scholarly journals Delta integrates 3D physical structure with topology and genomic data of chromosomes

2017 ◽  
Author(s):  
Bixia Tang ◽  
Feifei Li ◽  
Jing Li ◽  
Wenming Zhao ◽  
Zhihua Zhang
Keyword(s):  
3D Model ◽  
Globin Gene ◽  
3D Structure ◽  
Physical Structure ◽  
Supplementary Information ◽  
Contact Matrix ◽  
3D Architecture ◽  
Integrative Visualization ◽  
Analysis Platform

AbstractMotivationThe regulation of gene transcription and DNA replication are tightly associated with the 3D chromosomal structures and genomic features, e.g. epigenetic marks, transcription factor bindings and non-coding RNAs. The interaction between the features and the chromosomal structures forming a multilayer 3D regulatory network. Therefore, it is necessary to integrate the physical 3D architecture of genome and features to comprehensive depict their connection to gene regulation.ResultsHere, we present an integrative visualization and analysis platform, Delta, to facilitate visually annotating and exploring the 3D physical architecture of genomes. Delta takes Hi-C or ChIA-PET contact matrix as input and predicts the topology associated domains and chromatin loops in the genome, and generates a physical 3D model which represents the plausible consensus 3D structure of the genome. Delta features a highly interactive visualization tool, which enhanced the integration of genome topology/physical structure and extensive genome annotation, by juxtaposition of the 3D model with diverse genomic assay outputs. Finally, we showcased that Delta could be helpful to reveal potentially interesting findings by a case study on the β-globin gene region.Availability and implementationhttp://delta.big.ac.cn/[email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals PredMP: a web server for de novo prediction and visualization of membrane proteins

2018 ◽  
Vol 35 (4) ◽  
pp. 691-693 ◽  
Author(s):  
Sheng Wang ◽  
Shiyang Fei ◽  
Zongan Wang ◽  
Yu Li ◽  
Jinbo Xu ◽  
...  
Keyword(s):  
Deep Learning ◽  
Lipid Bilayer ◽  
3D Model ◽  
De Novo ◽  
3D Structure ◽  
Supplementary Information ◽  
Model Generation ◽  
Transmembrane Topology ◽  
Distance Restraints ◽  
Deep Learning Model

Abstract Motivation PredMP is the first web service, to our knowledge, that aims at de novo prediction of the membrane protein (MP) 3D structure followed by the embedding of the MP into the lipid bilayer for visualization. Our approach is based on a high-throughput Deep Transfer Learning (DTL) method that first predicts MP contacts by learning from non-MPs and then predicts the 3D model of the MP using the predicted contacts as distance restraints. This algorithm is derived from our previous Deep Learning (DL) method originally developed for soluble protein contact prediction, which has been officially ranked No. 1 in CASP12. The DTL framework in our approach overcomes the challenge that there are only a limited number of solved MP structures for training the deep learning model. There are three modules in the PredMP server: (i) The DTL framework followed by the contact-assisted folding protocol has already been implemented in RaptorX-Contact, which serves as the key module for 3D model generation; (ii) The 1D annotation module, implemented in RaptorX-Property, is used to predict the secondary structure and disordered regions; and (iii) the visualization module to display the predicted MPs embedded in the lipid bilayer guided by the predicted transmembrane topology. Results Tested on 510 non-redundant MPs, our server predicts correct folds for ∼290 MPs, which significantly outperforms existing methods. Tested on a blind and live benchmark CAMEO from September 2016 to January 2018, PredMP can successfully model all 10 MPs belonging to the hard category. Availability and implementation PredMP is freely accessed on the web at http://www.predmp.com. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals TomoSAR Mapping of 3D Forest Structure: Contributions of L-Band Configurations

2021 ◽  
Vol 13 (12) ◽  
pp. 2255
Author(s):  
Matteo Pardini ◽  
Victor Cazcarra-Bes ◽  
Konstantinos Papathanassiou
Keyword(s):  
Information Content ◽  
Forest Structure ◽  
Structural Information ◽  
3D Structure ◽  
Physical Structure ◽  
Structure Mapping ◽  
Structure Information ◽  
Forest Sites ◽  
L Band ◽  
Structure Indices

