Advanced Modelling Strategies: Challenges and pitfalls in robust causal inference with observational data

Advanced Modelling Strategies: Challenges and pitfalls in robust causal inference with observational data summarises the lecture notes prepared for a four-day workshop sponsored by the Society for Social Medicine and hosted by the Leeds Institute for Data Analytics (LIDA) at the University of Leeds on 17th-20th July 2017

How South Pacific mangroves may respond to predicted climate change and sea level rise

In the Pacific islands the total mangrove area is about 343,735 ha, with largest areas in Papua New Guinea, Solomon Islands, Fiji and New Caledonia. A total of 34 species of mangroves occur, as well as 3 hybrids. These are of the Indo-Malayan assemblage (with one exception), and decline in diversity from west to east across the Pacific, reaching a limit at American Samoa. Mangrove resources are traditionally exploited in the Pacific islands, for construction and fuel wood, herbal medicines, and the gathering of crabs and fish. There are two main environmental settings for mangroves in the Pacific, deltaic and estuarine mangroves of high islands, and embayment, lagoon and reef flat mangroves of low islands. It is indicated from past analogues that their close relationship with sea-level height renders these mangrove swamps particularly vulnerable to disruption by sea-level rise. Stratigraphic records of Pacific island mangrove ecosystems during sea-level changes of the Holocene Period demonstrate that low islands mangroves can keep up with a sea-level rise of up to 12 cm per 100 years. Mangroves of high islands can keep up with rates of sea-level rates of up to 45 cm per 100 years, according to the supply of fluvial sediment. When the rate of sea-level rise exceeds the rate of accretion, mangroves experience problems of substrate erosion, inundation stress and increased salinity. Rise in temperature and the direct effects of increased CO2 levels are likely to increase mangrove productivity, change phenological patterns (such as the timing of flowering and fruiting), and expand the ranges of mangroves into higher latitudes. Pacific island mangroves are expected to demonstrate a sensitive response to the predicted rise in sea-level. A regional monitoring system is needed to provide data on ecosystem changes in productivity, species composition and sedimentation. This has been the intention of a number of programs, but none has yet been implemented

Are we failing to protect threatened mangroves in the Sundarbans world heritage ecosystem?

The Sundarbans, the largest mangrove ecosystem in the world, is under threat from historical and future human exploitation and sea level rise. Limited scientific knowledge on the spatial ecology of the mangroves in this world heritage ecosystem has been a major impediment to conservation efforts. Here, for the first time, we report on habitat suitability analyses and spatial density maps for the four most prominent mangrove species - Heritiera fomes, Excoecaria agallocha, Ceriops decandra and Xylocarpus mekongensis. Globally endangered H. fomes abundances declined as salinity increased. Responses to nutrients, elevation, and stem density varied between species. H. fomes and X. mekongensis preferred upstream habitats. E. agallocha and C. decandra preferred down-stream and mid-stream habitats. Historical harvesting had negative influences on H. fomes, C. decandra and X. mekongensis abundances. The established protected area network does not support the most suitable habitats of these threatened species. We therefore recommend a reconfiguration of the network to include these suitable habitats and ensure their immediate protection. These novel habitat insights and spatial predictions can form the basis for future forest studies and spatial conservation planning, and have implications for more effective conservation of the Sundarbans mangroves and the many other species that rely on them

Intervention differential effects and regression to the mean in studies where sample selection is based on the initial value of the outcome variable: an evaluation of methods illustrated in weight-management studies

© 2020, © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. Background: Intervention differential effects (IDEs) occur where changes in an outcome depend upon the initial values of that outcome. Although methods to identify IDEs are well documented, there remains a lack of understanding about the circumstances under which these methods are robust. One context that has not been explored is the identification of intervention differential effect in studies where sample selection is based on the initial value of the outcome being evaluated. We hypothesise that, in such settings, established methods for detecting IDEs will struggle to discriminate these from regression to the mean. Methods: Using simulated datasets of weight-loss intervention programmes that recruit according to initial body mass index, we explore the reliability of Oldham's method and multilevel modelling (MLM) to detect IDEs. Results: In datasets simulated with no IDE, Oldham's method and MLM yield Type I error rates >90%, confirming that threshold selection/truncation leads to bias due to regression to the mean. Type I error rates return close to 5% for both methods when a control group is introduced. Conclusions: Oldham's method and MLM can robustly detect IDEs in this setting, but only if analyses incorporate a control group for comparison

