Project Hydra: Designing & Building a Reusable Framework for Multipurpose, Multifunction, Multi-institutional Repository-Powered Solutions

4th International Conference on Open RepositoriesThis presentation was part of the session : Fedora User Group PresentationsDate: 2009-05-20 03:30 PM – 05:00 PMThere is a clear business need in higher education for a flexible, reusable application framework that can support the rapid development of multiple systems tailored to distinct needs, but powered by a common underlying repository. Recognizing this common need, Stanford University, the University of Hull and the University of Virginia are collaborating on "Project Hydra", a three-year effort to create an application and middleware framework that, in combination with an underlying Fedora repository, will create a reusable environment for running multifunction, multipurpose repository-powered solutions. This paper details the collaborators' functional and technical design for such a framework, and will demonstrate the progress made to date on the initiative.JIS

Hydra: A Technical and Community Framework For Customized, Reusable, Repository Solutions

While repositories provide obvious benefits in hosting and managing content, it is equally clear that there is no "one size fits all" solution to the range of digital asset management needs at a typical institution, much less across institutions. A system that supports the submission, approval and dissemination of electronic theses and dissertations, for example, has demonstrably different requirements than a digitization workflow solution, an e-science data repository, or media preservation and access system. There is a clear need in the repository community to readily develop and deploy content-, domain-, and institution-specific solutions that integrate the flexibility and richness of customized applications and workflows with the underlying power of repositories for content management, access and preservation. Hydra is a multi-institutional, multi-functional, multi-purpose framework that addresses this need on twin fronts. As a technical framework, it provides a toolkit of reusable components that can be combined and configured in different arrays to meet a diversity of content management needs. As a community framework, Hydra provides like-minded institutions with the mechanism to combine their individual development efforts, resources and priorities into a collective solution with breadth and depth that exceeds the capacity of any single institution to create, maintain or enhance on its own

Hydra: A Technical and Community Framework For Customized, Reusable, Repository Solutions

While repositories provide obvious benefits in hosting and managing content, it is equally clear that there is no "one size fits all" solution to the range of digital asset management needs at a typical institution, much less across institutions. A system that supports the submission, approval and dissemination of electronic theses and dissertations, for example, has demonstrably different requirements than a digitization workflow solution, an e-science data repository, or media preservation and access system. There is a clear need in the repository community to readily develop and deploy content-, domain-, and institution-specific solutions that integrate the flexibility and richness of customized applications and workflows with the underlying power of repositories for content management, access and preservation. Hydra is a multi-institutional, multi-functional, multi-purpose framework that addresses this need on twin fronts. As a technical framework, it provides a toolkit of reusable components that can be combined and configured in different arrays to meet a diversity of content management needs. As a community framework, Hydra provides like-minded institutions with the mechanism to combine their individual development efforts, resources and priorities into a collective solution with breadth and depth that exceeds the capacity of any single institution to create, maintain or enhance on its own

Bapineuzumab for mild to moderate Alzheimer’s disease in two global, randomized, phase 3 trials

Background Our objective was to evaluate the efficacy (clinical and biomarker) and safety of intravenous bapineuzumab in patients with mild to moderate Alzheimer’s disease (AD). Methods Two of four phase 3, multicenter, randomized, double-blind, placebo-controlled, 18-month trials were conducted globally: one in apolipoprotein E ε4 carriers and another in noncarriers. Patients received bapineuzumab 0.5 mg/kg (both trials) or 1.0 mg/kg (noncarrier trial) or placebo every 13 weeks. Coprimary endpoints were change from baseline to week 78 on the 11-item Alzheimer’s Disease Assessment Scale–Cognitive subscale and the Disability Assessment for Dementia. Results A total of 683 and 329 patients completed the current carrier and noncarrier trials, respectively, which were terminated prematurely owing to lack of efficacy in the two other phase 3 trials of bapineuzumab in AD. The current trials showed no significant difference between bapineuzumab and placebo for the coprimary endpoints and no effect of bapineuzumab on amyloid load or cerebrospinal fluid phosphorylated tau. (Both measures were stable over time in the placebo group.) Amyloid-related imaging abnormalities with edema or effusion were confirmed as the most notable adverse event. Conclusions These phase 3 global trials confirmed lack of efficacy of bapineuzumab at tested doses on clinical endpoints in patients with mild to moderate AD. Some differences in the biomarker results were seen compared with the other phase 3 bapineuzumab trials. No unexpected adverse events were observed. Trial registration Noncarriers (3000) ClinicalTrials.gov identifier NCT00667810; registered 24 Apr 2008. Carriers (3001) ClinicalTrials.gov identifier NCT00676143; registered 2 May 2008

Genome-wide survey of parent-of-origin effects on DNA methylation identifies candidate imprinted loci in humans

Genomic imprinting is an epigenetic mechanism leading to parent-of-origin silencing of alleles. So far, the precise number of imprinted regions in humans is uncertain. In this study, we leveraged genome-wide DNA methylation in whole blood measured longitudinally at 3 time points (birth, childhood and adolescence) and GWAS data in 740 Mother-Child duos from the Avon Longitudinal Study of Parents and Children to identify candidate imprinted loci. We reasoned that cis-meQTLs at genomic regions that were imprinted would show strong evidence of parent-of-origin associations with DNA methylation, enabling the detection of imprinted regions. Using this approach, we identified genome-wide significant cis-meQTLs that exhibited parent-of-origin effects (POEs) at 82 loci, 34 novel and 48 regions previously implicated in imprinting (3.7-10< P

