CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets.

UNLABELLED: Promoter capture Hi-C (PCHi-C) allows the genome-wide interrogation of physical interactions between distal DNA regulatory elements and gene promoters in multiple tissue contexts. Visual integration of the resultant chromosome interaction maps with other sources of genomic annotations can provide insight into underlying regulatory mechanisms. We have developed Capture HiC Plotter (CHiCP), a web-based tool that allows interactive exploration of PCHi-C interaction maps and integration with both public and user-defined genomic datasets. AVAILABILITY AND IMPLEMENTATION: CHiCP is freely accessible from www.chicp.org and supports most major HTML5 compliant web browsers. Full source code and installation instructions are available from http://github.com/D-I-L/django-chicp CONTACT: [email protected] is the published version. It first appeared at http://bioinformatics.oxfordjournals.org/content/early/2016/04/26/bioinformatics.btw173

Dynamical mass generation in quantum field theory : some methods with application to the Gross-Neveu model and Yang-Mills theory

We introduce some techniques to investigate dynamical mass generation. The Gross-Neveu model (GN) is used as a toy model, because the GN mass gap is exactly known, making it possible to check reliability of the various methods. Very accurate results are obtained. Also application to SU(N) Yang-Mills (YM) is discussed.Comment: 8 LaTeX2e pages, uses Kluwer class file crckbked.cls. Kluwer package included. To appear in: Proceedings of the NATO Advanced Research Workshop on "Confinement, Topology, and other Non-Perturbative Aspects of QCD", Stara Lesna, Slovakia, 21-27 jan 200

Reflective Journaling: A Theoretical Model and Digital Prototype for Developing Resilience and Creativity

Reflection is commonly discussed as a tool for personal and professional development that is becoming increasingly important in today’s global and digital world. In this paper, we propose a model that suggests ways in which reflection, in the form of Reflective Journaling, can support the development of creativity and resilience, which are needed to enable individuals to function effectively in a fast-changing environment. In addition, the model proposes ways in which external support and progress monitoring can be used in conjunction with skills in adaptive resilience and structured creativity, to support the maintenance of reflective journaling as a habit, in the longer term, thus creating virtuous cycles of skills and behaviours that can reinforce each other. Based on our model, and additional user research, we describe the design of a first digital prototype that aims to support the use of Reflective Journaling and to develop creativity and resilience through suggested mechanisms. Initial evaluations of our prototype are positive. It has been well-received by early test users, and has the potential to address all the connections defined. We therefore suggest that the theoretical model can be used to develop digital tools, such as the one included, to help those who wish to develop the habit of reflective journaling, and through that a range of other skills associated with resilience and creative thinking. We see this as a starting point for investigating this potential in more depth

Near-field examination of perovskite-based superlenses and superlens-enhanced probe-object coupling

A planar slab of negative index material works as a superlens with sub-diffraction-limited imaging resolution, since propagating waves are focused and, moreover, evanescent waves are reconstructed in the image plane. Here, we demonstrate a superlens for electric evanescent fields with low losses using perovskites in the mid-infrared regime. The combination of near-field microscopy with a tunable free-electron laser allows us to address precisely the polariton modes, which are critical for super-resolution imaging. We spectrally study the lateral and vertical distributions of evanescent waves around the image plane of such a lens, and achieve imaging resolution of wavelength/14 at the superlensing wavelength. Interestingly, at certain distances between the probe and sample surface, we observe a maximum of these evanescent fields. Comparisons with numerical simulations indicate that this maximum originates from an enhanced coupling between probe and object, which might be applicable for multifunctional circuits, infrared spectroscopy, and thermal sensors.Comment: 20 pages, 6 figures, published as open access article in Nature Communications (see http://www.nature.com/ncomms/

Factors of Susceptibility of Human Myiasis Caused by the New World Screw-Worm, Cochliomyia hominivorax in São Gonçalo, Rio de Janeiro, Brazil

This study was carried out between July 2007 and June 2008 and reports on the occurrence of human myiasis caused by the New World screwworm, Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae) in São Gonçalo in the state of Rio de Janeiro, Brazil. Liquid or solid vaseline was used to suffocate the larvae, which were then preserved in 70% ethanol and sent to the Instituto Oswaldo Cruz for identification. C. hominivorax were identified in all 22 cases of myiasis. There were 12 male and 10 female patients with ages ranging from 03 to 71. Ethnically the highest incidence was among black people, with 17 cases. Open wounds were the main cause of the parasitosis, whereas poor personal hygiene, the low educational level, alcoholism, bedridden patients, and physical or mental disability were possibly secondary factors; in addition to all these factors the income of the patients was very low

Barriers to transformative adaptation: Responses to flood risk in Ireland

Barriers to climate change adaptation have received increased attention in recent years as researchers and policymakers attempt to understand their complex and interdependent nature and identify strategies for overcoming them. To date however, there is a paucity of research on barriers to transformative adaptation. Using two case studies of flood risk management from Ireland we identify and characterize barriers to transformative adaptation. Qualitative semi-structured interviews were conducted with key stakeholders connected to proposed transformative strategies in Skibbereen, County Cork and Clontarf, County Dublin. Across both case studies, where transformative strategies failed to materialize, we highlight three significant barriers that impede transformation including: (i) social and cultural values, particularly place attachment and identity; (ii) institutional reliance on technical expertise which fails to look beyond traditional technocratic approaches and; (iii) institutional regulatory practices. Findings illustrate that where social or institutional barriers emerge, transformation may more likely succeed through a series of incremental changes. This research has practical implications for future adaptation planning as facilitating transformation through incrementalism requires flexible adaptation strategies that are responsive to changing social values over time. While focused on flood risk management, our findings have applicability for other sectors adapting to climate change

The management of scabies outbreaks in residential care facilities for the elderly in England: a review of current health protection guidelines

Commonly thought of as a disease of poverty and overcrowding in resource-poor settings globally, scabies is also an important public health issue in residential care facilities for the elderly (RCFE) in high-income countries such as the UK. We compared and contrasted current local Health Protection Team (HPT) guidelines for the management of scabies outbreaks in RCFE throughout England. We performed content analysis on 20 guidelines, and used this to create a quantitative report of their variation in key dimensions. Although the guidelines were generally consistent on issues such as the treatment protocols for individual patients, there was substantial variation in their recommendations regarding the prophylactic treatment of contacts, infection control measures and the roles and responsibilities of individual stakeholders. Most guidelines did not adequately address the logistical challenges associated with mass treatment in this setting. We conclude that the heterogeneous nature of the guidelines reviewed is an argument in favour of national guidelines being produced

Teaching Africa and international studies: Forum introduction

Africa has often been defined and represented by outsiders. In International Studies, the continent is frequently viewed as peripheral and uninteresting. This is clearly a problem, and an increasingly apparent one as the number of courses on Africa and IS grow, both in Africa and beyond. Many academics who run these courses are keen to challenge the continent’s traditional marginalisation and perceived dependency, but they are limited by the resources available to them, and the fact that many are establishing new courses from scratch. This article outlines some of the key debates around teaching Africa and IS, setting the scene for the articles that follow