Shrinking a large dataset to identify variables associated with increased risk of Plasmodium falciparum infection in Western Kenya

Large datasets are often not amenable to analysis using traditional single-step approaches. Here, our general objective was to apply imputation techniques, principal component analysis (PCA), elastic net and generalized linear models to a large dataset in a systematic approach to extract the most meaningful predictors for a health outcome. We extracted predictors for Plasmodium falciparum infection, from a large covariate dataset while facing limited numbers of observations, using data from the People, Animals, and their Zoonoses (PAZ) project to demonstrate these techniques: data collected from 415 homesteads in western Kenya, contained over 1500 variables that describe the health, environment, and social factors of the humans, livestock, and the homesteads in which they reside. The wide, sparse dataset was simplified to 42 predictors of P. falciparum malaria infection and wealth rankings were produced for all homesteads. The 42 predictors make biological sense and are supported by previous studies. This systematic data-mining approach we used would make many large datasets more manageable and informative for decision-making processes and health policy prioritization

Measurement of the Bottom-Strange Meson Mixing Phase in the Full CDF Data Set

We report a measurement of the bottom-strange meson mixing phase \beta_s using the time evolution of B0_s -> J/\psi (->\mu+\mu-) \phi (-> K+ K-) decays in which the quark-flavor content of the bottom-strange meson is identified at production. This measurement uses the full data set of proton-antiproton collisions at sqrt(s)= 1.96 TeV collected by the Collider Detector experiment at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity. We report confidence regions in the two-dimensional space of \beta_s and the B0_s decay-width difference \Delta\Gamma_s, and measure \beta_s in [-\pi/2, -1.51] U [-0.06, 0.30] U [1.26, \pi/2] at the 68% confidence level, in agreement with the standard model expectation. Assuming the standard model value of \beta_s, we also determine \Delta\Gamma_s = 0.068 +- 0.026 (stat) +- 0.009 (syst) ps-1 and the mean B0_s lifetime, \tau_s = 1.528 +- 0.019 (stat) +- 0.009 (syst) ps, which are consistent and competitive with determinations by other experiments.Comment: 8 pages, 2 figures, Phys. Rev. Lett 109, 171802 (2012

W boson polarization measurement in the ttbar dilepton channel using the CDF II Detector

We present a measurement of $W$ boson polarization in top-quark decays in $t\bar{t}$ events with decays to dilepton final states using $5.1 {\rm fb^{-1}}$ of integrated luminosity in $p\bar{p}$ collisions collected by the CDF II detector at the Tevatron. A simultaneous measurement of the fractions of longitudinal ($f_0$) and right-handed ($f_+$) $W$ bosons yields the results $f_0 = 0.71 ^{+0.18}_{-0.17} {\rm (stat)} \pm 0.06 {\rm (syst)}$ and $f_+ = -0.07 \pm 0.09 {\rm (stat)} \pm 0.03 {\rm (syst)}$. Combining this measurement with our previous result based on single lepton final states, we obtain $f_0 = 0.84 \pm 0.09 {\rm (stat)} \pm 0.05 {\rm (syst)}$ and $f_{+} = -0.16 \pm 0.05 {\rm (stat)} \pm 0.04 {\rm (syst)}$. The results are consistent with standard model expectation.Comment: Published in Phys. Lett.

