On the Effective Dissemination and Use of Learning Objectives Catalogs for Health Information Curricula Development.

Catalogs of competency-based learning objectives (CLO) were introduced and promoted as a prerequisite for high-quality, systematic curriculum development. While this is common in medicine, the consistent use of CLO is not yet well established in epidemiology, biometry, medical informatics, biomedical informatics, and nursing informatics especially in Germany. This paper aims to identify underlying obstacles and give recommendations in order to promote the dissemination of CLO for curricular development in health data and information sciences. To determine these obstacles and recommendations a public online expert workshop was organized. This paper summarizes the findings.

Climate change disrupts core habitats of marine species.

Driven by climate change, marine biodiversity is undergoing a phase of rapid change that has proven to be even faster than changes observed in terrestrial ecosystems. Understanding how these changes in species composition will affect future marine life is crucial for conservation management, especially due to increasing demands for marine natural resources. Here, we analyse predictions of a multiparameter habitat suitability model covering the global projected ranges of >33,500 marine species from climate model projections under three CO2 emission scenarios (RCP2.6, RCP4.5, RCP8.5) up to the year 2100. Our results show that the core habitat area will decline for many species, resulting in a net loss of 50% of the core habitat area for almost half of all marine species in 2100 under the high-emission scenario RCP8.5. As an additional consequence of the continuing distributional reorganization of marine life, gaps around the equator will appear for 8% (RCP2.6), 24% (RCP4.5), and 88% (RCP8.5) of marine species with cross-equatorial ranges. For many more species, continuous distributional ranges will be disrupted, thus reducing effective population size. In addition, high invasion rates in higher latitudes and polar regions will lead to substantial changes in the ecosystem and food web structure, particularly regarding the introduction of new predators. Overall, our study highlights that the degree of spatial and structural reorganization of marine life with ensued consequences for ecosystem functionality and conservation efforts will critically depend on the realized greenhouse gas emission pathway.

Combining trapped ion mobility spectrometry with liquid chromatography and tandem mass spectrometry for analysis of isomeric PDE-5 inhibitor analogs.

The detection and identification of phosphodiesterase type 5 enzyme (PDE-5) inhibitors in dietary supplements poses an analytical challenge due to the large number of analogs and isomers currently available and the continued introduction of novel analogs. The use of trapped ion mobility spectrometry (TIMS) in conjunction with liquid chromatography (LC) and electrospray ionization tandem mass spectrometry (MS/MS) was explored for the analysis of two groups of isomeric PDE-5 inhibitor analogs using a 5-minute method. Of the eight compounds studied, six were resolved by a combination of LC and TIMS; the two remaining isomers were distinguished by one or more unique product ions in the MS/MS spectrum. The results revealed that separation by LC corresponded to differences in substitution on the piperazine moiety of the PDE-5 inhibitors, while separation by TIMS corresponded to the position of a nitrogen atom in the fused ring region of the molecules. Samples prepared by spiking mixtures of varying amounts of the Group 2 isomers into a representative dietary supplement matrix were analyzed and concentrations determined from the mobility-adjusted extracted ion chromatograms exhibited relative standard deviations of 6.0 % or less for 17 of 20 measurements and recoveries between 80 % and 120 % for all measurements. Quantitative measurements from a short LC gradient were possible due to the reduced chemical background associated with the TIMS separation of co-eluting matrix compounds, which enabled acquisition of rapid and qualitatively relevant broadband collision induced dissociation spectra that didn't require precursor ion isolation; the reduced chemical background permits non-targeted detection of novel analogs and eliminates the need for a separate method for quantitative measurement.

Compilation of different data sets of the Late Neolithic wetland site of Pestenacker and of the adjacent valley depositions.

This document contains data sets of the valley depositions of the Loosbach valley and data of the Late Neolithic wetland site of Pestenacker. It consists of raw data and graphical figures of direct push-based electrical conductivity and colour logs and driving core recoveries as well as hand drilling recoveries presented by Köhler et al. [1]. We reviewed unpublished archaeological profiles to determine the incision levels of former stream phases at Pestenacker site. Here, we provide the new, reusable and accessible data set. The data sets and figures of the valley depositions can be used for further analyses, including statistical ones, to improve the methods of the direct-push sensing and to compare it with the sedimentological features recovered from driving core and hand drillings. In addition, the data set is useful for further issues in Pestenacker as well as in the whole central Europe. Especially in the circum-Alpine region, as a comparison with other pile dwellings or stilt houses built from the Neolithic to the Bronce Age.

