A combined algorithm for analyzing structural controllability and observability of complex networks

In this paper a combined algorithm for analyzing structural controllability and observability of complex networks is presented. The algorithm addresses the two fundamental properties to guarantee structural controllability of a system: the absence of dilations and the accessibility of all nodes. The first problem is reformulated as a Maximum Matching search and it is addressed via the Hopcroft- Karp algorithm; the second problem is solved via a new wiring algorithm. Both algorithms can be combined to efficiently determine the number of required controllers and observers as well as the new required connections in order to guarantee controllability and observability in real complex networks. An application to a Twitter social network with over 100,000 nodes illustrates the proposed algorithms.

Agent-based modeling and simulation for the design of the future european Air Traffic Management system: the experience of CASSIOPEIA

The SESAR (Single European Sky ATM Research) program is an ambitious re-search and development initiative to design the future European air traffic man-agement (ATM) system. The study of the behavior of ATM systems using agent-based modeling and simulation tools can help the development of new methods to improve their performance. This paper presents an overview of existing agent-based approaches in air transportation (paying special attention to the challenges that exist for the design of future ATM systems) and, subsequently, describes a new agent-based approach that we proposed in the CASSIOPEIA project, which was developed according to the goals of the SESAR program. In our approach, we use agent models for different ATM stakeholders, and, in contrast to previous work, our solution models new collaborative decision processes for flow traffic management, it uses an intermediate level of abstraction (useful for simulations at larger scales), and was designed to be a practical tool (open and reusable) for the development of different ATM studies. It was successfully applied in three stud-ies related to the design of future ATM systems in Europe.

Conservation of the expression and function of apterous orthologs in Drosophila and mammals

The Drosophila apterous (ap) gene encodes a protein of the LIM-homeodomain family. Many transcription factors of this class have been conserved during evolution; however, the functional significance of their structural conservation is generally not known. ap is best known for its fundamental role as a dorsal selector gene required for patterning and growth of the wing, but it also has other important functions required for neuronal fasciculation, fertility, and normal viability. We isolated mouse (mLhx2) and human (hLhx2) ap orthologs, and we used transgenic animals and rescue assays to investigate the conservation of the Ap protein during evolution. We found that the human protein LHX2 is able to regulate correctly ap target genes in the fly, causes the same phenotypes as Ap when ectopically produced, and most importantly rescues ap mutant phenotypes as efficiently as the fly protein. In addition, we found striking similarities in the expression patterns of the Drosophila and murine genes. Both mLhx2 and ap are expressed in the respective nerve cords, eyes, olfactory organs, brain, and limbs. These results demonstrate the conservation of Ap protein function across phyla and argue that aspects of its expression pattern have also been conserved from a common ancestor of insects and vertebrates.

PALI—a database of Phylogeny and ALIgnment of homologous protein structures

PALI (release 1.2) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of homologous protein domains in various families. The data set of homologous protein structures has been derived by consulting the SCOP database (release 1.50) and the data set comprises 604 families of homologous proteins involving 2739 protein domain structures with each family made up of at least two members. Each member in a family has been structurally aligned with every other member in the same family (pairwise alignment) and all the members in the family are also aligned using simultaneous super­position (multiple alignment). The structural alignments are performed largely automatically, with manual interventions especially in the cases of distantly related proteins, using the program STAMP (version 4.2). Every family is also associated with two dendrograms, calculated using PHYLIP (version 3.5), one based on a structural dissimilarity metric defined for every pairwise alignment and the other based on similarity of topologically equivalent residues. These dendrograms enable easy comparison of sequence and structure-based relationships among the members in a family. Structure-based alignments with the details of structural and sequence similarities, superposed coordinate sets and dendrograms can be accessed conveniently using a web interface. The database can be queried for protein pairs with sequence or structural similarities falling within a specified range. Thus PALI forms a useful resource to help in analysing the relationship between sequence and structure variation at a given level of sequence similarity. PALI also contains over 653 ‘orphans’ (single member families). Using the web interface involving PSI_BLAST and PHYLIP it is possible to associate the sequence of a new protein with one of the families in PALI and generate a phylogenetic tree combining the query sequence and proteins of known 3-D structure. The database with the web interfaced search and dendrogram generation tools can be accessed at http://pa uling.mbu.iisc.ernet.in/~pali.

