OrganismTagger: detection, normalization and grounding of organism entities in biomedical documents

Motivation: Semantic tagging of organism mentions in full-text articles is an important part of literature mining and semantic enrichment solutions. Tagged organism mentions also play a pivotal role in disambiguating other entities in a text, such as proteins. A high-precision organism tagging system must be able to detect the numerous forms of organism mentions, including common names as well as the traditional taxonomic groups: genus, species and strains. In addition, such a system must resolve abbreviations and acronyms, assign the scientific name and if possible link the detected mention to the NCBI Taxonomy database for further semantic queries and literature navigation. Results: We present the OrganismTagger, a hybrid rule-based/machine learning system to extract organism mentions from the literature. It includes tools for automatically generating lexical and ontological resources from a copy of the NCBI Taxonomy database, thereby facilitating system updates by end users. Its novel ontology-based resources can also be reused in other semantic mining and linked data tasks. Each detected organism mention is normalized to a canonical name through the resolution of acronyms and abbreviations and subsequently grounded with an NCBI Taxonomy database ID. In particular, our system combines a novel machine-learning approach with rule-based and lexical methods for detecting strain mentions in documents. On our manually annotated OT corpus, the OrganismTagger achieves a precision of 95%, a recall of 94% and a grounding accuracy of 97.5%. On the manually annotated corpus of Linnaeus-100, the results show a precision of 99%, recall of 97% and grounding accuracy of 97.4%. Availability: The OrganismTagger, including supporting tools, resources, training data and manual annotations, as well as end user and developer documentation, is freely available under an open-source license at http://www.semanticsoftware.info/organism-tagger. Contact: [email protected]

Butane dihedral angle dynamics in water is dominated by internal friction

The dihedral dynamics of butane in water is known to be rather insensitive to the water viscosity; possible explanations for this involve inertial effects or Kramers’ turnover, the finite memory time of friction, and the presence of so-called internal friction. To disentangle these factors, we introduce a method to directly extract the friction memory function from unconstrained simulations in the presence of an arbitrary free-energy landscape. By analysis of the dihedral friction in butane for varying water viscosity, we demonstrate the existence of an internal friction contribution that does not scale linearly with water viscosity. At normal water viscosity, the internal friction turns out to be eight times larger than the solvent friction and thus completely dominates the effective friction. By comparison with simulations of a constrained butane molecule that has the dihedral as the only degree of freedom, we show that internal friction comes from the six additional degrees of freedom in unconstrained butane that are orthogonal to the dihedral angle reaction coordinate. While the insensitivity of butane’s dihedral dynamics to water viscosity is solely due to the presence of internal friction, inertial effects nevertheless crucially influence the resultant transition rates. In contrast, non-Markovian effects due to the finite memory time are present but do not significantly influence the dihedral barrier-crossing rate of butane. These results not only settle the character of dihedral dynamics in small solvated molecular systems such as butane, they also have important implications for the folding of polymers and proteins

Nickel partitioning in biogenic and abiogenic ferrihydrite: the influence of silica and implications for ancient environments

