Eigenvalue Decomposition of Time Series with Application to the Czech Business Cycle

We follow a Beveridge-Nelson like time series decomposition method (into trend, business cycle and irregular components), and examine a stylized model of price inflation determination using the Czech data. We characterize the estimated components of CPI, IPPI and import inflations, together with the real production wage and real output, and survey their basic correlation properties; furthermore we compute structural innovations imposing restrictions on their long-run effects, draw the impulse responses, and test the results by means of bootstrap simulation. We conclude that major room for further refinement of the research is found in two areas, First, from an economist's perspective, in the construction of real marginal cost indicators, and second, from a statistiacian's perspective, in further investigation of the robustness of the method.bootstrap, business cycle, inflation, structural VAR, time series decomposition

Euroisation in Serbia

Euroisation in Serbia is rooted in a long history of macroeconomic instability. Extreme inflation volatility has undermined trust in the dinar and discouraged dinar savings. At the same time, an abundant supply of foreign capital inflows has provided easy access to foreign currency lending at low interest rates in an environment of perceived exchange rate stability – a perception reinforced by the choice of exchange rate regime. As a result, both the asset and the liability side of banks’ balance sheets, and even those of the non-bank sector, is heavily foreign currency-denominated. This paper documents the forces that promote euroisation in Serbia. The paper argues that, in the wake of the global crisis, a window of opportunity has emerged that could foster a process of de-euroisation. The lack of foreign funding and recent exchange rate volatility has tilted borrower incentives towards local currency borrowing. If disinflationary macroeconomic policies gain credibility, with the possible support of regulatory options, euroisation could drop sharply.

Strategic Interactions, Social Optimality and Growth

We focus on the implications of strategic interactions among research intensive firms on the rates of growth when the number of competing firms is small and firms recognise the effects their investment decisions have on the production behaviour of their rivals. Similar to other results, we find that the mode of oligopolist competition can have a great effect on the rate of growth, but we present novel channels of these effects. More importantly and unlike standard results, we show that for the Cournot type of competition, a (constrained) socially optimal rate of growth can be attained. On the other hand, this can never be achieved under the more severe Bertrand competition. These findings are thus parallel to the conclusions in strategic trade literature. Our results demonstrate that conclusions from the "strategic trade" literature are robust enough, if ex- tended into an explicitly dynamic general equilibrium framework. More importantly, though, they make evident that the questions of optimal policy design related to organisational structure and strategic conduct are tractable in the framework of endogenous growth models in sufficient detail.

An Economy in Transition and DSGE: What the Czech National Bank’s New Projection Model Needs

Since the introduction of the inflation targeting regime in 1998 the Czech National Bank has made considerable progress in developing formal tools for supporting its Forecasting and Policy Analysis System. This paper documents the advances in the ongoing research aimed at developing a DSGE small open economy model designed to capture some of the most important features of the Czech economy - both the business-cycle regularities and the recent developments associated with the economy's transition and its convergence towards the industrialized European countries. The model in its current form is able to capture trends in relative prices, allow for medium-convergence in expenditure shares, and deal with the undercapitalization and investment inflow issues. Besides the model exhibits real and nominal rigidities that are in line with the recent New Open Economy Macroeconomics literature built fully on first principles. The innovative features of our model include the international currency pricing scheme permitting flexible calibration of import and export price elasticities along with the disconnect of the nominal exchange rate, the policy reaction function with a parameterized forecast horizon, and a generalized capital accumulation equation with imperfect intertemporal substitution of investment..

The Czech Economic Transition: Exploring Options Using a Macrosectoral Model

The processes that will drive the next stage of the Czech transition are likely to be similar to those promoting real convergence in the EU cohesion countries. We draw on previous modelling research on the cohesion economies to construct and calibrate a small macrosectoral model of the Czech Republic that serves to highlight key policy issues facing CEE-country decision-makers. Four scenarios are then explored by simulation: the first projects the current pattern of disequilibrium wage setting into the future, while a second looks at the consequences of labour market reform. The other scenarios highlight some of the differences between policy strategies based on indigenous versus FDI-driven export-led growth.

Space Environments Testbed

The Space Environments Testbed (SET) is a flight controller data system for the Common Carrier Assembly. The SET-1 flight software provides the command, telemetry, and experiment control to ground operators for the SET-1 mission. Modes of operation (see dia gram) include: a) Boot Mode that is initiated at application of power to the processor card, and runs memory diagnostics. It may be entered via ground command or autonomously based upon fault detection. b) Maintenance Mode that allows for limited carrier health monitoring, including power telemetry monitoring on a non-interference basis. c) Safe Mode is a predefined, minimum power safehold configuration with power to experiments removed and carrier functionality minimized. It is used to troubleshoot problems that occur during flight. d) Operations Mode is used for normal experiment carrier operations. It may be entered only via ground command from Safe Mode

CaverDock: Software tool for fast screening of un/binding of ligands in protein engineering

