scholarly journals Topological Map: An Efficient Tool to Compute Incrementally Topological Features on 3D Images

2006 ◽  
pp. 1-15 ◽  
Author(s):  
Guillaume Damiand ◽  
Samuel Peltier ◽  
Laurent Fuchs ◽  
Pascal Lienhardt
Keyword(s):  
Efficient Tool ◽  
Topological Map ◽  
3D Images ◽  
Topological Features

PEPRF: Identification of Essential Proteins by Integrating Topological Features of PPI Network and Sequence-based Features via Random Forest

2021 ◽  
Vol 16 ◽  
Author(s):  
Chuanyan Wu ◽  
Bentao Lin ◽  
Kai Shi ◽  
Qingju Zhang ◽  
Rui Gao ◽  
...  
Keyword(s):  
Random Forest ◽  
Feature Selection Method ◽  
Selection Method ◽  
Ppi Network ◽  
Efficient Tool ◽  
Essential Proteins ◽  
Protein Protein Interaction ◽  
Topological Features ◽  
Sequence Graph ◽  
Experimental Approaches

Background: Essential proteins play an important role in the process of life, which can be identified by experimental methods and computational approaches. Experimental approaches to identify essential proteins are of high accuracy but with the limitation of time and resource-consuming. Objective: Herein, we present a computational model (PEPRF) to identify essential proteins based on machine learning. Methods: Different features of proteins were extracted. Topological features of Protein-Protein Interaction (PPI) network-based were extracted. Based on the protein sequence, graph theory-based features, information-based features, composition, and physiochemical features, etc., were extracted. Finally, 282 features were constructed. In order to select the features that contributed most to the identification, the ReliefF-based feature selection method was adopted to measure the weights of these features. As a result, 212 features were curated to train random forest classifiers. Finally, PEPRF obtained an AUC of 0.71 and an accuracy of 0.742. Conclusion: Our results show that PEPRF may be applied as an efficient tool to identify essential proteins.

Imaging of platinum-shadowed macromolecular complexes in dark field

1984 ◽  
Vol 42 ◽  
pp. 146-147
Author(s):  
D.W. Andrews ◽  
F.P. Ottensmeyer
Keyword(s):  
Thin Film ◽  
Three Dimensional ◽  
Average Diameter ◽  
Dark Field ◽  
Bright Field ◽  
Field Mode ◽  
Macromolecular Complexes ◽  
Average Mass ◽  
Topological Features ◽  
Projection Images

Shadowing with heavy metals has been used for many years to enhance the topological features of biological macromolecular complexes. The three dimensional features present in directionaly shadowed specimens often simplifies interpretation of projection images provided by other techniques. One difficulty with the method is the relatively large amount of metal used to achieve sufficient contrast in bright field images. Thick shadow films are undesirable because they decrease resolution due to an increased tendency for microcrystalline aggregates to form, because decoration artefacts become more severe and increased cap thickness makes estimation of dimensions more uncertain.The large increase in contrast provided by the dark field mode of imaging allows the use of shadow replicas with a much lower average mass thickness. To form the images in Fig. 1, latex spheres of 0.087 μ average diameter were unidirectionally shadowed with platinum carbon (Pt-C) and a thin film of carbon was indirectly evaporated on the specimen as a support.

Measurements in 3D images

1991 ◽  
Vol 49 ◽  
pp. 408-409
Author(s):  
John C. Russ
Keyword(s):  
Three Dimensional ◽  
Image Plane ◽  
X Rays ◽  
Traditional Use ◽  
3D Images ◽  
Confocal Scanning Laser Microscope ◽  
Hard Materials ◽  
Depth Direction ◽  
Confocal Scanning ◽  
Confocal Scanning Laser

Three-dimensional (3D) images consisting of arrays of voxels can now be routinely obtained from several different types of microscopes. These include both the transmission and emission modes of the confocal scanning laser microscope (but not its most common reflection mode), the secondary ion mass spectrometer, and computed tomography using electrons, X-rays or other signals. Compared to the traditional use of serial sectioning (which includes sequential polishing of hard materials), these newer techniques eliminate difficulties of alignment of slices, and maintain uniform resolution in the depth direction. However, the resolution in the z-direction may be different from that within each image plane, which makes the voxels non-cubic and creates some difficulties for subsequent analysis.

Developments in 3D Echocardiography

2009 ◽  
Vol 5 (2) ◽  
pp. 10 ◽  
Author(s):  
Jose Luis Zamorano ◽  
Keyword(s):  
3D Echocardiography ◽  
Resonance Imaging ◽  
Clinical Tool ◽  
3D Images ◽  
Processing Power ◽  
2D Echocardiography ◽  
Automated Quantification ◽  
Heart Cycle ◽  
Functional Mechanisms ◽  
Full Volume

3D echocardiography (3DE) will gain increasing acceptance as a routine clinical tool as the technology evolves due to advances in technology and computer processing power. Images obtained from 3DE provide more accurate assessment of complex cardiac anatomy and sophisticated functional mechanisms compared with conventional 2D echocardiography (2DE), and are comparable to those achieved with magnetic resonance imaging. Many of the limitations associated with the early iterations of 3DE prevented their widespread clinical application. However, recent significant improvements in transducer and post-processing software technologies have addressed many of these issues. Furthermore, the most recent advances in the ability to image the entire heart in realtime and fully automated quantification have poised 3DE to become more ubiquitous in clinical routine. Realtime 3DE (RT3DE) systems offer further improvements in the diagnostic and treatment planning capabilities of cardiac ultrasound. Innovations such as the ability to acquire non-stitched, realtime, full-volume 3D images of the heart in a single heart cycle promise to overcome some of the current limitations of current RT3DE systems, which acquire images over four to seven cardiac cycles, with the need for gating and the potential for stitch artefacts.

