extracochlear electrodes were correctly identified audiologically in 60% of cases and in surgical reports in 6% of cases; however, it is possible that at least a portion of these cases involved postoperative electrode migration. Given these findings, postoperative CT scans can provide information regarding basal electrode location, which could help improve programming accuracy, associated frequency allocation, and audibility with appropriate deactivation of extracochlear electrodes.
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Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces
Zerbe, Brandon S.; Hall, David R.
2013-01-01
In the context of protein-protein interactions, the term “hot spot” refers to a residue or cluster of residues that makes a major contribution to the binding free energy, as determined by alanine scanning mutagenesis. In contrast, in pharmaceutical research a hot spot is a site on a target protein that has high propensity for ligand binding and hence is potentially important for drug discovery. Here we examine the relationship between these two hot spot concepts by comparing alanine scanning data for a set of 15 proteins with results from mapping the protein surfaces for sites that can bind fragment-sized small molecules. We find the two types of hot spots are largely complementary; the residues protruding into hot spot regions identified by computational mapping or experimental fragment screening are almost always themselves hot spot residues as defined by alanine scanning experiments. Conversely, a residue that is found by alanine scanning to contribute little to binding rarely interacts with hot spot regions on the partner protein identified by fragment mapping. In spite of the strong correlation between the two hot spot concepts, they fundamentally differ, however. In particular, while identification of a hot spot by alanine scanning establishes the potential to generate substantial interaction energy with a binding partner, there are additional topological requirements to be a hot spot for small molecule binding. Hence, only a minority of hot spots identified by alanine scanning represent sites that are potentially useful for small inhibitor binding, and it is this subset that is identified by experimental or computational fragment screening. PMID:22770357
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Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces.
Zerbe, Brandon S; Hall, David R; Vajda, Sandor; Whitty, Adrian; Kozakov, Dima
2012-08-27
In the context of protein-protein interactions, the term "hot spot" refers to a residue or cluster of residues that makes a major contribution to the binding free energy, as determined by alanine scanning mutagenesis. In contrast, in pharmaceutical research, a hot spot is a site on a target protein that has high propensity for ligand binding and hence is potentially important for drug discovery. Here we examine the relationship between these two hot spot concepts by comparing alanine scanning data for a set of 15 proteins with results from mapping the protein surfaces for sites that can bind fragment-sized small molecules. We find the two types of hot spots are largely complementary; the residues protruding into hot spot regions identified by computational mapping or experimental fragment screening are almost always themselves hot spot residues as defined by alanine scanning experiments. Conversely, a residue that is found by alanine scanning to contribute little to binding rarely interacts with hot spot regions on the partner protein identified by fragment mapping. In spite of the strong correlation between the two hot spot concepts, they fundamentally differ, however. In particular, while identification of a hot spot by alanine scanning establishes the potential to generate substantial interaction energy with a binding partner, there are additional topological requirements to be a hot spot for small molecule binding. Hence, only a minority of hot spots identified by alanine scanning represent sites that are potentially useful for small inhibitor binding, and it is this subset that is identified by experimental or computational fragment screening.
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Tree-centric mapping of forest carbon density from airborne laser scanning and hyperspectral data.
Dalponte, Michele; Coomes, David A
2016-10-01
Forests are a major component of the global carbon cycle, and accurate estimation of forest carbon stocks and fluxes is important in the context of anthropogenic global change. Airborne laser scanning (ALS) data sets are increasingly recognized as outstanding data sources for high-fidelity mapping of carbon stocks at regional scales.We develop a tree-centric approach to carbon mapping, based on identifying individual tree crowns (ITCs) and species from airborne remote sensing data, from which individual tree carbon stocks are calculated. We identify ITCs from the laser scanning point cloud using a region-growing algorithm and identifying species from airborne hyperspectral data by machine learning. For each detected tree, we predict stem diameter from its height and crown-width estimate. From that point on, we use well-established approaches developed for field-based inventories: above-ground biomasses of trees are estimated using published allometries and summed within plots to estimate carbon density.We show this approach is highly reliable: tests in the Italian Alps demonstrated a close relationship between field- and ALS-based estimates of carbon stocks ( r 2 = 0·98). Small trees are invisible from the air, and a correction factor is required to accommodate this effect.An advantage of the tree-centric approach over existing area-based methods is that it can produce maps at any scale and is fundamentally based on field-based inventory methods, making it intuitive and transparent. Airborne laser scanning, hyperspectral sensing and computational power are all advancing rapidly, making it increasingly feasible to use ITC approaches for effective mapping of forest carbon density also inside wider carbon mapping programs like REDD++.
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USDA-ARS?s Scientific Manuscript database
Watermelon (Citrullus lanatus var. lanatus) contains 88% water, sugars, and several important health-related compounds, including lycopene, citrulline, arginine, and glutathione. The current genetic diversity study uses microsatellites with known map positions to identify genomic regions that under...
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Lo, T Y; Sim, K S; Tso, C P; Nia, M E
2014-01-01
An improvement to the previously proposed adaptive Canny optimization technique for scanning electron microscope image colorization is reported. The additional feature, called pseudo-mapping technique, is that the grayscale markings are temporarily mapped to a set of pre-defined pseudo-color map as a mean to instill color information for grayscale colors in chrominance channels. This allows the presence of grayscale markings to be identified; hence optimization colorization of grayscale colors is made possible. This additional feature enhances the flexibility of scanning electron microscope image colorization by providing wider range of possible color enhancement. Furthermore, the nature of this technique also allows users to adjust the luminance intensities of selected region from the original image within certain extent. © 2014 Wiley Periodicals, Inc.
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NASA Astrophysics Data System (ADS)
Hoffman, Joanne; Liu, Jiamin; Turkbey, Evrim; Kim, Lauren; Summers, Ronald M.
2015-03-01
Station-labeling of mediastinal lymph nodes is typically performed to identify the location of enlarged nodes for cancer staging. Stations are usually assigned in clinical radiology practice manually by qualitative visual assessment on CT scans, which is time consuming and highly variable. In this paper, we developed a method that automatically recognizes the lymph node stations in thoracic CT scans based on the anatomical organs in the mediastinum. First, the trachea, lungs, and spines are automatically segmented to locate the mediastinum region. Then, eight more anatomical organs are simultaneously identified by multi-atlas segmentation. Finally, with the segmentation of those anatomical organs, we convert the text definitions of the International Association for the Study of Lung Cancer (IASLC) lymph node map into patient-specific color-coded CT image maps. Thus, a lymph node station is automatically assigned to each lymph node. We applied this system to CT scans of 86 patients with 336 mediastinal lymph nodes measuring equal or greater than 10 mm. 84.8% of mediastinal lymph nodes were correctly mapped to their stations.
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Elemental mapping of biological samples using a scanning proton microprobe
NASA Astrophysics Data System (ADS)
Watt, F.; Grime, G. W.
1988-03-01
Elemental mapping using a scanning proton microprobe (SPM) can be a powerful technique for probing trace elements in biology, allowing complex interfaces to be studied in detail, identifying contamination and artefacts present in the specimen, and in certain circumstances obtaining indirect chemical information. Examples used to illustrate the advantages of the technique include the elemental mapping of growing pollen tubes, honey bee brain section, a mouse macrophage cell, human liver section exhibiting primary biliary cirrhosis, and the attack by a mildew fungus on a pea leaf.
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Use of single nucleotide polymorphisms (SNP) to fine-map quantitative trait loci (QTL) in swine
USDA-ARS?s Scientific Manuscript database
Mapping quantitative trait loci (QTL) in swine at the US Meat Animal Research Center has relied heavily on linkage mapping in either F2 or Backcross families. QTL identified in the initial scans typically have very broad confidence intervals and further refinement of the QTL’s position is needed bef...
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Powers, Jarrod; Brewer, Shannon K.; Long, James M.; Campbell, Thomas
2015-01-01
Side-scan sonar is a valuable tool for mapping habitat features in many aquatic systems suggesting it may also be useful for locating sedentary biota. The objective of this study was to determine if side-scan sonar could be used to identify freshwater mussel (unionid) beds and the required environmental conditions. We used side-scan sonar to develop a series of mussel-bed reference images by placing mussel shells within homogenous areas of fine and coarse substrates. We then used side-scan sonar to map a 32-km river reach during spring and summer. Using our mussel-bed reference images, several river locations were identified where mussel beds appeared to exist in the scanned images and we chose a subset of sites (n = 17) for field validation. The validation confirmed that ~60% of the sites had mussel beds and ~80% had some mussels or shells present. Water depth was significantly related to our ability to predict mussel-bed locations: predictive ability was greatest at depths of 1–2 m, but decreased in water >2-m deep. We determined side-scan sonar is an effective tool for preliminary assessments of mussel presence during times when they are located at or above the substrate surface and in relatively fine substrates excluding fine silt.
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Page layout analysis and classification for complex scanned documents
NASA Astrophysics Data System (ADS)
Erkilinc, M. Sezer; Jaber, Mustafa; Saber, Eli; Bauer, Peter; Depalov, Dejan
2011-09-01
A framework for region/zone classification in color and gray-scale scanned documents is proposed in this paper. The algorithm includes modules for extracting text, photo, and strong edge/line regions. Firstly, a text detection module which is based on wavelet analysis and Run Length Encoding (RLE) technique is employed. Local and global energy maps in high frequency bands of the wavelet domain are generated and used as initial text maps. Further analysis using RLE yields a final text map. The second module is developed to detect image/photo and pictorial regions in the input document. A block-based classifier using basis vector projections is employed to identify photo candidate regions. Then, a final photo map is obtained by applying probabilistic model based on Markov random field (MRF) based maximum a posteriori (MAP) optimization with iterated conditional mode (ICM). The final module detects lines and strong edges using Hough transform and edge-linkages analysis, respectively. The text, photo, and strong edge/line maps are combined to generate a page layout classification of the scanned target document. Experimental results and objective evaluation show that the proposed technique has a very effective performance on variety of simple and complex scanned document types obtained from MediaTeam Oulu document database. The proposed page layout classifier can be used in systems for efficient document storage, content based document retrieval, optical character recognition, mobile phone imagery, and augmented reality.
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HapMap scanning of novel human minor histocompatibility antigens.
Kamei, Michi; Nannya, Yasuhito; Torikai, Hiroki; Kawase, Takakazu; Taura, Kenjiro; Inamoto, Yoshihiro; Takahashi, Taro; Yazaki, Makoto; Morishima, Satoko; Tsujimura, Kunio; Miyamura, Koichi; Ito, Tetsuya; Togari, Hajime; Riddell, Stanley R; Kodera, Yoshihisa; Morishima, Yasuo; Takahashi, Toshitada; Kuzushima, Kiyotaka; Ogawa, Seishi; Akatsuka, Yoshiki
2009-05-21
Minor histocompatibility antigens (mHags) are molecular targets of allo-immunity associated with hematopoietic stem cell transplantation (HSCT) and involved in graft-versus-host disease, but they also have beneficial antitumor activity. mHags are typically defined by host SNPs that are not shared by the donor and are immunologically recognized by cytotoxic T cells isolated from post-HSCT patients. However, the number of molecularly identified mHags is still too small to allow prospective studies of their clinical importance in transplantation medicine, mostly due to the lack of an efficient method for isolation. Here we show that when combined with conventional immunologic assays, the large data set from the International HapMap Project can be directly used for genetic mapping of novel mHags. Based on the immunologically determined mHag status in HapMap panels, a target mHag locus can be uniquely mapped through whole genome association scanning taking advantage of the unprecedented resolution and power obtained with more than 3 000 000 markers. The feasibility of our approach could be supported by extensive simulations and further confirmed by actually isolating 2 novel mHags as well as 1 previously identified example. The HapMap data set represents an invaluable resource for investigating human variation, with obvious applications in genetic mapping of clinically relevant human traits.
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NASA Astrophysics Data System (ADS)
Dredge, Paula; Ives, Simon; Howard, Daryl L.; Spiers, Kathryn M.; Yip, Andrew; Kenderdine, Sarah
2015-11-01
A portrait of Henry VIII on oak panel c. 1535 has recently undergone technical examination to inform questions regarding authorship and the painting's relationship to a group of similar works in the collections of the National Portrait Gallery, London, and the Society of Antiquaries. Due to previous conservation treatments of the painting, the conventional transmission X-radiograph image was difficult to interpret. As a result, the painting underwent high-definition X-ray fluorescence (XRF) elemental mapping on the X-ray fluorescence microscopy beamline of the Australian Synchrotron. Scans were conducted at 12.6 and 18.5 keV, below and above the lead (Pb) L edges, respectively. Typical scan parameters were 120 μm pixel size at 7 ms dwell time, with the largest scan covering an area 545 × 287 mm2 collected in 23 h (10.8 MP). XRF mapping of the panel has guided the conservation treatment of the painting and the revelation of previously obscured features. It has also provided insight into the process of making of the painting. The informative and detailed elemental maps, alongside ultra-high-definition scans of the painting undertaken before and after varnish and over-paint removal, have assisted in comparison of the finely painted details with the London paintings. The resolution offered by the combination of imaging techniques identifies pigment distribution at an extremely fine scale, enabling a new understanding of the artist's paint application.
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Automated volumetric segmentation of retinal fluid on optical coherence tomography
Wang, Jie; Zhang, Miao; Pechauer, Alex D.; Liu, Liang; Hwang, Thomas S.; Wilson, David J.; Li, Dengwang; Jia, Yali
2016-01-01
We propose a novel automated volumetric segmentation method to detect and quantify retinal fluid on optical coherence tomography (OCT). The fuzzy level set method was introduced for identifying the boundaries of fluid filled regions on B-scans (x and y-axes) and C-scans (z-axis). The boundaries identified from three types of scans were combined to generate a comprehensive volumetric segmentation of retinal fluid. Then, artefactual fluid regions were removed using morphological characteristics and by identifying vascular shadowing with OCT angiography obtained from the same scan. The accuracy of retinal fluid detection and quantification was evaluated on 10 eyes with diabetic macular edema. Automated segmentation had good agreement with manual segmentation qualitatively and quantitatively. The fluid map can be integrated with OCT angiogram for intuitive clinical evaluation. PMID:27446676
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Noguchi, Kyo; Itoh, Toshihide; Naruto, Norihito; Takashima, Shutaro; Tanaka, Kortaro; Kuroda, Satoshi
2017-01-01
We evaluated whether X-map, a novel imaging technique, can visualize ischemic lesions within 20 hours after the onset in patients with acute ischemic stroke, using noncontrast dual-energy computed tomography (DECT). Six patients with acute ischemic stroke were included in this study. Noncontrast head DECT scans were acquired with 2 X-ray tubes operated at 80 kV and Sn150 kV between 32 minutes and 20 hours after the onset. Using these DECT scans, the X-map was reconstructed based on 3-material decomposition and compared with a simulated standard (120 kV) computed tomography (CT) and diffusion-weighted imaging (DWI). The X-map showed more sensitivity to identify the lesions as an area of lower attenuation value than a simulated standard CT in all 6 patients. The lesions on the X-map correlated well with those on DWI. In 3 of 6 patients, the X-map detected a transient decrease in the attenuation value in the peri-infarct area within 1 day after the onset. The X-map is a powerful tool to supplement a simulated standard CT and characterize acute ischemic lesions. However, the X-map cannot replace a simulated standard CT to diagnose acute cerebral infarction. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
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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%).
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Scanning For Hotspots In Lamp Filaments
NASA Technical Reports Server (NTRS)
Powers, Charles E.; Van Sant, Tim; Leidecker, Henning
1993-01-01
Scanning photometer designed for use in investigation of failures of incandescent lamp filaments. Maps brightness as function of position along each filament to identify bright (hot) spots, occurring at notches and signifying incipient breaks or rewelds. Also used to measure nonuniformity in outputs of such linear devices as light-emitting diodes, and to measure diffraction patterns of lenses.
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A High-Density Admixture Map for Disease Gene Discovery in African Americans
Smith, Michael W. ; Patterson, Nick ; Lautenberger, James A. ; Truelove, Ann L. ; McDonald, Gavin J. ; Waliszewska, Alicja ; Kessing, Bailey D. ; Malasky, Michael J. ; Scafe, Charles ; Le, Ernest ; De Jager, Philip L. ; Mignault, Andre A. ; Yi, Zeng ; de Thé, Guy ; Essex, Myron ; Sankalé, Jean-Louis ; Moore, Jason H. ; Poku, Kwabena ; Phair, John P. ; Goedert, James J. ; Vlahov, David ; Williams, Scott M. ; Tishkoff, Sarah A. ; Winkler, Cheryl A. ; De La Vega, Francisco M. ; Woodage, Trevor ; Sninsky, John J. ; Hafler, David A. ; Altshuler, David ; Gilbert, Dennis A. ; O’Brien, Stephen J. ; Reich, David
2004-01-01
Admixture mapping (also known as “mapping by admixture linkage disequilibrium,” or MALD) provides a way of localizing genes that cause disease, in admixed ethnic groups such as African Americans, with ∼100 times fewer markers than are required for whole-genome haplotype scans. However, it has not been possible to perform powerful scans with admixture mapping because the method requires a dense map of validated markers known to have large frequency differences between Europeans and Africans. To create such a map, we screened through databases containing ∼450,000 single-nucleotide polymorphisms (SNPs) for which frequencies had been estimated in African and European population samples. We experimentally confirmed the frequencies of the most promising SNPs in a multiethnic panel of unrelated samples and identified 3,011 as a MALD map (1.2 cM average spacing). We estimate that this map is ∼70% informative in differentiating African versus European origins of chromosomal segments. This map provides a practical and powerful tool, which is freely available without restriction, for screening for disease genes in African American patient cohorts. The map is especially appropriate for those diseases that differ in incidence between the parental African and European populations. PMID:15088270
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Large-scale mapping of mutations affecting zebrafish development.
Geisler, Robert; Rauch, Gerd-Jörg; Geiger-Rudolph, Silke; Albrecht, Andrea; van Bebber, Frauke; Berger, Andrea; Busch-Nentwich, Elisabeth; Dahm, Ralf; Dekens, Marcus P S; Dooley, Christopher; Elli, Alexandra F; Gehring, Ines; Geiger, Horst; Geisler, Maria; Glaser, Stefanie; Holley, Scott; Huber, Matthias; Kerr, Andy; Kirn, Anette; Knirsch, Martina; Konantz, Martina; Küchler, Axel M; Maderspacher, Florian; Neuhauss, Stephan C; Nicolson, Teresa; Ober, Elke A; Praeg, Elke; Ray, Russell; Rentzsch, Brit; Rick, Jens M; Rief, Eva; Schauerte, Heike E; Schepp, Carsten P; Schönberger, Ulrike; Schonthaler, Helia B; Seiler, Christoph; Sidi, Samuel; Söllner, Christian; Wehner, Anja; Weiler, Christian; Nüsslein-Volhard, Christiane
2007-01-09
Large-scale mutagenesis screens in the zebrafish employing the mutagen ENU have isolated several hundred mutant loci that represent putative developmental control genes. In order to realize the potential of such screens, systematic genetic mapping of the mutations is necessary. Here we report on a large-scale effort to map the mutations generated in mutagenesis screening at the Max Planck Institute for Developmental Biology by genome scanning with microsatellite markers. We have selected a set of microsatellite markers and developed methods and scoring criteria suitable for efficient, high-throughput genome scanning. We have used these methods to successfully obtain a rough map position for 319 mutant loci from the Tübingen I mutagenesis screen and subsequent screening of the mutant collection. For 277 of these the corresponding gene is not yet identified. Mapping was successful for 80 % of the tested loci. By comparing 21 mutation and gene positions of cloned mutations we have validated the correctness of our linkage group assignments and estimated the standard error of our map positions to be approximately 6 cM. By obtaining rough map positions for over 300 zebrafish loci with developmental phenotypes, we have generated a dataset that will be useful not only for cloning of the affected genes, but also to suggest allelism of mutations with similar phenotypes that will be identified in future screens. Furthermore this work validates the usefulness of our methodology for rapid, systematic and inexpensive microsatellite mapping of zebrafish mutations.
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RAPTOR-scan: Identifying and Tracking Objects Through Thousands of Sky Images
DOE Office of Scientific and Technical Information (OSTI.GOV)
Davidoff, Sherri; Wozniak, Przemyslaw
2004-09-28
The RAPTOR-scan system mines data for optical transients associated with gamma-ray bursts and is used to create a catalog for the RAPTOR telescope system. RAPTOR-scan can detect and track individual astronomical objects across data sets containing millions of observed points.Accurately identifying a real object over many optical images (clustering the individual appearances) is necessary in order to analyze object light curves. To achieve this, RAPTOR telescope observations are sent in real time to a database. Each morning, a program based on the DBSCAN algorithm clusters the observations and labels each one with an object identifier. Once clustering is complete, themore » analysis program may be used to query the database and produce light curves, maps of the sky field, or other informative displays.Although RAPTOR-scan was designed for the RAPTOR optical telescope system, it is a general tool designed to identify objects in a collection of astronomical data and facilitate quick data analysis. RAPTOR-scan will be released as free software under the GNU General Public License.« less
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Mapping dynamic social networks in real life using participants' own smartphones.
Boonstra, Tjeerd W; E Larsen, Mark; Christensen, Helen
2015-11-01
Interpersonal relationships are vital for our daily functioning and wellbeing. Social networks may form the primary means by which environmental influences determine individual traits. Several studies have shown the influence of social networks on decision-making, behaviors and wellbeing. Smartphones have great potential for measuring social networks in a real world setting. Here we tested the feasibility of using people's own smartphones as a data collection platform for face-to-face interactions. We developed an application for iOS and Android to collect Bluetooth data and acquired one week of data from 14 participants in our organization. The Bluetooth scanning statistics were used to quantify the time-resolved connection strength between participants and define the weights of a dynamic social network. We used network metrics to quantify changes in network topology over time and non-negative matrix factorization to identify cliques or subgroups that reoccurred during the week. The scanning rate varied considerably between smartphones running Android and iOS and egocentric networks metrics were correlated with the scanning rate. The time courses of two identified subgroups matched with two meetings that took place that week. These findings demonstrate the feasibility of using participants' own smartphones to map social network, whilst identifying current limitations of using generic smartphones. The bias introduced by variations in scanning rate and missing data is an important limitation that needs to be addressed in future studies.
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Digital soils survey map of the Patagonia Mountains, Arizona
Norman, Laura; Wissler, Craig; Guertin, D. Phillip; Gray, Floyd
2002-01-01
The ‘Soil Survey of Santa Cruz and Parts of Cochise and Pima Counties, Arizona,' a product of the USDA’s Soil Conservation Service and the Forest Service in cooperation with the Arizona Agricultural Experiment Station, released in 1979, was created according to the site conditions in 1971, when soil scientists identified soils types on aerial photographs. The scale at which these maps were published is 1:20,000. These soil maps were automated for incorporation into the hydrologic modeling within a GIS. The aerial photos onto which the soils units were drawn had not been orthoganalized, and contained distortion. A total of 15 maps composed the study area. These maps were scanned into TIFF format using an 8-bit black and white drum scanner at 100 dpi. The images were imported into ERDAS IMAGINE and the white borders were removed through subset decollaring processes. Five CD-ROM’s containing Digital Orthophoto Quarter Quads (DOQQ’s) were used to register and rectify the scanned soils maps. Polygonal data was then attributed according to the datasets.
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Scanning and georeferencing historical USGS quadrangles
Davis, Larry R.; Allord, G.J.
2011-01-01
The USGS Historical Quadrangle Scanning Project (HQSP) is scanning all scales and all editions of approximately 250,000 topographic maps published by the U.S. Geological Survey (USGS) since the inception of the topographic mapping program in 1884. This scanning will provide a comprehensive digital repository of USGS topographic maps, available to the public at no cost. This project serves the dual purpose of creating a master catalog and digital archive copies of the irreplaceable collection of topographic maps in the USGS Reston Map Library as well as making the maps available for viewing and downloading from the USGS Store and The National Map Viewer.
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NASA Astrophysics Data System (ADS)
Sopori, Bhushan; Wei, Chen; Yi, Zhang; Madjdpour, Jamal
2000-03-01
A scanning system for mapping defects, and for measuring their influence on the photovoltaic of Si solar cells, is described. The system uses optical scattering patterns to identify the nature of defects. The local density of the defects is statistically determined from the integrated scattered light. The optical system can also measure the reflectance and the light-induced current which is then used to yield maps of the internal photoresponse of the device.
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Cotton phenotyping with lidar from a track-mounted platform
NASA Astrophysics Data System (ADS)
French, Andrew N.; Gore, Michael A.; Thompson, Alison
2016-05-01
High-Throughput Phenotyping (HTP) is a discipline for rapidly identifying plant architectural and physiological responses to environmental factors such as heat and water stress. Experiments conducted since 2010 at Maricopa, Arizona with a three-fold sensor group, including thermal infrared radiometers, active visible/near infrared reflectance sensors, and acoustic plant height sensors, have shown the validity of HTP with a tractor-based system. However, results from these experiments also show that accuracy of plant phenotyping is limited by the system's inability to discriminate plant components and their local environmental conditions. This limitation may be overcome with plant imaging and laser scanning which can help map details in plant architecture and sunlit/shaded leaves. To test the capability for mapping cotton plants with a laser system, a track-mounted platform was deployed in 2015 over a full canopy and defoliated cotton crop consisting of a scanning LIDAR driven by Arduinocontrolled stepper motors. Using custom Python and Tkinter code, the platform moved autonomously along a pipe-track at 0.1 m/s while collecting LIDAR scans at 25 Hz (0.1667 deg. beam). These tests showed that an autonomous LIDAR platform can reduce HTP logistical problems and provide the capability to accurately map cotton plants and cotton bolls. A prototype track-mounted platform was developed to test the use of LIDAR scanning for High- Throughput Phenotyping (HTP). The platform was deployed in 2015 at Maricopa, Arizona over a senescent cotton crop. Using custom Python and Tkinter code, the platform moved autonomously along a pipe-track at <1 m/s while collecting LIDAR scans at 25 Hz (0.1667 deg. beam). Scanning data mapped the canopy heights and widths, and detected cotton bolls.
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Semantic Labelling of Road Furniture in Mobile Laser Scanning Data
NASA Astrophysics Data System (ADS)
Li, F.; Oude Elberink, S.; Vosselman, G.
2017-09-01
Road furniture semantic labelling is vital for large scale mapping and autonomous driving systems. Much research has been investigated on road furniture interpretation in both 2D images and 3D point clouds. Precise interpretation of road furniture in mobile laser scanning data still remains unexplored. In this paper, a novel method is proposed to interpret road furniture based on their logical relations and functionalities. Our work represents the most detailed interpretation of road furniture in mobile laser scanning data. 93.3 % of poles are correctly extracted and all of them are correctly recognised. 94.3 % of street light heads are detected and 76.9 % of them are correctly identified. Despite errors arising from the recognition of other components, our framework provides a promising solution to automatically map road furniture at a detailed level in urban environments.
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NASA Astrophysics Data System (ADS)
Gontaszewska-Piekarz, Agnieszka; Mrówczyńska, Maria
2018-04-01
The paper presents the possibilities of using data obtained by airborne laser scanning for identifying areas where lignite used to be mined. The technology of airborne laser scanning presented in the paper as and its results have a vast potential in terms of identifying local terrain deformations. The paper also presents the history of lignite mining in the region of Ośno Lubuskie (the north-west of Ziemia Lubuska - western Poland). It describes underground mining in complicated geological conditions (glaciotectonic deformations). The paper is supplemented with historical maps showing the locations of the mines
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NASA Astrophysics Data System (ADS)
Sun, Chengjun; Jiang, Fenghua; Gao, Wei; Li, Xiaoyun; Yu, Yanzhen; Yin, Xiaofei; Wang, Yong; Ding, Haibing
2017-01-01
Detection of sulfur-oxidizing bacteria has largely been dependent on targeted gene sequencing technology or traditional cell cultivation, which usually takes from days to months to carry out. This clearly does not meet the requirements of analysis for time-sensitive samples and/or complicated environmental samples. Since energy-dispersive X-ray spectrometry (EDS) can be used to simultaneously detect multiple elements in a sample, including sulfur, with minimal sample treatment, this technology was applied to detect sulfur-oxidizing bacteria using their high sulfur content within the cell. This article describes the application of scanning electron microscopy imaging coupled with EDS mapping for quick detection of sulfur oxidizers in contaminated environmental water samples, with minimal sample handling. Scanning electron microscopy imaging revealed the existence of dense granules within the bacterial cells, while EDS identified large amounts of sulfur within them. EDS mapping localized the sulfur to these granules. Subsequent 16S rRNA gene sequencing showed that the bacteria detected in our samples belonged to the genus Chromatium, which are sulfur oxidizers. Thus, EDS mapping made it possible to identify sulfur oxidizers in environmental samples based on localized sulfur within their cells, within a short time (within 24 h of sampling). This technique has wide ranging applications for detection of sulfur bacteria in environmental water samples.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Cunliffe, Alexandra; Armato, Samuel G.; Castillo, Richard
2015-04-01
Purpose: To assess the relationship between radiation dose and change in a set of mathematical intensity- and texture-based features and to determine the ability of texture analysis to identify patients who develop radiation pneumonitis (RP). Methods and Materials: A total of 106 patients who received radiation therapy (RT) for esophageal cancer were retrospectively identified under institutional review board approval. For each patient, diagnostic computed tomography (CT) scans were acquired before (0-168 days) and after (5-120 days) RT, and a treatment planning CT scan with an associated dose map was obtained. 32- × 32-pixel regions of interest (ROIs) were randomly identifiedmore » in the lungs of each pre-RT scan. ROIs were subsequently mapped to the post-RT scan and the planning scan dose map by using deformable image registration. The changes in 20 feature values (ΔFV) between pre- and post-RT scan ROIs were calculated. Regression modeling and analysis of variance were used to test the relationships between ΔFV, mean ROI dose, and development of grade ≥2 RP. Area under the receiver operating characteristic curve (AUC) was calculated to determine each feature's ability to distinguish between patients with and those without RP. A classifier was constructed to determine whether 2- or 3-feature combinations could improve RP distinction. Results: For all 20 features, a significant ΔFV was observed with increasing radiation dose. Twelve features changed significantly for patients with RP. Individual texture features could discriminate between patients with and those without RP with moderate performance (AUCs from 0.49 to 0.78). Using multiple features in a classifier, AUC increased significantly (0.59-0.84). Conclusions: A relationship between dose and change in a set of image-based features was observed. For 12 features, ΔFV was significantly related to RP development. This study demonstrated the ability of radiomics to provide a quantitative, individualized measurement of patient lung tissue reaction to RT and assess RP development.« less
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Assessing Temporal Behavior in LIDAR Point Clouds of Urban Environments
NASA Astrophysics Data System (ADS)
Schachtschneider, J.; Schlichting, A.; Brenner, C.
2017-05-01
Self-driving cars and robots that run autonomously over long periods of time need high-precision and up-to-date models of the changing environment. The main challenge for creating long term maps of dynamic environments is to identify changes and adapt the map continuously. Changes can occur abruptly, gradually, or even periodically. In this work, we investigate how dense mapping data of several epochs can be used to identify the temporal behavior of the environment. This approach anticipates possible future scenarios where a large fleet of vehicles is equipped with sensors which continuously capture the environment. This data is then being sent to a cloud based infrastructure, which aligns all datasets geometrically and subsequently runs scene analysis on it, among these being the analysis for temporal changes of the environment. Our experiments are based on a LiDAR mobile mapping dataset which consists of 150 scan strips (a total of about 1 billion points), which were obtained in multiple epochs. Parts of the scene are covered by up to 28 scan strips. The time difference between the first and last epoch is about one year. In order to process the data, the scan strips are aligned using an overall bundle adjustment, which estimates the surface (about one billion surface element unknowns) as well as 270,000 unknowns for the adjustment of the exterior orientation parameters. After this, the surface misalignment is usually below one centimeter. In the next step, we perform a segmentation of the point clouds using a region growing algorithm. The segmented objects and the aligned data are then used to compute an occupancy grid which is filled by tracing each individual LiDAR ray from the scan head to every point of a segment. As a result, we can assess the behavior of each segment in the scene and remove voxels from temporal objects from the global occupancy grid.
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QTL Mapping and CRISPR/Cas9 Editing to Identify a Drug Resistance Gene in Toxoplasma gondii.
Shen, Bang; Powell, Robin H; Behnke, Michael S
2017-06-22
Scientific knowledge is intrinsically linked to available technologies and methods. This article will present two methods that allowed for the identification and verification of a drug resistance gene in the Apicomplexan parasite Toxoplasma gondii, the method of Quantitative Trait Locus (QTL) mapping using a Whole Genome Sequence (WGS) -based genetic map and the method of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 -based gene editing. The approach of QTL mapping allows one to test if there is a correlation between a genomic region(s) and a phenotype. Two datasets are required to run a QTL scan, a genetic map based on the progeny of a recombinant cross and a quantifiable phenotype assessed in each of the progeny of that cross. These datasets are then formatted to be compatible with R/qtl software that generates a QTL scan to identify significant loci correlated with the phenotype. Although this can greatly narrow the search window of possible candidates, QTLs span regions containing a number of genes from which the causal gene needs to be identified. Having WGS of the progeny was critical to identify the causal drug resistance mutation at the gene level. Once identified, the candidate mutation can be verified by genetic manipulation of drug sensitive parasites. The most facile and efficient method to genetically modify T. gondii is the CRISPR/Cas9 system. This system comprised of just 2 components both encoded on a single plasmid, a single guide RNA (gRNA) containing a 20 bp sequence complementary to the genomic target and the Cas9 endonuclease that generates a double-strand DNA break (DSB) at the target, repair of which allows for insertion or deletion of sequences around the break site. This article provides detailed protocols to use CRISPR/Cas9 based genome editing tools to verify the gene responsible for sinefungin resistance and to construct transgenic parasites.
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QTL Mapping and CRISPR/Cas9 Editing to Identify a Drug Resistance Gene in Toxoplasma gondii
Shen, Bang; Powell, Robin H.; Behnke, Michael S.
2017-01-01
Scientific knowledge is intrinsically linked to available technologies and methods. This article will present two methods that allowed for the identification and verification of a drug resistance gene in the Apicomplexan parasite Toxoplasma gondii, the method of Quantitative Trait Locus (QTL) mapping using a Whole Genome Sequence (WGS) -based genetic map and the method of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 -based gene editing. The approach of QTL mapping allows one to test if there is a correlation between a genomic region(s) and a phenotype. Two datasets are required to run a QTL scan, a genetic map based on the progeny of a recombinant cross and a quantifiable phenotype assessed in each of the progeny of that cross. These datasets are then formatted to be compatible with R/qtl software that generates a QTL scan to identify significant loci correlated with the phenotype. Although this can greatly narrow the search window of possible candidates, QTLs span regions containing a number of genes from which the causal gene needs to be identified. Having WGS of the progeny was critical to identify the causal drug resistance mutation at the gene level. Once identified, the candidate mutation can be verified by genetic manipulation of drug sensitive parasites. The most facile and efficient method to genetically modify T. gondii is the CRISPR/Cas9 system. This system comprised of just 2 components both encoded on a single plasmid, a single guide RNA (gRNA) containing a 20 bp sequence complementary to the genomic target and the Cas9 endonuclease that generates a double-strand DNA break (DSB) at the target, repair of which allows for insertion or deletion of sequences around the break site. This article provides detailed protocols to use CRISPR/Cas9 based genome editing tools to verify the gene responsible for sinefungin resistance and to construct transgenic parasites. PMID:28671645
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Panagopoulos, Ioannis; Gorunova, Ludmila; Bjerkehagen, Bodil; Heim, Sverre
2014-01-01
Whole transcriptome sequencing was used to study a small round cell tumor in which a t(4;19)(q35;q13) was part of the complex karyotype but where the initial reverse transcriptase PCR (RT-PCR) examination did not detect a CIC-DUX4 fusion transcript previously described as the crucial gene-level outcome of this specific translocation. The RNA sequencing data were analysed using the FusionMap, FusionFinder, and ChimeraScan programs which are specifically designed to identify fusion genes. FusionMap, FusionFinder, and ChimeraScan identified 1017, 102, and 101 fusion transcripts, respectively, but CIC-DUX4 was not among them. Since the RNA sequencing data are in the fastq text-based format, we searched the files using the "grep" command-line utility. The "grep" command searches the text for specific expressions and displays, by default, the lines where matches occur. The "specific expression" was a sequence of 20 nucleotides from the coding part of the last exon 20 of CIC (Reference Sequence: NM_015125.3) chosen since all the so far reported CIC breakpoints have occurred here. Fifteen chimeric CIC-DUX4 cDNA sequences were captured and the fusion between the CIC and DUX4 genes was mapped precisely. New primer combinations were constructed based on these findings and were used together with a polymerase suitable for amplification of GC-rich DNA templates to amplify CIC-DUX4 cDNA fragments which had the same fusion point found with "grep". In conclusion, FusionMap, FusionFinder, and ChimeraScan generated a plethora of fusion transcripts but did not detect the biologically important CIC-DUX4 chimeric transcript; they are generally useful but evidently suffer from imperfect both sensitivity and specificity. The "grep" command is an excellent tool to capture chimeric transcripts from RNA sequencing data when the pathological and/or cytogenetic information strongly indicates the presence of a specific fusion gene.
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Methods for the correction of vascular artifacts in PET O-15 water brain-mapping studies
NASA Astrophysics Data System (ADS)
Chen, Kewei; Reiman, E. M.; Lawson, M.; Yun, Lang-sheng; Bandy, D.; Palant, A.
1996-12-01
While positron emission tomographic (PET) measurements of regional cerebral blood flow (rCBF) can be used to map brain regions that are involved in normal and pathological human behaviors, measurements in the anteromedial temporal lobe can be confounded by the combined effects of radiotracer activity in neighboring arteries and partial-volume averaging. The authors now describe two simple methods to address this vascular artifact. One method utilizes the early frames of a dynamic PET study, while the other method utilizes a coregistered magnetic resonance image (MRI) to characterize the vascular region of interest (VROI). Both methods subsequently assign a common value to each pixel in the VROI for the control (baseline) scan and the activation scan. To study the vascular artifact and to demonstrate the ability of the proposed methods correcting the vascular artifact, four dynamic PET scans were performed in a single subject during the same behavioral state. For each of the four scans, a vascular scan containing vascular activity was computed as the summation of the images acquired 0-60 s after radiotracer administration, and a control scan containing minimal vascular activity was computed as the summation of the images acquired 20-80 s after radiotracer administration. t-score maps calculated from the four pairs of vascular and control scans were used to characterize regional blood flow differences related to vascular activity before and after the application of each vascular artifact correction method. Both methods eliminated the observed differences in vascular activity, as well as the vascular artifact observed in the anteromedial temporal lobes. Using PET data from a study of normal human emotion, these methods permitted the authors to identify rCBF increases in the anteromedial temporal lobe free from the potentially confounding, combined effects of vascular activity and partial-volume averaging.
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Parthasarathy, Meera; Pemaiah, Brindha; Natesan, Ravichandran; Padmavathy, Saralla R; Pachiappan, Jayaraman
2015-02-01
Salt glands are specialized organelles present in the leaf tissues of halophytes, which impart salt-tolerance capability to the plant species. These glands are usually identified only by their morphology using conventional staining procedures coupled with optical microscopy. In this work, we have employed scanning electrochemical microscopy to identify the salt glands not only by their morphology but also by their salt excretion behavior. Bermuda grass (Cynodon dactylon L.) species was chosen for the study as they are known to be salt-tolerant and contain salt glands on leaf surfaces. Scanning electrochemical microscopy performed in sodium chloride medium in the presence and absence of potassium ferrocyanide as redox mediator, reveals the identity of salt glands. More insight into the ion expulsion behavior of these glands was obtained by mapping lateral and vertical variations in ion concentrations using surface impedance measurements which indicated five times higher resistance over the salt glands compared to the surrounding tissues and bulk solution. The protocol could be used to understand the developmental processes in plants grown in different soil/water conditions in order to improve salt tolerance of food crops by genetic engineering and hence improve their agricultural productivity.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Guan, Xuefei; Zhou, S. Kevin; Rasselkorde, El Mahjoub
The study presents a data processing methodology for weld build-up using multiple scan patterns. To achieve an overall high probability of detection for flaws with different orientations, an inspection procedure with three different scan patterns is proposed. The three scan patterns are radial-tangential longitude wave pattern, axial-radial longitude wave pattern, and tangential shear wave pattern. Scientific fusion of the inspection data is implemented using volume reconstruction techniques. The idea is to perform spatial domain forward data mapping for all sampling points. A conservative scheme is employed to handle the case that multiple sampling points are mapped to one grid location.more » The scheme assigns the maximum value for the grid location to retain the largest equivalent reflector size for the location. The methodology is demonstrated and validated using a realistic ring of weld build-up. Tungsten balls and bars are embedded to the weld build-up during manufacturing process to represent natural flaws. Flat bottomed holes and side drilled holes are installed as artificial flaws. Automatic flaw identification and extraction are demonstrated. Results indicate the inspection procedure with multiple scan patterns can identify all the artificial and natural flaws.« less
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NASA Astrophysics Data System (ADS)
Guan, Xuefei; Rasselkorde, El Mahjoub; Abbasi, Waheed; Zhou, S. Kevin
2015-03-01
The study presents a data processing methodology for weld build-up using multiple scan patterns. To achieve an overall high probability of detection for flaws with different orientations, an inspection procedure with three different scan patterns is proposed. The three scan patterns are radial-tangential longitude wave pattern, axial-radial longitude wave pattern, and tangential shear wave pattern. Scientific fusion of the inspection data is implemented using volume reconstruction techniques. The idea is to perform spatial domain forward data mapping for all sampling points. A conservative scheme is employed to handle the case that multiple sampling points are mapped to one grid location. The scheme assigns the maximum value for the grid location to retain the largest equivalent reflector size for the location. The methodology is demonstrated and validated using a realistic ring of weld build-up. Tungsten balls and bars are embedded to the weld build-up during manufacturing process to represent natural flaws. Flat bottomed holes and side drilled holes are installed as artificial flaws. Automatic flaw identification and extraction are demonstrated. Results indicate the inspection procedure with multiple scan patterns can identify all the artificial and natural flaws.
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Sun, Hongbin; Pashoutani, Sepehr; Zhu, Jinying
2018-06-16
Delamanintions and reinforcement corrosion are two common problems in concrete bridge decks. No single nondestructive testing method (NDT) is able to provide comprehensive characterization of these defects. In this work, two NDT methods, acoustic scanning and Ground Penetrating Radar (GPR), were used to image a straight concrete bridge deck and a curved intersection ramp bridge. An acoustic scanning system has been developed for rapid delamination mapping. The system consists of metal-ball excitation sources, air-coupled sensors, and a GPS positioning system. The acoustic scanning results are presented as a two-dimensional image that is based on the energy map in the frequency range of 0.5⁻5 kHz. The GPR scanning results are expressed as the GPR signal attenuation map to characterize concrete deterioration and reinforcement corrosion. Signal processing algorithms for both methods are discussed. Delamination maps from the acoustic scanning are compared with deterioration maps from the GPR scanning on both bridges. The results demonstrate that combining the acoustic and GPR scanning results will provide a complementary and comprehensive evaluation of concrete bridge decks.
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NASA Astrophysics Data System (ADS)
Casas Planes, Á.; Garcia, M.; Siegel, R.; Koltunov, A.; Ramirez, C.; Ustin, S.
2015-12-01
Occupancy and habitat suitability models for snag-dependent wildlife species are commonly defined as a function of snag basal area. Although critical for predicting or assessing habitat suitability, spatially distributed estimates of snag basal area are not generally available across landscapes at spatial scales relevant for conservation planning. This study evaluates the use of airborne laser scanning (ALS) to 1) identify individual conifer snags and map their basal area across a recently burned forest, and 2) map habitat suitability for a wildlife species known to be dependent on snag basal area, specifically the black-backed woodpecker (Picoides arcticus). This study focuses on the Rim Fire, a megafire that took place in 2013 in the Sierra Nevada Mountains of California, creating large patches of medium- and high-severity burned forest. We use forest inventory plots, single-tree ALS-derived metrics and Gaussian processes classification and regression to identify conifer snags and estimate their stem diameter and basal area. Then, we use the results to map habitat suitability for the black-backed woodpecker using thresholds for conifer basal area from a previously published habitat suitability model. Local maxima detection and watershed segmentation algorithms resulted in 75% detection of trees with stem diameter larger than 30 cm. Snags are identified with an overall accuracy of 91.8 % and conifer snags are identified with an overall accuracy of 84.8 %. Finally, Gaussian process regression reliably estimated stem diameter (R2 = 0.8) using height and crown area. This work provides a fast and efficient methodology to characterize the extent of a burned forest at the tree level and a critical tool for early wildlife assessment in post-fire forest management and biodiversity conservation.
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Laser-Based Slam with Efficient Occupancy Likelihood Map Learning for Dynamic Indoor Scenes
NASA Astrophysics Data System (ADS)
Li, Li; Yao, Jian; Xie, Renping; Tu, Jinge; Feng, Chen
2016-06-01
Location-Based Services (LBS) have attracted growing attention in recent years, especially in indoor environments. The fundamental technique of LBS is the map building for unknown environments, this technique also named as simultaneous localization and mapping (SLAM) in robotic society. In this paper, we propose a novel approach for SLAMin dynamic indoor scenes based on a 2D laser scanner mounted on a mobile Unmanned Ground Vehicle (UGV) with the help of the grid-based occupancy likelihood map. Instead of applying scan matching in two adjacent scans, we propose to match current scan with the occupancy likelihood map learned from all previous scans in multiple scales to avoid the accumulation of matching errors. Due to that the acquisition of the points in a scan is sequential but not simultaneous, there unavoidably exists the scan distortion at different extents. To compensate the scan distortion caused by the motion of the UGV, we propose to integrate a velocity of a laser range finder (LRF) into the scan matching optimization framework. Besides, to reduce the effect of dynamic objects such as walking pedestrians often existed in indoor scenes as much as possible, we propose a new occupancy likelihood map learning strategy by increasing or decreasing the probability of each occupancy grid after each scan matching. Experimental results in several challenged indoor scenes demonstrate that our proposed approach is capable of providing high-precision SLAM results.
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Tsumura, Y; Uchiyama, K; Moriguchi, Y; Ueno, S; Ihara-Ujino, T
2012-12-01
Local adaptation is important in evolutionary processes and speciation. We used multiple tests to identify several candidate genes that may be involved in local adaptation from 1026 loci in 14 natural populations of Cryptomeria japonica, the most economically important forestry tree in Japan. We also studied the relationships between genotypes and environmental variables to obtain information on the selective pressures acting on individual populations. Outlier loci were mapped onto a linkage map, and the positions of loci associated with specific environmental variables are considered. The outlier loci were not randomly distributed on the linkage map; linkage group 11 was identified as a genomic island of divergence. Three loci in this region were also associated with environmental variables such as mean annual temperature, daily maximum temperature, maximum snow depth, and so on. Outlier loci identified with high significance levels will be essential for conservation purposes and for future work on molecular breeding.
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Ground mapping resolution accuracy of a scanning radiometer from a geostationary satellite.
Stremler, F G; Khalil, M A; Parent, R J
1977-06-01
Measures of the spatial and spatial rate (frequency) mapping of scanned visual imagery from an earth reference system to a spin-scan geostationary satellite are examined. Mapping distortions and coordinate inversions to correct for these distortions are formulated in terms of geometric transformations between earth and satellite frames of reference. Probabilistic methods are used to develop relations for obtainable mapping resolution when coordinate inversions are employed.
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Microanalysis of dental caries using laser-scanned fluorescence
NASA Astrophysics Data System (ADS)
Barron, Joseph R.; Paton, Barry E.; Zakariasen, Kenneth L.
1992-06-01
It is well known that enamel and dentin fluoresce when illuminated by short-wavelength optical radiation. Fluorescence emission from carious and non-carious regions of teeth have been studied using a new experimental scanning technique for fluorescence analysis of dental sections. Scanning in 2 dimensions will allow surface maps of dental caries to be created. These surface images are then enhanced using the conventional and newer image processing techniques. Carious regions can be readily identified and contour maps can be used to graphically display the degree of damage on both surfaces and transverse sections. Numerous studies have shown that carious fluorescence is significantly different than non-carious regions. The scanning laser fluorescence spectrometer focuses light from a 25 mW He-Cd laser at 442 nm through an objective lens onto a cross-section area as small as 3 micrometers in diameter. Microtome prepared dental samples 100 micrometers thick are laid flat onto an optical bench perpendicular to the incident beam. The sample is moved under computer control in X & Y with an absolute precision of 0.1 micrometers . The backscattered light is both spatial and wavelength filtered before being measured on a long wavelength sensitized photomultiplier tube. High precision analysis of dental samples allow detailed maps of carious regions to be determined. Successive images allow time studies of caries growth and even the potential for remineralization studies of decalcified regions.
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Improving fMRI reliability in presurgical mapping for brain tumours.
Stevens, M Tynan R; Clarke, David B; Stroink, Gerhard; Beyea, Steven D; D'Arcy, Ryan Cn
2016-03-01
Functional MRI (fMRI) is becoming increasingly integrated into clinical practice for presurgical mapping. Current efforts are focused on validating data quality, with reliability being a major factor. In this paper, we demonstrate the utility of a recently developed approach that uses receiver operating characteristic-reliability (ROC-r) to: (1) identify reliable versus unreliable data sets; (2) automatically select processing options to enhance data quality; and (3) automatically select individualised thresholds for activation maps. Presurgical fMRI was conducted in 16 patients undergoing surgical treatment for brain tumours. Within-session test-retest fMRI was conducted, and ROC-reliability of the patient group was compared to a previous healthy control cohort. Individually optimised preprocessing pipelines were determined to improve reliability. Spatial correspondence was assessed by comparing the fMRI results to intraoperative cortical stimulation mapping, in terms of the distance to the nearest active fMRI voxel. The average ROC-r reliability for the patients was 0.58±0.03, as compared to 0.72±0.02 in healthy controls. For the patient group, this increased significantly to 0.65±0.02 by adopting optimised preprocessing pipelines. Co-localisation of the fMRI maps with cortical stimulation was significantly better for more reliable versus less reliable data sets (8.3±0.9 vs 29±3 mm, respectively). We demonstrated ROC-r analysis for identifying reliable fMRI data sets, choosing optimal postprocessing pipelines, and selecting patient-specific thresholds. Data sets with higher reliability also showed closer spatial correspondence to cortical stimulation. ROC-r can thus identify poor fMRI data at time of scanning, allowing for repeat scans when necessary. ROC-r analysis provides optimised and automated fMRI processing for improved presurgical mapping. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/
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Utilizing multi-sensor fire detections to map fires in the United States
Howard, Stephen M.; Picotte, Joshua J.; Coan, Michael
2014-01-01
In 2006, the Monitoring Trends in Burn Severity (MTBS) project began a cooperative effort between the US Forest Service (USFS) and the U.S.Geological Survey (USGS) to map and assess burn severity all large fires that have occurred in the United States since 1984. Using Landsat imagery, MTBS is mandated to map wildfire and prescribed fire that meet specific size criteria: greater than 1000 acres in the west and 500 acres in the east, regardless of ownership. Relying mostly on federal and state fire occurrence records, over 15,300 individual fires have been mapped. While mapping recorded fires, an additional 2,700 “unknown” or undocumented fires were discovered and assessed. It has become apparent that there are perhaps thousands of undocumented fires in the US that are yet to be mapped. Fire occurrence records alone are inadequate if MTBS is to provide a comprehensive accounting of fire across the US. Additionally, the sheer number of fires to assess has overwhelmed current manual procedures. To address these problems, the National Aeronautics and Space Administration (NASA) Applied Sciences Program is helping to fund the efforts of the USGS and its MTBS partners (USFS, National Park Service) to develop, and implement a system to automatically identify fires using satellite data. In near real time, USGS will combine active fire satellite detections from MODIS, AVHRR and GOES satellites with Landsat acquisitions. Newly acquired Landsat imagery will be routinely scanned to identify freshly burned area pixels, derive an initial perimeter and tag the burned area with the satellite date and time of detection. Landsat imagery from the early archive will be scanned to identify undocumented fires. Additional automated fire assessment processes will be developed. The USGS will develop these processes using open source software packages in order to provide freely available tools to local land managers providing them with the capability to assess fires at the local level.
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Utilizing Multi-Sensor Fire Detections to Map Fires in the United States
NASA Astrophysics Data System (ADS)
Howard, S. M.; Picotte, J. J.; Coan, M. J.
2014-11-01
In 2006, the Monitoring Trends in Burn Severity (MTBS) project began a cooperative effort between the US Forest Service (USFS) and the U.S.Geological Survey (USGS) to map and assess burn severity all large fires that have occurred in the United States since 1984. Using Landsat imagery, MTBS is mandated to map wildfire and prescribed fire that meet specific size criteria: greater than 1000 acres in the west and 500 acres in the east, regardless of ownership. Relying mostly on federal and state fire occurrence records, over 15,300 individual fires have been mapped. While mapping recorded fires, an additional 2,700 "unknown" or undocumented fires were discovered and assessed. It has become apparent that there are perhaps thousands of undocumented fires in the US that are yet to be mapped. Fire occurrence records alone are inadequate if MTBS is to provide a comprehensive accounting of fire across the US. Additionally, the sheer number of fires to assess has overwhelmed current manual procedures. To address these problems, the National Aeronautics and Space Administration (NASA) Applied Sciences Program is helping to fund the efforts of the USGS and its MTBS partners (USFS, National Park Service) to develop, and implement a system to automatically identify fires using satellite data. In near real time, USGS will combine active fire satellite detections from MODIS, AVHRR and GOES satellites with Landsat acquisitions. Newly acquired Landsat imagery will be routinely scanned to identify freshly burned area pixels, derive an initial perimeter and tag the burned area with the satellite date and time of detection. Landsat imagery from the early archive will be scanned to identify undocumented fires. Additional automated fire assessment processes will be developed. The USGS will develop these processes using open source software packages in order to provide freely available tools to local land managers providing them with the capability to assess fires at the local level.
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OCT Expanded Clinical Data Analysis
NASA Technical Reports Server (NTRS)
Van Baalen, Mary; Tafreshi, Ali; Patel, Nimesh; Young, Millennia; Mason, Sara; Otto, Christian; Samuels, Brian; Koslovsky, Matthew; Schaefer, Caroline; Taiym, Wafa;
2017-01-01
Vision changes identified in long duration space fliers has led to a more comprehensive clinical monitoring protocol. Optical Coherence Tomography (OCT) was recently implemented on board the International Space Station in 2013. NASA is collaborating with Heidelberg Engineering to expand our current OCT data analysis capability by implementing a volumetric approach. Volumetric maps will be created by combining the circle scan, the disc block scan, and the radial scan. This assessment may provide additional information about the optic nerve and further characterize changes related microgravity exposure. We will discuss challenges with collection and analysis of OCT data, present the results of this reanalysis and outline the potential benefits and limitations of the additional data.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Cunliffe, A; Armato, S; Castillo, R
Purpose: To evaluate the consistency of computed tomography (CT) scan texture features, previously identified as stable in a healthy patient cohort, in esophageal cancer patient CT scans. Methods: 116 patients receiving radiation therapy (median dose: 50.4Gy) for esophageal cancer were retrospectively identified. For each patient, diagnostic-quality pre-therapy (0-183 days) and post-therapy (5-120 days) scans (mean voxel size: 0.8mm×0.8mm×2.5mm) and a treatment planning scan and associated dose map were collected. An average of 501 32x32-pixel ROIs were placed randomly in the lungs of each pre-therapy scan. ROI centers were mapped to corresponding locations in post-therapy and planning scans using the displacementmore » vector field output by demons deformable registration. Only ROIs with mean dose <5Gy were analyzed, as these were expected to contain minimal post-treatment damage. 140 texture features were calculated in pre-therapy and post-therapy scan ROIs and compared using Bland-Altman analysis. For each feature, the mean feature value change and the distance spanned by the 95% limits of agreement were normalized to the mean feature value, yielding normalized range of agreement (nRoA) and normalized bias (nBias). Using Wilcoxon signed rank tests, nRoA and nBias were compared with values computed previously in 27 healthy patient scans (mean voxel size: 0.67mm×0.67mm×1mm) acquired at a different institution. Results: nRoA was significantly (p<0.001) larger in cancer patients than healthy patients. Differences in nBias were not significant (p=0.23). The 20 features identified previously as having nRoA<20% for healthy patients had the lowest nRoA values in the current database, with an average increase of 5.6%. Conclusion: Despite differences in CT scanner type, scan resolution, and patient health status, the same 20 features remained stable (i.e., low variability and bias) in the absence of disease changes for databases from two institutions. Identification of these features is the first step towards quantifying radiation-induced changes between preand post-therapy scans. Supported, in part, by NIH Grant Nos. S10 RR021039, and P30 CA14599, the Virginia and D. K. Ludwig Fund for Cancer Research, Imaging Research Institute, Biological Sciences Division, The University of Chicago, and The Institute for Translational Medicine Pilot Award, The University of Chicago.« less
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Graded-threshold parametric response maps: towards a strategy for adaptive dose painting
NASA Astrophysics Data System (ADS)
Lausch, A.; Jensen, N.; Chen, J.; Lee, T. Y.; Lock, M.; Wong, E.
2014-03-01
Purpose: To modify the single-threshold parametric response map (ST-PRM) method for predicting treatment outcomes in order to facilitate its use for guidance of adaptive dose painting in intensity-modulated radiotherapy. Methods: Multiple graded thresholds were used to extend the ST-PRM method (Nat. Med. 2009;15(5):572-576) such that the full functional change distribution within tumours could be represented with respect to multiple confidence interval estimates for functional changes in similar healthy tissue. The ST-PRM and graded-threshold PRM (GT-PRM) methods were applied to functional imaging scans of 5 patients treated for hepatocellular carcinoma. Pre and post-radiotherapy arterial blood flow maps (ABF) were generated from CT-perfusion scans of each patient. ABF maps were rigidly registered based on aligning tumour centres of mass. ST-PRM and GT-PRM analyses were then performed on overlapping tumour regions within the registered ABF maps. Main findings: The ST-PRMs contained many disconnected clusters of voxels classified as having a significant change in function. While this may be useful to predict treatment response, it may pose challenges for identifying boost volumes or for informing dose-painting by numbers strategies. The GT-PRMs included all of the same information as ST-PRMs but also visualized the full tumour functional change distribution. Heterogeneous clusters in the ST-PRMs often became more connected in the GT-PRMs by voxels with similar functional changes. Conclusions: GT-PRMs provided additional information which helped to visualize relationships between significant functional changes identified by ST-PRMs. This may enhance ST-PRM utility for guiding adaptive dose painting.
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Characterization of Visual Scanning Patterns in Air Traffic Control
McClung, Sarah N.; Kang, Ziho
2016-01-01
Characterization of air traffic controllers' (ATCs') visual scanning strategies is a challenging issue due to the dynamic movement of multiple aircraft and increasing complexity of scanpaths (order of eye fixations and saccades) over time. Additionally, terminologies and methods are lacking to accurately characterize the eye tracking data into simplified visual scanning strategies linguistically expressed by ATCs. As an intermediate step to automate the characterization classification process, we (1) defined and developed new concepts to systematically filter complex visual scanpaths into simpler and more manageable forms and (2) developed procedures to map visual scanpaths with linguistic inputs to reduce the human judgement bias during interrater agreement. The developed concepts and procedures were applied to investigating the visual scanpaths of expert ATCs using scenarios with different aircraft congestion levels. Furthermore, oculomotor trends were analyzed to identify the influence of aircraft congestion on scan time and number of comparisons among aircraft. The findings show that (1) the scanpaths filtered at the highest intensity led to more consistent mapping with the ATCs' linguistic inputs, (2) the pattern classification occurrences differed between scenarios, and (3) increasing aircraft congestion caused increased scan times and aircraft pairwise comparisons. The results provide a foundation for better characterizing complex scanpaths in a dynamic task and automating the analysis process. PMID:27239190
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Characterization of Visual Scanning Patterns in Air Traffic Control.
McClung, Sarah N; Kang, Ziho
2016-01-01
Characterization of air traffic controllers' (ATCs') visual scanning strategies is a challenging issue due to the dynamic movement of multiple aircraft and increasing complexity of scanpaths (order of eye fixations and saccades) over time. Additionally, terminologies and methods are lacking to accurately characterize the eye tracking data into simplified visual scanning strategies linguistically expressed by ATCs. As an intermediate step to automate the characterization classification process, we (1) defined and developed new concepts to systematically filter complex visual scanpaths into simpler and more manageable forms and (2) developed procedures to map visual scanpaths with linguistic inputs to reduce the human judgement bias during interrater agreement. The developed concepts and procedures were applied to investigating the visual scanpaths of expert ATCs using scenarios with different aircraft congestion levels. Furthermore, oculomotor trends were analyzed to identify the influence of aircraft congestion on scan time and number of comparisons among aircraft. The findings show that (1) the scanpaths filtered at the highest intensity led to more consistent mapping with the ATCs' linguistic inputs, (2) the pattern classification occurrences differed between scenarios, and (3) increasing aircraft congestion caused increased scan times and aircraft pairwise comparisons. The results provide a foundation for better characterizing complex scanpaths in a dynamic task and automating the analysis process.
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Gautam, R; Srinath, I; Clavijo, A; Szonyi, B; Bani-Yaghoub, M; Park, S; Ivanek, R
2013-03-01
Coccidioidomycosis or Valley Fever (VF) is an emerging soil-borne fungal zoonosis affecting humans and animals. Most non-human cases of VF are found in dogs, which we hypothesize may serve as sentinels for estimating the human exposure risk. The objective of this study is to use the spatial and temporal distribution and clusters of dogs seropositive for VF to define the geographic area in Texas where VF is endemic, and thus presents a higher risk of exposure to humans. The included specimens were seropositive dogs tested at a major diagnostic laboratory between 1999 and 2009. Data were aggregated by zip code and smoothed by empirical Bayesian estimation to develop an isopleth map of VF seropositive rates using kriging. Clusters of seropositive dogs were identified using the spatial scan test. Both the isopleth map and the scan test identified an area with a high rate of VF-seropositive dogs in the western and southwestern parts of Texas (relative risk = 31). This location overlapped an area that was previously identified as a potential endemic region based on human surveys. Together, these data suggest that dogs may serve as sentinels for estimating the risk of human exposure to VF. © 2012 Blackwell Verlag GmbH.
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NASA Astrophysics Data System (ADS)
Krupnik, D.; Khan, S.; Crockett, M.
2017-12-01
Understanding the origin, genesis, as well as depositional and structural mechanisms of gold mineralization as well as detailed mapping of gold-bearing mineral phases at centimeter scale can be useful for exploration. This work was conducted in the Goldstrike mining district near St. George, UT, a structurally complex region which contains Carlin-style disseminated gold deposits in permeable sedimentary layers near high-angle fault zones. These fault zones are likely a conduit for gold-bearing hydrothermal fluids, are silicified, and are frequently gold-bearing. Alteration patterns are complex, difficult to distinguish visually, composed of several phases, and vary significantly over centimeter to meter scale distances. This makes identifying and quantifying the extent of the target zones costly, time consuming, and discontinuous with traditional geochemical methods. A ground-based hyperspectral scanning system with sensors collecting data in the Visible Near Infrared (VNIR) and Short-Wave Infrared (SWIR) portions of the electromagnetic spectrum are utilized for close-range outcrop scanning. Scans were taken of vertical exposures of both gold-bearing and barren silicified rocks (jasperoids), with the intent to produce images which delineate and quantify the extent of each phase of alteration, in combination with discrete geochemical data. This ongoing study produces mineralogical maps of surface minerals at centimeter scale, with the intent of mapping original and alteration minerals. This efficient method of outcrop characterization increases our understanding of fluid flow and alteration of economic deposits.
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Medina-Franco, José L.; Edwards, Bruce S.; Pinilla, Clemencia; Appel, Jon R.; Giulianotti, Marc A.; Santos, Radleigh G.; Yongye, Austin B.; Sklar, Larry A.; Houghten, Richard A.
2013-01-01
We present a general approach to describe the structure-activity relationships (SAR) of combinatorial data sets with activity for two biological endpoints with emphasis on the rapid identification of substitutions that have a large impact on activity and selectivity. The approach uses Dual-Activity Difference (DAD) maps that represent a visual and quantitative analysis of all pairwise comparisons of one, two, or more substitutions around a molecular template. Scanning the SAR of data sets using DAD maps allows the visual and quantitative identification of activity switches defined as specific substitutions that have an opposite effect on the activity of the compounds against two targets. The approach also rapidly identifies single- and double-target R-cliffs, i.e., compounds where a single or double substitution around the central scaffold dramatically modifies the activity for one or two targets, respectively. The approach introduced in this report can be applied to any analogue series with two biological activity endpoints. To illustrate the approach, we discuss the SAR of 106 pyrrolidine bis-diketopiperazines tested against two formylpeptide receptors obtained from positional scanning deconvolution methods of mixture-based libraries. PMID:23705689
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Vaughn, Justin N.; Nelson, Randall L.; Song, Qijian; Cregan, Perry B.; Li, Zenglu
2014-01-01
Soybean oil and meal are major contributors to world-wide food production. Consequently, the genetic basis for soybean seed composition has been intensely studied using family-based mapping. Population-based mapping approaches, in the form of genome-wide association (GWA) scans, have been able to resolve loci controlling moderately complex quantitative traits (QTL) in numerous crop species. Yet, it is still unclear how soybean’s unique population history will affect GWA scans. Using one of the populations in this study, we simulated phenotypes resulting from a range of genetic architectures. We found that with a heritability of 0.5, ∼100% and ∼33% of the 4 and 20 simulated QTL can be recovered, respectively, with a false-positive rate of less than ∼6×10−5 per marker tested. Additionally, we demonstrated that combining information from multi-locus mixed models and compressed linear-mixed models improves QTL identification and interpretation. We applied these insights to exploring seed composition in soybean, refining the linkage group I (chromosome 20) protein QTL and identifying additional oil QTL that may allow some decoupling of highly correlated oil and protein phenotypes. Because the value of protein meal is closely related to its essential amino acid profile, we attempted to identify QTL underlying methionine, threonine, cysteine, and lysine content. Multiple QTL were found that have not been observed in family-based mapping studies, and each trait exhibited associations across multiple populations. Chromosomes 1 and 8 contain strong candidate alleles for essential amino acid increases. Overall, we present these and additional data that will be useful in determining breeding strategies for the continued improvement of soybean’s nutrient portfolio. PMID:25246241
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Mapping Interaction Sites on Human Chemokine Receptors by Deep Mutational Scanning.
Heredia, Jeremiah D; Park, Jihye; Brubaker, Riley J; Szymanski, Steven K; Gill, Kevin S; Procko, Erik
2018-06-01
Chemokine receptors CXCR4 and CCR5 regulate WBC trafficking and are engaged by the HIV-1 envelope glycoprotein gp120 during infection. We combine a selection of human CXCR4 and CCR5 libraries comprising nearly all of ∼7000 single amino acid substitutions with deep sequencing to define sequence-activity landscapes for surface expression and ligand interactions. After consideration of sequence constraints for surface expression, known interaction sites with HIV-1-blocking Abs were appropriately identified as conserved residues following library sorting for Ab binding, validating the use of deep mutational scanning to map functional interaction sites in G protein-coupled receptors. Chemokine CXCL12 was found to interact with residues extending asymmetrically into the CXCR4 ligand-binding cavity, similar to the binding surface of CXCR4 recognized by an antagonistic viral chemokine previously observed crystallographically. CXCR4 mutations distal from the chemokine binding site were identified that enhance chemokine recognition. This included disruptive mutations in the G protein-coupling site that diminished calcium mobilization, as well as conservative mutations to a membrane-exposed site (CXCR4 residues H79 2.45 and W161 4.50 ) that increased ligand binding without loss of signaling. Compared with CXCR4-CXCL12 interactions, CCR5 residues conserved for gp120 (HIV-1 BaL strain) interactions map to a more expansive surface, mimicking how the cognate chemokine CCL5 makes contacts across the entire CCR5 binding cavity. Acidic substitutions in the CCR5 N terminus and extracellular loops enhanced gp120 binding. This study demonstrates how comprehensive mutational scanning can define functional interaction sites on receptors, and novel mutations that enhance receptor activities can be found simultaneously. Copyright © 2018 by The American Association of Immunologists, Inc.
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Assessing the impact of graphical quality on automatic text recognition in digital maps
NASA Astrophysics Data System (ADS)
Chiang, Yao-Yi; Leyk, Stefan; Honarvar Nazari, Narges; Moghaddam, Sima; Tan, Tian Xiang
2016-08-01
Converting geographic features (e.g., place names) in map images into a vector format is the first step for incorporating cartographic information into a geographic information system (GIS). With the advancement in computational power and algorithm design, map processing systems have been considerably improved over the last decade. However, the fundamental map processing techniques such as color image segmentation, (map) layer separation, and object recognition are sensitive to minor variations in graphical properties of the input image (e.g., scanning resolution). As a result, most map processing results would not meet user expectations if the user does not "properly" scan the map of interest, pre-process the map image (e.g., using compression or not), and train the processing system, accordingly. These issues could slow down the further advancement of map processing techniques as such unsuccessful attempts create a discouraged user community, and less sophisticated tools would be perceived as more viable solutions. Thus, it is important to understand what kinds of maps are suitable for automatic map processing and what types of results and process-related errors can be expected. In this paper, we shed light on these questions by using a typical map processing task, text recognition, to discuss a number of map instances that vary in suitability for automatic processing. We also present an extensive experiment on a diverse set of scanned historical maps to provide measures of baseline performance of a standard text recognition tool under varying map conditions (graphical quality) and text representations (that can vary even within the same map sheet). Our experimental results help the user understand what to expect when a fully or semi-automatic map processing system is used to process a scanned map with certain (varying) graphical properties and complexities in map content.
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Highly sensitive mode mapping of whispering-gallery modes by scanning thermocouple-probe microscopy.
Klein, Angela E; Schmidt, Carsten; Liebsch, Mattes; Janunts, Norik; Dobynde, Mikhail; Tünnermann, Andreas; Pertsch, Thomas
2014-03-01
We propose a method for mapping optical near-fields with the help of a thermocouple scanning-probe microscope tip. As the tip scans the sample surface, its apex is heated by light absorption, generating a thermovoltage. The thermovoltage map represents the intensity distribution of light at the sample surface. The measurement technique has been employed to map optical whispering-gallery modes in fused silica microdisk resonators operating at near-infrared wavelengths. The method could potentially be employed for near-field imaging of a variety of systems in the near-infrared and visible spectral range.
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Lunar UV-visible-IR mapping interferometric spectrometer
NASA Technical Reports Server (NTRS)
Smith, W. Hayden; Haskin, L.; Korotev, R.; Arvidson, R.; Mckinnon, W.; Hapke, B.; Larson, S.; Lucey, P.
1992-01-01
Ultraviolet-visible-infrared mapping digital array scanned interferometers for lunar compositional surveys was developed. The research has defined a no-moving-parts, low-weight and low-power, high-throughput, and electronically adaptable digital array scanned interferometer that achieves measurement objectives encompassing and improving upon all the requirements defined by the LEXSWIG for lunar mineralogical investigation. In addition, LUMIS provides a new, important, ultraviolet spectral mapping, high-spatial-resolution line scan camera, and multispectral camera capabilities. An instrument configuration optimized for spectral mapping and imaging of the lunar surface and provide spectral results in support of the instrument design are described.
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Holographic maps of quasiparticle interference
NASA Astrophysics Data System (ADS)
Dalla Torre, Emanuele G.; He, Yang; Demler, Eugene
2016-11-01
The analysis of Fourier-transformed scanning tunnelling microscopy images with subatomic resolution is a common tool for studying the properties of quasiparticle excitations in strongly correlated materials. Although Fourier amplitudes are generally complex valued, earlier analysis primarily focused on their absolute values. Their complex phases were often deemed random, and thus irrelevant, due to the unknown positions of the impurities in the sample. Here we show how to factor out these random phases by analysing overlaps between Fourier amplitudes that differ by reciprocal lattice vectors. The resulting holographic maps provide important and previously unknown information about the electronic structures. When applied to superconducting cuprates, our method solves a long-standing puzzle of the dichotomy between equivalent wavevectors. We show that d-wave Wannier functions of the conduction band provide a natural explanation for experimental results that were interpreted as evidence for competing unconventional charge modulations. Our work opens a new pathway to identify the nature of electronic states in scanning tunnelling microscopy.
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NASA Astrophysics Data System (ADS)
Liu, Jingbin; Liang, Xinlian; Hyyppä, Juha; Yu, Xiaowei; Lehtomäki, Matti; Pyörälä, Jiri; Zhu, Lingli; Wang, Yunsheng; Chen, Ruizhi
2017-04-01
Terrestrial laser scanning has been widely used to analyze the 3D structure of a forest in detail and to generate data at the level of a reference plot for forest inventories without destructive measurements. Multi-scan terrestrial laser scanning is more commonly applied to collect plot-level data so that all of the stems can be detected and analyzed. However, it is necessary to match the point clouds of multiple scans to yield a point cloud with automated processing. Mismatches between datasets will lead to errors during the processing of multi-scan data. Classic registration methods based on flat surfaces cannot be directly applied in forest environments; therefore, artificial reference objects have conventionally been used to assist with scan matching. The use of artificial references requires additional labor and expertise, as well as greatly increasing the cost. In this study, we present an automated processing method for plot-level stem mapping that matches multiple scans without artificial references. In contrast to previous studies, the registration method developed in this study exploits the natural geometric characteristics among a set of tree stems in a plot and combines the point clouds of multiple scans into a unified coordinate system. Integrating multiple scans improves the overall performance of stem mapping in terms of the correctness of tree detection, as well as the bias and the root-mean-square errors of forest attributes such as diameter at breast height and tree height. In addition, the automated processing method makes stem mapping more reliable and consistent among plots, reduces the costs associated with plot-based stem mapping, and enhances the efficiency.
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SU-F-BRB-05: Collision Avoidance Mapping Using Consumer 3D Camera
DOE Office of Scientific and Technical Information (OSTI.GOV)
Cardan, R; Popple, R
2015-06-15
Purpose: To develop a fast and economical method of scanning a patient’s full body contour for use in collision avoidance mapping without the use of ionizing radiation. Methods: Two consumer level 3D cameras used in electronic gaming were placed in a CT simulator room to scan a phantom patient set up in a high collision probability position. A registration pattern and computer vision algorithms were used to transform the scan into the appropriate coordinate systems. The cameras were then used to scan the surface of a gantry in the treatment vault. Each scan was converted into a polygon mesh formore » collision testing in a general purpose polygon interference algorithm. All clinically relevant transforms were applied to the gantry and patient support to create a map of all possible collisions. The map was then tested for accuracy by physically testing the collisions with the phantom in the vault. Results: The scanning fidelity of both the gantry and patient was sufficient to produce a collision prediction accuracy of 97.1% with 64620 geometry states tested in 11.5 s. The total scanning time including computation, transformation, and generation was 22.3 seconds. Conclusion: Our results demonstrate an economical system to generate collision avoidance maps. Future work includes testing the speed of the framework in real-time collision avoidance scenarios. Research partially supported by a grant from Varian Medical Systems.« less
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Cheng, Ching-Yu; Reich, David; Coresh, Josef; Boerwinkle, Eric; Patterson, Nick; Li, Man; North, Kari E.; Tandon, Arti; Bailey-Wilson, Joan E.; Wilson, James G.; Linda Kao, W. H.
2010-01-01
Obesity is an important cause of morbidity and mortality worldwide. In the U.S., the prevalence of obesity is higher in African Americans than whites, even after adjustment for socioeconomic status. This leads to the hypothesis that differences in genetic background may contribute to racial/ethnic differences in obesity-related traits. We tested this hypothesis by conducting a genome-wide admixture mapping scan using 1,350 ancestry-informative SNPs in 3,531 self-identified blacks from the Atherosclerosis Risk in Communities (ARIC) study. We used these markers to estimate the overall proportions of European ancestry (PEA) for each individual and then scanned for the association between PEA and obesity-related traits (both continuous and dichotomous) at each locus. The median (interquartile range) PEA was 0.151 (0.115). PEA was inversely correlated with continuous body mass index (BMI), weight, and subscapular skinfold thickness, even after adjusting for socioeconomic factors. In contrast, PEA was positively correlated with BMI-adjusted waist circumference. Using admixture mapping on dichotomized traits, we identified a locus on 2p23.3 to be suggestively associated with BMI (locus-specific LOD = 4.11) and weight (locus-specific LOD = 4.07). After adjusting for global PEA, each additional copy of a European ancestral allele at the 2p23.3 peak was associated with a BMI decrease of ∼0.92 kg/m2 (p = 2.9 × 10-5). Further mapping in this region on chromosome 2 may be able to uncover causative variants underlying obesity, which may offer insights into the control of energy homeostasis. PMID:19696751
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Multi-frequency parameter mapping of electrical impedance scanning using two kinds of circuit model.
