PDBsum: summaries and analyses of PDB structures

PDBsum is a web-based database providing a largely pictorial summary of the key information on each macromolecular structure deposited at the Protein Data Bank (PDB). It includes images of the structure, annotated plots of each protein chain’s secondary structure, detailed structural analyses generated by the PROMOTIF program, summary PROCHECK results and schematic diagrams of protein–ligand and protein–DNA interactions. RasMol scripts highlight key aspects of the structure, such as the protein’s domains, PROSITE patterns and protein–ligand interactions, for interactive viewing in 3D. Numerous links take the user to related sites. PDBsum is updated whenever any new structures are released by the PDB and is freely accessible via http://www.biochem.ucl.ac.uk/bsm/pdbsum.

GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources

GlycoSuiteDB is a relational database that curates information from the scientific literature on glyco­protein derived glycan structures, their biological sources, the references in which the glycan was described and the methods used to determine the glycan structure. To date, the database includes most published O-linked oligosaccharides from the last 50 years and most N-linked oligosaccharides that were published in the 1990s. For each structure, information is available concerning the glycan type, linkage and anomeric configuration, mass and composition. Detailed information is also provided on native and recombinant sources, including tissue and/or cell type, cell line, strain and disease state. Where known, the proteins to which the glycan structures are attached are reported, and cross-references to the SWISS-PROT/TrEMBL protein sequence databases are given if applicable. The GlycoSuiteDB annotations include literature references which are linked to PubMed, and detailed information on the methods used to determine each glycan structure are noted to help the user assess the quality of the structural assignment. GlycoSuiteDB has a user-friendly web interface which allows the researcher to query the database using mono­isotopic or average mass, monosaccharide composition, glycosylation linkages (e.g. N- or O-linked), reducing terminal sugar, attached protein, taxonomy, tissue or cell type and GlycoSuiteDB accession number. Advanced queries using combinations of these parameters are also possible. GlycoSuiteDB can be accessed on the web at http://www.glycosuite.com.

An approach to three-dimensional structures of biomolecules by using single-molecule diffraction images

We describe an approach to the high-resolution three-dimensional structural determination of macromolecules that utilizes ultrashort, intense x-ray pulses to record diffraction data in combination with direct phase retrieval by the oversampling technique. It is shown that a simulated molecular diffraction pattern at 2.5-Å resolution accumulated from multiple copies of single rubisco biomolecules, each generated by a femtosecond-level x-ray free electron laser pulse, can be successfully phased and transformed into an accurate electron density map comparable to that obtained by more conventional methods. The phase problem is solved by using an iterative algorithm with a random phase set as an initial input. The convergence speed of the algorithm is reasonably fast, typically around a few hundred iterations. This approach and phasing method do not require any ab initio information about the molecule, do not require an extended ordered lattice array, and can tolerate high noise and some missing intensity data at the center of the diffraction pattern. With the prospects of the x-ray free electron lasers, this approach could provide a major new opportunity for the high-resolution three-dimensional structure determination of single biomolecules.

Disruption of cellular signaling pathways by daunomycin through destabilization of nonlamellar membrane structures.

Albeit anthracyclines are widely used in the treatment of solid tumors and leukemias, their mechanism of action has not been elucidated. The present study gives relevant information about the role of nonlamellar membrane structures in signaling pathways, which could explain how anthracyclines can exert their cytocidal action without entering the cell [Tritton, T. R. & Yee, G. (1982) Science 217, 248-250]. The anthracycline daunomycin reduced the formation of the nonlamellar hexagonal (HII) phase (i.e., the hexagonal phase propensity), stabilizing the bilayer structure of the plasma membrane by a direct interaction with membrane phospholipids. As a consequence, various cellular events involved in signal transduction, such as membrane fusion and membrane association of peripheral proteins [e.g., guanine nucleotide-binding regulatory proteins (G proteins and protein kinase C-alpha beta)], where nonlamellar structures (negative intrinsic monolayer curvature strain) are required, were altered by the presence of daunomycin. Functionally, daunomycin also impaired the expression of the high-affinity state of a G protein-coupled receptor (ternary complex for the alpha 2-adrenergic receptor) due to G-protein dissociation from the plasma membrane. In vivo, daunomycin also decreased the levels of membrane-associated G proteins and protein kinase C-alpha beta in the heart. The occurrence of such nonlamellar structures favors the association of these peripheral proteins with the plasma membrane and prevents daunomycin-induced dissociation. These results reveal an important role of the lipid component of the cell membrane in signal transduction and its alteration by anthracyclines.

