Successive Coordinate Search and Component-by-Component Construction of Rank-1 Lattice Rules

The (fast) component-by-component (CBC) algorithm is an efficient tool for the construction of generating vectors for quasi-Monte Carlo rank-1 lattice rules in weighted reproducing kernel Hilbert spaces. We consider product weights, which assigns a weight to each dimension. These weights encode the effect a certain variable (or a group of variables by the product of the individual weights) has. Smaller weights indicate less importance. Kuo (2003) proved that the CBC algorithm achieves the optimal rate of convergence in the respective function spaces, but this does not imply the algorithm will find the generating vector with the smallest worst-case error. In fact it does not. We investigate a generalization of the component-by-component construction that allows for a general successive coordinate search (SCS), based on an initial generating vector, and with the aim of getting closer to the smallest worst-case error. The proposed method admits the same type of worst-case error bounds as the CBC algorithm, independent of the choice of the initial vector. Under the same summability conditions on the weights as in [Kuo,2003] the error bound of the algorithm can be made independent of the dimension $d$ and we achieve the same optimal order of convergence for the function spaces from [Kuo,2003]. Moreover, a fast version of our method, based on the fast CBC algorithm by Nuyens and Cools, is available, reducing the computational cost of the algorithm to $O(d \, n \log(n))$ operations, where $n$ denotes the number of function evaluations. Numerical experiments seeded by a Korobov-type generating vector show that the new SCS algorithm will find better choices than the CBC algorithm and the effect is better when the weights decay slower.Comment: 13 pages, 1 figure, MCQMC2016 conference (Stanford

Hot new directions for quasi-Monte Carlo research in step with applications

This article provides an overview of some interfaces between the theory of quasi-Monte Carlo (QMC) methods and applications. We summarize three QMC theoretical settings: first order QMC methods in the unit cube $[0,1]^s$ and in $\mathbb{R}^s$, and higher order QMC methods in the unit cube. One important feature is that their error bounds can be independent of the dimension $s$ under appropriate conditions on the function spaces. Another important feature is that good parameters for these QMC methods can be obtained by fast efficient algorithms even when $s$ is large. We outline three different applications and explain how they can tap into the different QMC theory. We also discuss three cost saving strategies that can be combined with QMC in these applications. Many of these recent QMC theory and methods are developed not in isolation, but in close connection with applications

Application of quasi-Monte Carlo methods to PDEs with random coefficients -- an overview and tutorial

This article provides a high-level overview of some recent works on the application of quasi-Monte Carlo (QMC) methods to PDEs with random coefficients. It is based on an in-depth survey of a similar title by the same authors, with an accompanying software package which is also briefly discussed here. Embedded in this article is a step-by-step tutorial of the required analysis for the setting known as the uniform case with first order QMC rules. The aim of this article is to provide an easy entry point for QMC experts wanting to start research in this direction and for PDE analysts and practitioners wanting to tap into contemporary QMC theory and methods.Comment: arXiv admin note: text overlap with arXiv:1606.0661

Murine HPV16 E7-expressing transgenic skin effectively emulates the cellular and molecular features of human high-grade squamous intraepithelial lesions.

Currently available vaccines prevent HPV infection and development of HPV-associated malignancies, but do not cure existing HPV infections and dysplastic lesions. Persistence of infection(s) in immunocompetent patients may reflect induction of local immunosuppressive mechanisms by HPV, providing a target for therapeutic intervention. We have proposed that a mouse, expressing HPV16 E7 oncoprotein under a Keratin 14 promoter (K14E7 mice), and which develops epithelial hyperplasia, may assist with understanding local immune suppression mechanisms that support persistence of HPV oncogene-induced epithelial hyperplasia. K14E7 skin grafts recruit immune cells from immunocompetent hosts, but consistently fail to be rejected. Here, we review the literature on HPV-associated local immunoregulation, and compare the findings with published observations on the K14E7 transgenic murine model, including comparison of the transcriptome of human HPV-infected pre-malignancies with that of murine K14E7 transgenic skin. We argue from the similarity of i) the literature findings and ii) the transcriptome profiles that murine K14E7 transgenic skin recapitulates the cellular and secreted protein profiles of high-grade HPV-associated lesions in human subjects. We propose that the K14E7 mouse may be an appropriate model to further study the immunoregulatory effects of HPV E7 expression, and can facilitate development and testing of therapeutic vaccines

