Current trends in the application of causal inference methods to pooled longitudinal observational infectious disease studies-A protocol for a methodological systematic review

INTRODUCTION: Pooling (or combining) and analysing observational, longitudinal data at the individual level facilitates inference through increased sample sizes, allowing for joint estimation of study- and individual-level exposure variables, and better enabling the assessment of rare exposures and diseases. Empirical studies leveraging such methods when randomization is unethical or impractical have grown in the health sciences in recent years. The adoption of so-called causal methods to account for both/either measured and/or unmeasured confounders is an important addition to the methodological toolkit for understanding the distribution, progression, and consequences of infectious diseases (IDs) and interventions on IDs. In the face of the Covid-19 pandemic and in the absence of systematic randomization of exposures or interventions, the value of these methods is even more apparent. Yet to our knowledge, no studies have assessed how causal methods involving pooling individual-level, observational, longitudinal data are being applied in ID-related research. In this systematic review, we assess how these methods are used and reported in ID-related research over the last 10 years. Findings will facilitate evaluation of trends of causal methods for ID research and lead to concrete recommendations for how to apply these methods where gaps in methodological rigor are identified. METHODS AND ANALYSIS: We will apply MeSH and text terms to identify relevant studies from EBSCO (Academic Search Complete, Business Source Premier, CINAHL, EconLit with Full Text, PsychINFO), EMBASE, PubMed, and Web of Science. Eligible studies are those that apply causal methods to account for confounding when assessing the effects of an intervention or exposure on an ID-related outcome using pooled, individual-level data from 2 or more longitudinal, observational studies. Titles, abstracts, and full-text articles, will be independently screened by two reviewers using Covidence software. Discrepancies will be resolved by a third reviewer. This systematic review protocol has been registered with PROSPERO (CRD42020204104)

Dependence of GAMA galaxy halo masses on the cosmic web environment from 100 deg2 of KiDS weak lensing data

Galaxies and their dark matter haloes are part of a complex network of mass structures, collectively called the cosmic web. Using the tidal tensor prescription these structures can be classified into four cosmic environments: voids, sheets, filaments and knots. As the cosmic web may influence the formation and evolution of dark matter haloes and the galaxies they host, we aim to study the effect of these cosmic environments on the average mass of galactic haloes. To this end we measure the galaxy–galaxy lensing profile of 91 195 galaxies, within 0.039 < z < 0.263, from the spectroscopic Galaxy And Mass Assembly survey, using ∼100deg2∼100deg2 of overlapping data from the Kilo-Degree Survey. In each of the four cosmic environments we model the contributions from group centrals, satellites and neighbouring groups to the stacked galaxy–galaxy lensing profiles. After correcting the lens samples for differences in the stellar mass distribution, we find no dependence of the average halo mass of central galaxies on their cosmic environment. We do find a significant increase in the average contribution of neighbouring groups to the lensing profile in increasingly dense cosmic environments. We show, however, that the observed effect can be entirely attributed to the galaxy density at much smaller scales (within 4 h−1 Mpc), which is correlated with the density of the cosmic environments. Within our current uncertainties we find no direct dependence of galaxy halo mass on their cosmic environment

The fourth data release of the Kilo-Degree Survey: ugri imaging and nine-band optical-IR photometry over 1000 square degrees

The Kilo-Degree Survey (KiDS) is an ongoing optical wide-field imaging survey with the OmegaCAM camera at the VLT Survey Telescope, specifically designed for measuring weak gravitational lensing by galaxies and large-scale structure. When completed it will consist of 1350 square degrees imaged in four filters (ugri). Here we present the fourth public data release which more than doubles the area of sky covered by data release 3. We also include aperture-matched ZYJHKs photometry from our partner VIKING survey on the VISTA telescope in the photometry catalogue. We illustrate the data quality and describe the catalogue content. Two dedicated pipelines are used for the production of the optical data. The Astro-WISE information system is used for the production of co-added images in the four survey bands, while a separate reduction of the r-band images using the theli pipeline is used to provide a source catalogue suitable for the core weak lensing science case. All data have been re-reduced for this data release using the latest versions of the pipelines. The VIKING photometry is obtained as forced photometry on the theli sources, using a re-reduction of the VIKING data that starts from the VISTA pawprints. Modifications to the pipelines with respect to earlier releases are described in detail. The photometry is calibrated to the Gaia DR2 G band using stellar locus regression. In this data release a total of 1006 square-degree survey tiles with stacked ugri images are made available, accompanied by weight maps, masks, and single-band source lists. We also provide a multi-band catalogue based on r-band detections, including homogenized photometry and photometric redshifts, for the whole dataset. Mean limiting magnitudes (5 sigma in a 2" aperture) are 24.23, 25.12, 25.02, 23.68 in ugri, respectively, and the mean r-band seeing is 0.70"

