8482892
Improving Sequence Alignments For Intrinsically Disordered Proteins
Here we analyze sequence alignments for intrinsically disordered proteins. For 55 disordered protein families we measure the performance of different scoring matrices and propose one adjusted to disordered regions. An iterative algorithm of realigning sequences and recalculating matrices is designed and tested. For each matrix we also test a wide range of gap penalties. Results show an improvement in the ability to detect and discriminate related disordered proteins whose average sequence identity with the other family members is below 50%.
12227821
DisProt: a database of protein disorder
UNLABELLED
The Database of Protein Disorder (DisProt) is a curated database that provides structure and function information about proteins that lack a fixed three-dimensional (3D) structure under putatively native conditions, either in their entirety or in part. Starting from the central premise that intrinsic disorder is an important structural class of protein and in order to meet the increasing interest thereof, DisProt is aimed at becoming a central repository of disorder-related information. For each disordered protein, the database includes the name of the protein, various aliases, accession codes, amino acid sequence, location of the disordered region(s), and methods used for structural (disorder) characterization. If applicable, most entries also list the biological function(s) of each disordered region, how each region of disorder is used for function, as well as provide links to PubMed abstracts and major protein databases.


AVAILABILITY
www.disprot.org
13531439
Combining Type Theory and Untyped Set Theory
We describe a dependent type theory with proof irrelevance. Within this framework, we give a representation of a form of Mac Lane set theory and discuss automated support for constructing proofs within this set theory. One of the novel aspects of the representation is that one is allowed to use any class (in the set theory) as a type (in the type theory). Such class types allow a natural way of representing partial functions (e.g., the first and second operators on the class of Kuratowski ordered pairs). We also discuss how automated search can be used to construct proofs. In particular, the first-order prover Vampire can be called to solve a challenge problem (the injective Cantor Theorem) which is notoriously difficult for higher-order automated provers.
31238264
The populated web: Browsing, searching and inhabiting the WWW using collaborative virtual environments
This paper presents new approaches for accessing the World Wide Web using multi-user three dimensional spaces, or collaborative virtual environments (CVEs.) The major sections of the paper deal with the aspects of browsing and navigating, searching, populating and displaying information within, and about the WWW. The methods described are illustrated with examples of working applications developed by the authors which together present an image of a possible future for Web access and collaboration based around the Web and its contents.
14987889
Optimal Camera Parameter Selection for State Estimation with Applications in Object Recognition
In this paper we introduce a formalism for optimal camera parameter selection for iterative state estimation. We consider a framework based on Shannon's information theory and select the camera parameters that maximize the mutual information, i.e. the information that the captured image conveys about the true state of the system. The technique explicitly takes into account the a priori probability governing the computation of the mutual information. Thus, a sequential decision process can be formed by treating the a posteriori probability at the current time step in the decision process as the a priori probability for the next time step. The convergence of the decision process can be proven. 
 
We demonstrate the benefits of our approach using an active object recognition scenario. The results show that the sequential decision process outperforms a random strategy, both in the sense of recognition rate and number of views necessary to return a decision.
16390848
A Fully Projective Formulation to Improve the Accuracy of Lowe's Pose-Estimation Algorithm
Both the original version of David Lowe's influential and classic algorithm for tracking known objects and a reformulation of it implemented by Ishiiet al. rely on (different) approximated imaging models. Removing their simplifying assumptions yields a fully projective solution with significantly improved accuracy and convergence, and arguably better computation-time properties.
529377
Encoding Functional Relations in Scunak
We describe how a set-theoretic foundation for mathematics can be encoded in the new system Scunak. We then discuss an encoding of the construction of functions as functional relations in untyped set theory. Using the dependent type theory of Scunak, we can define object level application and lambda abstraction operators (in the spirit of higher-order abstract syntax) mediating between functions in the (meta-level) type theory and (object-level) functional relations. The encoding has also been exported to Automath and Twelf.