DNA Extraction Method Development for Solid Tissues

Although germline variation testing is traditionally performed using DNA obtained from blood or other liquid samples, determining somatic variation in cancer samples requires DNA extraction directly from tissues. Additionally, epigenetic markers, such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are tissue-specific and change in selected disease states. However, several substances present in tissues are known to inhibit downstream reactions, including polymerase chain reaction PCR). For this project, we are assessing the quantity and quality of DNA obtained from extractions of various vital organs using 30 different commercially available DNA extraction kits to determine optimal kits for each tissue

RR Lyrae stars in the Sagittarius dwarf galaxy: Period analysis

(Abridged) We carried out a period analysis on ~3700 RR Lyrae stars spread over ~50 square degrees towards the Sagittarius dwarf galaxy (Sgr). The RR Lyraes are distributed almost evenly between Sgr and the Milky Way. For Sgr members, the average periods are 0.574 day and 0.322 day for RRab and RRc stars respectively. This places Sgr in the long-period tail of the Oosterhoff I group. We report the detection of 53 double-mode RR Lyrae stars (RRd) within our sample. The magnitude of 40 of these stars is consistent with membership in Sgr whereas 13 RRds are located within our Galaxy. We also found 13 RR Lyraes (5 in Sgr and 8 in the Galaxy) exhibiting two closely spaced frequencies, most probably related to non-radial pulsations. The period distribution of the RR Lyrae variables in Sgr is compared to those of other Milky Way satellites. We find a remarkable similarity between the RR Lyrae populations in Sgr and the Large Magellanic Cloud (LMC), suggesting that these galaxies have similar horizontal branch morphologies. This may indicate that Sgr and the LMC started their formation under similar conditions. Using various photometric indicators, we estimate the metallicity of the RR Lyrae stars in Sgr and find ~-1.6 dex with a dispersion of ~ +/-0.5 dex around this value and a minor but significant population at <-2.0 dex. We do not find evidence for a spatial metallicity gradient in the RR Lyrae population of Sgr. From the spatial distribution of RR Lyraes, we estimate the RRab content and total luminosity of this galaxy and find MV(Sgr)~-14.7 mag, a value that would be consistent with the empirical metallicity/luminosity relation for Dsph galaxies.Comment: 13 pages, 10 figures, 4 tables. Accepted for publication in A&

Complex Consequences of Herbivory and Interplant Cues in Three Annual Plants

Information exchange (or signaling) between plants following herbivore damage has recently been shown to affect plant responses to herbivory in relatively simple natural systems. In a large, manipulative field study using three annual plant species (Achyrachaena mollis, Lupinus nanus, and Sinapis arvensis), we tested whether experimental damage to a neighboring conspecific affected a plant's lifetime fitness and interactions with herbivores. By manipulating relatedness between plants, we assessed whether genetic relatedness of neighboring individuals influenced the outcome of having a damaged neighbor. Additionally, in laboratory feeding assays, we assessed whether damage to a neighboring plant specifically affected palatability to a generalist herbivore and, for S. arvensis, a specialist herbivore. Our study suggested a high level of contingency in the outcomes of plant signaling. For example, in the field, damaging a neighbor resulted in greater herbivory to A. mollis, but only when the damaged neighbor was a close relative. Similarly, in laboratory trials, the palatability of S. arvensis to a generalist herbivore increased after the plant was exposed to a damaged neighbor, while palatability to a specialist herbivore decreased. Across all species, damage to a neighbor resulted in decreased lifetime fitness, but only if neighbors were closely related. These results suggest that the outcomes of plant signaling within multi-species neighborhoods may be far more context-specific than has been previously shown. In particular, our study shows that herbivore interactions and signaling between plants are contingent on the genetic relationship between neighboring plants. Many factors affect the outcomes of plant signaling, and studies that clarify these factors will be necessary in order to assess the role of plant information exchange about herbivory in natural systems

Southern GEMS Groups I: Dynamical Properties

Here we present an investigation of the properties of 16 nearby galaxy groups and their constituent galaxies. The groups are selected from the Group Evolution Multi-wavelength Study (GEMS) and all have X-ray as well as wide-field neutral hydrogen (HI) observations. Group membership is determined using a friends-of-friends algorithm on the positions and velocities from the 6-degree Field Galaxy Survey (6dFGS) and NASA/IPAC Extra-galactic Database (NED). For each group we derive their physical properties using this membership, including: velocity dispersions (sigma_v), virial masses (M_V), total K-band luminosities (L_K(Tot)) and early-type fractions (f_early) and present these data for the individual groups. We find that the GEMS X-ray luminosity is proportional to the group velocity dispersions and virial masses: L_X(r_500)\propto\sigma_v^{3.11\pm0.59} and L_X(r_500)\propto M_V^{1.13\pm0.27}, consistent with the predictions of self-similarity between group and clusters. We also find that M_V\propto L_K(Tot)^{2.0\pm0.9}, i.e. mass grows faster than light and that the fraction of early-type galaxies in the groups is correlated with the group X-ray luminosities and velocity dispersions. We examine the brightest group galaxies (BGGs), finding that, while the luminosity of the BGG correlates with its total group luminosity, the fraction of group luminosity contained in the BGG decreases with increasing total group luminosity. This suggests that BGGs grow by mergers at early times in group evolution while the group continues to grow by accreting infalling galaxies. (Abridged)Comment: 30 pages, accepted for publication in MNRAS, Table 3 available at http://astronomy.swin.edu.au/~sbrough/landscape_table3.p

