An OER Architecture Framework: Needs and Design

ERIC Educational Resources Information Center

Khanna, Pankaj; Basak, P. C.

2013-01-01

This paper describes an open educational resources (OER) architecture framework that would bring significant improvements in a well-structured and systematic way to the educational practices of distance education institutions of India. The OER architecture framework is articulated with six dimensions: pedagogical, technological, managerial,…

OpenSeesPy: Python library for the OpenSees finite element framework

NASA Astrophysics Data System (ADS)

Zhu, Minjie; McKenna, Frank; Scott, Michael H.

2018-01-01

OpenSees, an open source finite element software framework, has been used broadly in the earthquake engineering community for simulating the seismic response of structural and geotechnical systems. The framework allows users to perform finite element analysis with a scripting language and for developers to create both serial and parallel finite element computer applications as interpreters. For the last 15 years, Tcl has been the primary scripting language to which the model building and analysis modules of OpenSees are linked. To provide users with different scripting language options, particularly Python, the OpenSees interpreter interface was refactored to provide multi-interpreter capabilities. This refactoring, resulting in the creation of OpenSeesPy as a Python module, is accomplished through an abstract interface for interpreter calls with concrete implementations for different scripting languages. Through this approach, users are able to develop applications that utilize the unique features of several scripting languages while taking advantage of advanced finite element analysis models and algorithms.

Energy-efficient skylight structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dame, J.V.

1988-03-29

This patent describes an energy-efficient skylight structure for attaching to a ceiling having a hole therein. The structure includes a roof membrane of light translucent material. The improvement comprises: a framework being larger in size than the hole in the ceiling, the framework adapted to receive a light-diffusing panel; means for attaching the framework over the hole in the ceiling to support beams for the ceiling; gasket means between the framework and the ceiling for sealing the framework to the ceiling around the hole; a light-diffusing panel held by the framework; sealing means between the light-diffusing panel and the frameworkmore » for sealing the perimeter of the light diffusing panel to the framework; and a light-channeling means attached at one end to the ceiling around the opening on the side opposite the framework and at the other end around the light translucent material of the roof membrane.« less

Clinical Knowledge Governance Framework for Nationwide Data Infrastructure Projects.

PubMed

Wulff, Antje; Haarbrandt, Birger; Marschollek, Michael

2018-01-01

The availability of semantically-enriched and interoperable clinical information models is crucial for reusing once collected data across institutions like aspired in the German HiGHmed project. Funded by the Federal Ministry of Education and Research, this nationwide data infrastructure project adopts the openEHR approach for semantic modelling. Here, strong governance is required to define high-quality and reusable models. Design of a clinical knowledge governance framework for openEHR modelling in cross-institutional settings like HiGHmed. Analysis of successful practices from international projects, published ideas on archetype governance and own modelling experiences as well as modelling of BPMN processes. We designed a framework by presenting archetype variations, roles and responsibilities, IT support and modelling workflows. Our framework has great potential to make the openEHR modelling efforts manageable. Because practical experiences are rare, prospectively our work will be predestinated to evaluate the benefits of such structured governance approaches.

Open architectures for formal reasoning and deductive technologies for software development

NASA Technical Reports Server (NTRS)

Mccarthy, John; Manna, Zohar; Mason, Ian; Pnueli, Amir; Talcott, Carolyn; Waldinger, Richard

1994-01-01

The objective of this project is to develop an open architecture for formal reasoning systems. One goal is to provide a framework with a clear semantic basis for specification and instantiation of generic components; construction of complex systems by interconnecting components; and for making incremental improvements and tailoring to specific applications. Another goal is to develop methods for specifying component interfaces and interactions to facilitate use of existing and newly built systems as 'off the shelf' components, thus helping bridge the gap between producers and consumers of reasoning systems. In this report we summarize results in several areas: our data base of reasoning systems; a theory of binding structures; a theory of components of open systems; a framework for specifying components of open reasoning system; and an analysis of the integration of rewriting and linear arithmetic modules in Boyer-Moore using the above framework.

Bi{sub 6}(SeO{sub 3}){sub 3}O{sub 5}Br{sub 2}: A new bismuth oxo-selenite bromide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berdonosov, Peter S., E-mail: berdonosov@inorg.chem.msu.ru; Olenev, Andrei V.; Kirsanova, Maria A.

2012-12-15

A new bismuth oxo-selenite bromide Bi{sub 6}(SeO{sub 3}){sub 3}O{sub 5}Br{sub 2} was synthesized and structurally characterized. The crystal structure belongs to the triclinic system (space group P1-bar , Z=2, a=7.1253(7) A, b=10.972(1) A, c=12.117(1) A, {alpha}=67.765(7) Degree-Sign , {beta}=82.188(8) Degree-Sign , {gamma}=78.445(7) Degree-Sign ) and is unrelated to those of other known oxo-selenite halides. It can be considered as an open framework composed of BiO{sub x} or BiO{sub y}Br{sub z} polyhedrons forming channels running along [1 0 0] direction which contain the selenium atoms in pyramidal shape oxygen coordination (SeO{sub 3}E). The spectroscopic properties and thermal stability were studied. Themore » new compound is stable up to 400 Degree-Sign C. - graphical abstract: New bismuth oxo-selenite bromide with new open framework structure. Highlights: Black-Right-Pointing-Pointer New bismuth oxo-selenite bromide was found and structurally characterized. Black-Right-Pointing-Pointer Bi{sub 6}(SeO{sub 3}){sub 3}O{sub 5}Br{sub 2} exhibit a new open framework structure type. Black-Right-Pointing-Pointer BiO{sub x} or BiO{sub y}Br{sub z} polyhedrons form channels in the structure which are decorated by [SeO{sub 3}E] groups.« less

Robust boundary treatment for open-channel flows in divergence-free incompressible SPH

NASA Astrophysics Data System (ADS)

Pahar, Gourabananda; Dhar, Anirban

2017-03-01

A robust Incompressible Smoothed Particle Hydrodynamics (ISPH) framework is developed to simulate specified inflow and outflow boundary conditions for open-channel flow. Being purely divergence-free, the framework offers smoothed and structured pressure distribution. An implicit treatment of Pressure Poison Equation and Dirichlet boundary condition is applied on free-surface to minimize error in velocity-divergence. Beyond inflow and outflow threshold, multiple layers of dummy particles are created according to specified boundary condition. Inflow boundary acts as a soluble wave-maker. Fluid particles beyond outflow threshold are removed and replaced with dummy particles with specified boundary velocity. The framework is validated against different cases of open channel flow with different boundary conditions. The model can efficiently capture flow evolution and vortex generation for random geometry and variable boundary conditions.

LiBSi2: a tetrahedral semiconductor framework from boron and silicon atoms bearing lithium atoms in the channels.

PubMed

Zeilinger, Michael; van Wüllen, Leo; Benson, Daryn; Kranak, Verina F; Konar, Sumit; Fässler, Thomas F; Häussermann, Ulrich

2013-06-03

Silicon swallows up boron: The novel open tetrahedral framework structure (OTF) of the Zintl phase LiBSi2 was made by applying high pressure to a mixture of LiB and elemental silicon. The compound represents a new topology in the B-Si net (called tum), which hosts Li atoms in the channels (see picture). LiBSi2 is the first example where B and Si atoms form an ordered common framework structure with B engaged exclusively in heteronuclear B-Si contacts.

Framework flexibility of ZIF-8 under liquid intrusion: discovering time-dependent mechanical response and structural relaxation.

PubMed

Sun, Yueting; Li, Yibing; Tan, Jin-Chong

2018-04-18

The structural flexibility of a topical zeolitic imidazolate framework with sodalite topology, termed ZIF-8, has been elucidated through liquid intrusion under moderate pressures (i.e. tens of MPa). By tracking the evolution of water intrusion pressure under cyclic conditions, we interrogate the role of the gate-opening mechanism controlling the size variation of the pore channels of ZIF-8. Interestingly, we demonstrate that its channel deformation is recoverable through structural relaxation over time, hence revealing the viscoelastic mechanical response in ZIF-8. We propose a simple approach employing a glycerol-water solution mixture, which can significantly enhance the sensitivity of intrusion pressure for the detection of structural deformation in ZIF-8. By leveraging the time-dependent gate-opening phenomenon in ZIF-8, we achieved a notable improvement (50%) in energy dissipation during multicycle mechanical deformation experiments.

Fragmentary and incidental behaviour of columns, slabs and crystals

PubMed Central

Whiteley, Walter

2014-01-01

Between the study of small finite frameworks and infinite incidentally periodic frameworks, we find the real materials which are large, but finite, fragments that fit into the infinite periodic frameworks. To understand these materials, we seek insights from both (i) their analysis as large frameworks with associated geometric and combinatorial properties (including the geometric repetitions) and (ii) embedding them into appropriate infinite periodic structures with motions that may break the periodic structure. A review of real materials identifies a number of examples with a local appearance of ‘unit cells’ which repeat under isometries but perhaps in unusual forms. These examples also refocus attention on several new classes of infinite ‘periodic’ frameworks: (i) columns—three-dimensional structures generated with one repeating isometry and (ii) slabs—three-dimensional structures with two independent repeating translations. With this larger vision of structures to be studied, we find some patterns and partial results that suggest new conjectures as well as many additional open questions. These invite a search for new examples and additional theorems. PMID:24379423

Fluid-structure coupling for wind turbine blade analysis using OpenFOAM

NASA Astrophysics Data System (ADS)

Dose, Bastian; Herraez, Ivan; Peinke, Joachim

2015-11-01

Modern wind turbine rotor blades are designed increasingly large and flexible. This structural flexibility represents a problem for the field of Computational Fluid Dynamics (CFD), which is used for accurate load calculations and detailed investigations of rotor aerodynamics. As the blade geometries within CFD simulations are considered stiff, the effect of blade deformation caused by aerodynamic loads cannot be captured by the common CFD approach. Coupling the flow solver with a structural solver can overcome this restriction and enables the investigation of flexible wind turbine blades. For this purpose, a new Finite Element (FE) solver was implemented into the open source CFD code OpenFOAM. Using a beam element formulation based on the Geometrically Exact Beam Theory (GEBT), the structural model can capture geometric non-linearities such as large deformations. Coupled with CFD solvers of the OpenFOAM package, the new framework represents a powerful tool for aerodynamic investigations. In this work, we investigated the aerodynamic performance of a state of the art wind turbine. For different wind speeds, aerodynamic key parameters are evaluated and compared for both, rigid and flexible blade geometries. The present work is funded within the framework of the joint project Smart Blades (0325601D) by the German Federal Ministry for Economic Affairs and Energy (BMWi) under decision of the German Federal Parliament.

Loading Ag nanoparticles on Cd(II) boron imidazolate framework for photocatalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Min; State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002; Zhang, De-Xiang

2016-05-15

An amine-functionalized Cd(II) boron imidazolate framework (BIF-77) with three-dimensional open structure has been successfully synthesized, which can load Ag nanoparticles (NPs) for photocatalytic degradation of methylene blue (MB). - Graphical abstract: An amine-functionalized neutral Cd(II) boron imidazolate framework can load Ag NPs and show excellent photocatalytic degradation behavious for MB. - Highlights: • Amine-functionalization. • Neutral boron imidazolate framework. • Loading Ag nanoparticles (NPs). • Photocatalytic degradation of methylene blue.

OpenStructure: a flexible software framework for computational structural biology.

PubMed

Biasini, Marco; Mariani, Valerio; Haas, Jürgen; Scheuber, Stefan; Schenk, Andreas D; Schwede, Torsten; Philippsen, Ansgar

2010-10-15

Developers of new methods in computational structural biology are often hampered in their research by incompatible software tools and non-standardized data formats. To address this problem, we have developed OpenStructure as a modular open source platform to provide a powerful, yet flexible general working environment for structural bioinformatics. OpenStructure consists primarily of a set of libraries written in C++ with a cleanly designed application programmer interface. All functionality can be accessed directly in C++ or in a Python layer, meeting both the requirements for high efficiency and ease of use. Powerful selection queries and the notion of entity views to represent these selections greatly facilitate the development and implementation of algorithms on structural data. The modular integration of computational core methods with powerful visualization tools makes OpenStructure an ideal working and development environment. Several applications, such as the latest versions of IPLT and QMean, have been implemented based on OpenStructure-demonstrating its value for the development of next-generation structural biology algorithms. Source code licensed under the GNU lesser general public license and binaries for MacOS X, Linux and Windows are available for download at http://www.openstructure.org. torsten.schwede@unibas.ch Supplementary data are available at Bioinformatics online.

Identifying the Role of Terahertz Vibrations in Metal-Organic Frameworks: From Gate-Opening Phenomenon to Shear-Driven Structural Destabilization

NASA Astrophysics Data System (ADS)

Ryder, Matthew R.; Civalleri, Bartolomeo; Bennett, Thomas D.; Henke, Sebastian; Rudić, Svemir; Cinque, Gianfelice; Fernandez-Alonso, Felix; Tan, Jin-Chong

2014-11-01

We present an unambiguous identification of low-frequency terahertz vibrations in the archetypal imidazole-based metal-organic framework (MOF) materials: ZIF-4, ZIF-7, and ZIF-8, all of which adopt a zeolite-like nanoporous structure. Using inelastic neutron scattering and synchrotron radiation far-infrared absorption spectroscopy, in conjunction with density functional theory (DFT), we have pinpointed all major sources of vibrational modes. Ab initio DFT calculations revealed the complex nature of the collective THz modes, which enable us to establish detailed correlations with experiments. We discover that low-energy conformational dynamics offers multiple pathways to elucidate novel physical phenomena observed in MOFs. New evidence demonstrates that THz modes are intrinsically linked, not only to anomalous elasticity underpinning gate-opening and pore-breathing mechanisms, but also to shear-induced phase transitions and the onset of structural instability.

Software Applications on the Peregrine System | High-Performance Computing

Science.gov Websites

programming and optimization. Gaussian Chemistry Program for calculating molecular electronic structure and Materials Science Open-source classical molecular dynamics program designed for massively parallel systems framework Q-Chem Chemistry ab initio quantum chemistry package for predictin molecular structures

Solvent-free synthesis of new metal phosphites with double-layered, pillared-layered, and framework structures

NASA Astrophysics Data System (ADS)

Liu, Lin; Zhang, Wei; Shi, Zhonghua; Chen, Yaoqiang; Lin, Zhien

2014-12-01

Three new metal phosphites, formulated as (H3O)2·Mn2(HPO3)3 (1), Co(bpy) (H2O) (HPO3) (2), and H2tmpda·Zn3(HPO3)4 (3), have been synthesized under solvent-free conditions, where bpy = 4,4‧-bipyridine, and tmpda = N,N,N‧,N‧-tetramethyl-1,3-propanediamine. Compound 1 has a double-layered structure with a thickness of 5.68 Å. Compound 2 has an inorganic-organic hybrid framework with cobalt phosphite layers pillared by bpy ligands. Compound 3 has a three-dimensional open-framework structure containing 8-ring channels. The temperature dependence of the magnetic susceptibility of compounds 1 and 2 were also investigated.

Developing a Novel Hydrogen Sponge with Ideal Binding Energy and High Surface Area for Practical Hydrogen Storage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, T. C. Mike

This Phase I (5 quarters) research project was to examine the validity of a new class of boron-containing polymer (B-polymer) frameworks, serving as the adsorbents for the practical onboard H2 storage applications. Three B-polymer frameworks were synthesized and investigated, which include B-poly(butyenylstyrene) (B-PBS) framework (A), B-poly(phenyldiacetyene) (B-PPDA) framework (B), and B-poly(phenyltriacetylene) (B-PPTA) framework (C). They are 2-D polymer structures with the repeating cyclic units that spontaneously form open morphology and the B-doped (p-type) π-electrons delocalized surfaces. The ideal B-polymer framework shall exhibit open micropores (pore size in the range of 1-1.5nm) with high surface area (>3000 m 2/g), and themore » B-dopants in the conjugated framework shall provide high surface energy for interacting with H 2 molecules (an ideal H 2 binding energy in the range of 15-25 kJ/mol). The pore size distribution and H2 binding energy were investigated at both Penn State and NREL laboratories. So far, the experimental results show the successful synthesis of B-polymer frameworks with the relatively well-defined planar (2-D) structures. The intrinsically formed porous morphology exhibits a broad pore size distribution (in the range of 0.5-10 nm) with specific surface area (~1000 m 2/g). The miss-alignment between 2-D layers may block some micropore channels and limit gas diffusion throughout the entire matrix. In addition, the 2-D planar conjugated structure may also allow free π-electrons delocalization throughout the framework, which significantly reduces the acidity of B-moieties (electron-deficiency).The resulting 2-D B-polymer frameworks only exhibit a small increase of H 2 binding energy in the range of 8-9 KJ/mole (quite constant over the whole sorption range).« less

Web Service Distributed Management Framework for Autonomic Server Virtualization

NASA Astrophysics Data System (ADS)

Solomon, Bogdan; Ionescu, Dan; Litoiu, Marin; Mihaescu, Mircea

Virtualization for the x86 platform has imposed itself recently as a new technology that can improve the usage of machines in data centers and decrease the cost and energy of running a high number of servers. Similar to virtualization, autonomic computing and more specifically self-optimization, aims to improve server farm usage through provisioning and deprovisioning of instances as needed by the system. Autonomic systems are able to determine the optimal number of server machines - real or virtual - to use at a given time, and add or remove servers from a cluster in order to achieve optimal usage. While provisioning and deprovisioning of servers is very important, the way the autonomic system is built is also very important, as a robust and open framework is needed. One such management framework is the Web Service Distributed Management (WSDM) system, which is an open standard of the Organization for the Advancement of Structured Information Standards (OASIS). This paper presents an open framework built on top of the WSDM specification, which aims to provide self-optimization for applications servers residing on virtual machines.

Design and synthesis of an exceptionally stable and highly porous metal-organic framework

NASA Astrophysics Data System (ADS)

Li, Hailian; Eddaoudi, Mohamed; O'Keeffe, M.; Yaghi, O. M.

1999-11-01

Open metal-organic frameworks are widely regarded as promising materials for applications in catalysis, separation, gas storage and molecular recognition. Compared to conventionally used microporous inorganic materials such as zeolites, these organic structures have the potential for more flexible rational design, through control of the architecture and functionalization of the pores. So far, the inability of these open frameworks to support permanent porosity and to avoid collapsing in the absence of guest molecules, such as solvents, has hindered further progress in the field. Here we report the synthesis of a metal-organic framework which remains crystalline, as evidenced by X-ray single-crystal analyses, and stable when fully desolvated and when heated up to 300°C. This synthesis is achieved by borrowing ideas from metal carboxylate cluster chemistry, where an organic dicarboxylate linker is used in a reaction that gives supertetrahedron clusters when capped with monocarboxylates. The rigid and divergent character of the added linker allows the articulation of the clusters into a three-dimensional framework resulting in a structure with higher apparent surface area and pore volume than most porous crystalline zeolites. This simple and potentially universal design strategy is currently being pursued in the synthesis of new phases and composites, and for gas-storage applications.

Trapping guests within a nanoporous metal-organic framework through pressure-induced amorphization.

PubMed

Chapman, Karena W; Sava, Dorina F; Halder, Gregory J; Chupas, Peter J; Nenoff, Tina M

2011-11-23

The release of guest species from within a nanoporous metal-organic framework (MOF) has been inhibited by amorphization of the guest-loaded framework structure under applied pressure. Thermogravimetric analyses have shown that by amorphizing ZIF-8 following sorption of molecular I(2), a hazardous radiological byproduct of nuclear energy production, the pore apertures in the framework are sufficiently distorted to kinetically trap I(2) and improve I(2) retention. Pair distribution function (PDF) analysis indicates that the local structure of the captive I(2) remains essentially unchanged upon amorphization of the framework, with the amorphization occurring under the same conditions for the vacant and guest-loaded framework. The low, accessible pressure range needed to effect this change in desorption is much lower than in tradition sorbents such as zeolites, opening the possibility for new molecular capture, interim storage, or controlled release applications.

Silver-induced reconstruction of an adeninate-based metal-organic framework for encapsulation of luminescent adenine-stabilized silver clusters.

PubMed

Jonckheere, Dries; Coutino-Gonzalez, Eduardo; Baekelant, Wouter; Bueken, Bart; Reinsch, Helge; Stassen, Ivo; Fenwick, Oliver; Richard, Fanny; Samorì, Paolo; Ameloot, Rob; Hofkens, Johan; Roeffaers, Maarten B J; De Vos, Dirk E

2016-05-21

Bright luminescent silver-adenine species were successfully stabilized in the pores of the MOF-69A (zinc biphenyldicarboxylate) metal-organic framework, starting from the intrinsically blue luminescent bio-MOF-1 (zinc adeninate 4,4'-biphenyldicarboxylate). Bio-MOF-1 is transformed to the MOF-69A framework by selectively leaching structural adenine linkers from the original framework using silver nitrate solutions in aqueous ethanol. Simultaneously, bright blue-green luminescent silver-adenine clusters are formed inside the pores of the recrystallized MOF-69A matrix in high local concentrations. The structural transition and concurrent changes in optical properties were characterized using a range of structural, physicochemical and spectroscopic techniques (steady-state and time-resolved luminescence, quantum yield determination, fluorescence microscopy). The presented results open new avenues for exploring the use of MOFs containing luminescent silver clusters for solid-state lighting and sensor applications.

Crystal structure of (NH4)2[Fe(II) 5(HPO3)6], a new open-framework phosphite.

PubMed

Berrocal, Teresa; Mesa, Jose Luis; Larrea, Edurne; Arrieta, Juan Manuel

2014-11-01

Di-ammonium hexa-phosphito-penta-ferrate(II), (NH4)2[Fe5(HPO3)6], was synthesized under mild hydro-thermal conditions and autogeneous pressure, yielding twinned crystals. The crystal structure exhibits an [Fe(II) 5(HPO3)6](2-) open framework with NH4 (+) groups as counter-cations. The anionic skeleton is based on (001) sheets of [FeO6] octa-hedra (one with point-group symmetry 3.. and one with .2.) linked along [001] through [HPO3](2-) oxoanions. Each sheet is constructed from 12-membered rings of edge-sharing [FeO6] octa-hedra, giving rise to channels with a radius of ca 3.1 Å in which the disordered NH4 (+) cations are located. The IR spectrum shows vibrational bands typical for phosphite and ammonium groups.

Intellect: a theoretical framework for personality traits related to intellectual achievements.

PubMed

Mussel, Patrick

2013-05-01

The present article develops a theoretical framework for the structure of personality traits related to intellectual achievements. We postulate a 2-dimensional model, differentiating between 2 processes (Seek and Conquer) and 3 operations (Think, Learn, and Create). The framework was operationalized by a newly developed measure, which was validated based on 2 samples. Subsequently, in 3 studies (overall N = 1,478), the 2-dimensional structure of the Intellect framework was generally supported. Additionally, subdimensions of the Intellect framework specifically predicted conceptually related criteria, including scholastic performance, vocational interest, and leisure activities. Furthermore, results from multidimensional scaling and higher order confirmatory factor analyses show that the framework allows for the incorporation of several constructs that have been proposed on different theoretical backgrounds, such as need for cognition, typical intellectual engagement, curiosity, intrinsic motivation, goal orientation, and openness to ideas. It is concluded that based on the Intellect framework, these constructs, which have been researched separately in the literature, can be meaningfully integrated.

Shrink wrapping redox-active crystals of polyoxometalate open frameworks with organic polymers via crystal induced polymerisation.

PubMed

Takashima, Yohei; Miras, Haralampos N; Glatzel, Stefan; Cronin, Leroy

2016-06-14

We report examples of crystal surface modification of polyoxometalate open frameworks whereby the use of pyrrole or aniline as monomers leads to the formation of the corresponding polymers via an oxidative polymerization process initiated by the redox active POM scaffolds. Guest-exchange experiments demonstrate that the polymers can finely tune the guest exchange rate and their structural integrity is retained after the surface modifications. In addition, the formation of polyoxometalate-based self-fabricating tubes by the dissolution of Keggin-based network crystals were also modulated by the polymers, allowing a new type of hybrid inorganic polymer with an organic coating to be fabricated.

CIT-7, a crystalline, molecular sieve with pores bounded by 8 and 10-membered rings

DOE PAGES

Schmidt, Joel E.; Xie, Dan; Rea, Thomas; ...

2015-01-23

A new crystalline molecular sieve, denoted CIT-7, is synthesized using an imidazolium-based diquaternary organic structure directing agent (OSDA). The framework structure is determined from a combination of rotation electron diffraction and synchrotron X-ray powder diffraction data. The structure has 10 crystallographically unique tetrahedral atoms (T-atoms) in the unit cell, and can be described as an ordered arrangement of the [4 25 46 2] mtw building unit and a previously unreported [4 45 2] building unit. The framework contains a 2-dimensional pore system that is bounded by 10 T-atom rings (10-ring, 5.1 Å × 6.2 Å opening) that are connected withmore » oval 8-rings (2.9 Å × 5.5 Å opening) through medium-sized cavities (~7.9 Å) at the channel intersections. CIT-7 can be synthesized over a broad range of compositions including pure-silica and heteroatom, e.g., aluminosilicate and titanosilicate, containing variants.« less

Handedness in shearing auxetics creates rigid and compliant structures

NASA Astrophysics Data System (ADS)

Lipton, Jeffrey Ian; MacCurdy, Robert; Manchester, Zachary; Chin, Lillian; Cellucci, Daniel; Rus, Daniela

2018-05-01

In nature, repeated base units produce handed structures that selectively bond to make rigid or compliant materials. Auxetic tilings are scale-independent frameworks made from repeated unit cells that expand under tension. We discovered how to produce handedness in auxetic unit cells that shear as they expand by changing the symmetries and alignments of auxetic tilings. Using the symmetry and alignment rules that we developed, we made handed shearing auxetics that tile planes, cylinders, and spheres. By compositing the handed shearing auxetics in a manner inspired by keratin and collagen, we produce both compliant structures that expand while twisting and deployable structures that can rigidly lock. This work opens up new possibilities in designing chemical frameworks, medical devices like stents, robotic systems, and deployable engineering structures.

First-Principles Study of Electronic Structure and Hydrogen Adsorption of 3d Transition Metal Exposed Paddle Wheel Frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bak, J. H.; Le, V. D.; Kang, J.

2012-04-05

Open-site paddle wheels, comprised of two transition metals bridged with four carboxylate ions, have been widely used for constructing metal-organic frameworks with large surface area and high binding energy sites. Using first-principles density functional theory calculations, we have investigated atomic and electronic structures of various 3d transition metal paddle wheels before and after metal exposure and their hydrogen adsorption properties at open metal sites. Notably, the hydrogen adsorption is impeded by covalent metal-metal bonds in early transition metal paddle wheels from Sc to Cr and by the strong ferromagnetic coupling of diatomic Mn and Fe in the paddle wheel configurations.more » A significantly enhanced H{sub 2} adsorption is predicted in the nonmagnetic Co{sub 2} and Zn{sub 2} paddle wheel with the binding energy of {approx}0.2 eV per H{sub 2}. We also propose the use of two-dimensional Co{sub 2} and Zn{sub 2} paddle wheel frameworks that could have strongly adsorbed dihydrogen up to 1.35 wt % for noncryogenic hydrogen storage applications.« less

Discrete particle model for cement infiltration within open-cell structures: Prevention of osteoporotic fracture.

PubMed

Ramos-Infante, Samuel Jesús; Ten-Esteve, Amadeo; Alberich-Bayarri, Angel; Pérez, María Angeles

2018-01-01

This paper proposes a discrete particle model based on the random-walk theory for simulating cement infiltration within open-cell structures to prevent osteoporotic proximal femur fractures. Model parameters consider the cement viscosity (high and low) and the desired direction of injection (vertical and diagonal). In vitro and in silico characterizations of augmented open-cell structures validated the computational model and quantified the improved mechanical properties (Young's modulus) of the augmented specimens. The cement injection pattern was successfully predicted in all the simulated cases. All the augmented specimens exhibited enhanced mechanical properties computationally and experimentally (maximum improvements of 237.95 ± 12.91% and 246.85 ± 35.57%, respectively). The open-cell structures with high porosity fraction showed a considerable increase in mechanical properties. Cement augmentation in low porosity fraction specimens resulted in a lesser increase in mechanical properties. The results suggest that the proposed discrete particle model is adequate for use as a femoroplasty planning framework.

The electromagnetic multipole moments of the charged open-flavor {Z}_{\\bar{c}q} states

NASA Astrophysics Data System (ADS)

Azizi, K.; Özdem, U.

2018-05-01

The electromagnetic multipole moments of the open-flavor {Z}\\bar{cq} states are investigated by assuming a diquark–antidiquark picture for their internal structure and quantum numbers {J}{PC}={1}+- for their spin-parity. In particular, their magnetic and quadrupole moments are extracted in the framework of light-cone QCD sum rule by the help of the photon distribution amplitudes. The electromagnetic multipole moments of the open-flavor {Z}\\bar{cq} states are important dynamical observables, which encode valuable information on their underlying structure. The results obtained for the magnetic moments of different structures are considerably large and can be measured in future experiments. We obtain very small values for the quadrupole moments of {Z}\\bar{cq} states indicating a nonspherical charge distribution.

Evaluation metrics for bone segmentation in ultrasound

NASA Astrophysics Data System (ADS)

Lougheed, Matthew; Fichtinger, Gabor; Ungi, Tamas

2015-03-01

Tracked ultrasound is a safe alternative to X-ray for imaging bones. The interpretation of bony structures is challenging as ultrasound has no specific intensity characteristic of bones. Several image segmentation algorithms have been devised to identify bony structures. We propose an open-source framework that would aid in the development and comparison of such algorithms by quantitatively measuring segmentation performance in the ultrasound images. True-positive and false-negative metrics used in the framework quantify algorithm performance based on correctly segmented bone and correctly segmented boneless regions. Ground-truth for these metrics are defined manually and along with the corresponding automatically segmented image are used for the performance analysis. Manually created ground truth tests were generated to verify the accuracy of the analysis. Further evaluation metrics for determining average performance per slide and standard deviation are considered. The metrics provide a means of evaluating accuracy of frames along the length of a volume. This would aid in assessing the accuracy of the volume itself and the approach to image acquisition (positioning and frequency of frame). The framework was implemented as an open-source module of the 3D Slicer platform. The ground truth tests verified that the framework correctly calculates the implemented metrics. The developed framework provides a convenient way to evaluate bone segmentation algorithms. The implementation fits in a widely used application for segmentation algorithm prototyping. Future algorithm development will benefit by monitoring the effects of adjustments to an algorithm in a standard evaluation framework.

A Fast, Open EEG Classification Framework Based on Feature Compression and Channel Ranking

PubMed Central

Han, Jiuqi; Zhao, Yuwei; Sun, Hongji; Chen, Jiayun; Ke, Ang; Xu, Gesen; Zhang, Hualiang; Zhou, Jin; Wang, Changyong

2018-01-01

Superior feature extraction, channel selection and classification methods are essential for designing electroencephalography (EEG) classification frameworks. However, the performance of most frameworks is limited by their improper channel selection methods and too specifical design, leading to high computational complexity, non-convergent procedure and narrow expansibility. In this paper, to remedy these drawbacks, we propose a fast, open EEG classification framework centralized by EEG feature compression, low-dimensional representation, and convergent iterative channel ranking. First, to reduce the complexity, we use data clustering to compress the EEG features channel-wise, packing the high-dimensional EEG signal, and endowing them with numerical signatures. Second, to provide easy access to alternative superior methods, we structurally represent each EEG trial in a feature vector with its corresponding numerical signature. Thus, the recorded signals of many trials shrink to a low-dimensional structural matrix compatible with most pattern recognition methods. Third, a series of effective iterative feature selection approaches with theoretical convergence is introduced to rank the EEG channels and remove redundant ones, further accelerating the EEG classification process and ensuring its stability. Finally, a classical linear discriminant analysis (LDA) model is employed to classify a single EEG trial with selected channels. Experimental results on two real world brain-computer interface (BCI) competition datasets demonstrate the promising performance of the proposed framework over state-of-the-art methods. PMID:29713262

Open-framework micro- and meso-structured chalcogenides and their ion exchange properties

NASA Astrophysics Data System (ADS)

Ding, Nan

2007-12-01

Micro- and meso- structured chalcogenides with open inorganic framework have driven tremendous attention and intense work during the last two decades. They belong to a special category of materials possessing multifunctional potential due to their large void space within the atomic skeletons and the novel physical properties brought by the chalcogen elements. The latter are not generally present in typical open-framework oxides. In addition, because of the different size and electronegativity of the chalcogen elements compared to oxygen, many new structural properties were expected to emerge when the work in this dissertation was undertaken. The major body of this work involves group 13 (e.g. Ga, In) or 14 (e.g. Ge, Sn) elements with chalcogen. Transition metals also are incorporated in a few examples. The first two groups of compounds reported belong to the latter case. Unique structure types have been obtained under hydrothermal conditions via the combination of M (M = Zn, Cd), Sn and Q (Q = S, Se) to build microporous A6M4Sn3Q13 (A = K, Rb) based on truncated penta-supertrahedral cluster [M4Sn4Q 17]10-. More surprisingly, the protonation of K 6Cd4Sn3Se13 led to another new compound K14Cd15Sn12Se46 which possesses a labyrinth-like void space within the compact [Cd15Sn12Se 46]14- anionic skeleton. This structural characteristic leads to an unusual stability of the compound in acid. Both the K6Cd 4Sn3Se13 and K14Cd15Sn 12Se46 are fast ion-exchangers and their K+ ions can be replaced by other alkali metal cations and even H+ for the latter. Other work reported was aimed at the heavier analogs of alumiophosphate, i.e. the open-frameworks based on group 13 (Ga, In), 15 (Sb) and chalcogen elements. Two groups of chalcoantimonates with two-dimensional architectures [M5Sb6S19]5- and polymorphic [M2Sb2Q7]2- (M = Ga, In; Q = S, Se) were obtained. With the help of bulky organic structure-directing agents, large windows were formed in some of these anionic slabs. The windows are aligned through each layer, adding a pseudo-3D feature to the compounds. This leads to excellent ion-exchange properties. More remarkably, these compounds showed exceptional selectivity for Cs+ ions than any other alkali metal and alkaline earth metal cations due to the soft acid (Cs +)/soft base (S2-) attraction and the size discrimination imposed by the open windows within the frameworks. These properties point to a new direction of designing compounds for possible radioactive 137Cs+ remediation. With the even larger surfactant molecules in water, metal cations In 3+, Zn2+ and Cd2+ can connect [SbSe 4]3- clusters via coordination chemistry to form cubic and hexagonal mesophases. In addition to the linking effect, these metal cations also played the role of Lewis acids and partially reduced [SbSe4] 3- to [SbSe3]3-, both of which are present in the long-range ordered mesostructures. Short range order in a mesostuctured chalcogenide was approached, when structurally rigid Chevrel clusters [Re 6Se6Br8]2- were linked by triselenide anions via metathesis. Higher angle Bragg reflections of this compound provided an opportunity to build a structural model for the first time for a chalcogen-based mesophase.

Guest-Induced Switchable Breathing Behavior in a Flexible Metal-Organic Framework with Pronounced Negative Gas Pressure.

PubMed

Shi, Yi-Xiang; Li, Wu-Xiang; Zhang, Wen-Hua; Lang, Jian-Ping

2018-06-29

Flexible metal-organic frameworks (MOFs) have attracted great interest for their dynamically structural transformability in response to external stimuli. Herein, we report a switchable "breathing" or "gate-opening" behavior associated with the phase transformation between a narrow pore (np) and a large pore (lp) in a flexible pillared-layered MOF, denoted as MOF-1 as, which is also confirmed by SCXRD and PXRD. The desolvated phase (MOF-1 des) features a unique stepwise adsorption isotherm for N 2 coupled with a pronounced negative gas adsorption pressure. For comparison, however, no appreciable CO 2 adsorption and gate-opening phenomenon with stepwise sorption can be observed. Furthermore, the polar micropore walls decorated with thiophene groups in MOF-1 des reveals the selective sorption of toluene over benzene and p-xylene associated with self-structural adjustment in spite of the markedly similar physicochemical properties of these vapor molecules.

An Extensible Schema-less Database Framework for Managing High-throughput Semi-Structured Documents

NASA Technical Reports Server (NTRS)

Maluf, David A.; Tran, Peter B.; La, Tracy; Clancy, Daniel (Technical Monitor)

2002-01-01

Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword searches of records for both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semi-structured documents existing within NASA enterprises. Today, NETMARK is a flexible, high throughput open database framework for managing, storing, and searching unstructured or semi structured arbitrary hierarchal models, XML and HTML.

Avoiding to Fit a Square Peg into a Round Hole: A Policy Framework for Operationalising Open Distance Education in Dual-Mode Universities

ERIC Educational Resources Information Center

Makoe, Mpine

2018-01-01

Although education policies in many African countries refer to the need for distance education to widen participation in universities, they have not articulated guidelines on how they plan to develop systems and structures that will support it. The purpose of this study was to develop a policy framework specific for distance education provision in…

Rapid development of entity-based data models for bioinformatics with persistence object-oriented design and structured interfaces.

PubMed

Ezra Tsur, Elishai

2017-01-01

Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed. The framework supports user-designed models of data encapsulation, objects persistency and structured interfaces to local and external data sources such as MalaCards, Biomodels and the National Centre for Biotechnology Information (NCBI) databases. The proposed framework was implemented using Java as the development environment, EclipseLink as the data persistency agent and Apache Derby as the database manager. Syntactic analysis was based on J3D, jsoup, Apache Commons and w3c.dom open libraries. Finally, a construction of a specialized database for aneurysms associated vascular diseases is demonstrated. This database contains 3-dimensional geometries of aneurysms, patient's clinical information, articles, biological models, related diseases and our recently published model of aneurysms' risk of rapture. Framework is available in: http://nbel-lab.com.

mdFoam+: Advanced molecular dynamics in OpenFOAM

NASA Astrophysics Data System (ADS)

Longshaw, S. M.; Borg, M. K.; Ramisetti, S. B.; Zhang, J.; Lockerby, D. A.; Emerson, D. R.; Reese, J. M.

2018-03-01

This paper introduces mdFoam+, which is an MPI parallelised molecular dynamics (MD) solver implemented entirely within the OpenFOAM software framework. It is open-source and released under the same GNU General Public License (GPL) as OpenFOAM. The source code is released as a publicly open software repository that includes detailed documentation and tutorial cases. Since mdFoam+ is designed entirely within the OpenFOAM C++ object-oriented framework, it inherits a number of key features. The code is designed for extensibility and flexibility, so it is aimed first and foremost as an MD research tool, in which new models and test cases can be developed and tested rapidly. Implementing mdFoam+ in OpenFOAM also enables easier development of hybrid methods that couple MD with continuum-based solvers. Setting up MD cases follows the standard OpenFOAM format, as mdFoam+ also relies upon the OpenFOAM dictionary-based directory structure. This ensures that useful pre- and post-processing capabilities provided by OpenFOAM remain available even though the fully Lagrangian nature of an MD simulation is not typical of most OpenFOAM applications. Results show that mdFoam+ compares well to another well-known MD code (e.g. LAMMPS) in terms of benchmark problems, although it also has additional functionality that does not exist in other open-source MD codes.

QuTiP: An open-source Python framework for the dynamics of open quantum systems

NASA Astrophysics Data System (ADS)

Johansson, J. R.; Nation, P. D.; Nori, Franco

2012-08-01

We present an object-oriented open-source framework for solving the dynamics of open quantum systems written in Python. Arbitrary Hamiltonians, including time-dependent systems, may be built up from operators and states defined by a quantum object class, and then passed on to a choice of master equation or Monte Carlo solvers. We give an overview of the basic structure for the framework before detailing the numerical simulation of open system dynamics. Several examples are given to illustrate the build up to a complete calculation. Finally, we measure the performance of our library against that of current implementations. The framework described here is particularly well suited to the fields of quantum optics, superconducting circuit devices, nanomechanics, and trapped ions, while also being ideal for use in classroom instruction. Catalogue identifier: AEMB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 16 482 No. of bytes in distributed program, including test data, etc.: 213 438 Distribution format: tar.gz Programming language: Python Computer: i386, x86-64 Operating system: Linux, Mac OSX, Windows RAM: 2+ Gigabytes Classification: 7 External routines: NumPy (http://numpy.scipy.org/), SciPy (http://www.scipy.org/), Matplotlib (http://matplotlib.sourceforge.net/) Nature of problem: Dynamics of open quantum systems. Solution method: Numerical solutions to Lindblad master equation or Monte Carlo wave function method. Restrictions: Problems must meet the criteria for using the master equation in Lindblad form. Running time: A few seconds up to several tens of minutes, depending on size of underlying Hilbert space.

A Good Beginning Makes a Good Market: The Effect of Different Market Opening Structures on Market Quality

PubMed Central

Hinterleitner, Gernot; Leopold-Wildburger, Ulrike

2015-01-01

This paper deals with the market structure at the opening of the trading day and its influence on subsequent trading. We compare a single continuous double auction and two complement markets with different call auction designs as opening mechanisms in a unified experimental framework. The call auctions differ with respect to their levels of transparency. We find that a call auction not only improves market efficiency and liquidity at the beginning of the trading day when compared to the stand-alone continuous double auction, but also causes positive spillover effects on subsequent trading. Concerning the design of the opening call auction, we find no significant differences between the transparent and nontransparent specification with respect to opening prices and liquidity. In the course of subsequent continuous trading, however, market quality is slightly higher after a nontransparent call auction. PMID:26351653

A Good Beginning Makes a Good Market: The Effect of Different Market Opening Structures on Market Quality.

PubMed

Hinterleitner, Gernot; Leopold-Wildburger, Ulrike; Mestel, Roland; Palan, Stefan

2015-01-01

This paper deals with the market structure at the opening of the trading day and its influence on subsequent trading. We compare a single continuous double auction and two complement markets with different call auction designs as opening mechanisms in a unified experimental framework. The call auctions differ with respect to their levels of transparency. We find that a call auction not only improves market efficiency and liquidity at the beginning of the trading day when compared to the stand-alone continuous double auction, but also causes positive spillover effects on subsequent trading. Concerning the design of the opening call auction, we find no significant differences between the transparent and nontransparent specification with respect to opening prices and liquidity. In the course of subsequent continuous trading, however, market quality is slightly higher after a nontransparent call auction.

Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

PubMed

Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

2012-01-01

The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

OpenDanubia - An integrated, modular simulation system to support regional water resource management

NASA Astrophysics Data System (ADS)

Muerth, M.; Waldmann, D.; Heinzeller, C.; Hennicker, R.; Mauser, W.

2012-04-01

The already completed, multi-disciplinary research project GLOWA-Danube has developed a regional scale, integrated modeling system, which was successfully applied on the 77,000 km2 Upper Danube basin to investigate the impact of Global Change on both the natural and anthropogenic water cycle. At the end of the last project phase, the integrated modeling system was transferred into the open source project OpenDanubia, which now provides both the core system as well as all major model components to the general public. First, this will enable decision makers from government, business and management to use OpenDanubia as a tool for proactive management of water resources in the context of global change. Secondly, the model framework to support integrated simulations and all simulation models developed for OpenDanubia in the scope of GLOWA-Danube are further available for future developments and research questions. OpenDanubia allows for the investigation of water-related scenarios considering different ecological and economic aspects to support both scientists and policy makers to design policies for sustainable environmental management. OpenDanubia is designed as a framework-based, distributed system. The model system couples spatially distributed physical and socio-economic process during run-time, taking into account their mutual influence. To simulate the potential future impacts of Global Change on agriculture, industrial production, water supply, households and tourism businesses, so-called deep actor models are implemented in OpenDanubia. All important water-related fluxes and storages in the natural environment are implemented in OpenDanubia as spatially explicit, process-based modules. This includes the land surface water and energy balance, dynamic plant water uptake, ground water recharge and flow as well as river routing and reservoirs. Although the complete system is relatively demanding on data requirements and hardware requirements, the modular structure and the generic core system (Core Framework, Actor Framework) allows the application in new regions and the selection of a reduced number of modules for simulation. As part of the Open Source Initiative in GLOWA-Danube (opendanubia.glowa-danube.de) a comprehensive documentation for the system installation was created and both the program code of the framework and of all major components is licensed under the GNU General Public License. In addition, some helpful programs and scripts necessary for the operation and processing of input and result data sets are provided.

Silver-induced reconstruction of an adeninate-based metal–organic framework for encapsulation of luminescent adenine-stabilized silver clusters† †Electronic supplementary information (ESI) available: Experimental details and additional structural, physicochemical and optical characterisation. See DOI: 10.1039/c6tc00260a Click here for additional data file.

PubMed Central

Jonckheere, Dries; Coutino-Gonzalez, Eduardo; Baekelant, Wouter; Bueken, Bart; Reinsch, Helge; Stassen, Ivo; Fenwick, Oliver; Richard, Fanny; Samorì, Paolo; Ameloot, Rob; Hofkens, Johan

2016-01-01

Bright luminescent silver-adenine species were successfully stabilized in the pores of the MOF-69A (zinc biphenyldicarboxylate) metal–organic framework, starting from the intrinsically blue luminescent bio-MOF-1 (zinc adeninate 4,4′-biphenyldicarboxylate). Bio-MOF-1 is transformed to the MOF-69A framework by selectively leaching structural adenine linkers from the original framework using silver nitrate solutions in aqueous ethanol. Simultaneously, bright blue-green luminescent silver-adenine clusters are formed inside the pores of the recrystallized MOF-69A matrix in high local concentrations. The structural transition and concurrent changes in optical properties were characterized using a range of structural, physicochemical and spectroscopic techniques (steady-state and time-resolved luminescence, quantum yield determination, fluorescence microscopy). The presented results open new avenues for exploring the use of MOFs containing luminescent silver clusters for solid-state lighting and sensor applications. PMID:28496980

`Dhara': An Open Framework for Critical Zone Modeling

NASA Astrophysics Data System (ADS)

Le, P. V.; Kumar, P.

2016-12-01

Processes in the Critical Zone, which sustain terrestrial life, are tightly coupled across hydrological, physical, biological, chemical, pedological, geomorphological and ecological domains over both short and long timescales. Observations and quantification of the Earth's surface across these domains using emerging high resolution measurement technologies such as light detection and ranging (lidar) and hyperspectral remote sensing are enabling us to characterize fine scale landscape attributes over large spatial areas. This presents a unique opportunity to develop novel approaches to model the Critical Zone that can capture fine scale intricate dependencies across the different processes in 3D. The development of interdisciplinary tools that transcend individual disciplines and capture new levels of complexity and emergent properties is at the core of Critical Zone science. Here we introduce an open framework for high-performance computing model (`Dhara') for modeling complex processes in the Critical Zone. The framework is designed to be modular in structure with the aim to create uniform and efficient tools to facilitate and leverage process modeling. It also provides flexibility to maintain, collaborate, and co-develop additional components by the scientific community. We show the essential framework that simulates ecohydrologic dynamics, and surface - sub-surface coupling in 3D using hybrid parallel CPU-GPU. We demonstrate that the open framework in Dhara is feasible for detailed, multi-processes, and large-scale modeling of the Critical Zone, which opens up exciting possibilities. We will also present outcomes from a Modeling Summer Institute led by Intensively Managed Critical Zone Observatory (IMLCZO) with representation from several CZOs and international representatives.

SCIFIO: an extensible framework to support scientific image formats.

PubMed

Hiner, Mark C; Rueden, Curtis T; Eliceiri, Kevin W

2016-12-07

No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation. SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats' OME-TIFF, within a unified environment. SCIFIO is a freely available software library developed to standardize the process of reading and writing scientific image formats.

Structure stability of HKUST-1 towards water and ethanol and their effect on its CO2 capture properties.

PubMed

Álvarez, J Raziel; Sánchez-González, Elí; Pérez, Eric; Schneider-Revueltas, Emilia; Martínez, Ana; Tejeda-Cruz, Adriana; Islas-Jácome, Alejandro; González-Zamora, Eduardo; Ibarra, Ilich A

2017-07-18

Water and ethanol stabilities of the crystal structure of the Cu-based metal-organic framework (MOF) HKUST-1 have been investigated. Vapour (water and ethanol) sorption isotherms and cyclability were measured by a dynamic strategy. The ethanol sorption capacity of HKUST-1 at 303 K remained unchanged contrasting water sorption (which decreased along with the sorption experiment time). Considering the binding energy of each sorbate with the open Cu(ii) sites, obtained by the use of diffusion coefficients, we showed the superior crystal stability of the HKUST-1 framework towards ethanol. Finally, a small quantity of ethanol (pre-adsorbed) slightly enhanced CO 2 capture without crystal structure degradation.

Molecule database framework: a framework for creating database applications with chemical structure search capability

PubMed Central

2013-01-01

Background Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Results Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes: • Support for multi-component compounds (mixtures) • Import and export of SD-files • Optional security (authorization) For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. Conclusions By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework. PMID:24325762

Molecule database framework: a framework for creating database applications with chemical structure search capability.

PubMed

Kiener, Joos

2013-12-11

Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.

OpenARC: Extensible OpenACC Compiler Framework for Directive-Based Accelerator Programming Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Seyong; Vetter, Jeffrey S

2014-01-01

Directive-based, accelerator programming models such as OpenACC have arisen as an alternative solution to program emerging Scalable Heterogeneous Computing (SHC) platforms. However, the increased complexity in the SHC systems incurs several challenges in terms of portability and productivity. This paper presents an open-sourced OpenACC compiler, called OpenARC, which serves as an extensible research framework to address those issues in the directive-based accelerator programming. This paper explains important design strategies and key compiler transformation techniques needed to implement the reference OpenACC compiler. Moreover, this paper demonstrates the efficacy of OpenARC as a research framework for directive-based programming study, by proposing andmore » implementing OpenACC extensions in the OpenARC framework to 1) support hybrid programming of the unified memory and separate memory and 2) exploit architecture-specific features in an abstract manner. Porting thirteen standard OpenACC programs and three extended OpenACC programs to CUDA GPUs shows that OpenARC performs similarly to a commercial OpenACC compiler, while it serves as a high-level research framework.« less

dsmcFoam+: An OpenFOAM based direct simulation Monte Carlo solver

NASA Astrophysics Data System (ADS)

White, C.; Borg, M. K.; Scanlon, T. J.; Longshaw, S. M.; John, B.; Emerson, D. R.; Reese, J. M.

2018-03-01

dsmcFoam+ is a direct simulation Monte Carlo (DSMC) solver for rarefied gas dynamics, implemented within the OpenFOAM software framework, and parallelised with MPI. It is open-source and released under the GNU General Public License in a publicly available software repository that includes detailed documentation and tutorial DSMC gas flow cases. This release of the code includes many features not found in standard dsmcFoam, such as molecular vibrational and electronic energy modes, chemical reactions, and subsonic pressure boundary conditions. Since dsmcFoam+ is designed entirely within OpenFOAM's C++ object-oriented framework, it benefits from a number of key features: the code emphasises extensibility and flexibility so it is aimed first and foremost as a research tool for DSMC, allowing new models and test cases to be developed and tested rapidly. All DSMC cases are as straightforward as setting up any standard OpenFOAM case, as dsmcFoam+ relies upon the standard OpenFOAM dictionary based directory structure. This ensures that useful pre- and post-processing capabilities provided by OpenFOAM remain available even though the fully Lagrangian nature of a DSMC simulation is not typical of most OpenFOAM applications. We show that dsmcFoam+ compares well to other well-known DSMC codes and to analytical solutions in terms of benchmark results.

A novel 3D framework indium phosphite-oxalate based on a pcu-type topology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zuo, Mengmeng; Zhou, Mingdong; Hu, Dianwen

2016-05-15

A new inorganic–organic hybrid indium phosphite-oxalate, formulated as H[In{sub 5}(HPO{sub 3}){sub 6}(H{sub 2}PO{sub 3}){sub 2}(C{sub 2}O{sub 4}){sub 2}]·(C{sub 4}N{sub 2}H{sub 11}){sub 2}·H{sub 2}O 1 has been hydrothermally synthesized in the presence of piperazine acting as a structure directing agent (SDA). The single crystal X-ray diffraction reveals that compound 1 shows three-dimensional open-framework with intersecting 12-ring channels along the [010] and [001] directions, which is constructed from strictly alternating double 6-ring units (D6Rs), [C{sub 2}O{sub 4}]{sup 2−} groups and [H{sub 2}PO{sub 3}]{sup −} pseudo-pyramids. It is noted that the classical D6R SBU is firstly reported in main metal phosphite/phosphite-oxalate. By regardingmore » D6R as the 6-connected nodes, the inorganic–organic hybrid framework is based on a pcu-type topology. The as-synthesized product was characterized by single-crystal X-ray diffraction, powder X-ray diffraction, IR spectroscopy, thermogravimetric analysis (TGA), ICP-AES and elemental analyses. - Graphical abstract: A 3D open-framework indium phosphite-oxalate has been synthesized under hydrothermal conditions. A classical SBU, D6R, is present in the structure. By regarding D6R as the 6-connected nodes, the inorganic–organic hybrid framework is based on a pcu-type topology. - Highlights: • A new indium phosphite-oxalate based on a pcu-type topology has been synthesized. • A classical SBU, D6R, is present in the structure. • The classical SBU is firstly reported in main metal phosphite/phosphite-oxalate.« less

Structure investigation of fluorinated aluminophosphate ULM-3 Al templated by 3-methylaminopropylamine

NASA Astrophysics Data System (ADS)

Zabukovec Logar, Natasa; Mali, Gregor; Rajic, Nevenka; Jevtic, Sanja; Rangus, Mojca; Golobic, Amalija; Kaucic, Venceslav

2010-05-01

A single-crystal X-ray diffraction analysis of an open-framework aluminophosphate ULM-3 Al prepared by 3-methylaminopropylamine (MAPA) as structure-directing agent revealed an orthorhombic Pcab symmetry ( a=9.9949(4) Å, b=15.8229(7) Å, c=18.1963(5) Å, R=0.0648, Z=8, unit cell formula [Al 24P 24O 96F 16·C 32H 112N 16]), which differs from the Pbc2 1 symmetry of the structural analogue prepared in the presence of 1,4-diaminobutane. The 27Al, 31P, 19F, 13C and 1H NMR investigations, which were performed to study in detail MAPA arrangement inside the framework as well as the interactions of MAPA with the aluminophosphate host, confirmed the crystal symmetry and the proposed hydrogen bonding scheme between the template and the framework.

Synthesis, characterization and thermodynamic study of carbon dioxide adsorption on akaganéite

DOE PAGES

Roque-Malherbe, R.; Lugo, F.; Rivera-Maldonado, C.; ...

2015-04-01

A mixture of akaganeite nanoparticles and sodium salts was synthesized and modi fied, first by washing, and then by Li exchange. The structural characterization of the produced materials was performed with: powder X-ray diffraction, scanning electron microscopy, energy dispersive X-ray analysis, thermogravimetric analysis, diffuse reflectance infrared Fourier transform spectrometry, Mossbauer spectros- € copy and magnetization measurements. Additionally low pressure nitrogen and high pressure carbon dioxide adsorption experiments were performed. The sum of the characterization information made possible to conclude that the produced akaganeite phases crystallized in a structure exhibiting the symmetry of the I2/m space group, where the measured equivalentmore » spherical diameter of the akaganeite crystallites yielded 9 nm, as well, the tested phases exhibited a standard behaviour under heating and displayed a superparamagnetic behaviour. Finally the high pressure carbon dioxide adsorption experiments demonstrated a pressure-responsive framework opening event due to a structural transformation of the adsorbent framework induced by the guest molecules. This fact opens new applications for akaganeite as a high pressure adsorbent.« less

Amine-controlled assembly of metal-sulfite architecture from 1D chains to 3D framework.

