In silico identification and characterization of protein-ligand binding sites

Protein–ligand binding site prediction methods aim to predict, from amino acid sequence, protein–ligand interactions, putative ligands, and ligand binding site residues using either sequence information, structural information, or a combination of both. In silico characterization of protein–ligand interactions has become extremely important to help determine a protein’s functionality, as in vivo-based functional elucidation is unable to keep pace with the current growth of sequence databases. Additionally, in vitro biochemical functional elucidation is time-consuming, costly, and may not be feasible for large-scale analysis, such as drug discovery. Thus, in silico prediction of protein–ligand interactions must be utilized to aid in functional elucidation. Here, we briefly discuss protein function prediction, prediction of protein–ligand interactions, the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated EvaluatiOn (CAMEO) competitions, along with their role in shaping the field. We also discuss, in detail, our cutting-edge web-server method, FunFOLD for the structurally informed prediction of protein–ligand interactions. Furthermore, we provide a step-by-step guide on using the FunFOLD web server and FunFOLD3 downloadable application, along with some real world examples, where the FunFOLD methods have been used to aid functional elucidation.

The water vapour continuum in near-infrared windows – current understanding and prospects for its inclusion in spectroscopic databases

Spectroscopic catalogues, such as GEISA and HITRAN, do not yet include information on the water vapour continuum that pervades visible, infrared and microwave spectral regions. This is partly because, in some spectral regions, there are rather few laboratory measurements in conditions close to those in the Earth’s atmosphere; hence understanding of the characteristics of the continuum absorption is still emerging. This is particularly so in the near-infrared and visible, where there has been renewed interest and activity in recent years. In this paper we present a critical review focusing on recent laboratory measurements in two near-infrared window regions (centred on 4700 and 6300 cm−1) and include reference to the window centred on 2600 cm−1 where more measurements have been reported. The rather few available measurements, have used Fourier transform spectroscopy (FTS), cavity ring down spectroscopy, optical-feedback – cavity enhanced laser spectroscopy and, in very narrow regions, calorimetric interferometry. These systems have different advantages and disadvantages. Fourier Transform Spectroscopy can measure the continuum across both these and neighbouring windows; by contrast, the cavity laser techniques are limited to fewer wavenumbers, but have a much higher inherent sensitivity. The available results present a diverse view of the characteristics of continuum absorption, with differences in continuum strength exceeding a factor of 10 in the cores of these windows. In individual windows, the temperature dependence of the water vapour self-continuum differs significantly in the few sets of measurements that allow an analysis. The available data also indicate that the temperature dependence differs significantly between different near-infrared windows. These pioneering measurements provide an impetus for further measurements. Improvements and/or extensions in existing techniques would aid progress to a full characterisation of the continuum – as an example, we report pilot measurements of the water vapour self-continuum using a supercontinuum laser source coupled to an FTS. Such improvements, as well as additional measurements and analyses in other laboratories, would enable the inclusion of the water vapour continuum in future spectroscopic databases, and therefore allow for a more reliable forward modelling of the radiative properties of the atmosphere. It would also allow a more confident assessment of different theoretical descriptions of the underlying cause or causes of continuum absorption.

Five New and Narrowly Distributed Species of Paepalanthus Section Diphyomene (Eriocaulaceae) from Central Brazil

Five new species of Paepalanthus section Diphyomene are described and illustrated: P. brevis, P. flexuosus, P. longiciliatus, P. macer, and P. stellatus. Paepalanthus brevis, similar to P. decussus, is easily distinguished by its short reproductive axis, and pilose and mucronate leaves. Paepalanthus flexuosus, morphologically related to P. urbanianus, possesses a distinctive short and tortuous reproductive axis. Paepalanthus longiciliatus, morphologically similar to P. weddellianus, possesses long trichomes on the margins of the reproductive axis bracts, considered a diagnostic feature. Paepalanthus macer shares similarities with P. amoenus, differing by its sulfurous capitula and adpressed reproductive axis bracts. Paepalanthus stellatus also has affinity with P. decussus, but possesses unique, membranaceous, reproductive-axis bracts and a punctual inner-capitulum arrangement of pistillate flowers. Four of the described species are narrowly distributed in the state of Goias, whereas P. brevis is endemic to Distrito Federal. All are considered critically endangered. Detailed comparisons of these species are presented in tables. Comments on phenology, distribution, habitat and etymology, along with an identification key, are provided.

