Automatic document classification of biological literature

Background: Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature. Results: We present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. Conclusions: We have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept

Oral Noetic and the Communicative Rubric in Beowulf .

Theoretically, this treatise is a study at the nexus of two fields: oral tradition and the philosophy of language. In application, it is a reading of the Anglo-Saxon epic narrative of Beowulf. It proceeds from the hypothesis that in its present, performative moment, the oral traditional narrative instantiates a moment of communicative meaning evincing characteristics of oral, thus speakerly, and thus intention-vitalized meaning, as defined by linguistic philosophers Austin, Grice, Searle, Schiffer, Strawson, and others. In the light of this theoretical perspective, the oral noetic and thus the communicative moment of the Beowulf poem is sought in its most dynamic and most illocutionary sense. In pursuit of these ends, the first chapter reviews the directions and conclusions of the highly contested question regarding the oral or written composition of Beowulf. The second chapter reviews the characteristics of orality as noetic, as articulated primarily by oral traditional theorists Walter Ong and Albert Lord, and develops further evidence of their voice in Beowulf. The third chapter reviews a number of the characteristics of language use and speaker meaning, as articulated primarily by linguistic philosophers J. L. Austin and H. P. Grice, expands upon them in consideration of the characteristics of oral poetry, and examines evidence of characteristics of oral communicative language in oral poetry. The fourth chapter, then, suggests a reading of the Beowulf poem through the paradigm of communicative meaning which grows out of the nexus of these two theoretical perspectives. Implicit in this discussion are several theoretical propositions, among which are these. First, language works. Second, the importance of the forms of orality is that they are the means through which oral peoples think and communicate, through which, in short, orality works. Third, the writing of an oral opus does not in itself or necessarily erase its oral working, its communicative force. Fourth, the reading of an oral work entails first and foremost the search for the ways in which its language works

The flavivirus NS1 protein: molecular and structural biology, immunology, role in pathogenesis and application as a diagnostic biomarker

The flavivirus nonstructural glycoprotein NS1 is an enigmatic protein whose structure and mechanistic function have remained somewhat elusive ever since it was first reported in 1970 as a viral antigen circulating in the sera of dengue-infected patients. All flavivirus NS1 genes share a high degree of homology, encoding a 352-amino-acid polypeptide that has a molecular weight of 46-55. kDa, depending on its glycosylation status. NS1 exists in multiple oligomeric forms and is found in different cellular locations: a cell membrane-bound form in association with virus-induced intracellular vesicular compartments, on the cell surface and as a soluble secreted hexameric lipoparticle. Intracellular NS1 co-localizes with dsRNA and other components of the viral replication complex and plays an essential cofactor role in replication. Although this makes NS1 an ideal target for inhibitor design, the precise nature of its cofactor function has yet to be elucidated. A plethora of potential interacting partners have been identified, particularly for the secreted form of NS1, with many being implicated in immune evasion strategies. Secreted and cell-surface-associated NS1 are highly immunogenic and both the proteins themselves and the antibodies they elicit have been implicated in the seemingly contradictory roles of protection and pathogenesis in the infected host. Finally, NS1 is also an important biomarker for early diagnosis of disease. In this article, we provide an overview of these somewhat disparate areas of research, drawing together the wealth of data generated over more than 40. years of study of this fascinating protein

Proposal for a Standardization of Mathematical Function Implementation in Floating-Point Arithmetic

Some aspects of what a standard for the implementation of the mathematical functions could be are presented. Firstly, the need for such a standard is motivated. Then the proposed standard is given. The question of roundings constitutes an important part of this paper: three levels are proposed, ranging from a level relatively easy to attain (with fixed maximal relative error) up to the best quality one, with correct rounding on the whole domain of every function. We do not claim that we always suggest the right choices, or that we have thought about all relevant issues. The mere goal of this paper is to raise questions and to launch the discussion towards a standard

A stabilized subunit vaccine for ebola virus

The ongoing Ebola epidemic in West Africa has claimed over eleven thousand lives and has highlighted our unpreparedness to counter emerging viral epidemics. While two recombinant vaccines have shown promising results in clinical trials, we have developed an alternate subunit vaccine candidate that could be called upon in the event that problems are encountered with regard to safety or protection efficacy. Our subunit vaccine candidate is based on a soluble version of the recombinant Ebola glycoprotein (GP) stabilized in its pre-fusion conformation. This protein is recognized by the neutralizing monoclonal antibody KZ52 and all three ZMapp antibodies (currently employed as a therapeutic for clinical treatment), indicating both GP1/2 and glycan cap domains are available and are presented in the desired conformation. Immunization via NanopatchTM (NP) microneedle delivery and intradermal injection were compared in C57 black mice. We assessed the antibody response elicited in immunized mice against Ebola virus (Zaire strain) using facilities at CSIRO’s Australian Animal Health Laboratories in Geelong (AAHL). Promising plaque reduction neutralization titers (PRNT50 = 1/80 sera dilution) were demonstrated. Furthermore, we have shown this vaccine is thermostable, retaining significant antigenicity after extended incubation at 37°C, indicating this vaccine strategy may not require cold chain delivery. In addition, the absence of any replicative elements ensures that it is likely to have a safer profile than live recombinant vaccines

Clinical and cost effectiveness of booklet based vestibular rehabilitation for chronic dizziness in primary care: single blind, parallel group, pragmatic, randomised controlled trial

Objective To determine the clinical and cost effectiveness of booklet based vestibular rehabilitation with and without telephone support for chronic dizziness, compared with routine care

Data Processing For Atomic Resolution EELS

The high beam current and sub-angstrom resolution of aberration-corrected scanning transmission electron microscopes has enabled electron energy loss spectroscopic (EELS) mapping with atomic resolution. These spectral maps are often dose-limited and spatially oversampled, leading to low counts/channel and are thus highly sensitive to errors in background estimation. However, by taking advantage of redundancy in the dataset map one can improve background estimation and increase chemical sensitivity. We consider two such approaches- linear combination of power laws and local background averaging-that reduce background error and improve signal extraction. Principal components analysis (PCA) can also be used to analyze spectrum images, but the poor peak-to-background ratio in EELS can lead to serious artifacts if raw EELS data is PCA filtered. We identify common artifacts and discuss alternative approaches. These algorithms are implemented within the Cornell Spectrum Imager, an open source software package for spectroscopic analysis