The non-farm economy in post-Soviet Georgia: A study of three rural communities

This report is based on qualitative fieldwork carried out between January 2001 and June 2002. The aim of the research has been to increase our understanding of the factors and dynamics of involvement in the non-farm sector in rural areas in Georgia since 1990, and to inform policymakers who aim to promote sustainable livelihood strategies in the rural non-farm economy (RNFE). Three communities were selected for study under this research project, situated in regions which are also the subject of quantitative research being conducted as part of the broader study of which this forms a part

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.

The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard-Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are significantly improved, and the modeling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined using traditional geometry restraints. In general it is found that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum-mechanical representation of active sites and improved geometric restraints for simulated annealing

Measurement of Seafloor Acoustic Backscatter Angular Dependence at 150 kHz Using a Multibeam Echosounder

Acoustic seafloor measurements with multibeam echosounders (MBESs) are currently often used for submarine habitat mapping, but the MBESs are usually not acoustically calibrated for backscattering strength (BBS) and cannot be used to infer absolute seafloor angular dependence. We present a study outlining the calibration and showing absolute backscattering strength values measured at a frequency of 150 kHz at around 10–20 m water depth. After recording bathymetry, the co-registered backscattering strength was corrected for true incidence and footprint reverberation area on a rough and tilted seafloor. Finally, absolute backscattering strength angular response curves (ARCs) for several seafloor types were constructed after applying sonar backscattering strength calibration and specific water column absorption for 150 kHz correction. Thus, we inferred specific 150 kHz angular backscattering responses that can discriminate among very fine sand, sandy gravel, and gravelly sand, as well as between bare boulders and boulders partially overgrown by red algae, which was validated by video ground-truthing. In addition, we provide backscatter mosaics using our algorithm (BBS-Coder) to correct the angle varying gain (AVG). The results of the work are compared and discussed with the published results of BBS measurements in the 100–400 kHz frequency range. The presented results are valuable in extending the very sparse angular response curves gathered so far and could contribute to a better understanding of the dependence of backscattering on the type of bottom habitat and improve their acoustic classificatio

Impact of the economic crisis on social, economic and territorial cohesion of the European Union

The impact of the economic and financial crisis that started in 2008 is still being felt. In November 2008, the European Commission launched a European Economic Recovery Plan with a view to coordinate Member States’ action in response to the crisis. In this context, the Study uses a combination of quantitative and qualitative methods in order to provide an overview of the impact of the crisis across four Member States and eight regions, in terms of economic, social and territorial cohesion, and to assess the responses of cohesion policy to counteract the crisis

Nearshore Benthic Habitat Mapping Based on Multi-Frequency, Multibeam Echosounder Data Using a Combined Object-Based Approach: A Case Study from the Rowy Site in the Southern Baltic Sea

Recently, the rapid development of the seabed mapping industry has allowed researchers to collect hydroacoustic data in shallow, nearshore environments. Progress in marine habitat mapping has also helped to distinguish the seafloor areas of varied acoustic properties. As a result of these new developments, we have collected a multi-frequency, multibeam echosounder dataset from the valuable nearshore environment of the southern Baltic Sea using two frequencies: 150 kHz and 400 kHz. Despite its small size, the Rowy area is characterized by diverse habitat conditions and the presence of red algae, unique on the Polish coast of the Baltic Sea. This study focused on the utilization of multibeam bathymetry and multi-frequency backscatter data to create reliable maps of the seafloor. Our approach consisted of the extraction of 70 secondary features of bathymetric and backscatter data, including statistic and textural attributes of different scales. Based on ground-truth samples, we have identified six habitat classes and selected the most relevant features of the bathymetric and backscatter data. Additionally, five types of image processing pixel-based and object-based classifiers were tested. We also evaluated the performance of algorithms using an accuracy assessment based on the validation subset of the ground-truth samples. Our best results reached 93% overall accuracy and a kappa coefficient of 0.90, confirming that nearshore seabed habitats can be accurately distinguished based on multi-frequency, multibeam echosounder measurements. Our predictive habitat mapping of shallow euphotic zones creates a new scientific perspective and provides relevant data for the management of natural resources. Object-based approaches previously used in various environments and areas suggest that methodology presented in this study may be scalable

IMPROVED LIGAND GEOMETRIES IN CRYSTALLOGRAPHIC REFINEMENT USING AFITT IN PHENIX

Modern crystal refinement programs rely on geometry restraints to overcome the challenge of a low data to parameter ratio. While the classical Engh & Huber restraints work well for standard residues, the chemical complexity of ligands and small molecules presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that lengthen refinement times and hinder automated refinement workflows. We present the results of combining AFITT and the Phenix software suite, which together generate more chemically accurate models for small molecules. A Phenix-AFITT refinement uses a full molecular mechanics force field for ligands during refinement. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, thus making it ideal for high throughput workflows. Phenix-AFITT refinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Refinements using AFITT significantly reduce ligand energies and lead to improved geometries without detriment to R-free factors

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

Abstract The refinement of biomolecular crystallographic models relies on geometric restraints to help address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here we present an integration of the full all-atom Amber molecular dynamics force field into Phenix crystallographic refinement, which enables a more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion angle potentials, an extensive and flexible set of atom types, Lennard-Jones treatment of non-bonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over twenty-two thousand protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better; clash scores and MolProbity scores are significantly improved; and the modelling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined with traditional geometry restraints. We find in general that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum mechanical representation of active sites and improved geometric restraints for simulated annealing. IMPORTANT this document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr Word tools (available from http://journals.iucr.org/services/docxtemplate/ ) are installed when editing this document. Synopsis The full Amber force field has been integrated into Phenix as an alternative refinement target. With a slight loss in speed, it achieves improved stereochemistry, fewer steric clashes and better hydrogen bonds

Peptide Crystal Simulations Reveal Hidden Dynamics

Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in X-ray diffraction data. We present here 9.6 μs of dynamics in a small helical peptide crystal with 36 independent copies of the unit cell. The average simulation structure agrees with experiment to within 0.28 Å backbone and 0.42 Å all-atom RMSD; a model refined against the average simulation density agrees with the experimental structure to within 0.20 Å backbone and 0.33 Å all-atom RMSD. The <i>R</i>-factor between the experimental structure factors and those derived from this unrestrained simulation is 23% to 1.0 Å resolution. The <i>B</i>-factors for most heavy atoms agree well with experiment (Pearson correlation of 0.90), but <i>B</i>-factors obtained by refinement against the average simulation density underestimate the coordinate fluctuations in the underlying simulation where the simulation samples alternate conformations. A dynamic flow of water molecules through channels within the crystal lattice is observed, yet the average water density is in remarkable agreement with experiment. A minor population of unit cells is characterized by reduced water content, 3₁₀ helical propensity and a <i>gauche</i>(-) side-chain rotamer for one of the valine residues. Careful examination of the experimental data suggests that transitions of the helices are a simulation artifact, although there is indeed evidence for alternate valine conformers and variable water content. This study highlights the potential for crystal simulations to detect dynamics and heterogeneity in experimental diffraction data as well as to validate computational chemistry methods