• A machine learning approach for ethnic classification: the British Pakistani face

      Khalid Jilani, Shelina; Ugail, Hassan; Bukar, Ali M.; Logan, Andrew J.; Munshi, Tasnim (2017)
      Ethnicity is one of the most salient clues to face identity. Analysis of ethnicity-specific facial data is a challenging problem and predominantly carried out using computer-based algorithms. Current published literature focusses on the use of frontal face images. We addressed the challenge of binary (British Pakistani or other ethnicity) ethnicity classification using profile facial images. The proposed framework is based on the extraction of geometric features using 10 anthropometric facial landmarks, within a purpose-built, novel database of 135 multi-ethnic and multi-racial subjects and a total of 675 face images. Image dimensionality was reduced using Principle Component Analysis and Partial Least Square Regression. Classification was performed using Linear Support Vector Machine. The results of this framework are promising with 71.11% ethnic classification accuracy using a PCA algorithm + SVM as a classifier, and 76.03% using PLS algorithm + SVM as a classifier.
    • Magnetic geophysical mapping of prehistoric iron production sites in central Norway

      Stamnes, A.A.; Stenvik, L.F.; Gaffney, Christopher F. (2019-08)
      The slag pit furnace of the Trøndelag tradition for iron production is a very specific cultural-historical tradition in central Norway in the Early Iron Age, but few of these iron production sites have been excavated in their entirety and there is therefore a lack of information about their size, spatial layout and organisation in the landscape. The aim of this paper is therefore to investigate how magnetic geophysical methods can be used as a way of locating, delimiting and characterising activity zones and specific archaeological features associated with this tradition of iron production. The NTNU University Museum in Trondheim performed geophysical surveys of four different iron production sites, combining topsoil volume magnetic susceptibility measurements and detailed fluxgate gradiometer surveys. Analysing and comparing the survey results with sketches and topographic survey results, as well as comparable geophysical survey data from iron production sites elsewhere in Norway, made it possible to gain new and valuable cultural-historical and methodological knowledge. The topsoil volume susceptibility measurements revealed a strong contrast between the main production areas and the natural background measurement values, often in the range of 7–27 times the median background values. The absolute highest measured values were usually in the area closest to the furnaces, and within the slag mounds. Satellites of high readings could be interpreted as roasting sites for iron ore, and even areas with known building remains related to the iron production sites had readings stronger than the median. The fluxgate gradiometer data helped to characterise individual features further, with strong geophysical contrast between features within the iron production sites and the areas surrounding them. Also, by analysing their physical placement, geophysical characteristics such as contrast, magnetic remanence and size, it was possible to gain further insight into the spatial organisation by indicating the potential location of furnaces, the spread of slag and the handling of iron ore. The latter involved both where the roasted iron ore was stored and where it was roasted. The geophysical characteristics of the furnaces were less uniform than situations reported elsewhere in Norway, which can be explained by the reuse of furnaces and slag pits. The spread of highly remanent material in and around the furnaces and elsewhere within the limits of the iron production sites also created a disturbed magnetic picture rendering it difficult to provide an unambiguous archaeological interpretation of all the geophysical anomalies identified. In conclusion, these results showed that the geophysical methods applied made it possible to indicate the physical size, layout and internal spatial organisation of iron production sites of the Trøndelag slag pit furnace tradition.
    • Magnetometry for Archaeologists

      Aspinall, A.; Gaffney, Christopher F.; Schmidt, Armin R. (2008)
    • A major advance in crystal structure prediction.

      Neumann, M.A.; Leusen, Frank J.J.; Kendrick, John (Wiley, 20/02/2008)
      A crystal ball? A new method for crystal structure prediction combines a tailor-made force field with a density functional theory method incorporating a van der Waals correction for dispersive interactions. In a blind test, the method predicts the correct crystal structure for all four compounds, one of which is a cocrystal. The picture shows the predicted structure of one of the compounds in green and the experimental structure in blue.
    • Making it work for me: beliefs about making a personal health record relevant and useable

