scholarly journals Hierarchical Reconstruction of High-Resolution 3D Models of Human Chromosomes

2018 ◽  
Author(s):  
Tuan Trieu ◽  
Oluwatosin Oluwadare ◽  
Jianlin Cheng
Keyword(s):  
High Resolution ◽  
Fluorescent In Situ Hybridization ◽  
Multiple Scales ◽  
3D Models ◽  
Human Chromosomes ◽  
Genome Research ◽  
Topologically Associated Domains ◽  
High Resolution Models ◽  
Human B Cell

Eukaryotic chromosomes are often composed of components organized into multiple scales, such as nucleosomes, chromatin fibers, topologically associated domains (TAD), chromosome compartments, and chromosome territories. Therefore, reconstructing detailed 3D models of chromosomes in high resolution is useful for advancing genome research. However, the task of constructing quality highresolution 3D models is still challenging with existing methods. Hence, we designed a hierarchical algorithm, called Hierarchical3DGenome, to reconstruct 3D chromosome models at high resolution (<=5 Kilobase (KB)). The algorithm first reconstructs high-resolution 3D models at TAD level. The TAD models are then assembled to form complete high-resolution chromosomal models. The assembly of TAD models is guided by a complete low-resolution chromosome model. The algorithm is successfully used to reconstruct 3D chromosome models at 5KB resolution for the human B-cell (GM12878). These high-resolution models satisfy Hi-C chromosomal contacts well and are consistent with models built at lower (i.e. 1MB) resolution, and with the data of fluorescent in situ hybridization experiments. The Java source code of Hierarchical3DGenome and its user manual are available here https://github.com/BDM-Lab/Hierarchical3DGenome.

scholarly journals Evaluation of the Apple iPhone 12 Pro LiDAR for an Application in Geosciences

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gregor Luetzenburg ◽  
Aart Kroon ◽  
Anders A. Bjørk
Keyword(s):  
High Resolution ◽  
Optical Sensors ◽  
Cost Effective ◽  
Point Clouds ◽  
3D Models ◽  
Absolute Accuracy ◽  
Wide Range ◽  
Financial Investments ◽  
Coastal Cliff ◽  
High Resolution Models

AbstractTraditionally, topographic surveying in earth sciences requires high financial investments, elaborate logistics, complicated training of staff and extensive data processing. Recently, off-the-shelf drones with optical sensors already reduced the costs for obtaining a high-resolution dataset of an Earth surface considerably. Nevertheless, costs and complexity associated with topographic surveying are still high. In 2020, Apple Inc. released the iPad Pro 2020 and the iPhone 12 Pro with novel build-in LiDAR sensors. Here we investigate the basic technical capabilities of the LiDAR sensors and we test the application at a coastal cliff in Denmark. The results are compared to state-of-the-art Structure from Motion Multi-View Stereo (SfM MVS) point clouds. The LiDAR sensors create accurate high-resolution models of small objects with a side length > 10 cm with an absolute accuracy of ± 1 cm. 3D models with the dimensions of up to 130 × 15 × 10 m of a coastal cliff with an absolute accuracy of ± 10 cm are compiled. Overall, the versatility in handling outweighs the range limitations, making the Apple LiDAR devices cost-effective alternatives to established techniques in remote sensing with possible fields of application for a wide range of geo-scientific areas and teaching.

High resolution ordering of DNA markers by multi-color fluorescent in situ hybridization of prophase chromosomes

1994 ◽  
Vol 65 (1-2) ◽  
pp. 130-135 ◽  
Author(s):  
J. Inazawa ◽  
T. Ariyama ◽  
T. Tokino ◽  
A. Tanigami ◽  
Y. Nakamura ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
High Resolution ◽  
Dna Markers ◽  
Fluorescent In Situ Hybridization

High-Resolution Fluorescent In Situ Hybridization of Drosophila Embryos and Tissues

2008 ◽  
Vol 2008 (6) ◽  
pp. pdb.prot5019-pdb.prot5019 ◽  
Author(s):  
E. Lecuyer ◽  
A. S. Necakov ◽  
L. Caceres ◽  
H. M. Krause
Keyword(s):  
In Situ Hybridization ◽  
High Resolution ◽  
Fluorescent In Situ Hybridization ◽  
Drosophila Embryos

scholarly journals Visualizing Votive Practice: Exploring Limestone and Terracotta Sculpture from Athienou-Malloura through 3D Models

2020 ◽  
Author(s):  
Derek B. Counts ◽  
Erik Walcek Averett ◽  
Kevin Garstki ◽  
Michael K. Toumazou
Keyword(s):  
High Resolution ◽  
Open Access ◽  
3D Visualization ◽  
Contextual Information ◽  
3D Models ◽  
Data Publishing ◽  
Archaeological Data ◽  
Archaeological Project ◽  
High Resolution Models ◽  
Visualization Techniques

Visualizing Votive Practice is an innovative, open-access, digital monograph that explores the limestone and terracotta sculptures excavated from a rural sanctuary at the site of Athienou-Malloura (Cyprus) by the Athienou Archaeological Project. Chapters on the archaeology of the site, the historiography of Cypriot sculpture, and perspectives on archaeological visualization provide context for the catalogue of 50 representative examples of votive sculpture from the sanctuary. The catalogue not only includes formal and contextual information for each object, but also embeds 3D models directly onto the page. Readers can not only view, but also manipulate, measure, zoom, and rotate each model. Additionally, links at the bottom of each entry unleash high-resolution models with accompanying metadata on the Open Context archaeological data publishing platform and on via the Sketchfab 3D viewing platform as well. This innovative monograph is aimed at a variety of audiences, from Mediterranean archaeologists and students to specialists interested in 3D visualization techniques.

