Enhancing the Usefulness of Open Governmental Data with Linked Data Viewing Techniques

Open Governmental Data publishing has had mixed success. While many governmental bodies are publishing an increasing number of datasets online, the potential usefulness is rather low. This paper describes action research conducted within the context of the Dutch Cadastre’s open data platform. We start by observing contemporary (Dutch) Open Data platforms and observe that dataset reuse is not always realized. We introduce Linked Open Data, which promises to deliver solutions to the lack of Open Data reuse. In the process of implementing Linked Data in practice, we observe that users face a knowledge and skill and that contemporary Linked Open Data tooling is often unable to properly advertise the usefulness of datasets to potential users, thereby hampering reuse. We therefore develop four components for Linked Data viewing to enhance the current situation, making it easier to observe what a dataset is about and which potential use cases it could serve

Structure of the PPARα and -γ Ligand Binding Domain in Complex with AZ 242; Ligand Selectivity and Agonist Activation in the PPAR Family

AbstractBackground: The peroxisome proliferator-activated receptors (PPAR) are ligand-activated transcription factors belonging to the nuclear receptor family. The roles of PPARα in fatty acid oxidation and PPARγ in adipocyte differentiation and lipid storage have been characterized extensively. PPARs are activated by fatty acids and eicosanoids and are also targets for antidyslipidemic drugs, but the molecular interactions governing ligand selectivity for specific subtypes are unclear due to the lack of a PPARα ligand binding domain structure.Results: We have solved the crystal structure of the PPARα ligand binding domain (LBD) in complex with the combined PPARα and -γ agonist AZ 242, a novel dihydro cinnamate derivative that is structurally different from thiazolidinediones. In addition, we present the crystal structure of the PPARγ_LBD/AZ 242 complex and provide a rationale for ligand selectivity toward the PPARα and -γ subtypes. Heteronuclear NMR data on PPARα in both the apo form and in complex with AZ 242 shows an overall stabilization of the LBD upon agonist binding. A comparison of the novel PPARα/AZ 242 complex with the PPARγ/AZ 242 complex and previously solved PPARγ structures reveals a conserved hydrogen bonding network between agonists and the AF2 helix.Conclusions: The complex of PPARα and PPARγ with the dual specificity agonist AZ 242 highlights the conserved interactions required for receptor activation. Together with the NMR data, this suggests a general model for ligand activation in the PPAR family. A comparison of the ligand binding sites reveals a molecular explanation for subtype selectivity and provides a basis for rational drug design

Narrowing the Gap between Open Standards Policy and Practice: The Dutch E-Government Experience \ud

Interoperability in the public sector can be improved by the use of open standards. Nonetheless, the openness of standards in government policies is debatable. This paper introduces the Dutch government policy on open standards, and will introduce a multi-dimensional view (and model) on openness rather than a one-dimensional strict definition. Applicability of the multi-dimensional model is tested in a case study, which demonstrates that this model has value for standardization organizations active in the government domain. In future cases the model helps in understanding how government-related standardization organizations can influence openness in a situation-specific way and the model therefore narrows the gap between open standards policy and practice. \u

Research on Quality of Transaction Standards: The Maturity of a Research Topic

This paper contains the results of a systematic literature review executed to determine the coverage of transaction standards in top information systems (IS) and management journals. Specifically, it aims to identify a research gap with respect to this topic. The top 25 journals are thoroughly searched and the selected publications are classified in order to make grounded statements. A moderate amount of literature found specifically aims at transaction standards. Hardly any research is found on quality aspects of transaction standards, which therefore counts as the research gap

Interaction of the replication terminator protein of Bacillus subtilis with DNA probed by NMR spectroscopy

Termination of DNA replication in Bacillus subtilis involves the polar arrest of replication forks by a specific complex formed between the dimeric 29 kDa replication terminator protein (RTP) and DNA terminator sites. We have used NMR spectroscopy to probe the changes in1H-15N correlation spectra of a15N-labelled RTP.C110S mutant upon the addition of a 21 base pair symmetrical DNA binding site. Assignment of the1H-15N correlations was achieved using a suite of triple resonance NMR experiments with15N,13C,70%2H enriched protein recorded at 800 MHz and using TROSY pulse sequences. Perturbations to1H-15N spectra revealed that the N-termini, α3-helices and several loops are affected by the binding interaction. An analysis of this data in light of the crystallographically determined apo- and DNA-bound forms of RTP.C110S revealed that the NMR spectral perturbations correlate more closely to protein structural changes upon complex formation rather than to interactions at the protein-DNA interface

Structure of the RTP-DNA complex and the mechanism of polar replication fork arrest

The coordinated termination of DNA replication is an important step in the life cycle of bacteria with circular chromosomes, but has only been defined at a molecular level in two systems to date. Here we report the structure of an engineered replication terminator protein (RTP) ot Bacillus subtilis in complex with a 21 base pair DNA by X-ray crystallography at 2.5 Å resolution. We also use NMR spectroscopic titration techniques. This work reveals a novel DNA interaction involving a dimeric 'winged helix' domain protein that differs from predictions. While the two recognition helices of RTP ate in close contact with the B-form DNA major grooves, the 'wings' and N-termini of RTP do not form intimate contacts with the DNA. This structure provides insight into the molecular basis of polar replication fork arrest based on a model of cooperative binding and differential binding affinities of RTP to the two adjacent binding sites in file complete terminator