      Fylan, F.; Caveney, L.; Cartwright, A.; Fylan, Beth (2018-06)
      Background: A Personal Health Record (PHR) is an electronic record that individuals use to manage and share their health information, e.g. data from their medical records and data collected by apps. However, engagement with their record can be low if people do not find it beneficial to their health, wellbeing or interactions with health and other services. We have explored the beliefs potential users have about a PHR, how it could be made personally relevant, and barriers to its use. Methods: A qualitative design comprising eight focus groups, each with 6–8 participants. Groups included adults with long-term health conditions, young people, physically active adults, data experts, and members of the voluntary sector. Each group lasted 60–90 min, was audio recorded and transcribed verbatim. We analysed the data using thematic analysis to address the question “What are people’s beliefs about making a Personal Health Record have relevance and impact?” Results: We found four themes. Making it work for me is about how to encourage individuals to actively engage with their PHR. I control my information is about individuals deciding what to share and who to share it with. My concerns is about individuals’ concerns about information security and if and how their information will be acted upon. Potential impact shows the potential benefits of a PHR such as increasing self-efficacy, uptake of health-protective behaviours, and professionals taking a more holistic approach to providing care and facilitating behaviour change. Conclusions: Our research shows the functionality that a PHR requires in order for people to engage with it. Interactive functions and integration with lifestyle and health apps are particularly important. A PHR could increase the effectiveness of behaviour change apps by specifying evidence-based behaviour change techniques that apps should incorporate. A PHR has the potential to increase health-protective behaviours and facilitate a more person-driven health and social care system. It could support patients to take responsibility for self-managing their health and treatment regimens, as well as helping patients to play a more active role when care transfers across boundaries of responsibility.
    • Making power explicit in sustainable water innovation: Re-linking subjectivity, institution and structure through environmental citizenship.

      Wong, S.; Sharp, Liz (2009)
      This article offers a new perspective on environmental citizenship by proposing the 'subjectivity-institution-structure' framework. Applying the framework to a sustainable water innovation project in north-west England, it argues that the meaning of environmental rights, the understanding of required environmental responsibilities, and the degree of public participation in decision-making, are shaped by individuals' subjective values, institutional arrangements and structural conditions. Our framework makes power explicit in the practice of environmental citizenship. It is intended to help set reasonable targets for sustainable development actions, which is particularly important when working with individuals with limited power.
    • Making sustainable water innovations work with the poor

      Wong, S.; Sharp, Liz; Kennedy, S.P.; Lewis, L. (2007)
    • MALDI analysis of Bacilli in spore mixtures by applying a quadrupole trap-time-of-flight tandem mass spectrometer.

      Warscheid, B.; Jackson, K.A.; Sutton, Chris W.; Fenselau, C. (2003)
      A novel ion trap time-of-flight hybrid mass spectrometer (qIT-TOF MS) has been applied for peptide sequencing in proteolytic digests generated from spore mixtures of Bacilli. The method of on-probe solubilization and in situ proteolytic digestion of small, acid-soluble spore proteins has been recently developed in our laboratory, and microorganism identification in less than 20 min was accomplished.1 In this study, tryptic peptides were generated in situ from complex spore mixtures of B. subtilis 168, B. globigii, B. thuringiensis subs. Kurstaki, and B. cereus T, respectively. MALDI analysis of bacterial peptides generated was performed with an average mass resolving power of 6200 and a mass accuracy of up to 10 ppm using a trap-TOF tandem configuration. Precursor ions of interest were usually selected and stored in the quadrupole ion trap with their complete isotope distribution by choosing a window of ±2 Da. Sequence-specific information on isolated protonated peptides was gained via tandem MS experiments with an average mass resolving power of 4450 for product ion analysis, and protein and bacterial sources were identified by database searching.
    • A male germ cell assay and supporting somatic cells: its application for the detection of phase specificity of genotoxins in vitro