Using Computational Modeling Derived From Micro CT Scanning for the Post-Implant Analyses of Various Cardiac Devices

2020 ◽  
Author(s):  
Thomas Valenzuela ◽  
Jorge Zhingre Sanchez ◽  
Mikayle Holm ◽  
Tinen Iles ◽  
Paul Iaizzo
Keyword(s):  
High Resolution ◽  
Medical Device ◽  
Medical Devices ◽  
Ct Scanning ◽  
3D Models ◽  
Micro Ct ◽  
Ct Scanner ◽  
Cardiac Devices ◽  
High Resolution Models ◽  
Implanted Devices

Abstract There are few medical devices currently utilized that have not had, at the very least, a second iteration. Medical device companies continually strive to improve their product to make it the best on the market. Medical devices are often optimized by defining the size of the device, making it more efficient and/or improving the device to tissue interface. Using the capabilities of the Visible Heart® Laboratories various cardiac devices can be implanted in reanimated swine and human hearts for the assessment of the various aforementioned parameters. After the implantation of these devices and assessment in functional anatomies, specimens were perfusion-fixed and then a micro-CT scanner was utilized to take high-resolution scans of the resultant device and tissue interfaces. These scans are used to generate high-resolution (∼20 microns) 3D models of the numerous implanted devices, measurement analyses, device simulations, and the creation of virtual reality scenes. All can then be used for detailed visual analyses. These abilities to render high-resolution models will allow medical device designers to closely evaluate their designs, in order to optimize their next iterations.

scholarly journals How Do Continuous High-Resolution Models of Patchy Seabed Habitats Enhance Classification Schemes?

Geosciences ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 237 ◽  
Author(s):  
Gustav Kågesten ◽  
Dario Fiorentino ◽  
Finn Baumgartner ◽  
Lovisa Zillén
Keyword(s):  
High Resolution ◽  
Multiple Scales ◽  
Natura 2000 ◽  
Boosted Regression Trees ◽  
Biological Information ◽  
Classification Schemes ◽  
Object Based ◽  
Thematic Resolution ◽  
High Resolution Models ◽  
The Baltic

Predefined classification schemes and fixed geographic scales are often used to simplify and cost-effectively map the spatial complexity of nature. These simplifications can however limit the usefulness of the mapping effort for users who need information across a different range of thematic and spatial resolutions. We demonstrate how substrate and biological information from point samples and photos, combined with continuous multibeam data, can be modeled to predictively map percentage cover conforming with multiple existing classification schemes (i.e., HELCOM HUB; Natura 2000), while also providing high-resolution (5 m) maps of individual substrate and biological components across a 1344 km2 offshore bank in the Baltic Sea. Data for substrate and epibenthic organisms were obtained from high-resolution photo mosaics, sediment grab samples, legacy data and expert annotations. Environmental variables included pixel and object based metrics at multiple scales (0.5 m–2 km), which improved the accuracy of models. We found that using Boosted Regression Trees (BRTs) to predict continuous models of substrate and biological components provided additional detail for each component without losing accuracy in the classified maps, compared with a thematic model. Results demonstrate the sensitivity of habitat maps to the effects of spatial and thematic resolution and the importance of high-resolution maps to management applications.

On-line sorting of human chromosomes by centromeric index, and identification of sorted populations by GTG-banding and fluorescent in situ hybridization

1990 ◽  
Vol 85 (1) ◽  
pp. 41-48 ◽  
Author(s):  
Gert A. Boschman ◽  
Wim Rens ◽  
Eric Manders ◽  
Carel van Oven ◽  
Gerrit W. Barendsen ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescent In Situ Hybridization ◽  
Human Chromosomes ◽  
Centromeric Index ◽  
On Line

scholarly journals SHARING HIGH-RESOLUTION MODELS AND INFORMATION ON WEB: THE WEB MODULE OF BIM3DSG SYSTEM

2016 ◽  
Vol XLI-B5 ◽  
pp. 703-710 ◽  
Author(s):  
F. Rechichi ◽  
A. Mandelli ◽  
C. Achille ◽  
F. Fassi
Keyword(s):  
High Resolution ◽  
Cultural Heritage ◽  
Efficient Solution ◽  
Ad Hoc ◽  
3D Models ◽  
High Resolution Models ◽  
The Web

BIM3DSG system is described here. It is an ad hoc designed BIM system created for Cultural Heritage applications. It proposes some solutions to solve some issues related to the use of BIM in this field. First, it tries to resolve the problem of managing huge, complex, high resolution and heterogeneous 3D models, and then it offers a practical, easy and efficient solution for a wide sharing of data and information.

scholarly journals Combined confocal and wide-field high-resolution cytometry of fluorescent in situ hybridization-stained cells

Cytometry ◽  
2001 ◽  
Vol 45 (1) ◽  
pp. 1-12 ◽  
Author(s):  
M. Kozubek ◽  
S. Kozubek ◽  
E. Luk�?ov� ◽  
E. B�rtov� ◽  
M. Skaln�kov� ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
High Resolution ◽  
Fluorescent In Situ Hybridization ◽  
Wide Field
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