From Side Chains Rattling on Picoseconds to Ensemble Simulations of Protein Folding

Simulations of biological macromolecules have evolved tremendously since the discoveries of the 1970s. The field has moved from simple simulations in vacuo on picosecond scales to milliseconds of accurate sampling of large proteins, and it has become a standard tool in biochemistry and biophysics, rather than a dedicated theoretical one. This is partly due to increasing computational power, but it would not have been possible without huge research efforts invested in new algorithms and software. Here, we illustrate some of this development, both past and future challenges, and in particular, discuss how the recent introduction of modern ensemble methods is breaking the trend of ever-longer simulations to instead focus on throughput and sampling. This has not only helped simulations become much more accurate, but it provides statistical error estimates, which are critical, as simulations are increasingly used to predict properties that have not yet been measured experimentally.     

Autogenous deformation and RH-change in perspective

Autogenous deformation and change of the relative humidity (RH-change) have been described and registered for a century. However, it is only within the last decade that these phenomena have received appreciable attention. The reason for this is that autogenous deformation and autogenous RH-change are phenomena of special importance within high-strength (high-performance) concrete technology, and a significant utilisation of these concretes did not take place until the early 1980s. In the present paper an historical overview of autogenous deformation and RH-change is given. In addition, due to the present status of this research field both terminology and measuring techniques are described in detail. Finally, some expectations for future research in this field are given.     

Durability of fire retardant treated wood products at humid and exterior conditions review of literature

Fire retardants may considerably improve the fire properties of wood products, but the durability, e.g. in exterior applications, has not been addressed fully. This paper reviews the existing knowledge and experience mainly from the USA with the aim of supporting further development in Europe. The review is concentrated on pressure impregnated fire retardant treated wood products which have the best opportunities for increased durability. Copyright © 2001 by John Wiley & Sons, Ltd.     

Integrating Ecological,Social and Cultural Dimensions in the Implementation of the Landscape Convention

Implementation of the European Landscape Convention requires new tools that link ecological, social and cultural dimensions in practical planning. Here, we propose connectivity as a conceptual tool to include different dimensions into landscape and spatial planning. We present a short review of the connectivity concept in relation to ecological, social and cultural dimensions and illustrate it by examples from a real landscape planning case.     

Metabolic versatility in full-scale wastewater treatment plants performing enhanced biological phosphorus removal

This study analysed the enhanced biological phosphorus removal (EBPR) microbial community and metabolic performance of five full-scale EBPR systems by using fluorescence in situ hybridisation combined with off-line batch tests fed with acetate under anaerobic–aerobic conditions. The phosphorus accumulating organisms (PAOs) in all systems were stable and showed little variability between each plant, while glycogen accumulating organisms (GAOs) were present in two of the plants. The metabolic activity of each sludge showed the frequent involvement of the anaerobic tricarboxylic acid cycle (TCA) in PAO metabolism for the anaerobic generation of reducing equivalents, in addition to the more frequently reported glycolysis pathway. Metabolic variability in the use of the two pathways was also observed, between different systems and in the same system over time. The metabolic dynamics was linked to the availability of glycogen, where a higher utilisation of the glycolysis pathway was observed in the two systems employing side-stream hydrolysis, and the TCA cycle was more active in the A²O systems. Full-scale plants that showed higher glycolysis activity also exhibited superior P removal performance, suggesting that promotion of the glycolysis pathway over the TCA cycle could be beneficial towards the optimisation of EBPR systems.     

Trajectory Analysis of Forest Cover Change in the Tropical Dry Forest of Burkina Faso,West Africa

Forest cover decline is one of the most important environmental issues in the tropics. The present study was carried out in Burkina Faso, West Africa, and aimed at assessing the trajectories of forest cover change and measuring landscape metrics of the trajectory classes in order to better understand the processes of change. Landsat and ASTER images acquired over a period of 30 years were used for cover change detection and the Fragstats package was used to compute landscape metrics with five unifying change classes. Results showed a substantial increase in cropland with concurrent decline in forest cover. Deforestation represented 63% of the Percentage of Landscape (PLAND) in 2006, while reforestation accounted for only 28%. Both of these classes had high Normalized Landscape Shape Index (NLSI) values, indicating that they were present as scattered small patches. The old cultivation (30-year permanent cropland) was aggregated (IJI ≈ 0) while deforestation exhibited highly interspersed patches. The old forest and old cultivation presented lower Area Weighted Fractal Dimension Index (FRAC_AM), but deforestation and reforestation had the higher FRAC_AM. These results confirmed that there was a high level of deforestation and fragmentation in southern Burkina Faso and justify the need for a proper management plan to ensure the sustainable use of forest resources.     

