Apellicon: a web-based tool for constructing and curating Textpresso databases.

As more research literature in the biological sciences is made available in electronic format, text mining systems are increasingly being used to improve the ability of investigators to retrieve relevant information. Through the use of advanced indexing techniques that utilize biological ontologies, semantic databases, and other formal representations of biological concepts text mining systems have been able to effectively parse biological literature. While text mining systems are increasingly effective at creating the linkages required to provide context-specific search results, the systems themselves are difficult to set up and use by novice computer users due to the highly technical nature of the applications. Because most researchers in the biological sciences do not have a strong computer science background we have focused on improving the quality of existing, proven text mining systems by implementing a web-based GUI that greatly improves the workflow of these systems. Textpresso in particular has an excellent web-based interface for searching literature but does not have an easy to use administrative interface. We developed the Apellicon interface to enable a wide range of users to build and manage a Textpresso database. An important feature of Apellicon is that it can enable groups to collaborate in building a Textpresso database

Matrix Stiffness Regulates Glial Cell Morphology and Differentiation

Studies from our laboratory have shown that inhibition of non-muscle myosin II (NMII) activity has opposite effects on the formation of myelin by oligodendrocytes (OL), the myelinating glia of the central nervous system (CNS) and Schwann cells (SC), which perform the same function in the peripheral nervous system (PNS). The decrease of NMII activity in SC impairs their ability to establish polarity and myelinate, while its inhibition in OL enhances process branching and increases the amount of myelin formed in vitro an in vivo. A growing number of studies have shown that NMII also plays a role in the ability of cells to sense and respond to the stiffness of the surrounding extracellular matrix (ECM). In the PNS, the ECM consists of a dense SC-secreted basal lamina, which displays significantly higher rigidity than the more loosely organized CNS matrix. In order to evaluate whether the opposing effects of inhibiting NMII in glial cell differentiation and myelination are partly the result of NMII-mediated sensing of ECM stiffness, we have grown cultures of primary rat OL and SC on variable rigidity polyacrylamide matrices coated with covalently bound ECM proteins. We found that stiffer matrices inhibit OL branching as well as their expression of differentiation markers, and that these effects are correlated with increased NMII activity. SC also respond to changes in ECM stiffness, and those grown on rigid matrices adopt a more polygonal morphology with fewer actin-based protrusions than those grown on soft matrices. Interestingly, and unlike what we have observed in the OL, stimulation of SC differentiation after cAMP treatment is not affected by differences in matrix stiffness alone. However, SC differentiation is potentiated on rigid matrices at high laminin concentration, which are conditions that mimic a mature basal lamina. Taken together, our data indicate that myelinating glial cell differentiation is sensitive to changes in the mechanical properties of the ECM and that in the case of SC, these responses may be modulated by the maturity and composition of their basal lamina

Differential forms on vector bundles

Abstract A bigraded algebra of polynomial forms on a vector bundle is introduced and a bidegree to each multivector-valued form is assigned. Numerous examples of polynomial forms appearing in various constructions in differential geometry are given. The Poincare lemma for polynomial forms is proved

Socratic Proofs for Propositional Linear-Time Logic

This paper presents a calculus of Socratic proofs for Propositional Linear-Time Logic (PLTL) and discusses potential automation of its proof search

Specification and verification of reconfiguration protocols in grid component systems

In this work we present an approach for the formal specification and verification of the reconfiguration protocols in Grid component systems. We consider Fractal, a modular and extensible component model. As a specification tool we invoke a specific temporal language, separated clausal normal form, which has been shown to be capable of expressing any ECTL+ expression thus, we are able to express the complex fairness properties of a component system. The structure of the normal enables us to directly apply the deductive verification technique, temporal resolution defined in the framework of branching-time temporal logic