The Astrolabe Project: Identifying and Curating Astronomical Dark Data through Development of Cyberinfrastructure Resources

As research datasets and analyses grow in complexity, data that could be valuable to other researchers and to support the integrity of published work remain uncurated across disciplines. These data are especially concentrated in the Long Tail of funded research, where curation resources and related expertise are often inaccessible. In the domain of astronomy, it is undisputed that uncurated dark data exist, but the scope of the problem remains uncertain. The Astrolabe Project is a collaboration between University of Arizona researchers, the CyVerse cyberinfrastructure environment, and American Astronomical Society, with a mission to identify and ingest previously-uncurated astronomical data, and to provide a robust computational environment for analysis and sharing of data, as well as services for authors wishing to deposit data associated with publications. Following expert feedback obtained through two workshops held in 2015 and 2016, Astrolabe is funded in part by National Science Foundation. The system is being actively developed within CyVerse, and Astrolabe collaborators are soliciting heterogeneous datasets and potential users for the prototype system. Astrolabe team members are currently working to characterize the properties of uncurated astronomical data, and to develop automated methods for locating potentially-useful data to be targeted for ingest into Astrolabe, while cultivating a user community for the new data management system.Comment: To be published in Proceedings of Library and Information Services in Astronomy (LISA) VIII; conference held in Strasbourg, France, June 6-9, 201

Astrolabe: Curating, Linking and Computing Astronomy's Dark Data

Where appropriate repositories are not available to support all relevant astronomical data products, data can fall into darkness: unseen and unavailable for future reference and re-use. Some data in this category are legacy or old data, but newer datasets are also often uncurated and could remain "dark". This paper provides a description of the design motivation and development of Astrolabe, a cyberinfrastructure project that addresses a set of community recommendations for locating and ensuring the long-term curation of dark or otherwise at-risk data and integrated computing. This paper also describes the outcomes of the series of community workshops that informed creation of Astrolabe. According to participants in these workshops, much astronomical dark data currently exist that are not curated elsewhere, as well as software that can only be executed by a few individuals and therefore becomes unusable because of changes in computing platforms. Astronomical research questions and challenges would be better addressed with integrated data and computational resources that fall outside the scope of existing observatory and space mission projects. As a solution, the design of the Astrolabe system is aimed at developing new resources for management of astronomical data. The project is based in CyVerse cyberinfrastructure technology and is a collaboration between the University of Arizona and the American Astronomical Society. Overall the project aims to support open access to research data by leveraging existing cyberinfrastructure resources and promoting scientific discovery by making potentially-useful data in a computable format broadly available to the astronomical community.Comment: Accepted for publication in the Astrophysical Journal Supplement Series, 22 pages, 2 figure

Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor

The presence of different transcripts of a gene across samples can be analysed by whole-transcriptome microarrays. Reproducing results from published microarray data represents a challenge due to the vast amounts of data and the large variety of pre-processing and filtering steps employed before the actual analysis is carried out. To guarantee a firm basis for methodological development where results with new methods are compared with previous results it is crucial to ensure that all analyses are completely reproducible for other researchers. We here give a detailed workflow on how to perform reproducible analysis of the GeneChip Human Exon 1.0 ST Array at probe and probeset level solely in R/Bioconductor, choosing packages based on their simplicity of use. To exemplify the use of the proposed workflow we analyse differential splicing and differential gene expression in a publicly available dataset using various statistical methods. We believe this study will provide other researchers with an easy way of accessing gene expression data at different annotation levels and with the sufficient details needed for developing their own tools for reproducible analysis of the GeneChip Human Exon 1.0 ST Array

Milankovitch frequencies in tephra records at volcanic arcs: The relation of kyr-scale cyclic variations in volcanism to global climate changes

