scholarly journals Integrating Transposable Elements in the 3D Genome

2019 ◽  
Author(s):  
Alexandros Bousios ◽  
Hans-Wilhelm Nuetzmann ◽  
Dorothy Buck ◽  
Davide Michieletto
Keyword(s):  
Transposable Elements ◽  
Cell Fate ◽  
Large Scale ◽  
Spatial Information ◽  
Experimental Studies ◽  
Three Dimensional ◽  
Predictive Modelling ◽  
Polymer Physics ◽  
Modelling Framework ◽  
Polymer Folding

Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Here, we propose a new predictive modelling framework for the study of the integration patterns of TEs based on extensions of widely employed polymer models for genome organisation. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, we now show that it can also offer orthogonal and generic insights into the integration and distribution profiles (or “topography”) of TEs across organisms. Here, we present polymer physics arguments and molecular dynamics simulations on TEs inserting into heterogeneously flexible polymers and show with a simple model that polymer folding and local flexibility affects TE integration patterns. The preliminary discussion presented herein lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome.

scholarly journals Cell fate transitions and the replication timing decision point

2010 ◽  
Vol 191 (5) ◽  
pp. 899-903 ◽  
Author(s):  
David M. Gilbert
Keyword(s):  
Cell Fate ◽  
Large Scale ◽  
Three Dimensional ◽  
Replication Timing ◽  
Window Of Opportunity ◽  
Decision Point ◽  
Stem Cell Fate ◽  
Cell Fate Decisions ◽  
Timing Decision ◽  
3D Architecture

Recent findings suggest that large-scale remodeling of three dimensional (3D) chromatin architecture occurs during a brief period in early G1 phase termed the replication timing decision point (TDP). In this speculative article, I suggest that the TDP may represent an as yet unappreciated window of opportunity for extracellular cues to influence 3D architecture during stem cell fate decisions. I also describe several testable predictions of this hypothesis.

Large-scale experimental evaluation of soil saturation effect on behaviour of buried pipes under operational loads

2020 ◽  
Vol 57 (2) ◽  
pp. 205-220
Author(s):  
Chamal Randeniya ◽  
D.J. Robert ◽  
Chun-Qing Li ◽  
Jayantha Kodikara
Keyword(s):  
Unsaturated Soil ◽  
Large Scale ◽  
Water Saturation ◽  
Experimental Studies ◽  
Three Dimensional ◽  
Past Research ◽  
Buried Pipe ◽  
Element Analysis ◽  
Buried Pipes ◽  
Soil Saturation

The behaviour of pipelines in unsaturated soil is fundamentally different from that of pipelines buried in dry or saturated soils. However, the effect of soil saturation on buried pipe behaviour has been overlooked in past research mainly due to the very limited large-scale experimental studies available. Most of the available studies on buried pipes in unsaturated soil are based on numerical modelling that analyses the pipe behaviour using a calibrated soil model developed on the basis of fundamental unsaturated soil characteristics. Investigations with such approaches may not be acceptable owing largely to unverified or complicated pipe–soil interactions and three-dimensional stress re-distributions. In this paper, the effect of soil saturation on buried pipe behaviour is investigated using a comprehensive large-scale experimental setup. A detailed methodology of large-scale testing, which was used to obtain pipe deformations as well as soil stresses with reference to a cast iron pipeline buried in low-plasticity clay under different soil saturation levels, is presented. The results obtained from large-scale experiments are compared with those of three-dimensional finite element analysis. Results produced in this paper reveal that the degree of water saturation of backfill soil can significantly affect the pipe deformation under internal and external loadings.

scholarly journals Development of framework for aggregation and visualization of three-dimensional (3D) spatial data

2021 ◽  
Author(s):  
Mihal Miu ◽  
Xiaokun Zhang ◽  
M. Ali Akber Dewan ◽  
Junye Wang
Keyword(s):  
Spatial Data ◽  
Large Scale ◽  
Spatial Information ◽  
Three Dimensional ◽  
Geospatial Data ◽  
Third Party ◽  
Data Sources ◽  
Multidimensional Data ◽  
Multiple Sources ◽  
Geospatial Information

Geospatial information plays an important role in environmental modelling, resource management, business operations, and government policy. However, very little or no commonality between formats of various geospatial data has led to difficulties in utilizing the available geospatial information. These disparate data sources must be aggregated before further extraction and analysis may be performed. The objective of this paper is to develop a framework called PlaniSphere, which aggregates various geospatial datasets, synthesizes raw data, and allows for third party customizations of the software. PlaniSphere uses NASA World Wind to access remote data and map servers using Web Map Service (WMS) as the underlying protocol that supports service-oriented architecture (SOA). The results show that PlaniSphere can aggregate and parses files that reside in local storage and conforms to the following formats: GeoTIFF, ESRI shape files, and KML. Spatial data retrieved using WMS from the Internet can create geospatial data sets (map data) from multiple sources, regardless of who the data providers are. The plug-in function of this framework can be expanded for wider uses, such as aggregating and fusing geospatial data from different data sources, by providing customizations to serve future uses, which the capacity of the commercial ESRI ArcGIS software is limited to add libraries and tools due to its closed-source architectures and proprietary data structures. Analysis and increasing availability of geo-referenced data may provide an effective way to manage spatial information by using large-scale storage, multidimensional data management, and Online Analytical Processing (OLAP) capabilities in one system.

