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Thilde Terkelsen, Vilde D Haakensen, Radka Saldova, Pavel Gromov, Merete Kjaer Hansen, Henning Stöckmann, Ole Christian Lingjaerde, Anne-Lise Børresen-Dale, Elena Papaleo, Åslaug Helland, Pauline M Rudd, Irina Gromova
Particular N-glycan structures are known to be associated with breast malignancies by coordinating various regulatory events within the tumor and corresponding microenvironment, thus implying that N-glycan patterns may be used for cancer stratification and as predictive or prognostic biomarkers. However, the association between N-glycans secreted by breast tumor and corresponding clinical relevance remain to be elucidated. We profiled N-glycans by HILIC UPLC across a discovery dataset composed of tumor interstitial fluids (TIF, n=85), paired normal interstitial fluids (NIF, n=54) and serum samples (n=28) followed by independent evaluation, with the ultimate goal of identifying tumor-related N-glycan patterns in blood of breast cancer patients...
April 26, 2018: Molecular Oncology
K Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-Young Choi, Michael Bada, William A Baumgartner, Natalya Panteleyeva, Karin Verspoor, Martha Palmer, Lawrence E Hunter
BACKGROUND: Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction from the scientific literature. In order to better understand the nature of the phenomenon of coreference in biomedical publications and to increase performance on the task, we annotated the Colorado Richly Annotated Full Text (CRAFT) corpus with coreference relations. RESULTS: The corpus was manually annotated with coreference relations, including identity and appositives for all coreferring base noun phrases...
August 17, 2017: BMC Bioinformatics
Ian Cunnings, Clare Patterson, Claudia Felser
A number of recent studies have investigated how syntactic and non-syntactic constraints combine to cue memory retrieval during anaphora resolution. In this paper we investigate how syntactic constraints and gender congruence interact to guide memory retrieval during the resolution of subject pronouns. Subject pronouns are always technically ambiguous, and the application of syntactic constraints on their interpretation depends on properties of the antecedent that is to be retrieved. While pronouns can freely corefer with non-quantified referential antecedents, linking a pronoun to a quantified antecedent is only possible in certain syntactic configurations via variable binding...
2015: Frontiers in Psychology
Koichi Suehiro, Katsuaki Tanaka, Mika Mikawa, Yuriko Uchihara, Taiki Matsuyama, Tadashi Matsuura, Tomoharu Funao, Tokuhiro Yamada, Takashi Mori, Kiyonobu Nishikawa
OBJECTIVES: The aims of this study were to compare cardiac output (CO) measured by the new fourth-generation FloTrac™/Vigileo™ system (Version 4.00) (COFVS) with that measured by a pulmonary artery catheter (COREF), and to investigate the ability of COFVS to track CO changes induced by increased peripheral resistance. DESIGN: Prospective study. SETTING: University Hospital. PARTICIPANTS: Twenty-three patients undergoing cardiac surgery...
2015: Journal of Cardiothoracic and Vascular Anesthesia
Yi Ting Huang, Joseph Hopfinger, Peter C Gordon
Two experiments examine the links between neural patterns in EEG (e.g., N400s, P600s) and their corresponding cognitive processes (e.g., lexical access, discourse integration) by varying the lexical and syntactic contexts of co-referential expressions. Experiment 1 examined coreferring expressions when they occurred within the same clause as their antecedents (John/Bill warmly dressed John). Experiment 2 examined between-clause co-referencing with expressions that also varied in lexical frequency (John/Weston went to the store so that John/Weston could buy milk)...
February 2014: Memory & Cognition
K Bendjelid, G Marx, N Kiefer, T P Simon, M Geisen, A Hoeft, N Siegenthaler, C K Hofer
BACKGROUND: A new calibrated pulse wave analysis method (VolumeView™/EV1000™, Edwards Lifesciences, Irvine, CA, USA) has been developed to continuously monitor cardiac output (CO). The aim of this study was to compare the performance of the VolumeView method, and of the PiCCO2™ pulse contour method (Pulsion Medical Systems, Munich, Germany), with reference transpulmonary thermodilution (TPTD) CO measurements. METHODS: This was a prospective, multicentre observational study performed in the surgical and interdisciplinary intensive care units of four tertiary hospitals...
October 2013: British Journal of Anaesthesia
Kazunori Uemura, Toru Kawada, Masashi Inagaki, Masaru Sugimachi
BACKGROUND: In managing patients with unstable hemodynamics, monitoring cardiac output (CO) can provide critical diagnostic data. However, conventional CO measurements are invasive, intermittent, and/or inaccurate. The purpose of this study was to validate our newly developed CO monitoring system. METHODS: This system automatically determines peak velocity of the ascending aortic flow using continuous-wave Doppler transthoracic echocardiography and estimates cardiac ejection time and aortic cross-sectional area using the pulse contour of the radial arterial pressure...