Synthetic Aperture Radar (SAR) measurements are unique for mapping forest 3D structure and its changes in time. Tomographic SAR (TomoSAR) configurations exploit this potential by reconstructing the 3D radar reflectivity. The frequency of the SAR measurements is one of the main parameters determining the information content of the reconstructed reflectivity in terms of penetration and sensitivity to the individual vegetation elements. This paper attempts to review and characterize the structural information content of L-band TomoSAR reflectivity reconstructions, and their potential to forest structure mapping. First, the challenges in the accurate TomoSAR reflectivity reconstruction of volume scatterers (which are expected to dominate at L-band) and to extract physical structure information from the reconstructed reflectivity is addressed. Then, the L-band penetration capability is directly evaluated by means of the estimation performance of the sub-canopy ground topography. The information content of the reconstructed reflectivity is then evaluated in terms of complementary structure indices. Finally, the dependency of the TomoSAR reconstruction and of its structural information to both the TomoSAR acquisition geometry and the temporal change of the reflectivity that may occur in the time between the TomoSAR measurements in repeat-pass or bistatic configurations is evaluated. The analysis is supported by experimental results obtained by processing airborne acquisitions performed over temperate forest sites close to the city of Traunstein in the south of Germany.

scholarly journals Adaptations in traditional courtyard houses in Baghdad, Iraq

2017 ◽  
Vol 35 (4) ◽  
pp. 348-363 ◽  
Author(s):  
Rand H.M. Agha ◽  
John M. Kamara
Keyword(s):  
Design Methodology ◽  
Full Range ◽  
Physical Structure ◽  
Structured Interviews ◽  
Content Type ◽  
Case Study Analysis ◽  
Physical Spaces ◽  
Adaptation Model

Purpose The purpose of this paper is to investigate the adaptations that have been made to traditional courtyard houses (TCHs) in Baghdad, Iraq. The aim is to develop an understanding of various factors in the adaptation of these buildings to suit contemporary lifestyles, which will contribute to the wider field of building adaptability. Design/methodology/approach Empirical evidence was collected through case studies of 12 TCHs in the Al-Kadhimiya area of Baghdad, which involved a physical survey of buildings and semi-structured interviews with 24 occupants. Findings Case study analysis show that building adaptability involves both a change to physical spaces and also to lifestyles; with the latter being more likely when there are limitations in how much change can be made to the physical structure. Research limitations/implications The focus of this research is mainly on users’ adaptation of spaces and therefore does not consider the full range of stakeholders involved in the adaptation process. The findings also only apply to the cases considered and may not be applicable to other house types or locations. Originality/value Studies on building adaptability mostly focus on the ease of change to the building fabric, although the role of users is acknowledged. This study provides insights into the complexity and variety of changes that users can make, which are influenced by lifestyles and driven by the need for comfort. These insights are represented in an adaptation model, which can serve as a basis for further research.

scholarly journals Smart energy monitoring based on IoT Lora-Wan on the campus buildings: Case study Indonesian Defence University (Unhan), Sentul, Bogor

2021 ◽  
Vol 878 (1) ◽  
pp. 012065
Author(s):  
S Ramadhan ◽  
L Lisapaly ◽  
D Boesrony
Keyword(s):  
Interconnection Networks ◽  
Electrical Energy ◽  
Physical Structure ◽  
Maximum Efficiency ◽  
Smart Devices ◽  
Energy Usage ◽  
Smart Building ◽  
Energy Meter ◽  
Campus Building

Abstract Smart building constructions such as Campus Buildings have been designed for use, where the physical structure and system components are interrelated and can maximize functionality for operation and maintenance. So that the Campus building can be used with a longer age. One of the sub-systems that can monitor and notify the range of energy usage on a campus building is a smart electrical energy meter (kWh meter), which is connected to all devices that consume electrical energy in campus buildings. These interconnected smart devices use IoT (Internet of Things) interconnection networks and low power wireless technology (Lora). In a case study of the use of this system at the Indonesian Defense University, Unhan, Sentul, Bogor, West Java, it can be seen how the maximum efficiency in the use of electrical energy can be obtained in the smart campus building construction, which runs automatically.

scholarly journals Rational Design for Mn3O4@carbon Foam Nanocomposite with 0D@3D Structure for Boosting Electrochemical Performance

2020 ◽  
Author(s):  
Zhu Yihan ◽  
Dongfeng Wang ◽  
Xuehua Yan ◽  
Yanli Li ◽  
Wending Zhou ◽  
...  
Keyword(s):  
Electrochemical Performance ◽  
Current Density ◽  
Rational Design ◽  
Hydrothermal Reaction ◽  
3D Structure ◽  
Carbon Foam ◽  
Transfer Path ◽  
3D Architecture ◽  
One Step ◽  
Mn3o4 Nanoparticles

