Efficient computer search of large-order multiple recursive pseudo-random number generators

AbstractUtilizing some results in number theory, we propose an efficient method to speed up the computer search of large-order maximum-period Multiple Recursive Generators (MRGs). We conduct the computer search and identify many efficient and portable MRGs of order up to 25,013, which have the equi-distribution property in up to 25,013 dimensions and the period lengths up to 10233,361 approximately. In addition, a theoretical test is adopted to further evaluate and compare these generators. An extensive empirical study shows that these generators behave well when tested with the stringent Crush battery of the test package TestU01

Explore Biological Pathways from Noisy Array Data by Directed Acyclic Boolean Networks

We consider the structure of directed acyclic Boolean (DAB) networks as a tool for exploring biological pathways. In a DAB network, the basic objects are binary elements and their Boolean duals. A DAB is characterized by two kinds of pairwise relations: similarity and prerequisite. The latter is a partial order relation, namely, the on-status of one element is necessary for the on-status of another element. A DAB network is uniquely determined by the state space of its elements. We arrange samples from the state space of a DAB network in a binary array and introduce a random mechanism of measurement error. Our inference strategy consists of two stages. First, we consider each pair of elements and try to identify their most likely relation. In the meantime, we assign a score, s-p-score, to this relation. Second, we rank the s-p-scores obtained from the first stage. We expect that relations with smaller s-p-scores are more likely to be true, and those with larger s-p-scores are more likely to be false. The key idea is the definition of s-scores (referring to similarity), p-scores (referring to prerequisite), and s-p-scores. As with classical statistical tests, control of false negatives and false positives are our primary concerns. We illustrate the method by a simulated example, the classical arginine biosynthetic pathway, and show some exploratory results on a published microarray expression dataset of yeast Saccharomyces cerevisiae obtained from experiments with activation and genetic perturbation of the pheromone response MAPK pathway

Multidimensional scaling for large genomic data sets

<p>Abstract</p> <p>Background</p> <p>Multi-dimensional scaling (MDS) is aimed to represent high dimensional data in a low dimensional space with preservation of the similarities between data points. This reduction in dimensionality is crucial for analyzing and revealing the genuine structure hidden in the data. For noisy data, dimension reduction can effectively reduce the effect of noise on the embedded structure. For large data set, dimension reduction can effectively reduce information retrieval complexity. Thus, MDS techniques are used in many applications of data mining and gene network research. However, although there have been a number of studies that applied MDS techniques to genomics research, the number of analyzed data points was restricted by the high computational complexity of MDS. In general, a non-metric MDS method is faster than a metric MDS, but it does not preserve the true relationships. The computational complexity of most metric MDS methods is over <it>O(N</it>²<it>)</it>, so that it is difficult to process a data set of a large number of genes <it>N</it>, such as in the case of whole genome microarray data.</p> <p>Results</p> <p>We developed a new rapid metric MDS method with a low computational complexity, making metric MDS applicable for large data sets. Computer simulation showed that the new method of split-and-combine MDS (SC-MDS) is fast, accurate and efficient. Our empirical studies using microarray data on the yeast cell cycle showed that the performance of K-means in the reduced dimensional space is similar to or slightly better than that of K-means in the original space, but about three times faster to obtain the clustering results. Our clustering results using SC-MDS are more stable than those in the original space. Hence, the proposed SC-MDS is useful for analyzing whole genome data.</p> <p>Conclusion</p> <p>Our new method reduces the computational complexity from <it>O</it>(<it>N</it>³) to <it>O</it>(<it>N</it>) when the dimension of the feature space is far less than the number of genes <it>N</it>, and it successfully reconstructs the low dimensional representation as does the classical MDS. Its performance depends on the grouping method and the minimal number of the intersection points between groups. Feasible methods for grouping methods are suggested; each group must contain both neighboring and far apart data points. Our method can represent high dimensional large data set in a low dimensional space not only efficiently but also effectively.</p

Adaptive Transmit Diversity with Quadrant Phase Constraining Feedback

An adaptive transmit scheme with quadrant phase constraining feedback is proposed in this paper. With simple linear operations at both transmitter and receiver, the proposed algorithm can achieve better system performances with only 2M- 2 bits of feedback information for systems with M transmit antennas. Theoretical performance bounds of the proposed transmit diversity scheme are derived. Simulation examples and theoretical analyses show that the proposed transmit diversity scheme outperforms not only the conventional open-loop transmit diversity techniques, but also some closed-loop transmit diversity techniques with more information transmitted in the feedback channel

Hepatitis B surface antigen quantification: Why and how to use it in 2011 – A core group report

Quantitative HBsAg had been suggested to be helpful in management of HBV, but assays were cumbersome. The recent availability of commercial quantitative assays has restarted the interest in quantitative serum hepatitis B surface antigen (HBsAg) as a biomarker for prognosis and treatment response in chronic hepatitis B. HBsAg level reflects the transcriptional activity of cccDNA rather than the absolute amount of cccDNA copies. Serum HBsAg level tends to be higher in hepatitis B e antigen (HBeAg)-positive than HBeAg-negative patients. Among patients with a low HBV DNA (<2000IU/ml), HBsAg <1000IU/ml in genotype D HBV infection and HBsAg <100IU/ml in genotype B/C HBV infection is associated with inactive carrier state in HBeAg-negative patients. The HBsAg reduction by nucleos(t)ide analogues (NA) is not as pronounced as by interferon treatment. On peginterferon treatment, sustained responders tend to show greater HBsAg decline than the non-responders. The optimal on-treatment HBsAg cutoff to predict response needs further evaluation in HBeAg-positive patients, but an absence of HBsAg decline together with a <2 log reduction in HBV DNA at week 12 can serve as stopping rule in HBeAg-negative patients with genotype D HBV infection. A rapid serum HBsAg decline during NA therapy may identify patients who will clear HBsAg in the long-term. There are early reports among Asian patients that an HBsAg level of <100IU/ml might predict lower risk of relapse after stopping NA treatment. In clinical practice, serum HBsAg level should be used together with, but not as a substitute for, HBV DNA

Obliquity pacing of the western Pacific Intertropical Convergence Zone over the past 282,000 years

The Intertropical Convergence Zone (ITCZ) encompasses the heaviest rain belt on the Earth. Few direct long-term records, especially in the Pacific, limit our understanding of long-term natural variability for predicting future ITCZ migration. Here we present a tropical precipitation record from the Southern Hemisphere covering the past 282,000 years, inferred from a marine sedimentary sequence collected off the eastern coast of Papua New Guinea. Unlike the precession paradigm expressed in its East Asian counterpart, our record shows that the western Pacific ITCZ migration was influenced by combined precession and obliquity changes. The obliquity forcing could be primarily delivered by a cross-hemispherical thermal/pressure contrast, resulting from the asymmetric continental configuration between Asia and Australia in a coupled East Asian-Australian circulation system. Our finding suggests that the obliquity forcing may play a more important role in global hydroclimate cycles than previously thought