Nanopublication-based semantic publishing and reviewing: a field study with formalization papers.

With the rapidly increasing amount of scientific literature, it is getting continuously more difficult for researchers in different disciplines to keep up-to-date with the recent findings in their field of study. Processing scientific articles in an automated fashion has been proposed as a solution to this problem, but the accuracy of such processing remains very poor for extraction tasks beyond the most basic ones (like locating and identifying entities and simple classification based on predefined categories). Few approaches have tried to change how we publish scientific results in the first place, such as by making articles machine-interpretable by expressing them with formal semantics from the start. In the work presented here, we propose a first step in this direction by setting out to demonstrate that we can formally publish high-level scientific claims in formal logic, and publish the results in a special issue of an existing journal. We use the concept and technology of nanopublications for this endeavor, and represent not just the submissions and final papers in this RDF-based format, but also the whole process in between, including reviews, responses, and decisions. We do this by performing a field study with what we call formalization papers, which contribute a novel formalization of a previously published claim. We received 15 submissions from 18 authors, who then went through the whole publication process leading to the publication of their contributions in the special issue. Our evaluation shows the technical and practical feasibility of our approach. The participating authors mostly showed high levels of interest and confidence, and mostly experienced the process as not very difficult, despite the technical nature of the current user interfaces. We believe that these results indicate that it is possible to publish scientific results from different fields with machine-interpretable semantics from the start, which in turn opens countless possibilities to radically improve in the future the effectiveness and efficiency of the scientific endeavor as a whole.

Experimental Band Structure of Pb(Zr,Ti)O3 : Mechanism of Ferroelectric Stabilization.

Pb(Zr,Ti)O3 (PZT) is the most common ferroelectric (FE) material widely used in solid-state technology. Despite intense studies of PZT over decades, its intrinsic band structure, electron energy depending on 3D momentum k, is still unknown. Here, Pb(Zr0.2 Ti0.8 )O3 using soft-X-ray angle-resolved photoelectron spectroscopy (ARPES) is explored. The enhanced photoelectron escape depth in this photon energy range allows sharp intrinsic definition of the out-of-plane momentum k and thereby of the full 3D band structure. Furthermore, the problem of sample charging due to the inherently insulating nature of PZT is solved by using thin-film PZT samples, where a thickness-induced self-doping results in their heavy doping. For the first time, the soft-X-ray ARPES experiments deliver the intrinsic 3D band structure of PZT as well as the FE-polarization dependent electrostatic potential profile across the PZT film deposited on SrTiO3 and Lax SrMn1- x O3 substrates. The negative charges near the surface, required to stabilize the FE state pointing away from the sample (P+), are identified as oxygen vacancies creating localized in-gap states below the Fermi energy. For the opposite polarization state (P-), the positive charges near the surface are identified as cation vacancies resulting from non-ideal stoichiometry of the PZT film as deduced from quantitative XPS measurements.

Sonogashira Synthesis of New Porous Aromatic Framework-Entrapped Palladium Nanoparticles as Heterogeneous Catalysts for Suzuki-Miyaura Cross-Coupling.

Palladium nanoparticles entrapped in porous aromatic frameworks (PAFs) or covalent organic frameworks may promote heterogeneous catalytic reactions. However, preparing such materials as active nanocatalysts usually requires additional steps for palladium entrapment and reduction. This paper reports as a new approach, a simple procedure leading to the self-entrapment of Pd nanoparticles within the PAF structure. Thus, the selected Sonogashira synthesis affords PAF-entrapped Pd nanoparticles that can catalyze the C-C Suzuki-Miyaura cross-coupling reactions. Following this new concept, PAFs were synthesized via Sonogashira cross-coupling of the tetraiodurated derivative of tetraphenyladamantane or spiro-9,9'-bifluorene with 1,6-diethynylpyrene, then characterized them using powder X-ray diffraction, diffuse reflectance infrared Fourier transform spectroscopy, X-ray photoelectron spectroscopy, high-resolution scanning transmission electron microscopy, and textural properties (i.e., adsorption-desorption isotherms). The PAF-entrapped Pd nanocatalysts showed high catalytic activity in Suzuki-Miyaura coupling reactions (demonstrated by preserving the turnover frequency values) and stability (demonstrated by palladium leaching and recycling experiments). This new approach presents a new class of PAFs with unique structural, topological, and compositional complexities as entrapped metal nanocatalysts or for other diverse applications.