Abstract A rational strategy was developed to prepare a nanocomposite with 0D/3D architecture. The composite containing Mn3O4 nanoparticles (0D) and carbon foam (3D) could be applied as an electrode material for supercapacitor by taking advantage of high conductivity of carbon foam (CF) and high pseudocapacitance of Mn3O4 nanoparticles. CF was prepared by a carbonization method using melamine foam, and then Mn3O4 nanoparticles were combined with carbon foam by a one-step hydrothermal method to prepare Mn3O4@CF nanocomposite. The 0D@3D hierarchical structure of Mn3O4@CF nanocomposite using CF as a 3D growing skeleton prevents agglomeration and increases reactive sites of Mn3O4 nanoparticles. In addition, CF as a conductive skeleton shortens the charge transfer path. The synergistic effect between CF and Mn3O4 improves the electrochemical performance of CF. Three Mn3O4@CF composites were prepared by adjusting the mass of the reactants in the processes of hydrothermal reaction. The Mn3O4 nanoparticles are uniformly grown on the CF surface with a diameter of 18 nm. Mn3O4@CF-2 composite has a specific capacitance of 212.8 F/g at a current density of 1 A/g, which is much higher than that of pristine CF (79.1 F/g) and Mn3O4 (112.7 F/g). The cyclic stability of Mn3O4@CF-2 is retained as 86.1% of initial capacitance after 2000 cycles at the current density of 1 A/g. It proves the feasibility of the as-mentioned strategy and broadens the application of carbon foam in supercapacitor.

scholarly journals True-orthophoto generation from UAV images: Implementation of a combined photogrammetric and computer vision approach

2014 ◽  
Vol II-5 ◽  
pp. 57-63 ◽  
Author(s):  
L. Barazzetti ◽  
R. Brumana ◽  
D. Oreni ◽  
M. Previtali ◽  
F. Roncoroni
Keyword(s):  
3D Model ◽  
Bundle Block Adjustment ◽  
Dense Matching ◽  
Automated Data Processing ◽  
Feature Based ◽  
Correlation Techniques ◽  
Uav Images ◽  
Image Orientation ◽  
Santa Maria

This paper presents a photogrammetric methodology for true-orthophoto generation with images acquired from UAV platforms. The method is an automated multistep workflow made up of three main parts: (i) image orientation through feature-based matching and collinearity equations / bundle block adjustment, (ii) dense matching with correlation techniques able to manage multiple images, and true-orthophoto mapping for 3D model texturing. It allows automated data processing of sparse blocks of convergent images in order to obtain a final true-orthophoto where problems such as self-occlusions, ghost effects, and multiple texture assignments are taken into consideration. <br><br> The different algorithms are illustrated and discussed along with a real case study concerning the UAV flight over the Basilica di Santa Maria di Collemaggio in L'Aquila (Italy). The final result is a rigorous true-orthophoto used to inspect the roof of the Basilica, which was seriously damaged by the earthquake in 2009.

Simulation of the 3D Structure of Pollutants Invading Sea Areas Based on 3DLIF Technology—A Case Study of the Round Tube Jet

2020 ◽  
Vol 111 (sp1) ◽  
Author(s):  
Jiaying Ren ◽  
Luhai Wang ◽  
Zhenli Huang ◽  
Xiaogang Wang ◽  
Haiying Li ◽  
...  
Keyword(s):  
3D Structure ◽  
Round Tube

scholarly journals Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations

2020 ◽  
Author(s):  
Swarnendu Tripathi ◽  
Nikita R Dsouza ◽  
Raul Urrutia ◽  
Michael T Zimmermann
Keyword(s):  
Hot Spot ◽  
Adult Population ◽  
3D Structure ◽  
Genetic Alterations ◽  
Genomic Variation ◽  
Supplementary Information ◽  
High Yield ◽  
Clinical Genetics ◽  
Ras Genes ◽  
Ras Family

Abstract Motivation Protein-coding genetic alterations are frequently observed in Clinical Genetics, but the high yield of variants of uncertain significance remains a limitation in decision making. RAS-family GTPases are cancer drivers, but only 54 variants, across all family members, fall within well-known hotspots. However, extensive sequencing has identified 881 non-hotspot variants for which significance remains to be investigated. Results Here, we evaluate 935 missense variants from seven RAS genes, observed in cancer, RASopathies and the healthy adult population. We characterized hotspot variants, previously studied experimentally, using 63 sequence- and 3D structure-based scores, chosen by their breadth of biophysical properties. Applying scores that display best correlation with experimental measures, we report new valuable mechanistic inferences for both hot-spot and non-hotspot variants. Moreover, we demonstrate that 3D scores have little-to-no correlation with those based on DNA sequence, which are commonly used in Clinical Genetics. Thus, combined, these new knowledge bear significant relevance. Availability and implementation All genomic and 3D scores, and markdown for generating figures, are provided in our supplemental data. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

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