The Oklahoma PetaStore: A Business Model for Big Data on a Small Budget

1. INTRODUCTION In the era of Big Data, and especially as research data management requirements are tightening, research productivity in many disciplines can be highly sensitive to the availability of large scale, long term storage sufficient to contain the many and varied datasets produced and/or consumed by research teams. At the University of Oklahoma (OU), the OU Supercomputing Center for Education & Research (OSCER), a division of OU Information Technology (IT), has been providing large scale archival storage to a growing population of researchers. This has been accomplished via a resource named the Oklahoma PetaStore, funded by a National Science Foundation (NSF) Major Research Instrumentation (MRI) grant (see Acknowledgements) and consisting of disk and tape hardware, software and media. By adopting an unusual business model, OSCER has made very large scale, long term storage available to researchers, at pricing substantially lower than could be accomplished on their own, and with management provided by IT professionals rather than by research team members (for example, graduate students).ABSTRACT In the era of Big Data, research productivity can be highly sensitive to the availability of large scale, long term archival storage. Unfortunately, many mass storage systems are prohibitively expensive at scales appropriate for individual institutions rather than for national centers. Furthermore, a key issue is the set of circumstances under which researchers can, and are willing to, adopt a centralized technology that, in a pure cost recovery model, might be, or might appear to be, more expensive than what the research teams could build on their own. This paper examines a business model that addresses these concerns in a comprehensive manner, distributing the costs among a funding agency, the institution and the research teams, thereby reducing the challenges faced by each. Categories and Subject Descriptors B.3.2 [Design Styles]: Mass storage General Terms Design, Economics, Reliability Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than the author(s) must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]. XSEDE '14, July 13 - 18 2014, Atlanta, GA, USA Copyright is held by the owner/author(s). Publication rights licensed to ACM. ACM 978-1-4503-2893-7/14/07…$15.00. http://dx.doi.org/10.1145/2616498.2616548 Keywords Archival storage, mass store, business modelN

U7 snRNA mutations in Drosophila block histone pre-mRNA processing and disrupt oogenesis

Metazoan replication-dependent histone mRNAs are not polyadenylated, and instead terminate in a conserved stem–loop structure generated by an endonucleolytic cleavage involving the U7 snRNP, which interacts with histone pre-mRNAs through base-pairing between U7 snRNA and a purine-rich sequence in the pre-mRNA located downstream of the cleavage site. Here we generate null mutations of the single Drosophila U7 gene and demonstrate that U7 snRNA is required in vivo for processing all replication-associated histone pre-mRNAs. Mutation of U7 results in the production of poly A+ histone mRNA in both proliferating and endocycling cells because of read-through to cryptic polyadenylation sites found downstream of each Drosophila histone gene. A similar molecular phenotype also results from mutation of Slbp, which encodes the protein that binds the histone mRNA 3′ stem–loop. U7 null mutants develop into sterile males and females, and these females display defects during oogenesis similar to germ line clones of Slbp null cells. In contrast to U7 mutants, Slbp null mutations cause lethality. This may reflect a later onset of the histone pre-mRNA processing defect in U7 mutants compared to Slbp mutants, due to maternal stores of U7 snRNA. A double mutant combination of a viable, hypomorphic Slbp allele and a viable U7 null allele is lethal, and these double mutants express polyadenylated histone mRNAs earlier in development than either single mutant. These data suggest that SLBP and U7 snRNP cooperate in the production of histone mRNA in vivo, and that disruption of histone pre-mRNA processing is detrimental to development

Engaging Citizen Scientists to Keep Transit Times Fresh and Ensure the Efficient Use of Transiting Exoplanet Characterization Missions

This white paper advocates for the creation of a community-wide program to maintain precise mid-transit times of exoplanets that would likely be targeted by future platforms. Given the sheer number of targets that will require careful monitoring between now and the launch of the next generation of exoplanet characterization missions, this network will initially be devised as a citizen science project -- focused on the numerous amateur astronomers, small universities and community colleges and high schools that have access to modest sized telescopes and off-the-shelf CCDs.Comment: White Paper submitted to Astro2020 Science Call, 5 pages, 3 figures, community comments and involvement are welcome