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

An audiomagnetotelluric survey of the Carnmenellis granite

The electrical resistivity of competent/unfractured rock depends mainly on porosity and the conductivity of the pore fluid. In fractured/jointed rocks a further degree of dependence on the degree of fluid saturation and permeability is observed; The audiomagnetotelluric survey described in this report is primarily concerned with mapping resistivity variations (i.e. rock/fluid properties) through the critical depth range (2 to 8 km) of geothermal energy extraction within and across the Carnmenellis granite. This report describes the audiomagnetotelluric experiment that was carried out during 1988. Two field surveys were performed. A main survey to assess the presence of a refractor (a wide-angle reflector) at about 7 to 8 km (Brooks et al., 1984) and a secondary survey to assess the depth e_xtent of a surface lineament. The principal results of the field experiment are now summarised. A seven-site investigation of a NW-SE surface lineament was carried out at spacings of 50m. To our knowledge, this is the first audiomagnetotelluric experiment involving such small spacings. The survey data were partially marred by an additive noise component in one of the electric field channels. Subsequent detailed analysis of these data revealed electric fence noise as the cause. Although such hindsight detection is unfortunate, the uncontaminated data offer valid constraints in relation to the detection of a fluid-filled fracture zone. The results presented indicate that it is highly unlikely that the target lineament can be associated with a conductive zone possessing a reasonable resistivity contrast which intersects the surface or near-surface. The results of the main experiment extend this null interpretation to the majority of surface lineaments as described below. The main granite survey consisted of 17 soundings in total. An E-W profile across the granite outcrop comprised 12 soundings and two further soundings were conducted off the outcrop for control. The two off-granite, soundings provided very different 'dimensional' characteristics to soundings on the granite. They therefore confirm the broad homogeneity of the geoelectric anisotropy on the granite. The two off-granite soundings also provided information on the resistivities of the Devonian cover rocks and the depth to granite. A further 3 soundings were performed in the vicinity of the Hot Dry Rock (HDR) reservoir at Rosemanowes quarry. Overall the Carnmenellis granite, as defined by its broad resistivity characteristics, appears predominantly homogeneous. A very consistent set of resistivity values are found for the whole granite structure below depths of 2 km. The majority of resistivity values are in the range 1000 to 10,000 ohm.m. When laboratory analyses of thermal and pressure dependence are taken into account the granite is found to correspond to a 'wet' granite saturated with several weight-percent of free water down to at least IO km. · The consistency of the resistivity values below 2 km across a major portion of the granite indicates that lateral geoelectric effects are likely to be confined to the near-surface (i.e. < 2 km). An examination of the lateral anisotropic behaviour across the granite confirms this general conclusion. We conclude that with the exception of one location the surface lineations, within the area surveyed, do not appear to represent deep vertical or sub-vertical zones with rock/fluid properties that would distinguish them from 'background' properties. Judging by the hydrogeological models for the near-surface granite, a spatially-complex hydrothermal circulation system can be considered to operate at depth (Gregory and Durrance 1987). The spatial distribution of such a system is likely to be closely tied to the distribution of major water-conducting fractures. Although the scale and degree of resistivity contrasts should be considered, the main survey profile has detected only one such near-surface feature. Significantly this conductive zone is spatially localised and is directed NE-SW. The zone appears ·to be correlated with a lineament and a main arterial alluvial fan of the survey region. The E-W survey profile intersects the NE-SW trending zone 0.5 km directly south of the village of Porkellis. There is an indication of a conductive layer at a depth of I km in the vicinity of this lineament. The sites defining the SE portion of the granite display anisotropic features which are different from those to the west. It is suggested that the cause is associated with boundary or off-granite variations rather than with variations across the outcrop although this cannot be ruled out. The features observed in the SE appear to define a broad, large-scale effect. Resistivity values through the granite also appear slightly larger in this region of the outcrop. The lateral geoelectric anisotropy transfers (i.e. azimuths rotate) from local and near-surface penetrations (e.g. 1 to 2 km) to a regional scale anisotropy at large-volume penetrations (e.g. in excess of 25 km). The rotation pattern is consistent