May 2013: Anesthesia and Analgesia
Ngan Nguyen, Jin-Dong Kim, Makoto Miwa, Takuya Matsuzaki, Junichi Tsujii
BACKGROUND: Current research has shown that major difficulties in event extraction for the biomedical domain are traceable to coreference. Therefore, coreference resolution is believed to be useful for improving event extraction. To address coreference resolution in molecular biology literature, the Protein Coreference (COREF) task was arranged in the BioNLP Shared Task (BioNLP-ST, hereafter) 2011, as a supporting task. However, the shared task results indicated that transferring coreference resolution methods developed for other domains to the biological domain was not a straight-forward task, due to the domain differences in the coreference phenomena...
2012: BMC Bioinformatics
Makoto Miwa, Paul Thompson, Sophia Ananiadou
MOTIVATION: In recent years, several biomedical event extraction (EE) systems have been developed. However, the nature of the annotated training corpora, as well as the training process itself, can limit the performance levels of the trained EE systems. In particular, most event-annotated corpora do not deal adequately with coreference. This impacts on the trained systems' ability to recognize biomedical entities, thus affecting their performance in extracting events accurately. Additionally, the fact that most EE systems are trained on a single annotated corpus further restricts their coverage...
July 1, 2012: Bioinformatics
Maria H Ledran, Anna Krassowska, Lyle Armstrong, Ian Dimmick, Jonas Renström, Roland Lang, Sun Yung, Mauro Santibanez-Coref, Elaine Dzierzak, Miodrag Stojkovic, Robert A J Oostendorp, Lesley Forrester, Majlinda Lako
Hematopoietic stem cells derived from human embryonic stem cells (hESCs) could provide a therapeutic alternative to bone marrow transplants, but the efficiency of currently available derivation protocols is low. In this study, we investigated whether coculture with monolayers of cells derived from mouse AGM and fetal liver, or with stromal cell lines derived from these tissues, can enhance hESC hematopoietic differentiation. We found that under such conditions hESC-derived differentiating cells formed early hematopoietic progenitors, with a peak at day 18-21 of differentiation that corresponded to the highest CD34 expression...
July 3, 2008: Cell Stem Cell
Angela Heine, Sascha Tamm, Markus Hofmann, Rainer M Bösel, Arthur M Jacobs
A recent eye-tracking study reported a reverse effect of a noun's lexical frequency in the context of the resolution of coreferring pronouns. Investigating the neurophysiological basis of this effect, the present electroencephalographic study found differential patterns in theta activation when participants read pronouns referring to nouns of different frequency classes. Evoked theta power after pronoun onset increased with the frequency of the critical noun. This finding suggests differential load on memory resources depending on the nouns' frequency...
December 18, 2006: Neuroreport
C Christine Camblin, Kerry Ledoux, Megan Boudewyn, Peter C Gordon, Tamara Y Swaab
Previous research has shown that the process of establishing coreference with a repeated name can affect basic repetition priming. Specifically, repetition priming on some measures can be eliminated for repeated names that corefer with an entity that is prominent in the discourse model. However, the exact nature and timing of this modulating effect of discourse are not yet understood. Here, we present two ERP studies that further probe the nature of repeated name coreference by using naturally produced connected speech and fast-rate RSVP methods of presentation...
May 18, 2007: Brain Research
Tamara Y Swaab, C Christine Camblin, Peter C Gordon
Effects of word repetition are extremely robust, but can these effects be modulated by discourse context? We examined this in an ERP experiment that tested coreferential processing (when two expressions refer to the same person) with repeated names. ERPs were measured to repeated names and pronoun controls in two conditions: (1) In the prominent condition the repeated name or pronoun coreferred with the subject of the preceding sentence and was therefore prominent in the preceding discourse (e.g., "John went to the store after John/he...
June 2004: Journal of Cognitive Neuroscience
L P Shapiro, A Hestvik
We describe two experiments that explored the on-line processing of coordinated (e.g., The policemen defended himself and the fireman did [e] too, according to someone who was there) and subordinated VP-ellipsis (e.g., The policeman defended himself because the fireman did [e], according to someone who was there). Such constructions have two possible interpretations: The "sloppy" reading is that the fireman defended himself, where himself corefers with the fireman. The "strict" reading is that the fireman defended him, where him corefers with the policeman...
November 1995: Journal of Psycholinguistic Research
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