      Habas, Khaled S.A.; Brinkworth, Martin H.; Anderson, Diana (2020-03)
      Male germ stem cells are responsible for transmission of genetic information to the next generation. Some chemicals exert a negative impact on male germ cells, either directly, or indirectly affecting them through their action on somatic cells. Ultimately, these effects might inhibit fertility, and may exhibit negative consequences on future offspring. Genotoxic anticancer agents may interact with DNA in germ cells potentially leading to a heritable germline mutation. Experimental information in support of this theory has not always been reproducible and suitable in vivo studies remain limited. Thus, alternative male germ cell tests, which are now able to detect phase specificity of such agents, might be used by regulatory agencies to help evaluate the potential risk of mutation. However, there is an urgent need for such approaches for identification of male reproductive genotoxins since this area has until recently been dependent on in vivo studies. Many factors drive alternative approaches, including the (1) commitment to the principles of the 3R's (Replacement, Reduction, and Refinement), (2) time-consuming nature and high cost of animal experiments, and (3) new opportunities presented by new molecular analytical assays. There is as yet currently no apparent appropriate model of full mammalian spermatogenesis in vitro, under the REACH initiative, where new tests introduced to assess genotoxicity and mutagenicity need to avoid unnecessary testing on animals. Accordingly, a battery of tests used in conjunction with the high throughput STAPUT gravity sedimentation was recently developed for purification of male germ cells to investigate genotoxicity for phase specificity in germ cells. This system might be valuable for the examination of phases previously only available in mammals with large-scale studies of germ cell genotoxicity in vivo. The aim of this review was to focus on this alternative approach and its applications as well as on chemicals of known in vivo phase specificities used during this test system development.
    • Male-mediated developmental toxicity

      Anderson, Diana; Schmid, Thomas E.; Baumgartner, Adolf (2014)
      Male-mediated developmental toxicity has been of concern for many years. The public became aware of male-mediated developmental toxicity in the early 1990s when it was reported that men working at Sellafield might be causing leukemia in their children. Human and animal studies have contributed to our current understanding of male-mediated effects. Animal studies in the 1980s and 1990s suggested that genetic damage after radiation and chemical exposure might be transmitted to offspring. With the increasing understanding that there is histone retention and modification, protamine incorporation into the chromatin and DNA methylation in mature sperm and that spermatozoal RNA transcripts can play important roles in the epigenetic state of sperm, heritable studies began to be viewed differently. Recent reports using molecular approaches have demonstrated that DNA damage can be transmitted to babies from smoking fathers, and expanded simple tandem repeats minisatellite mutations were found in the germline of fathers who were exposed to radiation from the Chernobyl nuclear power plant disaster. In epidemiological studies, it is possible to clarify whether damage is transmitted to the sons after exposure of the fathers. Paternally transmitted damage to the offspring is now recognized as a complex issue with genetic as well as epigenetic components.
    • The management of vegetation change on Ilkley Moor

      Hale, William H.G.; Cotton, David E. (1988)
    • Managing pain in prison: staff perspectives

      Walsh, E.; Butt, C.; Freshwater, D.; Dobson, R.; Wright, N.; Cahill, J.; Briggs, M.; Alldred, David P. (2014)
      The purpose of this paper is to present the findings of one part of a larger study, funded by the National Institute for Health Research, which explored the management of pain in adult male prisoners in one large category B prison in England. In this paper, the authors focus on the attitudes and perceptions of prison staff towards pain management in prison. A qualitative design was utilised to explore the staff perceptions of pain and pain management in one adult male prison. Questionnaires were provided for all staff with prisoner contact, and a follow up focus group was undertaken to further explore questionnaire data. The questionnaire and focus group findings demonstrated that staff had a good awareness of pain and pain management in prison, with both physical and emotional pain identified. The frequency of approaches by prisoners to staff for pain relief was noted to be high, whilst awareness of how the prison environment could potentially exacerbate pain was discussed. The acquisition of analgesia by prisoners for secondary gain was identified as a challenge to both assessing levels of pain and providing pain relief in prison, illustrating the complexity of providing care within a custodial culture. The effect on staff of caring for prisoners found to be confrontational and deceitful was significant for participants, with feelings of anger and frustration reported. This study was undertaken in one adult male category B prison with a very high turnover of prisoners. Staff working in other types of prison, for example, higher security or those more stable with longer sentenced prisoners could provide alternative views, as may staff caring for younger offenders and women. The challenges to undertaking research in prison with staff who can understandably be reluctant to engage in reflection on their practice cannot be underestimated and impact significantly on available methodologies. This qualitative research is the first of its kind to offer the perspectives of both health care professionals and prison staff working with prisoners complaining of pain in an English prison. It provides the groundwork for further research and development.
    • The many colours of ‘the dress’