Full-parallax 3D display using time-multiplexing projection technology

2020 ◽  
Vol 2020 (2) ◽  
pp. 100-1-100-6
Author(s):  
Takuya Omura ◽  
Hayato Watanabe ◽  
Naoto Okaichi ◽  
Hisayuki Sasaki ◽  
Masahiro Kawakita
Keyword(s):  
Incident Light ◽  
Polarization State ◽  
3D Image ◽  
3D Display ◽  
Time Division Multiplexing ◽  
3D Images ◽  
Polarization Gratings ◽  
Light Rays ◽  
Time Division

We enhanced the resolution characteristics of a threedimensional (3D) image using time-division multiplexing methods in a full-parallax multi-view 3D display. A time-division light-ray shifting (TDLS) method is proposed that uses two polarization gratings (PGs). As PG changes the diffraction direction of light rays according to the polarization state of the incident light, this method can shift light rays approximately 7 mm in a diagonal direction by switching the polarization state of incident light and adjusting the distance between the PGs. We verified the effect on the characteristics of 3D images based on the extent of the shift. As a result, the resolution of a 3D image with depth is improved by shifting half a pitch of a multi-view image using the TDLS method, and the resolution of the image displayed near the screen is improved by shifting half a pixel of each viewpoint image with a wobbling method. These methods can easily enhance 3D characteristics with a small number of projectors.

Forming Multiple Aerial 3D Images by Use of Infinity Mirror, AIRR, and DS3D Display

2019 ◽  
pp. 734
Author(s):  
Kazunari Chiba ◽  
Daiki Nishimura ◽  
Masayuki Shinohara ◽  
Hirotsugu Yamamoto
Keyword(s):  
3D Images

Forming Multiple Aerial 3D Images by Use of Infinity Mirror, AIRR, and DS3D Display

2019 ◽  
pp. 734
Author(s):  
Kazunari Chiba ◽  
Daiki Nishimura ◽  
Masayuki Shinohara ◽  
Hirotsugu Yamamoto
Keyword(s):  
3D Images

Analysis of Remote Sensing based Vegetation Indices (VIs) for Unmanned Aerial System (UAS): A Review

2020 ◽  
Vol 3 (2) ◽  
pp. 58-73
Author(s):  
Vijay Bhagat ◽  
Ajaykumar Kada ◽  
Suresh Kumar
Keyword(s):  
Remote Sensing ◽  
Spatial Data ◽  
Satellite Remote Sensing ◽  
Vegetation Indices ◽  
Unmanned Aerial System ◽  
Sustainable Land Management ◽  
Efficient Tool ◽  
Site Specific ◽  
The Earth ◽  
Interesting Area

Unmanned Aerial System (UAS) is an efficient tool to bridge the gap between high expensive satellite remote sensing, manned aerial surveys, and labors time consuming conventional fieldwork techniques of data collection. UAS can provide spatial data at very fine (up to a few mm) and desirable temporal resolution. Several studies have used vegetation indices (VIs) calculated from UAS based on optical- and MSS-datasets to model the parameters of biophysical units of the Earth surface. They have used different techniques of estimations, predictions and classifications. However, these results vary according to used datasets and techniques and appear very site-specific. These existing approaches aren’t optimal and applicable for all cases and need to be tested according to sensor category and different geophysical environmental conditions for global applications. UAS remote sensing is a challenging and interesting area of research for sustainable land management.

An Efficient Tool for Searching Maximal and Super Maximal Repeats in Large DNA/Protein Sequences via Induced-Enhanced Suffix Array

2019 ◽  
Vol 12 (2) ◽  
pp. 128-134
Author(s):  
Sanjeev Kumar ◽  
Suneeta Agarwal ◽  
Ranvijay
Keyword(s):  
Protein Sequences ◽  
Input Sequence ◽  
Suffix Array ◽  
Secondary Memory ◽  
Time And Space ◽  
Efficient Tool ◽  
Frequency Distributions ◽  
Alignment Algorithms ◽  
Common Prefix ◽  
Art Works

Background: DNA and Protein sequences of an organism contain a variety of repeated structures of various types. These repeated structures play an important role in Molecular biology as they are related to genetic backgrounds of inherited diseases. They also serve as a marker for DNA mapping and DNA fingerprinting. Efficient searching of maximal and super maximal repeats in DNA/Protein sequences can lead to many other applications in the area of genomics. Moreover, these repeats can also be used for identification of critical diseases by finding the similarity between frequency distributions of repeats in viruses and genomes (without using alignment algorithms). Objective: The study aims to develop an efficient tool for searching maximal and super maximal repeats in large DNA/Protein sequences. Methods: The proposed tool uses a newly introduced data structure Induced Enhanced Suffix Array (IESA). IESA is an extension of enhanced suffix array. It uses induced suffix array instead of classical suffix array. IESA consists of Induced Suffix Array (ISA) and an additional array-Longest Common Prefix (LCP) array. ISA is an array of all sorted suffixes of the input sequence while LCP array stores the lengths of the longest common prefixes between all pairs of consecutive suffixes in an induced suffix array. IESA is known to be efficient w.r.t. both time and space. It facilitates the use of secondary memory for constructing the large suffix-array. Results: An open source standalone tool named MSR-IESA for searching maximal and super maximal repeats in DNA/Protein sequences is provided at https://github.com/sanjeevalg/MSRIESA. Experimental results show that the proposed algorithm outperforms other state of the art works w.r.t. to both time and space. Conclusion: The proposed tool MSR-IESA is remarkably efficient for the analysis of DNA/Protein sequences, having maximal and super maximal repeats of any length. It can be used for identification of well-known diseases.

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