Highlights The increase in volcanic activity after the last glacial maximum observed on Iceland has led to one of the most fascinating hypothesis in science in the last decades: that deglaciation may force volcanism. We: - Re-analyzed four longer tephra records with the same statistical method and demonstrated that all contain the ∼41 kyr and ∼100 kyr Millankovitch periodicities. - The frequency spectra of the tephra and δ18O records are significantly correlated supporting the hypothesis that orbital-driven global climate changes interact with the volcanic eruption frequency regionally and globally. - However, the simultaneous analysis of the four best-characterized tephra records shows that correlations and associated time lags suffer from a number of uncertainties including the nature and quality of tephra time series, a wide range in geographic latitudes and geological settings, as well as applied statistical methods Therefore more precise tephra time series (preservation and age optimized) from different regions (glaciated versus non-glaciated) and geological settings (island arcs, continental arcs, intraplate) are needed together with standardized statistical analysis to decipher the impact of these factors on a global perspective of how climate may control volcanism. Abstract The increase in volcanic activity after the last glacial maximum observed on Iceland has led to one of the most fascinating hypothesis in science in the last decades: that deglaciation may force volcanism. Consequently, tephrostratigraphic records of sufficient length that cover multiple glacial cycles have been used to test whether such relationships hold systematically through the Quaternary. Here we review such tephra records that have been linked with climate proxy records such as δ18O in marine sediments, which is a measure of sea-level change and which is thought to be orbitally forced, as it exhibits the characteristic Milankovitch periodicities of precession (∼23 kyr), obliquity (∼41 kyr) and eccentricity (∼100 kyr). Statistical analyses have identified these periodicities also in long tephra records from different latitudes and geotectonic settings, as well as in compiled semi-global records. These studies detect Milankovitch periods in their tephra record, and also a phase shift relative to the δ18O record in such that periods of increased eruption frequencies coincide with the deglaciation period at the glacial/interglacial transition when ice and water loads on the lithosphere change most rapidly. However, there are also disparities in results and interpretations, which may be attributable to the different methods of analysis applied by the studies. We have therefore re-analyzed the four best-characterized tephra records by the same methods. We distinguish between analysis in the frequency domain, a novel approach, and analysis in the time domain, which has been used in previous studies. Analysis in the frequency domain identifies harmonic frequencies that arise from the binary nature of the tephra records and complicate the identification of primary frequencies. However, we show that all four records show spectral density peaks near the main Milankovitch periodicities of 41 and 100 kyr, and that they produce meaningful and significant statistical correlations with each other and the global δ18O record but not with random time series. Although the time-domain correlations with δ18O roughly confirm phase shifts implying peak volcanism during deglaciation, correlation coefficients arising from very noisy records are generally too low for precise constraints on the relative timing. These deficiencies presently hamper the recognition of the physical mechanisms through which global climate changes affect volcanism at both, high-latitude glaciated regions and low-latitude non-glaciated regions

Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na+ Ion Release

Monoamine transporters are responsible for termination of synaptic signaling and are involved in depression, control of appetite, and anxiety amongst other neurological processes. Despite extensive efforts, the structures of the monoamine transporters and the transport mechanism of ions and substrates are still largely unknown. Structural knowledge of the human serotonin transporter (hSERT) is much awaited for understanding the mechanistic details of substrate translocation and binding of antidepressants and drugs of abuse. The publication of the crystal structure of the homologous leucine transporter has resulted in homology models of the monoamine transporters. Here we present extended molecular dynamics simulations of an experimentally supported homology model of hSERT with and without the natural substrate yielding a total of more than 1.5 µs of simulation of the protein dimer. The simulations reveal a transition of hSERT from an outward-facing occluded conformation to an inward-facing conformation in a one-substrate-bound state. Simulations with a second substrate in the proposed symport effector site did not lead to conformational changes associated with translocation. The central substrate binding site becomes fully exposed to the cytoplasm leaving both the Na+-ion in the Na2-site and the substrate in direct contact with the cytoplasm through water interactions. The simulations reveal how sodium is released and show indications of early events of substrate transport. The notion that ion dissociation from the Na2-site drives translocation is supported by experimental studies of a Na2-site mutant. Transmembrane helices (TMs) 1 and 6 are identified as the helices involved in the largest movements during transport

