The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies

The latest version of CATH (class, architecture, topology, homology) (version 3.2), released in July 2008 (http://www.cathdb.info), contains 1 14215 domains, 2178 Homologous superfamilies and 1110 fold groups. We have assigned 20 330 new domains, 87 new homologous superfamilies and 26 new folds since CATH release version 3.1. A total of 28 064 new domains have been assigned since our NAR 2007 database publication (CATH version 3.0). The CATH website has been completely redesigned and includes more comprehensive documentation. We have revisited the CATH architecture level as part of the development of a `Protein Chart` and present information on the population of each architecture. The CATHEDRAL structure comparison algorithm has been improved and used to characterize structural diversity in CATH superfamilies and structural overlaps between superfamilies. Although the majority of superfamilies in CATH are not structurally diverse and do not overlap significantly with other superfamilies, similar to 4% of superfamilies are very diverse and these are the superfamilies that are most highly populated in both the PDB and in the genomes. Information on the degree of structural diversity in each superfamily and structural overlaps between superfamilies can now be downloaded from the CATH website.

PK/DB: database for pharmacokinetic properties and predictive in silico ADME models

The study of pharmacokinetic properties (PK) is of great importance in drug discovery and development. In the present work, PK/DB (a new freely available database for PK) was designed with the aim of creating robust databases for pharmacokinetic studies and in silico absorption, distribution, metabolism and excretion (ADME) prediction. Comprehensive, web-based and easy to access, PK/DB manages 1203 compounds which represent 2973 pharmacokinetic measurements, including five models for in silico ADME prediction (human intestinal absorption, human oral bioavailability, plasma protein binding, bloodbrain barrier and water solubility).

Elementary Petri net inside RFID distributed database (PNRD)

Usually, a Petri net is applied as an RFID model tool. This paper, otherwise, presents another approach to the Petri net concerning RFID systems. This approach, called elementary Petri net inside an RFID distributed database, or PNRD, is the first step to improve RFID and control systems integration, based on a formal data structure to identify and update the product state in real-time process execution, allowing automatic discovery of unexpected events during tag data capture. There are two main features in this approach: to use RFID tags as the object process expected database and last product state identification; and to apply Petri net analysis to automatically update the last product state registry during reader data capture. RFID reader data capture can be viewed, in Petri nets, as a direct analysis of locality for a specific transition that holds in a specific workflow. Following this direction, RFID readers storage Petri net control vector list related to each tag id is expected to be perceived. This paper presents PNRD cornerstones and a PNRD implementation example in software called DEMIS Distributed Environment in Manufacturing Information Systems.

Optimal Path Searching through Specified Routes using different Algorithms

To connect different electrical, network and data devices with the minimum cost and shortest path, is a complex job. In huge buildings, where the devices are placed at different locations on different floors and only some specific routes are available to pass the cables and buses, the shortest path search becomes more complex. The aim of this thesis project is, to develop an application which indentifies the best path to connect all objects or devices by following the specific routes.To address the above issue we adopted three algorithms Greedy Algorithm, Simulated Annealing and Exhaustive search and analyzed their results. The given problem is similar to Travelling Salesman Problem. Exhaustive search is a best algorithm to solve this problem as it checks each and every possibility and give the accurate result but it is an impractical solution because of huge time consumption. If no. of objects increased from 12 it takes hours to search the shortest path. Simulated annealing is emerged with some promising results with lower time cost. As of probabilistic nature, Simulated annealing could be non optimal but it gives a near optimal solution in a reasonable duration. Greedy algorithm is not a good choice for this problem. So, simulated annealing is proved best algorithm for this problem. The project has been implemented in C-language which takes input and store output in an Excel Workbook

A stopping rule while searching for optimal solution of facility-location

Solutions to combinatorial optimization, such as p-median problems of locating facilities, frequently rely on heuristics to minimize the objective function. The minimum is sought iteratively and a criterion is needed to decide when the procedure (almost) attains it. However, pre-setting the number of iterations dominates in OR applications, which implies that the quality of the solution cannot be ascertained. A small branch of the literature suggests using statistical principles to estimate the minimum and use the estimate for either stopping or evaluating the quality of the solution. In this paper we use test-problems taken from Baesley's OR-library and apply Simulated Annealing on these p-median problems. We do this for the purpose of comparing suggested methods of minimum estimation and, eventually, provide a recommendation for practioners. An illustration ends the paper being a problem of locating some 70 distribution centers of the Swedish Post in a region.

