AIDA: ab initio domain assembly server.

AIDA: ab initio domain assembly server, available at http://ffas.burnham.org/AIDA/ is a tool that can identify domains in multi-domain proteins and then predict their 3D structures and relative spatial arrangements. The server is free and open to all users, and there is an option for a user to provide an e-mail to get the link to result page. Domains are evolutionary conserved and often functionally independent units in proteins. Most proteins, especially eukaryotic ones, consist of multiple domains while at the same time, most experimentally determined protein structures contain only one or two domains. As a result, often structures of individual domains in multi-domain proteins can be accurately predicted, but the mutual arrangement of different domains remains unknown. To address this issue we have developed AIDA program, which combines steps of identifying individual domains, predicting (separately) their structures and assembling them into multiple domain complexes using an ab initio folding potential to describe domain-domain interactions. AIDA server not only supports the assembly of a large number of continuous domains, but also allows the assembly of domains inserted into other domains. Users can also provide distance restraints to guide the AIDA energy minimization

PubServer: literature searches by homology.

PubServer, available at http://pubserver.burnham.org/, is a tool to automatically collect, filter and analyze publications associated with groups of homologous proteins. Protein entries in databases such as Entrez Protein database at NCBI contain information about publications associated with a given protein. The scope of these publications varies a lot: they include studies focused on biochemical functions of individual proteins, but also reports from genome sequencing projects that introduce tens of thousands of proteins. Collecting and analyzing publications related to sets of homologous proteins help in functional annotation of novel protein families and in improving annotations of well-studied protein families or individual genes. However, performing such collection and analysis manually is a tedious and time-consuming process. PubServer automatically collects identifiers of homologous proteins using PSI-Blast, retrieves literature references from corresponding database entries and filters out publications unlikely to contain useful information about individual proteins. It also prepares simple vocabulary statistics from titles, abstracts and MeSH terms to identify the most frequently occurring keywords, which may help to quickly identify common themes in these publications. The filtering criteria applied to collected publications are user-adjustable. The results of the server are presented as an interactive page that allows re-filtering and different presentations of the output

Consumption of antimicrobials in the European Union and indications for their rational administration

Antimicrobials are essential for the medical care and health of animals and livestock populations. On the other hand it is generally accepted that the increase in prevalence of antimicrobial resistance is a worldwide problem. Therefore, in many countries of the world, the consumption of antibiotics and the resistance of pathogens isolated from humans and animals are monitored. Collected data indicate the need to reduce antimicrobial use in humans and in food-producing animals. This goal can only be achieved if antimicrobials will be used rationally and in accordance with the latest knowledge

Right Ventricular Compression Observed in Echocardiography from Pectus Excavatum Deformity

Pectus excavatum exists as varying anatomic deformities and compression of the right heart by the chest wall can lead to patient symptoms including dyspnea and chest pain with exertion. Echocardiography can be difficult but is critical to the evaluation and diagnosis of this patient population. Modifying standard views such as biplane transthoracic and 3-D transesophageal views may be necessary in some patients due to limitations from the abnormal anatomy of the deformed anterior chest wall. Apical four-chamber views when seen clearly can usually visualize any extrinsic compression to the right ventricle of the heart

FFAS server: novel features and applications.

The Fold and Function Assignment System (FFAS) server [Jaroszewski et al. (2005) FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Research, 33, W284-W288] implements the algorithm for protein profile-profile alignment introduced originally in [Rychlewski et al. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Science: a Publication of the Protein Society, 9, 232-241]. Here, we present updates, changes and novel functionality added to the server since 2005 and discuss its new applications. The sequence database used to calculate sequence profiles was enriched by adding sets of publicly available metagenomic sequences. The profile of a user's protein can now be compared with ∼20 additional profile databases, including several complete proteomes, human proteins involved in genetic diseases and a database of microbial virulence factors. A newly developed interface uses a system of tabs, allowing the user to navigate multiple results pages, and also includes novel functionality, such as a dotplot graph viewer, modeling tools, an improved 3D alignment viewer and links to the database of structural similarities. The FFAS server was also optimized for speed: running times were reduced by an order of magnitude. The FFAS server, http://ffas.godziklab.org, has no log-in requirement, albeit there is an option to register and store results in individual, password-protected directories. Source code and Linux executables for the FFAS program are available for download from the FFAS server

PDBFlex: exploring flexibility in protein structures.

The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software

LONG-TERM STUDY OF CHANGES OF PHYSICO-CHEMICAL PARAMETERS OF TRANSFORMER OILS

The average age of transformers in service is increasing and approaching the end of design life. Hence there is an increasing need to assess the condition of transformers. The utilities currently use a number of diagnostic techniques to assess the insulation condition of aged transformers. Among them physic-chemical analysis of transformer oil are frequently used. The article presents the results of many years of routine laboratory testing of oil transformers operated in the EnergiaPro energy company. Oil testing included measurements of total acidity, water content, breakdown voltage, resistivity, tgδ

EMI Shielding using Composite Materials with Plasma Layers

Electromagnetic compatibility, including the engineering of materials used for shielding from electromagnetic fields, is currently one of the most extensively developing field of applications of composite materials. The development of lightweight, mechanically resistant, shielding materials is possible as a result of using plasma technology. Due to rapid increase in the number of sources which generate the magnetic fields (like radio broadcasting, television, radio communication, cellular telephony), continuously extending range of applied frequencies and increasing power generated by PEM sources, the shielding is getting more and more difficult. This follows from the fact that complex power engineering systems are built of miniaturized electronic circuits. The progressing miniaturization reduces the resistance of the electronic circuits to electromagnetic exposure. Therefore, the choice of suitable materials for the shields and their appropriate arrangement have an essential meaning

The JCSG MR pipeline: optimized alignments, multiple models and parallel searches

The practical limits of molecular replacement can be extended by using several specifically designed protein models based on fold-recognition methods and by exhaustive searches performed in a parallelized pipeline. Updated results from the JCSG MR pipeline, which to date has solved 33 molecular-replacement structures with less than 35% sequence identity to the closest homologue of known structure, are presented