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Evolution: a view from the 21st century
Cathal Seoighe
Trends in Evolutionary Biology , 2012, DOI: 10.4081/eb.2012.e6
Modelling Financially Optimal Afforestation and Forest Management Scenarios Using a Bio-Economic Model  [PDF]
Mary Ryan, Cathal O’Donoghue, Henry Phillips
Open Journal of Forestry (OJF) , 2016, DOI: 10.4236/ojf.2016.61003
Abstract: The expansion of non-industrial private forests (NIPF) in Ireland is unique in the European context in which the almost doubling of forest cover within the last thirty years has taken place largely on farmland. This is not surprising as Ireland has some of the highest growth rates for conifers in Europe and also has a large proportion of land which is marginal for agriculture but highly productive under forests. However, in recent years, afforestation in Ireland as in many European countries has fallen well short of policy targets. As the farm afforestation decision essentially involves an inter-temporal land use change, farmers need comprehensive information on forest market returns under different environmental conditions and forest management regimes. This paper describes the systematic development of a cohort forest bio-economic model which examines financially optimal afforestation and management choices. Simulating a range of productivity and harvesting scenarios for Sitka spruce, we find that different objectives result in different outcomes. We see substantial differences between the biologically optimal rotation, the reduced rotation in common usage and the financially optimal rotation which maximises net present value and find that the results are particularly sensitive to the choice of management and methodological assumptions. Specifically, we find that better site productivity and thin versus no-thin options result in shorter rotations across all optimisations, reinforcing the usefulness of this type of financial modelling approach. This information is critical for future policy design to further incentivise afforestation of agricultural land.
Heritability in the Efficiency of Nonsense-Mediated mRNA Decay in Humans
Cathal Seoighe,Chris Gehring
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0011657
Abstract: In eukaryotes mRNA transcripts of protein-coding genes in which an intron has been retained in the coding region normally result in premature stop codons and are therefore degraded through the nonsense-mediated mRNA decay (NMD) pathway. There is evidence in the form of selective pressure for in-frame stop codons in introns and a depletion of length three introns that this is an important and conserved quality-control mechanism. Yet recent reports have revealed that the efficiency of NMD varies across tissues and between individuals, with important clinical consequences.
A flexible R package for nonnegative matrix factorization
Renaud Gaujoux, Cathal Seoighe
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-367
Abstract: Our objective is to provide the bioinformatics community with an open-source, easy-to-use and unified interface to standard NMF algorithms, as well as with a simple framework to help implement and test new NMF methods. For that purpose, we have developed a package for the R/BioConductor platform. The package ports public code to R, and is structured to enable users to easily modify and/or add algorithms. It includes a number of published NMF algorithms and initialization methods and facilitates the combination of these to produce new NMF strategies. Commonly used benchmark data and visualization methods are provided to help in the comparison and interpretation of the results.The NMF package helps realize the potential of Nonnegative Matrix Factorization, especially in bioinformatics, providing easy access to methods that have already yielded new insights in many applications. Documentation, source code and sample data are available from CRAN.The factorization of matrices representing complex multidimensional datasets is the basis of several commonly applied techniques for pattern recognition and unsupervised clustering. Similarly to principal components analysis (PCA) or independent component analysis (ICA), the objective of non-negative matrix factorization (NMF) is to explain the observed data using a limited number of basis components, which when combined together approximate the original data as accurately as possible. The distinguishing features of NMF are that both the matrix representing the basis components as well as the matrix of mixture coefficients are constrained to have non-negative entries, and that no orthogonality or independence constraints are imposed on the basis components. This leads to a simple and intuitive interpretation of the factors in NMF, and allows the basis components to overlap.Since its formal definition in [1,2], the NMF approach has been applied successfully in several fields including image and pattern recognition, signal process
Application of statistical process control to qualitative molecular diagnostic assays
Cathal P. O'Brien
Frontiers in Molecular Biosciences , 2014, DOI: 10.3389/fmolb.2014.00018
Abstract: Modern pathology laboratories and in particular high throughput laboratories such as clinical chemistry have developed a reliable system for statistical process control (SPC). Such a system is absent from the majority of molecular laboratories and where present is confined to quantitative assays. As the inability to apply SPC to an assay is an obvious disadvantage this study aimed to solve this problem by using a frequency estimate coupled with a confidence interval calculation to detect deviations from an expected mutation frequency. The results of this study demonstrate the strengths and weaknesses of this approach and highlight minimum sample number requirements. Notably, assays with low mutation frequencies and detection of small deviations from an expected value require greater sample numbers to mitigate a protracted time to detection. Modeled laboratory data was also used to highlight how this approach might be applied in a routine molecular laboratory. This article is the first to describe the application of SPC to qualitative laboratory data.