iProClass: an integrated, comprehensive and annotated protein classification database

The iProClass database is an integrated resource that provides comprehensive family relationships and structural and functional features of proteins, with rich links to various databases. It is extended from ProClass, a protein family database that integrates PIR superfamilies and PROSITE motifs. The iProClass currently consists of more than 200 000 non-redundant PIR and SWISS-PROT proteins organized with more than 28 000 superfamilies, 2600 domains, 1300 motifs, 280 post-translational modification sites and links to more than 30 databases of protein families, structures, functions, genes, genomes, literature and taxonomy. Protein and family summary reports provide rich annotations, including membership information with length, taxonomy and keyword statistics, full family relationships, comprehensive enzyme and PDB cross-references and graphical feature display. The database facilitates classification-driven annotation for protein sequence databases and complete genomes, and supports structural and functional genomic research. The iProClass is implemented in Oracle 8i object-relational system and available for sequence search and report retrieval at http://pir.georgetow n.edu/iproclass/.

Gardenification of tropical conserved wildlands: Multitasking, multicropping, and multiusers

Tropical wildlands and their biodiversity will survive in perpetuity only through their integration into human society. One protocol for integration is to explicitly recognize conserved tropical wildlands as wildland gardens. A major way to facilitate the generation of goods and services by a wildland garden is to generate a public-domain Yellow Pages for its organisms. Such a Yellow Pages is part and parcel of high-quality search-and-delivery from wildland gardens. And, as they and their organisms become better understood, they become higher quality biodiversity storage devices than are large freezers. One obstacle to wildland garden survival is that specific goods and services, such as biodiversity prospecting, lack development protocols that automatically shunt the profits back to the source. Other obstacles are that environmental services contracts have the unappealing trait of asking for the payment of environmental credit card bills and implying delegation of centralized governmental authority to decentralized social structures. Many of the potential conflicts associated with wildland gardens may be reduced by recognizing two sets of social rules for perpetuating biodiversity and ecosystems, one set for the wildland garden and one set for the agroscape. In the former, maintaining wildland biodiversity and ecosystem survival in perpetuity through minimally damaging use is paramount, while in the agroscape, wild biodiversity and ecosystems are tools for a healthy and productive agroecosystem, and the loss of much of the original is acceptable.

Gender sensitivity in national health plans in Latin America and the European Union

Objectives: To evaluate the situation regarding gender sensitivity in national health plans in Latin America and the European Union for the decade 2000–2010. Methods: A systematic search and content analysis of national health plans were carried out within 37 countries. Gender sensitivity, defined as the extent to which a health plan considers gender as a central category and develops measures to reduce any gender-related inequalities, was analysed through an ad hoc checklist. Results: The description of health problems by sex was more frequent than intervention proposals aimed at reducing gender health disparities. The greatest number of specific intervention proposals targeted at overcoming gender-based health inequalities were associated with sexual and/or reproductive health, gender based violence, the working environment and human resources training. Compared to the European Union member states, Latin American health plans were found to be generally more gender sensitive. Conclusions: National health plans are still generally lacking in gender sensitivity. Disparities exist in health policy formulation in favour of men, whilst women's health continues to be identified mainly with reproductive health. If gender sensitivity is not taken into account, efforts to improve the quality of clinical care will be insufficient as gender inequalities will persist.

Labour Market Reforms and Current Account Imbalances: Beggar-thy-neighbour policies in a currency union? CEPS Working Document No. 399/September 2014

Member countries of the Economic and Monetary Union (EMU) initiated wide-ranging labour market reforms in the last decade. This process is ongoing as countries that are faced with serious labour market imbalances perceive reforms as the fastest way to restore competitiveness within a currency union. This fosters fears among observers about a beggar-thy-neighbour policy that leaves non-reforming countries with a loss in competitiveness and an increase in foreign debt. Using a two-country, two-sector search and matching DSGE model, we analyse the impact of labour market reforms on the transmission of macroeconomic shocks in both non-reforming and reforming countries. By analysing the impact of reforms on foreign debt, we contribute to the debate on whether labour market reforms increase or reduce current account imbalances.