Gravitational lensing analysis of the Kilo-Degree Survey

The Kilo-Degree Survey (KiDS) is a multi-band imaging survey designed for cosmological studies from weak lensing and photometric redshifts. It uses the European Southern Observatory VLT Survey Telescope with its wide-field camera OmegaCAM. KiDS images are taken in four filters similar to the Sloan Digital Sky Survey ugri bands. The best seeing time is reserved for deep r-band observations. The median 5σ limiting AB magnitude is 24.9 and the median seeing is below 0.7 arcsec. Initial KiDS observations have concentrated on the Galaxy and Mass Assembly (GAMA) regions near the celestial equator, where extensive, highly complete redshift catalogues are available. A total of 109 survey tiles, 1 square degree each, form the basis of the first set of lensing analyses of halo properties of GAMA galaxies. Nine galaxies per square arcminute enter the lensing analysis, for an effective inverse shear variance of 69 arcmin−2. Accounting for the shape measurement weight, the median redshift of the sources is 0.53. KiDS data processing follows two parallel tracks, one optimized for weak lensing measurement and one for accurate matched-aperture photometry (for photometric redshifts). This technical paper describes the lensing and photometric redshift measurements (including a detailed description of the Gaussian aperture and photometry pipeline), summarizes the data quality and presents extensive tests for systematic errors that might affect the lensing analyses. We also provide first demonstrations of the suitability of the data for cosmological measurements, and describe our blinding procedure for preventing confirmation bias in the scientific analyses. The KiDS catalogues presented in this paper are released to the community through http://kids.strw.leidenuniv.nl

The first and second data releases of the Kilo-Degree Survey

Context. The Kilo-Degree Survey (KiDS) is an optical wide-field imaging survey carried out with the VLT Survey Telescope and the OmegaCAM camera. KiDS will image 1500 square degrees in four filters (ugri), and together with its near-infrared counterpart VIKING will produce deep photometry in nine bands. Designed for weak lensing shape and photometric redshift measurements, its core science driver is mapping the large-scale matter distribution in the Universe back to a redshift of ~0.5. Secondary science cases include galaxy evolution, Milky Way structure, and the detection of high-redshift clusters and quasars. Aims. KiDS is an ESO Public Survey and dedicated to serving the astronomical community with high-quality data products derived from the survey data. Public data releases, the first two of which are presented here, are crucial for enabling independent confirmation of the survey’s scientific value. The achieved data quality and initial scientific utilization are reviewed in order to validate the survey data. Methods. A dedicated pipeline and data management system based on ASTRO-WISE, combined with newly developed masking and source classification tools, is used for the production of the data products described here. Science projects based on these data products and preliminary results are outlined. Results. For 148 survey tiles (≈160 sq.deg.) stacked ugri images have been released, accompanied by weight maps, masks, source lists, and a multi-band source catalogue. Limiting magnitudes are typically 24.3, 25.1, 24.9, 23.8 (5σ in a 2′′ aperture) in ugri, respectively, and the typical r-band PSF size is less than 0.7′′. The photometry prior to global homogenization is stable at the ~2% (4%) level in gri (u) with some outliers due to non-photometric conditions, while the astrometry shows a typical 2D rms of 0.03′′. Early scientific results include the detection of nine high-z QSOs, fifteen candidate strong gravitational lenses, high-quality photometric redshifts and structural parameters for hundreds of thousands of galaxies

KiDS-450: cosmological parameter constraints from tomographic weak gravitational lensing

We present cosmological parameter constraints from a tomographic weak gravitational lensing analysis of ∼450 deg2 of imaging data from the Kilo Degree Survey (KiDS). For a flat Λ cold dark matter (ΛCDM) cosmology with a prior on H0 that encompasses the most recent direct measurements, we find S8≡σ8Ωm/0.3−−−−−−√=0.745±0.039⁠. This result is in good agreement with other low-redshift probes of large-scale structure, including recent cosmic shear results, along with pre-Planck cosmic microwave background constraints. A 2.3σ tension in S8 and ‘substantial discordance’ in the full parameter space is found with respect to the Planck 2015 results. We use shear measurements for nearly 15 million galaxies, determined with a new improved ‘self-calibrating’ version of lensFIT validated using an extensive suite of image simulations. Four-band ugri photometric redshifts are calibrated directly with deep spectroscopic surveys. The redshift calibration is confirmed using two independent techniques based on angular cross-correlations and the properties of the photometric redshift probability distributions. Our covariance matrix is determined using an analytical approach, verified numerically with large mock galaxy catalogues. We account for uncertainties in the modelling of intrinsic galaxy alignments and the impact of baryon feedback on the shape of the non-linear matter power spectrum, in addition to the small residual uncertainties in the shear and redshift calibration. The cosmology analysis was performed blind. Our high-level data products, including shear correlation functions, covariance matrices, redshift distributions, and Monte Carlo Markov chains are available at http://kids.strw.leidenuniv.nl