Computational studies of the extraction of visual spatial information from binocular and motion cues

1988 ◽  
Vol 66 (4) ◽  
pp. 464-477 ◽  
Author(s):  
Ellen C. Hildreth
Keyword(s):  
Computational Models ◽  
Spatial Information ◽  
Experimental Studies ◽  
Three Dimensional ◽  
Stereo Correspondence ◽  
Motion Cues ◽  
Visual Spatial ◽  
Binocular Stereo ◽  
Dimensional Shape ◽  
Three Dimensional Shape

This paper reviews some of the contributions that work in computational vision has made to the study of biological vision systems. We concentrate on two areas where there has been strong interaction between computational and experimental studies: the use of binocular stereo to recover the distances to surfaces in space, and the recovery of the three-dimensional shape of objects from relative motion in the image. With regard to stereo, we consider models proposed for solving the stereo correspondence problem, focussing on the way in which physical properties of the world constrain possible methods of solution. We also show how critical observations regarding human stereo vision have helped to shape these models. With regard to the recovery of structure from motion, we focus on how the constraint of object rigidity has been used in computational models of this process.

A model of the large-scale organization of chromatin

2013 ◽  
Vol 41 (2) ◽  
pp. 508-512 ◽  
Author(s):  
Mariano Barbieri ◽  
Mita Chotalia ◽  
James Fraser ◽  
Liron-Mark Lavitas ◽  
Josée Dostie ◽  
...  
Keyword(s):  
Experimental Data ◽  
Present Article ◽  
Cell Nucleus ◽  
Large Scale ◽  
Spatial Organization ◽  
Molecular Mechanisms ◽  
Three Dimensional ◽  
Polymer Physics ◽  
Self Organization ◽  
Dna Binding Factors

In the cell nucleus, chromosomes have a complex spatial organization, spanning several length scales, which serves vital functional purposes. It is unknown, however, how their three-dimensional architecture is orchestrated. In the present article, we review the application of a model based on classical polymer physics, the strings and binders switch model, to explain the molecular mechanisms of chromatin self-organization. We explore the scenario where chromatin architecture is shaped and regulated by the interactions of chromosomes with diffusing DNA-binding factors via thermodynamics mechanisms and compare it with available experimental data.

scholarly journals Development of framework for aggregation and visualization of three-dimensional (3D) spatial data

2021 ◽  
Author(s):  
Mihal Miu ◽  
Xiaokun Zhang ◽  
M. Ali Akber Dewan ◽  
Junye Wang
Keyword(s):  
Spatial Data ◽  
Large Scale ◽  
Spatial Information ◽  
Three Dimensional ◽  
Geospatial Data ◽  
Third Party ◽  
Data Sources ◽  
Multidimensional Data ◽  
Multiple Sources ◽  
Geospatial Information

Geospatial information plays an important role in environmental modelling, resource management, business operations, and government policy. However, very little or no commonality between formats of various geospatial data has led to difficulties in utilizing the available geospatial information. These disparate data sources must be aggregated before further extraction and analysis may be performed. The objective of this paper is to develop a framework called PlaniSphere, which aggregates various geospatial datasets, synthesizes raw data, and allows for third party customizations of the software. PlaniSphere uses NASA World Wind to access remote data and map servers using Web Map Service (WMS) as the underlying protocol that supports service-oriented architecture (SOA). The results show that PlaniSphere can aggregate and parses files that reside in local storage and conforms to the following formats: GeoTIFF, ESRI shape files, and KML. Spatial data retrieved using WMS from the Internet can create geospatial data sets (map data) from multiple sources, regardless of who the data providers are. The plug-in function of this framework can be expanded for wider uses, such as aggregating and fusing geospatial data from different data sources, by providing customizations to serve future uses, which the capacity of the commercial ESRI ArcGIS software is limited to add libraries and tools due to its closed-source architectures and proprietary data structures. Analysis and increasing availability of geo-referenced data may provide an effective way to manage spatial information by using large-scale storage, multidimensional data management, and Online Analytical Processing (OLAP) capabilities in one system.

scholarly journals Coupled SPH–FEM Modeling of Tsunami-Borne Large Debris Flow and Impact on Coastal Structures

