Access 3 project protocol: Young people and health system navigation in the digital age: A multifaceted, mixed methods study

© 2017 Article author(s). Background: The integration of digital technology into everyday lives of young people has become widespread. It is not known whether and how technology influences barriers and facilitators to healthcare, and whether and how young people navigate between face-to-face and virtual healthcare. To provide new knowledge essential to policy and practice, we designed a study that would explore health system access and navigation in the digital age. The study objectives are to: (1) describe experiences of young people accessing and navigating the health system in New South Wales (NSW), Australia; (2) identify barriers and facilitators to healthcare for young people and how these vary between groups; (3) describe health system inefficiencies, particularly for young people who are marginalised; (4) provide policy-relevant knowledge translation of the research data. Methods and analysis: This mixed methods study has four parts, including: (1) a cross-sectional survey of young people (12-24 years) residing in NSW, Australia; (2) a longitudinal, qualitative study of a subsample of marginalised young people (defined as young people who: identify as Aboriginal and/or Torres Strait Islander; are experiencing homelessness; identify as sexuality and/or gender diverse; are of refugee or vulnerable migrant background; and/or live in rural or remote NSW); (3) interviews with professionals; (4) a knowledge translation forum. Ethics and dissemination: Ethics approvals were sought and granted. Data collection commenced in March 2016 and will continue until June 2017. This study will gather practice and policy-relevant intelligence about contemporary experiences of young people and health services, with a unique focus on five different groups of marginalised young people, documenting their experiences over time. Access 3 will explore navigation around all levels of the health system, determine whether digital technology is integrated into this, and if so how, and will translate findings into policy-relevant recommendations

Real Time Global Tests of the ALICE High Level Trigger Data Transport Framework

The High Level Trigger (HLT) system of the ALICE experiment is an online event filter and trigger system designed for input bandwidths of up to 25 GB/s at event rates of up to 1 kHz. The system is designed as a scalable PC cluster, implementing several hundred nodes. The transport of data in the system is handled by an object-oriented data flow framework operating on the basis of the publisher-subscriber principle, being designed fully pipelined with lowest processing overhead and communication latency in the cluster. In this paper, we report the latest measurements where this framework has been operated on five different sites over a global north-south link extending more than 10,000 km, processing a ``real-time'' data flow.Comment: 8 pages 4 figure

A critical evaluation of automatic atom mapping algorithms and tools

The identification of the atoms which change their position in chemical reactions is an important knowledge within the field of Metabolic Engineering. This can lead to new advances at different levels from the reconstruction of metabolic networks to the classification of chemical reactions, through the identification of the atomic changes inside a reaction. The Atom Mapping approach was initially developed in the 1960s, but recently suffered important advances, being used in diverse biological and biotechnological studies. The main methodologies used for atom mapping are the Maximum Common Substructure and the Linear Optimization methods, which both require computational know-how and powerful resources to run the underlying tools. In this work, we assessed a number of previously implemented atom mapping frameworks, and built a framework able of managing the different data inputs and outputs, as well as the mapping process provided by each of these third-party tools. We evaluated the admissibility of the calculated atom maps from different algorithms, also assessing if with different approaches we were capable of returning equivalent atom maps for the same chemical reaction.ERDF -European Regional Development Fund(UID/BIO/04469/2013)info:eu-repo/semantics/publishedVersio

Calculation of magnetic anisotropy energy in SmCo5

SmCo5 is an important hard magnetic material, due to its large magnetic anisotropy energy (MAE). We have studied the magnetic properties of SmCo5 using density functional theory (DFT) calculations where the Sm f-bands, which are difficult to include in DFT calculations, have been treated within the LDA+U formalism. The large MAE comes mostly from the Sm f-shell anisotropy, stemming from an interplay between the crystal field and the spin-orbit coupling. We found that both are of similar strengths, unlike some other Sm compounds, leading to a partial quenching of the orbital moment (f-states cannot be described as either pure lattice harmonics or pure complex harmonics), an optimal situation for enhanced MAE. A smaller portion of the MAE can be associated with the Co-d band anisotropy, related to the peak in the density of states at the Fermi energy. Our result for the MAE of SmCo5, 21.6 meV/f.u., agrees reasonably with the experimental value of 13-16 meV/f.u., and the calculated magnetic moment (including the orbital component) of 9.4 mu_B agrees with the experimental value of 8.9 mu_B.Comment: Submitted to Phys. Rev.

Intersectionality: Social Marginalisation and Self-Reported Health Status in Young People.

