Comparison of roving-window and search-window techniques for characterising landscape morphometry

Brazil`s State of Sao Paulo Research Foundation

PARALLEL ALGORITHMS FOR MAXIMAL CLIQUES IN CIRCLE GRAPHS AND UNRESTRICTED DEPTH SEARCH

We present parallel algorithms on the BSP/CGM model, with p processors, to count and generate all the maximal cliques of a circle graph with n vertices and m edges. To count the number of all the maximal cliques, without actually generating them, our algorithm requires O(log p) communication rounds with O(nm/p) local computation time. We also present an algorithm to generate the first maximal clique in O(log p) communication rounds with O(nm/p) local computation, and to generate each one of the subsequent maximal cliques this algorithm requires O(log p) communication rounds with O(m/p) local computation. The maximal cliques generation algorithm is based on generating all maximal paths in a directed acyclic graph, and we present an algorithm for this problem that uses O(log p) communication rounds with O(m/p) local computation for each maximal path. We also show that the presented algorithms can be extended to the CREW PRAM model.

Screening the Schistosoma mansoni transcriptome for genes differentially expressed in the schistosomulum stage in search for vaccine candidates

Schistosomiasis affects more than 200 million people worldwide; another 600 million are at risk of infection. The schistosomulum stage is believed to be the target of protective immunity in the attenuated cercaria vaccine model. In an attempt to identify genes up-regulated in the schistosomulum stage in relation to cercaria, we explored the Schistosoma mansoni transcriptome by looking at the relative frequency of reads in EST libraries from both stages. The 400 genes potentially up-regulated in schistosomula were analyzed as to their Gene Ontology categorization, and we have focused on those encoding-predicted proteins with no similarity to proteins of other organisms, assuming they could be parasite-specific proteins important for survival in the host. Up-regulation in schistosomulum relative to cercaria was validated with real-time reverse transcription polymerase chain reaction (RT-PCR) for five out of nine selected genes (56%). We tested their protective potential in mice through immunization with DNA vaccines followed by a parasite challenge. Worm burden reductions of 16-17% were observed for one of them, indicating its protective potential. Our results demonstrate the value and caveats of using stage-associated frequency of ESTs as an indication of differential expression coupled to DNA vaccine screening in the identification of novel proteins to be further investigated as potential vaccine candidates.

Uncovering false positives on a virtual screening search for cruzain inhibitors

Some unexpected promiscuous inhibitors were observed in a virtual screening protocol applied to select cruzain inhibitors from the ZINC database. Physical-chemical and pharmacophore model filters were used to reduce the database size. The selected compounds were docked into the cruzain active site. Six hit compounds were tested as inhibitors. Although the compounds were designed to be nucleophilically attacked by the catalytic cysteine of cruzain, three of them showed typical promiscuous behavior, revealing that false positives are a prevalent concern in VS programs. (C) 2007 Elsevier Ltd. All rights reserved.

Scholarly E-book Across Disciplines: Content Analysis of Usage Reports and Search Terms

This presentation was offered as part of the CUNY Library Assessment Conference, Reinventing Libraries: Reinventing Assessment, held at the City University of New York in June 2014.

The Dynamics of The Firm : In Search for a General Model

This paper describe a model from system theory that can be used as a base for better understanding of different situations in the firms evolution. This change model is derived from the theory of organic systems and divides the evolution of the system into higher complexity of the system structure in three distinctive phases. These phases are a formative phase, a normative phase and an integrative phase. After a summary of different types of models of the dynamics of the firm the paper makes a theoretical presentation of the model and how this model is adaptable for better understanding of the need for change in strategic orientation, organization form and leadership style over time.

Semantic Distributed Messaging Middleware

Messaging middleware provides asynchronous communication between services in distributed environments. However, security, reliability and performance issues compel such middleware to be distributed, and distribution throws up its own problems such as identifying messaging channels which could then be subscribed to. In particular, interested parties need to identify channels defined in remote locations while not knowing details of how they are defined. A common vocabulary using semantic descriptions offers a solution to this problem. In this paper, we describe the design and implementation of federated messaging middleware using semantic description of channels.

Semantic and Personalised Service Discovery

One of the most pervasive classes of services needed to support e-Science applications are those responsible for the discovery of resources. We have developed a solution to the problem of service discovery in a Semantic Web/Grid setting. We do this in the context of bioinformatics, which is the use of computational and mathematical techniques to store, manage, and analyse the data from molecular biology in order to answer questions about biological phenomena. Our specific application is myGrid (www.mygrid.org.uk) that is developing open source, service-based middleware upon which bioinformatics applications can be built. myGrid is specifically targeted at developing open source high-level service Grid middleware for bioinformatics.

Semantic and Personalised Service Discovery

One of the most pervasive classes of services needed to support e-Science applications are those responsible for the discovery of resources. We have developed a solution to the problem of service discovery in a Semantic Web/Grid setting. We do this in the context of bioinformatics, which is the use of computational and mathematical techniques to store, manage, and analyse the data from molecular biology in order to answer questions about biological phenomena. Our specific application is myGrid (http: //www.mygrid.org.uk) that is developing open source, service-based middleware upon which bioin- formatics applications can be built. myGrid is specif- ically targeted at developing open source high-level service Grid middleware for bioinformatics.

Towards a Protocol for the Attachment of Semantic Descriptions to Grid Services

Service discovery in large scale, open distributed systems is difficult because of the need to filter out services suitable to the task at hand from a potentially huge pool of possibilities. Semantic descriptions have been advocated as the key to expressive service discovery, but the most commonly used service descriptions and registry protocols do not support such descriptions in a general manner. In this paper, we present a protocol, its implementation and an API for registering semantic service descriptions and other task/user-specific metadata, and for discovering services according to these. Our approach is based on a mechanism for attaching structured and unstructured metadata, which we show to be applicable to multiple registry technologies. The result is an extremely flexible service registry that can be the basis of a sophisticated semantically-enhanced service discovery engine, an essential component of a Semantic Grid.

Towards a Protocol for the Attachment of Metadata to Service Descriptions and its Use in Semantic Discovery

Service discovery in large scale, open distributed systems is difficult because of the need to filter out services suitable to the task at hand from a potentially huge pool of possibilities. Semantic descriptions have been advocated as the key to expressive service discovery, but the most commonly used service descriptions and registry protocols do not support such descriptions in a general manner. In this paper, we present a protocol, its implementation and an API for registering semantic service descriptions and other task/user-specific metadata, and for discovering services according to these. Our approach is based on a mechanism for attaching structured and unstructured metadata, which we show to be applicable to multiple registry technologies. The result is an extremely flexible service registry that can be the basis of a sophisticated semantically-enhanced service discovery engine, an essential component of a Semantic Grid.

A security architecture for a semantic Grid registry

Existing registry technologies such as UDDI can be enhanced to support capabilities for semantic reasoning and inquiry, which subsequently increases its usability range. The Grimoires registry was developed to provide such support through the use of metadata attachments to registry entities. The use of such attachments provides a way for allowing service operators to specify security assertions pertaining to registry entities owned by them. These assertions may however have to be reconciled with existing registry policies. A security architecture based on the XACML standard and deployed in the OMII framework is outlined to demonstrate how this goal is achieved in the registry.