TY - JOUR A1 - Datta, Suparno A1 - Sachs, Jan Philipp A1 - Freitas da Cruz, Harry A1 - Martensen, Tom A1 - Bode, Philipp A1 - Morassi Sasso, Ariane A1 - Glicksberg, Benjamin S. A1 - Böttinger, Erwin T1 - FIBER BT - enabling flexible retrieval of electronic health records data for clinical predictive modeling JF - JAMIA open N2 - Objectives: The development of clinical predictive models hinges upon the availability of comprehensive clinical data. Tapping into such resources requires considerable effort from clinicians, data scientists, and engineers. Specifically, these efforts are focused on data extraction and preprocessing steps required prior to modeling, including complex database queries. A handful of software libraries exist that can reduce this complexity by building upon data standards. However, a gap remains concerning electronic health records (EHRs) stored in star schema clinical data warehouses, an approach often adopted in practice. In this article, we introduce the FlexIBle EHR Retrieval (FIBER) tool: a Python library built on top of a star schema (i2b2) clinical data warehouse that enables flexible generation of modeling-ready cohorts as data frames. Materials and Methods: FIBER was developed on top of a large-scale star schema EHR database which contains data from 8 million patients and over 120 million encounters. To illustrate FIBER's capabilities, we present its application by building a heart surgery patient cohort with subsequent prediction of acute kidney injury (AKI) with various machine learning models. Results: Using FIBER, we were able to build the heart surgery cohort (n = 12 061), identify the patients that developed AKI (n = 1005), and automatically extract relevant features (n = 774). Finally, we trained machine learning models that achieved area under the curve values of up to 0.77 for this exemplary use case. Conclusion: FIBER is an open-source Python library developed for extracting information from star schema clinical data warehouses and reduces time-to-modeling, helping to streamline the clinical modeling process. KW - databases KW - factual KW - electronic health records KW - information storage and KW - retrieval KW - workflow KW - software/instrumentation Y1 - 2021 U6 - https://doi.org/10.1093/jamiaopen/ooab048 SN - 2574-2531 VL - 4 IS - 3 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Avetisyan, Serine A1 - Lago, Sol A1 - Vasishth, Shravan T1 - Does case marking affect agreement attraction in comprehension? JF - Journal of memory and language N2 - Previous studies have suggested that distinctive case marking on noun phrases reduces attraction effects in production, i.e., the tendency to produce a verb that agrees with a nonsubject noun. An important open question is whether attraction effects are modulated by case information in sentence comprehension. To address this question, we conducted three attraction experiments in Armenian, a language with a rich and productive case system. The experiments showed clear attraction effects, and they also revealed an overall role of case marking such that participants showed faster response and reading times when the nouns in the sentence had different case. However, we found little indication that distinctive case marking modulated attraction effects. We present a theoretical proposal of how case and number information may be used differentially during agreement licensing in comprehension. More generally, this work sheds light on the nature of the retrieval cues deployed when completing morphosyntactic dependencies. KW - subject-verb agreement KW - attraction KW - Case KW - Eastern Armenian KW - cue-based KW - retrieval KW - comprehension Y1 - 2020 U6 - https://doi.org/10.1016/j.jml.2020.104087 SN - 0749-596X SN - 1096-0821 VL - 112 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Fyndanis, Valantis A1 - Arcara, Giorgio A1 - Capasso, Rita A1 - Christidou, Paraskevi A1 - De Pellegrin, Serena A1 - Gandolfi, Marialuisa A1 - Messinis, Lambros A1 - Panagea, Evgenia A1 - Papathanasopoulos, Panagiotis A1 - Smania, Nicola A1 - Semenza, Carlo A1 - Miceli, Gabriele T1 - Time reference in nonfluent and fluent aphasia BT - a cross-linguistic test of the PAst Discourse Linking Hypothesis JF - Clinical linguistics & phonetics N2 - Recent studies by Bastiaanse and colleagues found that time reference is selectively impaired in people with nonfluent agrammatic aphasia, with reference to the past being more difficult to process than reference to the present or to the future. To account for this dissociation, they formulated the PAst DIscourse LInking Hypothesis (PADILIH), which posits that past reference is more demanding than present/future reference because it involves discourse linking. There is some evidence that this hypothesis can be applied to people with fluent aphasia as well. However, the existing evidence for the PADILIH is contradictory, and most of it has been provided by employing a test that predominantly taps retrieval processes, leaving largely unexplored the underlying ability to encode time reference-related prephonological features. Within a cross-linguistic approach, this study tests the PADILIH by means of a sentence completion task that 'equally' taps encoding and retrieval abilities. This study also investigates if the PADILIH’s scope can be extended to fluent aphasia. Greek- and Italian-speaking individuals with aphasia participated in the study. The Greek group consisted of both individuals with nonfluent agrammatic aphasia and individuals with fluent aphasia, who also presented signs of agrammatism. The Italian group consisted of individuals with agrammatic nonfluent aphasia only. The two Greek subgroups performed similarly. Neither language group of participants with aphasia exhibited a pattern of performance consistent with the predictions