Exercise-Induced Changes in Exhaled NO Differentiates Asthma With or Without Fixed Airway Obstruction From COPD With Dynamic Hyperinflation.

Asthmatic patients with fixed airway obstruction (FAO) and patients with chronic obstructive pulmonary disease (COPD) share similarities in terms of irreversible pulmonary function impairment. Exhaled nitric oxide (eNO) has been documented as a marker of airway inflammation in asthma, but not in COPD. To examine whether the basal eNO level and the change after exercise may differentiate asthmatics with FAO from COPD, 27 normal subjects, 60 stable asthmatics, and 62 stable COPD patients were studied. Asthmatics with FAO (n = 29) were defined as showing a postbronchodilator FEV(1)/forced vital capacity (FVC) ≤70% and FEV(1) less than 80% predicted after inhaled salbutamol (400 μg). COPD with dynamic hyperinflation (n = 31) was defined as a decrease in inspiratory capacity (ΔIC%) after a 6 minute walk test (6MWT). Basal levels of eNO were significantly higher in asthmatics and COPD patients compared to normal subjects. The changes in eNO after 6MWT were negatively correlated with the percent change in IC (r = −0.380, n = 29, P = 0.042) in asthmatics with FAO. Their levels of basal eNO correlated with the maximum mid-expiratory flow (MMEF % predicted) before and after 6MWT. In COPD patients with air-trapping, the percent change of eNO was positively correlated to ΔIC% (rs = 0.404, n = 31, P = 0.024). We conclude that asthma with FAO may represent residual inflammation in the airways, while dynamic hyperinflation in COPD may retain NO in the distal airspace. eNO changes after 6MWT may differentiate the subgroups of asthma or COPD patients and will help toward delivery of individualized therapy for airflow obstruction

FastPval: A fast and memory efficient program to calculate very low P-values from empirical distribution

Motivation: Resampling methods, such as permutation and bootstrap, have been widely used to generate an empirical distribution for assessing the statistical significance of a measurement. However, to obtain a very low P-value, a large size of resampling is required, where computing speed, memory and storage consumption become bottlenecks, and sometimes become impossible, even on a computer cluster. Results: We have developed a multiple stage P-value calculating program called FastPval that can efficiently calculate very low (up to 10-9) P-values from a large number of resampled measurements. With only two input files and a few parameter settings from the users, the program can compute P-values from empirical distribution very efficiently, even on a personal computer. When tested on the order of 109 resampled data, our method only uses 52.94% the time used by the conventional method, implemented by standard quicksort and binary search algorithms, and consumes only 0.11% of the memory and storage. Furthermore, our method can be applied to extra large datasets that the conventional method fails to calculate. The accuracy of the method was tested on data generated from Normal, Poison and Gumbel distributions and was found to be no different from the exact ranking approach. © The Author(s) 2010. Published by Oxford University Press.published_or_final_versio

dbPSHP: a database of recent positive selection across human populations

The dbPSHP database (http://jjwanglab.org/dbpshp) aims to help researchers to efficiently identify, validate and visualize putative positively selected loci in human evolution and further discover the mechanism governing these natural selections. Recent evolution of human populations at the genomic level reflects the adaptations to the living environments, including climate change and availability and stability of nutrients. Many genetic regions under positive selection have been identified, which assist us to understand how natural selection has shaped population differences. Here, we manually collect recent positive selections in different human populations, consisting of 15,472 loci from 132 publications. We further compiled a database that used 15 statistical terms of different evolutionary attributes for single nucleotide variant sites from the HapMap 3 and 1000 Genomes Project to identify putative regions under positive selection. These attributes include variant allele/genotype properties, variant heterozygosity, within population diversity, long-range haplotypes, pairwise population differentiation and evolutionary conservation. We also provide interactive pages for visualization and annotation of different selective signals. The database is freely available to the public and will be frequently updated.published_or_final_versio