Protein identification pipeline for the homology-driven proteomics

Homology-driven proteomics is a major tool to characterize proteomes of organisms with unsequenced genomes. This paper addresses practical aspects of automated homology-driven protein identifications by LC-MS/MS on a hybrid LTQ orbitrap mass spectrometer. All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download. (C) 2008 Elsevier B.V. All rights reserved.

Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

A novel approach for distributed application scheduling based on prediction of communication events

The evolution of commodity computing lead to the possibility of efficient usage of interconnected machines to solve computationally-intensive tasks, which were previously solvable only by using expensive supercomputers. This, however, required new methods for process scheduling and distribution, considering the network latency, communication cost, heterogeneous environments and distributed computing constraints. An efficient distribution of processes over such environments requires an adequate scheduling strategy, as the cost of inefficient process allocation is unacceptably high. Therefore, a knowledge and prediction of application behavior is essential to perform effective scheduling. In this paper, we overview the evolution of scheduling approaches, focusing on distributed environments. We also evaluate the current approaches for process behavior extraction and prediction, aiming at selecting an adequate technique for online prediction of application execution. Based on this evaluation, we propose a novel model for application behavior prediction, considering chaotic properties of such behavior and the automatic detection of critical execution points. The proposed model is applied and evaluated for process scheduling in cluster and grid computing environments. The obtained results demonstrate that prediction of the process behavior is essential for efficient scheduling in large-scale and heterogeneous distributed environments, outperforming conventional scheduling policies by a factor of 10, and even more in some cases. Furthermore, the proposed approach proves to be efficient for online predictions due to its low computational cost and good precision. (C) 2009 Elsevier B.V. All rights reserved.

EFFECTIVE NETWORKS FOR REAL-TIME DISTRIBUTED PROCESSING

This paper applies the concepts and methods of complex networks to the development of models and simulations of master-slave distributed real-time systems by introducing an upper bound in the allowable delivery time of the packets with computation results. Two representative interconnection models are taken into account: Uniformly random and scale free (Barabasi-Albert), including the presence of background traffic of packets. The obtained results include the identification of the uniformly random interconnectivity scheme as being largely more efficient than the scale-free counterpart. Also, increased latency tolerance of the application provides no help under congestion.

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.

THE EXTENT OF MULTIDISCIPLINARY AUTHORSHIP OF ARTICLES ON SCIENTOMETRICS AND BIBLIOMETRICS IN BRAZIL

The publications in scientometrics and bibliometrics with Brazilian authorship expanded exponentially in the 1990-2006 period, reaching 13 times in the Web of Science database and 19.5 times in the Google Scholar database. This increase is rather superior to that of the total Brazilian scientific production in the same time period (5.6 times in the Web of Science). Some characteristics to be noticed in this rise are: 1) The total number of articles during this period was 197; in that, 78% were published in 57 Brazilian journals and 22% in 13 international journals. 2) The national and international articles averaged 4.3 and 5.9 citations/article, respectively; two journals stood out among these, the national Ciencia da Informacao (44 articles averaging 6.7 citations/article) and the international Scientometrics (32 articles averaging 6.2 citations/article). 3) The articles encompass an impressive participation of authors from areas other than information science; only one-fourth of the authors are bound to the information science field, the remaining ones being distributed among the areas of humanities/business administration, biology/biomedicine, health and hard sciences. The occurrence of adventitious authors at this level of multidisciplinarity is uncommon in science. However, the possible benefits of such patterns are not clear in view of a fragmented intercommunication among the authors, as noticed through the citations. The advantages of changing this trend and of using other scientometric and bibliometric databases, such as SciELO, to avoid an almost exclusive use of the Web of Science database, are discussed.

