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https://www.readbyqxmd.com/read/29793060/a-computational-framework-for-the-detection-of-subcortical-brain-dysmaturation-in-neonatal-mri-using-3d-convolutional-neural-networks
#1
Rafael Ceschin, Alexandria Zahner, William Reynolds, Jenna Gaesser, Giulio Zuccoli, Cecilia W Lo, Vanathi Gopalakrishnan, Ashok Panigrahy
Deep neural networks are increasingly being used in both supervised learning for classification tasks and unsupervised learning to derive complex patterns from the input data. However, the successful implementation of deep neural networks using neuroimaging datasets requires adequate sample size for training and well-defined signal intensity based structural differentiation. There is a lack of effective automated diagnostic tools for the reliable detection of brain dysmaturation in the neonatal period, related to small sample size and complex undifferentiated brain structures, despite both translational research and clinical importance...
May 21, 2018: NeuroImage
https://www.readbyqxmd.com/read/29791361/no-reference-stereoscopic-image-quality-assessment-based-on-hue-summation-difference-mapping-image-and-binocular-joint-mutual-filtering
#2
Jiachen Yang, Kyohoon Sim, Bin Jiang, Wen Lu
The no-reference (NR) quality assessment for stereoscopic images plays a significant role in 3D technology, but it also faces great challenges. In this paper, a novel NR stereo image quality assessment (SIQA) method is proposed. Based on the human visual system, this method mimics the summation and difference channels, which consider the binocular interactive perception property, to process the visual information. Especially, the summation and difference images are calculated by the contrast of hue and luminance in color patches...
May 10, 2018: Applied Optics
https://www.readbyqxmd.com/read/29786614/a-novel-optimization-framework-for-vmat-with-dynamic-gantry-couch-rotation
#3
Qihui Lyu, Victoria Y Yu, Dan Ruan, Ryan Neph, Daniel O'Connor, Ke Sheng
Existing Volumetric Modulated Arc Therapy (VMAT) optimization using coplanar arcs is highly efficient but usually dosimetrically inferior to intensity modulated radiation therapy (IMRT) with optimized non-coplanar beams. To achieve both dosimetric quality and delivery efficiency, we proposed in this study, a novel integrated optimization method for non-coplanar VMAT (4πVMAT). 4πVMAT with Direct Aperture Optimization (DAO) was achieved by utilizing a least square dose fidelity objective, along with an anisotropic total variation term for regularizing the fluence smoothness, a single segment term for imposing simple apertures, and a group sparsity term for selecting beam angles...
May 22, 2018: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/29785293/planning-and-marking-for-thoracoscopic-anatomical-segmentectomies
#4
Agathe Seguin-Givelet, Madalina Grigoroiu, Emmanuel Brian, Dominique Gossot
Although sublobar resection (SLR) for treating non-small cell lung carcinoma (NSCLC) is still controversial, thoracoscopic segmentectomy is rising. Performing it by closed chest surgery is complex as it means confirming the location of the lesion, identifying vascular and bronchial structures, preserving venous drainage of adjacent segments, severing the intersegmental plane and ensuring an oncological safety margin with no manual palpation and different landmarks. Accurate planning is mandatory. We discuss in this article the interest of 3D reconstruction and mapping technics to enhance safety and reliability of these procedures...
April 2018: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29784681/use-of-intracardiac-echocardiography-in-interventional-cardiology-working-with-the-anatomy-rather-than-fighting-it
#5
REVIEW
Andres Enriquez, Luis C Saenz, Raphael Rosso, Frank E Silvestry, David Callans, Francis E Marchlinski, Fermin Garcia
The indications for catheter-based structural and electrophysiological procedures have recently expanded to more complex scenarios, in which an accurate definition of the variable individual cardiac anatomy is key to obtain optimal results. Intracardiac echocardiography (ICE) is a unique imaging modality able to provide high-resolution real-time visualization of cardiac structures, continuous monitoring of catheter location within the heart, and early recognition of procedural complications, such as pericardial effusion or thrombus formation...
