A linked data approach to publishing complex scientific workflows

Past data management practices in many fields of natural science, including climate research, have focused primarily on the final research output - the research publication - with less attention paid to the chain of intermediate data results and their associated metadata, including provenance. Data were often regarded merely as an adjunct to the publication, rather than a scientific resource in their own right. In this paper, we attempt to address the issues of capturing and publishing detailed workflows associated with the climate/research datasets held by the Climatic Research Unit (CRU) at the University of East Anglia. To this end, we present a customisable approach to exposing climate research workflows for the effective re-use of the associated data, through the adoption of linked-data principles, existing widely adopted citation techniques (Digital Object Identifier) and data exchange mechanisms (Open Archives Initiative Object Reuse and Exchange)

Appealing Politics? Using the Bully Pulpit to Change Opinions and Influence Policy

University of Minnesota Ph.D. dissertation. July 2016. Major: Political Science. Advisor: Andrew Karch. 1 computer file (PDF); vii, 165 pages.Recent political science research demonstrates that American politicians can use speeches to influence the political process. Despite this phenomenon's profound implications, our understanding of it remains underdeveloped in many respects. Most importantly, we lack compelling strategies that can outline the conditions under which speeches are most likely to be given, influence public opinion, and alter legislative behavior. Leveraging the unique variation provided by analysis at the state level, my dissertation does just that by assessing the impact of public statements by governors on the political process. It demonstrates that when governors speak out publicly on a policy issue, the speech can fundamentally alter the political process – influencing the way in which the public thinks about the issue and altering the behavior of legislators working on related public policy

Americans are divided on Medicaid work requirements, but it depends on recipients’ circumstances

This week the Biden administration requested a halt to a Trump-era Supreme Court challenge to state Medicaid work requirements. But how do Americans feel about work requirements for Medicaid recipients? In new research, Simon F. Haeder, Steven Sylvester and Timothy H. Callaghan find that while Americans are split in their support or opposition to Medicaid work requirements, public opinion is more nuanced when the public is asked who should be exempted from these requirements

Hadamard Products of Product Operators and the Design of Gradient-Diffusion Experiments for Simulating Decoherence by NMR Spectroscopy

An extension of the product operator formalism of NMR is introduced, which uses the Hadamard matrix product to describe many simple spin 1/2 relaxation processes. The utility of this formalism is illustrated by deriving NMR gradient-diffusion experiments to simulate several decoherence models of interest in quantum information processing, along with their Lindblad and Kraus representations. Gradient-diffusion experiments are also described for several more complex forms of decoherence, including the well-known collective isotropic model. Finally, it is shown that the Hadamard formalism gives a concise representation of decoherence with arbitrary correlations among the fluctuating fields at the different spins involved, and that this can be applied to both decoherence (T2) as well as nonadiabatic relaxation (T1) processes.Comment: RevTeX, 11 page single-spaced preprint, no figures. Version two has new title, abstract, introduction & conclusions, while the main body of the text remains substantially the sam

Cross-Linking Between Journal Publications and Data Repositories: A Selection of Examples

This article provides a selection of examples of the many ways that a link can be made between a journal article (whether in a data journal or otherwise) and a dataset held in a data repository. In some cases the method of linking is well established, while in others, they have yet to be rolled out uniformly across the journal landscape. We explore ways in which these examples might be implemented in a data journal, such as Geoscience Data Journal, as explored by the PREPARDE project

Opening Up Climate Research: A Linked Data Approach to Publishing Data Provenance

Traditionally, the formal scientific output in most fields of natural science has been limited to peer-reviewed academic journal publications, with less attention paid to the chain of intermediate data results and their associated metadata, including provenance. In effect, this has constrained the representation and verification of the data provenance to the confines of the related publications. Detailed knowledge of a dataset’s provenance is essential to establish the pedigree of the data for its effective re-use, and to avoid redundant re-enactment of the experiment or computation involved. It is increasingly important for open-access data to determine their authenticity and quality, especially considering the growing volumes of datasets appearing in the public domain. To address these issues, we present an approach that combines the Digital Object Identifier (DOI) – a widely adopted citation technique – with existing, widely adopted climate science data standards to formally publish detailed provenance of a climate research dataset as an associated scientific workflow. This is integrated with linked-data compliant data re-use standards (e.g. OAI-ORE) to enable a seamless link between a publication and the complete trail of lineage of the corresponding dataset, including the dataset itself

Evolution of Fitness Cost-Neutral Mutant PfCRT Conferring P. falciparum 4-Aminoquinoline Drug Resistance Is Accompanied by Altered Parasite Metabolism and Digestive Vacuole Physiology

Southeast Asia is an epicenter of multidrug-resistant Plasmodium falciparum strains. Selective pressures on the subcontinent have recurrently produced several allelic variants of parasite drug resistance genes, including the P. falciparum chloroquine resistance transporter (pfcrt). Despite significant reductions in the deployment of the 4-aminoquinoline drug chloroquine (CQ), which selected for the mutant pfcrt alleles that halted CQ efficacy decades ago, the parasite pfcrt locus is continuously evolving. This is highlighted by the presence of a highly mutated allele, Cam734 pfcrt, which has acquired the singular ability to confer parasite CQ resistance without an associated fitness cost. Here, we used pfcrt-specific zinc-finger nucleases to genetically dissect this allele in the pathogenic setting of asexual blood-stage infection. Comparative analysis of drug resistance and growth profiles of recombinant parasites that express Cam734 or variants thereof, Dd2 (the most common Southeast Asian variant), or wild-type pfcrt, revealed previously unknown roles for PfCRT mutations in modulating parasite susceptibility to multiple antimalarial agents. These results were generated in the GC03 strain, used in multiple earlier pfcrt studies, and might differ in natural isolates harboring this allele. Results presented herein show that Cam734-mediated CQ resistance is dependent on the rare A144F mutation that has not been observed beyond Southeast Asia, and reveal distinct impacts of this and other Cam734-specific mutations on CQ resistance and parasite growth rates. Biochemical assays revealed a broad impact of mutant PfCRT isoforms on parasite metabolism, including nucleoside triphosphate levels, hemoglobin catabolism and disposition of heme, as well as digestive vacuole volume and pH. Results from our study provide new insights into the complex molecular basis and physiological impact of PfCRT-mediated antimalarial drug resistance, and inform ongoing efforts to characterize novel pfcrt alleles that can undermine the efficacy of first-line antimalarial drug regimens