Prediction models for diagnosis and prognosis of covid-19: : systematic review and critical appraisal

Readers’ note This article is a living systematic review that will be updated to reflect emerging evidence. Updates may occur for up to two years from the date of original publication. This version is update 3 of the original article published on 7 April 2020 (BMJ 2020;369:m1328). Previous updates can be found as data supplements (https://www.bmj.com/content/369/bmj.m1328/related#datasupp). When citing this paper please consider adding the update number and date of access for clarity. Funding: LW, BVC, LH, and MDV acknowledge specific funding for this work from Internal Funds KU Leuven, KOOR, and the COVID-19 Fund. LW is a postdoctoral fellow of Research Foundation-Flanders (FWO) and receives support from ZonMw (grant 10430012010001). BVC received support from FWO (grant G0B4716N) and Internal Funds KU Leuven (grant C24/15/037). TPAD acknowledges financial support from the Netherlands Organisation for Health Research and Development (grant 91617050). VMTdJ was supported by the European Union Horizon 2020 Research and Innovation Programme under ReCoDID grant agreement 825746. KGMM and JAAD acknowledge financial support from Cochrane Collaboration (SMF 2018). KIES is funded by the National Institute for Health Research (NIHR) School for Primary Care Research. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, or the Department of Health and Social Care. GSC was supported by the NIHR Biomedical Research Centre, Oxford, and Cancer Research UK (programme grant C49297/A27294). JM was supported by the Cancer Research UK (programme grant C49297/A27294). PD was supported by the NIHR Biomedical Research Centre, Oxford. MOH is supported by the National Heart, Lung, and Blood Institute of the United States National Institutes of Health (grant R00 HL141678). ICCvDH and BCTvB received funding from Euregio Meuse-Rhine (grant Covid Data Platform (coDaP) interref EMR187). The funders played no role in study design, data collection, data analysis, data interpretation, or reporting.Peer reviewedPublisher PD

Gravitational lensing analysis of the Kilo-Degree Survey

Large scale structure and cosmolog

KiDS+2dFLenS+GAMA: testing the cosmological model with the EG statistic

We present a new measurement of EG, which combines measurements of weak gravitational lensing, galaxy clustering, and redshift-space distortions. This statistic was proposed as a consistency test of General Relativity (GR) that is insensitive to linear, deterministic galaxy bias, and the matter clustering amplitude. We combine deep imaging data from KiDS with overlapping spectroscopy from 2dFLenS, BOSS DR12, and GAMA and find EG(z = 0.267) = 0.43 ± 0.13 (GAMA), EG(z = 0.305) = 0.27 ± 0.08 (LOWZ+2dFLOZ), and EG(z = 0.554) = 0.26 ± 0.07 (CMASS+2dFHIZ). We demonstrate that the existing tension in the value of the matter density parameter hinders the robustness of this statistic as solely a test of GR. We find that our EG measurements, as well as existing ones in the literature, favour a lower matter density cosmology than the cosmic microwave background. For a flat CDM Universe, we find m(z = 0) = 0.25 ± 0.03. With this paper, we publicly release the 2dFLenS data set at: http://2dflens.swin.edu.au

KiDS-450: the tomographic weak lensing power spectrum and constraints on cosmological parameters

We present measurements of the weak gravitational lensing shear power spectrum based on $450$ sq. deg. of imaging data from the Kilo Degree Survey. We employ a quadratic estimator in two and three redshift bins and extract band powers of redshift auto-correlation and cross-correlation spectra in the multipole range $76 \leq \ell \leq 1310$. The cosmological interpretation of the measured shear power spectra is performed in a Bayesian framework assuming a $\Lambda$CDM model with spatially flat geometry, while accounting for small residual uncertainties in the shear calibration and redshift distributions as well as marginalising over intrinsic alignments, baryon feedback and an excess-noise power model. Moreover, massive neutrinos are included in the modelling. The cosmological main result is expressed in terms of the parameter combination $S_8 \equiv \sigma_8 \sqrt{\Omega_{\rm m}/0.3}$ yielding $S_8 = \ 0.651 \pm 0.058$(3 z-bins), confirming the recently reported tension in this parameter with constraints from Planck at$3.2\sigma$ (3 z-bins). We cross-check the results of the 3 z-bin analysis with the weaker constraints from the 2 z-bin analysis and find them to be consistent. The high-level data products of this analysis, such as the band power measurements, covariance matrices, redshift distributions, and likelihood evaluation chains are available at http://kids.strw.leidenuniv.nl/Comment: 23 pages, 18 figures, 5 tables; results unchanged, version accepted for publication by MNRAS. Data products available at http://kids.strw.leidenuniv.nl