Inhibition of glucocorticoid-induced apoptosis by targeting splice variants of \u3ci\u3eBIM\u3c/i\u3e mRNA with small interfering RNA and short hairpin RNA.

Glucocorticoids (GCs) induce apoptosis in lymphocytes and are effective agents for the treatment of leukemia. The activated glucocorticoid receptor (GR) initiates a transcriptional program leading to caspase activation and cell death, but the critical signaling intermediates in GC-induced apoptosis remain largely undefined. We have observed that GC induction of the three major protein products of the Bcl-2 relative Bim (BimEL, BimS and BimL) correlates with GC sensitivity in a panel of human pre-B acute lymphoblastic leukemia (ALL) cell lines. To test the hypothesis that Bim facilitates GC-induced apoptosis, we reduced BIM mRNA levels and Bim protein levels by RNA interference (RNAi) in highly GC-sensitive pre-B ALL cells. Reducing Bim proteins by either electroporation of synthetic siRNA duplexes or lentiviral-mediated stable expression of shRNA inhibited activation of caspase-3 and increased cell viability following GC exposure. We also observed that the extent of GC resistance correlated with siRNA silencing potency. siRNA duplexes that reduced only BimEL or BimEL and BimL (but not BimS) exhibited less GC resistance than a potent siRNA that silenced all three major isoforms, implying that induction of all three Bim proteins contributes to cell death. Finally, the modulation of GC-induced apoptosis caused by Bim silencing was independent of Bcl-2 expression levels, negating the hypothesis that the ratio of Bim to Bcl-2 regulates apoptosis. These results offer evidence that induction of Bim by GC is a required event for the complete apoptotic response in pre-B ALL cells

Coherent and generalized intelligent states for infinite square well potential and nonlinear oscillators

This article is an illustration of the construction of coherent and generalized intelligent states which has been recently proposed by us for an arbitrary quantum system $[ 1]$. We treat the quantum system submitted to the infinite square well potential and the nonlinear oscillators. By means of the analytical representation of the coherent states \`{a} la Gazeau-Klauder and those \`{a} la Klauder-Perelomov, we derive the generalized intelligent states in analytical ways

Are there any good digraph width measures?

Several different measures for digraph width have appeared in the last few years. However, none of them shares all the "nice" properties of treewidth: First, being \emph{algorithmically useful} i.e. admitting polynomial-time algorithms for all \MS1-definable problems on digraphs of bounded width. And, second, having nice \emph{structural properties} i.e. being monotone under taking subdigraphs and some form of arc contractions. As for the former, (undirected) \MS1 seems to be the least common denominator of all reasonably expressive logical languages on digraphs that can speak about the edge/arc relation on the vertex set.The latter property is a necessary condition for a width measure to be characterizable by some version of the cops-and-robber game characterizing the ordinary treewidth. Our main result is that \emph{any reasonable} algorithmically useful and structurally nice digraph measure cannot be substantially different from the treewidth of the underlying undirected graph. Moreover, we introduce \emph{directed topological minors} and argue that they are the weakest useful notion of minors for digraphs

Tweed in Martensites: A Potential New Spin Glass

We've been studying the ``tweed'' precursors above the martensitic transition in shape--memory alloys. These characteristic cross--hatched modulations occur for hundreds of degrees above the first--order shape--changing transition. Our two--dimensional model for this transition, in the limit of infinite elastic anisotropy, can be mapped onto a spin--glass Hamiltonian in a random field. We suggest that the tweed precursors are a direct analogy of the spin--glass phase. The tweed is intermediate between the high--temperature cubic phase and the low--temperature martensitic phase in the same way as the spin--glass phase can be intermediate between ferromagnet and antiferromagnet.Comment: 18 pages and four figures (included

Fixed-Parameter Tractability of Token Jumping on Planar Graphs

Suppose that we are given two independent sets $I_0$ and $I_r$ of a graph such that $|I_0| = |I_r|$, and imagine that a token is placed on each vertex in $I_0$. The token jumping problem is to determine whether there exists a sequence of independent sets which transforms $I_0$ into $I_r$ so that each independent set in the sequence results from the previous one by moving exactly one token to another vertex. This problem is known to be PSPACE-complete even for planar graphs of maximum degree three, and W[1]-hard for general graphs when parameterized by the number of tokens. In this paper, we present a fixed-parameter algorithm for the token jumping problem on planar graphs, where the parameter is only the number of tokens. Furthermore, the algorithm can be modified so that it finds a shortest sequence for a yes-instance. The same scheme of the algorithms can be applied to a wider class of graphs, $K_{3,t}$-free graphs for any fixed integer $t \ge 3$, and it yields fixed-parameter algorithms