PubMed

Austria, Cristina; Zhang, Jian; Valle, Henry; Zhang, Qichun; Chew, Emily; Nguyen, Dan-Tam; Gu, J Y; Feng, Pingyun; Bu, Xianhui

2007-08-06

Whereas open-framework materials have been made in a variety of chemical compositions, few are known in which 3-connected SO3(2)- anions serve as basic building units. Here, we report four new metal-sulfite polymeric structures, (ZnSO3)Py (1, py = pyridine), (ZnSO3)2(2,2'-bipy)H2O (2, 2,2'-bipy = 2,2'-bipyridine), (ZnSO3)2(TMDPy) (3, TMDPy = 4,4'-trimethylenedipyridine), and (MnSO3)2en (4, en = ethylenediamine) that have been synthesized hydrothermally and structurally characterized. In these compounds, low-dimensional 1D and 2D inorganic subunits are assembled into higher 2D or 3D covalent frameworks by organic ligands. In addition to the structure-directing effect of organic ligands, the flexible coordination chemistry of Zn2+ and SO3(2)- also contributes to the observed structural diversity. In compounds 1-3, Zn2+ sites alternate with trigonal pyramidal SO3(2)- anions to form three types of [ZnSO3]n chains, whereas in compound 4, a 2D-corrugated [MnSO3]n layer is present. Compound 1 features a rail-like chain with pendant pyridine rings. The pi-pi interaction between 2,2'-bipy ligands is found between adjacent chains in compound 2, resulting in 2D sheets that are further stacked through interlayer hydrogen bonds. Compound 3 exhibits a very interesting inorganic [(ZnSO3)2]n chain constructed from two chairlike subunits, and such chains are bridged by TMDPy ligands into a 2D sheet. In compound 4, side-by-side helical chains permeate through 2D-corrugated [MnSO3]n layers, which are pillared by neutral ethylenediamine molecules into a 3D framework that can be topologically represented as a (3,6)-connected net. The results presented here illustrate the rich structural chemistry of metal-sulfites and the potential of sulfite anions as a unique structural building block for the construction of novel open-framework materials, in particular, those containing polymeric inorganic subunits that may have interesting physical properties such as low-dimensional magnetism or electronic properties.

Two chain gallium fluorodiphosphates: synthesis, structure solution, and their transient presence during the hydrothermal crystallisation of a microporous gallium fluorophosphate.

PubMed

Millange, Franck; Walton, Richard I; Guillou, Nathalie; Loiseau, Thierry; O'Hare, Dermot; Férey, Gérard

2002-04-21

Two novel gallium fluorodiphosphates have been isolated and their structures solved ab initio from powder X-ray diffraction data; the materials readily interconvert under hydrothermal conditions, and are metastable with respect to an open-framework zeolitic gallium fluorophosphate, during the synthesis of which they are present as transient intermediates.

CIT-7, a crystalline, molecular sieve with pores bounded by 8 and 10-membered rings† †Electronic supplementary information (ESI) available: Details of the synthesis and characterization of all materials as well as details on the synchrotron and RED data collection and structure determination, including the cif file. See DOI: 10.1039/c4sc03935a Click here for additional data file.

PubMed Central

Schmidt, Joel E.; Xie, Dan; Rea, Thomas

2015-01-01

A new crystalline molecular sieve, denoted CIT-7, is synthesized using an imidazolium-based diquaternary organic structure directing agent (OSDA). The framework structure is determined from a combination of rotation electron diffraction and synchrotron X-ray powder diffraction data. The structure has 10 crystallographically unique tetrahedral atoms (T-atoms) in the unit cell, and can be described as an ordered arrangement of the [425462] mtw building unit and a previously unreported [4452] building unit. The framework contains a 2-dimensional pore system that is bounded by 10 T-atom rings (10-ring, 5.1 Å × 6.2 Å opening) that are connected with oval 8-rings (2.9 Å × 5.5 Å opening) through medium-sized cavities (∼7.9 Å) at the channel intersections. CIT-7 can be synthesized over a broad range of compositions including pure-silica and heteroatom, e.g., aluminosilicate and titanosilicate, containing variants. PMID:29163872

The Open-Ended Approach Framework

ERIC Educational Resources Information Center

Munroe, Lloyd

2015-01-01

This paper describes a pedagogical framework that teachers can use to support students who are engaged in solving open-ended problems, by explaining how two Japanese expert teachers successfully apply open-ended problems in their mathematics class. The Open-Ended Approach (OPA) framework consists of two main sections: Understanding Mathematical…

A software framework for real-time multi-modal detection of microsleeps.

PubMed

Knopp, Simon J; Bones, Philip J; Weddell, Stephen J; Jones, Richard D

2017-09-01

A software framework is described which was designed to process EEG, video of one eye, and head movement in real time, towards achieving early detection of microsleeps for prevention of fatal accidents, particularly in transport sectors. The framework is based around a pipeline structure with user-replaceable signal processing modules. This structure can encapsulate a wide variety of feature extraction and classification techniques and can be applied to detecting a variety of aspects of cognitive state. Users of the framework can implement signal processing plugins in C++ or Python. The framework also provides a graphical user interface and the ability to save and load data to and from arbitrary file formats. Two small studies are reported which demonstrate the capabilities of the framework in typical applications: monitoring eye closure and detecting simulated microsleeps. While specifically designed for microsleep detection/prediction, the software framework can be just as appropriately applied to (i) other measures of cognitive state and (ii) development of biomedical instruments for multi-modal real-time physiological monitoring and event detection in intensive care, anaesthesiology, cardiology, neurosurgery, etc. The software framework has been made freely available for researchers to use and modify under an open source licence.

A computational framework for automation of point defect calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goyal, Anuj; Gorai, Prashun; Peng, Haowei

We have developed a complete and rigorously validated open-source Python framework to automate point defect calculations using density functional theory. Furthermore, the framework provides an effective and efficient method for defect structure generation, and creation of simple yet customizable workflows to analyze defect calculations. This package provides the capability to compute widely-accepted correction schemes to overcome finite-size effects, including (1) potential alignment, (2) image-charge correction, and (3) band filling correction to shallow defects. Using Si, ZnO and In2O3 as test examples, we demonstrate the package capabilities and validate the methodology.

A computational framework for automation of point defect calculations

DOE PAGES

Goyal, Anuj; Gorai, Prashun; Peng, Haowei; ...

2017-01-13

We have developed a complete and rigorously validated open-source Python framework to automate point defect calculations using density functional theory. Furthermore, the framework provides an effective and efficient method for defect structure generation, and creation of simple yet customizable workflows to analyze defect calculations. This package provides the capability to compute widely-accepted correction schemes to overcome finite-size effects, including (1) potential alignment, (2) image-charge correction, and (3) band filling correction to shallow defects. Using Si, ZnO and In2O3 as test examples, we demonstrate the package capabilities and validate the methodology.

gadfly: A pandas-based Framework for Analyzing GADGET Simulation Data

NASA Astrophysics Data System (ADS)

Hummel, Jacob A.

2016-11-01

We present the first public release (v0.1) of the open-source gadget Dataframe Library: gadfly. The aim of this package is to leverage the capabilities of the broader python scientific computing ecosystem by providing tools for analyzing simulation data from the astrophysical simulation codes gadget and gizmo using pandas, a thoroughly documented, open-source library providing high-performance, easy-to-use data structures that is quickly becoming the standard for data analysis in python. Gadfly is a framework for analyzing particle-based simulation data stored in the HDF5 format using pandas DataFrames. The package enables efficient memory management, includes utilities for unit handling, coordinate transformations, and parallel batch processing, and provides highly optimized routines for visualizing smoothed-particle hydrodynamics data sets.

X-ray structures of LeuT in substrate-free outward-open and apo inward-open states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krishnamurthy, Harini; Gouaux, Eric

2012-08-09

Neurotransmitter sodium symporters are integral membrane proteins that remove chemical transmitters from the synapse and terminate neurotransmission mediated by serotonin, dopamine, noradrenaline, glycine and GABA ({gamma}-aminobutyric acid). Crystal structures of the bacterial homologue, LeuT, in substrate-bound outward-occluded and competitive inhibitor-bound outward-facing states have advanced our mechanistic understanding of neurotransmitter sodium symporters but have left fundamental questions unanswered. Here we report crystal structures of LeuT mutants in complexes with conformation-specific antibody fragments in the outward-open and inward-open states. In the absence of substrate but in the presence of sodium the transporter is outward-open, illustrating how the binding of substrate closes themore » extracellular gate through local conformational changes: hinge-bending movements of the extracellular halves of transmembrane domains 1, 2 and 6, together with translation of extracellular loop 4. The inward-open conformation, by contrast, involves large-scale conformational changes, including a reorientation of transmembrane domains 1, 2, 5, 6 and 7, a marked hinge bending of transmembrane domain 1a and occlusion of the extracellular vestibule by extracellular loop 4. These changes close the extracellular gate, open an intracellular vestibule, and largely disrupt the two sodium sites, thus providing a mechanism by which ions and substrate are released to the cytoplasm. The new structures establish a structural framework for the mechanism of neurotransmitter sodium symporters and their modulation by therapeutic and illicit substances.« less

The influence of different screw tightening forces on the vertical misfit of implant-supported frameworks.

PubMed

Vasconcellos, Diego Klee de; Bottino, Marco Antonio; Nishioka, Renato Sussumu; Valandro, Luiz Felipe; Costa, Elza Maria Valadares da

2005-06-01

The present in vitro study was designed to compare the differences in the vertical misfit of implant-supported frameworks using three different forces for tightening the bridge locking screws: fastening by hand until first resistance, and using torque drivers with 10 and 20Ncm. The investigation was conducted based on the results given by 9 six-unit nickel-chromium (2 abutments/ 4 pontics) screw-retained implant-supported frameworks. The structures were exposed to simulated porcelain firings. The marginal misfit measurements were made using a traveling measuring microscope at selected screw tightening forces: fastening by hand until first resistance, and using torque drivers with 10 and 20Ncm. The results were submitted to one-way ANOVA with repeated measures on one factor, and post hoc pairwise comparisons using Tukey test (5%). The mean marginal misfit of the frameworks, fastening the screws by hand until first resistance, was 41.56µm (SD±12.45µm). The use of torque driver devices caused a significant reduction in marginal opening (p<0.05). With the lowest torque available (10Ncm), the mean marginal discrepancy at the abutment-framework interface was reduced an average of 52% to a mean marginal opening of 19.71µm (SD±2.97µm). After the use of the 20Ncm torque driver, the mean marginal discrepancy of the frameworks was reduced an average of 69% to a mean marginal opening of 12.82µm (SD±4.0µm). Comparing the use of torque drivers with 10 and 20 Ncm torque, the means are not significantly different from one another. The seating force has an important effect on the vertical misfit measurements, once it may considerably narrow the vertical misfit gaps at the abutment-framework interface, thus leading to a misjudgment of the real marginal situation.

A distributed finite-element modeling and control approach for large flexible structures

NASA Technical Reports Server (NTRS)

Young, K. D.

1989-01-01

An unconventional framework is described for the design of decentralized controllers for large flexible structures. In contrast to conventional control system design practice which begins with a model of the open loop plant, the controlled plant is assembled from controlled components in which the modeling phase and the control design phase are integrated at the component level. The developed framework is called controlled component synthesis (CCS) to reflect that it is motivated by the well developed Component Mode Synthesis (CMS) methods which were demonstrated to be effective for solving large complex structural analysis problems for almost three decades. The design philosophy behind CCS is also closely related to that of the subsystem decomposition approach in decentralized control.

"Deviance, Selves and Others" Revisited.

ERIC Educational Resources Information Center

Stryker, Sheldon; Craft, Elizabeth A.

1982-01-01

Criticizes conceptual underpinnings of a 1970 study by Schwartz and Stryker. Proposes a framework more sensitive to interconnections between social structure and self-image and argues for a dimension of openness (to the impact of new relationships and experiences) that speaks to the modifiability of self-images. (CMG)

Structure-directing effects of ionic liquids in the ionothermal synthesis of metal-organic frameworks.

PubMed

Vaid, Thomas P; Kelley, Steven P; Rogers, Robin D

2017-07-01

Traditional synthesis of metal-organic frameworks (MOFs) involves the reaction of a metal-containing precursor with an organic linker in an organic solvent at an elevated temperature, in what is termed a 'solvothermal' reaction. More recently, many examples have been reported of MOF synthesis in ionic liquids (ILs), rather than an organic solvent, in 'ionothermal' reactions. The high concentration of both cations and anions in an ionic liquid allows for the formation of new MOF structures in which the IL cation or anion or both are incorporated into the MOF. Most commonly, the IL cation is included in the open cavities of the MOF, countering the anionic charge of the MOF framework itself and acting as a template around which the MOF structure forms. Ionic liquids can also serve other structure-directing roles, for example, when an IL containing a single enantiomer of a chiral anion leads to a homochiral MOF, even though the IL anion is not itself incorporated into the MOF. A comprehensive review of ionothermal syntheses of MOFs, and the structure-directing effects of the ILs, is given.

Vigi4Med Scraper: A Framework for Web Forum Structured Data Extraction and Semantic Representation

PubMed Central

Audeh, Bissan; Beigbeder, Michel; Zimmermann, Antoine; Jaillon, Philippe; Bousquet, Cédric

2017-01-01

The extraction of information from social media is an essential yet complicated step for data analysis in multiple domains. In this paper, we present Vigi4Med Scraper, a generic open source framework for extracting structured data from web forums. Our framework is highly configurable; using a configuration file, the user can freely choose the data to extract from any web forum. The extracted data are anonymized and represented in a semantic structure using Resource Description Framework (RDF) graphs. This representation enables efficient manipulation by data analysis algorithms and allows the collected data to be directly linked to any existing semantic resource. To avoid server overload, an integrated proxy with caching functionality imposes a minimal delay between sequential requests. Vigi4Med Scraper represents the first step of Vigi4Med, a project to detect adverse drug reactions (ADRs) from social networks founded by the French drug safety agency Agence Nationale de Sécurité du Médicament (ANSM). Vigi4Med Scraper has successfully extracted greater than 200 gigabytes of data from the web forums of over 20 different websites. PMID:28122056

Non-local currents and the structure of eigenstates in planar discrete systems with local symmetries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Röntgen, M., E-mail: mroentge@physnet.uni-hamburg.de; Morfonios, C.V., E-mail: christian.morfonios@physnet.uni-hamburg.de; Diakonos, F.K., E-mail: fdiakono@phys.uoa.gr

Local symmetries are spatial symmetries present in a subdomain of a complex system. By using and extending a framework of so-called non-local currents that has been established recently, we show that one can gain knowledge about the structure of eigenstates in locally symmetric setups through a Kirchhoff-type law for the non-local currents. The framework is applicable to all discrete planar Schrödinger setups, including those with non-uniform connectivity. Conditions for spatially constant non-local currents are derived and we explore two types of locally symmetric subsystems in detail, closed-loops and one-dimensional open ended chains. We find these systems to support locally similarmore » or even locally symmetric eigenstates. - Highlights: • We extend the framework of non-local currents to discrete planar systems. • Structural information about the eigenstates is gained. • Conditions for the constancy of non-local currents are derived. • We use the framework to design two types of example systems featuring locally symmetric eigenstates.« less

OpenCluster: A Flexible Distributed Computing Framework for Astronomical Data Processing

NASA Astrophysics Data System (ADS)

Wei, Shoulin; Wang, Feng; Deng, Hui; Liu, Cuiyin; Dai, Wei; Liang, Bo; Mei, Ying; Shi, Congming; Liu, Yingbo; Wu, Jingping

2017-02-01

The volume of data generated by modern astronomical telescopes is extremely large and rapidly growing. However, current high-performance data processing architectures/frameworks are not well suited for astronomers because of their limitations and programming difficulties. In this paper, we therefore present OpenCluster, an open-source distributed computing framework to support rapidly developing high-performance processing pipelines of astronomical big data. We first detail the OpenCluster design principles and implementations and present the APIs facilitated by the framework. We then demonstrate a case in which OpenCluster is used to resolve complex data processing problems for developing a pipeline for the Mingantu Ultrawide Spectral Radioheliograph. Finally, we present our OpenCluster performance evaluation. Overall, OpenCluster provides not only high fault tolerance and simple programming interfaces, but also a flexible means of scaling up the number of interacting entities. OpenCluster thereby provides an easily integrated distributed computing framework for quickly developing a high-performance data processing system of astronomical telescopes and for significantly reducing software development expenses.

Conjugated organic framework with three-dimensionally ordered stable structure and delocalized π clouds

NASA Astrophysics Data System (ADS)

Guo, Jia; Xu, Yanhong; Jin, Shangbin; Chen, Long; Kaji, Toshihiko; Honsho, Yoshihito; Addicoat, Matthew A.; Kim, Jangbae; Saeki, Akinori; Ihee, Hyotcherl; Seki, Shu; Irle, Stephan; Hiramoto, Masahiro; Gao, Jia; Jiang, Donglin

2013-11-01

Covalent organic frameworks are a class of crystalline organic porous materials that can utilize π-π-stacking interactions as a driving force for the crystallization of polygonal sheets to form layered frameworks and ordered pores. However, typical examples are chemically unstable and lack intrasheet π-conjugation, thereby significantly limiting their applications. Here we report a chemically stable, electronically conjugated organic framework with topologically designed wire frameworks and open nanochannels, in which the π conjugation-spans the two-dimensional sheets. Our framework permits inborn periodic ordering of conjugated chains in all three dimensions and exhibits a striking combination of properties: chemical stability, extended π-delocalization, ability to host guest molecules and hole mobility. We show that the π-conjugated organic framework is useful for high on-off ratio photoswitches and photovoltaic cells. Therefore, this strategy may constitute a step towards realizing ordered semiconducting porous materials for innovations based on two-dimensionally extended π systems.

An Extensible "SCHEMA-LESS" Database Framework for Managing High-Throughput Semi-Structured Documents

NASA Technical Reports Server (NTRS)

Maluf, David A.; Tran, Peter B.

2003-01-01

Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object-oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK, is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword search of records spanning across both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semistructured documents existing within NASA enterprises. Today, NETMARK is a flexible, high-throughput open database framework for managing, storing, and searching unstructured or semi-structured arbitrary hierarchal models, such as XML and HTML.

A malonitrile-functionalized metal-organic framework for hydrogen sulfide detection and selective amino acid molecular recognition

NASA Astrophysics Data System (ADS)

Li, Haiwei; Feng, Xiao; Guo, Yuexin; Chen, Didi; Li, Rui; Ren, Xiaoqian; Jiang, Xin; Dong, Yuping; Wang, Bo

2014-03-01

A novel porous polymeric fluorescence probe, MN-ZIF-90, has been designed and synthesized for quantitative hydrogen sulfide (H2S) fluorescent detection and highly selective amino acid recognition. This distinct crystalline structure, derived from rational design and malonitrile functionalization, can trigger significant enhancement of its fluorescent intensity when exposed to H2S or cysteine molecules. Indeed this new metal-organic framework (MOF) structure shows high selectivity of biothiols over other amino acids and exhibits favorable stability. Moreover, in vitro viability assays on HeLa cells show low cytotoxicity of MN-ZIF-90 and its imaging contrast efficiency is further demonstrated by fluorescence microscopy studies. This facile yet powerful strategy also offers great potential of using open-framework materials (i.e. MOFs) as the novel platform for sensing and other biological applications.

New anion-templated 3D heterobimetallic open frameworks based on lanthanide-carboxylate layers and copper pillars

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li Yunwu; Wang Yonghui; Li Yangguang

2008-06-15

A series of new three-dimensional (3D) lanthanide-transition metal (4f-3d) heterobimetallic open frameworks, [Ln{sub 2}(1,2-bdc){sub 2}(H{sub 2}O){sub 2} Cu(inic){sub 2}](ClO{sub 4}) (Ln=Eu (1), Tb (2), Nd (3) and Sm (4); 1,2-bdc=1,2-benzenedicarboxylate; Hinic=isonicotinic acid) have been hydrothermally synthesized and characterized by elemental analysis, IR, TG and single-crystal X-ray diffraction analysis. Compounds 1-4 are isostructural. They possess a new anion-templated 3D heterobimetallic open framework, which is observed for the first time in the {l_brace}Ln/TM/bdc/inic{r_brace} (TM=transition metal) system. Compounds 1 and 2 exhibit the characteristic fluorescent properties of Eu(III) and Tb(III), respectively. - Graphical abstract: A series of new anion-templated 3D heterobimetallic open frameworkmore » based on the lanthanide-carboxylate layers and copper(I)-inic pillars, [Ln{sub 2}(1,2-bdc){sub 2}(H{sub 2}O){sub 2}Cu(inic){sub 2}](ClO{sub 4}) (Ln=Eu (1), Tb (2), Nd (3) and Sm (4); 1,2-bdc=1,2-benzenedicarboxylate; Hinic=isonicotinic acid), have been hydrothermally synthesized and structurally characterized, among which compounds 1 and 2 exhibit good fluorescent properties.« less

High-throughput syntheses of iron phosphite open frameworks in ionic liquids

NASA Astrophysics Data System (ADS)

Wang, Zhixiu; Mu, Ying; Wang, Yilin; Bing, Qiming; Su, Tan; Liu, Jingyao

2017-02-01

Three open-framework iron phosphites: Feп5(NH4)2(HPO3)6 (1), Feп2Fe♯(NH4)(HPO3)4 (2) and Fe♯2(HPO3)3 (3) have been synthesized under ionothermal conditions. How the different synthesis parameters, such as the gel concentrations, synthetic times, reaction temperatures and solvents affect the products have been monitored by using high-throughput approaches. Within each type of experiment, relevant products have been investigated. The optimal reaction conditions are obtained from a series of experiments by high-throughput approaches. All the structures are determined by single-crystal X-ray diffraction analysis and further characterized by PXRD, TGA and FTIR analyses. Magnetic study reveals that those three compounds show interesting magnetic behavior at low temperature.

Targeting for Effect Analytical Framework for Counterland Operations

DTIC Science & Technology

1998-05-01

battlefield. Statistics from World War II show that in open terrain about 75 percent of combat casualties were caused by artillery; in mixed terrain this...34Petroleum as a Center of Gravity," Strategic Structures AY 96 Coursebook (Maxwell AFB, Ala.: Air Command and Staff College, 1996), 628. 31. Dunnigan, 458

Extra-large pore zeolite (ITQ-40) with the lowest framework density containing double four- and double three-rings

PubMed Central

Díaz-Cabañas, M. J.; Jiang, J.; Afeworki, M.; Dorset, D. L.; Soled, S. L.; Strohmaier, K. G.

2010-01-01

The first zeolite structure (ITQ-40) that contains double four (D4) and double three (D3) member ring secondary building units has been synthesized by introducing Ge and NH4F and working in concentrated synthesis gels. It is the first time that D3-Rs have been observed in a zeolite structure. As was previously analyzed [Brunner GO, Meier, WM (1989) Nature 337:146–147], such a structure has a very low framework density (10.1 T/1,000 Å3). Indeed, ITQ-40 has the lowest framework density ever achieved in oxygen-containing zeolites. Furthermore, it contains large pore openings, i.e., 15-member rings parallel to the [001] hexagonal axis and 16-member ring channels perpendicular to this axis. The results presented here push ahead the possibilities of zeolites for uses in electronics, control delivery of drugs and chemicals, as well as for catalysis. PMID:20660773

Rapid enrichment of rare-earth metals by carboxymethyl cellulose-based open-cellular hydrogel adsorbent from HIPEs template.

PubMed

Zhu, Yongfeng; Wang, Wenbo; Zheng, Yian; Wang, Feng; Wang, Aiqin

2016-04-20

A series of monolithic open-cellular hydrogel adsorbents based on carboxymethylcellulose (CMC) were prepared through high internal phase emulsions (HIPEs) and used to enrich the rare-earth metals La(3+) and Ce(3+). The changes of pore structure, and the effects of pH, contact time, initial concentration on the adsorption performance were systematically studied. The results show that the as-prepared monolithic hydrogel adsorbents possess good open-cellular framework structure and have fast adsorption kinetics and high adsorption capacity for La(3+) and Ce(3+). The involved adsorption system can reach equilibrium within 30min and the maximal adsorption capacity is determined to be 384.62mg/g for La(3+) and 333.33mg/g for Ce(3+). Moreover, these porous hydrogel adsorbents show an excellent adsorptive reusability for La(3+) and Ce(3+) through five adsorption-desorption cycles. Such a pore hierarchy structure makes this monolithic open-cellular hydrogel adsorbent be an effective adsorbent for effective enrichment of La(3+) and Ce(3+) from aqueous solution. Copyright © 2015 Elsevier Ltd. All rights reserved.

General and simple approach for control cage and cylindrical mesopores, and thermal/hydrothermal stable frameworks.

PubMed

El-Safty, Sherif A; Mizukami, Fujio; Hanaoka, Takaaki

2005-05-19

Highly ordered cage and cylindrical mesoporeous silica monoliths (HOM) with 2- and 3-dimensional (2D and 3D, respectively) structures, mesopore/micropore volumes, and thick-walled frameworks were successfully fabricated by instant direct templating of lyotropic phases of copolymer (EO(m)-PO(n)-EO(m)) surfactants. Large cage-like pores with uniform constriction sizes up to 10 nm and open cylindrical channel-like mesopores can be easily achieved by this simple and efficient synthesis design. Our results show that the cage-like pores could be fabricated at relatively lower copolymer concentrations used in the lyotropic phase domains at copolymer/TMOS ratios of 35 wt %. These ordered cage pore architectures underwent transition to open-cylindrical pores by increasing the copolymer concentration. High EO/PO block copolymers, in general, were crucially affected on the increase of the interior cavity sizes and on the stability of the cage mesopore characters. However, for F108 (EO(141)PO(44)EO(141)) systems, the fabrication of ordered and stable cage pore monoliths was achieved with significantly higher copolymer concentrations up to 90 wt %. Interestingly, the effective copolymer molecular nature was also observed in the ability to design various ordered mesophase geometries in large domain sizes. Our findings here show evidence that the synthetic strategy provides realistic control over a wide range of mesostructured phase geometries and their extended long-range ordering in the final replicas of the silica monolith frameworks. In addition, the HOM silica monoliths exhibited considerable structural stability against higher thermal temperature (up to 1000 degrees C) and longer hydrothermal treatment times under boiling water and steam. The remarkable structural findings of 3D frameworks, transparent monoliths, and micropores combined with large cage- and cylindrical-like mesopores are expected to find promising uses in materials chemistry.

Automatic Tool for Local Assembly Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whole community shotgun sequencing of total DNA (i.e. metagenomics) and total RNA (i.e. metatranscriptomics) has provided a wealth of information in the microbial community structure, predicted functions, metabolic networks, and is even able to reconstruct complete genomes directly. Here we present ATLAS (Automatic Tool for Local Assembly Structures) a comprehensive pipeline for assembly, annotation, genomic binning of metagenomic and metatranscriptomic data with an integrated framework for Multi-Omics. This will provide an open source tool for the Multi-Omic community at large.

Selective CO2 adsorption by a new metal-organic framework: synergy between open metal sites and a charged imidazolinium backbone.

PubMed

Kochetygov, Ilia; Bulut, Safak; Asgari, Mehrdad; Queen, Wendy L

2018-05-30

Metal-organic frameworks (MOFs) are porous, tunable crystalline materials that are attracting widespread scientific attention for their potential use in post-combustion CO2 capture. In this work, we report the synthesis of a new ligand, 1,3-bis(4-carboxyphenyl)-4,5-dihydro-1H-imidazol-3-ium tetrafluoroborate, H2Sp5-BF4, that is subsequently used for the construction of a novel MOF, Cu-Sp5-EtOH. This highly crystalline material has a charged framework that is expected to give rise to high CO2/N2 selectivity. However, the pores of the parent structure could not be accessed due to the presence of strongly coordinated ethanol molecules. After solvent exchange with methanol and subsequently heating Cu-Sp5-MeOH under vacuum, we are able to liberate the solvent providing other small molecules like CO2 access to the inside of the now porous structure, Cu-Sp5. The combination of open metal sites and framework charge leads to an exceptionally high CO2/N2 selectivity, as determined by Ideal Adsorbed Solution Theory (IAST) calculations performed on single-component adsorption isotherms. The CO2/N2 selectivity of Cu-Sp5 reaches a value of over 200 at pressures typically found in post-combustion flue gas (0.15 bar CO2/0.85 bar N2), a value that is among the highest reported to date.

An open ecosystem engagement strategy through the lens of global food safety

PubMed Central

Stacey, Paul; Fons, Garin; Bernardo, Theresa M

2015-01-01

The Global Food Safety Partnership (GFSP) is a public/private partnership established through the World Bank to improve food safety systems through a globally coordinated and locally-driven approach. This concept paper aims to establish a framework to help GFSP fully leverage the potential of open models. In preparing this paper the authors spoke to many different GFSP stakeholders who asked questions about open models such as: what is it?what’s in it for me?why use an open rather than a proprietary model?how will open models generate equivalent or greater sustainable revenue streams compared to the current “traditional” approaches?  This last question came up many times with assertions that traditional service providers need to see opportunity for equivalent or greater revenue dollars before they will buy-in. This paper identifies open value propositions for GFSP stakeholders and proposes a framework for creating and structuring that value. Open Educational Resources (OER) were the primary open practice GFSP partners spoke to us about, as they provide a logical entry point for collaboration. Going forward, funders should consider requiring that educational resources and concomitant data resulting from their sponsorship should be open, as a public good. There are, however, many other forms of open practice that bring value to the GFSP. Nine different open strategies and tactics (Appendix A) are described, including: open content (including OER and open courseware), open data, open access (research), open government, open source software, open standards, open policy, open licensing and open hardware. It is recommended that all stakeholders proactively pursue "openness" as an operating principle. This paper presents an overall GFSP Open Ecosystem Engagement Strategy within which specific local case examples can be situated. Two different case examples, China and Colombia, are presented to show both project-based and crowd-sourced, direct-to-public paths through this ecosystem. PMID:26213614

Tuning the formations of metal-1,3,5-benzenetricarboxylate frameworks via the assistance of amino acids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lei, Xiao-Ping; Lian, Ting-Ting; Chen, Shu-Mei, E-mail: csm@fzu.edu.cn

Seven new metal-1,3,5-benzenetricarboxylate coordination polymers have been synthesized by modification of auxiliary components during the assembly reactions. Their structures have been determined by single-crystal X-ray diffraction analyses and further characterized by XRD and TGA. Interestingly, they show fascinating topological structures. Compounds 1 and 2 possess the undulating layer structure with 3-connected hcb network and (3,6)-connected kgd network. Compound 3 possesses three-dimensional (3D) pillared-layer structure with 3-connected 2-fold interpenetrating srs net. Compound 4 also has the 3D 2-fold interpenetrating pillared-layer structure; however, it has (3,5)-connected hms topology because the Cd(II) center is 5-connected. Compound 5 possess 3D structure through hydrogen bondingmore » interactions between ladder-like layers. Compounds 6 and 7 have the similar 3D frameworks with 4-connected umc net and (3,7)-connected (3.4.5)(3{sup 2}.4{sup 6}.5{sup 5}.6{sup 8}) topology, respectively. The photoluminescent properties of compounds 2–7 were also investigated. - Graphical abstract: Presented here are seven new metal-1,3,5-benzenetricarboxylate coordination polymers with diverse structures from 2D layers to 3D open frameworks. The synthesis and structural diversity of these compounds are determined by the additional amino acids as unusual buffering agents. - Highlights: • Structural diversity of metal-1,3,5-benzenetricarboxylate frameworks. • Tuning structural topologies of MOFs via the assistance of amino acids. • Amino acids as unusual buffering agents for the synthesis of MOFs.« less

Materials Knowledge Systems in Python - A Data Science Framework for Accelerated Development of Hierarchical Materials.

PubMed

Brough, David B; Wheeler, Daniel; Kalidindi, Surya R

2017-03-01

There is a critical need for customized analytics that take into account the stochastic nature of the internal structure of materials at multiple length scales in order to extract relevant and transferable knowledge. Data driven Process-Structure-Property (PSP) linkages provide systemic, modular and hierarchical framework for community driven curation of materials knowledge, and its transference to design and manufacturing experts. The Materials Knowledge Systems in Python project (PyMKS) is the first open source materials data science framework that can be used to create high value PSP linkages for hierarchical materials that can be leveraged by experts in materials science and engineering, manufacturing, machine learning and data science communities. This paper describes the main functions available from this repository, along with illustrations of how these can be accessed, utilized, and potentially further refined by the broader community of researchers.

Materials Knowledge Systems in Python - A Data Science Framework for Accelerated Development of Hierarchical Materials

PubMed Central

Brough, David B; Wheeler, Daniel; Kalidindi, Surya R.

2017-01-01

There is a critical need for customized analytics that take into account the stochastic nature of the internal structure of materials at multiple length scales in order to extract relevant and transferable knowledge. Data driven Process-Structure-Property (PSP) linkages provide systemic, modular and hierarchical framework for community driven curation of materials knowledge, and its transference to design and manufacturing experts. The Materials Knowledge Systems in Python project (PyMKS) is the first open source materials data science framework that can be used to create high value PSP linkages for hierarchical materials that can be leveraged by experts in materials science and engineering, manufacturing, machine learning and data science communities. This paper describes the main functions available from this repository, along with illustrations of how these can be accessed, utilized, and potentially further refined by the broader community of researchers. PMID:28690971

Open Group Transformations

NASA Astrophysics Data System (ADS)

Batalin, Igor; Marnelius, Robert

Open groups whose generators are in arbitrary involutions may be quantized within a ghost extended framework in terms of a nilpotent BFV-BRST charge operator. Previously we have shown that generalized quantum Maurer-Cartan equations for arbitrary open groups may be extracted from the quantum connection operators and that they also follow from a simple quantum master equation involving an extended nilpotent BFV-BRST charge and a master charge. Here we give further details of these results. In addition we establish the general structure of the solutions of the quantum master equation. We also construct an extended formulation whose properties are determined by the extended BRST charge in the master equation.

AMBIT RESTful web services: an implementation of the OpenTox application programming interface.

PubMed

Jeliazkova, Nina; Jeliazkov, Vedrin

2011-05-16

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations.The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems.

AMBIT RESTful web services: an implementation of the OpenTox application programming interface

PubMed Central

2011-01-01

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations. The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems. PMID:21575202

Nektar++: An open-source spectral/ hp element framework

NASA Astrophysics Data System (ADS)

Cantwell, C. D.; Moxey, D.; Comerford, A.; Bolis, A.; Rocco, G.; Mengaldo, G.; De Grazia, D.; Yakovlev, S.; Lombard, J.-E.; Ekelschot, D.; Jordi, B.; Xu, H.; Mohamied, Y.; Eskilsson, C.; Nelson, B.; Vos, P.; Biotto, C.; Kirby, R. M.; Sherwin, S. J.

2015-07-01

Nektar++ is an open-source software framework designed to support the development of high-performance scalable solvers for partial differential equations using the spectral/ hp element method. High-order methods are gaining prominence in several engineering and biomedical applications due to their improved accuracy over low-order techniques at reduced computational cost for a given number of degrees of freedom. However, their proliferation is often limited by their complexity, which makes these methods challenging to implement and use. Nektar++ is an initiative to overcome this limitation by encapsulating the mathematical complexities of the underlying method within an efficient C++ framework, making the techniques more accessible to the broader scientific and industrial communities. The software supports a variety of discretisation techniques and implementation strategies, supporting methods research as well as application-focused computation, and the multi-layered structure of the framework allows the user to embrace as much or as little of the complexity as they need. The libraries capture the mathematical constructs of spectral/ hp element methods, while the associated collection of pre-written PDE solvers provides out-of-the-box application-level functionality and a template for users who wish to develop solutions for addressing questions in their own scientific domains.

Synthesis and time-resolved structural characterization of framework and mineral sulfides

NASA Astrophysics Data System (ADS)

Cahill, Christopher Langley

A new class of open-framework organic/inorganic hybrid materials based on In-S chemistry has been discovered. The compounds therein exhibit unprecedented structural diversity compared to known porous sulfides, primarily due to variation in framework building units. Further, large increases in pore dimensions (vs. zeolites, for example) are observed as these materials consist of comer and edge linked clusters, e.g. In10S20, In9S17, In4S10 and In6S 15. Choice of organic structure directing agents (templates) and careful control of reaction conditions (temperature, pH) both in the In-S and Ge-S systems is shown not only to dictate which building unit will form, but also to direct the resulting framework topology. Several of the compounds described herein crystallize either as powders, or as crystals too small for standard in-house X-ray structural analysis. Diffraction experiments have thus required synchrotron based single crystal techniques for structure determination. Further, certain reaction mixture compositions result in multi-phase end products, the formation pathways of which have been studied with time resolved, in situ synchrotron powder diffraction. An extension of the applicability of the in situ techniques investigated the role of oxygen in hydrothermal systems. Oxidation state is proposed to dictate speciation in the Ni-Ge-S system and to promote phase transformations in the Fe-S mineral system.

An Open Data Platform in the framework of the EGI-LifeWatch Competence Center

NASA Astrophysics Data System (ADS)

Aguilar Gómez, Fernando; de Lucas, Jesús Marco; Yaiza Rodríguez Marrero, Ana

2016-04-01

The working pilot of an Open Data Platform supporting the full data cycle in research is presented. It aims to preserve knowledge explicitly, starting with the description of the Case Studies, and integrating data and software management and preservation on equal basis. The uninterrupted support in the chain starts at the data acquisition level and covers up to the support for reuse and publication in an open framework, providing integrity and provenance controls. The Lifewatch Open Science Framework is a pilot web portal developed in collaboration with different commercial companies that tries to enrich and integrate different data lifecycle-related tools in order to address the management of the different steps: data planning, gathering, storing, curation, preservation, sharing, discovering, etc. To achieve this goal, the platform includes the following features: -Data Management Planning. Tool to set up an structure of the data, including what data will be generated, how it will be exploited, re-used, curated, preserved, etc. It has a semantic approach: includes reference to ontologies in order to express what data will be gathered. -Close to instrumentation. The portal includes a distributed storage system that can be used both for storing data from instruments and output data from analysis. All that data can be shared -Analysis. Resources from EGI Federated Cloud are accessible within the portal, so that users can exploit computing resources to perform analysis and other processes, including workflows. -Preservation. Data can be preserved in different systems and DOIs can be minted not only for datasets but also for software, DMPs, etc. The presentation will show the different components of the framework as well as how it can be extrapolated to other communities.

Examining Co-Teaching through a Socio-Technical Systems Lens

ERIC Educational Resources Information Center

Isherwood, Robert S.; Barger-Anderson, Richard; Erickson, Matthew

2012-01-01

Qualitative research was conducted in a large suburban school district implementing co-teaching as a new service delivery model for special education. Researchers examined the changes that resulted from the new service delivery model using a socio-technical systems lens. This framework views schools as open systems that contain a structural, task,…

Curriculum Reform in Post-Soviet Armenia: Balancing Local and Global Contexts in Armenian Secondary Schools

ERIC Educational Resources Information Center

Terzian, Shelley

2010-01-01

Structured according to the conceptual frameworks of nationalism and globalization, this study examined relationships between and among the Armenian Ministry of Education, the World Bank, the Open Society Institute Assistance Foundation-Armenia, and Armenian secondary school teachers and principals from 1991 to the present. Each group played a…

Competence-Based Approach in Value Chain Processes

NASA Astrophysics Data System (ADS)

Azevedo, Rodrigo Cambiaghi; D'Amours, Sophie; Rönnqvist, Mikael

There is a gap between competence theory and value chain processes frameworks. While individually considered as core elements in contemporary management thinking, the integration of the two concepts is still lacking. We claim that this integration would allow for the development of more robust business models by structuring value chain activities around aspects such as capabilities and skills, as well as individual and organizational knowledge. In this context, the objective of this article is to reduce this gap and consequently open a field for further improvements of value chain processes frameworks.

Implementation of highly parallel and large scale GW calculations within the OpenAtom software

NASA Astrophysics Data System (ADS)

Ismail-Beigi, Sohrab

The need to describe electronic excitations with better accuracy than provided by band structures produced by Density Functional Theory (DFT) has been a long-term enterprise for the computational condensed matter and materials theory communities. In some cases, appropriate theoretical frameworks have existed for some time but have been difficult to apply widely due to computational cost. For example, the GW approximation incorporates a great deal of important non-local and dynamical electronic interaction effects but has been too computationally expensive for routine use in large materials simulations. OpenAtom is an open source massively parallel ab initiodensity functional software package based on plane waves and pseudopotentials (http://charm.cs.uiuc.edu/OpenAtom/) that takes advantage of the Charm + + parallel framework. At present, it is developed via a three-way collaboration, funded by an NSF SI2-SSI grant (ACI-1339804), between Yale (Ismail-Beigi), IBM T. J. Watson (Glenn Martyna) and the University of Illinois at Urbana Champaign (Laxmikant Kale). We will describe the project and our current approach towards implementing large scale GW calculations with OpenAtom. Potential applications of large scale parallel GW software for problems involving electronic excitations in semiconductor and/or metal oxide systems will be also be pointed out.

Probing the structural flexibility of MOFs by constructing metal oxide@MOF-based heterostructures for size-selective photoelectrochemical response

NASA Astrophysics Data System (ADS)

Zhan, Wenwen; He, Yue; Guo, Jiangbin; Chen, Luning; Kong, Xiangjian; Zhao, Haixia; Kuang, Qin; Xie, Zhaoxiong; Zheng, Lansun

2016-07-01

It is becoming a challenge to achieve simpler characterization and wider application of flexible metal organic frameworks (MOFs) exhibiting the gate-opening or breathing behavior. Herein, we designed an intelligent MOF-based system where the gate-opening or breathing behavior of MOFs can be facially visualized in solution. Two types of metal oxide@MOF core-shell heterostructures, ZnO@ZIF-7 and ZnO@ZIF-71, were prepared using ZnO nanorods as self-sacrificial templates. The structural flexibility of both the MOFs can be easily judged from the distinct molecular-size-related formation modes and photoelectrochemical performances between the two ZnO@ZIF heterostructures. Moreover, the rotational dynamics of the flexible parts of ZIF-7 were studied by analyzing the intrinsic physical properties, such as dielectric constants, of the structure. The present work reminds us to pay particular attention to the influences of the structural flexibility of MOFs on the structure and properties of MOF-involved heterostructures in future studies.It is becoming a challenge to achieve simpler characterization and wider application of flexible metal organic frameworks (MOFs) exhibiting the gate-opening or breathing behavior. Herein, we designed an intelligent MOF-based system where the gate-opening or breathing behavior of MOFs can be facially visualized in solution. Two types of metal oxide@MOF core-shell heterostructures, ZnO@ZIF-7 and ZnO@ZIF-71, were prepared using ZnO nanorods as self-sacrificial templates. The structural flexibility of both the MOFs can be easily judged from the distinct molecular-size-related formation modes and photoelectrochemical performances between the two ZnO@ZIF heterostructures. Moreover, the rotational dynamics of the flexible parts of ZIF-7 were studied by analyzing the intrinsic physical properties, such as dielectric constants, of the structure. The present work reminds us to pay particular attention to the influences of the structural flexibility of MOFs on the structure and properties of MOF-involved heterostructures in future studies. Electronic supplementary information (ESI) available: Experimental details, XRD patterns and SEM images of products in other reactions, concentration-dependent photocurrent responses, and supplementary data of dielectric measurements. See DOI: 10.1039/c6nr02257j

Heptagraphene: Tunable dirac cones in a graphitic structure

DOE PAGES

Lopez-Bezanilla, Alejandro; Martin, Ivar; Littlewood, Peter B.

2016-09-13

Here, we predict the existence and dynamical stability of heptagraphene, a new graphitic structure formed of rings of 10 carbon atoms bridged by carbene groups yielding seven-membered rings. Despite the rectangular unit cell, the band structure is topologically equivalent to that of strongly distorted graphene. Density-functional-theory calculations demonstrate that heptagraphene has Dirac cones on symmetry lines that are robust against biaxial strain but which open a gap under shear. At high deformation values bond reconstructions lead to different electronic band arrangements in dynamically stable configurations. Within a tight-binding framework this richness of the electronic behavior is identified as a directmore » consequence of the symmetry breaking within the cell which, unlike other graphitic structures, leads to band gap opening. A combined approach of chemical and physical modification of graphene unit cell unfurls the opportunity to design carbon-based systems in which one aims to tune an electronic band gap.« less

Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter

NASA Astrophysics Data System (ADS)

Lee, Yongchan; Nishizawa, Tomohiro; Yamashita, Keitaro; Ishitani, Ryuichiro; Nureki, Osamu

2015-01-01

SWEET family proteins mediate sugar transport across biological membranes and play crucial roles in plants and animals. The SWEETs and their bacterial homologues, the SemiSWEETs, are related to the PQ-loop family, which is characterized by highly conserved proline and glutamine residues (PQ-loop motif). Although the structures of the bacterial SemiSWEETs were recently reported, the conformational transition and the significance of the conserved motif in the transport cycle have remained elusive. Here we report crystal structures of SemiSWEET from Escherichia coli, in the both inward-open and outward-open states. A structural comparison revealed that SemiSWEET undergoes an intramolecular conformational change in each protomer. The conserved PQ-loop motif serves as a molecular hinge that enables the ‘binder clip-like’ motion of SemiSWEET. The present work provides the framework for understanding the overall transport cycles of SWEET and PQ-loop family proteins.

Modelling multimedia teleservices with OSI upper layers framework: Short paper

NASA Astrophysics Data System (ADS)

Widya, I.; Vanrijssen, E.; Michiels, E.

The paper presents the use of the concepts and modelling principles of the Open Systems Interconnection (OSI) upper layers structure in the modelling of multimedia teleservices. It puts emphasis on the revised Application Layer Structure (OSI/ALS). OSI/ALS is an object based reference model which intends to coordinate the development of application oriented services and protocols in a consistent and modular way. It enables the rapid deployment and integrated use of these services. The paper emphasizes further on the nesting structure defined in OSI/ALS which allows the design of scalable and user tailorable/controllable teleservices. OSI/ALS consistent teleservices are moreover implementable on communication platforms of different capabilities. An analysis of distributed multimedia architectures which can be found in the literature, confirms the ability of the OSI/ALS framework to model the interworking functionalities of teleservices.

NETMARK: A Schema-less Extension for Relational Databases for Managing Semi-structured Data Dynamically

NASA Technical Reports Server (NTRS)

Maluf, David A.; Tran, Peter B.

2003-01-01

Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object-oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK, is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword search of records spanning across both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semi-structured documents existing within NASA enterprises. Today, NETMARK is a flexible, high-throughput open database framework for managing, storing, and searching unstructured or semi-structured arbitrary hierarchal models, such as XML and HTML.

Conjugated organic framework with three-dimensionally ordered stable structure and delocalized π clouds

PubMed Central

Guo, Jia; Xu, Yanhong; Jin, Shangbin; Chen, Long; Kaji, Toshihiko; Honsho, Yoshihito; Addicoat, Matthew A.; Kim, Jangbae; Saeki, Akinori; Ihee, Hyotcherl; Seki, Shu; Irle, Stephan; Hiramoto, Masahiro; Gao, Jia; Jiang, Donglin

2013-01-01

Covalent organic frameworks are a class of crystalline organic porous materials that can utilize π–π-stacking interactions as a driving force for the crystallization of polygonal sheets to form layered frameworks and ordered pores. However, typical examples are chemically unstable and lack intrasheet π-conjugation, thereby significantly limiting their applications. Here we report a chemically stable, electronically conjugated organic framework with topologically designed wire frameworks and open nanochannels, in which the π conjugation-spans the two-dimensional sheets. Our framework permits inborn periodic ordering of conjugated chains in all three dimensions and exhibits a striking combination of properties: chemical stability, extended π-delocalization, ability to host guest molecules and hole mobility. We show that the π-conjugated organic framework is useful for high on-off ratio photoswitches and photovoltaic cells. Therefore, this strategy may constitute a step towards realizing ordered semiconducting porous materials for innovations based on two-dimensionally extended π systems. PMID:24220603

FRED (a Framework for Reconstructing Epidemic Dynamics): an open-source software system for modeling infectious diseases and control strategies using census-based populations.

PubMed

Grefenstette, John J; Brown, Shawn T; Rosenfeld, Roni; DePasse, Jay; Stone, Nathan T B; Cooley, Phillip C; Wheaton, William D; Fyshe, Alona; Galloway, David D; Sriram, Anuroop; Guclu, Hasan; Abraham, Thomas; Burke, Donald S

2013-10-08

Mathematical and computational models provide valuable tools that help public health planners to evaluate competing health interventions, especially for novel circumstances that cannot be examined through observational or controlled studies, such as pandemic influenza. The spread of diseases like influenza depends on the mixing patterns within the population, and these mixing patterns depend in part on local factors including the spatial distribution and age structure of the population, the distribution of size and composition of households, employment status and commuting patterns of adults, and the size and age structure of schools. Finally, public health planners must take into account the health behavior patterns of the population, patterns that often vary according to socioeconomic factors such as race, household income, and education levels. FRED (a Framework for Reconstructing Epidemic Dynamics) is a freely available open-source agent-based modeling system based closely on models used in previously published studies of pandemic influenza. This version of FRED uses open-access census-based synthetic populations that capture the demographic and geographic heterogeneities of the population, including realistic household, school, and workplace social networks. FRED epidemic models are currently available for every state and county in the United States, and for selected international locations. State and county public health planners can use FRED to explore the effects of possible influenza epidemics in specific geographic regions of interest and to help evaluate the effect of interventions such as vaccination programs and school closure policies. FRED is available under a free open source license in order to contribute to the development of better modeling tools and to encourage open discussion of modeling tools being used to evaluate public health policies. We also welcome participation by other researchers in the further development of FRED.

PRISM: An open source framework for the interactive design of GPU volume rendering shaders.

PubMed

Drouin, Simon; Collins, D Louis

2018-01-01

Direct volume rendering has become an essential tool to explore and analyse 3D medical images. Despite several advances in the field, it remains a challenge to produce an image that highlights the anatomy of interest, avoids occlusion of important structures, provides an intuitive perception of shape and depth while retaining sufficient contextual information. Although the computer graphics community has proposed several solutions to address specific visualization problems, the medical imaging community still lacks a general volume rendering implementation that can address a wide variety of visualization use cases while avoiding complexity. In this paper, we propose a new open source framework called the Programmable Ray Integration Shading Model, or PRISM, that implements a complete GPU ray-casting solution where critical parts of the ray integration algorithm can be replaced to produce new volume rendering effects. A graphical user interface allows clinical users to easily experiment with pre-existing rendering effect building blocks drawn from an open database. For programmers, the interface enables real-time editing of the code inside the blocks. We show that in its default mode, the PRISM framework produces images very similar to those produced by a widely-adopted direct volume rendering implementation in VTK at comparable frame rates. More importantly, we demonstrate the flexibility of the framework by showing how several volume rendering techniques can be implemented in PRISM with no more than a few lines of code. Finally, we demonstrate the simplicity of our system in a usability study with 5 medical imaging expert subjects who have none or little experience with volume rendering. The PRISM framework has the potential to greatly accelerate development of volume rendering for medical applications by promoting sharing and enabling faster development iterations and easier collaboration between engineers and clinical personnel.

PRISM: An open source framework for the interactive design of GPU volume rendering shaders

PubMed Central

Collins, D. Louis

2018-01-01

Direct volume rendering has become an essential tool to explore and analyse 3D medical images. Despite several advances in the field, it remains a challenge to produce an image that highlights the anatomy of interest, avoids occlusion of important structures, provides an intuitive perception of shape and depth while retaining sufficient contextual information. Although the computer graphics community has proposed several solutions to address specific visualization problems, the medical imaging community still lacks a general volume rendering implementation that can address a wide variety of visualization use cases while avoiding complexity. In this paper, we propose a new open source framework called the Programmable Ray Integration Shading Model, or PRISM, that implements a complete GPU ray-casting solution where critical parts of the ray integration algorithm can be replaced to produce new volume rendering effects. A graphical user interface allows clinical users to easily experiment with pre-existing rendering effect building blocks drawn from an open database. For programmers, the interface enables real-time editing of the code inside the blocks. We show that in its default mode, the PRISM framework produces images very similar to those produced by a widely-adopted direct volume rendering implementation in VTK at comparable frame rates. More importantly, we demonstrate the flexibility of the framework by showing how several volume rendering techniques can be implemented in PRISM with no more than a few lines of code. Finally, we demonstrate the simplicity of our system in a usability study with 5 medical imaging expert subjects who have none or little experience with volume rendering. The PRISM framework has the potential to greatly accelerate development of volume rendering for medical applications by promoting sharing and enabling faster development iterations and easier collaboration between engineers and clinical personnel. PMID:29534069

Tunable reaction potentials in open framework nanoparticle battery electrodes for grid-scale energy storage.

PubMed

Wessells, Colin D; McDowell, Matthew T; Peddada, Sandeep V; Pasta, Mauro; Huggins, Robert A; Cui, Yi

2012-02-28

The electrical energy grid has a growing need for energy storage to address short-term transients, frequency regulation, and load leveling. Though electrochemical energy storage devices such as batteries offer an attractive solution, current commercial battery technology cannot provide adequate power, and cycle life, and energy efficiency at a sufficiently low cost. Copper hexacyanoferrate and nickel hexacyanoferrate, two open framework materials with the Prussian Blue structure, were recently shown to offer ultralong cycle life and high-rate performance when operated as battery electrodes in safe, inexpensive aqueous sodium ion and potassium ion electrolytes. In this report, we demonstrate that the reaction potential of copper-nickel alloy hexacyanoferrate nanoparticles may be tuned by controlling the ratio of copper to nickel in these materials. X-ray diffraction, TEM energy dispersive X-ray spectroscopy, and galvanostatic electrochemical cycling of copper-nickel hexacyanoferrate reveal that copper and nickel form a fully miscible solution at particular sites in the framework without perturbing the structure. This allows copper-nickel hexacyanoferrate to reversibly intercalate sodium and potassium ions for over 2000 cycles with capacity retentions of 100% and 91%, respectively. The ability to precisely tune the reaction potential of copper-nickel hexacyanoferrate without sacrificing cycle life will allow the development of full cells that utilize the entire electrochemical stability window of aqueous sodium and potassium ion electrolytes.

Molpher: a software framework for systematic chemical space exploration

PubMed Central

2014-01-01

Background Chemical space is virtual space occupied by all chemically meaningful organic compounds. It is an important concept in contemporary chemoinformatics research, and its systematic exploration is vital to the discovery of either novel drugs or new tools for chemical biology. Results In this paper, we describe Molpher, an open-source framework for the systematic exploration of chemical space. Through a process we term ‘molecular morphing’, Molpher produces a path of structurally-related compounds. This path is generated by the iterative application of so-called ‘morphing operators’ that represent simple structural changes, such as the addition or removal of an atom or a bond. Molpher incorporates an optimized parallel exploration algorithm, compound logging and a two-dimensional visualization of the exploration process. Its feature set can be easily extended by implementing additional morphing operators, chemical fingerprints, similarity measures and visualization methods. Molpher not only offers an intuitive graphical user interface, but also can be run in batch mode. This enables users to easily incorporate molecular morphing into their existing drug discovery pipelines. Conclusions Molpher is an open-source software framework for the design of virtual chemical libraries focused on a particular mechanistic class of compounds. These libraries, represented by a morphing path and its surroundings, provide valuable starting data for future in silico and in vitro experiments. Molpher is highly extensible and can be easily incorporated into any existing computational drug design pipeline. PMID:24655571

Molpher: a software framework for systematic chemical space exploration.