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

The Authors Respond

Although the studies highlighted in Kinlen and Peto’s letter describe situations they take to be “national in scope”, none of these adopted the ‘region-wide’ analysis we recommend. Rather, these studies have focussed on rural areas with small populations experiencing extreme levels of inward-migration that had been selected from larger regions/nation states. To definitively avoid bias, our study points to the need for comparisons of areas with varying levels of inward migration, either by comparing all areas within an entire region/nation state or random subsets thereof

The association between family and community social capital and health risk behaviours in young people: an integrative review

Background: Health risk behaviours known to result in poorer outcomes in adulthood are generally established in late childhood and adolescence. These ‘risky’ behaviours include smoking, alcohol and illicit drug use and sexual risk taking. While the role of social capital in the establishment of health risk behaviours in young people has been explored, to date, no attempt has been made to consolidate the evidence in the form of a review. Thus, this integrative review was undertaken to identify and synthesise research findings on the role and impact of family and community social capital on health risk behaviours in young people and provide a consolidated evidence base to inform multi-sectorial policy and practice.<p></p> Methods: Key electronic databases were searched (i.e. ASSIA, CINAHL, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, Database of Abstracts of Reviews of Effects, Embase, Medline, PsycINFO, Sociological Abstracts) for relevant studies and this was complemented by hand searching. Inclusion/exclusion criteria were applied and data was extracted from the included studies. Heterogeneity in study design and the outcomes assessed precluded meta-analysis/meta-synthesis; the results are therefore presented in narrative form.<p></p> Results: Thirty-four papers satisfied the review inclusion criteria; most were cross-sectional surveys. The majority of the studies were conducted in North America (n=25), with three being conducted in the UK. Sample sizes ranged from 61 to 98,340. The synthesised evidence demonstrates that social capital is an important construct for understanding the establishment of health risk behaviours in young people. The different elements of family and community social capital varied in terms of their saliency within each behavioural domain, with positive parent–child relations, parental monitoring, religiosity and school quality being particularly important in reducing risk.<p></p> Conclusions: This review is the first to systematically synthesise research findings about the association between social capital and health risk behaviours in young people. While providing evidence that may inform the development of interventions framed around social capital, the review also highlights key areas where further research is required to provide a fuller account of the nature and role of social capital in influencing the uptake of health risk behaviours.<p></p&gt

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO

Measurement of the top quark mass using the matrix element technique in dilepton final states

We present a measurement of the top quark mass in pp¯ collisions at a center-of-mass energy of 1.96 TeV at the Fermilab Tevatron collider. The data were collected by the D0 experiment corresponding to an integrated luminosity of 9.7  fb−1. The matrix element technique is applied to tt¯ events in the final state containing leptons (electrons or muons) with high transverse momenta and at least two jets. The calibration of the jet energy scale determined in the lepton+jets final state of tt¯ decays is applied to jet energies. This correction provides a substantial reduction in systematic uncertainties. We obtain a top quark mass of mt=173.93±1.84  GeV

Evolutionary genetics of immunological supertypes reveals two faces of the Red Queen

Red Queen host-parasite co-evolution can drive adaptations of immune-genes by positive selection that erodes genetic variation (Red Queen Arms Race), or result in a balanced polymorphism (Red Queen Dynamics) and the long-term preservation of genetic variation (trans-species polymorphism). These two Red Queen processes are opposite extremes of the co-evolutionary spectrum. Here we show that both Red Queen processes can operate simultaneously, analyzing the Major Histocompatibility Complex (MHC) in guppies (Poecilia reticulata and P. obscura), and swamp guppies (Micropoecilia picta). Sub-functionalization of MHC alleles into “supertypes” explains how polymorphisms persist during rapid host-parasite co-evolution. Simulations show the maintenance of supertypes as balanced polymorphisms, consistent with Red Queen Dynamics, whereas alleles within supertypes are subject to positive selection in a Red Queen Arms Race. Building on the Divergent Allele Advantage hypothesis, we show that functional aspects of allelic diversity help to elucidate the evolution of polymorphic genes involved in Red Queen co-evolution