Routes for breaching and protecting genetic privacy

We are entering the era of ubiquitous genetic information for research, clinical care, and personal curiosity. Sharing these datasets is vital for rapid progress in understanding the genetic basis of human diseases. However, one growing concern is the ability to protect the genetic privacy of the data originators. Here, we technically map threats to genetic privacy and discuss potential mitigation strategies for privacy-preserving dissemination of genetic data.Comment: Draft for comment

What we talk about when we talk about "global mindset": managerial cognition in multinational corporations

Recent developments in the global economy and in multinational corporations have placed significant emphasis on the cognitive orientations of managers, giving rise to a number of concepts such as “global mindset” that are presumed to be associated with the effective management of multinational corporations (MNCs). This paper reviews the literature on global mindset and clarifies some of the conceptual confusion surrounding the construct. We identify common themes across writers, suggesting that the majority of studies fall into one of three research perspectives: cultural, strategic, and multidimensional. We also identify two constructs from the social sciences that underlie the perspectives found in the literature: cosmopolitanism and cognitive complexity and use these two constructs to develop an integrative theoretical framework of global mindset. We then provide a critical assessment of the field of global mindset and suggest directions for future theoretical and empirical research

Evolutionary Dynamics of Co-Segregating Gene Clusters Associated with Complex Diseases

BACKGROUND: The distribution of human disease-associated mutations is not random across the human genome. Despite the fact that natural selection continually removes disease-associated mutations, an enrichment of these variants can be observed in regions of low recombination. There are a number of mechanisms by which such a clustering could occur, including genetic perturbations or demographic effects within different populations. Recent genome-wide association studies (GWAS) suggest that single nucleotide polymorphisms (SNPs) associated with complex disease traits are not randomly distributed throughout the genome, but tend to cluster in regions of low recombination. PRINCIPAL FINDINGS: Here we investigated whether deleterious mutations have accumulated in regions of low recombination due to the impact of recent positive selection and genetic hitchhiking. Using publicly available data on common complex diseases and population demography, we observed an enrichment of hitchhiked disease associations in conserved gene clusters subject to selection pressure. Evolutionary analysis revealed that these conserved gene clusters arose by multiple concerted rearrangements events across the vertebrate lineage. We observed distinct clustering of disease-associated SNPs in evolutionary rearranged regions of low recombination and high gene density, which harbor genes involved in immunity, that is, the interleukin cluster on 5q31 or RhoA on 3p21. CONCLUSIONS: Our results suggest that multiple lineage specific rearrangements led to a physical clustering of functionally related and linked genes exhibiting an enrichment of susceptibility loci for complex traits. This implies that besides recent evolutionary adaptations other evolutionary dynamics have played a role in the formation of linked gene clusters associated with complex disease traits

Galaxy-galaxy lensing with the DES-CMASS catalogue: measurement and constraints on the galaxy-matter cross-correlation

The DMASS sample is a photometric sample from the DES Year 1 data set designed to replicate the properties of the CMASS sample from BOSS, in support of a joint analysis of DES and BOSS beyond the small overlapping area. In this paper, we present the measurement of galaxy–galaxy lensing using the DMASS sample as gravitational lenses in the DES Y1 imaging data. We test a number of potential systematics that can bias the galaxy–galaxy lensing signal, including those from shear estimation, photometric redshifts, and observing conditions. After careful systematic tests, we obtain a highly significant detection of the galaxy–galaxy lensing signal, with total S/N = 25.7. With the measured signal, we assess the feasibility of using DMASS as gravitational lenses equivalent to CMASS, by estimating the galaxy-matter cross-correlation coefficient rcc. By jointly fitting the galaxy–galaxy lensing measurement with the galaxy clustering measurement from CMASS, we obtain rcc=1.09+0.12−0.11 for the scale cut of 4h−1Mpc and rcc=1.06+0.13−0.12 for 12h−1Mpc in fixed cosmology. By adding the angular galaxy clustering of DMASS, we obtain rcc = 1.06 ± 0.10 for the scale cut of 4h−1Mpc and rcc = 1.03 ± 0.11 for 12h−1Mpc⁠. The resulting values of rcc indicate that the lensing signal of DMASS is statistically consistent with the one that would have been measured if CMASS had populated the DES region within the given statistical uncertainty. The measurement of galaxy–galaxy lensing presented in this paper will serve as part of the data vector for the forthcoming cosmology analysis in preparation

