Prediction of protein B-factor profiles

The polypeptide backbones and side chains of proteins are constantly moving due to thermal motion and the kinetic energy of the atoms. The B-factors of protein crystal structures reflect the fluctuation of atoms about their average positions and provide important information about protein dynamics. Computational approaches to predict thermal motion are useful for analyzing the dynamic properties of proteins with unknown structures. In this article, we utilize a novel support vector regression (SVR) approach to predict the B-factor distribution (B-factor profile) of a protein from its sequence. We explore schemes for encoding sequences and various settings for the parameters used in SVR. Based on a large dataset of high-resolution proteins, our method predicts the B-factor distribution with a Pearson correlation coefficient (CC) of 0.53. In addition, our method predicts the B-factor profile with a CC of at least 0.56 for more than half of the proteins. Our method also performs well for classifying residues (rigid vs. flexible). For almost all predicted B-factor thresholds, prediction accuracies (percent of correctly predicted residues) are greater than 70%. These results exceed the best results of other sequence-based prediction methods. (C) 2005 Wiley-Liss, Inc.

Power perceptions and modes of complaining in higher education

This study examines the relationship between student perceptions of different types of educator power and different modes of student complaining behaviour in the case of university education. A large sample of marketing students in the business school responded to the study from a state university in Northeastern United States. Factor analysis and canonical correlation analysis are used to explore the relationships between five bases of power perceptions (referent, expert, reward, legitimate, and punishment) and four modes of complaining behaviour (voice, negative word of mouth, third party, and exit). The results indicate that students engage in different modes of complaining as they perceive different types of educator power. The predominant complaining mode is found to be voice under referent or expert power, third party under legitimate power, and exit under reward or punishment power. Our findings offer important implications for student satisfaction, retention, and completion rates in higher education.

Size frequency distributions of the florid prion protein aggregates in variant Creutzfeldt-Jakob disease follow a power-law function

The objective was to test the hypothesis that the size frequency distributions of the prion protein (PrP) plaques in cases of variant Creutzfeldt-Jakob disease (vCJD) follow a power-law function. The design was a retrospective neuropathological study. The patients were 11 cases of clinically and neuropathologically verified vCJD. Size distributions of the diffuse and florid-type plaques were measured in several areas of the cerebral cortex and hippocampus from each case and a power-law function fitted to each distribution. The size distributions of the florid and diffuse plaques were fitted successfully by a powerlaw function in 100% and 42% of brain areas investigated respectively. Processes of aggregation/disaggregation may be more important than surface diffusion in the pathogenesis of the florid plaques. By contrast, surface diffusion may be a more significant factor in the development of the diffuse plaques. © Springer-Verlag Italia 2006.

Role of power jitter induced by interchannel interactions in dispersion-managed lines

Collision induced power jitter is examined in dispersion-managed wavelength division-multiplexed transmission systems. The power jitter causes ’ a serious problem for a singly-periodic dispersion managed line having almost zero average dispersion, which can be reduced by applying doubly-periodic dispersion management.

Analysis of power jitter induced by interchannel interactions in dispersion-managed optical soliton transmission systems

Collision-induced power jitter is theoretically and numerically examined in dispersion-managed wavelength-division-multiplexed optical soliton transmission systems. The variational method is mainly used to develop a time efficient jitter calculation approach. The power jitter causes a serious problem for a singly periodic dispersion managed line having almost zero average dispersion, which can be reduced by applying doubly periodic dispersion management.