Speaker adaptation and adaptive training for jointly optimised tandem systems

Speaker independent (SI) Tandem systems trained by joint optimisation of bottleneck (BN) deep neural networks (DNNs) and Gaussian mixture models (GMMs) have been found to produce similar word error rates (WERs) to Hybrid DNN systems. A key advantage of using GMMs is that existing speaker adaptation methods, such as maximum likelihood linear regression (MLLR), can be used which to account for diverse speaker variations and improve system robustness. This paper investigates speaker adaptation and adaptive training (SAT) schemes for jointly optimised Tandem systems. Adaptation techniques investigated include constrained MLLR (CMLLR) transforms based on BN features for SAT as well as MLLR and parameterised sigmoid functions for unsupervised test-time adaptation. Experiments using English multi-genre broadcast (MGB3) data show that CMLLR SAT yields a 4% relative WER reduction over jointly trained Tandem and Hybrid SI systems, and further reductions in WER are obtained by system combination

Exploring the genome-wide roles of transcription factors and their complexes in chromosome interaction

Session - Bioinformatics and Genomic TechnologyThe tight regulation of genes in different cells is governed by temporal and spatial biological signals. It is very important to pinpoint the pattern of transcription factors (TFs) and their complexes in looping interactions and to detect TF complexes as well as the underlying cis-regulatory modules (CRMs) in different human cell types. Existing studies on analysis of TFs and their complexes were only performed at one dimension and not at genome-wide scale. Recently, the unbiased chromosome conformation capture, Hi-C, can detect the genome-wide chromatin interactions, but has restrictions on its resolution due to the variable cell-to-cell chromosome structures and inadequate sequencing depth. In this study, we provide a comprehensive analysis on TFs regulatory pattern within chromosome looping by combining Hi-C and ENCODE ChIP-Seq data from three human cell types (GM12878, H1-hESC and K562). We first devised a strategy to map ChIP-Seq peaks of each TF to a normalized 10kb Hi-C contact matrix and construct an interaction matrix for each participant TF. We observed tight correlation for TFs participant activities in high resolution chromosome looping between biological replicates, which indicate the TF activities is more stable than local DNA interactions. To check the enrichment of different chromatin marks and genomic features in the interaction region of each participant TF, we performed enrichment test on ...published_or_final_versio

Simultaneous demultiplexing of OTDM channels based on swept-pump fiber-optical parametric amplifier

Session - Quantum Information & Parametric Processing OM3B.2We experimentally demonstrate simultaneous demultiplexing of 80-Gb/s OTDM signal by transforming it into WDM idlers (spaced by 1.15 nm), based on a swept-pump fiber-optical parametric amplifier (FOPA), and 10-dB parametric gain is achieved. © 2012 OSApublished_or_final_versio

Local well-posedness for the nonlinear Schr\"odinger equation in the intersection of modulation spaces Mp,qs(Rd)∩M∞,1(Rd)M_{p, q}^s(\mathbb{R}^d) \cap M_{\infty, 1}(\mathbb{R}^d)

We introduce a Littlewood-Paley characterization of modulation spaces and use it to give an alternative proof of the algebra property, somehow implicitly contained in Sugimoto (2011), of the intersection $M^s_{p,q}(\mathbb{R}^d) \cap M_{\infty, 1}(\mathbb{R}^d)$ for $d \in \mathbb{N}$, $p, q \in [1, \infty]$ and $s \geq 0$. We employ this algebra property to show the local well-posedness of the Cauchy problem for the cubic nonlinear Schr\"odinger equation in the above intersection. This improves Theorem 1.1 by B\'enyi and Okoudjou (2009), where only the case $q = 1$ is considered, and closes a gap in the literature. If $q > 1$ and $s > d \left(1 - \frac{1}{q}\right)$ or if $q = 1$ and $s \geq 0$ then $M^s_{p,q}(\mathbb{R}^d) \hookrightarrow M_{\infty, 1}(\mathbb{R}^d)$ and the above intersection is superfluous. For this case we also reobtain a H\"older-type inequality for modulation spaces.Comment: 14 page