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3D mapping

Xuanang Xu, Fugen Zhou, Bo Liu
PURPOSE: Automatic approach for bladder segmentation from computed tomography (CT) images is highly desirable in clinical practice. It is a challenging task since the bladder usually suffers large variations of appearance and low soft-tissue contrast in CT images. In this study, we present a deep learning-based approach which involves a convolutional neural network (CNN) and a 3D fully connected conditional random fields recurrent neural network (CRF-RNN) to perform accurate bladder segmentation...
March 19, 2018: International Journal of Computer Assisted Radiology and Surgery
K Mohamathu Rafic, S Amalan, B S Timothy Peace, B Paul Ravindran
Background and aim: The practicability of computing dose calculation on cone beam CT (CBCT) has been widely investigated. In most clinical scenarios, the craniocaudal scanning length of CBCT is found to be inadequate for localization. This study aims to explore extended tomographic localization and adaptive dose calculation strategies using Hounsfield unit (HU) corrected CBCT image sets. Materials and methods: Planning CT (pCT) images of the Rando phantom (T12 -to-midthigh) were acquired with pelvic-protocol using Biograph CT-scanner...
March 2018: Reports of Practical Oncology and Radiotherapy
Nathaniel Narra, Shinya Abe, Vassil Dimitrov, Riku Nikander, Reijo Kouhia, Harri Sievänen, Jari Hyttinen
The causal relationship between habitual loading and adaptive response in bone morphology is commonly explored by analysing the spatial distribution of mechanically relevant features. In this study, 3D distribution of features in the proximal femur of 91 female athletes (5 exercise loading groups representing habitual loading) is contrasted with 20 controls. A femur specific Ricci-flow based conformal mapping procedure was developed for establishing correspondence among the periosteal surfaces. The procedure leverages the invariance of the conformal mapping method to isometric shape differences to align surfaces in the 2D parametric domain, to produce dense correspondences across an isotopological set of surfaces...
March 19, 2018: Scientific Reports
Oana Ursu, Nathan Boley, Maryna Taranova, Y X Rachel Wang, Galip Gurkan Yardimci, William Stafford Noble, Anshul Kundaje
Motivation: The three-dimensional organization of chromatin plays a critical role in gene regulation and disease. High-throughput chromosome conformation capture experiments such as Hi-C are used to obtain genome-wide maps of 3D chromatin contacts. However, robust estimation of data quality and systematic comparison of these contact maps is challenging due to the multi-scale, hierarchical structure of chromatin contacts and the resulting properties of experimental noise in the data. Measuring concordance of contact maps is important for assessing reproducibility of replicate experiments and for modeling variation between different cellular contexts...
March 15, 2018: Bioinformatics
Aida Niñerola-Baizán, Judith Gallego, Albert Cot, Pablo Aguiar, Francisco Lomeña, Javier Pavía, Domenec Ros
The aim of this work was to obtain a set of parameters to be applied in [123I]FP-CIT SPECT reconstruction in order to minimize the error between standardized and true values of the Specific Uptake Ratio (SUR) in dopaminergic neurotransmission SPECT studies. To this end, Monte Carlo simulation was used to generate a database of 1,380 projection data-sets from 23 subjects, including normal cases and a variety of pathologies. Studies were reconstructed using Filtered Back Projection (FBP) with attenuation correction and Ordered Subset Expectation Maximization (OSEM) with correction for different degradations (attenuation, scatter and PSF)...
March 19, 2018: Physics in Medicine and Biology
Shivani Patel, Palmi Modi, Mahesh Chhabria
Caspase-1 is a key endoprotease responsible for the post-translational processing of pro-inflammatory cytokines IL-1β, 18 & 33. Excessive secretion of IL-1β leads to numerous inflammatory and autoimmune diseases. Thus caspase-1 inhibition would be considered as an important therapeutic strategy for development of newer anti-inflammatory agents. Here we have employed an integrated virtual screening by combining pharmacophore mapping and docking to identify small molecules as caspase-1 inhibitors. The ligand based 3D pharmacophore model was generated having the essential structural features of (HBA, HY & RA) using a data set of 27 compounds...
March 8, 2018: Journal of Molecular Graphics & Modelling
Sen Wang, Xinxin Zuo, Chao Du, Runxiao Wang, Jiangbin Zheng, Ruigang Yang
This paper deals with the 3D reconstruction problem for dynamic non-rigid objects with a single RGB-D sensor. It is a challenging task as we consider the almost inevitable accumulation error issue in some previous sequential fusion methods and also the possible failure of surface tracking in a long sequence. Therefore, we propose a global non-rigid registration framework and tackle the drifting problem via an explicit loop closure. Our novel scheme starts with a fusion step to get multiple partial scans from the input sequence, followed by a pairwise non-rigid registration and loop detection step to obtain correspondences between neighboring partial pieces and those pieces that form a loop...