PubMed

Hoksza, David; Skoda, Petr; Voršilák, Milan; Svozil, Daniel

2014-03-21

Chemical space is virtual space occupied by all chemically meaningful organic compounds. It is an important concept in contemporary chemoinformatics research, and its systematic exploration is vital to the discovery of either novel drugs or new tools for chemical biology. In this paper, we describe Molpher, an open-source framework for the systematic exploration of chemical space. Through a process we term 'molecular morphing', Molpher produces a path of structurally-related compounds. This path is generated by the iterative application of so-called 'morphing operators' that represent simple structural changes, such as the addition or removal of an atom or a bond. Molpher incorporates an optimized parallel exploration algorithm, compound logging and a two-dimensional visualization of the exploration process. Its feature set can be easily extended by implementing additional morphing operators, chemical fingerprints, similarity measures and visualization methods. Molpher not only offers an intuitive graphical user interface, but also can be run in batch mode. This enables users to easily incorporate molecular morphing into their existing drug discovery pipelines. Molpher is an open-source software framework for the design of virtual chemical libraries focused on a particular mechanistic class of compounds. These libraries, represented by a morphing path and its surroundings, provide valuable starting data for future in silico and in vitro experiments. Molpher is highly extensible and can be easily incorporated into any existing computational drug design pipeline.

Crystal structure of K0.75[Fe(II) 3.75Fe(III) 1.25(HPO3)6]·0.5H2O, an open-framework iron phosphite with mixed-valent Fe(II)/Fe(III) ions.

PubMed

Larrea, Edurne S; Mesa, José Luis; Legarra, Estibaliz; Aguayo, Andrés Tomás; Arriortua, Maria Isabel

2016-01-01

Single crystals of the title compound, potassium hexa-phosphito-penta-ferrate(II,III) hemihydrate, K0.75[Fe(II) 3.75Fe(III) 1.25(HPO3)6]·0.5H2O, were grown under mild hydro-thermal conditions. The crystal structure is isotypic with Li1.43[Fe(II) 4.43Fe(III) 0.57(HPO3)6]·1.5H2O and (NH4)2[Fe(II) 5(HPO3)6] and exhibits a [Fe(II) 3.75Fe(III) 1.25(HPO3)6](0.75-) open framework with disordered K(+) (occupancy 3/4) as counter-cations. The anionic framework is based on (001) sheets of two [FeO6] octa-hedra (one with point group symmetry 3.. and one with point group symmetry .2.) linked along [001] through [HPO3](2-) oxoanions. Each sheet is constructed from 12-membered rings of edge-sharing [FeO6] octa-hedra, giving rise to channels with a radius of ca 3.1 Å where the K(+) cations and likewise disordered water mol-ecules (occupancy 1/4) are located. O⋯O contacts between the water mol-ecule and framework O atoms of 2.864 (5) Å indicate hydrogen-bonding inter-actions of medium strength. The infrared spectrum of the compound shows vibrational bands typical for phosphite and water groups. The Mössbauer spectrum is in accordance with the presence of Fe(II) and Fe(III) ions.

A framework for integration of scientific applications into the OpenTopography workflow

NASA Astrophysics Data System (ADS)

Nandigam, V.; Crosby, C.; Baru, C.

2012-12-01

The NSF-funded OpenTopography facility provides online access to Earth science-oriented high-resolution LIDAR topography data, online processing tools, and derivative products. The underlying cyberinfrastructure employs a multi-tier service oriented architecture that is comprised of an infrastructure tier, a processing services tier, and an application tier. The infrastructure tier consists of storage, compute resources as well as supporting databases. The services tier consists of the set of processing routines each deployed as a Web service. The applications tier provides client interfaces to the system. (e.g. Portal). We propose a "pluggable" infrastructure design that will allow new scientific algorithms and processing routines developed and maintained by the community to be integrated into the OpenTopography system so that the wider earth science community can benefit from its availability. All core components in OpenTopography are available as Web services using a customized open-source Opal toolkit. The Opal toolkit provides mechanisms to manage and track job submissions, with the help of a back-end database. It allows monitoring of job and system status by providing charting tools. All core components in OpenTopography have been developed, maintained and wrapped as Web services using Opal by OpenTopography developers. However, as the scientific community develops new processing and analysis approaches this integration approach is not scalable efficiently. Most of the new scientific applications will have their own active development teams performing regular updates, maintenance and other improvements. It would be optimal to have the application co-located where its developers can continue to actively work on it while still making it accessible within the OpenTopography workflow for processing capabilities. We will utilize a software framework for remote integration of these scientific applications into the OpenTopography system. This will be accomplished by virtually extending the OpenTopography service over the various infrastructures running these scientific applications and processing routines. This involves packaging and distributing a customized instance of the Opal toolkit that will wrap the software application as an OPAL-based web service and integrate it into the OpenTopography framework. We plan to make this as automated as possible. A structured specification of service inputs and outputs along with metadata annotations encoded in XML can be utilized to automate the generation of user interfaces, with appropriate tools tips and user help features, and generation of other internal software. The OpenTopography Opal toolkit will also include the customizations that will enable security authentication, authorization and the ability to write application usage and job statistics back to the OpenTopography databases. This usage information could then be reported to the original service providers and used for auditing and performance improvements. This pluggable framework will enable the application developers to continue to work on enhancing their application while making the latest iteration available in a timely manner to the earth sciences community. This will also help us establish an overall framework that other scientific application providers will also be able to use going forward.

The RISE Framework: Using Learning Analytics to Automatically Identify Open Educational Resources for Continuous Improvement

ERIC Educational Resources Information Center

Bodily, Robert; Nyland, Rob; Wiley, David

2017-01-01

The RISE (Resource Inspection, Selection, and Enhancement) Framework is a framework supporting the continuous improvement of open educational resources (OER). The framework is an automated process that identifies learning resources that should be evaluated and either eliminated or improved. This is particularly useful in OER contexts where the…

Educational opportunities based on the university-industry synergies in an open innovation framework

NASA Astrophysics Data System (ADS)

Lucia, Óscar; Burdio, José M.; Acero, Jesús; Barragán, Luis A.; Garcia, José R.

2012-03-01

Collaboration between Industry and University is becoming more important in order to improve the competitiveness of the research and development activities. Moreover, establishing synergies to bridge the gap between the academic and industrial spheres has demonstrated to be advantageous for both of them. Nowadays, Industry is moving towards an open innovation structure, in which external agents as universities play a key role. Besides, University is also seeking a more active learning methodology to improve the education of students for the real world. Considering this framework, a special effort should be done to take advantage of the collaborative work between Industry and University. The aim of this paper is to present the collaborative framework and the benefits obtained of the educational activities as a consequence of the long-term collaboration established between the University of Zaragoza and the Bosh and Siemens Home Appliances Group. The key stones of the collaboration are presented, and the positive outcomes for the students are highlighted. The strengths, weaknesses, opportunities, and threats of the proposed program are also discussed.

Unique (3,8)-connected lanthanide arenedisulfonate metal-organic frameworks containing benzimidazole-5,6-dicarboxylic acid co-ligand: Syntheses, structures and luminescence

NASA Astrophysics Data System (ADS)

Sun, Yan-Qiong; Liu, Qi; Zhong, Jie-Cen; Pan, Qun-Feng; Chen, Yi-Ping

2013-10-01

Two isostructural 3D lanthanide arenedisulfonate metal-organic frameworks (MOFs) [Ln(Hbidc)(nds)0.5(H2O)]n(Ln=Eu(1), La(2)) have been successfully synthesized by the hydrothermal reaction of lanthanide oxide with 2,6-naphthalenedisulfonate sodium (Na2nds) and an auxiliary ligand, 1H-benzimidazole-5,6-dicarboxylic acid (H3bidc). The two complexes are both constructed from 2D [Ln(Hbidc)]+ double layers pillared by nds2- ligands to generate 3D (3, 8)-connected open-framework structures with 1D long narrow channels running along the a axis. From topological point of view, the 3D framework is a (3, 8)-connected tfz-d net. The weak interactions including N-H⋯O, O-H⋯O hydrogen bonds and π-π stacking are observed in 1. The 2D IR correlation spectroscopy was applied to study the molecular interactions induced by thermal perturbation. The emission spectra of 1 exhibit the characteristic transition of 5D0→7FJ(J=0-4) of Eu(III).

Alternative Views of the Solar System among Turkish Students

ERIC Educational Resources Information Center

Cin, Mustafa

2007-01-01

This study examines middle-school students' alternative frameworks of the earth's shape, its relative size and its distance from the sun and the moon. The sample was selected in the province of Giresun in Turkey. Sixty-five 14-year-old students participated in the research. A structured interview consisting of open-ended questions was employed to…

Increasing Programme Effectiveness through Parent Empowerment: The Getting Ready for School Project in Tajikistan

ERIC Educational Resources Information Center

Whitsel, Christopher Michael; Lapham, Kate

2014-01-01

Within the development studies framework, empowerment involves increasing individual agency vis-à-vis the formal and informal opportunity structure. The Open Society Foundation's Early Childhood Programme developed the Getting Ready for School programme specifically for parents of preschool-age children to use at home in the year before school to…

Playing by the Rules: Instruction and Acculturation in Role-Playing Games

ERIC Educational Resources Information Center

Neuenschwander, Bryn

2008-01-01

The open-ended, informal, and socially negotiated nature of role-playing games creates a distinct learning challenge for newcomers to the hobby. The explicit rules of the game provide only an incomplete framework for structuring the actions of players, and the expectations and mores of a given group will add other, unspoken rules that discourage…

Porphyrin framework solids. Synthesis and structure of hybrid coordination polymers of tetra(carboxyphenyl)porphyrins and lanthanide-bridging ions.

PubMed

Muniappan, Sankar; Lipstman, Sophia; George, Sumod; Goldberg, Israel

2007-07-09

New types of porphyrin-based framework solids were constructed by reacting meso-tetra(3-carboxyphenyl)porphyrin and meso-tetra(4-carboxyphenyl)metalloporphyrins with common salts of lanthanide metal ions. The large size, high coordination numbers and strong affinity for oxo ligands of the latter, combined with favorable hydrothermal reaction conditions, allowed the formation of open three-dimensional single-framework architectures by coordination polymerization, in which the tetradentate porphyrin units are intercoordinated by multinuclear assemblies of the bridging metal ions. The latter serve as construction pillars of the supramolecular arrays, affording stable structures. Several modes of coordination polymerization were revealed by single-crystal X-ray diffraction. They differ by the spatial functionality of the porphyrin building blocks, the coordination patterns of the lanthanide-carboxylate assemblies, and the topology of the resulting frameworks. The seven new reported structures exhibit periodically spaced 0.4-0.6 nm wide channel voids that perforate the respective crystalline polymeric architectures and are accessible to solvent components. Materials based on the m-carboxyphenyl derivative reveal smaller channels than those based on the p-carboxyphenyl analogues. An additional complex of the former with a smaller third-row transition metal (Co) is characterized by coordination connectivity in two dimensions only. Thermal and powder-diffraction analyses confirm the stability of the lanthanide-TmCPP (TmCPP=tetra(m-carboxyphenyl)porphyrin) frameworks.

Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble

PubMed Central

Barnes, Christopher O.; Calero, Monica; Malik, Indranil; Graham, Brian W.; Spahr, Henrik; Lin, Guowu; Cohen, Aina; Brown, Ian S.; Zhang, Qiangmin; Pullara, Filippo; Trakselis, Michael A.; Kaplan, Craig D.; Calero, Guillermo

2015-01-01

Summary Notwithstanding numerous published structures of RNA Polymerase II (Pol II), structural details of Pol II engaging a complete nucleic acid scaffold have been lacking. Here, we report the structures of TFIIF stabilized transcribing Pol II complexes, revealing the upstream duplex and full transcription bubble. The upstream duplex lies over a wedge-shaped loop from Rpb2 that engages its minor groove, providing part of the structural framework for DNA tracking during elongation. At the upstream transcription bubble fork, rudder and fork loop-1 residues spatially coordinate strand annealing and the nascent RNA transcript. At the downstream fork, a network of Pol II interactions with the non-template strand forms a rigid domain with the Trigger Loop (TL), allowing visualization of its open state. Overall, our observations suggest that “open/closed” conformational transitions of the TL may be linked to interactions with the non-template strand, possibly in a synchronized ratcheting manner conducive to polymerase translocation. PMID:26186291

Adaption to Extreme Rainfall with Open Urban Drainage System: An Integrated Hydrological Cost-Benefit Analysis

NASA Astrophysics Data System (ADS)

Zhou, Qianqian; Panduro, Toke Emil; Thorsen, Bo Jellesmark; Arnbjerg-Nielsen, Karsten

2013-03-01

This paper presents a cross-disciplinary framework for assessment of climate change adaptation to increased precipitation extremes considering pluvial flood risk as well as additional environmental services provided by some of the adaptation options. The ability of adaptation alternatives to cope with extreme rainfalls is evaluated using a quantitative flood risk approach based on urban inundation modeling and socio-economic analysis of corresponding costs and benefits. A hedonic valuation model is applied to capture the local economic gains or losses from more water bodies in green areas. The framework was applied to the northern part of the city of Aarhus, Denmark. We investigated four adaptation strategies that encompassed laissez-faire, larger sewer pipes, local infiltration units, and open drainage system in the urban green structure. We found that when taking into account environmental amenity effects, an integration of open drainage basins in urban recreational areas is likely the best adaptation strategy, followed by pipe enlargement and local infiltration strategies. All three were improvements compared to the fourth strategy of no measures taken.

Adaption to extreme rainfall with open urban drainage system: an integrated hydrological cost-benefit analysis.

PubMed

Zhou, Qianqian; Panduro, Toke Emil; Thorsen, Bo Jellesmark; Arnbjerg-Nielsen, Karsten

2013-03-01

This paper presents a cross-disciplinary framework for assessment of climate change adaptation to increased precipitation extremes considering pluvial flood risk as well as additional environmental services provided by some of the adaptation options. The ability of adaptation alternatives to cope with extreme rainfalls is evaluated using a quantitative flood risk approach based on urban inundation modeling and socio-economic analysis of corresponding costs and benefits. A hedonic valuation model is applied to capture the local economic gains or losses from more water bodies in green areas. The framework was applied to the northern part of the city of Aarhus, Denmark. We investigated four adaptation strategies that encompassed laissez-faire, larger sewer pipes, local infiltration units, and open drainage system in the urban green structure. We found that when taking into account environmental amenity effects, an integration of open drainage basins in urban recreational areas is likely the best adaptation strategy, followed by pipe enlargement and local infiltration strategies. All three were improvements compared to the fourth strategy of no measures taken.

Tunable electrical conductivity in metal-organic framework thin film devices

DOEpatents

Talin, Albert Alec; Allendorf, Mark D.; Stavila, Vitalie; Leonard, Francois

2016-08-30

A composition including a porous metal organic framework (MOF) including an open metal site and a guest species capable of charge transfer that can coordinate with the open metal site, wherein the composition is electrically conductive. A method including infiltrating a porous metal organic framework (MOF) including an open metal site with a guest species that is capable of charge transfer; and coordinating the guest species to the open metal site to form a composition including an electrical conductivity greater than an electrical conductivity of the MOF.

Tunable electrical conductivity in metal-organic framework thin film devices

DOEpatents

Talin, Albert Alec; Allendorf, Mark D.; Stavila, Vitalie; Leonard, Francois

2016-05-24

A composition including a porous metal organic framework (MOF) including an open metal site and a guest species capable of charge transfer that can coordinate with the open metal site, wherein the composition is electrically conductive. A method including infiltrating a porous metal organic framework (MOF) including an open metal site with a guest species that is capable of charge transfer; and coordinating the guest species to the open metal site to form a composition including an electrical conductivity greater than an electrical conductivity of the MOF.

Opening up openness: a theoretical sort following critical incidents methodology and a meta-analytic investigation of the trait family measures.

PubMed

Connelly, Brian S; Ones, Deniz S; Davies, Stacy E; Birkland, Adib

2014-01-01

Existing taxonomies of Openness's facet structure have produced widely divergent results, and there is limited comprehensive empirical evidence about how Openness-related scales on existing personality inventories align within the 5-factor framework. In Study 1, we used a critical incidents sorting methodology to identify 11 categories of Openness measures; in Study 2, we meta-analyzed the relationships of these categories with global markers of the Big Five traits (utilizing data from 106 samples with a total sample size of N = 35,886). Our results identified 4 true facets of Openness: aestheticism, openness to sensations, nontraditionalism, and introspection. Measures of these facets were unadulterated by variance from other Big Five traits. Many traits frequently conceptualized as facets of Openness (e.g., innovation/creativity, variety-seeking, and tolerance) emerged as trait compounds that, although related to Openness, are also dependent on other Big Five traits. We discuss how Openness should be conceptualized, measured, and studied in light of the empirically based, refined taxonomy emerging from this research.

Reverse Micelle Based Synthesis of Microporous Materials in Microgravity

NASA Technical Reports Server (NTRS)

Dutta, Prabir K.

2001-01-01

Microporous materials include a large group of solids of varying chemical composition as well as porosity. These materials are characterized by channels and cavities of molecular dimensions. The framework structure is made up of interconnecting T-O-T' bonds, where T and T' can be Si, Al, P, Ga, Fe, Co, Zn, B and a host of other elements. Materials with Si-O-Al bonding in the framework are called zeolites and are extensively used in many applications. Ion-exchange properties of these materials are exploited in the consumer and environmental industries. Chemical and petroleum industries use zeolites as catalysts in hydrocarbon transform ations. Synthesis of new microporous frameworks has led to the development of new technologies, and thus considerable effort worldwide is expended in their discovery. Microporous materials are typically made under hydrothermal conditions. Influence of nature of starting reactants, structure directing agents, pH, temperature, and aging all have profound influence on the synthesis process. This is primarily because the most interesting open frameworks are not necessarily the stable structures in the reaction medium. Thus, the discovery of new frameworks is often tied to finding the right composition and synthesis conditions that allow for kinetic stabilization of the structure. This complexity of the synthesis process and limited understanding of it has made it difficult to develop directed is of microporous materials and most advances in this field have been made by trial and error. The basic issues in crystal growth of these materials include: (1) Nature of the nucleation process; (2) Molecular structure and assembly of nuclei; (3) Growth of nuclei into crystals; (4) Morphology control; and (5) Transformation of frameworks into other structures. The NASA-funded research described in this paper focuses on all the above issues and has been described in several publications. We present the highlights of our program, especially with the focus on possible experiments in microgravity.

Pb0.65Mn2.85Ga3S8 and Pb0.72Mn2.84Ga2.95Se8: Two Quaternary Metal Chalcognides with Open-Tunnel-Framework Structures Displaying Intense Second Harmonic Generation Responses and Interesting Magnetic Properties.

PubMed

Zhou, Molin; Jiang, Xingxing; Guo, Yangwu; Lin, Zheshuai; Yao, Jiyong; Wu, Yicheng

2017-07-17

By combining different nonlinear optical-active structural chromophores with transition metal Mn into a crystal structure, two novel quaternary metal chalcogenides Pb 0.65 Mn 2.85 Ga 3 S 8 (1) and Pb 0.72 Mn 2.84 Ga 2.95 Se 8 (2) were successfully synthesized. Compounds 1 and 2 are isostructural, and they represent a new structure type that crystallizes in the space group P6̅ (No. 174) in the hexagonal system. Their structures feature an interesting three-dimensional open-tunnel framework composed of bridged infinite chains with Pb 2+ cations filling in the biggest tunnels. Interestingly, both 1 and 2 demonstrate intense second harmonic generation responses at 2.09 μm that is about 1.5 and 4.4 times, respectively, of that of the benchmark material AgGaS 2 . However, 1 and 2 possess different optical diffuse reflectance spectra: 1 displays an evident multiband absorption characteristic with two distinguishing absorption edges of 738 and 551 nm, corresponding to two band gaps of 1.68 and 2.25 eV, respectively, while 2 exhibits only one sharp edge, and the corresponding band gap was estimated to be 1.65 eV. Moreover, apart from the considerable structural similarity between 1 and 2, the dc temperature dependent susceptibility measurements indicate that compound 1 is paramagnetic, while compound 2 exhibits spin-glass-like behavior.

Structural Modeling and Response of Command, Control and Communication Shelter Systems for Event DICE THROW.

DTIC Science & Technology

1980-03-01

Construction ... ........... ... 71 7 FkAEC"IWAG FitAZbL~ai-am naJ" LIST OF ILLUSTRATIONS (CONT’D) Figure Page 2.26 Grid Point System for AN/TRC-145...systems consists of a basic shelter structure whose side walls are of sandwich construction with internal stiffeners. Channel extrusions along each...free edge of the shelter provide additional strength and stiffening. The shelters contain electronic equipment racks of open framework construction using

Ordered macro-microporous metal-organic framework single crystals

NASA Astrophysics Data System (ADS)

Shen, Kui; Zhang, Lei; Chen, Xiaodong; Liu, Lingmei; Zhang, Daliang; Han, Yu; Chen, Junying; Long, Jilan; Luque, Rafael; Li, Yingwei; Chen, Banglin

2018-01-01

We constructed highly oriented and ordered macropores within metal-organic framework (MOF) single crystals, opening up the area of three-dimensional–ordered macro-microporous materials (that is, materials containing both macro- and micropores) in single-crystalline form. Our methodology relies on the strong shaping effects of a polystyrene nanosphere monolith template and a double-solvent–induced heterogeneous nucleation approach. This process synergistically enabled the in situ growth of MOFs within ordered voids, rendering a single crystal with oriented and ordered macro-microporous structure. The improved mass diffusion properties of such hierarchical frameworks, together with their robust single-crystalline nature, endow them with superior catalytic activity and recyclability for bulky-molecule reactions, as compared with conventional, polycrystalline hollow, and disordered macroporous ZIF-8.

An environmental decision framework applied to marine engine control technologies.

PubMed

Corbett, James J; Chapman, David

2006-06-01

This paper develops a decision framework for considering emission control technologies on marine engines, informed by standard decision theory, with an open structure that may be adapted by operators with specific vessel and technology attributes different from those provided here. Attributes relate objectives important to choosing control technologies with specific alternatives that may meet several of the objectives differently. The transparent framework enables multiple stakeholders to understand how different subjective judgments and varying attribute properties may result in different technology choices. Standard scoring techniques ensure that attributes are not biased by subjective scoring and that weights are the primary quantitative input where subjective preferences are exercised. An expected value decision structure is adopted that considers probabilities (likelihood) that a given alternative can meet its claims; alternative decision criteria are discussed. Capital and annual costs are combined using a net present value approach. An iterative approach is advocated that allows for screening and disqualifying alternatives that do not meet minimum conditions for acceptance, such as engine warranty or U.S. Coast Guard requirements. This decision framework assists vessel operators in considering explicitly important attributes and in representing choices clearly to other stakeholders concerned about reducing air pollution from vessels. This general decision structure may also be applied similarly to other environmental controls in marine applications.

A framework of analysis for field experiments with alternative materials in road construction.

PubMed

François, D; Jullien, A

2009-01-01

In France, a wide variety of alternative materials is produced or exists in the form of stockpiles built up over time. Such materials are distributed over various regions of the territory depending on local industrial development and urbanisation trends. The use of alternative materials at a national scale implies sharing local knowledge and experience. Building a national database on alternative materials for road construction is useful in gathering and sharing information. An analysis of feedback from onsite experiences (back analysis) is essential to improve knowledge on alternative material use in road construction. Back analysis of field studies has to be conducted in accordance with a single common framework. This could enable drawing comparisons between alternative materials and between road applications. A framework for the identification and classification of data used in back analyses is proposed. Since the road structure is an open system, this framework has been based on a stress-response approach at both the material and structural levels and includes a description of external factors applying during the road service life. The proposal has been shaped from a review of the essential characteristics of road materials and structures, as well as from the state of knowledge specific to alternative material characterisation.

Structural controllability of unidirectional bipartite networks

NASA Astrophysics Data System (ADS)

Nacher, Jose C.; Akutsu, Tatsuya

2013-04-01

The interactions between fundamental life molecules, people and social organisations build complex architectures that often result in undesired behaviours. Despite all of the advances made in our understanding of network structures over the past decade, similar progress has not been achieved in the controllability of real-world networks. In particular, an analytical framework to address the controllability of bipartite networks is still absent. Here, we present a dominating set (DS)-based approach to bipartite network controllability that identifies the topologies that are relatively easy to control with the minimum number of driver nodes. Our theoretical calculations, assisted by computer simulations and an evaluation of real-world networks offer a promising framework to control unidirectional bipartite networks. Our analysis should open a new approach to reverting the undesired behaviours in unidirectional bipartite networks at will.

eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows.

PubMed

Kiefer, Patrick; Schmitt, Uwe; Vorholt, Julia A

2013-04-01

The Python-based, open-source eMZed framework was developed for mass spectrometry (MS) users to create tailored workflows for liquid chromatography (LC)/MS data analysis. The goal was to establish a unique framework with comprehensive basic functionalities that are easy to apply and allow for the extension and modification of the framework in a straightforward manner. eMZed supports the iterative development and prototyping of individual evaluation strategies by providing a computing environment and tools for inspecting and modifying underlying LC/MS data. The framework specifically addresses non-expert programmers, as it requires only basic knowledge of Python and relies largely on existing successful open-source software, e.g. OpenMS. The framework eMZed and its documentation are freely available at http://emzed.biol.ethz.ch/. eMZed is published under the GPL 3.0 license, and an online discussion group is available at https://groups.google.com/group/emzed-users. Supplementary data are available at Bioinformatics online.

Deterministic Integration of Biological and Soft Materials onto 3D Microscale Cellular Frameworks

PubMed Central

McCracken, Joselle M.; Xu, Sheng; Badea, Adina; Jang, Kyung-In; Yan, Zheng; Wetzel, David J.; Nan, Kewang; Lin, Qing; Han, Mengdi; Anderson, Mikayla A.; Lee, Jung Woo; Wei, Zijun; Pharr, Matt; Wang, Renhan; Su, Jessica; Rubakhin, Stanislav S.; Sweedler, Jonathan V.

2018-01-01

Complex 3D organizations of materials represent ubiquitous structural motifs found in the most sophisticated forms of matter, the most notable of which are in life-sustaining hierarchical structures found in biology, but where simpler examples also exist as dense multilayered constructs in high-performance electronics. Each class of system evinces specific enabling forms of assembly to establish their functional organization at length scales not dissimilar to tissue-level constructs. This study describes materials and means of assembly that extend and join these disparate systems—schemes for the functional integration of soft and biological materials with synthetic 3D microscale, open frameworks that can leverage the most advanced forms of multilayer electronic technologies, including device-grade semiconductors such as monocrystalline silicon. Cellular migration behaviors, temporal dependencies of their growth, and contact guidance cues provided by the nonplanarity of these frameworks illustrate design criteria useful for their functional integration with living matter (e.g., NIH 3T3 fibroblast and primary rat dorsal root ganglion cell cultures). PMID:29552634

Formation of a new archetypal Metal-Organic Framework from a simple monatomic liquid

NASA Astrophysics Data System (ADS)

Metere, Alfredo; Oleynikov, Peter; Dzugutov, Mikhail; O'Keeffe, Michael

2014-12-01

We report a molecular-dynamics simulation of a single-component system of particles interacting via a spherically symmetric potential that is found to form, upon cooling from a liquid state, a low-density porous crystalline phase. Its structure analysis demonstrates that the crystal can be described by a net with a topology that belongs to the class of topologies characteristic of the Metal-Organic Frameworks (MOFs). The observed net is new, and it is now included in the Reticular Chemistry Structure Resource database. The observation that a net topology characteristic of MOF crystals, which are known to be formed by a coordination-driven self-assembly process, can be reproduced by a thermodynamically stable configuration of a simple single-component system of particles opens a possibility of using these models in studies of MOF nets. It also indicates that structures with MOF topology, as well as other low-density porous crystalline structures can possibly be produced in colloidal systems of spherical particles, with an appropriate tuning of interparticle interaction.

A cognitive perspective on health systems integration: results of a Canadian Delphi study.

PubMed

Evans, Jenna M; Baker, G Ross; Berta, Whitney; Barnsley, Jan

2014-05-19

Ongoing challenges to healthcare integration point toward the need to move beyond structural and process issues. While we know what needs to be done to achieve integrated care, there is little that informs us as to how. We need to understand how diverse organizations and professionals develop shared knowledge and beliefs - that is, we need to generate knowledge about normative integration. We present a cognitive perspective on integration, based on shared mental model theory, that may enhance our understanding and ability to measure and influence normative integration. The aim of this paper is to validate and improve the Mental Models of Integrated Care (MMIC) Framework, which outlines important knowledge and beliefs whose convergence or divergence across stakeholder groups may influence inter-professional and inter-organizational relations. We used a two-stage web-based modified Delphi process to test the MMIC Framework against expert opinion using a random sample of participants from Canada's National Symposium on Integrated Care. Respondents were asked to rate the framework's clarity, comprehensiveness, usefulness, and importance using seven-point ordinal scales. Spaces for open comments were provided. Descriptive statistics were used to describe the structured responses, while open comments were coded and categorized using thematic analysis. The Kruskall-Wallis test was used to examine cross-group agreement by level of integration experience, current workplace, and current role. In the first round, 90 individuals responded (52% response rate), representing a wide range of professional roles and organization types from across the continuum of care. In the second round, 68 individuals responded (75.6% response rate). The quantitative and qualitative feedback from experts was used to revise the framework. The re-named "Integration Mindsets Framework" consists of a Strategy Mental Model and a Relationships Mental Model, comprising a total of nineteen content areas. The Integration Mindsets Framework draws the attention of researchers and practitioners to how various stakeholders think about and conceptualize integration. A cognitive approach to understanding and measuring normative integration complements dominant cultural approaches and allows for more fine-grained analyses. The framework can be used by managers and leaders to facilitate the interpretation, planning, implementation, management and evaluation of integration initiatives.

Construction of a Hierarchical Architecture of Covalent Organic Frameworks via a Postsynthetic Approach.

PubMed

Zhang, Gen; Tsujimoto, Masahiko; Packwood, Daniel; Duong, Nghia Tuan; Nishiyama, Yusuke; Kadota, Kentaro; Kitagawa, Susumu; Horike, Satoshi

2018-02-21

Covalent organic frameworks (COFs) represent an emerging class of crystalline porous materials that are constructed by the assembly of organic building blocks linked via covalent bonds. Several strategies have been developed for the construction of new COF structures; however, a facile approach to fabricate hierarchical COF architectures with controlled domain structures remains a significant challenge, and has not yet been achieved. In this study, a dynamic covalent chemistry (DCC)-based postsynthetic approach was employed at the solid-liquid interface to construct such structures. Two-dimensional imine-bonded COFs having different aromatic groups were prepared, and a homogeneously mixed-linker structure and a heterogeneously core-shell hollow structure were fabricated by controlling the reactivity of the postsynthetic reactions. Solid-state nuclear magnetic resonance (NMR) spectroscopy and transmission electron microscopy (TEM) confirmed the structures. COFs prepared by a postsynthetic approach exhibit several functional advantages compared with their parent phases. Their Brunauer-Emmett-Teller (BET) surface areas are 2-fold greater than those of their parent phases because of the higher crystallinity. In addition, the hydrophilicity of the material and the stepwise adsorption isotherms of H 2 O vapor in the hierarchical frameworks were precisely controlled, which was feasible because of the distribution of various domains of the two COFs by controlling the postsynthetic reaction. The approach opens new routes for constructing COF architectures with functionalities that are not possible in a single phase.

Makahiki: An Open Source Serious Game Framework for Sustainability Education and Conservation

ERIC Educational Resources Information Center

Xu, Yongwen; Johnson, Philip M.; Lee, George E.; Moore, Carleton A.; Brewer, Robert S.

2014-01-01

Sustainability education and conservation have become an international imperative due to the rising cost of energy, increasing scarcity of natural resource and irresponsible environmental practices. This paper presents Makahiki, an open source serious game framework for sustainability, which implements an extensible framework for different…

A novel metal-organic framework for high storage and separation of acetylene at room temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duan, Xing, E-mail: star1987@hdu.edu.cn; Wang, Huizhen; Ji, Zhenguo

2016-09-15

A novel 3D microporous metal-organic framework with NbO topology, [Cu{sub 2}(L)(H{sub 2}O){sub 2}]∙(DMF){sub 6}·(H{sub 2}O){sub 2} (ZJU-10, ZJU = Zhejiang University; H{sub 4}L =2′-hydroxy-[1,1′:4′,1″-terphenyl]-3,3″,5,5″-tetracarboxylic acid; DMF =N,N-dimethylformamide), has been synthesized and structurally characterized. With suitable pore sizes and open Cu{sup 2+} sites, ZJU-10a exhibits high BET surface area of 2392 m{sup 2}/g, as well as moderately high C{sub 2}H{sub 2} volumetric uptake capacity of 132 cm{sup 3}/cm{sup 3}. Meanwhile, ZJU-10a is a promising porous material for separation of acetylene from methane and carbon dioxide gas mixtures at room temperature. - Graphical abstract: A new NbO-type microporous metal-organic framework ZJU-10 withmore » suitable pore size and open Cu{sup 2+} sites was synthesized to realize the strong interaction with acetylene molecules, which can separate the acetylene from methane and carbon dioxane gas mixtures at room temperature. Display Omitted - Highlights: • A novel 3D NbO-type microporous metal-organic framework ZJU-10 was solvothermally synthesized and structurally characterized. • ZJU-10a exhibits high BET surface area of 2392 m{sup 2}/g. • ZJU-10a shows a moderately high C{sub 2}H{sub 2} gravimetric (volumetric) uptake capacity of 174 (132) cm{sup 3}/g at 298 K and 1 bar. • ZJU-10a can separate acetylene from methane and carbon dioxide gas mixtures at room temperature.« less

Structural architecture of prothrombin in solution revealed by single molecule spectroscopy

DOE PAGES

Pozzi, Nicola; Bystranowska, Dominika; Zuo, Xiaobing; ...

2016-07-19

The coagulation factor prothrombin has a complex spatial organization of its modular assembly that comprises the N-terminal Gla domain, kringle-1, kringle-2, and the C-terminal protease domain connected by three intervening linkers. Here we use single molecule Förster resonance energy transfer to access the conformational landscape of prothrombin in solution and uncover structural features of functional significance that extend recent x-ray crystallographic analysis. Prothrombin exists in equilibrium between two alternative conformations, open and closed. The closed conformation predominates (70%) and features an unanticipated intramolecular collapse of Tyr 93 in kringle-1 onto Trp 547 in the protease domain that obliterates access tomore » the active site and protects the zymogen from autoproteolytic conversion to thrombin. The open conformation (30%) is more susceptible to chymotrypsin digestion and autoactivation, and features a shape consistent with recent x-ray crystal structures. Small angle x-ray scattering measurements of prothrombin wild type stabilized 70% in the closed conformation and of the mutant Y93A stabilized 80% in the open conformation directly document two envelopes that differ 50 Å in length. These findings reveal important new details on the conformational plasticity of prothrombin in solution and the drastic structural difference between its alternative conformations. Prothrombin uses the intramolecular collapse of kringle-1 onto the active site in the closed form to prevent autoactivation. As a result, the open-closed equilibrium also defines a new structural framework for the mechanism of activation of prothrombin by prothrombinase.« less

Three new d10 transition metal selenites containing PO4 tetrahedron: Cd7(HPO4)2(PO4)2(SeO3)2, Cd6(PO4)1.34(SeO3)4.66 and Zn3(HPO4)(SeO3)2(H2O)

NASA Astrophysics Data System (ADS)

Ma, Yun-Xiang; Gong, Ya-Ping; Hu, Chun-li; Mao, Jiang-Gao; Kong, Fang

2018-06-01

Three new d10 transition metal selenites containing PO4 tetrahedron, namely, Cd7(HPO4)2(PO4)2(SeO3)2 (1), Cd6(PO4)1.34(SeO3)4.66 (2) and Zn3(HPO4)(SeO3)2(H2O) (3), have been synthesized by hydrothermal reaction. They feature three different structural types. Compound 1 exhibits a novel 3D network composed of 3D cadmium selenite open framework with phosphate groups filled in the 1D helical tunnels. The structure of compound 2 displays a new 3D framework consisted of 2D cadmium oxide layers bridged by SeO3 and PO4 groups. Compound 3 is isostructural with the reported solids of Co3(SeO3)3-x(PO3OH)x(H2O) when x is equal to 1.0. Its structure could be viewed as a 3D zinc oxide open skeleton with SeO3 and HPO4 polyhedra attached on the wall of the tunnels. They represent the only examples in metal selenite phosphates in addition to the above cobalt compounds. Optical diffuse reflectance spectra revealed that these solids are insulators, which are consistent with the results of band structure computations based on DFT algorithm.

Topological framework for local structure analysis in condensed matter

PubMed Central

Lazar, Emanuel A.; Han, Jian; Srolovitz, David J.

2015-01-01

Physical systems are frequently modeled as sets of points in space, each representing the position of an atom, molecule, or mesoscale particle. As many properties of such systems depend on the underlying ordering of their constituent particles, understanding that structure is a primary objective of condensed matter research. Although perfect crystals are fully described by a set of translation and basis vectors, real-world materials are never perfect, as thermal vibrations and defects introduce significant deviation from ideal order. Meanwhile, liquids and glasses present yet more complexity. A complete understanding of structure thus remains a central, open problem. Here we propose a unified mathematical framework, based on the topology of the Voronoi cell of a particle, for classifying local structure in ordered and disordered systems that is powerful and practical. We explain the underlying reason why this topological description of local structure is better suited for structural analysis than continuous descriptions. We demonstrate the connection of this approach to the behavior of physical systems and explore how crystalline structure is compromised at elevated temperatures. We also illustrate potential applications to identifying defects in plastically deformed polycrystals at high temperatures, automating analysis of complex structures, and characterizing general disordered systems. PMID:26460045

A Framework for Open, Flexible and Distributed Learning.

ERIC Educational Resources Information Center

Khan, Badrul H.

Designing open, flexible distance learning systems on the World Wide Web requires thoughtful analysis and investigation combined with an understanding of both the Web's attributes and resources and the ways instructional design principles can be applied to tap the Web's potential. A framework for open, flexible, and distributed learning has been…

A Finite Element Framework for Studying the Mechanical Response of Macromolecules: Application to the Gating of the Mechanosensitive Channel MscL

PubMed Central

Tang, Yuye; Cao, Guoxin; Chen, Xi; Yoo, Jejoong; Yethiraj, Arun; Cui, Qiang

2006-01-01

The gating pathways of mechanosensitive channels of large conductance (MscL) in two bacteria (Mycobacterium tuberculosis and Escherichia coli) are studied using the finite element method. The phenomenological model treats transmembrane helices as elastic rods and the lipid membrane as an elastic sheet of finite thickness; the model is inspired by the crystal structure of MscL. The interactions between various continuum components are derived from molecular-mechanics energy calculations using the CHARMM all-atom force field. Both bacterial MscLs open fully upon in-plane tension in the membrane and the variation of pore diameter with membrane tension is found to be essentially linear. The estimated gating tension is close to the experimental value. The structural variations along the gating pathway are consistent with previous analyses based on structural models with experimental constraints and biased atomistic molecular-dynamics simulations. Upon membrane bending, neither MscL opens substantially, although there is notable and nonmonotonic variation in the pore radius. This emphasizes that the gating behavior of MscL depends critically on the form of the mechanical perturbation and reinforces the idea that the crucial gating parameter is lateral tension in the membrane rather than the curvature of the membrane. Compared to popular all-atom-based techniques such as targeted or steered molecular-dynamics simulations, the finite element method-based continuum-mechanics framework offers a unique alternative to bridge detailed intermolecular interactions and biological processes occurring at large spatial scales and long timescales. It is envisioned that such a hierarchical multiscale framework will find great value in the study of a variety of biological processes involving complex mechanical deformations such as muscle contraction and mechanotransduction. PMID:16731564

Ultra-flexible framework breathing in response to dehydration in liskeardite, [(Al,Fe){sub 16}(AsO{sub 4}){sub 9}(OH){sub 21}(H{sub 2}O){sub 11}]·26H{sub 2}O, a natural open-framework compound

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grey, Ian. E., E-mail: Ian.Grey@csiro.au; Brand, Helen E.A.; Rumsey, Michael S.

Dehydration of the natural open-framework compound, liskeardite, [(Al,Fe){sub 16}(AsO{sub 4}){sub 9}(OH){sub 21}(H{sub 2}O){sub 11}]·26H{sub 2}O, is accompanied by a change in the sign of the thermal expansion from positive to negative above room temperature, and at ~100 °C the structure undergoes a dramatic 2D contraction by co-operative rotation of heteropolyhedral columns that constitute the framework walls. Monoclinic liskeardite, I112 with a≈b≈24.7 Å, c ≈7.8 Å and β≈90° is transformed to a tetragonal phase, I-4 with a≈20.6 Å, c ≈7.7 Å. The associated 30% decrease in volume is unprecedented in inorganic microporous compounds. The flexibility of the contraction is related tomore » the double-hinged nature of the column rotations about [001]. Octahedra in adjacent columns are interconnected by corner-sharing with the two pairs of anions forming opposing edges of AsO{sub 4} tetrahedra, so a double-hinged rotation mechanism operates. Thermal analysis and mass spectroscopic results for liskeardite show that the phase transition at ~100 °C is related to removal of the channel water. The tetragonal phase shows exceptionally large NTE behaviour. Over the temperature range 148–178 the NTE along a and b is close to linear with a magnitude of the order of −900×10{sup −6} °C{sup −1}. The contraction along the channel direction is smaller but still appreciable at −200×10{sup −6} °C{sup −1}. - Graphical abstract: Structure of the collapsed liskeardite framework, formed on dehydration above 100 °C. - Highlights: • The thermal expansion of the mineral liskeardite changes + to − above ambient. • Dehydration at 100 °C results in a record reversible 30% volume reduction. • In situ synchrotron XRD has led to a structural model for the dehydrated phase. • Framework breathing flexibility is attributed to a double-hinge rotation mechanism. • The dehydrated phase shows unprecedented -ve expansion for inorganic materials.« less

“Manejar la Situacion”: Partner Notification, Partner Management, and Conceptual Frameworks for HIV/STI Control Among MSM in Peru

PubMed Central

Clark, Jesse L.; Perez-Brumer, Amaya; Salazar, Ximena

2015-01-01

Previous analyses of Partner Notification (PN) have addressed individual, interpersonal, social, and structural issues influencing PN outcomes but have paid less attention to the conceptual framework of PN itself. We conducted 18 individual interviews and 8 group discussions, in a two-stage qualitative research process, to explore the meanings and contexts of PN for sexually transmitted infections (STI) among men who have sex with men (MSM) and men who have sex with men and women (MSMW) in Lima, Peru. Participants described PN as the open disclosure of private, potentially stigmatizing information that could strengthen or disrupt a partnership, structured by the tension between concealment and revelation. In addition to informing partners of an STI diagnosis, the act of PN was believed to reveal other potentially stigmatizing information related to sexual identity and practices such as homosexuality, promiscuity, and HIV co-infection. In this context, the potential development of visible, biological STI symptoms represented a risk for disruption of the boundary between secrecy and disclosure that could result in involuntary disclosure of STI status. To address the conflict between concealment and disclosure, participants cited efforts to “manejar la situacion” [manage the situation] by controlling the biological risks of STI exposure without openly disclosing STI status. We use this concept of “managing the situation” as a practical and theoretical framework for comprehensive Partner Management for HIV/STI control systems among MSM in Latin America. PMID:25821149

An open-source framework for analyzing N-electron dynamics. II. Hybrid density functional theory/configuration interaction methodology.

PubMed

Hermann, Gunter; Pohl, Vincent; Tremblay, Jean Christophe

2017-10-30

In this contribution, we extend our framework for analyzing and visualizing correlated many-electron dynamics to non-variational, highly scalable electronic structure method. Specifically, an explicitly time-dependent electronic wave packet is written as a linear combination of N-electron wave functions at the configuration interaction singles (CIS) level, which are obtained from a reference time-dependent density functional theory (TDDFT) calculation. The procedure is implemented in the open-source Python program detCI@ORBKIT, which extends the capabilities of our recently published post-processing toolbox (Hermann et al., J. Comput. Chem. 2016, 37, 1511). From the output of standard quantum chemistry packages using atom-centered Gaussian-type basis functions, the framework exploits the multideterminental structure of the hybrid TDDFT/CIS wave packet to compute fundamental one-electron quantities such as difference electronic densities, transient electronic flux densities, and transition dipole moments. The hybrid scheme is benchmarked against wave function data for the laser-driven state selective excitation in LiH. It is shown that all features of the electron dynamics are in good quantitative agreement with the higher-level method provided a judicious choice of functional is made. Broadband excitation of a medium-sized organic chromophore further demonstrates the scalability of the method. In addition, the time-dependent flux densities unravel the mechanistic details of the simulated charge migration process at a glance. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

"Manejar la Situacion": Partner Notification, Partner Management, and Conceptual Frameworks for HIV/STI Control Among MSM in Peru.

PubMed

Clark, Jesse L; Perez-Brumer, Amaya; Salazar, Ximena

2015-12-01

Previous analyses of partner notification (PN) have addressed individual, interpersonal, social, and structural issues influencing PN outcomes but have paid less attention to the conceptual framework of PN itself. We conducted 18 individual interviews and 8 group discussions, in a two-stage qualitative research process, to explore the meanings and contexts of PN for sexually transmitted infections (STI) among men who have sex with men (MSM) and men who have sex with men and women (MSMW) in Lima, Peru. Participants described PN as the open disclosure of private, potentially stigmatizing information that could strengthen or disrupt a partnership, structured by the tension between concealment and revelation. In addition to informing partners of an STI diagnosis, the act of PN was believed to reveal other potentially stigmatizing information related to sexual identity and practices such as homosexuality, promiscuity, and HIV co-infection. In this context, the potential development of visible, biological STI symptoms represented a risk for disruption of the boundary between secrecy and disclosure that could result in involuntary disclosure of STI status. To address the conflict between concealment and disclosure, participants cited efforts to "manejar la situacion" (manage the situation) by controlling the biological risks of STI exposure without openly disclosing STI status. We use this concept of "managing the situation" as a practical and theoretical framework for comprehensive Partner Management for HIV/STI control systems among MSM in Latin America.

Uncovering the Local Magnesium Environment in the Metal–Organic Framework Mg 2 (dobpdc) Using 25 Mg NMR Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Jun; Blaakmeer, E. S. Merijn; Lipton, Andrew S.

The incorporation of N,N'-dimethylethylenediamine into an expanded MOF-74 framework has yielded a material (mmen-Mg2(dobpdc)) exhibiting “step-shaped” CO2 adsorption isotherms. The coordination of mmen at the Mg open metal center is essential for the unique cooperative adsorption mechanism elucidated for this material. Despite its importance for carbon capture, there is as yet no experimental structure determination available for the underlying metal– organic framework Mg2(dobpdc). Our 25Mg solid-state NMR data unravel the local Mg environments in several Mg2(dobpdc) samples, unambiguously confirming the formation of fivecoordinate Mg centers in the activated material and six-coordinate Mg centers in the solvent- or diamine-loaded samples, suchmore » as mmen-Mg2(dobpdc). A fraction of the Mg centers are locally disordered due to the framework deformation accompanied by the guest distributions and dynamics.« less

ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Richard A.; Brown, Joseph M.; Colby, Sean M.

ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multiomics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS provides robust taxonomy based onmore » majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.« less

OpenMDAO Framework Status

NASA Technical Reports Server (NTRS)

Naiman, Cynthia Gutierrez

2010-01-01

Advancing and exploring the science of Multidisciplinary Analysis & Optimization (MDAO) capabilities are high-level goals in the Fundamental Aeronautics Program s Subsonic Fixed Wing (SFW) project. The OpenMDAO team has made significant progress toward completing the Alpha OpenMDAO deliverable due in September 2010. Included in the presentation are: details of progress on developing the OpenMDAO framework, example usage of OpenMDAO, technology transfer plans, near term plans, progress toward establishing partnerships with external parties, and discussion of additional potential collaborations.

A 3D object-based model to simulate highly-heterogeneous, coarse, braided river deposits

NASA Astrophysics Data System (ADS)

Huber, E.; Huggenberger, P.; Caers, J.

2016-12-01

There is a critical need in hydrogeological modeling for geologically more realistic representation of the subsurface. Indeed, widely-used representations of the subsurface heterogeneity based on smooth basis functions such as cokriging or the pilot-point approach fail at reproducing the connectivity of high permeable geological structures that control subsurface solute transport. To realistically model the connectivity of high permeable structures of coarse, braided river deposits, multiple-point statistics and object-based models are promising alternatives. We therefore propose a new object-based model that, according to a sedimentological model, mimics the dominant processes of floodplain dynamics. Contrarily to existing models, this object-based model possesses the following properties: (1) it is consistent with field observations (outcrops, ground-penetrating radar data, etc.), (2) it allows different sedimentological dynamics to be modeled that result in different subsurface heterogeneity patterns, (3) it is light in memory and computationally fast, and (4) it can be conditioned to geophysical data. In this model, the main sedimentological elements (scour fills with open-framework-bimodal gravel cross-beds, gravel sheet deposits, open-framework and sand lenses) and their internal structures are described by geometrical objects. Several spatial distributions are proposed that allow to simulate the horizontal position of the objects on the floodplain as well as the net rate of sediment deposition. The model is grid-independent and any vertical section can be computed algebraically. Furthermore, model realizations can serve as training images for multiple-point statistics. The significance of this model is shown by its impact on the subsurface flow distribution that strongly depends on the sedimentological dynamics modeled. The code will be provided as a free and open-source R-package.

Synthesis, X-ray crystal structures, and gas sorption properties of pillared square grid nets based on paddle-wheel motifs: implications for hydrogen storage in porous materials.

PubMed

Chun, Hyungphil; Dybtsev, Danil N; Kim, Hyunuk; Kim, Kimoon

2005-06-06

A systematic modulation of organic ligands connecting dinuclear paddle-wheel motifs leads to a series of isomorphous metal-organic porous materials that have a three-dimensional connectivity and interconnected pores. Aromatic dicarboxylates such as 1,4-benzenedicarboxylate (1,4-bdc), tetramethylterephthalate (tmbdc), 1,4-naphthalenedicarboxylate (1,4-ndc), tetrafluoroterephthalate (tfbdc), or 2,6-naphthalenedicarboxylate (2,6-ndc) are linear linkers that form two-dimensional layers, and diamine ligands, 4-diazabicyclo[2.2.2]octane (dabco) or 4,4'-dipyridyl (bpy), coordinate at both sides of Zn(2) paddle-wheel units to bridge the layers vertically. The resulting open frameworks [Zn(2)(1,4-bdc)(2)(dabco)] (1), [Zn(2)(1,4-bdc)(tmbdc)(dabco)] (2), [Zn(2)(tmbdc)(2)(dabco)] (3), [Zn(2)(1,4-ndc)(2)(dabco)] (4), [Zn(2)(tfbdc)(2)(dabco)] (5), and [Zn(2)(tmbdc)(2)(bpy)] (8) possess varying size of pores and free apertures originating from the side groups of the 1,4-bdc derivatives. [Zn(2)(1,4-bdc)(2)(bpy)] (6) and [Zn(2)(2,6-ndc)(2)(bpy)] (7) have two- and threefold interpenetrating structures, respectively. The non-interpenetrating frameworks (1-5 and 8) possess surface areas in the range of 1450-2090 m(2)g(-1) and hydrogen sorption capacities of 1.7-2.1 wt % at 78 K and 1 atm. A detailed analysis of the sorption data in conjunction with structural similarities and differences concludes that porous materials with straight channels and large openings do not perform better than those with wavy channels and small openings in terms of hydrogen storage through physisorption.

An Integrated Framework Advancing Membrane Protein Modeling and Design

PubMed Central

Weitzner, Brian D.; Duran, Amanda M.; Tilley, Drew C.; Elazar, Assaf; Gray, Jeffrey J.

2015-01-01

Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a myriad of difficulties in overexpression and reconstitution into membrane mimetics severely limit our ability to determine their structures. Computational tools are therefore instrumental to membrane protein structure prediction, consequently increasing our understanding of membrane protein function and their role in disease. Here, we describe a general framework facilitating membrane protein modeling and design that combines the scientific principles for membrane protein modeling with the flexible software architecture of Rosetta3. This new framework, called RosettaMP, provides a general membrane representation that interfaces with scoring, conformational sampling, and mutation routines that can be easily combined to create new protocols. To demonstrate the capabilities of this implementation, we developed four proof-of-concept applications for (1) prediction of free energy changes upon mutation; (2) high-resolution structural refinement; (3) protein-protein docking; and (4) assembly of symmetric protein complexes, all in the membrane environment. Preliminary data show that these algorithms can produce meaningful scores and structures. The data also suggest needed improvements to both sampling routines and score functions. Importantly, the applications collectively demonstrate the potential of combining the flexible nature of RosettaMP with the power of Rosetta algorithms to facilitate membrane protein modeling and design. PMID:26325167

Theoretical Framework for Integrating Distributed Energy Resources into Distribution Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lian, Jianming; Wu, Di; Kalsi, Karanjit

This paper focuses on developing a novel theoretical framework for effective coordination and control of a large number of distributed energy resources in distribution systems in order to more reliably manage the future U.S. electric power grid under the high penetration of renewable generation. The proposed framework provides a systematic view of the overall structure of the future distribution systems along with the underlying information flow, functional organization, and operational procedures. It is characterized by the features of being open, flexible and interoperable with the potential to support dynamic system configuration. Under the proposed framework, the energy consumption of variousmore » DERs is coordinated and controlled in a hierarchical way by using market-based approaches. The real-time voltage control is simultaneously considered to complement the real power control in order to keep nodal voltages stable within acceptable ranges during real time. In addition, computational challenges associated with the proposed framework are also discussed with recommended practices.« less

Prussian Blue Nanocubes with an Open Framework Structure Coated with PEDOT as High-Capacity Cathodes for Lithium-Sulfur Batteries.

PubMed

Su, Dawei; Cortie, Michael; Fan, Hongbo; Wang, Guoxiu

2017-12-01

It is shown that Prussian blue analogues (PBAs) can be a very competitive sulfur host for lithium-sulfur (Li-S) batteries. Sulfur stored in the large interstitial sites of a PBA host can take advantage of reversible and efficient insertion/extraction of both Li + and electrons, due to the well-trapped mobile dielectron redox centers in the well-defined host. It is demonstrated that Na 2 Fe[Fe(CN) 6 ] has a large open framework, and as a cathode, it both stores sulfur and acts as a polysulfide diffusion inhibitor based on the Lewis acid-base bonding effect. The electrochemical testing shows that the S@Na 2 Fe[Fe(CN) 6 ]@poly(3,4-ethylenedioxythiophene) composite achieves excellent reversibility, good stability, and fast kinetics. Its outstanding electrochemical properties should be ascribed to the internal transport of Li +/e- , maximizing the utilization of sulfur. Moreover, the open metal centers serve as the Lewis acid sites with high affinity to the negatively charged polysulfide anions, reducing the diffusion of polysulfides out of the cathode and minimizing the shuttling effect. The fundamental basis of these exceptional performance characteristics is explored through a detailed analysis of the structural and electrochemical behavior of the material. It is believed that the PBAs will have a useful role in ensuring more effective and stable Li-S batteries. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Building biomedical web communities using a semantically aware content management system.