Measurement Bias in Caregiver-Report of Early Childhood Behavior Problems across Demographic Factors in an Echo-Wide Diverse Sample

BACKGROUND: Research and clinical practice rely heavily on caregiver-report measures, such as the Child Behavior Checklist 1.5-5 (CBCL/1.5-5), to gather information about early childhood behavior problems and to screen for child psychopathology. While studies have shown that demographic variables influence caregiver ratings of behavior problems, the extent to which the CBCL/1.5-5 functions equivalently at the item level across diverse samples is unknown. METHODS: Item-level data of CBCL/1.5-5 from a large sample of young children ( RESULTS: Items with the most impactful DIF across child and caregiver groupings were identified for Internalizing, Externalizing, and total Problems. The robust item sets, excluding the high DIF items, showed good reliability and high correlation with the original Internalizing and total Problems scales, with lower reliability for Externalizing. Language version of CBCL administration, education level and sex of the caregiver respondent showed the most significant impact on MI, followed by child age. Sensitivity analyses revealed that child race has a unique impact on DIF over and above socioeconomic status. CONCLUSIONS: The CBCL/1.5-5, a caregiver-report measure of early childhood behavior problems, showed bias across demographic groups. Robust item sets with less DIF can measure Internalizing and total Problems equally as well as the full item sets, with slightly lower reliability for Externalizing, and can be crosswalked to the metric of the full item set, enabling calculation of normed T scores based on more robust item sets

A new inhibitor of the β-arrestin/AP2 endocytic complex reveals interplay between GPCR internalization and signalling.

AbstractIn addition to G protein-coupled receptor (GPCR) desensitization and endocytosis, β-arrestin recruitment to ligand-stimulated GPCRs promotes non-canonical signalling cascades. Distinguishing the respective contributions of β-arrestin recruitment to the receptor and β-arrestin-promoted endocytosis in propagating receptor signalling has been limited by the lack of selective analytical tools. Here, using a combination of virtual screening and cell-based assays, we have identified a small molecule that selectively inhibits the interaction between β-arrestin and the β2-adaptin subunit of the clathrin adaptor protein AP2 without interfering with the formation of receptor/β-arrestin complexes. This selective β-arrestin/β2-adaptin inhibitor (Barbadin) blocks agonist-promoted endocytosis of the prototypical β2-adrenergic (β2AR), V2-vasopressin (V2R) and angiotensin-II type-1 (AT1R) receptors, but does not affect β-arrestin-independent (transferrin) or AP2-independent (endothelin-A) receptor internalization. Interestingly, Barbadin fully blocks V2R-stimulated ERK1/2 activation and blunts cAMP accumulation promoted by both V2R and β2AR, supporting the concept of β-arrestin/AP2-dependent signalling for both G protein-dependent and -independent pathways.</jats:p

Advancing the Selection of Neurodevelopmental Measures in Epidemiological Studies of Environmental Chemical Exposure and Health Effects

With research suggesting increasing incidence of pediatric neurodevelopmental disorders, questions regarding etiology continue to be raised. Neurodevelopmental function tests have been used in epidemiology studies to evaluate relationships between environmental chemical exposures and neurodevelopmental deficits. Limitations of currently used tests and difficulties with their interpretation have been described, but a comprehensive critical examination of tests commonly used in studies of environmental chemicals and pediatric neurodevelopmental disorders has not been conducted. We provide here a listing and critical evaluation of commonly used neurodevelopmental tests in studies exploring effects from chemical exposures and recommend measures that are not often used, but should be considered. We also discuss important considerations in selecting appropriate tests and provide a case study by reviewing the literature on polychlorinated biphenyls

Engaging Citizen Scientists to Keep Transit Times Fresh and Ensure the Efficient Use of Transiting Exoplanet Characterization Missions

This white paper advocates for the creation of a community-wide program to maintain precise mid-transit times of exoplanets that would likely be targeted by future platforms. Given the sheer number of targets that will require careful monitoring between now and the launch of the next generation of exoplanet characterization missions, this network will initially be devised as a citizen science project -- focused on the numerous amateur astronomers, small universities and community colleges and high schools that have access to modest sized telescopes and off-the-shelf CCDs