A Unified Load Generator for Geographically Distributed Generation ofNetwork Traffic

During the last decade, the Internet usage has been growing at an enormous rate which has beenaccompanied by the developments of network applications (e.g., video conference, audio/videostreaming, E-learning, E-Commerce and real-time applications) and allows several types ofinformation including data, voice, picture and media streaming. While end-users are demandingvery high quality of service (QoS) from their service providers, network undergoes a complex trafficwhich leads the transmission bottlenecks. Considerable effort has been made to study thecharacteristics and the behavior of the Internet. Simulation modeling of computer networkcongestion is a profitable and effective technique which fulfills the requirements to evaluate theperformance and QoS of networks. To simulate a single congested link, simulation is run with asingle load generator while for a larger simulation with complex traffic, where the nodes are spreadacross different geographical locations generating distributed artificial loads is indispensable. Onesolution is to elaborate a load generation system based on master/slave architecture.

Mjukvaruverktyg för loggning och analys avindustriella processer

This report discusses developing a software log tool for analysis of industrial processes. The target was to develop software that can help electro Engineers for monitor and fault finding in industrial processes. The tool is called PLS (Process log server), and is developed in Visual Studio.NET Framework 2005. PLS works as a client with Beijer Electronics OPC Server. The program is able to read data from PLC (Programmable Logic Controller), trough the OPC Server. PLS connects to all kind of controllers that is supported by the Beijer Electronics OPC Server. Signal data is stored in a database for later analysis. Chosen signals data can easily be exported into a text file. The text file is adopted for import to MS Office Excel. User manual [UM-07] is written as a separate document. The software acted stable through the function test. The final product becomes a first-rate tool that is simple to use. As an advantage, the software can be developed with more functions in the future.

Formgivning av magasin i ett redaktionellt utvecklingsarbete

Tidningskompaniet, a publishing agency in Göteborg, has during the spring of 2003 developed a customermagazine for Göteborgsvarvet, a Half Marathon Race in Göteborg. If realized the magazine shallbe distributed to former participants of the race twice a year and will be financed by adverts.As part of the editorial concept, development of a graphic profile will be made for the magazine. Thisdegree project will result in the production of a »dummy« magazine to be presented to the client and tobe used by the advertisement sales people in their work.The magazine, named »Varvet«, will convey the message that anyone can run Göteborgsvarvet. Theintention is to give the magazine a »youthful and sporty« image.The work in this degree project has comprised designing the magazine in co-operation with an editorialconcept developer and a project leader at Tidningskompaniet, and also the production of 18 magazinepages including prepress work. The magazine has been made into a strictly sectionized product,with a mix of short and long articles with lighter material and strict how-to-do-it guides. The designhas been made to complement the editorial concept, with typography and colours that feel modern and»active«.The dummy magazine has been digitally printed using a Xeikon digital press and has been distributedto the client and the advertisement sales bureau.

Developing a Communication link between Agents and cross Platform IDE

The main objective of this thesis work is to develop communication link between Runrev Revolution (IDE) and JADE (Multi-Agent System) through Socket programming using TCP/IP layer. These two independent platforms are connected using socket programming technique. Socket programming is considered to be newly emerging technology among these two platforms, the work done in this thesis work is considered to be a prototype.A Graphical simulation model is developed by salixphere (Company in Hedemora) to simulate logistic problems using Runrev Revolution (IDE). The simulation software/program is called “BIOSIM”. The logistic problems are complex, and conventional optimization techniques are unlikely very successful. “BIOSIM” can demonstrate the graphical representation of logistic problems depending upon the problem domains. As this simulation model is developed in revolution programming language (Transcript) which is dynamically typed and English-like language, it is quite slow compared to other high level programming languages. The object of this thesis work is to add intelligent behaviour in graphical objects and develop communication link between Runrev revolution (IDE) and JADE (Multi-Agent System) using TCP/IP layers.The test shows the intelligent behaviour in the graphical objects and successful communication between Runrev Revolution (IDE) and JADE (Multi-Agent System).