Addressing the project implementation challenges in the Saudi Arabian power supply industry: an investigative approach towards improving project delivery

For many decades, the Kingdom of Saudi Arabia has been widely known for being a reliable oil exporter. This fact, however, has not exempted it from facing significant domestic energy challenges. One of the most pressing of these challenges involves bridging the widening electricity supply-demand gap where, currently, the demand is growing at a very fast rate. One crucial means to address this challenge is through delivering power supply projects with maximum efficiency. Project delivery delay, however, is not uncommon in this highly capital-intensive industry, indicating electricity supplies are not coping with the demand increases. To provide a deeper insight into the challenges of project implementation and efficient practice, this research adopts a pragmatic approach by triangulating literature, questionnaires and semi-structured interviews. The research was conducted in the Saudi Arabian power supply industry – Western Operating Area. A total of 105 usable questionnaires were collected, and 28 recorded, semi-structured interviews were conducted, analysed and synthesised to produce a conceptual model of what constitutes the project implementation challenges in the investigated industry. This was achieved by conducting a comprehensive ranking analysis applied to all 58 identified and surveyed factors which, according to project practitioners in the investigated industry, contribute to project delay. 28 of these project delay factors were selected as the "most important" ones. Factor Analysis was employed to structure these 28 most important project delay factors into the following meaningful set of 7 project implementation challenges: Saudi Electricity Company's contractual commitments, Saudi Electricity Company's communication and coordination effectiveness, contractors' project planning and project control effectiveness, consultant-related aspects, manpower challenges and material uncertainties, Saudi Electricity Company's tendering system, and lack of project requirements clarity. The study has implications for industry policy in that it provides a coherent assessment of the key project stakeholders' central problems. From this analysis, pragmatic recommendations are proposed that, if enacted, will minimise the significance of the identified problems on future project outcomes, thus helping to ensure the electricity supply-demand gap is diminished.

Statnote 11: the two-factor analysis of variance

Experiments combining different groups or factors are a powerful method of investigation in applied microbiology. ANOVA enables not only the effect of individual factors to be estimated but also their interactions; information which cannot be obtained readily when factors are investigated separately. In addition, combining different treatments or factors in a single experiment is more efficient and often reduces the number of replications required to estimate treatment effects adequately. Because of the treatment combinations used in a factorial experiment, the degrees of freedom (DF) of the error term in the ANOVA is a more important indicator of the ‘power’ of the experiment than simply the number of replicates. A good method is to ensure, where possible, that sufficient replication is present to achieve 15 DF for each error term of the ANOVA. Finally, in a factorial experiment, it is important to define the design of the experiment in detail because this determines the appropriate type of ANOVA. We will discuss some of the common variations of factorial ANOVA in future statnotes. If there is doubt about which ANOVA to use, the researcher should seek advice from a statistician with experience of research in applied microbiology.

Statnote 13: a more complex analysis of variance incorporating a 'repeated measures' factor

Experiments combining different groups or factors and which use ANOVA are a powerful method of investigation in applied microbiology. ANOVA enables not only the effect of individual factors to be estimated but also their interactions; information which cannot be obtained readily when factors are investigated separately. In addition, combining different treatments or factors in a single experiment is more efficient and often reduces the sample size required to estimate treatment effects adequately. Because of the treatment combinations used in a factorial experiment, the degrees of freedom (DF) of the error term in the ANOVA is a more important indicator of the ‘power’ of the experiment than the number of replicates. A good method is to ensure, where possible, that sufficient replication is present to achieve 15 DF for the error term of the ANOVA testing effects of particular interest. Finally, it is important to always consider the design of the experiment because this determines the appropriate ANOVA to use. Hence, it is necessary to be able to identify the different forms of ANOVA appropriate to different experimental designs and to recognise when a design is a split-plot or incorporates a repeated measure. If there is any doubt about which ANOVA to use in a specific circumstance, the researcher should seek advice from a statistician with experience of research in applied microbiology.

