Source apportionment of PM2.5 in Cork Harbour, Ireland using a combination of single particle mass spectrometry and quantitative semi-continuous measurements

An aerosol time-of-flight mass spectrometer (ATOFMS) was deployed for the measurement of the size resolved chemical composition of single particles at a site in Cork Harbour, Ireland for three weeks in August 2008. The ATOFMS was co-located with a suite of semi-continuous instrumentation for the measurement of particle number, elemental carbon (EC), organic carbon (OC), sulfate and particulate matter smaller than 2.5 μm in diameter (PM2.5). The temporality of the ambient ATOFMS particle classes was subsequently used in conjunction with the semi-continuous measurements to apportion PM2.5 mass using positive matrix factorisation. The synergy of the single particle classification procedure and positive matrix factorisation allowed for the identification of six factors, corresponding to vehicular traffic, marine, long-range transport, various combustion, domestic solid fuel combustion and shipping traffic with estimated contributions to the measured PM2.5 mass of 23%, 14%, 13%, 11%, 5% and 1.5% respectively. Shipping traffic was found to contribute 18% of the measured particle number (20–600 nm mobility diameter), and thus may have important implications for human health considering the size and composition of ship exhaust particles. The positive matrix factorisation procedure enabled a more refined interpretation of the single particle results by providing source contributions to PM2.5 mass, while the single particle data enabled the identification of additional factors not possible with typical semi-continuous measurements, including local shipping traffic.

Statistical methods for polyhedral shape classification with incomplete data - application to cryo-electron tomographic images

A certain type of bacterial inclusion, known as a bacterial microcompartment, was recently identified and imaged through cryo-electron tomography. A reconstructed 3D object from single-axis limited angle tilt-series cryo-electron tomography contains missing regions and this problem is known as the missing wedge problem. Due to missing regions on the reconstructed images, analyzing their 3D structures is a challenging problem. The existing methods overcome this problem by aligning and averaging several similar shaped objects. These schemes work well if the objects are symmetric and several objects with almost similar shapes and sizes are available. Since the bacterial inclusions studied here are not symmetric, are deformed, and show a wide range of shapes and sizes, the existing approaches are not appropriate. This research develops new statistical methods for analyzing geometric properties, such as volume, symmetry, aspect ratio, polyhedral structures etc., of these bacterial inclusions in presence of missing data. These methods work with deformed and non-symmetric varied shaped objects and do not necessitate multiple objects for handling the missing wedge problem. The developed methods and contributions include: (a) an improved method for manual image segmentation, (b) a new approach to 'complete' the segmented and reconstructed incomplete 3D images, (c) a polyhedral structural distance model to predict the polyhedral shapes of these microstructures, (d) a new shape descriptor for polyhedral shapes, named as polyhedron profile statistic, and (e) the Bayes classifier, linear discriminant analysis and support vector machine based classifiers for supervised incomplete polyhedral shape classification. Finally, the predicted 3D shapes for these bacterial microstructures belong to the Johnson solids family, and these shapes along with their other geometric properties are important for better understanding of their chemical and biological characteristics.

The effects of agglomeration economies on the productivity of manufacturing local units in Ireland

The purpose of this study is to examine the effects of agglomeration economies on the productivity of manufacturing local units in Ireland. Four types of agglomeration economies are considered in this study. These are internal economies of scale, localization economies, related variety and urbanization economies. This study makes a number of contributions to the literature. Firstly, this is the first study to conduct an investigation of the effects of agglomeration economies on the productivity of manufacturing local units operating in Ireland. Secondly, this study distinguishes between indigenous and foreign-owned local units which is important given the dual nature of the Irish economy (Krugman, 1997). Thirdly, in addition to considering the effects of agglomeration economies, this study examines the impact of spurious agglomeration on the productivity of foreign-owned local units. Using data from the Census of Industrial Local Units and a series of IV GMM estimators to control for endogeneity, the results of the analysis conducted in Chapter 6 reveal that there are differences in the effects of agglomeration economies on the productivity of indigenous and foreign-owned local units. In Chapter 7 the Census of Industrial Local Units is supplemented by additional data sources and more in-depth measures are generated to capture the features of each of the external agglomeration economies considered in this analysis. There is some evidence to suggest that the availability of local inputs has a negative and significant impact on productivity. The NACE based measures of related variety reveal that the availability of local inputs and knowledge spillovers for related sectors have a negative and significant impact on productivity. There is clear evidence to suggest that urbanization economies are important for increasing the productivity of indigenous local units. The findings reveal that a 1% increase in population density in the NUTS 3 region leads to an increase in the productivity of indigenous local units of approximately 0.07% to 0.08%. The results also reveal that there is a significant difference in the effects of agglomeration economies on the productivity of low-tech and medium/high-tech indigenous local units. The more in-depth measures of agglomeration economies used in Chapter 7 are also used in Chapter 8. A series of IV GMM regressions are estimated in order to identify the impact of agglomeration economies and spurious agglomeration on the productivity of foreign-owned local units operating in Ireland. There is some evidence found to suggest that the availability of a pool of skilled labour has a positive and significant on productivity of foreign-owned local units. There is also evidence to suggest that localization knowledge spillovers have a negative impact on the productivity of foreign-owned local units. There is strong evidence to suggest that the availability of local inputs has a negative impact on the productivity. The negative impact is not confined to the NACE 4-digit sector but also extends into related sectors as determined by Porter’s (2003) cluster classification. The cluster based skills measure of related variety has a positive and significant impact on the productivity of foreign-owned local units. Similar to Chapter 7, there is clear evidence to suggest that urbanization economies are important for increasing the productivity of foreign-owned local units. Both the summary measure and each of the more in-depth measures of agglomeration economies have a positive and significant impact on productivity. Spurious agglomeration has a positive and significant impact on the productivity of foreign-owned local units. The results indicate that the more foreign-owned local units of the same nationality in the country the greater the levels of productivity for the local unit. From a policy perspective, urbanization economies are clearly important for increasing the productivity of both indigenous and foreign-owned local units. Furthermore, the availability of a pool of skilled labour appears to be important for increasing the productivity of foreign-owned local units. Another policy implication that arises from these results relates to the differences observed between indigenous local units and foreign-owned local units and also between low-tech and medium/high-tech indigenous local units. These findings indicate that ‘one-size-fits-all’ type policies are not appropriate for increasing the productivity of local units operating in Ireland. Policies should be tailored to the needs of either indigenous or foreign-owned local units and also to specific sectors. This positive finding for own country spurious agglomeration is important from a policy perspective and is one that IDA Ireland should take on board.

Comparative survey of the relative impact of mRNA features on local ribosome profiling read density

Ribosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization techniques in the presence of heterogeneous noise. We illustrate how RUST can be used for identifying mRNA sequence features that affect ribosome footprint densities globally. We show that a few parameters extracted with RUST are sufficient for predicting experimental densities with high accuracy. Importantly the application of RUST to 30 publicly available Ribo-seq data sets revealed a substantial variation in sequence determinants of ribosome footprint frequencies, questioning the reliability of Ribo-seq as an accurate representation of local ribosome densities without prior quality control. This emphasizes our incomplete understanding of how protocol parameters affect ribosome footprint densities.