Prediction of structural classes for protein sequences and domains—Impact of prediction algorithms, sequence representation and homology, and test procedures on accuracy

This paper addresses computational prediction of protein structural classes. Although in recent years progress in this field was made, the main drawback of the published prediction methods is a limited scope of comparison procedures, which in same cases were also improperly performed. Two examples include using protein datasets of varying homology, which has significant impact on the prediction accuracy, and comparing methods in pairs using different datasets. Based on extensive experimental work, the main aim of this paper is to revisit and reevaluate state of the art in this field. To this end, this paper performs a first-of-its-kind comprehensive and multi-goal study, which includes investigation of eight prediction algorithms, three protein sequence representations, three datasets with different homologies and finally three test procedures. Quality of several previously unused prediction algorithms, newly proposed sequence representation, and a new-to-the-field testing procedure is evaluated. Several important conclusions and findings are made. First, the logistic regression classifier, which was not previously used, is shown to perform better than other prediction algorithms, and high quality of previously used support vector machines is confirmed. The results also show that the proposed new sequence representation improves accuracy of the high quality prediction algorithms, while it does not improve results of the lower quality classifiers. The study shows that commonly used jackknife test is computationally expensive, and therefore computationally less demanding 10-fold cross-validation procedure is proposed. The results show that there is no statistically significant difference between these two procedures. The experiments show that sequence homology has very significant impact on the prediction accuracy, i.e. using highly homologous datasets results in higher accuracies. Thus, results of several past studies that use homologous datasets should not be perceived as reliable. The best achieved prediction accuracy for low homology datasets is about 57% and confirms results reported by Wang and Yuan [How good is the prediction of protein structural class by the component-coupled method?. Proteins 2000;38:165–175]. For a highly homologous dataset instance based classification is shown to be better than the previously reported results. It achieved 97% prediction accuracy demonstrating that homology is a major factor that can result in the overestimated prediction accuracy.     

Java enabling collaborative education,health care,and computing

Web technologies – in particular linked Java servers and clients – allow new dynamic collaborative environments linking people and computers. We describe the architecture of a system, TANGOsim, that combines a Java collaborative environment with an executive providing general message filters, and an event-driven simulator. The initial application is to command and control, but we describe how this approach can also be used in other areas, such as health care, scientific visualization and (distance) education. © 1997 John Wiley & Sons, Ltd.     

Antibacterial and Cytotoxicity Evaluation of New Hydroxyapatite-Based Granules Containing Silver or Gallium Ions with Potential Use as Bone Substitutes

The aim of the current work was to study the physicochemical properties and biological activity of different types of porous granules containing silver or gallium ions. Firstly, hydroxyapatites powders doped with Ga³⁺ or Ag⁺ were synthesized by the standard wet method. Then, the obtained powders were used to fabricate ceramic microgranules (AgM and GaM) and alginate/hydroxyapatite composite granules (AgT and GaT). The ceramic microgranules were also used to prepare a third type of granules (AgMT and GaMT) containing silver or gallium, respectively. All the granules turned out to be porous, except that the AgT and GaT granules were characterized by higher porosity and a better developed specific surface, whereas the microgranules had very fine, numerous micropores. The granules revealed a slow release of the substituted ions. All the granules except AgT were classified as non-cytotoxic according to the neutral red uptake (NRU) test and the MTT assay. The obtained powders and granules were subjected to various antibacterial test towards the following four different bacterial strains: Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas aeruginosa and Escherichia coli. The Ag-containing materials revealed high antibacterial activity.     

Energy policy and the role of bioenergy in Poland

Poland, as many other countries, has ambitions to increase the use of renewable energy sources. In this paper, we review the current status of bioenergy in Poland and make a critical assessment of the prospects for increasing the share of bioenergy in energy supply, including policy implications. Bioenergy use was about 4% (165 PJ) of primary energy use (3900 PJ) and 95% of renewable energy use (174 PJ) in 2003, mainly as firewood in the domestic sector. Targets have been set to increase the contribution of renewable energy to 7.5% in 2010, in accordance with the EU accession treaty, and to 14% in 2020. Bioenergy is expected to be the main contributor to reaching those targets. From a resource perspective, the use of bioenergy could at least double in the near term if straw, forestry residues, wood-waste, energy crops, biogas, and used wood were used for energy purposes. The long-term potential, assuming short rotation forestry on potentially available agricultural land is about one-third, or 1400 PJ, of current total primary energy use. However, in the near term, Poland is lacking fundamental driving forces for increasing the use of bioenergy (e.g., for meeting demand increases, improving supply security, or further reducing sulphur or greenhouse gas emissions). There is yet no coherent policy or strategy for supporting bioenergy. Co-firing with coal in large plants is an interesting option for creating demand and facilitating the development of a market for bioenergy. The renewable electricity quota obligation is likely to promote such co-firing but promising applications of bioenergy are also found in small- and medium-scale applications for heat production. Carbon taxes and, or, other financial support schemes targeted also at the heating sector are necessary in the near term in order to reach the 7.5% target. In addition, there is a need to support the development of supply infrastructure, change certain practices in forestry, coordinate RD&D efforts, and support general capacity building. The greatest challenge for the longer term lies in reforming and restructuring the agricultural sector.     