PubMed

Das, Sudeshna; Girard, Lisa; Green, Tom; Weitzman, Louis; Lewis-Bowen, Alister; Clark, Tim

2009-03-01

Web-based biomedical communities are becoming an increasingly popular vehicle for sharing information amongst researchers and are fast gaining an online presence. However, information organization and exchange in such communities is usually unstructured, rendering interoperability between communities difficult. Furthermore, specialized software to create such communities at low cost-targeted at the specific common information requirements of biomedical researchers-has been largely lacking. At the same time, a growing number of biological knowledge bases and biomedical resources are being structured for the Semantic Web. Several groups are creating reference ontologies for the biomedical domain, actively publishing controlled vocabularies and making data available in Resource Description Framework (RDF) language. We have developed the Science Collaboration Framework (SCF) as a reusable platform for advanced structured online collaboration in biomedical research that leverages these ontologies and RDF resources. SCF supports structured 'Web 2.0' style community discourse amongst researchers, makes heterogeneous data resources available to the collaborating scientist, captures the semantics of the relationship among the resources and structures discourse around the resources. The first instance of the SCF framework is being used to create an open-access online community for stem cell research-StemBook (http://www.stembook.org). We believe that such a framework is required to achieve optimal productivity and leveraging of resources in interdisciplinary scientific research. We expect it to be particularly beneficial in highly interdisciplinary areas, such as neurodegenerative disease and neurorepair research, as well as having broad utility across the natural sciences.

NMR crystallography to probe the breathing effect of the MIL-53(Al) metal-organic framework using solid-state NMR measurements of 13C-27Al distances.

PubMed

Giovine, Raynald; Volkringer, Christophe; Trébosc, Julien; Amoureux, Jean Paul; Loiseau, Thierry; Lafon, Olivier; Pourpoint, Frédérique

2017-03-01

The metal-organic framework MIL-53(Al) (aluminium terephthalate) exhibits a structural transition between two porous structures with large pore (lp) or narrow pore (np) configurations. This transition, called the breathing effect, is observed upon changes in temperature or external pressure, as well as with the adsorption of guest molecules, such as H 2 O, within the pores. We show here how these different pore openings can be detected by observing the dephasing of 13 C magnetization under 13 C- 27 Al dipolar couplings using Rotational-Echo Saturation-Pulse Double-Resonance (RESPDOR) solid-state NMR experiments with Simultaneous Frequency and Amplitude Modulation (SFAM) recoupling. These double-resonance NMR experiments between 13 C and 27 Al nuclei, which have close Larmor frequencies, are feasible thanks to the use of a frequency splitter. The experimental SFAM-RESPDOR signal fractions agree well with those simulated from the MIL-53(Al)-lp and -np crystal structures obtained from powder X-ray diffraction analysis. Hence, these 13 C- 27 Al solid-state NMR experiments validate these structures and confirm their rigidity. A similar agreement is reported for the framework ligands in the as-synthesized (as) MIL-53(Al), in which the pores contain free ligands. Furthermore, in this case, 13 C-{ 27 Al} SFAM-RESPDOR experiments allow an estimation of the average distance between the free ligands and the 27 Al nuclei of the framework.

A Computational Framework for Automation of Point Defect Calculations

NASA Astrophysics Data System (ADS)

Goyal, Anuj; Gorai, Prashun; Peng, Haowei; Lany, Stephan; Stevanovic, Vladan; National Renewable Energy Laboratory, Golden, Colorado 80401 Collaboration

A complete and rigorously validated open-source Python framework to automate point defect calculations using density functional theory has been developed. The framework provides an effective and efficient method for defect structure generation, and creation of simple yet customizable workflows to analyze defect calculations. The package provides the capability to compute widely accepted correction schemes to overcome finite-size effects, including (1) potential alignment, (2) image-charge correction, and (3) band filling correction to shallow defects. Using Si, ZnO and In2O3as test examples, we demonstrate the package capabilities and validate the methodology. We believe that a robust automated tool like this will enable the materials by design community to assess the impact of point defects on materials performance. National Renewable Energy Laboratory, Golden, Colorado 80401.

Computational modeling of Metal-Organic Frameworks

NASA Astrophysics Data System (ADS)

Sung, Jeffrey Chuen-Fai

In this work, the metal-organic frameworks MIL-53(Cr), DMOF-2,3-NH 2Cl, DMOF-2,5-NH2Cl, and HKUST-1 were modeled using molecular mechanics and electronic structure. The effect of electronic polarization on the adsorption of water in MIL-53(Cr) was studied using molecular dynamics simulations of water-loaded MIL-53 systems with both polarizable and non-polarizable force fields. Molecular dynamics simulations of the full systems and DFT calculations on representative framework clusters were utilized to study the difference in nitrogen adsorption between DMOF-2,3-NH2Cl and DMOF-2,5-NH 2Cl. Finally, the control of proton conduction in HKUST-1 by complexation of molecules to the Cu open metal site was investigated using the MS-EVB methodology.

Conductive framework of inverse opal structure for sulfur cathode in lithium-sulfur batteries.

PubMed

Jin, Lu; Huang, Xiaopeng; Zeng, Guobo; Wu, Hua; Morbidelli, Massimo

2016-09-07

As a promising cathode inheritor for lithium-ion batteries, the sulfur cathode exhibits very high theoretical volumetric capacity and energy density. In its practical applications, one has to solve the insulating properties of sulfur and the shuttle effect that deteriorates cycling stability. The state-of-the-art approaches are to confine sulfur in a conductive matrix. In this work, we utilize monodisperse polystyrene nanoparticles as sacrificial templates to build polypyrrole (PPy) framework of an inverse opal structure to accommodate (encapsulate) sulfur through a combined in situ polymerization and melting infiltration approach. In the design, the interconnected conductive PPy provides open channels for sulfur infiltration, improves electrical and ionic conductivity of the embedded sulfur, and reduces polysulfide dissolution in the electrolyte through physical and chemical adsorption. The flexibility of PPy and partial filling of the inverse opal structure endure possible expansion and deformation during long-term cycling. It is found that the long cycling stability of the cells using the prepared material as the cathode can be substantially improved. The result demonstrates the possibility of constructing a pure conductive polymer framework to accommodate insulate sulfur in ion battery applications.

Conductive framework of inverse opal structure for sulfur cathode in lithium-sulfur batteries

PubMed Central

Jin, Lu; Huang, Xiaopeng; Zeng, Guobo; Wu, Hua; Morbidelli, Massimo

2016-01-01

As a promising cathode inheritor for lithium-ion batteries, the sulfur cathode exhibits very high theoretical volumetric capacity and energy density. In its practical applications, one has to solve the insulating properties of sulfur and the shuttle effect that deteriorates cycling stability. The state-of-the-art approaches are to confine sulfur in a conductive matrix. In this work, we utilize monodisperse polystyrene nanoparticles as sacrificial templates to build polypyrrole (PPy) framework of an inverse opal structure to accommodate (encapsulate) sulfur through a combined in situ polymerization and melting infiltration approach. In the design, the interconnected conductive PPy provides open channels for sulfur infiltration, improves electrical and ionic conductivity of the embedded sulfur, and reduces polysulfide dissolution in the electrolyte through physical and chemical adsorption. The flexibility of PPy and partial filling of the inverse opal structure endure possible expansion and deformation during long-term cycling. It is found that the long cycling stability of the cells using the prepared material as the cathode can be substantially improved. The result demonstrates the possibility of constructing a pure conductive polymer framework to accommodate insulate sulfur in ion battery applications. PMID:27600885

Conceptual design of distillation-based hybrid separation processes.

PubMed

Skiborowski, Mirko; Harwardt, Andreas; Marquardt, Wolfgang

2013-01-01

Hybrid separation processes combine different separation principles and constitute a promising design option for the separation of complex mixtures. Particularly, the integration of distillation with other unit operations can significantly improve the separation of close-boiling or azeotropic mixtures. Although the design of single-unit operations is well understood and supported by computational methods, the optimal design of flowsheets of hybrid separation processes is still a challenging task. The large number of operational and design degrees of freedom requires a systematic and optimization-based design approach. To this end, a structured approach, the so-called process synthesis framework, is proposed. This article reviews available computational methods for the conceptual design of distillation-based hybrid processes for the separation of liquid mixtures. Open problems are identified that must be addressed to finally establish a structured process synthesis framework for such processes.

Development of an open metadata schema for prospective clinical research (openPCR) in China.

PubMed

Xu, W; Guan, Z; Sun, J; Wang, Z; Geng, Y

2014-01-01

In China, deployment of electronic data capture (EDC) and clinical data management system (CDMS) for clinical research (CR) is in its very early stage, and about 90% of clinical studies collected and submitted clinical data manually. This work aims to build an open metadata schema for Prospective Clinical Research (openPCR) in China based on openEHR archetypes, in order to help Chinese researchers easily create specific data entry templates for registration, study design and clinical data collection. Singapore Framework for Dublin Core Application Profiles (DCAP) is used to develop openPCR and four steps such as defining the core functional requirements and deducing the core metadata items, developing archetype models, defining metadata terms and creating archetype records, and finally developing implementation syntax are followed. The core functional requirements are divided into three categories: requirements for research registration, requirements for trial design, and requirements for case report form (CRF). 74 metadata items are identified and their Chinese authority names are created. The minimum metadata set of openPCR includes 3 documents, 6 sections, 26 top level data groups, 32 lower data groups and 74 data elements. The top level container in openPCR is composed of public document, internal document and clinical document archetypes. A hierarchical structure of openPCR is established according to Data Structure of Electronic Health Record Architecture and Data Standard of China (Chinese EHR Standard). Metadata attributes are grouped into six parts: identification, definition, representation, relation, usage guides, and administration. OpenPCR is an open metadata schema based on research registration standards, standards of the Clinical Data Interchange Standards Consortium (CDISC) and Chinese healthcare related standards, and is to be publicly available throughout China. It considers future integration of EHR and CR by adopting data structure and data terms in Chinese EHR Standard. Archetypes in openPCR are modularity models and can be separated, recombined, and reused. The authors recommend that the method to develop openPCR can be referenced by other countries when designing metadata schema of clinical research. In the next steps, openPCR should be used in a number of CR projects to test its applicability and to continuously improve its coverage. Besides, metadata schema for research protocol can be developed to structurize and standardize protocol, and syntactical interoperability of openPCR with other related standards can be considered.

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.

PubMed

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2014-01-01

pyOpenMS is an open-source, Python-based interface to the C++ OpenMS library, providing facile access to a feature-rich, open-source algorithm library for MS-based proteomics analysis. It contains Python bindings that allow raw access to the data structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping, and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ, and SWATH analysis tools). pyOpenMS thus allows fast prototyping and efficient workflow development in a fully interactive manner (using the interactive Python interpreter) and is also ideally suited for researchers not proficient in C++. In addition, our code to wrap a complex C++ library is completely open-source, allowing other projects to create similar bindings with ease. The pyOpenMS framework is freely available at https://pypi.python.org/pypi/pyopenms while the autowrap tool to create Cython code automatically is available at https://pypi.python.org/pypi/autowrap (both released under the 3-clause BSD licence). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

GiPSi:a framework for open source/open architecture software development for organ-level surgical simulation.

PubMed

Cavuşoğlu, M Cenk; Göktekin, Tolga G; Tendick, Frank

2006-04-01

This paper presents the architectural details of an evolving open source/open architecture software framework for developing organ-level surgical simulations. Our goal is to facilitate shared development of reusable models, to accommodate heterogeneous models of computation, and to provide a framework for interfacing multiple heterogeneous models. The framework provides an application programming interface for interfacing dynamic models defined over spatial domains. It is specifically designed to be independent of the specifics of the modeling methods used, and therefore facilitates seamless integration of heterogeneous models and processes. Furthermore, each model has separate geometries for visualization, simulation, and interfacing, allowing the model developer to choose the most natural geometric representation for each case. Input/output interfaces for visualization and haptics for real-time interactive applications have also been provided.

Multi-phase structural and tectonic evolution of the Andaman Sea Region

NASA Astrophysics Data System (ADS)

Masterton, Sheona; Hill, Catherine; Sagi, David Adam; Webb, Peter; Sevastjanova, Inga

2017-04-01

We present a new regional tectonic interpretation for Myanmar and the Andaman Sea, built within the framework of global plate motions. In our model the Present Day Andaman Sea region has been subjected to multiple phases of extension, culminating in its mid-Miocene to Present Day opening as a rhomboidal pull-apart basin. The Andaman Sea region is historically thought to have developed as a consequence of back-arc opening associated with plate convergence at the Andaman-Nicobar subduction system. We have undertaken detailed structural interpretation of potential field, Landsat and SRTM data, supported by 2-D crustal models of the Andaman Sea. From this analysis we identified several major north-south striking faults and a series of northeast-southwest striking structures across the region. We have also mapped the extent of the Andaman-Nicobar Accretionary Prism, a fore arc trough and volcanic arc, which we associate with a phase of traditional trench-parallel back-arc extension from the Paleocene to the middle Miocene. A regional tectonic event occurred during the middle Miocene that caused the cessation of back-arc extension in the Present Day Andaman Sea and an eastward shift in the locus of arc-related volcanism. At that time, N-S striking faults onshore and offshore Myanmar were reactivated with widespread right-lateral motion. This motion, accompanied by extension along new NE-SW striking faults, facilitated the opening of the Central Andaman Basin as a pull-apart basin (rhombochasm) in which a strike-slip tectonic regime has a greater impact on the mode of opening than the subduction process. The integration of our plate model solution within a global framework allows identification of major plate reorganisation events and their impact on a regional scale. We therefore attribute the onset of pull-apart opening in the Andaman Sea to ongoing clockwise rotation of the western Sundaland margin throughout the late Paleogene and early Miocene, possibly driven by the opening of the South China Sea to the east. Consequently, the obliquity of plate convergence along this margin increased, ultimately resulting in a change from minor strain partitioning to hyper oblique convergence and full strain partitioning by the mid-Miocene. Investigation into the effects of slab-steepening and dynamic subsidence in the Indochina region could be used as further tests of our proposed tectonic evolution of the Andaman Sea.

A computational study of CH 4 storage in porous framework materials with metalated linkers: connecting the atomistic character of CH 4 binding sites to usable capacity

DOE PAGES

Tsivion, Ehud; Mason, Jarad A.; Gonzalez, Miguel. I.; ...

2016-03-29

In order to store natural gas (NG) inexpensively at adequate densities for use as a fuel in the transportation sector, new porous materials are being developed. Our work uses computational methods to explore strategies for improving the usable methane storage capacity of adsorbents, including metal-organic frameworks (MOFs), that feature open-metal sites incorporated into their structure by postsynthetic modification. The adsorption of CH 4 on several open-metal sites is studied by calculating geometries and adsorption energies and analyzing the relevant interaction factors. Approximate site-specific adsorption isotherms are obtained, and the open-metal site contribution to the overall CH 4 usable capacity ismore » evaluated. It is found that sufficient ionic character is required, as exemplified by the strong CH 4 affinities of 2,2'-bipyridine-CaCl 2 and Mg, Ca-catecholate. In addition, it is found that the capacity of a single metal site depends not only on its affinity but also on its geometry, where trigonal or "bent" low-coordinate exposed sites can accommodate three or four methane molecules, as exemplified by Ca-decorated nitrilotriacetic acid. The effect of residual solvent molecules at the open-metal site is also explored, with some positive conclusions. Not only can residual solvent stabilize the open-metal site, surprisingly, solvent molecules do not necessarily reduce CH 4 affinity, but can contribute to increased usable capacity by modifying adsorption interactions.« less

Issues on Building Kazakhstan Geospatial Portal to Implement E-Government

NASA Astrophysics Data System (ADS)

Sagadiyev, K.; Kang, H. K.; Li, K. J.

2016-06-01

A main issue in developing e-government is about how to integrate and organize many complicated processes and different stakeholders. Interestingly geospatial information provides an efficient framework to integrate and organized them. In particular, it is very useful to integrate the process of land management in e-government with geospatial information framework, since most of land management tasks are related with geospatial properties. In this paper, we present a use-case on the e-government project in Kazakhstan for land management. We develop a geoportal to connect many tasks and different users via geospatial information framework. This geoportal is based on open source geospatial software including GeoServer, PostGIS, and OpenLayers. With this geoportal, we expect three achievements as follows. First we establish a transparent governmental process, which is one of main goal of e-government. Every stakeholder monitors what is happening in land management process. Second, we can significantly reduce the time and efforts in the government process. For example, a grant procedure for a building construction has taken more than one year with more than 50 steps. It is expected that this procedure would be reduced to 2 weeks by the geoportal framework. Third we provide a collaborative environment between different governmental structures via the geoportal, while many conflicts and mismatches have been a critical issue of governmental administration processes.

The Heliophysics Data Environment: Open Source, Open Systems and Open Data.

NASA Astrophysics Data System (ADS)

King, Todd; Roberts, Aaron; Walker, Raymond; Thieman, James

2012-07-01

The Heliophysics Data Environment (HPDE) is a place for scientific discovery. Today the Heliophysics Data Environment is a framework of technologies, standards and services which enables the international community to collaborate more effectively in space physics research. Crafting a framework for a data environment begins with defining a model of the tasks to be performed, then defining the functional aspects and the work flow. The foundation of any data environment is an information model which defines the structure and content of the metadata necessary to perform the tasks. In the Heliophysics Data Environment the information model is the Space Physics Archive Search and Extract (SPASE) model and available resources are described by using this model. A described resource can reside anywhere on the internet which makes it possible for a national archive, mission, data center or individual researcher to be a provider. The generated metadata is shared, reviewed and harvested to enable services. Virtual Observatories use the metadata to provide community based portals. Through unique identifiers and registry services tools can quickly discover and access data available anywhere on the internet. This enables a researcher to quickly view and analyze data in a variety of settings and enhances the Heliophysics Data Environment. To illustrate the current Heliophysics Data Environment we present the design, architecture and operation of the Heliophysics framework. We then walk through a real example of using available tools to investigate the effects of the solar wind on Earth's magnetosphere.

Geometry and Mechanics in the Opening of Chiral Seed Pods

NASA Astrophysics Data System (ADS)

Armon, Shahaf; Efrati, Efi; Kupferman, Raz; Sharon, Eran

2011-09-01

We studied the mechanical process of seed pods opening in Bauhinia variegate and found a chirality-creating mechanism, which turns an initially flat pod valve into a helix. We studied configurations of strips cut from pod valve tissue and from composite elastic materials that mimic its structure. The experiments reveal various helical configurations with sharp morphological transitions between them. Using the mathematical framework of “incompatible elasticity,” we modeled the pod as a thin strip with a flat intrinsic metric and a saddle-like intrinsic curvature. Our theoretical analysis quantitatively predicts all observed configurations, thus linking the pod’s microscopic structure and macroscopic conformation. We suggest that this type of incompatible strip is likely to play a role in the self-assembly of chiral macromolecules and could be used for the engineering of synthetic self-shaping devices.

Multi-Disciplinary Analysis and Optimization Frameworks

NASA Technical Reports Server (NTRS)

Naiman, Cynthia Gutierrez

2009-01-01

Since July 2008, the Multidisciplinary Analysis & Optimization Working Group (MDAO WG) of the Systems Analysis Design & Optimization (SAD&O) discipline in the Fundamental Aeronautics Program s Subsonic Fixed Wing (SFW) project completed one major milestone, Define Architecture & Interfaces for Next Generation Open Source MDAO Framework Milestone (9/30/08), and is completing the Generation 1 Framework validation milestone, which is due December 2008. Included in the presentation are: details of progress on developing the Open MDAO framework, modeling and testing the Generation 1 Framework, progress toward establishing partnerships with external parties, and discussion of additional potential collaborations

HERAFitter: Open source QCD fit project

DOE PAGES

Alekhin, S.; Behnke, O.; Belov, P.; ...

2015-07-01

HERAFitter is an open-source package that provides a framework for the determination of the parton distribution functions (PDFs) of the proton and for many different kinds of analyses in Quantum Chromodynamics (QCD). It encodes results from a wide range of experimental measurements in lepton-proton deep inelastic scattering and proton-proton (proton-antiproton) collisions at hadron colliders. These are complemented with a variety of theoretical options for calculating PDF-dependent cross section predictions corresponding to the measurements. The framework covers a large number of the existing methods and schemes used for PDF determination. The data and theoretical predictions are brought together through numerous methodologicalmore » options for carrying out PDF fits and plotting tools to help visualise the results. While primarily based on the approach of collinear factorisation, HERAFitter also provides facilities for fits of dipole models and transverse-momentum dependent PDFs. The package can be used to study the impact of new precise measurements from hadron colliders. This paper describes the general structure of HERAFitter and its wide choice of options.« less

Technical note: The Linked Paleo Data framework - a common tongue for paleoclimatology

NASA Astrophysics Data System (ADS)

McKay, Nicholas P.; Emile-Geay, Julien

2016-04-01

Paleoclimatology is a highly collaborative scientific endeavor, increasingly reliant on online databases for data sharing. Yet there is currently no universal way to describe, store and share paleoclimate data: in other words, no standard. Data standards are often regarded by scientists as mere technicalities, though they underlie much scientific and technological innovation, as well as facilitating collaborations between research groups. In this article, we propose a preliminary data standard for paleoclimate data, general enough to accommodate all the archive and measurement types encountered in a large international collaboration (PAGES 2k). We also introduce a vehicle for such structured data (Linked Paleo Data, or LiPD), leveraging recent advances in knowledge representation (Linked Open Data).The LiPD framework enables quick querying and extraction, and we expect that it will facilitate the writing of open-source community codes to access, analyze, model and visualize paleoclimate observations. We welcome community feedback on this standard, and encourage paleoclimatologists to experiment with the format for their own purposes.

QuantumOptics.jl: A Julia framework for simulating open quantum systems

NASA Astrophysics Data System (ADS)

Krämer, Sebastian; Plankensteiner, David; Ostermann, Laurin; Ritsch, Helmut

2018-06-01

We present an open source computational framework geared towards the efficient numerical investigation of open quantum systems written in the Julia programming language. Built exclusively in Julia and based on standard quantum optics notation, the toolbox offers speed comparable to low-level statically typed languages, without compromising on the accessibility and code readability found in dynamic languages. After introducing the framework, we highlight its features and showcase implementations of generic quantum models. Finally, we compare its usability and performance to two well-established and widely used numerical quantum libraries.

OpenDrift v1.0: a generic framework for trajectory modelling

NASA Astrophysics Data System (ADS)

Dagestad, Knut-Frode; Röhrs, Johannes; Breivik, Øyvind; Ådlandsvik, Bjørn

2018-04-01

OpenDrift is an open-source Python-based framework for Lagrangian particle modelling under development at the Norwegian Meteorological Institute with contributions from the wider scientific community. The framework is highly generic and modular, and is designed to be used for any type of drift calculations in the ocean or atmosphere. A specific module within the OpenDrift framework corresponds to a Lagrangian particle model in the traditional sense. A number of modules have already been developed, including an oil drift module, a stochastic search-and-rescue module, a pelagic egg module, and a basic module for atmospheric drift. The framework allows for the ingestion of an unspecified number of forcing fields (scalar and vectorial) from various sources, including Eulerian ocean, atmosphere and wave models, but also measurements or a priori values for the same variables. A basic backtracking mechanism is inherent, using sign reversal of the total displacement vector and negative time stepping. OpenDrift is fast and simple to set up and use on Linux, Mac and Windows environments, and can be used with minimal or no Python experience. It is designed for flexibility, and researchers may easily adapt or write modules for their specific purpose. OpenDrift is also designed for performance, and simulations with millions of particles may be performed on a laptop. Further, OpenDrift is designed for robustness and is in daily operational use for emergency preparedness modelling (oil drift, search and rescue, and drifting ships) at the Norwegian Meteorological Institute.

Open data models for smart health interconnected applications: the example of openEHR.

PubMed

Demski, Hans; Garde, Sebastian; Hildebrand, Claudia

2016-10-22

Smart Health is known as a concept that enhances networking, intelligent data processing and combining patient data with other parameters. Open data models can play an important role in creating a framework for providing interoperable data services that support the development of innovative Smart Health applications profiting from data fusion and sharing. This article describes a model-driven engineering approach based on standardized clinical information models and explores its application for the development of interoperable electronic health record systems. The following possible model-driven procedures were considered: provision of data schemes for data exchange, automated generation of artefacts for application development and native platforms that directly execute the models. The applicability of the approach in practice was examined using the openEHR framework as an example. A comprehensive infrastructure for model-driven engineering of electronic health records is presented using the example of the openEHR framework. It is shown that data schema definitions to be used in common practice software development processes can be derived from domain models. The capabilities for automatic creation of implementation artefacts (e.g., data entry forms) are demonstrated. Complementary programming libraries and frameworks that foster the use of open data models are introduced. Several compatible health data platforms are listed. They provide standard based interfaces for interconnecting with further applications. Open data models help build a framework for interoperable data services that support the development of innovative Smart Health applications. Related tools for model-driven application development foster semantic interoperability and interconnected innovative applications.

OpenNFT: An open-source Python/Matlab framework for real-time fMRI neurofeedback training based on activity, connectivity and multivariate pattern analysis.

PubMed

Koush, Yury; Ashburner, John; Prilepin, Evgeny; Sladky, Ronald; Zeidman, Peter; Bibikov, Sergei; Scharnowski, Frank; Nikonorov, Artem; De Ville, Dimitri Van

2017-08-01

Neurofeedback based on real-time functional magnetic resonance imaging (rt-fMRI) is a novel and rapidly developing research field. It allows for training of voluntary control over localized brain activity and connectivity and has demonstrated promising clinical applications. Because of the rapid technical developments of MRI techniques and the availability of high-performance computing, new methodological advances in rt-fMRI neurofeedback become possible. Here we outline the core components of a novel open-source neurofeedback framework, termed Open NeuroFeedback Training (OpenNFT), which efficiently integrates these new developments. This framework is implemented using Python and Matlab source code to allow for diverse functionality, high modularity, and rapid extendibility of the software depending on the user's needs. In addition, it provides an easy interface to the functionality of Statistical Parametric Mapping (SPM) that is also open-source and one of the most widely used fMRI data analysis software. We demonstrate the functionality of our new framework by describing case studies that include neurofeedback protocols based on brain activity levels, effective connectivity models, and pattern classification approaches. This open-source initiative provides a suitable framework to actively engage in the development of novel neurofeedback approaches, so that local methodological developments can be easily made accessible to a wider range of users. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

MollDE: a homology modeling framework you can click with.

PubMed

Canutescu, Adrian A; Dunbrack, Roland L

2005-06-15

Molecular Integrated Development Environment (MolIDE) is an integrated application designed to provide homology modeling tools and protocols under a uniform, user-friendly graphical interface. Its main purpose is to combine the most frequent modeling steps in a semi-automatic, interactive way, guiding the user from the target protein sequence to the final three-dimensional protein structure. The typical basic homology modeling process is composed of building sequence profiles of the target sequence family, secondary structure prediction, sequence alignment with PDB structures, assisted alignment editing, side-chain prediction and loop building. All of these steps are available through a graphical user interface. MolIDE's user-friendly and streamlined interactive modeling protocol allows the user to focus on the important modeling questions, hiding from the user the raw data generation and conversion steps. MolIDE was designed from the ground up as an open-source, cross-platform, extensible framework. This allows developers to integrate additional third-party programs to MolIDE. http://dunbrack.fccc.edu/molide/molide.php rl_dunbrack@fccc.edu.

Automated software system for checking the structure and format of ACM SIG documents

NASA Astrophysics Data System (ADS)

Mirza, Arsalan Rahman; Sah, Melike

2017-04-01

Microsoft (MS) Office Word is one of the most commonly used software tools for creating documents. MS Word 2007 and above uses XML to represent the structure of MS Word documents. Metadata about the documents are automatically created using Office Open XML (OOXML) syntax. We develop a new framework, which is called ADFCS (Automated Document Format Checking System) that takes the advantage of the OOXML metadata, in order to extract semantic information from MS Office Word documents. In particular, we develop a new ontology for Association for Computing Machinery (ACM) Special Interested Group (SIG) documents for representing the structure and format of these documents by using OWL (Web Ontology Language). Then, the metadata is extracted automatically in RDF (Resource Description Framework) according to this ontology using the developed software. Finally, we generate extensive rules in order to infer whether the documents are formatted according to ACM SIG standards. This paper, introduces ACM SIG ontology, metadata extraction process, inference engine, ADFCS online user interface, system evaluation and user study evaluations.

OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia

PubMed Central

2012-01-01

Background The OpenTox Framework, developed by the partners in the OpenTox project (http://www.opentox.org), aims at providing a unified access to toxicity data, predictive models and validation procedures. Interoperability of resources is achieved using a common information model, based on the OpenTox ontologies, describing predictive algorithms, models and toxicity data. As toxicological data may come from different, heterogeneous sources, a deployed ontology, unifying the terminology and the resources, is critical for the rational and reliable organization of the data, and its automatic processing. Results The following related ontologies have been developed for OpenTox: a) Toxicological ontology – listing the toxicological endpoints; b) Organs system and Effects ontology – addressing organs, targets/examinations and effects observed in in vivo studies; c) ToxML ontology – representing semi-automatic conversion of the ToxML schema; d) OpenTox ontology– representation of OpenTox framework components: chemical compounds, datasets, types of algorithms, models and validation web services; e) ToxLink–ToxCast assays ontology and f) OpenToxipedia community knowledge resource on toxicology terminology. OpenTox components are made available through standardized REST web services, where every compound, data set, and predictive method has a unique resolvable address (URI), used to retrieve its Resource Description Framework (RDF) representation, or to initiate the associated calculations and generate new RDF-based resources. The services support the integration of toxicity and chemical data from various sources, the generation and validation of computer models for toxic effects, seamless integration of new algorithms and scientifically sound validation routines and provide a flexible framework, which allows building arbitrary number of applications, tailored to solving different problems by end users (e.g. toxicologists). Availability The OpenTox toxicological ontology projects may be accessed via the OpenTox ontology development page http://www.opentox.org/dev/ontology; the OpenTox ontology is available as OWL at http://opentox.org/api/1 1/opentox.owl, the ToxML - OWL conversion utility is an open source resource available at http://ambit.svn.sourceforge.net/viewvc/ambit/branches/toxml-utils/ PMID:22541598

OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia.

PubMed

Tcheremenskaia, Olga; Benigni, Romualdo; Nikolova, Ivelina; Jeliazkova, Nina; Escher, Sylvia E; Batke, Monika; Baier, Thomas; Poroikov, Vladimir; Lagunin, Alexey; Rautenberg, Micha; Hardy, Barry

2012-04-24

The OpenTox Framework, developed by the partners in the OpenTox project (http://www.opentox.org), aims at providing a unified access to toxicity data, predictive models and validation procedures. Interoperability of resources is achieved using a common information model, based on the OpenTox ontologies, describing predictive algorithms, models and toxicity data. As toxicological data may come from different, heterogeneous sources, a deployed ontology, unifying the terminology and the resources, is critical for the rational and reliable organization of the data, and its automatic processing. The following related ontologies have been developed for OpenTox: a) Toxicological ontology - listing the toxicological endpoints; b) Organs system and Effects ontology - addressing organs, targets/examinations and effects observed in in vivo studies; c) ToxML ontology - representing semi-automatic conversion of the ToxML schema; d) OpenTox ontology- representation of OpenTox framework components: chemical compounds, datasets, types of algorithms, models and validation web services; e) ToxLink-ToxCast assays ontology and f) OpenToxipedia community knowledge resource on toxicology terminology.OpenTox components are made available through standardized REST web services, where every compound, data set, and predictive method has a unique resolvable address (URI), used to retrieve its Resource Description Framework (RDF) representation, or to initiate the associated calculations and generate new RDF-based resources.The services support the integration of toxicity and chemical data from various sources, the generation and validation of computer models for toxic effects, seamless integration of new algorithms and scientifically sound validation routines and provide a flexible framework, which allows building arbitrary number of applications, tailored to solving different problems by end users (e.g. toxicologists). The OpenTox toxicological ontology projects may be accessed via the OpenTox ontology development page http://www.opentox.org/dev/ontology; the OpenTox ontology is available as OWL at http://opentox.org/api/1 1/opentox.owl, the ToxML - OWL conversion utility is an open source resource available at http://ambit.svn.sourceforge.net/viewvc/ambit/branches/toxml-utils/

The anthroposphere as an anticipatory system: Open questions on steering the climate.

PubMed

Scolozzi, Rocco; Geneletti, Davide

2017-02-01

Climate change research and action counteracting it affect everyone and would involve cross-societal transformations reshaping the anthroposphere in its entirety. Scrutinizing climate-related science and policies, we recognize attempts to steer the evolution of climate according to expected (or modelled) futures. Such attempts would turn the anthroposphere into a large "anticipatory system", in which human society seeks to anticipate and, possibly, to govern climate dynamics. The chief aim of this discussion paper is to open a critical debate on the climate change paradigm (CCP) drawing on a strategic and systemic framework grounded in the concept of anticipatory system sensu Rosen (1991). The proposed scheme is ambitiously intended to turn an intricate issue into a complex but structured problem that is to say, to make such complexity clear and manageable. This framework emerges from concepts borrowed from different scientific fields (including future studies and system dynamics) and its background lies in a simple quantitative literature overview, relying upon a broad level of analysis. The proposed framework will assist researchers and policy makers in thinking of CCP in terms of an anticipatory system, and in disentangling its interrelated (and sometimes intricate) aspects. In point of fact, several strategic questions related to CCP were not subjected to an adequate transdisciplinary discussion: what are the interplays between physical processes and social-political interventions, who is the observer (what he/she is looking for), and which paradigm is being used (or who defines the desirable future). The proposed scheme allows to structure such various topics in an arrangement which is easier to communicate, highlighting the linkages in between, and making them intelligible and open to verification and discussion. Furthermore, ideally developments will help scientists and policy makers address the strategic gaps between the evidence-based climatological assessments and the plurality of possible answers as applied to the geopolitical contingencies. Copyright © 2016 Elsevier B.V. All rights reserved.

Structural Architecture of Prothrombin in Solution Revealed by Single Molecule Spectroscopy.

PubMed

Pozzi, Nicola; Bystranowska, Dominika; Zuo, Xiaobing; Di Cera, Enrico

2016-08-26

The coagulation factor prothrombin has a complex spatial organization of its modular assembly that comprises the N-terminal Gla domain, kringle-1, kringle-2, and the C-terminal protease domain connected by three intervening linkers. Here we use single molecule Förster resonance energy transfer to access the conformational landscape of prothrombin in solution and uncover structural features of functional significance that extend recent x-ray crystallographic analysis. Prothrombin exists in equilibrium between two alternative conformations, open and closed. The closed conformation predominates (70%) and features an unanticipated intramolecular collapse of Tyr(93) in kringle-1 onto Trp(547) in the protease domain that obliterates access to the active site and protects the zymogen from autoproteolytic conversion to thrombin. The open conformation (30%) is more susceptible to chymotrypsin digestion and autoactivation, and features a shape consistent with recent x-ray crystal structures. Small angle x-ray scattering measurements of prothrombin wild type stabilized 70% in the closed conformation and of the mutant Y93A stabilized 80% in the open conformation directly document two envelopes that differ 50 Å in length. These findings reveal important new details on the conformational plasticity of prothrombin in solution and the drastic structural difference between its alternative conformations. Prothrombin uses the intramolecular collapse of kringle-1 onto the active site in the closed form to prevent autoactivation. The open-closed equilibrium also defines a new structural framework for the mechanism of activation of prothrombin by prothrombinase. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Localized Symmetry Breaking for Tuning Thermal Expansion in ScF 3 Nanoscale Frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Lei; Qin, Feiyu; Sanson, Andrea

The local symmetry, beyond the averaged crystallographic structure, tends to bring unu-sual performances. Negative thermal expansion is a peculiar physical property of solids. Here, we report the delicate design of the localized symmetry breaking to achieve the controllable thermal expansion in ScF3 nano-scale frameworks. Intriguingly, an isotropic zero thermal expansion is concurrently engi-neered by localized symmetry breaking, with a remarkably low coefficient of thermal expansion of about +4.0×10-8/K up to 675K. This mechanism is investigated by the joint analysis of atomic pair dis-tribution function of synchrotron X-ray total scattering and extended X-ray absorption fine structure spectra. A localized rhombohedral distortionmore » presumably plays a critical role in stiffening ScF3 nano-scale frameworks and concomitantly suppressing transverse thermal vibrations of fluorine atoms. This physical scenario is also theoretically corroborated by the extinction of phonon modes with negative Grüneisen parameters in the rhombohedral ScF3. The present work opens an untraditional chemical modification to achieve controllable thermal expansion by breaking local symmetries of materials.« less

Application of preconditioned alternating direction method of multipliers in depth from focal stack

NASA Astrophysics Data System (ADS)

Javidnia, Hossein; Corcoran, Peter

2018-03-01

Postcapture refocusing effect in smartphone cameras is achievable using focal stacks. However, the accuracy of this effect is totally dependent on the combination of the depth layers in the stack. The accuracy of the extended depth of field effect in this application can be improved significantly by computing an accurate depth map, which has been an open issue for decades. To tackle this issue, a framework is proposed based on a preconditioned alternating direction method of multipliers for depth from the focal stack and synthetic defocus application. In addition to its ability to provide high structural accuracy, the optimization function of the proposed framework can, in fact, converge faster and better than state-of-the-art methods. The qualitative evaluation has been done on 21 sets of focal stacks and the optimization function has been compared against five other methods. Later, 10 light field image sets have been transformed into focal stacks for quantitative evaluation purposes. Preliminary results indicate that the proposed framework has a better performance in terms of structural accuracy and optimization in comparison to the current state-of-the-art methods.

The Thermal Hogan - A Means of Surviving the Lunar Night

NASA Technical Reports Server (NTRS)

Fruitwala, Neelay; Ungar, Eugene; Cornwell, John

2013-01-01

document describes the Thermal Hogan, a new shelter concept that would be used on the Moon to moderate the extreme nighttime temperatures, allowing survival of equipment with minimal heater power. It is lightweight, has few mechanical parts, and would be relatively easy to deploy on the Moon. The Lunar Hogan has two parts: an insulated shelter and a thermal mass. The shelter is constructed of multilayer insulation (MLI) draped over a structural framework. Entry and egress are accomplished either by raising the structure or via a door constructed of the same MLI material as the shelter. The thermal mass can be manufactured from locally available materials, either by piling substantially sized rocks to a depth of 0.25 meter, or by filling a 0.25-meter-deep conductive honeycomb-like structure with lunar dust. For ease of transport, the structural framework and honeycomb can be collapsible. The door can be opened by pushing on it in either direction. Gravity would cause it to close and it could be sealed via magnetic strips on the doorframe.

Crystal structure and cation exchanging properties of a novel open framework phosphate of Ce (IV)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bevara, Samatha; Achary, S. N., E-mail: sachary@barc.gov.in; Tyagi, A. K.

2016-05-23

Herein we report preparation, crystal structure and ion exchanging properties of a new phosphate of tetravalent cerium, K{sub 2}Ce(PO{sub 4}){sub 2}. A monoclinic structure having framework type arrangement of Ce(PO{sub 4}){sub 6} units formed by C2O{sub 8} square-antiprism and PO{sub 4} tetrahedra is assigned for K{sub C}e(PO{sub 4}){sub 2}. The K{sup +} ions are occupied in the channels formed by the Ce(PO{sub 4})6 and provide overall charge neutrality. The unique channel type arrangements of the K+ make them exchangeable with other cations. The ion exchanging properties of K2Ce(PO4)2 has been investigated by equilibrating with solution of 90Sr followed by radiometricmore » analysis. In optimum conditions, significant exchange of K+ with Sr2+ with Kd ~ 8000 mL/g is observed. The details of crystal structure and ion exchange properties are explained and a plausible mechanism for ion exchange is presented.« less

Formation of a new archetypal Metal-Organic Framework from a simple monatomic liquid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Metere, Alfredo, E-mail: alfredo.metere@mmk.su.se; Oleynikov, Peter; Dzugutov, Mikhail

2014-12-21

We report a molecular-dynamics simulation of a single-component system of particles interacting via a spherically symmetric potential that is found to form, upon cooling from a liquid state, a low-density porous crystalline phase. Its structure analysis demonstrates that the crystal can be described by a net with a topology that belongs to the class of topologies characteristic of the Metal-Organic Frameworks (MOFs). The observed net is new, and it is now included in the Reticular Chemistry Structure Resource database. The observation that a net topology characteristic of MOF crystals, which are known to be formed by a coordination-driven self-assembly process,more » can be reproduced by a thermodynamically stable configuration of a simple single-component system of particles opens a possibility of using these models in studies of MOF nets. It also indicates that structures with MOF topology, as well as other low-density porous crystalline structures can possibly be produced in colloidal systems of spherical particles, with an appropriate tuning of interparticle interaction.« less

Rationally Designed 2D Covalent Organic Framework with a Brick-Wall Topology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, Song-Liang; Zhang, Kai; Tan, Jing-Bo

In this paper, we report the design and synthesis of an imine-based two-dimensional covalent organic framework (2D COF) with a novel brick-wall topology by judiciously choosing a tritopic T-shaped building block and a ditopic linear linker. Unlike the main body of COF frameworks reported to-date, which consists of higher-symmetry 2D topologies, the unconventional layered brick-wall topology have only been proposed but never been realized experimentally. The brick-wall structure was characterized by powder X-ray diffraction analysis, FT-IR, solid state 13C NMR spectroscopy, nitrogen, and carbon oxide adsorption-desorption measurements as well as theoretical simulations. Lastly, our present work opens the door tomore » the design of novel 2D COFs and will broaden the scope of emerging COF materials.« less

Comparative SWOT analysis of strategic environmental assessment systems in the Middle East and North Africa region.

PubMed

Rachid, G; El Fadel, M

2013-08-15

This paper presents a SWOT analysis of SEA systems in the Middle East North Africa region through a comparative examination of the status, application and structure of existing systems based on country-specific legal, institutional and procedural frameworks. The analysis is coupled with the multi-attribute decision making method (MADM) within an analytical framework that involves both performance analysis based on predefined evaluation criteria and countries' self-assessment of their SEA system through open-ended surveys. The results show heterogenous status with a general delayed progress characterized by varied levels of weaknesses embedded in the legal and administrative frameworks and poor integration with the decision making process. Capitalizing on available opportunities, the paper highlights measures to enhance the development and enactment of SEA in the region. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bifunctional 3D porous Cu(I) metal-organic framework with gas sorption and luminescent properties

NASA Astrophysics Data System (ADS)

Xing, Guang'en; Zhang, Yan; Cao, Xiulian

2017-10-01

A new Cu(I) metal-organic framework, namely [Cu(L)]2n·n(H2O) (1 HL = 5-(4-Pyridyl)-1H-tetrazole), has been successfully synthesized via the solvothermal reactions of CuI and 5-(4-Pyridyl)-1H-tetrazole ligand, and further characterized by elemental analysis, powder X-ray diffraction analysis, thermal analysis and single crystal X-ray structural analysis. The L- ligand displays a μ4-N2, N3, N4, N5 coordination mode bridging Cu(I) ions into a 3D porous framework with the opened 1D channels filled by the lattice water molecules. Gas sorption investigations indicated that compound 1 can selectively adsorb CO2 over N2 at 298 K, and luminescent properties investigations revealed that compound 1 features luminescent sensing function for nitrobenzene.

Rationally Designed 2D Covalent Organic Framework with a Brick-Wall Topology

DOE PAGES

Cai, Song-Liang; Zhang, Kai; Tan, Jing-Bo; ...

2016-11-23

In this paper, we report the design and synthesis of an imine-based two-dimensional covalent organic framework (2D COF) with a novel brick-wall topology by judiciously choosing a tritopic T-shaped building block and a ditopic linear linker. Unlike the main body of COF frameworks reported to-date, which consists of higher-symmetry 2D topologies, the unconventional layered brick-wall topology have only been proposed but never been realized experimentally. The brick-wall structure was characterized by powder X-ray diffraction analysis, FT-IR, solid state 13C NMR spectroscopy, nitrogen, and carbon oxide adsorption-desorption measurements as well as theoretical simulations. Lastly, our present work opens the door tomore » the design of novel 2D COFs and will broaden the scope of emerging COF materials.« less

Structured Overlapping Grid Simulations of Contra-rotating Open Rotor Noise

NASA Technical Reports Server (NTRS)

Housman, Jeffrey A.; Kiris, Cetin C.

2015-01-01

Computational simulations using structured overlapping grids with the Launch Ascent and Vehicle Aerodynamics (LAVA) solver framework are presented for predicting tonal noise generated by a contra-rotating open rotor (CROR) propulsion system. A coupled Computational Fluid Dynamics (CFD) and Computational AeroAcoustics (CAA) numerical approach is applied. Three-dimensional time-accurate hybrid Reynolds Averaged Navier-Stokes/Large Eddy Simulation (RANS/LES) CFD simulations are performed in the inertial frame, including dynamic moving grids, using a higher-order accurate finite difference discretization on structured overlapping grids. A higher-order accurate free-stream preserving metric discretization with discrete enforcement of the Geometric Conservation Law (GCL) on moving curvilinear grids is used to create an accurate, efficient, and stable numerical scheme. The aeroacoustic analysis is based on a permeable surface Ffowcs Williams-Hawkings (FW-H) approach, evaluated in the frequency domain. A time-step sensitivity study was performed using only the forward row of blades to determine an adequate time-step. The numerical approach is validated against existing wind tunnel measurements.

Network Community Detection based on the Physarum-inspired Computational Framework.

PubMed

Gao, Chao; Liang, Mingxin; Li, Xianghua; Zhang, Zili; Wang, Zhen; Zhou, Zhili

2016-12-13

Community detection is a crucial and essential problem in the structure analytics of complex networks, which can help us understand and predict the characteristics and functions of complex networks. Many methods, ranging from the optimization-based algorithms to the heuristic-based algorithms, have been proposed for solving such a problem. Due to the inherent complexity of identifying network structure, how to design an effective algorithm with a higher accuracy and a lower computational cost still remains an open problem. Inspired by the computational capability and positive feedback mechanism in the wake of foraging process of Physarum, which is a large amoeba-like cell consisting of a dendritic network of tube-like pseudopodia, a general Physarum-based computational framework for community detection is proposed in this paper. Based on the proposed framework, the inter-community edges can be identified from the intra-community edges in a network and the positive feedback of solving process in an algorithm can be further enhanced, which are used to improve the efficiency of original optimization-based and heuristic-based community detection algorithms, respectively. Some typical algorithms (e.g., genetic algorithm, ant colony optimization algorithm, and Markov clustering algorithm) and real-world datasets have been used to estimate the efficiency of our proposed computational framework. Experiments show that the algorithms optimized by Physarum-inspired computational framework perform better than the original ones, in terms of accuracy and computational cost. Moreover, a computational complexity analysis verifies the scalability of our framework.

Inquiry-based science education: towards a pedagogical framework for primary school teachers

NASA Astrophysics Data System (ADS)

van Uum, Martina S. J.; Verhoeff, Roald P.; Peeters, Marieke

2016-02-01

Inquiry-based science education (IBSE) has been promoted as an inspiring way of learning science by engaging pupils in designing and conducting their own scientific investigations. For primary school teachers, the open nature of IBSE poses challenges as they often lack experience in supporting their pupils during the different phases of an open IBSE project, such as formulating a research question and designing and conducting an investigation. The current study aims to meet these challenges by presenting a pedagogical framework in which four domains of scientific knowledge are addressed in seven phases of inquiry. The framework is based on video analyses of pedagogical interventions by primary school teachers participating in open IBSE projects. Our results show that teachers can guide their pupils successfully through the process of open inquiry by explicitly addressing the conceptual, epistemic, social and/or procedural domain of scientific knowledge in the subsequent phases of inquiry. The paper concludes by suggesting further research to validate our framework and to develop a pedagogy for primary school teachers to guide their pupils through the different phases of open inquiry.

Critically Thinking about Harry Potter: A Framework for Discussing Controversial Works in the English Classroom.

ERIC Educational Resources Information Center

Marshall, Joanne M.

2003-01-01

Notes that at the school level and in the classroom, English educators can lead the way in open discussion, particularly discussion about books such as the Harry Potter series. Offers a seven-step framework as a way to begin an open discussion. Concludes that the framework acknowledges those concerns and provides a voice for them while also…

An open data mining framework for the analysis of medical images: application on obstructive nephropathy microscopy images.

PubMed

Doukas, Charalampos; Goudas, Theodosis; Fischer, Simon; Mierswa, Ingo; Chatziioannou, Aristotle; Maglogiannis, Ilias

2010-01-01

This paper presents an open image-mining framework that provides access to tools and methods for the characterization of medical images. Several image processing and feature extraction operators have been implemented and exposed through Web Services. Rapid-Miner, an open source data mining system has been utilized for applying classification operators and creating the essential processing workflows. The proposed framework has been applied for the detection of salient objects in Obstructive Nephropathy microscopy images. Initial classification results are quite promising demonstrating the feasibility of automated characterization of kidney biopsy images.

Porous framework of T{sub 2}[Fe(CN){sub 6}].xH{sub 2}O with T=Co, Ni, Cu, Zn, and H{sub 2} storage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Avila, M.; Reguera, L.; Rodriguez-Hernandez, J.

2008-11-15

The materials under study were prepared from aqueous solutions of ferrocyanic acid and salts of the involved transition metals and their crystal structure solved and refined from X-ray powder diffraction data. Complementary information from thermogravimetric, infrared and Moessbauer data was also used for the structural study. Three different crystal structures were found: hexagonal (P-3) for Zn with the zinc atom coordinated to three N ends of CN groups plus a water molecule, cubic (Pm-3m) for Ni and Cu, and monoclinic (P2{sub 1}/m) for Co. For Ni and Cu the obtained solids have an open channel framework related to 50% ofmore » vacancies for the building unit, [Fe(CN){sub 6}]. In the as-synthesized material the framework free volume is occupied by coordinated and hydrogen-bonded water molecules. These of hexacyanoferrates (II) have received certain attention as prototype of materials for the hydrogen storage. In the anhydrous phase of Ni and Cu, 50% of the metal (T) coordination sites, located at the cavities surface, will be available to interact with the hydrogen molecule. However, when the crystal waters are removed the porous frameworks collapse as it is suggested by H{sub 2} and CO{sub 2} adsorption data. For Co, a structure of stacked layers was found where the cobalt atoms have both tetrahedral and octahedral coordination. The layers remain together through a network of hydrogen-bonding interactions between coordinated and weakly bonded water molecules. No H{sub 2} adsorption was observed in the anhydrous phase of Co. For Zn, the porous framework remains stable on the water removal but with a system of narrow channels and a small available volume, also inaccessible to H{sub 2}. - Graphical abstract: Structure of stacked layers for CO{sub 2}[Fe(CN){sub 6}].xH{sub 2}O.« less

Growing a National Learning Environments and Resources Network for Science, Mathematics, Engineering, and Technology Education: Current Issues and Opportunities for the NSDL Program; Open Linking in the Scholarly Information Environment Using the OpenURL Framework; The HeadLine Personal Information Environment: Evaluation Phase One.

ERIC Educational Resources Information Center

Zia, Lee L.; Van de Sompel, Herbert; Beit-Arie, Oren; Gambles, Anne

2001-01-01

Includes three articles that discuss the National Science Foundation's National Science, Mathematics, Engineering, and Technology Education Digital Library (NSDL) program; the OpenURL framework for open reference linking in the Web-based scholarly information environment; and HeadLine (Hybrid Electronic Access and Delivery in the Library Networked…

Investigation of Oxygen Reduction Activity of Catalysts Derived from Co and Co/Zn Methyl-Imidazolate Frameworks in Proton Exchange Membrane Fuel Cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chong, Lina; Goenaga, Gabriel A.; Williams, Kia

We demonstrated that the oxygen reduction reaction (ORR) activity over the catalysts derived from pyrolyzed cobalt zeolitic imidazolate frameworks depends strongly on the imidazole ligand structure and cobalt content. The activity and durability of these catalysts were tested in the proton exchange membrane fuel cell for the first time. The membrane electrode assembly containing a catalyst derived from Co/Zn bimetallic ZIF at cathode achieved an open circuit voltage of 0.93 V, a current density of 28 mA cm-2 at 0.8 ViR-free and a peak power density of 374 mW cm-2.

SMILI?: A Framework for Interfaces to Learning Data in Open Learner Models, Learning Analytics and Related Fields

ERIC Educational Resources Information Center

Bull, Susan; Kay, Judy

2016-01-01

The SMILI? (Student Models that Invite the Learner In) Open Learner Model Framework was created to provide a coherent picture of the many and diverse forms of Open Learner Models (OLMs). The aim was for SMILI? to provide researchers with a systematic way to describe, compare and critique OLMs. We expected it to highlight those areas where there…

Sn Nanoparticles Encapsulated in 3D Nanoporous Carbon Derived from a Metal–Organic Framework for Anode Material in Lithium-Ion Batteries

DOE PAGES

Guo, Yuanyuan; Zeng, Xiaoqiao; Zhang, Yu; ...

2017-05-04

Three-dimensional nanoporous carbon frameworks encapsulated Sn nanoparticles (Sn@3D-NPC) are developed by a facile method as an improved lithium ion battery anode. The Sn@3D-NPC delivers a reversible capacity of 740 mAh g –1 after 200 cycles at a current density of 200 mA g –1, corresponding to a capacity retention of 85% (against the second capacity) and high rate capability (300 mAh g –1 at 5 A g –1). Compared to the Sn nanoparticles (SnNPs), such improvements are attributed to the 3D porous and conductive framework. The whole structure can provide not only the high electrical conductivity that facilities the electronmore » transfer but also the elasticity that will suppress the volume expansion and aggregation of SnNPs during the charge and discharge process. Lastly, this work opens a new application of metal–organic frameworks in energy storage.« less

Sn Nanoparticles Encapsulated in 3D Nanoporous Carbon Derived from a Metal-Organic Framework for Anode Material in Lithium-Ion Batteries.

PubMed

Guo, Yuanyuan; Zeng, Xiaoqiao; Zhang, Yu; Dai, Zhengfei; Fan, Haosen; Huang, Ying; Zhang, Weina; Zhang, Hua; Lu, Jun; Huo, Fengwei; Yan, Qingyu

2017-05-24

Three-dimensional nanoporous carbon frameworks encapsulated Sn nanoparticles (Sn@3D-NPC) are developed by a facile method as an improved lithium ion battery anode. The Sn@3D-NPC delivers a reversible capacity of 740 mAh g -1 after 200 cycles at a current density of 200 mA g -1 , corresponding to a capacity retention of 85% (against the second capacity) and high rate capability (300 mAh g -1 at 5 A g -1 ). Compared to the Sn nanoparticles (SnNPs), such improvements are attributed to the 3D porous and conductive framework. The whole structure can provide not only the high electrical conductivity that facilities the electron transfer but also the elasticity that will suppress the volume expansion and aggregation of SnNPs during the charge and discharge process. This work opens a new application of metal-organic frameworks in energy storage.

