In Testing Times: Conducting an Ethnographic Study of UK Animal Rights Protesters

This article reflects upon the experience of conducting research into a UK-based, though internationally-renowned, animal rights group. The article firstly rationalizes the ethnographic research methodology used to approach Stop Huntingdon Animal Cruelty (SHAC). Secondly, it describes the effect of unforeseen factors (from adverse media attention to ongoing criminal investigations) on the Author's ability to forge research relationships with informants within the movement, and how these challenges were overcome. Given the interdisciplinary focus of the project, this manuscript will be of interest to scholars wishing to investigate 'hard-to-reach' social groups, and particularly those who have written on reflexivity and power in research relationships.Animal Rights and Liberation, Protests, Ethnography, Field Relations, Overt Research

Rapid gravity filtration operational performance assessment and diagnosis for preventative maintenance from on-line data

Rapid gravity filters, the final particulate barrier in many water treatment systems, are typically monitored using on-line turbidity, flow and head loss instrumentation. Current metrics for assessing filtration performance from on-line turbidity data were critically assessed and observed not to effectively and consistently summarise the important properties of a turbidity distribution and the associated water quality risk. In the absence of a consistent risk function for turbidity in treated water, using on-line turbidity as an indicative rather than a quantitative variable appears to be more practical. Best practice suggests that filtered water turbidity should be maintained below 0.1 NTU, at higher turbidity we can be less confident of an effective particle and pathogen barrier. Based on this simple distinction filtration performance has been described in terms of reliability and resilience by characterising the likelihood, frequency and duration of turbidity spikes greater than 0.1 NTU. This view of filtration performance is then used to frame operational diagnosis of unsatisfactory performance in terms of a machine learning classification problem. Through calculation of operationally relevant predictor variables and application of the Classification and Regression Tree (CART) algorithm the conditions associated with the greatest risk of poor filtration performance can be effectively modelled and communicated in operational terms. This provides a method for an evidence based decision support which can be used to efficiently manage individual pathogen barriers in a multi-barrier system

Affymetrix probes containing runs of contiguous guanines are not gene-specific

High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in the designated probe set will provide a consistent message signifying the gene's presence. However, we demonstrate by data mining thousands of CEL files from NCBI's GEO database that 4G-probes (defined as probes containing sequences of four or more consecutive guanine (G) bases) do not react in the intended way. Rather, possibly due to the formation of G-quadruplexes, most 4G-probes are correlated, irrespective of the expression of the thousands of genes for which they were separately intended. It follows that 4G-probes should be ignored when calculating gene expression levels. Furthermore, future microarray designs should make no use of 4G-probes

THM and HAA formation from NOM in raw and treated surface waters

The disinfection by-product (DBP) formation potential (FP) of natural organic matter (NOM) in surface water sources has been studied with reference to the key water quality determinants (WQDs) of UV absorption (UV254), colour, and dissolved organic carbon (DOC) concentration. The data set used encompassed raw and treated water sampled over a 30-month period from 30 water treatment works (WTWs) across Scotland, all employing conventional clarification. Both trihalomethane (THM) and haloacetic acid (HAA) FPs were considered. In addition to the standard bulk WQDs, the DOC content was fractionated and analysed for the hydrophobic (HPO) and hydrophilic (HPI) fractions. Results were quantified in terms of the yield (dDBPFP/dWQD) and the linear regression coefficient R2 of the yield trend. The NOM in the raw waters was found to comprise 30–84% (average 66%) of the more reactive HPO material, with this proportion falling to 18–63% (average 50%) in the treated water. Results suggested UV254 to be as good an indicator of DBPFP as DOC or HPO for the raw waters, with R2 values ranging from 0.79 to 0.82 for THMs and from 0.71 to 0.73 for HAAs for these three determinants. For treated waters the corresponding values were significantly lower at 0.52–0.67 and 0.46–0.47 respectively, reflecting the lower HPO concentration and thus UV254 absorption and commensurately reduced precision due to the limit of detection of the analytical instrument. It is concluded that fractionation offers little benefit in attempting to discern or predict chlorinated carbonaceous DBP yield for the waters across the geographical region studied. UV254 offered an adequate estimate of DBPFP based on a mean yield of ∼2600 and ∼2800 μg per cm−1 absorbance for THMFP for the raw and treated waters respectively and ∼3800 and2900 μg cm−1 for HAAFP, albeit with reduced precision for the treated waters

