Core promoter short tandem repeats as evolutionary switch codes for primate speciation

Alteration in gene expression levels underlies many of the phenotypic differences across species. Because of their highly mutable nature, proximity to the +1 transcription start site (TSS), and the emerging evidence of functional impact on gene expression, core promoter short tandem repeats (STRs) may be considered an ideal source of variation across species. In a genome-scale analysis of the entire Homo sapiens protein-coding genes, we have previously identified core promoters with at least one STR of ≥6-repeats, with possible selective advantage in this species. In the current study, we performed reverse analysis of the entire Homo sapiens orthologous genes in mouse in the Ensembl database, in order to identify conserved STRs that have shrunk as an evolutionary advantage to humans. Two protocols were used to minimize ascertainment bias. Firstly, two species sharing a more recent ancestor with Homo sapiens (i.e. Pan troglodytes and Gorilla gorilla gorilla) were also included in the study. Secondly, four non-primate species encompassing the major orders across Mammals, including Scandentia, Laurasiatheria, Afrotheria, and Xenarthra were analyzed as out-groups. We introduce STR evolutionary events specifically identical in primates (i.e. Homo sapiens, Pan troglodytes, and Gorilla gorilla gorilla) vs. non-primate out-groups. The average frequency of the identically shared STR motifs across those primates ranged between 0.00005 and 0.06. The identified genes are involved in important evolutionary and developmental processes, such as normal craniofacial development (TFAP2B), regulation of cell shape (PALMD), learning and long-term memory (RGS14), nervous system development (GFRA2), embryonic limb morphogenesis (PBX2), and forebrain development (APAF1). We provide evidence of core promoter STRs as evolutionary switch codes for primate speciation, and the first instance of identity-by-descent for those motifs at the interspecies level. © 2014 Wiley Periodicals, Inc

Asymmetric Water Entry of Twin Wedges with Different Deadrises, Heel Angles, and Wedge Separations using Finite Element Based Finite Volume Method and VOF

Asymmetric water entry of twin wedges is investigated for deadrise angles of 30 and 50 degrees, and heel angles of 5, 10, 15, and 20 degrees as well as wedge separation ratios of 1 and 2. Finite Element based Finite Volume method (FEM-FVM) is used in conjunction with Volume of Fluid (VOF) scheme for the targeted analyses. Free surface evolution and impact forces versus time are determined and comparisons of the maximum force of the wedges against each other are presented for all the considered cases. It is demonstrated that the impact force on the second wedge is always greater than the first one by a minimum of 6% and maximum of 146% which is a very significant increase in the impact force and may cause high accelerations and damage to the structure. It is also observed that the mentioned effects increase with decreasing deadrise angle and increasing heel angle

Preliminary Experimental Investigation on a Low Profile Magneto-Hydrodynamic Propulsive Blanket, Considering Plasma Generation

The use of magnetohydrodynamic (MHD) blanket propulsion system in ships, even with low efficiencies, has particular benefits that can make them an appropriate option for the marine designers. Accordingly, any attempt to increase the efficiency of these systems requires full recognition of their performance in different conditions. In the present study, as a continuation of previous numerical works by the current authors, a magneto-hydrodynamic blanket propulsion system has been built and experimentally studied through examining the MHD forces produced in different voltages. Copper and gold have been used and compared as electrodes and the high advantage of gold has been demonstrated. The effect of electrolysis on the behavior of the blanket is analyzed. It has been demonstrated that although electrolysis restricts high currents in lower voltages (lower than ~140V) and the saturation of hydrogen decreases the MHD forces due to low electrical current (~140V up to ~160V), the saturation of hydrogen around cathode at high voltages (more than ~160V), makes a dielectric barrier which soon breaks down and make the production of plasma possible, which in turn highly increases the thrust force of the MHD blanket. Therefore, three regimes have been introduced and described for the MHD blanket; the electrolysis regime, the transition regime, and the hot plasma regime. Based on the obtained results, one may conclude that the present results have offered good evidence about the possibility of increasing the MHD blanket performance through plasma production in water

Statistical Analysis of Wedge Effect on the Seakeeping of a Planing Hull in Irregular Waves at the Onset of the Planing Region

