Dealing with partially observed covariates in propensity score analysis of observational data

Observational data, such as electronic health records, are a valuable source of information for researchers seeking to answer health-related questions. Since treatment allocation is not typically randomised in studies using observational data, there is confounding systematic differences in the characteristics of patients in different treatment groups. Propensity score analysis (PSA) can be used to handle confounding by modelling the probability of being allocated to a particular treatment, based on patient characteristics. However, a common issue in analyses of observational data is missing data. In general, not dealing appropriately with missing data can lead to loss of efficiency and biased estimates of the treatment effect. Furthermore, having partially observed covariate data can complicate the estimation of the propensity score. The missingness pattern approach (MPA) has been proposed to handle partially observed covariate data in PSA. One key objective of my thesis is to understand when the approach is appropriate, by exploring its underlying assumptions. I began by comparing different statements of the MPA's underlying assumptions given in the literature. I considered the plausibility of the MPA's assumptions in simple scenarios, finding that they are separate to the conventional classification of missingness mechanisms. I used d-separation (a rule for testing conditional independence statements) with single world intervention graphs, representing a variety of scenarios, in order to develop guidance for when the assumptions seem plausible. I also explored the connection between using the MPA and using missing indicators in the context of PSA, finding that the use of missing indicators is a simplification of the MPA. I extended this work to outcome regression, mathematically proving that using missing indicators is valid under the MPA's assumptions as well as an additional simplifying assumption. I also conducted simulation studies to assess bias when using missing indicators to handle partially observed covariate data in outcome regression

Mixing ratios of volatile organic compounds (VOCs) in the atmosphere of Karachi, Pakistan

Mixing ratios of carbon monoxide (CO), methane (CH4), non-methane hydrocarbons, halocarbons and alkyl nitrates (a total of 72 species) were determined for 78 whole air samples collected during the winter of 1998-1999 in Karachi, Pakistan. This is the first time that volatile organic compound (VOC) levels in Karachi have been extensively characterized. The overall air quality of the urban environment was determined using air samples collected at six locations throughout Karachi. Methane (6.3ppmv) and ethane (93ppbv) levels in Karachi were found to be much higher than in other cities that have been studied. The very high CH4 levels highlight the importance of natural gas leakage in Karachi. The leakage of liquefied petroleum gas contributes to elevated propane and butane levels in Karachi, although the propane and butane burdens were lower than in other cities (e.g., Mexico City, Santiago). High levels of benzene (0.3-19ppbv) also appear to be of concern in the Karachi urban area. Vehicular emissions were characterized using air samples collected along the busiest thoroughfare of the city (M.A. Jinnah Road). Emissions from vehicular exhaust were found to be the main source of many of the hydrocarbons reported here. Significant levels of isoprene (1.2ppbv) were detected at the roadside, and vehicular exhaust is estimated to account for about 20% of the isoprene observed in Karachi. 1,2-Dichloroethane, a lead scavenger added to leaded fuel, was also emitted by cars. The photochemical production of ozone (O3) was calculated for CO and the various VOCs using the Maximum Incremental Reactivity (MIR) scale. Based on the MIR scale, the leading contributors to O3 production in Karachi are ethene, CO, propene, m-xylene and toluene. © 2002 Elsevier Science Ltd. All rights reserved

Probabilistic linkage without personal information successfully linked national clinical datasets: Linkage of national clinical datasets without patient identifiers using probabilistic methods.

BACKGROUND: Probabilistic linkage can link patients from different clinical databases without the need for personal information. If accurate linkage can be achieved, it would accelerate the use of linked datasets to address important clinical and public health questions. OBJECTIVE: We developed a step-by-step process for probabilistic linkage of national clinical and administrative datasets without personal information, and validated it against deterministic linkage using patient identifiers. STUDY DESIGN AND SETTING: We used electronic health records from the National Bowel Cancer Audit (NBOCA) and Hospital Episode Statistics (HES) databases for 10,566 bowel cancer patients undergoing emergency surgery in the English National Health Service. RESULTS: Probabilistic linkage linked 81.4% of NBOCA records to HES, versus 82.8% using deterministic linkage. No systematic differences were seen between patients that were and were not linked, and regression models for mortality and length of hospital stay according to patient and tumour characteristics were not sensitive to the linkage approach. CONCLUSION: Probabilistic linkage was successful in linking national clinical and administrative datasets for patients undergoing a major surgical procedure. It allows analysts outside highly secure data environments to undertake linkage while minimising costs and delays, protecting data security, and maintaining linkage quality

Combustion of a coal char particle in a stream of dry gas.

