Jade Java Agent

Multi-agent systems are used in situations where you have to solve the problem of a diffuse character, or a complex calculation eg search information on the web, management of telecommunications networks, air traffic control, as well as in more mundane situations, which is eg control and running appliances. Java Agent Development framework, in short JADE is an environment that supports the construction of multi-agent systems written in Java. Allows you to construct and administer agents. This publication contains basic information about agents, the criteria for their creation and standards of JADE

Library for advanced functions in algorithms, data structures and AI implemented in C/C++ - Olib

Developers of one of most popular languages used for scientific computations which is C, have a lot of libraries at their disposal. Many of those allows usage of modern platforms equipped with advanced multicore processors. Among them is BLAS (Basic Linear Algebra Subprograms) and LAPACK (Linear Algebra PACKage). They contain mainly high performance procedures operating on matrix and vectors

An Atlas for Schistosoma mansoni Organs and Life-Cycle Stages Using Cell Type-Specific Markers and Confocal Microscopy

Schistosomiasis (bilharzia) is a tropical disease caused by trematode parasites (Schistosoma) that affects hundreds of millions of people in the developing world. Currently only a single drug (praziquantel) is available to treat this disease, highlighting the importance of developing new techniques to study Schistosoma. While molecular advances, including RNA interference and the availability of complete genome sequences for two Schistosoma species, will help to revolutionize studies of these animals, an array of tools for visualizing the consequences of experimental perturbations on tissue integrity and development needs to be made widely available. To this end, we screened a battery of commercially available stains, antibodies and fluorescently labeled lectins, many of which have not been described previously for analyzing schistosomes, for their ability to label various cell and tissue types in the cercarial stage of S. mansoni. This analysis uncovered more than 20 new markers that label most cercarial tissues, including the tegument, the musculature, the protonephridia, the secretory system and the nervous system. Using these markers we present a high-resolution visual depiction of cercarial anatomy. Examining the effectiveness of a subset of these markers in S. mansoni adults and miracidia, we demonstrate the value of these tools for labeling tissues in a variety of life-cycle stages. The methodologies described here will facilitate functional analyses aimed at understanding fundamental biological processes in these parasites

Eukaryotic Protein Kinases (ePKs) of the Helminth Parasite Schistosoma mansoni

<p>Abstract</p> <p>Background</p> <p>Schistosomiasis remains an important parasitic disease and a major economic problem in many countries. The <it>Schistosoma mansoni </it>genome and predicted proteome sequences were recently published providing the opportunity to identify new drug candidates. Eukaryotic protein kinases (ePKs) play a central role in mediating signal transduction through complex networks and are considered druggable targets from the medical and chemical viewpoints. Our work aimed at analyzing the <it>S. mansoni </it>predicted proteome in order to identify and classify all ePKs of this parasite through combined computational approaches. Functional annotation was performed mainly to yield insights into the parasite signaling processes relevant to its complex lifestyle and to select some ePKs as potential drug targets.</p> <p>Results</p> <p>We have identified 252 ePKs, which corresponds to 1.9% of the <it>S. mansoni </it>predicted proteome, through sequence similarity searches using HMMs (Hidden Markov Models). Amino acid sequences corresponding to the conserved catalytic domain of ePKs were aligned by MAFFT and further used in distance-based phylogenetic analysis as implemented in PHYLIP. Our analysis also included the ePK homologs from six other eukaryotes. The results show that <it>S. mansoni </it>has proteins in all ePK groups. Most of them are clearly clustered with known ePKs in other eukaryotes according to the phylogenetic analysis. None of the ePKs are exclusively found in <it>S. mansoni </it>or belong to an expanded family in this parasite. Only 16 <it>S. mansoni </it>ePKs were experimentally studied, 12 proteins are predicted to be catalytically inactive and approximately 2% of the parasite ePKs remain unclassified. Some proteins were mentioned as good target for drug development since they have a predicted essential function for the parasite.</p> <p>Conclusions</p> <p>Our approach has improved the functional annotation of 40% of <it>S. mansoni </it>ePKs through combined similarity and phylogenetic-based approaches. As we continue this work, we will highlight the biochemical and physiological adaptations of <it>S. mansoni </it>in response to diverse environments during the parasite development, vector interaction, and host infection.</p

Frequent co-infection among human group a rotaviruses in Thailand.

