Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes

Transposable elements (TEs) are major contributors of genetic material in mammalian genomes. These often include binding sites for architectural proteins, including the multifarious master protein, CTCF, which shapes the 3D genome by creating loops, domains, compartment borders, and RNA-DNA interactions. These play a role in the compact packaging of DNA and have the potential to facilitate regulatory function. In this study, we explore the widespread contribution of TEs to mammalian 3D genomes by quantifying the extent to which they give rise to loops and domain border differences across various cell types and species using several 3D genome mapping technologies. We show that specific families and subfamilies of TEs have contributed to lineage-specific 3D chromatin structures across mammalian species. In many cases, these loops may facilitate sustained interaction between distant cis-regulatory elements and target genes, and domains may segregate chromatin state to impact gene expression in a lineage-specific manner. An experimental validation of our analytical findings using CRISPR-Cas9 to delete a candidate TE resulted in disruption of species-specific 3D chromatin structure. Taken together, we comprehensively quantify and selectively validate our finding that TEs contribute to shaping 3D genome organization and may, in some cases, impact gene regulation during the course of mammalian evolution

Identifying The Potential Sources of Chemical Elements in Drainage and Rivers Using Google Earth Imageries and Posteriori Knowledge

This study attempts to identify the potential sources of the chemical elements in the river and drainage water using in-situ water quality sampling and public domain satellite data. Monitoring the physico-chemical level of urban streams and rivers is important to secure sufficient water resources, an indicator to the ecological degradation in urban areas and an indicator of environmental pollution. Nonetheless, identifying the potential sources of chemical pollutants by field observation is constrained by hard labor activities, time, and cost. Having satellite imagery that provides land use activity information would be useful in determining the chemical sources. Therefore, the objective of this paper is to utilize the publicly accessible Google satellite images in identifying the potential sources of the chemical elements' presence in the water that is physically sampled and measured over the selected urban rivers and drainage of Johor Bahru. Three chemical elements were identified, ammonia (NH3), nitrate (NO3-), and phosphate (PO43-). The identification of the chemical sources is conducted based on the interpretation of the satellite-derived information together with the posteriori knowledge, experience, and inputs in an environmental chemistry perspective. The findings revealed that the proportion of land used did not always have a significant impact on the chemical content of the waterways. For ammonia, areas with significant hotspots (aquaculture, wet market) are more significant, although the size of the area is not dominant. The nitrate content, on the other hand, showed quite a distinct pattern linked to oil palm, intensive farming, and industrial or commercial areas. There was no distinct land use pattern associated with phosphate level. However, locations with high residential areas were likely to have high phosphate content in their respective waterways or drainage to the onsite investigations with minimal labor works, cost effective, and time efficient

Identifying The Potential Sources of Chemical Elements in Drainage and Rivers Using Google Earth Imageries and Posteriori Knowledge

This study attempts to identify the potential sources of the chemical elements in the river and drainage water using in-situ water quality sampling and public domain satellite data. Monitoring the physico-chemical level of urban streams and rivers is important to secure sufficient water resources, an indicator to the ecological degradation in urban areas and an indicator of environmental pollution. Nonetheless, identifying the potential sources of chemical pollutants by field observation is constrained by hard labor activities, time, and cost. Having satellite imagery that provides land use activity information would be useful in determining the chemical sources. Therefore, the objective of this paper is to utilize the publicly accessible Google satellite images in identifying the potential sources of the chemical elements' presence in the water that is physically sampled and measured over the selected urban rivers and drainage of Johor Bahru. Three chemical elements were identified, ammonia (NH3), nitrate (NO3-), and phosphate (PO43-). The identification of the chemical sources is conducted based on the interpretation of the satellite-derived information together with the posteriori knowledge, experience, and inputs in an environmental chemistry perspective. The findings revealed that the proportion of land used did not always have a significant impact on the chemical content of the waterways. For ammonia, areas with significant hotspots (aquaculture, wet market) are more significant, although the size of the area is not dominant. The nitrate content, on the other hand, showed quite a distinct pattern linked to oil palm, intensive farming, and industrial or commercial areas. There was no distinct land use pattern associated with phosphate level. However, locations with high residential areas were likely to have high phosphate content in their respective waterways or drainage to the onsite investigations with minimal labor works, cost effective, and time efficient

A Survey on Approximation Mechanism Design without Money for Facility Games

In a facility game one or more facilities are placed in a metric space to serve a set of selfish agents whose addresses are their private information. In a classical facility game, each agent wants to be as close to a facility as possible, and the cost of an agent can be defined as the distance between her location and the closest facility. In an obnoxious facility game, each agent wants to be far away from all facilities, and her utility is the distance from her location to the facility set. The objective of each agent is to minimize her cost or maximize her utility. An agent may lie if, by doing so, more benefit can be obtained. We are interested in social choice mechanisms that do not utilize payments. The game designer aims at a mechanism that is strategy-proof, in the sense that any agent cannot benefit by misreporting her address, or, even better, group strategy-proof, in the sense that any coalition of agents cannot all benefit by lying. Meanwhile, it is desirable to have the mechanism to be approximately optimal with respect to a chosen objective function. Several models for such approximation mechanism design without money for facility games have been proposed. In this paper we briefly review these models and related results for both deterministic and randomized mechanisms, and meanwhile we present a general framework for approximation mechanism design without money for facility games

