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https://www.readbyqxmd.com/read/28710774/ucsf-chimerax-meeting-modern-challenges-in-visualization-and-analysis
#1
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
#2
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
#3
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...
June 29, 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
#4
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
#5
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
https://www.readbyqxmd.com/read/28625927/entrainment-and-high-density-three-dimensional-mapping-in-right-atrial-macroreentry-provide-critical-complementary-information-entrainment-may-unmask-visual-reentry-as-passive
#6
Bhupesh Pathik, Geoffrey Lee, Chrishan Nalliah, Stephen Joseph, Joseph B Morton, Paul B Sparks, Prashanthan Sanders, Peter M Kistler, Jonathan M Kalman
BACKGROUND: With the recent advent of high-density (HD) 3-dimensional (3D) mapping, the utility of entrainment is uncertain. However, the limitations of visual representation and interpretation of these high-resolution 3D maps are unclear. OBJECTIVE: The purpose of this study was to determine the strengths and limitations of both HD 3D mapping and entrainment mapping during mapping of right atrial macroreentry. METHODS: Fifteen patients were studied...
June 16, 2017: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/28597532/substrate-characterization-and-catheter-ablation-in-patients-with-scar-related-ventricular-tachycardia-using-ultra-high-density-3d-mapping
#7
Jana M Nührich, Lukas Kaiser, Ruken Özge Akbulak, Benjamin N Schäffer, Christian Eickholt, Michael Schwarzl, Pawel Kuklik, Julia Moser, Mario Jularic, Stephan Willems, Christian Meyer
BACKGROUND: Ablation of scar-related ventricular tachycardia (VT), especially in non-inducible VT or hemodynamically unstable patients, can be challenging. Thus, we evaluated feasibility of an ultra high-density 3D-mapping approach to characterize the ventricular substrate and, if possible, to map VT. METHODS AND RESULTS: Twenty-two patients (67±2 years, mean LV-EF 36±3%) with both ischemic and non-ischemic cardiomyopathy and documented VT underwent mapping and catheter ablation using a 64-electrode mini-basket catheter...
June 8, 2017: Journal of Cardiovascular Electrophysiology
https://www.readbyqxmd.com/read/28580758/nuclei-specific-deposits-of-iron-and-calcium-in-the-rat-thalamus-after-status-epilepticus-revealed-with-quantitative-susceptibility-mapping-qsm
#8
Manisha Aggarwal, Xu Li, Olli Gröhn, Alejandra Sierra
PURPOSE: To investigate pathological changes in the rat brain after pilocarpine-induced status epilepticus using quantitative susceptibility mapping (QSM). MATERIALS AND METHODS: 3D multiecho gradient-echo (GRE) data were acquired from ex vivo brains of pilocarpine-injected and age-matched control rats at 11.7T. Maps of R2* and quantitative susceptibility were calculated from the acquired 3D GRE magnitude and phase data, respectively. QSM and R2* maps were compared with Perls' (iron) and Alizarin-red-S (calcium) stainings in the same brains to investigate the pathophysiological basis of susceptibility contrast...
June 5, 2017: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/28514687/particulate-array-of-well-ordered-hiv-clade-c-env-trimers-elicits-neutralizing-antibodies-that-display-a-unique-v2-cap-approach
#9
Paola Martinez-Murillo, Karen Tran, Javier Guenaga, Gustaf Lindgren, Monika Àdori, Yu Feng, Ganesh E Phad, Néstor Vázquez Bernat, Shridhar Bale, Jidnyasa Ingale, Viktoriya Dubrovskaya, Sijy O'Dell, Lotta Pramanik, Mats Spångberg, Martin Corcoran, Karin Loré, John R Mascola, Richard T Wyatt, Gunilla B Karlsson Hedestam
The development of soluble envelope glycoprotein (Env) mimetics displaying ordered trimeric symmetry has ushered in a new era in HIV-1 vaccination. The recently reported native, flexibly linked (NFL) design allows the generation of native-like trimers from clinical isolates at high yields and homogeneity. As the majority of infections world-wide are of the clade C subtype, we examined responses in non-human primates to well-ordered subtype C 16055 trimers administered in soluble or high-density liposomal formats...
May 16, 2017: Immunity
https://www.readbyqxmd.com/read/28482032/structure-and-conformational-dynamics-of-scaffolded-dna-origami-nanoparticles
#10
Keyao Pan, William P Bricker, Sakul Ratanalert, Mark Bathe
Synthetic DNA is a highly programmable nanoscale material that can be designed to self-assemble into 3D structures that are fully determined by underlying Watson-Crick base pairing. The double crossover (DX) design motif has demonstrated versatility in synthesizing arbitrary DNA nanoparticles on the 5-100 nm scale for diverse applications in biotechnology. Prior computational investigations of these assemblies include all-atom and coarse-grained modeling, but modeling their conformational dynamics remains challenging due to their long relaxation times and associated computational cost...
