Christina S. Kim

Integration of Cardiac Proteome Biology and Medicine by a Specialized Knowledgebase

Rationale: Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts. Objective: The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine. Methods and Results: We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10 924 proteins in human myocardium. In addition, the Java-coded bioinformatics tools provided by COPaKB enable cardiovascular investigators in all disciplines to retrieve and analyze pertinent organellar protein properties of interest. Conclusions: COPaKB provides an innovative and interactive resource that connects research interests with the new biological discoveries in protein sciences. With an array of intuitive tools in this unified Web server, nonproteomics investigators can conveniently collaborate with proteomics specialists to dissect the molecular signatures of cardiovascular phenotypes.

Context-driven expectations about focus alternatives.

What is conveyed by a sentence frequently depends not only on the descriptive content carried by its words, but also on implicit alternatives determined by the context of use. Four visual world eye-tracking experiments examined how alternatives are generated based on aspects of the discourse context and used in interpreting sentences containing the focus operators only and also. Experiment 1 builds on previous reading time studies showing that the interpretations of only sentences are constrained by alternatives explicitly mentioned in the preceding discourse, providing fine-grained time course information about the expectations triggered by only. Experiments 2 and 3 show that, in the absence of explicitly mentioned alternatives, lexical and situation-based categories evoked by the context are possible sources of alternatives. While Experiments 1-3 all demonstrate the discourse dependence of alternatives, only explicit mention triggered expectations about alternatives that were specific to sentences with only. By comparing only with also, Experiment 4 begins to disentangle expectations linked to the meanings of specific operators from those generalizable to the class of focus-sensitive operators. Together, these findings show that the interpretation of sentences with focus operators draws on both dedicated mechanisms for introducing alternatives into the discourse context and general mechanisms associated with discourse processing.

Syntactic Priming without Lexical Overlap in Reading Comprehension

Syntactic priming without lexical overlap is well-documented in language production. In contrast, reading-time comprehension studies, which typically use locally ambiguous sentences, generally find syntactic priming only with lexical overlap. This asymmetry has led some researchers to propose that distinct mechanisms underlie the comprehension and production of syntactic structure. Instead, we propose that methodological differences in how priming is assessed are largely responsible for the asymmetry: in comprehension, lexical biases in a locally ambiguous target sentence may overwhelm the influence of syntactic priming effects on a reader’s interpretation. We addressed these issues in a self-paced reading study by (1) using target sentences containing global attachment ambiguities, (2) examining a syntactic structure which does not involve an argument of the verb, and (3) factoring out the unavoidable lexical biases associated with the target sentences in a mixed-effects regression model. Under these conditions, syntactic priming affected how ambiguous sentences were parsed, and facilitated reading times when target sentences were parsed using the primed structure. This resolves discrepancies among previous findings, and suggests that the same mechanism underlies syntactic priming in comprehension and production.

Presupposition Satisfaction, Locality and Discourse Constituency

The current study investigates presupposition-satisfying dependencies from the point of view of discourse processing. Using the presupposition trigger also as a case study, I ask to what extent the distance spanned by the trigger and the prior discourse content that satisfies the presupposition of also influences comprehenders’ interpretation of the discourse—specifically, whether comprehenders have a bias toward satisfying presuppositions using material in the discourse that is closer rather than more distant.