Characteristics of the Galaxy according to Cepheids

Classical and Type II Cepheids are used to reinvestigate specific properties of the Galaxy. A new Type II reddening-free Cepheid distance parameterization is formulated from LMC Cepheids (OGLE), with uncertainties typically no larger than 5-15%. A distance to the Galactic centre of R0=7.8+-0.6 kpc is derived from the median distance to Type II Cepheids in the bulge (OGLE), R0=7.7+-0.7 kpc from a distance to the near side of the bulge combined with an estimated bulge radius of 1.3+-0.3 kpc derived from planetary nebulae. The distance of the Sun from the Galactic plane inferred from classical Cepheid variables is Zsun=26+-3 pc, a result dependent on the sample's distance and direction because of the complicating effects of Gould's Belt and warping in the Galactic disk. Classical Cepheids and young open clusters delineate consistent and obvious spiral features, although their characteristics do not match conventional pictures of the Galaxy's spiral pattern. The Sagittarius-Carina arm is confirmed as a major spiral arm that appears to originate from a different Galactic region than suggested previously. Furthermore, a major feature is observed to emanate from Cygnus-Vulpecula and may continue locally near the Sun. Significant concerns related to the effects of metallicity on the VI-based reddening-free Cepheid distance relations used here are allayed by demonstrating that the computed distances to the Galactic centre, and to several globular clusters (M54, NGC 6441, M15, and M5) and galaxies (NGC 5128 and NGC 3198) which likely host Type II Cepheids: agree with literature results to within the uncertainties.Comment: Accepted for Publication (MNRAS

Precision measurement of the speed of propagation of neutrinos using the MINOS detectors

We report a two-detector measurement of the propagation speed of neutrinos over a baseline of 734 km. The measurement was made with the NuMI beam at Fermilab between the near and far MINOS detectors. The fractional difference between the neutrino speed and the speed of light is determined to be (v/c−1)=(1.0±1.1)×10−6, consistent with relativistic neutrinos

Transaction Costs, Liquidity Risk, and the CCAPM

In this paper, we make a liquidity adjustment to the consumption-based capital asset pricing model (CCAPM) and show that the liquidity-adjusted CCAPM is a generalized model of Acharya and Pedersen (2005). Using different proxies for transaction costs such as the effective trading costs measure of Hasbrouck (2009) and the bid-ask spread estimates of Corwin and Schultz (2012), we find that the liquidity-adjusted CCAPM explains a larger fraction of the cross-sectional return variations

The Community IntraVenous Antibiotic Study (CIVAS): a mixed methods evaluation of patient preferences for and cost effectiveness of different service models for delivering outpatient parenteral antimicrobial therapy

Background: Outpatient parenteral antimicrobial therapy (OPAT) is widely used in most developed countries, providing considerable opportunities for improved cost savings. However, it is implemented only partially in the UK, using a variety of service models. Objectives: The aims of this research were to (1) establish the extent of OPAT service models in England and identify their development; (2) evaluate patients’ preferences for different OPAT service delivery models; (3) assess the cost-effectiveness of different OPAT service delivery models; and (4) convene a consensus panel to consider our evidence and make recommendations. Methods: This mixed-methods study included seven centres providing OPAT using four main service models: (1) hospital outpatient (HO) attendance; (2) specialist nurse (SN) visiting at home; (3) general nurse (GN) visiting at home; and (4) self-administration (SA) or carer administration. Health-care providers were surveyed and interviewed to explore the implementation of OPAT services in England. OPAT patients were interviewed to determine key service attributes to develop a discrete choice experiment (DCE). This was used to perform a quantitative analysis of their preferences and attitudes. Anonymised OPAT case data were used to model cost-effectiveness with both Markov and simulation modelling methods. An expert panel reviewed the evidence and made recommendations for future service provision and further research. Results: The systematic review revealed limited robust literature but suggested that HO is least effective and SN is most effective. Qualitative study participants felt that different models of care were suited to different types of patient and they also identified key service attributes. The DCE indicated that type of service was the most important factor, with SN being strongly preferred to HO and SA. Preferences were influenced by attitudes to health care. The results from both Markov and simulation models suggest that a SN model is the optimal service for short treatment courses (up to 7 days). Net monetary benefit (NMB) values for HO, GN and SN services were £2493, £2547 and £2655, respectively. For longer treatment, SA appears to be optimal, although SNs provide slightly higher benefits at increased cost. NMB values for HO, GN, SN and SA services were £8240, £9550, £10,388 and £10,644, respectively. The simulation model provided useful information for planning OPAT services. The expert panel requested more guidance for service providers and commissioners. Overall, they agreed that mixed service models were preferable. Limitations: Recruitment to the qualitative study was suboptimal in the very elderly and ethnic minorities, so the preferences of patients from these groups might not be represented. The study recruited from Yorkshire, so the findings may not be applicable nationally. Conclusions: The quantitative preference analysis and economic modelling favoured a SN model, although there are differences between sociodemographic groups. SA provides cost savings for long-term treatment but is not appropriate for all. Future work: Further research is necessary to replicate our results in other regions and populations and to evaluate mixed service models. The simulation modelling and DCE methods used here may be applicable in other health-care settings. Funding: The National Institute for Health Research Health Service and Delivery Research programme