Raman spectroscopy for the detection of AGEs/ALEs

Raman spectroscopy is a noninvasive, nondestructive tool for capturing multiplexed biochemical information across diverse molecular species including proteins, lipids, DNA, and mineralizations. Based on light scattering from molecules, cells, and tissues, it is possible to detect molecular fingerprints and discriminate between subtly different members of each biochemical class. Raman spectroscopy is ideal for detecting perturbations from the expected molecular structure such as those occurring during senescence and the modification of long-lived proteins by metabolic intermediates as we age. Here, we describe the sample preparation, data acquisition, signal processing, data analysis and interpretation involved in using Raman spectroscopy for detecting age-related protein modifications in complex biological tissues.

Revolt and Revolution: the place of Islamism

The outbreak of revolt and revolution in the Middle East has given rise to a re-consideration of threat and security analyses as they pertain to the region and beyond. The resilience of some authoritarian regimes and the rapid collapse of others signal a significant transition within the region to which jihadi Islamist groups form one part of a powerful matrix. This article analyses the part and place of jihadi Islamism and Islamisms more generally in the revolts and revolutions. The article contends that events provide both opportunities and threats in strategies aimed at countering terrorism in the Middle East.

Cause-specific mortality adjudication in the UPLIFT® COPD trial:findings and recommendations

Mortality is an important endpoint in chronic obstructive pulmonary disease (COPD) trials, although accurately determining cause of death is difficult. In the Understanding the Potential Long-term Impacts on Function with Tiotropium (UPLIFT®) trial, a mortality adjudication committee (MAC) provided systematic, independent and blinded assessment of cause-specific mortality of all 981 reported deaths. Here we describe this process of mortality adjudication and methodological revisions introduced to help standardise the adjudication of two areas recognised to pose particular difficulty; firstly, the classification of fatal COPD exacerbations that occur in the setting of pneumonia and secondly, the categorisation of sudden death. In addition MAC determined cause of death was compared with that reported by site investigators (SIs). MAC-assigned causes of death were: respiratory, 35%; cancer, 25%; cardiovascular, 11%; sudden cardiac death, 4.4%; sudden death, 3.4%; other, 8.8%; unknown, 12.4%. Cancer/cardiac deaths were more common in Global Initiative for Chronic Obstructive Lung Disease stage II, respiratory deaths in stages III and IV. Agreement between MAC and SI regarding cause of death was complete (50.2%), incomplete (18.5%) or none (31.3%). The SI classified deaths as cardiac three-fold more frequently than MAC (incidence rate [IR]/100 patient-years 0.797 vs. 0.257), although IR ratios for cardiac deaths for tiotropium vs. control were similar between SI and MAC. Discrepancies between MAC- and SI-adjudicated causes of death are common, especially increased reporting of cardiac deaths by the SI. Future multicentre COPD trials should plan appropriate infrastructure before study initiation to ensure collection and interpretation of fatal events data.

A Cat's Lick: Democratisation and Minority Communities in the Post-Soviet Baltic

The research on Estonia, Latvia and Lithuania has pointed out some controversial social and political developments since the collapse of the Soviet Union. Crucially, there is a discrepancy between the governments' commitment to creating democratic political regimes, to ensuring harmonious social relations and to accommodating the ethno-cultural diversity of the resident communities. In reflecting on the legacies of the Soviet past, the book addresses the role non-titular populations have played in the process of democratisation and the relation between the states, societies and minorities in the post-Soviet Baltic states. The argument proceeds along three lines. Firstly, the book examines the institutional dimension of democratisation in the region, thereby addressing the processes of state- and nation-building as reflected in various policy-developments. Secondly, it compares the impact of ethno-cultural diversity on the development of the respective Baltic nation-states. The discussion makes clear that the framework of Baltic political communities was designed to suit the interests of the titular groups and thus resulted in the marginalisation of the minority communities. Thirdly, the book assesses the participation of minority communities in the development, criticism and improvement of state institutions and policies since independence. The analysis points out that, two decades after independence, the post-Soviet Baltic states and societies are seen by many members of the majority groups as primarily serving the interests of their ethnic community. In this situation, the members of the non-titular communities need to adapt to the majorities' perceptions in order to benefit from the achievements of democratisation.

