Variants of the Chandy-Misra-Bryant Distributed Discrete-Event Simulation Algorithm

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Reactive-Process Programming and Distributed Discrete-Event Simulation

The same forces that spurred the development of multicomputers - the demand for better performance and economy - are driving the evolution of multicomputers in the direction of more abundant and less expensive computing nodes - the direction of fine-grain multicomputers. This evolution in multicomputer architecture derives from advances in integrated circuit, packaging, and message-routing technologies, and carries far-reaching implications in programming and applications. This thesis pursues that trend with a balanced treatment of multicomputer programming and applications. First, a reactive- process programming system - Reactive-C - is investigated; then, a model application - discreteevent simulation - is developed; finally, a number of logic-circuit simulators written in the Reactive-C notation are evaluated. One difficulty in multicomputer applications is the inefficiency of many distributed algorithms compared to their sequential counterparts. When better formulations are developed, they often scale poorly with increasing numbers of nodes, and their beneficial effects eventually vanish when many nodes are used. However, rules for programming are quite different when nodes are plentiful and cheap: The primary concern is to utilize all of the concurrency available in an application, rather than to utilize all of the computing cycles available in a machine. We have shown in our research that it is possible to extract the maximum concurrency of a simulation subject, even one as difficult as a logic circuit, when one simulation element is assigned to each node. Despite the initial inefficiency of a straightforward algorithm, as the the number of nodes increases, the computation time decreases linearly until there are only a few elements in each node. We conclude by suggesting a, technique to further increase the available concurrency when there are many more nodes than simulation elements

A Bayesian measurement error model for two-channel cell-based RNAi data with replicates

RNA interference (RNAi) is an endogenous cellular process in which small double-stranded RNAs lead to the destruction of mRNAs with complementary nucleoside sequence. With the production of RNAi libraries, large-scale RNAi screening in human cells can be conducted to identify unknown genes involved in a biological pathway. One challenge researchers face is how to deal with the multiple testing issue and the related false positive rate (FDR) and false negative rate (FNR). This paper proposes a Bayesian hierarchical measurement error model for the analysis of data from a two-channel RNAi high-throughput experiment with replicates, in which both the activity of a particular biological pathway and cell viability are monitored and the goal is to identify short hair-pin RNAs (shRNAs) that affect the pathway activity without affecting cell activity. Simulation studies demonstrate the flexibility and robustness of the Bayesian method and the benefits of having replicates in the experiment. This method is illustrated through analyzing the data from a RNAi high-throughput screening that searches for cellular factors affecting HCV replication without affecting cell viability; comparisons of the results from this HCV study and some of those reported in the literature are included.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS496 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

The C Programmer's Abbreviated Guide to Multicomputer Programming

This abbreviated programmer's guide describes the essentials of writing multiple-process-message-passing C programs on UNIX hosts under a runtime system called the Cosmic Environment (version 7.2), and on multicomputers under a node operating systeni called the Reactive Kernel. It is our intention that a person who is already familiar with C and UNIX, and with the formulation of concurrent computations for multicomputers, will find a single reading of this guide to be sufficient preparation to start writing multicomputer programs. The Appendices include reference material and digression

Effects of resveratrol supplementation on methotrexate chemotherapy‐induced bone loss

Intensive cancer chemotherapy is known to cause bone defects, which currently lack treatments. This study investigated the effects of polyphenol resveratrol (RES) in preventing bone defects in rats caused by methotrexate (MTX), a commonly used antimetabolite in childhood oncology. Young rats received five daily MTX injections at 0.75 mg/kg/day. RES was orally gavaged daily for seven days prior to, and during, five‐day MTX administration. MTX reduced growth plate thickness, primary spongiosa height, trabecular bone volume, increased marrow adipocyte density, and increased mRNA expression of the osteogenic, adipogenic, and osteoclastogenic factors in the tibial bone. RES at 10 mg/kg was found not to affect bone health in normal rats, but to aggravate the bone damage in MTX‐treated rats. However, RES supplementation at 1 mg/kg preserved the growth plate, primary spongiosa, bone volume, and lowered the adipocyte density. It maintained expression of genes involved in osteogenesis and decreased expression of adipogenic and osteoclastogenic factors. RES suppressed osteoclast formation ex vivo of bone marrow cells from the treated rats. These data suggest that MTX can enhance osteoclast and adipocyte formation and cause bone loss, and that RES supplementation at 1 mg/kg may potentially prevent these bone defects

A Characterization of Topological Insulators: Chern Numbers for a Ground State Multiplet

