Compound heterozygous mutations in RIPPLY2 associated with vertebral segmentation defects

Segmentation defects of the vertebrae (SDV) are caused by aberrant somite formation during embryogenesis and result in irregular formation of the vertebrae and ribs. The Notch signal transduction pathway plays a critical role in somite formation and patterning in model vertebrates. In humans, mutations in several genes involved in the Notch pathway are associated with SDV, with both autosomal recessive (MESP2, DLL3, LFNG, HES7) and autosomal dominant (TBX6) inheritance. However, many individuals with SDV do not carry mutations in these genes. Using whole-exome capture and massive parallel sequencing, we identified compound heterozygous mutations in RIPPLY2 in two brothers with multiple regional SDV, with appropriate familial segregation. One novel mutation (c.A238T:p.Arg80*) introduces a premature stop codon. In transiently transfected C2C12 mouse myoblasts, the RIPPLY2 mutant protein demonstrated impaired transcriptional repression activity compared with wild-type RIPPLY2 despite similar levels of expression. The other mutation (c.240-4T>G), with minor allele frequency <0.002, lies in the highly conserved splice site consensus sequence 5' to the terminal exon. Ripply2 has a well-established role in somitogenesis and vertebral column formation, interacting at both gene and protein levels with SDV-associated Mesp2 and Tbx6. We conclude that compound heterozygous mutations in RIPPLY2 are associated with SDV, a new gene for this condition. © The Author 2014.

Geometric Representation of Graphs in Low Dimension Using Axis Parallel Boxes

An axis-parallel k-dimensional box is a Cartesian product R-1 x R-2 x...x R-k where R-i (for 1 <= i <= k) is a closed interval of the form [a(i), b(i)] on the real line. For a graph G, its boxicity box(G) is the minimum dimension k, such that G is representable as the intersection graph of (axis-parallel) boxes in k-dimensional space. The concept of boxicity finds applications in various areas such as ecology, operations research etc. A number of NP-hard problems are either polynomial time solvable or have much better approximation ratio on low boxicity graphs. For example, the max-clique problem is polynomial time solvable on bounded boxicity graphs and the maximum independent set problem for boxicity d graphs, given a box representation, has a left perpendicular1 + 1/c log n right perpendicular(d-1) approximation ratio for any constant c >= 1 when d >= 2. In most cases, the first step usually is computing a low dimensional box representation of the given graph. Deciding whether the boxicity of a graph is at most 2 itself is NP-hard. We give an efficient randomized algorithm to construct a box representation of any graph G on n vertices in left perpendicular(Delta + 2) ln nright perpendicular dimensions, where Delta is the maximum degree of G. This algorithm implies that box(G) <= left perpendicular(Delta + 2) ln nright perpendicular for any graph G. Our bound is tight up to a factor of ln n. We also show that our randomized algorithm can be derandomized to get a polynomial time deterministic algorithm. Though our general upper bound is in terms of maximum degree Delta, we show that for almost all graphs on n vertices, their boxicity is O(d(av) ln n) where d(av) is the average degree.

Shape effect on optimal geometric conditions in surface aeration systems

The performance of surface aeration systems, among other key design variables, depends upon the geometric parameters of the aeration tank. Efficient performance and scale up or scale down of the experimental results of an aeration ystem requires optimal geometric conditions. Optimal conditions refer to the conditions of maximum oxygen transfer rate, which assists in scaling up or down the system for ommercial utilization. The present work investigates the effect of an aeration tank's shape (unbaffled circular, baffled circular and unbaffled square) on oxygen transfer. Present results demonstrate that there is no effect of shape on the optimal geometric conditions for rotor position and rotor dimensions. This experimentation shows that circular tanks (baffled or unbaffled) do not have optimal geometric conditions for liquid transfer, whereas the square cross-section tank shows a unique geometric shape to optimize oxygen transfer.

A geometric approach for determining inner and exterior boundaries of workspaces of planar manipulators

In this paper a method to determine the internal and external boundaries of planar workspaces, represented with an ordered set of points, is presented. The sequence of points are grouped and can be interpreted to form a sequence of curves. Three successive curves are used for determining the instantaneous center of rotation for the second one of them. The two extremal points on the curve with respect to the instantaneous center are recognized as singular points. The chronological ordering of these singular points is used to generate the two envelope curves, which are potentially intersecting. Methods have been presented in the paper for the determination of the workspace boundary from the envelope curves. Strategies to deal with the manipulators with joint limits and various degenerate situations have also been discussed. The computational steps being completely geometric, the method does not require the knowledge about the manipulator's kinematics. Hence, it can be used for the workspace of arbitrary planar manipulators. A number of illustrative examples demonstrate the efficacy of the proposed method.

