Complications in Climate Data Classification: The Political and Cultural Production of Variable Names

Model intercomparison projects are a unique and highly specialized form of data—intensive collaboration in the earth sciences. Typically, a set of pre‐determined boundary conditions (scenarios) are agreed upon by a community of model developers that then test and simulate each of those scenarios with individual ‘runs’ of a climate model. Because both the human expertise, and the computational power needed to produce an intercomparison project are exceptionally expensive, the data they produce are often archived for the broader climate science community to use in future research. Outside of high energy physics and astronomy sky surveys, climate modeling intercomparisons are one of the largest and most rapid methods of producing data in the natural sciences (Overpeck et al., 2010).But, like any collaborative eScience project, the discovery and broad accessibility of this data is dependent on classifications and categorizations in the form of structured metadata—namely the Climate and Forecast (CF) metadata standard, which provides a controlled vocabulary to normalize the naming of a dataset’s variables. Intriguingly, the CF standard’s original publication notes, “…conventions have been developed only for things we know we need. Instead of trying to foresee the future, we have added features as required and will continue to do this” (Gregory, 2003). Yet, qualitatively we’ve observed that  this is not the case; although the time period of intercomparison projects remains stable (2-3 years), the scale and complexity of models and their output continue to grow—and thus, data creation and variable names consistently outpace the ratification of CF.

Supporting the long‐term curation and migration of natural history museum collections databases

Migration of data collections from one platform to another is an important component of data curation – yet, there is surprisingly little guidance for information professionals faced with this task. Data migration may be particularly challenging when these data collections are housed in relational databases, due to the complex ways that data, data schemas, and relational database management software become intertwined over time. Here we present results from a study of the maintenance, evolution and migration of research databases housed in Natural History Museums. We find that database migration is an on‐going – rather than occasional – process for many Collection managers, and that they creatively appropriate and innovate on many existing technologies in their migration work. This paper contributes descriptions of a preliminary set of common adaptations and “migration patterns” in the practices of database curators. It also outlines the strategies they use when facing collection‐level data migration and describes the limitations of existing tools in supporting LAM and “small science” research database migration. We conclude by outlining future research directions for the maintenance and migration of collections and complex digital objects.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147782/1/pra214505501055.pd

The Plastid Outer Envelope – A Highly Dynamic Interface between Plastid and Cytoplasm

Plastids are the defining organelles of all photosynthetic eukaryotes. They are the site of photosynthesis and of a large number of other essential metabolic pathways, such as fatty acid and amino acid biosyntheses, sulfur and nitrogen assimilation, and aromatic and terpenoid compound production, to mention only a few examples. The metabolism of plastids is heavily intertwined and connected with that of the surrounding cytosol, thus causing massive traffic of metabolic precursors, intermediates, and products. Two layers of biological membranes that are called the inner (IE) and the outer (OE) plastid envelope membranes bound the plastids of Archaeplastida. While the IE is generally accepted as the osmo-regulatory barrier between cytosol and stroma, the OE was considered to represent an unspecific molecular sieve, permeable for molecules of up to 10 kDa. However, after the discovery of small substrate specific pores in the OE, this view has come under scrutiny. In addition to controlling metabolic fluxes between plastid and cytosol, the OE is also crucial for protein import into the chloroplast. It contains the receptors and translocation channel of the TOC complex that is required for the canonical post-translational import of nuclear-encoded, plastid-targeted proteins. Further, the OE is a metabolically active compartment of the chloroplast, being involved in, e.g., fatty acid metabolism and membrane lipid production. Also, recent findings hint on the OE as a defense platform against several biotic and abiotic stress conditions, such as cold acclimation, freezing tolerance, and phosphate deprivation. Moreover, dynamic non-covalent interactions between the OE and the endomembrane system are thought to play important roles in lipid and non-canonical protein trafficking between plastid and endoplasmic reticulum. While proteomics and bioinformatics has provided us with comprehensive but still incomplete information on proteins localized in the plastid IE, the stroma, and the thylakoids, our knowledge of the protein composition of the plastid OE is far from complete. In this article, we report on the recent progress in discovering novel OE proteins to draw a conclusive picture of the OE. A “parts list” of the plastid OE will be presented, using data generated by proteomics of plastids isolated from various plant sources

The Phylogeny of a Dataset

ABSTRACT The field of evolutionary biology offers many approaches to study the changes that occur between and within generations of species; these methods have recently been adopted by cultural anthropologists, linguists and archaeologists to study the evolution of physical artifacts. In this paper, we further extend these approaches by using phylogenetic methods to model and visualize the evolution of a long-standing, widely used digital dataset in climate science. Our case study shows that clustering algorithms developed specifically for phylogenetic studies in evolutionary biology can be successfully adapted to the study of digital objects, and their known offspring. Although we note a number of limitations with our initial effort, we argue that a quantitative approach to studying how digital objects evolve, are reused, and spawn new digital objects represents an important direction for the future of Information Science

Genome-Wide Association Studies for the Detection of Genetic Variants Associated With Daptomycin and Ceftaroline Resistance in Staphylococcus aureus

