ThermoPhyl : a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples

The ability to specifically and sensitively target genotypes of interest is critical for the success of many PCR-based analyses of environmental or clinical samples that contain multiple templates.Next-generation sequence data clearly show that such samples can harbour hundreds to thousands of operational taxonomic units; a richness which precludes the manual evaluation of candidate assay specificity and sensitivity using multiple sequence alignments. To solve this problem we have developed and validated a free software tool which automates the identification of PCR assays targeting specific genotypes in complex samples. ThermoPhyl uses user-defined target and non-target sequence databases to assess the phylogenetic sensitivity and specificity of thermodynamically optimised candidate assays derived from primer design software packages. ThermoPhyl takes its name from its central premise of testing Thermodynamically optimal assays for Phylogenetic specificity and sensitivity and can be used for two primer (traditional PCR) or two primers with an internal probe (e.g. TaqMan® qPCR) applications and potentially for oligonucleotide probes.Here we describe the use of ThermoPhyl for traditional PCR and qPCR assays. PCR assays selected using ThermoPhyl were validated using 454 pyrosequencing of a traditional specific PCR assay and with a set of four genotype-specific qPCR assays applied to estuarine sediment samples

Chemistry and Apparent Quality of Surface Water and Ground Water Associated with Coal Basins

Personnel of the Arkansas Mining and Mineral Resources Research Institute conducted preliminary investigations on the chemistry and quality of surface and ground water associated with 12 coal-bearing sub-basins in the Arkansas Valley coal field. The coal field is approximately 60 miles long and 33 miles wide but only in 12 areas coal is thick enough and has proper quality to be termed commercial. Both surface and underground sample sites were established in each of the sub-basins with some minor variations in four areas where not all types of sites could be located. Water was collected from 19 surface points and 19 underground points in the established areas. Both field and laboratory analyses were made and elemental contents are reported herein. In the main, the chemistry and water quality suggests that all water is suitable for agricultural and industrial uses. To obtain potable water, treatment must be made to reduce calcium, magnesium, sodium sulfate and iron. The mineral content of the water is due to its contact with coal-bearing zones and, as such, reflects the mineral content of the coal. However, it is recommended that additional studies on the petrography and geochemistry of the coal, overburden and underburden is in order. Also, it is recommended that at least one detailed study be made of one of the coal sub-basins where geologic parameters can be completely established with regard to hydrogeology. This report is an important first step in determining the character and quality of Arkansas coal which must be fully understood to fully utilize this important mineral resource

Implementation of a local principal curves algorithm for neutrino interaction reconstruction in a liquid argon volume

A local principal curve algorithm has been implemented in three dimensions for automated track and shower reconstruction of neutrino interactions in a liquid argon time projection chamber. We present details of the algorithm and characterise its performance on simulated data sets.Comment: 14 pages, 17 figures; typing correction to Eq 5, the definition of the local covariance matri

Feminists really do count : the complexity of feminist methodologies

We are delighted to be presenting this special issue on the topic of feminism and quantitative methods. We believe that such an issue is exceptionally timely. This is not simply because of ongoing debates around quantification within the field of feminism and women‟s studies. It is also because of debates within the wider research community about the development of appropriate methodologies that take account of new technological and philosophical concerns and are fit-for-purpose for researching contemporary social, philosophical, cultural and global issues. Two areas serve as exemplars in this respect and both speak to these combined wider social science and specifically feminist methodological concerns. The first is the increasing concern amongst social scientists with how the complexity of social life can be captured and analysed. Within feminism, this can be seen in debates about intersectionality that recognise the concerns arising from multiple social positions/divisions and associated power issues. As Denis (2008: 688) comments in respect of intersectional analysis „The challenge of integrating multiple, concurrent, yet often contradictory social locations into analyses of power relations has been issued. Theorising to accomplish this end is evolving, and we are struggling to develop effective methodological tools in order to marry theorising with necessary complex analyses of empirical data.‟ Secondly, new techniques and new data sources are now coming on line. This includes work in the UK of the ESRC National Data Strategy which has been setting out the priorities for the development of research data resources both within and across the boundaries of the social sciences. This will facilitate historical, longitudinal, interdisciplinary and mixed methodological research. And it may be the case that these developments facilitate the achievement of a longstanding feminist aim not simply for interdisciplinarity but for transdisciplinarity in epistemological and methodological terms

