Grid computing and molecular simulations: the vision of the eMinerals Project

This paper discusses a number of aspects of using grid computing methods in support of molecular simulations, with examples drawn from the eMinerals project. A number of components for a useful grid infrastructure are discussed, including the integration of compute and data grids, automatic metadata capture from simulation studies, interoperability of data between simulation codes, management of data and data accessibility, management of jobs and workflow, and tools to support collaboration. Use of a grid infrastructure also brings certain challenges, which are discussed. These include making use of boundless computing resources, the necessary changes, and the need to be able to manage experimentation

System development guidelines from a review of motion-based technology for people with MCI or dementia

As the population ages and the number of people living with dementia or mild cognitive impairment (MCI) continues to increase, it is critical to identify creative and innovative ways to support and improve their quality of life. Motion-based technology has shown significant potential for people living with dementia or MCI by providing opportunities for cognitive stimulation, physical activity and participation in meaningful leisure activities, while simultaneously functioning as a useful tool for research and development of interventions. However, many of the current systems created using motion-based technology have not been designed specifically for people with dementia or MCI. Additionally, the usability and accessibility of these systems for these populations has not been thoroughly considered. This paper presents a set of system development guidelines derived from a review of the state of the art of motion-based technologies for people with dementia or MCI. These guidelines highlight three overarching domains of consideration for systems targeting people with dementia or MCI: (i) cognitive, (ii) physical, and (iii) social. We present the guidelines in terms of relevant design and use considerations within these domains and the emergent design themes within each domain. Our hope is that these guidelines will aid in designing motion-based software to meet the needs of people with dementia or MCI such that the potential of these technologies can be realized

The Effect of Carboxylates on the Mg Content of Calcites that Transform from ACC

AbstractIn some skeletal-forming and sedimentary environments, calcite and other CaCO3 polymorphs are produced from an amorphous calcium carbonate (ACC) phase. This experimental study determined the Mg content of calcites that grew in the presence of ACC with/without carboxylated biomolecules. The Mg content of the initial ACC obeys a simple fractionation for all conditions except in the presence of oxydiacetate. For all solution compositions, this ACC transforms into calcite crystallites that contain zero to 38 mole %MgCO3, without evidence of secondary polymorphs (Mg/Ca = 0-15). Mg is in the calcite structure within the resolution of the XRD method. The biomolecules slow the ACC to calcite transformation in proportion to their selectivity for Ca over Mg. Citrate, tartarate, and oxydiacetate increase the amount of Mg in both ACC and the resulting calcite. When the Mg2+/Ca2+ ratios of initial solutions are less than ∼5-8, the Mg content of the ACC and calcite products are similar

Modelling Primordial Gas in Numerical Cosmology

We have reviewed the chemistry and cooling behaviour of low-density (n<10^4 cm^-3) primordial gas and devised a cooling model wich involves 19 collisional and 9 radiative processes and is applicable for temperatures in the range (1 K < T < 10^8 K). We derived new fits of rate coefficients for the photo-attachment of neutral hydrogen, the formation of molecular hydrogen via H-, charge exchange between H2 and H+, electron detachment of H- by neutral hydrogen, dissociative recombination of H2 with slow electrons, photodissociation of H2+, and photodissociation of H2. Further it was found that the molecular hydrogen produced through the gas-phase processes, H2+ + H -> H2 + H+, and H- + H -> H2 + e-, is likely to be converted into its para configuration on a faster time scale than the formation time scale. We have tested the model extensively and shown it to agree well with former studies. We further studied the chemical kinetics in great detail and devised a minimal model which is substantially simpler than the full reaction network but predicts correct abundances. This minimal model shows convincingly that 12 collisional processes are sufficient to model the H, He, H+, H-, He+, He++, and H2 abundances in low density primordial gas for applications with no radiation fields.Comment: 26 pages of text, 4 tables, and 6 eps figures. The paper is also available at http://zeus.ncsa.uiuc.edu:8080/~abel/PGas/bib.html Submitted to New Astronomy. Note that some of the hyperlinks given in the paper are still under constructio