Long Range Dynamics Related to Magnetic Impurity in the 2D Heisenberg Antiferromagnet

We consider a magnetic impurity in the two-dimensional Heisenberg antifferomagnet with long range antiferromagnetic order. At low temperature the impurity magnetic susceptibility has a Curie term ($\propto 1/T$) and a logarithmic correction ($\propto \ln(T)$). We calculate the correction and derive related Ward identity for the impurity-spin-wave vertex.Comment: 5 pages, 6 figure

Driven Morse Oscillator: Model for Multi-photon Dissociation of Nitrogen Oxide

Within a one-dimensional semi-classical model with a Morse potential the possibility of infrared multi-photon dissociation of vibrationally excited nitrogen oxide was studied. The dissociation thresholds of typical driving forces and couplings were found to be similar, which indicates that the results were robust to variations of the potential and of the definition of dissociation rate. PACS: 42.50.Hz, 33.80.WzComment: old paper, 8 pages 6 eps file

Aero-Structural Modeling of the Truss-Braced Wing Aircraft Using Potential Method with Correction Methods for Transonic Viscous Flow and Wing-Strut Interference Aerodynamics

This paper describes an aero-structural modeling method for the Transonic Truss-Braced Wing (TTBW) aircraft using VSPAERO. A vortex-lattice model of the TTBW aircraft is developed, and a transonic and viscous flow correction method is implemented in the VSPAERO models to account for transonic and viscous flow effects. A correction method for the wing-strut interference aerodynamics is developed and applied to the VSPAERO solver. Also, a structural dynamic finite-element model of the TTBW aircraft is developed. This finite-element model includes the geometric nonlinear effect due to the tension in the struts which cause a deflection dependent nonlinear stiffness. The VSPAERO models are coupled to the finite-element model to provide a rapid capability for aero-structural modeling and flutter analysis. A flight-optimized jig twist model is being developed and will be applied for the purpose of generating a full flight dynamic model of the TTBW aircraft

Investigating evidence for different black hole accretion modes since redshift z~1

Chandra data in the COSMOS, AEGIS-XD and 4Ms CDFS are combined with optical/near-IR photometry to determine the rest-frame U-V vs V-J colours of X-ray AGN hosts at mean redshifts 0.40 and 0.85. This combination of colours (UVJ) provides an efficient means of separating quiescent from star-forming, including dust reddened, galaxies. Morphological information emphasises differences between AGN split by their UVJ colours. AGN in quiescent galaxies are dominated by spheroids, while star-forming hosts are split between bulges and disks. The UVJ diagram of AGN hosts is then used to set limits on the accretion density associated with evolved and star-forming systems. Most of the black hole growth since z~1 is associated with star-forming hosts. Nevertheless, ~15-20% of the X-ray luminosity density since z~1, is taking place in the quiescent region of the UVJ diagram. For the z~0.40 subsample, there is tentative evidence (2sigma significance), that AGN split by their UVJ colours differ in Eddington ratio. AGN in star-forming hosts dominate at high Eddington ratios, while AGN in quiescent hosts become increasingly important as a fraction of the total population toward low Eddington ratios. At higher redshift, z~0.8, such differences are significant at the 2sigma level only at Eddington ratios >1e-3. These findings are consistent with scenarios in which diverse accretion modes are responsible for the build-up of SMBHs at the centres of galaxies. We compare our results with the GALFORM semi-analytic model, which postulates two black hole fuelling modes, the first linked to star-formation and the second occuring in passive galaxies. GALFORM predicts a larger fraction of black hole growth in quiescent galaxies at z<1, compared to the data. Relaxing the strong assumption of the model that passive AGN hosts have zero star-formation rate could reconcile this disagreement.Comment: MNRAS accepte

Velocity field distributions due to ideal line vortices

We evaluate numerically the velocity field distributions produced by a bounded, two-dimensional fluid model consisting of a collection of parallel ideal line vortices. We sample at many spatial points inside a rigid circular boundary. We focus on ``nearest neighbor'' contributions that result from vortices that fall (randomly) very close to the spatial points where the velocity is being sampled. We confirm that these events lead to a non-Gaussian high-velocity ``tail'' on an otherwise Gaussian distribution function for the Eulerian velocity field. We also investigate the behavior of distributions that do not have equilibrium mean-field probability distributions that are uniform inside the circle, but instead correspond to both higher and lower mean-field energies than those associated with the uniform vorticity distribution. We find substantial differences between these and the uniform case.Comment: 21 pages, 9 figures. To be published in Physical Review E (http://pre.aps.org/) in May 200

Chern - Simons Gauge Field Theory of Two - Dimensional Ferromagnets

A Chern-Simons gauged Nonlinear Schr\"odinger Equation is derived from the continuous Heisenberg model in 2+1 dimensions. The corresponding planar magnets can be analyzed whithin the anyon theory. Thus, we show that static magnetic vortices correspond to the self-dual Chern - Simons solitons and are described by the Liouville equation. The related magnetic topological charge is associated with the electric charge of anyons. Furthermore, vortex - antivortex configurations are described by the sinh-Gordon equation and its conformally invariant extension. Physical consequences of these results are discussed.Comment: 15 pages, Plain TeX, Lecce, June 199