On Becoming a DNP user: Some Reflections on the Developing Use of a Computer

This paper considers the development of a tool to support the presentation of the material forming an ethnographic report. The paper focuses on the way in which use of the system has evolved to offer appropriate facilities. The use of viewpoints to present material from a number of studies is described. The paper concludes by reflecting on the need to consider the way in ethnographers have become users of the tool

Surprises in the Orbital Magnetic Moment and g-Factor of the Dynamic Jahn-Teller Ion C_{60}^-

We calculate the magnetic susceptibility and g-factor of the isolated C_{60}^- ion at zero temperature, with a proper treatment of the dynamical Jahn-Teller effect, and of the associated orbital angular momentum, Ham-reduced gyromagnetic ratio, and molecular spin-orbit coupling. A number of surprises emerge. First, the predicted molecular spin-orbit splitting is two orders of magnitude smaller than in the bare carbon atom, due to the large radius of curvature of the molecule. Second, this reduced spin-orbit splitting is comparable to Zeeman energies, for instance, in X-band EPR at 3.39KGauss, and a field dependence of the g-factor is predicted. Third, the orbital gyromagnetic factor is strongly reduced by vibron coupling, and so therefore are the effective weak-field g-factors of all low-lying states. In particular, the ground-state doublet of C_{60}^- is predicted to show a negative g-factor of \sim -0.1.Comment: 19 pages RevTex, 2 postscript figures include

Searching for DNA Lesions: Structural Evidence for Lower- and Higher-Affinity DNA Binding Conformations of Human Alkyladenine DNA Glycosylase

To efficiently repair DNA, human alkyladenine DNA glycosylase (AAG) must search the million-fold excess of unmodified DNA bases to find a handful of DNA lesions. Such a search can be facilitated by the ability of glycosylases, like AAG, to interact with DNA using two affinities: a lower-affinity interaction in a searching process and a higher-affinity interaction for catalytic repair. Here, we present crystal structures of AAG trapped in two DNA-bound states. The lower-affinity depiction allows us to investigate, for the first time, the conformation of this protein in the absence of a tightly bound DNA adduct. We find that active site residues of AAG involved in binding lesion bases are in a disordered state. Furthermore, two loops that contribute significantly to the positive electrostatic surface of AAG are disordered. Additionally, a higher-affinity state of AAG captured here provides a fortuitous snapshot of how this enzyme interacts with a DNA adduct that resembles a one-base loop.National Institutes of Health (U.S.) (grant no. P30-ES002109)National Institutes of Health (U.S.) (grant no. GM65337)National Institutes of Health (U.S.) (grant no. GM65337-03S2)National Institutes of Health (U.S.) (grant no. CA055042)National Institutes of Health (U.S.) (grant no. CA092584)Repligen Corporation (KIICR Graduate Fellowship

The acquisition of Sign Language: The impact of phonetic complexity on phonology

Research into the effect of phonetic complexity on phonological acquisition has a long history in spoken languages. This paper considers the effect of phonetics on phonological development in a signed language. We report on an experiment in which nonword-repetition methodology was adapted so as to examine in a systematic way how phonetic complexity in two phonological parameters of signed languages — handshape and movement — affects the perception and articulation of signs. Ninety-one Deaf children aged 3–11 acquiring British Sign Language (BSL) and 46 hearing nonsigners aged 6–11 repeated a set of 40 nonsense signs. For Deaf children, repetition accuracy improved with age, correlated with wider BSL abilities, and was lowest for signs that were phonetically complex. Repetition accuracy was correlated with fine motor skills for the youngest children. Despite their lower repetition accuracy, the hearing group were similarly affected by phonetic complexity, suggesting that common visual and motoric factors are at play when processing linguistic information in the visuo-gestural modality

