An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D

Background: The phenotypic effects of sequence variations in protein-coding regions come about primarily via their effects on the resulting structures, for example by disrupting active sites or affecting structural stability. In order better to understand the mechanisms behind known mutant phenotypes, and predict the effects of novel variations, biologists need tools to gauge the impacts of DNA mutations in terms of their structural manifestation. Although many mutations occur within domains whose structure has been solved, many more occur within genes whose protein products have not been structurally characterized.Results: Here we present 3DSim (3D Structural Implication of Mutations), a database and web application facilitating the localization and visualization of single amino acid polymorphisms (SAAPs) mapped to protein structures even where the structure of the protein of interest is unknown. The server displays information on 6514 point mutations, 4865 of them known to be associated with disease. These polymorphisms are drawn from SAAPdb, which aggregates data from various sources including dbSNP and several pathogenic mutation databases. While the SAAPdb interface displays mutations on known structures, 3DSim projects mutations onto known sequence domains in Gene3D. This resource contains sequences annotated with domains predicted to belong to structural families in the CATH database. Mappings between domain sequences in Gene3D and known structures in CATH are obtained using a MUSCLE alignment. 1210 three-dimensional structures corresponding to CATH structural domains are currently included in 3DSim; these domains are distributed across 396 CATH superfamilies, and provide a comprehensive overview of the distribution of mutations in structural space.Conclusion: The server is publicly available at http://3DSim.bioinfo.cnio.es/. In addition, the database containing the mapping between SAAPdb, Gene3D and CATH is available on request and most of the functionality is available through programmatic web service access

The ideal healthcare: priorities of people with chronic conditions and their carers

Background It is well established that health consumer opinions should be considered in the design, delivery, and evaluation of health services. However, the opinions of people with chronic conditions and their carers and what they actually consider as ideal healthcare is limited. The aim of this study is to investigate the healthcare priorities of consumers with chronic conditions and their carers, if there are differences between these two groups, and if priorities differ depending on geographical location. Methods The nominal group technique was used as a method to identify what is currently important to, or valued by, participants. This method was also particularly suited to learning about healthcare problems and generating important solutions, thereby helping to bridge the gap between research and policy. Recruitment was carried out via purposive sampling, with the assistance of community pharmacies, general practices, various health agencies, government and non-government organisations. A total of 11 nominal groups were conducted; five groups consisted predominantly of consumers (n = 33 participants), two groups consisted predominantly of carers (n = 12 participants) and four were mixed groups, i.e. consumers, carers, and both (n = 26 participants). Results The findings suggested that to create a model of ideal healthcare for people with chronic conditions and their carers, appropriate and timely healthcare access was of paramount importance. Continuity and coordinated care, patient-centred care and affordability were equally the second most important healthcare priorities for all groups. When compared with other groups, access was discussed more frequently among participants residing in the rural area of Mount Isa. Compared to consumers, carers also discussed priorities that were more reminiscent with their caring roles, such as increased access and continuity and coordinated care. Conclusions Access to healthcare is the most important priority for people with chronic conditions and their carers. In the event of inappropriate access for certain groups, all other efforts to increase the quality of healthcare delivery, e.g. patient-centred care, may be pointless. However, health professionals alone may be limited in their ability to address the concerns related to healthcare access; structural changes by health policy makers may be needed

Generating EQ-5D-3L health utility scores from the Edinburgh Postnatal Depression Scale: a perinatal mapping study

Background: Perinatal depression (PND) describes depression experienced by parents during pregnancy or in the first year after a baby is born. The EQ-5D instrument (a generic measure of health status) is not often collected in perinatal research, however disease-specific measures, such as the Edinburgh Postnatal Depression Scale (EPDS) are widely used. Mapping can be used to estimate generic health utility index values from disease-specific measures like the EPDS. Objective: To develop a mapping algorithm to estimate EQ-5D utility index values from the EPDS. Methods: Patient-level data from the BaBY PaNDA study (English observational cohort study) provided 1068 observations with paired EPDS and EQ-5D (3-level version; EQ-5D-3L) responses. We compared the performance of six alternative regression model types, each with four specifications of covariates (EPDS score and age: base, squared, and cubed). Model performance (ability to predict utility values) was assessed by ranking mean error, mean absolute error, and root mean square error. Algorithm performance in 3 external datasets was also evaluated. Results: There was moderate correlation between EPDS score and utility values (coefficient: – 0.42). The best performing model type was a two-part model, followed by ordinary least squared. Inclusion of squared and cubed covariates improved model performance. Based on graphs of observed and predicted utility values, the algorithm performed better when utility was above 0.6. Conclusions: This direct mapping algorithm allows the estimation of health utility values from EPDS scores. The algorithm has good external validity but is likely to perform better in samples with higher health status

Remote sensing of the mountain cryosphere: Current capabilities and future opportunities for research

Remote sensing technologies are integral to monitoring the mountain cryosphere in a warming world. Satellite missions and field-based platforms have transformed understanding of the processes driving changes in mountain glacier dynamics, snow cover, lake evolution, and the associated emergence of hazards (e.g. avalanches, floods, landslides). Sensors and platforms are becoming more bespoke, with innovation being driven by the commercial sector, and image repositories are more frequently open access, leading to the democratisation of data analysis and interpretation. Cloud computing, artificial intelligence, and machine learning are rapidly transforming our ability to handle this exponential increase in data. This review therefore provides a timely opportunity to synthesise current capabilities in remote sensing of the mountain cryosphere. Scientific and commercial applications were critically examined, recognising the technologies that have most advanced the discipline. Low-cost sensors can also be deployed in the field, using microprocessors and telecommunications equipment to connect mountain glaciers to stakeholders for real-time monitoring. The potential for novel automated pipelines that can process vast volumes of data is also discussed, from reimagining historical aerial imagery to produce elevation models, to automatically delineating glacier boundaries. Finally, the applications of these emerging techniques that will benefit scientific research avenues and real-world societal programmes are discussed