May 22, 2018: Circulation
https://www.readbyqxmd.com/read/29782796/resolution-measurement-from-a-single-reconstructed-cryo-em-density-map-with-multi-scale-spectral-analysis
#6
Yu-Jiao Yang, Shuai Wang, Biao Zhang, Hong-Bin Shen
As a relatively new technology to solve the 3D structure of a protein or protein complex, the Single-Particle Reconstruction (SPR) of cryo-EM images shows much superiority and is in a rapidly developing stage. Resolution measurement in SPR, which evaluates the quality of a reconstructed 3D density map, plays a critical role for promoting methodology development of SPR and structural biology. Due to there is no benchmark map in a new structure generation, how to realize the resolution estimation of a new map is still an open problem...
May 21, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29780855/magnetic-resonance-imaging-and-histopathological-visualization-of-human-dural-lymphatic-vessels
#7
Seung-Kwon Ha, Govind Nair, Martina Absinta, Nicholas J Luciano, Daniel S Reich
In this protocol, we describe a method to visualize and map dural lymphatic vessels in-vivo using magnetic resonance imaging (MRI) and ex-vivo using histopathological techniques. While MRI protocols for routine imaging of meningeal lymphatics include contrast-enhanced T2-FLAIR and T1- weighted black-blood imaging, a more specific 3D mapping of the lymphatic system can be obtained by administering two distinct gadolinium-based MRI contrast agents on different days (gadofosveset and gadobutrol) and subsequently processing images acquired before and after administration of each type of contrast...
April 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/29780511/through-tissue-imaging-of-a-live-breast-cancer-tumour-model-using-handheld-surface-enhanced-spatially-offset-resonance-raman-spectroscopy-sesorrs
#8
Fay Nicolson, Lauren E Jamieson, Samuel Mabbott, Konstantinos Plakas, Neil C Shand, Michael R Detty, Duncan Graham, Karen Faulds
In order to improve patient survival and reduce the amount of unnecessary and traumatic biopsies, non-invasive detection of cancerous tumours is of imperative and urgent need. Multicellular tumour spheroids (MTS) can be used as an ex vivo cancer tumour model, to model in vivo nanoparticle (NP) uptake by the enhanced permeability and retention (EPR) effect. Surface enhanced spatially offset Raman spectroscopy (SESORS) combines both surface enhanced Raman spectroscopy (SERS) and spatially offset Raman spectroscopy (SORS) to yield enhanced Raman signals at much greater sub-surface levels...
April 21, 2018: Chemical Science
https://www.readbyqxmd.com/read/29779177/computational-identification-of-structural-factors-affecting-the-mutagenic-potential-of-aromatic-amines-study-design-and-experimental-validation
#9
Svetoslav H Slavov, Iva Stoyanova-Slavova, William Mattes, Richard D Beger, Beat J Brüschweiler
A grid-based, alignment-independent 3D-SDAR (three-dimensional spectral data-activity relationship) approach based on simulated 13 C and 15 N NMR chemical shifts augmented with through-space interatomic distances was used to model the mutagenicity of 554 primary and 419 secondary aromatic amines. A robust modeling strategy supported by extensive validation including randomized training/hold-out test set pairs, validation sets, "blind" external test sets as well as experimental validation was applied to avoid over-parameterization and build Organization for Economic Cooperation and Development (OECD 2004) compliant models...
May 19, 2018: Archives of Toxicology
https://www.readbyqxmd.com/read/29775596/digital-museum-of-retinal-ganglion-cells-with-dense-anatomy-and-physiology
#10
J Alexander Bae, Shang Mu, Jinseop S Kim, Nicholas L Turner, Ignacio Tartavull, Nico Kemnitz, Chris S Jordan, Alex D Norton, William M Silversmith, Rachel Prentki, Marissa Sorek, Celia David, Devon L Jones, Doug Bland, Amy L R Sterling, Jungman Park, Kevin L Briggman, H Sebastian Seung
When 3D electron microscopy and calcium imaging are used to investigate the structure and function of neural circuits, the resulting datasets pose new challenges of visualization and interpretation. Here, we present a new kind of digital resource that encompasses almost 400 ganglion cells from a single patch of mouse retina. An online "museum" provides a 3D interactive view of each cell's anatomy, as well as graphs of its visual responses. The resource reveals two aspects of the retina's inner plexiform layer: an arbor segregation principle governing structure along the light axis and a density conservation principle governing structure in the tangential plane...