A Framework for Building and Reasoning with Adaptive and Interoperable PMESII Models

DTIC Science & Technology

2007-11-01

Description Logic SOA Service Oriented Architecture SPARQL Simple Protocol And RDF Query Language SQL Standard Query Language SROM Stability and...another by providing a more expressive ontological structure for one of the models, e.g., semantic networks can be mapped to first- order logical...Pellet is an open-source reasoner that works with OWL-DL. It accepts the SPARQL protocol and RDF query language ( SPARQL ) and provides a Java API to

Experiences with HPTN 067/ADAPT Study-Provided Open-Label PrEP Among Women in Cape Town: Facilitators and Barriers Within a Mutuality Framework.

PubMed

Amico, K Rivet; Wallace, Melissa; Bekker, Linda-Gail; Roux, Surita; Atujuna, Millicent; Sebastian, Elaine; Dye, Bonnie J; Elharrar, Vanessa; Grant, Robert M

2017-05-01

Placebo-controlled trials of pre-exposure prophylaxis (PrEP) have reported challenges with study-product uptake and use, with the greatest challenges reported in studies with young women in sub-Saharan Africa. We conducted a qualitative sub-study to explore experiences with open-label PrEP among young women in Cape Town, South Africa participating in HTPN 067/Alternative Dosing to Augment Pre-Exposure Prophylaxis Pill Taking (ADAPT). HPTN 067/ADAPT provided open label oral FTC/TDF PrEP to young women in Cape Town, South Africa who were randomized to daily and non-daily PrEP regimens. Following completion of study participation, women were invited into a qualitative sub-study including focus groups and in-depth interviews. Interviews and groups followed a semi-structured guide, were recorded, transcribed, and translated to English from isiXhosa, and coded using framework analysis. Sixty of the 179 women enrolled in HPTN 067/ADAPT participated in either a focus group (six groups for a total of 42 participants) or an in-depth interview (n = 18). This sample of mostly young, unmarried women identified facilitators of and barriers to PrEP use, as well as factors influencing study participation. Cross-cutting themes characterizing discourse suggested that women placed high value on contributing to the well-being of one's community (Ubuntu), experienced a degree of skepticism towards PrEP and the study more generally, and reported a wide range of approaches towards PrEP (ranging from active avoidance to high levels of persistence and adherence). A Mutuality Framework is proposed that identifies four dynamics (distrust, uncertainty, alignment, and mutuality) that represent distinct interactions between self, community and study and serve to contextualize women's experiences. Implications for better understanding PrEP use, and non-use, and intervention opportunities are discussed. In this sample of women, PrEP use in the context of an open-label research trial was heavily influenced by underlying beliefs about safety, reciprocity of contributions to community, and trust in transparency and integrity of the research. Greater attention to factors positioning women in the different dynamics of the proposed Mutuality Framework could direct intervention approaches in clinical trials, as well as open-label PrEP scale-up.

Moose: An Open-Source Framework to Enable Rapid Development of Collaborative, Multi-Scale, Multi-Physics Simulation Tools

NASA Astrophysics Data System (ADS)

Slaughter, A. E.; Permann, C.; Peterson, J. W.; Gaston, D.; Andrs, D.; Miller, J.

2014-12-01

The Idaho National Laboratory (INL)-developed Multiphysics Object Oriented Simulation Environment (MOOSE; www.mooseframework.org), is an open-source, parallel computational framework for enabling the solution of complex, fully implicit multiphysics systems. MOOSE provides a set of computational tools that scientists and engineers can use to create sophisticated multiphysics simulations. Applications built using MOOSE have computed solutions for chemical reaction and transport equations, computational fluid dynamics, solid mechanics, heat conduction, mesoscale materials modeling, geomechanics, and others. To facilitate the coupling of diverse and highly-coupled physical systems, MOOSE employs the Jacobian-free Newton-Krylov (JFNK) method when solving the coupled nonlinear systems of equations arising in multiphysics applications. The MOOSE framework is written in C++, and leverages other high-quality, open-source scientific software packages such as LibMesh, Hypre, and PETSc. MOOSE uses a "hybrid parallel" model which combines both shared memory (thread-based) and distributed memory (MPI-based) parallelism to ensure efficient resource utilization on a wide range of computational hardware. MOOSE-based applications are inherently modular, which allows for simulation expansion (via coupling of additional physics modules) and the creation of multi-scale simulations. Any application developed with MOOSE supports running (in parallel) any other MOOSE-based application. Each application can be developed independently, yet easily communicate with other applications (e.g., conductivity in a slope-scale model could be a constant input, or a complete phase-field micro-structure simulation) without additional code being written. This method of development has proven effective at INL and expedites the development of sophisticated, sustainable, and collaborative simulation tools.

WannierTools: An open-source software package for novel topological materials

NASA Astrophysics Data System (ADS)

Wu, QuanSheng; Zhang, ShengNan; Song, Hai-Feng; Troyer, Matthias; Soluyanov, Alexey A.

2018-03-01

We present an open-source software package WannierTools, a tool for investigation of novel topological materials. This code works in the tight-binding framework, which can be generated by another software package Wannier90 (Mostofi et al., 2008). It can help to classify the topological phase of a given material by calculating the Wilson loop, and can get the surface state spectrum, which is detected by angle resolved photoemission (ARPES) and in scanning tunneling microscopy (STM) experiments. It also identifies positions of Weyl/Dirac points and nodal line structures, calculates the Berry phase around a closed momentum loop and Berry curvature in a part of the Brillouin zone (BZ).

Chemical landscape analysis with the OpenTox framework.

PubMed

Jeliazkova, Nina; Jeliazkov, Vedrin

2012-01-01

The Structure-Activity Relationships (SAR) landscape and activity cliffs concepts have their origins in medicinal chemistry and receptor-ligand interactions modelling. While intuitive, the definition of an activity cliff as a "pair of structurally similar compounds with large differences in potency" is commonly recognized as ambiguous. This paper proposes a new and efficient method for identifying activity cliffs and visualization of activity landscapes. The activity cliffs definition could be improved to reflect not the cliff steepness alone, but also the rate of the change of the steepness. The method requires explicitly setting similarity and activity difference thresholds, but provides means to explore multiple thresholds and to visualize in a single map how the thresholds affect the activity cliff identification. The identification of the activity cliffs is addressed by reformulating the problem as a statistical one, by introducing a probabilistic measure, namely, calculating the likelihood of a compound having large activity difference compared to other compounds, while being highly similar to them. The likelihood is effectively a quantification of a SAS Map with defined thresholds. Calculating the likelihood relies on four counts only, and does not require the pairwise matrix storage. This is a significant advantage, especially when processing large datasets. The method generates a list of individual compounds, ranked according to the likelihood of their involvement in the formation of activity cliffs, and goes beyond characterizing cliffs by structure pairs only. The visualisation is implemented by considering the activity plane fixed and analysing the irregularities of the similarity itself. It provides a convenient analogy to a topographic map and may help identifying the most appropriate similarity representation for each specific SAR space. The proposed method has been applied to several datasets, representing different biological activities. Finally, the method is implemented as part of an existing open source Ambit package and could be accessed via an OpenTox API compliant web service and via an interactive application, running within a modern, JavaScript enabled web browser. Combined with the functionalities already offered by the OpenTox framework, like data sharing and remote calculations, it could be a useful tool for exploring chemical landscapes online.

Extreme Mechanics: Self-Folding Origami

NASA Astrophysics Data System (ADS)

Santangelo, Christian D.

2017-03-01

Origami has emerged as a tool for designing three-dimensional structures from flat films. Because they can be fabricated by lithographic or roll-to-roll processing techniques, they have great potential for the manufacture of complicated geometries and devices. This article discusses the mechanics of origami and kirigami with a view toward understanding how to design self-folding origami structures. Whether an origami structure can be made to fold autonomously depends strongly on the geometry and kinematics of the origami fold pattern. This article collects some of the results on origami rigidity into a single framework, and discusses how these aspects affect the foldability of origami. Despite recent progress, most problems in origami and origami design remain completely open.

ENKI - An Open Source environmental modelling platfom

NASA Astrophysics Data System (ADS)

Kolberg, S.; Bruland, O.

2012-04-01

The ENKI software framework for implementing spatio-temporal models is now released under the LGPL license. Originally developed for evaluation and comparison of distributed hydrological model compositions, ENKI can be used for simulating any time-evolving process over a spatial domain. The core approach is to connect a set of user specified subroutines into a complete simulation model, and provide all administrative services needed to calibrate and run that model. This includes functionality for geographical region setup, all file I/O, calibration and uncertainty estimation etc. The approach makes it easy for students, researchers and other model developers to implement, exchange, and test single routines and various model compositions in a fixed framework. The open-source license and modular design of ENKI will also facilitate rapid dissemination of new methods to institutions engaged in operational water resource management. ENKI uses a plug-in structure to invoke separately compiled subroutines, separately built as dynamic-link libraries (dlls). The source code of an ENKI routine is highly compact, with a narrow framework-routine interface allowing the main program to recognise the number, types, and names of the routine's variables. The framework then exposes these variables to the user within the proper context, ensuring that distributed maps coincide spatially, time series exist for input variables, states are initialised, GIS data sets exist for static map data, manually or automatically calibrated values for parameters etc. By using function calls and memory data structures to invoke routines and facilitate information flow, ENKI provides good performance. For a typical distributed hydrological model setup in a spatial domain of 25000 grid cells, 3-4 time steps simulated per second should be expected. Future adaptation to parallel processing may further increase this speed. New modifications to ENKI include a full separation of API and user interface, making it possible to run ENKI from GIS programs and other software environments. ENKI currently compiles under Windows and Visual Studio only, but ambitions exist to remove the platform and compiler dependencies.

Extended physics as a theoretical framework for systems biology?

PubMed

Miquel, Paul-Antoine

2011-08-01

In this essay we examine whether a theoretical and conceptual framework for systems biology could be built from the Bailly and Longo (2008, 2009) proposal. These authors aim to understand life as a coherent critical structure, and propose to develop an extended physical approach of evolution, as a diffusion of biomass in a space of complexity. Their attempt leads to a simple mathematical reconstruction of Gould's assumption (1989) concerning the bacterial world as a "left wall of least complexity" that we will examine. Extended physical systems are characterized by their constructive properties. Time is acting and new properties emerge by their history that can open the list of their initial properties. This conceptual and theoretical framework is nothing more than a philosophical assumption, but as such it provides a new and exciting approach concerning the evolution of life, and the transition between physics and biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

When Playing Meets Learning: Methodological Framework for Designing Educational Games

NASA Astrophysics Data System (ADS)

Linek, Stephanie B.; Schwarz, Daniel; Bopp, Matthias; Albert, Dietrich

Game-based learning builds upon the idea of using the motivational potential of video games in the educational context. Thus, the design of educational games has to address optimizing enjoyment as well as optimizing learning. Within the EC-project ELEKTRA a methodological framework for the conceptual design of educational games was developed. Thereby state-of-the-art psycho-pedagogical approaches were combined with insights of media-psychology as well as with best-practice game design. This science-based interdisciplinary approach was enriched by enclosed empirical research to answer open questions on educational game-design. Additionally, several evaluation-cycles were implemented to achieve further improvements. The psycho-pedagogical core of the methodology can be summarized by the ELEKTRA's 4Ms: Macroadaptivity, Microadaptivity, Metacognition, and Motivation. The conceptual framework is structured in eight phases which have several interconnections and feedback-cycles that enable a close interdisciplinary collaboration between game design, pedagogy, cognitive science and media psychology.

Investigating the Pressure-Induced Amorphization of Zeolitic Imidazolate Framework ZIF-8: Mechanical Instability Due to Shear Mode Softening.

PubMed

Ortiz, Aurélie U; Boutin, Anne; Fuchs, Alain H; Coudert, François-Xavier

2013-06-06

We provide the first molecular dynamics study of the mechanical instability that is the cause of pressure-induced amorphization of zeolitic imidazolate framework ZIF-8. By measuring the elastic constants of ZIF-8 up to the amorphization pressure, we show that the crystal-to-amorphous transition is triggered by the mechanical instability of ZIF-8 under compression, due to shear mode softening of the material. No similar softening was observed under temperature increase, explaining the absence of temperature-induced amorphization in ZIF-8. We also demonstrate the large impact of the presence of adsorbate in the pores on the mechanical stability and compressibility of the framework, increasing its shear stability. This first molecular dynamics study of ZIF mechanical properties under variations of pressure, temperature, and pore filling opens the way to a more comprehensive understanding of their mechanical stability, structural transitions, and amorphization.

Automated Analysis of Stateflow Models

NASA Technical Reports Server (NTRS)

Bourbouh, Hamza; Garoche, Pierre-Loic; Garion, Christophe; Gurfinkel, Arie; Kahsaia, Temesghen; Thirioux, Xavier

2017-01-01

Stateflow is a widely used modeling framework for embedded and cyber physical systems where control software interacts with physical processes. In this work, we present a framework a fully automated safety verification technique for Stateflow models. Our approach is two-folded: (i) we faithfully compile Stateflow models into hierarchical state machines, and (ii) we use automated logic-based verification engine to decide the validity of safety properties. The starting point of our approach is a denotational semantics of State flow. We propose a compilation process using continuation-passing style (CPS) denotational semantics. Our compilation technique preserves the structural and modal behavior of the system. The overall approach is implemented as an open source toolbox that can be integrated into the existing Mathworks Simulink Stateflow modeling framework. We present preliminary experimental evaluations that illustrate the effectiveness of our approach in code generation and safety verification of industrial scale Stateflow models.

Order-disorder antiferroelectric phase transition in a hybrid inorganic-organic framework with the perovskite architecture.

PubMed

Jain, Prashant; Dalal, Naresh S; Toby, Brian H; Kroto, Harold W; Cheetham, Anthony K

2008-08-13

[(CH3)2NH2]Zn(HCOO)3, 1, adopts a structure that is analogous to that of a traditional perovskite, ABX3, with A = [(CH3)2NH2], B = Zn, and X = HCOO. The hydrogen atoms of the dimethyl ammonium cation, which hydrogen bond to oxygen atoms of the formate framework, are disordered at room temperature. X-ray powder diffraction, dielectric constant, and specific heat data show that 1 undergoes an order-disorder phase transition on cooling below 156 K. We present evidence that this is a classical paraelectric to antiferroelectric phase transition that is driven by ordering of the hydrogen atoms. This sort of electrical ordering associated with order-disorder phase transition is unprecedented in hybrid frameworks and opens up an exciting new direction in rational synthetic strategies to create extended hybrid networks for applications in ferroic-related fields.

Discerning Thermodynamic Basis of Self-Organization in Critical Zone Structure and Function

NASA Astrophysics Data System (ADS)

Richardson, M.; Kumar, P.

2017-12-01

Self-organization characterizes the spontaneous emergence of order. Self-organization in the Critical Zone, the region of Earth's skin from below the groundwater table to the top of the vegetation canopy, involves the interaction of biotic and abiotic processes occurring through a hierarchy of temporal and spatial scales. The self-organization is sustained through input of energy and material in an open system framework, and the resulting formations are called dissipative structures. Why do these local states of organization form and how are they thermodynamically favorable? We hypothesize that structure formation is linked to energy conversion and matter throughput rates across driving gradients. Furthermore, we predict that structures in the Critical Zone evolve based on local availability of nutrients, water, and energy. By considering ecosystems as open thermodynamic systems, we model and study the throughput signatures on short times scales to determine origins and characteristics of ecosystem structure. This diagnostic approach allows us to use fluxes of matter and energy to understand the thermodynamic drivers of the system. By classifying the fluxes and dynamics in a system, we can identify patterns to determine the thermodynamic drivers for organized states. Additionally, studying the partitioning of nutrients, water, and energy throughout ecosystems through dissipative structures will help identify reasons for structure shapes and how these shapes impact major Critical Zone functions.

Ionothermal synthesis of open-framework metal phosphates with a Kagomé lattice network exhibiting canted anti-ferromagnetism† †Electronic supplementary information (ESI) available: Cif files, atomic parameters, X-ray diffraction patterns, IR spectra, TG curves, and thermal ellipsoid plot and atomic label schemes of compound 1–4. See DOI: 10.1039/c4tc00290c Click here for additional data file.

PubMed Central

Wang, Guangmei; Valldor, Martin; Mallick, Bert

2014-01-01

Four open-framework transition-metal phosphates; (NH4)2Co3(HPO4)2F4 (1), (NH4)Co3(HPO4)2(H2PO4)F2 (2), KCo3(HPO4)2(H2PO4)F2 (3), and KFe3(HPO4)2(H2PO4)F2 (4); are prepared by ionothermal synthesis using pyridinium hexafluorophosphate as the ionic liquid. Single-crystal X-ray diffraction analyses reveal that the four compounds contain cobalt/iron–oxygen/fluoride layers with Kagomé topology composed of interlinked face-sharing MO3F3/MO4F2 octahedra. PO3OH pseudo-tetrahedral groups augment the [M3O6F4] (1)/[M3O8F2] layers on both sides to give M3(HPO4)2F4 (1) and M3(HPO4)2F2 (2–4) layers. These layers are stacked along the a axis in a sequence AA…, resulting in the formation of a layer structure for (NH4)2Co3(HPO4)2F4(1). In NH4Co3(HPO4)2(H2PO4)F2 and KM3(HPO4)2(H2PO4)F2, the M3(HPO4)2F2 layers are stacked along the a axis in a sequence AAi… and are connected by [PO3(OH)] tetrahedra, giving rise to a 3-D open framework structure with 10-ring channels along the [001] direction. The negative charges of the inorganic framework are balanced by K+/NH4 + ions located within the channels. The magnetic transition metal cations themselves form layers with stair-case Kagomé topology. Magnetic susceptibility and magnetization measurements reveal that all four compounds exhibit a canted anti-ferromagnetic ground state (T c = 10 or 13 K for Co and T c = 27 K for Fe) with different canting angles. The full orbital moment is observed for both Co2+ and Fe2+. PMID:25580250

Open semantic annotation of scientific publications using DOMEO.

PubMed

Ciccarese, Paolo; Ocana, Marco; Clark, Tim

2012-04-24

Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model. The Domeo Annotation Tool was developed in tandem with this open model, the Annotation Ontology (AO). Development of both the Annotation Framework and the open model was driven by requirements of several different types of alpha users, including bench scientists and biomedical curators from university research labs, online scientific communities, publishing and pharmaceutical companies.Several use cases were incrementally implemented by the toolkit. These use cases in biomedical communications include personal note-taking, group document annotation, semantic tagging, claim-evidence-context extraction, reagent tagging, and curation of textmining results from entity extraction algorithms. We report on the Domeo user interface here. Domeo has been deployed in beta release as part of the NIH Neuroscience Information Framework (NIF, http://www.neuinfo.org) and is scheduled for production deployment in the NIF's next full release.Future papers will describe other aspects of this work in detail, including Annotation Framework Services and components for integrating with external textmining services, such as the NCBO Annotator web service, and with other textmining applications using the Apache UIMA framework.

Open semantic annotation of scientific publications using DOMEO

PubMed Central

2012-01-01

Background Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model. Methods The Domeo Annotation Tool was developed in tandem with this open model, the Annotation Ontology (AO). Development of both the Annotation Framework and the open model was driven by requirements of several different types of alpha users, including bench scientists and biomedical curators from university research labs, online scientific communities, publishing and pharmaceutical companies. Several use cases were incrementally implemented by the toolkit. These use cases in biomedical communications include personal note-taking, group document annotation, semantic tagging, claim-evidence-context extraction, reagent tagging, and curation of textmining results from entity extraction algorithms. Results We report on the Domeo user interface here. Domeo has been deployed in beta release as part of the NIH Neuroscience Information Framework (NIF, http://www.neuinfo.org) and is scheduled for production deployment in the NIF’s next full release. Future papers will describe other aspects of this work in detail, including Annotation Framework Services and components for integrating with external textmining services, such as the NCBO Annotator web service, and with other textmining applications using the Apache UIMA framework. PMID:22541592

Guest-Induced Two-Way Structural Transformation in a Layered Metal-Organic Framework Thin Film.

PubMed

Haraguchi, Tomoyuki; Otsubo, Kazuya; Sakata, Osami; Fujiwara, Akihiko; Kitagawa, Hiroshi

2016-12-28

Fabrication of thin films made of metal-organic frameworks (MOFs) has been intensively pursued for practical applications that use the structural response of MOFs. However, to date, only physisorption-induced structural response has been studied in these films. Chemisorption can be expected to provide a remarkable structural response because of the formation of bonds between guest molecules and reactive metal sites in host MOFs. Here, we report that chemisorption-induced two-way structural transformation in a nanometer-sized MOF thin film. We prepared a two-dimensional layered-type MOF Fe[Pt(CN) 4 ] thin film using a step-by-step approach. Although the as-synthesized film showed poor crystallinity, the dehydrated form of this thin film had a highly oriented crystalline nature (Film-D) as confirmed by synchrotron X-ray diffraction (XRD). Surprisingly, under water and pyridine vapors, Film-D showed chemisorption-induced dynamic structural transformations to Fe(L) 2 [Pt(CN) 4 ] thin films [L = H 2 O (Film-H), pyridine (Film-P)], where water and pyridine coordinated to the open Fe 2+ site. Dynamic structural transformations were also confirmed by in situ XRD, sorption measurement, and infrared reflection absorption spectroscopy. This is the first report of chemisorption-induced dynamic structural response in a MOF thin film, and it provides useful insights, which would lead to future practical applications of MOFs utilizing chemisorption-induced structural responses.

Toxicology ontology perspectives.

PubMed

Hardy, Barry; Apic, Gordana; Carthew, Philip; Clark, Dominic; Cook, David; Dix, Ian; Escher, Sylvia; Hastings, Janna; Heard, David J; Jeliazkova, Nina; Judson, Philip; Matis-Mitchell, Sherri; Mitic, Dragana; Myatt, Glenn; Shah, Imran; Spjuth, Ola; Tcheremenskaia, Olga; Toldo, Luca; Watson, David; White, Andrew; Yang, Chihae

2012-01-01

The field of predictive toxicology requires the development of open, public, computable, standardized toxicology vocabularies and ontologies to support the applications required by in silico, in vitro, and in vivo toxicology methods and related analysis and reporting activities. In this article we review ontology developments based on a set of perspectives showing how ontologies are being used in predictive toxicology initiatives and applications. Perspectives on resources and initiatives reviewed include OpenTox, eTOX, Pistoia Alliance, ToxWiz, Virtual Liver, EU-ADR, BEL, ToxML, and Bioclipse. We also review existing ontology developments in neighboring fields that can contribute to establishing an ontological framework for predictive toxicology. A significant set of resources is already available to provide a foundation for an ontological framework for 21st century mechanistic-based toxicology research. Ontologies such as ToxWiz provide a basis for application to toxicology investigations, whereas other ontologies under development in the biological, chemical, and biomedical communities could be incorporated in an extended future framework. OpenTox has provided a semantic web framework for the implementation of such ontologies into software applications and linked data resources. Bioclipse developers have shown the benefit of interoperability obtained through ontology by being able to link their workbench application with remote OpenTox web services. Although these developments are promising, an increased international coordination of efforts is greatly needed to develop a more unified, standardized, and open toxicology ontology framework.

eXframe: reusable framework for storage, analysis and visualization of genomics experiments

PubMed Central

2011-01-01

Background Genome-wide experiments are routinely conducted to measure gene expression, DNA-protein interactions and epigenetic status. Structured metadata for these experiments is imperative for a complete understanding of experimental conditions, to enable consistent data processing and to allow retrieval, comparison, and integration of experimental results. Even though several repositories have been developed for genomics data, only a few provide annotation of samples and assays using controlled vocabularies. Moreover, many of them are tailored for a single type of technology or measurement and do not support the integration of multiple data types. Results We have developed eXframe - a reusable web-based framework for genomics experiments that provides 1) the ability to publish structured data compliant with accepted standards 2) support for multiple data types including microarrays and next generation sequencing 3) query, analysis and visualization integration tools (enabled by consistent processing of the raw data and annotation of samples) and is available as open-source software. We present two case studies where this software is currently being used to build repositories of genomics experiments - one contains data from hematopoietic stem cells and another from Parkinson's disease patients. Conclusion The web-based framework eXframe offers structured annotation of experiments as well as uniform processing and storage of molecular data from microarray and next generation sequencing platforms. The framework allows users to query and integrate information across species, technologies, measurement types and experimental conditions. Our framework is reusable and freely modifiable - other groups or institutions can deploy their own custom web-based repositories based on this software. It is interoperable with the most important data formats in this domain. We hope that other groups will not only use eXframe, but also contribute their own useful modifications. PMID:22103807

Simulating the heterogeneity in braided channel belt deposits: 2. Examples of results and comparison to natural deposits

NASA Astrophysics Data System (ADS)

Guin, Arijit; Ramanathan, Ramya; Ritzi, Robert W.; Dominic, David F.; Lunt, Ian A.; Scheibe, Timothy D.; Freedman, Vicky L.

2010-04-01

In part 1 of this paper (Ramanathan et al., 2010b) we presented a methodology and a code for modeling the hierarchical sedimentary architecture in braided channel belt deposits. Here in part 2, the code was used to create a digital model of this architecture and the corresponding spatial distribution of permeability. The simulated architecture was compared to the real stratal architecture observed in an abandoned channel belt. The comparisons included assessments of similarity which were both qualitative and quantitative. The qualitative comparisons show that the geometries of unit types within the synthetic deposits are generally consistent with field observations. The unit types in the synthetic deposits would generally be recognized as representing their counterparts in nature, including cross stratasets, lobate and scroll bar deposits, and channel fills. Furthermore, the synthetic deposits have a hierarchical spatial relationship among these units consistent with observations from field exposures and geophysical images. In quantitative comparisons the proportions and the length, width, and height of unit types at different scales, across all levels of the stratal hierarchy, compare well between the synthetic and the natural deposits. A number of important attributes of the synthetic channel belt deposits are shown to be influenced by more than one level within the hierarchy of stratal architecture. First, the high-permeability open-framework gravels connected across all levels and thus formed preferential flow pathways; open-framework gravels are known to form preferential flow pathways in natural channel belt deposits. The nature of a connected cluster changed across different levels of the stratal hierarchy, and as a result of the geologic structure, the connectivity occurs at proportions of open-framework gravels below the theoretical percolation threshold for random infinite media. Second, when the channel belt model was populated with permeability distributions by lowest-level unit type, the composite permeability semivariogram contained structures that were identifiable at more than one scale, and each of these structures could be directly linked to unit types of different scales existing at different levels within the hierarchy of strata. These collective results are encouraging with respect to our goal that this model be relevant for testing ideas in future research on flow and transport in aquifers and reservoirs with multiscale heterogeneity.

A Copper(II)-Paddlewheel Metal-Organic Framework with Exceptional Hydrolytic Stability and Selective Adsorption and Detection Ability of Aniline in Water.

PubMed

Chen, Ya; Wang, Bin; Wang, Xiaoqing; Xie, Lin-Hua; Li, Jinping; Xie, Yabo; Li, Jian-Rong

2017-08-16

Copper(II)-paddlewheel-based metal-organic frameworks (CP-MOFs) represent a unique subclass of MOFs with highly predictable porous structures, facile syntheses, and functional open metal sites. However, the lack of high hydrolytic stability is an obstacle for CP-MOFs in many practical applications. In this work, we report a new CP-MOF, [Cu 4 (tdhb)] (BUT-155), which is constructed from a judiciously designed carboxylate ligand with high coordination connectivity (octatopic), abundant hydrophobic substituents (six methyl groups), and substituent constrained geometry (tetrahedral backbone), tdhb 8- [H 8 tdhb = 3,3',5,5'-tetrakis(3,5-dicarboxyphenyl)-2,2',4,4',6,6'-hexamethylbiphenyl)]. BUT-155 shows high porosity with a Brunauer-Emmett-Teller surface area of 2070 m 2 /g. Quite interestingly, this CP-MOF retains its structural integrity after being treated in water for 10 days at room temperature or in boiling water for 24 h. To the best of our knowledge, BUT-155 represents the first CP-MOF that is demonstrated to retain its structural integrity in boiling water. The high hydrolytic stability of BUT-155 allowed us to carry out adsorption studies of water vapor and aqueous organic pollutants on it. Water-vapor adsorption reveals a sigmoidal isotherm and a high uptake (46.7 wt %), which is highly reversible and regenerable. In addition, because of the availability of soft-acid-type open Cu(II) sites, BUT-155 shows a high performance for selective adsorption of soft-base-type aniline over water or phenol, and a naked-eye detectable color change for the MOF sample accompanies this. The adsorption selectivity and high adsorption capacity of aniline in BUT-155 are also well-interpreted by single-crystal structures of the water- and aniline-included phases of BUT-155.

A Fundamental Study of Inorganic Clathrate and Other Open-Framework Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nolas, George

Due to formidable synthetic challenges, many materials of scientific and technological interest are first obtained as microcrystalline powders. High purity, high yield processing techniques are often lacking and thus care must be taken in interpretation of the observed structural, chemical, and physical properties of powder or polycrystalline materials, which can be strongly influenced by extrinsic properties. Furthermore, the preparation of high-quality single crystals for many materials by traditional techniques can be especially challenging in cases where the elemental constituents have greatly differing melting points and/or vapor pressures, when the desired compound is thermodynamically metastable, or where growth with participation ofmore » the melt is generally not possible. New processing techniques are therefore imperative in order to investigate the intrinsic properties of these materials and elucidate their fundamental physical properties. Intermetallic clathrates constitute one such class of materials. The complex crystal structures of intermetallic clathrates are characterized by mainly group 14 host frameworks encapsulating guest-ions in polyhedral cages. The unique features of clathrate structures are intimately related to their physical properties, offering ideal systems for the study of structure-property relationships in crystalline solids. Moreover, intermetallic clathrates are being actively investigated due to their potential for application in thermoelectrics, photovoltaics and opto-electronics, superconductivity, and magnetocaloric technologies. We have developed different processing techniques in order to synthesize phase-pure high yield clathrates reproducibly, as well as grow single crystals for the first time. We also employed these techniques to synthesize new “open-framework” compounds. These advances in materials processing and crystal growth allowed for the investigation of the physical properties of a variety of different clathrate compositions for the first time.« less

ggCyto: Next Generation Open-Source Visualization Software for Cytometry.

PubMed

Van, Phu; Jiang, Wenxin; Gottardo, Raphael; Finak, Greg

2018-06-01

Open source software for computational cytometry has gained in popularity over the past few years. Efforts such as FlowCAP, the Lyoplate and Euroflow projects have highlighted the importance of efforts to standardize both experimental and computational aspects of cytometry data analysis. The R/BioConductor platform hosts the largest collection of open source cytometry software covering all aspects of data analysis and providing infrastructure to represent and analyze cytometry data with all relevant experimental, gating, and cell population annotations enabling fully reproducible data analysis. Data visualization frameworks to support this infrastructure have lagged behind. ggCyto is a new open-source BioConductor software package for cytometry data visualization built on ggplot2 that enables ggplot-like functionality with the core BioConductor flow cytometry data structures. Amongst its features are the ability to transform data and axes on-the-fly using cytometry-specific transformations, plot faceting by experimental meta-data variables, and partial matching of channel, marker and cell populations names to the contents of the BioConductor cytometry data structures. We demonstrate the salient features of the package using publicly available cytometry data with complete reproducible examples in a supplementary material vignette. https://bioconductor.org/packages/devel/bioc/html/ggcyto.html. gfinak@fredhutch.org. Supplementary data are available at Bioinformatics online and at http://rglab.org/ggcyto/.

MASTODON: A geosciences simulation tool built using the open-source framework MOOSE

NASA Astrophysics Data System (ADS)

Slaughter, A.

2017-12-01

The Department of Energy (DOE) is currently investing millions of dollars annually into various modeling and simulation tools for all aspects of nuclear energy. An important part of this effort includes developing applications based on the open-source Multiphysics Object Oriented Simulation Environment (MOOSE; mooseframework.org) from Idaho National Laboratory (INL).Thanks to the efforts of the DOE and outside collaborators, MOOSE currently contains a large set of physics modules, including phase field, level set, heat conduction, tensor mechanics, Navier-Stokes, fracture (extended finite-element method), and porous media, among others. The tensor mechanics and contact modules, in particular, are well suited for nonlinear geosciences problems. Multi-hazard Analysis for STOchastic time-DOmaiN phenomena (MASTODON; https://seismic-research.inl.gov/SitePages/Mastodon.aspx)--a MOOSE-based application--is capable of analyzing the response of 3D soil-structure systems to external hazards with current development focused on earthquakes. It is capable of simulating seismic events and can perform extensive "source-to-site" simulations including earthquake fault rupture, nonlinear wave propagation, and nonlinear soil-structure interaction analysis. MASTODON also includes a dynamic probabilistic risk assessment capability that enables analysts to not only perform deterministic analyses, but also easily perform probabilistic or stochastic simulations for the purpose of risk assessment. Although MASTODON has been developed for the nuclear industry, it can be used to assess the risk for any structure subjected to earthquakes.The geosciences community can learn from the nuclear industry and harness the enormous effort underway to build simulation tools that are open, modular, and share a common framework. In particular, MOOSE-based multiphysics solvers are inherently parallel, dimension agnostic, adaptive in time and space, fully coupled, and capable of interacting with other applications. The geosciences community could benefit from existing tools by enabling collaboration between researchers and practitioners throughout the world and advance the state-of-the-art in line with other scientific research efforts.

An open and extensible framework for spatially explicit land use change modelling: the lulcc R package

NASA Astrophysics Data System (ADS)

Moulds, S.; Buytaert, W.; Mijic, A.

2015-10-01

We present the lulcc software package, an object-oriented framework for land use change modelling written in the R programming language. The contribution of the work is to resolve the following limitations associated with the current land use change modelling paradigm: (1) the source code for model implementations is frequently unavailable, severely compromising the reproducibility of scientific results and making it impossible for members of the community to improve or adapt models for their own purposes; (2) ensemble experiments to capture model structural uncertainty are difficult because of fundamental differences between implementations of alternative models; and (3) additional software is required because existing applications frequently perform only the spatial allocation of change. The package includes a stochastic ordered allocation procedure as well as an implementation of the CLUE-S algorithm. We demonstrate its functionality by simulating land use change at the Plum Island Ecosystems site, using a data set included with the package. It is envisaged that lulcc will enable future model development and comparison within an open environment.

Hydrothermal synthesis, crystal structures, and enantioselective adsorption property of bis(L-histidinato)nickel(II) monohydrate

NASA Astrophysics Data System (ADS)

Ramos, Christian Paul L.; Conato, Marlon T.

2018-05-01

Despite the numerous researches in metal-organic frameworks (MOFs), there are only few reports on biologically important amino acids, histidine in particular, on its use as bridging ligand in the construction of open-framework architectures. In this work, hydrothermal synthesis was used to prepare a compound based on Ni2+ and histidine. The coordination assembly of imidazole side chain of histidine with divalent nickel ions in aqueous condition yielded purple prismatic solids. Single crystal X-ray diffraction (XRD) analysis of the product revealed structure for Ni(C6H8N3O2)2 • H2O that has a monoclinic (C2) structure with lattice parameters, a = 29.41, b = 8.27, c = 6.31 Å, β = 90.01 ˚. Circular dichroism - optical rotatory dispersion (CD-ORD), Powder X-ray diffraction (PXRD) and Fourier transform - infrared spectroscopy (FT-IR) analyses are conducted to further characterize the crystals. Enantioselective adsorption analysis using racemic mixture of 2-butanol confirmed bis(L-histidinato)nickel(II) monohydrate MOF crystal's enantioselective property preferentially favoring the adsorption of (S)-2-butanol isomer.

Synthesis, structure and topological analysis of glycine templated highly stable cadmium sulfate framework: A New Lewis Acid catalyst

NASA Astrophysics Data System (ADS)

Paul, Avijit Kumar

2018-04-01

One new open-framework two-dimensional layer, [Cd(NH3CH2COO)(SO4)], I, has been synthesized using amino acid as templating agent. Single crystal structural analysis shows that the compound crystallizes in monoclinic cell with non-centrosymmetric space group P21, a = 4.9513(1) Å, b = 7.9763(2) Å, c = 8.0967(2) Å, β = 105.917(1)° and V = 307.504(12) Å3. The compound has connectivity between the Cd-centers and the sulfate units forming a two-dimensional layer structure. Sulfate unit is coordinated to metal center with η3, μ4 mode possessing a coordination free oxygen atom. The zwitterionic form of glycine molecule is present in the structure bridging with two metal centers through μ2-mode by carboxylate oxygens. The topological analysis reveals that the two-dimensional network is formed with a novel 4- and 6-connected binodal net of (32,42,52)(34,44,54,63) topology. Although one end of the glycine molecule is free from coordination, the structure is highly stable up to 350 °C. Strong N-H⋯ O hydrogen bonding interactions play an important role in the stabilization and formation of three-dimensional supramolecular structure. The cyanosilylation of imines using the present compounds as heterogeneous catalyst indicates good catalytic behavior. The present study illustrates the usefulness of the amino acid for the structure building in less studied sulfate based framework materials as well as designing of new heterogeneous catalysts for the broad application. The compound has also been characterized through elemental analysis, PXRD, IR, SEM and TG-DT studies.

An open-source framework for large-scale, flexible evaluation of biomedical text mining systems.

PubMed

Baumgartner, William A; Cohen, K Bretonnel; Hunter, Lawrence

2008-01-29

Improved evaluation methodologies have been identified as a necessary prerequisite to the improvement of text mining theory and practice. This paper presents a publicly available framework that facilitates thorough, structured, and large-scale evaluations of text mining technologies. The extensibility of this framework and its ability to uncover system-wide characteristics by analyzing component parts as well as its usefulness for facilitating third-party application integration are demonstrated through examples in the biomedical domain. Our evaluation framework was assembled using the Unstructured Information Management Architecture. It was used to analyze a set of gene mention identification systems involving 225 combinations of system, evaluation corpus, and correctness measure. Interactions between all three were found to affect the relative rankings of the systems. A second experiment evaluated gene normalization system performance using as input 4,097 combinations of gene mention systems and gene mention system-combining strategies. Gene mention system recall is shown to affect gene normalization system performance much more than does gene mention system precision, and high gene normalization performance is shown to be achievable with remarkably low levels of gene mention system precision. The software presented in this paper demonstrates the potential for novel discovery resulting from the structured evaluation of biomedical language processing systems, as well as the usefulness of such an evaluation framework for promoting collaboration between developers of biomedical language processing technologies. The code base is available as part of the BioNLP UIMA Component Repository on SourceForge.net.

An open-source framework for large-scale, flexible evaluation of biomedical text mining systems

PubMed Central

Baumgartner, William A; Cohen, K Bretonnel; Hunter, Lawrence

2008-01-01

Background Improved evaluation methodologies have been identified as a necessary prerequisite to the improvement of text mining theory and practice. This paper presents a publicly available framework that facilitates thorough, structured, and large-scale evaluations of text mining technologies. The extensibility of this framework and its ability to uncover system-wide characteristics by analyzing component parts as well as its usefulness for facilitating third-party application integration are demonstrated through examples in the biomedical domain. Results Our evaluation framework was assembled using the Unstructured Information Management Architecture. It was used to analyze a set of gene mention identification systems involving 225 combinations of system, evaluation corpus, and correctness measure. Interactions between all three were found to affect the relative rankings of the systems. A second experiment evaluated gene normalization system performance using as input 4,097 combinations of gene mention systems and gene mention system-combining strategies. Gene mention system recall is shown to affect gene normalization system performance much more than does gene mention system precision, and high gene normalization performance is shown to be achievable with remarkably low levels of gene mention system precision. Conclusion The software presented in this paper demonstrates the potential for novel discovery resulting from the structured evaluation of biomedical language processing systems, as well as the usefulness of such an evaluation framework for promoting collaboration between developers of biomedical language processing technologies. The code base is available as part of the BioNLP UIMA Component Repository on SourceForge.net. PMID:18230184

An integrated domain specific language for post-processing and visualizing electrophysiological signals in Java.

PubMed

Strasser, T; Peters, T; Jagle, H; Zrenner, E; Wilke, R

2010-01-01

Electrophysiology of vision - especially the electroretinogram (ERG) - is used as a non-invasive way for functional testing of the visual system. The ERG is a combined electrical response generated by neural and non-neuronal cells in the retina in response to light stimulation. This response can be recorded and used for diagnosis of numerous disorders. For both clinical practice and clinical trials it is important to process those signals in an accurate and fast way and to provide the results as structured, consistent reports. Therefore, we developed a freely available and open-source framework in Java (http://www.eye.uni-tuebingen.de/project/idsI4sigproc). The framework is focused on an easy integration with existing applications. By leveraging well-established software patterns like pipes-and-filters and fluent interfaces as well as by designing the application programming interfaces (API) as an integrated domain specific language (DSL) the overall framework provides a smooth learning curve. Additionally, it already contains several processing methods and visualization features and can be extended easily by implementing the provided interfaces. In this way, not only can new processing methods be added but the framework can also be adopted for other areas of signal processing. This article describes in detail the structure and implementation of the framework and demonstrate its application through the software package used in clinical practice and clinical trials at the University Eye Hospital Tuebingen one of the largest departments in the field of visual electrophysiology in Europe.

Open-source framework for power system transmission and distribution dynamics co-simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Renke; Fan, Rui; Daily, Jeff

The promise of the smart grid entails more interactions between the transmission and distribution networks, and there is an immediate need for tools to provide the comprehensive modelling and simulation required to integrate operations at both transmission and distribution levels. Existing electromagnetic transient simulators can perform simulations with integration of transmission and distribution systems, but the computational burden is high for large-scale system analysis. For transient stability analysis, currently there are only separate tools for simulating transient dynamics of the transmission and distribution systems. In this paper, we introduce an open source co-simulation framework “Framework for Network Co-Simulation” (FNCS), togethermore » with the decoupled simulation approach that links existing transmission and distribution dynamic simulators through FNCS. FNCS is a middleware interface and framework that manages the interaction and synchronization of the transmission and distribution simulators. Preliminary testing results show the validity and capability of the proposed open-source co-simulation framework and the decoupled co-simulation methodology.« less

Open Architecture Framework for Improved Early Stage Submarine Design

DTIC Science & Technology

2010-06-01

Figure 12 Data Structure Example – VPH ..................................................................................... 41 Figure 13 SUBSTART Data...in the MIT SMM (e.g. – VPH -VB, pressure hull volume without volume of the in-hull variable ballast). Tables 4 and 5 list the variables by module...MUD1frac FFsurf θ(x,t) V(t) VPH ∆ff VCGLEADs BTf MUDfwd GMt R(x) Vambt VPHguess ∆mbt VCGnsc BTops OBambt ηa tenvsurf Vaux VPH -VB ∆nsc VCGVL

Discovering charge density functionals and structure-property relationships with PROPhet: A general framework for coupling machine learning and first-principles methods

DOE PAGES

Kolb, Brian; Lentz, Levi C.; Kolpak, Alexie M.

2017-04-26

Modern ab initio methods have rapidly increased our understanding of solid state materials properties, chemical reactions, and the quantum interactions between atoms. However, poor scaling often renders direct ab initio calculations intractable for large or complex systems. There are two obvious avenues through which to remedy this problem: (i) develop new, less expensive methods to calculate system properties, or (ii) make existing methods faster. This paper describes an open source framework designed to pursue both of these avenues. PROPhet (short for PROPerty Prophet) utilizes machine learning techniques to find complex, non-linear mappings between sets of material or system properties. Themore » result is a single code capable of learning analytical potentials, non-linear density functionals, and other structure-property or property-property relationships. These capabilities enable highly accurate mesoscopic simulations, facilitate computation of expensive properties, and enable the development of predictive models for systematic materials design and optimization. Here, this work explores the coupling of machine learning to ab initio methods through means both familiar (e.g., the creation of various potentials and energy functionals) and less familiar (e.g., the creation of density functionals for arbitrary properties), serving both to demonstrate PROPhet’s ability to create exciting post-processing analysis tools and to open the door to improving ab initio methods themselves with these powerful machine learning techniques.« less

Discovering charge density functionals and structure-property relationships with PROPhet: A general framework for coupling machine learning and first-principles methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolb, Brian; Lentz, Levi C.; Kolpak, Alexie M.

Modern ab initio methods have rapidly increased our understanding of solid state materials properties, chemical reactions, and the quantum interactions between atoms. However, poor scaling often renders direct ab initio calculations intractable for large or complex systems. There are two obvious avenues through which to remedy this problem: (i) develop new, less expensive methods to calculate system properties, or (ii) make existing methods faster. This paper describes an open source framework designed to pursue both of these avenues. PROPhet (short for PROPerty Prophet) utilizes machine learning techniques to find complex, non-linear mappings between sets of material or system properties. Themore » result is a single code capable of learning analytical potentials, non-linear density functionals, and other structure-property or property-property relationships. These capabilities enable highly accurate mesoscopic simulations, facilitate computation of expensive properties, and enable the development of predictive models for systematic materials design and optimization. Here, this work explores the coupling of machine learning to ab initio methods through means both familiar (e.g., the creation of various potentials and energy functionals) and less familiar (e.g., the creation of density functionals for arbitrary properties), serving both to demonstrate PROPhet’s ability to create exciting post-processing analysis tools and to open the door to improving ab initio methods themselves with these powerful machine learning techniques.« less

Brain maps 4.0—Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps

PubMed Central

2018-01-01

Abstract The fourth edition (following editions in 1992, 1998, 2004) of Brain maps: structure of the rat brain is presented here as an open access internet resource for the neuroscience community. One new feature is a set of 10 hierarchical nomenclature tables that define and describe all parts of the rat nervous system within the framework of a strictly topographic system devised previously for the human nervous system. These tables constitute a global ontology for knowledge management systems dealing with neural circuitry. A second new feature is an aligned atlas of bilateral flatmaps illustrating rat nervous system development from the neural plate stage to the adult stage, where most gray matter regions, white matter tracts, ganglia, and nerves listed in the nomenclature tables are illustrated schematically. These flatmaps are convenient for future development of online applications analogous to “Google Maps” for systems neuroscience. The third new feature is a completely revised Atlas of the rat brain in spatially aligned transverse sections that can serve as a framework for 3‐D modeling. Atlas parcellation is little changed from the preceding edition, but the nomenclature for rat is now aligned with an emerging panmammalian neuroanatomical nomenclature. All figures are presented in Adobe Illustrator vector graphics format that can be manipulated, modified, and resized as desired, and freely used with a Creative Commons license. PMID:29277900

An Open Source Simulation Model for Soil and Sediment Bioturbation

PubMed Central

Schiffers, Katja; Teal, Lorna Rachel; Travis, Justin Mark John; Solan, Martin

2011-01-01

Bioturbation is one of the most widespread forms of ecological engineering and has significant implications for the structure and functioning of ecosystems, yet our understanding of the processes involved in biotic mixing remains incomplete. One reason is that, despite their value and utility, most mathematical models currently applied to bioturbation data tend to neglect aspects of the natural complexity of bioturbation in favour of mathematical simplicity. At the same time, the abstract nature of these approaches limits the application of such models to a limited range of users. Here, we contend that a movement towards process-based modelling can improve both the representation of the mechanistic basis of bioturbation and the intuitiveness of modelling approaches. In support of this initiative, we present an open source modelling framework that explicitly simulates particle displacement and a worked example to facilitate application and further development. The framework combines the advantages of rule-based lattice models with the application of parameterisable probability density functions to generate mixing on the lattice. Model parameters can be fitted by experimental data and describe particle displacement at the spatial and temporal scales at which bioturbation data is routinely collected. By using the same model structure across species, but generating species-specific parameters, a generic understanding of species-specific bioturbation behaviour can be achieved. An application to a case study and comparison with a commonly used model attest the predictive power of the approach. PMID:22162997

An open source simulation model for soil and sediment bioturbation.

PubMed

Schiffers, Katja; Teal, Lorna Rachel; Travis, Justin Mark John; Solan, Martin

2011-01-01

Bioturbation is one of the most widespread forms of ecological engineering and has significant implications for the structure and functioning of ecosystems, yet our understanding of the processes involved in biotic mixing remains incomplete. One reason is that, despite their value and utility, most mathematical models currently applied to bioturbation data tend to neglect aspects of the natural complexity of bioturbation in favour of mathematical simplicity. At the same time, the abstract nature of these approaches limits the application of such models to a limited range of users. Here, we contend that a movement towards process-based modelling can improve both the representation of the mechanistic basis of bioturbation and the intuitiveness of modelling approaches. In support of this initiative, we present an open source modelling framework that explicitly simulates particle displacement and a worked example to facilitate application and further development. The framework combines the advantages of rule-based lattice models with the application of parameterisable probability density functions to generate mixing on the lattice. Model parameters can be fitted by experimental data and describe particle displacement at the spatial and temporal scales at which bioturbation data is routinely collected. By using the same model structure across species, but generating species-specific parameters, a generic understanding of species-specific bioturbation behaviour can be achieved. An application to a case study and comparison with a commonly used model attest the predictive power of the approach.

Open Governance in Higher Education: Extending the Past to the Future

ERIC Educational Resources Information Center

Masson, Patrick

2011-01-01

Open educational resources, open content, open access, open research, open courseware--all of these open initiatives share, and benefit from, a vision of access and a collaborative framework that often result in improved outcomes. Many of these open initiatives have gained adoption within higher education and are now serving in mission-critical…

A Knowledge Discovery framework for Planetary Defense

NASA Astrophysics Data System (ADS)

Jiang, Y.; Yang, C. P.; Li, Y.; Yu, M.; Bambacus, M.; Seery, B.; Barbee, B.

2016-12-01

Planetary Defense, a project funded by NASA Goddard and the NSF, is a multi-faceted effort focused on the mitigation of Near Earth Object (NEO) threats to our planet. Currently, there exists a dispersion of information concerning NEO's amongst different organizations and scientists, leading to a lack of a coherent system of information to be used for efficient NEO mitigation. In this paper, a planetary defense knowledge discovery engine is proposed to better assist the development and integration of a NEO responding system. Specifically, we have implemented an organized information framework by two means: 1) the development of a semantic knowledge base, which provides a structure for relevant information. It has been developed by the implementation of web crawling and natural language processing techniques, which allows us to collect and store the most relevant structured information on a regular basis. 2) the development of a knowledge discovery engine, which allows for the efficient retrieval of information from our knowledge base. The knowledge discovery engine has been built on the top of Elasticsearch, an open source full-text search engine, as well as cutting-edge machine learning ranking and recommendation algorithms. This proposed framework is expected to advance the knowledge discovery and innovation in planetary science domain.

The Pixhawk Open-Source Computer Vision Framework for Mavs

NASA Astrophysics Data System (ADS)

Meier, L.; Tanskanen, P.; Fraundorfer, F.; Pollefeys, M.

2011-09-01

Unmanned aerial vehicles (UAV) and micro air vehicles (MAV) are already intensively used in geodetic applications. State of the art autonomous systems are however geared towards the application area in safe and obstacle-free altitudes greater than 30 meters. Applications at lower altitudes still require a human pilot. A new application field will be the reconstruction of structures and buildings, including the facades and roofs, with semi-autonomous MAVs. Ongoing research in the MAV robotics field is focusing on enabling this system class to operate at lower altitudes in proximity to nearby obstacles and humans. PIXHAWK is an open source and open hardware toolkit for this purpose. The quadrotor design is optimized for onboard computer vision and can connect up to four cameras to its onboard computer. The validity of the system design is shown with a fully autonomous capture flight along a building.

Medical Subject Headings (MeSH) for indexing and retrieving open-source healthcare data.

PubMed

Marc, David T; Khairat, Saif S

2014-01-01

The US federal government initiated the Open Government Directive where federal agencies are required to publish high value datasets so that they are available to the public. Data.gov and the community site Healthdata.gov were initiated to disperse such datasets. However, data searches and retrieval for these sites are keyword driven and severely limited in performance. The purpose of this paper is to address the issue of extracting relevant open-source data by proposing a method of adopting the MeSH framework for indexing and data retrieval. A pilot study was conducted to compare the performance of traditional keywords to MeSH terms for retrieving relevant open-source datasets related to "mortality". The MeSH framework resulted in greater sensitivity with comparable specificity to the keyword search. MeSH showed promise as a method for indexing and retrieving data, yet future research should conduct a larger scale evaluation of the performance of the MeSH framework for retrieving relevant open-source healthcare datasets.

Pika: A snow science simulation tool built using the open-source framework MOOSE

NASA Astrophysics Data System (ADS)

Slaughter, A.; Johnson, M.

2017-12-01

The Department of Energy (DOE) is currently investing millions of dollars annually into various modeling and simulation tools for all aspects of nuclear energy. An important part of this effort includes developing applications based on the open-source Multiphysics Object Oriented Simulation Environment (MOOSE; mooseframework.org) from Idaho National Laboratory (INL).Thanks to the efforts of the DOE and outside collaborators, MOOSE currently contains a large set of physics modules, including phase-field, level set, heat conduction, tensor mechanics, Navier-Stokes, fracture and crack propagation (via the extended finite-element method), flow in porous media, and others. The heat conduction, tensor mechanics, and phase-field modules, in particular, are well-suited for snow science problems. Pika--an open-source MOOSE-based application--is capable of simulating both 3D, coupled nonlinear continuum heat transfer and large-deformation mechanics applications (such as settlement) and phase-field based micro-structure applications. Additionally, these types of problems may be coupled tightly in a single solve or across length and time scales using a loosely coupled Picard iteration approach. In addition to the wide range of physics capabilities, MOOSE-based applications also inherit an extensible testing framework, graphical user interface, and documentation system; tools that allow MOOSE and other applications to adhere to nuclear software quality standards. The snow science community can learn from the nuclear industry and harness the existing effort to build simulation tools that are open, modular, and share a common framework. In particular, MOOSE-based multiphysics solvers are inherently parallel, dimension agnostic, adaptive in time and space, fully coupled, and capable of interacting with other applications. The snow science community should build on existing tools to enable collaboration between researchers and practitioners throughout the world, and advance the state-of-the-art in line with other scientific research efforts.

A general theoretical framework for decoherence in open and closed systems

NASA Astrophysics Data System (ADS)

Castagnino, Mario; Fortin, Sebastian; Laura, Roberto; Lombardi, Olimpia

2008-08-01

A general theoretical framework for decoherence is proposed, which encompasses formalisms originally devised to deal just with open or closed systems. The conditions for decoherence are clearly stated and the relaxation and decoherence times are compared. Finally, the spin-bath model is developed in detail from the new perspective.

Open-Ended Learning Environments: A Theoretical Framework and Model for Design.

ERIC Educational Resources Information Center

Hill, Janette R.; Land, Susan M.

This paper presents a framework and model for design of open-ended learning environments (OELEs). First, an overview is presented that addresses key characteristics of OELEs, including: use of meaningful, complex contexts; provision of tools and resources; learner reflection and self-monitoring; and social, material, or technological scaffolding.…

Evidence of active region imprints on the solar wind structure

NASA Technical Reports Server (NTRS)

Hick, P.; Jackson, B. V.

