Data collection challenges in community settings: Insights from two field studies of patients with chronic disease

Purpose Collecting information about health and disease directly from patients can be fruitfully accomplished using contextual approaches, ones that combine more and less structured methods in home and community settings. This paper's purpose is to describe and illustrate a framework of the challenges of contextual data collection. Methods A framework is presented based on prior work in community-based participatory research and organizational science, comprised of ten types of challenges across four broader categories. Illustrations of challenges and suggestions for addressing them are drawn from two mixed-method, contextual studies of patients with chronic disease in two regions of the US. Results The first major category of challenges was concerned with the researcher-participant partnership, for example, the initial lack of mutual trust and understanding between researchers, patients, and family members. The second category concerned patient characteristics such as cognitive limitations and a busy personal schedule that created barriers to successful data collection. The third concerned research logistics and procedures such as recruitment, travel distances, and compensation. The fourth concerned scientific quality and interpretation, including issues of validity, reliability, and combining data from multiple sources. The two illustrative studies faced both common and diverse research challenges and used many different strategies to address them. Conclusion Collecting less structured data from patients and others in the community is potentially very productive but requires the anticipation, avoidance, or negotiation of various challenges. Future work is necessary to better understand these challenges across different methods and settings, as well as to test and identify strategies to address them

The Intracluster Medium in z > 1 Galaxy Clusters

The Chandra X-ray Observatory was used to obtain a 190 ks image of three high redshift galaxy clusters in one observation. The results of our analysis of these data are reported for the two z > 1 clusters in this Lynx field, including the most distant known X-ray selected cluster. Spatially-extended X-ray emission was detected from both these clusters, indicating the presence of hot gas in their intracluster media. A fit to the X-ray spectrum of RX J0849+4452, at z=1.26, yields a temperature of kT = 5.8^{+2.8}_{-1.7} keV. Using this temperature and the assumption of an isothermal sphere, the total mass of RX J0849+4452 is found to be 4.0^{+2.4}_{-1.9} X 10^{14} h_{65}^{-1} M_{\sun} within r = 1 h_{65}^{-1} Mpc. The T_x for RX J0849+4452 approximately agrees with the expectation based on its L_{bol} = 3.3^{+0.9}_{-0.5} X 10^{44}$erg s$^{-1} according to the low redshift L_x - T_x relation. The very different distributions of X-ray emitting gas and of the red member galaxies in the two z > 1 clusters, in contrast to the similarity of the optical/IR colors of those galaxies, suggests that the early-type galaxies mostly formed before their host clusters.Comment: 4 pages in emulateapj style plus 2 color jpegs for Figure 3. Accepted by The Astrophysical Journa

Oxygen isotopic heterogeneity in the Temora-2 reference zircon

For the past decade and a half, Geoscience Australia has distributed zircon from a portion of the Middledale Gabbroic Diorite under the label “Temora-2”. This reference zircon was originally developed as a reference material for use in ion microprobe U-Th-Pb geochronological analyses. As ion probe capability has increased to allow the measurements of other isotopic systems at geologically useful precision and accuracy, the Temora-2 zircon has remained a convenient reference material to use for those systems. However, the suitability of this material for non-geochronological applications must be continuously reassessed. This study demonstrates that some (but not all) aliquots of the Temora-2 zircon, distributed by Geoscience Australia to analytical laboratories worldwide, have δ18O values up to 1‰ lower than the reference laser fluorination δ18O value quoted in Black et al. (2004). Although the long and complex collection history of this material makes it difficult to pinpoint the cause of this discrepancy, we suspect it relates to material from two or more boulders from the Temora-2 site, with different δ18O values, being sampled and mixed together in the field prior to storage at Geoscience Australia. Therefore, oxygen isotope measurements on SIMS mounts where Temora is the only reference zircon may be biased towards heavier values by up to 1‰, unless there are additional constrains on the actual δ18O value of the specific aliquot of Temora-2 zircons placed on that particular ion probe mount. We recommend that future oxygen isotope work should use a reference zircon other than Temora-2, until Geoscience Australia can replace the current stock of heterogeneous Temora-2 material with zircon which has a uniform δ18O value

Dataset of Escherichia coli O157 : H7 genes enriched in adherence to spinach root tissue