May 17, 2018: Cell
https://www.readbyqxmd.com/read/29775352/three-dimensional-color-code-thresholds-via-statistical-mechanical-mapping
#11
Aleksander Kubica, Michael E Beverland, Fernando Brandão, John Preskill, Krysta M Svore
Three-dimensional (3D) color codes have advantages for fault-tolerant quantum computing, such as protected quantum gates with relatively low overhead and robustness against imperfect measurement of error syndromes. Here we investigate the storage threshold error rates for bit-flip and phase-flip noise in the 3D color code (3DCC) on the body-centered cubic lattice, assuming perfect syndrome measurements. In particular, by exploiting a connection between error correction and statistical mechanics, we estimate the threshold for 1D stringlike and 2D sheetlike logical operators to be p_{3DCC}^{(1)}≃1...
May 4, 2018: Physical Review Letters
https://www.readbyqxmd.com/read/29772275/5c-id-increased-resolution-chromosome-conformation-capture-carbon-copy-with-in-situ-3c-and-double-alternating-primer-design
#12
Ji Hun Kim, Katelyn R Titus, Wanfeng Gong, Jonathan A Beagan, Zhendong Cao, Jennifer E Phillips-Cremins
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library...
May 14, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29772173/quantitative-surface-enhanced-raman-spectroscopy-through-the-interface-assisted-self-assembly-of-three-dimensional-silver-nanorod-substrates
#13
Siying Liu, Xiang-Dong Tian, Yun Zhang, Jian-Feng Li
The realization of surface-enhanced Raman spectroscopy (SERS) to be a reliable quantitative analytical technique requires sensitive and reproducible enhancing substrates. Here, uniform three-dimensional (3D) Ag nanorod (AgNR) substrates with well-defined interlayer spacings are prepared through the air-liquid interface-assisted self-assembly of AgNR in a layer-by-layer manner. The correlation of the SERS performance with the 3D AgNR structures is performed by SERS mapping the substrates. SERS mapping reveals the excellent enhancement uniformity of the 3D substrates with the relative standard deviation (RSD) less than 10%...
May 17, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29772066/3d-specific-absorption-rate-estimation-from-high-intensity-focused-ultrasound-sonications-using-the-green-s-function-heat-kernel
#14
Nicholas J Freeman, Henrik Odéen, Dennis L Parker
PURPOSE: Evaluate a numerical inverse Green's function method of deriving specific absorption rates (SARs) from high intensity focused ultrasound (HIFU) sonications given tissue parameters (thermal conductivity, specific heat capacity, and mass density) and 3-D magnetic resonance imaging (MRI) temperature measurements. METHODS: SAR estimates were evaluated using simulations and MR temperature measurements from HIFU sonications. For simulations, a "true" SAR was calculated using the hybrid angular spectrum method for ultrasound simulations...
May 17, 2018: Medical Physics
https://www.readbyqxmd.com/read/29771683/an-individualized-strategy-to-estimate-the-effect-of-deformable-registration-uncertainty-on-accumulated-dose-in-the-upper-abdomen
#15
Yibing Wang, Steven F Petit, Eliana Vasquez Osorio, Vikas Gupta, Alejandra Méndez Romero, Ben J M Heijmen
In the abdomen, it is challenging to assess the accuracy of deformable image registration (DIR) for individual patients, due to the lack of clear anatomical landmarks, which can hamper clinical applications that require high accuracy DIR, such as adaptive radiotherapy. In this study, we propose and evaluate a methodology for estimating the impact of uncertainties in DIR on calculated accumulated dose in the upper abdomen, in order to aid decision making in adaptive treatment approaches. 