March 16, 2018: Sensors
Jung-Un Kim, Hang-Bong Kang
In object detection systems for autonomous driving, LIDAR sensors provide very useful information. However, problems occur because the object representation is greatly distorted by changes in distance. To solve this problem, we propose a LIDAR shape set that reconstructs the shape surrounding the object more clearly by using the LIDAR point information projected on the object. The LIDAR shape set restores object shape edges from a bird's eye view by filtering LIDAR points projected on a 2D pixel-based front view...
March 16, 2018: Sensors
Neta Blau, Eyal Klang, Nahum Kiryati, Marianne Amitai, Orith Portnoy, Arnaldo Mayer
PURPOSE: Simple renal cysts are a common benign finding in abdominal CT scans. However, since they may evolve in time, simple cysts need to be reported. With an ever-growing number of slices per CT scan, cysts are easily overlooked by the overloaded radiologist. In this paper, we address the detection of simple renal cysts as an incidental finding in a real clinical setting. METHODS: We propose a fully automatic framework for renal cyst detection, supported by a robust segmentation of the kidneys performed by a fully convolutional neural network...
March 15, 2018: International Journal of Computer Assisted Radiology and Surgery
Long Chen, Wen Tang, Nigel W John, Tao Ruan Wan, Jian Jun Zhang
BACKGROUND AND OBJECTIVE: While Minimally Invasive Surgery (MIS) offers considerable benefits to patients, it also imposes big challenges on a surgeon's performance due to well-known issues and restrictions associated with the field of view (FOV), hand-eye misalignment and disorientation, as well as the lack of stereoscopic depth perception in monocular endoscopy. Augmented Reality (AR) technology can help to overcome these limitations by augmenting the real scene with annotations, labels, tumour measurements or even a 3D reconstruction of anatomy structures at the target surgical locations...
May 2018: Computer Methods and Programs in Biomedicine
Eli Gibson, Wenqi Li, Carole Sudre, Lucas Fidon, Dzhoshkun I Shakir, Guotai Wang, Zach Eaton-Rosen, Robert Gray, Tom Doel, Yipeng Hu, Tom Whyntie, Parashkev Nachev, Marc Modat, Dean C Barratt, Sébastien Ourselin, M Jorge Cardoso, Tom Vercauteren
BACKGROUND AND OBJECTIVES: Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this domain of application requires substantial implementation effort. Consequently, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups...
May 2018: Computer Methods and Programs in Biomedicine
Samiul M Ansari, David S Palmer
Recently, Güssregen et al. used solute-solvent distribution functions calculated by the 3D Reference Interaction Site Model (3DRISM) in a 3D-QSAR approach to model activity data for a set of serine protease inhibitors; this approach was referred to as Comparative Analysis of 3D RISM MAps (CARMa). [J. Chem. Inf. MODEL: , 2017, 57, 1652-1666] Here we extend this idea by introducing probe atoms into the 3DRISM solvent model in order to directly capture other molecular interactions in addition to those related to hydration/dehydration...
March 15, 2018: Journal of Chemical Information and Modeling
S Kaiser, S V Radl, J Manhart, S Ayalur-Karunakaran, T Griesser, A Moser, C Ganser, C Teichert, W Kern, S Schlögl
The present work aims at the preparation of dry adhesives with switchable bonding properties by using the reversible nature of the [4πs+4πs] cycloaddition of anthracenes. Photo-responsive hydrogenated carboxylated nitrile butadiene rubber with photo-responsive pendant anthracene groups is prepared by one-pot synthesis. The formation of 3D networks relies on the photodimerization of the anthracene moieties upon UV exposure (λ > 300 nm). Controlled cleavage of the crosslink sites is achieved by either deep UV exposure (λ = 254 nm) or thermal dissociation at 70 °C...
March 15, 2018: Soft Matter
Perrine Chaurand, Wei Liu, Daniel Borschneck, Clément Levard, Mélanie Auffan, Emmanuel Paul, Blanche Collin, Isabelle Kieffer, Sophie Lanone, Jérôme Rose, Jeanne Perrin
In this methodological study, we demonstrated the relevance of 3D imaging performed at various scales for the ex vivo detection and location of cerium oxide nanomaterials (CeO2 -NMs) in mouse lung. X-ray micro-computed tomography (micro-CT) with a voxel size from 14 µm to 1 µm (micro-CT) was combined with X-ray nano-computed tomography with a voxel size of 63 nm (nano-CT). An optimized protocol was proposed to facilitate the sample preparation, to minimize the experimental artifacts and to optimize the contrast of soft tissues exposed to metal-based nanomaterials (NMs)...
