829668
Prediction of Boundaries Between Intrinsically Ordered and Disordered Protein Regions
Using proteins with both disordered and ordered regions collected through literature searches and database scanning, we assembled a set of 24-residue long segments centered on their order/disorder boundaries as well as a larger set of non-boundary segments consisting of either order or disorder. We analyzed position-specific amino acid compositions around the order/disorder boundaries and found more than thirty significant (p < 0.05) compositional differences between boundary and non-boundary data. From this analysis, we constructed several logistic regression predictors of order/disorder boundaries using slightly different data modeling approaches. Exact boundary prediction accuracies were estimated to be in the range from 74% to 80% for the different predictors.
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
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.
34334066
Haptics in augmented reality
An augmented reality system merges synthetic sensory information into a user's perception of a three-dimensional environment. An important performance goal for an augmented reality system is that the user perceives a single seamless environment. In most augmented reality systems the user views a real world augmented only with visual information and is not provided with a means to interact with the virtual objects. We describe an augmented reality system that, in addition to visual augmentation, merges synthetic haptic input into the user's perception of the real environment. Our system uses a PHANToM/sup TM/ haptic interface device to generate the haptic sensory input in real-time. The system allows user interactions such as moving or lifting a virtual object, and demonstrates interactions between virtual and real objects. Methods to provide proper visual occlusion between real and virtual objects are also described.
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.
18741005
Reasoning in Extensional Type Theory with Equality
We describe methods for automated theorem proving in extensional type theory with primitive equality. We discuss a complete, cut-free sequent calculus as well as a compact representation of cut-free (ground) proofs as extensional expansion dags. Automated proof search can be realized using a few operations to manipulate extensional expansion dags with variables. These search operations form a basis for complete search procedures. Procedures based on these ideas are implemented in the higher-order theorem prover Tps.
27008190
Tutorial: Using TPS for Higher-Order Theorem Proving and ETPS for Teaching Logic
TPS is an automated theorem proving system which can be used to prove theorems of first- or higher-order logic automatically, interactively, or in a combination of these modes of operation. Proofs in TPS are presented in natural deduction style. ETPS is a program which was obtained from TPS by deleting all the facilities for proving theorems automatically. ETPS can be used by students to learn how to prove theorems interactively. The objective of the tutorial is to teach participants how to make effective use of TPS and ETPS.