 Sixteen liver metastasis patients treated with SBRT were evaluated...
May 17, 2018: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/29771639/hic-5-expression-is-a-major-indicator-of-cancer-cell-morphology-migration-and-plasticity-in-three-dimensional-matrices
#16
Anushree C Gulvady, Fatemeh Dubois, Nicholas O Deakin, Gregory J Goreczny, Christopher E Turner
The focal adhesion proteins, Hic-5 and Paxillin have been previously identified as key regulators of MDA-MB-231 breast cancer cell migration and morphologic mesenchymal-amoeboid plasticity in three-dimensional extracellular matrices. However, their respective roles in other cancer cell types has not been evaluated. Herein, utilizing 3D cell-derived matrices and fibronectin-coated 1D substrates, we show that across a variety of cancer cell lines, the level of Hic-5 expression serves as the major indicator of the cells primary morphology, plasticity and in vitro invasiveness...
May 17, 2018: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/29769576/motion-compensated-micro-ct-reconstruction-for-in-situ-analysis-of-dynamic-processes
#17
Thomas De Schryver, Manuel Dierick, Marjolein Heyndrickx, Jeroen Van Stappen, Marijn A Boone, Luc Van Hoorebeke, Matthieu N Boone
This work presents a framework to exploit the synergy between Digital Volume Correlation (DVC) and iterative CT reconstruction to enhance the quality of high-resolution dynamic X-ray CT (4D-µCT) and obtain quantitative results from the acquired dataset in the form of 3D strain maps which can be directly correlated to the material properties. Furthermore, we show that the developed framework is capable of strongly reducing motion artifacts even in a dataset containing a single 360° rotation.
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769051/knee-dgemric-at-7-t-comparison-against-1-5-t-and-evaluation-of-t-1-mapping-methods
#18
Pernilla Peterson, Carl Johan Tiderius, Emma Olsson, Björn Lundin, Lars E Olsson, Jonas Svensson
BACKGROUND: dGEMRIC (delayed Gadolinium Enhanced Magnetic Resonance Image of Cartilage) is a well-established technique for cartilage quality assessment in osteoarthritis at clinical field strengths. The method is robust, but requires injection of contrast agent and a cumbersome examination procedure. New non-contrast-agent-based techniques for cartilage quality assessment are currently being developed at 7 T. However, dGEMRIC remains an important reference technique during this development...
May 16, 2018: BMC Musculoskeletal Disorders
https://www.readbyqxmd.com/read/29764378/grim-filter-fast-seed-location-filtering-in-dna-read-mapping-using-processing-in-memory-technologies
#19
Jeremie S Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
BACKGROUND: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read mappers 1) quickly generate possible mapping locations for seeds (i.e., smaller segments) within each read, 2) extract reference sequences at each of the mapping locations, and 3) check similarity between each read and its associated reference sequences with a computationally-expensive algorithm (i...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29763672/using-3d-spatial-correlations-to-improve-the-noise-robustness-of-multi-component-analysis-of-3d-multi-echo-quantitative-t2-relaxometry-data
#20
Dushyant Kumar, Hari Hariharan, Tobias D Faizy, Patrick Borchert, Susanne Siemonsen, Jens Fiehler, Ravinder Reddy, Jan Sedlacik
PURPOSE: We present a computationally feasible and iterative multi-voxel spatially regularized algorithm for myelin water fraction (MWF) reconstruction. This method utilizes 3D spatial correlations present in anatomical/pathological tissues and underlying B1+ -inhomogeneity or flip angle inhomogeneity to enhance the noise robustness of the reconstruction while intrinsically accounting for stimulated echo contributions using T2-distribution data alone. METHODS: Simulated data and in vivo data acquired using 3D non-selective multi-echo spin echo (3DNS-MESE) were used to compare the reconstruction quality of the proposed approach against those of the popular algorithm (the method by Prasloski et al...
May 12, 2018: NeuroImage
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