Rotavirus (RoV) is a non-enveloped dsRNA virus in the Reoviridae family, with a 18.5-kb genome of 11 segments encoding six structural (VP1–4, VP6 and VP7) and five or six non-structural proteins (NSP1-NSP5/6). Reassortment between human and/or animal RoVs plays an important role in the generation of genetic diversity in these viruses, and is presumed to result from co-infection in human or animal reservoirs. However, coinfection with heterologous RoV has rarely been documented, in part due to inadequate detection methods and a lack of largescale genomic investigations. Despite the availability of an efficacious vaccine, the burden of rotaviral diarrhea remains high in many developing countries, with rotavirus infection detected in 40–50% of all pediatric patients hospitalized with diarrhea. In addition to its cost, reduced vaccine effectiveness in developing country settings has contributed to its low uptake and the lack of government support for vaccination programs across Southeast Asia. The genetics and dynamics of rotavirus (RoV) have rarely been systematically investigated in these settings

Frequent co-infection among human group a rotaviruses in Thailand.

Rotavirus (RoV) is a non-enveloped dsRNA virus in the Reoviridae family, with a 18.5-kb genome of 11 segments encoding six structural (VP1–4, VP6 and VP7) and five or six non-structural proteins (NSP1-NSP5/6). Reassortment between human and/or animal RoVs plays an important role in the generation of genetic diversity in these viruses, and is presumed to result from co-infection in human or animal reservoirs. However, coinfection with heterologous RoV has rarely been documented, in part due to inadequate detection methods and a lack of largescale genomic investigations. Despite the availability of an efficacious vaccine, the burden of rotaviral diarrhea remains high in many developing countries, with rotavirus infection detected in 40–50% of all pediatric patients hospitalized with diarrhea. In addition to its cost, reduced vaccine effectiveness in developing country settings has contributed to its low uptake and the lack of government support for vaccination programs across Southeast Asia. The genetics and dynamics of rotavirus (RoV) have rarely been systematically investigated in these settings

Superthermal Al Atoms as a Reactive-Atom Probe of Fluorinated Surfaces

We demonstrate a proof-of-concept of a new analytical technique to measure relative F atom exposure at the surfaces of fluorinated materials. The method is based on reactive-atom scattering (RAS) of Al atoms, produced by pulsed laser ablation of solid Al at 532 nm. The properties of the incident ground-state Al were characterized by laser-induced fluorescence (LIF); at typical ablation fluences, the speed distribution is approximately Maxwellian at ∼45000 K, with a most-probable kinetic energy of 187 kJ mol-1 and a mean of 560 kJ mol-1 When these Al atoms impact the surfaces of perfluorinated solids (poly(tetrafluorethylene), PTFE) or liquids (perfluoropolyether, PFPE), gas-phase AlF products are clearly detectable by LIF on the AlF A-X band. Quantitative AlF yields were compared for a small representative set of a widely studied family of ionic liquids based on the common 1-alkyl-3-methylimidazolium ([Cnmim]+) cation. Yields of (1.9 ± 0.2):1 were found from [C2mim][Tf2N] and [C8mim][Tf2N], containing the common fluorinated bis(trifluoromethylsulfonyl)imide anion ([Tf2N]−). This is in quantitative agreement with previous independent low-energy ion scattering (LEIS) measurements and consistent with other independent results indicating that the longer cationic alkyl chains cover a larger fraction of the liquid surface and hence reduce anion exposure. The expected null result was obtained for the ionic liquid [C2mim][EtSO4] which contains no fluorine. These results open the way for further characterization and the potential application of this new variant of the RAS-LIF method

Identification and Characterization of vB_PreP_EPr2, a Lytic Bacteriophage of Pan-Drug Resistant <i>Providencia rettgeri</i>

Providencia rettgeri is an emerging opportunistic Gram-negative pathogen with reports of increasing antibiotic resistance. Pan-drug resistant (PDR) P. rettgeri infections are a growing concern, demonstrating a need for the development of alternative treatment options which is fueling a renewed interest in bacteriophage (phage) therapy. Here, we identify and characterize phage vB_PreP_EPr2 (EPr2) with lytic activity against PDR P. rettgeri MRSN 845308, a clinical isolate that carries multiple antibiotic resistance genes. EPr2 was isolated from an environmental water sample and belongs to the family Autographiviridae, subfamily Studiervirinae and genus Kayfunavirus, with a genome size of 41,261 base pairs. Additional phenotypic characterization showed an optimal MOI of 1 and a burst size of 12.3 ± 3.4 PFU per bacterium. EPr2 was determined to have a narrow host range against a panel of clinical P. rettgeri strains. Despite this fact, EPr2 is a promising lytic phage with potential for use as an alternative therapeutic for treatment of PDR P. rettgeri infections