Solidarity and power in German : language as political action : a contribution to the socio-cultural history of the German language

Germany's latest attempt at unification raises again the question of German nationhood and nationality. The present study examines the links between the development of the German language and the political history of Germany, principally in the nineteenth and twentieth centuries. By examining the role of language in the establishment and exercise of political power and in the creation of national and group solidarity in Germany, the study both provides insights into the nature of language as political action and contributes to the socio-cultural history of the German language. The language-theoretical hypothesis on which the study is based sees language as a central factor in political action, and opposes the notion that language is a reflection of underlying political 'realities' which exist independently of language. Language is viewed as language-in-text which performs identifiable functions. Following Leech, five functions are distinguished, two of which (the regulative and the phatic) are regarded as central to political processes. The phatic function is tested against the role of the German language as a creator and symbol of national identity, with particular attention being paid to concepts of the 'purity' of the language. The regulative function (under which a persuasive function is also subsumed) is illustrated using the examples of German fascist discourse and selected cases from German history post-1945. In addition, the interactions are examined between language change and socio-economic change by postulating that language change is both a condition and consequence of socio-economic change, in that socio-economic change both requires and conditions changes in the communicative environment. Finally, three politocolinguistic case studies from the eight and ninth decades of the twentieth century are introduced in order to demonstrate specific ways in which language has been deployed in an attempt to create political realities, thus verifying the initial hypothesis of the centrality of language to the political process.

Does stakeholder orientation matter? : empirical evidence about power and influence in local government decision-making

Despite being in the business agenda for almost thirty years, stakeholder management is still an under explored field in the public management context. The investigation presented in this doctoral thesis aims to ensure that stakeholder management is a useful technique able to raise issues about power and interests to public organisation’s strategic management processes. Stakeholder theory is tested in an exploratory study carried out with English Local Authorities whose focus is place on decision-making. The findings derive from two distinct and complementary studies: a cross-sectional survey undertaken with chief executives based on the quantitative approach and a qualitative investigation based on cross-sectional case studies and in-depth interviews of validation. While the first study aimed to produce a reliable and comprehensive list of stakeholders able to raise issues in decision-making, the second study aimed to depict the arena in which decision-making comes about. The findings indicate that local government decision-making is a multistakeholder process in which influences are exerted according to stakeholders’ power and interest. The findings also indicate that local government managers should take into account these tissues to avoid losing resources and legitimacy from its environmental supporters. Another issue raised by the investigation is related to the ethics upon which these types of relationships are based. According to the evidence gathered throughout the investigation, the formal model of accountability does not cover the whole set of stakeholders engaged in the process.

Attenuation of muscle atrophy by an N-terminal peptide of the receptor for proteolysis-inducing factor (PIF)

Background: Atrophy of skeletal muscle in cancer cachexia has been attributed to a tumour-produced highly glycosylated peptide called proteolysis-inducing factor (PIF). The action of PIF is mediated through a high-affinity membrane receptor in muscle. This study investigates the ability of peptides derived from the 20 N-terminal amino acids of the receptor to neutralise PIF action both in vitro and in vivo. Methods: Proteolysis-inducing factor was purified from the MAC16 tumour using an initial pronase digestion, followed by binding on DEAE cellulose, and the pronase was inactivated by heating to 80°C, before purification of the PIF using affinity chromatography. In vitro studies were carried out using C2C12 murine myotubes, while in vivo studies employed mice bearing the cachexia-inducing MAC16 tumour. Results: The process resulted in almost a 23?000-fold purification of PIF, but with a recovery of only 0.004%. Both the D- and L-forms of the 20mer peptide attenuated PIF-induced protein degradation in vitro through the ubiquitin-proteosome proteolytic pathway and increased expression of myosin. In vivo studies showed that neither the D- nor the L-peptides significantly attenuated weight loss, although the D-peptide did show a tendency to increase lean body mass. Conclusion: These results suggest that the peptides may be too hydrophilic to be used as therapeutic agents, but confirm the importance of the receptor in the action of the PIF on muscle protein degradation.