The Kinect project: group motion-based gaming for people living with dementia

Engaging in enjoyable activities is an essential part of well-being, but people with dementia can find participation increasingly difficult. Motion-based technologies can provide meaningful engagement in a wide range of activities, but for people with dementia to take advantage of these devices requires a good understanding of how best to select and present these activities to this population. The objective of this study was to explore the use of motion-based technology (Xbox Kinect) as a group activity for people with dementia who attend adult day programs. This qualitative study took place in an adult day program for older adults with age-related challenges. Participants (n=23) were observed while playing a digital bowling game presented on Xbox Kinect one hour per week for a period of 20 weeks, to capture naturalistic data. Field notes generated through observations were transcribed and analyzed to identify emerging themes. The findings revealed three predominant themes which illustrate the potential of motion-based technology as a group activity for people with dementia who attend adult day programs: (a) the importance of having a trained trainer, (b) learning vs. mastery, and (c) playing ‘independently together’. People with dementia can learn to play games presented on motion-based technology and enjoy doing so. Furthermore, using the technology in a group setting fostered an encouraging and supportive environment which further contributed to the leisure experience. However, to be used most effectively, staff must be trained to set-up and interact with the technology, as well as introduce, teach, and support people with dementia to use it

Metagenomic tools in microbial ecology research

Ability to directly sequence DNA from the environment permanently changed microbial ecology. Here, we review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function of complex microbial communities. While metagenomics is shaping our understanding of microbial functions in ecosystems via gene-centric and genome-centric methods, annotating functions, metagenome assembly and binning in heterogeneous samples remains challenging. Development of new analysis and sequencing platforms generating high-throughput long-read sequences and functional screening opportunities will aid in harnessing metagenomes to increase our understanding of microbial taxonomy, function, ecology, and evolution in the environment.publishedVersio

An overview on synthetic administrative data for research

Use of administrative data for research and for planning services has increased over recent decades due to the value of the large, rich information available. However, concerns about the release of sensitive or personal data and the associated disclosure risk can lead to lengthy approval processes and restricted data access. This can delay or prevent the production of timely evidence. A promising solution to facilitate more efficient data access is to create synthetic versions of the original datasets which do not hold any confidential information and can minimise disclosure risk. Such data may be used as an interim solution, allowing researchers to develop their analysis plans on non-disclosive data, whilst waiting for access to the real data. We aim to provide an overview of the background and uses of synthetic data, describe common methods used to generate synthetic data in the context of UK administrative research, propose a simplified terminology for categories of synthetic data, and illustrate challenges and future directions for research.&#x0D

Severe Plane-Form Enamel Hypoplasia in a Dentition from Roman Britain

Enamel defects can provide insight into the life histories of past individuals and populations, in-cluding information on a wide range of disturbances during childhood. This study investigates a particularly severe case of plane-form enamel hypoplasia from a Roman site in Gloucester, UK. Dentine protrudes above the occlusal enamel of upper central incisors, both upper canines, the lower left canine, lower right central incisor, and all four first molars. Given the morphology and location of these defects, along with the developmental tim-ing of the affected teeth, such factors as molar-incisor hypomineralization, amelogenesis imperfecta, and congen-ital syphilis can likely be ruled out. The defects resulted from a nonspecific but severe physiological disturbance during the second year of life. Severe plane-form defects of this kind, where enamel formation has completely ceased, are extremely rare in premodern populations, and this example is one of the earliest reported cases. It has been suggested that these defects generally occur only in individuals that survived a life-threatening illness, which would explain the scarcity in the archaeological record, i.e., the afflicted individual would not have lived long enough for the defects to manifest. Comparisons with clinical examples and pathogen DNA analysis may provide further insight into the etiology of these defects.</jats:p