IntPred: a structure-based predictor of protein-protein interaction sites

Motivation Protein–protein interactions are vital for protein function with the average protein having between three and ten interacting partners. Knowledge of precise protein–protein interfaces comes from crystal structures deposited in the Protein Data Bank (PDB), but only 50% of structures in the PDB are complexes. There is therefore a need to predict protein–protein interfaces in silico and various methods for this purpose. Here we explore the use of a predictor based on structural features and which exploits random forest machine learning, comparing its performance with a number of popular established methods. Results On an independent test set of obligate and transient complexes, our IntPred predictor performs well (MCC = 0.370, ACC = 0.811, SPEC = 0.916, SENS = 0.411) and compares favourably with other methods. Overall, IntPred ranks second of six methods tested with SPPIDER having slightly better overall performance (MCC = 0.410, ACC = 0.759, SPEC = 0.783, SENS = 0.676), but considerably worse specificity than IntPred. As with SPPIDER, using an independent test set of obligate complexes enhanced performance (MCC = 0.381) while performance is somewhat reduced on a dataset of transient complexes (MCC = 0.303). The trade-off between sensitivity and specificity compared with SPPIDER suggests that the choice of the appropriate tool is application-dependent

A deuterium nuclear magnetic resonance study of chain disorder in lamellar potassium palmitate: The effect of long and short chain guests

The deuterium magnetic resonance spectra of lamellar phases of host perdeuterated potassium palmitate mixed with varying amounts of guest protiated potassium octanoate and behenate and 86.3 mol% D2O are reported. At higher temperatures, the short chain guests give rise to more fluidity and the long chain guests give rise to less fluidity towards the end of the host chain. At low temperatures there are changes in the interaction between the polar head group and the water which depend on sample composition. The transition from the lamellar phase to the low temperature gel phase is investigated and in some cases the gel phase is found to be a complicated many-phase region, at least for the water. The spectral results are presented in detail but compact and empirical methods of analysis are also investigated

A deuterium nuclear magnetic resonance study of chain disorder in lamellar potassium palmitate: The effect of long and short chain guests

The deuterium magnetic resonance spectra of lamellar phases of host perdeuterated potassium palmitate mixed with varying amounts of guest protiated potassium octanoate and behenate and 86.3 mol% D2O are reported. At higher temperatures, the short chain guests give rise to more fluidity and the long chain guests give rise to less fluidity towards the end of the host chain. At low temperatures there are changes in the interaction between the polar head group and the water which depend on sample composition. The transition from the lamellar phase to the low temperature gel phase is investigated and in some cases the gel phase is found to be a complicated many-phase region, at least for the water. The spectral results are presented in detail but compact and empirical methods of analysis are also investigated

Phi-values in protein folding kinetics have energetic and structural components

Phi-values are experimental measures of how the kinetics of protein folding is changed by single-site mutations. Phi-values measure energetic quantities, but are often interpreted in terms of the structures of the transition state ensemble. Here we describe a simple analytical model of the folding kinetics in terms of the formation of protein substructures. The model shows that Phi-values have both structural and energetic components. In addition, it provides a natural and general interpretation of "nonclassical" Phi-values (i.e., less than zero, or greater than one). The model reproduces the Phi-values for 20 single-residue mutations in the alpha-helix of the protein CI2, including several nonclassical Phi-values, in good agreement with experiments.Comment: 15 pages, 3 figures, 1 tabl

Global copper cycles and greenhouse gas emissions in a 1.5 °C world

Moving towards a 1.5 °C world could fundamentally alter the future copper cycle through two key drivers: the implementation of decarbonization technologies and the imposition of an emissions budget on production activities. This study explores the impact of these drivers on the global copper cycle using a dynamic material flow analysis, coupled with an optimization technique. The results show that global final demand for copper could increase by a factor of 2.5 between 2015 and 2050, reaching 62 million metric tons, with approximately 4% of the increase coming from copper used in renewable energy-based power plants and 14% coming from electric vehicles. While there are sufficient resources to meet this growing demand, the greenhouse gas emissions of the copper cycle could account for approximately 2.7% of the total emissions budget by 2050, up from 0.3% today. Assessment of possible mitigation efforts by the copper industry shows that this can be halved, but will still be 35% short of the emissions budget target based on proportional responsibility, i.e., applying the same mitigation rate to all sectors. Rather, collective action is required by all stakeholders interacting with the copper cycle to bridge the mitigation gap, including through efforts to drive advanced sorting, higher fabrication yields, extended product lifetimes, and increased service efficiency of in-use copper stock