Impact of power allocation strategies in long-haul few-mode fiber transmission systems

We report for the first time on the limitations in the operational power range of few-mode fiber based transmission systems, employing 28Gbaud quadrature phase shift keying transponders, over 1,600km. It is demonstrated that if an additional mode is used on a preexisting few-mode transmission link, and allowed to optimize its performance, it will have a significant impact on the pre-existing mode. In particular, we show that for low mode coupling strengths (weak coupling regime), the newly added variable power mode does not considerably impact the fixed power existing mode, with performance penalties less than 2dB (in Q-factor). On the other hand, as mode coupling strength is increased (strong coupling regime), the individual launch power optimization significantly degrades the system performance, with penalties up to ∼6dB. Our results further suggest that mutual power optimization, of both fixed power and variable power modes, reduces power allocation related penalties to less than 3dB, for any given coupling strength, for both high and low differential mode delays. © 2013 Optical Society of America.

Estimation of productivity in Korean electric power plants:a semiparametric smooth coefficient model

This paper analyzes the impact of load factor, facility and generator types on the productivity of Korean electric power plants. In order to capture important differences in the effect of load policy on power output, we use a semiparametric smooth coefficient (SPSC) model that allows us to model heterogeneous performances across power plants and over time by allowing underlying technologies to be heterogeneous. The SPSC model accommodates both continuous and discrete covariates. Various specification tests are conducted to compare performance of the SPSC model. Using a unique generator level panel dataset spanning the period 1995-2006, we find that the impact of load factor, generator and facility types on power generation varies substantially in terms of magnitude and significance across different plant characteristics. The results have strong implication for generation policy in Korea as outlined in this study.

High rate growth of nanocrystalline diamond films using high microwave power and pure nitrogen/methane/hydrogen plasma

In this work, we investigate the impact of minute amounts of pure nitrogen addition into conventional methane/hydrogen mixtures on the growth characteristics of nanocrystalline diamond (NCD) films by microwave plasma assisted chemical vapour deposition (MPCVD), under high power conditions. The NCD films were produced from a gas mixture of 4% CH4/H2 with two different concentrations of N2 additive and microwave power ranging from 3.0 kW to 4.0 kW, while keeping all the other operating parameters constant. The morphology, grain size, microstructure and texture of the resulting NCD films were characterized by using scanning electron microscope (SEM), micro-Raman spectroscopy and X-ray diffraction (XRD) techniques. N2 addition was found to be the main parameter responsible for the formation and for the key change in the growth characteristics of NCD films under the employed conditions. Growth rates ranging from 5.4 μm/h up to 9.6 μm/h were achieved for the NCD films, much higher than those usually reported in the literature. The enhancing factor of nitrogen addition on NCD growth rate was obtained by comparing with the growth rate of large-grained microcrystalline diamond films grown without nitrogen and discussed by comparing with that of single crystal diamond through theoretical work in the literature. This achievement on NCD growth rate makes the technology interesting for industrial applications where fast coating of large substrates is highly desirable.

Effect of a tumour-derived lipid-mobilising factor on glucose and lipid metabolism in vivo

Treatment of ex-breeder male NMRI mice with lipid mobilising factor isolated from the urine of cachectic cancer patients, caused a significant increase in glucose oxidation to CO2, compared with control mice receiving phosphate buffered saline. Glucose utilisation by various tissues was determined by the 2-deoxyglucose tracer technique and shown to be elevated in brain, heart, brown adipose tissue and gastrocnemius muscle. The tissue glucose metabolic rate was increased almost three-fold in brain, accounting for the ability of lipid mobilising factor to decrease blood glucose levels. Lipid mobilising factor also increased overall lipid oxidation, as determined by the production of 14CO2 from [14C carboxy] triolein, being 67% greater than phosphate buffered saline controls over a 24 h period. There was a significant increase in [14C] lipid accumulation in plasma, liver and white and brown adipose tissue after administration of lipid mobilising factor. These results suggest that changes in carbohydrate metabolism and loss of adipose tissue, together with an increased whole body fatty acid oxidation in cachectic cancer patients, may arise from tumour production of lipid mobilising factor. © 2002 Cancer Research UK.