Prioritizing Software Inspection Results using Static Profiling
Cathal Boogerd,Leon Moonen
Computer Science , 2006,
Abstract: Static software checking tools are useful as an additional automated software inspection step that can easily be integrated in the development cycle and assist in creating secure, reliable and high quality code. However, an often quoted disadvantage of these tools is that they generate an overly large number of warnings, including many false positives due to the approximate analysis techniques. This information overload effectively limits their usefulness. In this paper we present ELAN, a technique that helps the user prioritize the information generated by a software inspection tool, based on a demand-driven computation of the likelihood that execution reaches the locations for which warnings are reported. This analysis is orthogonal to other prioritization techniques known from literature, such as severity levels and statistical analysis to reduce false positives. We evaluate feasibility of our technique using a number of case studies and assess the quality of our predictions by comparing them to actual values obtained by dynamic profiling.
Evidence for intron length conservation in a set of mammalian genes associated with embryonic development
Seoighe Cathal,Korir Paul K
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-s9-s16
Abstract: Background We carried out an analysis of intron length conservation across a diverse group of nineteen mammalian species. Motivated by recent research suggesting a role for time delays associated with intron transcription in gene expression oscillations required for early embryonic patterning, we searched for examples of genes that showed the most extreme conservation of total intron content in mammals. Results Gene sets annotated as being involved in pattern specification in the early embryo or containing the homeobox DNA-binding domain, were significantly enriched among genes with highly conserved intron content. We used ancestral sequences reconstructed with probabilistic models that account for insertion and deletion mutations to distinguish insertion and deletion events on lineages leading to human and mouse from their last common ancestor. Using a randomization procedure, we show that genes containing the homeobox domain show less change in intron content than expected, given the number of insertion and deletion events within their introns. Conclusions Our results suggest selection for gene expression precision or the existence of additional development-associated genes for which transcriptional delay is functionally significant.
Assessing the Geographic Representativity of Farm Accountancy Data
Stuart Green,Cathal O'Donoghue
ISPRS International Journal of Geo-Information , 2013, DOI: 10.3390/ijgi2010050
Abstract: The environment affects agriculture, via soils, weather, etc. and agriculture affects the environment locally at farm level and via its impact on climate change. Locating agriculture within its spatial environment is thus important for farmers and policy makers. Within the EU countries collect detailed farm data to understand the technical and financial performance of farms; the Farm Accountancy Data Network. However, knowledge of the spatial-environmental context of these farms is reported at gross scale. In this paper, Irish farm accounting data is geo-referenced using address matching to a national address database. An analysis of the geographic distribution of the survey farms, illustrated through a novel 2D ranked pair plot of the coordinates, compared to the national distribution of farms shows a trend in the location of survey farms that leads to a statistical difference in the climatic variables associated with the farm. The farms in the survey have significantly higher accumulated solar radiation values than the national average. As a result, the survey may not be representative spatially of the pattern of environment x farm system. This could have important considerations when using FADN data in modelling climate change impacts on agri-economic performance.
