The Art of Data Science

To flourish in the new data-intensive environment of 21st century science, we need to evolve new skills. These can be expressed in terms of the systemized framework that formed the basis of mediaeval education - the trivium (logic, grammar, and rhetoric) and quadrivium (arithmetic, geometry, music, and astronomy). However, rather than focusing on number, data is the new keystone. We need to understand what rules it obeys, how it is symbolized and communicated and what its relationship to physical space and time is. In this paper, we will review this understanding in terms of the technologies and processes that it requires. We contend that, at least, an appreciation of all these aspects is crucial to enable us to extract scientific information and knowledge from the data sets which threaten to engulf and overwhelm us.Comment: 12 pages, invited talk at Astrostatistics and Data Mining in Large Astronomical Databases workshop, La Palma, Spain, 30 May - 3 June 2011, to appear in Springer Series on Astrostatistic

Red clump stars and Gaia: calibration of the standard candle using a hierarchical probabilistic model

Distances to individual stars in our own Galaxy are critical in order to piece together the nature of its velocity and spatial structure. Core helium burning red clump (RC) stars have similar luminosities, are abundant throughout the Galaxy and thus constitute good standard candles. We build a hierarchical probabilistic model to quantify the quality of RC stars as standard candles using parallax measurements from the first Gaia data release. A unique aspect of our methodology is to fully account for (and marginalize over) parallax, photometry and dust correction uncertainties, which lead to more robust results than standard approaches. We determine the absolute magnitude and intrinsic dispersion of the RC in 2MASS bands J, H, Ks, GaiaG band and WISE bands W1, W2, W3 and W4. We find that the absolute magnitude of the RC is −1.61 ± 0.01 (in Ks), +0.44 ± 0.01 (in G), −0.93 ± 0.01 (in J), −1.46 ± 0.01 (in H), −1.68 ± 0.02 (in W1), −1.69 ± 0.02 (in W2), −1.67 ± 0.02 (in W3) and −1.76 ± 0.01 mag (in W4). The mean intrinsic dispersion is ∼0.17 ± 0.03 mag across all bands (yielding a typical distance precision of ∼8 per cent). Thus RC stars are reliable and precise standard candles. In addition, we have also re-calibrated the zero-point of the absolute magnitude of the RC in each band, which provides a benchmark for future studies to estimate distances to RC stars. Finally, the parallax error shrinkage in the hierarchical model outlined in this work can be used to obtain more precise parallaxes than Gaia for the most distant RC stars across the Galaxy

What happens if you single out? An experiment

We present an experiment investigating the effects of singling out an individual on trust and trustworthiness. We find that (a) trustworthiness falls if there is a singled out subject; (b) non-singled out subjects discriminate against the singled out subject when they are not responsible of the distinct status of this person; (c) under a negative frame, the singled out subject returns significantly less; (d) under a positive frame, the singled out subject behaves bimodally, either selecting very low or very high return rates. Overall, singling out induces a negligible effect on trust but is potentially disruptive for trustworthiness

Yule-Simpson's paradox in Galactic Archaeology

Simpson’s paradox, or Yule–Simpson effect, arises when a trend appears in different subsets of data but disappears or reverses when these subsets are combined. We describe here seven cases of this phenomenon for chemo-kinematical relations believed to constrain the Milky Way disc formation and evolution. We show that interpreting trends in relations, such as the radial and vertical chemical abundance gradients, the age–metallicity relation, and the metallicity–rotational velocity relation (MVR), can lead to conflicting conclusions about the Galaxy past if analyses marginalize over stellar age and/or birth radius. It is demonstrated that the MVR in RAVE giants is consistent with being always strongly negative, when narrow bins of [Mg/Fe] are considered. This is directly related to the negative radial metallicity gradients of stars grouped by common age (mono-age populations) due to the inside-out disc formation. The effect of the asymmetric drift can then give rise to a positive MVR trend in high-[α/Fe] stars, with a slope dependent on a given survey’s selection function and observational uncertainties. We also study the variation of lithium abundance, A(Li), with [Fe/H] of AMBRE:HARPS dwarfs. A strong reversal in the positive A(Li)–[Fe/H] trend of the total sample is found for mono-age populations, flattening for younger groups of stars. Dissecting by birth radius shows strengthening in the positive A(Li)–[Fe/H] trend, shifting to higher [Fe/H] with decreasing birth radius; these observational results suggest new constraints on chemical evolution models. This work highlights the necessity for precise age estimates for large stellar samples covering wide spatial regions

