ATM-deficient thymic lymphoma is associated with aberrant tcrd rearrangement and gene amplification

Ataxia telangiectasia mutated (ATM) deficiency predisposes humans and mice to T lineage lymphomas with recurrent chromosome 14 translocations involving the T cell receptor α/δ (Tcra/d) locus. Such translocations have been thought to result from aberrant repair of DNA double-strand breaks (DSBs) during Tcra locus V(D)J recombination, and to require the Tcra enhancer (Eα) for Tcra rearrangement or expression of the translocated oncogene. We now show that, in addition to the known chromosome 14 translocation, ATM-deficient mouse thymic lymphomas routinely contain a centromeric fragment of chromosome 14 that spans up to the 5′ boundary of the Tcra/d locus, at which position a 500-kb or larger region centromeric to Tcra/d is routinely amplified. In addition, they routinely contain a large deletion of the telomeric end of one copy of chromosome 12. In contrast to prior expectations, the recurrent translocations and amplifications involve V(D)J recombination–initiated breaks in the Tcrd locus, as opposed to the Tcra locus, and arise independently of the Eα. Overall, our studies reveal previously unexpected mechanisms that contribute to the oncogenic transformation of ATM-deficient T lineage cells

A characteristics framework for Semantic Information Systems Standards

Semantic Information Systems (IS) Standards play a critical role in the development of the networked economy. While their importance is undoubted by all stakeholders—such as businesses, policy makers, researchers, developers—the current state of research leaves a number of questions unaddressed. Terminological confusion exists around the notions of “business semantics”, “business-to-business interoperability”, and “interoperability standards” amongst others. And, moreover, a comprehensive understanding about the characteristics of Semantic IS Standards is missing. The paper addresses this gap in literature by developing a characteristics framework for Semantic IS Standards. Two case studies are used to check the applicability of the framework in a “real-life” context. The framework lays the foundation for future research in an important field of the IS discipline and supports practitioners in their efforts to analyze, compare, and evaluate Semantic IS Standard

Practical approximation scheme for the pion dynamics in the three-nucleon system

We discuss a working approximation scheme to a recently developed formulation of the coupled piNNN-NNN problem. The approximation scheme is based on the physical assumption that, at low energies, the 2N-subsystem dynamics in the elastic channel is conveniently described by the usual 2N-potential approach, while the explicit pion dynamics describes small, correction-type effects. Using the standard separable-expansion method, we obtain a dynamical equation of the Alt-Grassberger-Sandhas (AGS) type. This is an important result, because the computational techniques used for solving the normal AGS equation can also be used to describe the pion dynamics in the 3N system once the matrix dimension is increased by one component. We have also shown that this approximation scheme treats the conventional 3N problem once the pion degrees of freedom are projected out. Then the 3N system is described with an extended AGS-type equation where the spin-off of the pion dynamics (beyond the 2N potential) is taken into account in additional contributions to the driving term. These new terms are shown to reproduce the diagrams leading to modern 3N-force models. We also recover two sets of irreducible diagrams that are commonly neglected in 3N-force discussions, and conclude that these sets should be further investigated, because a claimed cancellation is questionable.Comment: 18 pages, including 5 figures, RevTeX, Eps

The pion-three-nucleon problem with two-cluster connected-kernel equations

It is found that the coupled piNNN-NNN system breaks into fragments in a nontrivial way. Assuming the particles as distinguishable, there are indeed four modes of fragmentation into two clusters, while in the standard three-body problem there are three possible two-cluster partitions and conversely the four-body problem has seven different possibilities. It is shown how to formulate the pion-three-nucleon collision problem through the integral-equation approach by taking into account the proper fragmentation of the system. The final result does not depend on the assumption of separability of the two-body t-matrices. Then, the quasiparticle method a' la Grassberger-Sandhas is applied and effective two-cluster connected-kernel equations are obtained. The corresponding bound-state problem is also formulated, and the resulting homogeneous equation provides a new approach which generalizes the commonly used techniques to describe the three-nucleon bound-state problem, where the meson degrees of freedom are usually suppressed.Comment: 20 pages, REVTeX, with 3 COLOR figures (PostScript

Analysis of Mice Lacking DNaseI Hypersensitive Sites at the 5′ End of the IgH Locus

