University College Cork

About: University College Cork is a education organization based out in Cork, Ireland. It is known for research contribution in the topics: Population & Context (language use). The organization has 12056 authors who have published 28452 publications receiving 958414 citations. The organization is also known as: Coláiste na hOllscoile Corcaigh & National University of Ireland, Cork.

A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function

Abstract: Thyroid hormone is essential for normal metabolism and development, and overt abnormalities in thyroid function lead to common endocrine disorders affecting approximately 10% of individuals over their life span. In addition, even mild alterations in thyroid function are associated with weight changes, atrial fibrillation, osteoporosis, and psychiatric disorders. To identify novel variants underlying thyroid function, we performed a large meta-analysis of genome-wide association studies for serum levels of the highly heritable thyroid function markers TSH and FT4, in up to 26,420 and 17,520 euthyroid subjects, respectively. Here we report 26 independent associations, including several novel loci for TSH (PDE10A, VEGFA, IGFBP5, NFIA, SOX9, PRDM11, FGF7, INSR, ABO, MIR1179, NRG1, MBIP, ITPK1, SASH1, GLIS3) and FT4 (LHX3, FOXE1, AADAT, NETO1/FBXO15, LPCAT2/CAPNS2). Notably, only limited overlap was detected between TSH and FT4 associated signals, in spite of the feedback regulation of their circulating levels by the hypothalamic-pituitary-thyroid axis. Five of the reported loci (PDE8B, PDE10A, MAF/LOC440389, NETO1/FBXO15, and LPCAT2/CAPNS2) show strong gender-specific differences, which offer clues for the known sexual dimorphism in thyroid function and related pathologies. Importantly, the TSH-associated loci contribute not only to variation within the normal range, but also to TSH values outside the reference range, suggesting that they may be involved in thyroid dysfunction. Overall, our findings explain, respectively, 5.64% and 2.30% of total TSH and FT4 trait variance, and they improve the current knowledge of the regulation of hypothalamic-pituitary-thyroid axis function and the consequences of genetic variation for hypo- or hyperthyroidism.

Insights into the taxonomy, genetics and physiology of bifidobacteria.

Abstract: Despite the generally accepted importance of bifidobacteria as probiotic components of the human intestinal microflora and their use in health promoting foods, there is only limited information about their phylogenetic position, physiology and underlying genetics. In the last few years numerous molecular approaches have emerged for the identification and characterization of bifidobacterial strains. Their use, in conjunction with traditional culturing methods, has led to a polyphasic taxonomy which has significantly enhanced our knowledge of the role played by these bacteria in the human intestinal ecosystem. The recent adaptation of culture-independent molecular tools to the fingerprinting of intestinal and food communities offers an exciting opportunity for revealing a more detailed picture of the true complexity of these environments. Furthermore, the availability of bifidobacterial genome sequences has advanced knowledge on the genetics of bifidobacteria and the effects of their metabolic activities on the intestinal ecosystem. The release of a complete Bifidobacterium longum genome sequence and the recent initiative to sequence additional strains are expected to open up a new era of comparative genomics in bifidobacterial biology. Moreover, the use of genomotyping allows a global comparative analysis of gene content between different bifidobacterial isolates of a given species without the necessity of sequencing many strains. Genomotyping provides useful information about the degree of relatedness among various strains of Bifidobacterium species and consequently can be used in a polyphasic identification approach. This review will deal mainly with the molecular tools described for bifidobacterial identification and the first insights into the underlying genetics involved in bifidobacterial physiology as well as genome variability.

Fabrication of Nanopore Array Electrodes by Focused Ion Beam Milling

Abstract: Single nanopore electrodes and nanopore electrode arrays have been fabricated using a focused ion beam (FIB) method. High aspect ratio pores (∼150−400-nm diameter and 500-nm depth) were fabricated using direct-write local ion milling of a silicon nitride layer over a buried platinum electrode. This local milling results in formation of a recessed platinum electrode at the base of each nanopore. The electrochemical properties of these nanopore metal electrodes have been characterized by voltammetry. Steady-state voltammograms were obtained for a range of array sizes as well as for single nanopore electrodes. High-resolution scanning electron microscopy imaging of the arrays showed that the pores had truncated cone, rather than cylindrical, conformations. A mathematical model describing diffusion to an electrode located at the base of a truncated conical pore was developed and applied to the analysis of the electrode geometries. The results imply that diffusion to the pore mouth is the dominant mass transpo...

Observation of dually decoded regions of the human genome using ribosome profiling data

Abstract: The recently developed ribosome profiling technique (Ribo-Seq) allows mapping of the locations of translating ribosomes on mRNAs with subcodon precision. When ribosome protected fragments (RPFs) are aligned to mRNA, a characteristic triplet periodicity pattern is revealed. We utilized the triplet periodicity of RPFs to develop a computational method for detecting transitions between reading frames that occur during programmed ribosomal frameshifting or in dual coding regions where the same nucleotide sequence codes for multiple proteins in different reading frames. Application of this method to ribosome profiling data obtained for human cells allowed us to detect several human genes where the same genomic segment is translated in more than one reading frame (from different transcripts as well as from the same mRNA) and revealed the translation of hitherto unpredicted coding open reading frames.

Making sense of experience

Abstract: When this chapter appeared in the first edition of Funology in 2003, there was an emerging interest in user experience. However, the information processing theories and models of interaction that were used at the time lacked the concepts and vocabulary necessary to understand how to design for experience. So, in ‘Making Sense of Experience’ we offered a vocabulary and a set of concepts to be used by HCI researchers and designers interested in user experience. When we were invited to revise the chapter for Funology 2, we decided to leave it as originally published but to add an endnote reflecting how our ideas have developed since 2003. This ‘endnote’ features as the preface to this chapter, and to also our other chapter, The Enchantments of Technology.