In vivo analysis of NHPX reveals a novel nucleolar localization pathway involving a transient accumulation in splicing speckles

The NHPX protein is a nucleolar factor that binds directly to a conserved RNA target sequence found in nucleolar box C/D snoRNAs and in U4 snRNA. Using enhanced yellow fluorescent protein (EYFP)– and enhanced cyan fluorescent protein–NHPX fusions, we show here that NHPX is specifically accumulated in both nucleoli and Cajal bodies (CBs) in vivo. The fusion proteins display identical localization patterns and RNA binding specificities to the endogenous NHPX. Analysis of a HeLa cell line stably expressing EYFP–NHPX showed that the nucleolar accumulation of NHPX was preceded by its transient accumulation in splicing speckles. Only newly expressed NHPX accumulated in speckles, and the nucleolar pool of NHPX did not interchange with the pool in speckles, consistent with a unidirectional pathway. The transient accumulation of NHPX in speckles prior to nucleoli was observed in multiple cell lines, including primary cells that lack CBs. Inhibitor studies indicated that progression of newly expressed NHPX from speckles to nucleoli was dependent on RNA polymerase II transcription, but not on RNA polymerase I activity. The data show a specific temporal pathway involving the sequential and directed accumulation of NHPX in distinct subnuclear compartments, and define a novel mechanism for nucleolar localization

Quantum-Mechanical Approach to Collision-Induced Radiative Emissions

Charge exchange is a process that occurs in an atomic collision where an electron from one of the colliding particles is transferred to the other; typically from a neutral atom or molecule to an ion. Electrons transferred into an excited energy state then decay into a lower-energy state and emit photons during this process. This phenomenon of collision-induced radiative emissions is of great interest in astrophysics and experimental x-ray spectroscopy research since it helps understand the production of x-rays in astrophysical settings. On the theoretical side, obtaining a description of these radiative emissions involves numerical work since a closed-form solution is not possible. Using standard numerical approaches, one needs to rely on models and approximations, especially in collision problems involving many-electron systems. Consequently, results obtained in this way can be at odds with experimental observations and/or results from different theoretical methods. In this dissertation, the main method is the two-centre basis generator method performed within the independent electron model. It is a dynamical approach to solving atomic collision problems and has shown to be reliable in describing charge exchange and other electronic processes. This work gives an extensive view on the applicability of this approach in the context of collision-induced radiative emissions where present results from a variety of ion-atom and ion-molecule collisions are benchmarked with results from previous studies

LU Factorization of Sparse, Unsymmetric Jacobian Matrices on Multicomputers: Experience, Strategies, Performance

Efficient sparse linear algebra cannot be achieved as a straightforward extension of the dense case, even for concurrent implementations. This paper details a new, general-purpose unsymmetric sparse LU factorization code built on the philosophy of Harwell’s MA28, with variations. We apply this code in the framework of Jacobian-matrix factorizations, arising from Newton iterations in the solution of nonlinear systems of equations. Serious attention has been paid to the data-structure requirements, complexity issues and communication features of the algorithm. Key results include reduced communication pivoting for both the “analyze” A-mode and repeated B-mode factorizations, and effective general-purpose data distributions useful incrementally to trade-off process-column load balance in factorization against triangular solve performance. Future planned efforts are cited in conclusion

A Portable Multicomputer Communication Library atop the Reactive Kernel

Sophisticated multicomputer applications require efficient, flexible, convenient underlying communication primitives. In the work described here, Zipcode, a new, portable communication library, has been designed, developed, articulated and evaluated. The primary goals were: high efficiency compared to lowest-level primitives, user-definable message receipt selectivity, as well as abstraction of collections of processes and message selectivity to allow multiple, independently conceived libraries to work together without conflict. Zipcode works atop the Caltech Reactive Kernel, a portable, minimalistic multicomputer node operating system. Presently, the Reactive Kernel is implemented for Intel iPSC/1, iPSC/2, and Symult s2010 multicomputers and emulated on shared-memory computers as well as networks of Sun workstations. Consequently, Zipcode addresses an equally wide audience, and can plausibly be run in other environments

