Enriching Existing Test Collections with OXPath

Extending TREC-style test collections by incorporating external resources is a time consuming and challenging task. Making use of freely available web data requires technical skills to work with APIs or to create a web scraping program specifically tailored to the task at hand. We present a light-weight alternative that employs the web data extraction language OXPath to harvest data to be added to an existing test collection from web resources. We demonstrate this by creating an extended version of GIRT4 called GIRT4-XT with additional metadata fields harvested via OXPath from the social sciences portal Sowiport. This allows the re-use of this collection for other evaluation purposes like bibliometrics-enhanced retrieval. The demonstrated method can be applied to a variety of similar scenarios and is not limited to extending existing collections but can also be used to create completely new ones with little effort.Comment: Experimental IR Meets Multilinguality, Multimodality, and Interaction - 8th International Conference of the CLEF Association, CLEF 2017, Dublin, Ireland, September 11-14, 201

Cooling rate, heating rate and aging effects in glassy water

We report a molecular dynamics simulation study of the properties of the potential energy landscape sampled by a system of water molecules during the process of generating a glass by cooling, and during the process of regenerating the equilibrium liquid by heating the glass. We study the dependence of these processes on the cooling/heating rates as well as on the role of aging (the time elapsed in the glass state). We compare the properties of the potential energy landscape sampled during these processes with the corresponding properties sampled in the liquid equilibrium state to elucidate under which conditions glass configurations can be associated with equilibrium liquid configurations.Comment: to be published in Phys. Rev. E (rapid comunication

Wetting and contact-line effects for spherical and cylindrical droplets on graphene layers: A comparative molecular-dynamics investigation

In Molecular Dynamics (MD) simulations, interactions between water molecules and graphitic surfaces are often modeled as a simple Lennard-Jones potential between oxygen and carbon atoms. A possible method for tuning this parameter consists of simulating a water nanodroplet on a flat graphitic surface, measuring the equilibrium contact angle, extrapolating it to the limit of a macroscopic droplet and finally matching this quantity to experimental results. Considering recent evidence demonstrating that the contact angle of water on a graphitic plane is much higher than what was previously reported, we estimate the oxygen-carbon interaction for the recent SPC/Fwwater model. Results indicate a value of about 0.2 kJ/mol, much lower than previous estimations. We then perform simulations of cylindrical water filaments on graphitic surfaces, in order to compare and correlate contact angles resulting from these two different systems. Results suggest that modified Young's equation does not describe the relation between contact angle and drop size in the case of extremely small systems and that contributions different from the one deriving from contact line tension should be taken into account.Comment: To be published on Physical Review E (http://pre.aps.org/

Perspective: How good is DFT for water?

Kohn-Sham density functional theory (DFT) has become established as an indispensable tool for investigating aqueous systems of all kinds, including those important in chemistry, surface science, biology and the earth sciences. Nevertheless, many widely used approximations for the exchange-correlation (XC) functional describe the properties of pure water systems with an accuracy that is not fully satisfactory. The explicit inclusion of dispersion interactions generally improves the description, but there remain large disagreements between the predictions of different dispersion-inclusive methods. We present here a review of DFT work on water clusters, ice structures and liquid water, with the aim of elucidating how the strengths and weaknesses of different XC approximations manifest themselves across this variety of water systems. Our review highlights the crucial role of dispersion in describing the delicate balance between compact and extended structures of many different water systems, including the liquid. By referring to a wide range of published work, we argue that the correct description of exchange-overlap interactions is also extremely important, so that the choice of semi-local or hybrid functional employed in dispersion-inclusive methods is crucial. The origins and consequences of beyond-2-body errors of approximate XC functionals are noted, and we also discuss the substantial differences between different representations of dispersion. We propose a simple numerical scoring system that rates the performance of different XC functionals in describing water systems, and we suggest possible future developments

Free energy of hydrophobic hydration:A molecular dynamics study of noble gases in water