Structure and formation energy of carbon nanotube caps

We present a detailed study of the geometry, structure and energetics of carbon nanotube caps. We show that the structure of a cap uniquely determines the chirality of the nanotube that can be attached to it. The structure of the cap is specified in a geometrical way by defining the position of six pentagons on a hexagonal lattice. Moving one (or more) pentagons systematically creates caps for other nanotube chiralities. For the example of the (10,0) tube we study the formation energy of different nanotube caps using ab-initio calculations. The caps with isolated pentagons have an average formation energy 0.29+/-0.01eV/atom. A pair of adjacent pentagons requires a much larger formation energy of 1.5eV. We show that the formation energy of adjacent pentagon pairs explains the diameter distribution in small-diameter nanotube samples grown by chemical vapor deposition.Comment: 8 pages, 8 figures (gray scale only due to space); submitted to Phys. Rev.

Arkansas Cotton Variety Test 2002

The primary aim of the Arkansas Cotton Variety Test is to provide unbiased data regarding the agronomic performance of cotton varieties and advanced breeding lines in the major cotton-growing areas of Arkansas. This information helps seed dealers establish marketing strategies and assists producers in choosing varieties to plant. In this way, the annual test facilitates the inclusion of new, improved genetic material into Arkansas cotton production. Variety adaptation is determined by evaluation of the varieties and lines at four University of Arkansas research stations located near Keiser, Clarkedale, Marianna, and Rohwer. Tests are duplicated in irrigated and non-irrigated culture at the Keiser and Marianna locations. In 2002, 37 entries were evaluated in the main test and 25 were evaluated in the first-year test. This report also includes the Mississippi County Cotton Variety Test (a large-plot, on-farm evaluation of 12 Round-up Ready varieties) and 12 other on-farm cotton variety tests conducted by the University of Arkansas Cooperative Extension Service

An FPT 2-Approximation for Tree-Cut Decomposition

The tree-cut width of a graph is a graph parameter defined by Wollan [J. Comb. Theory, Ser. B, 110:47-66, 2015] with the help of tree-cut decompositions. In certain cases, tree-cut width appears to be more adequate than treewidth as an invariant that, when bounded, can accelerate the resolution of intractable problems. While designing algorithms for problems with bounded tree-cut width, it is important to have a parametrically tractable way to compute the exact value of this parameter or, at least, some constant approximation of it. In this paper we give a parameterized 2-approximation algorithm for the computation of tree-cut width; for an input $n$-vertex graph $G$ and an integer $w$, our algorithm either confirms that the tree-cut width of $G$ is more than $w$ or returns a tree-cut decomposition of $G$ certifying that its tree-cut width is at most $2w$, in time $2^{O(w^2\log w)} \cdot n^2$. Prior to this work, no constructive parameterized algorithms, even approximated ones, existed for computing the tree-cut width of a graph. As a consequence of the Graph Minors series by Robertson and Seymour, only the existence of a decision algorithm was known.Comment: 17 pages, 3 figure

Maximum Edge-Disjoint Paths in kk-sums of Graphs

We consider the approximability of the maximum edge-disjoint paths problem (MEDP) in undirected graphs, and in particular, the integrality gap of the natural multicommodity flow based relaxation for it. The integrality gap is known to be $\Omega(\sqrt{n})$ even for planar graphs due to a simple topological obstruction and a major focus, following earlier work, has been understanding the gap if some constant congestion is allowed. In this context, it is natural to ask for which classes of graphs does a constant-factor constant-congestion property hold. It is easy to deduce that for given constant bounds on the approximation and congestion, the class of "nice" graphs is nor-closed. Is the converse true? Does every proper minor-closed family of graphs exhibit a constant factor, constant congestion bound relative to the LP relaxation? We conjecture that the answer is yes. One stumbling block has been that such bounds were not known for bounded treewidth graphs (or even treewidth 3). In this paper we give a polytime algorithm which takes a fractional routing solution in a graph of bounded treewidth and is able to integrally route a constant fraction of the LP solution's value. Note that we do not incur any edge congestion. Previously this was not known even for series parallel graphs which have treewidth 2. The algorithm is based on a more general argument that applies to $k$-sums of graphs in some graph family, as long as the graph family has a constant factor, constant congestion bound. We then use this to show that such bounds hold for the class of $k$-sums of bounded genus graphs