Accuracy and Reproducibility of Laboratory Diffuse Reflectance Measurements with Portable VNIR and MIR Spectrometers for Predictive Soil Organic Carbon Modeling.

Soil spectroscopy in the visible-to-near infrared (VNIR) and mid-infrared (MIR) is a cost-effective method to determine the soil organic carbon content (SOC) based on predictive spectral models calibrated to analytical-determined SOC reference data. The degree to which uncertainty in reference data and spectral measurements contributes to the estimated accuracy of VNIR and MIR predictions, however, is rarely addressed and remains unclear, in particular for current handheld MIR spectrometers. We thus evaluated the reproducibility of both the spectral reflectance measurements with portable VNIR and MIR spectrometers and the analytical dry combustion SOC reference method, with the aim to assess how varying spectral inputs and reference values impact the calibration and validation of predictive VNIR and MIR models. Soil reflectance spectra and SOC were measured in triplicate, the latter by different laboratories, for a set of 75 finely ground soil samples covering a wide range of parent materials and SOC contents. Predictive partial least-squares regression (PLSR) models were evaluated in a repeated, nested cross-validation approach with systematically varied spectral inputs and reference data, respectively. We found that SOC predictions from both VNIR and MIR spectra were equally highly reproducible on average and similar to the dry combustion method, but MIR spectra were more robust to calibration sample variation. The contributions of spectral variation (ΔRMSE < 0.4 g·kg−1) and reference SOC uncertainty (ΔRMSE < 0.3 g·kg−1) to spectral modeling errors were small compared to the difference between the VNIR and MIR spectral ranges (ΔRMSE ~1.4 g·kg−1 in favor of MIR). For reference SOC, uncertainty was limited to the case of biased reference data appearing in either the calibration or validation. Given better predictive accuracy, comparable spectral reproducibility and greater robustness against calibration sample selection, the portable MIR spectrometer was considered overall superior to the VNIR instrument for SOC analysis. Our results further indicate that random errors in SOC reference values are effectively compensated for during model calibration, while biased SOC calibration data propagates errors into model predictions. Reference data uncertainty is thus more likely to negatively impact the estimated validation accuracy in soil spectroscopy studies where archived data, e.g., from soil spectral libraries, are used for model building, but it should be negligible otherwise.

Hydro-sedimentary provenance analyses in the Weiße Elster catchment (Central Germany): The basic dataset.

This manuscript documents geological master data and X-ray fluorescence (XRF) data of a standardized 8*8 km sampling grid of the entire Weiße Elster catchment in Central Germany. Further, the manuscript documents XRF data of a refined 4*4 km sampling grid in the proximity of Salsitz floodplain transect as well as grain size data and XRF data of Salsitz SC40 core that was recovered from the Weiße Elster floodplain. The data provide opportunities for hydro-sedimentary provenance analyses as presented in the corresponding research article by Ballasus et al. [1].

Overbank silt-clay deposition and intensive Neolithic land use in a Central European catchment - Coupled or decoupled?

