Towards data warehousing and mining of protein unfolding simulation data

OBJECTIVES: The prediction of protein structure and the precise understanding of protein folding and unfolding processes remains one of the greatest challenges in structural biology and bioinformatics. Computer simulations based on molecular dynamics (MD) are at the forefront of the effort to gain a deeper understanding of these complex processes. Currently, these MD simulations are usually on the order of tens of nanoseconds, generate a large amount of conformational data and are computationally expensive. More and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. METHODS: To adequately organize, manage, and analyze the data generated by unfolding simulation studies, we designed a data warehouse system that is embedded in a grid environment to facilitate the seamless sharing of available computer resources and thus enable many groups to share complex molecular dynamics simulations on a more regular basis. RESULTS: To gain insight into the conformational fluctuations and stability of the monomeric forms of the amyloidogenic protein transthyretin (TTR), molecular dynamics unfolding simulations of the monomer of human TTR have been conducted. Trajectory data and meta-data of the wild-type (WT) protein and the highly amyloidogenic variant L55P-TTR represent the test case for the data warehouse. CONCLUSIONS: Web and grid services, especially pre-defined data mining services that can run on or 'near' the data repository of the data warehouse, are likely to play a pivotal role in the analysis of molecular dynamics unfolding data.

An in-depth view of the facets, antecedents and effects of leaders’ change competency: lessons from a case study

Leaders across companies initiate and implement change and thus are crucial for successful organizations. This study takes a competency perspective on leaders and investigates the competencies leaders show to facilitate effective change. The article explores the content of the construct of leaders’ change competency and examines its antecedents and effects. We conducted a case study in a German tourism company undergoing a major change process. The study identified (a) distinct content facets regarding the construct of leaders’ change competency along its two dimensions of leaders’ readiness for change and leaders’ change ability; (b) the construct’s antecedents, specifically contextual factors, leaders’ competency potentials, and attitudes toward change; and (c) beneficial effects of leaders’ change competency. The study ends with implications for research and leadership practice as well as suggestions for future studies on leaders’ change competency.

Extending Murty interferometry to the Terahertz part of the spectrum

We discuss some novel technologies that enable the implementation of shearing interferometry at the terahertz part of the spectrum. Possible applications include the direct measurement of lens parameters, the measurement of refractive index of materials that are transparent to terahertz frequencies, determination of homogeneity of samples, measurement of optical distortions and the non-contact evaluation of thermal expansion coefficient of materials buried inside media that are opaque to optical or infrared frequencies but transparent to THz frequencies. The introduction of a shear to a Gaussian free-space propagating terahertz beam in a controlled manner also makes possible a range of new encoding and optical signal processing modalities.

A 45 kyr palaeoclimate record from the lowland interior of tropical South America

We present a well-dated, high-resolution, ~ 45 kyr lake sediment record reflecting regional temperature and precipitation change in the continental interior of the Southern Hemisphere (SH) tropics of South America. The study site is Laguna La Gaiba (LLG), a large lake (95 km2) hydrologically-linked to the Pantanal, an immense, seasonally-flooded basin and the world's largest tropical wetland (135,000 km2). Lake-level changes at LLG are therefore reflective of regional precipitation. We infer past fluctuations in precipitation at this site through changes in: i) pollen-inferred extent of flood-tolerant forest; ii) relative abundance of terra firme humid tropical forest versus seasonally-dry tropical forest pollen types; and iii) proportions of deep- versus shallow-water diatoms. A probabilistic model, based on plant family and genus climatic optima, was used to generate quantitative estimates of past temperature from the fossil pollen data. Our temperature reconstruction demonstrates rising temperature (by 4 °C) at 19.5 kyr BP, synchronous with the onset of deglacial warming in the central Andes, strengthening the evidence that climatic warming in the SH tropics preceded deglacial warming in the Northern Hemisphere (NH) by at least 5 kyr. We provide unequivocal evidence that the climate at LLG was markedly drier during the last glacial period (45.0–12.2 kyr BP) than during the Holocene, contrasting with SH tropical Andean and Atlantic records that demonstrate a strengthening of the South American summer monsoon during the global Last Glacial Maximum (~ 21 kyr BP), in tune with the ~ 20 kyr precession orbital cycle. Holocene climate conditions occurred as early as 12.8–12.2 kyr BP, when increased precipitation in the Pantanal catchment caused heightened flooding and rising lake levels in LLG. In contrast to this strong geographic variation in LGM precipitation across the continent, expansion of tropical dry forest between 10 and 3 kyr BP at LLG strengthens the body of evidence for widespread early–mid Holocene drought across tropical South America.

Dementia and cancer: a review of the literature and current practice

Age is a risk factor for dementia, and also for most cancers. Surprisingly, rates of cancer appear to be lower in individuals with dementia and vice versa. Genetic mechanisms could underpin this inverse relationship and are outlined, but underdiagnosis must also be taken into account. Individuals with cancer and dementia pose unique challenges to healthcare professionals owing to the potential for impaired decision-making capacity, poor communication and difficulties following medication regimes. Mild cognitive impairment and ‘chemo brain’ should be differentiated from progressive neurodegeneration.