Protein tunnels, channels and gates are important for enzymatic catalysis and also represent attractive targets for rational protein design and drug design [1]. Drug molecules blocking the access of natural substrate or release of products are very efficient modulators of biological activity. Here we demonstrate the application of newly in-house developed software tool CaverDock [2,3] for the analysis of the transport of ligands through tunnels in biomolecular targets. Caverdock is a new addition to the Caver Suite [4-6]. We performed virtual screening of large databases of drugs against two pharmacologically relevant targets. We have used FDA-approved drugs for both targets. Oncological drugs (133 molecules), taken from the NIH website, and anti-inflammatory (56 molecules), taken from the Drugbank website, as the libraries of ligands for the two molecular targets: (i) cytochrome P450 17A1 and (ii) leukotriene A4 hydrolase/aminopeptidase. Moreover, we will also show the unbinding of the 2,3-dichloropropan-1-ol product from a buried active site of an haloalkane dehalogenase and its variant. With this study we identified hot-spots that may be used for directed evolution or site-directed mutagenesis to create new variants for faster 2,3-dichloropropan-1-ol release [7]. Finally, we will show the difference on ligand transportation when a protein is in an open and closed conformations [8]. We will show how CaverDock tackles the problem of protein flexibility. 1. Marques, S.M., et al., 2017: Enzyme Tunnels and Gates as Relevant Targets in Drug Design. Medicinal Research Reviews 37: 1095-1139. 2. Vavra, O., et al., 2019: CaverDock 1.0: A New Tool for Analysis of Ligand Binding and Unbinding Based on Molecular Docking. Bioinformatics (under review). 3. Filipovic, J., et al, 2019: A Novel Method for Analysis of Ligand Binding and Unbinding Based on Molecular Docking. Transactions on Computational Biology and Bioinformatics (under review) 4. Chovancova, E., et al., 2012: CAVER 3.0: A Tool for Analysis of Transport Pathways in Dynamic Protein Structures. PLOS Computational Biology 8: e1002708. 5. Jurcik, A., et al., 2018: CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. Bioinformatics 34: 3586-3588. 6. Stourac, J., et al., 2019: Caver Web 1.0: Identification of Tunnels and Channels in Proteins and Analysis of Ligand Transport. Nucleic Acids Research (under review). 7. Marques, S.M., et al., 2019: Computational Study of Protein-Ligand Unbinding for Enzyme Engineering. Frontiers in Chemistry 6: 650. 8. Kokkonen, P., et al., 2018: Molecular Gating of an Engineered Enzyme Captured in Real Time. Journal of the American Chemical Society 140: 17999–18008

CAVERDOCK: A new tool for analysis of ligand binding and unbinding based on molecular docking

Understanding the protein-ligand interactions is crucial for engineering improved catalysts. The interaction of a protein and a ligand molecule often takes place in enzymes active site. Such functional sites may be buried inside the protein core, and therefore a transport of a ligand from outside environment to the protein inside needs to be understood. Here we present the CaverDock [1], implementing a novel method for analysis of these important transport processes. Our method is based on a modified molecular docking algorithm. It iteratively places the ligand along the tunnel in such a way that the ligand movement is contiguous and its energy is minimized. The output of the calculation is ligand trajectory and energy profile of transport process. CaverDock uses a modified version of the program AutoDock Vina [2] for molecular docking and implements a parallel heuristic algorithm to search the space of possible trajectories. Our method lies in between of geometrical approaches and molecular dynamics simulations. Contrary to geometrical methods, it provides an evaluation of chemical forces. However, it is not as computationally demanding as the methods based on molecular dynamics. The typical input of CaverDock requires setup for molecular docking and tunnel geometry obtained from Caver [3]. Typical computational time is in dozens of minutes at a single node, allowing virtual screening of a large pool of molecules. We demonstrate CaverDock usability by comparison of a ligand trajectory in different tunnels of wild type and engineered proteins; and computation of energetic profiles for a large set of substrates and inhibitors. CaverDock is available from the web site http://www.caver.cz. 1. Vavra, O., Filipovic, J., Plhak, J., Bednar, D., Marques, S., Brezovsky, J., Matyska, L., Damborsky, J., CAVERDOCK: A New Tool for Analysis of Ligand Binding and Unbinding Based on Molecular Docking. PLOS Computational Biology (submitted). 2. Trott, O., Olson, A.J., AutoDock Vina: Improving the Speed and Accuracy of Docking with a New scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31: 455-461, 2010. 3. Chovancova, E., Pavelka, A., Benes, P., Strnad, O., Brezovsky, J., Kozlikova, B., Gora, A., Sustr, V., Klvana, M., Medek, P., Biedermannova, L., Sochor, J., Damborsky, J., 2012: CAVER 3.0: A Tool for Analysis of Transport Pathways in Dynamic Protein Structures. PLOS Computational Biology 8: e1002708

Molecular Epidemiology of Methicillin-Resistant Staphylococcus aureus, Rural Southwestern Alaska1

One-sentence summary for table of contents: Epidemiology of MRSA isolates in this region differs from that in the lower 48 states