1995-01-01

A common descriptive framework for discussing the solar wind structure in the inner heliosphere uses the global magnetic field as a reference: low density, high velocity solar wind emanates from open magnetic fields, with high density, low speed solar wind flowing outward near the current sheet. In this picture, active regions, underlying closed magnetic field structures in the streamer belt, leave little or no imprint on the solar wind. We present evidence from interplanetary scintillation measurements of the 'disturbance factor' g that active regions play a role in modulating the solar wind and possibly contribute to the solar wind mass output. Hence we find that the traditional view of the solar wind, though useful in understanding many features of solar wind structure, is oversimplified and possibly neglects important aspects of solar wind dynamics

Optimization of the structural configuration of ICBA/P3HT photovoltaic cells

NASA Astrophysics Data System (ADS)

Nemnes, G. A.; Iftimie, Sorina; Palici, Alexandra; Nicolaev, Adela; Mitran, T. L.; Radu, A.; Antohe, S.

2017-12-01

We investigate a possible route for optimization of organic P3HT:ICBA photovoltaic cells. In order to ensure a more efficient charge separation and collection at the electrodes, two- and three-layer structures are produced, where additional P3HT and ICBA single layers are placed adjacent to the mixed layer. The J-V characteristics are modeled using Monte-Carlo simulations in a flexible computational framework, reproducing the typical morphologies of the active layers. We discuss the implications of the structural modifications, in particular the enhancement of the open circuit voltage. Qualitative features of the theoretical simulations are validated by experiment. The proposed fabrication technique of using solvents with different boiling points for successive deposition of the individual layers may constitute an accessible route for producing optimized solar cell structures.

Long-Term Management Strategy for Dredged Material Disposal for Naval Weapons Station, Yorktown, Yorktown, Virginia; Naval Supply Center, Cheatham Annex, Williamsburg, Virginia; and Naval Amphibious Base, Little Creek, Norfolk, Virginia. Phase 2: Formulation of Alternatives

DTIC Science & Technology

1993-03-01

Regulatory Framework and Management Strategy ... .......... 11 Need for Criteria ............... ........................ .. 12 Criteria for Open-Water... Framework and Managetent Strategy 19. Because the Phase I results indicated that there is insufficient confined disposal capacity, the assessment of open...regulatory framework established for Sections 103 and 404. 11 20. All disposal options considered for this LTMS were examined using the Corps Management

Formal Provenance Representation of the Data and Information Supporting the National Climate Assessment

NASA Technical Reports Server (NTRS)

Tilmes, Curt

2014-01-01

The Global Change Information System (GCIS) provides a framework for the formal representation of structured metadata about data and information about global change. The pilot deployment of the system supports the National Climate Assessment (NCA), a major report of the U.S. Global Change Research Program (USGCRP). A consumer of that report can use the system to browse and explore that supporting information. Additionally, capturing that information into a structured data model and presenting it in standard formats through well defined open inter- faces, including query interfaces suitable for data mining and linking with other databases, the information becomes valuable for other analytic uses as well.

A New Framework for Analysis of Coevolutionary Systems-Directed Graph Representation and Random Walks.

PubMed

Chong, Siang Yew; Tiňo, Peter; He, Jun; Yao, Xin

2017-11-20

Studying coevolutionary systems in the context of simplified models (i.e., games with pairwise interactions between coevolving solutions modeled as self plays) remains an open challenge since the rich underlying structures associated with pairwise-comparison-based fitness measures are often not taken fully into account. Although cyclic dynamics have been demonstrated in several contexts (such as intransitivity in coevolutionary problems), there is no complete characterization of cycle structures and their effects on coevolutionary search. We develop a new framework to address this issue. At the core of our approach is the directed graph (digraph) representation of coevolutionary problems that fully captures structures in the relations between candidate solutions. Coevolutionary processes are modeled as a specific type of Markov chains-random walks on digraphs. Using this framework, we show that coevolutionary problems admit a qualitative characterization: a coevolutionary problem is either solvable (there is a subset of solutions that dominates the remaining candidate solutions) or not. This has an implication on coevolutionary search. We further develop our framework that provides the means to construct quantitative tools for analysis of coevolutionary processes and demonstrate their applications through case studies. We show that coevolution of solvable problems corresponds to an absorbing Markov chain for which we can compute the expected hitting time of the absorbing class. Otherwise, coevolution will cycle indefinitely and the quantity of interest will be the limiting invariant distribution of the Markov chain. We also provide an index for characterizing complexity in coevolutionary problems and show how they can be generated in a controlled manner.

Zeolitic imidazolate framework-7: Novel ammonia atmosphere-assisted synthesis, thermal and chemical durability, phase reversibility and potential as highly efficient nanophotocatalyst

NASA Astrophysics Data System (ADS)

Ebrahimi, Arash; Mansournia, Mohammadreza

2018-07-01

This is the first representation of novel sodalite zeolitic imidazolate framework-7 (ZIF-7) which has been made in ethanolic solution at room temperature via an ammonia atmosphere. High thermal stability up to 400 °C is representative of great persistence which has been proved by XRD and TG data. Chemical durability of the as-made ZIF-7 especially at boiled DMF exhibited by XRD patterns can present it as an interesting material without structural alteration after treatment in such harsh condition. Reversible phase transformation of ZIF-7 was totally checked by immersing in ethanol and DMF indicated that the framework can maintain its structural flexibility under heat and solvent treatment. Moreover, the "gate-opening" phenomenon performed by CO2 adsorption-desorption reveals structural breathing effect of ZIF-7 framework that makes it as potential material in CO2 adsorption/separation. In the end, the sacrificial metal-doped (Mn2+, Ni2+, Cu2+, Cd2+ and Ag+) ZIF-7 precursors were applied for preparation of their corresponded metal-doped ZnO as the heterogeneous catalyst to degrade Rhodamine-B (RhB) dye in water under UV-irradiation (up to 99% within 90 min by 0.5% Ag-ZnO (S15)). The recyclability experiment after 5 runs for the optimized catalyst demonstrated that the metal-doped ZnO can be operated consecutively without remarkable decreasing in its activity. These observations exhibit the excellent and beneficial properties of metal-doped ZnO can be as heterogeneous photocatalyst for the removal of organic contaminants in water.

A product lifecycle management framework to support the exchange of prototyping and testing information

NASA Astrophysics Data System (ADS)

Toche Fumchum, Luc Boris

2011-12-01

The modern perspective on product life cycle and the rapid evolution of Information and Communication Technologies in general have opened a new era in product representation and product information sharing between participants, both inside and outside the enterprise and throughout the product life. In particular, the Product Development Process relies on cross-functional activities involving different domains of expertise that each have their own dedicated tools. This has generated new challenges in terms of collaboration and dissemination of information at large between companies or even within the same organization. Within this context, the work reported herein focuses on a specific stakeholder within product development activities - the prototyping and testing department. Its business is typically related to the planning and building of prototypes in order to perform specific tests on the future product or one of its sub-assemblies. The research project aims at investigating an appropriate framework that leverages configured engineering product information, based on complementary information structures, to share and exchange prototyping and testing information in a Product Lifecycle Management (PLM) perspective. As a first step, a case study based on the retrofit of an aircraft engine is deployed to implement a scenario demonstrating the functionalities to be available within the intended framework. For this purpose, complementary and configurable structures are simulated within the project's PLM system. In a second step are considered the software interoperability issues that don't only affect Design -- Testing interactions, but many other interfaces within either the company -- due to the silo-arrangement -- or the consortiums with partners, in which case the whole PLM platforms could simply be incompatible. A study based on an open source initiative and relying on an improved model of communication is described to show how two natively disparate PLM tools can dialogue to merge information in a central environment. The principles applied in both steps are therefore transposed to introduce the Open Exchange Nest as a generic PLM-driven and web-based concept to support the collaborative work in the aforementioned context.

Pragmatic open space box utilization: asteroid survey model using distributed objects management based articulation (DOMBA)

NASA Astrophysics Data System (ADS)

Mohammad, Atif Farid; Straub, Jeremy

2015-05-01

A multi-craft asteroid survey has significant data synchronization needs. Limited communication speeds drive exacting performance requirements. Tables have been used in Relational Databases, which are structure; however, DOMBA (Distributed Objects Management Based Articulation) deals with data in terms of collections. With this, no read/write roadblocks to the data exist. A master/slave architecture is created by utilizing the Gossip protocol. This facilitates expanding a mission that makes an important discovery via the launch of another spacecraft. The Open Space Box Framework facilitates the foregoing while also providing a virtual caching layer to make sure that continuously accessed data is available in memory and that, upon closing the data file, recharging is applied to the data.

Synthesis, structure, and luminescent properties of microporous lanthanide metal-organic frameworks with inorganic rod-shaped building units.

PubMed

Guo, Xiaodan; Zhu, Guangshan; Sun, Fuxing; Li, Zhongyue; Zhao, Xiaojun; Li, Xiaotian; Wang, Hanchang; Qiu, Shilun

2006-03-20

A series of microporous lanthanide metal-organic frameworks, Tb3(BDC)(4.5)(DMF)2(H2O)3.(DMF)(H2O) (1) and Ln3(BDC)(4.5)(DMF)2(H2O)3.(DMF)(C2H5OH)(0.5)(H2O)(0.5) [Ln = Dy (2), Ho (3), Er (4)], have been synthesized by the reaction of the lanthanide metal ion (Ln3+) with 1,4-benzenedicarboxylic acid and triethylenetetramine in a mixed solution of N,N'-dimethylformamide (DMF), water, and C(2)H(5)OH. X-ray diffraction analyses reveal that they are extremely similar in structure and crystallized in triclinic space group P. An edge-sharing metallic dimer and 4 metallic monomers assemble with 18 carboxylate groups to form discrete inorganic rod-shaped building units [Ln6(CO2)18], which link to each other through phenyl groups to lead to three-dimensional open frameworks with approximately 4 x 6 A rhombic channels along the [0,-1,1] direction. A water sorption isotherm proves that guest molecules in the framework of complex 1 can be removed to create permanent microporosity and about four water molecules per formula unit can be adsorbed into the micropores. These complexes exhibit blue fluorescence, and complex 1 shows a Tb3+ characteristic emission in the range of 450-650 nm.

Combining formal and functional approaches to topic structure.

PubMed

Zellers, Margaret; Post, Brechtje

2012-03-01

Fragmentation between formal and functional approaches to prosodic variation is an ongoing problem in linguistic research. In particular, the frameworks of the Phonetics of Talk-in-Interaction (PTI) and Empirical Phonology (EP) take very different theoretical and methodological approaches to this kind of variation. We argue that it is fruitful to adopt the insights of both PTI's qualitative analysis and EP's quantitative analysis and combine them into a multiple-methods approach. One realm in which it is possible to combine these frameworks is in the analysis of discourse topic structure and the prosodic cues relevant to it. By combining a quantitative and a qualitative approach to discourse topic structure, it is possible to give a better account of the observed variation in prosody, for example in the case of fundamental frequency (F0) peak timing, which can be explained in terms of pitch accent distribution over different topic structure categories. Similarly, local and global patterns in speech rate variation can be better explained and motivated by adopting insights from both PTI and EP in the study of topic structure. Combining PTI and EP can provide better accounts of speech data as well as opening up new avenues of investigation which would not have been possible in either approach alone.

Two new three-dimensional zinc phosphites templated by piperazine: [H2pip][Zn3(HPO3)4(H2O)2] and K[H2pip]0.5[Zn3(HPO3)4

NASA Astrophysics Data System (ADS)

Zhang, Xiao; Wang, Guo-Ming; Wang, Zong-Hua; Wang, Ying-Xia; Lin, Jian-Hua

2014-01-01

Two three-dimensional open-framework zinc phosphites with the same organically templated, [H2pip][Zn3(HPO3)4(H2O)2] (1) and K[H2pip]0.5[Zn3(HPO3)4] (2) (pip = piperazine), have been solvothermally synthesized and structurally characterized by IR, elemental analysis, thermogravimetric analysis, powder and single-crystal X-ray diffractions. Compound 1 consists of ZnO4 tetrahedra, [HPO3] pseudopyramids and [ZnO4(H2O)2] octahedra, which are linked through their vertexes to generate three-dimensional architecture with intersecting 8-membered channels along the [1 0 0], [0 0 1] and [1 0 1] directions. Compound 2 is constructed from strictly alternating ZnO4 tetrahedra and [HPO3] pseudopyramids, and exhibits (3,4)-connected inorganic framework with 8-, and 12-membered channels, in which the K+ and diprotonated H2pip2+ extra-framework cations reside, respectively. The coexistence of inorganic K+ and organic piperazine mixed templates in the structure is unique and, to the best of our knowledge, firstly observed in metal-phosphite materials. In addition, the participation of left-handed and right-handed helical chains in construction of the puckered 4.82 sheet structure in 2 is also noteworthy.

A Framework for Daylighting Optimization in Whole Buildings with OpenStudio

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2016-08-12

We present a toolkit and workflow for leveraging the OpenStudio (Guglielmetti et al. 2010) platform to perform daylighting analysis and optimization in a whole building energy modeling (BEM) context. We have re-implemented OpenStudio's integrated Radiance and EnergyPlus functionality as an OpenStudio Measure. The OpenStudio Radiance Measure works within the OpenStudio Application and Parametric Analysis Tool, as well as the OpenStudio Server large scale analysis framework, allowing a rigorous daylighting simulation to be performed on a single building model or potentially an entire population of programmatically generated models. The Radiance simulation results can automatically inform the broader building energy model, andmore » provide dynamic daylight metrics as a basis for decision. Through introduction and example, this paper illustrates the utility of the OpenStudio building energy modeling platform to leverage existing simulation tools for integrated building energy performance simulation, daylighting analysis, and reportage.« less

pyGIMLi: An open-source library for modelling and inversion in geophysics

NASA Astrophysics Data System (ADS)

Rücker, Carsten; Günther, Thomas; Wagner, Florian M.

2017-12-01

Many tasks in applied geosciences cannot be solved by single measurements, but require the integration of geophysical, geotechnical and hydrological methods. Numerical simulation techniques are essential both for planning and interpretation, as well as for the process understanding of modern geophysical methods. These trends encourage open, simple, and modern software architectures aiming at a uniform interface for interdisciplinary and flexible modelling and inversion approaches. We present pyGIMLi (Python Library for Inversion and Modelling in Geophysics), an open-source framework that provides tools for modelling and inversion of various geophysical but also hydrological methods. The modelling component supplies discretization management and the numerical basis for finite-element and finite-volume solvers in 1D, 2D and 3D on arbitrarily structured meshes. The generalized inversion framework solves the minimization problem with a Gauss-Newton algorithm for any physical forward operator and provides opportunities for uncertainty and resolution analyses. More general requirements, such as flexible regularization strategies, time-lapse processing and different sorts of coupling individual methods are provided independently of the actual methods used. The usage of pyGIMLi is first demonstrated by solving the steady-state heat equation, followed by a demonstration of more complex capabilities for the combination of different geophysical data sets. A fully coupled hydrogeophysical inversion of electrical resistivity tomography (ERT) data of a simulated tracer experiment is presented that allows to directly reconstruct the underlying hydraulic conductivity distribution of the aquifer. Another example demonstrates the improvement of jointly inverting ERT and ultrasonic data with respect to saturation by a new approach that incorporates petrophysical relations in the inversion. Potential applications of the presented framework are manifold and include time-lapse, constrained, joint, and coupled inversions of various geophysical and hydrological data sets.

Creation of an Open Framework for Point-of-Care Computer-Assisted Reporting and Decision Support Tools for Radiologists.

PubMed

Alkasab, Tarik K; Bizzo, Bernardo C; Berland, Lincoln L; Nair, Sujith; Pandharipande, Pari V; Harvey, H Benjamin

2017-09-01

Decreasing unnecessary variation in radiology reporting and producing guideline-concordant reports is fundamental to radiology's success in value-based payment models and good for patient care. In this article, we present an open authoring system for point-of-care clinical decision support tools integrated into the radiologist reporting environment referred to as the computer-assisted reporting and decision support (CAR/DS) framework. The CAR/DS authoring system, described herein, includes: (1) a definition format for representing radiology clinical guidelines as structured, machine-readable Extensible Markup Language documents and (2) a user-friendly reference implementation to test the fidelity of the created definition files with the clinical guideline. The proposed definition format and reference implementation will enable content creators to develop CAR/DS tools that voice recognition software (VRS) vendors can use to extend the commercial tools currently in use. In making the definition format and reference implementation software freely available, we hope to empower individual radiologists, expert groups such as the ACR, and VRS vendors to develop a robust ecosystem of CAR/DS tools that can further improve the quality and efficiency of the patient care that our field provides. We hope that this initial effort can serve as the basis for a community-owned open standard for guideline definition that the imaging informatics and VRS vendor communities will embrace and strengthen. To this end, the ACR Assist™ initiative is intended to make the College's clinical content, including the Incidental Findings Committee White Papers, available for decision support tool creation based upon the herein described CAR/DS framework. Copyright © 2017 American College of Radiology. Published by Elsevier Inc. All rights reserved.

General Syntheses of Nanotubes Induced by Block Copolymer Self-Assembly.

PubMed

Zhao, Jianming; Huang, Wei; Si, Pengchao; Ulstrup, Jens; Diao, Fangyuan; Zhang, Jingdong

2018-06-01

Amphiphilic block copolymer templating strategies are extensively used for syntheses of mesoporous materials. However, monodisperse tubular nanostructures are limited. Here, a general method is developed to synthesize monodisperse nanotubes with narrow diameter distribution induced by self-assembly of block copolymer. 3-Aminophenol (AP) and formaldehyde (F) polymerize and self-assemble with cylindrical PS-b-PEO micelles into worm-like PS-b-PEO@APF composites with uniform diameter (49 ± 3 nm). After template extraction, worm-like APF polymer nanotubes are formed. The structure and morphology of the polymer nanotubes can be tuned by regulating the synthesis conditions. Furthermore, PS-b-PEO@APF composites are uniformly converted to isomorphic carbon nanotubes with large surface area of 662 m 2 g -1 , abundant hierarchical porous frameworks and nitrogen doping. The synthesis can be extended to silica nanotubes. These findings open an avenue to the design of porous materials with controlled structural framework, composition, and properties for a wide range of applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Managing crises through organisational development: a conceptual framework.

PubMed

Lalonde, Carole

2011-04-01

This paper presents a synthesis of the guiding principles in crisis management in accordance with the four configurational imperatives (strategy, structure, leadership and environment) defined by Miller (1987) and outlines interventions in organisational development (OD) that may contribute to their achievement. The aim is to build a conceptual framework at the intersection of these two fields that could help to strengthen the resilient capabilities of individuals, organisations and communities to face crises. This incursion into the field of OD--to generate more efficient configurations of practices in crisis management--seems particularly fruitful considering the system-wide application of OD, based on open-systems theory (Burke, 2008). Various interventions proposed by OD in terms of human processes, structural designs and human resource management, as well as strategy, may help leaders, members of organisations and civil society apply effectively, and in a more sustainable way, the crisis management guiding principles defined by researchers. © 2011 The Author(s). Disasters © Overseas Development Institute, 2011.

A "ship in a bottle" strategy to load a hydrophilic anticancer drug in porous metal organic framework nanoparticles: efficient encapsulation, matrix stabilization, and photodelivery.

PubMed

di Nunzio, Maria Rosaria; Agostoni, Valentina; Cohen, Boiko; Gref, Ruxandra; Douhal, Abderrazzak

2014-01-23

An essential challenge in the development of nanosized metal organic framework (nanoMOF) materials in biomedicine is to develop a strategy to stabilize their supramolecular structure in biological media while being able to control drug encapsulation and release. We have developed a method to efficiently encapsulate topotecan (TPT, 1), an important cytotoxic drug, in biodegradable nanoMOFs. Once inside the pores, 1 monomers aggregate in a "ship in a bottle" fashion, thus filling practically all of the nanoMOFs' available free volume and stabilizing their crystalline supramolecular structures. Highly efficient results have been found with the human pancreatic cell line PANC1, in contrast with free 1. We also demonstrate that one- and two-photon light irradiation emerges as a highly promising strategy to promote stimuli-dependent 1 release from the nanoMOFs, hence opening new standpoints for further developments in triggered drug delivery.

Crystal engineering on superpolyhedral building blocks in metal-organic frameworks applied in gas adsorption.

PubMed

Chen, Ying Pin; Liu, Tian Fu; Fordham, Stephen; Zhou, Hong Cai

2015-12-01

Two metal-organic frameworks [PCN-426(Ni) and PCN-427(Cu)] have been designed and synthesized to investigate the structure predictability using a SBB (supermolecular building blocks) approach. Tetratopic ligands featuring 120° angular carboxylate moieties were coordinated with a [Ni3(μ3-O)] cluster and a [Cu2O2] unit, respectively. As topologically predicted, 4-connected networks with square coordination adopted the nbo net for the Ni-MOF and ssb net for the Cu-MOF. PCN-426(Ni) was augmented with 12-connected octahedral SBBs, while PCN-427(Cu) was constructed with tetragonal open channels. After a CO2 supercritical drying procedure, the PCN-426(Ni) possessed a Brunauer-Emmett-Teller (BET) surface area as high as 3935 m(2) g(-1) and impressively high N2 uptake of 1500 cm(3) g(-1). This work demonstrates the generalization of the SBB strategy, finding an alternative to inconvenient synthetic processes to achieve the desired structural features.

Mechanical Properties in Metal-Organic Frameworks: Emerging Opportunities and Challenges for Device Functionality and Technological Applications.

PubMed

Burtch, Nicholas C; Heinen, Jurn; Bennett, Thomas D; Dubbeldam, David; Allendorf, Mark D

2017-11-17

Some of the most remarkable recent developments in metal-organic framework (MOF) performance properties can only be rationalized by the mechanical properties endowed by their hybrid inorganic-organic nanoporous structures. While these characteristics create intriguing application prospects, the same attributes also present challenges that will need to be overcome to enable the integration of MOFs with technologies where these promising traits can be exploited. In this review, emerging opportunities and challenges are identified for MOF-enabled device functionality and technological applications that arise from their fascinating mechanical properties. This is discussed not only in the context of their more well-studied gas storage and separation applications, but also for instances where MOFs serve as components of functional nanodevices. Recent advances in understanding MOF mechanical structure-property relationships due to attributes such as defects and interpenetration are highlighted, and open questions related to state-of-the-art computational approaches for quantifying their mechanical properties are critically discussed. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Studying Two-Dimensional Zeolites with the Tools of Surface Science: MFI Nanosheets on Au(111)

DOE PAGES

J. D. Kestell; Zhong, J. Q.; Shete, M.; ...

2016-07-26

While surface science has provided fundamental insights into a variety a materials, the most used catalysts in the industry, namely zeolites, still remain a challenge. The recent preparation of two-dimensional versions of MFI zeolite frameworks and the possibility of their deposition on electrically conductive supports provides for the first time a viable strategy to perform detailed studies on industrially relevant zeolites using the vast toolkit of surface science. In this work we demonstrate the use of infrared reflection absorption spectroscopy (IRRAS) and synchrotron-based x-ray photoelectron spectroscopy (XPS) to study these materials. Furthermore, polarization modulation IRRAS is used to study themore » adsorption of methanol and its effect in phonon vibrations of the zeolite framework. The possibility of using surface science methods, in particular under ambient pressure conditions, for the study of well-defined zeolites and other microporous structures opens new avenues to understand structural and mechanistic aspects of these materials as catalysts, adsorbents and molecular sieves.« less

Studying Two-Dimensional Zeolites with the Tools of Surface Science: MFI Nanosheets on Au(111)

DOE Office of Scientific and Technical Information (OSTI.GOV)

J. D. Kestell; Zhong, J. Q.; Shete, M.

While surface science has provided fundamental insights into a variety a materials, the most used catalysts in the industry, namely zeolites, still remain a challenge. The recent preparation of two-dimensional versions of MFI zeolite frameworks and the possibility of their deposition on electrically conductive supports provides for the first time a viable strategy to perform detailed studies on industrially relevant zeolites using the vast toolkit of surface science. In this work we demonstrate the use of infrared reflection absorption spectroscopy (IRRAS) and synchrotron-based x-ray photoelectron spectroscopy (XPS) to study these materials. Furthermore, polarization modulation IRRAS is used to study themore » adsorption of methanol and its effect in phonon vibrations of the zeolite framework. The possibility of using surface science methods, in particular under ambient pressure conditions, for the study of well-defined zeolites and other microporous structures opens new avenues to understand structural and mechanistic aspects of these materials as catalysts, adsorbents and molecular sieves.« less

Agent-based Large-Scale Emergency Evacuation Using Real-Time Open Government Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Wei; Liu, Cheng; Bhaduri, Budhendra L

The open government initiatives have provided tremendous data resources for the transportation system and emergency services in urban areas. This paper proposes a traffic simulation framework using high temporal resolution demographic data and real time open government data for evacuation planning and operation. A comparison study using real-world data in Seattle, Washington is conducted to evaluate the framework accuracy and evacuation efficiency. The successful simulations of selected area prove the concept to take advantage open government data, open source data, and high resolution demographic data in emergency management domain. There are two aspects of parameters considered in this study: usermore » equilibrium (UE) conditions of traffic assignment model (simple Non-UE vs. iterative UE) and data temporal resolution (Daytime vs. Nighttime). Evacuation arrival rate, average travel time, and computation time are adopted as Measure of Effectiveness (MOE) for evacuation performance analysis. The temporal resolution of demographic data has significant impacts on urban transportation dynamics during evacuation scenarios. Better evacuation performance estimation can be approached by integrating both Non-UE and UE scenarios. The new framework shows flexibility in implementing different evacuation strategies and accuracy in evacuation performance. The use of this framework can be explored to day-to-day traffic assignment to support daily traffic operations.« less

EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos.

PubMed

Schott, Benjamin; Traub, Manuel; Schlagenhauf, Cornelia; Takamiya, Masanari; Antritter, Thomas; Bartschat, Andreas; Löffler, Katharina; Blessing, Denis; Otte, Jens C; Kobitski, Andrei Y; Nienhaus, G Ulrich; Strähle, Uwe; Mikut, Ralf; Stegmaier, Johannes

2018-04-01

State-of-the-art light-sheet and confocal microscopes allow recording of entire embryos in 3D and over time (3D+t) for many hours. Fluorescently labeled structures can be segmented and tracked automatically in these terabyte-scale 3D+t images, resulting in thousands of cell migration trajectories that provide detailed insights to large-scale tissue reorganization at the cellular level. Here we present EmbryoMiner, a new interactive open-source framework suitable for in-depth analyses and comparisons of entire embryos, including an extensive set of trajectory features. Starting at the whole-embryo level, the framework can be used to iteratively focus on a region of interest within the embryo, to investigate and test specific trajectory-based hypotheses and to extract quantitative features from the isolated trajectories. Thus, the new framework provides a valuable new way to quantitatively compare corresponding anatomical regions in different embryos that were manually selected based on biological prior knowledge. As a proof of concept, we analyzed 3D+t light-sheet microscopy images of zebrafish embryos, showcasing potential user applications that can be performed using the new framework.

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.

PubMed

Jossinet, Fabrice; Ludwig, Thomas E; Westhof, Eric

2010-08-15

Assemble is an intuitive graphical interface to analyze, manipulate and build complex 3D RNA architectures. It provides several advanced and unique features within the framework of a semi-automated modeling process that can be performed by homology and ab initio with or without electron density maps. Those include the interactive editing of a secondary structure and a searchable, embedded library of annotated tertiary structures. Assemble helps users with performing recurrent and otherwise tedious tasks in structural RNA research. Assemble is released under an open-source license (MIT license) and is freely available at http://bioinformatics.org/assemble. It is implemented in the Java language and runs on MacOSX, Linux and Windows operating systems.

Stomatal Opening: The Role of Cell-Wall Mechanical Anisotropy and Its Analytical Relations to the Bio-composite Characteristics

PubMed Central

Marom, Ziv; Shtein, Ilana; Bar-On, Benny

2017-01-01

Stomata are pores on the leaf surface, which are formed by a pair of curved, tubular guard cells; an increase in turgor pressure deforms the guard cells, resulting in the opening of the stomata. Recent studies employed numerical simulations, based on experimental data, to analyze the effects of various structural, chemical, and mechanical features of the guard cells on the stomatal opening characteristics; these studies all support the well-known qualitative observation that the mechanical anisotropy of the guard cells plays a critical role in stomatal opening. Here, we propose a computationally based analytical model that quantitatively establishes the relations between the degree of anisotropy of the guard cell, the bio-composite constituents of the cell wall, and the aperture and area of stomatal opening. The model introduces two non-dimensional key parameters that dominate the guard cell deformations—the inflation driving force and the anisotropy ratio—and it serves as a generic framework that is not limited to specific plant species. The modeling predictions are in line with a wide range of previous experimental studies, and its analytical formulation sheds new light on the relations between the structure, mechanics, and function of stomata. Moreover, the model provides an analytical tool to back-calculate the elastic characteristics of the matrix that composes the guard cell walls, which, to the best of our knowledge, cannot be probed by direct nano-mechanical experiments; indeed, the estimations of our model are in good agreement with recently published results of independent numerical optimization schemes. The emerging insights from the stomatal structure-mechanics “design guidelines” may promote the development of miniature, yet complex, multiscale composite actuation mechanisms for future engineering platforms. PMID:29312365

Selective O 2 Sorption at Ambient Temperatures via Node Distortions in Sc-MIL-100

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sava Gallis, Dorina F.; Chapman, Karena W.; Rodriguez, Mark A.

2016-05-24

An open pored metal–organic framework (MOF) with oxygen selectivity at exceptionally high temperatures is confirmed by synthesis, sorption, and synchrotron structural analyses. The large-pore MIL-100 framework with access to the metal center (e.g., Sc and Fe) resulted in preferential O2 over N2 gas uptake at temperatures ranging from 77 K to ambient temperatures (258, 298, and 313 K). Most notably, Sc-MIL-100 shows exceptional O2 sorption; pair distribution function analyses indicate that this is due to distortions in the framework owing to the size of Sc atoms, in particular in the trimer metal cluster. Experimental studies also correlate very well withmore » GCMC simulations, confirming more favorable O2-framework interactions at pressures up to 1 bar, due to the close proximity of O2 to the high density of metal centers in the small tetrahedral cages. Both materials maintain their crystallinity upon gas adsorption cycling, are regenerable, and show exceptional promise for use in energy efficient oxygen purification processes, such as Pressure Swing Adsorption.« less

Co5In(BTC)4[B2O4(OH)]2: the first MOF material constructed by borate polyanions and carboxylate mixed ligands.

PubMed

Li, Sa-Ying; Liu, Zhi-Hong

2016-01-07

A novel heterometallic organic-inorganic hybrid MOF material, Co5In(BTC)4[B2O4(OH)]2, has been synthesized under ionothermal conditions. Its structure is characterized as a 3D open framework constructed by the Co2.5In0.5[B2O4(OH)] cluster and the 1,3,5-benzenetricarboxylate ligand. Furthermore, its fluorescent and adsorption properties have also been studied.

Graphene symmetry-breaking with molecular adsorbates: modeling and experiment

NASA Astrophysics Data System (ADS)

Groce, M. A.; Hawkins, M. K.; Wang, Y. L.; Cullen, W. G.; Einstein, T. L.

2012-02-01

Graphene's structure and electronic properties provide a framework for understanding molecule-substrate interactions and developing techniques for band gap engineering. Controlled deposition of molecular adsorbates can create superlattices which break the degeneracy of graphene's two-atom unit cell, opening a band gap. We simulate scanning tunneling microscopy and spectroscopy measurements for a variety of organic molecule/graphene systems, including pyridine, trimesic acid, and isonicotinic acid, based on density functional theory calculations using VASP. We also compare our simulations to ultra-high vacuum STM and STS results.

Open source data assimilation framework for hydrological modeling

NASA Astrophysics Data System (ADS)

Ridler, Marc; Hummel, Stef; van Velzen, Nils; Katrine Falk, Anne; Madsen, Henrik

2013-04-01

An open-source data assimilation framework is proposed for hydrological modeling. Data assimilation (DA) in hydrodynamic and hydrological forecasting systems has great potential to improve predictions and improve model result. The basic principle is to incorporate measurement information into a model with the aim to improve model results by error minimization. Great strides have been made to assimilate traditional in-situ measurements such as discharge, soil moisture, hydraulic head and snowpack into hydrologic models. More recently, remotely sensed data retrievals of soil moisture, snow water equivalent or snow cover area, surface water elevation, terrestrial water storage and land surface temperature have been successfully assimilated in hydrological models. The assimilation algorithms have become increasingly sophisticated to manage measurement and model bias, non-linear systems, data sparsity (time & space) and undetermined system uncertainty. It is therefore useful to use a pre-existing DA toolbox such as OpenDA. OpenDA is an open interface standard for (and free implementation of) a set of tools to quickly implement DA and calibration for arbitrary numerical models. The basic design philosophy of OpenDA is to breakdown DA into a set of building blocks programmed in object oriented languages. To implement DA, a model must interact with OpenDA to create model instances, propagate the model, get/set variables (or parameters) and free the model once DA is completed. An open-source interface for hydrological models exists capable of all these tasks: OpenMI. OpenMI is an open source standard interface already adopted by key hydrological model providers. It defines a universal approach to interact with hydrological models during simulation to exchange data during runtime, thus facilitating the interactions between models and data sources. The interface is flexible enough so that models can interact even if the model is coded in a different language, represent processes from a different domain or have different spatial and temporal resolutions. An open source framework that bridges OpenMI and OpenDA is presented. The framework provides a generic and easy means for any OpenMI compliant model to assimilate observation measurements. An example test case will be presented using MikeSHE, and OpenMI compliant fully coupled integrated hydrological model that can accurately simulate the feedback dynamics of overland flow, unsaturated zone and saturated zone.

Structural determinants of hydration, mechanics and fluid flow in freeze-dried collagen scaffolds.

PubMed

Offeddu, G S; Ashworth, J C; Cameron, R E; Oyen, M L

2016-09-01

Freeze-dried scaffolds provide regeneration templates for a wide range of tissues, due to their flexibility in physical and biological properties. Control of structure is crucial for tuning such properties, and therefore scaffold functionality. However, the common approach of modeling these scaffolds as open-cell foams does not fully account for their structural complexity. Here, the validity of the open-cell model is examined across a range of physical characteristics, rigorously linking morphology to hydration and mechanical properties. Collagen scaffolds with systematic changes in relative density were characterized using Scanning Electron Microscopy, X-ray Micro-Computed Tomography and spherical indentation analyzed in a time-dependent poroelastic framework. Morphologically, all scaffolds were mid-way between the open- and closed-cell models, approaching the closed-cell model as relative density increased. Although pore size remained constant, transport pathway diameter decreased. Larger collagen fractions also produced greater volume swelling on hydration, although the change in pore diameter was constant, and relatively small at ∼6%. Mechanically, the dry and hydrated scaffold moduli varied quadratically with relative density, as expected of open-cell materials. However, the increasing pore wall closure was found to determine the time-dependent nature of the hydrated scaffold response, with a decrease in permeability producing increasingly elastic rather than viscoelastic behavior. These results demonstrate that characterizing the deviation from the open-cell model is vital to gain a full understanding of scaffold biophysical properties, and provide a template for structural studies of other freeze-dried biomaterials. Freeze-dried collagen sponges are three-dimensional microporous scaffolds that have been used for a number of exploratory tissue engineering applications. The characterization of the structure-properties relationships of these scaffolds is necessary to understand their biophysical behavior in vivo. In this work, the relationship between morphology and physical properties in the dry and hydrated states was investigated across a range of solid concentrations in the scaffolds. The quantitative results provided can aid the design of scaffolds with a target trade-off between mechanical properties and structural features important for their biological activity. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

A New Framework for Massive Open Online Courses (MOOCs)

ERIC Educational Resources Information Center

Schoenack, Lindsie

2013-01-01

The challenges that massive open online courses (MOOCs) bring to the learning arena spur adult educators to improve delivery. A framework for a new type of MOOC is presented to address some of the challenges presented by earlier models. This new MOOC, called a mesoMOOC, can bridge several challenges that hinder current effective delivery of MOOCs…

Comparison of Physics Frameworks for WebGL-Based Game Engine

NASA Astrophysics Data System (ADS)

Yogya, Resa; Kosala, Raymond

2014-03-01

Recently, a new technology called WebGL shows a lot of potentials for developing games. However since this technology is still new, there are still many potentials in the game development area that are not explored yet. This paper tries to uncover the potential of integrating physics frameworks with WebGL technology in a game engine for developing 2D or 3D games. Specifically we integrated three open source physics frameworks: Bullet, Cannon, and JigLib into a WebGL-based game engine. Using experiment, we assessed these frameworks in terms of their correctness or accuracy, performance, completeness and compatibility. The results show that it is possible to integrate open source physics frameworks into a WebGLbased game engine, and Bullet is the best physics framework to be integrated into the WebGL-based game engine.

Multiscale Analysis of Open-Cell Aluminum Foam for Impact Energy Absorption

NASA Astrophysics Data System (ADS)

Kim, Ji Hoon; Kim, Daeyong; Lee, Myoung-Gyu; Lee, Jong Kook

2016-09-01

The energy-absorbing characteristics of crash members in automotive collision play an important role in controlling the amount of damage to the passenger compartment. Aluminum foams have high strength-to-weight ratio and high deformability, thus good crashworthiness is expected while maintaining or even saving weights when foams are implemented in crash members. In order to investigate the effect of the open-cell aluminum foam fillers on impact performance and weight saving, a multiscale framework for evaluating the crashworthiness of aluminum foam-filled members is used. To circumvent the difficulties of mechanical tests on foams, a micromechanical model of the aluminum foam is constructed using the x-ray micro tomography and virtual tests are conducted for the micromechanical model to characterize the behavior of the foam. In the macroscale, the aluminum foam is represented by the crushable foam constitutive model, which is then incorporated into the impact test simulation of the foam-filled crash member. The multiscale foam-filled crash member model was validated for the high-speed impact test, which confirms that the material model characterized by the micromechanical approach represents the behavior of the open-cell foam under impact loading well. Finally, the crash member design for maximizing the energy absorption is discussed by investigating various designs from the foam-only structure to the hollow tube structure. It was found that the foam structure absorbs more energy than the hollow tube or foam-filled structure with the same weight.

Multi-object segmentation framework using deformable models for medical imaging analysis.

PubMed

Namías, Rafael; D'Amato, Juan Pablo; Del Fresno, Mariana; Vénere, Marcelo; Pirró, Nicola; Bellemare, Marc-Emmanuel

2016-08-01

Segmenting structures of interest in medical images is an important step in different tasks such as visualization, quantitative analysis, simulation, and image-guided surgery, among several other clinical applications. Numerous segmentation methods have been developed in the past three decades for extraction of anatomical or functional structures on medical imaging. Deformable models, which include the active contour models or snakes, are among the most popular methods for image segmentation combining several desirable features such as inherent connectivity and smoothness. Even though different approaches have been proposed and significant work has been dedicated to the improvement of such algorithms, there are still challenging research directions as the simultaneous extraction of multiple objects and the integration of individual techniques. This paper presents a novel open-source framework called deformable model array (DMA) for the segmentation of multiple and complex structures of interest in different imaging modalities. While most active contour algorithms can extract one region at a time, DMA allows integrating several deformable models to deal with multiple segmentation scenarios. Moreover, it is possible to consider any existing explicit deformable model formulation and even to incorporate new active contour methods, allowing to select a suitable combination in different conditions. The framework also introduces a control module that coordinates the cooperative evolution of the snakes and is able to solve interaction issues toward the segmentation goal. Thus, DMA can implement complex object and multi-object segmentations in both 2D and 3D using the contextual information derived from the model interaction. These are important features for several medical image analysis tasks in which different but related objects need to be simultaneously extracted. Experimental results on both computed tomography and magnetic resonance imaging show that the proposed framework has a wide range of applications especially in the presence of adjacent structures of interest or under intra-structure inhomogeneities giving excellent quantitative results.

Extending the Territory: From Open Educational Resources to Open Educational Practices

ERIC Educational Resources Information Center

Ehlers, Ulf-Daniel

2011-01-01

This article examines the findings of the recent OPAL report "Beyond OER: Shifting Focus from Resources to Practices". In doing so, it defines current understanding of open educational resources and open educational practices, and highlights the shift from open content to open practice. The article includes a framework for supporting…

Industrially benign super-compressible piezoresistive carbon foams with predefined wetting properties: from environmental to electrical applications

NASA Astrophysics Data System (ADS)

Pham, Tung Ngoc; Samikannu, Ajaikumar; Kukkola, Jarmo; Rautio, Anne-Riikka; Pitkänen, Olli; Dombovari, Aron; Lorite, Gabriela Simone; Sipola, Teemu; Toth, Geza; Mohl, Melinda; Mikkola, Jyri-Pekka; Kordas, Krisztian

2014-11-01

In the present work electrically conductive, flexible, lightweight carbon sponge materials derived from open-pore structure melamine foams are studied and explored. Hydrophobic and hydrophilic surface properties - depending on the chosen treatment conditions - allow the separation and storage of liquid chemical compounds. Activation of the carbonaceous structures substantially increases the specific surface area from ~4 m2g-1 to ~345 m2g-1, while retaining the original three-dimensional, open-pore structure suitable for hosting, for example, Ni catalyst nanoparticles. In turn the structure is rendered suitable for hydrogenating acetone to 2-propanol and methyl isobutyl ketone as well for growing hierarchical carbon nanotube structures used as electric double-layer capacitor electrodes with specific capacitance of ~40 F/g. Mechanical stress-strain analysis indicates the materials are super-compressible (>70% volume reduction) and viscoelastic with excellent damping behavior (loss of 0.69 +/- 0.07), while piezoresistive measurements show very high gauge factors (from ~20 to 50) over a large range of deformations. The cost-effective, robust and scalable synthesis - in conjunction with their fascinating multifunctional utility - makes the demonstrated carbon foams remarkable competitors with other three-dimensional carbon materials typically based on pyrolyzed biopolymers or on covalently bonded graphene and carbon nanotube frameworks.

Industrially benign super-compressible piezoresistive carbon foams with predefined wetting properties: from environmental to electrical applications.

PubMed

Pham, Tung Ngoc; Samikannu, Ajaikumar; Kukkola, Jarmo; Rautio, Anne-Riikka; Pitkänen, Olli; Dombovari, Aron; Lorite, Gabriela Simone; Sipola, Teemu; Toth, Geza; Mohl, Melinda; Mikkola, Jyri-Pekka; Kordas, Krisztian

2014-11-06

In the present work electrically conductive, flexible, lightweight carbon sponge materials derived from open-pore structure melamine foams are studied and explored. Hydrophobic and hydrophilic surface properties - depending on the chosen treatment conditions - allow the separation and storage of liquid chemical compounds. Activation of the carbonaceous structures substantially increases the specific surface area from ~4 m(2)g(-1) to ~345 m(2)g(-1), while retaining the original three-dimensional, open-pore structure suitable for hosting, for example, Ni catalyst nanoparticles. In turn the structure is rendered suitable for hydrogenating acetone to 2-propanol and methyl isobutyl ketone as well for growing hierarchical carbon nanotube structures used as electric double-layer capacitor electrodes with specific capacitance of ~40 F/g. Mechanical stress-strain analysis indicates the materials are super-compressible (>70% volume reduction) and viscoelastic with excellent damping behavior (loss of 0.69 ± 0.07), while piezoresistive measurements show very high gauge factors (from ~20 to 50) over a large range of deformations. The cost-effective, robust and scalable synthesis - in conjunction with their fascinating multifunctional utility - makes the demonstrated carbon foams remarkable competitors with other three-dimensional carbon materials typically based on pyrolyzed biopolymers or on covalently bonded graphene and carbon nanotube frameworks.

Superconducting Open-Framework Allotrope of Silicon at Ambient Pressure

NASA Astrophysics Data System (ADS)

Sung, Ha-Jun; Han, W. H.; Lee, In-Ho; Chang, K. J.

2018-04-01

Diamond Si is a semiconductor with an indirect band gap that is the basis of modern semiconductor technology. Although many metastable forms of Si were observed using diamond anvil cells for compression and chemical precursors for synthesis, no metallic phase at ambient conditions has been reported thus far. Here we report the prediction of pure metallic Si allotropes with open channels at ambient pressure, unlike a cubic diamond structure in covalent bonding networks. The metallic phase termed P 6 /m -Si6 can be obtained by removing Na after pressure release from a novel Na-Si clathrate called P 6 /m -NaSi6 , which is predicted through first-principles study at high pressure. We identify that both P 6 /m -NaSi6 and P 6 /m -Si6 are stable and superconducting with the critical temperatures of about 13 and 12 K at ambient pressure, respectively. The prediction of new Na-Si and Si clathrate structures presents the possibility of exploring new exotic allotropes useful for Si-based devices.

Superconducting Open-Framework Allotrope of Silicon at Ambient Pressure.

PubMed

Sung, Ha-Jun; Han, W H; Lee, In-Ho; Chang, K J

2018-04-13

Diamond Si is a semiconductor with an indirect band gap that is the basis of modern semiconductor technology. Although many metastable forms of Si were observed using diamond anvil cells for compression and chemical precursors for synthesis, no metallic phase at ambient conditions has been reported thus far. Here we report the prediction of pure metallic Si allotropes with open channels at ambient pressure, unlike a cubic diamond structure in covalent bonding networks. The metallic phase termed P6/m-Si_{6} can be obtained by removing Na after pressure release from a novel Na-Si clathrate called P6/m-NaSi_{6}, which is predicted through first-principles study at high pressure. We identify that both P6/m-NaSi_{6} and P6/m-Si_{6} are stable and superconducting with the critical temperatures of about 13 and 12 K at ambient pressure, respectively. The prediction of new Na-Si and Si clathrate structures presents the possibility of exploring new exotic allotropes useful for Si-based devices.

Integrated System Modeling for Nuclear Thermal Propulsion (NTP)

NASA Technical Reports Server (NTRS)

Ryan, Stephen W.; Borowski, Stanley K.

2014-01-01

Nuclear thermal propulsion (NTP) has long been identified as a key enabling technology for space exploration beyond LEO. From Wernher Von Braun's early concepts for crewed missions to the Moon and Mars to the current Mars Design Reference Architecture (DRA) 5.0 and recent lunar and asteroid mission studies, the high thrust and specific impulse of NTP opens up possibilities such as reusability that are just not feasible with competing approaches. Although NTP technology was proven in the Rover / NERVA projects in the early days of the space program, an integrated spacecraft using NTP has never been developed. Such a spacecraft presents a challenging multidisciplinary systems integration problem. The disciplines that must come together include not only nuclear propulsion and power, but also thermal management, power, structures, orbital dynamics, etc. Some of this integration logic was incorporated into a vehicle sizing code developed at NASA's Glenn Research Center (GRC) in the early 1990s called MOMMA, and later into an Excel-based tool called SIZER. Recently, a team at GRC has developed an open source framework for solving Multidisciplinary Design, Analysis and Optimization (MDAO) problems called OpenMDAO. A modeling approach is presented that builds on previous work in NTP vehicle sizing and mission analysis by making use of the OpenMDAO framework to enable modular and reconfigurable representations of various NTP vehicle configurations and mission scenarios. This approach is currently applied to vehicle sizing, but is extensible to optimization of vehicle and mission designs. The key features of the code will be discussed and examples of NTP transfer vehicles and candidate missions will be presented.

Development of a competency framework for evidence-based practice in nursing.

PubMed

Leung, Kat; Trevena, Lyndal; Waters, Donna

2016-04-01

The measurement of competence in evidence-based practice (EBP) remains challenging to many educators and academics due to the lack of explicit competency criteria. Much uncertainty exists about what specific EBP competencies nurses should meet and how these should be measured. The objectives of this study are to develop a competency framework for measuring evidence-based knowledge and skills in nursing and to elicit the views of health educators/researchers about elements within the framework. A descriptive survey design with questionnaire. Between August and December 2013, forty-two health academics/educators, clinicians; and researchers from the medical and nursing schools at the University of Sydney and the Nurse Teacher's Society in Australia were invited to comment on proposed elements for measuring evidence-based knowledge and skills. The EBP competency framework was designed to measure nurses' knowledge and skills for using evidence in practice. Participants were invited to rate their agreement on the structure and relevance of the framework and to state their opinion about the measurement criteria for evidence-based nursing practice. Participant agreement on the structure and relevance of the framework was substantial, ICC: 0.80, 95% CI: 0.67-0.88, P<0.0001. Qualitative analysis of two open-ended survey questions revealed three common themes in participants' opinion of the competency elements: (1) a useful EBP framework; (2) varying expectations of EBP competence; and (3) challenges to EBP implementation. The findings of this study suggested that the EBP competency framework is of credible value for facilitating evidence-based practice education and research in nursing. However, there remains some uncertainty and disagreement about the levels of EBP competence required for nurses. These challenges further implicate the need for setting a reasonable competency benchmark with a broader group of stakeholders in nursing. Copyright © 2016 Elsevier Ltd. All rights reserved.

OpenElectrophy: An Electrophysiological Data- and Analysis-Sharing Framework

PubMed Central

Garcia, Samuel; Fourcaud-Trocmé, Nicolas

2008-01-01

Progress in experimental tools and design is allowing the acquisition of increasingly large datasets. Storage, manipulation and efficient analyses of such large amounts of data is now a primary issue. We present OpenElectrophy, an electrophysiological data- and analysis-sharing framework developed to fill this niche. It stores all experiment data and meta-data in a single central MySQL database, and provides a graphic user interface to visualize and explore the data, and a library of functions for user analysis scripting in Python. It implements multiple spike-sorting methods, and oscillation detection based on the ridge extraction methods due to Roux et al. (2007). OpenElectrophy is open source and is freely available for download at http://neuralensemble.org/trac/OpenElectrophy. PMID:19521545

A framework for streamlining research workflow in neuroscience and psychology

PubMed Central

Kubilius, Jonas

2014-01-01

Successful accumulation of knowledge is critically dependent on the ability to verify and replicate every part of scientific conduct. However, such principles are difficult to enact when researchers continue to resort on ad-hoc workflows and with poorly maintained code base. In this paper I examine the needs of neuroscience and psychology community, and introduce psychopy_ext, a unifying framework that seamlessly integrates popular experiment building, analysis and manuscript preparation tools by choosing reasonable defaults and implementing relatively rigid patterns of workflow. This structure allows for automation of multiple tasks, such as generated user interfaces, unit testing, control analyses of stimuli, single-command access to descriptive statistics, and publication quality plotting. Taken together, psychopy_ext opens an exciting possibility for a faster, more robust code development and collaboration for researchers. PMID:24478691

Two-Dimensional Covalent Organic Frameworks for Carbon Dioxide Capture through Channel-Wall Functionalization

PubMed Central

Huang, Ning; Chen, Xiong; Krishna, Rajamani; Jiang, Donglin

2015-01-01

Ordered open channels found in two-dimensional covalent organic frameworks (2D COFs) could enable them to adsorb carbon dioxide. However, the frameworks’ dense layer architecture results in low porosity that has thus far restricted their potential for carbon dioxide adsorption. Here we report a strategy for converting a conventional 2D COF into an outstanding platform for carbon dioxide capture through channel-wall functionalization. The dense layer structure enables the dense integration of functional groups on the channel walls, creating a new version of COFs with high capacity, reusability, selectivity, and separation productivity for flue gas. These results suggest that channel-wall functional engineering could be a facile and powerful strategy to develop 2D COFs for high-performance gas storage and separation. PMID:25613010

A compositional framework for reaction networks

NASA Astrophysics Data System (ADS)

Baez, John C.; Pollard, Blake S.

Reaction networks, or equivalently Petri nets, are a general framework for describing processes in which entities of various kinds interact and turn into other entities. In chemistry, where the reactions are assigned ‘rate constants’, any reaction network gives rise to a nonlinear dynamical system called its ‘rate equation’. Here we generalize these ideas to ‘open’ reaction networks, which allow entities to flow in and out at certain designated inputs and outputs. We treat open reaction networks as morphisms in a category. Composing two such morphisms connects the outputs of the first to the inputs of the second. We construct a functor sending any open reaction network to its corresponding ‘open dynamical system’. This provides a compositional framework for studying the dynamics of reaction networks. We then turn to statics: that is, steady state solutions of open dynamical systems. We construct a ‘black-boxing’ functor that sends any open dynamical system to the relation that it imposes between input and output variables in steady states. This extends our earlier work on black-boxing for Markov processes.

The RAVE/VERTIGO vertex reconstruction toolkit and framework

NASA Astrophysics Data System (ADS)

Waltenberger, W.; Mitaroff, W.; Moser, F.; Pflugfelder, B.; Riedel, H. V.

2008-07-01

A detector-independent toolkit for vertex reconstruction (RAVE1) is being developed, along with a standalone framework (VERTIGO2) for testing, analyzing and debugging. The core algorithms represent state-of-the-art for geometric vertex finding and fitting by both linear (Kalman filter) and robust estimation methods. Main design goals are ease of use, flexibility for embedding into existing software frameworks, extensibility, and openness. The implementation is based on modern object-oriented techniques, is coded in C++ with interfaces for Java and Python, and follows an open-source approach. A beta release is available.

Open source and open content: A framework for global collaboration in social-ecological research

Treesearch

Charles Schweik; Tom Evans; J. Morgan Grove

2005-01-01

This paper discusses opportunities for alternative collaborative approaches for social-ecological research in general and, in this context, for modeling land-use/land-cover change. In this field, the rate of progress in academic research is steady but perhaps not as rapid or efficient as might be possible with alternative organizational frameworks. The convergence of...

The Family as a Living Open System: An Emerging Conceptual Framework.

ERIC Educational Resources Information Center

Fawcett, Jacqueline

The conceptual framework of the family presented in this paper views the family as a reality in itself. The four-dimensional energy field that is the family system is a living open system, a dynamic whole engaged in mutual and simultaneous interaction with a four-dimensional energy field that is the environment. The family system is patterned and…

Functional Additive Mixed Models

PubMed Central

Scheipl, Fabian; Staicu, Ana-Maria; Greven, Sonja

2014-01-01

We propose an extensive framework for additive regression models for correlated functional responses, allowing for multiple partially nested or crossed functional random effects with flexible correlation structures for, e.g., spatial, temporal, or longitudinal functional data. Additionally, our framework includes linear and nonlinear effects of functional and scalar covariates that may vary smoothly over the index of the functional response. It accommodates densely or sparsely observed functional responses and predictors which may be observed with additional error and includes both spline-based and functional principal component-based terms. Estimation and inference in this framework is based on standard additive mixed models, allowing us to take advantage of established methods and robust, flexible algorithms. We provide easy-to-use open source software in the pffr() function for the R-package refund. Simulations show that the proposed method recovers relevant effects reliably, handles small sample sizes well and also scales to larger data sets. Applications with spatially and longitudinally observed functional data demonstrate the flexibility in modeling and interpretability of results of our approach. PMID:26347592

Trapping gases in metal-organic frameworks with a selective surface molecular barrier layer

DOE PAGES

Tan, Kui; Zuluaga, Sebastian; Fuentes, Erika; ...

2016-12-13

The main challenge for gas storage and separation in nanoporous materials is that many molecules of interest adsorb too weakly to be effectively retained. Instead of synthetically modifying the internal surface structure of the entire bulk—as is typically done to enhance adsorption—here we show that post exposure of a prototypical porous metal-organic framework to ethylenediamine can effectively retain a variety of weakly adsorbing molecules (for example, CO, CO 2, SO 2, C 2H 4, NO) inside the materials by forming a monolayer-thick cap at the external surface of microcrystals. Furthermore, this capping mechanism, based on hydrogen bonding as explained bymore » ab initio modelling, opens the door for potential selectivity. For example, water molecules are shown to disrupt the hydrogen-bonded amine network and diffuse through the cap without hindrance and fully displace/release the retained small molecules out of the metal-organic framework at room temperature. Lastly, these findings may provide alternative strategies for gas storage, delivery and separation.« less

A Sr2+-metal-organic framework with high chemical stability: synthesis, crystal structure and photoluminescence property.