A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia

We have previously discovered that probes containing runs of four or more contiguous guanines are not reliable for measuring gene expression in the Human HG_U133A Affymetrix GeneChip data. These probes are not correlated with other members of their probe set, but they are correlated with each other. We now extend our analysis to different3′GeneChip designs of mouse, rat, and human. We find that, in all these chip designs, the G-stack probes (probes with a run of exactly four consecutive guanines) are correlated highly with each other, indicating that such probes are not reliable measures of gene expression in mammalian studies. Furthermore, there is no specific position of G-stack where the correlation is highest in all the chips. We also find that the latest designs of rat and mouse chips have significantly fewer G-stack probes compared to their predecessors, whereas there has not been a similar reduction in G-stack density across the changes in human chips. Moreover, we find significant changes in RMA values (after removing G-stack probes) as the number of G-stack probes increases.</jats:p

Motif effects in Affymetrix GeneChips seriously affect probe intensities

An Affymetrix GeneChip consists of an array of hundreds of thousands of probes (each a sequence of 25 bases) with the probe values being used to infer the extent to which genes are expressed in the biological material under investigation. In this article, we demonstrate that these probe values are also strongly influenced by their precise base sequence. We use data from >28 000 CEL files relating to 10 different Affymetrix GeneChip platforms and involving nearly 1000 experiments. Our results confirm known effects (those due to the T7-primer and the formation of G-quadruplexes) but reveal other effects. We show that there can be huge variations from one experiment to another, and that there may also be sizeable disparities between batches within an experiment and between CEL files within a batch. © 2012 The Author(s)

Methods, measurements, and novel materials for improving depth filtration processes used in drinking water treatment.

Rapid media filtration is used to treat most surface water sources for municipal drinking water supply. This thesis presents results of an investigation into how media filters in Scottish Water, built decades ago to different standards, can meet increasingly stringent water quality requirements. A new method for efficient assessment of filter performance and diagnosis of issues using online data were developed. A recursive partitioning algorithm applied to operationally relevant predictor variables was shown to efficiently and effectively characterise the conditions associated with elevated turbidity over an extended period of operation. Tree models can then be used to communicate a diagnosis in operational terms to aid the efficient management of individual pathogen barriers in a multi-barrier system. Robust rapid filtration requires effective coagulation. An investigation was conducted at a water treatment works (WTW) to understand the influence of zeta potential. The effective zeta potential window was modelled & observed to change with conditions. The online measurement of zeta potential was shown to be useful for process optimisation by providing a quantitative measurement with a mechanistic basis for coagulation conditions. This provides advantages over jar testing which may poorly represent the system under investigation. Pilot and full-scale trials of an alternative expanded aluminosilicate media show that the additional bed expansion achieved by replacing sand with the lower density material can, at comparatively low cost, improve the performance of rapid gravity filters with a common design limitation. The effective application of new finer grade expanded aluminosilicate was shown at pilot and full scale. This thesis presents a suite of efficient solutions to ensure aging 20th century filters robustly meet challenges in 21st century. This is achieved by improving understanding of how and why specific constraints limit the performance of existing RGFs and developing strategic solutions to overcome common limitations to process performance.Engineering and Physical Sciences (EPSRC)STREAM EngD Programm

'I want to go back to the text': Response Strategies on the Reading Subtest of the New TOEFL

This post-peer-review, pre-copyedit version of the article submitted to IUPUI ScholarWorks as part of the OASIS Project. Article reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Permission granted through posted policies on copyright owner’s website or through direct contact with copyright owner.This study describes the reading and test-taking strategies that test takers used on the ‘Reading’ section of the LanguEdge Courseware (2002) materials developed to familiarize prospective respondents with the new TOEFL. The investigation focused on strategies used to respond to more traditional ‘single selection’ multiple-choice formats (i.e., Basic Comprehension and Inferencing questions) and the new selected-response (multiple selection, drag-and-drop) Reading to Learn items. The latter were designed to simulate the academic skill of forming a comprehensive and coherent representation of an entire text, rather than focusing on discrete points in the text. Verbal report data were collected from 32 students, representing four language groups (Chinese, Japanese, Korean, and ‘Other’) doing the Reading section tasks from the LanguEdge Courseware materials. Students were randomly assigned to two of the six reading subtests, each consisting of a 600–700 word text with 12–13 items, and subjects’ verbal reports accompanying items representing each of the ten item types were evaluated to determine strategy use. The findings provide insights into the response behaviors prompted by the reading tasks on the new TOEFL