We propose to use generic Chern numbers for a characterization of topological insulators. It is suitable for a numerical characterization of low dimensional quantum liquids where strong quantum fluctuations prevent from developing conventional orders. By twisting parameters of boundary conditions, the non-Abelian Chern number are defined for a few low lying states near the ground state in a finite system, which is a ground state multiplet with a possible (topological) degeneracy. We define the system as a topological insulator when energies of the multiplet are well separated from the above. Translational invariant twists up to a unitary equivalence are crutial to pick up only bulk properties without edge states. As a simple example, the setup is applied for a two-dimensional $XXZ$-spin system with an ising anisotropy where the ground state multiplet is composed of doubly almost degenerate states. It gives a vanishing Chern number due to a symmetry. Also Chern numbers for the generic fractional quantum Hall states are discussed shortly.Comment: 2 figure

Composite quasiparticle formation and the low-energy effective Hamiltonians of the one- and two-dimensional Hubbard Model

We investigate the effect of hole doping on the strong-coupling Hubbard model at half-filling in spatial dimensions $D\ge 1$. We start with an antiferromagnetic mean-field description of the insulating state, and show that doping creates solitons in the antiferromagnetic background. In one dimension, the soliton is topological, spinless, and decoupled from the background antiferromagnetic fluctuations at low energies. In two dimensions and above, the soliton is non-topological, has spin quantum number 1/2, and is strongly coupled to the antiferromagnetic fluctuations. We derive the effective action governing the quasiparticle motion, study the properties of a single carrier, and comment on a possible description at finite concentration.Comment: REVTEX 3.0, 22 pages with 14 figures in the PostScript format compressed using uufile. Submitted to Phys. Rev. B. The complete PostScript file including figures can be obtained via ftp at ftp://serval.berkeley.edu/hubbard.ps . It is also available via www at http://roemer.fys.ku.dk/recent.ht

Explicit Gauge Fixing for Degenerate Multiplets: A Generic Setup for Topological Orders

We supply basic tools for the study of the topological order of a multiplet which is an eigenspace of a finite-dimensional normal operator with continuous parameters. We allow intrinsic degeneracies within the multiplet where a well-known standard procedure does not work. As an important example, we give novel expressions for a spin Hall conductance for unitary superconductors with equal spin pairing. Generic topological orders will be treated in this unified manner particularly with nontrivial topological degeneracies.Comment: Almost final version. (Topological) Degeneracy is stresse

Establishing a nationwide emergency department-based syndromic surveillance system for better public health responses in Taiwan

Background. With international concern over emerging infectious diseases (EID) and bioterrorist attacks, public health is being required to have early outbreak detection systems. A disease surveillance team was organized to establish a hospital emergency department-based syndromic surveillance system (ED-SSS) capable of automatically transmitting patient data electronically from the hospitals responsible for emergency care throughout the country to the Centers for Disease Control in Taiwan (Taiwan-CDC) starting March, 2004. This report describes the challenges and steps involved in developing ED-SSS and the timely information it provides to improve in public health decision-making. Methods. Between June 2003 and March 2004, after comparing various surveillance systems used around the world and consulting with ED physicians, pediatricians and internal medicine physicians involved in infectious disease control, the Syndromic Surveillance Research Team in Taiwan worked with the Real-time Outbreak and Disease Surveillance (RODS) Laboratory at the University of Pittsburgh to create Taiwan's ED-SSS. The system was evaluated by analyzing daily electronic ED data received in real-time from the 189 hospitals participating in this system between April 1, 2004 and March 31, 2005. Results. Taiwan's ED-SSS identified winter and summer spikes in two syndrome groups: influenza-like illnesses and respiratory syndrome illnesses, while total numbers of ED visits were significantly higher on weekends, national holidays and the days of Chinese lunar new year than weekdays (p < 0.001). It also identified increases in the upper, lower, and total gastrointestinal (GI) syndrome groups starting in November 2004 and two clear spikes in enterovirus-like infections coinciding with the two school semesters. Using ED-SSS for surveillance of influenza-like illnesses and enteroviruses-related infections has improved Taiwan's pandemic flu preparedness and disease control capabilities. Conclusion. Taiwan's ED-SSS represents the first nationwide real-time syndromic surveillance system ever established in Asia. The experiences reported herein can encourage other countries to develop their own surveillance systems. The system can be adapted to other cultural and language environments for better global surveillance of infectious diseases and international collaboration. © 2008 Wu et al; licensee BioMed Central Ltd