Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra

Automated methods for NMR structure determination of proteins are continuously becoming more robust. However, current methods addressing larger, more complex targets rely on analyzing 6–10 complementary spectra, suggesting the need for alternative approaches. Here, we describe 4D-CHAINS/autoNOE-Rosetta, a complete pipeline for NOE-driven structure determination of medium- to larger-sized proteins. The 4D-CHAINS algorithm analyzes two 4D spectra recorded using a single, fully protonated protein sample in an iterative ansatz where common NOEs between different spin systems supplement conventional through-bond connectivities to establish assignments of sidechain and backbone resonances at high levels of completeness and with a minimum error rate. The 4D-CHAINS assignments are then used to guide automated assignment of long-range NOEs and structure refinement in autoNOE-Rosetta. Our results on four targets ranging in size from 15.5 to 27.3 kDa illustrate that the structures of proteins can be determined accurately and in an unsupervised manner in a matter of days

Cellular Automata Applications in Shortest Path Problem

Cellular Automata (CAs) are computational models that can capture the essential features of systems in which global behavior emerges from the collective effect of simple components, which interact locally. During the last decades, CAs have been extensively used for mimicking several natural processes and systems to find fine solutions in many complex hard to solve computer science and engineering problems. Among them, the shortest path problem is one of the most pronounced and highly studied problems that scientists have been trying to tackle by using a plethora of methodologies and even unconventional approaches. The proposed solutions are mainly justified by their ability to provide a correct solution in a better time complexity than the renowned Dijkstra's algorithm. Although there is a wide variety regarding the algorithmic complexity of the algorithms suggested, spanning from simplistic graph traversal algorithms to complex nature inspired and bio-mimicking algorithms, in this chapter we focus on the successful application of CAs to shortest path problem as found in various diverse disciplines like computer science, swarm robotics, computer networks, decision science and biomimicking of biological organisms' behaviour. In particular, an introduction on the first CA-based algorithm tackling the shortest path problem is provided in detail. After the short presentation of shortest path algorithms arriving from the relaxization of the CAs principles, the application of the CA-based shortest path definition on the coordinated motion of swarm robotics is also introduced. Moreover, the CA based application of shortest path finding in computer networks is presented in brief. Finally, a CA that models exactly the behavior of a biological organism, namely the Physarum's behavior, finding the minimum-length path between two points in a labyrinth is given.Comment: To appear in the book: Adamatzky, A (Ed.) Shortest path solvers. From software to wetware. Springer, 201

A New Framework for the Citation Indexing Paradigm

A new citation indexing paradigm is proposed: the cascading citation indexing framework (c2IF, for short). It improves the way research publications are assessed for their impact in promoting science and technology. Given a collection of articles and their citation graph, citations are considered at the (article, author) level. Each one article is uniquely identified by means of the Digital Object Identifier (DOI, http://www.doi.org). To identify each one author uniquely, a Universal Author Identifier (UAI) scheme is established. In addition to the citations directly made to a given (article, author) pair, citation paths that target each one citing article are also considered. The granularity of the paradigm is further increased by introducing the concept of the chord, whereby a citation path of length one co-exists with paths of length two or higher, involving the same source- and target- articles. The c2IF output emerges in the form of a medal standings table, analogous to the one that ranks teams at athletic events: when two (article, author) pairs receive the same number of (direct) citations, the one that is cited by more popular articles (i.e. articles that comprise targets to a larger number of paths in the citation graph), is assigned a higher rank value

Extrusion of Root Canal Sealer in Periapical Tissues - Report of Two Cases with Different Treatment Management and Literature Review

Background: Extrusion of root canal sealers may cause damage to the surrounding anatomic structures. Clinical symptoms like pain, swelling and paresthesia or anesthesia may be present. The purpose of this presentation is to describe two cases of root canal sealer penetration into periapical tissues. A different treatment management was followed in each case

A New Framework for the Citation Indexing Paradigm

A new citation indexing paradigm is proposed: the cascading citation indexing framework (c 2 IF, for short). It improves the way research publications are assessed for their impact in promoting science and technology. Given a collection of articles and their citation graph, citations are considered at the (article, author) level. Each one article is uniquely identified b

The Universal Author Identifier System (UAI_Sys)

One common problem in the scientific research literature is that each one author cannot easily be identified uniquely. The problem arises when there are authors with identical names, authors who have changed their name(s) in the course of time, and authors whose names appear in alternative versions (for example: Jaakko Hyvärinen, and J. P. Hyvärinen) across the publications they have (co-) authored. The issue becomes more of a problem when data analysis utilizing author names is to be conducted, for example: in citation analysis. In this paper we introduce the Universal Author Identifier system, codenamed UAI_Sys. The system is web based and publicly available, enabling each one author to register/update his/her own metadata, plus acquire a unique identifier (UAI code), ensuring name disambiguation. As soon as UAI_Sys becomes accepted and enjoys worldwide use, selected author metadata will become globally available to all interested parties. Care is taken so that UAI_Sys comprises more than just a database for storing and handling author identifiers. Provision is taken for the system to incorporate web services facilitating communication with third party applications, thus expanding the possibilities for web based co-functionality. Last but not least, the system supports role-based access and management (i.e. different user roles for authors, librarians, publishers, and administrators) for efficient and effective information dissemination and management, promoting research and collaboration. UAI_Sys is being designed/developed along the lines of the Cascading Citations Analysis Project (C-CAP) which is co-funded by the Alexander Technology Educational Institute (ATEI), and the University of Macedonia (UoM)

The Universal Author Identifier System (UAI_Sys)

One common problem in the scientific research literature is that each one author cannot easily be identified uniquely. The problem arises when there are authors with identical names, authors who have changed their name(s) in the course of time, and authors whose names appear in alternative versions (for example: Jaakko Hyvärinen, and J. P. Hyvärinen) across the publications they have (co-) authored. The issue becomes more of a problem when data analysis utilizing author names is to be conducted, for example: in citation analysis. In this paper we introduce the Universal Author Identifier system, codenamed UAI_Sys. The system is web based and publicly available, enabling each one author to register/update his/her own metadata, plus acquire a unique identifier (UAI code), ensuring name disambiguation. As soon as UAI_Sys becomes accepted and enjoys worldwide use, selected author metadata will become globally available to all interested parties. Care is taken so that UAI_Sys comprises more than just a database for storing and handling author identifiers. Provision i