Liu, Ruigang; Dong, Xiuzhen; Fu, Feng; You, Fusheng; Shi, Xuetao; Ji, Zhenyu; Wang, Kan
2007-07-01
Electrical impedance scanning (EIS) is a kind of potential bio-impedance measurement technology, especially aiding the diagnosis of breast cancer in women. By changing the frequency of the driving signal in turn while keeping the other conditions stable, multi-frequency measurement results on the object can be obtained. According to the least square method and circuit theory, the parameters in two models are deduced when measured with data at multiple driving frequencies. The arcs, in the real and imaginary parts of a trans-admittance coordinate, made by the evaluated parameters fit well the realistic data measured by our EIS device on female subjects. The Cole-Cole model in the form of admittance is closer to the measured data than the three-element model. Based on the evaluation of the multi-frequency parameters, we presented parameter mapping of EIS using two kinds of circuit model: one is the three-element model in the form of admittance and the other is the Cole-Cole model in the form of admittance. Comparing with classical admittance mapping at a single frequency, the multi-frequency parameter mapping will provide a novel vision to study EIS. The multi-frequency approach can provide the mappings of four parameters, which is helpful to identify different diseases with a similar characteristic in classical EIS mapping. From plots of the real and imaginary parts of the admittance, it is easy to make sure whether there exists abnormal tissue.
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NASA Astrophysics Data System (ADS)
George, Michael G.; Wang, Jian; Banerjee, Rupak; Bazylak, Aimy
2016-03-01
The novel application of scanning transmission X-ray microscopy (STXM) to the microporous layer (MPL) of a polymer electrolyte membrane fuel cell is investigated. A spatially resolved chemical component distribution map is obtained for the MPL of a commercially available SGL 25 BC sample. This is achieved with near edge X-ray absorption fine structure spectroscopic analysis. Prior to analysis the sample is embedded in non-reactive epoxy and ultra-microtomed to a thickness of 100 nm. Polytetrafluoroethylene (PTFE), carbon particle agglomerates, and supporting epoxy resin distributions are identified and reconstructed for a scanning area of 6 μm × 6 μm. It is observed that the spatial distribution of PTFE is strongly correlated to the carbon particle agglomerations. Additionally, agglomerate structures of PTFE are identified, possibly indicating the presence of a unique mesostructure in the MPL. STXM analysis is presented as a useful technique for the investigation of chemical species distributions in the MPL.
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Kobayashi, Akira; Yokogawa, Hideaki; Sugiyama, Kazuhisa
2012-01-01
The purpose of this study was to investigate pathological changes of the corneal cell layer in patients with map-dot-fingerprint (epithelial basement membrane) dystrophy by in vivo laser corneal confocal microscopy. Two patients were evaluated using a cornea-specific in vivo laser scanning confocal microscope (Heidelberg Retina Tomograph 2 Rostock Cornea Module, HRT 2-RCM). The affected corneal areas of both patients were examined. Image analysis was performed to identify corneal epithelial and stromal deposits correlated with this dystrophy. Variously shaped (linear, multilaminar, curvilinear, ring-shape, geographic) highly reflective materials were observed in the "map" area, mainly in the basal epithelial cell layer. In "fingerprint" lesions, multiple linear and curvilinear hyporeflective lines were observed. Additionally, in the affected corneas, infiltration of possible Langerhans cells and other inflammatory cells was observed as highly reflective Langerhans cell-like or dot images. Finally, needle-shaped materials were observed in one patient. HRT 2-RCM laser confocal microscopy is capable of identifying corneal microstructural changes related to map-dot-fingerprint corneal dystrophy in vivo. The technique may be useful in elucidating the pathogenesis and natural course of map-dot-fingerprint corneal dystrophy and other similar basement membrane abnormalities.
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Billingsley, George H.; Wellmeyer, Jessica L.
2003-01-01
The geologic map of the Mount Trumbull 30' x 60' quadrangle is a cooperative product of the U.S. Geological Survey, the National Park Service, and the Bureau of Land Management that provides geologic map coverage and regional geologic information for visitor services and resource management of Grand Canyon National Park, Lake Mead Recreational Area, and Grand Canyon Parashant National Monument, Arizona. This map is a compilation of previous and new geologic mapping that encompasses the Mount Trumbull 30' x 60' quadrangle of Arizona. This digital database, a compilation of previous and new geologic mapping, contains geologic data used to produce the 100,000-scale Geologic Map of the Mount Trumbull 30' x 60' Quadrangle, Mohave and Coconino Counties, Northwestern Arizona. The geologic features that were mapped as part of this project include: geologic contacts and faults, bedrock and surficial geologic units, structural data, fold axes, karst features, mines, and volcanic features. This map was produced using 1:24,000-scale 1976 infrared aerial photographs followed by extensive field checking. Volcanic rocks were mapped as separate units when identified on aerial photographs as mappable and distinctly separate units associated with one or more pyroclastic cones and flows. Many of the Quaternary alluvial deposits that have similar lithology but different geomorphic characteristics were mapped almost entirely by photogeologic methods. Stratigraphic position and amount of erosional degradation were used to determine relative ages of alluvial deposits having similar lithologies. Each map unit and structure was investigated in detail in the field to ensure accuracy of description. Punch-registered mylar sheets were scanned at the Flagstaff Field Center using an Optronics 5040 raster scanner at a resolution of 50 microns (508 dpi). The scans were output in .rle format, converted to .rlc, and then converted to ARC/INFO grids. A tic file was created in geographic coordinates and projected into the base map projection (Polyconic) using a central meridian of -113.500. The tic file was used to transform the grid into Universal Transverse Mercator projection. The linework was vectorized using gridline. Scanned lines were edited interactively in ArcEdit. Polygons were attributed in ArcEdit and all artifacts and scanning errors visible at 1:100,000 were removed. Point data were digitized onscreen. Due to the discovery of digital and geologic errors on the original files, the ARC/INFO coverages were converted to a personal geodatabase and corrected in ArcMap. The feature classes which define the geologic units, lines and polygons, are topologically related and maintained in the geodatabase by a set of validation rules. The internal database structure and feature attributes were then modified to match other geologic map databases being created for the Grand Canyon region. Faults were edited with the downthrown block, if known, on the 'right side' of the line. The 'right' and 'left' sides of a line are determined from 'starting' at the line's 'from node' and moving to the line's end or 'to node'.
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Correlation of ERTS MSS data and earth coordinate systems
NASA Technical Reports Server (NTRS)
Malila, W. A. (Principal Investigator); Hieber, R. H.; Mccleer, A. P.
1973-01-01
The author has identified the following significant results. Experience has revealed a problem in the analysis and interpretation of ERTS-1 multispectral scanner (MSS) data. The problem is one of accurately correlating ERTS-1 MSS pixels with analysis areas specified on aerial photographs or topographic maps for training recognition computers and/or evaluating recognition results. It is difficult for an analyst to accurately identify which ERTS-1 pixels on a digital image display belong to specific areas and test plots, especially when they are small. A computer-aided procedure to correlate coordinates from topographic maps and/or aerial photographs with ERTS-1 data coordinates has been developed. In the procedure, a map transformation from earth coordinates to ERTS-1 scan line and point numbers is calculated using selected ground control points nad the method of least squares. The map transformation is then applied to the earth coordinates of selected areas to obtain the corresponding ERTS-1 point and line numbers. An optional provision allows moving the boundaries of the plots inward by variable distances so the selected pixels will not overlap adjacent features.
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NASA Astrophysics Data System (ADS)
Galantowicz, J. F.; Picton, J.; Root, B.
2017-12-01
Passive microwave remote sensing can provided a distinct perspective on flood events by virtue of wide sensor fields of view, frequent observations from multiple satellites, and sensitivity through clouds and vegetation. During Hurricanes Harvey and Irma, we used AMSR2 (Advanced Microwave Scanning Radiometer 2, JAXA) data to map flood extents starting from the first post-storm rain-free sensor passes. Our standard flood mapping algorithm (FloodScan) derives flooded fraction from 22-km microwave data (AMSR2 or NASA's GMI) in near real time and downscales it to 90-m resolution using a database built from topography, hydrology, and Global Surface Water Explorer data and normalized to microwave data footprint shapes. During Harvey and Irma we tested experimental versions of the algorithm designed to map the maximum post-storm flood extent rapidly and made a variety of map products available immediately for use in storm monitoring and response. The maps have several unique features including spanning the entire storm-affected area and providing multiple post-storm updates as flood water shifted and receded. From the daily maps we derived secondary products such as flood duration, maximum flood extent (Figure 1), and flood depth. In this presentation, we describe flood extent evolution, maximum extent, and local details as detected by the FloodScan algorithm in the wake of Harvey and Irma. We compare FloodScan results to other available flood mapping resources, note observed shortcomings, and describe improvements made in response. We also discuss how best-estimate maps could be updated in near real time by merging FloodScan products and data from other remote sensing systems and hydrological models.
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NASA Astrophysics Data System (ADS)
Guthoff, Rudolf F.; Zhivov, Andrey; Stachs, Oliver
2010-02-01
The aim of the study was to produce two-dimensional reconstruction maps of the living corneal sub-basal nerve plexus by in vivo laser scanning confocal microscopy in real time. CLSM source data (frame rate 30Hz, 384x384 pixel) were used to create large-scale maps of the scanned area by selecting the Automatic Real Time (ART) composite mode. The mapping algorithm is based on an affine transformation. Microscopy of the sub-basal nerve plexus was performed on normal and LASIK eyes as well as on rabbit eyes. Real-time mapping of the sub-basal nerve plexus was performed in large-scale up to a size of 3.2mm x 3.2mm. The developed method enables a real-time in vivo mapping of the sub-basal nerve plexus which is stringently necessary for statistically firmed conclusions about morphometric plexus alterations.
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Sodium Channel Mutations and Susceptibility to Heart Failure and Atrial Fibrillation
Olson, Timothy M.; Michels, Virginia V.; Ballew, Jeffrey D.; Reyna, Sandra P.; Karst, Margaret L.; Herron, Kathleen J.; Horton, Steven C.; Rodeheffer, Richard J.; Anderson, Jeffrey L.
2007-01-01
Context Dilated cardiomyopathy (DCM), a genetically heterogeneous disorder, causes heart failure and rhythm disturbances. The majority of identified DCM genes encode structural proteins of the contractile apparatus and cytoskeleton. Recently, genetic defects in calcium and potassium regulation have been discovered in patients with DCM, implicating an alternative disease mechanism. The full spectrum of genetic defects in DCM, however, has not been established. Objectives To identify a novel gene for DCM at a previously mapped locus, define the spectrum of mutations in this gene within a DCM cohort, and determine the frequency of DCM among relatives inheriting a mutation in this gene. Design, Setting, and Participants Refined mapping of a DCM locus on chromosome 3p in a multigenerational family and mutation scanning in 156 unrelated pro-bands with DCM, prospectively identified at the Mayo Clinic between 1987 and 2004. Relatives underwent screening echocardiography and electrocardiography and DNA sample procurement. Main Outcome Measure Correlation of identified mutations with cardiac phenotype. Results Refined locus mapping revealed SCN5A, encoding the cardiac sodium channel, as a candidate gene. Mutation scans identified a missense mutation (D1275N) that cosegregated with an age-dependent, variably expressed phenotype of DCM, atrial fibrillation, impaired automaticity, and conduction delay. In the DCM cohort, additional missense (T220I, R814W, D1595H) and truncation (2550-2551insTG) SCN5A mutations, segregating with cardiac disease or arising de novo, were discovered in unrelated probands. Among individuals with an SCN5A mutation 27% had early features of DCM (mean age at diagnosis, 20.3 years), 38% had DCM (mean age at diagnosis, 47.9 years), and 43% had atrial fibrillation (mean age at diagnosis, 27.8 years). Conclusions Heritable SCN5A defects are associated with susceptibility to early-onset DCM and atrial fibrillation. Similar or even identical mutations may lead to heart failure, arrhythmia, or both. PMID:15671429
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The importance of source area mapping for rockfall hazard analysis
NASA Astrophysics Data System (ADS)
Valagussa, Andrea; Frattini, Paolo; Crosta, Giovanni B.
2013-04-01
A problem in the characterization of the area affected by rockfall is the correct source areas definition. Different positions or different size of the source areas along a cliff result in different possibilities of propagation and diverse interaction with passive countermeasures present in the area. Through the use of Hy-Stone (Crosta et al., 2004), a code able to perform 3D numerical modeling of rockfall processes, different types of source areas were tested on a case study slope along the western flank of the Mt. de La Saxe (Courmayeur, AO), developing between 1200 and 2055 m s.l.m. The first set of source areas consists of unstable rock masses identified on the basis of field survey and Terrestrial Laser Scanning (IMAGEO, 2011). A second set of source areas has been identified by using different thresholds of slope gradient. We tested slope thresholds between 50° and 75° at 5° intervals. The third source area dataset has been generating by performing a kinematic stability analysis. For this analysis, we mapped the join sets along the rocky cliff by means of the software COLTOP 3D (Jaboyedoff, 2004), and then we identified the portions of rocky cliff where planar/wedge and toppling failures are possible assuming an average friction angle of 35°. Through the outputs of the Hy-Stone models we extracted and analyzed the kinetic energy, height of fly and velocity of the blocks falling along the rocky cliff in order to compare the controls of different source areas. We observed strong variations of kinetic energy and fly height among the different models, especially when using unstable masses identified through Terrestrial Laser Scanning. This is mainly related to the size of the blocks identified as susceptible to failure. On the contrary, the slope gradient thresholds does not have a strong impact on rockfall propagation. This contribution highlights the importance of a careful and appropriate mapping of rockfall source area for rockfall hazard analysis and the design of passive countermeasures.
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NASA Astrophysics Data System (ADS)
Müller, Peter; Krause, Marita; Beck, Rainer; Schmidt, Philip
2017-10-01
Context. The venerable NOD2 data reduction software package for single-dish radio continuum observations, which was developed for use at the 100-m Effelsberg radio telescope, has been successfully applied over many decades. Modern computing facilities, however, call for a new design. Aims: We aim to develop an interactive software tool with a graphical user interface for the reduction of single-dish radio continuum maps. We make a special effort to reduce the distortions along the scanning direction (scanning effects) by combining maps scanned in orthogonal directions or dual- or multiple-horn observations that need to be processed in a restoration procedure. The package should also process polarisation data and offer the possibility to include special tasks written by the individual user. Methods: Based on the ideas of the NOD2 package we developed NOD3, which includes all necessary tasks from the raw maps to the final maps in total intensity and linear polarisation. Furthermore, plot routines and several methods for map analysis are available. The NOD3 package is written in Python, which allows the extension of the package via additional tasks. The required data format for the input maps is FITS. Results: The NOD3 package is a sophisticated tool to process and analyse maps from single-dish observations that are affected by scanning effects from clouds, receiver instabilities, or radio-frequency interference. The "basket-weaving" tool combines orthogonally scanned maps into a final map that is almost free of scanning effects. The new restoration tool for dual-beam observations reduces the noise by a factor of about two compared to the NOD2 version. Combining single-dish with interferometer data in the map plane ensures the full recovery of the total flux density. Conclusions: This software package is available under the open source license GPL for free use at other single-dish radio telescopes of the astronomical community. The NOD3 package is designed to be extendable to multi-channel data represented by data cubes in Stokes I, Q, and U.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Pope, D.L.; Wagner, J.B.
1988-09-01
Before siting oil and gas platforms on the sea floor as artificial reefs offshore Louisiana, potentially hazardous and unstable geologic conditions must be identified and evaluated to assess their possible impacts on platform stability. Geologic and man-made features can be identified and assessed from high-resolution geophysical techniques (3.5-7.0 kHz echograms, single-channel seismic, and side-scan sonar). Such features include faults, diapirs, scarps, channels, gas seeps, irregular sea floor topography, mass wasting deposits (slumps, slides, and debris flows), pipelines, and other subsea marine equipment. Geotechnical techniques are utilized to determine lithologic and physical properties of the sediments for correlation with the geophysicalmore » data. These techniques are used to develop a series of geologic maps, cross sections, and pipeline and platform-location maps. Construction of echo-character maps from 3.5-kHz data provides an analysis of near-bottom sedimentation processes (turbidity currents and debris flows).« less
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Chen, Alexander; Pastis, Nicholas; Furukawa, Brian; Silvestri, Gerard A
2015-05-01
Electromagnetic navigation has improved the diagnostic yield of peripheral bronchoscopy for pulmonary nodules. For these procedures, a thin-slice chest CT scan is performed prior to bronchoscopy at full inspiration and is used to create virtual airway reconstructions that are used as a map during bronchoscopy. Movement of the lung occurs with respiratory variation during bronchoscopy, and the location of pulmonary nodules during procedures may differ significantly from their location on the initial planning full-inspiratory chest CT scan. This study was performed to quantify pulmonary nodule movement from full inspiration to end-exhalation during tidal volume breathing in patients undergoing electromagnetic navigation procedures. A retrospective review of electromagnetic navigation procedures was performed for which two preprocedure CT scans were performed prior to bronchoscopy. One CT scan was performed at full inspiration, and a second CT scan was performed at end-exhalation during tidal volume breathing. Pulmonary lesions were identified on both CT scans, and distances between positions were recorded. Eighty-five pulmonary lesions were identified in 46 patients. Average motion of all pulmonary lesions was 17.6 mm. Pulmonary lesions located in the lower lobes moved significantly more than upper lobe nodules. Size and distance from the pleura did not significantly impact movement. Significant movement of pulmonary lesions occurs between full inspiration and end-exhalation during tidal volume breathing. This movement from full inspiration on planning chest CT scan to tidal volume breathing during bronchoscopy may significantly affect the diagnostic yield of electromagnetic navigation bronchoscopy procedures.
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NASA Technical Reports Server (NTRS)
Panda, Binayak
2009-01-01
Modern analytical tools can yield invaluable results during materials characterization and failure analysis. Scanning electron microscopes (SEMs) provide significant analytical capabilities, including angstrom-level resolution. These systems can be equipped with a silicon drift detector (SDD) for very fast yet precise analytical mapping of phases, as well as electron back-scattered diffraction (EBSD) units to map grain orientations, chambers that admit large samples, variable pressure for wet samples, and quantitative analysis software to examine phases. Advanced solid-state electronics have also improved surface and bulk analysis instruments: Secondary ion mass spectroscopy (SIMS) can quantitatively determine and map light elements such as hydrogen, lithium, and boron - with their isotopes. Its high sensitivity detects impurities at parts per billion (ppb) levels. X-ray photo-electron spectroscopy (XPS) can determine oxidation states of elements, as well as identifying polymers and measuring film thicknesses on coated composites. This technique is also known as electron spectroscopy for chemical analysis (ESCA). Scanning Auger electron spectroscopy (SAM) combines surface sensitivity, spatial lateral resolution (10 nm), and depth profiling capabilities to describe elemental compositions of near and below surface regions down to the chemical state of an atom.
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Bathymetry and acoustic backscatter data collected in 2010 from Cat Island, Mississippi
Buster, Noreen A.; Pfeiffer, William R.; Miselis, Jennifer L.; Kindinger, Jack G.; Wiese, Dana S.; Reynolds, B.J.
2012-01-01
Scientists from the U.S. Geological Survey (USGS), St. Petersburg Coastal and Marine Science Center (SPCMSC), in collaboration with the U.S. Army Corps of Engineers (USACE), conducted geophysical and sedimentological surveys around Cat Island, the westernmost island in the Mississippi-Alabama barrier island chain (fig. 1). The objectives of the study were to understand the geologic evolution of Cat Island relative to other barrier islands in the northern Gulf of Mexico and to identify relationships between the geologic history, present day morphology, and sediment distribution. This report contains data from the bathymetry and side-scan sonar portion of the study collected during two geophysical cruises. Interferometric swath bathymetry and side-scan sonar data were collected aboard the RV G.K. Gilbert September 7-15, 2010. Single-beam bathymetry was collected in shallow water around the island (< 2 meter (m)) from the RV Streeterville from September 28 to October 2, 2010, to cover the data gap between the landward limit of the previous cruise and the shoreline. This report serves as an archive of processed interferometric swath and single-beam bathymetry and side scan sonar data. GIS data products include a 50-m cell size interpolated gridded bathymetry surface, trackline maps, and an acoustic side-scan sonar image. Additional files include error analysis maps, Field Activity Collection System (FACS) logs, and formal Federal Geographic Data Committee (FDGC) metadata.
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Low temperature laser scanning microscopy of a superconducting radio-frequency cavity
Ciovati, G.; Anlage, Steven M.; Baldwin, C.; ...
2012-03-16
An apparatus was created to obtain, for the first time, 2D maps of the surface resistance of the inner surface of an operating superconducting radio-frequency niobium cavity by a low-temperature laser scanning microscopy technique. This allows identifying non-uniformities of the surface resistance with a spatial resolution of about one order of magnitude better than with earlier methods. A signal-to-noise ratio of about 10 dB was obtained with 240 mW laser power and 1 Hz modulation frequency. The various components of the apparatus, the experimental procedure and results are discussed in details in this contribution.
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Automated kidney detection for 3D ultrasound using scan line searching
NASA Astrophysics Data System (ADS)
Noll, Matthias; Nadolny, Anne; Wesarg, Stefan
2016-04-01
Ultrasound (U/S) is a fast and non-expensive imaging modality that is used for the examination of various anatomical structures, e.g. the kidneys. One important task for automatic organ tracking or computer-aided diagnosis is the identification of the organ region. During this process the exact information about the transducer location and orientation is usually unavailable. This renders the implementation of such automatic methods exceedingly challenging. In this work we like to introduce a new automatic method for the detection of the kidney in 3D U/S images. This novel technique analyses the U/S image data along virtual scan lines. Here, characteristic texture changes when entering and leaving the symmetric tissue regions of the renal cortex are searched for. A subsequent feature accumulation along a second scan direction produces a 2D heat map of renal cortex candidates, from which the kidney location is extracted in two steps. First, the strongest candidate as well as its counterpart are extracted by heat map intensity ranking and renal cortex size analysis. This process exploits the heat map gap caused by the renal pelvis region. Substituting the renal pelvis detection with this combined cortex tissue feature increases the detection robustness. In contrast to model based methods that generate characteristic pattern matches, our method is simpler and therefore faster. An evaluation performed on 61 3D U/S data sets showed, that in 55 cases showing none or minor shadowing the kidney location could be correctly identified.
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Teng, Chaoyi; Demers, Hendrix; Brodusch, Nicolas; Waters, Kristian; Gauvin, Raynald
2018-06-04
A number of techniques for the characterization of rare earth minerals (REM) have been developed and are widely applied in the mining industry. However, most of them are limited to a global analysis due to their low spatial resolution. In this work, phase map analyses were performed on REM with an annular silicon drift detector (aSDD) attached to a field emission scanning electron microscope. The optimal conditions for the aSDD were explored, and the high-resolution phase maps generated at a low accelerating voltage identify phases at the micron scale. In comparisons between an annular and a conventional SDD, the aSDD performed at optimized conditions, making the phase map a practical solution for choosing an appropriate grinding size, judging the efficiency of different separation processes, and optimizing a REM beneficiation flowsheet.
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The Registration and Segmentation of Heterogeneous Laser Scanning Data
NASA Astrophysics Data System (ADS)
Al-Durgham, Mohannad M.
Light Detection And Ranging (LiDAR) mapping has been emerging over the past few years as a mainstream tool for the dense acquisition of three dimensional point data. Besides the conventional mapping missions, LiDAR systems have proven to be very useful for a wide spectrum of applications such as forestry, structural deformation analysis, urban mapping, and reverse engineering. The wide application scope of LiDAR lead to the development of many laser scanning technologies that are mountable on multiple platforms (i.e., airborne, mobile terrestrial, and tripod mounted), this caused variations in the characteristics and quality of the generated point clouds. As a result of the increased popularity and diversity of laser scanners, one should address the heterogeneous LiDAR data post processing (i.e., registration and segmentation) problems adequately. Current LiDAR integration techniques do not take into account the varying nature of laser scans originating from various platforms. In this dissertation, the author proposes a methodology designed particularly for the registration and segmentation of heterogeneous LiDAR data. A data characterization and filtering step is proposed to populate the points' attributes and remove non-planar LiDAR points. Then, a modified version of the Iterative Closest Point (ICP), denoted by the Iterative Closest Projected Point (ICPP) is designed for the registration of heterogeneous scans to remove any misalignments between overlapping strips. Next, a region-growing-based heterogeneous segmentation algorithm is developed to ensure the proper extraction of planar segments from the point clouds. Validation experiments show that the proposed heterogeneous registration can successfully align airborne and terrestrial datasets despite the great differences in their point density and their noise level. In addition, similar testes have been conducted to examine the heterogeneous segmentation and it is shown that one is able to identify common planar features in airborne and terrestrial data without resampling or manipulating the data in any way. The work presented in this dissertation provides a framework for the registration and segmentation of airborne and terrestrial laser scans which has a positive impact on the completeness of the scanned feature. Therefore, the derived products from these point clouds have higher accuracy as seen in the full manuscript.
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Strain mapping in TEM using precession electron diffraction
Taheri, Mitra Lenore; Leff, Asher Calvin
2017-02-14
A sample material is scanned with a transmission electron microscope (TEM) over multiple steps having a predetermined size at a predetermined angle. Each scan at a predetermined step and angle is compared to a template, wherein the template is generated from parameters of the material and the scanning. The data is then analyzed using local mis-orientation mapping and/or Nye's tensor analysis to provide information about local strain states.
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Use of remote sensing for land use policy formulation
NASA Technical Reports Server (NTRS)
1982-01-01
Research projects described include: (1) identifying coniferous forest types in Michigan using LANDSAT imagery; (2) investigating synoptic temperature patterns in Michigan as determined via GOES and HCMM thermal imagery; (3) land surface change detection using satellite data and a geographic data base; (4) determining soil map unit composition by electronic scanning densitometry; and (5) delimiting areas of virus infection in vineyards and blueberry fields in southwestern and western Michigan. Contractual activities involve important farmlands inventory, changes in aquatic vegetation in Saginaw Bay, digitized soil association map of Michigan, and aerial photography for hybrid-poplar research. On-going projects are also being conducted in Jamaica, Honduras, the Dominican Republic and Kenya.
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Commeau, R.F.; Reynolds, Leslie A.; Poag, C.W.
1985-01-01
The composition of agglutinated foraminiferal tests vary remarkably in response to local substrate characteristics, physiochemical properties of the water column and species- dependant selectivity of test components. We have employed a technique that combines a scanning electron microscope with an energy dispersive X-ray spectrometer system to identify major and minor elemental constituents of agglutinated foraminiferal walls. As a sample is bombarded with a beam of high energy electrons, X-rays are generated that are characteristic of the elements present. As a result, X- ray density maps can be produced for each of several elements present in the tests of agglutinated foraminifers.
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Bathymetry and selected perspective views of 6 reef and coastal areas in Northern Lake Michigan
Barnes, Peter; Fleisher, Guy; Gardner, James V.; Lee, Kristen
2003-01-01
We apply state of the art laser technology and derivative imagery to map the detailed morphology and of principal lake trout spawning sites on reefs in Northern Lake Michigan and to provide a geologic interpretation. We sought to identify the presence of ideal spawning substrate: shallow, "clean" gravel/cobble substrate, adjacent to deeper water. This study is a pilot collaborative effort with the US Army Corps of Engineers SHOALS (Scanning Hydrographic Operational Airborne Lidar Survey) program. The high-definition maps are integrated with known and developing data on fisheries, as well as limited substrate sedimentologic information and underlying Paleozoic carbonate rocks.
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Elemental mapping with energy-dispersive X-ray spectroscopy (EDX) associated with scanning electron microscopy is highly useful for studying internally mixed atmospheric particles. Presented is a study of individual particles from urban airsheds and the analytical challenges in q...
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Lithology and aggregate quality attributes for the digital geologic map of Colorado
Knepper, Daniel H.; Green, Gregory N.; Langer, William H.
1999-01-01
This geologic map was prepared as a part of a study of digital methods and techniques as applied to complex geologic maps. The geologic map was digitized from the original scribe sheets used to prepare the published Geologic Map of Colorado (Tweto 1979). Consequently the digital version is at 1:500,000 scale using the Lambert Conformal Conic map projection parameters of the state base map. Stable base contact prints of the scribe sheets were scanned on a Tektronix 4991 digital scanner. The scanner automatically converts the scanned image to an ASCII vector format. These vectors were transferred to a VAX minicomputer, where they were then loaded into ARC/INFO. Each vector and polygon was given attributes derived from the original 1979 geologic map.
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EFFECTS OF GREEN MACROALGAE ON CLASSIFICATION OF SEAGRASS IN SIDE SCAN SONAR IMAGERY
High resolution maps of seagrass beds are useful for monitoring estuarine condition, managing fish habitats, and modeling estuarine processes. Side scan sonar (SSS) is one method for producing spatially accurate seagrass maps, although it has not been used widely. Our team rece...
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Klebe, Stephan; Azzedine, Hamid; Durr, Alexandra; Bastien, Patrick; Bouslam, Naima; Elleuch, Nizar; Forlani, Sylvie; Charon, Celine; Koenig, Michel; Melki, Judith; Brice, Alexis; Stevanin, Giovanni
2006-06-01
The hereditary spastic paraplegias (HSPs) are a clinically and genetically heterogeneous group of neurodegenerative diseases characterized by progressive spasticity in the lower limbs. Twenty-nine different loci (SPG) have been mapped so far, and 11 responsible genes have been identified. Clinically, one distinguishes between pure and complex HSP forms which are variably associated with numerous combinations of neurological and extra-neurological signs. Less is known about autosomal recessive forms (ARHSP) since the mapped loci have been identified often in single families and account for only a small percentage of patients. We report a new ARHSP locus (SPG30) on chromosome 2q37.3 in a consanguineous family with seven unaffected and four affected members of Algerian origin living in Eastern France with a significant multipoint lod score of 3.8. Ten other families from France (n = 4), Tunisia (n = 2), Algeria (n = 3) and the Czech Republic (n = 1) were not linked to the newly identified locus thus demonstrating further genetic heterogeneity. The phenotype of the linked family consists of spastic paraparesis and peripheral neuropathy associated with slight cerebellar signs confirmed by cerebellar atrophy on one CT scan.
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Solano, Rubén; Gómez-Barroso, Diana; Simón, Fernando; Lafuente, Sarah; Simón, Pere; Rius, Cristina; Gorrindo, Pilar; Toledo, Diana; Caylà, Joan A
2014-05-01
A retrospective, space-time study of whooping cough cases reported to the Public Health Agency of Barcelona, Spain between the years 2000 and 2011 is presented. It is based on 633 individual whooping cough cases and the 2006 population census from the Spanish National Statistics Institute, stratified by age and sex at the census tract level. Cluster identification was attempted using space-time scan statistic assuming a Poisson distribution and restricting temporal extent to 7 days and spatial distance to 500 m. Statistical calculations were performed with Stata 11 and SatScan and mapping was performed with ArcGis 10.0. Only clusters showing statistical significance (P <0.05) were mapped. The most likely cluster identified included five census tracts located in three neighbourhoods in central Barcelona during the week from 17 to 23 August 2011. This cluster included five cases compared with the expected level of 0.0021 (relative risk = 2436, P <0.001). In addition, 11 secondary significant space-time clusters were detected with secondary clusters occurring at different times and localizations. Spatial statistics is felt to be useful by complementing epidemiological surveillance systems through visualizing excess in the number of cases in space and time and thus increase the possibility of identifying outbreaks not reported by the surveillance system.
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Parasitism drives host genome evolution: Insights from the Pasteuria ramosa-Daphnia magna system.
Bourgeois, Yann; Roulin, Anne C; Müller, Kristina; Ebert, Dieter
2017-04-01
Because parasitism is thought to play a major role in shaping host genomes, it has been predicted that genomic regions associated with resistance to parasites should stand out in genome scans, revealing signals of selection above the genomic background. To test whether parasitism is indeed such a major factor in host evolution and to better understand host-parasite interaction at the molecular level, we studied genome-wide polymorphisms in 97 genotypes of the planktonic crustacean Daphnia magna originating from three localities across Europe. Daphnia magna is known to coevolve with the bacterial pathogen Pasteuria ramosa for which host genotypes (clonal lines) are either resistant or susceptible. Using association mapping, we identified two genomic regions involved in resistance to P. ramosa, one of which was already known from a previous QTL analysis. We then performed a naïve genome scan to test for signatures of positive selection and found that the two regions identified with the association mapping further stood out as outliers. Several other regions with evidence for selection were also found, but no link between these regions and phenotypic variation could be established. Our results are consistent with the hypothesis that parasitism is driving host genome evolution. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.
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Historical Topographic Map Collection bookmark
Fishburn, Kristin A.; Allord, Gregory J.
2017-06-29
The U.S. Geological Survey (USGS) National Geospatial Program is scanning published USGS 1:250,000-scale and larger topographic maps printed between 1884, the inception of the topographic mapping program, and 2006. The goal of this project, which began publishing the historical scanned maps in 2011, is to provide a digital repository of USGS topographic maps, available to the public at no cost. For more than 125 years, USGS topographic maps have accurately portrayed the complex geography of the Nation. The USGS is the Nation’s largest producer of printed topographic maps, and prior to 2006, USGS topographic maps were created using traditional cartographic methods and printed using a lithographic printing process. As the USGS continues the release of a new generation of topographic maps (US Topo) in electronic form, the topographic map remains an indispensable tool for government, science, industry, land management planning, and leisure.
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The NORDA MC&G Map Data Formatting Facility: Development of a Digital Map Data Base
1989-12-01
Lempel - Ziv compression . extract such features as roads, water, urban areas, and Also investigated were various transform encoding text from the scanned... Compression Ratios scanned maps revealed a small number of color classes and lar .e homogeneous regions. The original 24-bit Lempel Ziv Lempel Ziv pixel...Various high performance, lossless compression tech- Table 6. Compression ratios for VQ classification niques were tried. followed by Lempel Ziv
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M3RSM: Many-to-Many Multi-Resolution Scan Matching
2015-05-01
a localization problem), or may be derived from a LIDAR scan earlier in the robot’s trajectory (a SLAM problem). The reference map is generally...Mapping ( SLAM ) systems prevent the unbounded accumulation of error. A typical approach with laser range-finder data is to compute the posterior...even greater bottleneck than the SLAM optimiza- tion itself. In our multi-robot mapping system, over a dozen robots explored an area simultaneously [14
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Jung, Jaehoon; Yoon, Sanghyun; Ju, Sungha; Heo, Joon
2015-01-01
The growing interest and use of indoor mapping is driving a demand for improved data-acquisition facility, efficiency and productivity in the era of the Building Information Model (BIM). The conventional static laser scanning method suffers from some limitations on its operability in complex indoor environments, due to the presence of occlusions. Full scanning of indoor spaces without loss of information requires that surveyors change the scanner position many times, which incurs extra work for registration of each scanned point cloud. Alternatively, a kinematic 3D laser scanning system, proposed herein, uses line-feature-based Simultaneous Localization and Mapping (SLAM) technique for continuous mapping. Moreover, to reduce the uncertainty of line-feature extraction, we incorporated constrained adjustment based on an assumption made with respect to typical indoor environments: that the main structures are formed of parallel or orthogonal line features. The superiority of the proposed constrained adjustment is its reduction for uncertainties of the adjusted lines, leading to successful data association process. In the present study, kinematic scanning with and without constrained adjustment were comparatively evaluated in two test sites, and the results confirmed the effectiveness of the proposed system. The accuracy of the 3D mapping result was additionally evaluated by comparison with the reference points acquired by a total station: the Euclidean average distance error was 0.034 m for the seminar room and 0.043 m for the corridor, which satisfied the error tolerance for point cloud acquisition (0.051 m) according to the guidelines of the General Services Administration for BIM accuracy. PMID:26501292
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del-Moral-Martínez, Ignacio; Rosell-Polo, Joan R.; Company, Joaquim; Sanz, Ricardo; Escolà, Alexandre; Masip, Joan; Martínez-Casasnovas, José A.; Arnó, Jaume
2016-01-01
The leaf area index (LAI) is defined as the one-side leaf area per unit ground area, and is probably the most widely used index to characterize grapevine vigor. However, LAI varies spatially within vineyard plots. Mapping and quantifying this variability is very important for improving management decisions and agricultural practices. In this study, a mobile terrestrial laser scanner (MTLS) was used to map the LAI of a vineyard, and then to examine how different scanning methods (on-the-go or discontinuous systematic sampling) may affect the reliability of the resulting raster maps. The use of the MTLS allows calculating the enveloping vegetative area of the canopy, which is the sum of the leaf wall areas for both sides of the row (excluding gaps) and the projected upper area. Obtaining the enveloping areas requires scanning from both sides one meter length section along the row at each systematic sampling point. By converting the enveloping areas into LAI values, a raster map of the latter can be obtained by spatial interpolation (kriging). However, the user can opt for scanning on-the-go in a continuous way and compute 1-m LAI values along the rows, or instead, perform the scanning at discontinuous systematic sampling within the plot. An analysis of correlation between maps indicated that MTLS can be used discontinuously in specific sampling sections separated by up to 15 m along the rows. This capability significantly reduces the amount of data to be acquired at field level, the data storage capacity and the processing power of computers. PMID:26797618
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del-Moral-Martínez, Ignacio; Rosell-Polo, Joan R; Company, Joaquim; Sanz, Ricardo; Escolà, Alexandre; Masip, Joan; Martínez-Casasnovas, José A; Arnó, Jaume
2016-01-19
The leaf area index (LAI) is defined as the one-side leaf area per unit ground area, and is probably the most widely used index to characterize grapevine vigor. However, LAI varies spatially within vineyard plots. Mapping and quantifying this variability is very important for improving management decisions and agricultural practices. In this study, a mobile terrestrial laser scanner (MTLS) was used to map the LAI of a vineyard, and then to examine how different scanning methods (on-the-go or discontinuous systematic sampling) may affect the reliability of the resulting raster maps. The use of the MTLS allows calculating the enveloping vegetative area of the canopy, which is the sum of the leaf wall areas for both sides of the row (excluding gaps) and the projected upper area. Obtaining the enveloping areas requires scanning from both sides one meter length section along the row at each systematic sampling point. By converting the enveloping areas into LAI values, a raster map of the latter can be obtained by spatial interpolation (kriging). However, the user can opt for scanning on-the-go in a continuous way and compute 1-m LAI values along the rows, or instead, perform the scanning at discontinuous systematic sampling within the plot. An analysis of correlation between maps indicated that MTLS can be used discontinuously in specific sampling sections separated by up to 15 m along the rows. This capability significantly reduces the amount of data to be acquired at field level, the data storage capacity and the processing power of computers.
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NASA Technical Reports Server (NTRS)
Hutcheon, I. D.; Steele, I. M.; Smith, J. V.; Clayton, R. N.
1978-01-01
Three Type B inclusions from the Allende meteorite have been analyzed. A grain-to-grain characterization of mineral chemistry and isotopic content was made possible by the use of a range of techniques, including luminescence and scanning electron microscopy and electron and ion microprobe analysis. Cathodoluminescence was used in fine-grained, optically opaque regions to distinguish between sub-micrometer phases, such as garnet and Si-rich material, subsequently identified by electron probe and scanning electron microscope analyses. Four types of luminescence patterns, due to twinning, primary sector zoning, alteration of boundaries and fractures, and shock effects, were identified in Allende plagioclase. Luminescence color exhibited a strong correlation with Mg content and provided a guide for an electron probe quantitative map of Mg and Na distributions. Ion microprobe studies of individual grains revealed large excesses of Mg-26.
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The Safety Course Design and Operations of Composite Overwrapped Pressure Vessels (COPV)
NASA Technical Reports Server (NTRS)
Saulsberry, Regor; Prosser, William
2015-01-01
Following a Commercial Launch Vehicle On-Pad COPV (Composite Overwrapped Pressure Vessels) failure, a request was received by the NESC (NASA Engineering and Safety Center) June 14, 2014. An assessment was approved July 10, 2014, to develop and assess the capability of scanning eddy current (EC) nondestructive evaluation (NDE) methods for mapping thickness and inspection for flaws. Current methods could not identify thickness reduction from necking and critical flaw detection was not possible with conventional dye penetrant (PT) methods, so sensitive EC scanning techniques were needed. Developmental methods existed, but had not been fully developed, nor had the requisite capability assessment (i.e., a POD (Probability of Detection) study) been performed.
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NASA Astrophysics Data System (ADS)
Bártová, H.; Trojek, T.; Čechák, T.; Šefců, R.; Chlumská, Š.
2017-10-01
The presence of heavy chemical elements in old pigments is possible to identify in historical paintings using X-ray fluorescence analysis (XRF). This is a non-destructive analytical method frequently used in examination of objects that require in situ analysis, where it is necessary to avoid damaging the object by taking samples. Different modalities are available, such as microanalysis, scanning selected areas, or depth profiling techniques. Surface scanning is particularly profitable since 2D element distribution maps are much more understandable than the results of individual analyses. Information on the layered structure of the painting can be also obtained by handheld portable systems. Results presented in our paper combine 2D element distribution maps obtained by scanning analysis, and depth profiling using conventional XRF. The latter is very suitable for objects of art, as it can be evaluated from data measured with portable XRF device. Depth profiling by conventional XRF is based on the differences in X-ray absorption in paint layers. The XRF technique was applied for analysis of panel paintings of the Master of the St George Altarpiece who was active in Prague in the 1470s and 1480s. The results were evaluated by taking micro-samples and performing a material analysis.
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Abdelmagid, Nada; Bereczky-Veress, Biborka; Guerreiro-Cacais, André Ortlieb; Bergman, Petra; Luhr, Katarina M.; Bergström, Tomas; Sköldenberg, Birgit; Piehl, Fredrik
2012-01-01
Herpes simplex encephalitis (HSE) is a fatal infection of the central nervous system (CNS) predominantly caused by Herpes simplex virus type 1. Factors regulating the susceptibility to HSE are still largely unknown. To identify host gene(s) regulating HSE susceptibility we performed a genome-wide linkage scan in an intercross between the susceptible DA and the resistant PVG rat. We found one major quantitative trait locus (QTL), Hse1, on rat chromosome 4 (confidence interval 24.3–31 Mb; LOD score 29.5) governing disease susceptibility. Fine mapping of Hse1 using recombinants, haplotype mapping and sequencing, as well as expression analysis of all genes in the interval identified the calcitonin receptor gene (Calcr) as the main candidate, which also is supported by functional studies. Thus, using unbiased genetic approach variability in Calcr was identified as potentially critical for infection and viral spread to the CNS and subsequent HSE development. PMID:22761571
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Implementation of efficient trajectories for an ultrasonic scanner using chaotic maps
NASA Astrophysics Data System (ADS)
Almeda, A.; Baltazar, A.; Treesatayapun, C.; Mijarez, R.
2012-05-01
Typical ultrasonic methodology for nondestructive scanning evaluation uses systematic scanning paths. In many cases, this approach is time inefficient and also energy and computational power consuming. Here, a methodology for the scanning of defects using an ultrasonic echo-pulse scanning technique combined with chaotic trajectory generation is proposed. This is implemented in a Cartesian coordinate robotic system developed in our lab. To cover the entire search area, a chaotic function and a proposed mirror mapping were incorporated. To improve detection probability, our proposed scanning methodology is complemented with a probabilistic approach of discontinuity detection. The developed methodology was found to be more efficient than traditional ones used to localize and characterize hidden flaws.
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Marine habitat mapping at Labuan Marine Park, Federal Territory of Labuan, Malaysia
NASA Astrophysics Data System (ADS)
Mustajap, Fazliana; Saleh, Ejria; Madin, John; Hamid, Shahimah Abdul
2015-06-01
Marine habitat mapping has recently become essential in coastal marine science research. It is one of the efforts to understand marine ecosystems, and thus to protect them. Habitat mapping is integral to marine-related industries such as fisheries, aquaculture, forestry and tourism. An assessment of marine habitat mapping was conducted at Labuan Marine Park (LMP), a marine protected area in the Federal Territory of Labuan. It is surrounded by shallow water within its islands (Kuraman, Rusukan Kecil and Rusukan Besar) with an area of 39.7 km2. The objectives of the study are to identify the substrate and types of marine habitat present within the park. Side scan sonar (SSS) (Aquascan TM) was used to determine the substrates and habitat while ground truthings were done through field observation and SCUBA diving survey. Seabed classification and marine habitat was based on NOAA's biogeography program. Three substrate types (sand, rock, silt) were identified in this area. The major marine habitats identified are corals, macro algae and small patches of sea grass. The study area is an important refuge for spawning and juvenile fish and supports the livelihood of the coastal communities on Labuan Island. Therefore, proper management is crucial in order to better maintain the marine protected area. The findings are significant and provide detailed baseline information on marine habitat for conservation, protection and future management in LMP.
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Scanning and georeferencing historical USGS quadrangles
Fishburn, Kristin A.; Davis, Larry R.; Allord, Gregory J.
2017-06-23
The U.S. Geological Survey (USGS) National Geospatial Program is scanning published USGS 1:250,000-scale and larger topographic maps printed between 1884, the inception of the topographic mapping program, and 2006. The goal of this project, which began publishing the Historical Topographic Map Collection in 2011, is to provide access to a digital repository of USGS topographic maps that is available to the public at no cost. For more than 125 years, USGS topographic maps have accurately portrayed the complex geography of the Nation. The USGS is the Nation’s largest producer of traditional topographic maps, and, prior to 2006, USGS topographic maps were created using traditional cartographic methods and printed using a lithographic process. The next generation of topographic maps, US Topo, is being released by the USGS in digital form, and newer technologies make it possible to also deliver historical maps in the same electronic format that is more publicly accessible.
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2012-01-01
Background Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most important and challenging areas of research in animal genetics. However, currently there are relatively few genomic regions identified that have been subject to positive selection. In this study, a genome-wide scan using ~50,000 Single Nucleotide Polymorphisms (SNPs) was performed in an attempt to identify genomic regions associated with fat deposition in fat-tail breeds. This trait and its modification are very important in those countries grazing these breeds. Results Two independent experiments using either Iranian or Ovine HapMap genotyping data contrasted thin and fat tail breeds. Population differentiation using FST in Iranian thin and fat tail breeds revealed seven genomic regions. Almost all of these regions overlapped with QTLs that had previously been identified as affecting fat and carcass yield traits in beef and dairy cattle. Study of selection sweep signatures using FST in thin and fat tail breeds sampled from the Ovine HapMap project confirmed three of these regions located on Chromosomes 5, 7 and X. We found increased homozygosity in these regions in favour of fat tail breeds on chromosome 5 and X and in favour of thin tail breeds on chromosome 7. Conclusions In this study, we were able to identify three novel regions associated with fat deposition in thin and fat tail sheep breeds. Two of these were associated with an increase of homozygosity in the fat tail breeds which would be consistent with selection for mutations affecting fat tail size several thousand years after domestication. PMID:22364287
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2013-01-01
Background Flax is valued for its fiber, seed oil and nutraceuticals. Recently, the fiber industry has invested in the development of products made from linseed stems, making it a dual purpose crop. Simultaneous targeting of genomic regions controlling stem fiber and seed quality traits could enable the development of dual purpose cultivars. However, the genetic diversity, population structure and linkage disequilibrium (LD) patterns necessary for association mapping (AM) have not yet been assessed in flax because genomic resources have only recently been developed. We characterized 407 globally distributed flax accessions using 448 microsatellite markers. The data was analyzed to assess the suitability of this core collection for AM. Genomic scans to identify candidate genes selected during the divergent breeding process of fiber flax and linseed were conducted using the whole genome shotgun sequence of flax. Results Combined genetic structure analysis assigned all accessions to two major groups with six sub-groups. Population differentiation was weak between the major groups (FST = 0.094) and for most of the pairwise comparisons among sub-groups. The molecular coancestry analysis indicated weak relatedness (mean = 0.287) for most individual pairs. Abundant genetic diversity was observed in the total panel (5.32 alleles per locus), and some sub-groups showed a high proportion of private alleles. The average genome-wide LD (r2) was 0.036, with a relatively fast decay of 1.5 cM. Genomic scans between fiber flax and linseed identified candidate genes involved in cell-wall biogenesis/modification, xylem identity and fatty acid biosynthesis congruent with genes previously identified in flax and other plant species. Conclusions Based on the abundant genetic diversity, weak population structure and relatedness and relatively fast LD decay, we concluded that this core collection is suitable for AM studies targeting multiple agronomic and quality traits aiming at the improvement of flax as a true dual purpose crop. Our genomic scans provide the first insights into candidate regions affected by divergent selection in flax. In combination with AM, genomic scans have the ability to increase the power to detect loci influencing complex traits. PMID:23647851
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Soto-Cerda, Braulio J; Diederichsen, Axel; Ragupathy, Raja; Cloutier, Sylvie
2013-05-06
Flax is valued for its fiber, seed oil and nutraceuticals. Recently, the fiber industry has invested in the development of products made from linseed stems, making it a dual purpose crop. Simultaneous targeting of genomic regions controlling stem fiber and seed quality traits could enable the development of dual purpose cultivars. However, the genetic diversity, population structure and linkage disequilibrium (LD) patterns necessary for association mapping (AM) have not yet been assessed in flax because genomic resources have only recently been developed. We characterized 407 globally distributed flax accessions using 448 microsatellite markers. The data was analyzed to assess the suitability of this core collection for AM. Genomic scans to identify candidate genes selected during the divergent breeding process of fiber flax and linseed were conducted using the whole genome shotgun sequence of flax. Combined genetic structure analysis assigned all accessions to two major groups with six sub-groups. Population differentiation was weak between the major groups (F(ST) = 0.094) and for most of the pairwise comparisons among sub-groups. The molecular coancestry analysis indicated weak relatedness (mean = 0.287) for most individual pairs. Abundant genetic diversity was observed in the total panel (5.32 alleles per locus), and some sub-groups showed a high proportion of private alleles. The average genome-wide LD (r²) was 0.036, with a relatively fast decay of 1.5 cM. Genomic scans between fiber flax and linseed identified candidate genes involved in cell-wall biogenesis/modification, xylem identity and fatty acid biosynthesis congruent with genes previously identified in flax and other plant species. Based on the abundant genetic diversity, weak population structure and relatedness and relatively fast LD decay, we concluded that this core collection is suitable for AM studies targeting multiple agronomic and quality traits aiming at the improvement of flax as a true dual purpose crop. Our genomic scans provide the first insights into candidate regions affected by divergent selection in flax. In combination with AM, genomic scans have the ability to increase the power to detect loci influencing complex traits.
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Note: Electron energy spectroscopy mapping of surface with scanning tunneling microscope.
Li, Meng; Xu, Chunkai; Zhang, Panke; Li, Zhean; Chen, Xiangjun
2016-08-01
We report a novel scanning probe electron energy spectrometer (SPEES) which combines a double toroidal analyzer with a scanning tunneling microscope to achieve both topography imaging and electron energy spectroscopy mapping of surface in situ. The spatial resolution of spectroscopy mapping is determined to be better than 0.7 ± 0.2 μm at a tip sample distance of 7 μm. Meanwhile, the size of the field emission electron beam spot on the surface is also measured, and is about 3.6 ± 0.8 μm in diameter. This unambiguously demonstrates that the spatial resolution of SPEES technique can be much better than the size of the incident electron beam.
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Westermeier, Christian; Fiebig, Matthias; Nickel, Bert
2013-10-25
Frequency-resolved scanning photoresponse microscopy of pentacene thin-film transistors is reported. The photoresponse pattern maps the in-plane distribution of trap states which is superimposed by the level of trap filling adjusted by the gate voltage of the transistor. Local hotspots in the photoresponse map thus indicate areas of high trap densities within the pentacene thin film. © 2013 WILEY-VCH Verlag GmbH 8 Co. KGaA, Weinheim.
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Kim, Sangkyu; Welsh, David A; Myers, Leann; Cherry, Katie E; Wyckoff, Jennifer; Jazwinski, S Michal
2015-02-28
We have completed a genome-wide linkage scan for healthy aging using data collected from a family study, followed by fine-mapping by association in a separate population, the first such attempt reported. The family cohort consisted of parents of age 90 or above and their children ranging in age from 50 to 80. As a quantitative measure of healthy aging, we used a frailty index, called FI34, based on 34 health and function variables. The linkage scan found a single significant linkage peak on chromosome 12. Using an independent cohort of unrelated nonagenarians, we carried out a fine-scale association mapping of the region suggestive of linkage and identified three sites associated with healthy aging. These healthy-aging sites (HASs) are located in intergenic regions at 12q13-14. HAS-1 has been previously associated with multiple diseases, and an enhancer was recently mapped and experimentally validated within the site. HAS-2 is a previously uncharacterized site possessing genomic features suggestive of enhancer activity. HAS-3 contains features associated with Polycomb repression. The HASs also contain variants associated with exceptional longevity, based on a separate analysis. Our results provide insight into functional genomic networks involving non-coding regulatory elements that are involved in healthy aging and longevity.
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Kim, Sangkyu; Welsh, David A.; Myers, Leann; Cherry, Katie E.; Wyckoff, Jennifer; Jazwinski, S. Michal
2015-01-01
We have completed a genome-wide linkage scan for healthy aging using data collected from a family study, followed by fine-mapping by association in a separate population, the first such attempt reported. The family cohort consisted of parents of age 90 or above and their children ranging in age from 50 to 80. As a quantitative measure of healthy aging, we used a frailty index, called FI34, based on 34 health and function variables. The linkage scan found a single significant linkage peak on chromosome 12. Using an independent cohort of unrelated nonagenarians, we carried out a fine-scale association mapping of the region suggestive of linkage and identified three sites associated with healthy aging. These healthy-aging sites (HASs) are located in intergenic regions at 12q13–14. HAS-1 has been previously associated with multiple diseases, and an enhancer was recently mapped and experimentally validated within the site. HAS-2 is a previously uncharacterized site possessing genomic features suggestive of enhancer activity. HAS-3 contains features associated with Polycomb repression. The HASs also contain variants associated with exceptional longevity, based on a separate analysis. Our results provide insight into functional genomic networks involving non-coding regulatory elements that are involved in healthy aging and longevity. PMID:25682868
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Reddy, Umesh K.; Abburi, Lavanya; Abburi, Venkata Lakshmi; Saminathan, Thangasamy; Cantrell, Robert; Vajja, Venkata Gopinath; Reddy, Rishi; Tomason, Yan R.; Levi, Amnon; Wehner, Todd C.; Nimmakayala, Padma
2015-01-01
Our genetic diversity study uses microsatellites of known map position to estimate genome level population structure and linkage disequilibrium, and to identify genomic regions that have undergone selection during watermelon domestication and improvement. Thirty regions that showed evidence of selective sweep were scanned for the presence of candidate genes using the watermelon genome browser (www.icugi.org). We localized selective sweeps in intergenic regions, close to the promoters, and within the exons and introns of various genes. This study provided an evidence of convergent evolution for the presence of diverse ecotypes with special reference to American and European ecotypes. Our search for location of linked markers in the whole-genome draft sequence revealed that BVWS00358, a GA repeat microsatellite, is the GAGA type transcription factor located in the 5′ untranslated regions of a structure and insertion element that expresses a Cys2His2 Zinc finger motif, with presumed biological processes related to chitin response and transcriptional regulation. In addition, BVWS01708, an ATT repeat microsatellite, located in the promoter of a DTW domain-containing protein (Cla002761); and 2 other simple sequence repeats that association mapping link to fruit length and rind thickness. PMID:25425675
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NASA Astrophysics Data System (ADS)
Gillen, Rebecca; Firbank, Michael J.; Lloyd, Jim; O'Brien, John T.
2015-09-01
This study investigated if the appearance and diagnostic accuracy of HMPAO brain perfusion SPECT images could be improved by using CT-based attenuation and scatter correction compared with the uniform attenuation correction method. A cohort of subjects who were clinically categorized as Alzheimer’s Disease (n=38 ), Dementia with Lewy Bodies (n=29 ) or healthy normal controls (n=30 ), underwent SPECT imaging with Tc-99m HMPAO and a separate CT scan. The SPECT images were processed using: (a) correction map derived from the subject’s CT scan or (b) the Chang uniform approximation for correction or (c) no attenuation correction. Images were visually inspected. The ratios between key regions of interest known to be affected or spared in each condition were calculated for each correction method, and the differences between these ratios were evaluated. The images produced using the different corrections were noted to be visually different. However, ROI analysis found similar statistically significant differences between control and dementia groups and between AD and DLB groups regardless of the correction map used. We did not identify an improvement in diagnostic accuracy in images which were corrected using CT-based attenuation and scatter correction, compared with those corrected using a uniform correction map.
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Lawrence, J R; Swerhone, G D W; Leppard, G G; Araki, T; Zhang, X; West, M M; Hitchcock, A P
2003-09-01
Confocal laser scanning microscopy (CLSM), transmission electron microscopy (TEM), and soft X-ray scanning transmission X-ray microscopy (STXM) were used to map the distribution of macromolecular subcomponents (e.g., polysaccharides, proteins, lipids, and nucleic acids) of biofilm cells and matrix. The biofilms were developed from river water supplemented with methanol, and although they comprised a complex microbial community, the biofilms were dominated by heterotrophic bacteria. TEM provided the highest-resolution structural imaging, CLSM provided detailed compositional information when used in conjunction with molecular probes, and STXM provided compositional mapping of macromolecule distributions without the addition of probes. By examining exactly the same region of a sample with combinations of these techniques (STXM with CLSM and STXM with TEM), we demonstrate that this combination of multimicroscopy analysis can be used to create a detailed correlative map of biofilm structure and composition. We are using these correlative techniques to improve our understanding of the biochemical basis for biofilm organization and to assist studies intended to investigate and optimize biofilms for environmental remediation applications.
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NASA Astrophysics Data System (ADS)
Moscati, R. J.; Marshall, B. D.
2005-12-01
X-ray microfluorescence (XRMF) spectrometry is a rapid, accurate technique to map element abundances of rock surfaces (such as thin-section billets, the block remaining when a thin section is prepared). Scanning a specimen with a collimated primary X-ray beam (100 μm diameter) generates characteristic secondary X-rays that yield the relative chemical abundances for the major rock-/mineral-forming analytes (such as Si, Al, K, Ca, and Fe). When Cu-rich epoxy is used to impregnate billets, XRMF also can determine porosity from the Cu abundance. Common billet scan size is 30 x 15 mm and the typical mapping time rarely exceeds 2.5 hrs (much faster than traditional point-counting). No polishing or coating is required for the billets, although removing coarse striations or gross irregularities on billet surfaces should improve the spatial accuracy of the maps. Background counts, spectral artifacts, and diffraction peaks typically are inconsequential for maps of major elements. An operational check is performed after every 10 analyses on a standard that contains precisely measured areas of Mn and Mo. Reproducibility of the calculated area ratio of Mn:Mo is consistently within 5% of the known value. For each billet, the single element maps (TIFF files) generated by XRMF are imported into MultiSpec© (a program developed at Purdue University for analysis of multispectral image data, available from http://dynamo.ecn.purdue.edu/~biehl/MultiSpec/) where mineral phases can be spectrally identified and their relative abundances quantified. The element maps for each billet are layered to produce a multi-element file for mineral classification and statistical processing, including modal estimates of mineral abundance. Although mineral identification is possible even if the mineralogy is unknown, prior petrographic examination of the corresponding thin section yields more accurate maps because the software can be set to identify all similar pixels. Caution is needed when using MultiSpec© to distinguish mineral phases with similar chemistry (for example, opal and quartz) and minerals that occupy very small surface areas (<10 pixels). In either case, careful petrography and informed use of the software will allow rapid use of MultiSpec© to create accurate mineral maps of rock and thin-section billet surfaces. This technique, for example, has allowed quantitative estimates of calcite and silica abundances to be determined on about 200 samples of secondary mineral coatings from the unsaturated zone at Yucca Mountain, Nevada.
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Scanning evanescent electro-magnetic microscope
Xiang, Xiao-Dong; Gao, Chen; Schultz, Peter G.; Wei, Tao
2003-01-01
A novel scanning microscope is described that uses near-field evanescent electromagnetic waves to probe sample properties. The novel microscope is capable of high resolution imaging and quantitative measurements of the electrical properties of the sample. The inventive scanning evanescent wave electromagnetic microscope (SEMM) can map dielectric constant, tangent loss, conductivity, complex electrical impedance, and other electrical parameters of materials. The quantitative map corresponds to the imaged detail. The novel microscope can be used to measure electrical properties of both dielectric and electrically conducting materials.
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Scanning evanescent electro-magnetic microscope
Xiang, Xiao-Dong; Gao, Chen
2001-01-01
A novel scanning microscope is described that uses near-field evanescent electromagnetic waves to probe sample properties. The novel microscope is capable of high resolution imaging and quantitative measurements of the electrical properties of the sample. The inventive scanning evanescent wave electromagnetic microscope (SEMM) can map dielectric constant, tangent loss, conductivity, complex electrical impedance, and other electrical parameters of materials. The quantitative map corresponds to the imaged detail. The novel microscope can be used to measure electrical properties of both dielectric and electrically conducting materials.
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MapEdit: solution to continuous raster map creation
NASA Astrophysics Data System (ADS)
Rančić, Dejan; Djordjevi-Kajan, Slobodanka
2003-03-01
The paper describes MapEdit, MS Windows TM software for georeferencing and rectification of scanned paper maps. The software produces continuous raster maps which can be used as background in geographical information systems. Process of continuous raster map creation using MapEdit "mosaicking" function is also described as well as the georeferencing and rectification algorithms which are used in MapEdit. Our approach for georeferencing and rectification using four control points and two linear transformations for each scanned map part, together with nearest neighbor resampling method, represents low cost—high speed solution that produce continuous raster maps with satisfactory quality for many purposes (±1 pixel). Quality assessment of several continuous raster maps at different scales that have been created using our software and methodology, has been undertaken and results are presented in the paper. For the quality control of the produced raster maps we referred to three wide adopted standards: US Standard for Digital Cartographic Data, National Standard for Spatial Data Accuracy and US National Map Accuracy Standard. The results obtained during the quality assessment process are given in the paper and show that our maps meat all three standards.
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NASA Astrophysics Data System (ADS)
Qiu, Yuchen; Lu, Xianglan; Yan, Shiju; Tan, Maxine; Cheng, Samuel; Li, Shibo; Liu, Hong; Zheng, Bin
2016-03-01
Automated high throughput scanning microscopy is a fast developing screening technology used in cytogenetic laboratories for the diagnosis of leukemia or other genetic diseases. However, one of the major challenges of using this new technology is how to efficiently detect the analyzable metaphase chromosomes during the scanning process. The purpose of this investigation is to develop a computer aided detection (CAD) scheme based on deep learning technology, which can identify the metaphase chromosomes with high accuracy. The CAD scheme includes an eight layer neural network. The first six layers compose of an automatic feature extraction module, which has an architecture of three convolution-max-pooling layer pairs. The 1st, 2nd and 3rd pair contains 30, 20, 20 feature maps, respectively. The seventh and eighth layers compose of a multiple layer perception (MLP) based classifier, which is used to identify the analyzable metaphase chromosomes. The performance of new CAD scheme was assessed by receiver operation characteristic (ROC) method. A number of 150 regions of interest (ROIs) were selected to test the performance of our new CAD scheme. Each ROI contains either interphase cell or metaphase chromosomes. The results indicate that new scheme is able to achieve an area under the ROC curve (AUC) of 0.886+/-0.043. This investigation demonstrates that applying a deep learning technique may enable to significantly improve the accuracy of the metaphase chromosome detection using a scanning microscopic imaging technology in the future.
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[CT pulmonary density mapping: surgical utility].
Gavezzoli, D; Caputo, P; Manelli, A; Zuccon, W; Faccini, M; Bonandrini, L
2002-04-01
The present paper considers the technique of CT scan maps of pulmonary isodensity, examining lung density differences as a function of the type of disease and considering their significance for the purposes of refined, useful diagnosis in a surgical context. METHODS. The method is used to examine 3 groups of subjects selected on a clinical/anamnestic basis and a further group already admitted for surgery. For each patient we obtained 2 thoracic density scans during the phase of maximum inspiration and expiration. On each scan we constructed 50 isodensity maps, the equivalent of more than 2500 measurements: the preliminary standard was represented by 100 wide windows to produce total "illumination" of the pulmonary fields. The isodensity windows were then codified differently. Subsequently, the density scans were analysed with the technique of scalar decomposition. The CT scan maps of lung isodensity proved useful for certain lung diseases in which early diagnosis, topographic extent of the pathology and the refined definition of the pathological picture provide important solutions as regards the indication and planning of surgical treatment and for the evaluation of the operative risk and prognosis. We consider that the technique is rapidly performed, not complex and inexpensive and is able to supply detailed information on the lung parenchyma such as to be used not only as a routine technique but also in emergencies.
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NASA Astrophysics Data System (ADS)
Kislitsyn, Dmitry Anatolevich
This dissertation presents results of a project bringing Scanning Tunneling Microscope (STM) into a regime of unlimited operational time at cryogenic conditions. Freedom from liquid helium consumption was achieved and technical characteristics of the instrument are reported, including record low noise for a scanning probe instrument coupled to a close-cycle cryostat, which allows for atomically resolved imaging, and record low thermal drift. Subsequent studies showed that the new STM opened new prospects in nanoscience research by enabling Scanning Tunneling Spectroscopic (STS) spatial mapping to reveal details of the electronic structure in real space for molecules and low-dimensional nanomaterials, for which this depth of investigation was previously prohibitively expensive. Quantum-confined electronic states were studied in single-walled carbon nanotubes (SWCNTs) deposited on the Au(111) surface. Localization on the nanometer-scale was discovered to produce a local vibronic manifold resulting from the localization-enhanced electron-vibrational coupling. STS showed the vibrational overtones, identified as D-band Kekule vibrational modes and K-point transverse out-of plane phonons. This study experimentally connected the properties of well-defined localized electronic states to the properties of associated vibronic states. Electronic structures of alkyl-substituted oligothiophenes with different backbone lengths were studied and correlated with torsional conformations assumed on the Au(111) surface. The molecules adopted distinct planar conformations with alkyl ligands forming cis- or trans-mutual orientations and at higher coverage self-assembled into ordered structures, binding to each other via interdigitated alkyl ligands. STS maps visualized, in real space, particle-in-a-box-like molecular orbitals. Shorter quaterthiophenes have substantially varying orbital energies because of local variations in surface reactivity. Different conformers of longer oligothiophenes with significant geometrical distortions of the oligothiophene backbones surprisingly exhibited similar electronic structures, indicating insensitivity of interaction with the surface to molecular conformation. Electronic states for annealed ligand-free lead sulfide nanocrystals were investigated, as well as hydrogen-passivated silicon nanocrystals, supported on the Au(111) surface. Delocalized quantum-confined states and localized defect-related states were identified, for the first time, via STS spatial mapping. Physical mechanisms, involving surface reconstruction or single-atom defects, were proposed for surface state formation to explain the observed spatial behavior of the electronic density of states. This dissertation includes previously published co-authored material.
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Kameda, Hiroyuki; Kudo, Kohsuke; Matsuda, Tsuyoshi; Harada, Taisuke; Iwadate, Yuji; Uwano, Ikuko; Yamashita, Fumio; Yoshioka, Kunihiro; Sasaki, Makoto; Shirato, Hiroki
2017-12-04
Respiration-induced phase shift affects B 0 /B 1 + mapping repeatability in parallel transmission (pTx) calibration for 7T brain MRI, but is improved by breath-holding (BH). However, BH cannot be applied during long scans. To examine whether interleaved acquisition during calibration scanning could improve pTx repeatability and image homogeneity. Prospective. Nine healthy subjects. 7T MRI with a two-channel RF transmission system was used. Calibration scanning for B 0 /B 1 + mapping was performed under sequential acquisition/free-breathing (Seq-FB), Seq-BH, and interleaved acquisition/FB (Int-FB) conditions. The B 0 map was calculated with two echo times, and the B 1 + map was obtained using the Bloch-Siegert method. Actual flip-angle imaging (AFI) and gradient echo (GRE) imaging were performed using pTx and quadrature-Tx (qTx). All scans were acquired in five sessions. Repeatability was evaluated using intersession standard deviation (SD) or coefficient of variance (CV), and in-plane homogeneity was evaluated using in-plane CV. A paired t-test with Bonferroni correction for multiple comparisons was used. The intersession CV/SDs for the B 0 /B 1 + maps were significantly smaller in Int-FB than in Seq-FB (Bonferroni-corrected P < 0.05 for all). The intersession CVs for the AFI and GRE images were also significantly smaller in Int-FB, Seq-BH, and qTx than in Seq-FB (Bonferroni-corrected P < 0.05 for all). The in-plane CVs for the AFI and GRE images in Seq-FB, Int-FB, and Seq-BH were significantly smaller than in qTx (Bonferroni-corrected P < 0.01 for all). Using interleaved acquisition during calibration scans of pTx for 7T brain MRI improved the repeatability of B 0 /B 1 + mapping, AFI, and GRE images, without BH. 1 Technical Efficacy Stage 1 J. Magn. Reson. Imaging 2017. © 2017 International Society for Magnetic Resonance in Medicine.
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Ota, Miho; Ogawa, Shintaro; Kato, Koichi; Wakabayashi, Chisato; Kunugi, Hiroshi
2015-04-30
Previous studies demonstrated that patients with schizophrenia show greater sensitivity to psychostimulants than healthy subjects. Sensitization to psychostimulants and resultant alteration of dopaminergic neurotransmission in rodents have been suggested as a useful model of schizophrenia. This study was aimed to examine the use of methylphenidate as a psychostimulant to induce dopamine release and that of [18F]fallypride as a radioligand to estimate the release in a rat model of schizophrenia. Six rats were scanned by positron emission tomography (PET) twice before and after methylphenidate challenge to evaluate dopamine release. After the scans, these rats were sensitized by using repeated methamphetamine (MAP) administration. Then, they were re-scanned twice again before and after methylphenidate challenge to evaluate whether MAP-sensitized rats show greater sensitivity to methylphenidate. We revealed a main effect of MAP-pretreatment and that of metylphenidate challenge. We found that % change of distribution volume ratio after repeated administration of MAP was greater than that before sensitization. These results suggest that methylphenidate-induced striatal dopamine release increased after sensitization to MAP. PET scan using [18F]fallypride at methylphenidate-challenge may provide a biological marker for schizophrenia and be useful to diagnose schizophrenia. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
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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
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NASA Astrophysics Data System (ADS)
Koch, R.; May, S.; Nüchter, A.
2017-02-01
3D laser scanners are favoured sensors for mapping in mobile service robotics at indoor and outdoor applications, since they deliver precise measurements at a wide scanning range. The resulting maps are detailed since they have a high resolution. Based on these maps robots navigate through rough terrain, fulfil advanced manipulation, and inspection tasks. In case of specular reflective and transparent objects, e.g., mirrors, windows, shiny metals, the laser measurements get corrupted. Based on the type of object and the incident angle of the incoming laser beam there are three results possible: a measurement point on the object plane, a measurement behind the object plane, and a measurement of a reflected object. It is important to detect such situations to be able to handle these corrupted points. This paper describes why it is difficult to distinguish between specular reflective and transparent surfaces. It presents a 3DReflection- Pre-Filter Approach to identify specular reflective and transparent objects in point clouds of a multi-echo laser scanner. Furthermore, it filters point clouds from influences of such objects and extract the object properties for further investigations. Based on an Iterative-Closest-Point-algorithm reflective objects are identified. Object surfaces and points behind surfaces are masked according to their location. Finally, the processed point cloud is forwarded to a mapping module. Furthermore, the object surface corners and the type of the surface is broadcasted. Four experiments demonstrate the usability of the 3D-Reflection-Pre-Filter. The first experiment was made in a empty room containing a mirror, the second experiment was made in a stairway containing a glass door, the third experiment was made in a empty room containing two mirrors, the fourth experiment was made in an office room containing a mirror. This paper demonstrate that for single scans the detection of specular reflective and transparent objects in 3D is possible. It is more reliable in 3D as in 2D. Nevertheless, collect the data of multiple scans and post-filter them as soon as the object was bypassed should pursued. This is why future work concentrates on implementing a post-filter module. Besides, it is the aim to improve the discrimination between specular reflective and transparent objects.
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Valdigem, Bruno Pereira; da Silva, Nilton José Carneiro; Dietrich, Cristiano Oliveira; Moreira, Dalmo; Sasdelli, Roberto; Pinto, Ibraim M; Cirenza, Claudio; de Paola, Angelo Amato Vincenzo
2010-11-01
As damage to coronary arteries is a potential complication of epicardial RF catheter ablation (EPRFCA), the procedure must be associated with coronary angiography. Chronic Chagasic cardiomiopathy (CCC) is a disease where epicardial VT are common. Eletroanatomic mapping merged with computed totmography (CT) scan data is a useful tool for mapping the endocardium, and its accuracy in guiding ablation on the epicardium was not adequately evaluated so far. Compare electronatomic map merged with Heart CT to fluoroscopy for epicardial ablation of CCC. Describe the distribution of the scars on CCC. We performed epicardial and endocardial mapping and ablation using CARTO XP V8 on eight patients and merged the map with coronary arteries CT scan using at least three landmarks. To compare the 3D image obtained with CARTO MERGE and the 2D fluoroscopic image obtained during the ablation procedure, we used computer graphic software (Inkscape™) in order to prove that the images were equivalent and to compare the distance between the catheter tip on fluoroscopy to catheter tip on 3D EA map. EPRFCA was successfully performed in all patients and they did not present recurrence for at least 3-month follow-up. The mean difference between the tip of the catheter on fluoroscopy and on the 3D model was 6.03 ± 2.09 mm. Scars were present in the epicardium and endocardium and most of patients presented with posterior wall scars and RV scar. The combination of electroanatomic map and CT coronary artery scan data is feasible and can be an important tool for EPRFCA in patients with CCC and VT.
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Mapping gray-scale image to 3D surface scanning data by ray tracing
NASA Astrophysics Data System (ADS)
Li, Peng; Jones, Peter R. M.
1997-03-01
The extraction and location of feature points from range imaging is an important but difficult task in machine vision based measurement systems. There exist some feature points which are not able to be detected from pure geometric characteristics, particularly in those measurement tasks related to the human body. The Loughborough Anthropometric Shadow Scanner (LASS) is a whole body surface scanner based on structured light technique. Certain applications of LASS require accurate location of anthropometric landmarks from the scanned data. This is sometimes impossible from existing raw data because some landmarks do not appear in the scanned data. Identification of these landmarks has to resort to surface texture of the scanned object. Modifications to LASS were made to allow gray-scale images to be captured before or after the object was scanned. Two-dimensional gray-scale image must be mapped to the scanned data to acquire the 3D coordinates of a landmark. The method to map 2D images to the scanned data is based on the colinearity conditions and ray-tracing method. If the camera center and image coordinates are known, the corresponding object point must lie on a ray starting from the camera center and connecting to the image coordinate. By intersecting the ray with the scanned surface of the object, the 3D coordinates of a point can be solved. Experimentation has demonstrated the feasibility of the method.
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A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea
Kujur, Alice; Bajaj, Deepak; Upadhyaya, Hari D.; Das, Shouvik; Ranjan, Rajeev; Shree, Tanima; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C.L.L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.