Exploration and exploitation in project-based organizations: Development and diffusion of knowledge at different organizational levels in construction companies

Management studies highlight the importance of an organization's capability to both exploit existing knowledge and technologies for short-term profits and also explore new knowledge and technologies to enhance long-term innovation. Although this paradox recently has received escalating interest in management research, studies dealing with project-levels and project-based organizations (PBOs) are scarce. This conceptual paper discusses how PBOs in the construction industry can manage the exploration/exploitation paradox at different organizational levels. Short-term project focus and decentralization inhibits learning from one point in time and space to another, making it easier to reap the benefits of exploitation than of exploration. Current structural and sequential separation of exploration and exploitation activities at business unit, project portfolio, and project levels do not solve the paradox, due to lack of integrating mechanisms. Hence, PBOs in the construction industry may suffer from inadequate extent of exploration, while the extent of exploitation is not reaching its potential. Cooperative procurement procedures can serve as a basis for facilitating both exploration and exploitation of knowledge and technologies in construction projects.     

Evaluation of Gene Expression Knock-Down by Chemically and Structurally Modified Gapmer Antisense Oligonucleotides

We analyzed the effect of modified nucleotides within gapmer antisense oligonucleotides on RNase H mediated gene silencing. Additionally, short hairpins were introduced into antisense oligonucleotides as structural motifs, and their influence on biological and physicochemical properties of pre-structured gapmers was investigated for the first time. The results indicate that two LNA residues in specified positions of the gap flanking regions are sufficient and favorable for efficient knock-down of the β-actin gene. Furthermore, the introduction of other modified nucleotides, i. e. glycyl-amino-LNA−T, 2′-O-propagyluridine, polyamine functionalized uridine, and UNA, in specified positions, also increases the inhibition of β-actin expression. Importantly, the presence of hairpins within the gapmers improves their silencing properties.     

Acid Hydrogen Peroxide Treatment of Norway Spruce TMP: The Effect of an Extended pH Range when Catalyzed by Free Ferrous and Free or EDG/EDTA-Chelated Ferric Ions

The influence of different types of iron salts (i.e., ferrous or ferric cations with sulphate, nitrate or chloride anions) on the reaction between coarse thermomechanical pulp and acid hydrogen peroxide (Fenton chemistry) was studied when the initial pH was 3.2 and 5.3. Also, ferric ions chelated with EDTA or EDG at different molar ratios were compared with ferrous sulphate when the initial pH was extended from about 3 to 8. Different anions of ferric ion salt gave a similar catalytic effect. At an initial pH of 7–8, the ferric-EDTA catalyzed reaction resulted in similar or higher hydrogen peroxide consumption and more detectable hydroxyl radicals than the ferrous sulphate catalyzed reaction, but less reaction with the pulp was indicated. Between pH 5–8, using Fe-EDG as a catalyst gave higher hydrogen peroxide consumption and more detectable hydroxyl radicals than if using ferrous sulphate; however, the measured effect on the pulp was similar or less.     

Effect of the Degree of Phosphorylation on the Crystallinity of Native Potato Starch

X-ray diffraction technique, combined with digital image processing was used to compare the crystallinity of native starch from a number of potato varieties, differing in the degree of phosphorylation. The crystallinity was found to decrease linearily with an increased degree of phosphorylation. Based on earlier observations of the gelatinization enthalpies, it was assumed that the C-6 phosphates, which have an orientation out of the α-helices disturb the crystallization of the amylopectin during the starch synthesis. The C-3 phosphates, which are located in the interior parts of the α-helices, are not believed to interfere with the crystal structure.