- Behavioral and Decision Sciences Program
- Biological Basis of Behavior Program
- Center for Italian Studies
- Cinema and Media Studies Program
- Classical Studies at Penn
- College of Arts and Sciences
- Department of Anthropology
- Department of Biology
- Department of Chemistry
- Department of Criminology
- Department of Earth and Environmental Science
- Department of East Asian Languages and Civilizations
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Publication Using Syntactic Information in Document Filtering: A Comparative Study of Part-of-Speech Tagging and Supertagging(1996-12-01) Chandrasekar, R.; Srinivas, B.Any coherent text contains significant latent information, such as syntactic structure and patterns of language use. This information can be exploited to overcome the inadequacies of keyword-based retrieval and make information retrieval more efficient. In this paper, we demonstrate quantitatively how syntactic information is useful in filtering out irrelevant documents. We also compare two different syntactic labelings-- simple Part-of-Speech (POS) labeling and Supertag labeling-- and show how the richer (more fine-grained) representation of supertags leads to more efficient and effective document filtering. We have implemented a system which exploits syntactic information in a flexible manner to filter documents. The system has been tested on a large collection of news sentences, and achieves an F-score of 89 for filtering out irrelevant sentences. Its performance and modularity makes it a promising postprocessing addition to any Information Retrieval system.Publication Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome(2012-11-01) Li, Fan; Vandivier, Lee E; Willmann, Matthew R; Chen, Ying; Gregory, Brian DThe secondary structure of an RNA molecule plays an integral role in its maturation, regulation, and function. However, the global influence of this feature on plant gene expression is still largely unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach in conjunction with transcriptome-wide sequencing of rRNA-depleted (RNA sequencing), small RNA, and ribosome-bound RNA populations to investigate the impact of RNA secondary structure on gene expression regulation in Arabidopsis thaliana. From this analysis, we find that highly unpaired and paired RNAs are strongly correlated with euchromatic and heterochromatic epigenetic histone modifications, respectively, providing evidence that secondary structure is necessary for these RNA-mediated posttranscriptional regulatory pathways. Additionally, we uncover key structural patterns across protein-coding transcripts that indicate RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in this model plant. We further reveal that RNA folding is significantly anticorrelated with overall transcript abundance, which is often due to the increased propensity of highly structured mRNAs to be degraded and/or processed into small RNAs. Finally, we find that secondary structure affects mRNA translation, suggesting that this feature regulates plant gene expression at multiple levels. These findings provide a global assessment of RNA folding and its significant regulatory effects in a plant transcriptome.Publication Biological Oxygen Demand Optode Analysis of Coral Reef-Associated Microbial Communities Exposed to Algal Exudates(2013-07-16) Gregg, Allison K; Hatay, Mark; Haas, Andreas F; Robinett, Nathan L; Barott, Katie; Vermeij, Mark J.A; Marhaver, Kristen L; Meirelles, Pedro M; Thompson, Fabiano; Rohwer, ForestAlgae-derived dissolved organic matter has been hypothesized to induce mortality of reef building corals. One proposed killing mechanism is a zone of hypoxia created by rapidly growing microbes. To investigate this hypothesis, biological oxygen demand (BOD) optodes were used to quantify the change in oxygen concentrations of microbial communities following exposure to exudates generated by turf algae and crustose coralline algae (CCA). BOD optodes were embedded with microbial communities cultured from Montastraea annularis and Mussismilia hispida, and respiration was measured during exposure to turf and CCA exudates. The oxygen concentrations along the optodes were visualized with a low-cost Submersible Oxygen Optode Recorder (SOOpR) system. With this system we observed that exposure to exudates derived from turf algae stimulated higher oxygen drawdown by the coral-associated bacteria than CCA exudates or seawater controls. Furthermore, in both turf and CCA exudate treatments, all microbial communities (coral-, algae-associated and pelagic) contributed significantly to the observed oxygen drawdown. This suggests that the driving factor for elevated oxygen consumption rates is the source of exudates rather than the initially introduced microbial community. Our results demonstrate that exudates from turf algae may contribute to hypoxia-induced coral stress in two different coral genera as a result of increased biological oxygen demand of the local microbial community. Additionally, the SOOpR system developed here can be applied to measure the BOD of any culturable microbe or microbial community.Publication The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell(2017-02-20) Slabodnick, Mark M; Ruby, J. G; Reiff, Sarah B; Swart, Estienne C; Gosai, Sager J; Prabakaran, Sudhakaran; Witkowska, Ewa; Larue, Graham E; Gregory, Brian D; Nowacki, Mariusz; Derisi, Joseph; Roy, Scott W; Marshall, Wallace F; Sood, PranidhiThe giant, single-celled organism Stentor coeruleus has a long history as a model system for studying pattern formation and regeneration in single cells. Stentor [1, 2] is a heterotrichous ciliate distantly related to familiar ciliate models, such as Tetrahymena or Paramecium. The primary distinguishing feature of Stentor is its incredible size: a single cell is 1 mm long. Early developmental biologists, including T.H. Morgan [3], were attracted to the system because of its regenerative abilities—if large portions of a cell are surgically removed, the remnant reorganizes into a normal-looking but smaller cell with correct proportionality [2, 3]. These biologists were also drawn to Stentor because it exhibits a rich repertoire of behaviors, including light avoidance, mechanosensitive contraction, food selection, and even the ability to habituate to touch, a