1,110 research outputs found
The genome architecture of the Collaborative Cross mouse genetic reference population.
No full textThe Collaborative Cross Consortium reports here on the development of a unique genetic resource population. The Collaborative Cross (CC) is a multiparental recombinant inbred panel derived from eight laboratory mouse inbred strains. Breeding of the CC lines was initiated at multiple international sites using mice from The Jackson Laboratory. Currently, this innovative project is breeding independent CC lines at the University of North Carolina (UNC), at Tel Aviv University (TAU), and at Geniad in Western Australia (GND). These institutions aim to make publicly available the completed CC lines and their genotypes and sequence information. We genotyped, and report here, results from 458 extant lines from UNC, TAU, and GND using a custom genotyping array with 7500 SNPs designed to be maximally informative in the CC and used a novel algorithm to infer inherited haplotypes directly from hybridization intensity patterns. We identified lines with breeding errors and cousin lines generated by splitting incipient lines into two or more cousin lines at early generations of inbreeding. We then characterized the genome architecture of 350 genetically independent CC lines. Results showed that founder haplotypes are inherited at the expected frequency, although we also consistently observed highly significant transmission ratio distortion at specific loci across all three populations. On chromosome 2, there is significant overrepresentation of WSB/EiJ alleles, and on chromosome X, there is a large deficit of CC lines with CAST/EiJ alleles. Linkage disequilibrium decays as expected and we saw no evidence of gametic disequilibrium in the CC population as a whole or in random subsets of the population. Gametic equilibrium in the CC population is in marked contrast to the gametic disequilibrium present in a large panel of classical inbred strains. Finally, we discuss access to the CC population and to the associated raw data describing the genetic structure of individual lines. Integration of rich phenotypic and genomic data over time and across a wide variety of fields will be vital to delivering on one of the key attributes of the CC, a common genetic reference platform for identifying causative variants and genetic networks determining traits in mammals
Specifications and Development of Interoperability Solution dedicated to Multiple Expertise Collaboration in a Design Framework
No full textThis paper describes the specifications of an interoperability platform based on the PPO (Product Process Organization) model developed by the French community IPPOP in the context of collaborative and innovative design. By using PPO model as a reference, this work aims to connect together heterogonous tools used by experts easing data and information exchanges. After underlining the growing needs of collaborative design process, this paper focuses on interoperability concept by describing current solutions and their limits. Then a solution based on the flexibility of the PPO model adapted to the philosophy of interoperability is proposed. To illustrate these concepts, several examples are more particularly described (robustness analysis, CAD and Product Lifecycle Management systems connections)
The ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data
No full textThe Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Consortium is a collaborative network of researchers working together on a range of large-scale studies that integrate data from 70 institutions worldwide. Organized into Working Groups that tackle questions in neuroscience, genetics, and medicine, ENIGMA studies have analyzed neuroimaging data from over 12,826 subjects. In addition, data from 12,171 individuals were provided by the CHARGE consortium for replication of findings, in a total of 24,997 subjects. By meta-analyzing results from many sites, ENIGMA has detected factors that affect the brain that no individual site could detect on its own, and that require larger numbers of subjects than any individual neuroimaging study has currently collected. ENIGMA's first project was a genome-wide association study identifying common variants in the genome associated with hippocampal volume or intracranial volume. Continuing work is exploring genetic associations with subcortical volumes (ENIGMA2) and white matter microstructure (ENIGMA-DTI). Working groups also focus on understanding how schizophrenia, bipolar illness, major depression and attention deficit/hyperactivity disorder (ADHD) affect the brain. We review the current progress of the ENIGMA Consortium, along with challenges and unexpected discoveries made on the way
Co‐operative cross‐platform courseware development
No full textThe UKMCC (UK Mathematics Courseware Consortium) is a Consortium funded under TLTP (Training and Learning Technology Programme) to produce courseware for service mathematics teaching, using the SEFI (Société Européenne pour la Formation des Ingénieurs) syllabus. There are agreed courseware design guidelines and a simple courseware management system which allows cross‐referencing. Courseware is divided into modules, with an author as implementer for each. On any one hardware platform, a variety of authoring languages is possible. Across hardware platforms, the design guidelines ensure that conversion is possible, and will preserve look and feel. We argue here that these arrangements provide a basis for continued co‐operation between authors and future development as the technology changes
The Collaborative Cross, a community resource for the genetic analysis of complex traits
No full textThe goal of the Complex Trait Consortium is to promote the development of resources that can be used to understand, treat and ultimately prevent pervasive human diseases. Existing and proposed mouse resources that are optimized to study the actions of isolated genetic loci on a fixed background are less effective for studying intact polygenic networks and interactions among genes, environments, pathogens and other factors. The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease.