2015-01-01
We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23–47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea. PMID:26058368
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NASA Astrophysics Data System (ADS)
Zanetti, Michael; Wilk, Jakob; Joeleht, Argo; Välja, Rudolf; Losiak, Anna; Wisniowski, Tomek; Huber, Matthew; Pavel, Kristiina; Kriiska, Aivar; Plado, Jüri; Geppert, Wolf Dietrich; Kukko, Antero; Kaartinen, Harri
2015-04-01
Introduction: The Kaali Impact Crater on the island of Saaremaa, Estonia (58.37° N, 22.67° E) is part of a crater-strewn-field consisting of nine identified craters, ranging in size from 110m (Kaali Main) to a few meters in diameter [1-3]. The strewn field was formed by the breakup of an IAB iron meteorite during atmospheric entry [4]. The main crater is due to its size an important crater to study the effects of small asteroidal impacts on terrestrial planets. Despite some anthropomorphic changes, the crater is well preserved. During a scientific expedition in August 2014, we mapped the crater in unprecedented detail using 3D laser scanning tools and made detailed strike and dip measurements of all outcrops. Additional measurements using ground-penetrating radar and electro-resistivity tomography we also conducted to further refine the subsurface crater morphology. The results include a high resolution topographic map of the crater, previously unreported observations of overturned ejecta, and refined morphometric estimates of the crater. Additionally, research conducted as part of the expedition has provided a new, best-estimate for the formation of the crater (3200a +/- 30 BP) based on 14C AMS dating of charcoal from within the ejecta blanket [Losiak et al., 2015, this conference]. Structural Mapping: Although Kaali Main has been the subject of previous investigation (e.g. [2,5,6]), most of the structural descriptions of the crater pre-date modern crater investigations. Strongly inclined blocks were previously considered being affected by erosion and slope processes, our new observations show that most high dip-angle features fit well with overall dip-angle systematics. The existence of the overturned flap can be demonstrated in at least four areas around the crater. 3D Laser Scanning: A point cloud containing 16 million data points was created using 43 individual scans from a tripod mounted Faro 3D 330x laser scanner. Scans were processed using Trimble Realworks software. A DEM, Hillshade, Slope Map and Contour Map were created in ESRI ArcScene software. Photogrammetry: Photogrammetric techniques from images of key outcrops were used to create texture, photorealistic 3D representations using Agisoft PhotoScan software. Acknowledgements: We extend our sincerest gratitude to the Estonian National Heritage Board for permission to dig and make measurements at the crater. References: [1] I.Kolkun (1922) Üldine geologia. Tallin, 170. [2] J. A.Reinwald (1933) Publications of the Geological Institution of the University of Tartu, 30:1-20. [3] J.A.Reinwald (1928) thesis; Univ of Tartu [4] L.J.Spencer (1938) Miner. Mag., 25:75-80. [5] A.Aaloe (1959) ENSV TA Geoloogia Instituudi Uurimused, 2:105-117. [6] A.Raukas et al. (2002) Impact Studies 2005, 341-355.
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An Evaluation of Substrates for Tactile Maps and Diagrams: Scanning Speed and Users' Preferences
ERIC Educational Resources Information Center
Jehoel, Sandra; Ungar, Simon; McCallum, Don; Rowell, Jonathan
2005-01-01
This study evaluated the relative suitability of a range of base materials for producing tactile maps and diagrams via a new ink-jet process. The visually impaired and sighted participants tactilely scanned arrays of symbols that were printed on seven substrate materials, including paper, plastic, and aluminum. In general, the rougher substrates…
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High-speed multislice T1 mapping using inversion-recovery echo-planar imaging.
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.
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Retrieval Algorithms for Road Surface Modelling Using Laser-Based Mobile Mapping.
Jaakkola, Anttoni; Hyyppä, Juha; Hyyppä, Hannu; Kukko, Antero
2008-09-01
Automated processing of the data provided by a laser-based mobile mapping system will be a necessity due to the huge amount of data produced. In the future, vehiclebased laser scanning, here called mobile mapping, should see considerable use for road environment modelling. Since the geometry of the scanning and point density is different from airborne laser scanning, new algorithms are needed for information extraction. In this paper, we propose automatic methods for classifying the road marking and kerbstone points and modelling the road surface as a triangulated irregular network. On the basis of experimental tests, the mean classification accuracies obtained using automatic method for lines, zebra crossings and kerbstones were 80.6%, 92.3% and 79.7%, respectively.
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NASA Astrophysics Data System (ADS)
Chen, C.; Zou, X.; Tian, M.; Li, J.; Wu, W.; Song, Y.; Dai, W.; Yang, B.
2017-11-01
In order to solve the automation of 3D indoor mapping task, a low cost multi-sensor robot laser scanning system is proposed in this paper. The multiple-sensor robot laser scanning system includes a panorama camera, a laser scanner, and an inertial measurement unit and etc., which are calibrated and synchronized together to achieve simultaneously collection of 3D indoor data. Experiments are undertaken in a typical indoor scene and the data generated by the proposed system are compared with ground truth data collected by a TLS scanner showing an accuracy of 99.2% below 0.25 meter, which explains the applicability and precision of the system in indoor mapping applications.
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Note: Electron energy spectroscopy mapping of surface with scanning tunneling microscope
DOE Office of Scientific and Technical Information (OSTI.GOV)
Li, Meng; Xu, Chunkai, E-mail: xuck@ustc.edu.cn, E-mail: xjun@ustc.edu.cn; Zhang, Panke
We report a novel scanning probe electron energy spectrometer (SPEES) which combines a double toroidal analyzer with a scanning tunneling microscope to achieve both topography imaging and electron energy spectroscopy mapping of surface in situ. The spatial resolution of spectroscopy mapping is determined to be better than 0.7 ± 0.2 μm at a tip sample distance of 7 μm. Meanwhile, the size of the field emission electron beam spot on the surface is also measured, and is about 3.6 ± 0.8 μm in diameter. This unambiguously demonstrates that the spatial resolution of SPEES technique can be much better than themore » size of the incident electron beam.« less
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Spatial clustering and local risk of leprosy in São Paulo, Brazil.
Ramos, Antônio Carlos Vieira; Yamamura, Mellina; Arroyo, Luiz Henrique; Popolin, Marcela Paschoal; Chiaravalloti Neto, Francisco; Palha, Pedro Fredemir; Uchoa, Severina Alice da Costa; Pieri, Flávia Meneguetti; Pinto, Ione Carvalho; Fiorati, Regina Célia; Queiroz, Ana Angélica Rêgo de; Belchior, Aylana de Souza; Dos Santos, Danielle Talita; Garcia, Maria Concebida da Cunha; Crispim, Juliane de Almeida; Alves, Luana Seles; Berra, Thaís Zamboni; Arcêncio, Ricardo Alexandre
2017-02-01
Although the detection rate is decreasing, the proportion of new cases with WHO grade 2 disability (G2D) is increasing, creating concern among policy makers and the Brazilian government. This study aimed to identify spatial clustering of leprosy and classify high-risk areas in a major leprosy cluster using the SatScan method. Data were obtained including all leprosy cases diagnosed between January 2006 and December 2013. In addition to the clinical variable, information was also gathered regarding the G2D of the patient at diagnosis and after treatment. The Scan Spatial statistic test, developed by Kulldorff e Nagarwalla, was used to identify spatial clustering and to measure the local risk (Relative Risk-RR) of leprosy. Maps considering these risks and their confidence intervals were constructed. A total of 434 cases were identified, including 188 (43.31%) borderline leprosy and 101 (23.28%) lepromatous leprosy cases. There was a predominance of males, with ages ranging from 15 to 59 years, and 51 patients (11.75%) presented G2D. Two significant spatial clusters and three significant spatial-temporal clusters were also observed. The main spatial cluster (p = 0.000) contained 90 census tracts, a population of approximately 58,438 inhabitants, detection rate of 22.6 cases per 100,000 people and RR of approximately 3.41 (95%CI = 2.721-4.267). Regarding the spatial-temporal clusters, two clusters were observed, with RR ranging between 24.35 (95%CI = 11.133-52.984) and 15.24 (95%CI = 10.114-22.919). These findings could contribute to improvements in policies and programming, aiming for the eradication of leprosy in Brazil. The Spatial Scan statistic test was found to be an interesting resource for health managers and healthcare professionals to map the vulnerability of areas in terms of leprosy transmission risk and areas of underreporting.
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NASA Technical Reports Server (NTRS)
Cartmill, R. H. (Principal Investigator)
1973-01-01
The author has identified the following significant results. Using the 12S Digicol color additive viewer and eight color classification map has been produced of a portion of the study area. Channel 3 of the MSS produced the best map. Enlargements of the MSS data have been accomplished by using the Data Analysis Station. The attached film recorder has three color guns which are capable of placing 2400 square elements across a 9 inch film. It has been found that by repeating ERTS element 9 times and each scan line 13 times that a map of a scale approximately 1:62,000 can be produced as a color negative film strip. This can be contact printed to produce a color map of the scale. As yet this procedure does not correct for image skew caused by rotation which is believed to be the major source of distortion and blockiness in the image. However, the final product which has not undergone any photographic enlargement is superior to photographically enlarged maps of the same scale.
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VizieR Online Data Catalog: PACS photometry of FIR faint stars (Klaas+, 2018)
NASA Astrophysics Data System (ADS)
Klaas, U.; Balog, Z.; Nielbock, M.; Mueller, T. G.; Linz, H.; Kiss, Cs.
2018-01-01
70, 100 and 160um photometry of FIR faint stars from PACS scan map and chop/nod measurements. For scan maps also the photometry of the combined scan and cross-scan maps (at 160um there are usually two scan and cross-scan maps each as complements to the 70 and 100um maps) is given. Note: Not all stars have measured fluxes in all three filters. Scan maps: The main observing mode was the point-source mini-scan-map mode; selected scan map parameters are given in column mparam. An outline of the data processing using the high-pass filter (HPF) method is presented in Balog et al. (2014ExA....37..129B). Processing proceeded from Herschel Science Archive SPG v13.1.0 level 1 products with HIPE version 15 build 165 for 70 and 100um maps and from Herschel Science Archive SPG v14.2.0 level 1 products with HIPE version 15 build 1480 for 160um maps. Fluxes faper were obtained by aperture photometry with aperture radii of 5.6, 6.8 and 10.7 arcsec for the 70, 100 and 160um filter, respectively. Noise per pixel sigpix was determined with the histogram method, described in this paper, for coverage values greater than or equal to 0.5*maximum coverage. The number of map pixels (1.1, 1.4, and 2.1 arcsec pixel size, respectively) inside the photometric aperture is Naper = 81.42, 74.12, and 81.56, respectively. The corresponding correction factors for correlated noise are fcorr = 3.13, 2.76, and 4.12, respectively. The noise for the photometric aperture is calculated as sig_aper=sqrt(Naper)*fcorr*sigpix. Signal-to-noise ratios are determined as S/N=faper/sigaper. Aperture-correction factors to derive the total flux are caper = 1.61, 1.56 and 1.56 for the 70, 100 and 160um filter, respectively. Applied colour-correction factors for a 5000K black-body SED are cc = 1.016, 1.033, and 1.074 for the 70, 100, and 160um filter, respectively. The final stellar flux is derived as fstar=faper*caper/cc. Maximum and minimum FWHM of the star PSF are determined by an elliptical fit of the intensity profile. Chop/nod observations: The chop/nod point-source mode is described in this paper. An outline of the data processing is presented in Nielbock et al. (2013ExA....36..631N). Processing proceeded from Herschel Science Archive SPG v11.1.0 level 1 products with HIPE version 13 build 2768. Gyro correction was applied for most of the cases to improve the pointing reconstruction performance. Fluxes faper were obtained by aperture photometry with aperture radii of 5.6, 6.8 and 10.7 arcsec for the 70, 100 and 160um filter, respectively. Noise per pixel sigpix was determined with the histogram method, described in this paper, for coverage values greater than or equal to 0.5*maximum coverage. The number of map pixels (1.1, 1.4, and 2.1 arcsec pixel size, respectively) inside the photometric aperture is Naper = 81.42, 74.12, and 81.56, respectively. The corresponding correction factors for correlated noise are fcorr = 6.33, 4.22, and 7.81, respectively. The noise for the photometric aperture is calculated as sigaper=sqrt(Naper)*fcorr*sigpix. Signal-to-noise ratios are determined as S/N=faper/sigaper. Aperture-correction factors to derive the total flux are caper = 1.61, 1.56 and 1.56 for the 70, 100 and 160um filter, respectively. Applied colour-correction factors for a 5000K black-body SED are cc = 1.016, 1.033, and 1.074 for the 70, 100, and 160um filter, respectively. Maximum and minimum FWHM of the star PSF are determined by an elliptical fit of the intensity profile. (7 data files).
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Enhanced capture rate for haze defects in production wafer inspection
NASA Astrophysics Data System (ADS)
Auerbach, Ditza; Shulman, Adi; Rozentsvige, Moshe
2010-03-01
Photomask degradation via haze defect formation is an increasing troublesome yield problem in the semiconductor fab. Wafer inspection is often utilized to detect haze defects due to the fact that it can be a bi-product of process control wafer inspection; furthermore, the detection of the haze on the wafer is effectively enhanced due to the multitude of distinct fields being scanned. In this paper, we demonstrate a novel application for enhancing the wafer inspection tool's sensitivity to haze defects even further. In particular, we present results of bright field wafer inspection using the on several photo layers suffering from haze defects. One way in which the enhanced sensitivity can be achieved in inspection tools is by using a double scan of the wafer: one regular scan with the normal recipe and another high sensitivity scan from which only the repeater defects are extracted (the non-repeater defects consist largely of noise which is difficult to filter). Our solution essentially combines the double scan into a single high sensitivity scan whose processing is carried out along two parallel routes (see Fig. 1). Along one route, potential defects follow the standard recipe thresholds to produce a defect map at the nominal sensitivity. Along the alternate route, potential defects are used to extract only field repeater defects which are identified using an optimal repeater algorithm that eliminates "false repeaters". At the end of the scan, the two defect maps are merged into one with optical scan images available for all the merged defects. It is important to note, that there is no throughput hit; in addition, the repeater sensitivity is increased relative to a double scan, due to a novel runtime algorithm implementation whose memory requirements are minimized, thus enabling to search a much larger number of potential defects for repeaters. We evaluated the new application on photo wafers which consisted of both random and haze defects. The evaluation procedure involved scanning with three different recipe types: Standard Inspection: Nominal recipe with a low false alarm rate was used to scan the wafer and repeaters were extracted from the final defect map. Haze Monitoring Application: Recipe sensitivity was enhanced and run on a single field column from which on repeating defects were extracted. Enhanced Repeater Extractor: Defect processing included the two parallel routes: a nominal recipe for the random defects and the new high sensitive repeater extractor algorithm. The results showed that the new application (recipe #3) had the highest capture rate on haze defects and detected new repeater defects not found in the first two recipes. In addition, the recipe was much simpler to setup since repeaters are filtered separately from random defects. We expect that in the future, with the advent of mask-less lithography and EUV lithography, the monitoring of field and die repeating defects on the wafer will become a necessity for process control in the semiconductor fab.
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Ruiz-Narváez, Edward A; Sucheston-Campbell, Lara; Bensen, Jeannette T; Yao, Song; Haddad, Stephen; Haiman, Christopher A; Bandera, Elisa V; John, Esther M; Bernstein, Leslie; Hu, Jennifer J; Ziegler, Regina G; Deming, Sandra L; Olshan, Andrew F; Ambrosone, Christine B; Palmer, Julie R; Lunetta, Kathryn L
2016-01-01
Recent genetic admixture coupled with striking differences in incidence of estrogen receptor (ER) breast cancer subtypes, as well as severity, between women of African and European ancestry, provides an excellent rationale for performing admixture mapping in African American women with breast cancer risk. We performed the largest breast cancer admixture mapping study with in African American women to identify novel genomic regions associated with the disease. We conducted a genome-wide admixture scan using 2,624 autosomal ancestry informative markers (AIMs) in 3,629 breast cancer cases (including 1,968 ER-positive, 1093 ER-negative, and 601 triple-negative) and 4,658 controls from the African American Breast Cancer Epidemiology and Risk (AMBER) Consortium, a collaborative study of four large geographically different epidemiological studies of breast cancer in African American women. We used an independent case-control study to test for SNP association in regions with genome-wide significant admixture signals. We found two novel genome-wide significant regions of excess African ancestry, 4p16.1 and 17q25.1, associated with ER-positive breast cancer. Two regions known to harbor breast cancer variants, 10q26 and 11q13, were also identified with excess of African ancestry. Fine-mapping of the identified genome-wide significant regions suggests the presence of significant genetic associations with ER-positive breast cancer in 4p16.1 and 11q13. In summary, we identified three novel genomic regions associated with breast cancer risk by ER status, suggesting that additional previously unidentified variants may contribute to the racial differences in breast cancer risk in the African American population.
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Kobayashi, Akira; Yokogawa, Hideaki; Sugiyama, Kazuhisa
2012-01-01
Background: The purpose of this study was to investigate pathological changes of the corneal cell layer in patients with map-dot-fingerprint (epithelial basement membrane) dystrophy by in vivo laser corneal confocal microscopy. Methods: Two patients were evaluated using a cornea-specific in vivo laser scanning confocal microscope (Heidelberg Retina Tomograph 2 Rostock Cornea Module, HRT 2-RCM). The affected corneal areas of both patients were examined. Image analysis was performed to identify corneal epithelial and stromal deposits correlated with this dystrophy. Results: Variously shaped (linear, multilaminar, curvilinear, ring-shape, geographic) highly reflective materials were observed in the “map” area, mainly in the basal epithelial cell layer. In “fingerprint” lesions, multiple linear and curvilinear hyporeflective lines were observed. Additionally, in the affected corneas, infiltration of possible Langerhans cells and other inflammatory cells was observed as highly reflective Langerhans cell-like or dot images. Finally, needle-shaped materials were observed in one patient. Conclusion: HRT 2-RCM laser confocal microscopy is capable of identifying corneal microstructural changes related to map-dot-fingerprint corneal dystrophy in vivo. The technique may be useful in elucidating the pathogenesis and natural course of map-dot-fingerprint corneal dystrophy and other similar basement membrane abnormalities. PMID:22888214
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Wig, Gagan S.; Laumann, Timothy O.; Cohen, Alexander L.; Power, Jonathan D.; Nelson, Steven M.; Glasser, Matthew F.; Miezin, Francis M.; Snyder, Abraham Z.; Schlaggar, Bradley L.; Petersen, Steven E.
2014-01-01
We describe methods for parcellating an individual subject's cortical and subcortical brain structures using resting-state functional correlations (RSFCs). Inspired by approaches from social network analysis, we first describe the application of snowball sampling on RSFC data (RSFC-Snowballing) to identify the centers of cortical areas, subdivisions of subcortical nuclei, and the cerebellum. RSFC-Snowballing parcellation is then compared with parcellation derived from identifying locations where RSFC maps exhibit abrupt transitions (RSFC-Boundary Mapping). RSFC-Snowballing and RSFC-Boundary Mapping largely complement one another, but also provide unique parcellation information; together, the methods identify independent entities with distinct functional correlations across many cortical and subcortical locations in the brain. RSFC parcellation is relatively reliable within a subject scanned across multiple days, and while the locations of many area centers and boundaries appear to exhibit considerable overlap across subjects, there is also cross-subject variability—reinforcing the motivation to parcellate brains at the level of individuals. Finally, examination of a large meta-analysis of task-evoked functional magnetic resonance imaging data reveals that area centers defined by task-evoked activity exhibit correspondence with area centers defined by RSFC-Snowballing. This observation provides important evidence for the ability of RSFC to parcellate broad expanses of an individual's brain into functionally meaningful units. PMID:23476025
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NASA Technical Reports Server (NTRS)
Meier, M. F. (Principal Investigator)
1974-01-01
The author has identified the following significant results. Snowlines on a small drainage basin were accurately identified on bulk ERTS-1 images without use of digital processing, and results checked with high altitude and ground-based photography. The area and approximate shape of snow patches as small as 20,000 sq m could be correctly identified with a magnifying scanning densitometer. The resolution of ERTS is more than ample for most snow mapping needs. Mount Baker, Washington, has a large crater south of the summit and an area north of the summit which emit considerable geothermal heat in the form of fumaroles and hot ground. Temperatures are being monitored using an ERTS DCS. Debris flows are occassionally released from the crater due to water saturation at the base of a heavy snowpack lying on hydrothermally altered hot ground. These debris flows present a possible hazard to life and property, as they are discharged down the Boulder Glacier toward Baker Lake, the upper of two major hydroelectric power reservoirs which are situated above the populated Skagit River Valley. ERTS-1 images show that the most recent debris flow (20-21 August 1973) can be clearly discerned and mapped. ERTS images provide another important tool for monitoring this potential hazard.
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Effective use of ERTS multisensor data in the Great Plains
NASA Technical Reports Server (NTRS)
Myers, V. I. (Principal Investigator)
1972-01-01
The author has identified the following significant results. One unique advantage of ERTS imagery for delineating soil associations is the large area that can be scanned with one photo. Although soil associations usually are published at scales of 1:500,000 or 1:1,000,000, the delineations are drawn on much larger scale maps covering small pieces of the scene and then pieced together. Alluvial areas are usually swollen out of proportion to other soil areas. ERTS imagery puts alluvial areas into their proper size. A second feature of ERTS imagery is that a soil association map constructed with its aid assures that the cartographic level of the associations is more nearly the same. Another advantage of ERTS imagery is that the actual shape and configuration of soil associations are apparent. Also with ERTS imagery significant new delineations may become apparent which were missed when constructing soil association maps from conventional large scale photos.
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Geological Features Mapping Using PALSAR-2 Data in Kelantan River Basin, Peninsular Malaysia
NASA Astrophysics Data System (ADS)
Pour, A. B.; Hashim, M.
2016-09-01
In this study, the recently launched Phased Array type L-band Synthetic Aperture Radar-2 (PALSAR-2) onboard the Advanced Land Observing Satellite-2 (ALOS-2), remote sensing data were used to map geologic structural and topographical features in the Kelantan river basin for identification of high potential risk and susceptible zones for landslides and flooding areas. A ScanSAR and two fine mode dual polarization level 3.1 images cover Kelantan state were processed for comprehensive analysis of major geological structures and detailed characterizations of lineaments, drainage patterns and lithology at both regional and district scales. Red-Green-Blue (RGB) colour-composite was applied to different polarization channels of PALSAR-2 data to extract variety of geological information. Directional convolution filters were applied to the data for identifying linear features in particular directions and edge enhancement in the spatial domain. Results derived from ScanSAR image indicate that lineament occurrence at regional scale was mainly linked to the N-S trending of the Bentong-Raub Suture Zone (BRSZ) in the west and Lebir Fault Zone in the east of the Kelantan state. Combination of different polarization channels produced image maps contain important information related to water bodies, wetlands and lithological units for the Kelantan state using fine mode observation data. The N-S, NE-SW and NNE-SSW lineament trends were identified in the study area using directional filtering. Dendritic, sub-dendritic and rectangular drainage patterns were detected in the Kelantan river basin. The analysis of field investigations data indicate that many of flooded areas were associated with high potential risk zones for hydro-geological hazards such as wetlands, urban areas, floodplain scroll, meander bend, dendritic and sub-dendritic drainage patterns, which are located in flat topograghy regions. Numerous landslide points were located in rectangular drainage system that associated with topographic slope of metamorphic and Quaternary rock units. Some large landslides were associated with N-S, NNE-SSW and NE-SW trending fault zones. Consequently, structural and topographical geology maps were produced for Kelantan river basin using PALSAR-2 data, which could be broadly applicable for landslide hazard mapping and identification of high potential risk zone for hydro-geological hazards.
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Mapping Fearscapes of a Mammalian Herbivore using Terrestrial LiDAR and UAV Imagery
NASA Astrophysics Data System (ADS)
Olsoy, P.; Nobler, J. D.; Forbey, J.; Rachlow, J. L.; Burgess, M. A.; Glenn, N. F.; Shipley, L. A.
2013-12-01
Concealment allows prey animals to remain hidden from a predator and can influence both real and perceived risks of predation. The heterogeneous nature of vegetative structure can create a variable landscape of concealment - a 'fearscape' - that may influence habitat quality and use by prey. Traditional measurements of concealment rely on a limited number of distances, heights, and vantage points, resulting in small snapshots of concealment available to a prey animal. Our objective was to demonstrate the benefits of emerging remote sensing techniques to map fearscapes for pygmy rabbits (Brachylagus idahoensis) in sagebrush steppe habitat across a continuous range of scales. Specifically, we used vegetation height rasters derived from terrestrial laser scanning (TLS) to create viewsheds from multiple vantage points, representing predator visibility. The sum of all the viewsheds modeled horizontal concealment of prey at both the shrub and patch scales. We also used a small, unmanned aerial vehicle (UAV) to determine vertical concealment at a habitat scale. Terrestrial laser scanning provided similar estimates of horizontal concealment at the shrub scale when compared to photographic methods (R2 = 0.85). Both TLS and UAV provide the potential to quantify concealment of prey from multiple distances, heights, or vantage points, allowing the creation of a manipulable fearscape map that can be correlated with habitat use by prey animals. The predictive power of such a map also could identify shrubs or patches for fine scale nutritional and concealment analysis for future investigation and conservation efforts. Fearscape map at the mound-scale. Viewsheds were calculated from 100 equally spaced observer points located 4 m from the closest on-mound sagebrush of interest. Red areas offer low concealment, while green areas provide high concealment.
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NASA Astrophysics Data System (ADS)
Hofierka, Jaroslav; Gallay, Michal; Bandura, Peter; Šašak, Ján
2018-05-01
Karst sinkholes (dolines) play an important role in a karst landscape by controlling infiltration of surficial water, air flow or spatial distribution of solar energy. These landforms also present a limiting factor for human activities in agriculture or construction. Therefore, mapping such geomorphological forms is vital for appropriate landscape management and planning. There are several mapping techniques available; however, their applicability can be reduced in densely forested areas with poor accessibility and visibility of the landforms. In such conditions, airborne laser scanning (ALS) provides means for efficient and accurate mapping of both land and landscape canopy surfaces. Taking the benefits of ALS into account, we present an innovative method for identification and evaluation of karst sinkholes based on numerical water flow modelling. The suggested method was compared to traditional techniques for sinkhole mapping which use topographic maps and digital terrain modelling. The approach based on simulation of a rainfall event very closely matched the reference datasets derived by manual inspection of the ALS digital elevation model and field surveys. However, our process-based approach provides advantage of assessing the magnitude how sinkholes influence concentration of overland water flow during extreme rainfall events. This was performed by calculating the volume of water accumulated in sinkholes during the simulated rainfall. In this way, the influence of particular sinkholes on underground geomorphological systems can be assessed. The method was demonstrated in a case study of Slovak Karst in the West Carpathians where extreme rainfalls or snow-thaw events occur annually. We identified three spatially contiguous groups of sinkholes with a different effect on overland flow concentration. These results are discussed in relation to the known underground hydrological systems.
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Downer, Jonathan; Corkill, Rufus; Byrne, James V
2015-01-01
Introduction Cerebral vasospasm is the leading cause of morbidity and mortality in patients with aneurysmal subarachnoid haemorrhage (SAH) surviving the initial ictus. Commonly used techniques for vasospasm assessment are digital subtraction angiography and transcranial Doppler sonography. These techniques can reliably identify only the major vessel spasm and fail to estimate its haemodynamic significance. To overcome these issues and to enable comprehensive non-invasive assessment of vasospasm inside the interventional suite, a novel protocol involving measurement of parenchymal blood volume (PBV) using C-arm flat detector computed tomography (FDCT) was implemented. Materials and methods Patients from the neuro-intensive treatment unit (ITU) with suspected vasospasm following aneurysmal SAH were scanned with a biplane C-arm angiography system using an intravenous contrast injection protocol. The PBV maps were generated using prototype software. Contemporaneous clinically indicated MR scan including the diffusion- and perfusion-weighted sequences was performed. C-arm PBV maps were compared against the MR perfusion maps. Results Distribution of haemodynamic impairment on C-arm PBV maps closely matched the pattern of abnormality on MR perfusion maps. On visual comparison between the two techniques, the extent of abnormality indicated PBV to be both cerebral blood flow and cerebral blood volume weighted. Conclusion C-arm FDCT PBV measurements allow an objective assessment of the severity and localisation of cerebral hypoperfusion resulting from vasospasm. The technique has proved feasible and useful in very sick patients after aneurysmal SAH. The promise shown in this early study indicates that it deserves further evaluation both for post-SAH vasospasm and in other relevant clinical settings. PMID:26017197
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Kamran, Mudassar; Downer, Jonathan; Corkill, Rufus; Byrne, James V
2015-08-01
Cerebral vasospasm is the leading cause of morbidity and mortality in patients with aneurysmal subarachnoid haemorrhage (SAH) surviving the initial ictus. Commonly used techniques for vasospasm assessment are digital subtraction angiography and transcranial Doppler sonography. These techniques can reliably identify only the major vessel spasm and fail to estimate its haemodynamic significance. To overcome these issues and to enable comprehensive non-invasive assessment of vasospasm inside the interventional suite, a novel protocol involving measurement of parenchymal blood volume (PBV) using C-arm flat detector computed tomography (FDCT) was implemented. Patients from the neuro-intensive treatment unit (ITU) with suspected vasospasm following aneurysmal SAH were scanned with a biplane C-arm angiography system using an intravenous contrast injection protocol. The PBV maps were generated using prototype software. Contemporaneous clinically indicated MR scan including the diffusion- and perfusion-weighted sequences was performed. C-arm PBV maps were compared against the MR perfusion maps. Distribution of haemodynamic impairment on C-arm PBV maps closely matched the pattern of abnormality on MR perfusion maps. On visual comparison between the two techniques, the extent of abnormality indicated PBV to be both cerebral blood flow and cerebral blood volume weighted. C-arm FDCT PBV measurements allow an objective assessment of the severity and localisation of cerebral hypoperfusion resulting from vasospasm. The technique has proved feasible and useful in very sick patients after aneurysmal SAH. The promise shown in this early study indicates that it deserves further evaluation both for post-SAH vasospasm and in other relevant clinical settings. © The Author(s) 2015.
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Quantifying torso deformity in scoliosis
NASA Astrophysics Data System (ADS)
Ajemba, Peter O.; Kumar, Anish; Durdle, Nelson G.; Raso, V. James
2006-03-01
Scoliosis affects the alignment of the spine and the shape of the torso. Most scoliosis patients and their families are more concerned about the effect of scoliosis on the torso than its effect on the spine. There is a need to develop robust techniques for quantifying torso deformity based on full torso scans. In this paper, deformation indices obtained from orthogonal maps of full torso scans are used to quantify torso deformity in scoliosis. 'Orthogonal maps' are obtained by applying orthogonal transforms to 3D surface maps. (An 'orthogonal transform' maps a cylindrical coordinate system to a Cartesian coordinate system.) The technique was tested on 361 deformed computer models of the human torso and on 22 scans of volunteers (8 normal and 14 scoliosis). Deformation indices from the orthogonal maps correctly classified up to 95% of the volunteers with a specificity of 1.00 and a sensitivity of 0.91. In addition to classifying scoliosis, the system gives a visual representation of the entire torso in one view and is viable for use in a clinical environment for managing scoliosis.
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NASA Astrophysics Data System (ADS)
Debastiani, Rafaela; Simon, Rolf; Goettlicher, Joerg; Heissler, Stefan; Steininger, Ralph; Batchelor, David; Fiederle, Michael; Baumbach, Tilo
2016-10-01
Roman mural green pigment painting fragments from three Roman sites in the north of the Roman province Germania Superior: Koblenz Stadtwald Remstecken (KOSR), Weißenthurm " Am guten Mann" (WEIS) and Mendig Lungenkärchen (MELU), dating from second and third centuries AD were analyzed. The experiments were performed nondestructively using synchrotron-based scanning macro-X-ray fluorescence (SR-MA-XRF), synchrotron-based scanning micro-X-ray fluorescence (SR-μ-XRF), synchrotron-based X-ray diffraction (SR-XRD) and Raman spectroscopy. Correlation between SR-MA-XRF, SR-μ-XRF elemental map distributions and optical images of scanned areas was mainly found for the elements Ca, Fe and K. With XRF, Fe and K were identified correlated with green pigment, but in samples from two sites, Mendig Lungenkärchen and Weißenthurm " Am guten Mann", also Cu was detected in minor concentration. The results of SR-XRD and Raman spectroscopy were limited to one sample from Weißenthurm " Am guten Mann". In this sample, green earth and calcium carbonate were identified by SR-XRD and, additionally, malachite by Raman spectroscopy.
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Watts, Kristen; Lagalante, Anthony
2018-06-06
Art conservation science is in need of a relatively nondestructive way of rapidly identifying the binding media within a painting cross-section and isolating binding media to specific layers within the cross-section. Knowledge of the stratigraphy of cross-sections can be helpful for removing possible unoriginal paint layers on the artistic work. Desorption electrospray ionization-mass spectrometry (DESI-MS) was used in ambient mode to study cross-sections from mock-up layered paint samples and samples from a 17th century baroque painting. The DESI spray was raster scanned perpendicular to the cross-section layers to maximize lateral resolution then analyzed with a triple quadrupole mass analyzer in linear ion trap mode. From these scans, isobaric mass maps were created to map the locations of masses indicative of particular binding media onto the cross-sections. Line paint-outs of pigments in different binding media showed specific and unique ions to distinguish between the modern acrylic media and the lipid containing binding media. This included: OP (EO) 9 surfactant in positive ESI for acrylic (m/z 621), and oleic (m/z 281), stearic (m/z 283), and azelaic (m/z 187) acids in negative ESI for oil and egg tempera. DESI-MS maps of mock-up cross-sections of layered pigmented binding media showed correlation between these ions and the layers with a spatial resolution of 100 μm. DESI-MS is effective in monitoring binding media within an intact painting cross-section via mass spectrometric methods. This includes distinguishing between lipid-containing and modern binding materials present in a known mockup cross section matrix as well as identifying lipid binding media in a 17th century baroque era painting. This article is protected by copyright. All rights reserved.
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Scan angle calculation and image compositing for the Mexico forest mapping project
Zhiliang Zhu
1994-01-01
Data from the Advanced Very High Resolution Radiometer (AVHRR) were used in a cooperative project, sponsored by the U.S. Department of Agriculture, Forest Service, Southern Forest Experiment Station, and the United Nations, Food and Agriculture Organization (FAO), to map Mexicos forest cover types.To provide satisfactory AVHRR data sets for the project, the sensor scan...
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Kondo, Yukihito; Okunishi, Eiji
2014-10-01
Moiré method in scanning transmission electron microscopy allows observing a magnified two-dimensional atomic column elemental map of a higher pixel resolution with a lower electron dose unlike conventional atomic column mapping. The magnification of the map is determined by the ratio between the pixel size and the lattice spacing. With proper ratios for the x and y directions, we could observe magnified elemental maps, homothetic to the atomic arrangement in the sample of SrTiO3 [0 0 1]. The map showed peaks at all expected oxygen sites in SrTiO3 [0 0 1]. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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Multimodal connectivity of motor learning-related dorsal premotor cortex.
Hardwick, Robert M; Lesage, Elise; Eickhoff, Claudia R; Clos, Mareike; Fox, Peter; Eickhoff, Simon B
2015-12-01
The dorsal premotor cortex (dPMC) is a key region for motor learning and sensorimotor integration, yet we have limited understanding of its functional interactions with other regions. Previous work has started to examine functional connectivity in several brain areas using resting state functional connectivity (RSFC) and meta-analytical connectivity modelling (MACM). More recently, structural covariance (SC) has been proposed as a technique that may also allow delineation of functional connectivity. Here, we applied these three approaches to provide a comprehensive characterization of functional connectivity with a seed in the left dPMC that a previous meta-analysis of functional neuroimaging studies has identified as playing a key role in motor learning. Using data from two sources (the Rockland sample, containing resting state data and anatomical scans from 132 participants, and the BrainMap database, which contains peak activation foci from over 10,000 experiments), we conducted independent whole-brain functional connectivity mapping analyses of a dPMC seed. RSFC and MACM revealed similar connectivity maps spanning prefrontal, premotor, and parietal regions, while the SC map identified more widespread frontal regions. Analyses indicated a relatively consistent pattern of functional connectivity between RSFC and MACM that was distinct from that identified by SC. Notably, results indicate that the seed is functionally connected to areas involved in visuomotor control and executive functions, suggesting that the dPMC acts as an interface between motor control and cognition. Copyright © 2015 Elsevier Inc. All rights reserved.
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NASA Astrophysics Data System (ADS)
Li, Yan; Tan, Ou; Huang, David
2011-03-01
The detection of early-stage keratoconus is one of the most important safety issues in screening candidates for corneal refractive surgeries. We propose to use epithelial thickness maps to assist the diagnosis of keratoconus. The corneal epithelial thickness in normal and keratoconic eyes was mapped with optical coherence tomography (OCT). A Fourier-domain OCT system capable of acquiring 26,000 axial-scans per second was used. It has an axial resolution of 5μm in cornea. A pachymetry scan pattern (8 radials, 1024 axial-scans each, 6mm diameter, repeat 3 times) centered at the pupil center was used to image the cornea. The 3 repeated radial scans on each meridian were registered and averaged. Then the anterior corneal, posterior corneal and epithelial boundaries were segmented automatically with a computer algorithm by increased signal intensity at corresponding boundaries. The epithelial thickness map was generated by interpolating epithelial thickness profile calculated from each meridian. Normal and keratoconic eyes (24 eyes each) were scanned 3 times. The central epithelial thickness in normal eyes was thicker than those of keratoconic eyes (mean difference 2.1 μm, t-test p=0.05). The epithelium was thinner superiorly than inferiorly in normal eyes (mean difference -1.4+/-1.1μm, p<0.001) while thicker superiorly than inferiorly in keratoconic eyes (2.0+/-4.1 μm, p=0.02).
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Yao, Y; Nguyen, T D; Pandya, S; Zhang, Y; Hurtado Rúa, S; Kovanlikaya, I; Kuceyeski, A; Liu, Z; Wang, Y; Gauthier, S A
2018-02-01
A hyperintense rim on susceptibility in chronic MS lesions is consistent with iron deposition, and the purpose of this study was to quantify iron-related myelin damage within these lesions as compared with those without rim. Forty-six patients had 2 longitudinal quantitative susceptibility mapping with automatic zero reference scans with a mean interval of 28.9 ± 11.4 months. Myelin water fraction mapping by using fast acquisition with spiral trajectory and T2 prep was obtained at the second time point to measure myelin damage. Mixed-effects models were used to assess lesion quantitative susceptibility mapping and myelin water fraction values. Quantitative susceptibility mapping scans were on average 6.8 parts per billion higher in 116 rim-positive lesions compared with 441 rim-negative lesions ( P < .001). All rim-positive lesions retained a hyperintense rim over time, with increasing quantitative susceptibility mapping values of both the rim and core regions ( P < .001). Quantitative susceptibility mapping scans and myelin water fraction in rim-positive lesions decreased from rim to core, which is consistent with rim iron deposition. Whole lesion myelin water fractions for rim-positive and rim-negative lesions were 0.055 ± 0.07 and 0.066 ± 0.04, respectively. In the mixed-effects model, rim-positive lesions had on average 0.01 lower myelin water fraction compared with rim-negative lesions ( P < .001). The volume of the rim at the initial quantitative susceptibility mapping scan was negatively associated with follow-up myelin water fraction ( P < .01). Quantitative susceptibility mapping rim-positive lesions maintained a hyperintense rim, increased in susceptibility, and had more myelin damage compared with rim-negative lesions. Our results are consistent with the identification of chronic active MS lesions and may provide a target for therapeutic interventions to reduce myelin damage. © 2018 by American Journal of Neuroradiology.
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How Secure Is Your Radiology Department? Mapping Digital Radiology Adoption and Security Worldwide.
Stites, Mark; Pianykh, Oleg S
2016-04-01
Despite the long history of digital radiology, one of its most critical aspects--information security--still remains extremely underdeveloped and poorly standardized. To study the current state of radiology security, we explored the worldwide security of medical image archives. Using the DICOM data-transmitting standard, we implemented a highly parallel application to scan the entire World Wide Web of networked computers and devices, locating open and unprotected radiology servers. We used only legal and radiology-compliant tools. Our security-probing application initiated a standard DICOM handshake to remote computer or device addresses, and then assessed their security posture on the basis of handshake replies. The scan discovered a total of 2774 unprotected radiology or DICOM servers worldwide. Of those, 719 were fully open to patient data communications. Geolocation was used to analyze and rank our findings according to country utilization. As a result, we built maps and world ranking of clinical security, suggesting that even the most radiology-advanced countries have hospitals with serious security gaps. Despite more than two decades of active development and implementation, our radiology data still remains insecure. The results provided should be applied to raise awareness and begin an earnest dialogue toward elimination of the problem. The application we designed and the novel scanning approach we developed can be used to identify security breaches and to eliminate them before they are compromised.
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Ultrasonic thickness measuring and imaging system and method
Bylenok, Paul J.; Patmos, William M.; Wagner, Thomas A.; Martin, Francis H.
1992-08-04
An ultrasonic thickness measuring and imaging system uses an ultrasonic fsed beam probe for measuring thickness of an object, such as a wall of a tube, a computer for controlling movement of the probe in a scanning pattern within the tube and processing an analog signal produced by the probe which is proportional to the tube wall thickness in the scanning pattern, and a line scan recorder for producing a record of the tube wall thicknesses measured by the probe in the scanning pattern. The probe is moved in the scanning pattern to sequentially scan circumferentially the interior tube wall at spaced apart adjacent axial locations. The computer processes the analog signal by converting it to a digital signal and then quantifies the digital signal into a multiplicity of thickness points with each falling in one of a plurality of thickness ranges corresponding to one of a plurality of shades of grey. From the multiplicity of quantified thickness points, a line scan recorder connected to the computer generates a pictorial map of tube wall thicknesses with each quantified thickness point thus being obtained from a minute area, e.g. 0.010 inch by 0.010 inch, of tube wall and representing one pixel of the pictorial map. In the pictorial map of tube wall thicknesses, the pixels represent different wall thicknesses having different shades of grey.
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Ultrasonic thickness measuring and imaging system and method
Bylenok, Paul J.; Patmos, William M.; Wagner, Thomas A.; Martin, Francis H.
1992-01-01
An ultrasonic thickness measuring and imaging system uses an ultrasonic fsed beam probe for measuring thickness of an object, such as a wall of a tube, a computer for controlling movement of the probe in a scanning pattern within the tube and processing an analog signal produced by the probe which is proportional to the tube wall thickness in the scanning pattern, and a line scan recorder for producing a record of the tube wall thicknesses measured by the probe in the scanning pattern. The probe is moved in the scanning pattern to sequentially scan circumferentially the interior tube wall at spaced apart adjacent axial locations. The computer processes the analog signal by converting it to a digital signal and then quantifies the digital signal into a multiplicity of thickness points with each falling in one of a plurality of thickness ranges corresponding to one of a plurality of shades of grey. From the multiplicity of quantified thickness points, a line scan recorder connected to the computer generates a pictorial map of tube wall thicknesses with each quantified thickness point thus being obtained from a minute area, e.g. 0.010 inch by 0.010 inch, of tube wall and representing one pixel of the pictorial map. In the pictorial map of tube wall thicknesses, the pixels represent different wall thicknesses having different shades of grey.
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Rybicki, Benjamin A.; Levin, Albert M.; McKeigue, Paul; Datta, Indrani; Gray-McGuire, Courtney; Colombo, Marco; Reich, David; Burke, Robert R.; Iannuzzi, Michael C.
2010-01-01
Genome-wide linkage and association studies have uncovered variants associated with sarcoidosis, a multi-organ granulomatous inflammatory disease. African ancestry may influence disease pathogenesis since African Americans are more commonly affected by sarcoidosis. Therefore, we conducted the first sarcoidosis genome-wide ancestry scan using a map of 1,384 highly ancestry informative single nucleotide polymorphisms genotyped on 1,357 sarcoidosis cases and 703 unaffected controls self-identified as African American. The most significant ancestry association was at marker rs11966463 on chromosome 6p22.3 (ancestry association risk ratio (aRR)= 1.90; p=0.0002). When we restricted the analysis to biopsy-confirmed cases, the aRR for this marker increased to 2.01; p=0.00007. Among the eight other markers that demonstrated suggestive ancestry associations with sarcoidosis were rs1462906 on chromosome 8p12 which had the most significant association with European ancestry (aRR=0.65; p=0.002), and markers on chromosomes 5p13 (aRR=1.46; p=0.005) and 5q31 (aRR=0.67; p=0.005), which correspond to regions we previously identified through sib pair linkage analyses. Overall, the most significant ancestry association for Scadding stage IV cases was to marker rs7919137 on chromosome 10p11.22 (aRR=0.27; p=2×10−5), a region not associated with disease susceptibility. In summary, through admixture mapping of sarcoidosis we have confirmed previous genetic linkages and identified several novel putative candidate loci for sarcoidosis. PMID:21179114
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Direct mapping of local redox current density on a monolith electrode by laser scanning.
Lee, Seung-Woo; Lopez, Jeffrey; Saraf, Ravi F
2013-09-15
An optical method of mapping local redox reaction over a monolith electrode using simple laser scanning is described. As the optical signal is linearly proportional to the maximum redox current that is measured concomitantly by voltammetry, the optical signal quantitatively maps the local redox current density distribution. The method is demonstrated on two types of reactions: (1) a reversible reaction where the redox moieties are ionic, and (2) an irreversible reaction on two different types of enzymes immobilized on the electrode where the reaction moieties are nonionic. To demonstrate the scanning capability, the local redox behavior on a "V-shaped" electrode is studied where the local length scale and, hence, the local current density, is nonuniform. The ability to measure the current density distribution by this method will pave the way for multianalyte analysis on a monolith electrode using a standard three-electrode configuration. The method is called Scanning Electrometer for Electrical Double-layer (SEED). Copyright © 2013 Elsevier B.V. All rights reserved.
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Jing, Shengli; Zhang, Lei; Ma, Yinhua; Liu, Bingfang; Zhao, Yan; Yu, Hangjin; Zhou, Xi; Qin, Rui; Zhu, Lili; He, Guangcun
2014-01-01
Insects and plants have coexisted for over 350 million years and their interactions have affected ecosystems and agricultural practices worldwide. Variation in herbivorous insects' virulence to circumvent host resistance has been extensively documented. However, despite decades of investigation, the genetic foundations of virulence are currently unknown. The brown planthopper (Nilaparvata lugens) is the most destructive rice (Oryza sativa) pest in the world. The identification of the resistance gene Bph1 and its introduction in commercial rice varieties prompted the emergence of a new virulent brown planthopper biotype that was able to break the resistance conferred by Bph1. In this study, we aimed to construct a high density linkage map for the brown planthopper and identify the loci responsible for its virulence in order to determine their genetic architecture. Based on genotyping data for hundreds of molecular markers in three mapping populations, we constructed the most comprehensive linkage map available for this species, covering 96.6% of its genome. Fifteen chromosomes were anchored with 124 gene-specific markers. Using genome-wide scanning and interval mapping, the Qhp7 locus that governs preference for Bph1 plants was mapped to a 0.1 cM region of chromosome 7. In addition, two major QTLs that govern the rate of insect growth on resistant rice plants were identified on chromosomes 5 (Qgr5) and 14 (Qgr14). This is the first study to successfully locate virulence in the genome of this important agricultural insect by marker-based genetic mapping. Our results show that the virulence which overcomes the resistance conferred by Bph1 is controlled by a few major genes and that the components of virulence originate from independent genetic characters. The isolation of these loci will enable the elucidation of the molecular mechanisms underpinning the rice-brown planthopper interaction and facilitate the development of durable approaches for controlling this most destructive agricultural insect.
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Jing, Shengli; Zhang, Lei; Ma, Yinhua; Liu, Bingfang; Zhao, Yan; Yu, Hangjin; Zhou, Xi; Qin, Rui; Zhu, Lili; He, Guangcun
2014-01-01
Insects and plants have coexisted for over 350 million years and their interactions have affected ecosystems and agricultural practices worldwide. Variation in herbivorous insects' virulence to circumvent host resistance has been extensively documented. However, despite decades of investigation, the genetic foundations of virulence are currently unknown. The brown planthopper (Nilaparvata lugens) is the most destructive rice (Oryza sativa) pest in the world. The identification of the resistance gene Bph1 and its introduction in commercial rice varieties prompted the emergence of a new virulent brown planthopper biotype that was able to break the resistance conferred by Bph1. In this study, we aimed to construct a high density linkage map for the brown planthopper and identify the loci responsible for its virulence in order to determine their genetic architecture. Based on genotyping data for hundreds of molecular markers in three mapping populations, we constructed the most comprehensive linkage map available for this species, covering 96.6% of its genome. Fifteen chromosomes were anchored with 124 gene-specific markers. Using genome-wide scanning and interval mapping, the Qhp7 locus that governs preference for Bph1 plants was mapped to a 0.1 cM region of chromosome 7. In addition, two major QTLs that govern the rate of insect growth on resistant rice plants were identified on chromosomes 5 (Qgr5) and 14 (Qgr14). This is the first study to successfully locate virulence in the genome of this important agricultural insect by marker-based genetic mapping. Our results show that the virulence which overcomes the resistance conferred by Bph1 is controlled by a few major genes and that the components of virulence originate from independent genetic characters. The isolation of these loci will enable the elucidation of the molecular mechanisms underpinning the rice-brown planthopper interaction and facilitate the development of durable approaches for controlling this most destructive agricultural insect. PMID:24911169
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NASA Astrophysics Data System (ADS)
Rose, A.; McKee, J.; Weber, E.; Bhaduri, B. L.
2017-12-01
Leveraging decades of expertise in population modeling, and in response to growing demand for higher resolution population data, Oak Ridge National Laboratory is now generating LandScan HD at global scale. LandScan HD is conceived as a 90m resolution population distribution where modeling is tailored to the unique geography and data conditions of individual countries or regions by combining social, cultural, physiographic, and other information with novel geocomputation methods. Similarities among these areas are exploited in order to leverage existing training data and machine learning algorithms to rapidly scale development. Drawing on ORNL's unique set of capabilities, LandScan HD adapts highly mature population modeling methods developed for LandScan Global and LandScan USA, settlement mapping research and production in high-performance computing (HPC) environments, land use and neighborhood mapping through image segmentation, and facility-specific population density models. Adopting a flexible methodology to accommodate different geographic areas, LandScan HD accounts for the availability, completeness, and level of detail of relevant ancillary data. Beyond core population and mapped settlement inputs, these factors determine the model complexity for an area, requiring that for any given area, a data-driven model could support either a simple top-down approach, a more detailed bottom-up approach, or a hybrid approach.
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Validity and reliability of four language mapping paradigms.
Wilson, Stephen M; Bautista, Alexa; Yen, Melodie; Lauderdale, Stefanie; Eriksson, Dana K
2017-01-01
Language areas of the brain can be mapped in individual participants with functional MRI. We investigated the validity and reliability of four language mapping paradigms that may be appropriate for individuals with acquired aphasia: sentence completion, picture naming, naturalistic comprehension, and narrative comprehension. Five neurologically normal older adults were scanned on each of the four paradigms on four separate occasions. Validity was assessed in terms of whether activation patterns reflected the known typical organization of language regions, that is, lateralization to the left hemisphere, and involvement of the left inferior frontal gyrus and the left middle and/or superior temporal gyri. Reliability (test-retest reproducibility) was quantified in terms of the Dice coefficient of similarity, which measures overlap of activations across time points. We explored the impact of different absolute and relative voxelwise thresholds, a range of cluster size cutoffs, and limitation of analyses to a priori potential language regions. We found that the narrative comprehension and sentence completion paradigms offered the best balance of validity and reliability. However, even with optimal combinations of analysis parameters, there were many scans on which known features of typical language organization were not demonstrated, and test-retest reproducibility was only moderate for realistic parameter choices. These limitations in terms of validity and reliability may constitute significant limitations for many clinical or research applications that depend on identifying language regions in individual participants.
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Tang, Jian.; Chen, Yuwei.; Jaakkola, Anttoni.; Liu, Jinbing.; Hyyppä, Juha.; Hyyppä, Hannu.
2014-01-01
Laser scan matching with grid-based maps is a promising tool for real-time indoor positioning of mobile Unmanned Ground Vehicles (UGVs). While there are critical implementation problems, such as the ability to estimate the position by sensing the unknown indoor environment with sufficient accuracy and low enough latency for stable vehicle control, further development work is necessary. Unfortunately, most of the existing methods employ heuristics for quick positioning in which numerous accumulated errors easily lead to loss of positioning accuracy. This severely restricts its applications in large areas and over lengthy periods of time. This paper introduces an efficient real-time mobile UGV indoor positioning system for large-area applications using laser scan matching with an improved probabilistically-motivated Maximum Likelihood Estimation (IMLE) algorithm, which is based on a multi-resolution patch-divided grid likelihood map. Compared with traditional methods, the improvements embodied in IMLE include: (a) Iterative Closed Point (ICP) preprocessing, which adaptively decreases the search scope; (b) a totally brute search matching method on multi-resolution map layers, based on the likelihood value between current laser scan and the grid map within refined search scope, adopted to obtain the global optimum position at each scan matching; and (c) a patch-divided likelihood map supporting a large indoor area. A UGV platform called NAVIS was designed, manufactured, and tested based on a low-cost robot integrating a LiDAR and an odometer sensor to verify the IMLE algorithm. A series of experiments based on simulated data and field tests with NAVIS proved that the proposed IMEL algorithm is a better way to perform local scan matching that can offer a quick and stable positioning solution with high accuracy so it can be part of a large area localization/mapping, application. The NAVIS platform can reach an updating rate of 12 Hz in a feature-rich environment and 2 Hz even in a feature-poor environment, respectively. Therefore, it can be utilized in a real-time application. PMID:24999715
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Tang, Jian; Chen, Yuwei; Jaakkola, Anttoni; Liu, Jinbing; Hyyppä, Juha; Hyyppä, Hannu
2014-07-04
Laser scan matching with grid-based maps is a promising tool for real-time indoor positioning of mobile Unmanned Ground Vehicles (UGVs). While there are critical implementation problems, such as the ability to estimate the position by sensing the unknown indoor environment with sufficient accuracy and low enough latency for stable vehicle control, further development work is necessary. Unfortunately, most of the existing methods employ heuristics for quick positioning in which numerous accumulated errors easily lead to loss of positioning accuracy. This severely restricts its applications in large areas and over lengthy periods of time. This paper introduces an efficient real-time mobile UGV indoor positioning system for large-area applications using laser scan matching with an improved probabilistically-motivated Maximum Likelihood Estimation (IMLE) algorithm, which is based on a multi-resolution patch-divided grid likelihood map. Compared with traditional methods, the improvements embodied in IMLE include: (a) Iterative Closed Point (ICP) preprocessing, which adaptively decreases the search scope; (b) a totally brute search matching method on multi-resolution map layers, based on the likelihood value between current laser scan and the grid map within refined search scope, adopted to obtain the global optimum position at each scan matching; and (c) a patch-divided likelihood map supporting a large indoor area. A UGV platform called NAVIS was designed, manufactured, and tested based on a low-cost robot integrating a LiDAR and an odometer sensor to verify the IMLE algorithm. A series of experiments based on simulated data and field tests with NAVIS proved that the proposed IMEL algorithm is a better way to perform local scan matching that can offer a quick and stable positioning solution with high accuracy so it can be part of a large area localization/mapping, application. The NAVIS platform can reach an updating rate of 12 Hz in a feature-rich environment and 2 Hz even in a feature-poor environment, respectively. Therefore, it can be utilized in a real-time application.
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Jeong, Jong Seok; Mkhoyan, K Andre
2016-06-01
Acquiring an atomic-resolution compositional map of crystalline specimens has become routine practice, thus opening possibilities for extracting subatomic information from such maps. A key challenge for achieving subatomic precision is the improvement of signal-to-noise ratio (SNR) of compositional maps. Here, we report a simple and reliable solution for achieving high-SNR energy-dispersive X-ray (EDX) spectroscopy spectrum images for individual atomic columns. The method is based on standard cross-correlation aided by averaging of single-column EDX maps with modifications in the reference image. It produces EDX maps with minimal specimen drift, beam drift, and scan distortions. Step-by-step procedures to determine a self-consistent reference map with a discussion on the reliability, stability, and limitations of the method are presented here.
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Mapping QTL influencing gastrointestinal nematode burden in Dutch Holstein-Friesian dairy cattle
Coppieters, Wouter; Mes, Ted HM; Druet, Tom; Farnir, Frédéric; Tamma, Nico; Schrooten, Chris; Cornelissen, Albert WCA; Georges, Michel; Ploeger, Harm W
2009-01-01
Background Parasitic gastroenteritis caused by nematodes is only second to mastitis in terms of health costs to dairy farmers in developed countries. Sustainable control strategies complementing anthelmintics are desired, including selective breeding for enhanced resistance. Results and Conclusion To quantify and characterize the genetic contribution to variation in resistance to gastro-intestinal parasites, we measured the heritability of faecal egg and larval counts in the Dutch Holstein-Friesian dairy cattle population. The heritability of faecal egg counts ranged from 7 to 21% and was generally higher than for larval counts. We performed a whole genome scan in 12 paternal half-daughter groups for a total of 768 cows, corresponding to the ~10% most and least infected daughters within each family (selective genotyping). Two genome-wide significant QTL were identified in an across-family analysis, respectively on chromosomes 9 and 19, coinciding with previous findings in orthologous chromosomal regions in sheep. We identified six more suggestive QTL by within-family analysis. An additional 73 informative SNPs were genotyped on chromosome 19 and the ensuing high density map used in a variance component approach to simultaneously exploit linkage and linkage disequilibrium in an initial inconclusive attempt to refine the QTL map position. PMID:19254385
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[Application Progress of Three-dimensional Laser Scanning Technology in Medical Surface Mapping].
Zhang, Yonghong; Hou, He; Han, Yuchuan; Wang, Ning; Zhang, Ying; Zhu, Xianfeng; Wang, Mingshi
2016-04-01
The booming three-dimensional laser scanning technology can efficiently and effectively get spatial three-dimensional coordinates of the detected object surface and reconstruct the image at high speed,high precision and large capacity of information.Non-radiation,non-contact and the ability of visualization make it increasingly popular in three-dimensional surface medical mapping.This paper reviews the applications and developments of three-dimensional laser scanning technology in medical field,especially in stomatology,plastic surgery and orthopedics.Furthermore,the paper also discusses the application prospects in the future as well as the biomedical engineering problems it would encounter with.
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Cracking the genomic piggy bank: identifying secrets of the pig genome.
Mote, B E; Rothschild, M F
2006-01-01
Though researchers are uncovering valuable information about the pig genome at unprecedented speed, the porcine genome community is barely scratching the surface as to understanding interactions of the biological code. The pig genetic linkage map has nearly 5,000 loci comprised of genes, microsatellites, and amplified fragment length polymorphism markers. Likewise, the physical map is becoming denser with nearly 6,000 markers. The long awaited sequencing efforts are providing multidimensional benefits with sequence available for comparative genomics and identifying single nucleotide polymorphisms for use in linkage and trait association studies. Scientists are using exotic and commercial breeds for quantitative trait loci scans. Additionally, candidate gene studies continue to identify chromosomal regions or genes associated with economically important traits such as growth rate, leanness, feed intake, meat quality, litter size, and disease resistance. The commercial pig industry is actively incorporating these markers in marker-assisted selection along with traditional performance information to improve said traits. Researchers are utilizing novel tools including pig microarrays along with advanced bioinformatics to identify new candidate genes, understand gene function, and piece together gene networks involved in important biological processes. Advances in pig genomics and implications to the pork industry as well as human health are reviewed.
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Gold Nanoparticle Quantitation by Whole Cell Tomography.
Sanders, Aric W; Jeerage, Kavita M; Schwartz, Cindi L; Curtin, Alexandra E; Chiaramonti, Ann N
2015-12-22
Many proposed biomedical applications for engineered gold nanoparticles require their incorporation by mammalian cells in specific numbers and locations. Here, the number of gold nanoparticles inside of individual mammalian stem cells was characterized using fast focused ion beam-scanning electron microscopy based tomography. Enhanced optical microscopy was used to provide a multiscale map of the in vitro sample, which allows cells of interest to be identified within their local environment. Cells were then serially sectioned using a gallium ion beam and imaged using a scanning electron beam. To confirm the accuracy of single cross sections, nanoparticles in similar cross sections were imaged using transmission electron microscopy and scanning helium ion microscopy. Complete tomographic series were then used to count the nanoparticles inside of each cell and measure their spatial distribution. We investigated the influence of slice thickness on counting single particles and clusters as well as nanoparticle packing within clusters. For 60 nm citrate stabilized particles, the nanoparticle cluster packing volume is 2.15 ± 0.20 times the volume of the bare gold nanoparticles.
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Age of the Scan Basin (Scotia Sea)
NASA Astrophysics Data System (ADS)
Schreider, Al. A.; Schreider, A. A.; Galindo-Zaldivar, J.; Maldonado, A.; Sazhneva, A. E.; Evsenko, E. I.
2017-03-01
Integrated geological and geophysical analysis of the anomalous magnetic field along with the previously unpublished profiles of Spanish expeditions onboard the R/V Hesperides and international databases of geomagnetic data processed in the context of the global tectonics concepts made it possible to identify paleomagnetic anomalies C11-C15 and compile the first map of the bottom geochronology of the Scan Basin. Unlike in earlier known publications, the paleoaxis of spreading does extend northeast, but approximately at an angle of 345°. According to calculations, spreading began 35.294‒35.706 Ma ago during chron C15r, and the spreading paleoaxis was abandoned 29.527‒29.970 Ma ago during chron C11n.2n. Thus, the destruction of the American-Antarctic bridge in the region joining the Bruce and Discovery banks with formation of oceanic crust in the Scan Basin started about 36 Ma ago. Regular spreading of the bottom has been continuing for about 6 Ma at a average rate close to 1.8 cm/year.
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Zhang, Kui; Wiener, Howard; Beasley, Mark; George, Varghese; Amos, Christopher I; Allison, David B
2006-08-01
Individual genome scans for quantitative trait loci (QTL) mapping often suffer from low statistical power and imprecise estimates of QTL location and effect. This lack of precision yields large confidence intervals for QTL location, which are problematic for subsequent fine mapping and positional cloning. In prioritizing areas for follow-up after an initial genome scan and in evaluating the credibility of apparent linkage signals, investigators typically examine the results of other genome scans of the same phenotype and informally update their beliefs about which linkage signals in their scan most merit confidence and follow-up via a subjective-intuitive integration approach. A method that acknowledges the wisdom of this general paradigm but formally borrows information from other scans to increase confidence in objectivity would be a benefit. We developed an empirical Bayes analytic method to integrate information from multiple genome scans. The linkage statistic obtained from a single genome scan study is updated by incorporating statistics from other genome scans as prior information. This technique does not require that all studies have an identical marker map or a common estimated QTL effect. The updated linkage statistic can then be used for the estimation of QTL location and effect. We evaluate the performance of our method by using extensive simulations based on actual marker spacing and allele frequencies from available data. Results indicate that the empirical Bayes method can account for between-study heterogeneity, estimate the QTL location and effect more precisely, and provide narrower confidence intervals than results from any single individual study. We also compared the empirical Bayes method with a method originally developed for meta-analysis (a closely related but distinct purpose). In the face of marked heterogeneity among studies, the empirical Bayes method outperforms the comparator.
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Longitudinal stability of MRI for mapping brain change using tensor-based morphometry.
Leow, Alex D; Klunder, Andrea D; Jack, Clifford R; Toga, Arthur W; Dale, Anders M; Bernstein, Matt A; Britson, Paula J; Gunter, Jeffrey L; Ward, Chadwick P; Whitwell, Jennifer L; Borowski, Bret J; Fleisher, Adam S; Fox, Nick C; Harvey, Danielle; Kornak, John; Schuff, Norbert; Studholme, Colin; Alexander, Gene E; Weiner, Michael W; Thompson, Paul M
2006-06-01
Measures of brain change can be computed from sequential MRI scans, providing valuable information on disease progression, e.g., for patient monitoring and drug trials. Tensor-based morphometry (TBM) creates maps of these brain changes, visualizing the 3D profile and rates of tissue growth or atrophy, but its sensitivity depends on the contrast and geometric stability of the images. As part of the Alzheimer's Disease Neuroimaging Initiative (ADNI), 17 normal elderly subjects were scanned twice (at a 2-week interval) with several 3D 1.5 T MRI pulse sequences: high and low flip angle SPGR/FLASH (from which Synthetic T1 images were generated), MP-RAGE, IR-SPGR (N = 10) and MEDIC (N = 7) scans. For each subject and scan type, a 3D deformation map aligned baseline and follow-up scans, computed with a nonlinear, inverse-consistent elastic registration algorithm. Voxelwise statistics, in ICBM stereotaxic space, visualized the profile of mean absolute change and its cross-subject variance; these maps were then compared using permutation testing. Image stability depended on: (1) the pulse sequence; (2) the transmit/receive coil type (birdcage versus phased array); (3) spatial distortion corrections (using MEDIC sequence information); (4) B1-field intensity inhomogeneity correction (using N3). SPGR/FLASH images acquired using a birdcage coil had least overall deviation. N3 correction reduced coil type and pulse sequence differences and improved scan reproducibility, except for Synthetic T1 images (which were intrinsically corrected for B1-inhomogeneity). No strong evidence favored B0 correction. Although SPGR/FLASH images showed least deviation here, pulse sequence selection for the ADNI project was based on multiple additional image analyses, to be reported elsewhere.
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Longitudinal stability of MRI for mapping brain change using tensor-based morphometry
Leow, Alex D.; Klunder, Andrea D.; Jack, Clifford R.; Toga, Arthur W.; Dale, Anders M.; Bernstein, Matt A.; Britson, Paula J.; Gunter, Jeffrey L.; Ward, Chadwick P.; Whitwell, Jennifer L.; Borowski, Bret J.; Fleisher, Adam S.; Fox, Nick C.; Harvey, Danielle; Kornak, John; Schuff, Norbert; Studholme, Colin; Alexander, Gene E.; Weiner, Michael W.; Thompson, Paul M.
2007-01-01
Measures of brain change can be computed from sequential MRI scans, providing valuable information on disease progression, e.g., for patient monitoring and drug trials. Tensor-based morphometry (TBM) creates maps of these brain changes, visualizing the 3D profile and rates of tissue growth or atrophy, but its sensitivity depends on the contrast and geometric stability of the images. A s part of the Alzheimer’s Disease Neuroimaging Initiative (ADNI), 17 normal elderly subjects were scanned twice (at a 2-week interval) with several 3D 1.5 T MRI pulse sequences: high and low flip angle SPGR/FLASH (from which Synthetic T1 images were generated), MP-RAGE, IR-SPGR (N = 10) and MEDIC (N = 7) scans. For each subject and scan type, a 3D deformation map aligned baseline and follow-up scans, computed with a nonlinear, inverse-consistent elastic registration algorithm. Voxelwise statistics, in ICBM stereotaxic space, visualized the profile of mean absolute change and its cross-subject variance; these maps were then compared using permutation testing. Image stability depended on: (1) the pulse sequence; (2) the transmit/receive coil type (birdcage versus phased array); (3) spatial distortion corrections (using MEDIC sequence information); (4) B1-field intensity inhomogeneity correction (using N3). SPGR/FLASH images acquired using a birdcage coil had least overall deviation. N3 correction reduced coil type and pulse sequence differences and improved scan reproducibility, except for Synthetic T1 images (which were intrinsically corrected for B1-inhomogeneity). No strong evidence favored B0 correction. Although SPGR/FLASH images showed least deviation here, pulse sequence selection for the ADNI project was based on multiple additional image analyses, to be reported elsewhere. PMID:16480900
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Wu, Mon-Ju; Mwangi, Benson; Bauer, Isabelle E; Passos, Ives C; Sanches, Marsal; Zunta-Soares, Giovana B; Meyer, Thomas D; Hasan, Khader M; Soares, Jair C
2017-01-15
Diagnosis, clinical management and research of psychiatric disorders remain subjective - largely guided by historically developed categories which may not effectively capture underlying pathophysiological mechanisms of dysfunction. Here, we report a novel approach of identifying and validating distinct and biologically meaningful clinical phenotypes of bipolar disorders using both unsupervised and supervised machine learning techniques. First, neurocognitive data were analyzed using an unsupervised machine learning approach and two distinct clinical phenotypes identified namely; phenotype I and phenotype II. Second, diffusion weighted imaging scans were pre-processed using the tract-based spatial statistics (TBSS) method and 'skeletonized' white matter fractional anisotropy (FA) and mean diffusivity (MD) maps extracted. The 'skeletonized' white matter FA and MD maps were entered into the Elastic Net machine learning algorithm to distinguish individual subjects' phenotypic labels (e.g. phenotype I vs. phenotype II). This calculation was performed to ascertain whether the identified clinical phenotypes were biologically distinct. Original neurocognitive measurements distinguished individual subjects' phenotypic labels with 94% accuracy (sensitivity=92%, specificity=97%). TBSS derived FA and MD measurements predicted individual subjects' phenotypic labels with 76% and 65% accuracy respectively. In addition, individual subjects belonging to phenotypes I and II were distinguished from healthy controls with 57% and 92% accuracy respectively. Neurocognitive task variables identified as most relevant in distinguishing phenotypic labels included; Affective Go/No-Go (AGN), Cambridge Gambling Task (CGT) coupled with inferior fronto-occipital fasciculus and callosal white matter pathways. These results suggest that there may exist two biologically distinct clinical phenotypes in bipolar disorders which can be identified from healthy controls with high accuracy and at an individual subject level. We suggest a strong clinical utility of the proposed approach in defining and validating biologically meaningful and less heterogeneous clinical sub-phenotypes of major psychiatric disorders. Copyright © 2016 Elsevier Inc. All rights reserved.
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Onuki, Ritsuko; Yamaguchi, Rui; Shibuya, Tetsuo; Kanehisa, Minoru; Goto, Susumu
2017-01-01
Genome-wide scans for positive selection have become important for genomic medicine, and many studies aim to find genomic regions affected by positive selection that are associated with risk allele variations among populations. Most such studies are designed to detect recent positive selection. However, we hypothesize that ancient positive selection is also important for adaptation to pathogens, and has affected current immune-mediated common diseases. Based on this hypothesis, we developed a novel linkage disequilibrium-based pipeline, which aims to detect regions associated with ancient positive selection across populations from single nucleotide polymorphism (SNP) data. By applying this pipeline to the genotypes in the International HapMap project database, we show that genes in the detected regions are enriched in pathways related to the immune system and infectious diseases. The detected regions also contain SNPs reported to be associated with cancers and metabolic diseases, obesity-related traits, type 2 diabetes, and allergic sensitization. These SNPs were further mapped to biological pathways to determine the associations between phenotypes and molecular functions. Assessments of candidate regions to identify functions associated with variations in incidence rates of these diseases are needed in the future. PMID:28445522
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Wig, Gagan S; Laumann, Timothy O; Cohen, Alexander L; Power, Jonathan D; Nelson, Steven M; Glasser, Matthew F; Miezin, Francis M; Snyder, Abraham Z; Schlaggar, Bradley L; Petersen, Steven E
2014-08-01
We describe methods for parcellating an individual subject's cortical and subcortical brain structures using resting-state functional correlations (RSFCs). Inspired by approaches from social network analysis, we first describe the application of snowball sampling on RSFC data (RSFC-Snowballing) to identify the centers of cortical areas, subdivisions of subcortical nuclei, and the cerebellum. RSFC-Snowballing parcellation is then compared with parcellation derived from identifying locations where RSFC maps exhibit abrupt transitions (RSFC-Boundary Mapping). RSFC-Snowballing and RSFC-Boundary Mapping largely complement one another, but also provide unique parcellation information; together, the methods identify independent entities with distinct functional correlations across many cortical and subcortical locations in the brain. RSFC parcellation is relatively reliable within a subject scanned across multiple days, and while the locations of many area centers and boundaries appear to exhibit considerable overlap across subjects, there is also cross-subject variability-reinforcing the motivation to parcellate brains at the level of individuals. Finally, examination of a large meta-analysis of task-evoked functional magnetic resonance imaging data reveals that area centers defined by task-evoked activity exhibit correspondence with area centers defined by RSFC-Snowballing. This observation provides important evidence for the ability of RSFC to parcellate broad expanses of an individual's brain into functionally meaningful units. © The Author 2013. Published by Oxford University Press.
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King County Nearshore Habitat Mapping Data Report: Picnic Point to Shilshole Bay Marina
DOE Office of Scientific and Technical Information (OSTI.GOV)
Woodruff, Dana L.; Farley, Paul J.; Borde, Amy B.
2000-12-31
The objective of this study is to provide accurate, georeferenced maps of benthic habitats to assist in the siting of a new wastewater treatment plant outfall and the assessment of habitats of endangered, threatened, and economically important species. The mapping was conducted in the fall of 1999 using two complementary techniques: side-scan sonar and underwater videography. Products derived from these techniques include geographic information system (GIS) compatible polygon data of substrate type and vegetation cover, including eelgrass and kelp. Additional GIS overlays include underwater video track line data of total macroalgae, selected macroalgal species, fish, and macroinvertebrates. The combined toolsmore » of geo-referenced side-scan sonar and underwater video is a powerful technique for assessing and mapping of nearshore habitat in Puget Sound. Side-scan sonar offers the ability to map eelgrass with high spatial accuracy and resolution, and provides information on patch size, shape, and coverage. It also provides information on substrate change and location of specific targets (e.g., piers, docks, pilings, large boulders, debris piles). The addition of underwater video is a complementary tool providing both groundtruthing for the sonar and additional information on macro fauna and flora. As a groundtruthing technique, the video was able to confirm differences between substrate types, as well as detect subtle spatial changes in substrate. It also verified information related to eelgrass, including the density classification categories and the type of substrate associated with eelgrass, which could not be determined easily with side- scan sonar. Video is also a powerful tool for mapping the location of macroalgae, (including kelp and Ulva), fish and macroinvertebrates. The ability to geo-locate these resources in their functional habitat provides an added layer of information and analytical potential.« less
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Haacke, Jon E.; Barclay, C. S. Venable; Hettinger, Robert D.
2016-09-30
In the 1970s and 1980s, C.S. Venable Barclay conducted geologic mapping of areas primarily underlain by Cretaceous coals in the eastern part of the Little Snake River coal field (LSR) in Carbon County, southwest Wyoming. With some exceptions, most of the mapping data were never published. Subsequently, after his retirement from the U.S. Geological Survey (USGS), his field maps and field notebooks were archived in the USGS Field Records. Due to a pending USGS coal assessment of the Little Snake River coal field area and planned geological mapping to be conducted by the Wyoming State Geological Survey, Barclay’s mapping data needed to be published to support these efforts. Subsequently, geologic maps were scanned and georeferenced into a geographic information system, and project and field notes were scanned into Portable Document Format (PDF) files. Data for seventeen 7½-minute quadrangles are presented in this report. This publication is solely intended to compile the mapping data as it was last worked on by Barclay and provides no interpretation or modification of his work.
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NASA Technical Reports Server (NTRS)
Mcmurtry, G. J.; Petersen, G. W. (Principal Investigator); Kowalik, W. S.
1975-01-01
The author has identified the following significant results. The histogram peaks of lineaments mapped from Skylab photograph at a scale of 1:517,000 lie subparallel, within 20 deg, to major shale joints and coal cleats on part of the Allegheny Plateau. The Landsat lineament, mapped at 1:989,000 are biased by illumination and scan line directions. While there is an illumination bias in the Skylab photograph, its direction does not coincide with the main transverse lineament trend, thus providing an independent assessment of the illumination direction bias. The coincidence in direction regardless of scale of the linear features suggests a mechanical relationship between joints, fracture traces, and lineaments which is more consistent with a tensional model than a shear model of origin.
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Eidenschenk, Celine; Dunne, Jean; Jouanguy, Emmanuelle; Fourlinnie, Claire; Gineau, Laure; Bacq, Delphine; McMahon, Corrina; Smith, Owen; Casanova, Jean-Laurent; Abel, Laurent; Feighery, Conleth
2006-04-01
We describe four children with a novel primary immunodeficiency consisting of specific natural-killer (NK) cell deficiency and susceptibility to viral diseases. One child developed an Epstein-Barr virus-driven lymphoproliferative disorder; two others developed severe respiratory illnesses of probable viral etiology. The four patients are related and belong to a large inbred kindred of Irish nomadic descent, which suggests autosomal recessive inheritance of this defect. A genomewide scan identified a single 12-Mb region on chromosome 8p11.23-q11.21 that was linked to this immunodeficiency (maximum LOD score 4.51). The mapping of the disease-causing genomic region paves the way for the identification of a novel pathway governing NK cell differentiation in humans.
