Exploring provision for children identified with special educational needs: an international review of policy and practice

This project aimed to create a descriptive map of international research which explores the notion of the continuum of educational provision for children with special educational needs. It also aimed to determine and examine the nature of how the continuum of provision is conceptualised, operationalised and enacted in a sample of selected countries. Commissioned by the National Council for Special Education, it also identified implications for the development of provision within the Irish context. The research involved a systematic identification and thematic review of theory, identifying and examining literature associated with the conceptualisation of the continuum; it examined the policy and provision across 55 administrations as publically reported, primarily to international agencies; it carried out more detailed examination of policy and practice in 10 countries using a survey and vignette study; and it involved a series of interviews with a range of individuals in a range of settings in four countries with differing approaches to supporting children with special educational needs. This paper outlines the overall findings of the research. It focuses in particular upon the need to change how we think about provision associated with continua, recognising the lack of international coherence in approaches to support for pupils with special educational needs. It identifies in particular the opportunities presented by a reconceptualisation of the class and the management of class resources, and the role key personnel can play in creating links between diverse services

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease

Triple Store Databases and their role in high throughput, automated, extensible, data analysis

A critical component of high throughput experiments is the ability to store, retrieve, and analyse the resulting data. This is arguably best accomplished using a relational database. However, an elaborate relational database is founded on a complicated schema, and changing this schema requires a major act of redesign. This is incompatible with the scientific method, however, by which new hypotheses are devised and tested. Triple store databases, on the other hand, are able to be modified and extended without requiring a major redesign. In this presentation, the triple store method, and its application to the cheminformatics problem of solubility prediction, will be described

Modernisation of computational chemistry and cheminformatics with eScience techniques : applications to chemical property prediction

The prediction of macroscopic chemical properties is recognised as a valuable ability.  Statistical models such as Quantitative Structure-Property Relationships (QSPRs) are only as good as the data and assumptions upon which they are based.  In this thesis, a number of difficulties in handling large data sets, including trust, relevancy and interpretation are made clear and an approach to modernising chemical data storage is presented.  The use of Semantic Web technologies to increase the availability and usefulness of the chemical information is demonstrated, placing emphasis on issues of provenance and quality as well as machine-readability.  A method of allowing computers to understand scientific units is a significant part of this, solving many potential problems in data re-use. Existing methods of encoding scientific units are found to be of limited scope and a new representation is formulated to make full use of and reinforce the intrinsic value of units with their measurements. The new system for chemical data management is then used to assemble a unique data set combining data from many sources in order to gain new understanding of the problem of melting point prediction.  Solid state data forms the cornerstone of this approach.  Attempts to model melting point in a high throughput manner highlight the issues involved in solid state simulation and the limitations of simple descriptors.  Further experimental data and modelling reveals the importance of the interrelation of enthalpy and entropy, and the stringent requirements for accuracy in order to achieve useful errors of melting point prediction.</p

Modernisation of computational chemistry and cheminformatics with eScience techniques: applications to chemical property prediction

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Endüstride yangın güvenliği ve uygulamaları

The CombeChem project has designed and deployed an e-Science infrastructure using a combination of Grid and Semantic Web technologies. In this paper we describe the datagrid element of the project, which provides a platform for sophisticated scientific queries and a rich record of experimental data and its provenance. This datagrid constitutes a significant deployment of Semantic Web technologies and we propose it as an example of a ‘Semantic Datagrid’

Analysis of Phase of LUCIFERASE Expression Reveals Novel Circadian Quantitative Trait Loci in Arabidopsis

In response to exogenous rhythms of light and temperature, most organisms exhibit endogenous circadian rhythms (i.e. cycles of behavior and gene expression with a periodicity of approximately 24 h). One of the defining characteristics of the circadian clock is its ability to synchronize (entrain) to an environmental rhythm. Entrainment is arguably the most salient feature of the clock in evolutionary terms. Previous quantitative trait studies of circadian characteristics in Arabidopsis (Arabidopsis thaliana) considered leaf movement under constant (free-running) conditions. This study, however, addressed the important circadian parameter of phase, which reflects the entrained relationship between the clock and the external cycle. Here it is shown that, when exposed to the same photoperiod, Arabidopsis accessions differ dramatically in phase. Variation in the timing of circadian LUCIFERASE expression was used to map loci affecting the entrained phase of the clock in a recombinant population derived from two geographically distant accessions, Landsberg erecta and Cape Verde Islands. Four quantitative trait loci (QTL) were found with major effects on circadian phase. A QTL on chromosome 5 contained SIGNALING IN RED LIGHT REDUCED 1 and PSEUDORESPONSE REGULATOR 3, both genes known to affect the circadian clock. Previously unknown polymorphisms were found in both genes, making them candidates for the effect on phase. Fine mapping of two other QTL highlighted genomic regions not previously identified in any circadian screens, indicating their effects are likely due to genes not hitherto considered part of the circadian system

Bringing chemical data onto the semantic web

Present chemical data storage methodologies place many restrictions on the use of the stored data. The absence of sufficient high-quality metadata prevents intelligent computer access to the data without human intervention. This creates barriers to the automation of data mining in activities such as quantitative structure-activity relationship modelling. The application of Semantic Web technologies to chemical data is shown to reduce these limitations. The use of unique identifiers and relationships (represented as uniform resource identifiers, URIs, and resource description framework, RDF) held in a triplestore provides for greater detail and flexibility in the sharing and storage of molecular structures and properties

FAIRification of genomic track metadata [version 1; peer review: 2 approved]

Background: Many types of data from genomic analyses can be represented as genomic tracks, i.e. features linked to the genomic coordinates of a reference genome. Examples of such data are epigenetic DNA methylation data, ChIP-seq peaks, germline or somatic DNA variants, as well as RNA-seq expression levels. Researchers often face difficulties in locating, accessing and combining relevant tracks from external sources, as well as locating the raw data, reducing the value of the generated information. Description of work: We propose to advance the application of FAIR data principles (Findable, Accessible, Interoperable, and Reusable) to produce searchable metadata for genomic tracks. Findability and Accessibility of metadata can then be ensured by a track search service that integrates globally identifiable metadata from various track hubs in the Track Hub Registry and other relevant repositories. Interoperability and Reusability need to be ensured by the specification and implementation of a basic set of recommendations for metadata. We have tested this concept by developing such a specification in a JSON Schema, called FAIRtracks, and have integrated it into a novel track search service, called TrackFind. We demonstrate practical usage by importing datasets through TrackFind into existing examples of relevant analytical tools for genomic tracks: EPICO and the GSuite HyperBrowser. Conclusion: We here provide a first iteration of a draft standard for genomic track metadata, as well as the accompanying software ecosystem. It can easily be adapted or extended to future needs of the research community regarding data, methods and tools, balancing the requirements of both data submitters and analytical end-usersThe work was funded by ELIXIR through the ELIXIR Implementation Study: FAIRification of genomic tracks, and through ELIXIR Norway, ELIXIR Spain and EMBL-EBI core funding. SC-G and JMF received funding through the INB Grant (PT17/0009/0001 - ISCIII-SGEFI / ERDF). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer ReviewedPostprint (published version