      Gegenfurtner, K.R.; Bloj, Marina; Toscani, M. (2015-06-29)
      There has been an intense discussion among the public about the colour of a dress, shown in a picture posted originally on Tumblr (http://swiked. tumblr.com/post/112073818575/ guys-please-help-me-is-this-dress white-and; accessed on 10:56 am GMT on Tue 24 Mar 2015). Some people argue that they see a white dress with golden lace, while others describe the dress as blue with black lace. Here we show that the question “what colour is the dress?” has more than two answers.
    • Mapping the methylation status of the miR-145 promoter in saphenous vein smooth muscle cells from individuals with type 2 diabetes

      Riches-Suman, Kirsten; Huntriss, J.; Keeble, C.; Wood, I.C.; O'Regan, D.J.; Turner, N.A.; Porter, K.E. (2016)
      Type 2 diabetes mellitus prevalence is growing globally, and the leading cause of mortality in these patients is cardiovascular disease. Epigenetic mechanisms such as microRNAs (miRs) and DNA methylation may contribute to complications of type 2 diabetes mellitus. We discovered an aberrant type 2 diabetes mellitus–smooth muscle cell phenotype driven by persistent up-regulation of miR-145. This study aimed to determine whether elevated expression was due to changes in methylation at the miR-145 promoter. Smooth muscle cells were cultured from saphenous veins of 22 non-diabetic and 22 type 2 diabetes mellitus donors. DNA was extracted, bisulphite treated and pyrosequencing used to interrogate methylation at 11 CpG sites within the miR-145 promoter. Inter-patient variation was high irrespective of type 2 diabetes mellitus. Differential methylation trends were apparent between non-diabetic and type 2 diabetes mellitus–smooth muscle cells at most sites but were not statistically significant. Methylation at CpGs −112 and −106 was consistently lower than all other sites explored in non-diabetic and type 2 diabetes mellitus–smooth muscle cells. Finally, miR-145 expression per se was not correlated with methylation levels observed at any site. The persistent up-regulation of miR- 145 observed in type 2 diabetes mellitus–smooth muscle cells is not related to methylation at the miR-145 promoter. Crucially, miR-145 methylation is highly variable between patients, serving as a cautionary note for future studies of this region in primary human cell types.
    • Mapping the solid-state properties of crystalline lysozyme during pharmaceutical unit-operations

      Mohammad, Mohammad A.; Grimsey, Ian M.; Forbes, Robert T. (2015-10-10)
      Bulk crystallisation of protein therapeutic molecules towards their controlled drug delivery is of interest to the biopharmaceutical industry. The complexity of biotherapeutic molecules is likely to lead to complex material properties of crystals in the solid state and to complex transitions. This complexity is explored using batch crystallised lysozyme as a model. The effects of drying and milling on the solid-state transformations of lysozyme crystals were monitored using differential scanning calorimetry (DSC), X-ray powder diffraction (XRPD), FT-Raman, and enzymatic assay. XRPD was used to characterise crystallinity and these data supported those of crystalline lysozyme which gave a distinctive DSC thermogram. The apparent denaturation temperature (Tm) of the amorphous lysozyme was ∼201 °C, while the Tm of the crystalline form was ∼187 °C. Raman spectra supported a more α-helix rich structure of crystalline lysozyme. This structure is consistent with reduced cooperative unit sizes compared to the amorphous lysozyme and is consistent with a reduction in the Tm of the crystalline form. Evidence was obtained that milling also induced denaturation in the solid-state, with the denatured lysozyme showing no thermal transition. The denaturation of the crystalline lysozyme occurred mainly through its amorphous form. Interestingly, the mechanical denaturation of lysozyme did not affect its biological activity on dissolution. Lysozyme crystals on drying did not become amorphous, while milling-time played a crucial role in the crystalline-amorphous-denatured transformations of lysozyme crystals. DSC is shown to be a key tool to monitor quantitatively these transformations.
    • Mass spectra of halogenostyrylbenzoxazoles