The potential utility and limitations of two methods to determine free energy differences from molecular dynamics simulations (MD) are studied. The computation of the free energy of hydration of the inert gases serves as a simple but illustrative example. Good results are obtained for the inert gases from a perturbation treatment, using a reference ensemble obtained from a MD simulation of a cavity in water, if these atoms are comparable in size to the cavity and the calculated free energy differences are small. This limits the applicability of the perturbation treatment of a small number of cases. Larger free energy differences can be obtained with reasonable accuracy from MD simulations with continuously changing interaction parameters. This integration method is more generally applicable, but makes an additional simulation necessary

Effects of altered TatC proteins on protein secretion efficiency via the twin-arginine translocation pathway of Bacillus subtilis

Protein translocation via the Tat machinery in thylakoids and bacteria occurs through a cooperation between the TatA, TatB and TatC subunits, of which the TatC protein forms the initial Tat substrate-binding site. The Bacillus subtilis Tat machinery lacks TatB and comprises two separate TatAC complexes with distinct substrate specificities: PhoD is secreted by the TatAdCd complex, whereas YwbN is secreted by the TatAyCy complex. To study the role of the Gram-positive TatC proteins in Tat-dependent protein secretion efficiency, we applied several genetic engineering approaches to modify and analyse the B. subtilis TatCd and TatCy proteins. Cytoplasmic and transmembrane domain exchange between TatCd and TatCy resulted in stable chimeric proteins that were unable to secrete both known substrates of the B. subtilis Tat system. Site-directed mutagenesis of conserved residues in the N-terminal part of both TatC proteins revealed significant differences in the degree of importance of these residues between TatCd, TatCy and Escherichia coli TatC. In addition, two small C-terminal deletions in TatCy completely abolished YwbN translocation, indicating that this terminus is essential for Tat translocation activity. Important differences from previous observations for E. coli TatC and implications for substrate binding and translocation are discussed.

Webifying the computerized execution of Clinical Practice Guidelines

The means through which Clinical Practice Guidelines are dissemi-nated and become accessible are a crucial factor in their later adoption by health care professionals. Making these guidelines available in Clinical Decision Sup-port Systems renders their application more personal and thus acceptable at the moment of care. Web technologies may play an important role in increasing the reach and dissemination of guidelines, but this promise remains largely unful-filled. There is a need for a guideline computer model that can accommodate a wide variety of medical knowledge along with a platform for its execution that can be easily used in mobile devices. This work presents the CompGuide frame-work, a web-based and service-oriented platform for the execution of Computer-Interpretable Guidelines. Its architecture comprises different modules whose in-teraction enables the interpretation of clinical tasks and the verification of clinical constraints and temporal restrictions of guidelines represented in OWL. It allows remote guideline execution with data centralization, more suitable for a work en-vironment where physicians are mobile and not bound to a machine. The solution presented in this paper encompasses a computer-interpretable guideline model, a web-based framework for guideline execution and an Application Programming Interface for the development of other guideline execution systems.This work is part-funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT – Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within project FCOMP-01-0124-FEDER-028980 (PTDC/EEI-SII/1386/2012). The work of Tiago Oliveira is supported by doctoral grant by FCT (SFRH/BD/85291/2012)

A molecular dynamics simulation of polymer crystallization from oriented amorphous state

Molecular process of crystallization from an oriented amorphous state was reproduced by molecular dynamics simulation for a realistic polyethylene model. Initial oriented amorphous state was obtained by uniaxial drawing an isotropic glassy state at 100 K. By the temperature jump from 100 K to 330 K, there occurred the crystallization into the fiber structure, during the process of which we observed the developments of various order parameters. The real space image and its Fourier transform revealed that a hexagonally ordered domain was initially formed, and then highly ordered crystalline state with stacked lamellae developed after further adjustment of the relative heights of the chains along their axes.Comment: 4 pages, 3 figure