Background: As next generation sequencing (NGS) technologies have experienced a rapid development over the last decade, the investigation of the bacterial genetic architecture reveals a high potential to dissect causal loci of antibiotic resistance phenotypes. Although genome-wide association studies (GWAS) have been successfully applied for investigating the basis of resistance traits, complex resistance phenotypes have been omitted so far. For S. aureus this especially refers to antibiotics of last resort like daptomycin and ceftaroline. Therefore, we aimed to perform GWAS for the identification of genetic variants associated with DAP and CPT resistance in clinical S. aureus isolates. Materials/methods: To conduct microbial GWAS, we selected cases and controls according to their clonal background, date of isolation, and geographical origin. Association testing was performed with PLINK and SEER analysis. By using in silico analysis, we also searched for rare genetic variants in candidate loci that have previously been described to be involved in the development of corresponding resistance phenotypes. Results: GWAS revealed MprF P314L and L826F to be significantly associated with DAP resistance. These mutations were found to be homogenously distributed among clonal lineages suggesting convergent evolution. Additionally, rare and yet undescribed single nucleotide polymorphisms could be identified within mprF and putative candidate genes. Finally, we could show that each DAP resistant isolate exhibited at least one amino acid substitution within the open reading frame of mprF. Due to the presence of strong population stratification, no genetic variants could be associated with CPT resistance. However, the investigation of the staphylococcal cassette chromosome mec (SCCmec) revealed various mecA SNPs to be putatively linked with CPT resistance. Additionally, some CPT resistant isolates revealed no mecA mutations, supporting the hypothesis that further and still unknown resistance determinants are crucial for the development of CPT resistance in S. aureus. Conclusion: We hereby confirmed the potential of GWAS to identify genetic variants that are associated with antibiotic resistance traits in S. aureus. However, precautions need to be taken to prevent the detection of spurious associations. In addition, the implementation of different approaches is still essential to detect multiple forms of variations and mutations that occur with a low frequency.Peer Reviewe

Corrigendum: Genome-Wide Association Studies for the Detection of Genetic Variants Associated With Daptomycin and Ceftaroline Resistance in Staphylococcus aureus

Peer Reviewe

Source attribution of poly- and perfluoroalkyl substances (PFASs) in surface waters from Rhode Island and the New York Metropolitan Area

Exposure to poly- and perfluoroalkyl substances (PFASs) has been associated with adverse health effects in humans and wildlife. Understanding pollution sources is essential for environmental regulation, but source attribution for PFASs has been confounded by limited information about industrial releases and rapid changes in chemical production. Here we use principal component analysis (PCA), hierarchical clustering, and geospatial analysis to understand source contributions to 14 PFASs measured across 37 sites in the northeastern United States in 2014. PFASs are significantly elevated in urban areas compared to rural sites except for perfluorobutanesulfonate, N-methyl perfluorooctanesulfonamidoacetic acid, perfluoroundecanate, and perfluorododecanate. The highest PFAS concentrations across sites were those of perfluorooctanate (PFOA, 56 ng L−1) and perfluorohexanesulfonate (PFHxS, 43 ng L−1), and perfluorooctanesulfonate (PFOS) levels are lower than earlier measurements of U.S. surface waters. PCA and cluster analysis indicate three main statistical groupings of PFASs. Geospatial analysis of watersheds reveals the first component/cluster originates from a mixture of contemporary point sources such as airports and textile mills. Atmospheric sources from the waste sector are consistent with the second component, and the metal smelting industry plausibly explains the third component. We find this source-attribution technique is effective for better understanding PFAS sources in urban areas

Plastid Signals and the Bundle Sheath: Mesophyll Development in Reticulate Mutants

Lundquist PK, Rosar C, Bräutigam A, Weber APM. Plastid Signals and the Bundle Sheath: Mesophyll Development in Reticulate Mutants. Molecular Plant. 2014;7(1):14-29.The development of a plant leaf is a meticulously orchestrated sequence of events producing a complex organ comprising diverse cell types. The reticulate class of leaf variegation mutants displays contrasting pigmentation between veins and interveinal regions due to specific aberrations in the development of mesophyll cells. Thus, the reticulate mutants offer a potent tool to investigate cell-type-specific developmental processes. The discovery that most mutants are affected in plastid-localized, metabolic pathways that are strongly expressed in vasculature-associated tissues implicates a crucial role for the bundle sheath and their chloroplasts in proper development of the mesophyll cells. Here, we review the reticulate mutants and their phenotypic characteristics, with a focus on those in Arabidopsis thaliana. Two alternative models have been put forward to explain the relationship between plastid metabolism and mesophyll cell development, which we call here the supply and the signaling hypotheses. We critically assess these proposed models and discuss their implications for leaf development and bundle sheath function in C3 species. The characterization of the reticulate mutants supports the significance of plastid retrograde signaling in cell development and highlights the significance of the bundle sheath in C3 photosynthesis

The Product and System Specificities of Measuring Curation Impact

Using three datasets archived at the National Center for Atmospheric Research (NCAR), we describe the creation of a ‘data usage index’ for curation-specific impact assessments. Our work is focused on quantitatively evaluating climate and weather data used in earth and space science research, but we also discuss the application of this approach to other research data contexts. We conclude with some proposed future directions for metric-based work in data curation