Migration and Integration. Common Challenges and Responses from Europe and Asia

With the signing of the ASEAN Framework Agreement for the Integration of Priority Sectors (FA) in 2004, migration and integration issues gained significance on the agenda. Primarily concerned with increasing economic growth, this framework excludes the integration of low and unskilled migrant workers; instead, ASEAN efforts to address migration and integration issues have been limited to Mutual Recognition Agreements for skilled labour and professionals. After an analysis of migration policy in the region, we highlight specific barriers to the integration of labour migrants in two priority sectors – nursing, which is highly regulated by the state, and Information, Communications and Technology (ICT), which is typically selfregulated and privately run. Despite a MRA for nursing allowing registered nurses to practice in another ASEAN country under supervision of local nurses without registering with the host country’s nursing regulatory authority, in practice, there are major barriers to the free movement of nurses within ASEAN in terms of skills recognition, licensure requirements and other protectionist measures. Although regulations governing the inflow of ICT professionals are not as stringent as those for healthcare professionals, private costs associated with job search and gaining foreign employment are higher in the ICT sector, largely due to limited information on international mobility within the industry. Three sets of barriers to greater integration are discussed. First, the economic and political diversity within ASEAN makes integration more problematic than in the European Union. Second, the primary concern with value-adding economic growth means that regional agreements are focused on skilled and professional labour migration only. Third, the “ASEAN way” of doing things – via a strong emphasis on consensus and non-interference with domestic policies – often means that the FA provision for the free movement of labour is usually trumped by domestic policies that do not reflect the same desire for labour integration.

Oslo terrorist attacks: Analysis, consequences and lessons learned. Transatlantic Security Paper No. 4, August 2011

The attack in Norway, like every attack with a major impact, should and will be carefully analyzed, both by police and by terrorists. If the Norwegian authorities have officially called for a technical evaluation of Counter-terrorism (CT) and rescue national services, many sensitive aspects still remain unsure.

Knowledge Organization in Transmedia Fictional Worlds: A Study of Harry Potter, Lord of the Rings, Marvel Universe, and Star Wars

Currently there is no structured data standard for representing elements commonly found in transmedia fictional universes. There are websites dedicated to individual universes, however, information found on these sites separates the various formats into books, movies, comics, etc.; concentrate on only the bibliographic aspects of the material; and are only full-text searchable. We have created an ontological model that will allow researchers, fans, brand managers, and creators to search for and retrieve the information contained in these worlds based on how they are structured. We conducted a domain analysis and user studies based on the contents of Harry Potter, Lord of the Rings, the Marvel Universe, and Star Wars in order to build a new model using the Ontology Web Language (OWL) and an artificial intelligence reasoning engine. This model can infer connections between characters, elements of power, items, places, events, etc. This model will facilitate better search and retrieval of the information contained within these vast story universes for all users interested in them. The result of this project is and OWL ontology that is intuitive for users; can be used by AI systems; and has been updated to reflect real user needs based on user research.

The chemistry and biology of human relaxin-3

A novel member of the human relaxin subclass of the insulin superfamily was recently discovered during a genomics database search and named relaxin-3. Like human relaxin-1 and relaxin-2, relaxin-3 is predicted to consist of a two-chain structure and three disulfide bonds in a disposition identical to that of insulin. To undertake detailed biophysical and biological characterization of the peptide, its chemical synthesis was undertaken. In contrast to human relaxin-1 and relaxin-2, however, relaxin-3 could not be successfully prepared by simple combination of the individual chains, thus necessitating recourse to the use of a regioselective disulfide bond formation strategy. Solid phase synthesis of the separate, selectively S-protected A and B chains followed by their purification and the subsequent stepwise formation of each of the three disulfides led to the successful acquisition of human relaxin-3. Comprehensive chemical characterization confirmed both the correct chain orientation and the integrity of the synthetic product. Relaxin-3 was found to bind to and activate native relaxin receptors in vitro and stimulate water drinking through central relaxin receptors in vivo. Recent studies have demonstrated that relaxin-3 will bind to and activate human LGR7, but not LGR8, in vitro. Secondary structural analysis showed it to adopt a less ordered confirmation than either relaxin-1 or relaxin-2, reflecting the presence in the former of a greater percentage of nonhelical forming amino acids. NMR spectroscopy and simulated annealing calculations were used to determine the three-dimensional structure of relaxin-3 and to identify key structural differences between the human relaxins.