A geometric approach to stationary defect solutions in one space dimension

In this manuscript, we consider the impact of a small jump-type spatial heterogeneity on the existence of stationary localized patterns in a system of partial dierential equations in one spatial dimension...

Capturability analysis of a geometric guidance law in relative velocity space

In this paper, a relative velocity approach is used to analyze the capturability of a geometric guidance law. Point mass models are assumed for both the missile and the target. The speeds of the missile and target are assumed to remain constant throughout the engagement. Lateral acceleration, obtained from the guidance law, is applied to change the path of the missile. The kinematic equations for engagements in the horizontal plane are derived in the relative velocity space. Some analytical results for the capture region are obtained for non-maneuvering and maneuvering targets. For non-maneuvering targets it is enough for the navigation gain to be a constant to intercept the target, while for maneuvering targets a time varying navigation gain is needed for interception. These results are then verified through numerical simulations.

Dimethyl sulfide and other biogenic volatile organic compound emissions from branching coral and reef seawater: Potential sources of secondary aerosol over the Great Barrier Reef

Volatile organic compounds (VOCs) in the headspace of bubble chambers containing branches of live coral in filtered reef seawater were analysed using gas chromatography with mass spectrometry (GC-MS). When the coral released mucus it was a source of dimethyl sulfide (DMS) and isoprene; however, these VOCs were not emitted to the chamber headspace from mucus-free coral. This finding, which suggests that coral is an intermittent source of DMS and isoprene, was supported by the observation of occasional large pulses of atmospheric DMS (DMSa) over Heron Island reef on the southern Great Barrier Reef (GBR), Australia, in the austral winter. The highest DMSa pulse (320 ppt) was three orders of magnitude less than the DMS mixing ratio (460 ppb) measured in the headspace of a dynamically purged bubble chamber containing a mucus-coated branch of Acropora aspera indicating that coral reefs can be strong point sources of DMSa. Static headspace GC-MS analysis of coral fragments identified mainly DMS and seven other minor reduced sulfur compounds including dimethyl disulfide, methyl mercaptan, and carbon disulfide, while coral reef seawater was an indicated source of methylene chloride, acetone, and methyl ethyl ketone. The VOCs emitted by coral and reef seawater are capable of producing new atmospheric particles < 15 nm diameter as observed at Heron Island reef. DMS and isoprene are known to play a role in low-level cloud formation, so aerosol precursors such as these could influence regional climate through a sea surface temperature regulation mechanism hypothesized to operate over the GBR.

Topological properties of the one dimensional exponential random geometric graph

In this article we study the one-dimensional random geometric (random interval) graph when the location of the nodes are independent and exponentially distributed. We derive exact results and limit theorems for the connectivity and other properties associated with this random graph. We show that the asymptotic properties of a graph with a truncated exponential distribution can be obtained using the exponential random geometric graph. © 2007 Wiley Periodicals, Inc. Random Struct. Alg., 2008.

Diffusion of Be, Co and Mn impurities in compound semiconductors and glassy carbon studied by the modified radiotracer technique

The main method of modifying properties of semiconductors is to introduce small amount of impurities inside the material. This is used to control magnetic and optical properties of materials and to realize p- and n-type semiconductors out of intrinsic material in order to manufacture fundamental components such as diodes. As diffusion can be described as random mixing of material due to thermal movement of atoms, it is essential to know the diffusion behavior of the impurities in order to manufacture working components. In modified radiotracer technique diffusion is studied using radioactive isotopes of elements as tracers. The technique is called modified as atoms are deployed inside the material by ion beam implantation. With ion implantation, a distinct distribution of impurities can be deployed inside the sample surface with good con- trol over the amount of implanted atoms. As electromagnetic radiation and other nuclear decay products emitted by radioactive materials can be easily detected, only very low amount of impurities can be used. This makes it possible to study diffusion in pure materials without essentially modifying the initial properties by doping. In this thesis a modified radiotracer technique is used to study the diffusion of beryllium in GaN, ZnO, SiGe and glassy carbon. GaN, ZnO and SiGe are of great interest to the semiconductor industry and beryllium as a small and possibly rapid dopant hasn t been studied previously using the technique. Glassy carbon has been added to demonstrate the feasibility of the technique. In addition, the diffusion of magnetic impurities, Mn and Co, has been studied in GaAs and ZnO (respectively) with spintronic applications in mind.