An analysis of Samoan reaction to The Orator (O Le Tulafale)’s Fāgogo defining Samoan identity

The Orator (O Le Tulafale) was promoted as the first Samoan language film shot in Samoa with a Samoan cast and crew. Written and directed by Samoan filmmaker Tusi Tamasese, the film succeeded at several of the movie industry’s prestigious festivals. The Orator (O Le Tulafale) is about an outcast family of a dwarf (Saili), his wife and her teenage daughter. As the main protagonist, Saili battles to overcome his fears to become a chief to save his family and land. The film’s themes are courage, love, honour , as well as hypocrisy, violence, and discrimination. A backlash by Samoans was predicted ; however, the opposite occurred. This raised the following questions: first, what is it about the film causing this reaction? It is a 106 -minute film shot in Samoa about Samoans and the Samoan culture . D espite promotional claims about the film , there have been Samoan -produced films in Samoa . Secondly, to what are Samoans really responding? Is it 1) just to the film because it is about Samoa, or 2) are they responding to themselves , and how they reacted during the act of watching the film? This implies levels of reactions in the act of watching, and examining the dominant level of response is important. To explore this, t he Samoan story telling technique of Fāgogo was used to analyse the film’s narration and narrative techniques. R. Allen’s (1993, 1997) concept of projected illusion was employed to discuss the relationship between Samoans and the film developed during the act of watching. An examination of the term Samoan and a description of the framework of Fa’a Samoa (Samoan culture) were provided. Also included were discussions of memory and its impact on Samoan cultural identity. The analysis indicated that The Orator (O Le Tulafale) acted as a memory prompt through which Samoans recalled memories confirming and defining cultural bonds. These memories constituted the essence of being Samoan. These memories were awakened, and shared as oral histories as fāgogo. The receivers appeared to interpret the shared memories to create their own memories and stories to suit their contexts, according to Facebook postings. An interpretation is that the organic sharing of memories as fā gogo created a global definition of Samoan that Samoans internationally claimed.

Depicting the interplay between organisational tiers in the use of a national quality registry to develop quality of care in Sweden

BACKGROUND: With a pending need to identify potential means to improved quality of care, national quality registries (NQRs) are identified as a promising route. Yet, there is limited evidence with regards to what hinders and facilitates the NQR innovation, what signifies the contexts in which NQRs are applied and drive quality improvement. Supposedly, barriers and facilitators to NQR-driven quality improvement may be found in the healthcare context, in the politico-administrative context, as well as with an NQR itself. In this study, we investigated the potential variation with regards to if and how an NQR was applied by decision-makers and users in regions and clinical settings. The aim was to depict the interplay between the clinical and the politico-administrative tiers in the use of NQRs to develop quality of care, examining an established registry on stroke care as a case study. METHODS: We interviewed 44 individuals representing the clinical and the politico-administrative settings of 4 out of 21 regions strategically chosen for including stroke units representing a variety of outcomes in the NQR on stroke (Riksstroke) and a variety of settings. The transcribed interviews were analysed by applying The Consolidated Framework for Implementation Research (CFIR). RESULTS: In two regions, decision-makers and/or administrators had initiated healthcare process projects for stroke, engaging the health professionals in the local stroke units who contributed with, for example, local data from Riksstroke. The Riksstroke data was used for identifying improvement issues, for setting goals, and asserting that the stroke units achieved an equivalent standard of care and a certain level of quality of stroke care. Meanwhile, one region had more recently initiated such a project and the fourth region had no similar collaboration across tiers. Apart from these projects, there was limited joint communication across tiers and none that included all individuals and functions engaged in quality improvement with regards to stroke care. CONCLUSIONS: If NQRs are to provide for quality improvement and learning opportunities, advances must be made in the links between the structures and processes across all organisational tiers, including decision-makers, administrators and health professionals engaged in a particular healthcare process.

Searching for Invariants Using Temporal Resolution

In this paper, we show how the clausal temporal resolution technique developed for temporal logic provides an effective method for searching for invariants, and so is suitable for mechanising a wide class of temporal problems. We demonstrate that this scheme of searching for invariants can be also applied to a class of multi-predicate induction problems represented by mutually recursive definitions. Completeness of the approach, examples of the application of the scheme, and overview of the implementation are described.