Asymptotic analysis of the dominant mechanisms in the coffee extraction process

peer-reviewedExtraction of coffee solubles from roast and ground coffee is a highly complex process, depending on a large number of brewing parameters. We consider a recent, experimentally validated, model of coffee extraction, describing extraction from a coffee bed using a double porosity model, which includes dissolution and transport of coffee. It was shown that this model can accurately describe coffee extraction in two situations: extraction from a dilute suspension of coffee grains and extraction from a packed coffee bed. Despite being based on some simplifying assumptions, this model can only be solved numerically. In this paper we consider asymptotic solutions of the model describing extraction from a packed coffee bed. Such solutions can explicitly relate coffee concentration to the process parameters. For an individual coffee grain, extraction is controlled by a rapid dissolution of coffee from the surface of the grain, in conjunction with a slower diffusion of coffee through the intragranular pore network to the grain surface. Extraction of coffee from the bed also depends on the speed of advection of coffee from the bed. We utilize the small parameter resulting from the ratio of the advection timescale to the grain diffusion timescale to construct asymptotic solutions using the method of matched asymptotic expansions. The asymptotic solutions are compared to numerical solutions and data from coffee extraction experiments. The asymptotic solutions depend on a small number of dimensionless parameters and so are useful to quickly fit extraction curves and investigate the influence of various process parameters on the extraction.PUBLISHEDpeer-reviewe

Evaluation of a co-culture of rapidly isolated chondrocytes and stem cells seeded on tri-layered collagen-based scaffolds in a caprine osteochondral defect model

Cartilage has poor regenerative capacity and thus damage to the joint surfaces presents a major clinical challenge. Recent research has focussed on the development of tissue-engineered and cell-based approaches for the treatment of cartilage and osteochondral injuries, with current clinically available cell-based approaches including autologous chondrocyte implantation and matrix-assisted autologous chondrocyte implantation. However, these approaches have significant disadvantages due to the requirement for a two-stage surgical procedure and an in vitro chondrocyte expansion phase which increases logistical challenges, hospital times and costs. In this study, we hypothesized that seeding biomimetic tri-layered scaffolds, with proven regenerative potential, with chondrocyte/infrapatellar fat pad stromal cell co-cultures would improve their regenerative capacity compared to scaffolds implanted cell-free. Rapid cell isolation techniques, without the requirement for long term in vitro culture, were utilised to achieve co-cultures of chondrocytes and stromal cells and thus overcome the limitations of existing cell-based techniques. Cell-free and cell-seeded scaffolds were implanted in osteochondral defects, created within the femoral condyle and trochlear ridge, in a translational large animal goat model. While analysis showed trends towards delayed subchondral bone healing in the cell-seeded scaffold group, by the 12 month timepoint the cell-free and cell-seeded groups yield cartilage and bone tissue with comparable quality and quantity. The results of the study reinforce the potential of the biomimetic tri-layered scaffold to repair joint defects but failed to demonstrate a clear benefit from the addition of the CC/FPMSC co-culture to this scaffold. Taking into consideration the additional cost and complexity associated with the cell-seeded scaffold approach, this study demonstrates that the treatment of osteochondral defects using cell-free tri-layered scaffolds may represent a more prudent clinical approach

Diagnostics of the Early Explosion Phase of a Classical Nova Using Its X-ray Emission: A Model for the X-ray Outburst of CI Camelopardalis in 1998

We have computed a spherically symmetric model for the interaction of matter ejected during the outburst of a classical nova with the stellar wind from its optical component.This model is used to describe the intense X-ray outburst (the peak 3-20 keV flux was ~2 Crab) of the binary system CI Camelopardalis in 1998. According to our model, the stellar wind from the optical component heated by a strong shock wave produced when matter is ejected from the white dwarf as the result of a thermonuclear explosion on its surface is the emission source in the standard X-ray band. Comparison of the calculated and observed time dependences of the mean radiation temperature and luminosity of the binary system during its outburst has yielded very important characteristics of the explosion.We have been able to measure the velocity of the ejected matter immediately after the onset of the explosion for the first time: it follows from our model that the ejected matter had a velocity of ~2700 km/s even on 0.1-0.5 day after the outburst onset and it flew with such a velocity for the first 1-1.5 day under an external force, possibly, the radiation pressure from the white dwarf. Subsequently, the matter probably became transparent and began to decelerate. The time dependence of the mean radiation temperature at late expansion phases has allowed us to estimate the mass of the ejected matter, ~10^{-7}-10^{-6} Msun. The mass loss rate in the stellar wind required to explain the observed peak luminosity of the binary system during its outburst has been estimated to be dM/dt ~(1-2)x10^{-6} Msun/yr.Comment: 19 pages, 24 figures; unimportant correction of the formul