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

Microencapsulated Dopamine (DA)-Induced Restitution of Function in 6-OHDA-Denervated Rat Striatum in vivo: Comparison Between Two Microsphere Excipients

Biodegradable controlled-release microsphere systems made with the biocompatible biodegradable polyester excipient poly [DL lactide-co-glycolide] constitute an exciting new technology for drug delivery to the central nervous system (CNS). The present study describes functional observations indicating that implantation of dopamine (DA) microspheres encapsulated within two different polymer excipients into denervated- striatal tissue assures a prolonged release of the transmitter in vivo. Moreover, in this regard, the results show that there were clear cut temporal differences in the effect of the two DA microsphere formulations compared in this study, probably reflecting variations in the actual composition (i.e., lactide to glycolide ratio) of the two copolymer excipients examined. This technology has considerable potential for basic research with possible clinical application

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

Building a Quantum Engineering Undergraduate Program

Contribution: A roadmap is provided for building a quantum engineering education program to satisfy U.S. national and international workforce needs. Background: The rapidly growing quantum information science and engineering (QISE) industry will require both quantum-aware and quantum-proficient engineers at the bachelor\u27s level. Research Question: What is the best way to provide a flexible framework that can be tailored for the full academic ecosystem? Methodology: A workshop of 480 QISE researchers from across academia, government, industry, and national laboratories was convened to draw on best practices; representative authors developed this roadmap. Findings: 1) For quantum-aware engineers, design of a first quantum engineering course, accessible to all STEM students, is described; 2) for the education and training of quantum-proficient engineers, both a quantum engineering minor accessible to all STEM majors, and a quantum track directly integrated into individual engineering majors are detailed, requiring only three to four newly developed courses complementing existing STEM classes; 3) a conceptual QISE course for implementation at any postsecondary institution, including community colleges and military schools, is delineated; 4) QISE presents extraordinary opportunities to work toward rectifying issues of inclusivity and equity that continue to be pervasive within engineering. A plan to do so is presented, as well as how quantum engineering education offers an excellent set of education research opportunities; and 5) a hands-on training plan on quantum hardware is outlined, a key component of any quantum engineering program, with a variety of technologies, including optics, atoms and ions, cryogenic and solid-state technologies, nanofabrication, and control and readout electronics

Building a Quantum Engineering Undergraduate Program

The rapidly growing quantum information science and engineering (QISE) industry will require both quantum-aware and quantum-proficient engineers at the bachelor's level. We provide a roadmap for building a quantum engineering education program to satisfy this need. For quantum-aware engineers, we describe how to design a first quantum engineering course accessible to all STEM students. For the education and training of quantum-proficient engineers, we detail both a quantum engineering minor accessible to all STEM majors, and a quantum track directly integrated into individual engineering majors. We propose that such programs typically require only three or four newly developed courses that complement existing engineering and science classes available on most larger campuses. We describe a conceptual quantum information science course for implementation at any post-secondary institution, including community colleges and military schools. QISE presents extraordinary opportunities to work towards rectifying issues of inclusivity and equity that continue to be pervasive within engineering. We present a plan to do so and describe how quantum engineering education presents an excellent set of education research opportunities. Finally, we outline a hands-on training plan on quantum hardware, a key component of any quantum engineering program, with a variety of technologies including optics, atoms and ions, cryogenic and solid-state technologies, nanofabrication, and control and readout electronics. Our recommendations provide a flexible framework that can be tailored for academic institutions ranging from teaching and undergraduate-focused two- and four-year colleges to research-intensive universities.Comment: 25 pages, 2 figure

The clinical and genetic spectrum of autosomal-recessive TOR1A-related disorders.

