Surface properties of the clean and Au/Pd covered Fe3_3O4_4(111): a DFT and DFT+UU study

The spin-density functional theory (DFT) and DFT+$U$ with Hubbard $U$ term accounting for on-site Coulomb interactions were applied to investigate structure, stability, and electronic properties of different terminations of the Fe$_3$O$_4$(111) surface. All terminations of the ferrimagnetic Fe$_3$O$_4$(111) surface exhibit very large (up to 90%) relaxations of the first four interlayer distances, decreasing with the oxide layer depth. Our calculations predict the iron terminated surface to be most stable in a wide range of the accessible values of the oxygen chemical potential. The adsorption of Au and Pd on two stable Fe- and O-terminated surfaces is studied. Our results show that Pd binds stronger than Au both to the Fe- and O-terminated surface. DFT+$U$ gives stronger bonding than DFT. The bonding of both adsorbates to the O-terminated magnetite surface is by 1.5-2.5 eV stronger than to the Fe-terminated surface

Requirement for Specific Proteases in Cancer Cell Intravasation as Revealed by a Novel Semiquantitative PCR-Based Assay

AbstractProteases are crucial for cancer metastasis, but due to lack of assays, their role in intravasation has not yet been tested. We have developed a human Alu sequence PCR-based assay to quantitate intravasated cells in an in vivo model. We demonstrated that metalloproteinases (MMPs), and most likely MMP-9, are required for intravasation by showing that marimastat, an inhibitor of MMPs, reduced intravasation by more than 90%, and that only tumor cell lines expressing MMP-9 intravasated. Cells with low surface urokinase plasminogen activator (uPA) and uPA receptor (uPAR) were also incapable of intravasation, despite the presence of high levels of MMP-9. We concluded that breaching of the vascular wall is a rate-limiting step for intravasation, and consequently for metastasis, and that cooperation between uPA/uPAR and MMP-9 is required to complete this step

Metallographic and corrosion research of copper from archaeological sites

In this study, copper slabs - ingots, from both Gdańsk and Krakow were examined. Besides metallographic examinations, attention was focused on analyses of corrosion products. The following techniques were applied: scanning electron microscopy with fluorescent X-ray microanalysis and X-ray diffraction. The conducted investigations enabled determination of the causes of corrosion in the old copper slabs, due mainly to the mediaeval alloying techniques and copper processing technologies

Order-Disorder Phase Transitions in KNO2 , CsNO2, and TlNO2 crystals: A Molecular Dynamics Study

The order-disorder phase transitions of KNO2 , CsNO2, and TlNO2 have been studied using parameter-free molecular dynamics simulation. It is found that the phase transitions in nitrites investigated are driven by the rotations of the NO2 2 ions about different axes together with displacements of cations and anions. We successfully reproduce the high-temperature phases of these nitrites, i.e., the NaCl-like structure for KNO2 and CsCl-like structure for Cs(Tl)NO2. Based on the investigation of the radial distribution function of the cations and anions, we explain why KNO2 and Cs(Tl)NO2 form quite different low-temperature phases

Molecular Dynamics Simulations of Phase Transition in AgNO3

Structural phase transition in AgNO3 at high temperature is simulated by molecular dynamics. The simulations are based on the potentials calculated from the Gordon–Kim modified electron-gas formalism extended to molecular ionic crystals. AgNO3 transforms into rhombohedral structure at high temperature and the phase transition is associated with the rotations of the NO3 ions and displacements of the NO3 and Ag ions

The Presampler for the Forward and Rear Calorimeter in the ZEUS Detector

The ZEUS detector at HERA has been supplemented with a presampler detector in front of the forward and rear calorimeters. It consists of a segmented scintillator array read out with wavelength-shifting fibers. We discuss its desi gn, construction and performance. Test beam data obtained with a prototype presampler and the ZEUS prototype calorimeter demonstrate the main function of this detector, i.e. the correction for the energy lost by an electron interacting in inactive material in front of the calorimeter.Comment: 20 pages including 16 figure

Downregulation of urokinase plasminogen activator receptor expression inhibits Erk signalling with concomitant suppression of invasiveness due to loss of uPAR–β1 integrin complex in colon cancer cells