Clues from nearby galaxies to a better theory of cosmic evolution

The great advances in the network of cosmological tests show that the relativistic Big Bang theory is a good description of our expanding universe. But the properties of nearby galaxies that can be observed in greatest detail suggest a still better theory would more rapidly gather matter into galaxies and groups of galaxies. This happens in theoretical ideas now under discussion.Comment: published in Natur

Early Antiretroviral Therapy Reduces AIDS Progression/Death in Individuals with Acute Opportunistic Infections: A Multicenter Randomized Strategy Trial

Background: Optimal timing of ART initiation for individuals presenting with AIDS-related OIs has not been defined. Methods and Findings: A5164 was a randomized strategy trial of ‘‘early ART’’ - given within 14 days of starting acute OI treatment versus ‘‘deferred ART’’ - given after acute OI treatment is completed. Randomization was stratified by presenting OI and entry CD4 count. The primary week 48 endpoint was 3-level ordered categorical variable: 1. Death/AIDS progression; 2. No progression with incomplete viral suppression (ie HIV viral load (VL) [greater than or equal to] 50 copies/ml); 3. No progression with optimal viral suppression (ie HIV VL <50 copies/ml). Secondary endpoints included: AIDS progression/death; plasma HIV RNA and CD4 responses and safety parameters including IRIS. 282 subjects were evaluable; 141 per arm. Entry OIs included Pneumocytis jirovecii pneumonia 63%, cryptococcal meningitis 12%, and bacterial infections 12%. The early and deferred arms started ART a median of 12 and 45 days after start of OI treatment, respectively. The difference in the primary endpoint did not reach statistical significance: AIDS progression/death was seen in 20 (14%) vs. 34 (24%); whereas no progression but with incomplete viral suppression was seen in 54 (38%) vs. 44 (31%); and no progression with optimal viral suppression in 67 (48%) vs 63 (45%) in the early vs. deferred arm, respectively (p = 0.22). However, the early ART arm had fewer AIDS progression/deaths (OR = 0.51; 95% CI = 0.27–0.94) and a longer time to AIDS progression/death (stratified HR = 0.53; 95% CI = 0.30–0.92). The early ART had shorter time to achieving a CD4 count above 50 cells/mL (p<0.001) and no increase in adverse events. Conclusions: Early ART resulted in less AIDS progression/death with no increase in adverse events or loss of virologic response compared to deferred ART. These results support the early initiation of ART in patients presenting with acute AIDS-related OIs, absent major contraindications

The RAVE-on Catalog of Stellar Atmospheric Parameters and Chemical Abundances for Chemo-dynamic Studies in the Gaia Era

The orbits, atmospheric parameters, chemical abundances, and ages of individual stars in the Milky Way provide the most comprehensive illustration of galaxy formation available. The Tycho-Gaia Astrometric Solution (TGAS) will deliver astrometric parameters for the largest ever sample of Milky Way stars, though its full potential cannot be realized without the addition of complementary spectroscopy. Among existing spectroscopic surveys, the RAdial Velocity Experiment (RAVE) has the largest overlap with TGAS ($\gtrsim$200,000 stars). We present a data-driven re-analysis of 520,781 RAVE spectra using The Cannon. For red giants, we build our model using high-fidelity APOGEE stellar parameters and abundances for stars that overlap with RAVE. For main-sequence and sub-giant stars, our model uses stellar parameters from the K2/EPIC. We derive and validate effective temperature $T_{\rm eff}$, surface gravity $\log{g}$, and chemical abundances of up to seven elements (O, Mg, Al, Si, Ca, Fe, Ni). We report a total of 1,685,851 elemental abundances with a typical precision of 0.07 dex, a substantial improvement over previous RAVE data releases. The synthesis of RAVE-on and TGAS is the most powerful data set for chemo-dynamic analyses of the Milky Way ever produced

Vessel-Associated Transforming Growth Factor-Beta1 (TGF-β1) Is Increased in the Bronchial Reticular Basement Membrane in COPD and Normal Smokers