of the PADILIH. However, a double dissociation observed within the Greek group suggests a hypothesis that may reconcile the present results with the PADILIH. KW - Time reference KW - past reference KW - future reference KW - encoding KW - retrieval Y1 - 2018 U6 - https://doi.org/10.1080/02699206.2018.1445291 SN - 0269-9206 SN - 1464-5076 VL - 32 IS - 9 SP - 823 EP - 843 PB - Taylor & Francis Group CY - Philadelphia ER - TY - JOUR A1 - Weymar, Mathias A1 - Bradley, Margaret M. A1 - Sege, Christopher T. A1 - Lang, Peter J. T1 - Neural activation and memory for natural scenes BT - explicit and spontaneous retrieval JF - Psychophysiology : journal of the Society for Psychophysiological Research N2 - Stimulus repetition elicits either enhancement or suppression in neural activity, and a recent fMRI meta-analysis of repetition effects for visual stimuli (Kim, 2017) reported cross-stimulus repetition enhancement in medial and lateral parietal cortex, as well as regions of prefrontal, temporal, and posterior cingulate cortex. Repetition enhancement was assessed here for repeated and novel scenes presented in the context of either an explicit episodic recognition task or an implicit judgment task, in order to study the role of spontaneous retrieval of episodic memories. Regardless of whether episodic memory was explicitly probed or not, repetition enhancement was found in medial posterior parietal (precuneus/cuneus), lateral parietal cortex (angular gyrus), as well as in medial prefrontal cortex (frontopolar), which did not differ by task. Enhancement effects in the posterior cingulate cortex were significantly larger during explicit compared to implicit task, primarily due to a lack of functional activity for new scenes. Taken together, the data are consistent with an interpretation that medial and (ventral) lateral parietal cortex are associated with spontaneous episodic retrieval, whereas posterior cingulate cortical regions may reflect task or decision processes. KW - fMRI KW - posterior parietal KW - repetition KW - retrieval KW - spontaneous memory Y1 - 2018 U6 - https://doi.org/10.1111/psyp.13197 SN - 0048-5772 SN - 1469-8986 VL - 55 IS - 10 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Paape, Dario L. J. F. T1 - Filling the Silence: Reactivation, not Reconstruction JF - Frontiers in psychology N2 - In a self-paced reading experiment, we investigated the processing of sluicing constructions ("sluices") whose antecedent contained a known garden path structure in German. Results showed decreased processing times for sluices with garden-path antecedents as well as a disadvantage for antecedents with non-canonical word order downstream from the ellipsis site. A post-hoc analysis showed the garden-path advantage also to be present in the region right before the ellipsis site. While no existing account of ellipsis processing explicitly predicted the results, we argue that they are best captured by combining a local antecedent mismatch effect with memory trace reactivation through reanalysis. KW - ellipsis processing KW - garden-path effect KW - German KW - retrieval KW - reconstruction KW - self-paced reading Y1 - 2016 U6 - https://doi.org/10.3389/fpsyg.2016.00027 SN - 1664-1078 VL - 7 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Hofmeister, Philip A1 - Vasishth, Shravan T1 - Distinctiveness and encoding effects in online sentence comprehension JF - Frontiers in psychology N2 - In explicit memory recall and recognition tasks, elaboration and contextual isolation both facilitate memory performance. Here, we investigate these effects in the context of sentence processing: targets for retrieval during online sentence processing of English object relative clause constructions differ in the amount of elaboration associated with the target noun phrase, or the homogeneity of superficial features (text color). Experiment 1 shows that greater elaboration for targets during the encoding phase reduces reading times at retrieval sites, but elaboration of non-targets has considerably weaker effects. Experiment 2 illustrates that processing isolated superficial features of target noun phrases-here, a green word in a sentence with words colored white-does not lead to enhanced memory performance, despite triggering longer encoding times. These results are interpreted in the light of the memory models of Nairne, 1990, 2001, 2006, which state that encoding remnants contribute to the set of retrieval cues that provide the basis for similarity-based interference effects. KW - encoding KW - retrieval KW - similarity KW - distinctiveness KW - sentence processing Y1 - 2014 U6 - https://doi.org/10.3389/fpsyg.2014.01237 SN - 1664-1078 VL - 5 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Paape, Dario L. J. F. T1 - Filling the Silence BT - Reactivation, not Reconstruction JF - Frontiers in psychology N2 - In a self-paced reading experiment, we investigated the processing of sluicing constructions (“sluices”) whose antecedent contained a known garden-path structure in German. Results showed decreased processing times for sluices with garden-path antecedents as well as a disadvantage for antecedents with non-canonical word order downstream from the ellipsis site. A post-hoc analysis showed the garden-path advantage also to be present in the region right before the ellipsis site. While no existing account of ellipsis processing explicitly predicted the results, we argue that they are best captured by combining a local antecedent mismatch effect with memory trace reactivation through reanalysis. KW - ellipsis processing KW - garden-path effect KW - German KW - retrieval KW - reconstruction KW - self-paced reading Y1 - 2016 U6 - https://doi.org/10.3389/fpsyg.2016.00027 SN - 1664-1078 VL - 7 SP - 1 EP - 18 PB - Frontiers Research Foundation CY - Lausanne ER -