The art of innovation: How fine arts graduates contribute to innovation

This report gives insights into how fine arts graduates contribute to innovation in the creative industries and beyond, and what policymakers can do to support their contribution. In the 21st century, the UK's economic competitiveness and social wellbeing will increasingly depend on our ability to innovate. A significant part of the innovation process revolves around 'creativity' - the ability to generate new ideas, or to restructure and redeploy old ones. But how important really is creativity to UK innovation? The UK has long been a leader in many of the more obvious 'creative industries': music, design, fine art, architecture and so on. Indeed, such activities can be argued to be at the heart of what the United Kingdom is about. Champions of the arts and of economic development have recently developed an alliance: they have linked this type of creativity to the type required for global competitiveness. The question is: is this link true? Nesta has explored this question in a series of research reports. This time, we have been privileged to work with an outstanding team centred on the Central Saint Martins College of Art & Design in surveying and interviewing a host of fine arts graduates of the University of Arts London from the past several decades

Antigen depot is not required for alum adjuvanticity

Alum adjuvants have been in continuous clinical use for more than 80 yr. While the prevailing theory has been that depot formation and the associated slow release of antigen and/or inflammation are responsible for alum enhancement of antigen presentation and subsequent T- and B-cell responses, this has never been formally proven. To examine antigen persistence, we used the chimeric fluorescent protein EαGFP, which allows assessment of antigen presentation in situ, using the Y-Ae antibody. We demonstrate that alum and/or CpG adjuvants induced similar uptake of antigen, and in all cases, GFP signal did not persist beyond 24 h in draining lymph node antigen-presenting cells. Antigen presentation was first detectable on B cells within 6–12 h of antigen administration, followed by conventional dendritic cells (DCs) at 12–24 h, then finally plasmacytoid DCs at 48 h or later. Again, alum and/or CpG adjuvants did not have an effect on the magnitude or sequence of this response; furthermore, they induced similar antigen-specific T-cell activation in vivo. Notably, removal of the injection site and associated alum depot, as early as 2 h after administration, had no appreciable effect on antigen-specific T- and B-cell responses. This study clearly rules out a role for depot formation in alum adjuvant activity

Academic motherhood and fieldwork: Juggling time, emotions and competing demands

The idea and practice of going ‘into the field’ to conduct research and gather data is a deeply rooted aspect of Geography as a discipline. For global North Development Geographers, amongst others, this usually entails travelling to, and spending periods of time in, often far-flung parts of the global South. Forging a successful academic career as a Development Geographer in the UK, is therefore to some extent predicated on mobility. This paper aims to critically engage with the gendered aspects of this expected mobility, focusing on the challenges and time constraints that are apparent when conducting overseas fieldwork as a mother, unaccompanied by her children. The paper emphasises the emotion work that is entailed in balancing the competing demands of overseas fieldwork and mothering, and begins to think through the implications of these challenges in terms of the types of knowledge we produce, as well as in relation to gender equality within the academy

Story in health and social care

This paper offers a brief consideration of how narrative, in the form of people‟s own stories, potentially figures in health and social care provision as part of the impulse towards patient-centred care. The rise of the epistemological legitimacy of patients‟ stories is sketched here. The paper draws upon relevant literature and original writing to consider the ways in which stories can mislead as well as illuminate the process of making individual treatment care plans

International Public Health Research Involving Interpreters: a Case Study from Bangladesh

Background: Cross-cultural and international research are important components of public health research, but the challenges of language barriers and working with interpreters are often overlooked, particularly in the case of qualitative research. Methods: A case-study approach was used to explore experiences of working with an interpreter in Bangladesh as part of a research project investigating women's experiences of emergency obstetric care. The case study: Data from the researcher's field notes provided evidence of experiences in working with an interpreter and show how the model of interviewing was adapted over time to give a more active role to the interpreter. The advantages of a more active role were increased rapport and "flow" in interviews. The disadvantages included reduced control from the researcher's perspective. Some tensions between the researcher and interpreter remained hard to overcome, irrespective of the model used. Independent transcription and translation of the interviews also raised questions around accuracy in translation. Conclusion: The issues examined in this case study have broader implications for public health research. Further work is needed in three areas: 1) developing effective relationships with interpreters; 2) the impact of the interpreter on the research process; and 3) the accuracy of the translation and level of analysis needed in any specific public health research. Finally, this paper highlights the importance to authors of reflecting on the potential impact of translation and interpretation on the research process when disseminating their research