March 13, 2018: Scientific Reports
Margaux Alazard, Jérôme Lacotte, Jérôme Horvilleur, Mina Ait-Said, Fiorella Salerno, Vladimir Manenti, Jean-François Piechaud, Jérôme Garot, Damien Bonnet, Alice Maltret
PURPOSE: To evaluate various strategies in order to minimize the risk of coronary injury during posteroseptal accessory pathways ablation in children. METHODS: We retrospectively reviewed 68 posteroseptal accessory pathways ablation procedures (20 decremental and 48 typical accessory pathways) performed in 62 pediatric patients at our institution between July 2009 and December 2016. Only posteroseptal accessory pathways targeted near or within the coronary sinus were included and ablation was mostly performed using irrigated tip radiofrequency...
March 12, 2018: Journal of Interventional Cardiac Electrophysiology: An International Journal of Arrhythmias and Pacing
Tarek Zghaib, Ashkan A Malayeri, Esra G Ipek, Mohammadali Habibi, Dong Huang, Muhammad A Balouch, David A Bluemke, Hugh Calkins, Saman Nazarian, Stefan L Zimmerman
BACKGROUND: Ablation-induced left atrial (LA) edema may result in procedural failure due to reversible pulmonary vein (PV) isolation. Conventional T2-weighted magnetic resonance edema imaging is limited by low spatial resolution. OBJECTIVE: In this pilot study, our goal was to 1) optimize and validate a 3D-SPACE sequence for quantification of T2-signal in the LA and 2) apply in recently ablated patients, comparing myocardial edema on T2-SPACE to tissue damage on late gadolinium-enhancement (LGE) imaging...
March 9, 2018: Heart Rhythm: the Official Journal of the Heart Rhythm Society
Yang Ju, Zhangyu Ren, Lingtao Mao, Fu-Pen Chiang
Providing a quantitative description of the whole-field stress evolution in complex structures subjected to continuous loading processes using traditional photoelastic approaches is a significant challenge because of the difficulties with fabricating complex structures, identifying the stress distribution and evolution, and unwrapping isochromatic phase maps. To overcome the challenges, we proposed a novel method to quantify the continuous whole-field stress evolution in a complex porous structure that was fabricated with 3D printing technology...
March 5, 2018: Optics Express
Asli Yildirim, Michael Feig
High-resolution three-dimensional models of Caulobacter crescentus nucleoid structures were generated via a multi-scale modeling protocol. Models were built as a plectonemically supercoiled circular DNA and by incorporating chromosome conformation capture based data to generate an ensemble of base pair resolution models consistent with the experimental data. Significant structural variability was found with different degrees of bending and twisting but with overall similar topologies and shapes that are consistent with C...
February 26, 2018: Nucleic Acids Research
Yue Yan, Jinzhong Yang, Sam Beddar, Geoffrey S Ibbott, Zhifei Wen, Laurence E Court, Ken-Pin Hwang, Mo Kadbi, Sunil Krishnan, Clifton Fuller, Steven J Frank, James N Yang, Peter A Balter, Rajat J Kudchadker, Jihong Wang
We developed a novel technique to study the impact of geometric distortion of magnetic resonance imaging (MRI) on intensity-modulated radiation therapy treatment planning.
 The measured 3D datasets of residual geometric distortion (a 1.5-T MRI component of an MRI linear accelerator system) was fitted with a second-order polynomial model to map the spatial dependence of geometric distortions. Then the geometric distortion model was applied to computed tomography (CT) image and structure data to simulate the distortion of MRI data and structures...
March 12, 2018: Physics in Medicine and Biology
Zaheer Ul-Haq, Sajda Ashraf, Majdi M Bkhaitan
Casein kinase-II, a member of protein kinase family, plays significant role in different cellular processes such as cell growth, differentiation, proliferation, gene expression and embryogenesis. Being a potent suppressor of apoptosis, it serves as a significant link for its association with various types of malignancies such as colorectal and breast cancer. To overcome its pathological role in various cancerous diseases, CK-II procures great consideration as a therapeutic target. This study aimed at understanding the binding mechanism and structural properties of benzimidazole derivatives by utilizing various computational tools including docking simulation, 3-dimensional quantitative structure activity relationships and molecular dynamic simulation...
March 12, 2018: Journal of Biomolecular Structure & Dynamics
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