Towards a career in bioinformatics

The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation from 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 9-11, 2009 at Biopolis, Singapore. InCoB has actively engaged researchers from the area of life sciences, systems biology and clinicians, to facilitate greater synergy between these groups. To encourage bioinformatics students and new researchers, tutorials and student symposium, the Singapore Symposium on Computational Biology (SYMBIO) were organized, along with the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and the Clinical Bioinformatics (CBAS) Symposium. However, to many students and young researchers, pursuing a career in a multi-disciplinary area such as bioinformatics poses a Himalayan challenge. A collection to tips is presented here to provide signposts on the road to a career in bioinformatics. An overview of the application of bioinformatics to traditional and emerging areas, published in this supplement, is also presented to provide possible future avenues of bioinformatics investigation. A case study on the application of e-learning tools in undergraduate bioinformatics curriculum provides information on how to go impart targeted education, to sustain bioinformatics in the Asia-Pacific region. The next InCoB is scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010

Introduction of a strong temperature-sensitive phenotype into enterovirus 71 by altering an amino acid of virus 3D polymerase

AbstractIn 1998, an enterovirus 71 (EV71) epidemic in Taiwan resulted in 78 deaths; however, the molecular basis of EV71 pathogenicity remains poorly understood. Comparison of the deduced amino acid sequences in 3D polymerases of EV71clinical isolates showed the T251V or T251I substitution from 1986 and 1998 outbreaks. An EV71 replicon system showed that introducing an I251T mutation did not affect luciferase activities at 35 °C when compared with wild type; however, lower luciferase activities were observed when they were incubated at 39.5 °C. In addition, the I251T mutation in the EV71 infectious clone not only reduced viral replication at 39.5 °C in vitro but also decreased the virulence of the mouse adaptive strain MP4 in neonatal mice in an i.p. infection model. Therefore, these results suggested that the threonine at position 251 results in a temperature sensitivity phenotype of EV71 which may contribute to the attenuation of circulating strains

Cytotoxic Phenylpropanoids and a New Triterpene, Turformosinic Acid, from Turpinia formosana Nakai

One new phenylpropanoid, turformosin A (1), and one new triterpene, turformosinic acid (2), together with 16 known compounds, were isolated from the stems of Turpinia formosana Nakai. All structures were elucidated on the basis of spectroscopic analysis, including 1D- and 2D-NMR techniques and MS analysis. Selected isolated compounds were evaluated for in vitro cytotoxicity against four human cancer cell lines and antioxidant scavenging effects on DPPH. (-)-(7'S,8'S)-threo-carolignan X (3) exhibited cytotoxicity against Hep2, WiDr, Daoy, and MCF-7 cell lines with ED(50) values of 3.60, 4.45, 6.07, and 13.7 μg/mL, respectively. Turformosin A (1), (-)-(7'S,8'S)- threo-carolignan X (3), methoxyhydroquinone-4-β-D-glucopyranoside (5), and methoxy-hydroquinone-1-β-D-glucopyranoside (6), exhibited similar anti-oxidative activity. Hep2 cells treated with 10 μg/mL of 3 showed elevation of sub-G1 population (from 20% at 8 h to 60% at 48 h), and activation of caspase-9/caspase-3/PARP cascade. Compound 3 induced intrinsic apoptotic pathway in Hep2 cells with dose and time dependence (10 μg/mL for 8 h)

Body Temperature Monitoring and SARS Fever Hotline, Taiwan

In Taiwan, a temperature-monitoring campaign and hotline for severe acute respiratory syndrome (SARS) fever were implemented in June 2003. Among 1,966 calls, fever was recorded in 19% (n = 378); 18 persons at high risk for SARS were identified. In a cross-sectional telephone survey, 95% (n = 1,060) of households knew about the campaign and 7 households reported fever