Dark energy survey year 1 results: weak lensing shape catalogues

We present two galaxy shape catalogues from the Dark Energy Survey Year 1 data set, covering 1500 deg2 with a median redshift of 0.59. The catalogues cover two main fields: Stripe 82, and an area overlapping the South Pole Telescope survey region. We describe our data analysis process and in particular our shape measurement using two independent shear measurement pipelines, METACALIBRATION and IM3SHAPE. The METACALIBRATION catalogue uses a Gaussian model with an innovative internal calibration scheme, and was applied to riz bands, yielding 34.8M objects. The IM3SHAPE catalogue uses amaximum-likelihood bulge/disc model calibrated using simulations, and was applied to r-band data, yielding 21.9M objects. Both catalogues pass a suite of null tests that demonstrate their fitness for use in weak lensing science. We estimate the 1σ uncertainties in multiplicative shear calibration to be 0.013 and 0.025 for the METACALIBRATION and IM3SHAPE catalogues, respectively

Dark Energy Survey Year 3 Results: Measuring the Survey Transfer Function with Balrog

We describe an updated calibration and diagnostic framework, Balrog, used to directly sample the selection and photometric biases of the Dark Energy Survey (DES) Year 3 (Y3) data set. We systematically inject onto the single-epoch images of a random 20% subset of the DES footprint an ensemble of nearly 30 million realistic galaxy models derived from DES Deep Field observations. These augmented images are analyzed in parallel with the original data to automatically inherit measurement systematics that are often too difficult to capture with generative models. The resulting object catalog is a Monte Carlo sampling of the DES transfer function and is used as a powerful diagnostic and calibration tool for a variety of DES Y3 science, particularly for the calibration of the photometric redshifts of distant "source" galaxies and magnification biases of nearer "lens" galaxies. The recovered Balrog injections are shown to closely match the photometric property distributions of the Y3 GOLD catalog, particularly in color, and capture the number density fluctuations from observing conditions of the real data within 1% for a typical galaxy sample. We find that Y3 colors are extremely well calibrated, typically within ∼1–8 mmag, but for a small subset of objects, we detect significant magnitude biases correlated with large overestimates of the injected object size due to proximity effects and blending. We discuss approaches to extend the current methodology to capture more aspects of the transfer function and reach full coverage of the survey footprint for future analyses

Dark Energy Survey Year 3 results: marginalization over redshift distribution uncertainties using ranking of discrete realizations

Cosmological information from weak lensing surveys is maximized by sorting source galaxies into tomographic redshift subsamples. Any uncertainties on these redshift distributions must be correctly propagated into the cosmological results. We present hyperrank, a new method for marginalizing over redshift distribution uncertainties, using discrete samples from the space of all possible redshift distributions, improving over simple parametrized models. In hyperrank, the set of proposed redshift distributions is ranked according to a small (between one and four) number of summary values, which are then sampled, along with other nuisance parameters and cosmological parameters in the Monte Carlo chain used for inference. This approach can be regarded as a general method for marginalizing over discrete realizations of data vector variation with nuisance parameters, which can consequently be sampled separately from the main parameters of interest, allowing for increased computational efficiency. We focus on the case of weak lensing cosmic shear analyses and demonstrate our method using simulations made for the Dark Energy Survey (DES). We show that the method can correctly and efficiently marginalize over a wide range of models for the redshift distribution uncertainty. Finally, we compare hyperrank to the common mean-shifting method of marginalizing over redshift uncertainty, validating that this simpler model is sufficient for use in the DES Year 3 cosmology results presented in companion papers

Dark Energy Survey year 3 results: Constraints on cosmological parameters and galaxy-bias models from galaxy clustering and galaxy-galaxy lensing using the redMaGiC sample