Hydro-sedimentary processes such as soil erosion, sediment transport, deposition, and re-deposition influence the environmental evolution of floodplains, especially in loess-covered catchments. Holocene floodplain deposits are thus a source of information on previous hydro-sedimentary dynamics and land use in the catchment. Resulting from forest clearings in the catchment, the onset of overbank silt-clay deposition is considered as an initial and significant human-induced process affecting Central European floodplain evolution and ecosystems. However, it is difficult to separate climate-related from anthropogenic forces on depositional environments, and the complexity of the hydro-sedimentary responses is part of an ongoing debate in geoscientific, ecological, and archaeological communities. This study focuses on the Central European Weiße Elster river system, where humans have been influencing hydro-sedimentary processes since the Early Neolithic due to land-use-induced soil erosion predominantly in the loess-covered sub-basin of the middle course. A catchment-scale XRF element record of fluvial sediment sources combined with the geochemical characterisation of Holocene floodplain deposits aim for a better understanding of the interplay between past soil erosion, overbank deposition in the floodplain, and potential changes in sediment provenances. The Weiße Elster floodplain chronosequences show a geochemical differentiation into a lower (Neolithic) and an upper (post-Neolithic) overbank silt-clay deposition. The construction of a sediment source fingerprinting mixing model yields the significant finding that the Neolithic overbank silt-clay deposition reveals a remote provenance signal from the upper catchment and less from the proximal loess-covered sub-catchment. According to a systematic archaeological data survey, the upper catchment was not permanently settled and used for agriculture in the Neolithic period. This contradicts the previous assumption that Neolithic overbank silt-clay deposition primarily originates from forest clearings and subsequent farming-induced soil erosion in the catchment. From a more general perspective, further examination of existing hypotheses concerning overbank silt-clay deposition in Central European floodplains is thus in order.

Health Informatics Learning Objectives on an Interoperable, Collaborative Platform.

Catalogues of learning objectives for Biomedical and Health Informatics are relevant prerequisites for systematic and effective qualification. Catalogue management needs to integrate different catalogues and support collaborative revisioning. The Health Informatics Learning Objectives Navigator (HI-LONa) offers an open, interoperable platform based on Semantic Web Technology. At present HI-LONa contains 983 learning objectives of three relevant catalogues. HI-LONa successfully supported a multiprofessional consensus process.

Towards Precise Descriptions of Medical Free/Libre and Open Source Software.

The web portal Medfloss.org lists over 360 medical free/libre and open source software (MEDFLOSS) projects. These projects are described with the help of a self-developed nomenclature. Due to inconsistencies, the nomenclature shall be replaced by HITO, the Health IT Ontology. HITO is developed iteratively based on different use cases. This paper aims to describe methods and results of the second HITO use case in which HITO is extended to improve the description, retrieval and comparisons of MEDFLOSS projects on Medfloss.org. We use a mixed-methods approach to add concepts and relationships to describe MEDFLOSS precisely. The resulting HITO version stresses functional descriptions based on features and supported enterprise functions, rather than just describing technical characteristics. However, describing a larger number of MEDFLOSS projects requires the commitment of the community.

Catchment soils as a factor of trace metal accumulation in sediments of the reservoir Klingenberg (eastern Ore Mountains, Germany).

The release and accumulation dynamics of trace metals in soils and aquatic sediments were exemplarily investigated in the catchment area of the Reservoir Klingenberg (Germany). Catchment soils were examined for mobilizable and total concentrations of arsenic (As), cadmium (Cd), chrome (Cr), iron (Fe), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn) and compared with trace metal quantities accumulated in riverbed and reservoir sediments. The comparison of all samples showed relatively small variations of Cr (7.96-46.0 mg/kg), Fe (7.79-40.4 g/kg), and Ni (6.06-56.5 mg/kg), while stronger differences were found for As (11.2-164 mg/kg), Cd (0.14-30.5 mg/kg), Mn (0.08-1.84 g/kg), Pb (20.7-183 mg/kg), and Zn (69.1-916 mg/kg). The catchment soils were slightly enriched by Cd, Pb, and Zn. Especially Cd and Zn were characterized by large mobilizable proportions. The mean trace metal concentrations in riverbed sediments were higher than in catchment soils, while reservoir sediments accumulated the highest amounts of the analyzed elements. The enrichment of trace metals in reservoir sediments was generally determined by the sedimentation of fine particles, while the distribution of As, Fe, and Mn was additionally impacted by redox conditions. For Cd and Zn, which in comparison were most enriched in riverbed and reservoir sediments, a significant release from soils by leaching processes was observed. The accumulation of As and Pb in reservoir sediments was influenced to a greater extent by soil erosion and by anthropogenic or chalcogen sources in the catchment.

Open and Linkable Knowledge About Management of Health Information Systems.