BACKGROUND:The aim of this study was to measure young people's health status and explore associations between health status and belonging to one or more socio-culturally marginalised group. METHODS:part of the Access 3 project, this cross-sectional survey of young people aged 12-24 years living in New South Wales, Australia, oversampled young people from one or more of the following groups: Aboriginal and or Torres Strait Islander; living in rural and remote areas; homeless; refugee; and/or, sexuality and/or gender diverse. This paper reports on findings pertaining to health status, presence of chronic health conditions, psychological distress, and wellbeing measures. RESULTS:1416 participants completed the survey; 897 (63.3%) belonged to at least one marginalised group; 574 (40.5%) to one, 281 (19.8%) to two and 42 (3.0%) to three or four groups. Belonging to more marginalised groups was significantly associated with having more chronic health conditions (p = 0.001), a greater likelihood of high psychological distress (p = 0.001) and of illness or injury related absence from school or work (p < 0.05). CONCLUSIONS:increasing marginalisation is associated with decreasing health status. Using an intersectional lens can to be a useful way to understand disadvantage for young people belonging to multiple marginalised groups

Building evidence into youth health policy: a case study of the Access 3 knowledge translation forum.

BACKGROUND: Effective integration of evidence and youth perspectives into policy is crucial for supporting the future health and well-being of young people. The aim of this project was to translate evidence from the Access 3 project to support development of a new state policy on youth health and well-being within New South Wales (NSW), Australia. Ensuring the active contribution of young people within policy development was a key objective of the knowledge translation (KT) process. METHODS: The KT activity consisted of a 1-day facilitated forum with 64 purposively sampled stakeholders. Participants included eight young people, 14 policy-makers, 15 academics, 22 clinicians or managers from NSW health services, four general practitioners and one mental health service worker. Research to be translated came from the synthesized findings of the NSW Access 3 project. The design of the forum included stakeholder presentations and group workshops, guided by the 2003 Lavis et al. KT framework that was improved by the Grimshaw et al. KT framework in 2012. Members of the Access 3 research team took on the role of knowledge brokers throughout the KT process. Participant satisfaction with the workshop was evaluated using a brief self-report survey. Policy uptake was determined through examination of the subsequent NSW Youth Health Framework 2017-2024. RESULTS: A total of 25 policy recommendations were established through the workshop, and these were grouped into six themes that broadly aligned with the synthesized findings from the Access 3 project. The six policy themes were (1) technology solutions, (2) integrated care and investment to build capacity, (3) adolescent health checks, (4) workforce, (5) youth participation and (6) youth health indicators. Forum members were asked to vote on the importance of individual recommendations. These policy recommendations were subsequently presented to the NSW Ministry of Health, with some evidence of policy uptake identified. The majority of participants rated the forum positively. CONCLUSIONS: The utilization of KT theories and active youth engagement led to the successful translation of research evidence and youth perspectives into NSW youth health policy. Future research should examine the implementation of policy arising from these KT efforts

Bioclipse: an open source workbench for chemo- and bioinformatics

BACKGROUND: There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. RESULTS: Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. CONCLUSION: Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at

Updates in Rhea-a manually curated resource of biochemical reactions.

Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Rhea has been designed for the functional annotation of enzymes and the description of genome-scale metabolic networks, providing stoichiometrically balanced enzyme-catalyzed reactions (covering the IUBMB Enzyme Nomenclature list and additional reactions), transport reactions and spontaneously occurring reactions. Rhea reactions are extensively curated with links to source literature and are mapped to other publicly available enzyme and pathway databases such as Reactome, BioCyc, KEGG and UniPathway, through manual curation and computational methods. Here we describe developments in Rhea since our last report in the 2012 database issue of Nucleic Acids Research. These include significant growth in the number of Rhea reactions and the inclusion of reactions involving complex macromolecules such as proteins, nucleic acids and other polymers that lie outside the scope of ChEBI. Together these developments will significantly increase the utility of Rhea as a tool for the description, analysis and reconciliation of genome-scale metabolic models

Self-organizing ontology of biochemically relevant small molecules

<p>Abstract</p> <p>Background</p> <p>The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest.</p> <p>Results</p> <p>To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development.</p> <p>Conclusions</p> <p>We conclude that the proposed methodology can ease the burden of chemical data annotators and dramatically increase their productivity. We anticipate that the use of formal logic in our proposed framework will make chemical classification criteria more transparent to humans and machines alike and will thus facilitate predictive and integrative bioactivity model development.</p