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Eidenschenk, Céline; Dunne, Jean; Jouanguy, Emmanuelle; Fourlinnie, Claire; Gineau, Laure; Bacq, Delphine; McMahon, Corrina; Smith, Owen; Casanova, Jean-Laurent; Abel, Laurent; Feighery, Conleth
2006-01-01
We describe four children with a novel primary immunodeficiency consisting of specific natural-killer (NK) cell deficiency and susceptibility to viral diseases. One child developed an Epstein-Barr virus–driven lymphoproliferative disorder; two others developed severe respiratory illnesses of probable viral etiology. The four patients are related and belong to a large inbred kindred of Irish nomadic descent, which suggests autosomal recessive inheritance of this defect. A genomewide scan identified a single 12-Mb region on chromosome 8p11.23-q11.21 that was linked to this immunodeficiency (maximum LOD score 4.51). The mapping of the disease-causing genomic region paves the way for the identification of a novel pathway governing NK cell differentiation in humans. PMID:16532402
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NASA Astrophysics Data System (ADS)
Chiariotti, P.; Martarelli, M.; Revel, G. M.
2017-12-01
A novel non-destructive testing procedure for delamination detection based on the exploitation of the simultaneous time and spatial sampling provided by Continuous Scanning Laser Doppler Vibrometry (CSLDV) and the feature extraction capability of Multi-Level wavelet-based processing is presented in this paper. The processing procedure consists in a multi-step approach. Once the optimal mother-wavelet is selected as the one maximizing the Energy to Shannon Entropy Ratio criterion among the mother-wavelet space, a pruning operation aiming at identifying the best combination of nodes inside the full-binary tree given by Wavelet Packet Decomposition (WPD) is performed. The pruning algorithm exploits, in double step way, a measure of the randomness of the point pattern distribution on the damage map space with an analysis of the energy concentration of the wavelet coefficients on those nodes provided by the first pruning operation. A combination of the point pattern distributions provided by each node of the ensemble node set from the pruning algorithm allows for setting a Damage Reliability Index associated to the final damage map. The effectiveness of the whole approach is proven on both simulated and real test cases. A sensitivity analysis related to the influence of noise on the CSLDV signal provided to the algorithm is also discussed, showing that the processing developed is robust enough to measurement noise. The method is promising: damages are well identified on different materials and for different damage-structure varieties.
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Exploring the Nuclear Phase Diagram with Beam Energy Scans
NASA Astrophysics Data System (ADS)
Horvat, Stephen
2017-04-01
The nuclear phase diagram is mapped using beam energy scans of relativistic heavy-ion collisions. This mapping is possible because different collision energies develop along different trajectories through the phase diagram. High energy collisions will evolve though a crossover phase transition according to lattice QCD, but lower collision energies may traverse a first order phase transition. There are hints for this first order phase transition and its critical endpoint, but further measurements and theoretical guidance is needed. In addition to mapping the phase transition, beam energy scans allow us to see if we can turn off the signatures of deconfinement. If an observable is a real signature for the formation of the deconfined state called quark-gluon plasma, then it should turn off at sufficiently low collision energies. In this summary talk I will show the current state of the field using beam energy scan results from RHIC and SPS, I will show where precise theoretical guidance is needed for understanding recent measurements, and I will motivate the need for more data and new measurements from FAIR, NICA, RHIC, and the SPS.
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Choi, Kyongsik; Chon, James W; Gu, Min; Lee, Byoungho
2007-08-20
In this paper, a simple confocal laser scanning microscopic (CLSM) image mapping technique based on the finite-difference time domain (FDTD) calculation has been proposed and evaluated for characterization of a subwavelength-scale three-dimensional (3D) void structure fabricated inside polymer matrix. The FDTD simulation method adopts a focused Gaussian beam incident wave, Berenger's perfectly matched layer absorbing boundary condition, and the angular spectrum analysis method. Through the well matched simulation and experimental results of the xz-scanned 3D void structure, we first characterize the exact position and the topological shape factor of the subwavelength-scale void structure, which was fabricated by a tightly focused ultrashort pulse laser. The proposed CLSM image mapping technique based on the FDTD can be widely applied from the 3D near-field microscopic imaging, optical trapping, and evanescent wave phenomenon to the state-of-the-art bio- and nanophotonics.
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Long-range side scan sonar and geophysical survey of the Aleutian Basin
NASA Astrophysics Data System (ADS)
Carlson, P. R.; Cooper, , A. K.; Gardner, J. V.; Karl, H. A.; Marlow, M. S.; Stevenson, A. J.; Huggett, Q.; Kenyon, N. H.; Parson, L. M.
In 1983, President Ronald Reagan established the Exclusive Economic Zone, an area of 3.9 billion acres (˜1.6 billion hectares) that gives the United States exclusive rights to energy and mineral resources on and under the seafloor for a distance of 200 nautical miles (˜370 km) from its coastline and in its territorial seas [Rowland et al., 1983]. The U.S. Geological Survey established a program, EEZ-Scan, in spring 1984 to map this new undersea territory [Gardner, 1984; EEZ-Scan Group, 1985]. The results of the first field season of mapping the EEZ off the conterminous west coast of the United States have been published as an atlas [EEZ-Scan 84 Scientific Staff, 1986] that is the first volume of a series.
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Kook, Michael S; Cho, Hyun-soo; Seong, Mincheol; Choi, Jaewan
2005-11-01
To evaluate the ability of scanning laser polarimetry parameters and a novel deviation map algorithm to discriminate between healthy and early glaucomatous eyes with localized visual field (VF) defects confined to one hemifield. Prospective case-control study. Seventy glaucomatous eyes with localized VF defects and 66 normal controls. A Humphrey field analyzer 24-2 full-threshold test and scanning laser polarimetry with variable corneal compensation were used. We assessed the sensitivity and specificity of scanning laser polarimetry parameters, sensitivity and cutoff values for scanning laser polarimetry deviation map algorithms at different specificity values (80%, 90%, and 95%) in the detection of glaucoma, and correlations between the algorithms of scanning laser polarimetry and of the pattern deviation derived from Humphrey field analyzer testing. There were significant differences between the glaucoma group and normal subjects in the mean parametric values of the temporal, superior, nasal, inferior, temporal (TSNIT) average, superior average, inferior average, and TSNIT standard deviation (SD) (P<0.05). The sensitivity and specificity of each scanning laser polarimetry variable was as follows: TSNIT, 44.3% (95% confidence interval [CI], 39.8%-49.8%) and 100% (95.4%-100%); superior average, 30% (25.5%-34.5%) and 97% (93.5%-100%); inferior average, 45.7% (42.2%-49.2%) and 100% (95.8%-100%); and TSNIT SD, 30% (25.9%-34.1%) and 97% (93.2%-100%), respectively (when abnormal was defined as P<0.05). Based on nerve fiber indicator cutoff values of > or =30 and > or =51 to indicate glaucoma, sensitivities were 54.3% (50.1%-58.5%) and 10% (6.4%-13.6%), and specificities were 97% (93.2%-100%) and 100% (95.8%-100%), respectively. The range of areas under the receiver operating characteristic curves using the scanning laser polarimetry deviation map algorithm was 0.790 to 0.879. Overall sensitivities combining each probability scale and severity score at 80%, 90%, and 95% specificities were 90.0% (95% CI, 86.4%-93.6%), 71.4% (67.4%-75.4%), and 60.0% (56.2%-63.8%), respectively. There was a statistically significant correlation between the scanning laser polarimetry severity score and the VF severity score (R2 = 0.360, P<0.001). Scanning laser polarimetry parameters may not be sufficiently sensitive to detect glaucomatous patients with localized VF damage. Our algorithm using the scanning laser polarimetry deviation map may enhance the understanding of scanning laser polarimetry printouts in terms of the locality, deviation size, and severity of localized retinal nerve fiber layer defects in eyes with localized VF loss.
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Coolen, Bram F; Poot, Dirk H J; Liem, Madieke I; Smits, Loek P; Gao, Shan; Kotek, Gyula; Klein, Stefan; Nederveen, Aart J
2016-03-01
A novel three-dimensional (3D) T1 and T2 mapping protocol for the carotid artery is presented. A 3D black-blood imaging sequence was adapted allowing carotid T1 and T2 mapping using multiple flip angles and echo time (TE) preparation times. B1 mapping was performed to correct for spatially varying deviations from the nominal flip angle. The protocol was optimized using simulations and phantom experiments. In vivo scans were performed on six healthy volunteers in two sessions, and in a patient with advanced atherosclerosis. Compensation for patient motion was achieved by 3D registration of the inter/intrasession scans. Subsequently, T1 and T2 maps were obtained by maximum likelihood estimation. Simulations and phantom experiments showed that the bias in T1 and T2 estimation was < 10% within the range of physiological values. In vivo T1 and T2 values for carotid vessel wall were 844 ± 96 and 39 ± 5 ms, with good repeatability across scans. Patient data revealed altered T1 and T2 values in regions of atherosclerotic plaque. The 3D T1 and T2 mapping of the carotid artery is feasible using variable flip angle and variable TE preparation acquisitions. We foresee application of this technique for plaque characterization and monitoring plaque progression in atherosclerotic patients. © 2015 Wiley Periodicals, Inc.
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A Novel Real-Time Reference Key Frame Scan Matching Method.
Mohamed, Haytham; Moussa, Adel; Elhabiby, Mohamed; El-Sheimy, Naser; Sesay, Abu
2017-05-07
Unmanned aerial vehicles represent an effective technology for indoor search and rescue operations. Typically, most indoor missions' environments would be unknown, unstructured, and/or dynamic. Navigation of UAVs in such environments is addressed by simultaneous localization and mapping approach using either local or global approaches. Both approaches suffer from accumulated errors and high processing time due to the iterative nature of the scan matching method. Moreover, point-to-point scan matching is prone to outlier association processes. This paper proposes a low-cost novel method for 2D real-time scan matching based on a reference key frame (RKF). RKF is a hybrid scan matching technique comprised of feature-to-feature and point-to-point approaches. This algorithm aims at mitigating errors accumulation using the key frame technique, which is inspired from video streaming broadcast process. The algorithm depends on the iterative closest point algorithm during the lack of linear features which is typically exhibited in unstructured environments. The algorithm switches back to the RKF once linear features are detected. To validate and evaluate the algorithm, the mapping performance and time consumption are compared with various algorithms in static and dynamic environments. The performance of the algorithm exhibits promising navigational, mapping results and very short computational time, that indicates the potential use of the new algorithm with real-time systems.
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Raman and CT scan mapping of chalcogenide glass diffusion generated gradient index profiles
NASA Astrophysics Data System (ADS)
Lindberg, G. P.; Berg, R. H.; Deegan, J.; Benson, R.; Salvaggio, P. S.; Gross, N.; Weinstein, B. A.; Gibson, D.; Bayya, S.; Sanghera, J.; Nguyen, V.; Kotov, M.
2016-05-01
Metrology of a gradient index (GRIN) material is non-trivial, especially in the realm of infrared and large refractive index. Traditional methods rely on index matching fluids which are not available for indexes as high as those found in the chalcogenide glasses (2.4-3.2). By diffusing chalcogenide glasses of similar composition one can blend the properties in a continuous way. In an effort to measure this we will present data from both x-ray computed tomography scans (CT scans) and Raman mapping scans of the diffusion profiles. Proof of concept measurements on undiffused bonded sheets of chalcogenide glasses were presented previously. The profiles measured will be of axially stacked sheets of chalcogenide glasses diffused to create a linear GRIN profile and nested tubes of chalcogenide glasses diffused to create a radial parabolic GRIN profile. We will show that the x-ray absorption in the CT scan and the intensity of select Raman peaks spatially measured through the material are indicators of the concentration of the diffusion ions and correlate to the spatial change in refractive index. We will also present finite element modeling (FEM) results and compare them to post precision glass molded (PGM) elements that have undergone CT and Raman mapping.
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Occupancy Grid Map Merging Using Feature Maps
2010-11-01
each robot begins exploring at different starting points, once two robots can communicate, they send their odometry data, LIDAR observations, and maps...robots [11]. Moreover, it is relevant to mention that significant success has been achieved in solving SLAM problems when using hybrid maps [12...represents the environment by parametric features. Our method is capable of representing a LIDAR scanned environment map in a parametric fashion. In general
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A Locus for Autosomal Dominant Hereditary Spastic Ataxia, SAX1, Maps to Chromosome 12p13
Meijer, I. A.; Hand, C. K.; Grewal, K. K.; Stefanelli, M. G.; Ives, E. J.; Rouleau, G. A.
2002-01-01
The hereditary spastic ataxias (HSA) are a group of clinically heterogeneous neurodegenerative disorders characterized by lower-limb spasticity and generalized ataxia. HSA was diagnosed in three unrelated autosomal dominant families from Newfoundland, who presented mainly with severe leg spasticity, dysarthria, dysphagia, and ocular-movement abnormalities. A genomewide scan was performed on one family, and linkage to a novel locus for HSA on chromosome 12p13, which contains the as-yet-unidentified gene locus SAX1, was identified. Fine mapping confirmed linkage in the two large families, and the third, smaller family showed LOD scores suggestive of linkage. Haplotype construction by use of 13 polymorphic markers revealed that all three families share a disease haplotype, which key recombinants and overlapping haplotypes refine to ∼5 cM, flanked by markers D12S93 and GATA151H05. SAX1 is the first locus mapped for autosomal dominant HSA. PMID:11774073
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NASA Astrophysics Data System (ADS)
Karagiannis, Georgios Th.
2016-04-01
The development of non-destructive techniques is a reality in the field of conservation science. These techniques are usually not so accurate, as the analytical micro-sampling techniques, however, the proper development of soft-computing techniques can improve their accuracy. In this work, we propose a real-time fast acquisition spectroscopic mapping imaging system that operates from the ultraviolet to mid infrared (UV/Vis/nIR/mIR) area of the electromagnetic spectrum and it is supported by a set of soft-computing methods to identify the materials that exist in a stratigraphic structure of paint layers. Particularly, the system acquires spectra in diffuse-reflectance mode, scanning in a Region-Of-Interest (ROI), and having wavelength range from 200 up to 5000 nm. Also, a fuzzy c-means clustering algorithm, i.e., the particular soft-computing algorithm, produces the mapping images. The evaluation of the method was tested on a byzantine painted icon.
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NASA Astrophysics Data System (ADS)
Luo, Haibo; Teng, Jie; Chen, Shuang; Wang, Yu; Zhang, Hui
2017-10-01
Hot compression tests of 8009Al alloy reinforced with 15% SiC particles (8009Al/15%SiCp composites) prepared by powder metallurgy (direct hot extrusion methods) were performed on Gleeble-3500 system in the temperature range of 400-550 °C and strain rate range of 0.001-1 s-1. The processing map based on the dynamic material model was established to evaluate the flow instability regime and optimize processing parameters; the associated microstructural changes were studied by the observations of optical metallographic and scanning electron microscopy. The results showed that the flow stress increased initially and reached a plateau after peak stress value with increasing strain. The peak stress increased as the strain rate increased and deformation temperature decreased. The optimum parameters were identified to be deformation temperature range of 500-550 °C and strain rate range of 0.001-0.02 s-1 by combining the processing map with microstructural observation.
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Scanning Probe Platform | Materials Science | NREL
level; this image obtained using a scanning tunneling microscope shows gray and white clusters of produce high-resolution color images or maps like this one obtained using scanning tunneling luminescence gray clusters. Gold substrate: (Left) STM image reveals the terraces of the H2 flamed substrate. (Right
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Automatic concrete cracks detection and mapping of terrestrial laser scan data
NASA Astrophysics Data System (ADS)
Rabah, Mostafa; Elhattab, Ahmed; Fayad, Atef
2013-12-01
Terrestrial laser scanning has become one of the standard technologies for object acquisition in surveying engineering. The high spatial resolution of imaging and the excellent capability of measuring the 3D space by laser scanning bear a great potential if combined for both data acquisition and data compilation. Automatic crack detection from concrete surface images is very effective for nondestructive testing. The crack information can be used to decide the appropriate rehabilitation method to fix the cracked structures and prevent any catastrophic failure. In practice, cracks on concrete surfaces are traced manually for diagnosis. On the other hand, automatic crack detection is highly desirable for efficient and objective crack assessment. The current paper submits a method for automatic concrete cracks detection and mapping from the data that was obtained during laser scanning survey. The method of cracks detection and mapping is achieved by three steps, namely the step of shading correction in the original image, step of crack detection and finally step of crack mapping and processing steps. The detected crack is defined in a pixel coordinate system. To remap the crack into the referred coordinate system, a reverse engineering is used. This is achieved by a hybrid concept of terrestrial laser-scanner point clouds and the corresponding camera image, i.e. a conversion from the pixel coordinate system to the terrestrial laser-scanner or global coordinate system. The results of the experiment show that the mean differences between terrestrial laser scan and the total station are about 30.5, 16.4 and 14.3 mms in x, y and z direction, respectively.
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Scan Line Based Road Marking Extraction from Mobile LiDAR Point Clouds.
Yan, Li; Liu, Hua; Tan, Junxiang; Li, Zan; Xie, Hong; Chen, Changjun
2016-06-17
Mobile Mapping Technology (MMT) is one of the most important 3D spatial data acquisition technologies. The state-of-the-art mobile mapping systems, equipped with laser scanners and named Mobile LiDAR Scanning (MLS) systems, have been widely used in a variety of areas, especially in road mapping and road inventory. With the commercialization of Advanced Driving Assistance Systems (ADASs) and self-driving technology, there will be a great demand for lane-level detailed 3D maps, and MLS is the most promising technology to generate such lane-level detailed 3D maps. Road markings and road edges are necessary information in creating such lane-level detailed 3D maps. This paper proposes a scan line based method to extract road markings from mobile LiDAR point clouds in three steps: (1) preprocessing; (2) road points extraction; (3) road markings extraction and refinement. In preprocessing step, the isolated LiDAR points in the air are removed from the LiDAR point clouds and the point clouds are organized into scan lines. In the road points extraction step, seed road points are first extracted by Height Difference (HD) between trajectory data and road surface, then full road points are extracted from the point clouds by moving least squares line fitting. In the road markings extraction and refinement step, the intensity values of road points in a scan line are first smoothed by a dynamic window median filter to suppress intensity noises, then road markings are extracted by Edge Detection and Edge Constraint (EDEC) method, and the Fake Road Marking Points (FRMPs) are eliminated from the detected road markings by segment and dimensionality feature-based refinement. The performance of the proposed method is evaluated by three data samples and the experiment results indicate that road points are well extracted from MLS data and road markings are well extracted from road points by the applied method. A quantitative study shows that the proposed method achieves an average completeness, correctness, and F-measure of 0.96, 0.93, and 0.94, respectively. The time complexity analysis shows that the scan line based road markings extraction method proposed in this paper provides a promising alternative for offline road markings extraction from MLS data.
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Scan Line Based Road Marking Extraction from Mobile LiDAR Point Clouds†
Yan, Li; Liu, Hua; Tan, Junxiang; Li, Zan; Xie, Hong; Chen, Changjun
2016-01-01
Mobile Mapping Technology (MMT) is one of the most important 3D spatial data acquisition technologies. The state-of-the-art mobile mapping systems, equipped with laser scanners and named Mobile LiDAR Scanning (MLS) systems, have been widely used in a variety of areas, especially in road mapping and road inventory. With the commercialization of Advanced Driving Assistance Systems (ADASs) and self-driving technology, there will be a great demand for lane-level detailed 3D maps, and MLS is the most promising technology to generate such lane-level detailed 3D maps. Road markings and road edges are necessary information in creating such lane-level detailed 3D maps. This paper proposes a scan line based method to extract road markings from mobile LiDAR point clouds in three steps: (1) preprocessing; (2) road points extraction; (3) road markings extraction and refinement. In preprocessing step, the isolated LiDAR points in the air are removed from the LiDAR point clouds and the point clouds are organized into scan lines. In the road points extraction step, seed road points are first extracted by Height Difference (HD) between trajectory data and road surface, then full road points are extracted from the point clouds by moving least squares line fitting. In the road markings extraction and refinement step, the intensity values of road points in a scan line are first smoothed by a dynamic window median filter to suppress intensity noises, then road markings are extracted by Edge Detection and Edge Constraint (EDEC) method, and the Fake Road Marking Points (FRMPs) are eliminated from the detected road markings by segment and dimensionality feature-based refinement. The performance of the proposed method is evaluated by three data samples and the experiment results indicate that road points are well extracted from MLS data and road markings are well extracted from road points by the applied method. A quantitative study shows that the proposed method achieves an average completeness, correctness, and F-measure of 0.96, 0.93, and 0.94, respectively. The time complexity analysis shows that the scan line based road markings extraction method proposed in this paper provides a promising alternative for offline road markings extraction from MLS data. PMID:27322279
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Mosaic of Digital Raster Soviet Topographic Maps of Afghanistan
Chirico, Peter G.; Warner, Michael B.
2005-01-01
EXPLANATION The data contained in this publication include scanned, geographically referenced digital raster graphics (DRGs) of Soviet 1:200,000 - scale topographic map quadrangles. The original Afghanistan topographic map series at 1:200,000 scale, for the entire country, was published by the Soviet military between 1985 and 1991(MTDGS, 85-91). Hard copies of these original paper maps were scanned using a large format scanner, reprojected into Geographic Coordinate System (GCS) coordinates, and then clipped to remove the map collars to create a seamless, topographic map base for the entire country. An index of all available topographic map sheets is displayed here: Index_Geo_DD.pdf. This publication also includes the originial topographic map quadrangles projected in Universal Transverse Mercator (UTM) projection. The country of Afghanistan spans three UTM Zones: Zone 41, Zone 42, and Zone 43. Maps are stored as GeoTIFFs in their respective UTM zone projection. Indexes of all available topographic map sheets in their respective UTM zone are displayed here: Index_UTM_Z41.pdf, Index_UTM_Z42.pdf, Index_UTM_Z43.pdf. An Adobe Acrobat PDF file of the U.S. Department of the Army's Technical Manual 30-548, is available (U.S. Army, 1958). This document has been translated into English for assistance in reading Soviet topographic map symbols.
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Krenner, Wolfgang; Kühne, Dirk; Klappenberger, Florian; Barth, Johannes V.
2013-01-01
Scanning tunneling spectroscopy (STS) enables the local, energy-resolved investigation of a samples surface density of states (DOS) by measuring the differential conductance (dI/dV) being approximately proportional to the DOS. It is popular to examine the electronic structure of elementary samples by acquiring dI/dV maps under constant current conditions. Here we demonstrate the intricacy of STS mapping of samples exhibiting a strong corrugation originating from electronic density and local work function changes. The confinement of the Ag(111) surface state by a porous organic network is studied with maps obtained under constant-current (CC) as well as open-feedback-loop (OFL) conditions. We show how the CC maps deviate markedly from the physically more meaningful OFL maps. By applying a renormalization procedure to the OFL data we can mimic the spurious effects of the CC mode and thereby rationalize the physical effects evoking the artefacts in the CC maps. PMID:23503526
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NASA Astrophysics Data System (ADS)
Retscher, G.
2017-09-01
Positioning of mobile users in indoor environments with Wireless Fidelity (Wi-Fi) has become very popular whereby location fingerprinting and trilateration are the most commonly employed methods. In both the received signal strength (RSS) of the surrounding access points (APs) are scanned and used to estimate the user's position. Within the scope of this study the advantageous qualities of both methods are identified and selected to benefit their combination. By a fusion of these technologies a higher performance for Wi-Fi positioning is achievable. For that purpose, a novel approach based on the well-known Differential GPS (DGPS) principle of operation is developed and applied. This approach for user localization and tracking is termed Differential Wi-Fi (DWi-Fi) by analogy with DGPS. From reference stations deployed in the area of interest differential measurement corrections are derived and applied at the mobile user side. Hence, range or coordinate corrections can be estimated from a network of reference station observations as it is done in common CORS GNSS networks. A low-cost realization with Raspberry Pi units is employed for these reference stations. These units serve at the same time as APs broadcasting Wi-Fi signals as well as reference stations scanning the receivable Wi-Fi signals of the surrounding APs. As the RSS measurements are carried out continuously at the reference stations dynamically changing maps of RSS distributions, so-called radio maps, are derived. Similar as in location fingerprinting this radio maps represent the RSS fingerprints at certain locations. From the areal modelling of the correction parameters in combination with the dynamically updated radio maps the location of the user can be estimated in real-time. The novel approach is presented and its performance demonstrated in this paper.
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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.
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Investigations on the Bundle Adjustment Results from Sfm-Based Software for Mapping Purposes
NASA Astrophysics Data System (ADS)
Lumban-Gaol, Y. A.; Murtiyoso, A.; Nugroho, B. H.
2018-05-01
Since its first inception, aerial photography has been used for topographic mapping. Large-scale aerial photography contributed to the creation of many of the topographic maps around the world. In Indonesia, a 2013 government directive on spatial management has re-stressed the need for topographic maps, with aerial photogrammetry providing the main method of acquisition. However, the large need to generate such maps is often limited by budgetary reasons. Today, SfM (Structure-from-Motion) offers quicker and less expensive solutions to this problem. However, considering the required precision for topographic missions, these solutions need to be assessed to see if they provide enough level of accuracy. In this paper, a popular SfM-based software Agisoft PhotoScan is used to perform bundle adjustment on a set of large-scale aerial images. The aim of the paper is to compare its bundle adjustment results with those generated by more classical photogrammetric software, namely Trimble Inpho and ERDAS IMAGINE. Furthermore, in order to provide more bundle adjustment statistics to be compared, the Damped Bundle Adjustment Toolbox (DBAT) was also used to reprocess the PhotoScan project. Results show that PhotoScan results are less stable than those generated by the two photogrammetric software programmes. This translates to lower accuracy, which may impact the final photogrammetric product.
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Pulmonary ventilation/perfusion scan
... take a ventilation and perfusion scan and then evaluate it with a chest x-ray. All parts ... ADAM Health Solutions. About MedlinePlus Site Map FAQs Customer Support Get email updates Subscribe to RSS Follow ...
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Smith, C; Cunliffe, A; Al-Hallaq, H
Purpose: To determine the stability of eight first-order texture features following the deformable registration of serial computed tomography (CT) scans. Methods: CT scans at two different time points from 10 patients deemed to have no lung abnormalities by a radiologist were collected. Following lung segmentation using an in-house program, texture maps were calculated from 32×32-pixel regions of interest centered at every pixel in the lungs. The texture feature value of the ROI was assigned to the center pixel of the ROI in the corresponding location of the texture map. Pixels in the square ROI not contained within the segmented lungmore » were not included in the calculation. To quantify the agreement between ROI texture features in corresponding pixels of the baseline and follow-up texture maps, the Fraunhofer MEVIS EMPIRE10 deformable registration algorithm was used to register the baseline and follow-up scans. Bland-Altman analysis was used to compare registered scan pairs by computing normalized bias (nBias), defined as the feature value change normalized to the mean feature value, and normalized range of agreement (nRoA), defined as the range spanned by the 95% limits of agreement normalized to the mean feature value. Results: Each patient’s scans contained between 6.8–15.4 million ROIs. All of the first-order features investigated were found to have an nBias value less than 0.04% and an nRoA less than 19%, indicating that the variability introduced by deformable registration was low. Conclusion: The eight first-order features investigated were found to be registration stable. Changes in CT texture maps could allow for temporal-spatial evaluation of the evolution of lung abnormalities relating to a variety of diseases on a patient-by-patient basis. SGA and HA receives royalties and licensing fees through the University of Chicago for computer-aided diagnosis technology. Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award Number R25GM109439.« less
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Farr, J B; Dessy, F; De Wilde, O; Bietzer, O; Schönenberg, D
2013-07-01
The purpose of this investigation was to compare and contrast the measured fundamental properties of two new types of modulated proton scanning systems. This provides a basis for clinical expectations based on the scanned beam quality and a benchmark for computational models. Because the relatively small beam and fast scanning gave challenges to the characterization, a secondary purpose was to develop and apply new approaches where necessary to do so. The following performances of the proton scanning systems were investigated: beamlet alignment, static in-air beamlet size and shape, scanned in-air penumbra, scanned fluence map accuracy, geometric alignment of scanning system to isocenter, maximum field size, lateral and longitudinal field uniformity of a 1 l cubic uniform field, output stability over time, gantry angle invariance, monitoring system linearity, and reproducibility. A range of detectors was used: film, ionization chambers, lateral multielement and longitudinal multilayer ionization chambers, and a scintillation screen combined with a digital video camera. Characterization of the scanned fluence maps was performed with a software analysis tool. The resulting measurements and analysis indicated that the two types of delivery systems performed within specification for those aspects investigated. The significant differences were observed between the two types of scanning systems where one type exhibits a smaller spot size and associated penumbra than the other. The differential is minimum at maximum energy and increases inversely with decreasing energy. Additionally, the large spot system showed an increase in dose precision to a static target with layer rescanning whereas the small spot system did not. The measured results from the two types of modulated scanning types of system were consistent with their designs under the conditions tested. The most significant difference between the types of system was their proton spot size and associated resolution, factors of magnetic optics, and vacuum length. The need and benefit of mutielement detectors and high-resolution sensors was also shown. The use of a fluence map analytical software tool was particularly effective in characterizing the dynamic proton energy-layer scanning.
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Mars, Mokhtar; Bouaziz, Mouna; Tbini, Zeineb; Ladeb, Fethi; Gharbi, Souha
2018-06-12
This study aims to determine how Magnetic Resonance Imaging (MRI) acquisition techniques and calculation methods affect T2 values of knee cartilage at 1.5 Tesla and to identify sequences that can be used for high-resolution T2 mapping in short scanning times. This study was performed on phantom and twenty-nine patients who underwent MRI of the knee joint at 1.5 Tesla. The protocol includes T2 mapping sequences based on Single Echo Spin Echo (SESE), Multi-Echo Spin Echo (MESE), Fast Spin Echo (FSE) and Turbo Gradient Spin Echo (TGSE). The T2 relaxation times were quantified and evaluated using three calculation methods (MapIt, Syngo Offline and monoexponential fit). Signal to Noise Ratios (SNR) were measured in all sequences. All statistical analyses were performed using the t-test. The average T2 values in phantom were 41.7 ± 13.8 ms for SESE, 43.2 ± 14.4 ms for MESE, 42.4 ± 14.1 ms for FSE and 44 ± 14.5 ms for TGSE. In the patient study, the mean differences were 6.5 ± 8.2 ms, 7.8 ± 7.6 ms and 8.4 ± 14.2 ms for MESE, FSE and TGSE compared to SESE respectively; these statistical results were not significantly different (p > 0.05). The comparison between the three calculation methods showed no significant difference (p > 0.05). t-Test showed no significant difference between SNR values for all sequences. T2 values depend not only on the sequence type but also on the calculation method. None of the sequences revealed significant differences compared to the SESE reference sequence. TGSE with its short scanning time can be used for high-resolution T2 mapping. ©2018The Author(s). Published by S. Karger AG, Basel.
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Zhang, Jingwei; Zhou, Dong; Nguyen, Thanh D; Spincemaille, Pascal; Gupta, Ajay; Wang, Yi
2017-05-01
Our objective was to demonstrate the feasibility of using hyperventilation as an efficient vasoconstrictive challenge and prior knowledge as denoising constraints for cerebral metabolic rate of oxygen (CMRO 2 ) mapping based upon quantitative susceptibility mapping (QSM). Three-dimensional (3D) multi-echo gradient echo and arterial spin labeling imaging were performed to calculate QSM and perfusion maps before and after a hyperventilation challenge in 11 healthy subjects. For comparison, this was repeated using a caffeine challenge. Whole-brain CMRO 2 and oxygen extraction fraction (OEF) maps were computed using constrained optimization. Hyperventilation scans were repeated to measure reproducibility. Regional agreement of CMRO 2 and OEF maps was analyzed within the cortical gray matter (CGM) using t-test and Bland-Altman plots. Hyperventilation challenge eliminates the 30-min waiting time needed for caffeine to exert its vasoconstrictive effects. Mean CMRO 2 (in µmol/100g/min) obtained in CGM using the caffeine and repeated hyperventilation scans were 149 ± 16, 153 ± 19, and 150 ± 20, respectively. This corresponded to an OEF of 33.6 ± 3.4%, 32.3 ± 3.2%, and 34.1 ± 3.8% at baseline state and 39.8 ± 4.8%, 43.6 ± 6.2%, and 42.8 ± 6.8% at challenged state, respectively. Hyperventilation scans produced a good agreement of CMRO 2 and OEF values. Hyperventilation is a feasible, reproducible, and efficient vasoconstrictive challenge for QSM-based quantitative CMRO 2 mapping. Magn Reson Med 77:1762-1773, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.
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Near-real-time mosaics from high-resolution side-scan sonar
Danforth, William W.; O'Brien, Thomas F.; Schwab, W.C.
1991-01-01
High-resolution side-scan sonar has proven to be a very effective tool for stuyding and understanding the surficial geology of the seafloor. Since the mid-1970s, the US Geological Survey has used high-resolution side-scan sonar systems for mapping various areas of the continental shelf. However, two problems typically encountered included the short range and the high sampling rate of high-resolution side-scan sonar systems and the acquisition and real-time processing of the enormous volume of sonar data generated by high-resolution suystems. These problems were addressed and overcome in August 1989 when the USGS conducted a side-scan sonar and bottom sampling survey of a 1000-sq-km section of the continental shelf in the Gulf of Farallones located offshore of San Francisco. The primary goal of this survey was to map an area of critical interest for studying continental shelf sediment dynamics. This survey provided an opportunity to test an image processing scheme that enabled production of a side-scan sonar hard-copy mosaic during the cruise in near real-time.
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Zhang, Shengyu; Hu, Qiang; Tang, Tao; Liu, Chao; Li, Chengchong; Zang, Yin-Yin; Cai, Wei-Xiong
2018-06-13
BACKGROUND Using regional homogeneity (ReHo) blood oxygen level-dependent functional MR (BOLD-fMRI), we investigated the structural and functional alterations of brain regions among patients with methamphetamine-associated psychosis (MAP). MATERIAL AND METHODS This retrospective study included 17 MAP patients, 16 schizophrenia (SCZ) patients, and 18 healthy controls. Informed consent was obtained from all patients before the clinical assessment, the severity of clinical symptoms was evaluated prior to the fMRI scanning, and then images were acquired and preprocessed after each participant received 6-min fRMI scanning. The participants all underwent BOLD-fMRI scanning. Voxel-based morphometry was used to measure gray matter density (GMD). Resting-state fMRI (rs-fMRI) was conducted to analyze functional MR, ReHo, and functional connectivity (FC). RESULTS GMD analysis results suggest that MAP patients, SCZ patients, and healthy volunteers show different GMDs within different brain regions. Similarly, the ReHo analysis results suggest that MAP patients, SCZ patients, and healthy volunteers have different GMDs within different brain regions. Negative correlations were found between ReHo- and the PANSS-positive scores within the left orbital interior frontal gyrus (L-orb-IFG) of MAP patients. ReHo- and PANSS-negative scores of R-SFG were negatively correlated among SCZ patients. The abnormal FC of R-MFG showed a negative correlation with the PANSS score among MAP patients. CONCLUSIONS The abnormalities in brain structure and FC were associated with the development of MAP.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Price, R.
1984-12-18
A method of mapping herpes simplex viral infection comprising administering a radiolabeled antiviral active 5-substituted 1-(2'-deoxy-2'-substituted-D-arabinofuranosyl) pyrimidine nucleoside to the infected subject, and scanning the area in which the infection is to be mapped for the radiolabel.
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Majeski, Stephanie A; Steffey, Michele A; Fuller, Mark; Hunt, Geraldine B; Mayhew, Philipp D; Pollard, Rachel E
2017-05-01
Sentinel lymph node mapping can help to direct surgical oncologic staging and metastatic disease detection in patients with complex lymphatic pathways. We hypothesized that indirect computed tomographic lymphography (ICTL) with a water-soluble iodinated contrast agent would successfully map lymphatic pathways of the iliosacral lymphatic center in dogs with anal sac gland carcinoma, providing a potential preoperative method for iliosacral sentinel lymph node identification in dogs. Thirteen adult dogs diagnosed with anal sac gland carcinoma were enrolled in this prospective, pilot study, and ICTL was performed via peritumoral contrast injection with serial caudal abdominal computed tomography scans for iliosacral sentinel lymph node identification. Technical and descriptive details for ICTL were recorded, including patient positioning, total contrast injection volume, timing of contrast visualization, and sentinel lymph nodes and lymphatic pathways identified. Indirect CT lymphography identified lymphatic pathways and sentinel lymph nodes in 12/13 cases (92%). Identified sentinel lymph nodes were ipsilateral to the anal sac gland carcinoma in 8/12 and contralateral to the anal sac gland carcinoma in 4/12 cases. Sacral, internal iliac, and medial iliac lymph nodes were identified as sentinel lymph nodes, and patterns were widely variable. Patient positioning and timing of imaging may impact successful sentinel lymph node identification. Positioning in supported sternal recumbency is recommended. Results indicate that ICTL may be a feasible technique for sentinel lymph node identification in dogs with anal sac gland carcinoma and offer preliminary data to drive further investigation of iliosacral lymphatic metastatic patterns using ICTL and sentinel lymph node biopsy. © 2017 American College of Veterinary Radiology.
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Mapping atomic contact between pentacene and a Au surface using scanning tunneling spectroscopy.
Song, Young Jae; Lee, Kyuho; Kim, Seong Heon; Choi, Byoung-Young; Yu, Jaejun; Kuk, Young
2010-03-10
We mapped spatially varying intramolecular electronic structures on a pentacene-gold interface using scanning tunneling spectroscopy. Along with ab initio calculations based on density functional theory, we found that the directional nature of the d orbitals of Au atoms plays an important role in the interaction at the pentacene-gold contact. The gold-induced interface states are broadened and shifted by various pentacene-gold distances determined by the various registries of a pentacene molecule on a gold substrate.
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Chu, Ming-Wen; Chen, Cheng Hsuan
2013-06-25
With innovative modern material-growth methods, a broad spectrum of fascinating materials with reduced dimensions-ranging from single-atom catalysts, nanoplasmonic and nanophotonic materials to two-dimensional heterostructural interfaces-is continually emerging and extending the new frontiers of materials research. A persistent central challenge in this grand scientific context has been the detailed characterization of the individual objects in these materials with the highest spatial resolution, a problem prompting the need for experimental techniques that integrate both microscopic and spectroscopic capabilities. To date, several representative microscopy-spectroscopy combinations have become available, such as scanning tunneling microscopy, tip-enhanced scanning optical microscopy, atom probe tomography, scanning transmission X-ray microscopy, and scanning transmission electron microscopy (STEM). Among these tools, STEM boasts unique chemical and electronic sensitivity at unparalleled resolution. In this Perspective, we elucidate the advances in STEM and chemical mapping applications at the atomic scale by energy-dispersive X-ray spectroscopy and electron energy loss spectroscopy with a focus on the ultimate challenge of chemical quantification with atomic accuracy.
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NASA Astrophysics Data System (ADS)
Liewald, C.; Reiser, D.; Westermeier, C.; Nickel, B.
2016-08-01
We use a pentacene transistor with asymmetric source drain contacts to test the sensitivity of scanning photocurrent microscopy (SPCM) for contact resistance and charge traps. The drain current of the device strongly depends on the choice of the drain electrode. In one case, more than 94% of the source drain voltage is lost due to contact resistance. Here, SPCM maps show an enhanced photocurrent signal at the hole-injecting contact. For the other bias condition, i.e., for ohmic contacts, the SPCM signal peaks heterogeneously along the channel. We argue from basic transport models that bright areas in SPCM maps indicate areas of large voltage gradients or high electric field strength caused by injection barriers or traps. Thus, SPCM allows us to identify and image the dominant voltage loss mechanism in organic field-effect transistors.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Gros, S; Roeske, J; Surucu, M
Purpose: To develop a novel method to monitor external anatomical changes in head and neck cancer patients in order to help guide adaptive radiotherapy decisions. Methods: The method, developed in MATLAB, reveals internal anatomical changes based on variations observed in external anatomy. Weekly kV-CBCT scans from 11 Head and neck patients were retrospectively analyzed. The pre-processing step first corrects each CBCT for artifacts and removes pixels from the immobilization mask to produce an accurate external contour of the patient’s skin. After registering the CBCTs to the initial planning CT, the external contours from each CBCT (CBCTn) are transferred to themore » first week — reference — CBCT{sub 1}. Contour radii, defined as the distances between an external contour and the central pixel of each CBCT slice, are calculated for each scan at angular increments of 1 degree. The changes in external anatomy are then quantified by the difference in radial distance between the external contours of CBCT1 and CBCTn. The radial difference is finally displayed on a 2D intensity map (angle vs radial distance difference) in order to highlight regions of interests with significant changes. Results: The 2D radial difference maps provided qualitative and quantitative information, such as the location and the magnitude of external contour divergences and the rate at which these deviations occur. With this method, anatomical changes due to tumor volume shrinkage and patient weight loss were clearly identified and could be correlated with the under-dosage of targets or over-dosage of OARs. Conclusion: This novel method provides an efficient tool to visualize 3D external anatomical modification on a single 2D map. It quickly pinpoints the location of differences in anatomy during the course of radiotherapy, which can help determine if a treatment plan needs to be adapted.« less
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NASA Technical Reports Server (NTRS)
Panda, Binayak; Gorti, Sridhar
2013-01-01
A number of research instruments are available at NASA's Marshall Space Flight Center (MSFC) to support ISS researchers and their investigations. These modern analytical tools yield valuable and sometimes new informative resulting from sample characterization. Instruments include modern scanning electron microscopes equipped with field emission guns providing analytical capabilities that include angstron-level image resolution of dry, wet and biological samples. These microscopes are also equipped with silicon drift X-ray detectors (SDD) for fast yet precise analytical mapping of phases, as well as electron back-scattered diffraction (EBSD) units to map grain orientations in crystalline alloys. Sample chambers admit large samples, provide variable pressures for wet samples, and quantitative analysis software to determine phase relations. Advances in solid-state electronics have also facilitated improvements for surface chemical analysis that are successfully employed to analyze metallic materials and alloys, ceramics, slags, and organic polymers. Another analytical capability at MSFC is a mganetic sector Secondary Ion Mass Spectroscopy (SIMS) that quantitatively determines and maps light elements such as hydrogen, lithium, and boron along with their isotopes, identifies and quantifies very low level impurities even at parts per billion (ppb) levels. Still other methods available at MSFC include X-ray photo-electron spectroscopy (XPS) that can determine oxidation states of elements as well as identify polymers and measure film thicknesses on coated materials, Scanning Auger electron spectroscopy (SAM) which combines surface sensitivity, spatial lateral resolution (approximately 20 nm), and depth profiling capabilities to describe elemental compositions in near surface regions and even the chemical state of analyzed atoms. Conventional Transmission Electron Microscope (TEM) for observing internal microstructures at very high magnifications and the Electron Probe Micro-analyzer (EPMA) for very precise microanalysis are available as needed by the researcher. Space Station researchers are invited to work with MSFC in analyzing their samples using these techniques.
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NASA Astrophysics Data System (ADS)
Murphy, Shane; Bauer, Karl; Sloan, Peter A.; Lawton, James J.; Tang, Lin; Palmer, Richard E.
2015-12-01
We demonstrate plasmon mapping of Ag nanostructures on graphite using scanning probe energy loss spectroscopy (SPELS) with a spatial resolution of 100 nm. In SPELS, an STM tip is used as a localized source of field-emitted electrons to probe the sample surface. The energy loss spectrum of the backscattered electrons is measured to provide a chemical signature of the surface under the tip. We acquire three images simultaneously with SPELS: i) constant-current field-emission images, which provide topographical information; ii) backscattered electron images, which display material contrast; and iii) SPELS images, where material-dependent features such as plasmons are mapped.
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Depth inpainting by tensor voting.
Kulkarni, Mandar; Rajagopalan, Ambasamudram N
2013-06-01
Depth maps captured by range scanning devices or by using optical cameras often suffer from missing regions due to occlusions, reflectivity, limited scanning area, sensor imperfections, etc. In this paper, we propose a fast and reliable algorithm for depth map inpainting using the tensor voting (TV) framework. For less complex missing regions, local edge and depth information is utilized for synthesizing missing values. The depth variations are modeled by local planes using 3D TV, and missing values are estimated using plane equations. For large and complex missing regions, we collect and evaluate depth estimates from self-similar (training) datasets. We align the depth maps of the training set with the target (defective) depth map and evaluate the goodness of depth estimates among candidate values using 3D TV. We demonstrate the effectiveness of the proposed approaches on real as well as synthetic data.
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Agemura, Toshihide; Sekiguchi, Takashi
2018-02-01
Collection efficiency and acceptance maps of typical detectors in modern scanning electron microscopes (SEMs) were investigated. Secondary and backscattered electron trajectories from a specimen to through-the-lens and under-the-lens detectors placed on an electron optical axis and an Everhart-Thornley detector mounted on a specimen chamber were simulated three-dimensionally. The acceptance maps were drawn as the relationship between the energy and angle of collected electrons under different working distances. The collection efficiency considering the detector sensitivity was also estimated for the various working distances. These data indicated that the acceptance maps and collection efficiency are keys to understand the detection mechanism and image contrast for each detector in the modern SEMs. Furthermore, the working distance is the dominant parameter because electron trajectories are drastically changed with the working distance.
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Cavanagh, Colin R; Jonas, Elisabeth; Hobbs, Matthew; Thomson, Peter C; Tammen, Imke; Raadsma, Herman W
2010-09-16
An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3), 15 significant (LOD ≥ 2), and 11 suggestive QTL (1.7 ≤ LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.
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Improved AFM Mapping of ICF Target Surfaces
NASA Astrophysics Data System (ADS)
Olson, D. K.; Drake, T.; Frey, D.; Huang, H.; Stephens, R. B.
2003-10-01
Targets for Inertial Confinement Fusion (ICF) research are made from spherical shells with very strict requirements on surface smoothness. Hydrodynamic instabilities are amplified by the presence of surface defects, greatly reducing the gain of ICF targets. Sub-micron variations in the surface can be examined using an Atomic Force Microscope. The current sphere mapping assembly at General Atomics is designed to trace near the equator of a rotating sphere under the AFM head. Spheres are traced on three mutually orthogonal planes. The ˜10 mm piezo-electric actuator range limits how far off the equator we can scan spheres of millimeter diameter. Because only a small fraction of the target's surface can be covered, localized high-mode defects are difficult to detect. In order to meet the needs of ICF research, we need to scan more surface area of the sphere with the AFM. By integrating an additional stepping motor to the sphere mapping assembly, we will be able to recenter the piezo driver of the AFM while mapping. This additional ability allows us to increase the amount of the sphere's surface we are able to scan with the AFM by extending the range of the AFM from the sphere's equator.
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A Novel Real-Time Reference Key Frame Scan Matching Method
Mohamed, Haytham; Moussa, Adel; Elhabiby, Mohamed; El-Sheimy, Naser; Sesay, Abu
2017-01-01
Unmanned aerial vehicles represent an effective technology for indoor search and rescue operations. Typically, most indoor missions’ environments would be unknown, unstructured, and/or dynamic. Navigation of UAVs in such environments is addressed by simultaneous localization and mapping approach using either local or global approaches. Both approaches suffer from accumulated errors and high processing time due to the iterative nature of the scan matching method. Moreover, point-to-point scan matching is prone to outlier association processes. This paper proposes a low-cost novel method for 2D real-time scan matching based on a reference key frame (RKF). RKF is a hybrid scan matching technique comprised of feature-to-feature and point-to-point approaches. This algorithm aims at mitigating errors accumulation using the key frame technique, which is inspired from video streaming broadcast process. The algorithm depends on the iterative closest point algorithm during the lack of linear features which is typically exhibited in unstructured environments. The algorithm switches back to the RKF once linear features are detected. To validate and evaluate the algorithm, the mapping performance and time consumption are compared with various algorithms in static and dynamic environments. The performance of the algorithm exhibits promising navigational, mapping results and very short computational time, that indicates the potential use of the new algorithm with real-time systems. PMID:28481285
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Eileen H. Helmer; Thomas S. Ruzycki; Jay Benner; Shannon M. Voggesser; Barbara P. Scobie; Courtenay Park; David W. Fanning; Seepersad Ramnarine
2012-01-01
Tropical forest managers need detailed maps of forest types for REDD+, but spectral similarity among forest types; cloud and scan-line gaps; and scarce vegetation ground plots make producing such maps with satellite imagery difficult. How can managers map tropical forest tree communities with satellite imagery given these challenges? Here we describe a case study of...
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Time-efficient high-resolution whole-brain three-dimensional macromolecular proton fraction mapping
Yarnykh, Vasily L.
2015-01-01
Purpose Macromolecular proton fraction (MPF) mapping is a quantitative MRI method that reconstructs parametric maps of a relative amount of macromolecular protons causing the magnetization transfer (MT) effect and provides a biomarker of myelination in neural tissues. This study aimed to develop a high-resolution whole-brain MPF mapping technique utilizing a minimal possible number of source images for scan time reduction. Methods The described technique is based on replacement of an actually acquired reference image without MT saturation by a synthetic one reconstructed from R1 and proton density maps, thus requiring only three source images. This approach enabled whole-brain three-dimensional MPF mapping with isotropic 1.25×1.25×1.25 mm3 voxel size and scan time of 20 minutes. The synthetic reference method was validated against standard MPF mapping with acquired reference images based on data from 8 healthy subjects. Results Mean MPF values in segmented white and gray matter appeared in close agreement with no significant bias and small within-subject coefficients of variation (<2%). High-resolution MPF maps demonstrated sharp white-gray matter contrast and clear visualization of anatomical details including gray matter structures with high iron content. Conclusions Synthetic reference method improves resolution of MPF mapping and combines accurate MPF measurements with unique neuroanatomical contrast features. PMID:26102097
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Hamill, Daniel; Buscombe, Daniel; Wheaton, Joseph M
2018-01-01
Side scan sonar in low-cost 'fishfinder' systems has become popular in aquatic ecology and sedimentology for imaging submerged riverbed sediment at coverages and resolutions sufficient to relate bed texture to grain-size. Traditional methods to map bed texture (i.e. physical samples) are relatively high-cost and low spatial coverage compared to sonar, which can continuously image several kilometers of channel in a few hours. Towards a goal of automating the classification of bed habitat features, we investigate relationships between substrates and statistical descriptors of bed textures in side scan sonar echograms of alluvial deposits. We develop a method for automated segmentation of bed textures into between two to five grain-size classes. Second-order texture statistics are used in conjunction with a Gaussian Mixture Model to classify the heterogeneous bed into small homogeneous patches of sand, gravel, and boulders with an average accuracy of 80%, 49%, and 61%, respectively. Reach-averaged proportions of these sediment types were within 3% compared to similar maps derived from multibeam sonar.
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PET attenuation correction for flexible MRI surface coils in hybrid PET/MRI using a 3D depth camera
NASA Astrophysics Data System (ADS)
Frohwein, Lynn J.; Heß, Mirco; Schlicher, Dominik; Bolwin, Konstantin; Büther, Florian; Jiang, Xiaoyi; Schäfers, Klaus P.
2018-01-01
PET attenuation correction for flexible MRI radio frequency surface coils in hybrid PET/MRI is still a challenging task, as position and shape of these coils conform to large inter-patient variabilities. The purpose of this feasibility study is to develop a novel method for the incorporation of attenuation information about flexible surface coils in PET reconstruction using the Microsoft Kinect V2 depth camera. The depth information is used to determine a dense point cloud of the coil’s surface representing the shape of the coil. From a CT template—acquired once in advance—surface information of the coil is extracted likewise and converted into a point cloud. The two point clouds are then registered using a combination of an iterative-closest-point (ICP) method and a partially rigid registration step. Using the transformation derived through the point clouds, the CT template is warped and thereby adapted to the PET/MRI scan setup. The transformed CT template is converted into an attenuation map from Hounsfield units into linear attenuation coefficients. The resulting fitted attenuation map is then integrated into the MRI-based patient-specific DIXON-based attenuation map of the actual PET/MRI scan. A reconstruction of phantom PET data acquired with the coil present in the field-of-view (FoV), but without the corresponding coil attenuation map, shows large artifacts in regions close to the coil. The overall count loss is determined to be around 13% compared to a PET scan without the coil present in the FoV. A reconstruction using the new μ-map resulted in strongly reduced artifacts as well as increased overall PET intensities with a remaining relative difference of about 1% to a PET scan without the coil in the FoV.
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Artist Concept of MAVEN Imaging Ultraviolet Spectrograph at Work
2014-11-07
This artist concept depicts the Imaging Ultraviolet Spectrograph IUVS on NASA MAVEN spacecraft scanning the upper atmosphere of Mars. IUVS uses limb scans to map the chemical makeup and vertical structure across Mars upper atmosphere.
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Gai, Neville D; Malayeri, Ashkan A; Bluemke, David A
2017-04-01
To develop and assess a new technique for three-dimensional (3D) full lung T1 and T2* mapping using a single free breathing scan during a clinically feasible time. A 3D stack of dual-echo ultrashort echo time (UTE) radial acquisition interleaved with and without a WET (water suppression enhanced through T1 effects) saturation pulse was used to map T1 and T2* simultaneously in a single scan. Correction for modulation due to multiple views per segment was derived. Bloch simulations were performed to study saturation pulse excitation profile on lung tissue. Optimization of the saturation delay time (for T1 mapping) and echo time (for T2* mapping) was performed. Monte Carlo simulation was done to predict accuracy and precision of the sequence with signal-to-noise ratio of in vivo images used in the simulation. A phantom study was carried out using the 3D interleaved saturation recovery with dual echo ultrashort echo time imaging (ITSR-DUTE) sequence and reference standard inversion recovery spin echo sequence (IR-SE) to compare accuracy of the sequence. Nine healthy volunteers were imaged and mean (SD) of T1 and T2* in lung parenchyma at 3T were estimated through manually assisted segmentation. 3D lung coverage with a resolution of 2.5 × 2.5 × 6 mm 3 was performed and nominal scan time was recorded for the scans. Repeatability was assessed in three of the volunteers. Regional differences in T1/T2* values were also assessed. The phantom study showed accuracy of T1 values to be within 2.3% of values obtained from IR-SE. Mean T1 value in lung parenchyma was 1002 ± 82 ms while T2* was 0.85 ± 0.1 ms. Scan time was ∼10 min for volunteer scans. Mean coefficient of variation (CV) across slices was 0.057 and 0.09, respectively. Regional variation along the gravitational direction and between right and left lung were not significant (P = 0.25 and P = 0.06, respectively) for T1. T2* showed significant variation (P = 0.03) along the gravitational direction. Repeatability for three volunteers was within 0.7% for T1 and 1.9% for T2*. 3D T1 and T2* maps of the entire lung can be obtained in a single scan of ∼10 min with a resolution of 2.5 × 2.5 × 6 mm 3 . 2 J. Magn. Reson. Imaging 2017;45:1097-1104. 2016 International Society for Magnetic Resonance in Medicine.
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Mapping PDB chains to UniProtKB entries.
Martin, Andrew C R
2005-12-01
UniProtKB/SwissProt is the main resource for detailed annotations of protein sequences. This database provides a jumping-off point to many other resources through the links it provides. Among others, these include other primary databases, secondary databases, the Gene Ontology and OMIM. While a large number of links are provided to Protein Data Bank (PDB) files, obtaining a regularly updated mapping between UniProtKB entries and PDB entries at the chain or residue level is not straightforward. In particular, there is no regularly updated resource which allows a UniProtKB/SwissProt entry to be identified for a given residue of a PDB file. We have created a completely automatically maintained database which maps PDB residues to residues in UniProtKB/SwissProt and UniProtKB/trEMBL entries. The protocol uses links from PDB to UniProtKB, from UniProtKB to PDB and a brute-force sequence scan to resolve PDB chains for which no annotated link is available. Finally the sequences from PDB and UniProtKB are aligned to obtain a residue-level mapping. The resource may be queried interactively or downloaded from http://www.bioinf.org.uk/pdbsws/.
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Satellite Data Sets in the Polar Regions
NASA Technical Reports Server (NTRS)
Comiso, Josefino C.; Busalacchi, Antonio J. (Technical Monitor)
2000-01-01
We have generated about two decades of consistently derived geophysical parameters in the polar regions. The key parameters are sea ice concentration, surface temperature, albedo, and cloud cover statistics. Sea ice concentrations were derived from the Scanning Multichannel Microwave Radiometer (SMMR) data and the Special Scanning Cl Microwave Imager (SSM/I) data from several platforms using the enhanced Bootstrap Algorithm for the period 1978 through 1999. The new algorithm reduces the errors associated with spatial and temporal variations in the emissivity and surface temperatures of sea ice. Also, bad data at ocean/land interfaces are identified and deleted in an unsupervised manner. Surface ice temperature, albedo and cloud cover statistics are derived simultaneously from the Advanced Very High Resolution Radiometer (AVHRR) data from 1981 through 1999 and mapped at a higher resolution but the same format as the ice concentration data. The technique makes use these co-registered ice concentration maps to enable cloud masking to be done separately for open ocean, sea ice and land areas. The effect of inversion is minimized by taking into consideration the expected changes in the effect of inversion with altitude, especially in the Antarctic. A technique for ice type regional classification has also been developed using multichannel cluster analysis and a neural network. This provide a means to identify large areas of thin ice, first year ice, and older ice types. The data sets have been shown to be coherent with each other and provide a powerful tool for in depth studies of the currently changing Arctic and Antarctic environment.
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Surface registration technique for close-range mapping applications
NASA Astrophysics Data System (ADS)
Habib, Ayman F.; Cheng, Rita W. T.
2006-08-01
Close-range mapping applications such as cultural heritage restoration, virtual reality modeling for the entertainment industry, and anatomical feature recognition for medical activities require 3D data that is usually acquired by high resolution close-range laser scanners. Since these datasets are typically captured from different viewpoints and/or at different times, accurate registration is a crucial procedure for 3D modeling of mapped objects. Several registration techniques are available that work directly with the raw laser points or with extracted features from the point cloud. Some examples include the commonly known Iterative Closest Point (ICP) algorithm and a recently proposed technique based on matching spin-images. This research focuses on developing a surface matching algorithm that is based on the Modified Iterated Hough Transform (MIHT) and ICP to register 3D data. The proposed algorithm works directly with the raw 3D laser points and does not assume point-to-point correspondence between two laser scans. The algorithm can simultaneously establish correspondence between two surfaces and estimates the transformation parameters relating them. Experiment with two partially overlapping laser scans of a small object is performed with the proposed algorithm and shows successful registration. A high quality of fit between the two scans is achieved and improvement is found when compared to the results obtained using the spin-image technique. The results demonstrate the feasibility of the proposed algorithm for registering 3D laser scanning data in close-range mapping applications to help with the generation of complete 3D models.
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Molecular beam epitaxy of InN nanowires on Si
NASA Astrophysics Data System (ADS)
Golam Sarwar, A. T. M.; Carnevale, Santino D.; Kent, Thomas F.; Laskar, Masihhur R.; May, Brelon J.; Myers, Roberto C.
2015-10-01
We report on a systematic growth study of the nucleation process of InN nanowires on Si(1 1 1) substrates using plasma assisted molecular beam epitaxy (PAMBE). Samples are grown with various substrate temperatures and III/V ratios. Scanning electron microscopy, X-ray diffraction spectroscopy, energy dispersive X-ray spectroscopy, and photoluminescence are carried out to map out the variation in structural and optical properties versus growth conditions. Statistical averages of areal density, height, and radius are mapped as a function of substrate temperature and III/V ratio. Three different morphological phases are identified on the growth surface: InN, α-In and β-In. Based on SEM image analysis of samples grown at different conditions, the formation mechanism of these phases is proposed. Finally, the growth phase diagram of PAMBE grown InN on Si under N-rich condition is presented, and tapered versus non-tapered growth conditions are identified. It is found that high growth temperature and low III/V ratio plays a critical role in the growth of non-tapered InN nanowires.
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Advances in QTL Mapping in Pigs
Rothschild, Max F.; Hu, Zhi-liang; Jiang, Zhihua
2007-01-01
Over the past 15 years advances in the porcine genetic linkage map and discovery of useful candidate genes have led to valuable gene and trait information being discovered. Early use of exotic breed crosses and now commercial breed crosses for quantitative trait loci (QTL) scans and candidate gene analyses have led to 110 publications which have identified 1,675 QTL. Additionally, these studies continue to identify genes associated with economically important traits such as growth rate, leanness, feed intake, meat quality, litter size, and disease resistance. A well developed QTL database called PigQTLdb is now as a valuable tool for summarizing and pinpointing in silico regions of interest to researchers. The commercial pig industry is actively incorporating these markers in marker-assisted selection along with traditional performance information to improve traits of economic performance. The long awaited sequencing efforts are also now beginning to provide sequence available for both comparative genomics and large scale single nucleotide polymorphism (SNP) association studies. While these advances are all positive, development of useful new trait families and measurement of new or underlying traits still limits future discoveries. A review of these developments is presented. PMID:17384738
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WRIS: a resource information system for wildland management
Robert M. Russell; David A. Sharpnack; Elliot Amidon
1975-01-01
WRIS (Wildland Resource Information System) is a computer system for processing, storing, retrieving, updating, and displaying geographic data. The polygon, representing a land area boundary, forms the building block of WRIS. Polygons form a map. Maps are digitized manually or by automatic scanning. Computer programs can extract and produce polygon maps and can overlay...
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Raman mapping of intact biofilms on stainless steel surfaces
USDA-ARS?s Scientific Manuscript database
Each slide under the Raman Microscope was mapped for approximately 18.5 hours with a dimension of 36x36 that provides a greater result compared to doing a smaller dimension scan. The results from the Raman Mapping show the location and position of how the bacteria are growing scattered or straight a...
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Footprint Map Partitioning Using Airborne Laser Scanning Data
NASA Astrophysics Data System (ADS)
Xiong, B.; Oude Elberink, S.; Vosselman, G.
2016-06-01
Nowadays many cities and countries are creating their 3D building models for a better daily management and smarter decision making. The newly created 3D models are required to be consistent with existing 2D footprint maps. Thereby the 2D maps are usually combined with height data for the task of 3D reconstruction. Many buildings are often composed by parts that are discontinuous over height. Building parts can be reconstructed independently and combined into a complete building. Therefore, most of the state-of-the-art work on 3D building reconstruction first decomposes a footprint map into parts. However, those works usually change the footprint maps for easier partitioning and cannot detect building parts that are fully inside the footprint polygon. In order to solve those problems, we introduce two methodologies, one more dependent on height data, and the other one more dependent on footprints. We also experimentally evaluate the two methodologies and compare their advantages and disadvantages. The experiments use Airborne Laser Scanning (ALS) data and two vector maps, one with 1:10,000 scale and another one with 1:500 scale.
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Utsunomiya, Satoshi; Ewing, Rodney C
2003-02-15
A major challenge to the development of a fundamental understanding of transport and retardation mechanisms of trace metal contaminants (<10 ppm) is their identification and characterization at the nanoscale. Atomic-scale techniques, such as conventional transmission electron microscopy, although powerful, are limited by the extremely small amounts of material that are examined. However, recent advances in electron microscopy provide a number of new analytical techniques that expand its application in environmental studies, particularly those concerning heavy metals on airborne particulates or water-borne colloids. High-angle annular dark field scanning transmission electron microscopy (HAADF-STEM), STEM-energy-dispersive X-ray spectrometry (EDX), and energy-filtered TEM (EFTEM) can be effectively used to identify and characterize nanoparticles. The image contrast in HAADF-STEM is strongly correlated to the atomic mass: heavier elements contribute to brighter contrast. Gold nanocrystals in pyrite and uranium nanocrystals in atmospheric aerosols have been identified by HAADF-STEM and STEM-EDX mapping and subsequently characterized by high-resolution TEM (HRTEM). EFTEM was used to identify U and Fe nanocrystals embedded in an aluminosilicate. A rare, As-bearing nanophase, westerveldite (FeAs), was identified by STEM-EDX and HRTEM. The combined use of these techniques greatly expands the effective application of electron microscopy in environmental studies, especially when applied to metals of very low concentrations. This paper describes examples of how these electron microbeam techniques can be used in combination to characterize a low concentration of heavy metals (a few ppm) on nanoscale particles.
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Suto, Jun-ichi
2013-07-31
DDD.Cg-A(y) female mice developed massive obesity as compared with B6.Cg-A(y) female mice. We previously identified quantitative trait loci (QTLs) for obesity on chromosomes 1, 6, 9 and 17 in F2 female mice, including F2A(y) (F2 mice with the A(y) allele) and F2 non- A(y) mice (F2 mice without the A(y) allele), produced by crossing C57BL/6J and DDD.Cg-A(y) strains. We here addressed the question whether the obesity QTLs share genetic bases with putative QTLs for plasma glucose, insulin and leptin concentrations. We performed QTL analyses for the first principal component (PC1) extracted from these metabolic measurements to identify the genes that contributed to the comprehensive evaluation of metabolic traits. By single QTL scans, we identified two significant QTLs for insulin concentration on chromosomes 6 and 12, three for leptin concentration on chromosomes 1, 6 and 17, and five for PC1 on chromosomes 1, 6, 12 (two loci) and 17. Although insulin and leptin concentrations and PC1 were not normally distributed in combined F2 mice, results of single QTL scans by parametric and non-parametric methods were very similar. Therefore, QTL scan by the parametric method was performed with the agouti locus genotype as a covariate. A significant QTL × covariate interaction was found for PC1 on chromosome 9. All obesity QTLs had significant metabolic effects. Thus, obesity- and diabetes-related traits in DDD.Cg-A(y) mice were largely controlled by QTLs on chromosomes 1, 6, 9, 12 and 17.
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Krause, F F; Rosenauer, A; Barthel, J; Mayer, J; Urban, K; Dunin-Borkowski, R E; Brown, H G; Forbes, B D; Allen, L J
2017-10-01
This paper addresses a novel approach to atomic resolution elemental mapping, demonstrating a method that produces elemental maps with a similar resolution to the established method of electron energy-loss spectroscopy in scanning transmission electron microscopy. Dubbed energy-filtered imaging scanning transmission electron microscopy (EFISTEM) this mode of imaging is, by the quantum mechanical principle of reciprocity, equivalent to tilting the probe in energy-filtered transmission electron microscopy (EFTEM) through a cone and incoherently averaging the results. In this paper we present a proof-of-principle EFISTEM experimental study on strontium titanate. The present approach, made possible by chromatic aberration correction, has the advantage that it provides elemental maps which are immune to spatial incoherence in the electron source, coherent aberrations in the probe-forming lens and probe jitter. The veracity of the experiment is supported by quantum mechanical image simulations, which provide an insight into the image-forming process. Elemental maps obtained in EFTEM suffer from the effect known as preservation of elastic contrast, which, for example, can lead to a given atomic species appearing to be in atomic columns where it is not to be found. EFISTEM very substantially reduces the preservation of elastic contrast and yields images which show stability of contrast with changing thickness. The experimental application is demonstrated in a proof-of-principle study on strontium titanate. Copyright © 2017 Elsevier B.V. All rights reserved.
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A convenient method for large-scale STM mapping of freestanding atomically thin conductive membranes
NASA Astrophysics Data System (ADS)
Uder, B.; Hartmann, U.
2017-06-01
Two-dimensional atomically flat sheets with a high flexibility are very attractive as ultrathin membranes but are also inherently challenging for microscopic investigations. We report on a method using Scanning Tunneling Microscopy (STM) under ultra-high vacuum conditions for large-scale mapping of several-micrometer-sized freestanding single and multilayer graphene membranes. This is achieved by operating the STM at unusual parameters. We found that large-scale scanning on atomically thin membranes delivers valuable results using very high tip-scan speeds combined with high feedback-loop gain and low tunneling currents. The method ultimately relies on the particular behavior of the freestanding membrane in the STM which is much different from that of a solid substrate.
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NASA Technical Reports Server (NTRS)
Larson, L. A.; Soria, F.; Poppa, H.
1980-01-01
A particularly simple conversion of a scanning Auger system for ESD ion energy distributions and scanning ESD has been developed. This approach combines the advantages of the small spot-size electron guns and mapping systems developed for SAM with the capability of ESD for the detection of hydrogen. Our intended use for the device is detection and mapping of surface concentrations of hydrogen on metals. The characteristics of SESD are illustrated with the preliminary results of an investigation into the ESD properties of hydrogenic adsorbates on Nb. It is shown that the ESDIED exhibit distinct differences indicative of the surface preparation, and that the ESD ion angular distributions have an effect on the observed contrast relationships in SESD.
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Pilot performance: assessing how scan patterns & navigational assessments vary by flight expertise.
Yang, Ji Hyun; Kennedy, Quinn; Sullivan, Joseph; Fricker, Ronald D
2013-02-01
Helicopter overland navigation is a cognitively complex task that requires continuous monitoring of system and environmental parameters and many hours of training to master. This study investigated the effect of expertise on pilots' gaze measurements, navigation accuracy, and subjective assessment of their navigation accuracy in overland navigation on easy and difficult routes. A simulated overland task was completed by 12 military officers who ranged in flight experience as measured by total flight hours (TFH). They first studied a map of a route that included both easy and difficult route sections, and then had to 'fly' this simulated route in a fixed-base helicopter simulator. They also completed pre-task estimations and post-task assessments of the navigational difficulty of the transit to each waypoint in the route. Their scan pattern was tracked via eye tracking systems, which captured both the subject's out-the-window (OTW) and topographical map scan data. TFH was not associated with navigation accuracy or root mean square (RMS) error for any route section. For the easy routes, experts spent less time scanning out the window (p = 0.61) and had shorter OTW dwell (p = -0.66). For the difficult routes, experts appeared to slow down their scan by spending as much time scanning out the window as the novices while also having fewer Map fixations (p = -0.65) and shorter OTW dwell (p = -0.69). However, TFH was not significantly correlated with more accurate estimates of route difficulty. This study found that TFH did not predict navigation accuracy or subjective assessment, but was correlated with some gaze parameters.
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NASA Astrophysics Data System (ADS)
Roggenstein, E. B.; Gray, G.
2013-12-01
The National Oceanic and Atmospheric Administration (NOAA) National Ocean Service (NOS) Center for Operational Oceanographic Products and Services (COOPS) manages three national observing system programs. These are the National Water level Observation Network (NWLON) (210 stations), the 23 NOAA/Physical Oceanographic Real-Time Systems (PORTS), and National Currents Observing Program (NCOP) (approximately 70 deployments/year). In support of its mission COOPS operates and maintains a number of small boats. During vessel operations, side-scan sonar data are at times needed to provide information about bottom structure for future work in the area. For example, potential hazards, obstructions, or bottom morphology features that have not been identified on localized charts for a given area could be used to inform decisions on planned installations. Side-scan sonar capability is also important when attempting to reacquire bottom mounts that fail to surface at the conclusion of a current meter survey. Structure mapping and side-scan capabilities have been added to recent consumer-level, commercial, off-the-shelf fathometers, generally intended for recreational, commercial fishing, and diving applications. We are proposing to investigate these systems' viability for meeting survey requirements. We assess their ability to provide a flexible alternative to research/commercial oceanographic level side-scan system at a significant cost savings. Such systems could provide important information to support scientific missions that require qualitative seafloor imagery.
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Yang, B; Navarro, N; Noguera, J L; Muñoz, M; Guo, T F; Yang, K X; Ma, J W; Folch, J M; Huang, L S; Pérez-Enciso, M
2011-10-01
Models in QTL mapping can be improved by considering all potential variables, i.e. we can use remaining traits other than the trait under study as potential predictors. QTL mapping is often conducted by correcting for a few fixed effects or covariates (e.g. sex, age), although many traits with potential causal relationships between them are recorded. In this work, we evaluate by simulation several procedures to identify optimum models in QTL scans: forward selection, undirected dependency graph and QTL-directed dependency graph (QDG). The latter, QDG, performed better in terms of power and false discovery rate and was applied to fatty acid (FA) composition and fat deposition traits in two pig F2 crosses from China and Spain. Compared with the typical QTL mapping, QDG approach revealed several new QTL. To the contrary, several FA QTL on chromosome 4 (e.g. Palmitic, C16:0; Stearic, C18:0) detected by typical mapping vanished after adjusting for phenotypic covariates in QDG mapping. This suggests that the QTL detected in typical mapping could be indirect. When a QTL is supported by both approaches, there is an increased confidence that the QTL have a primary effect on the corresponding trait. An example is a QTL for C16:1 on chromosome 8. In conclusion, mapping QTL based on causal phenotypic networks can increase power and help to make more biologically sound hypothesis on the genetic architecture of complex traits. © 2011 Blackwell Verlag GmbH.
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Study of spin-scan imaging for outer planets missions: Executive summary
NASA Technical Reports Server (NTRS)
Russell, E. E.; Chandos, R. A.; Kodak, J. C.; Pellicori, S. F.; Tomasko, M. G.
1974-01-01
The development and characteristics of spin-scan imagers for interplanetary exploration are discussed. The spin-scan imaging photopolarimeter instruments of Pioneer 10 and 11 are described. In addition to the imaging function, the instruments are also used in a faint-light mode to take sky maps in both radiance and polarization. The performance of a visible-infrared spin-scan radiometer (VISSR), which operates in both visible and infrared wavelengths, is reported.
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NASA Astrophysics Data System (ADS)
Wang, Jui-Kai; Kardon, Randy H.; Garvin, Mona K.
2015-03-01
In cases of optic-nerve-head edema, the presence of the swelling reduces the visibility of the underlying neural canal opening (NCO) within spectral-domain optical coherence tomography (SD-OCT) volumes. Consequently, traditional SD-OCT-based NCO segmentation methods often overestimate the size of the NCO. The visibility of the NCO can be improved using high-definition 2D raster scans, but such scans do not provide 3D contextual image information. In this work, we present a semi-automated approach for the segmentation of the NCO in cases of optic disc edema by combining image information from volumetric and high-definition raster SD-OCT image sequences. In particular, for each subject, five high-definition OCT B-scans and the OCT volume are first separately segmented, and then the five high-definition B-scans are automatically registered to the OCT volume. Next, six NCO points are placed (manually, in this work) in the central three high-definition OCT B-scans (two points for each central B-scans) and are automatically transferred into the OCT volume. Utilizing a combination of these mapped points and the 3D image information from the volumetric scans, a graph-based approach is used to identify the complete NCO on the OCT en-face image. The segmented NCO points using the new approach were significantly closer to expert-marked points than the segmented NCO points using a traditional approach (root mean square differences in pixels: 5.34 vs. 21.71, p < 0.001).
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A Scan of CDC-Authored Articles on Legal Epidemiology, 2011-2015.
Martini, Leila; Presley, David; Klieger, Sarah; Burris, Scott
2016-11-01
The Centers for Disease Control and Prevention (CDC) conducts research on legal epidemiology, the scientific study of law as a factor in the cause, distribution, and prevention of disease. This study describes a scan of articles written by CDC staff members to characterize the frequency and key features of legal epidemiology articles and their distribution across CDC departments and divisions. CDC librarians searched an internal repository for journal articles by CDC staff published from January 1, 2011, to May 31, 2015. Researchers reviewed and coded the abstracts to produce data on key features of the articles. Researchers identified 158 CDC-authored legal epidemiology articles published in 83 journals, most frequently in Preventing Chronic Disease (14 publications), Journal of Public Health Management Practice (10 publications), and Morbidity and Mortality Weekly Report (9 publications). Most articles concerned the use and impact of law as a deliberate tool of intervention. Thirteen articles addressed the legal infrastructure of public health, and 3 assessed the incidental or unintended effects of nonhealth laws. CDC-authored articles encompassed policy making, implementation, and impact. Literature reviews and studies mapping laws across multiple jurisdictions constituted one-quarter of all publications. Studies addressed laws at the international, national, state, local, and organizational levels. Results of the scan can be used to identify opportunities for the agency to better support research, professional development, networking, publication, and tracking of publication in this emerging field.
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Basic Operating Mode | Materials Science | NREL
indium diselenide thin film, showing elemental maps of copper (left) and indium (right). CuInSe2 thin film. Cu and In elemental maps obtained by EDS. In its basic operating mode, scanning electron
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Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy
Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong
2016-01-01
Local surface charge density of lipid membranes influences membrane–protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values. PMID:27561322
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Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy
NASA Astrophysics Data System (ADS)
Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong
2016-08-01
Local surface charge density of lipid membranes influences membrane-protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values.
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Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy.
Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong
2016-08-26
Local surface charge density of lipid membranes influences membrane-protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values.
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Harvesting geographic features from heterogeneous raster maps
NASA Astrophysics Data System (ADS)
Chiang, Yao-Yi
2010-11-01
Raster maps offer a great deal of geospatial information and are easily accessible compared to other geospatial data. However, harvesting geographic features locked in heterogeneous raster maps to obtain the geospatial information is challenging. This is because of the varying image quality of raster maps (e.g., scanned maps with poor image quality and computer-generated maps with good image quality), the overlapping geographic features in maps, and the typical lack of metadata (e.g., map geocoordinates, map source, and original vector data). Previous work on map processing is typically limited to a specific type of map and often relies on intensive manual work. In contrast, this thesis investigates a general approach that does not rely on any prior knowledge and requires minimal user effort to process heterogeneous raster maps. This approach includes automatic and supervised techniques to process raster maps for separating individual layers of geographic features from the maps and recognizing geographic features in the separated layers (i.e., detecting road intersections, generating and vectorizing road geometry, and recognizing text labels). The automatic technique eliminates user intervention by exploiting common map properties of how road lines and text labels are drawn in raster maps. For example, the road lines are elongated linear objects and the characters are small connected-objects. The supervised technique utilizes labels of road and text areas to handle complex raster maps, or maps with poor image quality, and can process a variety of raster maps with minimal user input. The results show that the general approach can handle raster maps with varying map complexity, color usage, and image quality. By matching extracted road intersections to another geospatial dataset, we can identify the geocoordinates of a raster map and further align the raster map, separated feature layers from the map, and recognized features from the layers with the geospatial dataset. The road vectorization and text recognition results outperform state-of-art commercial products, and with considerably less user input. The approach in this thesis allows us to make use of the geospatial information of heterogeneous maps locked in raster format.
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Breast tumour visualization using 3D quantitative ultrasound methods
NASA Astrophysics Data System (ADS)
Gangeh, Mehrdad J.; Raheem, Abdul; Tadayyon, Hadi; Liu, Simon; Hadizad, Farnoosh; Czarnota, Gregory J.
2016-04-01
Breast cancer is one of the most common cancer types accounting for 29% of all cancer cases. Early detection and treatment has a crucial impact on improving the survival of affected patients. Ultrasound (US) is non-ionizing, portable, inexpensive, and real-time imaging modality for screening and quantifying breast cancer. Due to these attractive attributes, the last decade has witnessed many studies on using quantitative ultrasound (QUS) methods in tissue characterization. However, these studies have mainly been limited to 2-D QUS methods using hand-held US (HHUS) scanners. With the availability of automated breast ultrasound (ABUS) technology, this study is the first to develop 3-D QUS methods for the ABUS visualization of breast tumours. Using an ABUS system, unlike the manual 2-D HHUS device, the whole patient's breast was scanned in an automated manner. The acquired frames were subsequently examined and a region of interest (ROI) was selected in each frame where tumour was identified. Standard 2-D QUS methods were used to compute spectral and backscatter coefficient (BSC) parametric maps on the selected ROIs. Next, the computed 2-D parameters were mapped to a Cartesian 3-D space, interpolated, and rendered to provide a transparent color-coded visualization of the entire breast tumour. Such 3-D visualization can potentially be used for further analysis of the breast tumours in terms of their size and extension. Moreover, the 3-D volumetric scans can be used for tissue characterization and the categorization of breast tumours as benign or malignant by quantifying the computed parametric maps over the whole tumour volume.
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Theoretical analysis of a dual-probe scanning tunneling microscope setup on graphene.
Settnes, Mikkel; Power, Stephen R; Petersen, Dirch H; Jauho, Antti-Pekka
2014-03-07
Experimental advances allow for the inclusion of multiple probes to measure the transport properties of a sample surface. We develop a theory of dual-probe scanning tunneling microscopy using a Green's function formalism, and apply it to graphene. Sampling the local conduction properties at finite length scales yields real space conductance maps which show anisotropy for pristine graphene systems and quantum interference effects in the presence of isolated impurities. Spectral signatures in the Fourier transforms of real space conductance maps include characteristics that can be related to different scattering processes. We compute the conductance maps of graphene systems with different edge geometries or height fluctuations to determine the effects of nonideal graphene samples on dual-probe measurements.
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Wood, Andrew R; Perry, John R B; Tanaka, Toshiko; Hernandez, Dena G; Zheng, Hou-Feng; Melzer, David; Gibbs, J Raphael; Nalls, Michael A; Weedon, Michael N; Spector, Tim D; Richards, J Brent; Bandinelli, Stefania; Ferrucci, Luigi; Singleton, Andrew B; Frayling, Timothy M
2013-01-01
Genome-wide association (GWA) studies have been limited by the reliance on common variants present on microarrays or imputable from the HapMap Project data. More recently, the completion of the 1000 Genomes Project has provided variant and haplotype information for several million variants derived from sequencing over 1,000 individuals. To help understand the extent to which more variants (including low frequency (1% ≤ MAF <5%) and rare variants (<1%)) can enhance previously identified associations and identify novel loci, we selected 93 quantitative circulating factors where data was available from the InCHIANTI population study. These phenotypes included cytokines, binding proteins, hormones, vitamins and ions. We selected these phenotypes because many have known strong genetic associations and are potentially important to help understand disease processes. We performed a genome-wide scan for these 93 phenotypes in InCHIANTI. We identified 21 signals and 33 signals that reached P<5×10(-8) based on HapMap and 1000 Genomes imputation, respectively, and 9 and 11 that reached a stricter, likely conservative, threshold of P<5×10(-11) respectively. Imputation of 1000 Genomes genotype data modestly improved the strength of known associations. Of 20 associations detected at P<5×10(-8) in both analyses (17 of which represent well replicated signals in the NHGRI catalogue), six were captured by the same index SNP, five were nominally more strongly associated in 1000 Genomes imputed data and one was nominally more strongly associated in HapMap imputed data. We also detected an association between a low frequency variant and phenotype that was previously missed by HapMap based imputation approaches. An association between rs112635299 and alpha-1 globulin near the SERPINA gene represented the known association between rs28929474 (MAF = 0.007) and alpha1-antitrypsin that predisposes to emphysema (P = 2.5×10(-12)). Our data provide important proof of principle that 1000 Genomes imputation will detect novel, low frequency-large effect associations.
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Wood, Andrew R.; Perry, John R. B.; Tanaka, Toshiko; Hernandez, Dena G.; Zheng, Hou-Feng; Melzer, David; Gibbs, J. Raphael; Nalls, Michael A.; Weedon, Michael N.; Spector, Tim D.; Richards, J. Brent; Bandinelli, Stefania; Ferrucci, Luigi; Singleton, Andrew B.; Frayling, Timothy M.
2013-01-01
Genome-wide association (GWA) studies have been limited by the reliance on common variants present on microarrays or imputable from the HapMap Project data. More recently, the completion of the 1000 Genomes Project has provided variant and haplotype information for several million variants derived from sequencing over 1,000 individuals. To help understand the extent to which more variants (including low frequency (1% ≤ MAF <5%) and rare variants (<1%)) can enhance previously identified associations and identify novel loci, we selected 93 quantitative circulating factors where data was available from the InCHIANTI population study. These phenotypes included cytokines, binding proteins, hormones, vitamins and ions. We selected these phenotypes because many have known strong genetic associations and are potentially important to help understand disease processes. We performed a genome-wide scan for these 93 phenotypes in InCHIANTI. We identified 21 signals and 33 signals that reached P<5×10−8 based on HapMap and 1000 Genomes imputation, respectively, and 9 and 11 that reached a stricter, likely conservative, threshold of P<5×10−11 respectively. Imputation of 1000 Genomes genotype data modestly improved the strength of known associations. Of 20 associations detected at P<5×10−8 in both analyses (17 of which represent well replicated signals in the NHGRI catalogue), six were captured by the same index SNP, five were nominally more strongly associated in 1000 Genomes imputed data and one was nominally more strongly associated in HapMap imputed data. We also detected an association between a low frequency variant and phenotype that was previously missed by HapMap based imputation approaches. An association between rs112635299 and alpha-1 globulin near the SERPINA gene represented the known association between rs28929474 (MAF = 0.007) and alpha1-antitrypsin that predisposes to emphysema (P = 2.5×10−12). Our data provide important proof of principle that 1000 Genomes imputation will detect novel, low frequency-large effect associations. PMID:23696881
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Final report: Mapping Interactions in Hybrid Systems with Active Scanning Probes
DOE Office of Scientific and Technical Information (OSTI.GOV)
Berezovsky, Jesse
2017-09-29
This project aimed to study and map interactions between components of hybrid nanodevices using a novel scanning probe approach. To enable this work, we initially constructed a flexible experimental apparatus allowing for simultaneous scanning probe and confocal optical microscopy measurements. This setup was first used for all-optical measurements of nanostructures, with the focus then shifting to hybrid devices in which single coherent electron spins are coupled to micron-scale ferromagnetic elements, which may prove useful for addressing single spins, enhanced sensing, or spin-wave-mediated coupling of spins for quantum information applications. A significant breakthrough was the realization that it is not necessarymore » to fabricate a magnetic structure on a scanning probe – instead a ferromagnetic vortex core can act as an integrated, solid state, scanning probe. The core of the vortex produces a very strong, localized fringe field which can be used analogously to an MFM tip. Unlike a traditional MFM tip, however, the vortex core is scanned within an integrated device (eliminating drift), and can be moved on vastly faster timescales. This approach allows the detailed investigation of interactions between single spins and complex driven ferromagnetic dynamics.« less
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Resolution-enhanced Mapping Spectrometer
NASA Technical Reports Server (NTRS)
Kumer, J. B.; Aubrun, J. N.; Rosenberg, W. J.; Roche, A. E.
1993-01-01
A familiar mapping spectrometer implementation utilizes two dimensional detector arrays with spectral dispersion along one direction and spatial along the other. Spectral images are formed by spatially scanning across the scene (i.e., push-broom scanning). For imaging grating and prism spectrometers, the slit is perpendicular to the spatial scan direction. For spectrometers utilizing linearly variable focal-plane-mounted filters the spatial scan direction is perpendicular to the direction of spectral variation. These spectrometers share the common limitation that the number of spectral resolution elements is given by the number of pixels along the spectral (or dispersive) direction. Resolution enhancement by first passing the light input to the spectrometer through a scanned etalon or Michelson is discussed. Thus, while a detector element is scanned through a spatial resolution element of the scene, it is also temporally sampled. The analysis for all the pixels in the dispersive direction is addressed. Several specific examples are discussed. The alternate use of a Michelson for the same enhancement purpose is also discussed. Suitable for weight constrained deep space missions, hardware systems were developed including actuators, sensor, and electronics such that low-resolution etalons with performance required for implementation would weigh less than one pound.
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Lin, Yi; Hyyppä, Juha; Kukko, Antero
2013-01-01
This study was dedicated to illustrating the significance of sensor manipulation in the case of terrestrial laser scanning, which is a field now in quick development. In fact, this quickness was mainly rooted in the emergence of new sensors with better performance, while the implications of sensor manipulation have not been fully recognized by the whole community. For this technical gap, the stop-and-go mapping mode can be reckoned as one of the potential solution plans. Stop-and-go was first proposed to handle the low efficiency of traditional static terrestrial laser scanning, and then, it was re-emphasized to improve the stability of sample collections for the state-of-the-art technology of mobile laser scanning. This work reviewed the previous efforts of trying the stop-and-go mode for improving the performance of static and mobile terrestrial laser scanning and generalized their principles respectively. This work also analyzed its advantages compared to the fully-static and fully-kinematic terrestrial laser scanning, and suggested the plans with more automatic measures for raising the efficacy of terrestrial laser scanning. Overall, this literature review indicated that the stop-and-go mapping mode as a case with generic sense can verify the presumption of sensor manipulation as essential as sensor development. PMID:23799493
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CT thermometry for cone-beam CT guided ablation
NASA Astrophysics Data System (ADS)
DeStefano, Zachary; Abi-Jaoudeh, Nadine; Li, Ming; Wood, Bradford J.; Summers, Ronald M.; Yao, Jianhua
2016-03-01
Monitoring temperature during a cone-beam CT (CBCT) guided ablation procedure is important for prevention of over-treatment and under-treatment. In order to accomplish ideal temperature monitoring, a thermometry map must be generated. Previously, this was attempted using CBCT scans of a pig shoulder undergoing ablation.1 We are extending this work by using CBCT scans of real patients and incorporating more processing steps. We register the scans before comparing them due to the movement and deformation of organs. We then automatically locate the needle tip and the ablation zone. We employ a robust change metric due to image noise and artifacts. This change metric takes windows around each pixel and uses an equation inspired by Time Delay Analysis to calculate the error between windows with the assumption that there is an ideal spatial offset. Once the change map is generated, we correlate change data with measured temperature data at the key points in the region. This allows us to transform our change map into a thermal map. This thermal map is then able to provide an estimate as to the size and temperature of the ablation zone. We evaluated our procedure on a data set of 12 patients who had a total of 24 ablation procedures performed. We were able to generate reasonable thermal maps with varying degrees of accuracy. The average error ranged from 2.7 to 16.2 degrees Celsius. In addition to providing estimates of the size of the ablation zone for surgical guidance, 3D visualizations of the ablation zone and needle are also produced.
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NASA Astrophysics Data System (ADS)
Dolezalova, J.; Popelka, S.
2016-06-01
The paper is dealing with scanpath comparison of eye-tracking data recorded during case study focused on the evaluation of 2D and 3D city maps. The experiment contained screenshots from three map portals. Two types of maps were used - standard map and 3D visualization. Respondents' task was to find particular point symbol on the map as fast as possible. Scanpath comparison is one group of the eye-tracking data analyses methods used for revealing the strategy of the respondents. In cartographic studies, the most commonly used application for scanpath comparison is eyePatterns that output is hierarchical clustering and a tree graph representing the relationships between analysed sequences. During an analysis of the algorithm generating a tree graph, it was found that the outputs do not correspond to the reality. We proceeded to the creation of a new tool called ScanGraph. This tool uses visualization of cliques in simple graphs and is freely available at www.eyetracking.upol.cz/scangraph. Results of the study proved the functionality of the tool and its suitability for analyses of different strategies of map readers. Based on the results of the tool, similar scanpaths were selected, and groups of respondents with similar strategies were identified. With this knowledge, it is possible to analyse the relationship between belonging to the group with similar strategy and data gathered from the questionnaire (age, sex, cartographic knowledge, etc.) or type of stimuli (2D, 3D map).
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Mumcuoglu, Tarkan; Wollstein, Gadi; Wojtkowski, Maciej; Kagemann, Larry; Ishikawa, Hiroshi; Gabriele, Michelle L.; Srinivasan, Vivek; Fujimoto, James G.; Duker, Jay S.; Schuman, Joel S.
2009-01-01
Purpose To test if improving optical coherence tomography (OCT) resolution and scanning speed improves the visualization of glaucomatous structural changes as compared with conventional OCT. Design Prospective observational case series. Participants Healthy and glaucomatous subjects in various stages of disease. Methods Subjects were scanned at a single visit with commercially available OCT (StratusOCT) and high-speed ultrahigh-resolution (hsUHR) OCT. The prototype hsUHR OCT had an axial resolution of 3.4 μm (3 times higher than StratusOCT), with an A-scan rate of 24 000 hertz (60 times faster than StratusOCT). The fast scanning rate allowed the acquisition of novel scanning patterns such as raster scanning, which provided dense coverage of the retina and optic nerve head. Main Outcome Measures Discrimination of retinal tissue layers and detailed visualization of retinal structures. Results High-speed UHR OCT provided a marked improvement in tissue visualization as compared with StratusOCT. This allowed the identification of numerous retinal layers, including the ganglion cell layer, which is specifically prone to glaucomatous damage. Fast scanning and the enhanced A-scan registration properties of hsUHR OCT provided maps of the macula and optic nerve head with unprecedented detail, including en face OCT fundus images and retinal nerve fiber layer thickness maps. Conclusion High-speed UHR OCT improves visualization of the tissues relevant to the detection and management of glaucoma. PMID:17884170
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A multi-scale segmentation approach to filling gaps in Landsat ETM+ SLC-off images
Maxwell, S.K.; Schmidt, Gail L.; Storey, James C.
2007-01-01
On 31 May 2003, the Landsat Enhanced Thematic Plus (ETM+) Scan Line Corrector (SLC) failed, causing the scanning pattern to exhibit wedge-shaped scan-to-scan gaps. We developed a method that uses coincident spectral data to fill the image gaps. This method uses a multi-scale segment model, derived from a previous Landsat SLC-on image (image acquired prior to the SLC failure), to guide the spectral interpolation across the gaps in SLC-off images (images acquired after the SLC failure). This paper describes the process used to generate the segment model, provides details of the gap-fill algorithm used in deriving the segment-based gap-fill product, and presents the results of the gap-fill process applied to grassland, cropland, and forest landscapes. Our results indicate this product will be useful for a wide variety of applications, including regional-scale studies, general land cover mapping (e.g. forest, urban, and grass), crop-specific mapping and monitoring, and visual assessments. Applications that need to be cautious when using pixels in the gap areas include any applications that require per-pixel accuracy, such as urban characterization or impervious surface mapping, applications that use texture to characterize landscape features, and applications that require accurate measurements of small or narrow landscape features such as roads, farmsteads, and riparian areas.
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Direct three-dimensional observation of the microstructure and chemistry of C{sub 3}S hydration
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hu, Qinang; Aboustait, Mohammed; Kim, Taehwan
Disagreements about the mechanisms of cement hydration remain despite the fact that portland cement has been studied extensively for over 100 years. One reason for this is that direct observation of the change in microstructure and chemistry are challenging for many experimental techniques. This paper presents results from synchrotron nano X-ray tomography and fluorescence imaging. The data show unprecedented direct observations of small collections of C{sub 3}S particles before and after different periods of hydration in 15 mmol/L lime solution. X-ray absorption contrast is used to make three dimensional maps of the changes of these materials with time. The chemicalmore » compositions of hydration products are then identified with X-ray fluorescence mapping and scanning electron microscopy. These experiments are used to provide insight into the rate and morphology of the microstructure formation.« less
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Space-time patterns of Campylobacter spp. colonization in broiler flocks, 2002-2006.
Jonsson, M E; Norström, M; Sandberg, M; Ersbøll, A K; Hofshagen, M
2010-09-01
This study was performed to investigate space-time patterns of Campylobacter spp. colonization in broiler flocks in Norway. Data on the Campylobacter spp. status at the time of slaughter of 16 054 broiler flocks from 580 farms between 2002 and 2006 was included in the study. Spatial relative risk maps together with maps of space-time clustering were generated, the latter by using spatial scan statistics. These maps identified the same areas almost every year where there was a higher risk for a broiler flock to test positive for Campylobacter spp. during the summer months. A modified K-function analysis showed significant clustering at distances between 2.5 and 4 km within different years. The identification of geographical areas with higher risk for Campylobacter spp. colonization in broilers indicates that there are risk factors associated with Campylobacter spp. colonization in broiler flocks varying with region and time, e.g. climate, landscape or geography. These need to be further explored. The results also showed clustering at shorter distances indicating that there are risk factors for Campylobacter spp. acting in a more narrow scale as well.
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Gabrieli, Francesca; Dooley, Kathryn A; Zeibel, Jason G; Howe, James D; Delaney, John K
2018-06-18
Microscale mid-infrared (mid-IR) imaging spectroscopy is used for the mapping of chemical functional groups. The extension to macroscale imaging requires that either the mid-IR radiation reflected off or that emitted by the object be greater than the radiation from the thermal background. Reflectance spectra can be obtained using an active IR source to increase the amount of radiation reflected off the object, but rapid heating of greater than 4 °C can occur, which is a problem for paintings. Rather than using an active source, by placing a highly reflective tube between the painting and camera and introducing a low temperature source, thermal radiation from the room can be reduced, allowing the IR radiation emitted by the painting to dominate. Thus, emissivity spectra of the object can be recovered. Using this technique, mid-IR emissivity image cubes of paintings were collected at high collection rates with a low-noise, line-scanning imaging spectrometer, which allowed pigments and paint binders to be identified and mapped. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Evidence of a novel quantitative-trait locus for obesity on chromosome 4p in Mexican Americans.
Arya, Rector; Duggirala, Ravindranath; Jenkinson, Christopher P; Almasy, Laura; Blangero, John; O'Connell, Peter; Stern, Michael P
2004-02-01
Although several genomewide scans have identified quantitative-trait loci influencing several obesity-related traits in humans, genes influencing normal variation in obesity phenotypes have not yet been identified. We therefore performed a genome scan of body mass index (BMI) on Mexican Americans, a population prone to obesity and diabetes, using a variance-components linkage analysis to identify loci that influence BMI. We used phenotypic data from 430 individuals (26% diabetics, 59% females, mean age +/- SD = 43 +/- 17 years, mean BMI +/- SD = 30.0 +/- 6.7, mean leptin (ng/ml) +/- SD = 22.1 +/- 17.1) distributed across 27 low-income Mexican American pedigrees who participated in the San Antonio Family Diabetes Study (SAFDS) for whom a 10-15-cM map is available. In this genomewide search, after accounting for the covariate effects of age, sex, diabetes, and leptin, we identified a genetic region exhibiting the most highly significant evidence for linkage (LOD 4.5) with BMI on chromosome 4p (4p15.1) at 42 cM, near marker D4S2912. This linkage result has been confirmed in an independent linkage study of severe obesity in Utah pedigrees. Two strong positional candidates, the human peroxisome proliferator-activated receptor gamma coactivator 1 (PPARGC1) and cholecystokinin A receptor (CCKAR) with major roles in the development of obesity, are located in this region. In conclusion, we identified a major genetic locus influencing BMI on chromosome 4p in Mexican Americans.
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Lu, Ping; Moya, Jaime M.; Yuan, Renliang; ...
2018-03-01
The delocalization of x-ray signals limits the spatial resolution in atomic-scale elemental mapping by scanning transmission electron microscopy (STEM) using energy-dispersive x-ray spectroscopy (EDS). In this study, using a SrTiO 3 [001] single crystal, we show that the x-ray localization to atomic columns is strongly dependent on crystal thickness, and a thin crystal is critical for improving the spatial resolution in atomic-scale EDS mapping. A single-frame scanning technique is used in this study instead of the multiple-frame technique to avoid peak broadening due to tracking error. The strong thickness dependence is realized by measuring the full width at half maximamore » (FWHM) as well as the peak-to-valley (P/V) ratio of the EDS profiles for Ti K and Sr K+L, obtained at several crystal thicknesses. A FWHM of about 0.16 nm and a P/V ratio of greater than 7.0 are obtained for Ti K for a crystal thickness of less than 20 nm. In conclusion, with increasing crystal thickness, the FWHM and P/V ratio increases and decreases, respectively, indicating the advantage of using a thin crystal for high-resolution EDS mapping.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Lu, Ping; Moya, Jaime M.; Yuan, Renliang
The delocalization of x-ray signals limits the spatial resolution in atomic-scale elemental mapping by scanning transmission electron microscopy (STEM) using energy-dispersive x-ray spectroscopy (EDS). In this study, using a SrTiO 3 [001] single crystal, we show that the x-ray localization to atomic columns is strongly dependent on crystal thickness, and a thin crystal is critical for improving the spatial resolution in atomic-scale EDS mapping. A single-frame scanning technique is used in this study instead of the multiple-frame technique to avoid peak broadening due to tracking error. The strong thickness dependence is realized by measuring the full width at half maximamore » (FWHM) as well as the peak-to-valley (P/V) ratio of the EDS profiles for Ti K and Sr K+L, obtained at several crystal thicknesses. A FWHM of about 0.16 nm and a P/V ratio of greater than 7.0 are obtained for Ti K for a crystal thickness of less than 20 nm. In conclusion, with increasing crystal thickness, the FWHM and P/V ratio increases and decreases, respectively, indicating the advantage of using a thin crystal for high-resolution EDS mapping.« less
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Lu, Ping; Moya, Jaime M; Yuan, Renliang; Zuo, Jian Min
2018-03-01
The delocalization of x-ray signals limits the spatial resolution in atomic-scale elemental mapping by scanning transmission electron microscopy (STEM) using energy-dispersive x-ray spectroscopy (EDS). In this study, using a SrTiO 3 [001] single crystal, we show that the x-ray localization to atomic columns is strongly dependent on crystal thickness, and a thin crystal is critical for improving the spatial resolution in atomic-scale EDS mapping. A single-frame scanning technique is used in this study instead of the multiple-frame technique to avoid peak broadening due to tracking error. The strong thickness dependence is realized by measuring the full width at half maxima (FWHM) as well as the peak-to-valley (P/V) ratio of the EDS profiles for Ti K and Sr K + L, obtained at several crystal thicknesses. A FWHM of about 0.16 nm and a P/V ratio of greater than 7.0 are obtained for Ti K for a crystal thickness of less than 20 nm. With increasing crystal thickness, the FWHM and P/V ratio increases and decreases, respectively, indicating the advantage of using a thin crystal for high-resolution EDS mapping. Published by Elsevier B.V.
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3D model assisted fully automated scanning laser Doppler vibrometer measurements
NASA Astrophysics Data System (ADS)
Sels, Seppe; Ribbens, Bart; Bogaerts, Boris; Peeters, Jeroen; Vanlanduit, Steve
2017-12-01
In this paper, a new fully automated scanning laser Doppler vibrometer (LDV) measurement technique is presented. In contrast to existing scanning LDV techniques which use a 2D camera for the manual selection of sample points, we use a 3D Time-of-Flight camera in combination with a CAD file of the test object to automatically obtain measurements at pre-defined locations. The proposed procedure allows users to test prototypes in a shorter time because physical measurement locations are determined without user interaction. Another benefit from this methodology is that it incorporates automatic mapping between a CAD model and the vibration measurements. This mapping can be used to visualize measurements directly on a 3D CAD model. The proposed method is illustrated with vibration measurements of an unmanned aerial vehicle
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Suto, Jun-Ichi; Kojima, Misaki
2017-01-01
DDD/Sgn mice have significantly higher plasma lipid concentrations than C57BL/6J mice. In the present study, we performed quantitative trait loci (QTL) mapping for plasma total-cholesterol (CHO) and triglyceride (TG) concentrations in reciprocal F 2 male intercross populations between the two strains. By single-QTL scans, we identified four significant QTL on chromosomes (Chrs) 1, 5, 17, and 19 for CHO and two significant QTL on Chrs 1 and 12 for TG. By including cross direction as an interactive covariate, we identified separate significant QTL on Chr 17 for CHO but none for TG. When the large phenotypic effect of QTL on Chr 1 was controlled by composite interval mapping, we identified three additional significant QTL on Chrs 3, 4, and 9 for CHO but none for TG. QTL on Chr 19 was a novel QTL for CHO and the allelic effect of this QTL significantly differed between males and females. Whole-exome sequence analysis in DDD/Sgn mice suggested that Apoa2 and Acads were the plausible candidate genes underlying CHO QTL on Chrs 1 and 5, respectively. Thus, we identified a multifactorial basis for plasma lipid concentrations in male mice. These findings will provide insight into the genetic mechanisms of plasma lipid metabolism.
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Kojima, Misaki
2017-01-01
DDD/Sgn mice have significantly higher plasma lipid concentrations than C57BL/6J mice. In the present study, we performed quantitative trait loci (QTL) mapping for plasma total-cholesterol (CHO) and triglyceride (TG) concentrations in reciprocal F2 male intercross populations between the two strains. By single-QTL scans, we identified four significant QTL on chromosomes (Chrs) 1, 5, 17, and 19 for CHO and two significant QTL on Chrs 1 and 12 for TG. By including cross direction as an interactive covariate, we identified separate significant QTL on Chr 17 for CHO but none for TG. When the large phenotypic effect of QTL on Chr 1 was controlled by composite interval mapping, we identified three additional significant QTL on Chrs 3, 4, and 9 for CHO but none for TG. QTL on Chr 19 was a novel QTL for CHO and the allelic effect of this QTL significantly differed between males and females. Whole-exome sequence analysis in DDD/Sgn mice suggested that Apoa2 and Acads were the plausible candidate genes underlying CHO QTL on Chrs 1 and 5, respectively. Thus, we identified a multifactorial basis for plasma lipid concentrations in male mice. These findings will provide insight into the genetic mechanisms of plasma lipid metabolism. PMID:28642824
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Shryock, Daniel F.; Havrilla, Caroline A.; DeFalco, Lesley; Esque, Todd C.; Custer, Nathan; Wood, Troy E.
2015-01-01
Local adaptation influences plant species’ responses to climate change and their performance in ecological restoration. Fine-scale physiological or phenological adaptations that direct demographic processes may drive intraspecific variability when baseline environmental conditions change. Landscape genomics characterize adaptive differentiation by identifying environmental drivers of adaptive genetic variability and mapping the associated landscape patterns. We applied such an approach to Sphaeralcea ambigua, an important restoration plant in the arid southwestern United States, by analyzing variation at 153 amplified fragment length polymorphism loci in the context of environmental gradients separating 47 Mojave Desert populations. We identified 37 potentially adaptive loci through a combination of genome scan approaches. We then used a generalized dissimilarity model (GDM) to relate variability in potentially adaptive loci with spatial gradients in temperature, precipitation, and topography. We identified non-linear thresholds in loci frequencies driven by summer maximum temperature and water stress, along with continuous variation corresponding to temperature seasonality. Two GDM-based approaches for mapping predicted patterns of local adaptation are compared. Additionally, we assess uncertainty in spatial interpolations through a novel spatial bootstrapping approach. Our study presents robust, accessible methods for deriving spatially-explicit models of adaptive genetic variability in non-model species that will inform climate change modelling and ecological restoration.
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Vectorial nanoscale mapping of optical antenna fields by single molecule dipoles.
Singh, Anshuman; Calbris, Gaëtan; van Hulst, Niek F
2014-08-13
Optical nanoantennas confine light on the nanoscale, enabling strong light-matter interactions and ultracompact optical devices. Such confined nanovolumes of light have nonzero field components in all directions (x, y, and z). Unfortunately mapping of the actual nanoscale field vectors has so far remained elusive, though antenna hotspots have been explored by several techniques. In this paper, we present a novel method to probe all three components of the local antenna field. To this end a resonant nanoantenna is fabricated at the vertex of a scanning tip. Next, the nanoantenna is deterministically scanned in close proximity to single fluorescent molecules, whose fixed excitation dipole moment reads out the local field vector. With nanometer molecular resolution, we distinctly map x-, y-, and z-field components of the dipole antenna, i.e. a full vectorial mode map, and show good agreement with full 3D FDTD simulations. Moreover, the fluorescence polarization maps the localized coupling, with emission through the longitudinal antenna mode. Finally, the resonant antenna probe is used for single molecule imaging with 40 nm fwhm response function. The total fluorescence enhancement is 7.6 times, while out-of-plane molecules, almost undetectable in far-field, are made visible by the strong antenna z-field with a fluorescence enhancement up to 100 times. Interestingly, the apparent position of molecules shifts up to 20 nm depending on their orientation. The capability to resolve orientational information on the single molecule level makes the scanning resonant antenna an ideal tool for extreme resolution bioimaging.
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Laser Pyrometer For Spot Temperature Measurements
NASA Technical Reports Server (NTRS)
Elleman, D. D.; Allen, J. L.; Lee, M. C.
1988-01-01
Laser pyrometer makes temperature map by scanning measuring spot across target. Scanning laser pyrometer passively measures radiation emitted by scanned spot on target and calibrated by similar passive measurement on blackbody of known temperature. Laser beam turned on for active measurements of reflectances of target spot and reflectance standard. From measurements, temperature of target spot inferred. Pyrometer useful for non-contact measurement of temperature distributions in processing of materials.
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Buscombe, Daniel; Wheaton, Joseph M.
2018-01-01
Side scan sonar in low-cost ‘fishfinder’ systems has become popular in aquatic ecology and sedimentology for imaging submerged riverbed sediment at coverages and resolutions sufficient to relate bed texture to grain-size. Traditional methods to map bed texture (i.e. physical samples) are relatively high-cost and low spatial coverage compared to sonar, which can continuously image several kilometers of channel in a few hours. Towards a goal of automating the classification of bed habitat features, we investigate relationships between substrates and statistical descriptors of bed textures in side scan sonar echograms of alluvial deposits. We develop a method for automated segmentation of bed textures into between two to five grain-size classes. Second-order texture statistics are used in conjunction with a Gaussian Mixture Model to classify the heterogeneous bed into small homogeneous patches of sand, gravel, and boulders with an average accuracy of 80%, 49%, and 61%, respectively. Reach-averaged proportions of these sediment types were within 3% compared to similar maps derived from multibeam sonar. PMID:29538449
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Zheng, Changlin; Zhu, Ye; Lazar, Sorin; Etheridge, Joanne
2014-04-25
We introduce off-axis chromatic scanning confocal electron microscopy, a technique for fast mapping of inelastically scattered electrons in a scanning transmission electron microscope without a spectrometer. The off-axis confocal mode enables the inelastically scattered electrons to be chromatically dispersed both parallel and perpendicular to the optic axis. This enables electrons with different energy losses to be separated and detected in the image plane, enabling efficient energy filtering in a confocal mode with an integrating detector. We describe the experimental configuration and demonstrate the method with nanoscale core-loss chemical mapping of silver (M4,5) in an aluminium-silver alloy and atomic scale imaging of the low intensity core-loss La (M4,5@840 eV) signal in LaB6. Scan rates up to 2 orders of magnitude faster than conventional methods were used, enabling a corresponding reduction in radiation dose and increase in the field of view. If coupled with the enhanced depth and lateral resolution of the incoherent confocal configuration, this offers an approach for nanoscale three-dimensional chemical mapping.
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NASA Astrophysics Data System (ADS)
Bentaieb, Samia; Ouamri, Abdelaziz; Nait-Ali, Amine; Keche, Mokhtar
2018-01-01
We propose and evaluate a three-dimensional (3D) face recognition approach that applies the speeded up robust feature (SURF) algorithm to the depth representation of shape index map, under real-world conditions, using only a single gallery sample for each subject. First, the 3D scans are preprocessed, then SURF is applied on the shape index map to find interest points and their descriptors. Each 3D face scan is represented by keypoints descriptors, and a large dictionary is built from all the gallery descriptors. At the recognition step, descriptors of a probe face scan are sparsely represented by the dictionary. A multitask sparse representation classification is used to determine the identity of each probe face. The feasibility of the approach that uses the SURF algorithm on the shape index map for face identification/authentication is checked through an experimental investigation conducted on Bosphorus, University of Milano Bicocca, and CASIA 3D datasets. It achieves an overall rank one recognition rate of 97.75%, 80.85%, and 95.12%, respectively, on these datasets.
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3D Reconstruction of Irregular Buildings and Buddha Statues
NASA Astrophysics Data System (ADS)
Zhang, K.; Li, M.-j.
2014-04-01
Three-dimensional laser scanning could acquire object's surface data quickly and accurately. However, the post-processing of point cloud is not perfect and could be improved. Based on the study of 3D laser scanning technology, this paper describes the details of solutions to modelling irregular ancient buildings and Buddha statues in Jinshan Temple, which aiming at data acquisition, modelling and texture mapping, etc. In order to modelling irregular ancient buildings effectively, the structure of each building is extracted manually by point cloud and the textures are mapped by the software of 3ds Max. The methods clearly combine 3D laser scanning technology with traditional modelling methods, and greatly improves the efficiency and accuracy of the ancient buildings restored. On the other hand, the main idea of modelling statues is regarded as modelling objects in reverse engineering. The digital model of statues obtained is not just vivid, but also accurate in the field of surveying and mapping. On this basis, a 3D scene of Jinshan Temple is reconstructed, which proves the validity of the solutions.
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Spatiotemporal analysis of dengue fever in Nepal from 2010 to 2014.
Acharya, Bipin Kumar; Cao, ChunXiang; Lakes, Tobia; Chen, Wei; Naeem, Shahid
2016-08-22
Due to recent emergence, dengue is becoming one of the major public health problems in Nepal. The numbers of reported dengue cases in general and the area with reported dengue cases are both continuously increasing in recent years. However, spatiotemporal patterns and clusters of dengue have not been investigated yet. This study aims to fill this gap by analyzing spatiotemporal patterns based on monthly surveillance data aggregated at district. Dengue cases from 2010 to 2014 at district level were collected from the Nepal government's health and mapping agencies respectively. GeoDa software was used to map crude incidence, excess hazard and spatially smoothed incidence. Cluster analysis was performed in SaTScan software to explore spatiotemporal clusters of dengue during the above-mentioned time period. Spatiotemporal distribution of dengue fever in Nepal from 2010 to 2014 was mapped at district level in terms of crude incidence, excess risk and spatially smoothed incidence. Results show that the distribution of dengue fever was not random but clustered in space and time. Chitwan district was identified as the most likely cluster and Jhapa district was the first secondary cluster in both spatial and spatiotemporal scan. July to September of 2010 was identified as a significant temporal cluster. This study assessed and mapped for the first time the spatiotemporal pattern of dengue fever in Nepal. Two districts namely Chitwan and Jhapa were found highly affected by dengue fever. The current study also demonstrated the importance of geospatial approach in epidemiological research. The initial result on dengue patterns and risk of this study may assist institutions and policy makers to develop better preventive strategies.
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NASA Astrophysics Data System (ADS)
Chang, Yu Min; Lu, Nien Hua; Wu, Tsung Chiang
2005-06-01
This study applies 3D Laser scanning technology to develop a high-precision measuring system for digital survey of historical building. It outperformed other methods in obtaining abundant high-precision measuring points and computing data instantly. In this study, the Pei-tien Temple, a Chinese Taoism temple in southern Taiwan famous for its highly intricate architecture and more than 300-year history, was adopted as the target to proof the high accuracy and efficiency of this system. By using French made MENSI GS-100 Laser Scanner, numerous measuring points were precisely plotted to present the plane map, vertical map and 3D map of the property. Accuracies of 0.1-1 mm in the digital data have consistently been achieved for the historical heritage measurement.
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The Infrared Astronomical Satellite /IRAS/ Scientific Data Analysis System /SDAS/ sky flux subsystem
NASA Technical Reports Server (NTRS)
Stagner, J. R.; Girard, M. A.
1980-01-01
The sky flux subsystem of the Infrared Astronomical Satellite Scientific Data Analysis System is described. Its major output capabilities are (1) the all-sky lune maps (8-arcminute pixel size), (2) galactic plane maps (2-arcminute pixel size) and (3) regional maps of small areas such as extended sources greater than 1-degree in extent. The major processing functions are to (1) merge the CRDD and pointing data, (2) phase the detector streams, (3) compress the detector streams in the in-scan and cross-scan directions, and (4) extract data. Functional diagrams of the various capabilities of the subsystem are given. Although this device is inherently nonimaging, various calibrated and geometrically controlled imaging products are created, suitable for quantitative and qualitative scientific interpretation.
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High-Resolution Underwater Mapping Using Side-Scan Sonar
2016-01-01
The goal of this study is to generate high-resolution sea floor maps using a Side-Scan Sonar(SSS). This is achieved by explicitly taking into account the SSS operation as follows. First, the raw sensor data is corrected by means of a physics-based SSS model. Second, the data is projected to the sea-floor. The errors involved in this projection are thoroughfully analysed. Third, a probabilistic SSS model is defined and used to estimate the probability of each sea-floor region to be observed. This probabilistic information is then used to weight the contribution of each SSS measurement to the map. Because of these models, arbitrary map resolutions can be achieved, even beyond the sensor resolution. Finally, a geometric map building method is presented and combined with the probabilistic approach. The resulting map is composed of two layers. The echo intensity layer holds the most likely echo intensities at each point in the sea-floor. The probabilistic layer contains information about how confident can the user or the higher control layers be about the echo intensity layer data. Experimental results have been conducted in a large subsea region. PMID:26821379
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NASA Astrophysics Data System (ADS)
Ko, Tony H.; Hartl, Ingmar; Drexler, Wolfgang; Ghanta, Ravi K.; Fujimoto, James G.
2002-06-01
Quantitative, three-dimensional mapping of retinal architectural morphology was achieved using an ultrahigh resolution ophthalmic OCT system. This OCT system utilizes a broad bandwidth titanium-sapphire laser light source generating bandwidths of up to 300 nm near 800 nm center wavelength. The system enables real-time cross-sectional imaging of the retina with ~3 micrometers axial resolution. The macula and the papillomacular axis of a normal human subject were systematically mapped using a series of linear scans. Edge detection and segmentation algorithms were developed to quantify retinal and intraretinal thicknesses. Topographic mapping of the total retinal thickness and the total ganglion cell/inner plexiform layer thickness was achieved around the macula. A topographic mapping quantifying the progressive thickening of the nerve fiber layer (NFL) nasally approaching the optic disk was also demonstrated. The ability to create three-dimensional topographic mapping of retinal architectural morphology at ~3 micrometers axial resolution will be relevant for the diagnosis of many retinal diseases. The topographic quantification of these structures can serve as a powerful tool for developing algorithms and clinical scanning protocols for the screening and staging of ophthalmic diseases such as glaucoma.
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Fractional CO₂ Laser Pretreatment Facilitates Transdermal Delivery of Two Vitamin C Derivatives.
Hsiao, Chien-Yu; Sung, Hsin-Ching; Hu, Sindy; Huang, Yau-Li; Huang, Chun-Hsun
2016-11-16
Topical vitamin C derivatives have been used to treat melasma and used as a skin whitener. The aim of this study was to compare skin histology and permeation of l-ascorbic acid 2-phosphate sesquimagnesium salt (MAP-1) and magnesium l-ascorbic acid-2-phosphate (MAP-2) after fractional CO₂ laser pretreatment. The effect of fractional laser treatment on porcine skin was examined by scanning electron microscopy and confocal laser scanning electron microscopy. The effect of fractional CO₂ laser treatment of different fluencies and pass numbers on transdermal flux of the two vitamin C derivatives through porcine skin was examined in vitro using a Franz diffusion chamber. Fluxes of MAP-1 and MAP-2 across fractional CO₂ laser-treated (5 W) skin were eight- to 13-fold, and 20- to 22-fold higher, respectively, than the fluxes of these compounds across intact skin. Fluxes of MAP-1 and MAP-2 across fractional CO₂ laser-treated (9 W) skin were 14- to 19-fold, and 30- to 42-fold higher, respectively, than their fluxes across intact skin. Fractional CO₂ laser treatment is an effective way of delivering vitamin C derivatives into the skin.
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Gandhi, S D; Kishore, V K; Crane, J M; Slabaugh, M B; Knapp, S J
2009-06-01
Erucic acid (22:1(13)) has been identified as an anti-nutritional compound in meadowfoam (Limnanthes alba) and other oilseeds in the Brassicales, a classification which has necessitated the development of low erucic acid cultivars for human consumption. The erucic acid concentrations of meadowfoam wild types (8%-24%) surpass industry standards for human consumption (
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Radiation hybrid mapping of genes in the lithium-sensitive wnt signaling pathway.
Rhoads, A R; Karkera, J D; Detera-Wadleigh, S D
1999-09-01
Lithium, an effective drug in the treatment of bipolar disorder, has been proposed to disrupt the Wnt signaling pathway. To facilitate analysis of the possible involvement of elements of the Wnt pathway in human bipolar disorder, a high resolution radiation hybrid mapping (RHM) of these genes was performed. A fine physical location has been obtained for Wnt 7A, frizzled 3, 4 and 5, dishevelled 1, 2 and 3, GSK3beta, axin, alpha-catenin, the Armadillo repeat-containing genes (delta-catenin and ARVCF), and a frizzled-like protein (frpHE) using the Stanford Human Genome Center (SHGC) G3 panel. Most of these genes were previously mapped by fluorescence in situ hybridization (FISH). Frizzled 4, axin and frpHE did not have a previous chromosomal assignment and were linked by RHM to chromosome markers, SHGC-35131 at 11q22.1, NIB1488 at 16p13.3 and D7S2919 at 7p15.2, respectively. Interestingly, some of these genes were found to map within potential regions underlying susceptibility to bipolar disorder and schizophrenia as well as disorders of neurodevelopmental origin. This alternative approach of establishing the precise location of selected genetic components of a candidate pathway and determining if they map within previously defined susceptibility loci should help to identify plausible candidate genes that warrant further analysis through association and mutational scanning.
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Bayesian Deconvolution for Angular Super-Resolution in Forward-Looking Scanning Radar
Zha, Yuebo; Huang, Yulin; Sun, Zhichao; Wang, Yue; Yang, Jianyu
2015-01-01
Scanning radar is of notable importance for ground surveillance, terrain mapping and disaster rescue. However, the angular resolution of a scanning radar image is poor compared to the achievable range resolution. This paper presents a deconvolution algorithm for angular super-resolution in scanning radar based on Bayesian theory, which states that the angular super-resolution can be realized by solving the corresponding deconvolution problem with the maximum a posteriori (MAP) criterion. The algorithm considers that the noise is composed of two mutually independent parts, i.e., a Gaussian signal-independent component and a Poisson signal-dependent component. In addition, the Laplace distribution is used to represent the prior information about the targets under the assumption that the radar image of interest can be represented by the dominant scatters in the scene. Experimental results demonstrate that the proposed deconvolution algorithm has higher precision for angular super-resolution compared with the conventional algorithms, such as the Tikhonov regularization algorithm, the Wiener filter and the Richardson–Lucy algorithm. PMID:25806871
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Brodusch, N; Demers, H; Gauvin, R
2013-04-01
A charge-coupled device camera of an electron backscattered diffraction system in a scanning electron microscope was positioned below a thin specimen and transmission Kikuchi patterns were collected. Contrary to electron backscattered diffraction, transmission electron forward scatter diffraction provides phase identification and orientation mapping at the nanoscale. The minimum Pd particle size for which a Kikuchi diffraction pattern was detected and indexed reliably was 5.6 nm. An orientation mapping resolution of 5 nm was measured at 30 kV. The resolution obtained with transmission electron forward scatter diffraction was of the same order of magnitude than that reported in electron nanodiffraction in the transmission electron microscope. An energy dispersive spectrometer X-ray map and a transmission electron forward scatter diffraction orientation map were acquired simultaneously. The high-resolution chemical, phase and orientation maps provided at once information on the chemical form, orientation and coherency of precipitates in an aluminium-lithium 2099 alloy. © 2013 The Authors Journal of Microscopy © 2013 Royal Microscopical Society.
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Geographical Clusters of Rape in the United States: 2000-2012
Amin, Raid; Nabors, Nicole S.; Nelson, Arlene M.; Saqlain, Murshid; Kulldorff, Martin
2016-01-01
Background While rape is a very serious crime and public health problem, no spatial mapping has been attempted for rape on the national scale. This paper addresses the three research questions: (1) Are reported rape cases randomly distributed across the USA, after being adjusted for population density and age, or are there geographical clusters of reported rape cases? (2) Are the geographical clusters of reported rapes still present after adjusting for differences in poverty levels? (3) Are there geographical clusters where the proportion of reported rape cases that lead to an arrest is exceptionally low or exceptionally high? Methods We studied the geographical variation of reported rape events (2003-2012) and rape arrests (2000-2012) in the 48 contiguous states of the USA. The disease Surveillance software SaTScan™ with its spatial scan statistic is used to evaluate the spatial variation in rapes. The spatial scan statistic has been widely used as a geographical surveillance tool for diseases, and we used it to identify geographical areas with clusters of reported rape and clusters of arrest rates for rape. Results The spatial scan statistic was used to identify geographical areas with exceptionally high rates of reported rape. The analyses were adjusted for age, and in secondary analyses, for both age and poverty level. We also identified geographical areas with either a low or a high proportion of reported rapes leading to an arrest. Conclusions We have identified geographical areas with exceptionally high (low) rates of reported rape. The geographical problem areas identified are prime candidates for more intensive preventive counseling and criminal prosecution efforts by public health, social service, and law enforcement agencies Geographical clusters of high rates of reported rape are prime areas in need of expanded implementation of preventive measures, such as changing attitudes in our society toward rape crimes, in addition to having the criminal justice system play an even larger role in preventing rape. PMID:28078318
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Geographical Clusters of Rape in the United States: 2000-2012.
Amin, Raid; Nabors, Nicole S; Nelson, Arlene M; Saqlain, Murshid; Kulldorff, Martin
2015-01-01
While rape is a very serious crime and public health problem, no spatial mapping has been attempted for rape on the national scale. This paper addresses the three research questions: (1) Are reported rape cases randomly distributed across the USA, after being adjusted for population density and age, or are there geographical clusters of reported rape cases? (2) Are the geographical clusters of reported rapes still present after adjusting for differences in poverty levels? (3) Are there geographical clusters where the proportion of reported rape cases that lead to an arrest is exceptionally low or exceptionally high? We studied the geographical variation of reported rape events (2003-2012) and rape arrests (2000-2012) in the 48 contiguous states of the USA. The disease Surveillance software SaTScan™ with its spatial scan statistic is used to evaluate the spatial variation in rapes. The spatial scan statistic has been widely used as a geographical surveillance tool for diseases, and we used it to identify geographical areas with clusters of reported rape and clusters of arrest rates for rape. The spatial scan statistic was used to identify geographical areas with exceptionally high rates of reported rape. The analyses were adjusted for age, and in secondary analyses, for both age and poverty level. We also identified geographical areas with either a low or a high proportion of reported rapes leading to an arrest. We have identified geographical areas with exceptionally high (low) rates of reported rape. The geographical problem areas identified are prime candidates for more intensive preventive counseling and criminal prosecution efforts by public health, social service, and law enforcement agencies Geographical clusters of high rates of reported rape are prime areas in need of expanded implementation of preventive measures, such as changing attitudes in our society toward rape crimes, in addition to having the criminal justice system play an even larger role in preventing rape.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Patton, T; Du, K; Bayouth, J
2015-06-15
Purpose: Longitudinal changes in lung ventilation following radiation therapy can be mapped using four-dimensional computed tomography(4DCT) and image registration. This study aimed to predict ventilation changes caused by radiation therapy(RT) as a function of pre-RT ventilation and delivered dose. Methods: 4DCT images were acquired before and 3 months after radiation therapy for 13 subjects. Jacobian ventilation maps were calculated from the 4DCT images, warped to a common coordinate system, and a Jacobian ratio map was computed voxel-by-voxel as the ratio of post-RT to pre-RT Jacobian calculations. A leave-one-out method was used to build a response model for each subject: post-RTmore » to pre-RT Jacobian ratio data and dose distributions of 12 subjects were applied to the subject’s pre-RT Jacobian map to predict the post-RT Jacobian. The predicted Jacobian map was compared to the actual post-RT Jacobian map to evaluate efficacy. Within this cohort, 8 subjects had repeat pre-RT scans that were compared as a reference for no ventilation change. Maps were compared using gamma pass rate criteria of 2mm distance-to-agreement and 6% ventilation difference. Gamma pass rates were compared using paired t-tests to determine significant differences. Further analysis masked non-radiation induced changes by excluding voxels below specified dose thresholds. Results: Visual inspection demonstrates the predicted post-RT ventilation map is similar to the actual map in magnitude and distribution. Quantitatively, the percentage of voxels in agreement when excluding voxels receiving below specified doses are: 74%/20Gy, 73%/10Gy, 73%/5Gy, and 71%/0Gy. By comparison, repeat scans produced 73% of voxels within the 6%/2mm criteria. The agreement of the actual post-RT maps with the predicted maps was significantly better than agreement with pre-RT maps (p<0.02). Conclusion: This work validates that significant changes to ventilation post-RT can be predicted. The differences between the predicted and actual outcome are similar to differences between repeat scans with equivalent ventilation. This work was supported by NIH grant CA166703 and a Pilot Grant from University of Iowa Carver College of Medicine.« less
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Bulluck, Heerajnarain; Hammond-Haley, Matthew; Fontana, Marianna; Knight, Daniel S; Sirker, Alex; Herrey, Anna S; Manisty, Charlotte; Kellman, Peter; Moon, James C; Hausenloy, Derek J
2017-08-01
A comprehensive cardiovascular magnetic resonance (CMR) in reperfused ST-segment myocardial infarction (STEMI) patients can be challenging to perform and can be time-consuming. We aimed to investigate whether native T1-mapping can accurately delineate the edema-based area-at-risk (AAR) and post-contrast T1-mapping and synthetic late gadolinium (LGE) images can quantify MI size at 1.5 T. Conventional LGE imaging and T2-mapping could then be omitted, thereby shortening the scan duration. Twenty-eight STEMI patients underwent a CMR scan at 1.5 T, 3 ± 1 days following primary percutaneous coronary intervention. The AAR was quantified using both native T1 and T2-mapping. MI size was quantified using conventional LGE, post-contrast T1-mapping and synthetic magnitude-reconstructed inversion recovery (MagIR) LGE and synthetic phase-sensitive inversion recovery (PSIR) LGE, derived from the post-contrast T1 maps. Native T1-mapping performed as well as T2-mapping in delineating the AAR (41.6 ± 11.9% of the left ventricle [% LV] versus 41.7 ± 12.2% LV, P = 0.72; R 2 0.97; ICC 0.986 (0.969-0.993); bias -0.1 ± 4.2% LV). There were excellent correlation and inter-method agreement with no bias, between MI size by conventional LGE, synthetic MagIR LGE (bias 0.2 ± 2.2%LV, P = 0.35), synthetic PSIR LGE (bias 0.4 ± 2.2% LV, P = 0.060) and post-contrast T1-mapping (bias 0.3 ± 1.8% LV, P = 0.10). The mean scan duration was 58 ± 4 min. Not performing T2 mapping (6 ± 1 min) and conventional LGE (10 ± 1 min) would shorten the CMR study by 15-20 min. T1-mapping can accurately quantify both the edema-based AAR (using native T1 maps) and acute MI size (using post-contrast T1 maps) in STEMI patients without major cardiovascular risk factors. This approach would shorten the duration of a comprehensive CMR study without significantly compromising on data acquisition and would obviate the need to perform T2 maps and LGE imaging.
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Wiltshire, Steven; Hattersley, Andrew T.; Hitman, Graham A.; Walker, Mark; Levy, Jonathan C.; Sampson, Michael; O’Rahilly, Stephen; Frayling, Timothy M.; Bell, John I.; Lathrop, G. Mark; Bennett, Amanda; Dhillon, Ranjit; Fletcher, Christopher; Groves, Christopher J.; Jones, Elizabeth; Prestwich, Philip; Simecek, Nikol; Rao, Pamidighantam V. Subba; Wishart, Marie; Foxon, Richard; Howell, Simon; Smedley, Damian; Cardon, Lon R.; Menzel, Stephan; McCarthy, Mark I.
2001-01-01
Improved molecular understanding of the pathogenesis of type 2 diabetes is essential if current therapeutic and preventative options are to be extended. To identify diabetes-susceptibility genes, we have completed a primary (418-marker, 9-cM) autosomal-genome scan of 743 sib pairs (573 pedigrees) with type 2 diabetes who are from the Diabetes UK Warren 2 repository. Nonparametric linkage analysis of the entire data set identified seven regions showing evidence for linkage, with allele-sharing LOD scores ⩾1.18 (P⩽.01). The strongest evidence was seen on chromosomes 8p21-22 (near D8S258 [LOD score 2.55]) and 10q23.3 (near D10S1765 [LOD score 1.99]), both coinciding with regions identified in previous scans in European subjects. This was also true of two lesser regions identified, on chromosomes 5q13 (D5S647 [LOD score 1.22] and 5q32 (D5S436 [LOD score 1.22]). Loci on 7p15.3 (LOD score 1.31) and 8q24.2 (LOD score 1.41) are novel. The final region showing evidence for linkage, on chromosome 1q24-25 (near D1S218 [LOD score 1.50]), colocalizes with evidence for linkage to diabetes found in Utah, French, and Pima families and in the GK rat. After dense-map genotyping (mean marker spacing 4.4 cM), evidence for linkage to this region increased to a LOD score of 1.98. Conditional analyses revealed nominally significant interactions between this locus and the regions on chromosomes 10q23.3 (P=.01) and 5q32 (P=.02). These data, derived from one of the largest genome scans undertaken in this condition, confirm that individual susceptibility-gene effects for type 2 diabetes are likely to be modest in size. Taken with genome scans in other populations, they provide both replication of previous evidence indicating the presence of a diabetes-susceptibility locus on chromosome 1q24-25 and support for the existence of additional loci on chromosomes 5, 8, and 10. These data should accelerate positional cloning efforts in these regions of interest. PMID:11484155
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Site assessment using echo sounding, side scan sonar and sub-bottom profiling.
DOT National Transportation Integrated Search
2014-02-01
The primary objective of this research is to use multifaceted geophysical data techniques in order to better map karst terrain beneath : standing bodies of water. This study may help providing stronger mapping techniques for future bridge and dam con...
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Identification of polymorphic inversions from genotypes
2012-01-01
Background Polymorphic inversions are a source of genetic variability with a direct impact on recombination frequencies. Given the difficulty of their experimental study, computational methods have been developed to infer their existence in a large number of individuals using genome-wide data of nucleotide variation. Methods based on haplotype tagging of known inversions attempt to classify individuals as having a normal or inverted allele. Other methods that measure differences between linkage disequilibrium attempt to identify regions with inversions but unable to classify subjects accurately, an essential requirement for association studies. Results We present a novel method to both identify polymorphic inversions from genome-wide genotype data and classify individuals as containing a normal or inverted allele. Our method, a generalization of a published method for haplotype data [1], utilizes linkage between groups of SNPs to partition a set of individuals into normal and inverted subpopulations. We employ a sliding window scan to identify regions likely to have an inversion, and accumulation of evidence from neighboring SNPs is used to accurately determine the inversion status of each subject. Further, our approach detects inversions directly from genotype data, thus increasing its usability to current genome-wide association studies (GWAS). Conclusions We demonstrate the accuracy of our method to detect inversions and classify individuals on principled-simulated genotypes, produced by the evolution of an inversion event within a coalescent model [2]. We applied our method to real genotype data from HapMap Phase III to characterize the inversion status of two known inversions within the regions 17q21 and 8p23 across 1184 individuals. Finally, we scan the full genomes of the European Origin (CEU) and Yoruba (YRI) HapMap samples. We find population-based evidence for 9 out of 15 well-established autosomic inversions, and for 52 regions previously predicted by independent experimental methods in ten (9+1) individuals [3,4]. We provide efficient implementations of both genotype and haplotype methods as a unified R package inveRsion. PMID:22321652
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Recent Coselection in Human Populations Revealed by Protein–Protein Interaction Network
Qian, Wei; Zhou, Hang; Tang, Kun
2015-01-01
Genome-wide scans for signals of natural selection in human populations have identified a large number of candidate loci that underlie local adaptations. This is surprising given the relatively short evolutionary time since the divergence of the human population. One hypothesis that has not been formally examined is whether and how the recent human evolution may have been shaped by coselection in the context of complex molecular interactome. In this study, genome-wide signals of selection were scanned in East Asians, Europeans, and Africans using 1000 Genome data, and subsequently mapped onto the protein–protein interaction (PPI) network. We found that the candidate genes of recent positive selection localized significantly closer to each other on the PPI network than expected, revealing substantial clustering of selected genes. Furthermore, gene pairs of shorter PPI network distances showed higher similarities of their recent evolutionary paths than those further apart. Last, subnetworks enriched with recent coselection signals were identified, which are substantially overrepresented in biological pathways related to signal transduction, neurogenesis, and immune function. These results provide the first genome-wide evidence for association of recent selection signals with the PPI network, shedding light on the potential mechanisms of recent coselection in the human genome. PMID:25532814
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Spatial Analysis of Hemorrhagic Fever with Renal Syndrome in Zibo City, China, 2009–2012
Wang, Ling; Yang, Shuxia; Zhang, Ling; Cao, Haixia; Zhang, Yan; Hu, Haodong; Zhai, Shenyong
2013-01-01
Background Hemorrhagic fever with renal syndrome (HFRS) is highly endemic in mainland China, where human cases account for 90% of the total global cases. Zibo City is one of the most serious affected areas in Shandong Province China with the HFRS incidence increasing sharply from 2009 to 2012. However, the hotspots of HFRS in Zibo remained unclear. Thus, a spatial analysis was conducted with the aim to explore the spatial, spatial-temporal and seasonal patterns of HFRS in Zibo from 2009 to 2012, and to provide guidance for formulating regional prevention and control strategies. Methods The study was based on the reported cases of HFRS from the National Notifiable Disease Surveillance System. Annualized incidence maps and seasonal incidence maps were produced to analyze the spatial and seasonal distribution of HFRS in Zibo City. Then spatial scan statistics and space-time scan statistics were conducted to identify clusters of HFRS. Results There were 200 cases reported in Zibo City during the 4-year study period. One most likely cluster and one secondary cluster for high incidence of HFRS were identified by the space-time analysis. And the most likely cluster was found to exist at Yiyuan County in October to December 2012. The human infections in the fall and winter reflected a seasonal characteristic pattern of Hantaan virus (HTNV) transmission. The secondary cluster was detected at the center of Zibo in May to June 2009, presenting a seasonal characteristic of Seoul virus (SEOV) transmission. Conclusion To control and prevent HFRS in Zibo city, the comprehensive preventive strategy should be implemented in the southern areas of Zibo in autumn and in the northern areas of Zibo in spring. PMID:23840719
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Lillie, Elizabeth M; Urban, Jillian E; Lynch, Sarah K; Whitlow, Christopher T; Stitzel, Joel D
2013-01-01
Diffuse axonal injury (DAI) is a common traumatic brain injury (TBI) often seen as a result of motor vehicle crashes (MVC). Twelve (12) cases of DAI were selected from the Crash Injury Research and Engineering Network (CIREN) to determine the extent and distribution of injury with respect to the head contact location. Head computed tomography (CT) scans were collected for each subject and segmented using semi-automated methods to establish the volumes of DAI. The impacted area on the subject's head was approximated from evidence of a soft tissue scalp contusion on the CT scan. This was used in conjunction with subject images and identified internal vehicle contact locations to ascertain a label map of the contact location. A point cloud was developed from the contact location label map and the centroid of the point cloud was calculated as the subject's head impact location. The injury and contact location were evaluated in spherical coordinates and grouped into 0.2 by 0.2 radial increments of azimuth and elevation. The radial increments containing DAI were projected onto a meshed sphere to evaluate the radial distance from the impact location to primary location of DAI and approximate anatomical location. Of the 170 injuries observed, 123 were identified in the frontal lobe and 36 in the parietal lobe. The distribution of the DAI in relation to the change in azimuth from the contact loca y correlated with contact to the head superficial to this lobe. Results from this study provide further insight into the biomechanics of traumatic brain injury and can be used in future work as an aid to validate finite element models of the head.
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Multielement mapping of alpha-SiC by scanning Auger microscopy
NASA Technical Reports Server (NTRS)
Browning, Ray; Smialek, James L.; Jacobson, Nathan S.
1987-01-01
Fine second-phase particles, numerous in sintered alpha-SiC, were analyzed by scanning Auger microscopy and conventional techniques. The Auger analysis utilized computer-controlled data acquisition, multielement correlation diagrams, and a high spatial resolution of 100 nm. This procedure enabled construction of false color maps and the detection of fine compositional details within these particles. Carbon, silicon oxide, and boron-rich particles (qualitatively as BN or B4C) predominated. The BN particles, sometimes having a carbon core, are believed to result from reaction between B4C additives and nitrogen sintering atmospheres.
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Innovative method for optimizing Side-Scan Sonar mapping: The blind band unveiled
NASA Astrophysics Data System (ADS)
Pergent, Gérard; Monnier, Briac; Clabaut, Philippe; Gascon, Gilles; Pergent-Martini, Christine; Valette-Sansevin, Audrey
2017-07-01
Over the past few years, the mapping of Mediterranean marine habitats has become a priority for scientists, environment managers and stakeholders, in particular in order to comply with European directives (Water Framework Directive and Marine Strategy Framework Directive) and to implement legislation to ensure their conservation. Side-scan sonar (SSS) is recognised as one of the most effective tool for underwater mapping. However, interpretation of acoustic data (sonograms) requires extensive field calibration and the ground-truthing process remains essential. Several techniques are commonly used, with sampling methods involving grabs, scuba diving observations or Remotely Operated Vehicle (ROV) underwater video recordings. All these techniques are time consuming, expensive and only provide sporadic informations. In the present study, the possibility of coupling a camera with a SSS and acquiring underwater videos in a continuous way has been tested. During the 'PosidCorse' oceanographic survey carried out along the eastern coast of Corsica, optical and acoustic data were respectively obtained using a GoPro™ camera and a Klein 3000™ SSS. Thereby, five profiles were performed between 10 and 50 m depth, corresponding to more than 20 km of data acquisition. The vertical images recorded with the camera fixed under the SSS and positioned facing downwards provided photo mosaics of very good quality corresponding to the entire sonograms's blind band. From the photo mosaics, 94% of the different bottom types and main habitats have been identified; specific structures linked to hydrodynamics conditions, anthropic and biological activities have also been observed as well as the substrate on which the Posidonia oceanica meadow grows. The association between acoustic data and underwater videos has proved to be a non-destructive and cost-effective method for ground-truthing in marine habitats mapping. Nevertheless, in order to optimize the results over the next surveys, certain limitations will need to be remedied.
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NASA Astrophysics Data System (ADS)
Ryou, Heonjune
2011-12-01
In this study Dynamic Mechanical Analysis (DMA) was applied to dentin, the macro hybrid layer and intact hybrid layers of the bonded dental restorative interface using nanoindentation. Both intertubular and peritubular dentin were evaluated by DMA using discrete and scanning mode nanoindentation. The complex (E*), loss (E"), and storage (E') moduli were quantified over a range of indentation loads and scanning frequencies. The storage modulus of the peritubular cuff (22.19 GPa
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Exploring the architectural trade space of NASAs Space Communication and Navigation Program
NASA Astrophysics Data System (ADS)
Sanchez, M.; Selva, D.; Cameron, B.; Crawley, E.; Seas, A.; Seery, B.
NASAs Space Communication and Navigation (SCaN) Program is responsible for providing communication and navigation services to space missions and other users in and beyond low Earth orbit. The current SCaN architecture consists of three independent networks: the Space Network (SN), which contains the TDRS relay satellites in GEO; the Near Earth Network (NEN), which consists of several NASA owned and commercially operated ground stations; and the Deep Space Network (DSN), with three ground stations in Goldstone, Madrid, and Canberra. The first task of this study is the stakeholder analysis. The goal of the stakeholder analysis is to identify the main stakeholders of the SCaN system and their needs. Twenty-one main groups of stakeholders have been identified and put on a stakeholder map. Their needs are currently being elicited by means of interviews and an extensive literature review. The data will then be analyzed by applying Cameron and Crawley's stakeholder analysis theory, with a view to highlighting dominant needs and conflicting needs. The second task of this study is the architectural tradespace exploration of the next generation TDRSS. The space of possible architectures for SCaN is represented by a set of architectural decisions, each of which has a discrete set of options. A computational tool is used to automatically synthesize a very large number of possible architectures by enumerating different combinations of decisions and options. The same tool contains models to evaluate the architectures in terms of performance and cost. The performance model uses the stakeholder needs and requirements identified in the previous steps as inputs, and it is based in the VASSAR methodology presented in a companion paper. This paper summarizes the current status of the MIT SCaN architecture study. It starts by motivating the need to perform tradespace exploration studies in the context of relay data systems through a description of the history NASA's space communicati- n networks. It then presents the generalities of possible architectures for future space communication and navigation networks. Finally, it describes the tools and methods being developed, clearly indicating the architectural decisions that have been taken into account as well as the systematic approach followed to model them. The purpose of this study is to explore the SCaN architectural tradespace by means of a computational tool. This paper describes the tool, while the tradespace exploration is underway.
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The pig genome project has plenty to squeal about.
Fan, B; Gorbach, D M; Rothschild, M F
2011-01-01
Significant progress on pig genetics and genomics research has been witnessed in recent years due to the integration of advanced molecular biology techniques, bioinformatics and computational biology, and the collaborative efforts of researchers in the swine genomics community. Progress on expanding the linkage map has slowed down, but the efforts have created a higher-resolution physical map integrating the clone map and BAC end sequence. The number of QTL mapped is still growing and most of the updated QTL mapping results are available through PigQTLdb. Additionally, expression studies using high-throughput microarrays and other gene expression techniques have made significant advancements. The number of identified non-coding RNAs is rapidly increasing and their exact regulatory functions are being explored. A publishable draft (build 10) of the swine genome sequence was available for the pig genomics community by the end of December 2010. Build 9 of the porcine genome is currently available with Ensembl annotation; manual annotation is ongoing. These drafts provide useful tools for such endeavors as comparative genomics and SNP scans for fine QTL mapping. A recent community-wide effort to create a 60K porcine SNP chip has greatly facilitated whole-genome association analyses, haplotype block construction and linkage disequilibrium mapping, which can contribute to whole-genome selection. The future 'systems biology' that integrates and optimizes the information from all research levels can enhance the pig community's understanding of the full complexity of the porcine genome. These recent technological advances and where they may lead are reviewed. Copyright © 2011 S. Karger AG, Basel.
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Automatic detection of cardiovascular risk in CT attenuation correction maps in Rb-82 PET/CTs
NASA Astrophysics Data System (ADS)
Išgum, Ivana; de Vos, Bob D.; Wolterink, Jelmer M.; Dey, Damini; Berman, Daniel S.; Rubeaux, Mathieu; Leiner, Tim; Slomka, Piotr J.
2016-03-01
CT attenuation correction (CTAC) images acquired with PET/CT visualize coronary artery calcium (CAC) and enable CAC quantification. CAC scores acquired with CTAC have been suggested as a marker of cardiovascular disease (CVD). In this work, an algorithm previously developed for automatic CAC scoring in dedicated cardiac CT was applied to automatic CAC detection in CTAC. The study included 134 consecutive patients undergoing 82-Rb PET/CT. Low-dose rest CTAC scans were acquired (100 kV, 11 mAs, 1.4mm×1.4mm×3mm voxel size). An experienced observer defined the reference standard with the clinically used intensity level threshold for calcium identification (130 HU). Five scans were removed from analysis due to artifacts. The algorithm extracted potential CAC by intensity-based thresholding and 3D connected component labeling. Each candidate was described by location, size, shape and intensity features. An ensemble of extremely randomized decision trees was used to identify CAC. The data set was randomly divided into training and test sets. Automatically identified CAC was quantified using volume and Agatston scores. In 33 test scans, the system detected on average 469mm3/730mm3 (64%) of CAC with 36mm3 false positive volume per scan. The intraclass correlation coefficient for volume scores was 0.84. Each patient was assigned to one of four CVD risk categories based on the Agatston score (0-10, 11-100, 101-400, <400). The correct CVD category was assigned to 85% of patients (Cohen's linearly weighted κ0.82). Automatic detection of CVD risk based on CAC scoring in rest CTAC images is feasible. This may enable large scale studies evaluating clinical value of CAC scoring in CTAC data.
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Functional connectivity density mapping: comparing multiband and conventional EPI protocols.
Cohen, Alexander D; Tomasi, Dardo; Shokri-Kojori, Ehsan; Nencka, Andrew S; Wang, Yang
2018-06-01
Functional connectivity density mapping (FCDM) is a newly developed data-driven technique that quantifies the number of local and global functional connections for each voxel in the brain. In this study, we evaluated reproducibility, sensitivity, and specificity of both local functional connectivity density (lFCD) and global functional connectivity density (gFCD). We compared these metrics using the human connectome project (HCP) compatible high-resolution (2 mm isotropic, TR = 0.8 s) multiband (MB), and more typical, lower resolution (3.5 mm isotropic, TR = 2.0 s) single-band (SB) resting state functional MRI (rs-fMRI) acquisitions. Furthermore, in order to be more clinically feasible, only rs-fMRI scans that lasted seven minutes were tested. Subjects were scanned twice within a two-week span. We found sensitivity and specificity increased and reproducibility either increased or did not change for the MB compared to the SB acquisitions. The MB scans also showed improved gray matter/white matter contrast compared to the SB scans. The lFCD and gFCD patterns were similar across MB and SB scans and confined predominantly to gray matter. We also observed a strong spatial correlation of FCD between MB and SB scans indicating the two acquisitions provide similar information. These findings indicate high-resolution MB acquisitions improve the quality of FCD data, and seven minute rs-fMRI scan can provide robust FCD measurements.
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Griffis, Joseph C; Allendorfer, Jane B; Szaflarski, Jerzy P
2016-01-15
Manual lesion delineation by an expert is the standard for lesion identification in MRI scans, but it is time-consuming and can introduce subjective bias. Alternative methods often require multi-modal MRI data, user interaction, scans from a control population, and/or arbitrary statistical thresholding. We present an approach for automatically identifying stroke lesions in individual T1-weighted MRI scans using naïve Bayes classification. Probabilistic tissue segmentation and image algebra were used to create feature maps encoding information about missing and abnormal tissue. Leave-one-case-out training and cross-validation was used to obtain out-of-sample predictions for each of 30 cases with left hemisphere stroke lesions. Our method correctly predicted lesion locations for 30/30 un-trained cases. Post-processing with smoothing (8mm FWHM) and cluster-extent thresholding (100 voxels) was found to improve performance. Quantitative evaluations of post-processed out-of-sample predictions on 30 cases revealed high spatial overlap (mean Dice similarity coefficient=0.66) and volume agreement (mean percent volume difference=28.91; Pearson's r=0.97) with manual lesion delineations. Our automated approach agrees with manual tracing. It provides an alternative to automated methods that require multi-modal MRI data, additional control scans, or user interaction to achieve optimal performance. Our fully trained classifier has applications in neuroimaging and clinical contexts. Copyright © 2015 Elsevier B.V. All rights reserved.
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Matsumoto, Hideyuki; Terao, Yasuo; Yugeta, Akihiro; Fukuda, Hideki; Emoto, Masaki; Furubayashi, Toshiaki; Okano, Tomoko; Hanajima, Ritsuko; Ugawa, Yoshikazu
2011-01-01
The aim of this study was to investigate where neurologists look when they view brain computed tomography (CT) images and to evaluate how they deploy their visual attention by comparing their gaze distribution with saliency maps. Brain CT images showing cerebrovascular accidents were presented to 12 neurologists and 12 control subjects. The subjects' ocular fixation positions were recorded using an eye-tracking device (Eyelink 1000). Heat maps were created based on the eye-fixation patterns of each group and compared between the two groups. The heat maps revealed that the areas on which control subjects frequently fixated often coincided with areas identified as outstanding in saliency maps, while the areas on which neurologists frequently fixated often did not. Dwell time in regions of interest (ROI) was likewise compared between the two groups, revealing that, although dwell time on large lesions was not different between the two groups, dwell time in clinically important areas with low salience was longer in neurologists than in controls. Therefore it appears that neurologists intentionally scan clinically important areas when reading brain CT images showing cerebrovascular accidents. Both neurologists and control subjects used the “bottom-up salience” form of visual attention, although the neurologists more effectively used the “top-down instruction” form. PMID:22174928
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Das, Shouvik; Singh, Mohar; Srivastava, Rishi; Bajaj, Deepak; Saxena, Maneesha S.; Rana, Jai C.; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.
2016-01-01
The present study used a whole-genome, NGS resequencing-based mQTL-seq (multiple QTL-seq) strategy in two inter-specific mapping populations (Pusa 1103 × ILWC 46 and Pusa 256 × ILWC 46) to scan the major genomic region(s) underlying QTL(s) governing pod number trait in chickpea. Essentially, the whole-genome resequencing of low and high pod number-containing parental accessions and homozygous individuals (constituting bulks) from each of these two mapping populations discovered >8 million high-quality homozygous SNPs with respect to the reference kabuli chickpea. The functional significance of the physically mapped SNPs was apparent from the identified 2,264 non-synonymous and 23,550 regulatory SNPs, with 8–10% of these SNPs-carrying genes corresponding to transcription factors and disease resistance-related proteins. The utilization of these mined SNPs in Δ (SNP index)-led QTL-seq analysis and their correlation between two mapping populations based on mQTL-seq, narrowed down two (CaqaPN4.1: 867.8 kb and CaqaPN4.2: 1.8 Mb) major genomic regions harbouring robust pod number QTLs into the high-resolution short QTL intervals (CaqbPN4.1: 637.5 kb and CaqbPN4.2: 1.28 Mb) on chickpea chromosome 4. The integration of mQTL-seq-derived one novel robust QTL with QTL region-specific association analysis delineated the regulatory (C/T) and coding (C/A) SNPs-containing one pentatricopeptide repeat (PPR) gene at a major QTL region regulating pod number in chickpea. This target gene exhibited anther, mature pollen and pod-specific expression, including pronounced higher up-regulated (∼3.5-folds) transcript expression in high pod number-containing parental accessions and homozygous individuals of two mapping populations especially during pollen and pod development. The proposed mQTL-seq-driven combinatorial strategy has profound efficacy in rapid genome-wide scanning of potential candidate gene(s) underlying trait-associated high-resolution robust QTL(s), thereby expediting genomics-assisted breeding and genetic enhancement of crop plants, including chickpea. PMID:26685680
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Pendleton, Michael W; Washburn, Dorothy K; Ellis, E Ann; Pendleton, Bonnie B
2014-03-01
The same sherd was analyzed using a scanning electron microscope with energy dispersive spectroscopy (SEM-EDS) and a micro X-ray fluorescence tube attached to a scanning electron microscope (Micro-XRF-SEM) to compare the effectiveness of elemental detection of iron-based pigment. To enhance SEM-EDS mapping, the sherd was carbon coated. The carbon coating was not required to produce Micro-XRF-SEM maps but was applied to maintain an unbiased comparison between the systems. The Micro-XRF-SEM analysis was capable of lower limits of detection than that of the SEM-EDS system, and therefore the Micro-XRF-SEM system could produce elemental maps of elements not easily detected by SEM-EDS mapping systems. Because SEM-EDS and Micro-XRF-SEM have been used for imaging and chemical analysis of biological samples, this comparison of the detection systems should be useful to biologists, especially those involved in bone or tooth (hard tissue) analysis.
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Pendleton, Michael W.; Washburn, Dorothy K.; Ellis, E. Ann; Pendleton, Bonnie B.
2014-01-01
The same sherd was analyzed using a scanning electron microscope with energy dispersive spectroscopy (SEM-EDS) and a micro X-ray fluorescence tube attached to a scanning electron microscope (Micro-XRF-SEM) to compare the effectiveness of elemental detection of iron-based pigment. To enhance SEM-EDS mapping, the sherd was carbon coated. The carbon coating was not required to produce Micro-XRF-SEM maps but was applied to maintain an unbiased comparison between the systems. The Micro-XRF-SEM analysis was capable of lower limits of detection than that of the SEM-EDS system, and therefore the Micro-XRF-SEM system could produce elemental maps of elements not easily detected by SEM-EDS mapping systems. Because SEM-EDS and Micro-XRF-SEM have been used for imaging and chemical analysis of biological samples, this comparison of the detection systems should be useful to biologists, especially those involved in bone or tooth (hard tissue) analysis. PMID:24600333
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Dissecting enzyme function with microfluidic-based deep mutational scanning.
Romero, Philip A; Tran, Tuan M; Abate, Adam R
2015-06-09
Natural enzymes are incredibly proficient catalysts, but engineering them to have new or improved functions is challenging due to the complexity of how an enzyme's sequence relates to its biochemical properties. Here, we present an ultrahigh-throughput method for mapping enzyme sequence-function relationships that combines droplet microfluidic screening with next-generation DNA sequencing. We apply our method to map the activity of millions of glycosidase sequence variants. Microfluidic-based deep mutational scanning provides a comprehensive and unbiased view of the enzyme function landscape. The mapping displays expected patterns of mutational tolerance and a strong correspondence to sequence variation within the enzyme family, but also reveals previously unreported sites that are crucial for glycosidase function. We modified the screening protocol to include a high-temperature incubation step, and the resulting thermotolerance landscape allowed the discovery of mutations that enhance enzyme thermostability. Droplet microfluidics provides a general platform for enzyme screening that, when combined with DNA-sequencing technologies, enables high-throughput mapping of enzyme sequence space.
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Contour-Driven Atlas-Based Segmentation
Wachinger, Christian; Fritscher, Karl; Sharp, Greg; Golland, Polina
2016-01-01
We propose new methods for automatic segmentation of images based on an atlas of manually labeled scans and contours in the image. First, we introduce a Bayesian framework for creating initial label maps from manually annotated training images. Within this framework, we model various registration- and patch-based segmentation techniques by changing the deformation field prior. Second, we perform contour-driven regression on the created label maps to refine the segmentation. Image contours and image parcellations give rise to non-stationary kernel functions that model the relationship between image locations. Setting the kernel to the covariance function in a Gaussian process establishes a distribution over label maps supported by image structures. Maximum a posteriori estimation of the distribution over label maps conditioned on the outcome of the atlas-based segmentation yields the refined segmentation. We evaluate the segmentation in two clinical applications: the segmentation of parotid glands in head and neck CT scans and the segmentation of the left atrium in cardiac MR angiography images. PMID:26068202
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Cancer diagnosis using a conventional x-ray fluorescence camera with a cadmium-telluride detector
NASA Astrophysics Data System (ADS)
Sato, Eiichi; Enomoto, Toshiyuki; Hagiwara, Osahiko; Abudurexiti, Abulajiang; Sato, Koetsu; Sato, Shigehiro; Ogawa, Akira; Onagawa, Jun
2011-10-01
X-ray fluorescence (XRF) analysis is useful for mapping various atoms in objects. Bremsstrahlung X-rays are selected using a 3.0 mm-thick aluminum filter, and these rays are absorbed by indium, cerium and gadolinium atoms in objects. Then XRF is produced from the objects, and photons are detected by a cadmium-telluride detector. The Kα photons are discriminated using a multichannel analyzer, and the number of photons is counted by a counter card. The objects are moved and scanned by an x-y stage in conjunction with a two-stage controller, and X-ray images obtained by atomic mapping are shown on a personal computer monitor. The scan steps of the x and y axes were both 2.5 mm, and the photon-counting time per mapping point was 0.5 s. We carried out atomic mapping using the X-ray camera, and Kα photons from cerium and gadolinium atoms were produced from cancerous regions in nude mice.
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NASA Astrophysics Data System (ADS)
Enomoto, Toshiyuki; Sato, Eiichi; Abderyim, Purkhet; Abudurexiti, Abulajiang; Hagiwara, Osahiko; Matsukiyo, Hiroshi; Osawa, Akihiro; Watanabe, Manabu; Nagao, Jiro; Sato, Shigehiro; Ogawa, Akira; Onagawa, Jun
2011-04-01
X-ray fluorescence (XRF) analysis is useful for mapping various molecules in objects. Bremsstrahlung X-rays are selected using a 3.0-mm-thick aluminum filter, and these rays are absorbed by iodine, cerium, and gadolinium molecules in objects. Next, XRF is produced from the objects, and photons are detected by a cadmium-telluride detector. The Kα photons are discriminated using a multichannel analyzer, and the number of photons is counted by a counter card. The objects are moved and scanned by an x- y stage in conjunction with a two-stage controller, and X-ray images obtained by molecular mapping are shown on a personal computer monitor. The scan steps of x and y axes were both 2.5 mm, and the photon-counting time per mapping point was 0.5 s. We carried out molecular mapping using the X-ray camera, and Kα photons from cerium and gadolinium molecules were produced from cancerous regions in nude mice.
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NASA Astrophysics Data System (ADS)
Zheng, Y.
2015-08-01
Peng Xi county, Sichuan province, the Bao Fan temple mural digitization survey mapping project: we use three-dimensional laserscanning, multi-baseline definition digital photography, multi-spectral digital image acquisition and other technologies for digital survey mapping. The purpose of this project is to use modern mathematical reconnaissance mapping means to obtain accurate mural shape, color, quality and other data. Combined with field investigation and laboratory analysis results, and based on a comprehensive survey and study, a comprehensive analysis of the historical Bao Fan Temple mural artistic and scientific value was conducted. A study of the mural's many qualities (structural, material, technique, preservation environment, degradation, etc.) reveal all aspects of the information carried by the Bao Fan Temple mural. From multiple angles (archeology, architecture, surveying, conservation science and other disciplines) an assessment for the Bao Fan Temple mural provides basic data and recommendations for conservation of the mural. In order to achieve the conservation of cultural relics in the Bao Fan Temple mural digitization survey mapping process, we try to apply the advantages of three-dimensional laser scanning equipment. For wall murals this means obtaining three-dimensional scale data from the scan of the building and through the analysis of these data to help determine the overall condition of the settlement as well as the deformation of the wall structure. Survey analysis provides an effective set of conclusions and suggestions for appropriate mural conservation. But before data collection, analysis and research need to first to select the appropriate scanning equipment, set the appropriate scanning accuracy and layout position of stations necessary to determine the scope of required data. We use the fine features of the three-dimensional laser scanning measuring arm to scan the mural surface deformation degradation to reflect the actual state of the mural surface patch model. For the degradation of the surface of the pigment layer, we use the patch model to simulate the scan obtained from an analysis. Statistics calculated relatively objective mural surface area from volume data, providing more accurate quantitative data for the mural conservation, especially, providing a viable technology for accurate monitoring of continued degradation. We believe, in order to make use of the three-dimensional laser scanning technology in a digital heritage conservation application, the technology should not only be used to record the object geometry and play a role in record keeping aspects, but, rather, should be used during the investigation to protect against targeted degradation and a more meaningful interpretation function. Like the development of the medical application of X-ray technology not only retains a picture, but more importantly, through this technical interpretation of patient pathology, guides doctors in carrying out the treatment work. Therefore, in the process of digitization of cultural heritage research, the focus should shift to the use of digital technology in the analysis of heritage object degradation and degradation monitoring surveys can promote the application of digital technology in the conservation of cultural heritage.
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Highlighting material structure with transmission electron diffraction correlation coefficient maps.
Kiss, Ákos K; Rauch, Edgar F; Lábár, János L
2016-04-01
Correlation coefficient maps are constructed by computing the differences between neighboring diffraction patterns collected in a transmission electron microscope in scanning mode. The maps are shown to highlight material structural features like grain boundaries, second phase particles or dislocations. The inclination of the inner crystal interfaces are directly deduced from the resulting contrast. Copyright © 2016 Elsevier B.V. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Reed, Valerie K.; Cavalcanti, Jose L.; Strom, Eric A.
Purpose: To determine the anatomic distribution of gross supraclavicular nodes within the supraclavicular fossa using 2-deoxy-2-[F-18] fluoro-d-glucose (FDG) positron emission tomography/computed tomography (PET/CT) scans, and to evaluate likely coverage of specific regions of the supraclavicular fossa using standard radiation fields. Methods and Materials: We identified 33 patients with advanced or metastatic breast cancer who had a PET/CT scan demonstrating hypermetabolic supraclavicular lymph nodes in 2005. The locations of the involved lymph nodes were mapped onto a single CT set of images of the supraclavicular fossa. These lymph nodes were also mapped onto the treatment-planning CT dataset of 4 patients treatedmore » in our institution (2 patients with biopsy-proven supraclavicular nodes and 2 patients with clinically negative supraclavicular nodes). Results: We were able to determine the distribution of 52 supraclavicular lymph nodes in 32 patients. Of 32 patients, 28 (87%) had a history of metastatic disease, and 2 patients had isolated nodal recurrences. Five patients had supraclavicular nodes posterior to the vertebral body transverse process, and several lymph nodes were in close proximity to the medial field border, raising the possibility of geographic miss in these areas. Conclusions: In patients with locally advanced disease, increased coverage of the supraclavicular fossa medially and posteriorly may be warranted.« less
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The Impact of Sources of Variability on Parametric Response Mapping of Lung CT Scans
Boes, Jennifer L.; Bule, Maria; Hoff, Benjamin A.; Chamberlain, Ryan; Lynch, David A.; Stojanovska, Jadranka; Martinez, Fernando J.; Han, Meilan K.; Kazerooni, Ella A.; Ross, Brian D.; Galbán, Craig J.
2015-01-01
Parametric response mapping (PRM) of inspiration and expiration computed tomography (CT) images improves the radiological phenotyping of chronic obstructive pulmonary disease (COPD). PRM classifies individual voxels of lung parenchyma as normal, emphysematous, or nonemphysematous air trapping. In this study, bias and noise characteristics of the PRM methodology to CT and clinical procedures were evaluated to determine best practices for this quantitative technique. Twenty patients of varying COPD status with paired volumetric inspiration and expiration CT scans of the lungs were identified from the baseline COPD-Gene cohort. The impact of CT scanner manufacturer and reconstruction kernels were evaluated as potential sources of variability in PRM measurements along with simulations to quantify the impact of inspiration/expiration lung volume levels, misregistration, and image spacing on PRM measurements. Negligible variation in PRM metrics was observed when CT scanner type and reconstruction were consistent and inspiration/expiration lung volume levels were near target volumes. CT scanner Hounsfield unit drift occurred but remained difficult to ameliorate. Increasing levels of image misregistration and CT slice spacing were found to have a minor effect on PRM measurements. PRM-derived values were found to be most sensitive to lung volume levels and mismatched reconstruction kernels. As with other quantitative imaging techniques, reliable PRM measurements are attainable when consistent clinical and CT protocols are implemented. PMID:26568983
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A Scan of CDC-Authored Articles on Legal Epidemiology, 2011-2015
Martini, Leila; Presley, David; Klieger, Sarah
2016-01-01
Objective: The Centers for Disease Control and Prevention (CDC) conducts research on legal epidemiology, the scientific study of law as a factor in the cause, distribution, and prevention of disease. This study describes a scan of articles written by CDC staff members to characterize the frequency and key features of legal epidemiology articles and their distribution across CDC departments and divisions. Methods: CDC librarians searched an internal repository for journal articles by CDC staff published from January 1, 2011, to May 31, 2015. Researchers reviewed and coded the abstracts to produce data on key features of the articles. Results: Researchers identified 158 CDC-authored legal epidemiology articles published in 83 journals, most frequently in Preventing Chronic Disease (14 publications), Journal of Public Health Management Practice (10 publications), and Morbidity and Mortality Weekly Report (9 publications). Most articles concerned the use and impact of law as a deliberate tool of intervention. Thirteen articles addressed the legal infrastructure of public health, and 3 assessed the incidental or unintended effects of nonhealth laws. CDC-authored articles encompassed policy making, implementation, and impact. Literature reviews and studies mapping laws across multiple jurisdictions constituted one-quarter of all publications. Studies addressed laws at the international, national, state, local, and organizational levels. Conclusion: Results of the scan can be used to identify opportunities for the agency to better support research, professional development, networking, publication, and tracking of publication in this emerging field. PMID:28123227
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The Scanning Nanoprobe Beamline Nanoscopium at Synchrotron Soleil
NASA Astrophysics Data System (ADS)
Somogyi, A.; Kewish, C. M.; Polack, F.; Moreno, T.
2011-09-01
The Nanoscopium beamline at Synchrotron Soleil will offer advanced scanning-based hard x-ray imaging techniques in the 5- to 20-keV energy range, for user communities working in the earth, environmental, and life sciences. Two dedicated end stations will exploit x-ray coherence to produce images in which contrast is based on a range of physical processes. In the first experiment hutch, coherent scatter imaging techniques will produce images in which contrast arises from spatial variations in the complex refractive index, and orientation in the nanostructure of samples. In the second experiment hutch, elemental mapping will be carried out at the trace (ppm) level by scanning x-ray fluorescence, speciation mapping by XANES, and phase gradient mapping by scanning differential phase contrast imaging. The beamline aims to reach sub-micrometric, down to 30 nm, spatial resolution. This ˜155-meter-long beamline will share the straight section with a future tomography beamline by using canted undulators having 6.5-mrad separation angle. The optical design of Nanoscopium aims to reduce the effect of instabilities on the probing nanobeam by utilizing an all-horizontal geometry for the reflections of the primary beamline mirrors, which focus onto a slit, creating an over-filled secondary source. Kirkpatrick-Baez mirrors and Fresnel zone plates will be used as focusing devices in the experiment hutches. Nanoscopium is expected to commence user operation in 2013.
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Non-random mate choice in humans: insights from a genome scan.
Laurent, R; Toupance, B; Chaix, R
2012-02-01
Little is known about the genetic factors influencing mate choice in humans. Still, there is evidence for non-random mate choice with respect to physical traits. In addition, some studies suggest that the Major Histocompatibility Complex may affect pair formation. Nowadays, the availability of high density genomic data sets gives the opportunity to scan the genome for signatures of non-random mate choice without prior assumptions on which genes may be involved, while taking into account socio-demographic factors. Here, we performed a genome scan to detect extreme patterns of similarity or dissimilarity among spouses throughout the genome in three populations of African, European American, and Mexican origins from the HapMap 3 database. Our analyses identified genes and biological functions that may affect pair formation in humans, including genes involved in skin appearance, morphogenesis, immunity and behaviour. We found little overlap between the three populations, suggesting that the biological functions potentially influencing mate choice are population specific, in other words are culturally driven. Moreover, whenever the same functional category of genes showed a significant signal in two populations, different genes were actually involved, which suggests the possibility of evolutionary convergences. © 2011 Blackwell Publishing Ltd.
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Teoh, Raymond; Johnson, Raleigh F; Nishino, Thomas K; Ethridge, Richard T
2007-01-01
The deep inferior epigastric perforator flap procedure has become a popular alternative for women who require breast reconstruction. One of the difficulties with this procedure is identifying perforator arteries large enough to ensure that the harvested tissue is well vascularized. Current techniques involve imaging the perforator arteries with computed tomography (CT) to produce a grid mapping the locations of the perforator arteries relative to the umbilicus. To compare the time it takes to produce a map of the perforators using either two-dimensional (2D) or three-dimensional (3D) CT, and to see whether there is a benefit in using a 3D model. Patient CT abdomen and pelvis scans were acquired from a GE 64-slice scanner. CT image processing was performed with the GE 3D Advantage Workstation v4.2 software. Maps of the perforators were generated both as 2D and 3D representations. Perforators within a region 5 cm rostral and 7 cm caudal to the umbilicus were measured and the times to perform these measurements using both 2D and 3D images were recorded by a stopwatch. Although the 3D method took longer than the 2D method (mean [+/- SD] time 1:51+/-0:35 min versus 1:08+/-0:16 min per perforator artery, respectively), producing a 3D image provides much more information than the 2D images alone. Additionally, an actual-sized 3D image can be printed out, removing the need to make measurements and producing a grid. Although it took less time to create a grid of the perforators using 2D axial CT scans, the 3D reconstruction of the abdomen allows the plastic surgeons to better visualize the patient's anatomy and has definite clinical utility.
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Fine Mapping of 6q23.1 Identifies TULP4 as Contributing to Clefts.
Vieira, Alexandre R; de Carvalho, Flavia M; Johnson, Lindsay; DeVos, Lauren; Swailes, Alexa L; Weber, Megan L; Deeley, Kathleen
2015-03-01
Objective : The aim of this work was to fine-map the region 6q23.1, which obtained suggestive linkage signal (logarithm of the odds [LOD] score = 2.22 under a recessive model) to cleft lip with or without cleft palate (CL±P) in our previous genome-wide linkage scan to identify possible genetic variants that may contribute to CL±P. Design : We used densely spaced markers spanning the entire 6q23.1 region to test for association with CL±P in a family cohort sample. Setting : Clinical information and DNA samples were obtained from families in the Philippines at their homes or primary health care clinics. Participants : The study sample consisted of 477 subjects (224 females and 253 males), segregating isolated CL±P, from 72 living in the same area in the Philippines. Main Outcome Measure : Overtransmission of alleles to persons born with CL±P. Results : We found statistical evidence of association between a marker of TULP4 (rs651333) with CL±P (P = .00007). Conclusions : Our results further support the linkage results for the chromosome 6q region and reveal a novel candidate gene for CL±P.
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Data-driven inference for the spatial scan statistic.
Almeida, Alexandre C L; Duarte, Anderson R; Duczmal, Luiz H; Oliveira, Fernando L P; Takahashi, Ricardo H C
2011-08-02
Kulldorff's spatial scan statistic for aggregated area maps searches for clusters of cases without specifying their size (number of areas) or geographic location in advance. Their statistical significance is tested while adjusting for the multiple testing inherent in such a procedure. However, as is shown in this work, this adjustment is not done in an even manner for all possible cluster sizes. A modification is proposed to the usual inference test of the spatial scan statistic, incorporating additional information about the size of the most likely cluster found. A new interpretation of the results of the spatial scan statistic is done, posing a modified inference question: what is the probability that the null hypothesis is rejected for the original observed cases map with a most likely cluster of size k, taking into account only those most likely clusters of size k found under null hypothesis for comparison? This question is especially important when the p-value computed by the usual inference process is near the alpha significance level, regarding the correctness of the decision based in this inference. A practical procedure is provided to make more accurate inferences about the most likely cluster found by the spatial scan statistic.
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Application of 3D Laser Scanning Technology in Complex Rock Foundation Design
NASA Astrophysics Data System (ADS)
Junjie, Ma; Dan, Lu; Zhilong, Liu
2017-12-01
Taking the complex landform of Tanxi Mountain Landscape Bridge as an example, the application of 3D laser scanning technology in the mapping of complex rock foundations is studied in this paper. A set of 3D laser scanning technologies are formed and several key engineering problems are solved. The first is 3D laser scanning technology of complex landforms. 3D laser scanning technology is used to obtain a complete 3D point cloud data model of the complex landform. The detailed and accurate results of the surveying and mapping decrease the measuring time and supplementary measuring times. The second is 3D collaborative modeling of the complex landform. A 3D model of the complex landform is established based on the 3D point cloud data model. The super-structural foundation model is introduced for 3D collaborative design. The optimal design plan is selected and the construction progress is accelerated. And the last is finite-element analysis technology of the complex landform foundation. A 3D model of the complex landform is introduced into ANSYS for building a finite element model to calculate anti-slide stability of the rock, and provides a basis for the landform foundation design and construction.
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Lina Ma,; Sherrod, David R.; Scott, William E.
2014-01-01
This geodatabase contains information derived from legacy mapping that was published in 1995 as U.S. Geological Survey Open-File Report 95-219. The main component of this publication is a geologic map database prepared using geographic information system (GIS) applications. Included are pdf files to view or print the map sheet, the accompanying pamphlet from Open-File Report 95-219, and links to the original publication, which is available as scanned files in pdf format.
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Real-Time Occupancy Change Analyzer
DOE Office of Scientific and Technical Information (OSTI.GOV)
2005-03-30
The Real-Time Occupancy Change Analyzer (ROCA) produces an occupancy grid map of an environment around the robot, scans the environment to generate a current obstacle map relative to a current robot position, and converts the current obstacle map to a current occupancy grid map. Changes in the occupancy grid can be reported in real time to support a number of tracking capabilities. The benefit of ROCA is that rather than only providing a vector to the detected change, it provides the actual x,y position of the change.
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Martín-Fabiani, Ignacio; Rebollar, Esther; García-Gutiérrez, Mari Cruz; Rueda, Daniel R; Castillejo, Marta; Ezquerra, Tiberio A
2015-02-11
In this work we present an accurate mapping of the structural order of laser-induced periodic surface structures (LIPSS) in spin-coated thin polymer films, via a microfocus beam grazing incidence small-angle X-ray scattering (μGISAXS) scan, GISAXS modeling, and atomic force microscopy imaging all along the scanned area. This combined study has allowed the evaluation of the effects on LIPSS formation due to nonhomogeneous spatial distribution of the laser pulse energy, mapping with micrometric resolution the evolution of the period and degree of structural order of LIPSS across the laser beam diameter in a direction perpendicular to the polarization vector. The experiments presented go one step further toward controlling nanostructure formation in LIPSS through a deep understanding of the parameters that influence this process.
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NASA Technical Reports Server (NTRS)
Comiso, Josefino C.; Zwally, H. Jay
1989-01-01
A time series of daily brightness temperature gridded maps (October 25, 1978 through August 15, 1987) were generated from all ten channels of the Nimbus-7 Scanning Multichannel Microwave Radiometer orbital data. This unique data set can be utilized in a wide range of applications including heat flux, ocean circulation, ice edge productivity, and climate studies. Two sets of data in polar stereographic format are created for the Arctic region: one with a grid size of about 30 km on a 293 by 293 array similar to that previously utilized for the Nimbus-5 Electrically Scanning Microwave Radiometer, while the other has a grid size of about 25 km on a 448 by 304 array identical to what is now being used for the DMSP Scanning Multichannel Microwave Imager. Data generated for the Antaractic region are mapped using the 293 by 293 grid only. The general technique for mapping, and a quality assessment of the data set are presented. Monthly and yearly averages are also generated from the daily data and sample geophysical ice images and products derived from the data are given. Contour plots of monthly ice concentrations derived from the data for October 1978 through August 1987 are presented to demonstrate spatial and temporal detail which this data set can offer, and to show potential research applications.
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NASA Astrophysics Data System (ADS)
Yanbe, Yutaka; Sato, Eiichi; Chiba, Hiraku; Maeda, Tomoko; Matsushita, Ryo; Oda, Yasuyuki; Hagiwara, Osahiko; Matsukiyo, Hiroshi; Osawa, Akihiro; Enomoto, Toshiyuki; Watanabe, Manabu; Kusachi, Shinya; Sato, Shigehiro; Ogawa, Akira
2013-09-01
X-ray fluorescence (XRF) analysis is useful for mapping various atoms in objects. Bremsstrahlung X-rays with energies beyond tantalum (Ta) K-edge energy 67.4 keV are absorbed effectively using a 100-µm-thick Ta filter, and the filtered X-rays including tungsten (W) Kα rays are absorbed by gadolinium (Gd) atoms in objects. The Gd XRF is then produced from Gd atoms in the objects and is counted by a cadmium telluride (CdTe) detector. Gd Kα photons with a maximum count rate of 1 kilo counts per second are dispersed using a multichannel analyzer, and the number of photons is counted by a counter card. The distance between the CdTe detector and the object is minimized to 40 mm to increase the count rate. The object is scanned using an x-y stage with a velocity of 5.0 mm/s, and Gd mapping are shown on a computer monitor. The scan steps of the x- and y-axes were both 2.5 mm, and the photon-counting time per mapping point was 0.5 s. We obtained Gd XRF images at high contrast, and Gd Kα photons were easily detected from cancerous regions in a nude mouse placed behind a 20-mm-thick poly(methyl methacrylate) plate.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Yin, Zhye, E-mail: yin@ge.com; De Man, Bruno; Yao, Yangyang
Purpose: Traditionally, 2D radiographic preparatory scan images (scout scans) are used to plan diagnostic CT scans. However, a 3D CT volume with a full 3D organ segmentation map could provide superior information for customized scan planning and other purposes. A practical challenge is to design the volumetric scout acquisition and processing steps to provide good image quality (at least good enough to enable 3D organ segmentation) while delivering a radiation dose similar to that of the conventional 2D scout. Methods: The authors explored various acquisition methods, scan parameters, postprocessing methods, and reconstruction methods through simulation and cadaver data studies tomore » achieve an ultralow dose 3D scout while simultaneously reducing the noise and maintaining the edge strength around the target organ. Results: In a simulation study, the 3D scout with the proposed acquisition, preprocessing, and reconstruction strategy provided a similar level of organ segmentation capability as a traditional 240 mAs diagnostic scan, based on noise and normalized edge strength metrics. At the same time, the proposed approach delivers only 1.25% of the dose of a traditional scan. In a cadaver study, the authors’ pictorial-structures based organ localization algorithm successfully located the major abdominal-thoracic organs from the ultralow dose 3D scout obtained with the proposed strategy. Conclusions: The authors demonstrated that images with a similar degree of segmentation capability (interpretability) as conventional dose CT scans can be achieved with an ultralow dose 3D scout acquisition and suitable postprocessing. Furthermore, the authors applied these techniques to real cadaver CT scans with a CTDI dose level of less than 0.1 mGy and successfully generated a 3D organ localization map.« less
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Cross-Disciplinary Analysis of Lymph Node Classification in Lung Cancer on CT Scanning.
El-Sherief, Ahmed H; Lau, Charles T; Obuchowski, Nancy A; Mehta, Atul C; Rice, Thomas W; Blackstone, Eugene H
2017-04-01
Accurate and consistent regional lymph node classification is an important element in the staging and multidisciplinary management of lung cancer. Regional lymph node definition sets-lymph node maps-have been created to standardize regional lymph node classification. In 2009, the International Association for the Study of Lung Cancer (IASLC) introduced a lymph node map to supersede all preexisting lymph node maps. Our aim was to study if and how lung cancer specialists apply the IASLC lymph node map when classifying thoracic lymph nodes encountered on CT scans during lung cancer staging. From April 2013 through July 2013, invitations were distributed to all members of the Fleischner Society, Society of Thoracic Radiology, General Thoracic Surgical Club, and the American Association of Bronchology and Interventional Pulmonology to participate in an anonymous online image-based and text-based 20-question survey regarding lymph node classification for lung cancer staging on CT imaging. Three hundred thirty-seven people responded (approximately 25% participation). Respondents consisted of self-reported thoracic radiologists (n = 158), thoracic surgeons (n = 102), and pulmonologists who perform endobronchial ultrasonography (n = 77). Half of the respondents (50%; 95% CI, 44%-55%) reported using the IASLC lymph node map in daily practice, with no significant differences between subspecialties. A disparity was observed between the IASLC definition sets and their interpretation and application on CT scans, in particular for lymph nodes near the thoracic inlet, anterior to the trachea, anterior to the tracheal bifurcation, near the ligamentum arteriosum, between the bronchus intermedius and esophagus, in the internal mammary space, and adjacent to the heart. Use of older lymph node maps and inconsistencies in interpretation and application of definitions in the IASLC lymph node map may potentially lead to misclassification of stage and suboptimal management of lung cancer in some patients. Published by Elsevier Inc.
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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.
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N'Diaye, Amidou; Haile, Jemanesh K; Cory, Aron T; Clarke, Fran R; Clarke, John M; Knox, Ron E; Pozniak, Curtis J
2017-01-01
Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat.
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Inventory of forest and rangeland and detection of forest stress
NASA Technical Reports Server (NTRS)
Heller, R. C.; Aldrich, R. C.; Weber, F. P.; Driscoll, R. S. (Principal Investigator)
1972-01-01
There are no author-identified significant results in this report. Some ERTS-1 imagery has been received for each of the test sites: Black Hills, Atlanta, and Manitou. Only small portions of each site are covered and clouds have precluded capturing good imagery over the center of each site. Discoloration infestations of ponderosa pine are being located and sized on CIR transparencies. A computer program was completed from microdensitometer scans of CIR photos which maps areas of an image which are spectrally similar. Decided differences between forest types are present as well as differences between forest and other vegetative and nonvegetative land classes.
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Low dose dynamic CT myocardial perfusion imaging using a statistical iterative reconstruction method
DOE Office of Scientific and Technical Information (OSTI.GOV)
Tao, Yinghua; Chen, Guang-Hong; Hacker, Timothy A.
Purpose: Dynamic CT myocardial perfusion imaging has the potential to provide both functional and anatomical information regarding coronary artery stenosis. However, radiation dose can be potentially high due to repeated scanning of the same region. The purpose of this study is to investigate the use of statistical iterative reconstruction to improve parametric maps of myocardial perfusion derived from a low tube current dynamic CT acquisition. Methods: Four pigs underwent high (500 mA) and low (25 mA) dose dynamic CT myocardial perfusion scans with and without coronary occlusion. To delineate the affected myocardial territory, an N-13 ammonia PET perfusion scan wasmore » performed for each animal in each occlusion state. Filtered backprojection (FBP) reconstruction was first applied to all CT data sets. Then, a statistical iterative reconstruction (SIR) method was applied to data sets acquired at low dose. Image voxel noise was matched between the low dose SIR and high dose FBP reconstructions. CT perfusion maps were compared among the low dose FBP, low dose SIR and high dose FBP reconstructions. Numerical simulations of a dynamic CT scan at high and low dose (20:1 ratio) were performed to quantitatively evaluate SIR and FBP performance in terms of flow map accuracy, precision, dose efficiency, and spatial resolution. Results: Forin vivo studies, the 500 mA FBP maps gave −88.4%, −96.0%, −76.7%, and −65.8% flow change in the occluded anterior region compared to the open-coronary scans (four animals). The percent changes in the 25 mA SIR maps were in good agreement, measuring −94.7%, −81.6%, −84.0%, and −72.2%. The 25 mA FBP maps gave unreliable flow measurements due to streaks caused by photon starvation (percent changes of +137.4%, +71.0%, −11.8%, and −3.5%). Agreement between 25 mA SIR and 500 mA FBP global flow was −9.7%, 8.8%, −3.1%, and 26.4%. The average variability of flow measurements in a nonoccluded region was 16.3%, 24.1%, and 937.9% for the 500 mA FBP, 25 mA SIR, and 25 mA FBP, respectively. In numerical simulations, SIR mitigated streak artifacts in the low dose data and yielded flow maps with mean error <7% and standard deviation <9% of mean, for 30×30 pixel ROIs (12.9 × 12.9 mm{sup 2}). In comparison, low dose FBP flow errors were −38% to +258%, and standard deviation was 6%–93%. Additionally, low dose SIR achieved 4.6 times improvement in flow map CNR{sup 2} per unit input dose compared to low dose FBP. Conclusions: SIR reconstruction can reduce image noise and mitigate streaking artifacts caused by photon starvation in dynamic CT myocardial perfusion data sets acquired at low dose (low tube current), and improve perfusion map quality in comparison to FBP reconstruction at the same dose.« less
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Evidence of a Novel Quantitative-Trait Locus for Obesity on Chromosome 4p in Mexican Americans
Arya, Rector; Duggirala, Ravindranath; Jenkinson, Christopher P.; Almasy, Laura; Blangero, John; O’Connell, Peter; Stern, Michael P.
2004-01-01
Although several genomewide scans have identified quantitative-trait loci influencing several obesity-related traits in humans, genes influencing normal variation in obesity phenotypes have not yet been identified. We therefore performed a genome scan of body mass index (BMI) on Mexican Americans, a population prone to obesity and diabetes, using a variance-components linkage analysis to identify loci that influence BMI. We used phenotypic data from 430 individuals (26% diabetics, 59% females, mean age ± SD = 43 ± 17 years, mean BMI ± SD = 30.0 ± 6.7, mean leptin (ng/ml) ± SD = 22.1 ± 17.1) distributed across 27 low-income Mexican American pedigrees who participated in the San Antonio Family Diabetes Study (SAFDS) for whom a 10–15-cM map is available. In this genomewide search, after accounting for the covariate effects of age, sex, diabetes, and leptin, we identified a genetic region exhibiting the most highly significant evidence for linkage (LOD 4.5) with BMI on chromosome 4p (4p15.1) at 42 cM, near marker D4S2912. This linkage result has been confirmed in an independent linkage study of severe obesity in Utah pedigrees. Two strong positional candidates, the human peroxisome proliferator-activated receptor gamma coactivator 1 (PPARGC1) and cholecystokinin A receptor (CCKAR) with major roles in the development of obesity, are located in this region. In conclusion, we identified a major genetic locus influencing BMI on chromosome 4p in Mexican Americans. PMID:14740316
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Tlou, Boikhutso; Sartorius, Benn; Tanser, Frank
2017-01-01
The aim of the study was to identify the key determinants of child mortality 'hot-spots' in space and time. Comprehensive population-based mortality data collected between 2000 and 2014 by the Africa Centre Demographic Information System located in the UMkhanyakude District of KwaZulu-Natal Province, South Africa, was analysed. We assigned all mortality events and person-time of observation for children <5 years of age to an exact homestead of residence (mapped to <2m accuracy as part of the DSA platform). Using these exact locations, both the Kulldorff and Tango spatial scan statistics for regular and irregular shaped cluster detection were used to identify clusters of childhood mortality events in both space and time. Of the 49 986 children aged < 5 years who resided in the study area between 2000 and 2014, 2010 (4.0%) died. Childhood mortality decreased by 80% over the period from >20 per 1000 person-years in 2001-2003 to 4 per 1000 person-years in 2014. The two scanning spatial techniques identified two high-risk clusters for child mortality along the eastern border of the study site near the national highway, with a relative risk of 2.10 and 1.91 respectively. The high-risk communities detected in this work, and the differential risk factor profile of these communities, can assist public health professionals to identify similar populations in other parts of rural South Africa. Identifying child mortality hot-spots will potentially guide policy interventions in rural, resource-limited settings.
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NASA Astrophysics Data System (ADS)
Yamanari, Masahiro; Miura, Masahiro; Makita, Shuichi; Yatagai, Toyohiko; Yasuno, Yoshiaki
2007-02-01
Birefringence of retinal nerve fiber layer is measured by polarization-sensitive spectral domain optical coherence tomography using the B-scan-oriented polarization modulation method. Birefringence of the optical fiber and the cornea is compensated by Jones matrix based analysis. Three-dimensional phase retardation map around the optic nerve head and en-face phase retardation map of the retinal nerve fiber layer are shown. Unlike scanning laser polarimetry, our system can measure the phase retardation quantitatively without using bow-tie pattern of the birefringence in the macular region, which enables diagnosis of glaucoma even if the patients have macular disease.
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An acoustic backscatter thermometer for remotely mapping seafloor water temperature
NASA Astrophysics Data System (ADS)
Jackson, Darrell R.; Dworski, J. George
1992-01-01
A bottom-mounted, circularly scanning sonar operating at 40 kHz has been used to map changes in water sound speed over a circular region 150 m in diameter. If it is assumed that the salinity remains constant, the change in sound speed can be converted to a change in temperature. For the present system, the spatial resolution is 7.5 m and the temperature resolution is 0.05°C. The technique is based on comparison of successive sonar scans by means of a correlation algorithm. The algorithm is illustrated using data from the Sediment Transport Events on Slopes and Shelves (STRESS) experiment.
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Miyata, Tomohiro; Mizoguchi, Teruyasu
2018-03-01
Understanding structures and spatial distributions of molecules in liquid phases is crucial for the control of liquid properties and to develop efficient liquid-phase processes. Here, real-space mapping of molecular distributions in a liquid was performed. Specifically, the ionic liquid 1-Ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide (C2mimTFSI) was imaged using atomic-resolution scanning transmission electron microscopy. Simulations revealed network-like bright regions in the images that were attributed to the TFSI- anion, with minimal contributions from the C2mim+ cation. Simple visualization of the TFSI- distribution in the liquid sample was achieved by binarizing the experimental image.
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Calculation of laser pulse distribution maps for corneal reshaping with a scanning beam
NASA Astrophysics Data System (ADS)
Manns, Fabrice; Shen, Jin-Hui; Soederberg, Per G.; Matsui, Takaaki; Parel, Jean-Marie A.
1995-05-01
A method for calculating pulse distribution maps for scanning laser corneal surgery is presented. The accuracy, the smoothness of the corneal shape, and the duration of surgery were evaluated for corrections of myopia by using computer simulations. The accuracy and the number of pulses were computed as a function of the beam diameter, the diameter of the treatment zone, and the amount of attempted flattening. The ablation is smooth when the spot overlap is 80% or more. The accuracy does not depend on the beam diameter or on the diameter of the ablation zone when the ablation zone is larger than 5 mm. With an overlap of 80% and an ablation zone larger than 5 mm, the error is 5% of the attempted flattening, and 610 pulses are needed per Diopter of correction with a beam diameter of 1 mm. Pulse maps for the correction of astigmatism were computed and evaluated. The simulations show that with 60% overlap, a beam diameter of 1 mm, and a 5 mm treatment zone, 6 D of astigmatism can be corrected with an accuracy better than 1.8 D. This study shows that smooth and accurate ablations can be produced with a scanning spot.
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Land-Based Mobile Laser Scanning Systems: a Review
NASA Astrophysics Data System (ADS)
Puente, I.; González-Jorge, H.; Arias, P.; Armesto, J.
2011-09-01
Mobile mapping has been using various photogrammetric techniques for many years. In recent years, there has been an increase in the number of mobile mapping systems using laser scanners available in the market, partially because of the improvement in GNSS/INS performance for direct georeferencing. In this article, some of the most important land-based mobile laser scanning (MLS) systems are reviewed. Firstly, the main characteristics of MLS systems vs. airborne (ALS) and terrestrial laser scanning (TLS) systems are compared. Secondly, a short overview of the mobile mapping technology is also provided so that the reader can fully grasp the complexity and operation of these devices. As we put forward in this paper, a comparison of different systems is briefly carried out regarding specifications provided by the manufacturers. Focuses on the current research are also addressed with emphasis on the practical applications of these systems. Most of them have been utilized for data collection on road infrastructures or building façades. This article shows that MLS technology is nowadays well established and proven, since the demand has grown to the point that there are several systems suppliers offering their products to satisfy this particular market.
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Multimodal Registration of White Matter Brain Data via Optimal Mass Transport.
Rehman, Tauseefur; Haber, Eldad; Pohl, Kilian M; Haker, Steven; Halle, Mike; Talos, Florin; Wald, Lawrence L; Kikinis, Ron; Tannenbaum, Allen
2008-09-01
The elastic registration of medical scans from different acquisition sequences is becoming an important topic for many research labs that would like to continue the post-processing of medical scans acquired via the new generation of high-field-strength scanners. In this note, we present a parameter-free registration algorithm that is well suited for this scenario as it requires no tuning to specific acquisition sequences. The algorithm encompasses a new numerical scheme for computing elastic registration maps based on the minimizing flow approach to optimal mass transport. The approach utilizes all of the gray-scale data in both images, and the optimal mapping from image A to image B is the inverse of the optimal mapping from B to A . Further, no landmarks need to be specified, and the minimizer of the distance functional involved is unique. We apply the algorithm to register the white matter folds of two different scans and use the results to parcellate the cortex of the target image. To the best of our knowledge, this is the first time that the optimal mass transport function has been applied to register large 3D multimodal data sets.
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Multimodal Registration of White Matter Brain Data via Optimal Mass Transport
Rehman, Tauseefur; Haber, Eldad; Pohl, Kilian M.; Haker, Steven; Halle, Mike; Talos, Florin; Wald, Lawrence L.; Kikinis, Ron; Tannenbaum, Allen
2017-01-01
The elastic registration of medical scans from different acquisition sequences is becoming an important topic for many research labs that would like to continue the post-processing of medical scans acquired via the new generation of high-field-strength scanners. In this note, we present a parameter-free registration algorithm that is well suited for this scenario as it requires no tuning to specific acquisition sequences. The algorithm encompasses a new numerical scheme for computing elastic registration maps based on the minimizing flow approach to optimal mass transport. The approach utilizes all of the gray-scale data in both images, and the optimal mapping from image A to image B is the inverse of the optimal mapping from B to A. Further, no landmarks need to be specified, and the minimizer of the distance functional involved is unique. We apply the algorithm to register the white matter folds of two different scans and use the results to parcellate the cortex of the target image. To the best of our knowledge, this is the first time that the optimal mass transport function has been applied to register large 3D multimodal data sets. PMID:28626844
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A novel visual pipework inspection system
NASA Astrophysics Data System (ADS)
Summan, Rahul; Jackson, William; Dobie, Gordon; MacLeod, Charles; Mineo, Carmelo; West, Graeme; Offin, Douglas; Bolton, Gary; Marshall, Stephen; Lille, Alexandre
2018-04-01
The interior visual inspection of pipelines in the nuclear industry is a safety critical activity conducted during outages to ensure the continued safe and reliable operation of plant. Typically, the video output by a manually deployed probe is viewed by an operator looking to identify and localize surface defects such as corrosion, erosion and pitting. However, it is very challenging to estimate the nature and extent of defects by viewing a large structure through a relatively small field of view. This work describes a new visual inspection system employing photogrammetry using a fisheye camera and a structured light system to map the internal geometry of pipelines by generating a photorealistic, geometrically accurate surface model. The error of the system output was evaluated through comparison to a ground truth laser scan (ATOS GOM Triple Scan) of a nuclear grade split pipe sample (stainless steel 304L, 80mm internal diameter) containing defects representative of the application - the error was found to be submillimeter across the sample.
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Mapping Inhibitory Neuronal Circuits by Laser Scanning Photostimulation
Ikrar, Taruna; Olivas, Nicholas D.; Shi, Yulin; Xu, Xiangmin
2011-01-01
Inhibitory neurons are crucial to cortical function. They comprise about 20% of the entire cortical neuronal population and can be further subdivided into diverse subtypes based on their immunochemical, morphological, and physiological properties1-4. Although previous research has revealed much about intrinsic properties of individual types of inhibitory neurons, knowledge about their local circuit connections is still relatively limited3,5,6. Given that each individual neuron's function is shaped by its excitatory and inhibitory synaptic input within cortical circuits, we have been using laser scanning photostimulation (LSPS) to map local circuit connections to specific inhibitory cell types. Compared to conventional electrical stimulation or glutamate puff stimulation, LSPS has unique advantages allowing for extensive mapping and quantitative analysis of local functional inputs to individually recorded neurons3,7-9. Laser photostimulation via glutamate uncaging selectively activates neurons perisomatically, without activating axons of passage or distal dendrites, which ensures a sub-laminar mapping resolution. The sensitivity and efficiency of LSPS for mapping inputs from many stimulation sites over a large region are well suited for cortical circuit analysis. Here we introduce the technique of LSPS combined with whole-cell patch clamping for local inhibitory circuit mapping. Targeted recordings of specific inhibitory cell types are facilitated by use of transgenic mice expressing green fluorescent proteins (GFP) in limited inhibitory neuron populations in the cortex3,10, which enables consistent sampling of the targeted cell types and unambiguous identification of the cell types recorded. As for LSPS mapping, we outline the system instrumentation, describe the experimental procedure and data acquisition, and present examples of circuit mapping in mouse primary somatosensory cortex. As illustrated in our experiments, caged glutamate is activated in a spatially restricted region of the brain slice by UV laser photolysis; simultaneous voltage-clamp recordings allow detection of photostimulation-evoked synaptic responses. Maps of either excitatory or inhibitory synaptic input to the targeted neuron are generated by scanning the laser beam to stimulate hundreds of potential presynaptic sites. Thus, LSPS enables the construction of detailed maps of synaptic inputs impinging onto specific types of inhibitory neurons through repeated experiments. Taken together, the photostimulation-based technique offers neuroscientists a powerful tool for determining the functional organization of local cortical circuits. PMID:22006064
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Airborne laser scanning for high-resolution mapping of Antarctica
NASA Astrophysics Data System (ADS)
Csatho, Bea; Schenk, Toni; Krabill, William; Wilson, Terry; Lyons, William; McKenzie, Garry; Hallam, Cheryl; Manizade, Serdar; Paulsen, Timothy
In order to evaluate the potential of airborne laser scanning for topographic mapping in Antarctica and to establish calibration/validation sites for NASA's Ice, Cloud and land Elevation Satellite (ICESat) altimeter mission, NASA, the U.S. National Science Foundation (NSF), and the U.S. Geological Survey (USGS) joined forces to collect high-resolution airborne laser scanning data.In a two-week campaign during the 2001-2002 austral summer, NASA's Airborne Topographic Mapper (ATM) system was used to collect data over several sites in the McMurdo Sound area of Antarctica (Figure 1a). From the recorded signals, NASA computed laser points and The Ohio State University (OSU) completed the elaborate computation/verification of high-resolution Digital Elevation Models (DEMs) in 2003. This article reports about the DEM generation and some exemplary results from scientists using the geomorphologic information from the DEMs during the 2003-2004 field season.
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Response phase mapping of nonlinear joint dynamics using continuous scanning LDV measurement method
NASA Astrophysics Data System (ADS)
Di Maio, D.; Bozzo, A.; Peyret, Nicolas
2016-06-01
This study aims to present a novel work aimed at locating discrete nonlinearities in mechanical assemblies. The long term objective is to develop a new metric for detecting and locating nonlinearities using Scanning LDV systems (SLDV). This new metric will help to improve the modal updating, or validation, of mechanical assemblies presenting discrete and sparse nonlinearities. It is well established that SLDV systems can scan vibrating structures with high density of measurement points and produc e highly defined Operational Deflection Shapes (ODSs). This paper will present some insights on how to use response phase mapping for locating nonlinearities of a bolted flange. This type of structure presents two types of nonlinearities, which are geometr ical and frictional joints. The interest is focussed on the frictional joints and, therefore, the ability to locate which joint s are responsible for nonlinearity is seen highly valuable for the model validation activities.
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Ramos, Rogelio; Zlatev, Roumen; Valdez, Benjamin; Stoytcheva, Margarita; Carrillo, Mónica; García, Juan-Francisco
2013-01-01
A virtual instrumentation (VI) system called VI localized corrosion image analyzer (LCIA) based on LabVIEW 2010 was developed allowing rapid automatic and subjective error-free determination of the pits number on large sized corroded specimens. The VI LCIA controls synchronously the digital microscope image taking and its analysis, finally resulting in a map file containing the coordinates of the detected probable pits containing zones on the investigated specimen. The pits area, traverse length, and density are also determined by the VI using binary large objects (blobs) analysis. The resulting map file can be used further by a scanning vibrating electrode technique (SVET) system for rapid (one pass) "true/false" SVET check of the probable zones only passing through the pit's centers avoiding thus the entire specimen scan. A complete SVET scan over the already proved "true" zones could determine the corrosion rate in any of the zones.
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ACCELERATING MR PARAMETER MAPPING USING SPARSITY-PROMOTING REGULARIZATION IN PARAMETRIC DIMENSION
Velikina, Julia V.; Alexander, Andrew L.; Samsonov, Alexey
2013-01-01
MR parameter mapping requires sampling along additional (parametric) dimension, which often limits its clinical appeal due to a several-fold increase in scan times compared to conventional anatomic imaging. Data undersampling combined with parallel imaging is an attractive way to reduce scan time in such applications. However, inherent SNR penalties of parallel MRI due to noise amplification often limit its utility even at moderate acceleration factors, requiring regularization by prior knowledge. In this work, we propose a novel regularization strategy, which utilizes smoothness of signal evolution in the parametric dimension within compressed sensing framework (p-CS) to provide accurate and precise estimation of parametric maps from undersampled data. The performance of the method was demonstrated with variable flip angle T1 mapping and compared favorably to two representative reconstruction approaches, image space-based total variation regularization and an analytical model-based reconstruction. The proposed p-CS regularization was found to provide efficient suppression of noise amplification and preservation of parameter mapping accuracy without explicit utilization of analytical signal models. The developed method may facilitate acceleration of quantitative MRI techniques that are not suitable to model-based reconstruction because of complex signal models or when signal deviations from the expected analytical model exist. PMID:23213053
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Barnhardt, W.A.; Kelley, J.T.; Dickson, S.M.; Belknap, D.F.
1998-01-01
The bedrock-framed seafloor in the northwestern Gulf of Maine is characterized by extreme changes in bathymetric relief and covered with a wide variety of surficial materials. Traditional methods of mapping cannot accurately represent the great heterogeneity of such a glaciated region. A new mapping scheme for complex seafloors, based primarily on the interpretation of side-scan sonar imagery, utilizes four easily recognized units: rock, gravel, sand and mud. In many places, however, the seafloor exhibits a complicated mixture or extremely 'patchy' distribution of the four basic units, which are too small to map individually. Twelve composite units, each a two-component mixture of the basic units, were established to represent this patchiness at a small scale (1:100,000). Using a geographic information system, these and all other available data (seismic profiles, grab samples, submersible dives and cores) were referenced to a common geographic base, superimposed on bathymetric contours and then integrated into surficial geologic maps of the regional inner continental shelf. This digital representation of the seafloor comprises a multidimensional, interactive model complete with explicit attributes (depth, bottom type) that allow for detailed analysis of marine environments.
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Wen, Weie; He, Zhonghu; Gao, Fengmei; Liu, Jindong; Jin, Hui; Zhai, Shengnan; Qu, Yanying; Xia, Xianchun
2017-01-01
A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat (Triticum aestivum L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be used as a reference for quantitative trait loci (QTL) mapping to facilitate exploitation of genes and QTL in wheat breeding. PMID:28848588
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The Sounds of Nanoscience: Acoustic STM Analogues
ERIC Educational Resources Information Center
Euler, Manfred
2013-01-01
A hands-on model of scanning tunnelling microscopy (STM) is presented. It uses near-field imaging with sound and computer assisted visualization to create acoustic mappings of resonator arrangements. Due to the (partial) analogy of matter and sound waves the images closely resemble STM scans of atoms. Moreover, the method can be extended to build…
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USDA-ARS?s Scientific Manuscript database
Laser scanning data streams, when linked with multi-spectral, hyperspectral, apparent soil electro-conductivity (ECa), or other kinds of geo-referenced data streams, aid in the creation of maps that allow useful applications in agricultural systems. These combinations of georeferenced information p...
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Characterizing underwater habitat and other features is difficult and costly, especially in the large St. Louis River Estuary. We are using side-scan sonar (SSS), first developed in the 1960s to remotely sense underwater habitat features from reflected acoustic signals (backscatt...
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Ito, K; Kadoya, N; Chiba, M
2016-06-15
Purpose: The aim of this study is to develop radiation treatment planning using magnetic susceptibility obtained from quantitative susceptibility mapping (QSM) via MR imaging. This study demonstrates the feasibility of a method for generating a substitute for a CT image from an MRI. Methods: The head of a healthy volunteer was scanned using a CT scanner and a 3.0 T MRI scanner. The CT imaging was performed with a slice thickness of 2.5 mm at 80 and 120 kV (dual-energy scan). These CT images were converted to relative electron density (rED) using the CT-rED conversion table generated by a previousmore » dual-energy CT scan. The CT-rED conversion table was generated using the conversion of the energy-subtracted CT number to rED via a single linear relationship. One T2 star-weighted 3D gradient echo-based sequence with four different echo times images was acquired using the MRI scanner. These T2 star-weighted images were used to estimate the phase data. To estimate the local field map, a Laplacian unwrapping of the phase and background field removal algorithm were implemented to process phase data. To generate a magnetic susceptibility map from the local field map, we used morphology enabled dipole inversion method. The rED map was resampled to the same resolution as magnetic susceptibility, and the magnetic susceptibility-rED conversion table was obtained via voxel-by-voxel mapping between the magnetic susceptibility and rED maps. Results: A correlation between magnetic susceptibility and rED is not observed through our method. Conclusion: Our results show that the correlation between magnetic susceptibility and rED is not observed. As the next step, we assume that the voxel of the magnetic susceptibility map comprises two materials, such as water (0 ppm) and bone (-2.2 ppm) or water and marrow (0.81ppm). The elements of each voxel were estimated from the ratio of the two materials.« less
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Site-directed DNA crosslinking of large multisubunit protein-DNA complexes.
Persinger, Jim; Bartholomew, Blaine
2009-01-01
Several methods have been developed to site-specifically incorporate photoreactive nucleotide analogs into DNA for the purpose of identifying the proteins and their domains that are in contact with particular regions of DNA. The synthesis of several deoxynucleotide analogs that have a photoreactive group tethered to the nucleotide base and the incorporation of these analogs into DNA are described. In a second approach, oligonucleotide with a photoreactive group attached to the phosphate backbone is chemically synthesized. The photoreactive oligonucleotide is then enzymatically incorporated into DNA by annealing it to a complementary DNA template and extending with DNA polymerase. Both approaches have been effectively used to map protein-DNA interactions in large multisubunit complexes such as the eukaryotic transcription or ATP-dependent chromatin remodeling complexes. Not only do these techniques map the binding sites of the various subunits in these complexes, but when coupled with peptide mapping also determine the protein domain that is in close proximity to the different DNA sites. The strength of these techniques is the ability to scan a large number of potential sites by making combinations of different DNA probes and is facilitated by using an immobilized DNA template for synthesis.
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NASA Astrophysics Data System (ADS)
Alexander, Cici; Korstjens, Amanda H.; Hill, Ross A.
2017-03-01
Mapping and monitoring tropical rainforests and quantifying their carbon stocks are important, both for devising strategies for their conservation and mitigating the effects of climate change. Airborne Laser Scanning (ALS) has advantages over other remote sensing techniques for describing the three-dimensional structure of forests. This study identifies forest patches using ALS-based structural attributes in a tropical rainforest in Sumatra, Indonesia. A method to group trees with similar attributes into forest patches based on Thiessen polygons and k-medoids clustering is developed, combining the advantages of both raster and individual tree-based methods. The structural composition of the patches could be an indicator of habitat type and quality. The patches could also be a basis for developing allometric models for more accurate estimation of carbon stock than is currently possible with generalised models.
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Mutation Scanning in Wheat by Exon Capture and Next-Generation Sequencing.
King, Robert; Bird, Nicholas; Ramirez-Gonzalez, Ricardo; Coghill, Jane A; Patil, Archana; Hassani-Pak, Keywan; Uauy, Cristobal; Phillips, Andrew L
2015-01-01
Targeted Induced Local Lesions in Genomes (TILLING) is a reverse genetics approach to identify novel sequence variation in genomes, with the aims of investigating gene function and/or developing useful alleles for breeding. Despite recent advances in wheat genomics, most current TILLING methods are low to medium in throughput, being based on PCR amplification of the target genes. We performed a pilot-scale evaluation of TILLING in wheat by next-generation sequencing through exon capture. An oligonucleotide-based enrichment array covering ~2 Mbp of wheat coding sequence was used to carry out exon capture and sequencing on three mutagenised lines of wheat containing previously-identified mutations in the TaGA20ox1 homoeologous genes. After testing different mapping algorithms and settings, candidate SNPs were identified by mapping to the IWGSC wheat Chromosome Survey Sequences. Where sequence data for all three homoeologues were found in the reference, mutant calls were unambiguous; however, where the reference lacked one or two of the homoeologues, captured reads from these genes were mis-mapped to other homoeologues, resulting either in dilution of the variant allele frequency or assignment of mutations to the wrong homoeologue. Competitive PCR assays were used to validate the putative SNPs and estimate cut-off levels for SNP filtering. At least 464 high-confidence SNPs were detected across the three mutagenized lines, including the three known alleles in TaGA20ox1, indicating a mutation rate of ~35 SNPs per Mb, similar to that estimated by PCR-based TILLING. This demonstrates the feasibility of using exon capture for genome re-sequencing as a method of mutation detection in polyploid wheat, but accurate mutation calling will require an improved genomic reference with more comprehensive coverage of homoeologues.
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Whankaew, Sukhuman; Poopear, Supannee; Kanjanawattanawong, Supanath; Tangphatsornruang, Sithichoke; Boonseng, Opas; Lightfoot, David A; Triwitayakorn, Kanokporn
2011-05-25
Cassava (Manihot esculenta Crantz) can produce cyanide, a toxic compound, without self-injury. That ability was called the cyanogenic potential (CN). This project aimed to identify quantitative trait loci (QTL) associated with the CN in an outbred population derived from 'Hanatee' × 'Huay Bong 60', two contrasting cultivars. CN was evaluated in 2008 and in 2009 at Rayong province, and in 2009 at Lop Buri province, Thailand. CN was measured using a picrate paper kit. QTL analysis affecting CN was performed with 303 SSR markers. The phenotypic values showed continuous variation with transgressive segregation events with more (115 ppm) and less CN (15 ppm) than either parent ('Hanatee' had 33 ppm and 'Huay Bong 60' had 95 ppm). The linkage map consisted of 303 SSR markers, on 27 linkage groups with a map that encompassed 1,328 cM. The average marker interval was 5.8 cM. Five QTL underlying CN were detected. CN08R1from 2008 at Rayong, CN09R1and CN09R2 from 2009 at Rayong, and CN09L1 and CN09L2 from 2009 at Lop Buri were mapped on linkage group 2, 5, 10 and 11, respectively. Among all the identified QTL, CN09R1 was the most significantly associated with the CN trait with LOD score 5.75 and explained the greatest percentage of phenotypic variation (%Expl.) of 26%. Five new QTL affecting CN were successfully identified from 4 linkage groups. Discovery of these QTL can provide useful markers to assist in cassava breeding and studying genes affecting the trait.
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2011-01-01
Background Cassava (Manihot esculenta Crantz) can produce cyanide, a toxic compound, without self-injury. That ability was called the cyanogenic potential (CN). This project aimed to identify quantitative trait loci (QTL) associated with the CN in an outbred population derived from 'Hanatee' × 'Huay Bong 60', two contrasting cultivars. CN was evaluated in 2008 and in 2009 at Rayong province, and in 2009 at Lop Buri province, Thailand. CN was measured using a picrate paper kit. QTL analysis affecting CN was performed with 303 SSR markers. Results The phenotypic values showed continuous variation with transgressive segregation events with more (115 ppm) and less CN (15 ppm) than either parent ('Hanatee' had 33 ppm and 'Huay Bong 60' had 95 ppm). The linkage map consisted of 303 SSR markers, on 27 linkage groups with a map that encompassed 1,328 cM. The average marker interval was 5.8 cM. Five QTL underlying CN were detected. CN08R1from 2008 at Rayong, CN09R1and CN09R2 from 2009 at Rayong, and CN09L1 and CN09L2 from 2009 at Lop Buri were mapped on linkage group 2, 5, 10 and 11, respectively. Among all the identified QTL, CN09R1 was the most significantly associated with the CN trait with LOD score 5.75 and explained the greatest percentage of phenotypic variation (%Expl.) of 26%. Conclusions Five new QTL affecting CN were successfully identified from 4 linkage groups. Discovery of these QTL can provide useful markers to assist in cassava breeding and studying genes affecting the trait. PMID:21609492
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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
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Probabilistic change mapping from airborne LiDAR for post-disaster damage assessment
NASA Astrophysics Data System (ADS)
Jalobeanu, A.; Runyon, S. C.; Kruse, F. A.
2013-12-01
When both pre- and post-event LiDAR point clouds are available, change detection can be performed to identify areas that were most affected by a disaster event, and to obtain a map of quantitative changes in terms of height differences. In the case of earthquakes in built-up areas for instance, first responders can use a LiDAR change map to help prioritize search and recovery efforts. The main challenge consists of producing reliable change maps, robust to collection conditions, free of processing artifacts (due for instance to triangulation or gridding), and taking into account the various sources of uncertainty. Indeed, datasets acquired within a few years interval are often of different point density (sometimes an order of magnitude higher for recent data), different acquisition geometries, and very likely suffer from georeferencing errors and geometric discrepancies. All these differences might not be important for producing maps from each dataset separately, but they are crucial when performing change detection. We have developed a novel technique for the estimation of uncertainty maps from the LiDAR point clouds, using Bayesian inference, treating all variables as random. The main principle is to grid all points on a common grid before attempting any comparison, as working directly with point clouds is cumbersome and time consuming. A non-parametric approach based on local linear regression was implemented, assuming a locally linear model for the surface. This enabled us to derive error bars on gridded elevations, and then elevation differences. In this way, a map of statistically significant changes could be computed - whereas a deterministic approach would not allow testing of the significance of differences between the two datasets. This approach allowed us to take into account not only the observation noise (due to ranging, position and attitude errors) but also the intrinsic roughness of the observed surfaces occurring when scanning vegetation. As only elevation differences above a predefined noise level are accounted for (according to a specified confidence interval related to the allowable false alarm rate) the change detection is robust to all these sources of noise. To first validate the approach, we built small-scale models and scanned them using a terrestrial laser scanner to establish 'ground truth'. Changes were manually applied to the models then new scans were performed and analyzed. Additionally, two airborne datasets of the Monterey Peninsula, California, were processed and analyzed. The first one was acquired during 2010 (with relatively low point density, 1-3 pts/m2), and the second one was acquired during 2012 (with up to 30 pts/m2). To perform the comparison, a new point cloud registration technique was developed and the data were registered to a common 1 m grid. The goal was to correct systematic shifts due to GPS and INS errors, and focus on the actual height differences regardless of the absolute planimetric accuracy of the datasets. Though no major disaster event occurred between the two acquisition dates, sparse changes were detected and interpreted mostly as construction and natural landscape evolution.
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Scan path entropy and arrow plots: capturing scanning behavior of multiple observers
Hooge, Ignace; Camps, Guido
2013-01-01
Designers of visual communication material want their material to attract and retain attention. In marketing research, heat maps, dwell time, and time to AOI first hit are often used as evaluation parameters. Here we present two additional measures (1) “scan path entropy” to quantify gaze guidance and (2) the “arrow plot” to visualize the average scan path. Both are based on string representations of scan paths. The latter also incorporates transition matrices and time required for 50% of the observers to first hit AOIs (T50). The new measures were tested in an eye tracking study (48 observers, 39 advertisements). Scan path entropy is a sensible measure for gaze guidance and the new visualization method reveals aspects of the average scan path and gives a better indication in what order global scanning takes place. PMID:24399993
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Scanning measurement of Seebeck coefficient of a heated sample
DOE Office of Scientific and Technical Information (OSTI.GOV)
Snyder, G. Jeffrey; Iwanaga, Shiho
2016-04-19
A novel scanning Seebeck coefficient measurement technique is disclosed utilizing a cold scanning thermocouple probe tip on heated bulk and thin film samples. The system measures variations in the Seebeck coefficient within the samples. The apparatus may be used for two dimensional mapping of the Seebeck coefficient on the bulk and thin film samples. This technique can be utilized for detection of defective regions, as well as phase separations in the sub-mm range of various thermoelectric materials.
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Scanning fluorescent microthermal imaging apparatus and method
Barton, Daniel L.; Tangyunyong, Paiboon
1998-01-01
A scanning fluorescent microthermal imaging (FMI) apparatus and method is disclosed, useful for integrated circuit (IC) failure analysis, that uses a scanned and focused beam from a laser to excite a thin fluorescent film disposed over the surface of the IC. By collecting fluorescent radiation from the film, and performing point-by-point data collection with a single-point photodetector, a thermal map of the IC is formed to measure any localized heating associated with defects in the IC.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Jones, Michael W. M.; Phillips, Nicholas W.; van Riessen, Grant A.
2016-08-11
Owing to its extreme sensitivity, quantitative mapping of elemental distributionsviaX-ray fluorescence microscopy (XFM) has become a key microanalytical technique. The recent realisation of scanning X-ray diffraction microscopy (SXDM) meanwhile provides an avenue for quantitative super-resolved ultra-structural visualization. The similarity of their experimental geometries indicates excellent prospects for simultaneous acquisition. Here, in both step- and fly-scanning modes, robust, simultaneous XFM-SXDM is demonstrated.
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NASA Astrophysics Data System (ADS)
Larson, Bjorg; Abeytunge, Sanjeewa; Glazowski, Chris; Rajadhyaksha, Milind
2012-02-01
Confocal point-scanning microscopy has been showing promise in the detection, diagnosing and mapping of skin lesions in clinical settings. The noninvasive technique allows provides optical sectioning and cellular resolution for in vivo diagnosis of melanoma and basal cell carcinoma and pre-operative and intra-operative mapping of margins. The imaging has also enabled more accurate "guided" biopsies while minimizing the otherwise large number of "blind" biopsies. Despite these translational advances, however, point-scanning technology remains relatively complex and expensive. Line-scanning technology may offer an alternative approach to accelerate translation to the clinic. Line-scanning, using fewer optical components, inexpensive linear-array detectors and custom electronics, may enable smaller, simpler and lower-cost confocal microscopes. A line is formed using a cylindrical lens and scanned through the back focal plane of the objective with a galvanometric scanner. A linear CCD is used for detection. Two pupil configurations were compared for performance in imaging human tissue. In the full-pupil configuration, illumination and detection is made through the full objective pupil. In the divided pupil approach, half the pupil is illuminated and the other half is used for detection. The divided pupil configuration loses spatial and axial resolution due to a diminished NA, but the sectioning capability and rejection of background is improved. Imaging in skin and oral mucosa illustrate the performance of the two configurations.
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Classification of Mobile Laser Scanning Point Clouds from Height Features
NASA Astrophysics Data System (ADS)
Zheng, M.; Lemmens, M.; van Oosterom, P.
2017-09-01
The demand for 3D maps of cities and road networks is steadily growing and mobile laser scanning (MLS) systems are often the preferred geo-data acquisition method for capturing such scenes. Because MLS systems are mounted on cars or vans they can acquire billions of points of road scenes within a few hours of survey. Manual processing of point clouds is labour intensive and thus time consuming and expensive. Hence, the need for rapid and automated methods for 3D mapping of dense point clouds is growing exponentially. The last five years the research on automated 3D mapping of MLS data has tremendously intensified. In this paper, we present our work on automated classification of MLS point clouds. In the present stage of the research we exploited three features - two height components and one reflectance value, and achieved an overall accuracy of 73 %, which is really encouraging for further refining our approach.
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Wu, J.S.; Kim, A. M.; Bleher, R.; Myers, B.D.; Marvin, R. G.; Inada, H.; Nakamura, K.; Zhang, X.F.; Roth, E.; Li, S.Y.; Woodruff, T. K.; O'Halloran, T. V.; Dravid, Vinayak P.
2013-01-01
A dedicated analytical scanning transmission electron microscope (STEM) with dual energy dispersive spectroscopy (EDS) detectors has been designed for complementary high performance imaging as well as high sensitivity elemental analysis and mapping of biological structures. The performance of this new design, based on a Hitachi HD-2300A model, was evaluated using a variety of biological specimens. With three imaging detectors, both the surface and internal structure of cells can be examined simultaneously. The whole-cell elemental mapping, especially of heavier metal species that have low cross-section for electron energy loss spectroscopy (EELS), can be faithfully obtained. Optimization of STEM imaging conditions is applied to thick sections as well as thin sections of biological cells under low-dose conditions at room- and cryogenic temperatures. Such multimodal capabilities applied to soft/biological structures usher a new era for analytical studies in biological systems. PMID:23500508
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NASA Technical Reports Server (NTRS)
Bonacuse, Peter J.; Kantzos, Peter T.
2002-01-01
An automated two-degree-of-freedom specimen positioning stage has been developed at the NASA Glenn Research Center to map and monitor defects in fatigue specimens. This system expedites the examination of the entire gauge section of fatigue specimens so that defects can be found using scanning electron microscopy (SEM). Translation and rotation stages are driven by microprocessor-based controllers that are, in turn, interfaced to a computer running custom-designed software. This system is currently being used to find and record the location of ceramic inclusions in powder metallurgy materials. The mapped inclusions are periodically examined during interrupted fatigue experiments. The number of cycles to initiate cracks from these inclusions and the rate of growth of initiated cracks can then be quantified. This information is necessary to quantify the effect of this type of defect on the durability of powder metallurgy materials. This system was developed with support of the Ultra Safe program.
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Wang, Chunhao; Subashi, Ergys; Yin, Fang-Fang; Chang, Zheng
2016-01-01
Purpose: To develop a dynamic fractal signature dissimilarity (FSD) method as a novel image texture analysis technique for the quantification of tumor heterogeneity information for better therapeutic response assessment with dynamic contrast-enhanced (DCE)-MRI. Methods: A small animal antiangiogenesis drug treatment experiment was used to demonstrate the proposed method. Sixteen LS-174T implanted mice were randomly assigned into treatment and control groups (n = 8/group). All mice received bevacizumab (treatment) or saline (control) three times in two weeks, and one pretreatment and two post-treatment DCE-MRI scans were performed. In the proposed dynamic FSD method, a dynamic FSD curve was generated to characterize the heterogeneity evolution during the contrast agent uptake, and the area under FSD curve (AUCFSD) and the maximum enhancement (MEFSD) were selected as representative parameters. As for comparison, the pharmacokinetic parameter Ktrans map and area under MR intensity enhancement curve AUCMR map were calculated. Besides the tumor’s mean value and coefficient of variation, the kurtosis, skewness, and classic Rényi dimensions d1 and d2 of Ktrans and AUCMR maps were evaluated for heterogeneity assessment for comparison. For post-treatment scans, the Mann–Whitney U-test was used to assess the differences of the investigated parameters between treatment/control groups. The support vector machine (SVM) was applied to classify treatment/control groups using the investigated parameters at each post-treatment scan day. Results: The tumor mean Ktrans and its heterogeneity measurements d1 and d2 values showed significant differences between treatment/control groups in the second post-treatment scan. In contrast, the relative values (in reference to the pretreatment value) of AUCFSD and MEFSD in both post-treatment scans showed significant differences between treatment/control groups. When using AUCFSD and MEFSD as SVM input for treatment/control classification, the achieved accuracies were 93.8% and 93.8% at first and second post-treatment scan days, respectively. In comparison, the classification accuracies using d1 and d2 of Ktrans map were 87.5% and 100% at first and second post-treatment scan days, respectively. Conclusions: As quantitative metrics of tumor contrast agent uptake heterogeneity, the selected parameters from the dynamic FSD method accurately captured the therapeutic response in the experiment. The potential application of the proposed method is promising, and its addition to the existing DCE-MRI techniques could improve DCE-MRI performance in early assessment of treatment response. PMID:26936718
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Nanoscopium: a Scanning Hard X-ray Nanoprobe Beamline at Synchrotron Soleil
NASA Astrophysics Data System (ADS)
Somogyi, A.; Polack, F.; Moreno, T.
2010-06-01
Nanoscopium is the single scanning hard X-ray nano-probe beamline planned at SOLEIL. This ˜155 m long beamline will fully exploit the high brilliance and coherence characteristics of the X-ray beam both for diffraction limited focusing and for contrast formation. It will offer the most advanced imaging techniques in multimodal mode and will be a research tool for a wide user community working in the fields of earth-, environmental-, and life-sciences. The different μ-μnano-probe techniques offered by the beamline will permit elemental mapping at trace (ppm) levels (scanning XRF), speciation mapping (XANES), phase gradient mapping (scanning differential phase contrast), and density-contrast based imaging of internal structures (coherent diffraction imaging) in the 30 nm to 1 μm spatial resolution range, also in "in situ conditions". Nanoscopium will cover the 5-20 keV energy range. The stability of the nanobeam will be ensured by horizontally reflecting beamline optics (a sagitally and a tangentially pre-focusing mirror, horizontally reflecting monochromators) in front of the overfilled secondary source. Trade-off between high energy resolution (ΔE/E˜10-4) and high flux (1011 ph/s with ΔE/E˜10-2) will be achieved by two interchangeable monochromators (a double crystal and a double multilayer one). KB mirror and FZP lenses will be used as focusing devices. The beamline is in the design and construction phase. It is foreseen to be open for users at the beginning of 2013.
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Quasiparticle interference mapping of ZrSiS
NASA Astrophysics Data System (ADS)
Lodge, Michael; Hosen, Md Mofazzle; Neupane, Madhab; Ishigami, Masa; Chang, Guoqing; Singh, Bahadur; Lin, Hsin; Weber, Bent; Hellerstedt, Jack; Edmonds, Mark; Fuhrer, Michael; Kaczorowski, Dariusz
The emergent class of 3D Dirac semimetals presents intriguing new systems in which to study the rich physics of the robust, topologically-protected quasiparticles hosted within their bulk. For example, in nodal-line Dirac semimetals, the conductance and valence bands meet along a closed loop in momentum space and disperse linearly in the vicinity of the resultant line node. This results in novel scattering phenomena, owing to the unique Fermi surfaces and scattering selection rules of these systems. Here, we have performed scanning tunneling microscopy and spectroscopy of ZrSiS, one such nodal-line Dirac semimetal,at 4.5 K. We have visualized quasiparticle scattering using differential conductance mapping. In conjunction with numerical modeling, we identify at least six allowed scattering vectors in the material, which gives insight into the scattering selection rules of these novel materials. This work is based upon research supported by the National Science Foundation under Grant No. 0955625 (MSL and MI) and Fellowship No. 1614303 (MSL), and by the Australian Research Council under DECRA Fellowship No. DE160101334 (BW).
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Clop, Alex; Marcq, Fabienne; Takeda, Haruko; Pirottin, Dimitri; Tordoir, Xavier; Bibé, Bernard; Bouix, Jacques; Caiment, Florian; Elsen, Jean-Michel; Eychenne, Francis; Larzul, Catherine; Laville, Elisabeth; Meish, Françoise; Milenkovic, Dragan; Tobin, James; Charlier, Carole; Georges, Michel
2006-07-01
Texel sheep are renowned for their exceptional meatiness. To identify the genes underlying this economically important feature, we performed a whole-genome scan in a Romanov x Texel F2 population. We mapped a quantitative trait locus with a major effect on muscle mass to chromosome 2 and subsequently fine-mapped it to a chromosome interval encompassing the myostatin (GDF8) gene. We herein demonstrate that the GDF8 allele of Texel sheep is characterized by a G to A transition in the 3' UTR that creates a target site for mir1 and mir206, microRNAs (miRNAs) that are highly expressed in skeletal muscle. This causes translational inhibition of the myostatin gene and hence contributes to the muscular hypertrophy of Texel sheep. Analysis of SNP databases for humans and mice demonstrates that mutations creating or destroying putative miRNA target sites are abundant and might be important effectors of phenotypic variation.
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Mapping bright and dark modes in gold nanoparticle chains using electron energy loss spectroscopy.
Barrow, Steven J; Rossouw, David; Funston, Alison M; Botton, Gianluigi A; Mulvaney, Paul
2014-07-09
We present a scanning transmission electron microscopy-electron energy loss spectroscopy (STEM-EELS) investigation of gold nanosphere chains with lengths varying from 1 to 5 particles. We show localized EELS signals from the chains and identify energy-loss peaks arising due to l = 1, 2, 3, 4, and 5 plasmon modes through the use of EELS mapping. We also show the evolution of the energy of these modes as the length of a given chain increases, and we find that a chain containing N particles can accommodate at least N experimentally observable modes, in addition to the transverse mode. As the chain length is increased by the addition of one more gold particle to the chain, the new N + 1 mode becomes the highest energy mode, while the existing modes lower their energy and eventually asymptote as they delocalize along the chain. We also show that modes become increasingly difficult to detect with the EELS technique as l approaches N. The data are compared to numerical simulations.
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NASA Technical Reports Server (NTRS)
Hoffer, R. M. (Principal Investigator)
1979-01-01
The spatial characteristics of the data were evaluated. A program was developed to reduce the spatial distortions resulting from variable viewing distance, and geometrically adjusted data sets were generated. The potential need for some level of radiometric adjustment was evidenced by an along track band of high reflectance across different cover types in the Varian imagery. A multiple regression analysis was employed to explore the viewing angle effect on measured reflectance. Areas in the data set which appeared to have no across track stratification of cover type were identified. A program was developed which computed the average reflectance by column for each channel, over all of the scan lines in the designated areas. A regression analysis was then run using the first, second, and third degree polynomials, for each channel. An atmospheric effect as a component of the viewing angle source of variance is discussed. Cover type maps were completed and training and test field selection was initiated.
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Tracking footprints of artificial selection in the dog genome.
Akey, Joshua M; Ruhe, Alison L; Akey, Dayna T; Wong, Aaron K; Connelly, Caitlin F; Madeoy, Jennifer; Nicholas, Thomas J; Neff, Mark W
2010-01-19
The size, shape, and behavior of the modern domesticated dog has been sculpted by artificial selection for at least 14,000 years. The genetic substrates of selective breeding, however, remain largely unknown. Here, we describe a genome-wide scan for selection in 275 dogs from 10 phenotypically diverse breeds that were genotyped for over 21,000 autosomal SNPs. We identified 155 genomic regions that possess strong signatures of recent selection and contain candidate genes for phenotypes that vary most conspicuously among breeds, including size, coat color and texture, behavior, skeletal morphology, and physiology. In addition, we demonstrate a significant association between HAS2 and skin wrinkling in the Shar-Pei, and provide evidence that regulatory evolution has played a prominent role in the phenotypic diversification of modern dog breeds. Our results provide a first-generation map of selection in the dog, illustrate how such maps can rapidly inform the genetic basis of canine phenotypic variation, and provide a framework for delineating the mechanistic basis of how artificial selection promotes rapid and pronounced phenotypic evolution.
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Zou, Qiang; Wu, Zhiming; Fu, Mingming; ...
2017-02-03
Combined scanning tunneling microscopy, spectroscopy, and local barrier height (LBH) studies show that low-temperature-cleaved optimally doped Ba(Fe 1–xCo x) 2As 2 crystals with x = 0.06, with T c = 22 K, have complicated morphologies. Although the cleavage surface and hence the morphologies are variable, the superconducting gap maps show the same gap widths and nanometer size inhomogeneities irrelevant to the morphology. Based on the spectroscopy and LBH maps, the bright patches and dark stripes in the morphologies are identified as Ba- and As-dominated surface terminations, respectively. Magnetic impurities, possibly due to Co or Fe atoms, are believed to createmore » local in-gap state and, in addition, suppress the superconducting coherence peaks. Lastly, this study will clarify the confusion on the cleavage surface terminations of the Fe-based superconductors and its relation with the electronic structures.« less
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NASA Astrophysics Data System (ADS)
Beegle, L. W.; Bhartia, R.; DeFlores, L. P.; Abbey, W.; Asher, S. A.; Burton, A. S.; Fries, M.; Conrad, P. G.; Clegg, S. M.; Wiens, R. C.; Edgett, K. S.; Ehlmann, B. L.; Nealson, K. H.; Minitti, M. E.; Popp, J.; Langenhorst, F.; Sobron, P.; Steele, A.; Williford, K. H.; Yingst, R. A.
2017-12-01
The Scanning Habitable Environments with Raman & Luminescence for Organics & Chemicals (SHERLOC) investigation is part of the Mars 2020 integrated payload. SHERLOC enables non-contact, spatially resolved, and highly sensitivity detection and characterization of organics and minerals in the Martian surface and near subsurface. SHERLOC is an arm-mounted, Deep UV (DUV) resonance Raman and fluorescence spectrometer utilizing a 248.6-nm DUV laser. Deep UV induced native fluorescence is very sensitive to condensed carbon and aromatic organics, enabling detection at or below 10-6 w/w (1 ppm) at <100 µm spatial scales. SHERLOC's deep UV resonance Raman enables detection and classification of aromatic and aliphatic organics with sensitivities of 10-2 to below 10-4 w/w. In addition to organics, the deep UV Raman enables detection and classification of minerals relevant to aqueous chemistry with grain sizes below 20 µm. SHERLOC will be able to map the distribution of organic material with respect to visible features and minerals that are identifiable with the Raman spectrometer. These maps will enable analysis of the distribution of organics with minerals.
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Mesoscale monitoring of the soil freeze/thaw boundary from orbital microwave radiometry
NASA Technical Reports Server (NTRS)
Dobson, Craig; Ulaby, Fawwaz T.; Zuerndorfer, Brian; England, Anthony W.
1990-01-01
A technique was developed for mapping the spatial extent of frozen soils from the spectral characteristics of the 10.7 to 37 GHz radiobrightness. Through computational models for the spectral radiobrightness of diurnally heated freesing soils, a distinctive radiobrightness signature was identified for frozen soils, and the signature was cast as a discriminant for unsupervised classification. In addition to large area images, local area spatial averages of radiobrightness were calculated for each radiobrightness channel at 7 meteorologic sites within the test region. Local area averages at the meteorologic sites were used to define the preliminary boundaries in the Freeze Indicator discriminate. Freeze Indicator images based upon Nimbus 7, Scanning Multichannel Microwave Radiometer (SMMR) data effectively map temporal variations in the freeze/thaw pattern for the northern Great Plains at the time scale of days. Diurnal thermal gradients have a small but measurable effect upon the SMMR spectral gradient. Scale-space filtering can be used to improve the spatial resolution of a freeze/thaw classified image.
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Wu, Jianhui; Huang, Shuo; Zeng, Qingdong; Liu, Shengjie; Wang, Qilin; Mu, Jingmei; Yu, Shizhou; Han, Dejun; Kang, Zhensheng
2018-06-16
A major stripe rust resistance QTL on chromosome 4BL was localized to a 4.5-Mb interval using comparative QTL mapping methods and validated in 276 wheat genotypes by haplotype analysis. CYMMIT-derived wheat line P10103 was previously identified to have adult plant resistance (APR) to stripe rust in the greenhouse and field. The conventional approach for QTL mapping in common wheat is laborious. Here, we performed QTL detection of APR using a combination of genome-wide scanning and extreme pool-genotyping. SNP-based genetic maps were constructed using the Wheat55 K SNP array to genotype a recombinant inbred line (RIL) population derived from the cross Mingxian 169 × P10103. Five stable QTL were detected across multiple environments. A fter comparing SNP profiles from contrasting, extreme DNA pools of RILs six putative QTL were located to approximate chromosome positions. A major QTL on chromosome 4B was identified in F 2:4 contrasting pools from cross Zhengmai 9023 × P10103. A consensus QTL (LOD = 26-40, PVE = 42-55%), named QYr.nwafu-4BL, was defined and localized to a 4.5-Mb interval flanked by SNP markers AX-110963704 and AX-110519862 in chromosome arm 4BL. Based on stripe rust response, marker genotypes, pedigree analysis and mapping data, QYr.nwafu-4BL is likely to be a new APR QTL. The applicability of the SNP-based markers flanking QYr.nwafu-4BL was validated on a diversity panel of 276 wheat lines. The additional minor QTL on chromosomes 4A, 5A, 5B and 6A enhanced the level of resistance conferred by QYr.nwafu-4BL. Marker-assisted pyramiding of QYr.nwafu-4BL and other favorable minor QTL in new wheat cultivars should improve the level of APR to stripe rust.
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Photoreceptor layer map using spectral-domain optical coherence tomography.
Lee, Ji Eun; Lim, Dae Won; Bae, Han Yong; Park, Hyun Jin
2009-12-01
To develop a novel method for analysis of the photoreceptor layer map (PLM) generated using spectral-domain optical coherence tomography (OCT). OCT scans were obtained from 20 eyes, 10 with macular holes (MH) and 10 with central serous chorioretinopathy (CSC) using the Macular Cube (512 x 128) protocol of the Cirrus HD-OCT (Carl Zeiss). The scanned data were processed using embedded tools of the advanced visualization. A partial thickness OCT fundus image of the photoreceptor layer was generated by setting the region of interest to a 50-microm thick layer that was parallel and adjacent to the retinal pigment epithelium. The resulting image depicted the photoreceptor layer as a map of the reflectivity in OCT. The PLM was compared with fundus photography, auto-fluorescence, tomography, and retinal thickness map. The signal from the photoreceptor layer of every OCT scan in each case was demonstrated as a single image of PLM in a fundus photograph fashion. In PLM images, detachment of the sensory retina is depicted as a hypo-reflective area, which represents the base of MH and serous detachment in CSC. Relative hypo-reflectivity, which was also noted at closed MH and at recently reattached retina in CSC, was associated with reduced signal from the junction between the inner and outer segments of photoreceptors in OCT images. Using PLM, changes in the area of detachment and reflectivity of the photoreceptor layer could be efficiently monitored. The photoreceptor layer can be analyzed as a map using spectral-domain OCT. In the treatment of both MH and CSC, PLM may provide new pathological information about the photoreceptor layer to expand our understanding of these diseases.
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Meng, Yu; Li, Gang; Gao, Yaozong; Lin, Weili; Shen, Dinggang
2016-11-01
Longitudinal neuroimaging analysis of the dynamic brain development in infants has received increasing attention recently. Many studies expect a complete longitudinal dataset in order to accurately chart the brain developmental trajectories. However, in practice, a large portion of subjects in longitudinal studies often have missing data at certain time points, due to various reasons such as the absence of scan or poor image quality. To make better use of these incomplete longitudinal data, in this paper, we propose a novel machine learning-based method to estimate the subject-specific, vertex-wise cortical morphological attributes at the missing time points in longitudinal infant studies. Specifically, we develop a customized regression forest, named dynamically assembled regression forest (DARF), as the core regression tool. DARF ensures the spatial smoothness of the estimated maps for vertex-wise cortical morphological attributes and also greatly reduces the computational cost. By employing a pairwise estimation followed by a joint refinement, our method is able to fully exploit the available information from both subjects with complete scans and subjects with missing scans for estimation of the missing cortical attribute maps. The proposed method has been applied to estimating the dynamic cortical thickness maps at missing time points in an incomplete longitudinal infant dataset, which includes 31 healthy infant subjects, each having up to five time points in the first postnatal year. The experimental results indicate that our proposed framework can accurately estimate the subject-specific vertex-wise cortical thickness maps at missing time points, with the average error less than 0.23 mm. Hum Brain Mapp 37:4129-4147, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
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Matsuyama, Tomoki; Kimura, Makoto T.; Koike, Kuniaki; Abe, Tomoko; Nakano, Takeshi; Asami, Tadao; Ebisuzaki, Toshikazu; Held, William A.; Yoshida, Shigeo; Nagase, Hiroki
2003-01-01
Understanding the role of ‘epigenetic’ changes such as DNA methylation and chromatin remodeling has now become critical in understanding many biological processes. In order to delineate the global methylation pattern in a given genomic DNA, computer software has been developed to create a virtual image of restriction landmark genomic scanning (Vi-RLGS). When using a methylation- sensitive enzyme such as NotI as the restriction landmark, the comparison between real and in silico RLGS profiles of the genome provides a methylation map of genomic NotI sites. A methylation map of the Arabidopsis genome was created that could be confirmed by a methylation-sensitive PCR assay. The method has also been applied to the mouse genome. Although a complete methylation map has not been completed, a region of methylation difference between two tissues has been tested and confirmed by bisulfite sequencing. Vi-RLGS in conjunction with real RLGS will make it possible to develop a more complete map of genomic sites that are methylated or demethylated as a consequence of normal or abnormal development. PMID:12888509
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Geomorphometric analysis of cave ceiling channels mapped with 3-D terrestrial laser scanning
NASA Astrophysics Data System (ADS)
Gallay, Michal; Hochmuth, Zdenko; Kaňuk, Ján; Hofierka, Jaroslav
2016-05-01
The change of hydrological conditions during the evolution of caves in carbonate rocks often results in a complex subterranean geomorphology, which comprises specific landforms such as ceiling channels, anastomosing half tubes, or speleothems organized vertically in different levels. Studying such complex environments traditionally requires tedious mapping; however, this is being replaced with terrestrial laser scanning technology. Laser scanning overcomes the problem of reaching high ceilings, providing new options to map underground landscapes with unprecedented level of detail and accuracy. The acquired point cloud can be handled conveniently with dedicated software, but applying traditional geomorphometry to analyse the cave surface is limited. This is because geomorphometry has been focused on parameterization and analysis of surficial terrain. The theoretical and methodological concept has been based on two-dimensional (2-D) scalar fields, which are sufficient for most cases of the surficial terrain. The terrain surface is modelled with a bivariate function of altitude (elevation) and represented by a raster digital elevation model. However, the cave is a 3-D entity; therefore, a different approach is required for geomorphometric analysis. In this paper, we demonstrate the benefits of high-resolution cave mapping and 3-D modelling to better understand the palaeohydrography of the Domica cave in Slovakia. This methodological approach adopted traditional geomorphometric methods in a unique manner and also new methods used in 3-D computer graphics, which can be applied to study other 3-D geomorphological forms.
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Guehl, Nicolas J; Normandin, Marc D; Wooten, Dustin W; Rozen, Guy; Ruskin, Jeremy N; Shoup, Timothy M; Woo, Jonghye; Ptaszek, Leon M; Fakhri, Georges El; Alpert, Nathaniel M
2017-09-01
We have recently reported a method for measuring rest-stress myocardial blood flow (MBF) using a single, relatively short, PET scan session. The method requires two IV tracer injections, one to initiate rest imaging and one at peak stress. We previously validated absolute flow quantitation in ml/min/cc for standard bull's eye, segmental analysis. In this work, we extend the method for fast computation of rest-stress MBF parametric images. We provide an analytic solution to the single-scan rest-stress flow model which is then solved using a two-dimensional table lookup method (LM). Simulations were performed to compare the accuracy and precision of the lookup method with the original nonlinear method (NLM). Then the method was applied to 16 single scan rest/stress measurements made in 12 pigs: seven studied after infarction of the left anterior descending artery (LAD) territory, and nine imaged in the native state. Parametric maps of rest and stress MBF as well as maps of left (f LV ) and right (f RV ) ventricular spill-over fractions were generated. Regions of interest (ROIs) for 17 myocardial segments were defined in bull's eye fashion on the parametric maps. The mean of each ROI was then compared to the rest (K 1r ) and stress (K 1s ) MBF estimates obtained from fitting the 17 regional TACs with the NLM. In simulation, the LM performed as well as the NLM in terms of precision and accuracy. The simulation did not show that bias was introduced by the use of a predefined two-dimensional lookup table. In experimental data, parametric maps demonstrated good statistical quality and the LM was computationally much more efficient than the original NLM. Very good agreement was obtained between the mean MBF calculated on the parametric maps for each of the 17 ROIs and the regional MBF values estimated by the NLM (K 1map LM = 1.019 × K 1 ROI NLM + 0.019, R 2 = 0.986; mean difference = 0.034 ± 0.036 mL/min/cc). We developed a table lookup method for fast computation of parametric imaging of rest and stress MBF. Our results show the feasibility of obtaining good quality MBF maps using modest computational resources, thus demonstrating that the method can be applied in a clinical environment to obtain full quantitative MBF information. © 2017 American Association of Physicists in Medicine.
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Chen, Yongsheng; Liu, Saifeng; Wang, Yu; Kang, Yan; Haacke, E Mark
2018-02-01
To provide whole brain grey matter (GM) to white matter (WM) contrast enhanced T1W (T1WE) images, multi-echo quantitative susceptibility mapping (QSM), proton density (PD) weighted images, T1 maps, PD maps, susceptibility weighted imaging (SWI), and R2* maps with minimal misregistration in scanning times <5min. Strategically acquired gradient echo (STAGE) imaging includes two fully flow compensated double echo gradient echo acquisitions with a resolution of 0.67×1.33×2.0mm 3 acquired in 5min for 64 slices. Ten subjects were recruited and scanned at 3 Tesla. The optimum pair of flip angles (6° and 24° with TR=25ms at 3T) were used for both T1 mapping with radio frequency (RF) transmit field correction and creating enhanced GM/WM contrast (the T1WE). The proposed T1WE image was created from a combination of the proton density weighted (6°, PDW) and T1W (24°) images and corrected for RF transmit field variations. Prior to the QSM calculation, a multi-echo phase unwrapping strategy was implemented using the unwrapped short echo to unwrap the longer echo to speed up computation. R2* maps were used to mask deep grey matter and veins during the iterative QSM calculation. A weighted-average sum of susceptibility maps was generated to increase the signal-to-noise ratio (SNR) and the contrast-to-noise ratio (CNR). The proposed T1WE image has a significantly improved CNR both for WM to deep GM and WM to cortical GM compared to the acquired T1W image (the first echo of 24° scan) and the T1MPRAGE image. The weighted-average susceptibility maps have 80±26%, 55±22%, 108±33% SNR increases across the ten subjects compared to the single echo result of 17.5ms for the putamen, caudate nucleus, and globus pallidus, respectively. STAGE imaging offers the potential to create a standardized brain imaging protocol providing four pieces of quantitative tissue property information and multiple types of qualitative information in just 5min. Published by Elsevier Inc.
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Olin, Anders; Ladefoged, Claes N; Langer, Natasha H; Keller, Sune H; Löfgren, Johan; Hansen, Adam E; Kjær, Andreas; Langer, Seppo W; Fischer, Barbara M; Andersen, Flemming L
2018-06-01
Quantitative PET/MRI is dependent on reliable and reproducible MR-based attenuation correction (MR-AC). In this study, we evaluated the quality of current vendor-provided thoracic MR-AC maps and further investigated the reproducibility of their impact on 18 F-FDG PET quantification in patients with non-small cell lung cancer. Methods: Eleven patients with inoperable non-small cell lung cancer underwent 2-5 thoracic PET/MRI scan-rescan examinations within 22 d. 18 F-FDG PET data were acquired along with 2 Dixon MR-AC maps for each examination. Two PET images (PET A and PET B ) were reconstructed using identical PET emission data but with MR-AC from these intrasubject repeated attenuation maps. In total, 90 MR-AC maps were evaluated visually for quality and the occurrence of categorized artifacts by 2 PET/MRI-experienced physicians. Each tumor was outlined by a volume of interest (40% isocontour of maximum) on PET A , which was then projected onto the corresponding PET B SUV mean and SUV max were assessed from the PET images. Within-examination coefficients of variation and Bland-Altman analyses were conducted for the assessment of SUV variations between PET A and PET B Results: Image artifacts were observed in 86% of the MR-AC maps, and 30% of the MR-AC maps were subjectively expected to affect the tumor SUV. SUV mean and SUV max resulted in coefficients of variation of 5.6% and 6.6%, respectively, and scan-rescan SUV variations were within ±20% in 95% of the cases. Substantial SUV variations were seen mainly for scan-rescan examinations affected by respiratory motion. Conclusion: Artifacts occur frequently in standard thoracic MR-AC maps, affecting the reproducibility of PET/MRI. These, in combination with other well-known sources of error associated with PET/MRI examinations, lead to inconsistent SUV measurements in serial studies, which may affect the reliability of therapy response assessment. A thorough visual inspection of the thoracic MR-AC map and Dixon images from which it is derived remains crucial for the detection of MR-AC artifacts that may influence the reliability of SUV. © 2018 by the Society of Nuclear Medicine and Molecular Imaging.
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Scanning fluorescent microthermal imaging apparatus and method
Barton, D.L.; Tangyunyong, P.
1998-01-06
A scanning fluorescent microthermal imaging (FMI) apparatus and method is disclosed, useful for integrated circuit (IC) failure analysis, that uses a scanned and focused beam from a laser to excite a thin fluorescent film disposed over the surface of the IC. By collecting fluorescent radiation from the film, and performing point-by-point data collection with a single-point photodetector, a thermal map of the IC is formed to measure any localized heating associated with defects in the IC. 1 fig.
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NASA Astrophysics Data System (ADS)
Okyay, Unal; Khan, Shuhab D.
2016-02-01
Well-exposed eolian units of the Jurassic system on the Colorado Plateau including the Wingate Sandstone, show prominent color variations throughout southeastern Utah due to diagenetic changes that include precipitation and/or removal of iron oxide, clay, and carbonate cement. Spatially variable characteristic diagenetic changes suggest fluid-rock interactions through the sandstone. Distinctive spectral signatures of diagenetic minerals can be used to map diagenetic mineral variability and possibly fluid-flow pathways. The main objective of this work was to identify characteristic diagenetic minerals, and map their spatial variability from regional to outcrop scale in Wingate Sandstone exposures of Lisbon Valley, Utah. Laboratory reflectance spectroscopy analysis of the samples facilitated identification of diagnostic spectral characteristics of the common diagenetic minerals and their relative abundances between altered and unaltered Wingate Sandstone. Comparison of reflectance spectroscopy with satellite, airborne, and ground-based imaging spectroscopy data provided a method for mapping and evaluating spatial variations of diagenetic minerals. The Feature-oriented Principal Component Selection method was used on Advanced Spaceborne Thermal Emission and Reflection Radiometer data so as to map common mineral groups throughout the broader Wingate Sandstone exposure in the area. The Minimum Noise Fraction and Spectral Angle Mapper methods were applied on airborne HyMap and ground-based hyperspectral imaging data to identify and map mineralogical changes. The satellite and airborne data showed that out of 25.55 km2 total exposure of Wingate Sandstone in Lisbon Valley, unaltered sandstone cover 12.55 km2, and altered sandstone cover 8.90 km2 in the northwest flank and 5.09 km2 in the southern flank of the anticline. The ground-based hyperspectral data demonstrated the ability to identify and map mineral assemblages with two-dimensional lateral continuity on near-vertical rock faces. The results showed that 39.71% of the scanned outcrop is bleached and 20.60% is unbleached while 6.33% remain unclassified, and 33.36% is masked-out as vegetation. The bleached and unbleached areas are alternating throughout the vertical face of the outcrop. The relative hematite abundance observed in the unbleached areas are somewhat symmetrical. This indicates fairly similar reaction intensities along the upper and lower reaction fronts observed in the vertical section. The distribution geometry and relative abundances of diagenetic minerals not only suggest multiple paths of fluid-flow in Wingate Sandstone but also provides some insight about relative direction of past fluid-flow.
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Savini, Alessandra; Vertino, Agostina; Marchese, Fabio; Beuck, Lydia; Freiwald, André
2014-01-01
In this study, we mapped the distribution of Cold-Water Coral (CWC) habitats on the northern Ionian Margin (Mediterranean Sea), with an emphasis on assessing coral coverage at various spatial scales over an area of 2,000 km(2) between 120 and 1,400 m of water depth. Our work made use of a set of data obtained from ship-based research surveys. Multi-scale seafloor mapping data, video inspections, and previous results from sediment samples were integrated and analyzed using Geographic Information System (GIS)-based tools. Results obtained from the application of spatial and textural analytical techniques to acoustic meso-scale maps (i.e. a Digital Terrain Model (DTM) of the seafloor at a 40 m grid cell size and associated terrain parameters) and large-scale maps (i.e. Side-Scan Sonar (SSS) mosaics of 1 m in resolution ground-truthed using underwater video observations) were integrated and revealed that, at the meso-scale level, the main morphological pattern (i.e. the aggregation of mound-like features) associated with CWC habitat occurrences was widespread over a total area of 600 km(2). Single coral mounds were isolated from the DTM and represented the geomorphic proxies used to model coral distributions within the investigated area. Coral mounds spanned a total area of 68 km(2) where different coral facies (characterized using video analyses and mapped on SSS mosaics) represent the dominant macro-habitat. We also mapped and classified anthropogenic threats that were identifiable within the examined videos, and, here, discuss their relationship to the mapped distribution of coral habitats and mounds. The combined results (from multi-scale habitat mapping and observations of the distribution of anthropogenic threats) provide the first quantitative assessment of CWC coverage for a Mediterranean province and document the relevant role of seafloor geomorphology in influencing habitat vulnerability to different types of human pressures.
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Low-Cost Peptide Microarrays for Mapping Continuous Antibody Epitopes.
McBride, Ryan; Head, Steven R; Ordoukhanian, Phillip; Law, Mansun
2016-01-01
With the increasing need for understanding antibody specificity in antibody and vaccine research, pepscan assays provide a rapid method for mapping and profiling antibody responses to continuous epitopes. We have developed a relatively low-cost method to generate peptide microarray slides for studying antibody binding. Using a setup of an IntavisAG MultiPep RS peptide synthesizer, a Digilab MicroGrid II 600 microarray printer robot, and an InnoScan 1100 AL scanner, the method allows the interrogation of up to 1536 overlapping, alanine-scanning, and mutant peptides derived from the target antigens. Each peptide is tagged with a polyethylene glycol aminooxy terminus to improve peptide solubility, orientation, and conjugation efficiency to the slide surface.
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2008-09-01
6 maps such as those shown in Fig. 4 ; typical examples of the cumulative misorientation are given in Figs. 5 and 6 , respectively...misorientation line scans shown in Figs. 5 and 6 . Fig. 5. Typical line scans from EBSD maps in Fig. 4 showing the variation of orientation over a long...e g 0 2 4 6 8 10 12 14 16 (b) Distance, μm 0 20 40 60 80 100 C u m u l a t i v e m i s o r i e n t a t i o n , d e g 0 5 10 15
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Chen, L G; Zhang, C; Zhang, R; Zhang, X L; Dong, Z C
2013-06-01
We report the development of a custom scanning tunneling microscope equipped with photon collection and detection systems. The optical optimization includes the comprehensive design of aspherical lens for light collimation and condensing, the sophisticated piezo stages for in situ lens adjustment inside ultrahigh vacuum, and the fiber-free coupling of collected photons directly onto the ultrasensitive single-photon detectors. We also demonstrate submolecular photon mapping for the molecular islands of porphyrin on Ag(111) under small tunneling currents down to 10 pA and short exposure time down to 1.2 ms/pixel. A high quantum efficiency up to 10(-2) was also observed.
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Santos, Carla Santana; Kowaltowski, Alicia J; Bertotti, Mauro
2017-09-12
We developed a highly sensitive oxygen consumption scanning microscopy system using platinized platinum disc microelectrodes. The system is capable of reliably detecting single-cell respiration, responding to classical regulators of mitochondrial oxygen consumption activity as expected. Comparisons with commercial multi-cell oxygen detection systems show that the system has comparable errors (if not smaller), with the advantage of being able to monitor inter and intra-cell heterogeneity in oxygen consumption characteristics. Our results uncover heterogeneous oxygen consumption characteristics between cells and within the same cell´s microenvironments. Single Cell Oxygen Mapping (SCOM) is thus capable of reliably studying mitochondrial oxygen consumption characteristics and heterogeneity at a single-cell level.
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Airborne Laser Swath Mapping: Improved Penetration of Dense Vegetation Opens New Applications
NASA Astrophysics Data System (ADS)
Carter, W. E.; Shrestha, R. L.; Slatton, K. C.
2009-12-01
Historically, mapping structures and terrain obscured by dense forests has been problematical, because shadows limit or prevent the use of airborne photogrammetric techniques, and ground surveying techniques are slow, labor intensive, and too costly for many applications. Airborne laser swath mapping (ALSM) units with pulse rates of a few thousand to a few tens of thousands of pulses per second typically resulted in 1 or 2 points per square meter of terrain, which worked reasonably well in sparse to moderately forested areas. For example, data collected with a 30 kHz laser, provided sufficient returns from the ground in areas covered with redwood, mixed hardwoods, and conifer forests, to create 1 to 2 meter resolution bare earth digital elevation models (DEM). These DEMs were useful in studies of forest covered landslides, terraces, and fault lines. However, in dense semi-tropical areas of Florida, with primary and secondary canopies that include dense brush such as palmetto, the DEMs were significantly degraded, and in many areas it was not possible to derive bare earth DEMs that were reliable in height to better than 0.5 to 1.0 meter. In 2007 the UF purchased a second generation Optech ALSM unit that has decimeter accuracy ranging with pulse rates of 100 to 125 kHz. Flying at 600 meters AGL, 60 meters per second, and using a scan angle of ± 20 degrees and scan rate of 40 Hz, results in about 5 laser pulses per square meter within a single swath. In April 2009 a UF team collected ALSM observations covering approximately 2000 acres at Caracol, Belize, to support archaeological studies of the ancient (650 to 900AD) Mayan city, which is largely covered with dense jungle. By overlapping adjacent swaths by 50%, and flying the project area twice with orthogonal flight lines, an accumulated data set containing approximately 20 pulses per square meter, with a distribution of incident angles was realized. The Caracol area has been under study for 25 years and traditional mapping techniques involved cutting pathways through the jungle, typically at 50 meter intervals, and using transits, electronic distance measuring instruments and total stations to map visible features. Without completely clearing the vegetation, it was difficult for ground surveyors to identify and map all of the pertinent features, and preliminary analysis suggest that the ALSM data display areas of previously unmapped mounded settlement, as well as subtle features in the terrain, including shallow agricultural terraces. The ability to map structures and terrain in areas covered with semi-tropical and tropical forests and jungles opens new opportunities for archaeological studies, and promises to impact geological and geophysical studies in these difficult to map regions as well.
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Optimized efficient liver T1ρ mapping using limited spin lock times
NASA Astrophysics Data System (ADS)
Yuan, Jing; Zhao, Feng; Griffith, James F.; Chan, Queenie; Wang, Yi-Xiang J.
2012-03-01
T1ρ relaxation has recently been found to be sensitive to liver fibrosis and has potential to be used for early detection of liver fibrosis and grading. Liver T1ρ imaging and accurate mapping are challenging because of the long scan time, respiration motion and high specific absorption rate. Reduction and optimization of spin lock times (TSLs) are an efficient way to reduce scan time and radiofrequency energy deposition of T1ρ imaging, but maintain the near-optimal precision of T1ρ mapping. This work analyzes the precision in T1ρ estimation with limited, in particular two, spin lock times, and explores the feasibility of using two specific operator-selected TSLs for efficient and accurate liver T1ρ mapping. Two optimized TSLs were derived by theoretical analysis and numerical simulations first, and tested experimentally by in vivo rat liver T1ρ imaging at 3 T. The simulation showed that the TSLs of 1 and 50 ms gave optimal T1ρ estimation in a range of 10-100 ms. In the experiment, no significant statistical difference was found between the T1ρ maps generated using the optimized two-TSL combination and the maps generated using the six TSLs of [1, 10, 20, 30, 40, 50] ms according to one-way ANOVA analysis (p = 0.1364 for liver and p = 0.8708 for muscle).
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NASA Astrophysics Data System (ADS)
Kinkingnehun, Serge R. J.; du Boisgueheneuc, Foucaud; Golmard, Jean-Louis; Zhang, Sandy X.; Levy, Richard; Dubois, Bruno
2004-04-01
We have developed a new technique to analyze correlations between brain anatomy and its neurological functions. The technique is based on the anatomic MRI of patients with brain lesions who are administered neuropsychological tests. Brain lesions of the MRI scans are first manually segmented. The MRI volumes are then normalized to a reference map, using the segmented area as a mask. After normalization, the brain lesions of the MRI are segmented again in order to redefine the border of the lesions in the context of the normalized brain. Once the MRI is segmented, the patient's score on the neuropsychological test is assigned to each voxel in the lesioned area, while the rest of the voxels of the image are set to 0. Subsequently, the individual patient's MRI images are superimposed, and each voxel is reassigned the average score of the patients who have a lesion at that voxel. A threshold is applied to remove regions having less than three overlaps. This process leads to an anatomo-functional map that links brain areas to functional loss. Other maps can be created to aid in analyzing the functional maps, such as one that indicates the 95% confidence interval of the averaged scores for each area. This anatomo-clinical overlapping map (AnaCOM) method was used to obtain functional maps from patients with lesions in the superior frontal gyrus. By finding particular subregions more responsible for a particular deficit, this method can generate new hypotheses to be tested by conventional group methods.
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Dual-pathway multi-echo sequence for simultaneous frequency and T2 mapping
NASA Astrophysics Data System (ADS)
Cheng, Cheng-Chieh; Mei, Chang-Sheng; Duryea, Jeffrey; Chung, Hsiao-Wen; Chao, Tzu-Cheng; Panych, Lawrence P.; Madore, Bruno
2016-04-01
Purpose: To present a dual-pathway multi-echo steady state sequence and reconstruction algorithm to capture T2, T2∗ and field map information. Methods: Typically, pulse sequences based on spin echoes are needed for T2 mapping while gradient echoes are needed for field mapping, making it difficult to jointly acquire both types of information. A dual-pathway multi-echo pulse sequence is employed here to generate T2 and field maps from the same acquired data. The approach might be used, for example, to obtain both thermometry and tissue damage information during thermal therapies, or susceptibility and T2 information from a same head scan, or to generate bonus T2 maps during a knee scan. Results: Quantitative T2, T2∗ and field maps were generated in gel phantoms, ex vivo bovine muscle, and twelve volunteers. T2 results were validated against a spin-echo reference standard: A linear regression based on ROI analysis in phantoms provided close agreement (slope/R2 = 0.99/0.998). A pixel-wise in vivo Bland-Altman analysis of R2 = 1/T2 showed a bias of 0.034 Hz (about 0.3%), as averaged over four volunteers. Ex vivo results, with and without motion, suggested that tissue damage detection based on T2 rather than temperature-dose measurements might prove more robust to motion. Conclusion: T2, T2∗ and field maps were obtained simultaneously, from the same datasets, in thermometry, susceptibility-weighted imaging and knee-imaging contexts.
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How Scientists Differentiate Between Land Cover Types
NASA Technical Reports Server (NTRS)
2002-01-01
Before scientists can transform raw satellite image data into land cover maps, they must decide on what categories of land cover they would like to use. Categories are simply the types of landscape that the scientists are trying to map and can vary greatly from map to map. For flood maps, there may be only two categories-dry land and wet land-while a standard global land cover map may have seventeen categories including closed shrub lands, savannas, evergreen needle leaf forest, urban areas, and ice/snow. The only requirement for any land cover category is that it have a distinct spectral signature that a satellite can record. As can be seen through a prism, many different colors (wavelengths) make up the spectra of sunlight. When sunlight strikes objects, certain wavelengths are absorbed and others are reflected or emitted. The unique way in which a given type of land cover reflects and absorbs light is known as its spectral signature. Anyone who has flown over the midwestern United States has seen evidence of this phenomenon. From an airplane window, the ground appears as a patchwork of different colors formed by the fields of crops planted there. The varying pigments of the leaves, the amount of foliage per square foot, the age of the plants, and many other factors create this tapestry. Most imaging satellites are sensitive to specific wavelengths of light, including infrared wavelengths that cannot be seen with the naked eye. Passive satellite remote sensors-such as those flown on Landsat 5, Landsat 7, and Terra-have a number of light detectors (photoreceptors) on board that measure the energy reflected or emitted by the Earth. One light detector records only the blue part of the spectrum coming off the Earth. Another observes all the yellow-green light and still another picks up on all the near-infrared light. The detectors scan the Earth's surface as the satellite travels in a circular orbit very nearly from pole-to-pole. To differentiate between types of land cover and their attributes, researchers manipulate the colors recorded by the satellite to get the combination of wavelengths that best distinguishes the spectral signature of the land cover they wish to identify. After an area of forest or water or grass is identified, they can outline the category on an easy-to-analyze, color-coded map. To verify their results, the scientists will often travel to the regions of interest and compare the results of the map with test sites on the ground. next: The Basic Vegetation Map back: Mapping Earth's Diverse Landscapes
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NASA Astrophysics Data System (ADS)
Newbury, Dale E.; Ritchie, Nicholas W. M.
2012-06-01
Scanning electron microscopy with energy dispersive x-ray spectrometry (SEM/EDS) is a powerful and flexible elemental analysis method that can identify and quantify elements with atomic numbers > 4 (Be) present as major constituents (where the concentration C > 0.1 mass fraction, or 10 weight percent), minor (0.01<= C <= 0.1) and trace (C < 0.01, with a minimum detectable limit of ~+/- 0.0005 - 0.001 under routine measurement conditions, a level which is analyte and matrix dependent ). SEM/EDS can select specimen volumes with linear dimensions from ~ 500 nm to 5 μm depending on composition (masses ranging from ~ 10 pg to 100 pg) and can provide compositional maps that depict lateral elemental distributions. Despite the maturity of SEM/EDS, which has a history of more than 40 years, and the sophistication of modern analytical software, the method is vulnerable to serious shortcomings that can lead to incorrect elemental identifications and quantification errors that significantly exceed reasonable expectations. This paper will describe shortcomings in peak identification procedures, limitations on the accuracy of quantitative analysis due to specimen topography or failures in physical models for matrix corrections, and quantitative artifacts encountered in xray elemental mapping. Effective solutions to these problems are based on understanding the causes and then establishing appropriate measurement science protocols. NIST DTSA II and Lispix are open source analytical software available free at www.nist.gov that can aid the analyst in overcoming significant limitations to SEM/EDS.
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Lu, Qing; Bi, Kun; Liu, Chu; Luo, Guoping; Tang, Hao; Yao, Zhijian
2013-10-16
Abnormal inter-regional causalities can be mapped for the objective diagnosis of various diseases. These inter-regional connectivities are usually calculated over an entire scan and used to characterize the stationary strength of the connections. However, the connectivity within networks may undergo substantial changes during a scan. In this study, we developed an objective depression recognition approach using the dynamic regional interactions that occur in response to sad facial stimuli. The whole time-period magnetoencephalography (MEG) signals from the visual cortex, amygdala, anterior cingulate cortex (ACC) and inferior frontal gyrus (IFG) were separated into sequential time intervals. The Granger causality mapping method was used to identify the pairwise interaction pattern within each time interval. Feature selection was then undertaken within a minimum redundancy-maximum relevance (mRMR) framework. Typical classifiers were utilized to predict those patients who had depression. The overall performances of these classifiers were similar, and the highest classification accuracy rate was 87.5%. The best discriminative performance was obtained when the number of features was within a robust range. The discriminative network pattern obtained through support vector machine (SVM) analyses displayed abnormal causal connectivities that involved the amygdala during the early and late stages. These early and late connections in the amygdala appear to reveal a negative bias to coarse expression information processing and abnormal negative modulation in patients with depression, which may critically affect depression discrimination. © 2013 Elsevier B.V. All rights reserved.
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Chui, Toco Yuen Ping; Pinhas, Alexander; Gan, Alexander; Razeen, Moataz; Shah, Nishit; Cheang, Eric; Liu, Chun L; Dubra, Alfredo; Rosen, Richard B
2016-05-01
To characterise longitudinal changes in the retinal microvasculature of type 2 diabetes mellitus (T2DM) as exemplified in a patient with proliferative diabetic retinopathy (PDR) using an adaptive optics scanning light ophthalmoscope (AOSLO). A 35-year-old T2DM patient with PDR treated with scatter pan-retinal photocoagulation at the inferior retina 1 day prior to initial AOSLO imaging along with a 24-year-old healthy control were imaged in this study. AOSLO vascular structural and perfusion maps were acquired at four visits over a 20-week period. Capillary diameter and microaneurysm area changes were measured on the AOSLO structural maps. Imaging repeatability was established using longitudinal imaging of microvasculature in the healthy control. Capillary occlusion and recanalisation, capillary dilatation, resolution of local retinal haemorrhage, capillary hairpin formation, capillary bend formation, microaneurysm formation, progression and regression were documented over time in a region 2° superior to the fovea in the PDR patient. An identical microvascular network with same capillary diameter was observed in the control subject over time. High-resolution serial AOSLO imaging enables in vivo observation of vasculopathic changes seen in diabetes mellitus. The implications of this methodology are significant, providing the opportunity for studying the dynamics of the pathological process, as well as the possibility of identifying highly sensitive and non-invasive biomarkers of end organ damage and response to treatment. © 2016 The Authors Ophthalmic & Physiological Optics © 2016 The College of Optometrists.
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Mapping Diffusion in a Living Cell via the Phasor Approach
Ranjit, Suman; Lanzano, Luca; Gratton, Enrico
2014-01-01
Diffusion of a fluorescent protein within a cell has been measured using either fluctuation-based techniques (fluorescence correlation spectroscopy (FCS) or raster-scan image correlation spectroscopy) or particle tracking. However, none of these methods enables us to measure the diffusion of the fluorescent particle at each pixel of the image. Measurement using conventional single-point FCS at every individual pixel results in continuous long exposure of the cell to the laser and eventual bleaching of the sample. To overcome this limitation, we have developed what we believe to be a new method of scanning with simultaneous construction of a fluorescent image of the cell. In this believed new method of modified raster scanning, as it acquires the image, the laser scans each individual line multiple times before moving to the next line. This continues until the entire area is scanned. This is different from the original raster-scan image correlation spectroscopy approach, where data are acquired by scanning each frame once and then scanning the image multiple times. The total time of data acquisition needed for this method is much shorter than the time required for traditional FCS analysis at each pixel. However, at a single pixel, the acquired intensity time sequence is short; requiring nonconventional analysis of the correlation function to extract information about the diffusion. These correlation data have been analyzed using the phasor approach, a fit-free method that was originally developed for analysis of FLIM images. Analysis using this method results in an estimation of the average diffusion coefficient of the fluorescent species at each pixel of an image, and thus, a detailed diffusion map of the cell can be created. PMID:25517145
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Reliability of fMRI for Studies of Language in Post-Stroke Aphasia Subjects
Eaton, Kenneth P.; Szaflarski, Jerzy P.; Altaye, Mekibib; Ball, Angel L.; Kissela, Brett M.; Banks, Christi; Holland, Scott K.
2008-01-01
Quantifying change in brain activation patterns associated with post-stroke recovery and reorganization of language function over time requires accurate understanding of inter-scan and inter-subject variability. Here we report inter-scan variability measures for fMRI activation patterns associated with verb generation (VG) and semantic decision/tone decision (SDTD) tasks in 4 healthy controls and 4 aphasic left middle cerebral artery (LMCA) stroke subjects. A series of 10 fMRI scans was completed on a 4T Varian scanner for each task for each subject, except for one stroke subject who completed 5 and 6 scans for SDTD and VG, thus yielding 35 and 36 total stroke subject scans for SDTD and VG, respectively. Group composite and intraclass correlation coefficient (ICC) maps were computed across all subjects and trials for each task. The patterns of reliable activation for the VG and SDTD tasks correspond well to those regions typically activated by these tasks in healthy and aphasic subjects. ICCs for activation were consistently high (R0.05 ≈ 0.8) for individual tasks among both control and aphasic subjects. These voxel-wise measures of reliability highlight regions of low inter-scan variability within language circuitry for control and post-recovery stroke subjects. ICCs computed from the combination of the SDTD/VG data were markedly reduced for both control and aphasic subjects as compared with the ICCs for the individual tasks. These quantitative measures of inter-scan variability support the proposed use of these fMRI paradigms for longitudinal mapping of neural reorganization of language processing following left hemispheric insult. PMID:18411061
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Uncovering archaeological landscapes at Angkor using lidar.
Evans, Damian H; Fletcher, Roland J; Pottier, Christophe; Chevance, Jean-Baptiste; Soutif, Dominique; Tan, Boun Suy; Im, Sokrithy; Ea, Darith; Tin, Tina; Kim, Samnang; Cromarty, Christopher; De Greef, Stéphane; Hanus, Kasper; Bâty, Pierre; Kuszinger, Robert; Shimoda, Ichita; Boornazian, Glenn
2013-07-30
Previous archaeological mapping work on the successive medieval capitals of the Khmer Empire located at Angkor, in northwest Cambodia (∼9th to 15th centuries in the Common Era, C.E.), has identified it as the largest settlement complex of the preindustrial world, and yet crucial areas have remained unmapped, in particular the ceremonial centers and their surroundings, where dense forest obscures the traces of the civilization that typically remain in evidence in surface topography. Here we describe the use of airborne laser scanning (lidar) technology to create high-precision digital elevation models of the ground surface beneath the vegetation cover. We identify an entire, previously undocumented, formally planned urban landscape into which the major temples such as Angkor Wat were integrated. Beyond these newly identified urban landscapes, the lidar data reveal anthropogenic changes to the landscape on a vast scale and lend further weight to an emerging consensus that infrastructural complexity, unsustainable modes of subsistence, and climate variation were crucial factors in the decline of the classical Khmer civilization.
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Kong, Jessica; Giridharagopal, Rajiv; Harrison, Jeffrey S; Ginger, David S
2018-05-31
Correlating nanoscale chemical specificity with operational physics is a long-standing goal of functional scanning probe microscopy (SPM). We employ a data analytic approach combining multiple microscopy modes, using compositional information in infrared vibrational excitation maps acquired via photoinduced force microscopy (PiFM) with electrical information from conductive atomic force microscopy. We study a model polymer blend comprising insulating poly(methyl methacrylate) (PMMA) and semiconducting poly(3-hexylthiophene) (P3HT). We show that PiFM spectra are different from FTIR spectra, but can still be used to identify local composition. We use principal component analysis to extract statistically significant principal components and principal component regression to predict local current and identify local polymer composition. In doing so, we observe evidence of semiconducting P3HT within PMMA aggregates. These methods are generalizable to correlated SPM data and provide a meaningful technique for extracting complex compositional information that are impossible to measure from any one technique.
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Uncovering archaeological landscapes at Angkor using lidar
Evans, Damian H.; Fletcher, Roland J.; Pottier, Christophe; Chevance, Jean-Baptiste; Soutif, Dominique; Tan, Boun Suy; Im, Sokrithy; Ea, Darith; Tin, Tina; Kim, Samnang; Cromarty, Christopher; De Greef, Stéphane; Hanus, Kasper; Bâty, Pierre; Kuszinger, Robert; Shimoda, Ichita; Boornazian, Glenn
2013-01-01
Previous archaeological mapping work on the successive medieval capitals of the Khmer Empire located at Angkor, in northwest Cambodia (∼9th to 15th centuries in the Common Era, C.E.), has identified it as the largest settlement complex of the preindustrial world, and yet crucial areas have remained unmapped, in particular the ceremonial centers and their surroundings, where dense forest obscures the traces of the civilization that typically remain in evidence in surface topography. Here we describe the use of airborne laser scanning (lidar) technology to create high-precision digital elevation models of the ground surface beneath the vegetation cover. We identify an entire, previously undocumented, formally planned urban landscape into which the major temples such as Angkor Wat were integrated. Beyond these newly identified urban landscapes, the lidar data reveal anthropogenic changes to the landscape on a vast scale and lend further weight to an emerging consensus that infrastructural complexity, unsustainable modes of subsistence, and climate variation were crucial factors in the decline of the classical Khmer civilization. PMID:23847206
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The digital geologic map of Colorado in ARC/INFO format, Part A. Documentation
Green, Gregory N.
1992-01-01
This geologic map was prepared as a part of a study of digital methods and techniques as applied to complex geologic maps. The geologic map was digitized from the original scribe sheets used to prepare the published Geologic Map of Colorado (Tweto 1979). Consequently the digital version is at 1:500,000 scale using the Lambert Conformal Conic map projection parameters of the state base map. Stable base contact prints of the scribe sheets were scanned on a Tektronix 4991 digital scanner. The scanner automatically converts the scanned image to an ASCII vector format. These vectors were transferred to a VAX minicomputer, where they were then loaded into ARC/INFO. Each vector and polygon was given attributes derived from the original 1979 geologic map. This database was developed on a MicroVAX computer system using VAX V 5.4 nd ARC/INFO 5.0 software. UPDATE: April 1995, The update was done solely for the purpose of adding the abilitly to plot to an HP650c plotter. Two new ARC/INFO plot AMLs along with a lineset and shadeset for the HP650C design jet printer have been included. These new files are COLORADO.650, INDEX.650, TWETOLIN.E00 and TWETOSHD.E00. These files were created on a UNIX platform with ARC/INFO 6.1.2. Updated versions of INDEX.E00, CONTACT.E00, LINE.E00, DECO.E00 and BORDER.E00 files that included the newly defined HP650c items are also included. * Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Descriptors: The Digital Geologic Map of Colorado in ARC/INFO Format Open-File Report 92-050
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Lee, Won June; Na, Kyeong Ik; Kim, Young Kook; Jeoung, Jin Wook; Park, Ki Ho
2017-06-01
To evaluate the diagnostic ability of wide-field retinal nerve fiber layer (RNFL) maps with swept-source optical coherence tomography (SS-OCT) for detection of preperimetric (PPG) and early perimetric glaucoma (EG). One hundred eighty-four eyes, including 67 healthy eyes, 43 eyes with PPG, and 74 eyes with EG, were analyzed. Patients underwent a comprehensive ocular examination including red-free RNFL photography, visual field testing and wide-field SS-OCT scanning (DRI-OCT-1 Atlantis; Topcon, Tokyo, Japan). SS-OCT provides a wide-field RNFL thickness map and a SuperPixel map, which are composed of the RNFL deviation map of the peripapillary area and the deviation map of the composition of the ganglion cell layer with the inner plexiform layer and RNFL (GC-IPL+RNFL) in the macular area. The ability to discriminate PPG and EG from healthy eyes was assessed using sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) for all parameters and criteria provided by the wide-field SS-OCT scan. The wide-field RNFL thickness map using SS-OCT showed the highest sensitivity of PPG-diagnostic and EG-diagnostic performance compared with the other SS-OCT criteria based on the internal normative base (93.0 and 97.3%, respectively). Among the SS-OCT continuous parameters, the RFNL thickness of the 7 clock-hour, inferior and inferotemporal macular ganglion cell analyses showed the largest AUC of PPG-diagnostic and EG-diagnostic performance (AUC=0.809 to 0.865). The wide-field RNFL thickness map using SS-OCT performed well in distinguishing eyes with PPG and EG from healthy eyes. In the clinical setting, wide-field RNFL maps of SS-OCT can be useful tools for detection of early-stage glaucoma.
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The digital geologic map of Colorado in ARC/INFO format, Part B. Common files
Green, Gregory N.
1992-01-01
This geologic map was prepared as a part of a study of digital methods and techniques as applied to complex geologic maps. The geologic map was digitized from the original scribe sheets used to prepare the published Geologic Map of Colorado (Tweto 1979). Consequently the digital version is at 1:500,000 scale using the Lambert Conformal Conic map projection parameters of the state base map. Stable base contact prints of the scribe sheets were scanned on a Tektronix 4991 digital scanner. The scanner automatically converts the scanned image to an ASCII vector format. These vectors were transferred to a VAX minicomputer, where they were then loaded into ARC/INFO. Each vector and polygon was given attributes derived from the original 1979 geologic map. This database was developed on a MicroVAX computer system using VAX V 5.4 nd ARC/INFO 5.0 software. UPDATE: April 1995, The update was done solely for the purpose of adding the abilitly to plot to an HP650c plotter. Two new ARC/INFO plot AMLs along with a lineset and shadeset for the HP650C design jet printer have been included. These new files are COLORADO.650, INDEX.650, TWETOLIN.E00 and TWETOSHD.E00. These files were created on a UNIX platform with ARC/INFO 6.1.2. Updated versions of INDEX.E00, CONTACT.E00, LINE.E00, DECO.E00 and BORDER.E00 files that included the newly defined HP650c items are also included. * Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Descriptors: The Digital Geologic Map of Colorado in ARC/INFO Format Open-File Report 92-050
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Laiba, Efrat; Glikaite, Ilana; Levy, Yael; Pasternak, Zohar; Fridman, Eyal
2016-04-01
The overdominant model of heterosis explains the superior phenotype of hybrids by synergistic allelic interaction within heterozygous loci. To map such genetic variation in yeast, we used a population doubling time dataset of Saccharomyces cerevisiae 16 × 16 diallel and searched for major contributing heterotic trait loci (HTL). Heterosis was observed for the majority of hybrids, as they surpassed their best parent growth rate. However, most of the local heterozygous loci identified by genome scan were surprisingly underdominant, i.e., reduced growth. We speculated that in these loci adverse effects on growth resulted from incompatible allelic interactions. To test this assumption, we eliminated these allelic interactions by creating hybrids with local hemizygosity for the underdominant HTLs, as well as for control random loci. Growth of hybrids was indeed elevated for most hemizygous to HTL genes but not for control genes, hence validating the results of our genome scan. Assessing the consequences of local heterozygosity by reciprocal hemizygosity and allele replacement assays revealed the influence of genetic background on the underdominant effects of HTLs. Overall, this genome-wide study on a multi-parental hybrid population provides a strong argument against single gene overdominance as a major contributor to heterosis, and favors the dominance complementation model.
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NASA Astrophysics Data System (ADS)
Castellini, Paolo; Esposito, Enrico; Marchetti, Barbara; Paone, Nicola; Tomasini, Enrico P.
2001-10-01
During the last years the growing importance of the correct determination of the state of conservation of artworks has been stated by all personalities in care of Cultural Heritage. There exist many analytical methodologies and techniques to individuate the physical and chemical characteristics of artworks, but at present their structural diagnostics mainly rely on the expertise of the restorer and the typical diagnostic process is accomplished mainly through manual and visual inspection of the object surface. The basic idea behind the proposed technique is to substitute human senses with measurement instruments: surfaces are very slightly vibrated by mechanical actuators, while a laser Doppler vibrometer scans the objects measuring surface velocity and producing 2D or 3D maps. Where a defect occurs velocity is higher than neighboring areas so defects can be easily spotted. Laser vibrometers also identify structural resonance frequencies thus leading to a complete characterization of defects. This work will present the most recent results coming out of the application of Scanning Laser Doppler Vibrometers (SLDV) to different types of artworks: mosaics, ceramics, inlaid wood and easel painting. Real artworks and samples realized on purpose have been studied using the proposed technique and different measuring issues resulting from each artwork category will be described.
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NASA Astrophysics Data System (ADS)
Butler, D. J.; Stevenson, A. W.; Wright, T. E.; Harty, P. D.; Lehmann, J.; Livingstone, J.; Crosbie, J. C.
2015-11-01
Small circular beams of synchrotron radiation (0.1 mm and 0.4 mm in diameter) were used to irradiate ionization chambers of the types commonly used in radiotherapy. By scanning the chamber through the beam and measuring the ionization current, a spatial map of the dosimetric response of the chamber was recorded. The technique is able to distinguish contributions to the large-field ionization current from the chamber walls, central electrode and chamber stem. Scans were recorded for the NE 2571 Farmer chamber, the PTW 30013, IBA FC65-G Farmer-type chambers, the NE 2611A and IBA CC13 thimble chambers, the PTW 31006 and 31014 pinpoint chambers, the PTW Roos and Advanced Markus plane-parallel chambers, and the PTW 23342 thin-window soft x-ray chamber. In all cases, large contributions to the response arise from areas where the incident beam grazes the cavity surfaces. Quantitative as well as qualitative information about the relative chamber response was extracted from the maps, including the relative contribution of the central electrode. Line scans using monochromatic beams show the effect of the photon energy on the chamber response. For Farmer-type chambers, a simple Monte Carlo model was in good agreement with the measured response.
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Performance analysis of a compact and low-cost mapping-grade mobile laser scanning system
NASA Astrophysics Data System (ADS)
Julge, Kalev; Vajakas, Toivo; Ellmann, Artu
2017-10-01
The performance of a low-cost, self-contained, compact, and easy to deploy mapping-grade mobile laser scanning (MLS) system, which is composed of a light detection and ranging sensor Velodyne VLP-16 and a dual antenna global navigation satellite system/inertial navigation system SBG Systems Ellipse-D, is analyzed. The field tests were carried out in car-mounted and backpack modes for surveying road engineering structures (such as roads, parking lots, underpasses, and tunnels) and coastal erosion zones, respectively. The impact of applied calculation principles on trajectory postprocessing, direct georeferencing, and the theoretical accuracy of the system is analyzed. A calibration method, based on Bound Optimization BY Quadratic Approximation, for finding the boresight angles of an MLS system is proposed. The resulting MLS point clouds are compared with high-accuracy static terrestrial laser scanning data and survey-grade MLS data from a commercially manufactured MLS system. The vertical, horizontal, and relative accuracy are assessed-the root-mean-square error (RMSE) values were determined to be 8, 15, and 3 cm, respectively. Thus, the achieved mapping-grade accuracy demonstrates that this relatively compact and inexpensive self-assembled MLS can be successfully used for surveying the geometry and deformations of terrain, buildings, road, and other engineering structures.
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NASA Astrophysics Data System (ADS)
Lam, Mie K.; de Greef, Martijn; Bouwman, Job G.; Moonen, Chrit T. W.; Viergever, Max A.; Bartels, Lambertus W.
2015-10-01
The multi-gradient echo MR thermometry (MGE MRT) method is proposed to use at the interface of the muscle and fat layers found in the abdominal wall, to monitor MR-HIFU heating. As MGE MRT uses fat as a reference, it is field-drift corrected. Relative temperature maps were reconstructed by subtracting absolute temperature maps. Because the absolute temperature maps are reconstructed of individual scans, MGE MRT provides the flexibility of interleaved mapping of temperature changes between two arbitrary time points. The method’s performance was assessed in an ex vivo water bath experiment. An ex vivo HIFU experiment was performed to show the method’s ability to monitor heating of consecutive HIFU sonications and to estimate cooling time constants, in the presence of field drift. The interleaved use between scans of a clinical protocol was demonstrated in vivo in a patient during a clinical uterine fibroid treatment. The relative temperature measurements were accurate (mean absolute error 0.3 °C) and provided excellent visualization of the heating of consecutive HIFU sonications. Maps were reconstructed of estimated cooling time constants and mean ROI values could be well explained by the applied heating pattern. Heating upon HIFU sonication and subsequent cooling could be observed in the in vivo demonstration.
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Evaluation of MRI sequences for quantitative T1 brain mapping
NASA Astrophysics Data System (ADS)
Tsialios, P.; Thrippleton, M.; Glatz, A.; Pernet, C.
2017-11-01
T1 mapping constitutes a quantitative MRI technique finding significant application in brain imaging. It allows evaluation of contrast uptake, blood perfusion, volume, providing a more specific biomarker of disease progression compared to conventional T1-weighted images. While there are many techniques for T1-mapping there is a wide range of reported T1-values in tissues, raising the issue of protocols reproducibility and standardization. The gold standard for obtaining T1-maps is based on acquiring IR-SE sequence. Widely used alternative sequences are IR-SE-EPI, VFA (DESPOT), DESPOT-HIFI and MP2RAGE that speed up scanning and fitting procedures. A custom MRI phantom was used to assess the reproducibility and accuracy of the different methods. All scans were performed using a 3T Siemens Prisma scanner. The acquired data processed using two different codes. The main difference was observed for VFA (DESPOT) which grossly overestimated T1 relaxation time by 214 ms [126 270] compared to the IR-SE sequence. MP2RAGE and DESPOT-HIFI sequences gave slightly shorter time than IR-SE (~20 to 30ms) and can be considered as alternative and time-efficient methods for acquiring accurate T1 maps of the human brain, while IR-SE-EPI gave identical result, at a cost of a lower image quality.
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Recent Results from Galileo PPR at Io: Orbits I31 and I32
NASA Technical Reports Server (NTRS)
Rathbun, J. A.; Spencer, J. R.; Tamppari, L. K.; Martin, T. Z.; Barnard, L.; Travis, L. D.
2002-01-01
Recent Galileo PPR (Photo-Polarimeter Radiometer) results will be shown, including global day and nighttime maps, high latitude regional maps, and high-resolution scans across hotspots and from pole to pole. SO2 vapor pressure, global heatflow, and hotspot power outputs are estimated. Additional information is contained in the original extended abstract.
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Roussis, S G
2001-08-01
The automated acquisition of the product ion spectra of all precursor ions in a selected mass range by using a magnetic sector/orthogonal acceleration time-of-flight (oa-TOF) tandem mass spectrometer for the characterization of complex petroleum mixtures is reported. Product ion spectra are obtained by rapid oa-TOF data acquisition and simultaneous scanning of the magnet. An analog signal generator is used for the scanning of the magnet. Slow magnet scanning rates permit the accurate profiling of precursor ion peaks and the acquisition of product ion spectra for all isobaric ion species. The ability of the instrument to perform both high- and low-energy collisional activation experiments provides access to a large number of dissociation pathways useful for the characterization of precursor ions. Examples are given that illustrate the capability of the method for the characterization of representative petroleum mixtures. The structural information obtained by the automated MS/MS experiment is used in combination with high-resolution accurate mass measurement results to characterize unknown components in a polar extract of a refinery product. The exhaustive mapping of all precursor ions in representative naphtha and middle-distillate fractions is presented. Sets of isobaric ion species are separated and their structures are identified by interpretation from first principles or by comparison with standard 70-eV EI libraries of spectra. The utility of the method increases with the complexity of the samples.
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A multimodal imaging framework for enhanced robot-assisted partial nephrectomy guidance
NASA Astrophysics Data System (ADS)
Halter, Ryan J.; Wu, Xiaotian; Hartov, Alex; Seigne, John; Khan, Shadab
2015-03-01
Robot-assisted laparoscopic partial nephrectomies (RALPN) are performed to treat patients with locally confined renal carcinoma. There are well-documented benefits to performing partial (opposed to radical) kidney resections and to using robot-assisted laparoscopic (opposed to open) approaches. However, there are challenges in identifying tumor margins and critical benign structures including blood vessels and collecting systems during current RALPN procedures. The primary objective of this effort is to couple multiple image and data streams together to augment visual information currently provided to surgeons performing RALPN and ultimately ensure complete tumor resection and minimal damage to functional structures (i.e. renal vasculature and collecting systems). To meet this challenge we have developed a framework and performed initial feasibility experiments to couple pre-operative high-resolution anatomic images with intraoperative MRI, ultrasound (US) and optical-based surface mapping and kidney tracking. With these registered images and data streams, we aim to overlay the high-resolution contrast-enhanced anatomic (CT or MR) images onto the surgeon's view screen for enhanced guidance. To date we have integrated the following components of our framework: 1) a method for tracking an intraoperative US probe to extract the kidney surface and a set of embedded kidney markers, 2) a method for co-registering intraoperative US scans with pre-operative MR scans, and 3) a method for deforming pre-op scans to match intraoperative scans. These components have been evaluated through phantom studies to demonstrate protocol feasibility.
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Method of composing two-dimensional scanned spectra observed by the New Vacuum Solar Telescope
NASA Astrophysics Data System (ADS)
Cai, Yun-Fang; Xu, Zhi; Chen, Yu-Chao; Xu, Jun; Li, Zheng-Gang; Fu, Yu; Ji, Kai-Fan
2018-04-01
In this paper we illustrate the technique used by the New Vacuum Solar Telescope (NVST) to increase the spatial resolution of two-dimensional (2D) solar spectroscopy observations involving two dimensions of space and one of wavelength. Without an image stabilizer at the NVST, large scale wobble motion is present during the spatial scanning, whose instantaneous amplitude can reach 1.3″ due to the Earth’s atmosphere and the precision of the telescope guiding system, and seriously decreases the spatial resolution of 2D spatial maps composed with scanned spectra. We make the following effort to resolve this problem: the imaging system (e.g., the TiO-band) is used to record and detect the displacement vectors of solar image motion during the raster scan, in both the slit and scanning directions. The spectral data (e.g., the Hα line) which are originally obtained in time sequence are corrected and re-arranged in space according to those displacement vectors. Raster scans are carried out in several active regions with different seeing conditions (two rasters are illustrated in this paper). Given a certain spatial sampling and temporal resolution, the spatial resolution of the composed 2D map could be close to that of the slit-jaw image. The resulting quality after correction is quantitatively evaluated with two methods. A physical quantity, such as the line-of-sight velocities in multiple layers of the solar atmosphere, is also inferred from the re-arranged spectrum, demonstrating the advantage of this technique.
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A GENOME-WIDE LINKAGE AND ASSOCIATION SCAN REVEALS NOVEL LOCI FOR AUTISM
Weiss, Lauren A.; Arking, Dan E.
2009-01-01
Summary Although autism is a highly heritable neurodevelopmental disorder, attempts to identify specific susceptibility genes have thus far met with limited success 1. Genome-wide association studies (GWAS) using half a million or more markers, particularly those with very large sample sizes achieved through meta-analysis, have shown great success in mapping genes for other complex genetic traits (http://www.genome.gov/26525384). Consequently, we initiated a linkage and association mapping study using half a million genome-wide SNPs in a common set of 1,031 multiplex autism families (1,553 affected offspring). We identified regions of suggestive and significant linkage on chromosomes 6q27 and 20p13, respectively. Initial analysis did not yield genome-wide significant associations; however, genotyping of top hits in additional families revealed a SNP on chromosome 5p15 (between SEMA5A and TAS2R1) that was significantly associated with autism (P = 2 × 10−7). We also demonstrated that expression of SEMA5A is reduced in brains from autistic patients, further implicating SEMA5A as an autism susceptibility gene. The linkage regions reported here provide targets for rare variation screening while the discovery of a single novel association demonstrates the action of common variants. PMID:19812673
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Mapping selected general literature of international nursing.
Shams, Marie-Lise Antoun; Dixon, Lana S
2007-01-01
This study, part of a wider project to map the literature of nursing, identifies core journals cited in non-US nursing journals and determines the extent of their coverage by indexing services. Four general English-language journals were analyzed for format types and publication dates. Core titles were identified and nine bibliographic databases were scanned for indexing coverage. Findings show that 57.5% (13,391/23,271) of the cited references from the 4 core journals were to journal articles, 27.8% (6,471/23,271) to books, 9.5% (2,208/23,271) to government documents, 4.9% (1,131/23,271) to miscellaneous sources, and less than 1% (70/23,271) to Internet resources. Eleven journals produced one-third of the citations; the next third included 146 journals, followed by a dispersion of 1,622 titles. PubMed received the best database coverage scores, followed by CINAHL and Science Citation Index. None of the databases provided complete coverage of all 11 core titles. The four source journals contain a diverse group of cited references. The currency of citations to government documents makes these journals a good source for regulatory and legislative awareness. Nurses consult nursing and biomedical journals and must search both nursing and biomedical databases to cover the literature.
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NASA Astrophysics Data System (ADS)
Belianinov, Alex; Ganesh, Panchapakesan; Lin, Wenzhi; Sales, Brian C.; Sefat, Athena S.; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V.
2014-12-01
Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1-xSex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.
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Data on the genome-wide identification of CNL R-genes in Setaria italica (L.) P. Beauv.
Andersen, Ethan J; Nepal, Madhav P
2017-08-01
We report data associated with the identification of 242 disease resistance genes (R-genes) in the genome of Setaria italica as presented in "Genetic diversity of disease resistance genes in foxtail millet ( Setaria italica L.)" (Andersen and Nepal, 2017) [1]. Our data describe the structure and evolution of the Coiled-coil, Nucleotide-binding site, Leucine-rich repeat (CNL) R-genes in foxtail millet. The CNL genes were identified through rigorous extraction and analysis of recently available plant genome sequences using cutting-edge analytical software. Data visualization includes gene structure diagrams, chromosomal syntenic maps, a chromosomal density plot, and a maximum-likelihood phylogenetic tree comparing Sorghum bicolor , Panicum virgatum , Setaria italica , and Arabidopsis thaliana . Compilation of InterProScan annotations, Gene Ontology (GO) annotations, and Basic Local Alignment Search Tool (BLAST) results for the 242 R-genes identified in the foxtail millet genome are also included in tabular format.
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Robinson, Nicholas; Baranski, Matthew; Mahapatra, Kanta Das; Saha, Jatindra Nath; Das, Sweta; Mishra, Jashobanta; Das, Paramananda; Kent, Matthew; Arnyasi, Mariann; Sahoo, Pramoda Kumar
2014-06-30
Production of carp dominates world aquaculture. More than 1.1 million tonnes of rohu carp, Labeo rohita (Hamilton), were produced in 2010. Aeromonas hydrophila is a bacterial pathogen causing aeromoniasis in rohu, and is a major problem for carp production worldwide. There is a need to better understand the genetic mechanisms affecting resistance to this disease, and to develop tools that can be used with selective breeding to improve resistance. Here we use a 6 K SNP array to genotype 21 full-sibling families of L. rohita that were experimentally challenged intra-peritoneally with a virulent strain of A. hydrophila to scan the genome for quantitative trait loci associated with disease resistance. In all, 3193 SNPs were found to be informative and were used to create a linkage map and to scan for QTL affecting resistance to A. hydrophila. The linkage map consisted of 25 linkage groups, corresponding to the number of haploid chromosomes in L. rohita. Male and female linkage maps were similar in terms of order, coverage (1384 and 1393 cM, respectively) and average interval distances (1.32 and 1.35 cM, respectively). Forty-one percent of the SNPs were annotated with gene identity using BLAST (cut off E-score of 0.001). Twenty-one SNPs mapping to ten linkage groups showed significant associations with the traits hours of survival and dead or alive (P <0.05 after Bonferroni correction). Of the SNPs showing significant or suggestive associations with the traits, several were homologous to genes of known immune function or were in close linkage to such genes. Genes of interest included heat shock proteins (70, 60, 105 and "small heat shock proteins"), mucin (5b precursor and 2), lectin (receptor and CD22), tributyltin-binding protein, major histocompatibility loci (I and II), complement protein component c7-1, perforin 1, ubiquitin (ligase, factor e4b isoform 2 and conjugation enzyme e2 c), proteasome subunit, T-cell antigen receptor and lymphocyte specific protein tyrosine kinase. A panel of markers has been identified that will be validated for use with both genomic and marker-assisted selection to improve resistance of L. rohita to A. hydrophila.
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Laser microbeam CT scanning of dosimetry gels
NASA Astrophysics Data System (ADS)
Maryanski, Marek J.; Ranade, Manisha K.
2001-06-01
A novel design of an optical tomographic scanner is described that can be used for 3D mapping of optical attenuation coefficient within translucent cylindrical objects with spatial resolution on the order of 100 microns. Our scanner design utilizes the cylindrical geometry of the imaged object to obtain the desired paths of the scanning light rays. A rotating mirror and a photodetector are placed at two opposite foci of the translucent cylinder that acts as a cylindrical lens. A He-Ne laser beam passes first through a focusing lens and then is reflected by the rotating mirror, so as to scan the interior of the cylinder with focused and parallel paraxial rays that are subsequently collected by the photodetector to produce the projection data, as the cylinder rotates in small angle increments between projections. Filtered backprojection is then used to reconstruct planar distributions of optical attenuation coefficient in the cylinder. Multiplanar scans are used to obtain a complete 3D tomographic reconstruction. Among other applications, the scanner can be used in radiation therapy dosimetry and quality assurance for mapping 3D radiation dose distributions in various types of tissue-equivalent gel phantoms that change their optical attenuation coefficients in proportion to the absorbed radiation dose.
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Reliability Correction for Functional Connectivity: Theory and Implementation
Mueller, Sophia; Wang, Danhong; Fox, Michael D.; Pan, Ruiqi; Lu, Jie; Li, Kuncheng; Sun, Wei; Buckner, Randy L.; Liu, Hesheng
2016-01-01
Network properties can be estimated using functional connectivity MRI (fcMRI). However, regional variation of the fMRI signal causes systematic biases in network estimates including correlation attenuation in regions of low measurement reliability. Here we computed the spatial distribution of fcMRI reliability using longitudinal fcMRI datasets and demonstrated how pre-estimated reliability maps can correct for correlation attenuation. As a test case of reliability-based attenuation correction we estimated properties of the default network, where reliability was significantly lower than average in the medial temporal lobe and higher in the posterior medial cortex, heterogeneity that impacts estimation of the network. Accounting for this bias using attenuation correction revealed that the medial temporal lobe’s contribution to the default network is typically underestimated. To render this approach useful to a greater number of datasets, we demonstrate that test-retest reliability maps derived from repeated runs within a single scanning session can be used as a surrogate for multi-session reliability mapping. Using data segments with different scan lengths between 1 and 30 min, we found that test-retest reliability of connectivity estimates increases with scan length while the spatial distribution of reliability is relatively stable even at short scan lengths. Finally, analyses of tertiary data revealed that reliability distribution is influenced by age, neuropsychiatric status and scanner type, suggesting that reliability correction may be especially important when studying between-group differences. Collectively, these results illustrate that reliability-based attenuation correction is an easily implemented strategy that mitigates certain features of fMRI signal nonuniformity. PMID:26493163
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NASA Astrophysics Data System (ADS)
Gangeh, Mehrdad J.; Fung, Brandon; Tadayyon, Hadi; Tran, William T.; Czarnota, Gregory J.
2016-03-01
A non-invasive computer-aided-theragnosis (CAT) system was developed for the early assessment of responses to neoadjuvant chemotherapy in patients with locally advanced breast cancer. The CAT system was based on quantitative ultrasound spectroscopy methods comprising several modules including feature extraction, a metric to measure the dissimilarity between "pre-" and "mid-treatment" scans, and a supervised learning algorithm for the classification of patients to responders/non-responders. One major requirement for the successful design of a high-performance CAT system is to accurately measure the changes in parametric maps before treatment onset and during the course of treatment. To this end, a unified framework based on Hilbert-Schmidt independence criterion (HSIC) was used for the design of feature extraction from parametric maps and the dissimilarity measure between the "pre-" and "mid-treatment" scans. For the feature extraction, HSIC was used to design a supervised dictionary learning (SDL) method by maximizing the dependency between the scans taken from "pre-" and "mid-treatment" with "dummy labels" given to the scans. For the dissimilarity measure, an HSIC-based metric was employed to effectively measure the changes in parametric maps as an indication of treatment effectiveness. The HSIC-based feature extraction and dissimilarity measure used a kernel function to nonlinearly transform input vectors into a higher dimensional feature space and computed the population means in the new space, where enhanced group separability was ideally obtained. The results of the classification using the developed CAT system indicated an improvement of performance compared to a CAT system with basic features using histogram of intensity.
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Ding, Ting; Zhang, Siyuan; Fu, Quanyou; Xu, Zhian; Wan, Mingxi
2014-01-01
This paper presented an ultrasound line-by-line scanning method of spatial-temporal active cavitation mapping applicable in a liquid or liquid filled tissue cavities exposed by high-intensity focused ultrasound (HIFU). Scattered signals from cavitation bubbles were obtained in a scan line immediately after one HIFU exposure, and then there was a waiting time of 2 s long enough to make the liquid back to the original state. As this pattern extended, an image was built up by sequentially measuring a series of such lines. The acquisition of the beamformed radiofrequency (RF) signals for a scan line was synchronized with HIFU exposure. The duration of HIFU exposure, as well as the delay of the interrogating pulse relative to the moment while HIFU was turned off, could vary from microseconds to seconds. The feasibility of this method was demonstrated in tap-water and a tap-water filled cavity in the tissue-mimicking gelatin-agar phantom as capable of observing temporal evolutions of cavitation bubble cloud with temporal resolution of several microseconds, lateral and axial resolution of 0.50 mm and 0.29 mm respectively. The dissolution process of cavitation bubble cloud and spatial distribution affected by cavitation previously generated were also investigated. Although the application is limited by the requirement for a gassy fluid (e.g. tap water, etc.) that allows replenishment of nuclei between HIFU exposures, the technique may be a useful tool in spatial-temporal cavitation mapping for HIFU with high precision and resolution, providing a reference for clinical therapy. Copyright © 2013 Elsevier B.V. All rights reserved.