Given a care delivery organization, its health information system can be defined as the part of the organization that processes and stores data, information, and knowledge. There is an enormous number of frameworks, textbooks and articles that describe the scope of health information system management from the perspective of medical informatics. Transforming this knowledge to Linked Open Data results in a structured data representation that is accessible for both humans and machines, the Semantic Network of Information Management in Hospitals (SNIK). We present interfaces that are useful for researchers, practitioners and students, depending on their objectives and their Semantic Web skills.

The SNIK Graph: Visualization of a Medical Informatics Ontology.

SNIK, a medical informatics ontology, combines knowledge from different literature sources dealing with the management of hospital information systems (HIS). Concepts and relations were extracted from literature, modeled as an ontology and visualized as a graph on a website. We demonstrate the potential of the graph visualization for tuitional scenarios. SNIK complements teaching and learning with conventional literature by concentrating knowledge that is scattered over different pieces of text around one node of a graph.

Technical Environment for Developing the SNIK Ontology of Information Management in Hospitals.

The SNIK project converts textbooks about information management in hospitals to a domain ontology that provides a shared vocabulary for institutions to model and integrate processes, data and infrastructure. To accommodate user groups with different requirements and technical backgrounds, and to support incremental and cooperative development, we create a system architecture to publish, visualize, browse and query the ontology, as well as to evaluate and improve the data quality.

Structural investigation of the C-terminal catalytic fragment of presenilin 1.

The gamma-secretase complex has a decisive role in the development of Alzheimer's disease, in that it cleaves a precursor to create the amyloid beta peptide whose aggregates form the senile plaques encountered in the brains of patients. Gamma-secretase is a member of the intramembrane-cleaving proteases which process their transmembrane substrates within the bilayer. Many of the mutations encountered in early onset familial Alzheimer's disease are linked to presenilin 1, the catalytic component of gamma-secretase, whose active form requires its endoproteolytic cleavage into N-terminal and C-terminal fragments. Although there is general agreement regarding the topology of the N-terminal fragment, studies of the C-terminal fragment have yielded ambiguous and contradictory results that may be difficult to reconcile in the absence of structural information. Here we present the first structure of the C-terminal fragment of human presenilin 1, as obtained from NMR studies in SDS micelles. The structure reveals a topology where the membrane is likely traversed three times in accordance with the more generally accepted nine transmembrane domain model of presenilin 1, but contains unique structural features adapted to accommodate the unusual intramembrane catalysis. These include a putative half-membrane-spanning helix N-terminally harboring the catalytic aspartate, a severely kinked helical structure toward the C terminus as well as a soluble helix in the assumed-to-be unstructured N-terminal loop.

Membrane protein expression in cell-free systems.

Cell-free expression has emerged as a promising tool for the fast and efficient production of membrane proteins. The rapidly growing number of successfully produced targets in combination with the continuous development of new applications significantly promotes the distribution of this technology. Membrane protein synthesis by cell-free expression does not appear to be restricted by origin, size or topology of the target, and its global application is therefore a highly valuable characteristic. The technology is relatively fast to establish in standard biochemical labs, and it does not require expensive equipment. Moreover, it enables the production of membrane proteins in completely new modes, like the direct translation into detergent micelles, which is not possible with any other expression system. In this protocol, we focus on the currently most efficient cell-free expression system for membrane proteins based on Escherichia coli extracts.

Spatial and temporal small-scale variability of nitrogen mobilization in a forest ecosystem with high N deposition in NW-Germany.

For conifer stands in NW-Germany with high DIN load (23-35 kg N ha(-1) a(-1)) and a long history of nitrogen export the risk of N mobilization were investigated. Ammonium is the most mobilized N species, pointing towards either conditions not favoring nitrification or, more likely - under the dominant aerobic conditions - a very high amount of ammonium in the forest floor. Independence of net nitrification and net ammonification from each other indicates the existence of two separate systems. The nitrifying system depends very much on biotic conditions - as a function of energy and moisture - and seems not to be directly related to N deposition. In contrast, for the ammonification system (Oe horizon) a correlation with the sum of ammonium deposition three months prior to sampling was found. However, the role of disturbance, i.e. nitrogen export, during the last centuries and the role of recovery of the N balance during the last 150 years is still not clear.