      Ayrton, Stephen T.; Panova, Jekaterina; Michalik, Adam R.; Martin, William H.C.; Gallagher, R.T.; Bowen, Richard D. (2013-07-01)
      Several series of styrylbenzoxazoles of general formula XC6H3(NCO)CH=CHC6H4Y [X= F, Cl or Br; Y = H, F, Cl, Br, CH3 or CH3O] have been investigated by positive ion electrospray and electron ionization mass spectrometry. These compounds, many of which are biologically active or have pharmaceutical potential, show in their electrospray spectra strong peaks for MH+ ions, which undergo relatively little fragmentation. The electron ionization spectra are extremely clean, being dominated by the loss of an atom or radical, Y*, from the ortho position of the pendant ring, by a rearrangement that may be interpreted as a proximity effect. The resultant [M-Y](+) ions are exceptionally stable and rarely undergo further fragmentation. The analytical value of this proximity effect, which is analogous to intramolecular aromatic substitution, in revealing the presence of a substituent in the pendant ring and determining its position, is emphasized. Elimination of a species (including H* or F*) derived from an ortho substituent in the pendant ring occurs even when apparently more favourable alternative fragmentation is possible by direct cleavage of the C-X bond (X = Cl or Br) in the benzoxazole ring.
    • A massive, Late Neolithic pit structure associated with Durrington Walls Henge

      Gaffney, Vincent L.; Baldwin, E.; Bates, M.; Bates, C.R.; Gaffney, Christopher F.; Hamilton, D.; Kinnaird, T.; Neubauer, W.; Yorston, R.; Allaby, R.; et al. (2020-06)
      A series of massive geophysical anomalies, located south of the Durrington Walls henge monument, were identified during fluxgate gradiometer survey undertaken by the Stonehenge Hidden Landscapes Project (SHLP). Initially interpreted as dewponds, these data have been re-evaluated, along with information on similar features revealed by archaeological contractors undertaking survey and excavation to the north of the Durrington Walls henge. Analysis of the available data identified a total of 20 comparable features, which align within a series of arcs adjacent to Durrington Walls. Further geophysical survey, supported by mechanical coring, was undertaken on several geophysical anomalies to assess their nature, and to provide dating and environmental evidence. The results of fieldwork demonstrate that some of these features, at least, were massive, circular pits with a surface diameter of 20m or more and a depth of at least 5m. Struck flint and bone were recovered from primary silts and radiocarbon dating indicates a Late Neolithic date for the lower silts of one pit. The degree of similarity across the 20 features identified suggests that they could have formed part of a circuit of large pits around Durrington Walls, and this may also have incorporated the recently discovered Larkhill causewayed enclosure. The diameter of the circuit of pits exceeds 2km and there is some evidence that an intermittent, inner post alignment may have existed within the circuit of pits. One pit may provide evidence for a recut; suggesting that some of these features could have been maintained through to the Middle Bronze Age. Together, these features represent a unique group of features related to the henge at Durrington Walls, executed at a scale not previously recorded.
    • Materiality

      Taylor, Timothy F. (2008)
    • Mathematical and computational models of drug transport in tumours

      Groh, C.M.; Hubbard, M.E.; Jones, P.F.; Loadman, Paul M.; Periasamy, Nagarajan; Sleeman, B.D.; Smye, S.W.; Twelves, Christopher J.; Phillips, Roger M. (2014-05-06)
      The ability to predict how far a drug will penetrate into the tumour microenvironment within its pharmacokinetic (PK) lifespan would provide valuable information about therapeutic response. As the PK profile is directly related to the route and schedule of drug administration, an in silico tool that can predict the drug administration schedule that results in optimal drug delivery to tumours would streamline clinical trial design. This paper investigates the application of mathematical and computational modelling techniques to help improve our understanding of the fundamental mechanisms underlying drug delivery, and compares the performance of a simple model with more complex approaches. Three models of drug transport are developed, all based on the same drug binding model and parametrized by bespoke in vitro experiments. Their predictions, compared for a ‘tumour cord’ geometry, are qualitatively and quantitatively similar. We assess the effect of varying the PK profile of the supplied drug, and the binding affinity of the drug to tumour cells, on the concentration of drug reaching cells and the accumulated exposure of cells to drug at arbitrary distances from a supplying blood vessel. This is a contribution towards developing a useful drug transport modelling tool for informing strategies for the treatment of tumour cells which are ‘pharmacokinetically resistant’ to chemotherapeutic strategies.