Cancer invasion is regulated by cell surface proteinases and adhesion molecules. Interaction between specific cell surface molecules such as urokinase plasminogen activator receptor (uPAR) and integrins is crucial for tumour invasion and metastasis. In this study, we examined whether uPAR and beta1 integrin form a functional complex to mediate signalling required for tumour invasion. We assessed the expression of uPAR/beta1 integrin complex, Erk signalling pathway, adhesion, uPA and matrix metalloproteinase (MMP) expression, migration/invasion and matrix degradation in a colon cancer cell line in which uPAR expression was modified. Antisense inhibition of the cell surface expression of uPAR by 50% in human colon carcinoma HCT116 cells (A/S) suppressed Erk-MAP kinase activity by two-fold. Urokinase plasminogen activator receptor antisense treatment of HCT116 cells was associated with a 1.3-fold inhibition of adhesion, approximately four-fold suppression of HMW-uPA secretion and inhibition of pro-MMP-9 secretion. At a functional level, uPAR antisense resulted in a four-fold decline in migration/invasion and abatement of plasmin-mediated matrix degradation. In empty vector-transfected cells (mock), uPA strongly elevated basal Erk activation. In contrast, in A/S cells, uPA induction of Erk activation was not observed. Urokinase plasminogen activator receptor associated with beta1 integrin in mock-transfected cells. Disruption of uPAR-beta1 integrin complex in mock-transfected cells with a specific peptide (P25) inhibited uPA-mediated Erk-MAP kinase pathway and inhibited migration/invasion and plasmin-dependent matrix degradation through suppression of pro-MMP-9/MMP-2 expression. This novel paradigm of uPAR-integrin signalling may afford opportunities for alternative therapeutic strategies for the treatment of cancer

Functional Diversity and Structural Disorder in the Human Ubiquitination Pathway

The ubiquitin-proteasome system plays a central role in cellular regulation and protein quality control (PQC). The system is built as a pyramid of increasing complexity, with two E1 (ubiquitin activating), few dozen E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase) enzymes. By collecting and analyzing E3 sequences from the KEGG BRITE database and literature, we assembled a coherent dataset of 563 human E3s and analyzed their various physical features. We found an increase in structural disorder of the system with multiple disorder predictors (IUPred - E1: 5.97%, E2: 17.74%, E3: 20.03%). E3s that can bind E2 and substrate simultaneously (single subunit E3, ssE3) have significantly higher disorder (22.98%) than E3s in which E2 binding (multi RING-finger, mRF, 0.62%), scaffolding (6.01%) and substrate binding (adaptor/substrate recognition subunits, 17.33%) functions are separated. In ssE3s, the disorder was localized in the substrate/adaptor binding domains, whereas the E2-binding RING/HECT-domains were structured. To demonstrate the involvement of disorder in E3 function, we applied normal modes and molecular dynamics analyses to show how a disordered and highly flexible linker in human CBL (an E3 that acts as a regulator of several tyrosine kinase-mediated signalling pathways) facilitates long-range conformational changes bringing substrate and E2-binding domains towards each other and thus assisting in ubiquitin transfer. E3s with multiple interaction partners (as evidenced by data in STRING) also possess elevated levels of disorder (hubs, 22.90% vs. non-hubs, 18.36%). Furthermore, a search in PDB uncovered 21 distinct human E3 interactions, in 7 of which the disordered region of E3s undergoes induced folding (or mutual induced folding) in the presence of the partner. In conclusion, our data highlights the primary role of structural disorder in the functions of E3 ligases that manifests itself in the substrate/adaptor binding functions as well as the mechanism of ubiquitin transfer by long-range conformational transitions. © 2013 Bhowmick et al