Zeros and Os:Silence, Absence and Erasure in an Intercultural O-thello

The performative function of sound and music has received little attention in performance theory and criticism and certainly much less so in studies of intercultural theatre. Such an absence is noteworthy particularly since interculturalism is an appropriative Western theatrical form that absorbs Eastern sources to re-create the targeted Western mise en scene. Consequently, a careful consideration of the employment of sound and music are imperative for sound and music form the vertebrae of Asian traditional performance practices. In acoustemological and ethnomusicological studies, sound and music demarcate cultural boundaries and locate cultures by an auditory (dis)recognition. In the light of this need for a more considered understanding of the performative function of sound and music in intercultural performance, this paper seeks to examine the soundscapes of an intercultural production of Shakespeare’s Othello – Desdemona. Directed by Singaporean Ong Keng Sen, Desdemona was a re-scripting of Shakespeare’s text and a self-conscious performance an identity politics. Staged with a multi-ethnic, multi-national cast, Desdemona employed various Asian performance traditions such as Sanskrit Kutiyattam, Myanmarese puppetry, and Korean p’ansori to create the intercultural spectacle. The spectacle was not only a visual aesthetic but an aural one as well. By examining the soundscapes of fractured silences and eruptive cultural sounds the paper hopes to establish the ways in which Desdemona performs absences and erasures of ‘Asia’ in a simultaneous act of performing an Asian Shakespeare.

Interpretation on Humphrey's visual field tests. Is it glaucoma?

This article describes a step-wise approach for the understanding and interpretation of Humphrey's SITA visual field tests. The goal of this article is to help the reader to differentiate between non-specific abnormalities of the visual field and changes of the visual field that are suggestive of glaucoma.

An Examination of Transformation Techniques to Investigate and Interpret Multivariate Geochemical Data Analysis: Tellus Case Study

This research aims to use the multivariate geochemical dataset, generated by the Tellus project, to investigate the appropriate use of transformation methods to maintain the integrity of geochemical data and inherent constrained behaviour in multivariate relationships. The widely used normal score transform is compared with the use of a stepwise conditional transform technique. The Tellus Project, managed by GSNI and funded by the Department of Enterprise Trade and Development and the EU’s Building Sustainable Prosperity Fund, involves the most comprehensive geological mapping project ever undertaken in Northern Ireland. Previous study has demonstrated spatial variability in the Tellus data but geostatistical analysis and interpretation of the datasets requires use of an appropriate methodology that reproduces the inherently complex multivariate relations. Previous investigation of the Tellus geochemical data has included use of Gaussian-based techniques. However, earth science variables are rarely Gaussian, hence transformation of data is integral to the approach. The multivariate geochemical dataset generated by the Tellus project provides an opportunity to investigate the appropriate use of transformation methods, as required for Gaussian-based geostatistical analysis. In particular, the stepwise conditional transform is investigated and developed for the geochemical datasets obtained as part of the Tellus project. The transform is applied to four variables in a bivariate nested fashion due to the limited availability of data. Simulation of these transformed variables is then carried out, along with a corresponding back transformation to original units. Results show that the stepwise transform is successful in reproducing both univariate statistics and the complex bivariate relations exhibited by the data. Greater fidelity to multivariate relationships will improve uncertainty models, which are required for consequent geological, environmental and economic inferences.

DiveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors

Summary: We present a new R package, diveRsity, for the calculation of various diversity statistics, including common diversity partitioning statistics (?, G) and population differentiation statistics (D, GST ', ? test for population heterogeneity), among others. The package calculates these estimators along with their respective bootstrapped confidence intervals for loci, sample population pairwise and global levels. Various plotting tools are also provided for a visual evaluation of estimated values, allowing users to critically assess the validity and significance of statistical tests from a biological perspective. diveRsity has a set of unique features, which facilitate the use of an informed framework for assessing the validity of the use of traditional F-statistics for the inference of demography, with reference to specific marker types, particularly focusing on highly polymorphic microsatellite loci. However, the package can be readily used for other co-dominant marker types (e.g. allozymes, SNPs). Detailed examples of usage and descriptions of package capabilities are provided. The examples demonstrate useful strategies for the exploration of data and interpretation of results generated by diveRsity. Additional online resources for the package are also described, including a GUI web app version intended for those with more limited experience using R for statistical analysis. © 2013 British Ecological Society.

Statistics sunspots and settlement: Influences on sum of probability curves

Large data sets of radiocarbon dates are becoming a more common feature of archaeological research. The sheer numbers of radiocarbon dates produced, however, raise issues of representation and interpretation. This paper presents a methodology which both reduces the visible impact of dating fluctuations, but also takes into consideration the influence of the underlying radiocarbon calibration curve. By doing so, it may be possible to distinguish between periods of human activity in early medieval Ireland and the statistical tails produced by radiocarbon calibration.

Extremely Complex Populations of Small RNAs in the Mouse Retina and RPE/Choroid

Purpose: MicroRNAs (miRNAs) are small non-coding RNAs of ~18-22 nucleotides in length that regulate gene expression. They are widely expressed in the retina, being both required for its normal development and perturbed in disease. The aim of this study was to apply new high-throughput sequencing techniques to more fully characterise the microRNAs and other small RNAs expressed in the retina and retinal pigment epithelium (RPE)/choroid of the mouse.

