Nucleosome positioning: resources and tools online

Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely, to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info

Impact of Macroeconomic Announcements on Implied Volatility Slope of SPX Options and VIX

Cataloged from PDF version of article.This paper examines the impact of macroeconomic announcements on the high-frequency behavior of the observed implied volatility skew of S&P 500 index options and VIX. We document that macroeconomic announcements affect VIX significantly and slope at a lesser extent. We also find evidence that good and bad announcements significantly and asymmetrically change implied volatility slope and VIX. 2014 Elsevier Inc. All rights reserved

A Novel Broadband Multilevel Fast Multipole Algorithm With Incomplete-Leaf Tree Structures for Multiscale Electromagnetic Problems

An efficient and versatile broadband multilevel fast multipole algorithm (MLFMA), which is capable of handling large multiscale electromagnetic problems with a wide dynamic range of mesh sizes, is presented. By invoking a novel concept of incomplete-leaf tree structures, where only the overcrowded boxes are divided into smaller ones for a given population threshold, versatility of using variable-sized boxes is achieved. Consequently, for geometries containing highly overmeshed local regions, the proposed method is always more efficient than the conventional MLFMA for the same accuracy, while it is always more accurate if the efficiency is comparable. Furthermore, in such a population-based clustering scenario, the error is controllable regardless of the number of levels. Several canonical examples are provided to demonstrate the superior efficiency and accuracy of the proposed algorithm in comparison with the conventional MLFMA

An Approach for Time-aware Domain-based Analysis of Users Trustworthiness in Big Social Data

In Online Social Networks (OSNs) there is a need for better understanding of social trust in order to improve the analysis process and mining credibility of social media data. Given the open environment and fewer restrictions associated with OSNs, the medium allows legitimate users as well as spammers to publish their content. Hence, it is essential to measure users’ credibility in various domains and accordingly define influential users in a particular domain(s). Most of the existing approaches of trustworthiness evaluation of users in OSNs are generic-based approaches. There is a lack of domain-based trustworthiness evaluation mechanisms. In OSNs, discovering users’ influence in a specific domain has been motivated by its significance in a broad range of applications such as personalized recommendation systems and expertise retrieval. The aim of this paper is to present an approach to analysing domain-based user’s trustworthiness in OSNs. We provide a novel distinguishing measurement for users in a set of knowledge domains. Domains are extracted from the user’s content using semantic analysis. In order to obtain the level of trustworthiness, a metric incorporating a number of attributes extracted from content analysis and user analysis is consolidated and formulated by considering temporal factor. We show the accuracy of the proposed algorithm by providing a fine-grained trustworthiness analysis of users and their domains of interest in the OSNs using big data Infrastructure

High-Q-factor Al [subscript 2]O[subscript 3] micro-trench cavities integrated with silicon nitride waveguides on silicon

We report on the design and performance of high-Q integrated optical micro-trench cavities on silicon. The microcavities are co-integrated with silicon nitride bus waveguides and fabricated using wafer-scale silicon-photonics-compatible processing steps. The amorphous aluminum oxide resonator material is deposited via sputtering in a single straightforward post-processing step. We examine the theoretical and experimental optical properties of the aluminum oxide micro-trench cavities for different bend radii, film thicknesses and near-infrared wavelengths and demonstrate experimental Q factors of > 10[superscript 6]. We propose that this high-Q micro-trench cavity design can be applied to incorporate a wide variety of novel microcavity materials, including rare-earth-doped films for microlasers, into wafer-scale silicon photonics platforms

Prevalence, knowledge, attitude, and practices associated with influenza vaccination among healthcare workers in primary care centers in Jazan, Saudi Arabia: A crosssectional study

Purpose: To assess the prevalence, knowledge, attitude and practices of health care workers (HCWs) in Jazan Province regarding the annual influenza vaccination program.Methods: A cross-sectional, self-administered questionnaire-based study was conducted among HCWs (n = 368) at the primary 18 health care centers in Jazan, Saudi Arabia during the period January – April, 2016.Results: The overall vaccination coverage was 87.0 % in the previous year and 79.9 % in the last 5 years. In all, 97 % of males and 59.5 % of females considered influenza as a serious disease (p = 0.005). Regarding prevention of influenza infection, 91.2 % of respondents believed that HCWs were at risk of influenza infection, while 62.5 % considered vaccination as the best preventive measure (p = 0.003). The most common reasons for receiving vaccine were “to protect oneself or one’s family” (99.4 %), while the most common reason for not taking the vaccine was “fear of side effects” (49 %).Conclusion: HCWs exhibit positive attitudes toward influenza vaccine, and notwithstanding the high vaccine coverage in Jazan Province. However, influenza vaccine campaigns should include information to enhance the awareness of HCWs about the risk of exposure to influenza, and information about the adverse reactions to influenza vaccine.Keywords: Healthcare workers, Influenza vaccine, Risk of exposure, Adverse reactions

Single unconfined compression of cellular dense collagen scaffolds for cartilage and bone tissue engineering

Cell seeded collagen matrix scaffolds have been extensively evaluated recently as potential systems for de-novo tissue regeneration and repair for a variety of tissue types. While collagen gels are biologically excellent as starting point scaffold materials, their use is limited by the lack of cohesive structure and inherently weak mechanical properties due to a high liquid content (>99%). An ingenious method of combining unconfined plastic compression (PC) with capillary action has shown that these scaffolds can be rapidly processed into tissue like structures, which can be immediately implanted into the host[1]. It has been shown that the rapid increase in fibrillar collagen density dramatically enhanced the mechanical properties of such scaffolds thus potentially eliminating the need for long term cellular action. This simple project investigated the effect of single unconfined compression on cartilage-cell seeded collagen matrices in terms of cell viability, proliferation and oxygen consumption

h-deformation of Gr(2)

The $h$-deformation of functions on the Grassmann matrix group $Gr(2)$ is presented via a contraction of $Gr_q(2)$. As an interesting point, we have seen that, in the case of the $h$-deformation, both R-matrices of $GL_h(2)$ and $Gr_h(2)$ are the same