Efficient mining of myxobacterial metabolite profiles enabled by liquid chromatography-electrospray ionisation-time-of-flight mass spectrometry and compound-based principal component analysis.

Bacteria producing secondary metabolites are an important source of natural products with highly diverse structures and biological activities. Developing methods to efficiently mine procaryotic secondary metabolomes for the presence of potentially novel natural products is therefore of considerable interest. Modern mass spectrometry-coupled liquid chromatography can effectively capture microbial metabolic diversity with ever improving sensitivity and accuracy. In addition, computational and statistical tools increasingly enable the targeted analysis and exploration of information-rich LC-MS datasets. In this article, we describe the use of such techniques for the characterization of myxobacterial secondary metabolomes. Using accurate mass data from high-resolution ESI-TOF measurements, target screening has facilitated the rapid identification of known myxobacterial metabolites in extracts from nine Myxococcus species. Furthermore, principal component analysis (PCA), implementing an advanced compound-based bucketing approach, readily revealed the presence of further compounds which contribute to variation among the metabolite profiles under investigation. The generation of molecular formulae for putative novel compounds with high confidence due to evaluation of both exact mass position and isotopic pattern, is exemplified as an important key for de-replication and prioritization of candidates for further characterization.

Transmembrane segment enhanced labeling as a tool for the backbone assignment of alpha-helical membrane proteins.

Recent advances in cell-free expression protocols have opened a new avenue toward high-resolution structural investigations of membrane proteins by x-ray crystallography and NMR spectroscopy. One of the biggest challenges for liquid-state NMR-based structural investigations of membrane proteins is the significant peak overlap in the spectra caused by large line widths and limited chemical shift dispersion of alpha-helical proteins. Contributing to the limited chemical shift dispersion is the fact that approximately 60% of the amino acids in transmembrane regions consist of only six different amino acid types. This principle disadvantage, however, can be exploited to aid in the assignment of the backbone resonances of membrane proteins; by (15)N/(13)C-double-labeling of these six amino acid types, sequential connectivities can be obtained for large stretches of the transmembrane segments where number and length of stretches consisting exclusively of these six amino acid types are enhanced compared with the remainder of the protein. We show by experiment as well as by statistical analysis that this labeling scheme provides a large number of sequential connectivities in transmembrane regions and thus constitutes a tool for the efficient assignment of membrane protein backbone resonances.

Preparative scale expression of membrane proteins in Escherichia coli-based continuous exchange cell-free systems.

Cell-free expression is emerging as a prime method for the rapid production of preparative quantities of high-quality membrane protein samples. The technology facilitates easy access to large numbers of proteins that have been extremely difficult to obtain. Most frequently used are cell-free systems based on extracts of Escherichia coli cells, and the reaction procedures are reliable and efficient. This protocol describes the preparation of all essential reaction components such as the E. coli cell extract, T7 RNA polymerase, DNA templates as well as the individual stock solutions. The setups of expression reactions in analytical and preparative scales, including a variety of reaction designs, are illustrated. We provide detailed reaction schemes that allow the preparation of milligram amounts of functionally folded membrane proteins of prokaryotic and eukaryotic origin in less than 24 h.

Preparative scale cell-free expression systems: new tools for the large scale preparation of integral membrane proteins for functional and structural studies.

Cell-free expression techniques have emerged as promising tools for the production of membrane proteins for structural and functional analysis. Elimination of toxic effects and a variety of options to stabilize the synthesized proteins enable the synthesis of otherwise difficult to obtain proteins. Modifications in the reaction design result in preparative scale production rates of cell-free reactions and yield in milligram amounts of membrane proteins per one millilitre of reaction volume. A diverse selection of detergents can be supplied into the reaction system without inhibitory effects to the translation machinery. This offers the unique opportunity to produce a membrane protein directly into micelles of a detergent of choice. We present detailed protocols for the cell-free production of membrane proteins in different modes and we summarize the current knowledge of this technique. A special emphasize will be on the production of soluble and functionally folded membrane proteins in presence of suitable detergents. In addition, we will highlight the advantages of cell-free expression for the structural analysis of membrane proteins especially by liquid state nuclear magnetic resonance spectroscopy and we will discuss new strategies for structural approaches.