2021 ◽  
Vol 9 (10) ◽  
pp. 1068
Author(s):  
Anis Hasanpour ◽  
Denis Istrati ◽  
Ian Buckle
Keyword(s):  
Turbulent Flows ◽  
Large Scale ◽  
Experimental Studies ◽  
Three Dimensional ◽  
Fem Modeling ◽  
Vertical Column ◽  
Initial Water ◽  
Modeling Approach ◽  
Non Linear ◽  
The Impact

Field surveys in recent tsunami events document the catastrophic effects of large waterborne debris on coastal infrastructure. Despite the availability of experimental studies, numerical studies investigating these effects are very limited due to the need to simulate different domains (fluid, solid), complex turbulent flows and multi-physics interactions. This study presents a coupled SPH–FEM modeling approach that simulates the fluid with particles, and the flume, the debris and the structure with mesh-based finite elements. The interaction between the fluid and solid bodies is captured via node-to-solid contacts, while the interaction of the debris with the flume and the structure is defined via a two-way segment-based contact. The modeling approach is validated using available large-scale experiments in the literature, in which a restrained shipping container is transported by a tsunami bore inland until it impacts a vertical column. Comparison of the experimental data with the two-dimensional numerical simulations reveals that the SPH–FEM models can predict (i) the non-linear transformation of the tsunami wave as it propagates towards the coast, (ii) the debris–fluid interaction and (iii) the impact on a coastal structure, with reasonable accuracy. Following the validation of the models, a limited investigation was conducted, which demonstrated the generation of significant debris pitching that led to a non-normal impact on the column with a reduced contact area and impact force. While the exact level of debris pitching is highly dependent on the tsunami characteristics and the initial water depth, it could potentially result in a non-linear force–velocity trend that has not been considered to date, highlighting the need for further investigation preferably with three-dimensional models.

scholarly journals insideOutside: an accessible algorithm for classifying interior and exterior points, with applications in embryology

2021 ◽  
Author(s):  
Stanley E. Strawbridge ◽  
Agata Kurowski ◽  
Elena Corujo-Simon ◽  
Alexander G. Fletcher ◽  
Jennifer Nichols
Keyword(s):  
Cell Fate ◽  
Spatial Information ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Three Dimensional ◽  
Mathematical Framework ◽  
Cell Fate Decision ◽  
Machine Learning Approach ◽  
Quantitative Immunofluorescence ◽  
Fate Decision

AbstractA crucial aspect of embryology is relating the position of individual cells to the broader geometry of the embryo. A classic example can be seen in the first cell-fate decision of the mouse embryo, where interior cells become inner cell mass and exterior cells become trophectoderm. Advances in image acquisition and processing technology used by quantitative immunofluorescence have resulted in the production of embryo images with increasingly rich spatial information that demand accessible analytical methods. Here, we describe a simple mathematical framework and an unsupervised machine learning approach for classifying interior and exterior points of a three-dimensional point-cloud. We benchmark our method to demonstrate that it yields higher classification rates for pre-implantation mouse embryos and greater accuracy when challenged with local surface concavities. This method should prove useful to experimentalists within and beyond embryology, with broader applications in the biological and life sciences.

scholarly journals Leisure Time Sports Activities and Life Satisfaction: Deeper Insights Based on a Representative Survey from Germany

2020 ◽  
Author(s):  
Michael Mutz ◽  
Anne K. Reimers ◽  
Yolanda Demetriou
Keyword(s):  
Life Satisfaction ◽  
Large Scale ◽  
Leisure Time ◽  
Organizational Context ◽  
Experimental Studies ◽  
Well Being ◽  
Activity Level ◽  
Leisure Satisfaction ◽  
General Life Satisfaction ◽  
Sports Activities

Abstract Observational and experimental studies show that leisure time sporting activity (LTSA) is associated with higher well-being. However, scholars often seem to assume that 1) LTSA fosters “general” life satisfaction, thereby ignoring effects on domain satisfaction; 2) the effect of LTSA on well-being is linear and independent of a person’s general activity level; 3) the amount of LTSA is more important than the repertoire of LTSA, i.e. the number of different activities; 4) all kinds of LTSA are equal in their effects, irrespective of spatial and organisational context conditions. Using data from the German SALLSA-Study (“Sport, Active Lifestyle and Life Satisfaction”), a large-scale CAWI-Survey (N = 1008) representing the population ≥ 14 years, the paper takes a closer look on these assumptions. Findings demonstrate that LTSA is associated with general life satisfaction and domain-specific satisfaction (concerning relationships, appearance, leisure, work and health), but that the relationship is most pronounced for leisure satisfaction. Associations of sport with life satisfaction, leisure satisfaction and subjective health are non-linear, approaching an injection point from which on additional LTSA is no longer beneficial. Moreover, findings lend support to the notion that diversity in LTSA matters, as individuals with higher variation in sports activities are more satisfied. Finally, results with regard to spatial and organizational context suggest that outdoor sports and club-organized sports have additional benefits.

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