In the current paper, different experiments are conducted on a high speed planing craft in irregular waves, with and without a wedge. Performance and seakeeping aspects of these planing hulls in the form of trim, rise-up, and resistance in regular waves and heave, pitch, bow, and center of gravity (CG) acceleration in irregular waves are extracted in time series. Irregular waves represent sea state 3 with 12cm height and peak period of 1.66. A model length of 2.63m and 1:5 scale is considered and all data for irregular waves are scaled, as well. The deadrise angle is constant and is taken to be 24 degrees. The targeted experimental tests are conducted for four longitudinal Froude numbers of 1.0, 1.18, 1.37, and 1.57, which are all in the planing regime. The results are analyzed for the mean height of wave, significant wave height, RMS, and spectrum. The comprehensive study of wedges' effects is also presented which indicates that a wedge can decrease the motions and accelerations, exceedingly. Ultimately, the obtained results are compared against those by Fridsma (1971) and Soletic (2010) and it is demonstrated that motions and accelerations are indeed reduced

Applying Different Strategies within OpenFOAM to Investigate the Effects of Breakup and Collision Model on the Spray and in-Cylinder Gas Mixture Attribute

In the current study, a 3-D numerical simulation of two-phase flow has been conducted in a direct injection CI engine using the Eularian-Lagrangian approach and a new breakup model. The newly modified breakup scheme has been implemented for simulating the ultra-high pressure diesel injection. The effects of droplet breakup and collision model on the spray and in-cylinder gas characteristics have been examined using the open source code OpenFOAM. Spray penetration and cone angle are investigated as spray properties and surrounding gas motion are studied by in-cylinder gas velocity and pressure distribution for non-evaporating conditions. In addition, vapor penetration of the evaporating spray is presented to study the effects of current scheme on the evaporating condition. The continuous field is described by RANS equations and dynamics of the dispersed droplet is modeled by Lagrangian tracking scheme. Results of the proposed modified KHRT model are compared against other default methods in OpenFOAM and favorable agreement is achieved. Robustness and accuracy of different breakup schemes and collision models are also verified using the published experimental data. It is demonstrated that the proposed breakup scheme and Nordin collision model display very accurate results in the case of ultra-high pressure injection

Particle and Gas Flow Modeling of Wall-impinging Diesel Spray under Ultra-high Fuel Injection Pressures

Advanced models of spray breakup and droplet collision are implemented in OpenFOAM code for comparing the flat-wall impinging and free fuel sprays under ultra-high pressure direct injection diesel engines. The non-evaporating spray and ambient gas flow characteristics are analyzed by a combination of Eulerian and Lagrangian methods for continuous and dispersed phase, respectively. Various injection pressures and two different impinging distances are used. Reynolds Averaged Navier Stokes (RANS) equations are solved using standard k-ε turbulence model. Computational domain and grid size are determined based on a mesh study. Numerical results are validated by published experimental data for free and wall-impinging sprays. The robustness and accuracy of the proposed scheme are confirmed by comparing the main characteristics of spray and surrounding gas against published experimental data. To accomplish this, spray shape, penetration and gas velocity vectors are compared with experimental data and insightful understanding of the spray characteristics are provided. In comparison with free spray, tip penetration has been limited in impinging sprays. Turbulent flow in impinging sprays leads to more induced air motion. Also, impinging spray leads to more pushed-out gas velocity. The obtained results indicate that the numerical findings are generally in good agreement with experimental data in case of ultra-high injection pressures and micro-hole injectors

Curvature Effects on the Electromagnetic Force, Efficiency, and Heat Transfer of a Weak Low Profile Magneto-Hydrodynamic Blanket Propulsion System

The present study concerns the numerical assessment of the effects of longitudinal and lateral curvature of a flexible low profile magneto-hydrodynamic blanket on its thrust, performance, and heat transfer. To this end, after validating the solver with the analytical solution of the Hartman problem, negative and positive curvatures are taken into consideration in lateral and longitudinal directions on the blanket and electromagnetic and velocity fields, temperature distributions, force density fields and profiles are extracted and compared to the flat MHD blanket. It is demonstrated that negative curvatures increase the thrust force and temperature of the blanket and the reverse occurs for the positive curvatures. It is also shown that the longitudinal curvature affects the blanket thrust by -2.5% up to 5.2%, its efficiency by nearly 6% and the temperature change from -25 up to 28%. On the other hand, for the lateral curvatures, the overall thrust produced by the blanket is affected by about -6% to +6%, the efficiency is affected by -10% to 25% and temperature change is affected by -2 to 6%