BACKGROUND: Transforming growth factor-beta1 (TGF-β1) is a multipotential cytokine with angiogenic activity. There are only limited data about its role in airway remodeling in COPD. We have previously shown that the reticular basement membrane (Rbm) is hypervascular in the airways of current smokers either with or without chronic obstructive pulmonary disease (COPD). This study evaluated TGF-β1 immunostaining in the Rbm and its relationship to vascularity in smokers with or without COPD. METHODOLOGY/PRINCIPAL FINDINGS: Bronchial biopsies from 15 smokers with normal lung function, 19 current and 14 ex-smokers with COPD were immunostained for TGF-β1 antibody and compared to 17 healthy controls. The percentage area of tissue and also number and area of vessels staining positively for TGF-β1 were measured and compared between groups. Some bronchial biopsies from current smoking COPD subjects were also stained for phosphorylated (active) Smad2/3. Epithelial TGF- β1 staining was not different between COPD current smokers and normal controls. TGF-β1 stained vessels in the Rbm were increased in smokers with normal lung function, current smoking COPD and ex-smokers with COPD compared to controls [median (range) for number of vessels/mm Rbm 2.5 (0.0-12.7), 3.4 (0.0-8.1) and 1.0 (0.0-6.3) vs. 0.0 (0.0-7.0), p<0.05]. Percentage of vessels stained was also increased in these clinical groups. Preliminary data suggest that in current smoking COPD subjects endothelial cells and cells in the Rbm stain positively for phosphorylated Smad2/3 suggesting TGF-β1 is functionally active in this situation. CONCLUSIONS/SIGNIFICANCE: Vessel-associated TGF-β1 activity is increased in the bronchial Rbm in smokers and especially those with COPD

Allergic inflammation does not impact chemical-induced carcinogenesis in the lungs of mice

<p>Abstract</p> <p>Background</p> <p>Although the relationship between allergic inflammation and lung carcinogenesis is not clearly defined, several reports suggest an increased incidence of lung cancer in patients with asthma. We aimed at determining the functional impact of allergic inflammation on chemical carcinogenesis in the lungs of mice.</p> <p>Methods</p> <p>Balb/c mice received single-dose urethane (1 g/kg at day 0) and two-stage ovalbumin during tumor initiation (sensitization: days -14 and 0; challenge: daily at days 6-12), tumor progression (sensitization: days 70 and 84; challenge: daily at days 90-96), or chronically (sensitization: days -14 and 0; challenge: daily at days 6-12 and thrice weekly thereafter). In addition, interleukin (IL)-5 deficient and wild-type C57BL/6 mice received ten weekly urethane injections. All mice were sacrificed after four months. Primary end-points were number, size, and histology of lung tumors. Secondary end-points were inflammatory cells and mediators in the airspace compartment.</p> <p>Results</p> <p>Ovalbumin provoked acute allergic inflammation and chronic remodeling of murine airways, evident by airspace eosinophilia, IL-5 up-regulation, and airspace enlargement. Urethane resulted in formation of atypical alveolar hyperplasias, adenomas, and adenocarcinomas in mouse lungs. Ovalbumin-induced allergic inflammation during tumor initiation, progression, or continuously did not impact the number, size, or histologic distribution of urethane-induced pulmonary neoplastic lesions. In addition, genetic deficiency in IL-5 had no effect on urethane-induced lung tumorigenesis.</p> <p>Conclusions</p> <p>Allergic inflammation does not impact chemical-induced carcinogenesis of the airways. These findings suggest that not all types of airway inflammation influence lung carcinogenesis and cast doubt on the idea of a mechanistic link between asthma and lung cancer.</p

Farmer attitudes and livestock disease: exploring citizenship behaviour and peer monitoring across two BVD control schemes in the UK

The eradication of BVD in the UK is technically possible but appears to be socially untenable. The following study explored farmer attitudes to BVD control schemes in relation to advice networks and information sharing, shared aims and goals, motivation and benefits of membership, notions of BVD as a priority disease and attitudes toward regulation. Two concepts from the organisational management literature framed the study: citizenship behaviour where actions of individuals support the collective good (but are not explicitly recognised as such) and peer to peer monitoring (where individuals evaluate other’s behaviour). Farmers from two BVD control schemes in the UK participated in the study: Orkney Livestock Association BVD Eradication Scheme and Norfolk and Suffolk Cattle Breeders Association BVD Eradication Scheme. In total 162 farmers participated in the research (109 in-scheme and 53 out of scheme). The findings revealed that group helping and information sharing among scheme members was low with a positive BVD status subject to social censure. Peer monitoring in the form of gossip with regard to the animal health status of other farms was high. Interestingly, farmers across both schemes supported greater regulation with regard to animal health, largely due to the mistrust of fellow farmers following voluntary disease control measures. While group cohesiveness varied across the two schemes, without continued financial inducements, longer-term sustainability is questionabl