Fe(III) (oxyhydr)oxides are ubiquitous in modern soils and sediments, and their large surface area leads to scavenging of trace elements. Experimental trace element partitioning between Fe(III) (oxyhydr)oxides and aqueous solutions have been used to elucidate the geochemical composition of the Precambrian oceans based on the trace element concentrations in Precambrian banded iron formations (BIFs). However, previous partitioning experiments did not consider the potential influence of microbially-derived organic material, even though it is widely believed that bacterial phytoplankton was involved in Fe(II) oxidation and the deposition of BIF primary minerals. Therefore, the present study focuses on sorption of Ni to, and co-precipitation of Ni with, both biogenic ferrihydrite (Fe(OH)3) precipitated by the freshwater photoferrotroph Rhodobacter ferrooxidans SW2 and the marine photoferrotroph Rhodovulum iodosum, as well as chemically synthesized ferrihydrite. We considered the influence of cellular organic material, medium composition and the availability of dissolved silica. Our results show a preferential association of Ni with ferrihydrite, and not with the microbial cells or extracellular organic substances. We found that the addition of silica (2 mM) did not influence Ni partitioning but led to the encrustation of some cells with ferrihydrite and amorphous silica. The two- to threefold lower Ni/Fe ratio in biogenic as compared to abiogenic ferrihydrite is probably due to a competition between Ni and organic matter for sorption sites on the mineral surface. Additionally, the competition of ions present at high concentrations in marine medium for sorption sites led to decreased Ni sorption or co-precipitation. Based on our data we conclude that, if the Fe(III) minerals deposited in BIFs were – at least to some extent – biological, then the Ni concentrations in the early ocean would have been higher than previously suggested. This study shows the importance of considering the presence of microbial biomass and seawater ions in paleomarine reconstructions

Corporate Governance, Opaque Bank Activities, and Risk/Return Efficiency: Pre- and Post-Crisis Evidence from Turkey

Does better corporate governance unambiguously improve the risk/return efficiency of banks? Or does either a re-orientation of banks' revenue mix towards more opaque products, an economic downturn, or tighter supervision create off-setting or reinforcing effects? The authors relate bank efficiency to shortfalls from a stochastic risk/return frontier. They analyze how internal governance mechanisms (CEO duality, board experience, political connections, and education profile) and external governance mechanisms (discipline exerted by shareholders, depositors, or skilled employees) determine efficiency in a sample of Turkish banks. The 2000 financial crisis was a wakeup call for bank efficiency and corporate governance. As a result, better corporate governance mechanisms have been able to improve risk/return efficiency when the economic, regulatory, and supervisory environments are more stable and bank products are more complex.corporate governance;bank risk;noninterest income;crisis;frontier

Non-Markovian modeling of protein folding.

We extract the folding free energy landscape and the time-dependent friction function, the two ingredients of the generalized Langevin equation (GLE), from explicit-water molecular dynamics (MD) simulations of the α-helix forming polypeptide [Formula: see text] for a one-dimensional reaction coordinate based on the sum of the native H-bond distances. Folding and unfolding times from numerical integration of the GLE agree accurately with MD results, which demonstrate the robustness of our GLE-based non-Markovian model. In contrast, Markovian models do not accurately describe the peptide kinetics and in particular, cannot reproduce the folding and unfolding kinetics simultaneously, even if a spatially dependent friction profile is used. Analysis of the GLE demonstrates that memory effects in the friction significantly speed up peptide folding and unfolding kinetics, as predicted by the Grote-Hynes theory, and are the cause of anomalous diffusion in configuration space. Our methods are applicable to any reaction coordinate and in principle, also to experimental trajectories from single-molecule experiments. Our results demonstrate that a consistent description of protein-folding dynamics must account for memory friction effects

Alternative fuels from forest residues for passenger cars - an assessment under German framework conditions

Background Due to the available volumes, biogenic residues are a promising resource for renewable fuels for passenger cars to reduce greenhouse gas (GHG) emissions. In this study, we compare three fuels from forest residues under German framework conditions: biogenic electricity, substitute natural gas (SNG), and Fischer-Tropsch (FT) diesel. Methods Fuels from forest residues are compared with regard to their technical efficiency (here defined as ‘pkm per kg biomass’), costs, and environmental impacts with a focus on GHG emissions. We took into consideration the real-life driving conditions and corresponding car classes as well as market penetration scenarios for electric and gaseous fuel cars. Results Our results show that the technical efficiency of biogenic electricity is high, while the economic and environmental results strongly depend on the car size and market penetration assumptions. Furthermore, it is essential to clearly define the main goal of introducing fuels from forest residues. If the goal is to reduce GHG emissions at the lowest cost, SNG (and natural gas) in bigger cars is preferable. For high GHG reductions at the lowest forest residue consumption, biogenic electricity in smaller commuter-type cars are found to be a good solution. This also proves true for the aggregated environmental impact score ReCiPe Total. Conclusions It is important to include mobility patterns and a clear goal definition when comparing biogenic fuels. In Germany, biogenic electricity, SNG, and FT diesel can reduce GHG emissions at reduction costs of around 100 €/t CO2-Eq when used the right way