Spacers to improve performance and porosity of graphene based polymer electrolyte fuel cells

Graphene has been suggested as a potential support material to replace commercial carbon black due to its carbon corrosion resistance. However, graphene-based electrodes typically perform poorly in MEA testing due to restacking of the graphitic sheets. In this study we investigate the introduction of carbon black and their effects on the porosity and current density of graphene-based supports

PI controller tuning for load disturbance rejection using constrained optimization

© 2016, Springer-Verlag Berlin Heidelberg. In this paper, a simple and effective PI controller tuning method is presented. To take both performance requirements and robustness issues into consideration, the design technique is based on optimization of load disturbance rejection with a constraint either on the gain margin or phase margin. In addition, a simplified form of the resulting tuning formulae is obtained for first order plus dead time models. To demonstrate the ability of the proposed tuning technique in dealing with a wide range of plants, simulation results for several examples, including integrating, non-minimum phase and long dead time models, are provided

Comparison of the prognostic value of selected markers of the systemic inflammatory response in patients with colorectal cancer

There is increasing evidence that the presence of a systemic inflammatory response plays an important role in predicting survival in patients with colorectal cancer. However, it is not clear what components of the systemic inflammatory response best predict survival. The aim of the present study was to compare the prognostic value of an inflammation-based prognostic score (modified Glasgow Prognostic Score (Mgps) 0=C-reactive protein <10 mg l−1, 1=C-reactive protein >10 mg l−1, and 2=C-reactive protein >10 mg l−1 and albumin<35 g l−1) with that of components of the white cell count (neutrophils, lymphocytes, monocytes and platelets using standard thresholds) in patients with colorectal cancer. Two patient groups were studied: 149 patients who underwent potentially curative resection for colorectal cancer and 84 patients who had synchronous unresectable liver metastases. In those patients who underwent potentially curative resection the minimum follow-up was 36 months and 20 patients died of their cancer. On multivariate survival analysis only TNM stage (HR 3.75, 95% CI 1.54–9.17, P=0.004), monocyte count (HR 3.79, 95% CI 1.29–11.12, P=0.015) and mGPS (HR 2.21, 95% CI 1.11–4.41, P=0.024) were independently associated with cancer-specific survival. In patients with synchronous unresectable liver metastases the minimum follow-up was 6 months and 71 patients died of their cancer. On multivariate survival analysis only single liver metastasis >5 cm (HR 1.78, 95% CI 0.99–3.21, P=0.054), extra-hepatic disease (HR 2.09, 95% CI 1.05–4.17, P=0.036), chemotherapy treatment (HR 2.40, 95% CI 1.82–3.17, P<0.001) and mGPS (HR 1.44, 95% CI 1.01–2.04, P=0.043) were independently associated with cancer-specific survival. In summary, markers of the systemic inflammatory response are associated with poor outcome in patients with either primary operable or synchronous unresectable colorectal cancer. An acute-phase protein-based prognostic score, the mGPS, appears to be a superior predictor of survival compared with the cellular components of the systemic inflammatory response

Formation of an ion-free crystalline carbon nitride and its reversible intercalation with ionic species and molecular water

The development of processes to tune the properties of materials is essential for the progression of nextgeneration technologies for catalysis, optoelectronics and sustainability including energy harvesting and conversion. Layered carbon nitrides have also been identified as of significant interest within these fields of application. However, most carbon nitride materials studied to date have poor crystallinity and therefore their properties cannot be readily controlled or easily related to their molecular level or nanoscale structures. Here we report a process for forming a range of crystalline layered carbon nitrides with polytriazine imide (PTI) structures that can be interconverted by simple ion exchange processes, permitting the tunability of their optoelectronic and chemical properties. Notable outcomes of our work are (a) the creation of a crystalline, guest-ion-free PTI compound that (b) can be re-intercalated with ions or molecules using “soft chemistry” approaches. This includes the intercalation of HCl, demonstrating a new ambient pressure route to the layered PTI$xHCl material that was previously only available by a high-pressure-high-temperature route (c). Our work also shows (d) that the intercalantfree (IF-) PTI material spontaneously absorbs up to 10 weight% H2O from the ambient atmosphere and that this process is reversible, leading to potential applications for membranes and water capture in dry environment

Star Clusters

This review concentrates almost entirely on globular star clusters. It emphasises the increasing realisation that few of the traditional problems of star cluster astronomy can be studied in isolation: the influence of the Galaxy affects dynamical evolution deep in the core, and the spectrum of stellar masses; in turn the evolution of the core determines the highest stellar densities, and the rate of encounters. In this way external tidal effects indirectly influence the formation and evolution of blue stragglers, binary pulsars, X-ray sources, etc. More controversially, the stellar density appears to influence the relative distribution of normal stars. In the opposite sense, the evolution of individual stars governs much of the early dynamics of a globular cluster, and the existence of large numbers of primordial binary stars has changed important details of our picture of the dynamical evolution. New computational tools which will become available in the next few years will help dynamical theorists to address these questions.Comment: 10 pages, 3 figures, Te