PubMed

Jia, Yan-Yuan; Liu, Xiao-Ting; Wang, Wen-He; Zhang, Li-Zhu; Zhang, Ying-Hui; Bu, Xian-He

2017-01-13

Metal-organic frameworks (MOFs) are typically built by assembly of metal centres and organic linkers, and have emerged as promising crystalline materials in a variety of fields. However, the stability of MOFs is a key limitation for their practical applications. Herein, we report a novel Sr 2+: -MOF [Sr 4 (Tdada) 2 (H 2 O) 3 (DMF) 2 ] (denoted as NKU- 105: , NKU = Nankai University; H 4 Tdada = 5,5'-((thiophene-2,5-dicar bonyl)bis(azanediyl))diisophthalic acid; DMF = N,N-dimethylformamide) featuring an open square channel of about 6 Å along the c-axis. Notably, NKU- 105: exhibits much outstanding chemical stability against common organic solvents, boiling water, acids and bases, relative to most MOF materials. Furthermore, NKU- 105: is an environment-friendly luminescent material with a bright cyan emission.This article is part of the themed issue 'Coordination polymers and metal-organic frameworks: materials by design'. © 2016 The Author(s).

A Sr2+-metal–organic framework with high chemical stability: synthesis, crystal structure and photoluminescence property

PubMed Central

Jia, Yan-Yuan; Liu, Xiao-Ting; Wang, Wen-He; Zhang, Li-Zhu; Bu, Xian-He

2017-01-01

Metal–organic frameworks (MOFs) are typically built by assembly of metal centres and organic linkers, and have emerged as promising crystalline materials in a variety of fields. However, the stability of MOFs is a key limitation for their practical applications. Herein, we report a novel Sr2+-MOF [Sr4(Tdada)2(H2O)3(DMF)2] (denoted as NKU-105, NKU = Nankai University; H4Tdada = 5,5'-((thiophene-2,5-dicar bonyl)bis(azanediyl))diisophthalic acid; DMF = N,N-dimethylformamide) featuring an open square channel of about 6 Å along the c-axis. Notably, NKU-105 exhibits much outstanding chemical stability against common organic solvents, boiling water, acids and bases, relative to most MOF materials. Furthermore, NKU-105 is an environment-friendly luminescent material with a bright cyan emission. This article is part of the themed issue ‘Coordination polymers and metal–organic frameworks: materials by design’. PMID:27895256

Functional Additive Mixed Models.

PubMed

Scheipl, Fabian; Staicu, Ana-Maria; Greven, Sonja

2015-04-01

We propose an extensive framework for additive regression models for correlated functional responses, allowing for multiple partially nested or crossed functional random effects with flexible correlation structures for, e.g., spatial, temporal, or longitudinal functional data. Additionally, our framework includes linear and nonlinear effects of functional and scalar covariates that may vary smoothly over the index of the functional response. It accommodates densely or sparsely observed functional responses and predictors which may be observed with additional error and includes both spline-based and functional principal component-based terms. Estimation and inference in this framework is based on standard additive mixed models, allowing us to take advantage of established methods and robust, flexible algorithms. We provide easy-to-use open source software in the pffr() function for the R-package refund. Simulations show that the proposed method recovers relevant effects reliably, handles small sample sizes well and also scales to larger data sets. Applications with spatially and longitudinally observed functional data demonstrate the flexibility in modeling and interpretability of results of our approach.

Tight-binding model for materials at mesoscale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tai, Yuan-Yen; Choi, Hongchul; Zhu, Wei

2016-12-21

TBM3 is an open source package for computational simulations of quantum materials at multiple scales in length and time. The project originated to investigate the multiferroic behavior in transition-metal oxide heterostructures. The framework has also been designed to study emergent phemona in other quantum materials like 2-dimensional transition-metal dichalcogenides, graphene, topological insulators, and skyrmion in materials, etc. In the long term, we will enable the package for transport and time-resolved phenomena. TBM3 is currently a C++ based numerical tool package and framework for the design and construction of any kind of lattice structures with multi-orbital and spin degrees of freedom.more » The fortran based portion of the package will be added in the near future. The design of TBM3 is in a highly flexible and reusable framework and the tight-binding parameters can be modeled or informed by DFT calculations. It is currently GPU enabled and feature of CPU enabled MPI will be added in the future.« less

Emptying and filling a tunnel bronze

DOE PAGES

Marley, Peter M.; Abtew, Tesfaye A.; Farley, Katie E.; ...

2015-01-13

The classical orthorhombic layered phase of V 2O 5 has long been regarded as the thermodynamic sink for binary vanadium oxides and has found great practical utility as a result of its open framework and easily accessible redox states. Herein, we exploit a cation-exchange mechanism to synthesize a new stable tunnel-structured polymorph of V 2O 5 (ζ-V 2O 5) and demonstrate the subsequent ability of this framework to accommodate Li and Mg ions. The facile extraction and insertion of cations and stabilization of the novel tunnel framework is facilitated by the nanometer-sized dimensions of the materials, which leads to accommodationmore » of strain without amorphization. The topotactic approach demonstrated here indicates not just novel intercalation chemistry accessible at nanoscale dimensions but also suggests a facile synthetic route to ternary vanadium oxide bronzes (MxV 2O 5) exhibiting intriguing physical properties that range from electronic phase transitions to charge ordering and superconductivity.« less

a Framework for AN Open Source Geospatial Certification Model

NASA Astrophysics Data System (ADS)

Khan, T. U. R.; Davis, P.; Behr, F.-J.

2016-06-01

The geospatial industry is forecasted to have an enormous growth in the forthcoming years and an extended need for well-educated workforce. Hence ongoing education and training play an important role in the professional life. Parallel, in the geospatial and IT arena as well in the political discussion and legislation Open Source solutions, open data proliferation, and the use of open standards have an increasing significance. Based on the Memorandum of Understanding between International Cartographic Association, OSGeo Foundation, and ISPRS this development led to the implementation of the ICA-OSGeo-Lab imitative with its mission "Making geospatial education and opportunities accessible to all". Discussions in this initiative and the growth and maturity of geospatial Open Source software initiated the idea to develop a framework for a worldwide applicable Open Source certification approach. Generic and geospatial certification approaches are already offered by numerous organisations, i.e., GIS Certification Institute, GeoAcademy, ASPRS, and software vendors, i. e., Esri, Oracle, and RedHat. They focus different fields of expertise and have different levels and ways of examination which are offered for a wide range of fees. The development of the certification framework presented here is based on the analysis of diverse bodies of knowledge concepts, i.e., NCGIA Core Curriculum, URISA Body Of Knowledge, USGIF Essential Body Of Knowledge, the "Geographic Information: Need to Know", currently under development, and the Geospatial Technology Competency Model (GTCM). The latter provides a US American oriented list of the knowledge, skills, and abilities required of workers in the geospatial technology industry and influenced essentially the framework of certification. In addition to the theoretical analysis of existing resources the geospatial community was integrated twofold. An online survey about the relevance of Open Source was performed and evaluated with 105 respondents worldwide. 15 interviews (face-to-face or by telephone) with experts in different countries provided additional insights into Open Source usage and certification. The findings led to the development of a certification framework of three main categories with in total eleven sub-categories, i.e., "Certified Open Source Geospatial Data Associate / Professional", "Certified Open Source Geospatial Analyst Remote Sensing & GIS", "Certified Open Source Geospatial Cartographer", "Certified Open Source Geospatial Expert", "Certified Open Source Geospatial Associate Developer / Professional Developer", "Certified Open Source Geospatial Architect". Each certification is described by pre-conditions, scope and objectives, course content, recommended software packages, target group, expected benefits, and the methods of examination. Examinations can be flanked by proofs of professional career paths and achievements which need a peer qualification evaluation. After a couple of years a recertification is required. The concept seeks the accreditation by the OSGeo Foundation (and other bodies) and international support by a group of geospatial scientific institutions to achieve wide and international acceptance for this Open Source geospatial certification model. A business case for Open Source certification and a corresponding SWOT model is examined to support the goals of the Geo-For-All initiative of the ICA-OSGeo pact.

New anion-templated 3D heterobimetallic open frameworks based on lanthanide-carboxylate layers and copper pillars

NASA Astrophysics Data System (ADS)

Li, Yun-Wu; Wang, Yong-Hui; Li, Yang-Guang; Wang, En-Bo

2008-06-01

A series of new three-dimensional (3D) lanthanide-transition metal (4 f-3 d) heterobimetallic open frameworks, [ Ln2(1,2-bdc) 2(H 2O) 2 Cu(inic) 2](ClO 4) ( Ln=Eu (1), Tb (2), Nd (3) and Sm (4); 1,2-bdc=1,2-benzenedicarboxylate; Hinic=isonicotinic acid) have been hydrothermally synthesized and characterized by elemental analysis, IR, TG and single-crystal X-ray diffraction analysis. Compounds 1-4 are isostructural. They possess a new anion-templated 3D heterobimetallic open framework, which is observed for the first time in the { Ln/ TM/bdc/inic} ( TM=transition metal) system. Compounds 1 and 2 exhibit the characteristic fluorescent properties of Eu(III) and Tb(III), respectively.

Implementing a competence framework for administering medication: reporting the experiences of mental health nurses and students in the UK.

PubMed

Hemingway, Steve; White, Jacqueline; Baxter, Hazel; Smith, George; Turner, James; McCann, Terence

2012-10-01

Medicine administration is a high risk activity that most nurses undertake frequently. In this paper, the views of registered mental health nurses and final year student nurses are evaluated about the usefulness of the Medicines with Respect Assessment of the Administration of Medicines Competency Framework. A questionnaire using 22 items with closed and open response questions was distributed to 827 practising mental health nurses and 44 final year mental health nursing students. This article presents a content analysis of written replies to the open response questions. Four overlapping themes were identified in response to the open questions posed in the survey: (1) reasons for undertaking the Medicines with Respect Framework; (2) positive aspects; (3) negative aspects; and (4) service user benefits.

DEVELOP MULTI-STRESSOR, OPEN ARCHITECTURE MODELING FRAMEWORK FOR ECOLOGICAL EXPOSURE FROM SITE TO WATERSHED SCALE

EPA Science Inventory

A number of multimedia modeling frameworks are currently being developed. The Multimedia Integrated Modeling System (MIMS) is one of these frameworks. A framework should be seen as more of a multimedia modeling infrastructure than a single software system. This infrastructure do...

Brain maps 4.0-Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps.

PubMed

Swanson, Larry W

2018-04-15

The fourth edition (following editions in 1992, 1998, 2004) of Brain maps: structure of the rat brain is presented here as an open access internet resource for the neuroscience community. One new feature is a set of 10 hierarchical nomenclature tables that define and describe all parts of the rat nervous system within the framework of a strictly topographic system devised previously for the human nervous system. These tables constitute a global ontology for knowledge management systems dealing with neural circuitry. A second new feature is an aligned atlas of bilateral flatmaps illustrating rat nervous system development from the neural plate stage to the adult stage, where most gray matter regions, white matter tracts, ganglia, and nerves listed in the nomenclature tables are illustrated schematically. These flatmaps are convenient for future development of online applications analogous to "Google Maps" for systems neuroscience. The third new feature is a completely revised Atlas of the rat brain in spatially aligned transverse sections that can serve as a framework for 3-D modeling. Atlas parcellation is little changed from the preceding edition, but the nomenclature for rat is now aligned with an emerging panmammalian neuroanatomical nomenclature. All figures are presented in Adobe Illustrator vector graphics format that can be manipulated, modified, and resized as desired, and freely used with a Creative Commons license. © 2018 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

Development of AN Open-Source Automatic Deformation Monitoring System for Geodetical and Geotechnical Measurements

NASA Astrophysics Data System (ADS)

Engel, P.; Schweimler, B.

2016-04-01

The deformation monitoring of structures and buildings is an important task field of modern engineering surveying, ensuring the standing and reliability of supervised objects over a long period. Several commercial hardware and software solutions for the realization of such monitoring measurements are available on the market. In addition to them, a research team at the Neubrandenburg University of Applied Sciences (NUAS) is actively developing a software package for monitoring purposes in geodesy and geotechnics, which is distributed under an open source licence and free of charge. The task of managing an open source project is well-known in computer science, but it is fairly new in a geodetic context. This paper contributes to that issue by detailing applications, frameworks, and interfaces for the design and implementation of open hardware and software solutions for sensor control, sensor networks, and data management in automatic deformation monitoring. It will be discussed how the development effort of networked applications can be reduced by using free programming tools, cloud computing technologies, and rapid prototyping methods.

3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE FEM Model.

PubMed

Spühler, Jeannette H; Jansson, Johan; Jansson, Niclas; Hoffman, Johan

2018-01-01

Due to advances in medical imaging, computational fluid dynamics algorithms and high performance computing, computer simulation is developing into an important tool for understanding the relationship between cardiovascular diseases and intraventricular blood flow. The field of cardiac flow simulation is challenging and highly interdisciplinary. We apply a computational framework for automated solutions of partial differential equations using Finite Element Methods where any mathematical description directly can be translated to code. This allows us to develop a cardiac model where specific properties of the heart such as fluid-structure interaction of the aortic valve can be added in a modular way without extensive efforts. In previous work, we simulated the blood flow in the left ventricle of the heart. In this paper, we extend this model by placing prototypes of both a native and a mechanical aortic valve in the outflow region of the left ventricle. Numerical simulation of the blood flow in the vicinity of the valve offers the possibility to improve the treatment of aortic valve diseases as aortic stenosis (narrowing of the valve opening) or regurgitation (leaking) and to optimize the design of prosthetic heart valves in a controlled and specific way. The fluid-structure interaction and contact problem are formulated in a unified continuum model using the conservation laws for mass and momentum and a phase function. The discretization is based on an Arbitrary Lagrangian-Eulerian space-time finite element method with streamline diffusion stabilization, and it is implemented in the open source software Unicorn which shows near optimal scaling up to thousands of cores. Computational results are presented to demonstrate the capability of our framework.

Synthesis, crystal structure, and magnetic properties of a two-fold interpenetrated diamondoid open framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Jing-Yun, E-mail: jyunwu@ncnu.edu.tw; Cheng, Fu-Yin; Chiang, Ming-Hsi, E-mail: mhchiang@chem.sinica.edu.tw

2016-10-15

Self-assembly of an enlarged angular pyridinecarboxylate ligand and cobalt(II) acetate under mild conditions afforded a three-dimensional open-framework coordination polymer, [Co{sub 2}(μ-H{sub 2}O)(pyca-43){sub 4}]{sub n} (1, Hpyca-43=(E)−3-((pyridin-4-yl)methyleneamino)benzoic acid). The molecular structure of 1 has rationalized to be a porous two-fold interpenetrated diamondoid-like network, with dinuclear Co{sub 2}(μ-H{sub 2}O)(O{sub 2}C){sub 4}N{sub 4} clusters as tetrahedral secondary building units (SBUs), possessing highly solvent accessible volume of approximately 53.0%. Least-squares fit of the magnetic susceptibility data (20–300 K) of 1 yields Curie constant C=6.15 cm{sup 3} mol{sup –1} K and Weiss constant θ=–11.6 K. Every Co{sub 2} subunit within the network is magnetically insulatedmore » to other dimers. The magnetic exchange parameter between Co(II) centers is estimated to −0.72 cm{sup –1}, suggesting a weak antiferromagnetic interaction. The g{sub av} value of 4.65 from fitting to the Lines model indicates that the decrease of the χ{sub M}T value upon cooling is dominated by depopulation of the excited Kramer's states to the effective ground singlet. In addition, the thermal stability and adsorption properties of 1 are also reported. - Graphical abstract: This work has synthesized and structurally characterized a porous two-fold interpenetrated diamondoid-like network, which possesses highly solvent accessible volume of approximately 53.0% and shows a weak antiferromagnetic interaction between the Co(II) centers.« less

3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE FEM Model

PubMed Central

Spühler, Jeannette H.; Jansson, Johan; Jansson, Niclas; Hoffman, Johan

2018-01-01

Due to advances in medical imaging, computational fluid dynamics algorithms and high performance computing, computer simulation is developing into an important tool for understanding the relationship between cardiovascular diseases and intraventricular blood flow. The field of cardiac flow simulation is challenging and highly interdisciplinary. We apply a computational framework for automated solutions of partial differential equations using Finite Element Methods where any mathematical description directly can be translated to code. This allows us to develop a cardiac model where specific properties of the heart such as fluid-structure interaction of the aortic valve can be added in a modular way without extensive efforts. In previous work, we simulated the blood flow in the left ventricle of the heart. In this paper, we extend this model by placing prototypes of both a native and a mechanical aortic valve in the outflow region of the left ventricle. Numerical simulation of the blood flow in the vicinity of the valve offers the possibility to improve the treatment of aortic valve diseases as aortic stenosis (narrowing of the valve opening) or regurgitation (leaking) and to optimize the design of prosthetic heart valves in a controlled and specific way. The fluid-structure interaction and contact problem are formulated in a unified continuum model using the conservation laws for mass and momentum and a phase function. The discretization is based on an Arbitrary Lagrangian-Eulerian space-time finite element method with streamline diffusion stabilization, and it is implemented in the open source software Unicorn which shows near optimal scaling up to thousands of cores. Computational results are presented to demonstrate the capability of our framework. PMID:29713288

Knowledge and Theme Discovery across Very Large Biological Data Sets Using Distributed Queries: A Prototype Combining Unstructured and Structured Data

PubMed Central

Repetski, Stephen; Venkataraman, Girish; Che, Anney; Luke, Brian T.; Girard, F. Pascal; Stephens, Robert M.

2013-01-01

As the discipline of biomedical science continues to apply new technologies capable of producing unprecedented volumes of noisy and complex biological data, it has become evident that available methods for deriving meaningful information from such data are simply not keeping pace. In order to achieve useful results, researchers require methods that consolidate, store and query combinations of structured and unstructured data sets efficiently and effectively. As we move towards personalized medicine, the need to combine unstructured data, such as medical literature, with large amounts of highly structured and high-throughput data such as human variation or expression data from very large cohorts, is especially urgent. For our study, we investigated a likely biomedical query using the Hadoop framework. We ran queries using native MapReduce tools we developed as well as other open source and proprietary tools. Our results suggest that the available technologies within the Big Data domain can reduce the time and effort needed to utilize and apply distributed queries over large datasets in practical clinical applications in the life sciences domain. The methodologies and technologies discussed in this paper set the stage for a more detailed evaluation that investigates how various data structures and data models are best mapped to the proper computational framework. PMID:24312478

Knowledge and theme discovery across very large biological data sets using distributed queries: a prototype combining unstructured and structured data.

PubMed

Mudunuri, Uma S; Khouja, Mohamad; Repetski, Stephen; Venkataraman, Girish; Che, Anney; Luke, Brian T; Girard, F Pascal; Stephens, Robert M

2013-01-01

As the discipline of biomedical science continues to apply new technologies capable of producing unprecedented volumes of noisy and complex biological data, it has become evident that available methods for deriving meaningful information from such data are simply not keeping pace. In order to achieve useful results, researchers require methods that consolidate, store and query combinations of structured and unstructured data sets efficiently and effectively. As we move towards personalized medicine, the need to combine unstructured data, such as medical literature, with large amounts of highly structured and high-throughput data such as human variation or expression data from very large cohorts, is especially urgent. For our study, we investigated a likely biomedical query using the Hadoop framework. We ran queries using native MapReduce tools we developed as well as other open source and proprietary tools. Our results suggest that the available technologies within the Big Data domain can reduce the time and effort needed to utilize and apply distributed queries over large datasets in practical clinical applications in the life sciences domain. The methodologies and technologies discussed in this paper set the stage for a more detailed evaluation that investigates how various data structures and data models are best mapped to the proper computational framework.

Synthesis, crystal structure and thermal study of the hybrid nickel sulfate: C6N2H16[Ni(H2O)6(SO4)2].2H2O

NASA Astrophysics Data System (ADS)

Ngopoh, F. A. I.; Hamdi, N.; Chaouch, S.; Lachkar, M.; da Silva, I.; El Bali, B.

2018-03-01

A new inorganic-organic hybrid open framework nickel sulfate C6N2H16[Ni(H2O)6(SO4)2].2H2O has been synthesized by slow evaporation in aqueous solution using trans-1,4-diaminocyclohexane as structure-directing agent. It was characterized by single-crystal X-ray diffraction, infrared spectroscopy and analyzed by TGA-DSC. The compound crystallizes in the monoclinic space group P21/n, with the unit cell parameters of a = 6.2586 Å, b = 12.3009 Å, c = 13.2451 Å, β = 98,047°, Z = 4. Its crystal structure consists of isolated polyhedrons [Ni(H2O)6]2+ and [SO4]2- and free water which connects through hydrogen bonds. This association results in the porous framework where the protonated organic molecule trans-1,4-diaminocyclohexane is located as a counter ion. The IR spectra Shows the bands corresponding to the sulfate anion, water molecule and diprotonated trans-1-4-diaminocyclohexane. Thermal study indicates the loss of water molecules and the degradation of trans-1-4-diaminocyclohexane.

Structural and magnetic characterization of three tetranuclear Cu(II) complexes with face-sharing-dicubane/double-open-cubane like core framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paul, Aparup; Bertolasi, Valerio; Figuerola, Albert

Three novel tetranuclear copper(II) complexes namely [Cu{sub 4}(L{sup 1}){sub 4}]∙2(dmf) (1), [Cu{sub 4}(L{sup 1}){sub 4}] (2) and [Cu{sub 4}(L{sup 2}){sub 2}(HL{sup 2}){sub 2}(H{sub 2}O){sub 2}]∙2(ClO{sub 4})·6(H{sub 2}O) (3) (H{sub 2}L{sup 1}, (E)−2-((1-hydroxybutan-2-ylimino)methyl)phenol; H{sub 2}L{sup 2}, (E)−2-((1-hydroxybutan-2-ylimino)methyl)−6-methoxyphenol)) were synthesized from the self-assembly of copper(II) perchlorate and the tridentate Schiff base ligands. The structural determination reveals that crystallizes in the monoclinic system with space group C2/c, whereas both the and crystallize in the triclinic system with space group P-1. and possess face-sharing dicubane core, on the other hand complex 3 has double open cubane core structure. The copper(II) ions in the cubanemore » core are in distorted square planar geometries, and weak π…π and C–H…π interactions lead to formation of a 2D supramolecular architecture for and . At room temperature and , exhibit fluorescence with a quantum yield (Φ{sub s}) of 0.47, 0.49 and 0.38, respectively. Variable temperature magnetic susceptibility measurements in the range 2–300 K indicate an overall weak antiferromagnetic exchange coupling in all complexes. The PHI program was used to study their magnetic behaviour. In agreement with their face-sharing dicubane structure, a Hamiltonian of the type H =– J{sub 1}(S{sub 1}S{sub 2}+S{sub 1}S{sub 2’}+S{sub 1'}S{sub 2}+S{sub 1'}S{sub 2’}) – J{sub 2}S{sub 1}S{sub 1’}, where S{sub 1} = S{sub 1’} = S{sub 2} = S{sub 2’} = S{sub Cu} =1/2, was used for studying and . Simulations performed suggest magnetic exchange constants with values close to J{sub 1} =−20 cm{sup −1} and J{sub 2} =0 cm{sup -1} for these complexes. On the other hand, the spin Hamiltonian H =– J{sub 1}(S{sub 1}S{sub 4}+S{sub 2}S{sub 3}) – J{sub 2}(S{sub 1}S{sub 3}+S{sub 2}S{sub 4}) – J{sub 3}S{sub 1}S{sub 2}, where S{sub 1} = S{sub 2} = S{sub 3} = S{sub 4} = S{sub Cu} =1/2, was used to study the magnetic behaviour of the double open cubane core of and a good agreement between the experimental and simulated results was found by using the parameters g{sub 1} = g{sub 2} =2.20, g{sub 3} = g{sub 4} =2.18, J{sub 1} =−36 cm{sup -1}, J{sub 2} =−44 cm{sup -1} and J{sub 3} =0 cm{sup -1}. - Graphical abstract: Tetranuclear Cu(II) complexes with face-sharing-dicubane / double-open-cubane like core frameworks were synthesized and characterized by crystal structure and magnetic analysis. Variable temperature magnetic properties corroborate with their structural arrangement. - Highlights: • Novel tetranuclear copper(II) complexes have been structurally characterized. • Complexes possess face-sharing dicubane/double open cubane core structures. • Variable temperature magnetic measurements reveal antiferromagnetic coupling. • PHI program was used to explain the observed magnetic properties.« less

Coordination Covalent Frameworks: A New Route for Synthesis and Expansion of Functional Porous Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elsaidi, Sameh K.; Mohamed, Mona H.; Loring, John S.

The synthetic approaches for fine-tuning the structural properties of coordination polymers or metal organic frameworks have exponentially grown during the last decade. This is due to the control over the properties of the resulting structures such as stability, pore size, pore chemis-try and surface area for myriad possible applications. Herein, we present a new class of porous materials called Covalent Coordination Frameworks (CCFs) that were designed and effectively synthesized using a two-step reticular chemistry approach. During the first step, trigonal prismatic molecular building block was isolated using 4-aminobenazoic acid and Cr (III) salt, subsequently in the second step the polymerizationmore » of the isolated molecular building blocks (MBBs) takes place by the formation of strong covalent bonds where small organic molecules can connect the MBBs forming extended porous CCF materials. All the isolated CCFs were found to be permanently porous while the discrete MBB were non-porous. This approach would inevitably open a feasible path for the applications of reticular chemistry and the synthesis of novel porous materials with various topologies under ambient conditions using simple organic molecules and versatile MBBs with different functionalities which would not be possible using the traditional one step approach« less

A patient-specific aortic valve model based on moving resistive immersed implicit surfaces.

PubMed

Fedele, Marco; Faggiano, Elena; Dedè, Luca; Quarteroni, Alfio

2017-10-01

In this paper, we propose a full computational framework to simulate the hemodynamics in the aorta including the valve. Closed and open valve surfaces, as well as the lumen aorta, are reconstructed directly from medical images using new ad hoc algorithms, allowing a patient-specific simulation. The fluid dynamics problem that accounts from the movement of the valve is solved by a new 3D-0D fluid-structure interaction model in which the valve surface is implicitly represented through level set functions, yielding, in the Navier-Stokes equations, a resistive penalization term enforcing the blood to adhere to the valve leaflets. The dynamics of the valve between its closed and open position is modeled using a reduced geometric 0D model. At the discrete level, a finite element formulation is used and the SUPG stabilization is extended to include the resistive term in the Navier-Stokes equations. Then, after time discretization, the 3D fluid and 0D valve models are coupled through a staggered approach. This computational framework, applied to a patient-specific geometry and data, allows to simulate the movement of the valve, the sharp pressure jump occurring across the leaflets, and the blood flow pattern inside the aorta.

Software for MR image overlay guided needle insertions: the clinical translation process

NASA Astrophysics Data System (ADS)

Ungi, Tamas; U-Thainual, Paweena; Fritz, Jan; Iordachita, Iulian I.; Flammang, Aaron J.; Carrino, John A.; Fichtinger, Gabor

2013-03-01

PURPOSE: Needle guidance software using augmented reality image overlay was translated from the experimental phase to support preclinical and clinical studies. Major functional and structural changes were needed to meet clinical requirements. We present the process applied to fulfill these requirements, and selected features that may be applied in the translational phase of other image-guided surgical navigation systems. METHODS: We used an agile software development process for rapid adaptation to unforeseen clinical requests. The process is based on iterations of operating room test sessions, feedback discussions, and software development sprints. The open-source application framework of 3D Slicer and the NA-MIC kit provided sufficient flexibility and stable software foundations for this work. RESULTS: All requirements were addressed in a process with 19 operating room test iterations. Most features developed in this phase were related to workflow simplification and operator feedback. CONCLUSION: Efficient and affordable modifications were facilitated by an open source application framework and frequent clinical feedback sessions. Results of cadaver experiments show that software requirements were successfully solved after a limited number of operating room tests.

A cognitive perspective on health systems integration: results of a Canadian Delphi study

PubMed Central

2014-01-01

Background Ongoing challenges to healthcare integration point toward the need to move beyond structural and process issues. While we know what needs to be done to achieve integrated care, there is little that informs us as to how. We need to understand how diverse organizations and professionals develop shared knowledge and beliefs – that is, we need to generate knowledge about normative integration. We present a cognitive perspective on integration, based on shared mental model theory, that may enhance our understanding and ability to measure and influence normative integration. The aim of this paper is to validate and improve the Mental Models of Integrated Care (MMIC) Framework, which outlines important knowledge and beliefs whose convergence or divergence across stakeholder groups may influence inter-professional and inter-organizational relations. Methods We used a two-stage web-based modified Delphi process to test the MMIC Framework against expert opinion using a random sample of participants from Canada’s National Symposium on Integrated Care. Respondents were asked to rate the framework’s clarity, comprehensiveness, usefulness, and importance using seven-point ordinal scales. Spaces for open comments were provided. Descriptive statistics were used to describe the structured responses, while open comments were coded and categorized using thematic analysis. The Kruskall-Wallis test was used to examine cross-group agreement by level of integration experience, current workplace, and current role. Results In the first round, 90 individuals responded (52% response rate), representing a wide range of professional roles and organization types from across the continuum of care. In the second round, 68 individuals responded (75.6% response rate). The quantitative and qualitative feedback from experts was used to revise the framework. The re-named “Integration Mindsets Framework” consists of a Strategy Mental Model and a Relationships Mental Model, comprising a total of nineteen content areas. Conclusions The Integration Mindsets Framework draws the attention of researchers and practitioners to how various stakeholders think about and conceptualize integration. A cognitive approach to understanding and measuring normative integration complements dominant cultural approaches and allows for more fine-grained analyses. The framework can be used by managers and leaders to facilitate the interpretation, planning, implementation, management and evaluation of integration initiatives. PMID:24885659

Revisiting the configuration of small satellites structures in the framework of 3D Additive Manufacturing

NASA Astrophysics Data System (ADS)

Gaudenzi, P.; Atek, S.; Cardini, V.; Eugeni, M.; Graterol Nisi, G.; Lampani, L.; Pasquali, M.; Pollice, L.

2018-05-01

In this paper the AM-induced evolution of the design process for small satellites is investigated, leading to the identification of optimal design strategies and the definition of a new MAIT concept. A review of the open literature is presented and some introductory concepts are exposed to highlight the effect of the introduction of AM technologies in the development of new satellites systems. In particular, an innovative structural configuration for the CubeSat class of satellites is proposed, with the ultimate goal of minimizing system complexity via parts reduction and the integration of subsystems through an innovative assembly configuration, as an example to be considered for larger satellites.

Lowering the barrier to a decentralized NHIN using the open healthcare framework.

PubMed

Smith, Eishay; Kaufman, James H

2006-01-01

In this paper, we discuss two important elements to lowering the barrier to creation of a National Health Information Network. The first element is the adoption of standards that will enable interoperability while guarantee open interfaces (and preventing vendor lock-in). The second element is the role of open source. While adoption of open standards by large EMR vendors is critically important to enterprise healthcare providers and payors, the availability of inexpensive (or free) standardized Healthcare Information Technology for small physician practices is critical. By analogy to the emergence of the World Wide Web, a framework for creating inexpensive and open source applications for physicians will be as important to realizing a National Health Information Network as availability of free browser technology was to the growth of the internet.

Simulating the Heterogeneity in Braided Channel Belt Deposits: 2. Examples of Results and Comparison to Natural Deposits

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guin, Arijit; Ramanathan, Ramya; Ritzi, Robert W.

In Part 1 of this series we presented a methodology and a code for modeling the hierarchical sedimentary architecture in braided channel belt deposits. Here, in Part 2, the code was used to create a digital model of this architecture, and the corresponding spatial distribution of permeability. The simulated architecture was compared to the real stratal architecture observed in an abandoned channel belt of the Sagavanirktok River, Alaska by Lunt et al. (2004). The comparisons included assessments of similarity which were both qualitative and quantitative. From the qualitative comparisons we conclude that a synthetic deposit created by the code hasmore » unit types, at each level, with a geometry which is generally consistent with the geometry of unit types observed in the field. The digital unit types would generally be recognized as representing their counterparts in nature, including cross stratasets, lobate and scroll bar deposits, channel fills, etc. Furthermore, the synthetic deposit has a hierarchical spatial relationship among these units which represents how the unit types are observed in field exposures and in geophysical images. In quantitative comparisons the proportions and the length, width, and height of unit types at different scales, across all levels of the stratal hierarchy compare well between the digital and the natural deposits. A number of important attributes of the channel belt model were shown to be influenced by more than one level within the hierarchy of stratal architecture. First, the high-permeability open-framework gravels percolated at all levels and thus formed preferential flow pathways. Open framework gravels are indeed known to form preferential flow pathways in natural channel belt deposits. The nature of a percolating cluster changed across different levels of the hierarchy of stratal architecture. As a result of this geologic structure, the percolation occurs at proportions of open-framework gravels below the theoretical percolation threshold for random infinite media. Second, when the channel belt model was populated with permeability distributions by lowest-level unit type, the composite permeability semivariogram contained structures that were identifiable at more than one scale, and each of these structures could be directly linked to unit types of different scales existing at different levels within the hierarchy of strata. These collective results are encouraging with respect to our goal that this model be relevant as a base case in future studies for testing ideas in research addressing the upscaling problem in aquifers and reservoirs with multi-scale heterogeneity.« less

Automated visualization of rule-based models

PubMed Central

Tapia, Jose-Juan; Faeder, James R.

2017-01-01

Frameworks such as BioNetGen, Kappa and Simmune use “reaction rules” to specify biochemical interactions compactly, where each rule specifies a mechanism such as binding or phosphorylation and its structural requirements. Current rule-based models of signaling pathways have tens to hundreds of rules, and these numbers are expected to increase as more molecule types and pathways are added. Visual representations are critical for conveying rule-based models, but current approaches to show rules and interactions between rules scale poorly with model size. Also, inferring design motifs that emerge from biochemical interactions is an open problem, so current approaches to visualize model architecture rely on manual interpretation of the model. Here, we present three new visualization tools that constitute an automated visualization framework for rule-based models: (i) a compact rule visualization that efficiently displays each rule, (ii) the atom-rule graph that conveys regulatory interactions in the model as a bipartite network, and (iii) a tunable compression pipeline that incorporates expert knowledge and produces compact diagrams of model architecture when applied to the atom-rule graph. The compressed graphs convey network motifs and architectural features useful for understanding both small and large rule-based models, as we show by application to specific examples. Our tools also produce more readable diagrams than current approaches, as we show by comparing visualizations of 27 published models using standard graph metrics. We provide an implementation in the open source and freely available BioNetGen framework, but the underlying methods are general and can be applied to rule-based models from the Kappa and Simmune frameworks also. We expect that these tools will promote communication and analysis of rule-based models and their eventual integration into comprehensive whole-cell models. PMID:29131816

Supporting openEHR Java desktop application developers.

PubMed

Kashfi, Hajar; Torgersson, Olof

2011-01-01

The openEHR community suggests that an appropriate approach for creating a graphical user interface for an openEHR-based application is to generate forms from the underlying archetypes and templates. However, current generation techniques are not mature enough to be able to produce high quality interfaces with good usability. Therefore, developing efficient ways to combine manually designed and developed interfaces to openEHR backends is an interesting alternative. In this study, a framework for binding a pre-designed graphical user interface to an openEHR-based backend is proposed. The proposed framework contributes to the set of options available for developers. In particular we believe that the approach of combining user interface components with an openEHR backend in the proposed way might be useful in situations where the quality of the user interface is essential and for creating small scale and experimental systems.

Defining and using open architecture levels

NASA Astrophysics Data System (ADS)

Cramer, M. A.; Morrison, A. W.; Cordes, B.; Stack, J. R.

2012-05-01

Open architecture (OA) within military systems enables delivery of increased warfighter capabilities in a shorter time at a reduced cost.i In fact in today's standards-aware environment, solutions are often proposed to the government that include OA as one of its basics design tenets. Yet the ability to measure and assess OA in an objective manner, particularly at the subsystem/component level within a system, remains an elusive proposition. Furthermore, it is increasingly apparent that the establishment of an innovation ecosystem of an open business model that leverages thirdparty development requires more than just technical modifications that promote openness. This paper proposes a framework to migrate not only towards technical openness, but also towards enabling and facilitating an open business model, driven by third party development, for military systems. This framework was developed originally for the U.S. Navy Littoral and Mine Warfare community; however, the principles and approach may be applied elsewhere within the Navy and Department of Defense.

OpenDrift - an open source framework for ocean trajectory modeling

NASA Astrophysics Data System (ADS)

Dagestad, Knut-Frode; Breivik, Øyvind; Ådlandsvik, Bjørn

2016-04-01

We will present a new, open source tool for modeling the trajectories and fate of particles or substances (Lagrangian Elements) drifting in the ocean, or even in the atmosphere. The software is named OpenDrift, and has been developed at Norwegian Meteorological Institute in cooperation with Institute of Marine Research. OpenDrift is a generic framework written in Python, and is openly available at https://github.com/knutfrode/opendrift/. The framework is modular with respect to three aspects: (1) obtaining input data, (2) the transport/morphological processes, and (3) exporting of results to file. Modularity is achieved through well defined interfaces between components, and use of a consistent vocabulary (CF conventions) for naming of variables. Modular input implies that it is not necessary to preprocess input data (e.g. currents, wind and waves from Eulerian models) to a particular file format. Instead "reader modules" can be written/used to obtain data directly from any original source, including files or through web based protocols (e.g. OPeNDAP/Thredds). Modularity of processes implies that a model developer may focus on the geophysical processes relevant for the application of interest, without needing to consider technical tasks such as reading, reprojecting, and colocating input data, rotation and scaling of vectors and model output. We will show a few example applications of using OpenDrift for predicting drifters, oil spills, and search and rescue objects.

eTOXlab, an open source modeling framework for implementing predictive models in production environments.

PubMed

Carrió, Pau; López, Oriol; Sanz, Ferran; Pastor, Manuel

2015-01-01

Computational models based in Quantitative-Structure Activity Relationship (QSAR) methodologies are widely used tools for predicting the biological properties of new compounds. In many instances, such models are used as a routine in the industry (e.g. food, cosmetic or pharmaceutical industry) for the early assessment of the biological properties of new compounds. However, most of the tools currently available for developing QSAR models are not well suited for supporting the whole QSAR model life cycle in production environments. We have developed eTOXlab; an open source modeling framework designed to be used at the core of a self-contained virtual machine that can be easily deployed in production environments, providing predictions as web services. eTOXlab consists on a collection of object-oriented Python modules with methods mapping common tasks of standard modeling workflows. This framework allows building and validating QSAR models as well as predicting the properties of new compounds using either a command line interface or a graphic user interface (GUI). Simple models can be easily generated by setting a few parameters, while more complex models can be implemented by overriding pieces of the original source code. eTOXlab benefits from the object-oriented capabilities of Python for providing high flexibility: any model implemented using eTOXlab inherits the features implemented in the parent model, like common tools and services or the automatic exposure of the models as prediction web services. The particular eTOXlab architecture as a self-contained, portable prediction engine allows building models with confidential information within corporate facilities, which can be safely exported and used for prediction without disclosing the structures of the training series. The software presented here provides full support to the specific needs of users that want to develop, use and maintain predictive models in corporate environments. The technologies used by eTOXlab (web services, VM, object-oriented programming) provide an elegant solution to common practical issues; the system can be installed easily in heterogeneous environments and integrates well with other software. Moreover, the system provides a simple and safe solution for building models with confidential structures that can be shared without disclosing sensitive information.

Personality assessment and model comparison with behavioral data: A statistical framework and empirical demonstration with bonobos (Pan paniscus).

PubMed

Martin, Jordan S; Suarez, Scott A

2017-08-01

Interest in quantifying consistent among-individual variation in primate behavior, also known as personality, has grown rapidly in recent decades. Although behavioral coding is the most frequently utilized method for assessing primate personality, limitations in current statistical practice prevent researchers' from utilizing the full potential of their coding datasets. These limitations include the use of extensive data aggregation, not modeling biologically relevant sources of individual variance during repeatability estimation, not partitioning between-individual (co)variance prior to modeling personality structure, the misuse of principal component analysis, and an over-reliance upon exploratory statistical techniques to compare personality models across populations, species, and data collection methods. In this paper, we propose a statistical framework for primate personality research designed to address these limitations. Our framework synthesizes recently developed mixed-effects modeling approaches for quantifying behavioral variation with an information-theoretic model selection paradigm for confirmatory personality research. After detailing a multi-step analytic procedure for personality assessment and model comparison, we employ this framework to evaluate seven models of personality structure in zoo-housed bonobos (Pan paniscus). We find that differences between sexes, ages, zoos, time of observation, and social group composition contributed to significant behavioral variance. Independently of these factors, however, personality nonetheless accounted for a moderate to high proportion of variance in average behavior across observational periods. A personality structure derived from past rating research receives the strongest support relative to our model set. This model suggests that personality variation across the measured behavioral traits is best described by two correlated but distinct dimensions reflecting individual differences in affiliation and sociability (Agreeableness) as well as activity level, social play, and neophilia toward non-threatening stimuli (Openness). These results underscore the utility of our framework for quantifying personality in primates and facilitating greater integration between the behavioral ecological and comparative psychological approaches to personality research. © 2017 Wiley Periodicals, Inc.

Global OpenSearch

NASA Astrophysics Data System (ADS)

Newman, D. J.; Mitchell, A. E.

2015-12-01

At AGU 2014, NASA EOSDIS demonstrated a case-study of an OpenSearch framework for Earth science data discovery. That framework leverages the IDN and CWIC OpenSearch API implementations to provide seamless discovery of data through the 'two-step' discovery process as outlined by the Federation for Earth Sciences (ESIP) OpenSearch Best Practices. But how would an Earth Scientist leverage this framework and what are the benefits? Using a client that understands the OpenSearch specification and, for further clarity, the various best practices and extensions, a scientist can discovery a plethora of data not normally accessible either by traditional methods (NASA Earth Data Search, Reverb, etc) or direct methods (going to the source of the data) We will demonstrate, via the CWICSmart web client, how an earth scientist can access regional data on a regional phenomena in a uniform and aggregated manner. We will demonstrate how an earth scientist can 'globalize' their discovery. You want to find local data on 'sea surface temperature of the Indian Ocean'? We can help you with that. 'European meteorological data'? Yes. 'Brazilian rainforest satellite imagery'? That too. CWIC allows you to get earth science data in a uniform fashion from a large number of disparate, world-wide agencies. This is what we mean by Global OpenSearch.

OpenDA-WFLOW framework for improving hydrologic predictions using distributed hydrologic models

NASA Astrophysics Data System (ADS)

Weerts, Albrecht; Schellekens, Jaap; Kockx, Arno; Hummel, Stef

2017-04-01

Data assimilation (DA) holds considerable potential for improving hydrologic predictions (Liu et al., 2012) and increase the potential for early warning and/or smart water management. However, advances in hydrologic DA research have not yet been adequately or timely implemented in operational forecast systems to improve the skill of forecasts for better informed real-world decision making. The objective of this work is to highlight the development of a generic linkage of the open source OpenDA package and the open source community hydrologic modeling framework Openstreams/WFLOW and its application in operational hydrological forecasting on various spatial scales. The coupling between OpenDA and Openstreams/wflow framework is based on the emerging standard Basic Model Interface (BMI) as advocated by CSDMS using cross-platform webservices (i.e. Apache Thrift) developed by Hut et al. (2016). The potential application of the OpenDA-WFLOW for operational hydrologic forecasting including its integration with Delft-FEWS (used by more than 40 operational forecast centers around the world (Werner et al., 2013)) is demonstrated by the presented case studies. We will also highlight the possibility to give real-time insight into the working of the DA methods applied for supporting the forecaster as mentioned as one of the burning issues by Liu et al., (2012).

Development of an Analysis and Design Optimization Framework for Marine Propellers

NASA Astrophysics Data System (ADS)

Tamhane, Ashish C.

In this thesis, a framework for the analysis and design optimization of ship propellers is developed. This framework can be utilized as an efficient synthesis tool in order to determine the main geometric characteristics of the propeller but also to provide the designer with the capability to optimize the shape of the blade sections based on their specific criteria. A hybrid lifting-line method with lifting-surface corrections to account for the three-dimensional flow effects has been developed. The prediction of the correction factors is achieved using Artificial Neural Networks and Support Vector Regression. This approach results in increased approximation accuracy compared to existing methods and allows for extrapolation of the correction factor values. The effect of viscosity is implemented in the framework via the coupling of the lifting line method with the open-source RANSE solver OpenFOAM for the calculation of lift, drag and pressure distribution on the blade sections using a transition kappa-o SST turbulence model. Case studies of benchmark high-speed propulsors are utilized in order to validate the proposed framework for propeller operation in open-water conditions but also in a ship's wake.

JTSA: an open source framework for time series abstractions.

PubMed

Sacchi, Lucia; Capozzi, Davide; Bellazzi, Riccardo; Larizza, Cristiana

2015-10-01

The evaluation of the clinical status of a patient is frequently based on the temporal evolution of some parameters, making the detection of temporal patterns a priority in data analysis. Temporal abstraction (TA) is a methodology widely used in medical reasoning for summarizing and abstracting longitudinal data. This paper describes JTSA (Java Time Series Abstractor), a framework including a library of algorithms for time series preprocessing and abstraction and an engine to execute a workflow for temporal data processing. The JTSA framework is grounded on a comprehensive ontology that models temporal data processing both from the data storage and the abstraction computation perspective. The JTSA framework is designed to allow users to build their own analysis workflows by combining different algorithms. Thanks to the modular structure of a workflow, simple to highly complex patterns can be detected. The JTSA framework has been developed in Java 1.7 and is distributed under GPL as a jar file. JTSA provides: a collection of algorithms to perform temporal abstraction and preprocessing of time series, a framework for defining and executing data analysis workflows based on these algorithms, and a GUI for workflow prototyping and testing. The whole JTSA project relies on a formal model of the data types and of the algorithms included in the library. This model is the basis for the design and implementation of the software application. Taking into account this formalized structure, the user can easily extend the JTSA framework by adding new algorithms. Results are shown in the context of the EU project MOSAIC to extract relevant patterns from data coming related to the long term monitoring of diabetic patients. The proof that JTSA is a versatile tool to be adapted to different needs is given by its possible uses, both as a standalone tool for data summarization and as a module to be embedded into other architectures to select specific phenotypes based on TAs in a large dataset. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

MetaboLights: An Open-Access Database Repository for Metabolomics Data.

PubMed

Kale, Namrata S; Haug, Kenneth; Conesa, Pablo; Jayseelan, Kalaivani; Moreno, Pablo; Rocca-Serra, Philippe; Nainala, Venkata Chandrasekhar; Spicer, Rachel A; Williams, Mark; Li, Xuefei; Salek, Reza M; Griffin, Julian L; Steinbeck, Christoph

2016-03-24

MetaboLights is the first general purpose, open-access database repository for cross-platform and cross-species metabolomics research at the European Bioinformatics Institute (EMBL-EBI). Based upon the open-source ISA framework, MetaboLights provides Metabolomics Standard Initiative (MSI) compliant metadata and raw experimental data associated with metabolomics experiments. Users can upload their study datasets into the MetaboLights Repository. These studies are then automatically assigned a stable and unique identifier (e.g., MTBLS1) that can be used for publication reference. The MetaboLights Reference Layer associates metabolites with metabolomics studies in the archive and is extensively annotated with data fields such as structural and chemical information, NMR and MS spectra, target species, metabolic pathways, and reactions. The database is manually curated with no specific release schedules. MetaboLights is also recommended by journals for metabolomics data deposition. This unit provides a guide to using MetaboLights, downloading experimental data, and depositing metabolomics datasets using user-friendly submission tools. Copyright © 2016 John Wiley & Sons, Inc.

Design and Implementation of a Modern Automatic Deformation Monitoring System

NASA Astrophysics Data System (ADS)

Engel, Philipp; Schweimler, Björn

2016-03-01

The deformation monitoring of structures and buildings is an important task field of modern engineering surveying, ensuring the standing and reliability of supervised objects over a long period. Several commercial hardware and software solutions for the realization of such monitoring measurements are available on the market. In addition to them, a research team at the University of Applied Sciences in Neubrandenburg (NUAS) is actively developing a software package for monitoring purposes in geodesy and geotechnics, which is distributed under an open source licence and free of charge. The task of managing an open source project is well-known in computer science, but it is fairly new in a geodetic context. This paper contributes to that issue by detailing applications, frameworks, and interfaces for the design and implementation of open hardware and software solutions for sensor control, sensor networks, and data management in automatic deformation monitoring. It will be discussed how the development effort of networked applications can be reduced by using free programming tools, cloud computing technologies, and rapid prototyping methods.

Steps in the open space planning process

Treesearch

Stephanie B. Kelly; Melissa M. Ryan

1995-01-01

This paper presents the steps involved in developing an open space plan. The steps are generic in that the methods may be applied various size communities. The intent is to provide a framework to develop an open space plan that meets Massachusetts requirements for funding of open space acquisition.

75 FR 34450 - FCC to Hold Open Commission Meeting Thursday, June 17, 2010

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-17

... FEDERAL COMMUNICATIONS COMMISSION FCC to Hold Open Commission Meeting Thursday, June 17, 2010 DATES: June 10, 2010. The Federal Communications Commission will hold an Open Meeting on the subject... consider a Notice of Inquiry to begin an open, public process to consider possible legal frameworks for...

The Ecology of the Open Practitioner: A Conceptual Framework for Open Research

ERIC Educational Resources Information Center

Stagg, Adrian

2017-01-01

Open Educational Practices (OEP) have gained traction internationally over the last fifteen years, with individuals, institutions, and governments increasingly interested in the affordances of openness. Whilst initiatives, policies, and support mechanisms are evident, there is an ever-present danger of localised contexts being unintentionally…

Conductive open frameworks

DOEpatents

Yaghi, Omar M.; Wan, Shun; Doonan, Christian J.; Wang, Bo; Deng, Hexiang

2016-02-23

The disclosure relates generally to materials that comprise conductive covalent organic frameworks. The disclosure also relates to materials that are useful to store and separate gas molecules and sensors.

Conductive open frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yaghi, Omar M.; Wan, Shun; Doonan, Christian J.

The disclosure relates generally to materials that comprise conductive covalent organic frameworks. The disclosure also relates to materials that are useful to store and separate gas molecules and sensors.

Colorometric detection of water using MOF-polymer films and composites

DOEpatents

Allendorf, Mark D.; Talin, Albert Alec

2016-05-24

A method including exposing a mixture of a porous metal organic framework (MOF) and a polymer to a predetermined molecular species, wherein the MOF has an open metal site for the predetermined molecular species and the polymer has a porosity for the predetermined molecular species; and detecting a color change of the MOF in the presence of the predetermined molecular species. A method including combining a porous metal organic framework (MOF) and a polymer, wherein the MOF has an open metal site for a predetermined molecular species and the polymer has a porosity for the predetermined molecular species. An article of manufacture including a mixture of a porous metal organic framework (MOF) and a polymer, wherein the MOF has an open metal site for a predetermined molecular species and the polymer has a porosity for the predetermined molecular species.

Radical covalent organic frameworks: a general strategy to immobilize open-accessible polyradicals for high-performance capacitive energy storage.

PubMed

Xu, Fei; Xu, Hong; Chen, Xiong; Wu, Dingcai; Wu, Yang; Liu, Hao; Gu, Cheng; Fu, Ruowen; Jiang, Donglin

2015-06-01

Ordered π-columns and open nanochannels found in covalent organic frameworks (COFs) could render them able to store electric energy. However, the synthetic difficulty in achieving redox-active skeletons has thus far restricted their potential for energy storage. A general strategy is presented for converting a conventional COF into an outstanding platform for energy storage through post-synthetic functionalization with organic radicals. The radical frameworks with openly accessible polyradicals immobilized on the pore walls undergo rapid and reversible redox reactions, leading to capacitive energy storage with high capacitance, high-rate kinetics, and robust cycle stability. The results suggest that channel-wall functional engineering with redox-active species will be a facile and versatile strategy to explore COFs for energy storage. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

BioContainers: an open-source and community-driven framework for software standardization.

PubMed

da Veiga Leprevost, Felipe; Grüning, Björn A; Alves Aflitos, Saulo; Röst, Hannes L; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I; Perez-Riverol, Yasset

2017-08-15

BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). The software is freely available at github.com/BioContainers/. yperez@ebi.ac.uk. © The Author(s) 2017. Published by Oxford University Press.

BioContainers: an open-source and community-driven framework for software standardization

PubMed Central

da Veiga Leprevost, Felipe; Grüning, Björn A.; Alves Aflitos, Saulo; Röst, Hannes L.; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C.; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I.; Perez-Riverol, Yasset

2017-01-01

Abstract Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/. Contact yperez@ebi.ac.uk PMID:28379341

WE-AB-209-02: A New Inverse Planning Framework with Principle-Based Modeling of Inter-Structural Dosimetric Tradeoffs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, H; Dong, P; Xing, L

Purpose: Traditional radiotherapy inverse planning relies on the weighting factors to phenomenologically balance the conflicting criteria for different structures. The resulting manual trial-and-error determination of the weights has long been recognized as the most time-consuming part of treatment planning. The purpose of this work is to develop an inverse planning framework that parameterizes the inter-structural dosimetric tradeoff among with physically more meaningful quantities to simplify the search for a clinically sensible plan. Methods: A permissible dosimetric uncertainty is introduced for each of the structures to balance their conflicting dosimetric requirements. The inverse planning is then formulated as a convex feasibilitymore » problem, which aims to generate plans with acceptable dosimetric uncertainties. A sequential procedure (SP) is derived to decompose the model into three submodels to constrain the uncertainty in the planning target volume (PTV), the critical structures, and all other structures to spare, sequentially. The proposed technique is applied to plan a liver case and a head-and-neck case and compared with a conventional approach. Results: Our results show that the strategy is able to generate clinically sensible plans with little trial-and-error. In the case of liver IMRT, the fractional volumes to liver and heart above 20Gy are found to be 22% and 10%, respectively, which are 15.1% and 33.3% lower than that of the counterpart conventional plan while maintaining the same PTV coverage. The planning of the head and neck IMRT show the same level of success, with the DVHs for all organs at risk and PTV very competitive to a counterpart plan. Conclusion: A new inverse planning framework has been established. With physically more meaningful modeling of the inter-structural tradeoff, the technique enables us to substantially reduce the need for trial-and-error adjustment of the model parameters and opens new opportunities of incorporating prior knowledge to facilitate the treatment planning process.« less

The dynamic relationship between structural change and CO2 emissions in Malaysia: a cointegrating approach.