Direct Evidence of the Role of Hybridization in the X-Ray Magnetic Circular Dichroism of a-Ce

We present an x-ray magnetic circular dichroism (XMCD) study of a [Ce(10 Å)/Fe(30 Å)] multilayer performed at the Ce-M4,5 absorption edges. In this system the Ce-4f electrons are strongly hybridized with the valence band. XMCD experiments show that they carry an ordered magnetic moment. The differences of the shape of the XMCD signals of a typical g-like compound (CeCuSi) and of the Ce/ Fe multilayer highlight the role of hybridization in determining the ground state of cerium atoms in the multilayer, which results in a mixing of J = 5/2 and J = 7/2 coupled states

A Development Environment for Visual Physics Analysis

The Visual Physics Analysis (VISPA) project integrates different aspects of physics analyses into a graphical development environment. It addresses the typical development cycle of (re-)designing, executing and verifying an analysis. The project provides an extendable plug-in mechanism and includes plug-ins for designing the analysis flow, for running the analysis on batch systems, and for browsing the data content. The corresponding plug-ins are based on an object-oriented toolkit for modular data analysis. We introduce the main concepts of the project, describe the technical realization and demonstrate the functionality in example applications

Authigenic iron oxide proxies for marine zinc over geological time and implications for eukaryotic metallome evolution

Author Posting. © The Author(s), 2012. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Geobiology 11 (2013): 295-306, doi:10.1111/gbi.12036.Here we explore enrichments in paleomarine Zn as recorded by authigenic iron oxides including Precambrian iron formations, ironstones and Phanerozoic hydrothermal exhalites. This compilation of new and literature-based iron formation analyses track dissolved Zn abundances and constrain the magnitude of the marine reservoir over geological time. Overall, the iron formation record is characterized by a fairly static range in Zn/Fe ratios throughout the Precambrian, consistent with the shale record (Scott et al., 2013, Nature Geoscience, 6, 125-128). When hypothetical partitioning scenarios are applied to this record, paleomarine Zn concentrations within about an order of magnitude of modern are indicated. We couple this examination with new chemical speciation models used to interpret the iron formation record. We present two scenarios: first, under all but the most sulfidic conditions and with Zn binding organic ligand concentrations similar to modern oceans, the amount of bioavailable Zn remained relatively unchanged through time. Late proliferation of Zn in eukaryotic metallomes has previously been linked to marine Zn biolimitation, but under this scenario, the expansion in eukaryotic Zn metallomes may be better linked to biologically intrinsic evolutionary factors. In this case zinc’s geochemical and biological evolution may be decoupled, and viewed as a function of increasing need for genome regulation and diversification of Zn-binding transcription factors. In the second scenario, we consider Archean organic ligand complexation in such excess that it may render Zn bioavailability low. However, this is dependent on Zn organic ligand complexes not being bioavailable, which remains unclear. In this case, although bioavailability may be low, sphalerite precipitation is prevented, thereby maintaining a constant Zn inventory throughout both ferruginous and euxinic conditions. These results provide new perspectives and constraints 50 on potential couplings between the trajectory of biological and marine geochemical coevolution.This work was supported by a NSERC Discovery Grant to KOK, a NSERC PDF to SVL, a NSERC CGSM to LJR, and an NSF-EAR-PDF to NJP. MAS acknowledges support from the Gordon and Betty Moore Foundation Grant #2724. This work was also supported by grants from the Deutsche Forschungsgemeinschaft (DFG) to A.K. (KA 1736/4-1 and 12-1)