Advances in infrastructures and tools for multiagent systems

In the last few years, information system technologies have focused on solving challenges in order to develop distributed applications. Distributed systems can be viewed as collections of service-provider and ser vice-consumer components interlinked by dynamically defined workflows (Luck and McBurney 2008).Alberola Oltra, JM.; Botti Navarro, VJ.; Such Aparicio, JM. (2014). Advances in infrastructures and tools for multiagent systems. Information Systems Frontiers. 16:163-167. doi:10.1007/s10796-014-9493-6S16316716Alberola, J. M., Búrdalo, L., Julián, V., Terrasa, A., & García-Fornes, A. (2014). An adaptive framework for monitoring agent organizations. Information Systems Frontiers, 16(2). doi: 10.1007/s10796-013-9478-x .Alfonso, B., Botti, V., Garrido, A., & Giret, A. (2014). A MAS-based infrastructure for negotiation and its application to a water-right market. Information Systems Frontiers, 16(2). doi: 10.1007/s10796-013-9443-8 .Andrighetto, G., Castelfranchi, C., Mayor, E., McBreen, J., López-Sánchez, M., & Parsons, S. (2013). (Social) norm dynamics. In G. Andrighetto, G. Governatori, P. Noriega, & L. W. van der Torre (Eds.), Normative multi-agent systems (pp. 135–170). Dagstuhl: Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik.Baarslag, T., Fujita, K., Gerding, E. H., Hindriks, K., Ito, T., Jennings, N. R., et al. (2013). Evaluating practical negotiating agents: results and analysis of the 2011 international competition. Artificial Intelligence, 198, 73–103.Boissier, O., Bordini, R. H., Hübner, J. F., Ricci, A., & Santi, A. (2013). Multi-agent oriented programming with JaCaMo. Science of Computer Programming, 78(6), 747–761.Campos, J., Esteva, M., López-Sánchez, M., Morales, J., & Salamó, M. (2011). Organisational adaptation of multi-agent systems in a peer-to-peer scenario. Computing, 91(2), 169–215.Carrera, A., Iglesias, C. A., & Garijo, M. (2014). Beast methodology: an agile testing methodology for multi-agent systems based on behaviour driven development. Information Systems Frontiers, 16(2). doi: 10.1007/s10796-013-9438-5 .Criado, N., Such, J. M., & Botti, V. (2014). Norm reasoning services. Information Systems Frontiers, 16(2). doi: 10.1007/s10796-013-9444-7 .Del Val, E., Rebollo, M., & Botti, V. (2014). Enhancing decentralized service discovery in open service-oriented multi-agent systems. Journal of Autonomous Agents and Multi-Agent Systems, 28(1), 1–30.Denti, E., Omicini, A., & Ricci, A. (2002). Coordination tools for MAS development and deployment. Applied Artificial Intelligence, 16(9–10), 721–752.Dignum, V., & Dignum, F. (2012). A logic of agent organizations. Logic Journal of IGPL, 20(1), 283–316.Ferber, J., & Gutknecht, O. (1998). A meta-model for the analysis and design of organizations in multi-agent systems. In Multi agent systems. Proceedings. International Conference on (pp. 128–135). IEEE.Fogués, R. L., Such, J. M., Espinosa, A., & Garcia-Fornes, A. (2014). BFF: a tool for eliciting tie strength and user communities in social networking services. Information Systems Frontiers, 16(2). doi: 10.1007/s10796-013-9453-6 .Garcia, E., Giret, A., & Botti, V. (2011). Evaluating software engineering techniques for developing complex systems with multiagent approaches. Information and Software Technology, 53(5), 494–506.Garcia-Fornes, A., Hübner, J., Omicini, A., Rodriguez-Aguilar, J., & Botti, V. (2011). Infrastructures and tools for multiagent systems for the new generation of distributed systems. Engineering Applications of Articial Intelligence, 24(7), 1095–1097.Jennings, N., Faratin, P., Lomuscio, A., Parsons, S., Sierra, C., & Wooldridge, M. (2001). Automated negotiation: prospects, methods and challenges. International Journal of Group Decision and Negotiation, 10(2), 199–215.Jung, Y., Kim, M., Masoumzadeh, A., & Joshi, J. B. (2012). A survey of security issue in multi-agent systems. Artificial Intelligence Review, 37(3), 239–260.Kota, R., Gibbins, N., & Jennings, N. R. (2012). Decentralized approaches for self-adaptation in agent organizations. ACM Transactions on Autonomous and Adaptive Systems (TAAS), 7(1), 1.Kraus, S. (1997). Negotiation and cooperation in multi-agent environments. Artificial Intelligence, 94(1), 79–97.Lin, Y. I., Chou, Y. W., Shiau, J. Y., & Chu, C. H. (2013). Multi-agent negotiation based on price schedules algorithm for distributed collaborative design. Journal of Intelligent Manufacturing, 24(3), 545–557.Luck, M., & McBurney, P. (2008). Computing as interaction: agent and agreement technologies.Luck, M., McBurney, P., Shehory, O., & Willmott, S. (2005). Agent technology: Computing as interaction (A roadmap for agent based computing). AgentLink.Ossowski, S., & Menezes, R. (2006). On coordination and its significance to distributed and multiagent systems. Concurrency and Computation: Practice and Experience, 18(4), 359–370.Ossowski, S., Sierra, C., & Botti. (2013). Agreement technologies: A computing perspective. In Agreement Technologies (pp. 3–16). Springer Netherlands.Pinyol, I., & Sabater-Mir, J. (2013). Computational trust and reputation models for open multi-agent systems: a review. Artificial Intelligence Review, 40(1), 1–25.Ricci, A., Piunti, M., & Viroli, M. (2011). Environment programming in multi-agent systems: an artifact-based perspective. Autonomous Agents and Multi-Agent Systems, 23(2), 158–192.Sierra, C., & Debenham, J. (2006). Trust and honour in information-based agency. In Proceedings of the 5th international conference on autonomous agents and multi agent systems, (p. 1225–1232). New York: ACM.Sierra, C., Botti, V., & Ossowski, S. (2011). Agreement computing. KI-Knstliche Intelligenz, 25(1), 57–61.Vasconcelos, W., García-Camino, A., Gaertner, D., Rodríguez-Aguilar, J. A., & Noriega, P. (2012). Distributed norm management for multi-agent systems. Expert Systems with Applications, 39(5), 5990–5999.Wooldridge, M. (2002). An introduction to multiagent systems. New York: Wiley.Wooldridge, M., & Jennings, N. R. (1995). Intelligent agents: theory and practice. Knowledge Engineering Review, 10(2), 115–152