Gender and authority in British women hymn-writers' use of metre, 1760-1900

This article is part of a cluster that draws material from the recent conference Metre Matters: New Approaches to Prosody, 1780–1914. It comprises an introduction by Jason David Hall and six articles presented at the conference, whose aim was to address renewed scholarly interest in versification and form across the long nineteenth century, as well as some of the methodologies underpinning it. The papers included in the cluster look both to the minutiae of Romantic and Victorian metres and to their cultural intertexts. The conference, hosted by the University of Exeter's Centre for Victorian Studies, was held 3–5 July 2008

Higher order clustering coefficients in Barabasi-Albert networks

Higher order clustering coefficients $C(x)$ are introduced for random networks. The coefficients express probabilities that the shortest distance between any two nearest neighbours of a certain vertex $i$ equals $x$, when one neglects all paths crossing the node $i$. Using $C(x)$ we found that in the Barab\'{a}si-Albert (BA) model the average shortest path length in a node's neighbourhood is smaller than the equivalent quantity of the whole network and the remainder depends only on the network parameter $m$. Our results show that small values of the standard clustering coefficient in large BA networks are due to random character of the nearest neighbourhood of vertices in such networks.Comment: 10 pages, 4 figure

pH driven colloidal transformation of MS2 virus particles for water purification

Viral infection due to contaminated drinking water is the main cause of infantile death by diarrheal disease [1]. Viruses are difficult to remove by common gravity driven filters due to their nanometer scale size. With the global goal of improving virus removal in drinking water treatments, the colloidal structure of a virus model, MS2 bacteriophage, has been investigated; the effects of pH and Suwannee River natural organic matter in water have been studied [2]. Dynamic light scattering, small angle X-ray scattering and cryogenic transmission electron microscopy were used to characterize the colloidal structure of MS2 in water. The results show that the bacteriophage MS2 is a spherical particle with a core-shell type structure and a total diameter of 27nm. The RNA core has a radius of about 8nm and the protein shell forming the virus capsid is about 6nm thick. The water pH was discovered to have a major influence on the colloidal structure of the virus: at pH above 5, interparticle repulsions stabilize the virus solution. A decrease in pH to 3 led to diminishing of the repulsion forces and micrometer sized virus aggregates. This aggregation process was reversible upon circulating the water pH. In addition, the presence of Suwannee River natural organic matter that simulates the organic components in surface water was found to sterically stabilize the virus particles, reducing aggregates size and promoting disaggregation with pH increase. These findings will allow a better understanding of virus interactions and can guide the design of advanced water filtration processes for virus removal. Please click Additional Files below to see the full abstract

A modern look at a medieval bilayer metal leaf: nanotomography of Zwischgold

Many European sculptures and altarpieces from the Middle Ages were decorated with Zwischgold, a bilayer metal leaf with an ultra-thin gold face backed by silver. Zwischgold corrodes quickly when exposed to air, causing the surface of the artefact to darken and lose gloss. The conservation of such Zwischgold applied artefacts has been an obstinate problem. We have acquired quantitative, 3D nanoscale images of Zwischgold samples from 15th century artefacts and modern materials using ptychographic X-ray computed tomography (PXCT), a recently developed coherent diffractive imaging technique, to investigate the leaf structure and chemical state of Zwischgold. The measurements clearly demonstrate decreasing density (increasing porosity) of the leaf materials and their corrosion products, as well as delamination of the leaves from their substrate. Each of these effects speak to typically observed issues in the conservation of such Zwischgold applied artefacts. Further, a rare variant of Zwischgold that contains extremely thin multiple gold layers and an overlapping phenomenon of Zwischgold with other metal leaves are observed through PXCT. As supportive data, scanning electron microscopy (SEM) and scanning transmission electron microscopy (STEM) coupled with energy dispersive X-ray analysis (EDX) were performed on the medieval samples