Integrative Analysis of mRNA Expression and Half-Life Data Reveals Trans-Acting Genetic Variants Associated with Increased Expression of Stable Transcripts
Thong T. Nguyen, Cathal Seoighe
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0079627
Abstract: Genetic variation in gene expression makes an important contribution to phenotypic variation and susceptibility to disease. Recently, a subset of cis-acting expression quantitative loci (eQTLs) has been found to result from polymorphisms that affect RNA stability. Here we carried out a search for trans-acting variants that influence RNA stability. We first demonstrate that differences in the activity of trans-acting factors that stabilize RNA can be detected by comparing the expression levels of long-lived (stable) and short-lived (unstable) transcripts in high-throughput gene expression experiments. Using gene expression microarray data generated from eight HapMap3 populations, we calculated the relative expression ranks of long-lived transcripts versus short-lived transcripts in each sample. Treating this as a quantitative trait, we applied genome-wide association and identified a single nucleotide polymorphism (SNP), rs6137010, on chromosome 20p13 with which it is strongly associated in two Asian populations (p = 4×10?10 in CHB – Han Chinese from Beijing; p = 1×10?4 in JPT – Japanese from Tokyo). This SNP is a cis-eQTL for SNRPB in CHB and JPT but not in the other six HapMap3 populations. SNRPB is a core component of the spliceosome, and has previously been shown to affect the expression of many RNA processing factors. We propose that a cis-eQTL of SNRPB may be directly responsible for inter-individual variation in relative expression of long-lived versus short-lived transcript in Asian populations. In support of this hypothesis, knockdown of SNRPB results in a significant reduction in the relative expression of long-lived versus short-lived transcripts. Samples with higher relative expression of long-lived transcripts also had higher relative expression of coding compared to non-coding RNA and of RNA from housekeeping compared to non-housekeeping genes, due to the lower decay rates of coding RNAs, particularly those that perform housekeeping functions, compared to non-coding RNAs.
Conserved Molecular Mechanisms Underlying Homeostasis of the Golgi Complex
Cathal Wilson,Antonella Ragnini-Wilson
International Journal of Cell Biology , 2010, DOI: 10.1155/2010/758230
Abstract: The Golgi complex performs a central function in the secretory pathway in the sorting and sequential processing of a large number of proteins destined for other endomembrane organelles, the plasma membrane, or secretion from the cell, in addition to lipid metabolism and signaling. The Golgi apparatus can be regarded as a self-organizing system that maintains a relatively stable morphofunctional organization in the face of an enormous flux of lipids and proteins. A large number of the molecular players that operate in these processes have been identified, their functions and interactions defined, but there is still debate about many aspects that regulate protein trafficking and, in particular, the maintenance of these highly dynamic structures and processes. Here, we consider how an evolutionarily conserved underlying mechanism based on retrograde trafficking that uses lipids, COPI, SNAREs, and tethers could maintain such a homeodynamic system. 1. Introduction Despite the ancient origin of the Golgi and the differences in its structure across species, there is a striking conservation of a number of molecular machineries and principles that appear to operate in intra-Golgi trafficking. We sought to use these observations as a starting point from which to discuss how the maintenance of Golgi structure might be intrinsically related with the conservation of the basic molecular machineries that regulate intra-Golgi trafficking. In most organisms the Golgi apparatus is composed of a series of flattened, membrane-bounded sacks (cisternae) arranged in a cis-to-trans fashion to form a stack. These stacks are laterally linked to form a ribbon-like membrane system in mammalian cells [1] but this ribbon-like structure does not link the Golgi stacks in plants and Drosophila [2, 3]. In the yeast Saccharomyces cerevisiae the Golgi compartments are not arranged as a stack at all but exist as separate scattered compartments in the cell [4, 5] while in some developmental stages of Drosophila no stacks are present [3]. Yet, the basic functions of the Golgi in transport and sorting appear to be conserved across species, so neither the stacked structure nor the ribbon can be considered as fundamental for the basic functions of the Golgi apparatus in transport and sorting of secretory cargo molecules. In addition, it is possible to argue that ER-to-Golgi transport and the COPII complex, which is required for cargo selection and packaging at the ER [6], is not part of the self-organizing system per se. Many, but not all, Golgi-associated proteins recycle through the ER and
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