NOTCH signaling specifies arterial-type definitive hemogenic endothelium from human pluripotent stem cells

NOTCH signaling is required for the arterial specification and formation of hematopoietic stem cells (HSCs) and lympho-myeloid progenitors in the embryonic aorta-gonad-mesonephros region and extraembryonic vasculature from a distinct lineage of vascular endothelial cells with hemogenic potential. However, the role of NOTCH signaling in hemogenic endothelium (HE) specification from human pluripotent stem cell (hPSC) has not been studied. Here, using a chemically defined hPSC differentiation system combined with the use of DLL1-Fc and DAPT to manipulate NOTCH, we discover that NOTCH activation in hPSC-derived immature HE progenitors leads to formation of CD144+CD43−CD73−DLL4+Runx1 + 23-GFP+ arterial-type HE, which requires NOTCH signaling to undergo endothelial-to-hematopoietic transition and produce definitive lympho-myeloid and erythroid cells. These findings demonstrate that NOTCH-mediated arterialization of HE is an essential prerequisite for establishing definitive lympho-myeloid program and suggest that exploring molecular pathways that lead to arterial specification may aid in vitro approaches to enhance definitive hematopoiesis from hPSCs

A Comparison of the SOCIT and DebriSat Experiments

This paper explores the differences between, and shares the lessons learned from, two hypervelocity impact experiments critical to the update of orbital debris environment models. The procedures and processes of the fourth Satellite Orbital Debris Characterization Impact Test (SOCIT) were analyzed and related to the ongoing DebriSat experiment. SOCIT was the first hypervelocity impact test designed specifically for satellites in Low Earth Orbit (LEO). It targeted a 1960's U.S. Navy satellite, from which data was obtained to update pre-existing NASA and DOD breakup models. DebriSat is a comprehensive update to these satellite breakup models- necessary since the material composition and design of satellites have evolved from the time of SOCIT. Specifically, DebriSat utilized carbon fiber, a composite not commonly used in satellites during the construction of the US Navy Transit satellite used in SOCIT. Although DebriSat is an ongoing activity, multiple points of difference are drawn between the two projects. Significantly, the hypervelocity tests were conducted with two distinct satellite models and test configurations, including projectile and chamber layout. While both hypervelocity tests utilized soft catch systems to minimize fragment damage to its post-impact shape, SOCIT only covered 65% of the projected area surrounding the satellite, whereas, DebriSat was completely surrounded cross-range and downrange by the foam panels to more completely collect fragments. Furthermore, utilizing lessons learned from SOCIT, DebriSat's post-impact processing varies in methodology (i.e., fragment collection, measurement, and characterization). For example, fragment sizes were manually determined during the SOCIT experiment, while DebriSat utilizes automated imaging systems for measuring fragments, maximizing repeatability while minimizing the potential for human error. In addition to exploring these variations in methodologies and processes, this paper also presents the challenges DebriSat has encountered thus far and how they were addressed. Accomplishing DebriSat's goal of collecting 90% of the debris, which constitutes well over 100,000 fragments, required addressing many challenges stemming from the very large number of fragments. One of these challenges arose in identifying the foam-embedded fragments. DebriSat addressed this by X-raying all of the panels once the loose debris were removed, and applying a detection algorithm developed in-house to automate the embedded fragment identification process. It is easy to see how the amount of data being compiled would be outstanding. Creating an efficient way to catalog each fragment, as well as archiving the data for reproducibility also posed a great challenge for DebriSat. Barcodes to label each fragment were introduced with the foresight that once the characterization process began, the datasheet for each fragment would have to be accessed again quickly and efficiently. The DebriSat experiment has benefited significantly by leveraging lessons learned from the SOCIT experiment along with the technological advancements that have occurred during the time between the experiments. The two experiments represent two ages of satellite technology and, together, demonstrate the continuous efforts to improve the experimental techniques for fragmentation debris characterization