The Influence of Heteroatom Dopants Nitrogen, Boron, Sulfur, and Phosphorus on Carbon Electrocatalysts for the Oxygen Reduction Reaction.

A hard templating method, using SBA-15 in combination with glucose solution and different heteroatom precursors, has been employed to investigate the influence of the different heteroatom dopants nitrogen, boron, sulfur, and phosphorus on carbon electrocatalysts for the oxygen reduction reaction. Samples were synthesized under the same conditions and resulted in a similar morphology and surface areas around 1000 m2 /g. Incorporating nitrogen into the carbon matrix was found to be easier than for boron or phosphorus, while sulfur doping proved problematic and only yielded 2 at% of sulfur or less. Different dopant concentrations as well as a combination of dopants suggested that nitrogen was the only heteroatom exerting an actual influence on the catalytic activity, resulting in higher electron transfer numbers. The other dopants exhibited a similar performance regardless of the dopant content, though slightly improved when compared to an undoped control sample. These findings indicate that incorporated nitrogen can act as catalytic sites, while boron, sulfur and phosphorus can enhance the catalytic activity by possibly creating defects in the carbon matrix.

Homogeneity assessment for grass samples used for organically bound tritium proficiency test.

The paper presents homogeneity check for dried grass batch to be used in an inter-comparison exercise. When carrying out an inter-comparison exercise, the organizer must guarantee that the unsatisfactory result will not be imputed to the sample and sample's changeability. Therefore, in an inter-comparison exercise must carry on the homogeneity testing. In our study, the homogeneity was checked for two parameters, the hydrogen percentage (%H) and the organically bound tritium (OBT) activity concentration. Ten subsamples of 50g from bulk material were chosen using a stratified random selection. Two replicates from each package were analyzed for hydrogen content and OBT analysis. The homogeneity parameters were evaluated according to ISO 13528:2015. The two checked properties confirm that the batch of dried grass is sufficiently homogenous.

eXamine: exploring annotated modules in networks.

BACKGROUND: Biological networks have a growing importance for the interpretation of high-throughput "omics" data. Integrative network analysis makes use of statistical and combinatorial methods to extract smaller subnetwork modules, and performs enrichment analysis to annotate the modules with ontology terms or other available knowledge. This process results in an annotated module, which retains the original network structure and includes enrichment information as a set system. A major bottleneck is a lack of tools that allow exploring both network structure of extracted modules and its annotations. RESULTS: This paper presents a visual analysis approach that targets small modules with many set-based annotations, and which displays the annotations as contours on top of a node-link diagram. We introduce an extension of self-organizing maps to lay out nodes, links, and contours in a unified way. An implementation of this approach is freely available as the Cytoscape app eXamine CONCLUSIONS: eXamine accurately conveys small and annotated modules consisting of several dozens of proteins and annotations. We demonstrate that eXamine facilitates the interpretation of integrative network analysis results in a guided case study. This study has resulted in a novel biological insight regarding the virally-encoded G-protein coupled receptor US28.

Perioperative management of patients with lung carcinoma and cerebral metastases.

OBJECTIVE: The present study proposes to present the importance of perioperative therapeutic management in survival prolongation and the quality of life for patients that have undergone surgery for cerebral metastases secondary to pulmonary tumors. METHOD: During 2001-2009, 40 patients with ages between 43-74 years have been diagnosed in our clinic with pulmonary tumor and cerebral metastases. The patients presented single cerebral lesion (excepting one patient with 2 cerebral metastases) and pulmonary tumor. Intracranial pressure (ICP) was high in all cases. All patients have undergone operation with general anesthesia. RESULTS: For all patients the reduction of ICP and keeping an optimal CPP (cerebral perfusion pressure) was pursued. In 38 cases, general anesthesia was performed with Sevoflurane and opioids (fentanyl, remifentanyl, sufentanyl) and in 2 cases the TIVA (total intravenous anesthesia) technique was used with propofol and remifentanyl. 14 of the patients required intraoperative depletive treatment through administering mannitol 20%. 37 patients (92%) have been discharged with improved neurological condition without showing signs of intracranial hypertension, convulsive seizures and with partially or totally remitted hemiparesis and one patient had worse postoperative neurological status. CONCLUSION: Pulmonary tumor with cerebral metastases represent an important cause for death rate. To solve secondary cerebral lesions, the perioperative management must include assesment and choosing an anesthesia technique with a proper intraoperative management.