Fénix: a flexible information exchange data model for natural language processing

In this paper we describe Fénix, a data model for exchanging information between Natural Language Processing applications. The format proposed is intended to be flexible enough to cover both current and future data structures employed in the field of Computational Linguistics. The Fénix architecture is divided into four separate layers: conceptual, logical, persistence and physical. This division provides a simple interface to abstract the users from low-level implementation details, such as programming languages and data storage employed, allowing them to focus in the concepts and processes to be modelled. The Fénix architecture is accompanied by a set of programming libraries to facilitate the access and manipulation of the structures created in this framework. We will also show how this architecture has been already successfully applied in different research projects.

Structures, Systems and Organizational Communication Processes in Franchises in times of crisis: the Spanish case

Current economic crisis together with the Internet revolution has had direct impacts on the franchise sector of Spain: in particular on its unique communication network. The aim of this research is to analyse how Spanish franchise companies have adapted to these changes through its corporate communications management. We want to determine whether the management of communications is ideal to the growth and consolidation of companies in the market. Corporate communications plans and organizational structures were analyzed to verify whether or not information technology (i.e. the use of the Internet) is maximized: the communications aspect being a critical area of company growth. We found that most franchise companies surveyed had adapted well to the changes in information technology, despite economic challenges. The Internet as a communications tool has been limited to its utility as a “bulletin board” for information. The marketing advantage of Internet communication, or its use as an avenue for customer exchange and exchange of goods and services has yet to be maximized. Future research may look into the details of how companies are able to maximize the communications-marketing advantage that Online/Internet can contribute to the franchise sector.

Workshops in “Construction of Structures I”: A new teaching methodology in the Building Engineering Degree

Both the current economic situation in the construction sector and the continuous normative changes in the building area imply the use of new methodologies to enhance students’ competences in the degree of Building Engineer. The aim of this paper is to present, analyse and discuss the development of constructive workshops as a new teaching methodology used in the subject of Construction of Structures I at the University of Alicante to complement the constructive and technical knowledge acquired by our students and to enhance their communicative and representation skills essential for their professional practice in the future. The used methodology is based on the development of three-dimensional construction details (in groups of 3 or 4 students) to be shown in two A1-pannels exposed in the corridors of the Polytechnic School. Thus, students’ work approaches constructive problems in a global way by discussing simultaneously with teachers and other groups about the most suitable solution on each case. This contribution has multiperspective results and improves criticism of students in different areas, encouraging new learning strategies and active participation. What is more, on-line information and web applications have been used to prepare and organize this kind of workshops, allowing students to use new technologies as a complementary learning methodology. In conclusion, the use of these new workshops in the Degree of Building Engineer stimulates an interactive class versus a traditional lecture where the participative groups´ attitude and the development of oral presentations dissolve the traditional boundaries regarding public communication skills of the students in the Degree.

The devil is in the details. Information warfare in the light of Russia's military doctrine. OSW Point of View 50, May 2015

By highlighting informational threats and giving them a military dimension, the authors of the Russian Federation's military doctrine have outlined the concept of information warfare. It is a kind of combat conducted by both conventional and indirect methods, open and concealed, using military and civilian structures. It has two dimensions: broader ("non-nuclear containment", i.e. combat waged on various levels - political, economic, diplomatic, humanitarian, military) and narrower (as an element supporting of action). An analysis of these issues enables us to identify several rising trends over the period 2000-2014 in Russian security policy. These boil down to a blurring of the boundaries between internal and external threats, introducing non-military methods and organisational structures to armed combat, and conferring an ideological character on this combat. This leads to a blurring of the contours of inter-state conflicts, which allows Russia to take part in armed conflicts in which it is not officially a party.

The effect of structures and lake level on bluff and shore erosion in Berrien County, Michigan, 1970-74 /

Cover title.

Determining discharge-coefficient ratings for selected coastal control structures in Broward and Palm Beach counties, Florida /

Shipping list no.: 99-0001-P.

Durability/corrosion of soil reinforced structures /

"December 1990."

The use of lithium to prevent or mitigate alkali-silica reaction in concrete pavements and structures /

"March 2007."

An analysis of transfer and development lengths for pretensioned concrete structures /

"December 1994."

a The application of modular/sectional structures to ground effect machines. /

"Task 9R99-01-005-06. Contract DA 44-177-TC-727."

Simple models for computing dynamic responses of complex frame structures /

"NSF/RA-780529."