The effects of cross-border and cross-industry mergers and acquisitions on home-region and global multinational enterprises

We examine the effects of international and product diversification through mergers and acquisitions (M&As) on the firm's risk–return profile. We identify the rewards from different types of M&As and investigate whether becoming a global firm is a value-enhancing strategy. Drawing on the theoretical work of Vachani (Journal of International Business Studies, 22 (1991), pp. 307−222) and on Rugman and Verbeke's (Journal of International Business Studies, 35 (2004), pp. 3−18) metrics, we classify firms according to their degree of international and product diversification. To account for the endogeneity of M&As, we develop a panel vector autoregression. We find that global and host-region multinational enterprises benefit from cross-border M&As that reinforce their geographical footprint. Cross-industry M&As enhance the risk–return profile of home-region firms. This effect depends on the degree of product diversification. Hence there is no value-enhancing M&A strategy for home-region and bi-regional firms to become ‘truly global’.

A cross-cultural examination of the psychometric properties of responses to the Achievement Goal Questionnaire

The psychometric properties of scores from the Achievement Goal Questionnaire were examined in samples of Japanese (N = 326) and Canadian (N = 307) post secondary students. Previous research found evidence of a four-factor structure of achievement goals in U.S. samples. Using confirmatory factor-analytic techniques, the authors found strong evidence for the four-factor structure of achievement goals in both the Canadian and Japanese populations. Subsequent multi group structural equation modeling indicated the metric invariance of this four-factor structure across the two populations.

Messages about antibiotic resistance in different newspaper genres

Poorer people are more likely to use antibiotics; inappropriate antibiotic use causes resistance, and health campaigns attempt to change behaviour through education. However, fuelled by the media, the public think antibiotic resistance is outside their control. Differences in the attribution of blame for antibiotic resistance in two genres of UK newspapers, targeting distinct socioeconomic groups, were examined using a mixed methods approach. Firstly, depiction of blame was categorised as either external to the lay public (outside their control) or internal (lay person accountable) and subjected to a chi-square test. Secondly, using critical discourse analysis, we examined the portrayal of the main agents through newspaper language. Data from 597 articles (307 broadsheets) analysed revealed a significant association between newspaper genre and attribution of blame for antibiotic resistance. While both newspaper types blamed antibiotic resistance predominantly on factors external to the lay public, broadsheets were more likely to acknowledge internal factors than tabloids. Tabloids provided a more skewed representation, exposing readers to inaccurate explanations about antibiotic resistance. They highlighted ineptitude in health professionals, victimising patients and blaming others, while broadsheets used less emotive language. Pharmacists should take special care to communicate the importance of appropriate antibiotic use against this backdrop of distortion.

Ecosystem effects of CO2 concentration: evidence from past climates

Atmospheric CO2 concentration has varied from minima of 170-200 ppm in glacials to maxima of 280-300 ppm in the recent interglacials. Photosynthesis by C-3 plants is highly sensitive to CO2 concentration variations in this range. Physiological consequences of the CO2 changes should therefore be discernible in palaeodata. Several lines of evidence support this expectation. Reduced terrestrial carbon storage during glacials, indicated by the shift in stable isotope composition of dissolved inorganic carbon in the ocean, cannot be explained by climate or sea-level changes. It is however consistent with predictions of current process-based models that propagate known physiological CO2 effects into net primary production at the ecosystem scale. Restricted forest cover during glacial periods, indicated by pollen assemblages dominated by non-arboreal taxa, cannot be reproduced accurately by palaeoclimate models unless CO2 effects on C-3-C-4 plant competition are also modelled. It follows that methods to reconstruct climate from palaeodata should account for CO2 concentration changes. When they do so, they yield results more consistent with palaeoclimate models. In conclusion, the palaeorecord of the Late Quaternary, interpreted with the help of climate and ecosystem models, provides evidence that CO2 effects at the ecosystem scale are neither trivial nor transient.

Testing for non-linearity in daily sterling exchange rates

A number of tests for non-linear dependence in time series are presented and implemented on a set of 10 daily sterling exchange rates covering the entire post Bretton-Woods era until the present day. Irrefutable evidence of non-linearity is shown in many of the series, but most of this dependence can apparently be explained by reference to the GARCH family of models. It is suggested that the literature in this area has reached an impasse, with the presence of ARCH effects clearly demonstrated in a large number of papers, but with the tests for non-linearity which are currently available being unable to classify any additional non-linear structure.

Energy exchange in a dense urban environment Part II: impact of spatial heterogeneity of the surface

The centre of cities, characterised by spatial and temporal complexity, are challenging environments for micrometeorological research. This paper considers the impact of sensor location and heterogeneity of the urban surface on flux observations in the dense city centre of London, UK. Data gathered at two sites in close vicinity, but with different measurement heights, were analysed to investigate the influence of source area characteristics on long-term radiation and turbulent heat fluxes. Combining consideration of diffuse radiation and effects of specular reflections, the non-Lambertian urban surface is found to impact the measurements of surface albedo. Comparisons of observations from the two sites reveal that turbulent heat fluxes are similar under some flow conditions. However, they mostly observe processes at different scales due to their differing measurement heights, highlighting the critical impact of siting sensors in urban areas. A detailed source area analysis is presented to investigate the surface controls influencing the energy exchanges at the different scales