Amygdala and dlPFC abnormalities, with aberrant connectivity and habituation in response to emotional stimuli in females with BPD

Background: Little is known about the frontolimbic abnormalities thought to underlie borderline personality disorder (BPD). We endeavoured to study regional responses, as well as their connectivity and habituation during emotion processing. Methods: 14 BPD patients and 14 normal female controls (NC) controlled for menstrual phase underwent emotion-induction during an fMRI task using standardised images in a block design. We then performed psychophysiological interaction (PPI) analysis to investigate functional connectivity. Results: BPD patients reported more disgust in questionnaires compared to controls. Relative to NC, they showed reduced left amygdala and increased dorsolateral prefrontal cortex (dlPFC) activation to all emotions collapsed versus neutral. Habituation of ventral striatal activity to repeated emotional stimuli was observed in controls but not in BPD. Finally, in the context of disgust (but not other emotions) versus neutral, BPD patients displayed enhanced left amygdala coupling with the dlPFC and ventral striatum. Limitations: Strict inclusion criteria reduced the sample size. Conclusions: In summary, BPD showed abnormal patterns of activation, habituation and connectivity in regions linked to emotion regulation. Amygdala deactivation may be mediated by abnormal top-down regulatory control from the dorsolateral prefrontal cortex. Aberrant emotion processing may play a unique role in the pathophysiology of BPD

Decoding Brain Activity Associated with Literal and Metaphoric Sentence Comprehension Using Distributional Semantic Models

Recent years have seen a growing interest within the natural language processing (NLP)community in evaluating the ability of semantic models to capture human meaning representation in the brain. Existing research has mainly focused on applying semantic models to de-code brain activity patterns associated with the meaning of individual words, and, more recently, this approach has been extended to sentences and larger text fragments. Our work is the first to investigate metaphor process-ing in the brain in this context. We evaluate a range of semantic models (word embeddings, compositional, and visual models) in their ability to decode brain activity associated with reading of both literal and metaphoric sentences. Our results suggest that compositional models and word embeddings are able to capture differences in the processing of literal and metaphoric sentences, providing sup-port for the idea that the literal meaning is not fully accessible during familiar metaphor comprehension

Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation

Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. In the present study, we describe results of DNAm quantitative trait locus (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTLs, of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15–17% of the additive genetic variance of DNAm. We show that the genetic architecture of DNAm levels is highly polygenic. Using shared genetic control between distal DNAm sites, we constructed networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic variants are associated with both DNAm levels and complex diseases, but only in a minority of cases do these associations reflect causal relationships from DNAm to trait or vice versa, indicating a more complex genotype–phenotype map than previously anticipated

Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation.

Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. In the present study, we describe results of DNAm quantitative trait locus (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTLs, of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15–17% of the additive genetic variance of DNAm. We show that the genetic architecture of DNAm levels is highly polygenic. Using shared genetic control between distal DNAm sites, we constructed networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic variants are associated with both DNAm levels and complex diseases, but only in a minority of cases do these associations reflect causal relationships from DNAm to trait or vice versa, indicating a more complex genotype–phenotype map than previously anticipated.C.L.R., G.D.S., G.S., J.L.M., K.B., M. Suderman, T.G.R. and T.R.G. are supported by the UK Medical Research Council (MRC) Integrative Epidemiology Unit at the University of Bristol (MC_UU_00011/1, MC_UU_00011/4, MC_UU_00011/5). C.L.R. receives support from a Cancer Research UK Programme grant (no. C18281/A191169). G.H. is funded by the Wellcome Trust and the Royal Society (208806/Z/17/Z). E.H. and J.M. were supported by MRC project grants (nos. MR/K013807/1 and MR/R005176/1 to J.M.) and an MRC Clinical Infrastructure award (no. MR/M008924/1 to J.M.). B.T.H. is supported by the Netherlands CardioVascular Research Initiative (the Dutch Heart Foundation, Dutch Federation of University Medical Centres, the Netherlands Organisation for Health Research and Development, and the Royal Netherlands Academy of Sciences) for the GENIUS project ‘Generating the best evidence-based pharmaceutical targets for atherosclerosis’ (CVON2011-19, CVON2017-20). J.T.B. was supported by the Economic and Social Research Council (grant no. ES/N000404/1). The present study was also supported by JPI HDHL-funded DIMENSION project (administered by the BBSRC UK, grant no. BB/S020845/1 to J.T.B., and by ZonMW the Netherlands, grant no. 529051021 to B.T.H). A.D.B. has been supported by a Wellcome Trust PhD Training Fellowship for Clinicians and the Edinburgh Clinical Academic Track programme (204979/Z/16/Z). J. Klughammer was supported by a DOC fellowship of the Austrian Academy of Sciences. Cohort-specific acknowledgements and funding are presented in the Supplementary Note