Dublin City University

About: Dublin City University is a education organization based out in Dublin, Ireland. It is known for research contribution in the topics: Machine translation & Laser. The organization has 5904 authors who have published 17178 publications receiving 389376 citations. The organization is also known as: National Institute for Higher Education, Dublin & DCU.

Mechanisms of strontium uptake by laboratory and brewing strains of Saccharomyces cerevisiae.

Abstract: Laboratory and brewing strains of Saccharomyces cerevisiae were compared for metabolism-independent and -dependent Sr2+ uptake. Cell surface adsorption of Sr2+ to live cells was greater in the brewing than in the laboratory strain examined. However, uptake levels were greater in denatured (dried and ground) S. cerevisiae, and the relative affinities of Sr2+ for the two strains were reversed. Results for the brewing S. cerevisiae strain were similar whether the organism was obtained fresh from brewery waste or after culturing under the same conditions as for the laboratory strain. Reciprocal Langmuir plots of uptake data for live biomass were not linear, whereas those for denatured biomass were. The more complex Sr2+ binding mechanism inferred for live S. cerevisiae was underlined by cation displacement experiments. Sr2+ adsorption to live cells resulted in release of Mg2+, Ca2+, and H+, suggesting a combination of ionic and covalent bonding of Sr2+. In contrast, Mg2+ was the predominant exchangeable cation on denatured biomass, indicating primarily electrostatic attraction of Sr2+. Incubation of live S. cerevisiae in the presence of glucose resulted in a stimulation of Sr2+ uptake. Cell fractionation revealed that this increased Sr2+ uptake was mostly due to sequestration of Sr2+ in the vacuole, although a small increase in cytoplasmic Sr2+ was also evident. No stimulation or inhibition of active H+ efflux resulted from metabolism-dependent Sr2+ accumulation. However, a decline in cytoplasmic, and particularly vacuolar, Mg2+, in comparison with that of cells incubated with Sr2+ in the absence of glucose, was apparent. This was most marked for the laboratory S. cerevisiae strain, which contained higher Mg2+ levels than the brewing strain.

HER-2 signaling and inhibition in breast cancer.

Abstract: Amplification of the HER-2 gene occurs in approximately 25% of breast cancers, causing up-regulation of key signaling pathways which control cell growth and survival. In breast cancer patients, HER-2 overexpression correlates with an aggressive phenotype and poor prognosis. HER-2, therefore, has become the focus of many anti-cancer therapeutic approaches. Trastuzumab (Herceptin), a humanized monoclonal antibody directed against the extracellular domain of HER-2, was the first FDA-approved HER-2-targeted therapy for the treatment of metastatic breast cancer. However, not all HER-2-overexpressing patients respond to trastuzumab and most that initially respond develop resistance within one year of treatment. Trastuzumab resistance has been studied in cell line models of resistance and several mechanisms of resistance have been proposed. More recent anti-HER-2 strategies involve targeting its tyrosine kinase domain; for example, lapatinib (Tykerb) is a dual HER-2 and EGFR tyrosine kinase inhibitor and has shown efficacy as a single agent and in combination with other therapeutics. A number of novel HER-2 antagonists are currently in preclinical or clinical development, including both monoclonal antibodies and small molecule inhibitors. Increased understanding of HER-2 signaling in breast cancer, and of response and resistance to HER-2 antagonists, will aid the development of strategies to overcome resistance to HER-2 targeted therapies.

#hardtoparse: POS tagging and parsing the twitterverse

Abstract: We evaluate the statistical dependency parser, Malt, on a new dataset of sentences taken from tweets. We use a version of Malt which is trained on gold standard phrase structure Wall Street Journal (WSJ) trees converted to Stanford labelled dependencies. We observe a drastic drop in performance moving from our in-domain WSJ test set to the new Twitter dataset, much of which has to do with the propagation of part-of-speech tagging errors. Retraining Malt on dependency trees produced by a state-of-the-art phrase structure parser, which has itself been self-trained on Twitter material, results in a significant improvement. We analyse this improvement by examining in detail the effect of the retraining on individual dependency types.

Overexpression of the microRNA miR-433 promotes resistance to paclitaxel through the induction of cellular senescence in ovarian cancer cells.

Abstract: Annually, ovarian cancer (OC) affects 240,000 women worldwide and is the most lethal gynecological malignancy. High-grade serous OC (HGSOC) is the most common and aggressive OC subtype, characterized by widespread genome changes and chromosomal instability and is consequently poorly responsive to chemotherapy treatment. The objective of this study was to investigate the role of the microRNA miR-433 in the cellular response of OC cells to paclitaxel treatment. We show that stable miR-433 expression in A2780 OC cells results in the induction of cellular senescence demonstrated by morphological changes, downregulation of phosphorylated retinoblastoma (p-Rb), and an increase in β-galactosidase activity. Furthermore, in silico analysis identified four possible miR-433 target genes associated with cellular senescence: cyclin-dependent kinase 6 (CDK6), MAPK14, E2F3, and CDKN2A. Mechanistically, we demonstrate that downregulation of p-Rb is attributable to a miR-433-dependent downregulation of CDK6, establishing it as a novel miR-433 associated gene. Interestingly, we show that high miR-433 expressing cells release miR-433 into the growth media via exosomes which in turn can induce a senescence bystander effect. Furthermore, in relation to a chemotherapeutic response, quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed that only PEO1 and PEO4 OC cells with the highest miR-433 expression survive paclitaxel treatment. Our data highlight how the aberrant expression of miR-433 can adversely affect intracellular signaling to mediate chemoresistance in OC cells by driving cellular senescence.

Getting Gender Right in Neural Machine Translation

Abstract: Speakers of different languages must attend to and encode strikingly different aspects of the world in order to use their language correctly (Sapir, 1921; Slobin, 1996). One such difference is related to the way gender is expressed in a language. Saying “I am happy” in English, does not encode any additional knowledge of the speaker that uttered the sentence. However, many other languages do have grammatical gender systems and so such knowledge would be encoded. In order to correctly translate such a sentence into, say, French, the inherent gender information needs to be retained/recovered. The same sentence would become either “Je suis heureux”, for a male speaker or “Je suis heureuse” for a female one. Apart from morphological agreement, demographic factors (gender, age, etc.) also influence our use of language in terms of word choices or even on the level of syntactic constructions (Tannen, 1991; Pennebaker et al., 2003). We integrate gender information into NMT systems. Our contribution is twofold: (1) the compilation of large datasets with speaker information for 20 language pairs, and (2) a simple set of experiments that incorporate gender information into NMT for multiple language pairs. Our experiments show that adding a gender feature to an NMT system significantly improves the translation quality for some language pairs.