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

BACKGROUND: Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools is now available for both isotopically labeled and label-free liquid chromatography mass spectrometry (LC-MS) based quantitative proteomics. However, they are generally not comparable to each other in terms of functionality, user interfaces, information input/output, and do not readily facilitate appropriate statistical data analysis. These limitations, along with the array of choices, present a daunting prospect for biologists, and other researchers not trained in bioinformatics, who wish to use LC-MS-based quantitative proteomics. RESULTS: We have developed Corra, a computational framework and tools for discovery-based LC-MS proteomics. Corra extends and adapts existing algorithms used for LC-MS-based proteomics, and statistical algorithms, originally developed for microarray data analyses, appropriate for LC-MS data analysis. Corra also adapts software engineering technologies (e.g. Google Web Toolkit, distributed processing) so that computationally intense data processing and statistical analyses can run on a remote server, while the user controls and manages the process from their own computer via a simple web interface. Corra also allows the user to output significantly differentially abundant LC-MS-detected peptide features in a form compatible with subsequent sequence identification via tandem mass spectrometry (MS/MS). We present two case studies to illustrate the application of Corra to commonly performed LC-MS-based biological workflows: a pilot biomarker discovery study of glycoproteins isolated from human plasma samples relevant to type 2 diabetes, and a study in yeast to identify in vivo targets of the protein kinase Ark1 via phosphopeptide profiling. CONCLUSION: The Corra computational framework leverages computational innovation to enable biologists or other researchers to process, analyze and visualize LC-MS data with what would otherwise be a complex and not user-friendly suite of tools. Corra enables appropriate statistical analyses, with controlled false-discovery rates, ultimately to inform subsequent targeted identification of differentially abundant peptides by MS/MS. For the user not trained in bioinformatics, Corra represents a complete, customizable, free and open source computational platform enabling LC-MS-based proteomic workflows, and as such, addresses an unmet need in the LC-MS proteomics field

Cloud computing mobile application for remote monitoring of Bell's palsy

Mobile applications provide the healthcare industry with a means of connecting with patients in their own home utilizing their own personal mobile devices such as tablets and phones. This allows therapists to monitor the progress of people under their care from a remote location and all with the added benefit that patients are familiar with their own mobile devices; thereby reducing the time required to train patients with the new technology. There is also the added benefit to the health service that there is no additional cost required to purchase devices for use. The Facial Remote Activity Monitoring Eyewear (FRAME) mobile application and web service framework has been designed to work on the IOS and android platforms, the two most commonly used today. Results: The system utilizes secure cloud based data storage to collect, analyse and store data, this allows for near real time, secure access remotely by therapists to monitor their patients and intervene when required. The underlying framework has been designed to be secure, anonymous and flexible to ensure compliance with the data protection act and the latest General Data Protection Regulation (GDPR); this new standard came into effect in April 2018 and replaces the Data Protection Act in the UK and Europe

Architecture and secondary structure of an entire HIV-1 RNA genome

Single-stranded RNA viruses encompass broad classes of infectious agents and cause the common cold, cancer, AIDS, and other serious health threats. Viral replication is regulated at many levels, including using conserved genomic RNA structures. Most potential regulatory elements within viral RNA genomes are uncharacterized. Here we report the structure of an entire HIV-1 genome at single nucleotide resolution using SHAPE, a high-throughput RNA analysis technology. The genome encodes protein structure at two levels. In addition to the correspondence between RNA and protein primary sequences, a correlation exists between high levels of RNA structure and sequences that encode inter-domain loops in HIV proteins. This correlation suggests RNA structure modulates ribosome elongation to promote native protein folding. Some simple genome elements previously shown to be important, including the ribosomal gag-pol frameshift stem-loop, are components of larger RNA motifs. We also identify organizational principles for unstructured RNA regions. Highly used splice acceptors lie in unstructured motifs and hypervariable regions are sequestered from flanking genome regions by stable insulator helices. These results emphasize that the HIV-1 genome and, potentially, many coding RNAs are punctuated by numerous previously unrecognized regulatory motifs and that extensive RNA structure may constitute an additional level of the genetic code