PubMed

Ali, Wajahat; Abdullah, Azrai; Azam, Muhammad

2017-05-01

The current study investigates the dynamic relationship between structural changes, real GDP per capita, energy consumption, trade openness, population density, and carbon dioxide (CO 2 ) emissions within the EKC framework over a period 1971-2013. The study used the autoregressive distributed lagged (ARDL) approach to investigate the long-run relationship between the selected variables. The study also employed the dynamic ordinary least squared (DOLS) technique to obtain the robust long-run estimates. Moreover, the causal relationship between the variables is explored using the VECM Granger causality test. Empirical results reveal a negative relationship between structural change and CO 2 emissions in the long run. The results indicate a positive relationship between energy consumption, trade openness, and CO 2 emissions. The study applied the turning point formula of Itkonen (2012) rather than the conventional formula of the turning point. The empirical estimates of the study do not support the presence of the EKC relationship between income and CO 2 emissions. The Granger causality test indicates the presence of long-run bidirectional causality between energy consumption, structural change, and CO 2 emissions in the long run. Economic growth, openness to trade, and population density unidirectionally cause CO 2 emissions. These results suggest that the government should focus more on information-based services rather than energy-intensive manufacturing activities. The feedback relationship between energy consumption and CO 2 emissions suggests that there is an ominous need to refurbish the energy-related policy reforms to ensure the installations of some energy-efficient modern technologies.

Development of a Framework to Characterise the Openness of Mathematical Tasks

ERIC Educational Resources Information Center

Yeo, Joseph B. W.

2017-01-01

Educators usually mean different constructs when they speak of open tasks: some may refer to pure-mathematics investigative tasks while others may have authentic real-life tasks in mind; some may think of the answer being open while others may refer to an open method. On the other hand, some educators use different terms, e.g. open and open-ended,…

Actualizing a provider alliance to expand health services access to a low-income urban community.

PubMed

Tataw, David; Bazargan-Hejazi, Shahrzad; James, Frederick W

2011-01-01

Social change to facilitate health care access for vulnerable populations sometimes involves model-driven innovative structures and innovative planning and implementation approaches. This paper described and analyzed the rationale, conceptual framework, program components, and implementation of the South Central Health Care Alliance (SCHCA) implemented in South Los Angeles from January 2002 to December 2004. The program development and implementation was guided by an integrated framework linking the Open Systems Theory, the Social Cognitive Theory, the Health Belief Model, and the Preventive Health Education and Medical Home Project. The performance of the SCHCA as a social system, partnership, and participatory implementation program is also presented. While the SCHCA was found to be a dynamic social system that responded well to contingencies, its performance as a partnership and participatory implementation program was wanting in many respects.

Parallel scalability and efficiency of vortex particle method for aeroelasticity analysis of bluff bodies

NASA Astrophysics Data System (ADS)

Tolba, Khaled Ibrahim; Morgenthal, Guido

2018-01-01

This paper presents an analysis of the scalability and efficiency of a simulation framework based on the vortex particle method. The code is applied for the numerical aerodynamic analysis of line-like structures. The numerical code runs on multicore CPU and GPU architectures using OpenCL framework. The focus of this paper is the analysis of the parallel efficiency and scalability of the method being applied to an engineering test case, specifically the aeroelastic response of a long-span bridge girder at the construction stage. The target is to assess the optimal configuration and the required computer architecture, such that it becomes feasible to efficiently utilise the method within the computational resources available for a regular engineering office. The simulations and the scalability analysis are performed on a regular gaming type computer.

An open-source framework for testing tracking devices using Lego Mindstorms

NASA Astrophysics Data System (ADS)

Jomier, Julien; Ibanez, Luis; Enquobahrie, Andinet; Pace, Danielle; Cleary, Kevin

2009-02-01

In this paper, we present an open-source framework for testing tracking devices in surgical navigation applications. At the core of image-guided intervention systems is the tracking interface that handles communication with the tracking device and gathers tracking information. Given that the correctness of tracking information is critical for protecting patient safety and for ensuring the successful execution of an intervention, the tracking software component needs to be thoroughly tested on a regular basis. Furthermore, with widespread use of extreme programming methodology that emphasizes continuous and incremental testing of application components, testing design becomes critical. While it is easy to automate most of the testing process, it is often more difficult to test components that require manual intervention such as tracking device. Our framework consists of a robotic arm built from a set of Lego Mindstorms and an open-source toolkit written in C++ to control the robot movements and assess the accuracy of the tracking devices. The application program interface (API) is cross-platform and runs on Windows, Linux and MacOS. We applied this framework for the continuous testing of the Image-Guided Surgery Toolkit (IGSTK), an open-source toolkit for image-guided surgery and shown that regression testing on tracking devices can be performed at low cost and improve significantly the quality of the software.

Crossing levels in systems ergonomics: a framework to support 'mesoergonomic' inquiry.

PubMed

Karsh, Ben-Tzion; Waterson, Patrick; Holden, Richard J

2014-01-01

In this paper we elaborate and articulate the need for what has been termed 'mesoergonomics'. In particular, we argue that the concept has the potential to bridge the gap between, and integrate, established work within the domains of micro- and macroergonomics. Mesoergonomics is defined as an open systems approach to human factors and ergonomics (HFE) theory and research whereby the relationship between variables in at least two different system levels or echelons is studied, and where the dependent variables are human factors and ergonomic constructs. We present a framework which can be used to structure a set of questions for future work and prompt further empirical and conceptual inquiry. The framework consists of four steps: (1) establishing the purpose of the mesoergonomic investigation; (2) selecting human factors and ergonomics variables; (3) selecting a specific type of mesoergonomic investigation; and (4) establishing relationships between system levels. In addition, we describe two case studies which illustrate the workings of the framework and the value of adopting a mesoergonomic perspective within HFE. The paper concludes with a set of issues which could form part of a future agenda for research within systems ergonomics. Copyright © 2013 Elsevier Ltd and The Ergonomics Society. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Guangmei; Valldor, Martin; Mallick, Bert

Four open-framework transition-metal phosphates; (NH4)2Co3(HPO4)2F4 (1), (NH4)Co3(HPO4)2(H2PO4)F2 (2), KCo3(HPO4)2(H2PO4)F2 (3), and KFe3(HPO4)2(H2PO4)F2 (4); are prepared by ionothermal synthesis using pyridinium hexafluorophosphate as the ionic liquid. Single-crystal X-ray diffraction analyses reveal that the four compounds contain cobalt/iron–oxygen/fluoride layers with Kagomé topology composed of interlinked face-sharing MO3F3/MO4F2 octahedra. PO3OH pseudo-tetrahedral groups augment the [M3O6F4] (1)/[M3O8F2] layers on both sides to give M3(HPO4)2F4 (1) and M3(HPO4)2F2 (2–4) layers. These layers are stacked along the a axis in a sequence AA…, resulting in the formation of a layer structure for (NH4)2Co3(HPO4)2F4(1). In NH4Co3(HPO4)2(H2PO4)F2 and KM3(HPO4)2(H2PO4)F2, the M3(HPO4)2F2 layers are stacked along the a axismore » in a sequence AAi… and are connected by [PO3(OH)] tetrahedra, giving rise to a 3-D open framework structure with 10-ring channels along the [001] direction. The negative charges of the inorganic framework are balanced by K+/NH4+ ions located within the channels. The magnetic transition metal cations themselves form layers with stair-case Kagomé topology. Magnetic susceptibility and magnetization measurements reveal that all four compounds exhibit a canted anti-ferromagnetic ground state (Tc = 10 or 13 K for Co and Tc = 27 K for Fe) with different canting angles. The full orbital moment is observed for both Co2+ and Fe2+.« less

Processes of recovery through routine or specialist treatment for borderline personality disorder (BPD): a qualitative study.

PubMed

Katsakou, Christina; Pistrang, Nancy; Barnicot, Kirsten; White, Hayley; Priebe, Stefan

2017-07-04

Recovery processes in borderline personality disorder (BPD) are poorly understood. This study explored how recovery in BPD occurs through routine or specialist treatment, as perceived by service users (SUs) and therapists. SUs were recruited from two specialist BPD services, three community mental health teams, and one psychological therapies service. Semi-structured interviews were conducted with 48 SUs and 15 therapists. The "framework" approach was used to analyse the data. The findings were organized into two domains of themes. The first domain described three parallel processes that constituted SUs' recovery journey: fighting ambivalence and committing to taking action; moving from shame to self-acceptance and compassion; and moving from distrust and defensiveness to opening up to others. The second domain described four therapeutic challenges that needed to be addressed to support this journey: balancing self-exploration and finding solutions; balancing structure and flexibility; confronting interpersonal difficulties and practicing new ways of relating; and balancing support and independence. Therapies facilitating the identified processes may promote recovery. The recovery processes and therapeutic challenges identified in this study could provide a framework to guide future research.

Synthesis, structural characterization and high pressure phase transitions of monolithium hydronium sulfate

NASA Astrophysics Data System (ADS)

Banerjee, Debasis; Plonka, Anna M.; Kim, Sun Jin; Xu, Wenqian; Parise, John B.

2013-01-01

A three dimensional lithium hydronium sulfate LiSO4·H3O [1], [space group Pna21a=8.7785(12) Å, b=9.1297(12) Å, c=5.2799(7) Å, V=423.16(10) Å3] was synthesized via solvothermal methods using 1,5-naphthalenedisulfonic acid (1,5-NSA) as the source of sulfate ions. The structure of [1], determined by single crystal X-ray diffraction techniques, consists of corner sharing LiO4 and SO4 tetrahedra, forming an anionic 3-D open framework that is charge balanced by hydronium ions positioned within channels running along [001] and forming strong H-bonding with the framework oxygen atoms. Compound [1] undergoes two reversible phase transitions, involving reorientation of SO42- ions at pressures of approximately 2.5 and 5 GPa at room temperature, as evident from characteristic discontinuous frequency drops in the ν1 mode of the Raman spectra. Additionally, compound [1] forms dense β-lithium sulfate at 300 °C, as evident from temperature dependent powder XRD and combined reversible TGA-DSC experiments.

Crossing the Virtual World Barrier with OpenAvatar

NASA Technical Reports Server (NTRS)

Joy, Bruce; Kavle, Lori; Tan, Ian

2012-01-01

There are multiple standards and formats for 3D models in virtual environments. The problem is that there is no open source platform for generating models out of discrete parts; this results in the process of having to "reinvent the wheel" when new games, virtual worlds and simulations want to enable their users to create their own avatars or easily customize in-world objects. OpenAvatar is designed to provide a framework to allow artists and programmers to create reusable assets which can be used by end users to generate vast numbers of complete models that are unique and functional. OpenAvatar serves as a framework which facilitates the modularization of 3D models allowing parts to be interchanged within a set of logical constraints.

ooi: OpenStack OCCI interface

NASA Astrophysics Data System (ADS)

López García, Álvaro; Fernández del Castillo, Enol; Orviz Fernández, Pablo

In this document we present an implementation of the Open Grid Forum's Open Cloud Computing Interface (OCCI) for OpenStack, namely ooi (Openstack occi interface, 2015) [1]. OCCI is an open standard for management tasks over cloud resources, focused on interoperability, portability and integration. ooi aims to implement this open interface for the OpenStack cloud middleware, promoting interoperability with other OCCI-enabled cloud management frameworks and infrastructures. ooi focuses on being non-invasive with a vanilla OpenStack installation, not tied to a particular OpenStack release version.

Open Badges for Education: What Are the Implications at the Intersection of Open Systems and Badging?

ERIC Educational Resources Information Center

Ahn, June; Pellicone, Anthony; Butler, Brian S.

2014-01-01

Badges have garnered great interest among scholars of digital media and learning. In addition, widespread initiatives such as Mozilla's Open Badge Framework expand the potential of badging into the realm of open education. In this paper, we explicate the concept of open badges. We highlight some of the ways that researchers have examined…

Open-source Framework for Storing and Manipulation of Plasma Chemical Reaction Data

NASA Astrophysics Data System (ADS)

Jenkins, T. G.; Averkin, S. N.; Cary, J. R.; Kruger, S. E.

2017-10-01

We present a new open-source framework for storage and manipulation of plasma chemical reaction data that has emerged from our in-house project MUNCHKIN. This framework consists of python scripts and C + + programs. It stores data in an SQL data base for fast retrieval and manipulation. For example, it is possible to fit cross-section data into most widely used analytical expressions, calculate reaction rates for Maxwellian distribution functions of colliding particles, and fit them into different analytical expressions. Another important feature of this framework is the ability to calculate transport properties based on the cross-section data and supplied distribution functions. In addition, this framework allows the export of chemical reaction descriptions in LaTeX format for ease of inclusion in scientific papers. With the help of this framework it is possible to generate corresponding VSim (Particle-In-Cell simulation code) and USim (unstructured multi-fluid code) input blocks with appropriate cross-sections.

Open Distribution of Virtual Containers as a Key Framework for Open Educational Resources and STEAM Subjects

ERIC Educational Resources Information Center

Corbi, Alberto; Burgos, Daniel

2017-01-01

This paper presents how virtual containers enhance the implementation of STEAM (science, technology, engineering, arts, and math) subjects as Open Educational Resources (OER). The publication initially summarizes the limitations of delivering open rich learning contents and corresponding assignments to students in college level STEAM areas. The…

BioASF: a framework for automatically generating executable pathway models specified in BioPAX.

PubMed

Haydarlou, Reza; Jacobsen, Annika; Bonzanni, Nicola; Feenstra, K Anton; Abeln, Sanne; Heringa, Jaap

2016-06-15

Biological pathways play a key role in most cellular functions. To better understand these functions, diverse computational and cell biology researchers use biological pathway data for various analysis and modeling purposes. For specifying these biological pathways, a community of researchers has defined BioPAX and provided various tools for creating, validating and visualizing BioPAX models. However, a generic software framework for simulating BioPAX models is missing. Here, we attempt to fill this gap by introducing a generic simulation framework for BioPAX. The framework explicitly separates the execution model from the model structure as provided by BioPAX, with the advantage that the modelling process becomes more reproducible and intrinsically more modular; this ensures natural biological constraints are satisfied upon execution. The framework is based on the principles of discrete event systems and multi-agent systems, and is capable of automatically generating a hierarchical multi-agent system for a given BioPAX model. To demonstrate the applicability of the framework, we simulated two types of biological network models: a gene regulatory network modeling the haematopoietic stem cell regulators and a signal transduction network modeling the Wnt/β-catenin signaling pathway. We observed that the results of the simulations performed using our framework were entirely consistent with the simulation results reported by the researchers who developed the original models in a proprietary language. The framework, implemented in Java, is open source and its source code, documentation and tutorial are available at http://www.ibi.vu.nl/programs/BioASF CONTACT: j.heringa@vu.nl. © The Author 2016. Published by Oxford University Press.

An open-framework thorium sulfate hydrate with 11.5 A voids.

PubMed

Wilson, Richard E; Skanthakumar, S; Knope, Karah E; Cahill, Christopher L; Soderholm, L

2008-10-20

We report the synthesis of a thorium sulfate hydrate with 11.5 A open channels that propagate through the structure. The compound crystallizes in the tetragonal space group P4(2)/nmc, a = b = 25.890(4) A, c = 9.080(2) A, Z = 8, V = 6086.3(2) A(3). The thermal stability of the compound was investigated using thermogravimetric analysis and high-energy X-ray scattering (HEXS) revealing that the compound begins to undergo decomposition near 200 degrees C with an accompanied loss in crystallinity. The immediate coordination environment about the thorium atoms remains intact through heating to 500 degrees C as demonstrated by HEXS. Further heating reveals the formation of at least two crystalline phases, Th(SO4)2 and ThO2, which ultimately decompose to ThO2.

Gate-opening gas adsorption and host-guest interacting gas trapping behavior of porous coordination polymers under applied AC electric fields.

PubMed

Kosaka, Wataru; Yamagishi, Kayo; Zhang, Jun; Miyasaka, Hitoshi

2014-09-03

The gate-opening adsorption behavior of the one-dimensional chain compound [Ru2(4-Cl-2-OMePhCO2)4(phz)] (1; 4-Cl-2-OMePhCO2(-) = 4-chloro-o-anisate; phz = phenazine) for various gases (O2, NO, and CO2) was electronically monitored in situ by applying ac electric fields to pelletized samples attached to a cryostat, which was used to accurately control the temperature and gas pressure. The gate-opening and -closing transitions induced by gas adsorption/desorption, respectively, were accurately monitored by a sudden change in the real part of permittivity (ε'). The transition temperature (TGO) was also found to be dependent on the applied temperature and gas pressure according to the Clausius-Clapeyron equation. This behavior was also observed in the isostructural compound [Rh2(4-Cl-2-OMePhCO2)4(phz)] (2), which exhibited similar gate-opening adsorption properties, but was not detected in the nonporous gate-inactive compound [Ru2(o-OMePhCO2)4(phz)] (3). Furthermore, the imaginary part of permittivity (ε″) effectively captured the electronic perturbations of the samples induced by the introduced guest molecules. Only the introduction of NO resulted in the increase of the sample's electronic conductivity for 1 and 3, but not for 2. This behavior indicates that electronic host-guest interactions were present, albeit very weak, at the surface of sample 1 and 3, i.e., through grain boundaries of the sample, which resulted in perturbation of the conduction band of this material's framework. This technique involving the in situ application of ac electric fields is useful not only for rapidly monitoring gas sorption responses accompanied by gate-opening/-closing structural transitions but also potentially for the development of molecular framework materials as chemically driven electronic devices.

Understanding Hawking radiation in the framework of open quantum systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu Hongwei; Zhang Jialin

2008-01-15

We study the Hawking radiation in the framework of open quantum systems by examining the time evolution of a detector (modeled by a two-level atom) interacting with vacuum massless scalar fields. The dynamics of the detector is governed by a master equation obtained by tracing over the field degrees of freedom from the complete system. The nonunitary effects are studied by analyzing the time behavior of a particular observable of the detector, i.e., its admissible state, in the Unruh, Hartle-Hawking, as well as Boulware vacua outside a Schwarzschild black hole. We find that the detector in both the Unruh andmore » Hartle-Hawking vacua would spontaneously excite with a nonvanishing probability the same as what one would obtain if there is thermal radiation at the Hawking temperature from the black hole, thus reproducing the basic results concerning the Hawking effect in the framework of open quantum systems.« less

Applications of the MapReduce programming framework to clinical big data analysis: current landscape and future trends

PubMed Central

2014-01-01

The emergence of massive datasets in a clinical setting presents both challenges and opportunities in data storage and analysis. This so called “big data” challenges traditional analytic tools and will increasingly require novel solutions adapted from other fields. Advances in information and communication technology present the most viable solutions to big data analysis in terms of efficiency and scalability. It is vital those big data solutions are multithreaded and that data access approaches be precisely tailored to large volumes of semi-structured/unstructured data. The MapReduce programming framework uses two tasks common in functional programming: Map and Reduce. MapReduce is a new parallel processing framework and Hadoop is its open-source implementation on a single computing node or on clusters. Compared with existing parallel processing paradigms (e.g. grid computing and graphical processing unit (GPU)), MapReduce and Hadoop have two advantages: 1) fault-tolerant storage resulting in reliable data processing by replicating the computing tasks, and cloning the data chunks on different computing nodes across the computing cluster; 2) high-throughput data processing via a batch processing framework and the Hadoop distributed file system (HDFS). Data are stored in the HDFS and made available to the slave nodes for computation. In this paper, we review the existing applications of the MapReduce programming framework and its implementation platform Hadoop in clinical big data and related medical health informatics fields. The usage of MapReduce and Hadoop on a distributed system represents a significant advance in clinical big data processing and utilization, and opens up new opportunities in the emerging era of big data analytics. The objective of this paper is to summarize the state-of-the-art efforts in clinical big data analytics and highlight what might be needed to enhance the outcomes of clinical big data analytics tools. This paper is concluded by summarizing the potential usage of the MapReduce programming framework and Hadoop platform to process huge volumes of clinical data in medical health informatics related fields. PMID:25383096

Applications of the MapReduce programming framework to clinical big data analysis: current landscape and future trends.

PubMed

Mohammed, Emad A; Far, Behrouz H; Naugler, Christopher

2014-01-01

The emergence of massive datasets in a clinical setting presents both challenges and opportunities in data storage and analysis. This so called "big data" challenges traditional analytic tools and will increasingly require novel solutions adapted from other fields. Advances in information and communication technology present the most viable solutions to big data analysis in terms of efficiency and scalability. It is vital those big data solutions are multithreaded and that data access approaches be precisely tailored to large volumes of semi-structured/unstructured data. THE MAPREDUCE PROGRAMMING FRAMEWORK USES TWO TASKS COMMON IN FUNCTIONAL PROGRAMMING: Map and Reduce. MapReduce is a new parallel processing framework and Hadoop is its open-source implementation on a single computing node or on clusters. Compared with existing parallel processing paradigms (e.g. grid computing and graphical processing unit (GPU)), MapReduce and Hadoop have two advantages: 1) fault-tolerant storage resulting in reliable data processing by replicating the computing tasks, and cloning the data chunks on different computing nodes across the computing cluster; 2) high-throughput data processing via a batch processing framework and the Hadoop distributed file system (HDFS). Data are stored in the HDFS and made available to the slave nodes for computation. In this paper, we review the existing applications of the MapReduce programming framework and its implementation platform Hadoop in clinical big data and related medical health informatics fields. The usage of MapReduce and Hadoop on a distributed system represents a significant advance in clinical big data processing and utilization, and opens up new opportunities in the emerging era of big data analytics. The objective of this paper is to summarize the state-of-the-art efforts in clinical big data analytics and highlight what might be needed to enhance the outcomes of clinical big data analytics tools. This paper is concluded by summarizing the potential usage of the MapReduce programming framework and Hadoop platform to process huge volumes of clinical data in medical health informatics related fields.

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.

PubMed

Glusman, Gustavo; Rose, Peter W; Prlić, Andreas; Dougherty, Jennifer; Duarte, José M; Hoffman, Andrew S; Barton, Geoffrey J; Bendixen, Emøke; Bergquist, Timothy; Bock, Christian; Brunk, Elizabeth; Buljan, Marija; Burley, Stephen K; Cai, Binghuang; Carter, Hannah; Gao, JianJiong; Godzik, Adam; Heuer, Michael; Hicks, Michael; Hrabe, Thomas; Karchin, Rachel; Leman, Julia Koehler; Lane, Lydie; Masica, David L; Mooney, Sean D; Moult, John; Omenn, Gilbert S; Pearl, Frances; Pejaver, Vikas; Reynolds, Sheila M; Rokem, Ariel; Schwede, Torsten; Song, Sicheng; Tilgner, Hagen; Valasatava, Yana; Zhang, Yang; Deutsch, Eric W

2017-12-18

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods.

National Qualification Frameworks: Developing Research Perspectives

ERIC Educational Resources Information Center

Fernie, Scott; Pilcher, Nick

2009-01-01

Arguments for National Qualification Frameworks (NQF) are compelling. Indeed, such frameworks are now an international phenomenon. Yet, few studies take a critical perspective and challenge the broad assumptions underpinning NQF. Arguments presented in this paper attempt to open a debate within the higher education community that draws attention…

Origin of negative thermal expansion in Zn2GeO4 revealed by high pressure study

NASA Astrophysics Data System (ADS)

Cheng, Xuerui; Yuan, Jie; Zhu, Xiang; Yang, Kun; Liu, Miao; Qi, Zeming

2018-03-01

Zn2GeO4, as an open-framework structure compound, exhibits negative thermal expansion (NTE) below room temperature. In this work, we investigated the structural stability and phonon modes employing the x-ray diffraction and Raman spectroscopy under high pressure up to 23.0 GPa within a diamond anvil cell, and we observed that a pressure-induced irreversible amorphization took place around 10.1 GPa. Bulk modulus, pressure coefficients, and Grüneisen parameters were measured for the initial rhombohedral structure. Several low-frequency rigid-unit modes are found to have negative Grüneisen parameter, which accounts for the primary part of NTE in Zn2GeO4. These results further confirm the hypothesis that the pressure-induced amorphization and the negative thermal expansion are correlated phenomena.

Pseudogap and electronic structure of electron-doped Sr2IrO4

NASA Astrophysics Data System (ADS)

Moutenet, Alice; Georges, Antoine; Ferrero, Michel

2018-04-01

We present a theoretical investigation of the effects of correlations on the electronic structure of the Mott insulator Sr2IrO4 upon electron doping. A rapid collapse of the Mott gap upon doping is found, and the electronic structure displays a strong momentum-space differentiation at low doping level: The Fermi surface consists of pockets centered around (π /2 ,π /2 ) , while a pseudogap opens near (π ,0 ) . Its physical origin is shown to be related to short-range spin correlations. The pseudogap closes upon increasing doping, but a differentiated regime characterized by a modulation of the spectral intensity along the Fermi surface persists to higher doping levels. These results, obtained within the cellular dynamical mean-field-theory framework, are discussed in comparison to recent photoemission experiments and an overall good agreement is found.

QmeQ 1.0: An open-source Python package for calculations of transport through quantum dot devices

NASA Astrophysics Data System (ADS)

Kiršanskas, Gediminas; Pedersen, Jonas Nyvold; Karlström, Olov; Leijnse, Martin; Wacker, Andreas

2017-12-01

QmeQ is an open-source Python package for numerical modeling of transport through quantum dot devices with strong electron-electron interactions using various approximate master equation approaches. The package provides a framework for calculating stationary particle or energy currents driven by differences in chemical potentials or temperatures between the leads which are tunnel coupled to the quantum dots. The electronic structures of the quantum dots are described by their single-particle states and the Coulomb matrix elements between the states. When transport is treated perturbatively to lowest order in the tunneling couplings, the possible approaches are Pauli (classical), first-order Redfield, and first-order von Neumann master equations, and a particular form of the Lindblad equation. When all processes involving two-particle excitations in the leads are of interest, the second-order von Neumann approach can be applied. All these approaches are implemented in QmeQ. We here give an overview of the basic structure of the package, give examples of transport calculations, and outline the range of applicability of the different approximate approaches.

Global magnetosphere simulations using constrained-transport Hall-MHD with CWENO reconstruction

NASA Astrophysics Data System (ADS)

Lin, L.; Germaschewski, K.; Maynard, K. M.; Abbott, S.; Bhattacharjee, A.; Raeder, J.

2013-12-01

We present a new CWENO (Centrally-Weighted Essentially Non-Oscillatory) reconstruction based MHD solver for the OpenGGCM global magnetosphere code. The solver was built using libMRC, a library for creating efficient parallel PDE solvers on structured grids. The use of libMRC gives us access to its core functionality of providing an automated code generation framework which takes a user provided PDE right hand side in symbolic form to generate an efficient, computer architecture specific, parallel code. libMRC also supports block-structured adaptive mesh refinement and implicit-time stepping through integration with the PETSc library. We validate the new CWENO Hall-MHD solver against existing solvers both in standard test problems as well as in global magnetosphere simulations.

Coupling movement and landscape ecology for animal conservation in production landscapes.

PubMed

Doherty, Tim S; Driscoll, Don A

2018-01-10

Habitat conversion in production landscapes is among the greatest threats to biodiversity, not least because it can disrupt animal movement. Using the movement ecology framework, we review animal movement in production landscapes, including areas managed for agriculture and forestry. We consider internal and external drivers of altered animal movement and how this affects navigation and motion capacities and population dynamics. Conventional management approaches in fragmented landscapes focus on promoting connectivity using structural changes in the landscape. However, a movement ecology perspective emphasizes that manipulating the internal motivations or navigation capacity of animals represents untapped opportunities to improve movement and the effectiveness of structural connectivity investments. Integrating movement and landscape ecology opens new opportunities for conservation management in production landscapes. © 2018 The Authors.

OpenMDAO: Framework for Flexible Multidisciplinary Design, Analysis and Optimization Methods

NASA Technical Reports Server (NTRS)

Heath, Christopher M.; Gray, Justin S.

2012-01-01

The OpenMDAO project is underway at NASA to develop a framework which simplifies the implementation of state-of-the-art tools and methods for multidisciplinary design, analysis and optimization. Foremost, OpenMDAO has been designed to handle variable problem formulations, encourage reconfigurability, and promote model reuse. This work demonstrates the concept of iteration hierarchies in OpenMDAO to achieve a flexible environment for supporting advanced optimization methods which include adaptive sampling and surrogate modeling techniques. In this effort, two efficient global optimization methods were applied to solve a constrained, single-objective and constrained, multiobjective version of a joint aircraft/engine sizing problem. The aircraft model, NASA's nextgeneration advanced single-aisle civil transport, is being studied as part of the Subsonic Fixed Wing project to help meet simultaneous program goals for reduced fuel burn, emissions, and noise. This analysis serves as a realistic test problem to demonstrate the flexibility and reconfigurability offered by OpenMDAO.

Rapid development of medical imaging tools with open-source libraries.

PubMed

Caban, Jesus J; Joshi, Alark; Nagy, Paul

2007-11-01

Rapid prototyping is an important element in researching new imaging analysis techniques and developing custom medical applications. In the last ten years, the open source community and the number of open source libraries and freely available frameworks for biomedical research have grown significantly. What they offer are now considered standards in medical image analysis, computer-aided diagnosis, and medical visualization. A cursory review of the peer-reviewed literature in imaging informatics (indeed, in almost any information technology-dependent scientific discipline) indicates the current reliance on open source libraries to accelerate development and validation of processes and techniques. In this survey paper, we review and compare a few of the most successful open source libraries and frameworks for medical application development. Our dual intentions are to provide evidence that these approaches already constitute a vital and essential part of medical image analysis, diagnosis, and visualization and to motivate the reader to use open source libraries and software for rapid prototyping of medical applications and tools.

IMHOTEP: virtual reality framework for surgical applications.

PubMed

Pfeiffer, Micha; Kenngott, Hannes; Preukschas, Anas; Huber, Matthias; Bettscheider, Lisa; Müller-Stich, Beat; Speidel, Stefanie

2018-05-01

The data which is available to surgeons before, during and after surgery is steadily increasing in quantity as well as diversity. When planning a patient's treatment, this large amount of information can be difficult to interpret. To aid in processing the information, new methods need to be found to present multimodal patient data, ideally combining textual, imagery, temporal and 3D data in a holistic and context-aware system. We present an open-source framework which allows handling of patient data in a virtual reality (VR) environment. By using VR technology, the workspace available to the surgeon is maximized and 3D patient data is rendered in stereo, which increases depth perception. The framework organizes the data into workspaces and contains tools which allow users to control, manipulate and enhance the data. Due to the framework's modular design, it can easily be adapted and extended for various clinical applications. The framework was evaluated by clinical personnel (77 participants). The majority of the group stated that a complex surgical situation is easier to comprehend by using the framework, and that it is very well suited for education. Furthermore, the application to various clinical scenarios-including the simulation of excitation propagation in the human atrium-demonstrated the framework's adaptability. As a feasibility study, the framework was used during the planning phase of the surgical removal of a large central carcinoma from a patient's liver. The clinical evaluation showed a large potential and high acceptance for the VR environment in a medical context. The various applications confirmed that the framework is easily extended and can be used in real-time simulation as well as for the manipulation of complex anatomical structures.

Data dictionary services in XNAT and the Human Connectome Project.

PubMed

Herrick, Rick; McKay, Michael; Olsen, Timothy; Horton, William; Florida, Mark; Moore, Charles J; Marcus, Daniel S

2014-01-01

The XNAT informatics platform is an open source data management tool used by biomedical imaging researchers around the world. An important feature of XNAT is its highly extensible architecture: users of XNAT can add new data types to the system to capture the imaging and phenotypic data generated in their studies. Until recently, XNAT has had limited capacity to broadcast the meaning of these data extensions to users, other XNAT installations, and other software. We have implemented a data dictionary service for XNAT, which is currently being used on ConnectomeDB, the Human Connectome Project (HCP) public data sharing website. The data dictionary service provides a framework to define key relationships between data elements and structures across the XNAT installation. This includes not just core data representing medical imaging data or subject or patient evaluations, but also taxonomical structures, security relationships, subject groups, and research protocols. The data dictionary allows users to define metadata for data structures and their properties, such as value types (e.g., textual, integers, floats) and valid value templates, ranges, or field lists. The service provides compatibility and integration with other research data management services by enabling easy migration of XNAT data to standards-based formats such as the Resource Description Framework (RDF), JavaScript Object Notation (JSON), and Extensible Markup Language (XML). It also facilitates the conversion of XNAT's native data schema into standard neuroimaging vocabularies and structures.

Data dictionary services in XNAT and the Human Connectome Project

PubMed Central

Herrick, Rick; McKay, Michael; Olsen, Timothy; Horton, William; Florida, Mark; Moore, Charles J.; Marcus, Daniel S.

2014-01-01

The XNAT informatics platform is an open source data management tool used by biomedical imaging researchers around the world. An important feature of XNAT is its highly extensible architecture: users of XNAT can add new data types to the system to capture the imaging and phenotypic data generated in their studies. Until recently, XNAT has had limited capacity to broadcast the meaning of these data extensions to users, other XNAT installations, and other software. We have implemented a data dictionary service for XNAT, which is currently being used on ConnectomeDB, the Human Connectome Project (HCP) public data sharing website. The data dictionary service provides a framework to define key relationships between data elements and structures across the XNAT installation. This includes not just core data representing medical imaging data or subject or patient evaluations, but also taxonomical structures, security relationships, subject groups, and research protocols. The data dictionary allows users to define metadata for data structures and their properties, such as value types (e.g., textual, integers, floats) and valid value templates, ranges, or field lists. The service provides compatibility and integration with other research data management services by enabling easy migration of XNAT data to standards-based formats such as the Resource Description Framework (RDF), JavaScript Object Notation (JSON), and Extensible Markup Language (XML). It also facilitates the conversion of XNAT's native data schema into standard neuroimaging vocabularies and structures. PMID:25071542

Structural graph-based morphometry: A multiscale searchlight framework based on sulcal pits.

PubMed

Takerkart, Sylvain; Auzias, Guillaume; Brun, Lucile; Coulon, Olivier

2017-01-01

Studying the topography of the cortex has proved valuable in order to characterize populations of subjects. In particular, the recent interest towards the deepest parts of the cortical sulci - the so-called sulcal pits - has opened new avenues in that regard. In this paper, we introduce the first fully automatic brain morphometry method based on the study of the spatial organization of sulcal pits - Structural Graph-Based Morphometry (SGBM). Our framework uses attributed graphs to model local patterns of sulcal pits, and further relies on three original contributions. First, a graph kernel is defined to provide a new similarity measure between pit-graphs, with few parameters that can be efficiently estimated from the data. Secondly, we present the first searchlight scheme dedicated to brain morphometry, yielding dense information maps covering the full cortical surface. Finally, a multi-scale inference strategy is designed to jointly analyze the searchlight information maps obtained at different spatial scales. We demonstrate the effectiveness of our framework by studying gender differences and cortical asymmetries: we show that SGBM can both localize informative regions and estimate their spatial scales, while providing results which are consistent with the literature. Thanks to the modular design of our kernel and the vast array of available kernel methods, SGBM can easily be extended to include a more detailed description of the sulcal patterns and solve different statistical problems. Therefore, we suggest that our SGBM framework should be useful for both reaching a better understanding of the normal brain and defining imaging biomarkers in clinical settings. Copyright © 2016 Elsevier B.V. All rights reserved.

A Modular Framework for Transforming Structured Data into HTML with Machine-Readable Annotations

NASA Astrophysics Data System (ADS)

Patton, E. W.; West, P.; Rozell, E.; Zheng, J.

2010-12-01

There is a plethora of web-based Content Management Systems (CMS) available for maintaining projects and data, i.a. However, each system varies in its capabilities and often content is stored separately and accessed via non-uniform web interfaces. Moving from one CMS to another (e.g., MediaWiki to Drupal) can be cumbersome, especially if a large quantity of data must be adapted to the new system. To standardize the creation, display, management, and sharing of project information, we have assembled a framework that uses existing web technologies to transform data provided by any service that supports the SPARQL Protocol and RDF Query Language (SPARQL) queries into HTML fragments, allowing it to be embedded in any existing website. The framework utilizes a two-tier XML Stylesheet Transformation (XSLT) that uses existing ontologies (e.g., Friend-of-a-Friend, Dublin Core) to interpret query results and render them as HTML documents. These ontologies can be used in conjunction with custom ontologies suited to individual needs (e.g., domain-specific ontologies for describing data records). Furthermore, this transformation process encodes machine-readable annotations, namely, the Resource Description Framework in attributes (RDFa), into the resulting HTML, so that capable parsers and search engines can extract the relationships between entities (e.g, people, organizations, datasets). To facilitate editing of content, the framework provides a web-based form system, mapping each query to a dynamically generated form that can be used to modify and create entities, while keeping the native data store up-to-date. This open framework makes it easy to duplicate data across many different sites, allowing researchers to distribute their data in many different online forums. In this presentation we will outline the structure of queries and the stylesheets used to transform them, followed by a brief walkthrough that follows the data from storage to human- and machine-accessible web page. We conclude with a discussion on content caching and steps toward performing queries across multiple domains.

Generalized Intelligent Framework for Tutoring (GIFT) Cloud/Virtual Open Campus Quick Start Guide (Revision 1)

DTIC Science & Technology

2017-06-01

for GIFT Cloud, the web -based application version of the Generalized Intelligent Framework for Tutoring (GIFT). GIFT is a modular, open-source...external applications. GIFT is available to users with a GIFT Account at no cost. GIFT Cloud is an implementation of GIFT. This web -based application...section. Approved for public release; distribution is unlimited. 3 3. Requirements for GIFT Cloud GIFT Cloud is accessed via a web browser

openBIS: a flexible framework for managing and analyzing complex data in biology research

PubMed Central

2011-01-01

Background Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it. Results We have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies. Conclusions openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain. PMID:22151573

A qualitative study of parents' perceptions of a behavioural sleep intervention.

PubMed

Tse, L; Hall, W

2008-03-01

A study, entitled Evaluation of an Intervention Aimed at Resolving Behavioural Sleep Problems in 6- to 12-month-old Infants: A Pilot Study, was undertaken to evaluate the efficacy of a behavioural sleep intervention. This descriptive qualitative study aimed to describe parents' perceptions of the sleep intervention and any burden associated with participating in the study. Fourteen of the 35 families who had participated in the quantitative study were interviewed. Respondents comprised well-educated, middle-class and mixed-ethnicity families. Data were collected through semi-structured interviews, with open-ended trigger questions, and were analysed using inductive content analysis. Nine themes, which subsumed a number of categories, were constructed. Parents changed their perspectives about sleep and parenting styles; they experienced many challenges and inadvertent benefits; and they welcomed a structured framework for assisting with sleep problems. The parents fitted intervention strategies into their realities; many factors interfered with their success; and their support systems and their expectations of the study varied. These parents' previous education about normal infant sleep cycles and behavioural sleep problems was inadequate. The parents who were able to use the structured framework, flexible strategies and access to healthcare professionals for problem solving not only excelled in resolving their infants' sleep problems, but also gained confidence about their parenting skills and success.

Porting plasma physics simulation codes to modern computing architectures using the libmrc framework

NASA Astrophysics Data System (ADS)

Germaschewski, Kai; Abbott, Stephen

2015-11-01

Available computing power has continued to grow exponentially even after single-core performance satured in the last decade. The increase has since been driven by more parallelism, both using more cores and having more parallelism in each core, e.g. in GPUs and Intel Xeon Phi. Adapting existing plasma physics codes is challenging, in particular as there is no single programming model that covers current and future architectures. We will introduce the open-source libmrc framework that has been used to modularize and port three plasma physics codes: The extended MHD code MRCv3 with implicit time integration and curvilinear grids; the OpenGGCM global magnetosphere model; and the particle-in-cell code PSC. libmrc consolidates basic functionality needed for simulations based on structured grids (I/O, load balancing, time integrators), and also introduces a parallel object model that makes it possible to maintain multiple implementations of computational kernels, on e.g. conventional processors and GPUs. It handles data layout conversions and enables us to port performance-critical parts of a code to a new architecture step-by-step, while the rest of the code can remain unchanged. We will show examples of the performance gains and some physics applications.

Construction of hierarchically porous monoliths from covalent organic frameworks (COFs) and their application for bisphenol A removal.

PubMed

Liu, Zhongshan; Wang, Hongwei; Ou, Junjie; Chen, Lianfang; Ye, Mingliang

2018-05-11

Subject to synthetic conditions, covalent organic frameworks (COFs) are usually in powder form. Herein, taking an azine-linked COF as an example, detailed characterizations indicated that accessible aldehyde groups and hydrazine groups (CNNH 2 , 88 μmol g -1 ) concurrently existed on its surface. Intrigued by such feature, we have developed an approach based on ring-opening polymerization to shape COF powder into monoliths. The crystallinity and micropore of COF in monoliths were well remained, meanwhile, the ring-opening polymerization remarkably generated macropores ranging from 0.43 to 3.51 μm, indicating a hierarchically porous structure. The BET surface area of resultant monoliths with different COF mass fractions of 16%, 28% and 43% ranged from 105 to 281 m 2  g -1 . Due to the π-π interaction and hydrogen bond interaction, COF-based monoliths exhibited strong retention and rapid adsorption for bisphenol A (BPA) in aqueous medium. When 29 mL BPA solution (22.8 mg L -1 ) passed through COF-based monolith (28%), the adsorption capacity was up to 61.3 mg g -1 . Furthermore, the COF-based monolith demonstrated excellent cycle use for catalyzing Suzuki-Miyaura coupling reaction after being coordinated with palladium acetate. Copyright © 2018 Elsevier B.V. All rights reserved.

Lakes, landscapes, and R: A framework for open science on freshwater cyanobacteria

EPA Science Inventory

In the last several years scientific reproducibility has been a hot topic with several fields openly struggling with reproducing and replicating research results. One of the key tools to address reproducibility is the use of open source software. Increasingly in ecology, the R ...

Analysis and characterization of graphene-on-substrate devices

NASA Astrophysics Data System (ADS)

Berdebes, Dionisis

The purpose of this MS Thesis is the analysis and characterization of graphene on substrate structures prepared at the Birck Nanotechnology Center-Purdue University/IBM Watson Research Center-N.Y., and characterized under low-field transport conditions. First, a literature survey is conducted, both in theoretical and experimental work on graphene transport phenomena, and the open issues are reported. Next, the theory of low-field transport in graphene is reviewed within a Landauer framework. Experimental results of back-gated graphene-on-substrate devices, prepared by the Appenzeller group, are then presented, followed by an extraction of an energy/temperature dependent backscattering mean free path as the main characterization parameter. A key conclusion is the critical role of contacts in two-probe measurements. In this framework, a non-self-consistent Non Equilibrium Green's Function method is employed for the calculation of the odd and even metal-graphene ballistic interfacial resistance. A good agreement with the relevant experimental work is observed.

Defect-Engineered Metal–Organic Frameworks

PubMed Central

Fang, Zhenlan; Bueken, Bart; De Vos, Dirk E; Fischer, Roland A

2015-01-01

Defect engineering in metal–organic frameworks (MOFs) is an exciting concept for tailoring material properties, which opens up novel opportunities not only in sorption and catalysis, but also in controlling more challenging physical characteristics such as band gap as well as magnetic and electrical/conductive properties. It is challenging to structurally characterize the inherent or intentionally created defects of various types, and there have so far been few efforts to comprehensively discuss these issues. Based on selected reports spanning the last decades, this Review closes that gap by providing both a concise overview of defects in MOFs, or more broadly coordination network compounds (CNCs), including their classification and characterization, together with the (potential) applications of defective CNCs/MOFs. Moreover, we will highlight important aspects of “defect-engineering” concepts applied for CNCs, also in comparison with relevant solid materials such as zeolites or COFs. Finally, we discuss the future potential of defect-engineered CNCs. PMID:26036179

Electronegative Guests in CoSb 3

DOE PAGES

Duan, Bo; Yang, Jiong; Salvador, James R.; ...

2016-04-19

Introducing guests into a host framework to form a so called inclusion compound can be used to design materials with new and fascinating functionalities. The vast majority of inclusion compounds have electropositive guests with neutral or negatively charged frameworks. Here, we show a series of electronegative guest filled skutterudites with inverse polarity. The strong covalent guest-host interactions observed for the electronegative group VIA guests, i.e., S and Se, feature a unique localized cluster vibration which significantly influences the lattice dynamics, together with the point-defect scattering caused by element substitutions, resulting in very low lattice thermal conductivity values. The findings ofmore » electronegative guests provide a new perspective for guest-filling in skutterudites, and the covalent filler/lattice interactions lead to an unusual lattice dynamics phenomenon which can be used for designing high-efficiency thermoelectric materials and novel functional inclusion compounds with open structures.« less

Structuration and sensemaking: frameworks for understanding the management of health information systems in the ICU.

PubMed

Ghosh, Tip

2007-01-01

This paper will describe two alternate conceptual frameworks (i.e. Structuration and Sensemaking) that will help to describe and provide insight into how best to implement health information systems in ICUs throughout the globe. Structuration and sensemaking are two competing ways to view the social world within hospitals. To examine the impact of information technology in health care organizations, it is important to explore the dynamic interplay between clinical decisionmaking, outcomes of HIT implementation, and individual characteristics of the organizational setting. The adaptation of information technology within health care organizations is by its very nature quite complex. The recursive pattern of social interactions that shape the implementation of technologies within that setting is key. Structuration theory provides an understanding of human work as social interaction within that organizational culture, mediated by artifacts such as tools, language, rules and procedures, and open to change. The ICU provides multiple opportunities for sensemaking. It involves caring for multiple patients simultaneously; is subject to high levels of uncertainty and is provided under significant time constraints. It is highly interdependent work, necessitating shared sensemaking as well as individual sensemaking. Sensemaking is made partially visible in this context as clinicians communicate to each other what they think is the cause of the patient's symptoms and how to treat them in the form of discussions about patient care, consultation requests, ancillary testing, and the electronic medical record. The collaborative nature of work in the ICU lends itself to the application of sensemaking and structuration theories.

Emergence of structured communities through evolutionary dynamics.

PubMed

Shtilerman, Elad; Kessler, David A; Shnerb, Nadav M

2015-10-21

Species-rich communities, in which many competing species coexist in a single trophic level, are quite frequent in nature, but pose a formidable theoretical challenge. In particular, it is known that complex competitive systems become unstable and unfeasible when the number of species is large. Recently, many studies have attributed the stability of natural communities to the structure of the interspecific interaction network, yet the nature of such structures and the underlying mechanisms responsible for them remain open questions. Here we introduce an evolutionary model, based on the generic Lotka-Volterra competitive framework, from which a stable, structured, diverse community emerges spontaneously. The modular structure of the competition matrix reflects the phylogeny of the community, in agreement with the hierarchial taxonomic classification. Closely related species tend to have stronger niche overlap and weaker fitness differences, as opposed to pairs of species from different modules. The competitive-relatedness hypothesis and the idea of emergent neutrality are discussed in the context of this evolutionary model. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structural Basis of Mitochondrial Transcription Initiation.

PubMed

Hillen, Hauke S; Morozov, Yaroslav I; Sarfallah, Azadeh; Temiakov, Dmitry; Cramer, Patrick

2017-11-16

Transcription in human mitochondria is driven by a single-subunit, factor-dependent RNA polymerase (mtRNAP). Despite its critical role in both expression and replication of the mitochondrial genome, transcription initiation by mtRNAP remains poorly understood. Here, we report crystal structures of human mitochondrial transcription initiation complexes assembled on both light and heavy strand promoters. The structures reveal how transcription factors TFAM and TFB2M assist mtRNAP to achieve promoter-dependent initiation. TFAM tethers the N-terminal region of mtRNAP to recruit the polymerase to the promoter whereas TFB2M induces structural changes in mtRNAP to enable promoter opening and trapping of the DNA non-template strand. Structural comparisons demonstrate that the initiation mechanism in mitochondria is distinct from that in the well-studied nuclear, bacterial, or bacteriophage transcription systems but that similarities are found on the topological and conceptual level. These results provide a framework for studying the regulation of gene expression and DNA replication in mitochondria. Copyright © 2017 Elsevier Inc. All rights reserved.

Crystal structure of a Schistosoma mansoni septin reveals the phenomenon of strand slippage in septins dependent on the nature of the bound nucleotide.

PubMed

Zeraik, Ana E; Pereira, Humberto M; Santos, Yuri V; Brandão-Neto, José; Spoerner, Michael; Santos, Maiara S; Colnago, Luiz A; Garratt, Richard C; Araújo, Ana P U; DeMarco, Ricardo

2014-03-14

Septins are filament-forming GTP-binding proteins involved in important cellular events, such as cytokinesis, barrier formation, and membrane remodeling. Here, we present two crystal structures of the GTPase domain of a Schistosoma mansoni septin (SmSEPT10), one bound to GDP and the other to GTP. The structures have been solved at an unprecedented resolution for septins (1.93 and 2.1 Å, respectively), which has allowed for unambiguous structural assignment of regions previously poorly defined. Consequently, we provide a reliable model for functional interpretation and a solid foundation for future structural studies. Upon comparing the two complexes, we observe for the first time the phenomenon of a strand slippage in septins. Such slippage generates a front-back communication mechanism between the G and NC interfaces. These data provide a novel mechanistic framework for the influence of nucleotide binding to the GTPase domain, opening new possibilities for the study of the dynamics of septin filaments.

Dielectric anomaly and relaxation natures in a Zn-Cr pillar−layered metal−organic framework with cages and channels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xue, Chen; Yao, Zhi-Yuan; Liu, Shao-Xian

A bimetallic metal–organic framework (MOF) with the formula [Zn{sub 3}btc{sub 2}(Cr{sub 3}O(isonic){sub 6}(H{sub 2}O){sub 2}(OH))]·(DMF){sub 15.5}(H{sub 2}O){sub 8} (H{sub 3}btc=1,3,5-benzenetricarboxylic acid; isonic=isonicotinicate) shows a pillar-layered structure. The monolayer consists of hexagon-like rings formed by the [Zn(isonic){sub 2}(btc){sub 2}] tetrahedral and the consecutive monolayers are pillared by trigonal–prismatic clusters of [Cr{sub 3}O(isonic){sub 6}(H{sub 2}O){sub 2}(OH)]through the remaining binding sites of the Zn{sup 2+} ions. DMF and water molecules are confined in the cages and channels. TGA indicates that the lattice DMF and water molecules begin to be released at temperatures above 363 K. Dielectric measurements were carried out in the rangemore » of 173–363 K and 1–10{sup 7} Hz for three successive thermal cycles. The dielectric spectroscopy obtained in the first thermal cycle was different from that observed in the next two thermal cycles, while the dielectric spectra in the last two thermal cycles were almost identical. The dielectric nature of this MOF is discussed in detail for each thermal cycle. Since MOFs are unique host–guest systems in which the structure of the host framework is designable and the guests are exchangeable, it is no doubt those MOFs are materials with a variety of dielectric natures. This study gives a fresh impetus to achieve MOFs–based dielectric materials. - Graphical abstract: The bimetallic MOF [Zn{sub 3}btc{sub 2}(Cr{sub 3}O(isonic){sub 6}(H{sub 2}O){sub 2}(OH))]·(DMF){sub 15.5}(H{sub 2}O){sub 8}1, shows a pillar-layered open-framework structure. The dielectric spectra of 1 are almost identical in the last two thermal cycles, whereas significantly different from that observed in the first thermal cycle. The novel dielectric anomaly associated with a stacked structure transformation of the disordered guests. - Highlights: • A bimetallic metal-organic framework shows a pillar-layered structure. • The MOF displays novel dielectric anomaly and relaxation behaviors. • The dielectric anomaly arises from the stacking structure transformation of guests. • The dielectric relaxation is related to the dipole dynamics of guests.« less

Organizational Context and Capabilities for Integrating Care: A Framework for Improvement.

PubMed

Evans, Jenna M; Grudniewicz, Agnes; Baker, G Ross; Wodchis, Walter P

2016-08-31

Interventions aimed at integrating care have become widespread in healthcare; however, there is significant variability in their success. Differences in organizational contexts and associated capabilities may be responsible for some of this variability. This study develops and validates a conceptual framework of organizational capabilities for integrating care, identifies which of these capabilities may be most important, and explores the mechanisms by which they influence integrated care efforts. The Context and Capabilities for Integrating Care (CCIC) Framework was developed through a literature review, and revised and validated through interviews with leaders and care providers engaged in integrated care networks in Ontario, Canada. Interviews involved open-ended questions and graphic elicitation. Quantitative content analysis was used to summarize the data. The CCIC Framework consists of eighteen organizational factors in three categories: Basic Structures, People and Values, and Key Processes. The three most important capabilities shaping the capacity of organizations to implement integrated care interventions include Leadership Approach, Clinician Engagement and Leadership, and Readiness for Change. The majority of hypothesized relationships among organizational capabilities involved Readiness for Change and Partnering, emphasizing the complexity, interrelatedness and importance of these two factors to integrated care efforts. Organizational leaders can use the framework to determine readiness to integrate care, develop targeted change management strategies, and select appropriate partners with overlapping or complementary profiles on key capabilities. Researchers may use the results to test and refine the proposed framework, with a focus on the hypothesized relationships among organizational capabilities and between organizational capabilities and performance outcomes.

In Search for the Open Educator: Proposal of a Definition and a Framework to Increase Openness Adoption among University Educators

ERIC Educational Resources Information Center

Nascimbeni, Fabio; Burgos, Daniel

2016-01-01

The paper explores the change process that university teachers need to go through in order to become fluent with Open Education approaches. Based on a literature review and a set of interviews with a number of leading experts in the field of Open Educational Resources and Open Education, the paper puts forward an original definition of Open…

Developing Conceptual Framework for Revising Self-Learning Materials (SLMs) of the Open School (OS) of Bangladesh Open University (BOU) at a Digital Environment

ERIC Educational Resources Information Center

Yeasmin, Sabina; Murthy, C. R. K.

2011-01-01

Bangladesh Open University (BOU) runs school programs as part of its academic activities through open schooling since its inception. As of today, the Open School uses the first generation self-learning materials (SLMs) written, before an era, following an in-house style and template. The concerned faculty member corrects, every year, texts before…

Developing Conceptual Framework for Revising Self-Learning Materials (SLMs) of the Open School (OS) of Bangladesh Open University (BOU) at a Digital Environment

ERIC Educational Resources Information Center

Yeasmin, Sabina; Murthy, C. R. K.

2012-01-01

Bangladesh Open University (BOU) runs school programs as part of its academic activities through open schooling since its inception. As of today, the Open School uses the first generation self-learning materials (SLMs) written, before an era, following an in-house style and template. The concerned faculty member corrects, every year, texts before…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Seyong; Kim, Jungwon; Vetter, Jeffrey S

This paper presents a directive-based, high-level programming framework for high-performance reconfigurable computing. It takes a standard, portable OpenACC C program as input and generates a hardware configuration file for execution on FPGAs. We implemented this prototype system using our open-source OpenARC compiler; it performs source-to-source translation and optimization of the input OpenACC program into an OpenCL code, which is further compiled into a FPGA program by the backend Altera Offline OpenCL compiler. Internally, the design of OpenARC uses a high- level intermediate representation that separates concerns of program representation from underlying architectures, which facilitates portability of OpenARC. In fact, thismore » design allowed us to create the OpenACC-to-FPGA translation framework with minimal extensions to our existing system. In addition, we show that our proposed FPGA-specific compiler optimizations and novel OpenACC pragma extensions assist the compiler in generating more efficient FPGA hardware configuration files. Our empirical evaluation on an Altera Stratix V FPGA with eight OpenACC benchmarks demonstrate the benefits of our strategy. To demonstrate the portability of OpenARC, we show results for the same benchmarks executing on other heterogeneous platforms, including NVIDIA GPUs, AMD GPUs, and Intel Xeon Phis. This initial evidence helps support the goal of using a directive-based, high-level programming strategy for performance portability across heterogeneous HPC architectures.« less

The Open Ed Tech: Never Mind the Edupunks; or, The Great Web 2.0 Swindle

ERIC Educational Resources Information Center

Lamb, