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High-density 3D mapping

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https://www.readbyqxmd.com/read/29196268/developing-3d-microscopy-with-clarity-on-human-brain-tissue-towards-a-tool-for-informing-and-validating-mri-based-histology
#1
Markus Morawski, Evgeniya Kirilina, Nico Scherf, Carsten Jäger, Katja Reimann, Robert Trampel, Filippos Gavriilidis, Stefan Geyer, Bernd Biedermann, Thomas Arendt, Nikolaus Weiskopf
Recent breakthroughs in magnetic resonance imaging (MRI) enabled quantitative relaxometry and diffusion-weighted imaging with sub-millimeter resolution. Combined with biophysical models of MR contrast the emerging methods promise in vivo mapping of cyto- and myelo-architectonics, i.e., in vivo histology using MRI (hMRI) in humans. The hMRI methods require histological reference data for model building and validation. This is currently provided by MRI on post mortem human brain tissue in combination with classical histology on sections...
November 28, 2017: NeuroImage
https://www.readbyqxmd.com/read/29169344/genome-wide-association-mapping-of-black-point-reaction-in-common-wheat-triticum-aestivum-l
#2
Jindong Liu, Zhonghu He, Awais Rasheed, Weie Wen, Jun Yan, Pingzhi Zhang, Yingxiu Wan, Yong Zhang, Chaojie Xie, Xianchun Xia
BACKGROUND: Black point is a serious threat to wheat production and can be managed by host resistance. Marker-assisted selection (MAS) has the potential to accelerate genetic improvement of black point resistance in wheat breeding. We performed a genome-wide association study (GWAS) using the high-density wheat 90 K and 660 K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of black point resistance and identify associated molecular markers. RESULTS: Black point reactions were evaluated in 166 elite wheat cultivars in five environments...
November 23, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29163559/genome-wide-association-study-of-calcium-accumulation-in-grains-of-european-wheat-cultivars
#3
Dalia Z Alomari, Kai Eggert, Nicolaus von Wirén, Klaus Pillen, Marion S Röder
Mineral concentrations in cereals are important for human health, especially for people who depend mainly on consuming cereal diet. In this study, we carried out a genome-wide association study (GWAS) of calcium concentrations in wheat (Triticum aestivum L.) grains using a European wheat diversity panel of 353 varieties [339 winter wheat (WW) plus 14 of spring wheat (SW)] and phenotypic data based on two field seasons. High genotyping densities of single-nucleotide polymorphism (SNP) markers were obtained from the application of the 90k iSELECT ILLUMINA chip and a 35k Affymetrix chip...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29067730/simultaneous-qsm-and-metabolic-imaging-of-the-brain-using-spice
#4
Xi Peng, Fan Lam, Yudu Li, Bryan Clifford, Zhi-Pei Liang
PURPOSE: To map brain metabolites and tissue magnetic susceptibility simultaneously using a single three-dimensional (1) H-MRSI acquisition without water suppression. METHODS: The proposed technique builds on a subspace imaging method called spectroscopic imaging by exploiting spatiospectral correlation (SPICE), which enables ultrashort echo time (TE)/short pulse repetition time (TR) acquisitions for (1) H-MRSI without water suppression. This data acquisition scheme simultaneously captures both the spectral information of brain metabolites and the phase information of the water signals that is directly related to tissue magnetic susceptibility variations...
October 24, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/29043295/three-dimensional-supercritical-resolved-light-induced-magnetic-holography
#5
Chenglong Hao, Zhongquan Nie, Huapeng Ye, Hao Li, Yang Luo, Rui Feng, Xia Yu, Feng Wen, Ying Zhang, Changyuan Yu, Jinghua Teng, Boris Luk'yanchuk, Cheng-Wei Qiu
In the era of big data, there exists a growing gap between data generated and storage capacity using two-dimensional (2D) magnetic storage technologies (for example, hard disk drives), because they have reached their performance saturation. 3D volumetric all-optical magnetic holography is emerging rapidly as a promising road map to realizing high-density capacity for its fast magnetization control and subwavelength magnetization volume. However, most of the reported light-induced magnetization confronts the problems of impurely longitudinal magnetization, diffraction-limited spot, and uncontrollable magnetization reversal...
October 2017: Science Advances
https://www.readbyqxmd.com/read/29024200/novel-automated-point-collection-software-facilitates-rapid-high-density-electroanatomical-mapping-with-multiple-catheter-types
#6
Leon M Ptaszek, Boyce Moon, Guy Rozen, Srijoy Mahapatra, Moussa Mansour
INTRODUCTION: Manual, point-by-point electroanatomical mapping requires the operator to directly evaluate each point during map construction. Consequently, point collection can be a slow process. An automated 3D mapping system was developed with the goal of improving key mapping metrics, including map completion time and point density. METHODS: Automated 3D mapping software that includes morphology and cycle length discrimination functions for surface and intracardiac electrograms was developed...
October 12, 2017: Journal of Cardiovascular Electrophysiology
https://www.readbyqxmd.com/read/28889004/quantitative-vascular-neuroimaging-of-the-rat-brain-using-superparamagnetic-nanoparticles-new-insights-on-vascular-organization-and-brain-function
#7
Codi A Gharagouzloo, Liam Timms, Ju Qiao, Zihang Fang, Joseph Nneji, Aniket Pandya, Praveen Kulkarni, Anne L van de Ven, Craig Ferris, Srinivas Sridhar
A method called Quantitative Ultra-Short Time-to-Echo Contrast Enhanced (QUTE-CE) Magnetic Resonance Imaging (MRI) which utilizes superparamagnetic iron oxide nanoparticles (SPIONs) as a contrast agent to yield positive contrast angiograms with high clarity and definition is applied to the whole live rat brain. QUTE-CE MRI intensity data are particularly well suited for measuring quantitative cerebral blood volume (qCBV). A global map of qCBV in the awake resting-state with unprecedented detail was created via application of a 3D MRI rat brain atlas with 173 segmented and annotated brain areas...
September 6, 2017: NeuroImage
https://www.readbyqxmd.com/read/28885152/multimodal-breast-parenchymal-patterns-correlation-using-a-patient-specific-biomechanical-model
#8
Eloy Garcia, Yago Diez, Oliver Diaz, Xavier Llado, Albert Gubern-Merida, Robert Marti, Joan Marti, Arnau Oliver
In this paper we aim to produce a realistic 2D projection of the breast parenchymal distribution from a 3D breast magnetic resonance image (MRI). To evaluate the accuracy of our simulation, we compare our results with the local breast density (i.e. density map) obtained from the complementary fullfield digital mammogram. To achieve this goal, we have developed a fully automatic framework which registers MRI volumes to X-ray mammograms using a subject-specific biomechanical model of the breast. The optimization step modifies the position, orientation and elastic parameters of the breast model to perform the alignment between the images...
September 7, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28842384/3d-mr-fingerprinting-with-accelerated-stack-of-spirals-and-hybrid-sliding-window-and-grappa-reconstruction
#9
Congyu Liao, Berkin Bilgic, Mary Kate Manhard, Bo Zhao, Xiaozhi Cao, Jianhui Zhong, Lawrence L Wald, Kawin Setsompop
PURPOSE: Whole-brain high-resolution quantitative imaging is extremely encoding intensive, and its rapid and robust acquisition remains a challenge. Here we present a 3D MR fingerprinting (MRF) acquisition with a hybrid sliding-window (SW) and GRAPPA reconstruction strategy to obtain high-resolution T1, T2 and proton density (PD) maps with whole brain coverage in a clinically feasible timeframe. METHODS: 3D MRF data were acquired using a highly under-sampled stack-of-spirals trajectory with a steady-state precession (FISP) sequence...
August 24, 2017: NeuroImage
https://www.readbyqxmd.com/read/28833436/fast-3d-magnetic-resonance-fingerprinting-for-a-whole-brain-coverage
#10
Dan Ma, Yun Jiang, Yong Chen, Debra McGivney, Bhairav Mehta, Vikas Gulani, Mark Griswold
PURPOSE: The purpose of this study was to accelerate the acquisition and reconstruction time of 3D magnetic resonance fingerprinting scans. METHODS: A 3D magnetic resonance fingerprinting scan was accelerated by using a single-shot spiral trajectory with an undersampling factor of 48 in the x-y plane, and an interleaved sampling pattern with an undersampling factor of 3 through plane. Further acceleration came from reducing the waiting time between neighboring partitions...
August 22, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28821300/t1-refblochi-high-resolution-3d-post-contrast-t1-myocardial-mapping-based-on-a-single-3d-late-gadolinium-enhancement-volume-bloch-equations-and-a-reference-t1
#11
Chenxi Hu, Albert J Sinusas, Steffen Huber, Stephanie Thorn, Mitchel R Stacy, Hamid Mojibian, Dana C Peters
BACKGROUND: High resolution 3D T1 mapping is important for assessment of diffuse myocardial fibrosis in left atrium or other thin-walled structures. In this work, we investigated a fast single-TI 3D high resolution T1 mapping method that directly transforms a 3D late gadolinium enhancement (LGE) volume to a 3D T1 map. METHODS: The proposed method, T1-refBlochi, is based on Bloch equation modeling of the LGE signal, a single-point calibration, and assumptions that proton density and T2* are relatively uniform in the heart...
August 18, 2017: Journal of Cardiovascular Magnetic Resonance
https://www.readbyqxmd.com/read/28776822/ripple-mapping-initial-multicenter-experience-of-an-intuitive-approach-to-overcoming-the-limitations-of-3d-activation-mapping
#12
Vishal Luther, Nuno Cortez-Dias, Luís Carpinteiro, João de Sousa, Richard Balasubramaniam, Sharad Agarwal, David Farwell, Mark Sopher, Girish Babu, Richard Till, Nikki Jones, Stuart Tan, Anthony Chow, Martin Lowe, Jem Lane, Naveen Pappachan, Nicholas Linton, Prapa Kanagaratnam
BACKGROUND: Ripple mapping (RM) displays electrograms as moving bars over a three-dimensional surface displaying bipolar voltage, and has shown in a single-center series to be effective for atrial tachycardia (AT) mapping without annotation of local activation time or window-of-interest assignment. We tested the reproducibility of these findings in operators naïve to RM, using it for the first time in postablation AT. METHODS: Maps were collected with multielectrode catheters and CARTO ConfiDENSE...
November 2017: Journal of Cardiovascular Electrophysiology
https://www.readbyqxmd.com/read/28740215/quantitative-analysis-of-3d-alignment-quality-its-impact-on-soft-validation-particle-pruning-and-homogeneity-analysis
#13
J Vargas, R Melero, J Gómez-Blanco, J M Carazo, C O S Sorzano
Single Particle Analysis using cryo-electron microscopy is a structural biology technique aimed at capturing the three-dimensional (3D) conformation of biological macromolecules. Projection images used to construct the 3D density map are characterized by a very low signal-to-noise ratio to minimize radiation damage in the samples. As a consequence, the 3D image alignment process is a challenging and error prone task which usually determines the success or failure of obtaining a high quality map. In this work, we present an approach able to quantify the alignment precision and accuracy of the 3D alignment process, which is then being used to help the reconstruction process in a number of ways, such as: (1) Providing quality indicators of the macromolecular map for soft validation, (2) Assessing the degree of homogeneity of the sample and, (3), Selecting subsets of representative images...
July 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28735424/a-novel-3d-anatomic-mapping-approach-using-multipoint-high-density-voltage-gradient-mapping-to-quickly-localize-and-terminate-typical-atrial-flutter
#14
William C Choe, Sri Sundaram, J Ryan Jordan, Nate Mullins, Charles Boorman, Austin Davies, Alex C Tiftickjian, Sunil Nath
PURPOSE: The purposes of the study were to evaluate and characterize the cavotricuspid isthmus using multipoint high density voltage gradient mapping (HD-VGM) to see if this would improve on current ablation techniques compared to standard cavotricuspid isthmus ablation techniques. METHODS: Group 1, 25 patients who underwent ablation using standard methods of 3D mapping and ablation, was compared to group 2, 33 patients undergoing ablation using HD-VGM and ablation...
September 2017: Journal of Interventional Cardiac Electrophysiology: An International Journal of Arrhythmias and Pacing
https://www.readbyqxmd.com/read/28724077/physical-map-of-the-short-arm-of-bread-wheat-chromosome-3d
#15
Kateřina Holušová, Jan Vrána, Jan Šafář, Hana Šimková, Barbora Balcárková, Zeev Frenkel, Benoit Darrier, Etienne Paux, Federica Cattonaro, Helene Berges, Thomas Letellier, Michael Alaux, Jaroslav Doležel, Jan Bartoš
Bread wheat ( L.) is one of the most important crops worldwide. Although a reference genome sequence would represent a valuable resource for wheat improvement through genomics-assisted breeding and gene cloning, its generation has long been hampered by its allohexaploidy, high repeat content, and large size. As a part of a project coordinated by the International Wheat Genome Sequencing Consortium (IWGSC), a physical map of the short arm of wheat chromosome 3D (3DS) was prepared to facilitate reference genome assembly and positional gene cloning...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28710774/ucsf-chimerax-meeting-modern-challenges-in-visualization-and-analysis
#16
Thomas D Goddard, Conrad C Huang, Elaine C Meng, Eric F Pettersen, Gregory S Couch, John H Morris, Thomas E Ferrin
UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This paper highlights some specific advances in the areas of visualization and usability, performance, and extensibility...
July 14, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28708060/synem-automated-synapse-detection-for-connectomics
#17
Benedikt Staffler, Manuel Berning, Kevin M Boergens, Anjali Gour, Patrick van der Smagt, Moritz Helmstaedter
Nerve tissue contains a high density of chemical synapses, about 1 per µm(3) in the mammalian cerebral cortex. Thus, even for small blocks of nerve tissue, dense connectomic mapping requires the identification of millions to billions of synapses. While the focus of connectomic data analysis has been on neurite reconstruction, synapse detection becomes limiting when datasets grow in size and dense mapping is required. Here, we report SynEM, a method for automated detection of synapses from conventionally en-bloc stained 3D electron microscopy image stacks...
July 14, 2017: ELife
https://www.readbyqxmd.com/read/28664343/catheter-ablation-of-atypical-atrial-flutter-a-novel-3d-anatomic-mapping-approach-to-quickly-localize-and-terminate-atypical-atrial-flutter
#18
Sri Sundaram, William Choe, J Ryan Jordan, Nate Mullins, Charles Boorman, Eric J Kessler, Sunil Nath
PURPOSE: This study aims to describe a novel method of High Density Activation Sequence Mapping combined with Voltage Gradient Mapping Overlay (HD-VGM) to quickly localize and terminate atypical atrial flutter. METHODS: Twenty-one patients presenting with 26 different atypical atrial flutter circuits after a previous catheter or surgical AF ablation were studied. HD-VGM was performed with a commercially available impedance-based mapping system to locate and successfully ablate the critical isthmus of each tachycardia circuit...
September 2017: Journal of Interventional Cardiac Electrophysiology: An International Journal of Arrhythmias and Pacing
https://www.readbyqxmd.com/read/28636340/three-dimensional-modeling-of-quasicrystal-structures-from-x-ray-diffraction-an-icosahedral-al-cu-fe-alloy
#19
Seung-Tae Hong
Quasicrystals (QCs) are well-ordered but aperiodic crystals with classically forbidden symmetries (such as 5-fold). High-dimensional (HD) crystallography is a standard method to locate atom positions explicitly. However, in practice, it is still challenging because of its complexity. Here, we report a new simple approach to three-dimensional (3D) atomic modeling derived from X-ray diffraction data, and apply it to the icosahedral QC Al0.63Cu0.25Fe0.12. Electron density maps were calculated directly from 3D diffraction data indexed with noninteger (fractional) numbers as measured, with proper phases; each of 2(5) = 32 possible phase assignments for the five strongest reflections was used for Fourier synthesis...
June 21, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28636001/wataa-atlas-of-protein-hydration-exploring-synergies-between-data-mining-and-ab-initio-calculations
#20
Jiří Černý, Bohdan Schneider, Lada Biedermannová
Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
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