The 5′ end of the IgH locus contains a cluster of DNaseI hypersensitive sites, one of which (HS1) was shown to be pro-B cell specific and to contain binding sites for the transcription factors PU.1, E2A, and Pax5. These data as well as the location of the hypersensitive sites at the 5′ border of the IgH locus suggested a possible regulatory function for these elements with respect to the IgH locus. To test this notion, we generated mice carrying targeted deletions of either the pro-B cell specific site HS1 or the whole cluster of DNaseI hypersensitive sites. Lymphocytes carrying these deletions appear to undergo normal development, and mutant B cells do not exhibit any obvious defects in V(D)J recombination, allelic exclusion, or class switch recombination. We conclude that deletion of these DNaseI hypersensitive sites does not have an obvious impact on the IgH locus or B cell development

Structure and reactions of pentaquark baryons

We review the current status of the exotic pentaquark baryons. After a brief look at experiments of both positive and negative results, we discuss theoretical methods to study the structure and reactions for the pentaquarks. First we introduce the quark model and the chiral soliton model, where we discuss the relation of mass spectrum and parity with some emphasis on the role of chiral symmetry. It is always useful to picture the structure of the pentaquarks in terms of quarks. As for other methods, we discuss a model independent method, and briefly mention the results from the lattice and QCD sum rule. Decay properties are then studied in some detail, which is one of the important properties of Theta+. We investigate the relation between the decay width and the quark structure having certain spin-parity quantum numbers. Through these analyses, we consider as plausible quantum numbers of Theta+, JP = 3/2-. In the last part of this note, we discuss production reactions of Theta+ which provide links between the theoretical models and experimental information. We discuss photoproductions and hadron-induced reactions which are useful to explore the nature of Theta+Comment: 20 pages, proceedings for the workshop on HADRON PHYSICS, March 7 - 17, (2005) Puri, Indi

A Naturally Narrow Positive Parity Theta^+

We present a consistent color-flavor-spin-orbital wave function for a positive parity Theta^+ that naturally explains the observed narrowness of the state. The wave function is totally symmetric in its flavor-spin part and totally antisymmetric in its color-orbital part. If flavor-spin interactions dominate, this wave function renders the positive parity Theta^+ lighter than its negative parity counterpart. We consider decays of the Theta^+ and compute the overlap of this state with the kinematically allowed final states. Our results are numerically small. We note that dynamical correlations between quarks are not necessary to obtain narrow pentaquark widths.Comment: 10 pages, 1 figure, Revtex4, two-column format, version to be published in Phys. Rev. D, includes numerical estimates of decay width

Z^* Resonances: Phenomenology and Models

We explore the phenomenology of, and models for, the Z^* resonances, the lowest of which is now well established, and called the Theta. We provide an overview of three models which have been proposed to explain its existence and/or its small width, and point out other relevant predictions, and potential problems, for each. The relation to what is known about KN scattering, including possible resonance signals in other channels, is also discussed.Comment: 29 pages, uses RevTeX4; expanded version (published form

Benchmarking implementations of functional languages with ‘Pseudoknot', a float-intensive benchmark

Over 25 implementations of different functional languages are benchmarked using the same program, a floating-point intensive application taken from molecular biology. The principal aspects studied are compile time and execution time for the various implementations that were benchmarked. An important consideration is how the program can be modified and tuned to obtain maximal performance on each language implementation. With few exceptions, the compilers take a significant amount of time to compile this program, though most compilers were faster than the then current GNU C compiler (GCC version 2.5.8). Compilers that generate C or Lisp are often slower than those that generate native code directly: the cost of compiling the intermediate form is normally a large fraction of the total compilation time. There is no clear distinction between the runtime performance of eager and lazy implementations when appropriate annotations are used: lazy implementations have clearly come of age when it comes to implementing largely strict applications, such as the Pseudoknot program. The speed of C can be approached by some implementations, but to achieve this performance, special measures such as strictness annotations are required by non-strict implementations. The benchmark results have to be interpreted with care. Firstly, a benchmark based on a single program cannot cover a wide spectrum of ‘typical' applications. Secondly, the compilers vary in the kind and level of optimisations offered, so the effort required to obtain an optimal version of the program is similarly varie