In the field of rare diseases, progress in molecular diagnostics led to the recognition that variants linked to autosomal-dominant neurodegenerative diseases of later onset can, in the context of biallelic inheritance, cause devastating neurodevelopmental disorders and infantile or childhood-onset neurodegeneration. TOR1A-associated arthrogryposis multiplex congenita 5 (AMC5) is a rare neurodevelopmental disorder arising from biallelic variants in TOR1A, a gene that in the heterozygous state is associated to torsion dystonia-1 (DYT1 or DYT-TOR1A), an early-onset dystonia with reduced penetrance. While 15 individuals with TOR1A-AMC5 have been reported (less than 10 in detail), a systematic investigation of the full disease-associated spectrum has not been conducted. Here, we assess the clinical, radiological and molecular characteristics of 57 individuals from 40 families with biallelic variants in TOR1A. Median age at last follow-up was 3 years (0-24 years). Most individuals presented with severe congenital flexion contractures (95%) and variable developmental delay (79%). Motor symptoms were reported in 79% and included lower limb spasticity and pyramidal signs, as well as gait disturbances. Facial dysmorphism was an integral part of the phenotype, with key features being a broad/full nasal tip, narrowing of the forehead and full cheeks. Analysis of disease-associated manifestations delineated a phenotypic spectrum ranging from normal cognition and mild gait disturbance to congenital arthrogryposis, global developmental delay, intellectual disability, absent speech and inability to walk. In a subset, the presentation was consistent with fetal akinesia deformation sequence with severe intrauterine abnormalities. Survival was 71% with higher mortality in males. Death occurred at a median age of 1.2 months (1 week - 9 years) due to respiratory failure, cardiac arrest, or sepsis. Analysis of brain MRI studies identified non-specific neuroimaging features, including a hypoplastic corpus callosum (72%), foci of signal abnormality in the subcortical and periventricular white matter (55%), diffuse white matter volume loss (45%), mega cisterna magna (36%) and arachnoid cysts (27%). The molecular spectrum included 22 distinct variants, defining a mutational hotspot in the C-terminal domain of the Torsin-1A protein. Genotype-phenotype analysis revealed an association of missense variants in the 3-helix bundle domain to an attenuated phenotype, while missense variants near the Walker A/B motif as well as biallelic truncating variants were linked to early death. In summary, this systematic cross-sectional analysis of a large cohort of individuals with biallelic TOR1A variants across a wide age-range delineates the clinical and genetic spectrum of TOR1A-related autosomal-recessive disease and highlights potential predictors for disease severity and survival

Prevalence and architecture of de novo mutations in developmental disorders.

The genomes of individuals with severe, undiagnosed developmental disorders are enriched in damaging de novo mutations (DNMs) in developmentally important genes. Here we have sequenced the exomes of 4,293 families containing individuals with developmental disorders, and meta-analysed these data with data from another 3,287 individuals with similar disorders. We show that the most important factors influencing the diagnostic yield of DNMs are the sex of the affected individual, the relatedness of their parents, whether close relatives are affected and the parental ages. We identified 94 genes enriched in damaging DNMs, including 14 that previously lacked compelling evidence of involvement in developmental disorders. We have also characterized the phenotypic diversity among these disorders. We estimate that 42% of our cohort carry pathogenic DNMs in coding sequences; approximately half of these DNMs disrupt gene function and the remainder result in altered protein function. We estimate that developmental disorders caused by DNMs have an average prevalence of 1 in 213 to 1 in 448 births, depending on parental age. Given current global demographics, this equates to almost 400,000 children born per year

The contribution of X-linked coding variation to severe developmental disorders

Abstract: Over 130 X-linked genes have been robustly associated with developmental disorders, and X-linked causes have been hypothesised to underlie the higher developmental disorder rates in males. Here, we evaluate the burden of X-linked coding variation in 11,044 developmental disorder patients, and find a similar rate of X-linked causes in males and females (6.0% and 6.9%, respectively), indicating that such variants do not account for the 1.4-fold male bias. We develop an improved strategy to detect X-linked developmental disorders and identify 23 significant genes, all of which were previously known, consistent with our inference that the vast majority of the X-linked burden is in known developmental disorder-associated genes. Importantly, we estimate that, in male probands, only 13% of inherited rare missense variants in known developmental disorder-associated genes are likely to be pathogenic. Our results demonstrate that statistical analysis of large datasets can refine our understanding of modes of inheritance for individual X-linked disorders