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Photogrammetry of the Viking-Lander imagery.
Wu, S.S.C.; Schafer, F.J.
1982-01-01
We have solved the problem of photogrammetric mapping from the Viking Lander photography in two ways: 1) by converting the azimuth and elevation scanning imagery to the equivalent of a frame picture by means of computerized rectification; and 2) by interfacing a high-speed, general-purpose computer to the AS-11A analytical plotter so that all computations of corrections can be performed in real time during the process of model orientation and map compilation. Examples are presented of photographs and maps of Earth and Mars. -from Authors
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Use of IKONOS Data for Mapping Cultural Resources of Stennis Space Center, Mississippi
NASA Technical Reports Server (NTRS)
Spruce, Joseph P.; Giardino, Marco
2002-01-01
Cultural resource surveys are important for compliance with Federal and State law. Stennis Space Center (SSC) in Mississippi is researching, developing, and validating remote sensing and Geographical Information System (GIS) methods for aiding cultural resource assessments on the center's own land. The suitability of IKONOS satellite imagery for georeferencing scanned historic maps is examined in this viewgraph presentation. IKONOS data can be used to map historic buildings and farmland in Gainsville, MS, and plan archaeological surveys.
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draco: Analysis and simulation of drift scan radio data
NASA Astrophysics Data System (ADS)
Shaw, J. Richard
2017-12-01
draco analyzes transit radio data with the m-mode formalism. It is telescope agnostic, and is used as part of the analysis and simulation pipeline for the CHIME (Canadian Hydrogen Intensity Mapping Experiment) telescope. It can simulate time stream data from maps of the sky (using the m-mode formalism) and add gain fluctuations and correctly correlated instrumental noise (i.e. Wishart distributed). Further, it can perform various cuts on the data and make maps of the sky from data using the m-mode formalism.
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NASA Astrophysics Data System (ADS)
Shaw, Adam; Nunn, John
2010-06-01
In treatment planning for ultrasound therapy, it is desirable to know the 3D structure of the ultrasound field. However, mapping an ultrasound field in 3D is very slow, with even a single planar raster scan taking typically several hours. Additionally, hydrophones that are used for field mapping are expensive and can be damaged in some therapy fields. So there is value in rapid methods which enable visualization and mapping of the ultrasound field in about 1 min. In this note we explore the feasibility of mapping the intensity distribution by measuring the temperature distribution produced in a thin sheet of absorbing material. A 0.2 mm thick acetate sheet forms a window in the wall of a water tank containing the transducer. The window is oriented at 45° to the beam axis, and the distance from the transducer to the window can be varied. The temperature distribution is measured with an infrared camera; thermal images of the inclined plane could be viewed in real time or images could be captured for later analysis and 3D field reconstruction. We conclude that infrared thermography can be used to gain qualitative information about ultrasound fields. Thermal images are easily visualized with good spatial and thermal resolutions (0.044 mm and 0.05 °C in our system). The focus and field structure such as side lobes can be identified in real time from the direct video output. 3D maps and image planes at arbitrary orientations to the beam axis can be obtained and reconstructed within a few minutes. In this note we are primarily interested in the technique for characterization of high intensity focused ultrasound (HIFU) fields, but other applications such as physiotherapy fields are also possible.
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The feasibility of an infrared system for real-time visualization and mapping of ultrasound fields.
Shaw, Adam; Nunn, John
2010-06-07
In treatment planning for ultrasound therapy, it is desirable to know the 3D structure of the ultrasound field. However, mapping an ultrasound field in 3D is very slow, with even a single planar raster scan taking typically several hours. Additionally, hydrophones that are used for field mapping are expensive and can be damaged in some therapy fields. So there is value in rapid methods which enable visualization and mapping of the ultrasound field in about 1 min. In this note we explore the feasibility of mapping the intensity distribution by measuring the temperature distribution produced in a thin sheet of absorbing material. A 0.2 mm thick acetate sheet forms a window in the wall of a water tank containing the transducer. The window is oriented at 45 degrees to the beam axis, and the distance from the transducer to the window can be varied. The temperature distribution is measured with an infrared camera; thermal images of the inclined plane could be viewed in real time or images could be captured for later analysis and 3D field reconstruction. We conclude that infrared thermography can be used to gain qualitative information about ultrasound fields. Thermal images are easily visualized with good spatial and thermal resolutions (0.044 mm and 0.05 degrees C in our system). The focus and field structure such as side lobes can be identified in real time from the direct video output. 3D maps and image planes at arbitrary orientations to the beam axis can be obtained and reconstructed within a few minutes. In this note we are primarily interested in the technique for characterization of high intensity focused ultrasound (HIFU) fields, but other applications such as physiotherapy fields are also possible.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Wang, T; Zhu, L
Purpose: Conventional dual energy CT (DECT) reconstructs CT and basis material images from two full-size projection datasets with different energy spectra. To relax the data requirement, we propose an iterative DECT reconstruction algorithm using one full scan and a second sparse-view scan by utilizing redundant structural information of the same object acquired at two different energies. Methods: We first reconstruct a full-scan CT image using filtered-backprojection (FBP) algorithm. The material similarities of each pixel with other pixels are calculated by an exponential function about pixel value differences. We assume that the material similarities of pixels remains in the second CTmore » scan, although pixel values may vary. An iterative method is designed to reconstruct the second CT image from reduced projections. Under the data fidelity constraint, the algorithm minimizes the L2 norm of the difference between pixel value and its estimation, which is the average of other pixel values weighted by their similarities. The proposed algorithm, referred to as structure preserving iterative reconstruction (SPIR), is evaluated on physical phantoms. Results: On the Catphan600 phantom, SPIR-based DECT method with a second 10-view scan reduces the noise standard deviation of a full-scan FBP CT reconstruction by a factor of 4 with well-maintained spatial resolution, while iterative reconstruction using total-variation regularization (TVR) degrades the spatial resolution at the same noise level. The proposed method achieves less than 1% measurement difference on electron density map compared with the conventional two-full-scan DECT. On an anthropomorphic pediatric phantom, our method successfully reconstructs the complicated vertebra structures and decomposes bone and soft tissue. Conclusion: We develop an effective method to reduce the number of views and therefore data acquisition in DECT. We show that SPIR-based DECT using one full scan and a second 10-view scan can provide high-quality DECT images and accurate electron density maps as conventional two-full-scan DECT.« less
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Non-laser-based scanner for three-dimensional digitization of historical artifacts
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hahn, Daniel V.; Baldwin, Kevin C.; Duncan, Donald D
2007-05-20
A 3D scanner, based on incoherent illumination techniques, and associated data-processing algorithms are presented that can be used to scan objects at lateral resolutions ranging from 5 to100 {mu}m (or more) and depth resolutions of approximately 2 {mu}m.The scanner was designed with the specific intent to scan cuneiform tablets but can be utilized for other applications. Photometric stereo techniques are used to obtain both a surface normal map and a parameterized model of the object's bidirectional reflectance distribution function. The normal map is combined with height information,gathered by structured light techniques, to form a consistent 3D surface. Data from Lambertianmore » and specularly diffuse spherical objects are presented and used to quantify the accuracy of the techniques. Scans of a cuneiform tablet are also presented. All presented data are at a lateral resolution of 26.8 {mu}m as this is approximately the minimum resolution deemed necessary to accurately represent cuneiform.« less
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Ramos, Rogelio; Zlatev, Roumen; Valdez, Benjamin; Stoytcheva, Margarita; Carrillo, Mónica; García, Juan-Francisco
2013-01-01
A virtual instrumentation (VI) system called VI localized corrosion image analyzer (LCIA) based on LabVIEW 2010 was developed allowing rapid automatic and subjective error-free determination of the pits number on large sized corroded specimens. The VI LCIA controls synchronously the digital microscope image taking and its analysis, finally resulting in a map file containing the coordinates of the detected probable pits containing zones on the investigated specimen. The pits area, traverse length, and density are also determined by the VI using binary large objects (blobs) analysis. The resulting map file can be used further by a scanning vibrating electrode technique (SVET) system for rapid (one pass) “true/false” SVET check of the probable zones only passing through the pit's centers avoiding thus the entire specimen scan. A complete SVET scan over the already proved “true” zones could determine the corrosion rate in any of the zones. PMID:23691434
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Development of an external beam nuclear microprobe on the Aglae facility of the Louvre museum
NASA Astrophysics Data System (ADS)
Calligaro, T.; Dran, J.-C.; Ioannidou, E.; Moignard, B.; Pichon, L.; Salomon, J.
2000-03-01
The external beam line of our facility has been recently equipped with the focusing system previously mounted on a classical nuclear microprobe. When using a 0.1 μm thick Si 3N 4 foil for the exit window and flowing helium on the sample under analysis, a beam spot as small as 10 μm is attainable at a distance of 3 mm from the window. Elemental micromapping is performed by mechanical scanning. An electronic device has been designed which allows XY scanning by moving the sample under the beam by steps down to 0.1 μm. Beam monitoring is carried out by means of the weak X-ray signal emitted by the exit foil and detected by a specially designed Si(Li) detector cooled by Peltier effect. The characteristics of external beams of protons and alpha particles are evaluated by means of resonance scanning and elemental mapping of a grid. An example of application is presented, dealing with elemental micro-mapping of inclusions in gemstones.
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Spatial modelling and mapping of female genital mutilation in Kenya.
Achia, Thomas N O
2014-03-25
Female genital mutilation/cutting (FGM/C) is still prevalent in several communities in Kenya and other areas in Africa, as well as being practiced by some migrants from African countries living in other parts of the world. This study aimed at detecting clustering of FGM/C in Kenya, and identifying those areas within the country where women still intend to continue the practice. A broader goal of the study was to identify geographical areas where the practice continues unabated and where broad intervention strategies need to be introduced. The prevalence of FGM/C was investigated using the 2008 Kenya Demographic and Health Survey (KDHS) data. The 2008 KDHS used a multistage stratified random sampling plan to select women of reproductive age (15-49 years) and asked questions concerning their FGM/C status and their support for the continuation of FGM/C. A spatial scan statistical analysis was carried out using SaTScan™ to test for statistically significant clustering of the practice of FGM/C in the country. The risk of FGM/C was also modelled and mapped using a hierarchical spatial model under the Integrated Nested Laplace approximation approach using the INLA library in R. The prevalence of FGM/C stood at 28.2% and an estimated 10.3% of the women interviewed indicated that they supported the continuation of FGM. On the basis of the Deviance Information Criterion (DIC), hierarchical spatial models with spatially structured random effects were found to best fit the data for both response variables considered. Age, region, rural-urban classification, education, marital status, religion, socioeconomic status and media exposure were found to be significantly associated with FGM/C. The current FGM/C status of a woman was also a significant predictor of support for the continuation of FGM/C. Spatial scan statistics confirm FGM clusters in the North-Eastern and South-Western regions of Kenya (p<0.001). This suggests that the fight against FGM/C in Kenya is not yet over. There are still deep cultural and religious beliefs to be addressed in a bid to eradicate the practice. Interventions by government and other stakeholders must address these challenges and target the identified clusters.
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Global Variability of Mesoscale Convective System Anvil Structure from A-Train Satellite Data
NASA Technical Reports Server (NTRS)
Yuan, Jian; Houze, Robert A.
2010-01-01
Mesoscale convective systems (MCSs) in the tropics produce extensive anvil clouds, which significantly affect the transfer of radiation. This study develops an objective method to identify MCSs and their anvils by combining data from three A-train satellite instruments: Moderate Resolution Imaging Spectroradiometer (MODIS) for cloud-top size and coldness, Advanced Microwave Scanning Radiometer for Earth Observing System (AMSR-E) for rain area size and intensity, and CloudSat for horizontal and vertical dimensions of anvils. The authors distinguish three types of MCSs: small and large separated MCSs and connected MCSs. The latter are MCSs sharing a contiguous rain area. Mapping of the objectively identified MCSs shows patterns of MCSs that are consistent with previous studies of tropical convection, with separated MCSs dominant over Africa and the Amazon regions and connected MCSs favored over the warm pool of the Indian and west Pacific Oceans. By separating the anvil from the raining regions of MCSs, this study leads to quantitative global maps of anvil coverage. These maps are consistent with the MCS analysis, and they lay the foundation for estimating the global radiative effects of anvil clouds. CloudSat radar data show that the modal thickness of MCS anvils is about 4-5 km. Anvils are mostly confined to within 1.5-2 times the equivalent radii of the primary rain areas of the MCSs. Over the warm pool, they may extend out to about 5 times the rain area radii. The warm ocean MCSs tend to have thicker non-raining and lightly raining anvils near the edges
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Fan, Zhen; Dani, Melanie; Femminella, Grazia D; Wood, Melanie; Calsolaro, Valeria; Veronese, Mattia; Turkheimer, Federico; Gentleman, Steve; Brooks, David J; Hinz, Rainer; Edison, Paul
2018-07-01
Neuroinflammation and microglial activation play an important role in amnestic mild cognitive impairment (MCI) and Alzheimer's disease. In this study, we investigated the spatial distribution of neuroinflammation in MCI subjects, using spectral analysis (SA) to generate parametric maps and quantify 11 C-PBR28 PET, and compared these with compartmental and other kinetic models of quantification. Thirteen MCI and nine healthy controls were enrolled in this study. Subjects underwent 11 C-PBR28 PET scans with arterial cannulation. Spectral analysis with an arterial plasma input function was used to generate 11 C-PBR28 parametric maps. These maps were then compared with regional 11 C-PBR28 V T (volume of distribution) using a two-tissue compartment model and Logan graphic analysis. Amyloid load was also assessed with 18 F-Flutemetamol PET. With SA, three component peaks were identified in addition to blood volume. The 11 C-PBR28 impulse response function (IRF) at 90 min produced the lowest coefficient of variation. Single-subject analysis using this IRF demonstrated microglial activation in five out of seven amyloid-positive MCI subjects. IRF parametric maps of 11 C-PBR28 uptake revealed a group-wise significant increase in neuroinflammation in amyloid-positive MCI subjects versus HC in multiple cortical association areas, and particularly in the temporal lobe. Interestingly, compartmental analysis detected group-wise increase in 11 C-PBR28 binding in the thalamus of amyloid-positive MCI subjects, while Logan parametric maps did not perform well. This study demonstrates for the first time that spectral analysis can be used to generate parametric maps of 11 C-PBR28 uptake, and is able to detect microglial activation in amyloid-positive MCI subjects. IRF parametric maps of 11 C-PBR28 uptake allow voxel-wise single-subject analysis and could be used to evaluate microglial activation in individual subjects.
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High-throughput physical mapping of chromosomes using automated in situ hybridization.
George, Phillip; Sharakhova, Maria V; Sharakhov, Igor V
2012-06-28
Projects to obtain whole-genome sequences for 10,000 vertebrate species and for 5,000 insect and related arthropod species are expected to take place over the next 5 years. For example, the sequencing of the genomes for 15 malaria mosquitospecies is currently being done using an Illumina platform. This Anopheles species cluster includes both vectors and non-vectors of malaria. When the genome assemblies become available, researchers will have the unique opportunity to perform comparative analysis for inferring evolutionary changes relevant to vector ability. However, it has proven difficult to use next-generation sequencing reads to generate high-quality de novo genome assemblies. Moreover, the existing genome assemblies for Anopheles gambiae, although obtained using the Sanger method, are gapped or fragmented. Success of comparative genomic analyses will be limited if researchers deal with numerous sequencing contigs, rather than with chromosome-based genome assemblies. Fragmented, unmapped sequences create problems for genomic analyses because: (i) unidentified gaps cause incorrect or incomplete annotation of genomic sequences; (ii) unmapped sequences lead to confusion between paralogous genes and genes from different haplotypes; and (iii) the lack of chromosome assignment and orientation of the sequencing contigs does not allow for reconstructing rearrangement phylogeny and studying chromosome evolution. Developing high-resolution physical maps for species with newly sequenced genomes is a timely and cost-effective investment that will facilitate genome annotation, evolutionary analysis, and re-sequencing of individual genomes from natural populations. Here, we present innovative approaches to chromosome preparation, fluorescent in situ hybridization (FISH), and imaging that facilitate rapid development of physical maps. Using An. gambiae as an example, we demonstrate that the development of physical chromosome maps can potentially improve genome assemblies and, thus, the quality of genomic analyses. First, we use a high-pressure method to prepare polytene chromosome spreads. This method, originally developed for Drosophila, allows the user to visualize more details on chromosomes than the regular squashing technique. Second, a fully automated, front-end system for FISH is used for high-throughput physical genome mapping. The automated slide staining system runs multiple assays simultaneously and dramatically reduces hands-on time. Third, an automatic fluorescent imaging system, which includes a motorized slide stage, automatically scans and photographs labeled chromosomes after FISH. This system is especially useful for identifying and visualizing multiple chromosomal plates on the same slide. In addition, the scanning process captures a more uniform FISH result. Overall, the automated high-throughput physical mapping protocol is more efficient than a standard manual protocol.
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A non-linear regression method for CT brain perfusion analysis
NASA Astrophysics Data System (ADS)
Bennink, E.; Oosterbroek, J.; Viergever, M. A.; Velthuis, B. K.; de Jong, H. W. A. M.
2015-03-01
CT perfusion (CTP) imaging allows for rapid diagnosis of ischemic stroke. Generation of perfusion maps from CTP data usually involves deconvolution algorithms providing estimates for the impulse response function in the tissue. We propose the use of a fast non-linear regression (NLR) method that we postulate has similar performance to the current academic state-of-art method (bSVD), but that has some important advantages, including the estimation of vascular permeability, improved robustness to tracer-delay, and very few tuning parameters, that are all important in stroke assessment. The aim of this study is to evaluate the fast NLR method against bSVD and a commercial clinical state-of-art method. The three methods were tested against a published digital perfusion phantom earlier used to illustrate the superiority of bSVD. In addition, the NLR and clinical methods were also tested against bSVD on 20 clinical scans. Pearson correlation coefficients were calculated for each of the tested methods. All three methods showed high correlation coefficients (>0.9) with the ground truth in the phantom. With respect to the clinical scans, the NLR perfusion maps showed higher correlation with bSVD than the perfusion maps from the clinical method. Furthermore, the perfusion maps showed that the fast NLR estimates are robust to tracer-delay. In conclusion, the proposed fast NLR method provides a simple and flexible way of estimating perfusion parameters from CT perfusion scans, with high correlation coefficients. This suggests that it could be a better alternative to the current clinical and academic state-of-art methods.
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Xu, Zhe; Chen, Sisi; Yang, Chun; Huang, Shenghai; Shen, Meixiao; Wang, Yuanyuan
2018-01-01
To investigate the repeatability and reproducibility of mapping the entire corneal thickness using spectral domain optical coherence tomography (SD-OCT). Thirty normal eyes, 30 post-laser in situ keratomileusis (LASIK) surgery eyes, and 30 keratoconus eyes were analyzed. A custom-built long scan depth SD-OCT device was used to obtain entire corneal images. Ten-millimeter-diameter corneal thickness maps were generated by an automated segmentation algorithm. Intraclass correlation coefficients of repeatability (ICC1) and reproducibility (ICC2), and coefficients of repeatability (CoR1) and reproducibility (CoR2), were calculated to quantify the precision and accuracy of corneal pachymetry measurements using the Bland-Altman method. For SD-OCT measurements in healthy subjects, CoR1 and CoR2 were less than 5.00 and 5.53 μm. ICC1 and ICC2 were more than 0.997 and 0.996. For SD-OCT measurements in LASIK patients, CoR1 and CoR2 were less than 5.09 and 5.34 μm. ICC1 and ICC2 were more than 0.997 and 0.996. For SD-OCT measurements in keratoconus patients, CoR1 and CoR2 were less than 11.57 and 10.92 μm. ICC1 and ICC2 were more than 0.995 and 0.996. The measurements of corneal pachymetric mapping by long scan depth SD-OCT can be assessed over the entire corneal area with good repeatability and reproducibility. © 2017 S. Karger AG, Basel.
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Robust isotropic super-resolution by maximizing a Laplace posterior for MRI volumes
NASA Astrophysics Data System (ADS)
Han, Xian-Hua; Iwamoto, Yutaro; Shiino, Akihiko; Chen, Yen-Wei
2014-03-01
Magnetic resonance imaging can only acquire volume data with finite resolution due to various factors. In particular, the resolution in one direction (such as the slice direction) is much lower than others (such as the in-plane direction), yielding un-realistic visualizations. This study explores to reconstruct MRI isotropic resolution volumes from three orthogonal scans. This proposed super- resolution reconstruction is formulated as a maximum a posterior (MAP) problem, which relies on the generation model of the acquired scans from the unknown high-resolution volumes. Generally, the deviation ensemble of the reconstructed high-resolution (HR) volume from the available LR ones in the MAP is represented as a Gaussian distribution, which usually results in some noise and artifacts in the reconstructed HR volume. Therefore, this paper investigates a robust super-resolution by formulating the deviation set as a Laplace distribution, which assumes sparsity in the deviation ensemble based on the possible insight of the appeared large values only around some unexpected regions. In addition, in order to achieve reliable HR MRI volume, we integrates the priors such as bilateral total variation (BTV) and non-local mean (NLM) into the proposed MAP framework for suppressing artifacts and enriching visual detail. We validate the proposed robust SR strategy using MRI mouse data with high-definition resolution in two direction and low-resolution in one direction, which are imaged in three orthogonal scans: axial, coronal and sagittal planes. Experiments verifies that the proposed strategy can achieve much better HR MRI volumes than the conventional MAP method even with very high-magnification factor: 10.
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Transmission imaging for integrated PET-MR systems.
Bowen, Spencer L; Fuin, Niccolò; Levine, Michael A; Catana, Ciprian
2016-08-07
Attenuation correction for PET-MR systems continues to be a challenging problem, particularly for body regions outside the head. The simultaneous acquisition of transmission scan based μ-maps and MR images on integrated PET-MR systems may significantly increase the performance of and offer validation for new MR-based μ-map algorithms. For the Biograph mMR (Siemens Healthcare), however, use of conventional transmission schemes is not practical as the patient table and relatively small diameter scanner bore significantly restrict radioactive source motion and limit source placement. We propose a method for emission-free coincidence transmission imaging on the Biograph mMR. The intended application is not for routine subject imaging, but rather to improve and validate MR-based μ-map algorithms; particularly for patient implant and scanner hardware attenuation correction. In this study we optimized source geometry and assessed the method's performance with Monte Carlo simulations and phantom scans. We utilized a Bayesian reconstruction algorithm, which directly generates μ-map estimates from multiple bed positions, combined with a robust scatter correction method. For simulations with a pelvis phantom a single torus produced peak noise equivalent count rates (34.8 kcps) dramatically larger than a full axial length ring (11.32 kcps) and conventional rotating source configurations. Bias in reconstructed μ-maps for head and pelvis simulations was ⩽4% for soft tissue and ⩽11% for bone ROIs. An implementation of the single torus source was filled with (18)F-fluorodeoxyglucose and the proposed method quantified for several test cases alone or in comparison with CT-derived μ-maps. A volume average of 0.095 cm(-1) was recorded for an experimental uniform cylinder phantom scan, while a bias of <2% was measured for the cortical bone equivalent insert of the multi-compartment phantom. Single torus μ-maps of a hip implant phantom showed significantly less artifacts and improved dynamic range, and differed greatly for highly attenuating materials in the case of the patient table, compared to CT results. Use of a fixed torus geometry, in combination with translation of the patient table to perform complete tomographic sampling, generated highly quantitative measured μ-maps and is expected to produce images with significantly higher SNR than competing fixed geometries at matched total acquisition time.
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Transmission imaging for integrated PET-MR systems
NASA Astrophysics Data System (ADS)
Bowen, Spencer L.; Fuin, Niccolò; Levine, Michael A.; Catana, Ciprian
2016-08-01
Attenuation correction for PET-MR systems continues to be a challenging problem, particularly for body regions outside the head. The simultaneous acquisition of transmission scan based μ-maps and MR images on integrated PET-MR systems may significantly increase the performance of and offer validation for new MR-based μ-map algorithms. For the Biograph mMR (Siemens Healthcare), however, use of conventional transmission schemes is not practical as the patient table and relatively small diameter scanner bore significantly restrict radioactive source motion and limit source placement. We propose a method for emission-free coincidence transmission imaging on the Biograph mMR. The intended application is not for routine subject imaging, but rather to improve and validate MR-based μ-map algorithms; particularly for patient implant and scanner hardware attenuation correction. In this study we optimized source geometry and assessed the method’s performance with Monte Carlo simulations and phantom scans. We utilized a Bayesian reconstruction algorithm, which directly generates μ-map estimates from multiple bed positions, combined with a robust scatter correction method. For simulations with a pelvis phantom a single torus produced peak noise equivalent count rates (34.8 kcps) dramatically larger than a full axial length ring (11.32 kcps) and conventional rotating source configurations. Bias in reconstructed μ-maps for head and pelvis simulations was ⩽4% for soft tissue and ⩽11% for bone ROIs. An implementation of the single torus source was filled with 18F-fluorodeoxyglucose and the proposed method quantified for several test cases alone or in comparison with CT-derived μ-maps. A volume average of 0.095 cm-1 was recorded for an experimental uniform cylinder phantom scan, while a bias of <2% was measured for the cortical bone equivalent insert of the multi-compartment phantom. Single torus μ-maps of a hip implant phantom showed significantly less artifacts and improved dynamic range, and differed greatly for highly attenuating materials in the case of the patient table, compared to CT results. Use of a fixed torus geometry, in combination with translation of the patient table to perform complete tomographic sampling, generated highly quantitative measured μ-maps and is expected to produce images with significantly higher SNR than competing fixed geometries at matched total acquisition time.
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Kim, Sangmin; Kim, Jeonghyun; Jung, Jaehoon; Heo, Joon
2015-12-09
The cadastral system provides land ownership information by registering and representing land boundaries on a map. The current cadastral system in Korea, however, focuses mainly on the management of 2D land-surface boundaries. It is not yet possible to provide efficient or reliable land administration, as this 2D system cannot support or manage land information on 3D properties (including architectures and civil infrastructures) for both above-ground and underground facilities. A geometrical model of the 3D parcel, therefore, is required for registration of 3D properties. This paper, considering the role of the cadastral system, proposes a framework for a 3D underground cadastral system that can register various types of 3D underground properties using indoor mapping for as-built Building Information Modeling (BIM). The implementation consists of four phases: (1) geometric modeling of a real underground infrastructure using terrestrial laser scanning data; (2) implementation of as-built BIM based on geometric modeling results; (3) accuracy assessment for created as-built BIM using reference points acquired by total station; and (4) creation of three types of 3D underground cadastral map to represent underground properties. The experimental results, based on indoor mapping for as-built BIM, show that the proposed framework for a 3D underground cadastral system is able to register the rights, responsibilities, and restrictions corresponding to the 3D underground properties. In this way, clearly identifying the underground physical situation enables more reliable and effective decision-making in all aspects of the national land administration system.
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NASA Astrophysics Data System (ADS)
Emter, Thomas; Petereit, Janko
2014-05-01
An integrated multi-sensor fusion framework for localization and mapping for autonomous navigation in unstructured outdoor environments based on extended Kalman filters (EKF) is presented. The sensors for localization include an inertial measurement unit, a GPS, a fiber optic gyroscope, and wheel odometry. Additionally a 3D LIDAR is used for simultaneous localization and mapping (SLAM). A 3D map is built while concurrently a localization in a so far established 2D map is estimated with the current scan of the LIDAR. Despite of longer run-time of the SLAM algorithm compared to the EKF update, a high update rate is still guaranteed by sophisticatedly joining and synchronizing two parallel localization estimators.
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Classification of fMRI resting-state maps using machine learning techniques: A comparative study
NASA Astrophysics Data System (ADS)
Gallos, Ioannis; Siettos, Constantinos
2017-11-01
We compare the efficiency of Principal Component Analysis (PCA) and nonlinear learning manifold algorithms (ISOMAP and Diffusion maps) for classifying brain maps between groups of schizophrenia patients and healthy from fMRI scans during a resting-state experiment. After a standard pre-processing pipeline, we applied spatial Independent component analysis (ICA) to reduce (a) noise and (b) spatial-temporal dimensionality of fMRI maps. On the cross-correlation matrix of the ICA components, we applied PCA, ISOMAP and Diffusion Maps to find an embedded low-dimensional space. Finally, support-vector-machines (SVM) and k-NN algorithms were used to evaluate the performance of the algorithms in classifying between the two groups.
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NASA Technical Reports Server (NTRS)
Xing, W.; Heinrich, B.; Zhou, HU; Fife, A. A.; Cragg, A. R.; Grant, P. D.
1995-01-01
Mapping of the magnetic flux density B(sub z) (perpendicular to the film plane) for a YBa2Cu3O7 thin-film sample was carried out using a scanning micro-Hall probe. The sheet magnetization and sheet current densities were calculated from the B(sub z) distributions. From the known sheet magnetization, the tangential (B(sub x,y)) and normal components of the flux density B were calculated in the vicinity of the film. It was found that the sheet current density was mostly determined by 2B(sub x,y)/d, where d is the film thickness. The evolution of flux penetration as a function of applied field will be shown.
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Lilliu, S; Maragliano, C; Hampton, M; Elliott, M; Stefancich, M; Chiesa, M; Dahlem, M S; Macdonald, J E
2013-11-27
We report a simple technique for mapping Electrostatic Force Microscopy (EFM) bias sweep data into 2D images. The method allows simultaneous probing, in the same scanning area, of the contact potential difference and the second derivative of the capacitance between tip and sample, along with the height information. The only required equipment consists of a microscope with lift-mode EFM capable of phase shift detection. We designate this approach as Scanning Probe Potential Electrostatic Force Microscopy (SPP-EFM). An open-source MATLAB Graphical User Interface (GUI) for images acquisition, processing and analysis has been developed. The technique is tested with Indium Tin Oxide (ITO) and with poly(3-hexylthiophene) (P3HT) nanowires for organic transistor applications.
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Tropical rain mapping radar on the Space Station
NASA Technical Reports Server (NTRS)
Im, Eastwood; Li, Fuk
1989-01-01
The conceptual design for a tropical rain mapping radar for flight on the manned Space Station is discussed. In this design the radar utilizes a narrow, dual-frequency (9.7 GHz and 24.1 GHz) beam, electronically scanned antenna to achieve high spatial (4 km) and vertical (250 m) resolutions and a relatively large (800 km) cross-track swath. An adaptive scan strategy will be used for better utilization of radar energy and dwell time. Such a system can detect precipitation at rates of up to 100 mm/hr with accuracies of roughly 15 percent. With the proposed space-time sampling strategy, the monthly averaged rainfall rate can be estimated to within 8 percent, which is essential for many climatological studies.
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Progress in the development of shallow-water mapping systems
Bergeron, E.; Worley, C.R.; O'Brien, T.
2007-01-01
The USGS (US Geological Survey) Coastal and Marine Geology has deployed an advance autonomous shallow-draft robotic vehicle, Iris, for shallow-water mapping in Apalachicola Bay, Florida. The vehicle incorporates a side scan sonar system, seismic-reflection profiler, single-beam echosounder, and global positioning system (GPS) navigation. It is equipped with an onboard microprocessor-based motor controller, delivering signals for speed and steering to hull-mounted brushless direct-current thrusters. An onboard motion sensor in the Sea Robotics vehicle control system enclosure has been integrated in the vehicle to measure the vehicle heave, pitch, roll, and heading. Three water-tight enclosures are mounted along the vehicle axis for the Edgetech computer and electronics system including the Sea Robotics computer, a control and wireless communications system, and a Thales ZXW real-time kinematic (RTK) GPS receiver. The vehicle has resulted in producing high-quality seismic reflection and side scan sonar data, which will help in developing the baseline oyster habitat maps.
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Transcript mapping for handwritten English documents
NASA Astrophysics Data System (ADS)
Jose, Damien; Bharadwaj, Anurag; Govindaraju, Venu
2008-01-01
Transcript mapping or text alignment with handwritten documents is the automatic alignment of words in a text file with word images in a handwritten document. Such a mapping has several applications in fields ranging from machine learning where large quantities of truth data are required for evaluating handwriting recognition algorithms, to data mining where word image indexes are used in ranked retrieval of scanned documents in a digital library. The alignment also aids "writer identity" verification algorithms. Interfaces which display scanned handwritten documents may use this alignment to highlight manuscript tokens when a person examines the corresponding transcript word. We propose an adaptation of the True DTW dynamic programming algorithm for English handwritten documents. The integration of the dissimilarity scores from a word-model word recognizer and Levenshtein distance between the recognized word and lexicon word, as a cost metric in the DTW algorithm leading to a fast and accurate alignment, is our primary contribution. Results provided, confirm the effectiveness of our approach.
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Wide-Field Raman Imaging of Dental Lesions
Yang, Shan; Li, Bolan; Akkus, Anna; Akkus, Ozan; Lang, Lisa
2014-01-01
Detection of dental caries at the onset remains as a great challenge in dentistry. Raman spectroscopy could be successfully applied towards detecting caries since it is sensitive to the amount of the Raman active mineral crystals, the most abundant component of enamel. Effective diagnosis requires full examination of a tooth surface via a Raman mapping. Point-scan Raman mapping is not clinically relevant (feasible) due to lengthy data acquisition time. In this work, a wide-field Raman imaging system was assembled based on a high-sensitivity 2D CCD camera for imaging the mineralization status of teeth with lesions. Wide-field images indicated some lesions to be hypomineralized and others to be hypermineralized. The observations of wide-field Raman imaging were in agreement with point-scan Raman mapping. Therefore, sound enamel and lesions can be discriminated by Raman imaging of the mineral content. In conclusion, wide-field Raman imaging is a potentially useful tool for visualization of dental lesions in the clinic. PMID:24781363
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Wu, J S; Kim, A M; Bleher, R; Myers, B D; Marvin, R G; Inada, H; Nakamura, K; Zhang, X F; Roth, E; Li, S Y; Woodruff, T K; O'Halloran, T V; Dravid, Vinayak P
2013-05-01
A dedicated analytical scanning transmission electron microscope (STEM) with dual energy dispersive spectroscopy (EDS) detectors has been designed for complementary high performance imaging as well as high sensitivity elemental analysis and mapping of biological structures. The performance of this new design, based on a Hitachi HD-2300A model, was evaluated using a variety of biological specimens. With three imaging detectors, both the surface and internal structure of cells can be examined simultaneously. The whole-cell elemental mapping, especially of heavier metal species that have low cross-section for electron energy loss spectroscopy (EELS), can be faithfully obtained. Optimization of STEM imaging conditions is applied to thick sections as well as thin sections of biological cells under low-dose conditions at room and cryogenic temperatures. Such multimodal capabilities applied to soft/biological structures usher a new era for analytical studies in biological systems. Copyright © 2013 Elsevier B.V. All rights reserved.
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NASA Astrophysics Data System (ADS)
Miller, D.; Trembanis, A. C.; Kennedy, E.; Rusch, H.; Rothermel, E.
2016-02-01
The National Park Service has partnered with faculty and students at the University of Delaware to map the length of Assateague Island and sample benthic communities there for two purposes: (1) to provide a complete inventory of benthic habitats and their biota, and (2) to determine if any changes from a pre-storm survey can be ascribed to Superstorm Sandy in 2012. During the 2014 and 2015 field seasons over 75 km2 of high-resolution ( 50 cm/pixel) side-scan sonar and collocated bathymetry were collected with a surface vessel mounted bathy side-scan sonar (EdgeTech 6205), spanning the shore from depths of less than 2 m out to a distance of approximately 1 nautical mile and depths of 10-12 m. Furthermore, we have resampled using standard methodology (modified Young grab and 0.5-mm sieve) a subset of the previously sampled benthic stations that represent all sediment classes identified in prior studies. Additionally, we have obtained novel data with our ROV and AUV assets, including finer scale bottom video and multibeam bathymetry, at specifically chosen locations in order to enhance understanding of the benthic habitat and bottom type changes. In addition to providing a habitat and faunal inventory for resource management purposes, we will compare our side scan and benthic survey data to the pre-storm 2011 data products with comparable coverage. To date we have found that ArcGIS and ENVI sediment classifications agree well with those from the 2011 study, but spatially we note more areas of finer sediments and less of gravel. As was expected, 2014 benthic assemblages differ significantly among sediment classes (PRIMER ANOSIM), and sediment class is the best predictor of the benthic community (PERMANOVA+ distance-based RDA). Our goal here is to use consistent analytical approaches to characterize changes that occur over season and inter-annual time scales. This is a critical step toward attributing sediment, habitat and biological changes to Superstorm Sandy.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Patton, T; Du, K; Bayouth, J
Purpose: Four-dimensional computed tomography (4DCT) can be used to evaluate longitudinal changes in pulmonary function. The sensitivity of such measurements to identify function change may be improved with reproducible breathing patterns. The purpose of this study was to determine if inhale was more consistent than exhale, i.e., lung expansion during inhalation compared to lung contraction during exhalation. Methods: Repeat 4DCT image data acquired within a short time interval from 8 patients. Using a tissue volume preserving deformable image registration algorithm, Jacobian ventilation maps in two scanning sessions were computed and compared on the same coordinate for reproducibility analysis. Equivalent lungmore » volumes (ELV) were used for 5 subjects and equivalent title volumes (ETV) for the 3 subjects who experienced a baseline shift between scans. In addition, gamma pass rate was calculated from a modified gamma index evaluation between two ventilation maps, using acceptance criterions of 2mm distance-to-agreement and 5% ventilation difference. The gamma pass rates were then compared using paired t-test to determine if there was a significant difference. Results: Inhalation was more reproducible than exhalation. In the 5 ELV subjects 78.5% of the lung voxels met the gamma criteria for expansion during inhalation when comparing the two scans, while significantly fewer (70.9% of the lung voxels) met the gamma criteria for contraction during exhalation (p = .027). In the 8 total subjects analyzed the average gamma pass rate for expansion during inhalation was 75.2% while for contraction during exhalation it was 70.3%; which trended towards significant (p = .064). Conclusion: This work implies inhalation is more reproducible than exhalation, when equivalent respiratory volumes are considered. The reason for this difference is unknown. Longitudinal investigation of pulmonary function change based on inhalation images appears appropriate for Jacobian-based measure of lung tissue expansion. NIH Grant: R01 CA166703.« less
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Scanning three-dimensional x-ray diffraction microscopy using a high-energy microbeam
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hayashi, Y., E-mail: y-hayashi@mosk.tytlabs.co.jp; Hirose, Y.; Seno, Y.
2016-07-27
A scanning three-dimensional X-ray diffraction (3DXRD) microscope apparatus with a high-energy microbeam was installed at the BL33XU Toyota beamline at SPring-8. The size of the 50 keV beam focused using Kirkpatrick-Baez mirrors was 1.3 μm wide and 1.6 μm high in full width at half maximum. The scanning 3DXRD method was tested for a cold-rolled carbon steel sheet sample. A three-dimensional orientation map with 37 {sup 3} voxels was obtained.
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Jara, Hernán; Mian, Asim; Sakai, Osamu; Anderson, Stephan W; Horn, Mitchel J; Norbash, Alexander M; Soto, Jorge A
2016-12-01
Gadolinium-based contrast agents have associated risks. Normal saline (NS) is a nontoxic sodium chloride water solution that can significantly increase the magnetic resonance imaging (MRI) relaxation times of blood via transient hemodilution (THD). The purpose of this pilot study was to test in vivo in the head the potential of normal saline as a safer, exogenous perfusion contrast agent. This Health Insurance Portability and Accountability Act (HIPAA)-compliant prospective study was approved by the local Institutional Review Board (IRB): 12 patients were scanned with T 1 -weighted inversion recovery turbo spin echo pulse sequence at 1.5T. The dynamic inversion recovery pulse sequence was run before, during, and after the NS injection for up to 5 minutes: 100 ml of NS was power-injected via antecubital veins at 3-4 ml/s. Images were processed to map maximum enhancement area-under-the-curve, time-to-peak, and mean-transit-time. These maps were used to identify the areas showing significant NS injection-related signal and to generate enhancement time curves. Hardware and pulse sequence stability were studied via phantom experimentation. Main features of the time curves were tested against theoretical modeling of THD signal effects using inversion recovery pulse sequences. Pearson correlation coefficient (R) mapping was used to differentiate genuine THD effects from motion confounders and noise. The scans of 8 out of 12 patients showed NS injection-related effects that correlate in magnitude with tissue type (gray matter ∼15% and white matter ∼3%). Motion artifacts prevented ascertaining NS signal effects in the remaining four patients. Positive and negative time curves were observed in vivo and this dual THD signal polarity was also observed in the theoretical simulations. R-histograms that were approximately constant in the range 0.1 < |R| < 0.8 and leading to correlation fractions of F corr (|R| > 0.5) = 0.45 and 0.59 were found to represent scans with genuine THD signal effects. A measurable perfusion effect in brain tissue was demonstrated in vivo using NS as an injectable intravascular contrast agent. J. Magn. Reson. Imaging 2016;44:1580-1591. © 2016 International Society for Magnetic Resonance in Medicine.
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Diffusion tensor magnetic resonance imaging of the pancreas.
Nissan, Noam; Golan, Talia; Furman-Haran, Edna; Apter, Sara; Inbar, Yael; Ariche, Arie; Bar-Zakay, Barak; Goldes, Yuri; Schvimer, Michael; Grobgeld, Dov; Degani, Hadassa
2014-01-01
To develop a diffusion-tensor-imaging (DTI) protocol that is sensitive to the complex diffusion and perfusion properties of the healthy and malignant pancreas tissues. Twenty-eight healthy volunteers and nine patients with pancreatic-ductal-adenocacinoma (PDAC), were scanned at 3T with T2-weighted and DTI sequences. Healthy volunteers were also scanned with multi-b diffusion-weighted-imaging (DWI), whereas a standard clinical protocol complemented the PDAC patients' scans. Image processing at pixel resolution yielded parametric maps of three directional diffusion coefficients λ1, λ2, λ3, apparent diffusion coefficient (ADC), and fractional anisotropy (FA), as well as a λ1-vector map, and a main diffusion-direction map. DTI measurements of healthy pancreatic tissue at b-values 0,500 s/mm² yielded: λ1 = (2.65±0.35)×10⁻³, λ2 = (1.87±0.22)×10⁻³, λ3 = (1.20±0.18)×10⁻³, ADC = (1.91±0.22)×10⁻³ (all in mm²/s units) and FA = 0.38±0.06. Using b-values of 100,500 s/mm² led to a significant reduction in λ1, λ2, λ3 and ADC (p<.0001) and a significant increase (p<0.0001) in FA. The reduction in the diffusion coefficients suggested a contribution of a fast intra-voxel-incoherent-motion (IVIM) component at b≤100 s/mm², which was confirmed by the multi-b DWI results. In PDACs, λ1, λ2, λ3 and ADC in both 0,500 s/mm² and 100,500 s/mm² b-values sets, as well as the reduction in these diffusion coefficients between the two sets, were significantly lower in comparison to the distal normal pancreatic tissue, suggesting higher cellularity and diminution of the fast-IVIM component in the cancer tissue. DTI using two reference b-values 0 and 100 s/mm² enabled characterization of the water diffusion and anisotropy of the healthy pancreas, taking into account a contribution of IVIM. The reduction in the diffusion coefficients of PDAC, as compared to normal pancreatic tissue, and the smaller change in these coefficients in PDAC when the reference b-value was modified from 0 to 100 s/mm², helped identifying the presence of malignancy.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Thomas, D; Neylon, J; Dou, T
Purpose: A recently proposed 4D-CT protocol uses deformable registration of free-breathing fast-helical CT scans to generate a breathing motion model. In order to allow accurate registration, free-breathing images are required to be free of doubling-artifacts, which arise when tissue motion is greater than scan speed. This work identifies the minimum scanner parameters required to successfully generate free-breathing fast-helical scans without doubling-artifacts. Methods: 10 patients were imaged under free breathing conditions 25 times in alternating directions with a 64-slice CT scanner using a low dose fast helical protocol. A high temporal resolution (0.1s) 4D-CT was generated using a patient specific motionmore » model and patient breathing waveforms, and used as the input for a scanner simulation. Forward projections were calculated using helical cone-beam geometry (800 projections per rotation) and a GPU accelerated reconstruction algorithm was implemented. Various CT scanner detector widths and rotation times were simulated, and verified using a motion phantom. Doubling-artifacts were quantified in patient images using structural similarity maps to determine the similarity between axial slices. Results: Increasing amounts of doubling-artifacts were observed with increasing rotation times > 0.2s for 16×1mm slice scan geometry. No significant increase in doubling artifacts was observed for 64×1mm slice scan geometry up to 1.0s rotation time although blurring artifacts were observed >0.6s. Using a 16×1mm slice scan geometry, a rotation time of less than 0.3s (53mm/s scan speed) would be required to produce images of similar quality to a 64×1mm slice scan geometry. Conclusion: The current generation of 16 slice CT scanners, which are present in most Radiation Oncology departments, are not capable of generating free-breathing sorting-artifact-free images in the majority of patients. The next generation of CT scanners should be capable of at least 53mm/s scan speed in order to use a fast-helical 4D-CT protocol to generate a motion-artifact free 4D-CT. NIH R01CA096679.« less
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TH-A-BRF-09: Integration of High-Resolution MRSI Into Glioblastoma Treatment Planning
DOE Office of Scientific and Technical Information (OSTI.GOV)
Schreibmann, E; Cordova, J; Shu, H
2014-06-15
Purpose: Identification of a metabolite signature that shows significant tumor cell infiltration into normal brain in regions that do not appear abnormal on standard MRI scans would be extremely useful for radiation oncologists to choose optimal regions of brain to treat, and to quantify response beyond the MacDonald criteria. We report on integration of high-resolution magnetic resonance spectroscopic imaging (HR-MRSI) with radiation dose escalation treatment planning to define and target regions at high risk for recurrence. Methods: We propose to supplement standard MRI with a special technique performed on an MRI scanner to measure the metabolite levels within defined volumes.more » Metabolite imaging was acquired using an advanced MRSI technique combining 3D echo-planar spectroscopic imaging (EPSI) with parallel acquisition (GRAPPA) using a multichannel head coil that allows acquisition of whole brain metabolite maps with 108 μl resolution in 12 minutes implemented on a 3T MR scanner. Elevation in the ratio of two metabolites, choline (Cho, elevated in proliferating high-grade gliomas) and N-acetyl aspartate (NAA, a normal neuronal metabolite), was used to image infiltrating high-grade glioma cells in vivo. Results: The metabolite images were co-registered with standard contrast-enhanced T1-weighted MR images using in-house registration software and imported into the treatment-planning system. Regions with tumor infiltration are identified on the metabolic images and used to create adaptive IMRT plans that deliver a standard dose of 60 Gy to the standard target volume and an escalated dose of 75 Gy (or higher) to the most suspicious regions, identified as areas with elevated Cho/NAA ratio. Conclusion: We have implemented a state-of-the-art HR-MRSI technology that can generate metabolite maps of the entire brain in a clinically acceptable scan time, coupled with introduction of an imaging co-registration/ analysis program that combines MRSI data with standard imaging studies in a clinically useful fashion.« less
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NASA Astrophysics Data System (ADS)
Saputra, Aditya; Rahardianto, Trias; Gomez, Christopher
2017-07-01
Adequate knowledge of geological structure is an essential for most studies in geoscience, mineral exploration, geo-hazard and disaster management. The geological map is still one the datasets the most commonly used to obtain information about the geological structure such as fault, joint, fold, and unconformities, however in rural areas such as Central Java data is still sparse. Recent progress in data acquisition technologies and computing have increased the interest in how to capture the high-resolution geological data effectively and for a relatively low cost. Some methods such as Airborne Laser Scanning (ALS), Terrestrial Laser Scanning (TLS), and Unmanned Aerial Vehicles (UAVs) have been widely used to obtain this information, however, these methods need a significant investment in hardware, software, and time. Resolving some of those issues, the photogrammetric method structure from motion (SfM) is an image-based method, which can provide solutions equivalent to laser technologies for a relatively low-cost with minimal time, specialization and financial investment. Using SfM photogrammetry, it is possible to generate high resolution 3D images rock surfaces and outcrops, in order to improve the geological understanding of Indonesia. In the present contribution, it is shown that the information about fault and joint can be obtained at high-resolution and in a shorter time than with the conventional grid mapping and remotely sensed topographic surveying. The SfM method produces a point-cloud through image matching and computing. This task can be run with open- source or commercial image processing and 3D reconstruction software. As the point cloud has 3D information as well as RGB values, it allows for further analysis such as DEM extraction and image orthorectification processes. The present paper describes some examples of SfM to identify the fault in the outcrops and also highlight the future possibilities in terms of earthquake hazard assessment, based on fieldwork in the South of Yogyakarta City.
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Monitoring forests at the speed of light.
Valerie Rapp
2005-01-01
Airborne laser scanning is a technology developed in the last 15 years. Commonly referred to as light detection and ranging, or LIDAR, these systems can map ground with up to a 6-inch elevation accuracy in open, flat terrain. LIDAR is being rapidly adopted for topographical and flood-plain mapping and the detection of earthquake faults hidden by vegetation, among other...
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Sex Differences during Visual Scanning of Occlusion Events in Infants
ERIC Educational Resources Information Center
Wilcox, Teresa; Alexander, Gerianne M.; Wheeler, Lesley; Norvell, Jennifer M.
2012-01-01
A growing number of sex differences in infancy have been reported. One task on which they have been observed reliably is the event-mapping task. In event mapping, infants view an occlusion event involving 1 or 2 objects, the occluder is removed, and then infants see 1 object. Typically, boys are more likely than girls to detect an inconsistency…
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Sampling and mapping forest volume and biomass using airborne LIDARs
Erik Naesset; Terje Gobakken; Ross Nelson
2009-01-01
Since around 1995, extensive research efforts have been made in Scandinavia to develop airborne Light Detection and Ranging (LIDAR) as an operational tool for wall-to-wall mapping of forest stands for planning purposes. Scanning LIDAR has the ability to capture the entire three-dimensional structure of forest canopies and has therefore proved to be a very efficient...
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Material Properties of Human Ocular Tissue at 7-µm Resolution.
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.
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Phased-array ultrasonic surface contour mapping system and method for solids hoppers and the like
Fasching, George E.; Smith, Jr., Nelson S.
1994-01-01
A real time ultrasonic surface contour mapping system is provided including a digitally controlled phased-array of transmitter/receiver (T/R) elements located in a fixed position above the surface to be mapped. The surface is divided into a predetermined number of pixels which are separately scanned by an arrangement of T/R elements by applying phase delayed signals thereto that produce ultrasonic tone bursts from each T/R that arrive at a point X in phase and at the same time relative to the leading edge of the tone burst pulse so that the acoustic energies from each T/R combine in a reinforcing manner at point X. The signals produced by the reception of the echo signals reflected from point X back to the T/Rs are also delayed appropriately so that they add in phase at the input of a signal combiner. This combined signal is then processed to determine the range to the point X using density-corrected sound velocity values. An autofocusing signal is developed from the computed average range for a complete scan of the surface pixels. A surface contour map is generated in real time form the range signals on a video monitor.
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X-ray fluorescence camera for imaging of iodine media in vivo.
Matsukiyo, Hiroshi; Watanabe, Manabu; Sato, Eiichi; Osawa, Akihiro; Enomoto, Toshiyuki; Nagao, Jiro; Abderyim, Purkhet; Aizawa, Katsuo; Tanaka, Etsuro; Mori, Hidezo; Kawai, Toshiaki; Ehara, Shigeru; Sato, Shigehiro; Ogawa, Akira; Onagawa, Jun
2009-01-01
X-ray fluorescence (XRF) analysis is useful for measuring density distributions of contrast media in vivo. An XRF camera was developed for carrying out mapping for iodine-based contrast media used in medical angiography. Objects are exposed by an X-ray beam from a cerium target. Cerium K-series X-rays are absorbed effectively by iodine media in objects, and iodine fluorescence is produced from the objects. Next, iodine Kalpha fluorescence is selected out by use of a 58-microm-thick stannum filter and is detected by a cadmium telluride (CdTe) detector. The Kalpha rays are discriminated out by a multichannel analyzer, and the number of photons is counted by a counter card. The objects are moved and scanned by an x-y stage in conjunction with a two-stage controller, and X-ray images obtained by iodine mapping are shown on a personal computer monitor. The scan pitch of the x and y axes was 2.5 mm, and the photon counting time per mapping point was 2.0 s. We carried out iodine mapping of non-living animals (phantoms), and iodine Kalpha fluorescence was produced from weakly remaining iodine elements in a rabbit skin cancer.
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Complexity of genetic mechanisms conferring nonuniformity of recombination in maize.
Pan, Qingchun; Deng, Min; Yan, Jianbing; Li, Lin
2017-04-26
Recombinations occur nonuniformly across the maize genome. To dissect the genetic mechanisms underlying the nonuniformity of recombination, we performed quantitative trait locus (QTL) mapping using recombinant inbred line populations. Genome-wide QTL scan identified hundreds of QTLs with both cis-prone and trans- effects for recombination number variation. To provide detailed insights into cis- factors associated with recombination variation, we examined the genomic features around recombination hot regions, including density of genes, DNA transposons, retrotransposons, and some specific motifs. Compared to recombination variation in whole genome, more QTLs were mapped for variations in recombination hot regions. The majority QTLs for recombination hot regions are trans-QTLs and co-localized with genes from the recombination pathway. We also found that recombination variation was positively associated with the presence of genes and DNA transposons, but negatively related to the presence of long terminal repeat retrotransposons. Additionally, 41 recombination hot regions were fine-mapped. The high-resolution genotyping of five randomly selected regions in two F 2 populations verified that they indeed have ultra-high recombination frequency, which is even higher than that of the well-known recombination hot regions sh1-bz and a1-sh2. Taken together, our results further our understanding of recombination variation in plants.
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Robust Multipoint Water-Fat Separation Using Fat Likelihood Analysis
Yu, Huanzhou; Reeder, Scott B.; Shimakawa, Ann; McKenzie, Charles A.; Brittain, Jean H.
2016-01-01
Fat suppression is an essential part of routine MRI scanning. Multiecho chemical-shift based water-fat separation methods estimate and correct for Bo field inhomogeneity. However, they must contend with the intrinsic challenge of water-fat ambiguity that can result in water-fat swapping. This problem arises because the signals from two chemical species, when both are modeled as a single discrete spectral peak, may appear indistinguishable in the presence of Bo off-resonance. In conventional methods, the water-fat ambiguity is typically removed by enforcing field map smoothness using region growing based algorithms. In reality, the fat spectrum has multiple spectral peaks. Using this spectral complexity, we introduce a novel concept that identifies water and fat for multiecho acquisitions by exploiting the spectral differences between water and fat. A fat likelihood map is produced to indicate if a pixel is likely to be water-dominant or fat-dominant by comparing the fitting residuals of two different signal models. The fat likelihood analysis and field map smoothness provide complementary information, and we designed an algorithm (Fat Likelihood Analysis for Multiecho Signals) to exploit both mechanisms. It is demonstrated in a wide variety of data that the Fat Likelihood Analysis for Multiecho Signals algorithm offers highly robust water-fat separation for 6-echo acquisitions, particularly in some previously challenging applications. PMID:21842498
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Antarctic Ultraviolet Radiation Climatology from Total Ozone Mapping Spectrometer Data
NASA Technical Reports Server (NTRS)
Lubin, Dan
2004-01-01
This project has successfully produced a climatology of local noon spectral surface irradiance covering the Antarctic continent and the Southern Ocean, the spectral interval 290-700 nm (UV-A, UV-B, and photosynthetically active radiation, PAR), and the entire sunlit part of the year for November 1979-December 1999. Total Ozone Mapping Spectrometer (TOMS) data were used to specify column ozone abundance and UV-A (360- or 380-nm) reflectivity, and passive microwave (MW) sea ice concentrations were used to specify the surface albedo over the Southern Ocean. For this latter task, sea ice concentration retrievals from the Nimbus-7 Scanning Multichannel Microwave Radiometer (SMMR) and its successor, the Defense Meteorological Satellite Program (DMSP) Special Sensor Microwave Imager (SSM/I) were identified with ultraviolet/visible-wavelength albedos based on an empirical TOMS/MW parameterization developed for this purpose (Lubin and Morrow, 2001). The satellite retrievals of surface albedo and UV-A reflectivity were used in a delta-Eddington radiative transfer model to estimate cloud effective optical depth. These optical depth estimates were then used along with the total ozone and surface albedo to calculate the downwelling spectral UV and PAR irradiance at the surface. These spectral irradiance maps were produced for every usable day of TOMS data between 1979-1999 (every other day early in the TOMS program, daily later on).
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NASA Astrophysics Data System (ADS)
Liang, Cunren; Zeng, Qiming; Jia, Jianying; Jiao, Jian; Cui, Xi'ai
2013-02-01
Scanning synthetic aperture radar (ScanSAR) mode is an efficient way to map large scale geophysical phenomena at low cost. The work presented in this paper is dedicated to ScanSAR interferometric processing and its implementation by making full use of existing standard interferometric synthetic aperture radar (InSAR) software. We first discuss the properties of the ScanSAR signal and its phase-preserved focusing using the full aperture algorithm in terms of interferometry. Then a complete interferometric processing flow is proposed. The standard ScanSAR product is decoded subswath by subswath with burst gaps padded with zero-pulses, followed by a Doppler centroid frequency estimation for each subswath and a polynomial fit of all of the subswaths for the whole scene. The burst synchronization of the interferometric pair is then calculated, and only the synchronized pulses are kept for further interferometric processing. After the complex conjugate multiplication of the interferometric pair, the residual non-integer pulse repetition interval (PRI) part between adjacent bursts caused by zero padding is compensated by resampling using a sinc kernel. The subswath interferograms are then mosaicked, in which a method is proposed to remove the subswath discontinuities in the overlap area. Then the following interferometric processing goes back to the traditional stripmap processing flow. A processor written with C and Fortran languages and controlled by Perl scripts is developed to implement these algorithms and processing flow based on the JPL/Caltech Repeat Orbit Interferometry PACkage (ROI_PAC). Finally, we use the processor to process ScanSAR data from the Envisat and ALOS satellites and obtain large scale deformation maps in the radar line-of-sight (LOS) direction.
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NASA Astrophysics Data System (ADS)
Lima, E. A.; Bruno, A. C.; Carvalho, H. R.; Weiss, B. P.
2014-10-01
Scanning magnetic microscopy is a new methodology for mapping magnetic fields with high spatial resolution and field sensitivity. An important goal has been to develop high-performance instruments that do not require cryogenic technology due to its high cost, complexity, and limitation on sensor-to-sample distance. Here we report the development of a low-cost scanning magnetic microscope based on commercial room-temperature magnetic tunnel junction (MTJ) sensors that typically achieves spatial resolution better than 7 µm. By comparing different bias and detection schemes, optimal performance was obtained when biasing the MTJ sensor with a modulated current at 1.0 kHz in a Wheatstone bridge configuration while using a lock-in amplifier in conjunction with a low-noise custom-made preamplifier. A precision horizontal (x-y) scanning stage comprising two coupled nanopositioners controls the position of the sample and a linear actuator adjusts the sensor-to-sample distance. We obtained magnetic field sensitivities better than 150 nT/Hz1/2 between 0.1 and 10 Hz, which is a critical frequency range for scanning magnetic microscopy. This corresponds to a magnetic moment sensitivity of 10-14 A m2, a factor of 100 better than achievable with typical commercial superconducting moment magnetometers. It also represents an improvement in sensitivity by a factor between 10 and 30 compared to similar scanning MTJ microscopes based on conventional bias-detection schemes. To demonstrate the capabilities of the instrument, two polished thin sections of representative geological samples were scanned along with a synthetic sample containing magnetic microparticles. The instrument is usable for a diversity of applications that require mapping of samples at room temperature to preserve magnetic properties or viability, including paleomagnetism and rock magnetism, nondestructive evaluation of materials, and biological assays.
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Nishiyama, Yuichi; Kanayama, Hidekazu; Mori, Hiroshi; Tada, Keiji; Yamamoto, Yasushi; Katsube, Takashi; Takeshita, Haruo; Kawakami, Kazunori; Kitagaki, Hajime
2017-06-01
This study examined the usefulness of statistical parametric mapping (SPM) for investigating postmortem changes on brain computed tomography (CT). This retrospective study included 128 patients (23 - 100 years old) without cerebral abnormalities who underwent unenhanced brain CT before and after death. The antemortem CT (AMCT) scans and postmortem CT (PMCT) scans were spatially normalized using our original brain CT template, and postmortem changes of CT values (in Hounsfield units; HU) were analysed by the SPM technique. Compared with AMCT scans, 58.6 % and 98.4 % of PMCT scans showed loss of the cerebral sulci and an unclear grey matter (GM)-white matter (WM) interface, respectively. SPM analysis revealed a significant decrease in cortical GM density within 70 min after death on PMCT scans, suggesting cytotoxic brain oedema. Furthermore, there was a significant increase in the density of the WM, lenticular nucleus and thalamus more than 120 min after death. The SPM technique demonstrated typical postmortem changes on brain CT scans, and revealed that the unclear GM-WM interface on early PMCT scans is caused by a rapid decrease in cortical GM density combined with a delayed increase in WM density. SPM may be useful for assessment of whole brain postmortem changes. • The original brain CT template achieved successful normalization of brain morphology. • Postmortem changes in the brain were independent of sex. • Cortical GM density decreased rapidly after death. • WM and deep GM densities increased following cortical GM density change. • SPM could be useful for assessment of whole brain postmortem changes.
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Haile, Jemanesh K.; Cory, Aron T.; Clarke, Fran R.; Clarke, John M.; Knox, Ron E.; Pozniak, Curtis J.
2017-01-01
Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat. PMID:28135299
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Evaluation of ERTS-1 image sensor spatial resolution in photographic form
NASA Technical Reports Server (NTRS)
Slater, P. N. (Principal Investigator); Schowengerdt, R. A.
1975-01-01
The author has identified the following significant results. The digital Optical Transfer Function (OTF) measurements showed the following: (1) there are no significant differences in optical performance, in terms of OTF, among all four bands of the multispectral scanner, (2) no substantial changes in the OTF's of bands 4, 5, and 6 during the period November 1972 to May 1973, and (3) comparison between the photographic and digital (CCT) two-dimensional OTF's indicated a strong asymmetry in the photographic product OTF between the MSS scan direction and across scan direction. The coherent light Fourier analysis program showed the following: (1) for agricultural areas, bands 5 and 7 of the MSS are superior in terms of image definition, and therefore mapping and acreage estimation, (2) amplitude modulation in imagery from MSS bands 4 and 5 is between 65 to 90 percent of that in corresponding bands of Apollo 9 imagery (SO65), and (3) MSS band 5 imagery has a ground resolution between 55 to 75 percent of that exhibited in the corresponding band of Apollo 9 imagery (SO65).
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Clustering of color map pixels: an interactive approach
NASA Astrophysics Data System (ADS)
Moon, Yiu Sang; Luk, Franklin T.; Yuen, K. N.; Yeung, Hoi Wo
2003-12-01
The demand for digital maps continues to arise as mobile electronic devices become more popular nowadays. Instead of creating the entire map from void, we may convert a scanned paper map into a digital one. Color clustering is the very first step of the conversion process. Currently, most of the existing clustering algorithms are fully automatic. They are fast and efficient but may not work well in map conversion because of the numerous ambiguous issues associated with printed maps. Here we introduce two interactive approaches for color clustering on the map: color clustering with pre-calculated index colors (PCIC) and color clustering with pre-calculated color ranges (PCCR). We also introduce a memory model that could enhance and integrate different image processing techniques for fine-tuning the clustering results. Problems and examples of the algorithms are discussed in the paper.
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Occupancy change detection system and method
Bruemmer, David J [Idaho Falls, ID; Few, Douglas A [Idaho Falls, ID
2009-09-01
A robot platform includes perceptors, locomotors, and a system controller. The system controller executes instructions for producing an occupancy grid map of an environment around the robot, scanning the environment to generate a current obstacle map relative to a current robot position, and converting the current obstacle map to a current occupancy grid map. The instructions also include processing each grid cell in the occupancy grid map. Within the processing of each grid cell, the instructions include comparing each grid cell in the occupancy grid map to a corresponding grid cell in the current occupancy grid map. For grid cells with a difference, the instructions include defining a change vector for each changed grid cell, wherein the change vector includes a direction from the robot to the changed grid cell and a range from the robot to the changed grid cell.
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Digital Archives - Thomas M. Bown's Bighorn Basin Maps: The Suite of Forty-Four Office Master Copies
McKinney, Kevin C.
2001-01-01
This CD-ROM is a digitally scanned suite of master 'locality' maps produced by Dr. Thomas M. Bown. The maps are archived in the US Geological Survey Field Records. The maps feature annual compilations of newly established fossil (nineteen 7.5 degree maps) of central basin data collections. This master suite of forty-four maps represents a considerably broader geographic range within the basin. Additionally, three field seasons of data were compiled into the master suite of maps after the final editing of the Professional Paper. These maps are the culmination of Dr. Bown's Bighorn Basin research as a vertebrate paleontologist for the USGS. Data include Yale, Wyoming, Duke, Michigan and USGS localities. Practical topographic features are also indicated, such as jeep=trail access, new reservoirs, rerouted roadbeds, measured sections, fossil reconnaissance evaluations (G=good, NG=no good and H=hideous), faults, palcosol stages, and occasionally 'camp' vernacular for locality names.
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Farber, Joshua M; Totterman, Saara M S; Martinez-Torteya, Antonio; Tamez-Peña, Jose G
2016-02-01
Subchondral bone (SCB) undergoes changes in the shape of the articulating bone surfaces and is currently recognized as a key target in osteoarthritis (OA) treatment. The aim of this study was to present an automated system that determines the curvature of the SCB regions of the knee and to evaluate its cross-sectional and longitudinal scan-rescan precision Six subjects with OA and six control subjects were selected from the Osteoarthritis Initiative (OAI) pilot study database. As per OAI protocol, these subjects underwent 3T MRI at baseline and every twelve months thereafter, including a 3D DESS WE sequence. We analyzed the baseline and twenty-four month images. Each subject was scanned twice at these visits, thus generating scan-rescan information. Images were segmented with an automated multi-atlas framework platform and then 3D renderings of the bone structure were created from the segmentations. Curvature maps were extracted from the 3D renderings and morphed into a reference atlas to determine precision, to generate population statistics, and to visualize cross-sectional and longitudinal curvature changes. The baseline scan-rescan root mean square error values ranged from 0.006mm(-1) to 0.013mm(-1), and from 0.007mm(-1) to 0.018mm(-1) for the SCB of the femur and the tibia, respectively. The standardized response of the mean of the longitudinal changes in curvature in these regions ranged from -0.09 to 0.02 and from -0.016 to 0.015, respectively. The fully automated system produces accurate and precise curvature maps of femoral and tibial SCB, and will provide a valuable tool for the analysis of the curvature changes of articulating bone surfaces during the course of knee OA. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Mechanical Twinning and Microstructures in Experimentally Stressed Quartzite
NASA Astrophysics Data System (ADS)
Minor, A.; Sintubin, M.; Wenk, H. R.; Rybacki, E.
2015-12-01
Since Dauphiné twins in quartz have been identified as a stress-related intracrystalline microstructure, several electron backscatter diffraction (EBSD) studies revealed that Dauphiné twins are present in naturally deformed quartz-bearing rocks in a wide range of tectono-metamorphic conditions. EBSD studies on experimentally stressed quartzite showed that crystals with particular crystallographic orientations contain many Dauphiné twin boundaries, while neighboring crystals with different orientations are largely free of twin boundaries. To understand the relationship between stress direction and orientation of Dauphiné twinned quartz crystals, a detailed EBSD study was performed on experimentally stressed quartzite samples and compared with an undeformed reference sample. We stressed 4 cylindrical samples in triaxial compression in a Paterson type gas deformation apparatus at GFZ Potsdam. Experimental conditions were 300MPa confining pressure, 500°C temperature and axial stresses of 145MPa, 250MPa and 460MPa for about 30 hours, resulting in a minor strain <0.04%. EBSD scans were obtained with a Zeiss Evo scanning electron microscope and TSL software at UC Berkeley. The EBSD maps show that Dauphiné twinning is present in the starting material as well as in experimentally stressed samples. Pole figures of the bulk orientation of the reference sample compared with stressed samples show a significant difference regarding the distribution for the r and z directions. The reference sample shows an indistinct maximum for r and z, whereas the stressed samples show a maximum for r poles and a minimum for z poles in the axial stress direction. EBSD scans of the reference and stressed samples were further analyzed manually to identify the orientations of single grains, which are free of twin boundaries and those, which contain twin boundaries. This analysis aims to quantify the relationship of crystal orientation and stress magnitude to initiate mechanical twinning.
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2013-01-01
Background Cardiovascular magnetic resonance (CMR) T1 mapping indices, such as T1 time and partition coefficient (λ), have shown potential to assess diffuse myocardial fibrosis. The purpose of this study was to investigate how scanner and field strength variation affect the accuracy and precision/reproducibility of T1 mapping indices. Methods CMR studies were performed on two 1.5T and three 3T scanners. Eight phantoms were made to mimic the T1/T2 of pre- and post-contrast myocardium and blood at 1.5T and 3T. T1 mapping using MOLLI was performed with simulated heart rate of 40-100 bpm. Inversion recovery spin echo (IR-SE) was the reference standard for T1 determination. Accuracy was defined as the percent error between MOLLI and IR-SE, and scan/re-scan reproducibility was defined as the relative percent mean difference between repeat MOLLI scans. Partition coefficient was estimated by ΔR1myocardium phantom/ΔR1blood phantom. Generalized linear mixed model was used to compare the accuracy and precision/reproducibility of T1 and λ across field strength, scanners, and protocols. Results Field strength significantly affected MOLLI T1 accuracy (6.3% error for 1.5T vs. 10.8% error for 3T, p<0.001) but not λ accuracy (8.8% error for 1.5T vs. 8.0% error for 3T, p=0.11). Partition coefficients of MOLLI were not different between two 1.5T scanners (47.2% vs. 47.9%, p=0.13), and showed only slight variation across three 3T scanners (49.2% vs. 49.8% vs. 49.9%, p=0.016). Partition coefficient also had significantly lower percent error for precision (better scan/re-scan reproducibility) than measurement of individual T1 values (3.6% for λ vs. 4.3%-4.8% for T1 values, approximately, for pre/post blood and myocardium values). Conclusion Based on phantom studies, T1 errors using MOLLI ranged from 6-14% across various MR scanners while errors for partition coefficient were less (6-10%). Compared with absolute T1 times, partition coefficient showed less variability across platforms and field strengths as well as higher precision. PMID:23890156
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Optimising EEG-fMRI for Localisation of Focal Epilepsy in Children.
Centeno, Maria; Tierney, Tim M; Perani, Suejen; Shamshiri, Elhum A; StPier, Kelly; Wilkinson, Charlotte; Konn, Daniel; Banks, Tina; Vulliemoz, Serge; Lemieux, Louis; Pressler, Ronit M; Clark, Christopher A; Cross, J Helen; Carmichael, David W
2016-01-01
Early surgical intervention in children with drug resistant epilepsy has benefits but requires using tolerable and minimally invasive tests. EEG-fMRI studies have demonstrated good sensitivity for the localization of epileptic focus but a poor yield although the reasons for this have not been systematically addressed. While adults EEG-fMRI studies are performed in the "resting state"; children are commonly sedated however, this has associated risks and potential confounds. In this study, we assessed the impact of the following factors on the tolerability and results of EEG-fMRI in children: viewing a movie inside the scanner; movement; occurrence of interictal epileptiform discharges (IED); scan duration and design efficiency. This work's motivation is to optimize EEG-fMRI parameters to make this test widely available to paediatric population. Forty-six children with focal epilepsy and 20 controls (6-18) underwent EEG-fMRI. For two 10 minutes sessions subjects were told to lie still with eyes closed, as it is classically performed in adult studies ("rest sessions"), for another two sessions, subjects watched a child friendly stimulation i.e. movie ("movie sessions"). IED were mapped with EEG-fMRI for each session and across sessions. The resulting maps were classified as concordant/discordant with the presumed epileptogenic focus for each subject. Movement increased with scan duration, but the movie reduced movement by ~40% when played within the first 20 minutes. There was no effect of movie on the occurrence of IED, nor in the concordance of the test. Ability of EEG-fMRI to map the epileptogenic region was similar for the 20 and 40 minute scan durations. Design efficiency was predictive of concordance. A child friendly natural stimulus improves the tolerability of EEG-fMRI and reduces in-scanner movement without having an effect on IED occurrence and quality of EEG-fMRI maps. This allowed us to scan children as young as 6 and obtain localising information without sedation. Our data suggest that ~20 minutes is the optimal length of scanning for EEG-fMRI studies in children with frequent IED. The efficiency of the fMRI design derived from spontaneous IED generation is an important factor for producing concordant results.
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NASA Astrophysics Data System (ADS)
Meijs, M.; Debats, O.; Huisman, H.
2015-03-01
In prostate cancer, the detection of metastatic lymph nodes indicates progression from localized disease to metastasized cancer. The detection of positive lymph nodes is, however, a complex and time consuming task for experienced radiologists. Assistance of a two-stage Computer-Aided Detection (CAD) system in MR Lymphography (MRL) is not yet feasible due to the large number of false positives in the first stage of the system. By introducing a multi-structure, multi-atlas segmentation, using an affine transformation followed by a B-spline transformation for registration, the organ location is given by a mean density probability map. The atlas segmentation is semi-automatically drawn with ITK-SNAP, using Active Contour Segmentation. Each anatomic structure is identified by a label number. Registration is performed using Elastix, using Mutual Information and an Adaptive Stochastic Gradient optimization. The dataset consists of the MRL scans of ten patients, with lymph nodes manually annotated in consensus by two expert readers. The feature map of the CAD system consists of the Multi-Atlas and various other features (e.g. Normalized Intensity and multi-scale Blobness). The voxel-based Gentleboost classifier is evaluated using ROC analysis with cross validation. We show in a set of 10 studies that adding multi-structure, multi-atlas anatomical structure likelihood features improves the quality of the lymph node voxel likelihood map. Multiple structure anatomy maps may thus make MRL CAD more feasible.
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Schmid, Gregor; Zeitvogel, Fabian; Hao, Likai; Ingino, Pablo; Adaktylou, Irini; Eickhoff, Merle; Obst, Martin
2016-01-05
Fe(II)-oxidizing bacteria form biogenic cell-mineral aggregates (CMAs) composed of microbial cells, extracellular organic compounds, and ferric iron minerals. CMAs are capable of immobilizing large quantities of heavy metals, such as nickel, via sorption processes. CMAs play an important role for the fate of heavy metals in the environment, particularly in systems characterized by elevated concentrations of dissolved metals, such as mine drainage or contaminated sediments. We applied scanning transmission (soft) X-ray microscopy (STXM) spectrotomography for detailed 3D chemical mapping of nickel sorbed to CMAs on the submicron scale. We analyzed different CMAs produced by phototrophic or nitrate-reducing microbial Fe(II) oxidation and, in addition, a twisted stalk structure obtained from an environmental biofilm. Nickel showed a heterogeneous distribution and was found to be preferentially sorbed to biogenically precipitated iron minerals such as Fe(III)-(oxyhydr)oxides and, to a minor extent, associated with organic compounds. Some distinct nickel accumulations were identified on the surfaces of CMAs. Additional information obtained from scatter plots and angular distance maps, showing variations in the nickel-iron and nickel-organic carbon ratios, also revealed a general correlation between nickel and iron. Although a high correlation between nickel and iron was observed in 2D maps, 3D maps revealed this to be partly due to projection artifacts. In summary, by combining different approaches for data analysis, we unambiguously showed the heterogeneous sorption behavior of nickel to CMAs.