The burning rate, surface temperature, drag, and extinction conditions of a single char particle moving in a gas are computed numerically. The effects of the size and velocity of the particle and of the temperature and composition of the gas are examined in the framework of a simple model that includes O2 and CO2 heterogeneous reactions and, in some cases, a diffusion-controlled CO oxidation flame in the gas around the particle. In agreement with known results, the burning rate is found to increase with the velocity of the particle when the Reynolds number of the gas flow ceases to be small. The temperature of the particle increases with the temperature and oxygen mass fraction of the gas and is little affected by the size and velocity of the particle, except in the vicinity of extinction. The drag coefficient is a decreasing function of the particle size and velocity in the range of Reynolds numbers that has been analyzed. The presence of CO2 in the gas may have an important effect on the gasification of small particles

Detection of hexavalent uranium with inline and field-portable immunosensors

An antibody that recognizes a chelated form of hexavalent uranium was used in the development of two different immunosensors for uranium detection. Specifically, these sensors were utilized for the analysis of groundwater samples collected during a 2007 field study of in situ bioremediation in a aquifer located at Rifle, CO. The antibody-based sensors provided data comparable to that obtained using Kinetic Phosphorescence Analysis (KPA). Thus, these novel instruments and associated reagents should provide field researchers and resource managers with valuable new tools for on-site data acquisition

On the Mysterious Propulsion of Synechococcus

We propose a model for the self-propulsion of the marine bacterium Synechococcus utilizing a continuous looped helical track analogous to that found in Myxobacteria [1]. In our model cargo-carrying protein motors, driven by proton-motive force, move along a continuous looped helical track. The movement of the cargo creates surface distortions in the form of small amplitude traveling ridges along the S-layer above the helical track. The resulting fluid motion adjacent to the helical ribbon provides the propulsive thrust. A variation on the helical rotor model of [1] allows the motors to be anchored to the peptidoglycan layer, where they drive rotation of the track creating traveling helical waves along the S-layer. We derive expressions relating the swimming speed to the amplitude, wavelength, and velocity of the surface waves induced by the helical rotor, and show that they fall in reasonable ranges to explain the velocity and rotation rate of swimming Synechococcus

A major genetic locus in <i>Trypanosoma brucei</i> is a determinant of host pathology

The progression and variation of pathology during infections can be due to components from both host or pathogen, and/or the interaction between them. The influence of host genetic variation on disease pathology during infections with trypanosomes has been well studied in recent years, but the role of parasite genetic variation has not been extensively studied. We have shown that there is parasite strain-specific variation in the level of splenomegaly and hepatomegaly in infected mice and used a forward genetic approach to identify the parasite loci that determine this variation. This approach allowed us to dissect and identify the parasite loci that determine the complex phenotypes induced by infection. Using the available trypanosome genetic map, a major quantitative trait locus (QTL) was identified on T. brucei chromosome 3 (LOD = 7.2) that accounted for approximately two thirds of the variance observed in each of two correlated phenotypes, splenomegaly and hepatomegaly, in the infected mice (named &lt;i&gt;TbOrg1&lt;/i&gt;). In addition, a second locus was identified that contributed to splenomegaly, hepatomegaly and reticulocytosis (&lt;i&gt;TbOrg2&lt;/i&gt;). This is the first use of quantitative trait locus mapping in a diploid protozoan and shows that there are trypanosome genes that directly contribute to the progression of pathology during infections and, therefore, that parasite genetic variation can be a critical factor in disease outcome. The identification of parasite loci is a first step towards identifying the genes that are responsible for these important traits and shows the power of genetic analysis as a tool for dissecting complex quantitative phenotypic traits

Can disordered mobile phone use be considered a behavioral addiction? An update on current evidence and a comprehensive model for future research

Despite the many positive outcomes, excessive mobile phone use is now often associated with potentially harmful and/or disturbing behaviors (e.g., symptoms of deregulated use, negative impact on various aspects of daily life such as relationship problems, and work intrusion). Problematic mobile phone use (PMPU) has generally been considered as a behavioral addiction that shares many features with more established drug addictions. In light of the most recent data, the current paper reviews the validity of the behavioral addiction model when applied to PMPU. On the whole, it is argued that the evidence supporting PMPU as an addictive behavior is scarce. In particular, it lacks studies that definitively show behavioral and neurobiological similarities between mobile phone addiction and other types of legitimate addictive behaviors. Given this context, an integrative pathway model is proposed that aims to provide a theoretical framework to guide future research in the field of PMPU. This model highlights that PMPU is a heterogeneous and multi-faceted condition

Graphene Photonics and Optoelectronics

The richness of optical and electronic properties of graphene attracts enormous interest. Graphene has high mobility and optical transparency, in addition to flexibility, robustness and environmental stability. So far, the main focus has been on fundamental physics and electronic devices. However, we believe its true potential to be in photonics and optoelectronics, where the combination of its unique optical and electronic properties can be fully exploited, even in the absence of a bandgap, and the linear dispersion of the Dirac electrons enables ultra-wide-band tunability. The rise of graphene in photonics and optoelectronics is shown by several recent results, ranging from solar cells and light emitting devices, to touch screens, photodetectors and ultrafast lasers. Here we review the state of the art in this emerging field.Comment: Review Nature Photonics, in pres