We constrain cosmological parameters and galaxy-bias parameters using the combination of galaxy clustering and galaxy-galaxy lensing measurements from the Dark Energy Survey (DES) year-3 data. We describe our modeling framework and choice of scales analyzed, validating their robustness to theoretical uncertainties in small-scale clustering by analyzing simulated data. Using a linear galaxy-bias model and redMaGiC galaxy sample, we obtain 10% constraints on the matter density of the Universe. We also implement a nonlinear galaxy-bias model to probe smaller scales that includes parametrization based on hybrid perturbation theory and find that it leads to a 17% gain in cosmological constraining power. We perform robustness tests of our methodology pipeline and demonstrate stability of the constraints to changes in the theory model. Using the redMaGiC galaxy sample as foreground lens galaxies and adopting the best-fitting cosmological parameters from DES year-1 data, we find the galaxy clustering and galaxy-galaxy lensing measurements to exhibit significant signals akin to decorrelation between galaxies and mass on large scales, which is not expected in any current models. This likely systematic measurement error biases our constraints on galaxy bias and the S8 parameter. We find that a scale-, redshift-and sky-Area-independent phenomenological decorrelation parameter can effectively capture this inconsistency between the galaxy clustering and galaxy-galaxy lensing. We trace the source of this correlation to a color-dependent photometric issue and minimize its impact on our result by changing the selection criteria of redMaGiC galaxies. Using this new sample, our constraints on the S8 parameter are consistent with previous studies and we find a small shift in the ωm constraints compared to the fiducial redMaGiC sample. We infer the constraints on the mean host-halo mass of the redMaGiC galaxies in this new sample from the large-scale bias constraints, finding the galaxies occupy halos of mass approximately 1.6×10 13 M⊙/h

Dark Energy Survey Y3 results: Blending shear and redshift biases in image simulations

As the statistical power of galaxy weak lensing reaches per cent level precision, large, realistic, and robust simulations are required to calibrate observational systematics, especially given the increased importance of object blending as survey depths increase. To capture the coupled effects of blending in both shear and photometric redshift calibration, we define the effective redshift distribution for lensing, nγ(z), and describe how to estimate it using image simulations. We use an extensive suite of tailored image simulations to characterize the performance of the shear estimation pipeline applied to the Dark Energy Survey (DES) Year 3 data set. We describe the multiband, multi-epoch simulations, and demonstrate their high level of realism through comparisons to the real DES data. We isolate the effects that generate shear calibration biases by running variations on our fiducial simulation, and find that blending-related effects are the dominant contribution to the mean multiplicative bias of approximately $-2{{ rm per cent}}$. By generating simulations with input shear signals that vary with redshift, we calibrate biases in our estimation of the effective redshift distribution, and demonstrate the importance of this approach when blending is present. We provide corrected effective redshift distributions that incorporate statistical and systematic uncertainties, ready for use in DES Year 3 weak lensing analyses

SPT clusters with des and HST weak lensing. I. Cluster lensing and Bayesian population modeling of multiwavelength cluster datasets

We present a Bayesian population modeling method to analyze the abundance of galaxy clusters identified by the South Pole Telescope (SPT) with a simultaneous mass calibration using weak gravitational lensing data from the Dark Energy Survey (DES) and the Hubble Space Telescope (HST). We discuss and validate the modeling choices with a particular focus on a robust, weak-lensing-based mass calibration using DES data. For the DES Year 3 data, we report a systematic uncertainty in weak-lensing mass calibration that increases from 1% at z=0.25 to 10% at z=0.95, to which we add 2% in quadrature to account for uncertainties in the impact of baryonic effects. We implement an analysis pipeline that joins the cluster abundance likelihood with a multiobservable likelihood for the Sunyaev-Zel'dovich effect, optical richness, and weak-lensing measurements for each individual cluster. We validate that our analysis pipeline can recover unbiased cosmological constraints by analyzing mocks that closely resemble the cluster sample extracted from the SPT-SZ, SPTpol ECS, and SPTpol 500d surveys and the DES Year 3 and HST-39 weak-lensing datasets. This work represents a crucial prerequisite for the subsequent cosmological analysis of the real dataset