Defining freshwater as a natural resource: a framework linking water use to the area of protection natural resources

© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. Purpose: While many examples have shown unsustainable use of freshwater resources, existing LCIA methods for water use do not comprehensively address impacts to natural resources for future generations. This framework aims to (1) define freshwater resource as an item to protect within the Area of Protection (AoP) natural resources, (2) identify relevant impact pathways affecting freshwater resources, and (3) outline methodological choices for impact characterization model development. Methods: Considering the current scope of the AoP natural resources, the complex nature of freshwater resources and its important dimensions to safeguard safe future supply, a definition of freshwater resource is proposed, including water quality aspects. In order to clearly define what is to be protected, the freshwater resource is put in perspective through the lens of the three main safeguard subjects defined by Dewulf et al. (2015). In addition, an extensive literature review identifies a wide range of possible impact pathways to freshwater resources, establishing the link between different inventory elementary flows (water consumption, emissions, and land use) and their potential to cause long-term freshwater depletion or degradation. Results and discussion: Freshwater as a resource has a particular status in LCA resource assessment. First, it exists in the form of three types of resources: flow, fund, or stock. Then, in addition to being a resource for human economic activities (e.g., hydropower), it is above all a non-substitutable support for life that can be affected by both consumption (source function) and pollution (sink function). Therefore, both types of elementary flows (water consumption and emissions) should be linked to a damage indicator for freshwater as a resource. Land use is also identified as a potential stressor to freshwater resources by altering runoff, infiltration, and erosion processes as well as evapotranspiration. It is suggested to use the concept of recovery period to operationalize this framework: when the recovery period lasts longer than a given period of time, impacts are considered to be irreversible and fall into the concern of freshwater resources protection (i.e., affecting future generations), while short-term impacts effect the AoP ecosystem quality and human health directly. It is shown that it is relevant to include this concept in the impact assessment stage in order to discriminate the long-term from the short-term impacts, as some dynamic fate models already do. Conclusions: This framework provides a solid basis for the consistent development of future LCIA methods for freshwater resources, thereby capturing the potential long-term impacts that could warn decision makers about potential safe water supply issues in the future

Physical activity to improve cognition in older adults: can physical activity programs enriched with cognitive challenges enhance the effects? A systematic review and meta-analysis

: EPHPP quality rating scores (DOCX 38 kb

Sentinel surveillance for travellers' diarrhoea in primary care

<p>Abstract</p> <p>Background</p> <p>Travellers' diarrhoea is the most common health problem among international travellers and much of the burden falls on general practitioners. We assessed whether sentinel surveillance based in primary care could be used to monitor changes in the epidemiology of travellers' diarrhoea.</p> <p>Methods</p> <p>A sentinel surveillance scheme of 30 volunteer general practices distributed throughout Wales provides weekly reports of consultations for eight infectious diseases to the national Communicable Disease Surveillance Centre. Travellers' diarrhoea was introduced as a new reportable infection in July 2002.</p> <p>Results</p> <p>Between 1 July 2002 and 31 March 2005 there were 90 reports of travellers' diarrhoea. The mean annual consultation rate was 15.2 per 100,000 population (95% confidence interval: 12.2–18.7), with the highest rates in summer, in people aged 15–24 years, and in travellers to Southern Europe. A higher proportion of travellers than expected had visited destinations outside Europe and North America when compared to the proportion of all United Kingdom travellers visiting these destinations (38% vs. 11%; Chi²= 53.3, p < 0.0001).</p> <p>Conclusion</p> <p>Sentinel surveillance has the potential to monitor secular trends in travellers' diarrhoea and to help characterise population groups or travel destinations associated with higher risk.</p