A high-throughput positive-selection approach was taken to generate a dataset of Shigatoxigenic Escherichia coli (STEC) O157:H7 genes enriched in adherence to plant tissue. The approach generates a differential dataset based on BAC clones enriched in the output, after adherence, compared to the inoculum used as the input. A BAC clone library derived from STEC isolate 'Sakai' was used since this isolate is associated with a very large-scale outbreak of human disease from consumption of contaminated fresh produce; white radish sprouts. Spinach was used for the screen since it is associated with STEC outbreaks, and the roots provide a suitable site for bacterial colonisation. Four successive of rounds of Sakai BAC clone selection and amplification were applied for spinach root adherence, in parallel to a non-plant control. Genomic DNA was obtained from a total of 7.17 x 108 cfu/ml of bacteria from the plant treatment and 1.13 x 109 cfu/ml of bacteria from the no-plant control. Relative gene abundance of the output compared to the input pools was obtained using an established E. coli DNA microarray chip for STEC. The dataset enables screening for genes enriched under the treatment condition and informs on genes that may play a role in plant-microbe interactions

Shear dynamics in Bianchi I cosmologies with R^n-gravity

We give the equations governing the shear evolution in Bianchi spacetimes for general f(R)-theories of gravity. We consider the case of R^n-gravity and perform a detailed analysis of the dynamics in Bianchi I cosmologies which exhibit local rotational symmetry. We find exact solutions and study their behaviour and stability in terms of the values of the parameter n. In particular, we found a set of cosmic histories in which the universe is initially isotropic, then develops shear anisotropies which approaches a constant value.Comment: 25 pages LaTeX, 6 figures. Revised to match the final version accepted for publication in CQ

Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy.

The success of immunotherapy has led to a myriad of clinical trials accompanied by efforts to gain mechanistic insight and identify predictive signatures for personalization. However, many immune monitoring technologies face investigator bias, missing unanticipated cellular responses in limited clinical material. We present here a mass cytometry (CyTOF) workflow for standardized, systems-level biomarker discovery in immunotherapy trials. To broadly enumerate immune cell identity and activity, we established and extensively assessed a reference panel of 33 antibodies to cover major cell subsets, simultaneously quantifying activation and immune checkpoint molecules in a single assay. This assay enumerates ≥98% of peripheral immune cells with ≥4 positively identifying antigens. Robustness and reproducibility are demonstrated on multiple samples types, across two research centers and by orthogonal measurements. Using automated analysis, we identify stratifying immune signatures in bone marrow transplantation-associated graft-versus-host disease. Together, this validated workflow ensures comprehensive immunophenotypic analysis and data comparability and will accelerate biomarker discovery

Building a traceable climate model hierarchy with multi-level emulators

To study climate change on multi-millennial timescales or to explore a model’s parameter space, efficient models with simplified and parameterised processes are required. However, the reduction in explicitly modelled processes can lead to underestimation of some atmospheric responses that are essential to the understanding of the climate system. While more complex general circulations are available and capable of simulating a more realistic climate, they are too computationally intensive for these purposes. In this work, we propose a multi-level Gaussian emulation technique to efficiently estimate the outputs of steady-state simulations of an expensive atmospheric model in response to changes in boundary forcing. The link between a computationally expensive atmospheric model, PLASIM (Planet Simulator), and a cheaper model, EMBM (energy–moisture balance model), is established through the common boundary condition specified by an ocean model, allowing for information to be propagated from one to the other. This technique allows PLASIM emulators to be built at a low cost. The method is first demonstrated by emulating a scalar summary quantity, the global mean surface air temperature. It is then employed to emulate the dimensionally reduced 2-D surface air temperature field. Even though the two atmospheric models chosen are structurally unrelated, Gaussian process emulators of PLASIM atmospheric variables are successfully constructed using EMBM as a fast approximation. With the extra information gained from the cheap model, the multi-level emulator of PLASIM’s 2-D surface air temperature field is built using only one-third the amount of expensive data required by the normal single-level technique. The constructed emulator is shown to capture 93.2% of the variance across the validation ensemble, with the averaged RMSE of 1.33 °C. Using the method proposed, quantities from PLASIM can be constructed and used to study the effects introduced by PLASIM’s atmosphere