simple form of learning usually seen in higher organisms [4]. While early microsurgical approaches demonstrated a startling array of regenerative and morphogenetic processes in this single-celled organism, Stentor was never developed as a molecular model system. We report the sequencing of the Stentor coeruleus macronuclear genome and reveal key features of the genome. First, we find that Stentor uses the standard genetic code, suggesting that ciliate-specific genetic codes arose after Stentor branched from other ciliates. We also discover that ploidy correlates with Stentor’s cell size. Finally, in the Stentor genome, we discover the smallest spliceosomal introns reported for any species. The sequenced genome opens the door to molecular analysis of single-cell regeneration in Stentor.Publication On Relational Completeness of Multi-Modal Categories Logics(1998-09-01) Jäger, GerhardSeveral recent results show that the Lambek Calculus L and its close relative L1 is sound and complete under (possibly relativized) relational interpretation. The paper transfers these results to L◊, the multi-modal extension of the Lambek Calculus that was proposed in Moortgat 1996. Two natural relational interpretations of L◊ are proposed and shown to be sound and complete. The completeness proofs make heavy use of the method of relational labeling from Kurtonina 1995. Finally, it is demonstrated that relational interpretation provides a semantic justification for the translation from L◊ to L from Versmissen 1996.Publication CoRAL: Predicting Non-Coding RNAs from Small RNA-Sequencing Data(2013-08-01) Leung, Yuk Y; Ryvkin, Paul; Ungar, Lyle H; Gregory, Brian D; Wang, Li-SanThe surprising observation that virtually the entire human genome is transcribed means we know little about the function of many emerging classes of RNAs, except their astounding diversities. Traditional RNA function prediction methods rely on sequence or alignment information, which are limited in their abilities to classify the various collections of non-coding RNAs (ncRNAs). To address this, we developed Classification of RNAs by Analysis of Length (CoRAL), a machine learning-based approach for classification of RNA molecules. CoRAL uses biologically interpretable features including fragment length and cleavage specificity to distinguish between different ncRNA populations. We evaluated CoRAL using genome-wide small RNA sequencing data sets from four human tissue types and were able to classify six different types of RNAs with ∼80% cross-validation accuracy. Analysis by CoRAL revealed that microRNAs, small nucleolar and transposon-derived RNAs are highly discernible and consistent across all human tissue types assessed, whereas long intergenic ncRNAs, small cytoplasmic RNAs and small nuclear RNAs show less consistent patterns. The ability to reliably annotate loci across tissue types demonstrates the potential of CoRAL to characterize ncRNAs using small RNA sequencing data in less well-characterized organisms.Publication Modal Logic Over Finite Structures(1995-10-01) Rosen, EricIn this paper, we develop various aspects of the finite model theory of propositional modal logic. In particular, we show that certain results about the expressive power of modal logic over the class of all structures, due to van Benthem and his collaborators, remain true over the class of finite structures. We establish that a first-order definable class of finite models is closed under bisimulations if it is definable by a `modal first-order sentence’. We show that a class of finite models that is defined by a modal sentence is closed under extensions if it is defined by a diamond-modal sentence. In sharp contrast, it is well known that many classical results for first-order logic, including various preservation theorems, fail for the class of finite models.Publication Immunolocalization of Proteins in Corals: The V-Type H+-ATPase Proton Pump(2015-09-05) Barott, Katie; Tresguerres, MartinHere we describe the immunolocalization of a membrane-bound proton pump, the V-type H+-ATPase (VHA), in tissues and isolated cells of scleractinian corals. Immunolocalization of coral proteins requires additional steps not required for various model organisms, such as decalcification of the coral skeleton for immunohistochemistry or removal of cells away from the skeleton for immunocytochemistry. The tissue and cell preparation techniques described here can be adapted for localization of other coral proteins, provided the appropriate validation steps have been taken for the primary antibodies and species of coral used. These techniques are important for improving our understanding of coral cell physiology.Publication The Anaphoric Parallel between Modality and Tense(1997-05-01) Stone, MatthewIn modal subordination, a modal sentence is interpreted relative to a hypothetical scenario introduced in an earlier sentence. In this paper, I argue that this phenomenon reflects the fact that the interpretation of modals is an ANAPHORIC process, precisely analogous to the anaphoric interpretation of tense. Modal morphemes introduce alternative scenarios as entities into the discourse model; their interpretation depends on evoking scenarios for described, reference and speech points, and relating them to one another. Although this account formalizes anaphoric connections using dynamic semantics, it invokes a novel and direct encoding of scenarios as ordinary, static objects (competing analyses take modal referents to be inherently dynamic objects, unlike the referents of pronouns and tenses). The result is a simpler proposal with better empirical coverage.Publication Some Novel Applications of Explanation-Based Learning to Parsing Lexicalized Tree-Adjoining Grammars(1995-05-01) Srinivas, B.; Joshi, Aravind KIn this paper we present some novel applications of Explanation-Based Learning (EBL) technique to parsing Lexicalized Tree-Adjoining grammars. The novel aspects are (a) immediate generalization of parses in the training set, (b) generalization over recursive structures and (c) representation of generalized parses as Finite State Transducers. A highly impoverished parser called a “stapler” has also been introduced. We present experimental results using EBL for different corpora and architectures to show the effectiveness of our approach.