May 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28479513/epicardial-endocardial-breakthrough-during-stable-atrial-macroreentry-evidence-from-ultra-high-resolution-3-dimensional-mapping
#11
Bhupesh Pathik, Geoffrey Lee, Frédéric Sacher, Michel Haïssaguerre, Pierre Jaïs, Grégoire Massoullié, Nicolas Derval, Prashanthan Sanders, Peter Kistler, Jonathan M Kalman
BACKGROUND: Evidence for epicardial-endocardial breakthrough (EEB) is derived from mapping inferences in patients with atrial fibrillation who may also have focal activations. OBJECTIVE: The purpose of this study was to investigate whether EEB could be discerned during stable right atrial (RA) macroreentry using high-density high-spatial resolution 3-dimensional mapping. METHODS: Macroreentry was diagnosed using 3-dimensional mapping and entrainment...
May 4, 2017: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/28463257/high-precision-real-time-3d-shape-measurement-using-a-bi-frequency-scheme-and-multi-view-system
#12
Tianyang Tao, Qian Chen, Shijie Feng, Yan Hu, Jian Da, Chao Zuo
High-speed and high-precision 3D shape measurement plays a central role in diverse applications such as automatic online inspection, robotics control, and human-computer interaction. Conventional multi-frame phase-shifting-based fringe projection profilometry techniques face inherent trade-offs between the speed and measurement precision, which are fundamentally limited by the fringe density and extra pattern projections used for de-ambiguity of fringe orders. Increasing the frequency of the projection fringes can obviously improve the measurement precision; however, it creates difficulties in the subsequent phase unwrapping...
May 1, 2017: Applied Optics
https://www.readbyqxmd.com/read/28463188/tumor-cell-load-and-heterogeneity-estimation-from-diffusion-weighted-mri-calibrated-with-histological-data-an-example-from-lung-cancer
#13
Yi Yin, Oliver Sedlaczek, Benedikt Muller, Arne Warth, Margarita Gonzalez-Vallinas, Niels Grabe, Hans-Ulrich Kauczor, Kai Breuhahn, Irene Vignon-Clemental, Dirk Drasdo
Diffusion-weighted magnetic resonance imaging (DWI) is a key non-invasive imaging technique for cancer diagnosis and tumor treatment assessment, reflecting Brownian movement of water molecules in tissues. Since densely packed cells restrict molecule mobility, tumor tissues produce usually higher signal (a.k.a less attenuated signal) on isotropic maps compared to normal tissues. However, no general quantitative relation between DWI data and the cell density has been established. In order to link low-resolution clinical cross-sectional data with high-resolution histological information, we developed an image processing and analysis chain, which was used to study the correlation between the diffusion coefficient (D value) estimated from DWI and tumor cellularity from serial histological slides of a resected non-small cell lung cancer (NSCLC) tumor...
April 27, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28460192/proton-density-fat-fraction-of-rotator-cuff-muscles-is-associated-with-isometric-strength-10-years-after-rotator-cuff-repair-a-quantitative-magnetic-resonance-imaging-study-of-the-shoulder
#14
Dimitrios C Karampinos, Christian Holwein, Stefan Buchmann, Thomas Baum, Stefan Ruschke, Alexandra S Gersing, Reto Sutter, Andreas B Imhoff, Ernst J Rummeny, Pia M Jungmann
BACKGROUND: Quantitative muscle fat-fraction magnetic resonance (MR) imaging techniques correlate with semiquantitative Goutallier scores with failure after rotator cuff (RC) repair. PURPOSE: To investigate the relationship of proton density fat fraction (PDFF) of the RC muscles with semiquantitative MR scores, cartilage T2 relaxation times, and clinical isometric strength measurements in patients 10 years after unilateral RC repair. STUDY DESIGN: Cross-sectional study; Level of evidence, 3...
April 1, 2017: American Journal of Sports Medicine
https://www.readbyqxmd.com/read/28436918/an-integrated-and-highly-sensitive-ultrafast-acoustoelectric-imaging-system-for-biomedical-applications
#15
Beatrice Berthon, Pierre-Marc Dansette, Mickael Tanter, Mathieu Pernot, Jean Provost
PURPOSE: Direct imaging of cardiac electrical activation is crucial to better understand and diagnose diseases linked to arrhythmias. This work presents an Ultrafast Acoustoelectric Imaging (UAI) system for direct and non-invasive ultrafast mapping of propagating current densities. MATERIALS AND METHODS: Acoustoelectric imaging is based on the acoustoelectric effect, the modulation of the medium's electrical impedance by a propagating ultrasonic wave. UAI triggers this effect with plane wave emissions to image current densities...