Optimal guidance law development for an advanced launch system

The proposed investigation on a Matched Asymptotic Expansion (MAE) method was carried out. It was concluded that the method of MAE is not applicable to launch vehicle ascent trajectory optimization due to a lack of a suitable stretched variable. More work was done on the earlier regular perturbation approach using a piecewise analytic zeroth order solution to generate a more accurate approximation. In the meantime, a singular perturbation approach using manifold theory is also under current investigation. Work on a general computational environment based on the use of MACSYMA and the weak Hamiltonian finite element method continued during this period. This methodology is capable of the solution of a large class of optimal control problems

Proton impact on ground and excited states of atomic hydrogen

The processes of electron excitation, capture, and ionization were investigated in proton collisions with atomic hydrogen in the initial $n=1$ and $n=2$ states at impact energies from 1 to 300 keV. The theoretical analysis is based on the close-coupling two-center basis generator method in the semiclassical approximation. Calculated cross sections are compared with previous results which include data obtained from classical-trajectory Monte Carlo, convergent close-coupling, and other two-center atomic orbital expansion approaches. There is an overall good agreement in the capture and excitation cross sections while there are some discrepancies in the ionization results at certain impact energies. These discrepancies in the present results can be partially understood through the use of a $1/n^{3}$ scaling model.Comment: 7 pages, 4 figures, Eur. Phys. J. D. Final Accepted Versio

Source Code for the Nihongo Tutor

This document contains a listing of the Pascal source code for the Nihongo Tutor program. This code is designed to be executed on Macintosh computers under the Kanjitalk operating system. It was written by Kei Wai Leung under the supervision of Anthony A. Maciejewski as part of the Nihongo Tutorial System, a set of programs designed to assist scientists and engineers acquire a reading knowledge of technical Japanese. As this is an ongoing project, portions of this code are under revision. This project is funded by the National Science Foundation under Grant No. INT-8818039. The government has certain rights in this material

Technical Specifications of the Nihongo Tutorial System

The Nihongo tutorial system presented here is an intelligent tutorial system designed to use a computer to assist scientists and engineers in developing reading competence in technical Japanese. It is comprised of three applications: the Nihongo Tutor, the Parse Tree Editor and the Administrator. The Nihongo Tutor provides useful information about an article such as an English translation, syntax, and pronunciation to help the student to comprehend the text of a personalized lesson. It also records the student\u27s performance into his personal database which reflects his current Japanese language proficiency. The Administrator uses the personal data of a student to assign an article that is related to his technical interests and at his current level of Japanese competence. The Parse Tree Editor is used to prepare technical articles for the tutorial system by incorporating semantic, syntactic, phonetic, and morphological information into the parse tree of a sentence in each article. This report presents the technical details of the implementation of the Nihongo Tutorial System including both the data structures and algorithms employed

Quantifying argonaute proteins in and out of GW/P-bodies: Implications in microRNA activities

MicroRNAs (miRNAs) are a class of ∼22nt non-coding RNAs that regulate the translational potential and stability of mRNAs. Though constituting only 1-4% of human genes, miRNAs are predicted to regulate more than 60% of all mRNAs. The action of miRNAs is mediated through their associations with Argonaute proteins and mRNA targets. Previous studies indicated that though the majority of Argonaute proteins is diffusely distributed in the cytoplasm, a small fraction is consistently observed to be concentrated in a cytoplasmic compartment called GW/P-bodies. In this chapter, we will provide a quantitative and dynamic view of the subcellular localization of miRNA function, followed by a discussion on the possible roles of PBs in miRNA silencing.National Institutes of Health (U.S.) (Grant R01-CA133404)National Cancer Institute (U.S.) (Grant P01-CA42063)National Cancer Institute (U.S.) (Grant P30-CA14051