TTA school-based research consortium initiative, the evaluation, final report
No full textThis is the final report of the evaluation of th School-Based Research Consortium Initiative which ran in England from 1998 to 2001. The initiative was sponsored via a public/private partnership between the Teacher Training Agency (TTA), a UK Government agency, and the Centre for British Teachers (CfBT), a private not-for-profit company. The aim of the initiative was to create local infrastructures of support and action for teachers to engage ‘in and with’ research. Those infrastructures were made up of consortia, consisting in each case of a small number of schools together with a university department of education and at least one local education authority (LEA). Over the three years that it ran, the initiative spawned a considerable range and volume of research activities, including peer observation of teaching, peer review of videos of teaching, interview-based study, surveys measuring such things as rewards and sanctions in the classroom. In addition to well-developed teacher-university collaborations and some joint work with local education authorities, there were many examples of teacher-teacher collaboration (some of it between different schools), and also times when teachers and pupils worked together to devise, carry out or interpret research activity. In practice, the initiative created an environment in which it was possible to develop new research relationships across a range of partners, rather than merely transfer the locus of research to schools. Three aspects of teacher experience of the initiative are important to highlight. The first was the overwhelming testimony of teachers that the value of the initiative for them was the rediscovery of their professional confidence in a climate of low trust accountability, characterised by constant monitoring, target setting and bureaucratic demands. The second was the growth of familiarity with research practices that teachers gained through working collaboratively with their peers, with pupils, and with colleagues from the university. The third was how the process of research itself was necessarily situated in teachers’ own practices
BioBlitz: Promoting cross border Research and collaborative Practices for Biodiversity Conservation
No full textThis brief covers policy and research topics in biodiversity conservation (e.g., species and protected areas), invasive alien species, coastal and marine management, and strategies for public engagement. The purpose of the policy brief is to synthesise evidence of the Bioblitz approach, highlight the valuable contribution it makes to public engagement, the scientific process, and environmental management and policy, and explore how these potentials of the BioBlitz methodology can be enhanced by increasing cross-boundary cooperation and exchanges. The policy brief has been developed as collaborative process by a newly founded ECSA working group on BioBlitzes that brings together organisers of such activities from around the world
A genome-wide association study of upper aerodigestive tract cancers conducted within the INHANCE consortium
No full textGenome-wide association studies (GWAS) have been successful in identifying common genetic variation involved in susceptibility to etiologically complex disease. We conducted a GWAS to identify common genetic variation involved in susceptibility to upper aero-digestive tract (UADT) cancers. Genome-wide genotyping was carried out using the Illumina HumanHap300 beadchips in 2,091 UADT cancer cases and 3,513 controls from two large European multi-centre UADT cancer studies, as well as 4,821 generic controls. The 19 top-ranked variants were investigated further in an additional 6,514 UADT cancer cases and 7,892 controls of European descent from an additional 13 UADT cancer studies participating in the INHANCE consortium. Five common variants presented evidence for significant association in the combined analysis (p≤5×10−7). Two novel variants were identified, a 4q21 variant (rs1494961, p = 1×10−8) located near DNA repair related genes HEL308 and FAM175A (or Abraxas) and a 12q24 variant (rs4767364, p = 2×10−8) located in an extended linkage disequilibrium region that contains multiple genes including the aldehyde dehydrogenase 2 (ALDH2) gene. Three remaining variants are located in the ADH gene cluster and were identified previously in a candidate gene study involving some of these samples. The association between these three variants and UADT cancers was independently replicated in 5,092 UADT cancer cases and 6,794 controls non-overlapping samples presented here (rs1573496-ADH7, p = 5×10−8; rs1229984-ADH1B, p = 7×10−9; and rs698-ADH1C, p = 0.02). These results implicate two variants at 4q21 and 12q24 and further highlight three ADH variants in UADT cancer susceptibility
The Collaborative Cross: Rationale, Implementation, and Costs
No full text“Most genetic traits of interest in populations of humans and other organisms are determined by many factors, including genetic and environmental components, which interact in often unpredictable ways. For such complex traits, the whole is not only greater than the sum of its parts, it may be different from the sum of its parts. Thus, complex traits have a genetic architecture that consists of all of the genetic and environmental factors that contribute to the trait, as well as their magnitude and their interactions.” National Institute of General Medical Sciences, 1998, Complex Trait Workshop Report: www.nigms.nih.gov/news/reports/genetic_arch.html The goal of the Complex Trait Consortium (CTC) is to promote the development of resources that can be used to understand, treat, and ultimately prevent pervasive human diseases. Essentially all human diseases are complex in the sense that incidence, severity, and outcome are determined by interactions among many gene variants and environmental factors. Cancer, diabetes, heart and lung disease, Alzheimer’s, and infectious diseases fall into this category. Members of the CTC have spent the past year devising a detailed plan to generate a collaborative genetic resource that will greatly accelerate the study of mouse models of human disease. The resource is called the Collaborative Cross. This Report explains our objectives and provides an outline of the methods and costs associated with making the Collaborative Cross
CBCS: A Scalable Consortium Blockchain Architecture Based on World State Collaborative Storage
No full textIn the big data environment, data are characterized by a large volume, various types, and rapid changes. The consortium blockchain applied in this environment faces the problem of excessive storage of the ledger, and the ledger handling different types of business needs to be isolated to ensure the ledger’s security. To this end, this paper proposes a scalable consortium blockchain architecture based on world state collaborative storage (CBCS). First, a business world state database update method is designed based on sparse Merkle multiproofs, where the collaborative storage of world state is realized under the premise of mutual isolation of the ledger between business domains. Then, a world state consistency verification method based on the rank B+ tree is designed to verify the consistency of the business world state in business domains by the checking sidechain, and a main-side chain cross-anchoring structure is designed to realize secure anchoring of the mainchain and the checking sidechain. Meanwhile, a blockchain transaction trusted tracing method based on two-level certification is developed to enable business nodes to obtain complete blockchain transactions. Finally, the feasibility and efficiency of the proposed mechanism to solve the storage scalability problem in the consortium blockchain are verified through experiments
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