April 24, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28416035/measuring-the-autocorrelation-function-of-nanoscale-three-dimensional-density-distribution-in-individual-cells-using-scanning-transmission-electron-microscopy-atomic-force-microscopy-and-a-new-deconvolution-algorithm
#16
Yue Li, Di Zhang, Ilker Capoglu, Karl A Hujsak, Dhwanil Damania, Lusik Cherkezyan, Eric Roth, Reiner Bleher, Jinsong S Wu, Hariharan Subramanian, Vinayak P Dravid, Vadim Backman
Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass-density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass-density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction...
April 18, 2017: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/28410679/dual-energy-imaging-method-to-improve-the-image-quality-and-the-accuracy-of-dose-calculation-for-cone-beam-computed-tomography
#17
Kuo Men, Jianrong Dai, Xinyuan Chen, Minghui Li, Ke Zhang, Peng Huang
PURPOSE: To improve the image quality and accuracy of dose calculation for cone-beam computed tomography (CT) images through implementation of a dual-energy cone-beam computed tomography method (DE-CBCT), and evaluate the improvement quantitatively. METHODS: Two sets of CBCT projections were acquired using the X-ray volumetric imaging (XVI) system on a Synergy (Elekta, Stockholm, Sweden) system with 120kV (high) and 70kV (low) X-rays, respectively. Then, the electron density relative to water (relative electron density (RED)) of each voxel was calculated using a projection-based dual-energy decomposition method...
April 2017: Physica Medica: PM
https://www.readbyqxmd.com/read/28407062/voltage-gradient-mapping-and-electrophysiologically-guided-cryoablation-in-children-with-avnrt
#18
Fabrizio Drago, Irma Battipaglia, Mario Salvatore Russo, Romolo Remoli, Vincenzo Pazzano, Gino Grifoni, Greta Allegretti, Massimo Stefano Silvetti
Aims: Recently, voltage gradient mapping of Koch's triangle to find low-voltage connections, or 'voltage bridges', corresponding to the anatomic position of the slow pathway, has been introduced as a method to ablate atrioventricular nodal reentry tachycardia (AVNRT) in children. Thus, we aimed to assess the effectiveness of voltage mapping of Koch's triangle, combined with the search for the slow potential signal in 'low-voltage bridges', to guide cryoablation of AVNRT in children. Methods and results: From June 2015 to May 2016, 35 consecutive paediatric patients (mean age 12...
April 12, 2017: Europace: European Pacing, Arrhythmias, and Cardiac Electrophysiology
https://www.readbyqxmd.com/read/28401432/feasibility-assessment-of-a-maldi-fticr-imaging-approach-for-the-3d-reconstruction-of-a-mouse-lung
#19
E Ellen Jones, Cristine Quiason, Stephanie Dale, Sheerin K Shahidi-Latham
Matrix assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) has proven to be a quick, robust, and label-free tool to produce two-dimensional (2D) ion-density maps representing the distribution of a variety of analytes across a tissue section of interest. In addition, three-dimensional (3D) imaging mass spectrometry workflows have been developed that are capable of visualizing these same analytes throughout an entire volume of a tissue rather than a single cross-section. Until recently, the use of Fourier transform ion cyclotron resonance (FTICR) mass spectrometers for 3D volume reconstruction has been impractical due to software limitations, such as inadequate capacity to manipulate the extremely large data files produced during an imaging experiment...
August 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28388052/mapping-charge-distribution-in-single-pbs-core-cds-arm-nano-multipod-heterostructures-by-off-axis-electron-holography
#20
Rajesh Chalasani, Alexander Pekin, Alexander Rabkin, Ran E Abutbul, Oswaldo Diéguez, Yaron Kauffmann, Yuval Golan, Amit Kohn
We synthesized PbS core-CdS arm nanomultipod heterostructures (NMHs) that exhibit PbS{111}/CdS{0002} epitaxial relations. The PbS-CdS interface is chemically sharp as determined by aberration corrected transmission electron microscopy (TEM) and compared to density functional theory (DFT) calculations. Ensemble fluorescence measurements show quenching of the optical signal from the CdS arms indicating charge separation due to the heterojunction with PbS. A finite-element three-dimensional (3D) calculation of the Poisson equation shows a type-I heterojunction, which would prevent recombination in the CdS arm after optical excitation...
April 13, 2017: Nano Letters
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