High neonatal blood iron content is associated with the risk of childhood type 1 diabetes mellitus

(1) Background: Iron requirement increases during pregnancy and iron supplementation is therefore recommended in many countries. However, excessive iron intake may lead to destruction of pancreatic β-cells. Therefore, we aim to test if higher neonatal iron content in blood is associated with the risk of developing type 1 diabetes mellitus (T1D) in childhood; (2) Methods: A case-control study was conducted, including 199 children diagnosed with T1D before the age of 16 years from 1991 to 2005 and 199 controls matched on date of birth. Information on confounders was available in 181 cases and 154 controls. Iron was measured on a neonatal single dried blood spot sample and was analyzed by laser ablation inductively coupled plasma mass spectrometry. Multivariate logistic regression was used to evaluate if iron content in whole blood was associated with the risk of T1D; (3) Results: A doubling of iron content increased the odds of developing T1D more than two-fold (odds ratio (95% CI), 2.55 (1.04; 6.24)). Iron content increased with maternal age (p = 0.04) and girls had higher content than boys (p = 0.01); (4) Conclusions: Higher neonatal iron content associates to an increased risk of developing T1D before the age of 16 years. Iron supplementation during early childhood needs further investigation, including the causes of high iron in neonates

«Man må regne med å dø når man er over 60 år». En KLoK-oppgave om utfylling av dødsattest og unaturlige dødsfall

Gruppen har valgt utfylling av Legeerklæring om dødsfall/Melding om unaturlig dødsfall (dødsattest) som tema i denne prosjektoppgaven, nærmere bestemt delen som omhandler registrering og melding av unaturlige dødsfall. Problemstillingen lyder som følger: Hvordan endre dødsattesten for å forbedre registrering ,og melding til politiet, av unaturlige dødsfall? Kunnskapsgrunnlaget for oppgaven baseres i stor grad på det norske lovverket, i tillegg også publiserte forskningsresultater fra Akershus Universitetssykehus (Ahus). Kvalitetsforbedringsprosjektet finner sted på Ahus og skal gjennomføres ved å gjøre endringer i dødsattestskjemaet i DIPS. Gruppen planlegger å benytte seg av en resultatindikator der man sammenligner andel unaturlige dødsfall som blir registrert og meldt til politiet før og etter prosjektperioden. Vi vurderer vårt tiltak til å være gjennomførbart. Hvis tiltaket fungerer på Ahus, bør det også innføres på nasjonalt plan

Association between Neonatal Whole Blood Iron Content and Cytokines, Adipokines, and Other Immune Response Proteins

(1) Background: High iron associates with inflammation and type 1 diabetes (T1D). Iron is essential not only for neonatal development but also for infectious microorganisms. The neonatal immune system is immature, and innate immunity prevails before immunocompetence develops. (2) Methods: In 398 newborns from the Danish Newborn Screening Biobank, we examined if whole blood iron (WB-Iron) content were associated with cytokines, adipokines, C-reactive protein (CRP), and mannose-binding lectin (MBL) in non-infected healthy neonates, and if these associations differed in newborns who later developed T1D (cases) (n = 199). WB-Iron was quantified using laser ablation inductively coupled plasma mass spectrometry on the neonatal dried blood spots. For each analyte, the relative change (RC) in the mean level was modeled by robust log-normal regression. (3) Results: A one unit increase in neonatal WB-Iron was associated with a 38% decrease in mean interleukin (IL)-6 levels (0.62; 95% CI: 0.40–0.95, p = 0.03), and a 37% decrease in mean MBL levels (0.63; 95% CI: 0.41–0.95, p = 0.03), but was not statistically significant after correction for multiple testing. (4) Conclusions: In summary, we found that higher neonatal WB-iron content was inversely associated with IL-6 and MBL, which may increase susceptibility to infections