Chandra Detection of a TypeII Quasar at z=3.288

We report on observations of a TypeII quasar at redshift z=3.288, identified as a hard X-ray source in a 185 ks observation with the Chandra X-ray Observatory and as a high-redshift photometric candidate from deep, multiband optical imaging. CXOJ084837.9+445352 (hereinafter CXO52) shows an unusually hard X-ray spectrum from which we infer an absorbing column density N(H) = (4.8+/-2.1)e23 / cm2 (90% confidence) and an implied unabsorbed 2-10 keV rest-frame luminosity of L(2-10) = 3.3e44 ergs/s, well within the quasar regime. Hubble Space Telescope imaging shows CXO52 to be elongated with slight morphological differences between the WFPC2 F814W and NICMOS F160W bands. Optical and near-infrared spectroscopy of CXO52 show high-ionization emission lines with velocity widths ~1000 km/s and flux ratios similar to a Seyfert2 galaxy or radio galaxy. The latter are the only class of high-redshift TypeII luminous AGN which have been extensively studied to date. Unlike radio galaxies, however, CXO52 is radio quiet, remaining undetected at radio wavelengths to fairly deep limits, f(4.8GHz) < 40 microJy. High-redshift TypeII quasars, expected from unification models of active galaxies and long-thought necessary to explain the X-ray background, are poorly constrained observationally with few such systems known. We discuss recent observations of similar TypeII quasars and detail search techniques for such systems: namely (1) X-ray selection, (2) radio selection, (3) multi-color imaging selection, and (4) narrow-band imaging selection. Such studies are likely to begin identifying luminous, high-redshift TypeII systems in large numbers. We discuss the prospects for these studies and their implications to our understanding of the X-ray background.Comment: 28 pages, 5 figures; to appear in The Astrophysical Journa

Hydrologically driven ecosystem processes determine the distribution and persistence of ecosystem-specialist predators under climate change

Climate change has the capacity to alter physical and biological ecosystem processes, jeopardizing the survival of associated species. This is a particular concern in cool, wet northern peatlands that could experience warmer, drier conditions. Here we show that climate, ecosystem processes and food chains combine to influence the population performance of species in British blanket bogs. Our peatland process model accurately predicts water-table depth, which predicts abundance of craneflies (keystone invertebrates), which in turn predicts observed abundances and population persistence of three ecosystem-specialist bird species that feed on craneflies during the breeding season. Climate change projections suggest that falling water tables could cause 56–81% declines in cranefly abundance and, hence, 15–51% reductions in the abundances of these birds by 2051–2080. We conclude that physical (precipitation, temperature and topography), biophysical (evapotranspiration and desiccation of invertebrates) and ecological (food chains) processes combine to determine the distributions and survival of ecosystem-specialist predators

Evolution of the Color-Magnitude Relation in Galaxy Clusters at z ~1 from the ACS Intermediate Redshift Cluster Survey

We apply detailed observations of the Color-Magnitude Relation (CMR) with the ACS/HST to study galaxy evolution in eight clusters at z~1. The early-type red sequence is well defined and elliptical and lenticular galaxies lie on similar CMRs. We analyze CMR parameters as a function of redshift, galaxy properties and cluster mass. For bright galaxies (M_B < -21mag), the CMR scatter of the elliptical population in cluster cores is smaller than that of the S0 population, although the two become similar at faint magnitudes. While the bright S0 population consistently shows larger scatter than the ellipticals, the scatter of the latter increases in the peripheral cluster regions. If we interpret these results as due to age differences, bright elliptical galaxies in cluster cores are on average older than S0 galaxies and peripheral elliptical galaxies (by about 0.5Gyr). CMR zero point, slope, and scatter in the (U-B)_z=0 rest-frame show no significant evolution out to redshift z~1.3 nor significant dependence on cluster mass. Two of our clusters display CMR zero points that are redder (by ~2sigma) than the average (U-B)_z=0 of our sample. We also analyze the fraction of morphological early-type and late-type galaxies on the red sequence. We find that, while in the majority of the clusters most (80% to 90%) of the CMR population is composed of early-type galaxies, in the highest redshift, low mass cluster of our sample, the CMR late-type/early-type fractions are similar (~50%), with most of the late-type population composed of galaxies classified as S0/a. This trend is not correlated with the cluster's X-ray luminosity, nor with its velocity dispersion, and could be a real evolution with redshift.Comment: ApJ, in press, 27 pages, 22 figure