Electrical Properties of Carbon Nanotube Based Fibers and Their Future Use in Electrical Wiring

The production of continuous fibers made purely of carbon nanotubes has paved the way for new macro‐scale applications which utilize the superior properties of individual carbon nanotubes. These wire‐like macroscopic assemblies of carbon nanotubes were recognized to have a potential to be used in electrical wiring. Carbon nanotube wiring may be extremely light and mechanically stronger and more efficient in transferring high frequency signals than any conventional conducting material, being cost‐effective simultaneously. However, transfer of the unique properties of individual CNTs to the macro‐scale proves to be quite challenging. This Feature Article gives an overview of the potential of using carbon nanotube fibers as next generation wiring, state of the art developments in this field, and goals to be achieved before carbon nanotubes may be transformed into competitive products.     

An adaptive calibration and beamforming technique for a GEO satellite data relay

High throughput data links from low Earth orbit satellites through a geostationary orbit satellite data relay have been proposed to increase the available contact times to ground stations. Accurate antenna beam pointing and tracking of moving targets are key requirements for the relay satellite. In this work, we propose an adaptive calibration and beamforming methodology on the basis of least mean squares, which is suitable for a geostationary orbit data relay. The target system consists of the combination of a high gain reflector fed by a digitally steerable patch antenna array. The proposed method is first presented by numerical cosimulation of the antenna and the calibration algorithm. The results are then validated in an outdoor experimental setup with all digital signal processing implemented in a field‐programmable gate array. We demonstrate the tracking ability and pointing performance of the digitally enhanced reflector antenna with gain fluctuations smaller than 3 dB over a field of view of at least 2,5°. The demonstrated performance shows that the digitally enhanced reflector antenna is a suitable candidate for long‐distance space communications.     

Replacing Copper Wires with Carbon Nanotube Wires in Electrical Transformers

Carbon nanotubes, with their unique physical properties, have the potential to outperform conventionally used electrical wiring metals. Any improvement in this area of technology would be of great importance to industry, the economy, and the environment, as the global need for electrical energy and its efficient transfer and conversion rapidly increases. Carbon nanotube fibers, which are assemblies made purely of carbon nanotubes, can uniquely be used in macroscopic electrical applications including electrical wires and devices where the operation is enabled by these conductors. This paper presents details of the working prototype of an electrical machine, a transformer, where conventional copper wires have been replaced with conducting wires made purely of carbon nanotube fibers.     

Thrombin Inhibition Prevents Endothelial Dysfunction and Reverses 20-HETE Overproduction without Affecting Blood Pressure in Angiotensin II-Induced Hypertension in Mice

Angiotensin II (Ang II) induces hypertension and endothelial dysfunction, but the involvement of thrombin in these responses is not clear. Here, we assessed the effects of the inhibition of thrombin activity by dabigatran on Ang II-induced hypertension and endothelial dysfunction in mice with a particular focus on NO- and 20-HETE-dependent pathways. As expected, dabigatran administration significantly delayed thrombin generation (CAT assay) in Ang II-treated hypertensive mice, and interestingly, it prevented endothelial dysfunction development, but it did not affect elevated blood pressure nor excessive aortic wall thickening. Dabigatran’s effects on endothelial function in Ang II-treated mice were evidenced by improved NO-dependent relaxation in the aorta in response to acetylcholine in vivo (MRI measurements) and increased systemic NO bioavailability (NO₂⁻ quantification) with a concomitant increased ex vivo production of endothelium-derived NO (EPR analysis). Dabigatran treatment also contributed to the reduction in the endothelial expression of pro-inflammatory vWF and ICAM-1. Interestingly, the fall in systemic NO bioavailability in Ang II-treated mice was associated with increased 20-HETE concentration in plasma (UPLC-MS/MS analysis), which was normalised by dabigatran treatment. Taking together, the inhibition of thrombin activity in Ang II-induced hypertension in mice improves the NO-dependent function of vascular endothelium and normalises the 20-HETE-depedent pathway without affecting the blood pressure and vascular remodelling.     

Effect of impact angle and projectile size on sputtering efficiency of solid benzene investigated by molecular dynamics simulations

Molecular dynamics computer simulations have been used to investigate the effect of the cluster size on the sputtering yield dependence on the impact angle. Ar₃₆₆ and Ar₂₉₅₃ cluster projectiles with 14.75 keV of incident energy are directed at the surface of a solid benzene crystal described by a coarse-grained representation at angles between 0° and 70°. It is observed that the shape of the angular dependence of sputtering efficiency is strongly affected by the cluster size. For the Ar₃₆₆ cluster, the sputtering yield only slightly increases with the impact angle, has a broad maximum around 40°, and decreases at larger angles. For the Ar₂₉₅₃ cluster, the yield strongly increases with the impact angle, has a maximum around 45° followed by a steep decrease at larger angles. For both investigated cluster projectiles the primary energy is deposited so close to the surface so that the sputtering efficiency only weekly benefits from the shift of the deposited energy profile toward the surface which occurs at larger impact angles. In this study, molecular dynamics computer simulations are used to probe the effect of the impact angle on the efficiency of ejection molecules emitted from solid benzene by 14.75 keV Ar₃₆₆ and Ar₂₉₅₃ clusters.