Methods: Retina and RPE/choroid were dissected from eyes of 3 month-old C57BL/6J mice. Small RNA libraries were prepared and deep sequencing performed on a Genome Analyzer (Illumina). Reads were annotated by alignment to miRBase, other non-coding RNA databases and the mouse genome.

Results: Annotation of 9 million reads to 320 microRNAs in retina and 340 in RPE/choroid provides the most comprehensive profiling of microRNAs to date. Two novel microRNAs were identified in retina. Members of the sensory organ specific miR-183,-182,-96 cluster were amongst the most highly expressed, retina-enriched microRNAs. Remarkably, microRNA 'isomiRs', which vary slightly in length and are differentially detected by Taqman RT-PCR assays, existed for all the microRNAs identified in both tissues. More variation occurred at the 3' ends, including non-templated additions of T and A. Drosha-independent mirtron microRNAs and other small RNAs derived from snoRNAs were also detected.

Conclusions: Deep sequencing has revealed the complexity of small RNA expression in the mouse retina and RPE/choroid. This knowledge will improve the design and interpretation of future functional studies of the role of microRNAs and other small RNAs in retinal disease.

Scientific standards for human intervention trials evaluating health benefits of foods, and their application to infants, children and adolescents

Associations between the consumption of particular foods and health outcomes may be indicated by observational studies. However, intervention trials that evaluate the health benefits of foods provide the strongest evidence to support dietary recommendations for health. Thus, it is important that these trials are carried out safely, and to high scientific standards. Accepted standards for the reporting of the health benefits of pharmaceutical and other medical interventions have been provided by the Consolidated Standards of Reporting Trials (CONSORT) statement. However, there are no generally accepted standards for trials to evaluate the health benefits of foods. Trials with foods differ from medical trials in issues related to safety, ethics, research governance and practical implementation. Furthermore, these important issues can deter the conduct of both medical and nutrition trials in infants, children and adolescents. This paper provides standards for the planning, design, conduct, statistical analysis and interpretation of human intervention trials to evaluate the health benefits of foods that are based on the CONSORT guidelines, and outlines the key issues that need to be addressed in trials in participants in the paediatric age range.

Doing Focus Groups and Interviews with Recent Migrants to Northern Ireland: A Dynamic Interplay of Ethics, Language and Access

This case describes a qualitative social science research project that was conducted in 2009 and that examined the experiences of recent migrants to Northern Ireland. While background to the research and key findings are presented, the topic forms a backdrop to the case. The following aspects of the study are presented: the theoretical context; formulating the research question, design and methodology; key methodological issues; data collection and analysis; project dissemination; and research funding and reporting. The case pays particular attention to the needs and impact of different groups including the researcher, the funding body, the researcher’s employer and the researched. The significance of access, language and ethics to this study are examined. Finally, the way in which the research unfolded in an often-unpredictable way throughout the implementation process is highlighted in the narrative.

RAS testing of colorectal carcinoma—a guidance document from the Association of Clinical Pathologists Molecular Pathology and Diagnostics Group

Analysis of colorectal carcinoma (CRC) tissue for KRAS codon 12 or 13 mutations to guide use of anti-epidermal growth factor receptor (EGFR) therapy is now considered mandatory in the UK. The scope of this practice has been recently extended because of data indicating that NRAS mutations and additional KRAS mutations also predict for poor response to anti-EGFR therapy. The following document provides guidance on RAS (i.e., KRAS and NRAS) testing of CRC tissue in the setting of personalised medicine within the UK and particularly within the NHS. This guidance covers issues related to case selection, preanalytical aspects, analysis and interpretation of such RAS testing.

From the past to the Future: integrating archaeology and conflict resolution in Northern Ireland

Contested understandings about the past continue to reify the divided character of post-Troubles Northern Ireland. In particular, the unresolved legacies of the extension of English control over Ireland in the late sixteenth and early seventeenth centuries through warfare and plantation continue to structure daily lives in the province. Yet the archaeological record of this period complicates the accepted dichotomous narratives through highlighting complexity. These nuances, however, have been lost in recent decades as an overly simplistic model of colonizer versus colonized has emerged as the dominant political paradigm. The management and presentation of sites associated with the process of plantation can arguably create the space necessary to bridge the divide, and to challenge accepted understandings. Cross-community engagement in the process of archaeological discovery and interpretation on plantation-period sites in Northern Ireland highlights the critical role archaeology can play in peace and reconciliation in post-conflict societies.