at the majority of survey locations beginning NE/ENE at depths of about l km to NINE at depths of 6 to 10 km and thence to NW/N at depths in excess of 25 km. The information on geoelectric anisotropy has been compared with the principal joint and stress directions of the granite in order to identify the mechanism controlling the resistivity variations. The main conclusion is that the directions of resistivity anisotropy do not display any persistent alignment with the principal horizontal stress directions. Such a conclusion assumes that the present indicators of stress directions are representative of the in situ stress at depths in excess of 2.5 km. On this basis then the mechanism of aligned microcracks does not appear to control the observed geoelectric anisotropy. The results indicate that within the upper 1.5 km (at least), resistivity is controlled by one of the two principal joint systems of the granite. The results identify the fracture system parallel to the NW-SE master joints as being preferentially 'open' and containing enhanced concentrations of fluids. A definitive interpretation (from geoelectric anisotropy) at greater depths appears to be restricted by the observed 'intermediate' rotations as other larger-scale (regional) effects become more dominant. The vertical field is, however, influenced by a major resistivity contrast striking NW-SE beyond, and to the SW, of the Carnmenellis outcrop. Below a depth of 2 km resistivity values increase slowly with depth attaining maximum values by about 6 km. The anticipated linear decrease of resistivity with increasing temperature is not observed and a more dominant pressure/stress dependence must control the spatially-consistent. depth dependence observed. Laboratory measurements on a wide range of granitic rocks indicate that transfer from crack-dominated behaviour to pore-dominated behaviour will be complete by an applied pressure of 200 MPa. The extrapolated overburden and stress magnitudes, from the HDR borehole measurements. suggest that this will be achieved within the Carnmenellis by about 6 km. The resistivity profiles are therefore consistent with the completion of crack closure by a depth of 6 km and a transfer to a pore-dominated resistivity mechanism below this depth. Thus, in simple terms, if a 'joint' can be defined as a feature that is capable of 'closing' (and closed here means an inability to support ionic conduction of interstitial fluids) the observations suggest the absence of such joints below 6 km. A comparison of the vertical geoelectric profiles across the granite with the boundary reflector (RI) of the deep low-velocity zone modelled by Brooks et al. (1984) is possible. The resistivity profiles however do not reveal any spatially-consistent major discontinuities in the upper 12 km. The depth interval of the low-velocity zone appears merely to be associated with an interval of approximately constant and maximum resistivity. We conclude that no detectable geoelectric variations in rock/fluid properties can be identified at a depth associated with the Rl reflector. Thus RI does not appear to represent the upper surface of a fractured zone with an associated enhancement of conducting fluids. The three sounding sites above and around the HDR reservoir provide interesting results in the upper 5 km. The identical resistivity profiles at two of the sites display a more conductive profile when compared with a third site some 1.1 km away. The two sites, 500 m apart, appear to define a 'reservoir-influenced' section down to depths of 4 to 5 km. This depth appears consistent with the termination depth of the microseismic zone defined during hydrofracturing. The finite lateral extent of the low-resistivity reservoir volume is also apparent in the azimuthal (anisotropic) behaviour across the three locations. Thus the zone of enhanced fluid concentration (i.e. the reservoir) has been shown to have finite dimensions both laterally and vertically

The upgrade of base orcadas magnetic observatory

In January 2012 new absolute magnetometers, fluxgate variometers and recording hardware to monitor and record changes in the Earth’s magnetic field have been installed at Base Orcadas Observatory, in a collaborative project between the Argentine National Weather Service (SMN), the British Geological Survey (BGS) in Edinburgh and the Institut Royal Météorologique de Belgique, Dourbes as part of the INTERMAGNET Digital Geomagnetic Observatory (INDIGO) program. This observatory is located on the Argentine Antarctic Base on the South Orkney Islands (Orcadas del Sur), with the new equipment replacing existing photographic recording equipment which was damaged by an earthquake in 2003. The equipment is designed to meet INTERMAGNET standards for data quality providing a one-minute data set which will be corrected to absolute through a program of absolute observations. The original magnetic observatory at Base Orcadas (the oldest in Antarctica) was installed by the Scottish National Antarctic Expedition in (SNAE) 1902-04 and recordings of variations in the Earth’s magnetic field have continued since that time at this remote location