Tourists and beach safety in Queensland, Australia

Surf Life Saving Queensland (SLSQ) is a leading authority on beach safety, providing patrol, education, and rescue services to both tourists and local residents along the coast of Queensland, Australia. SLSQ recognizes that tourists are a target group requiring special attention due to their unfamiliarity with ocean beaches and surfing activities, and in some cases having the additional challenge of poor swimming skills, language barriers, and disorientation in a foreign vacation environment. This article describes SLSQ initiatives to provide beach safety for tourists through a focus on service delivery and partnerships with the tourism industry and relevant government agencies. The positive involvement of SLSQ in tourism is a model for other coastal destinations, given that drowning is the second most frequent cause of injury death among international travelers.

Acquisition of negative valence and modified attentional processing by non fear relevant stimuli

The current research examined valence and attentional processing of a priori fear relevant stimuli and investigated the extent to which these characteristics can be acquired by non fear relevant stimuli across an aversive learning episode. The first experiment compared pictures of snakes and spiders with pictures of birds and fish using affective priming, visual search and detection of a dot probe. Snakes and spiders were more negative than birds and fish as indexed by affective priming, and were preferentially attended to in the visual search task. The second experiment exposed the non fear relevant animal pictures, birds and fish, in an aversive learning episode involving an aversive shock US. Skin conductance responding was measured during acquisition. After acquisition, conditioned non fear relevant animal stimuli, CS1, and non conditioned, non fear relevant animal stimuli, CS, were compared across affective priming, visual search and dot probe tasks. During acquisition, skin conductance responses were larger during CS1 than during CS across all three response intervals. After acquisition, CS1 non fear relevant animal pictures were more negative than CS non fear relevant animal pictures as indexed by affective priming, and were preferentially attended to in a dot probe task. These studies provide evidence that negative valence and modified attentional processing can be acquired in a brief aversive learning episode.

Hierarchical indexing structure for efficient similarity search in video retrieval

With the rapid increase in both centralized video archives and distributed WWW video resources, content-based video retrieval is gaining its importance. To support such applications efficiently, content-based video indexing must be addressed. Typically, each video is represented by a sequence of frames. Due to the high dimensionality of frame representation and the large number of frames, video indexing introduces an additional degree of complexity. In this paper, we address the problem of content-based video indexing and propose an efficient solution, called the Ordered VA-File (OVA-File) based on the VA-file. OVA-File is a hierarchical structure and has two novel features: 1) partitioning the whole file into slices such that only a small number of slices are accessed and checked during k Nearest Neighbor (kNN) search and 2) efficient handling of insertions of new vectors into the OVA-File, such that the average distance between the new vectors and those approximations near that position is minimized. To facilitate a search, we present an efficient approximate kNN algorithm named Ordered VA-LOW (OVA-LOW) based on the proposed OVA-File. OVA-LOW first chooses possible OVA-Slices by ranking the distances between their corresponding centers and the query vector, and then visits all approximations in the selected OVA-Slices to work out approximate kNN. The number of possible OVA-Slices is controlled by a user-defined parameter delta. By adjusting delta, OVA-LOW provides a trade-off between the query cost and the result quality. Query by video clip consisting of multiple frames is also discussed. Extensive experimental studies using real video data sets were conducted and the results showed that our methods can yield a significant speed-up over an existing VA-file-based method and iDistance with high query result quality. Furthermore, by incorporating temporal correlation of video content, our methods achieved much more efficient performance.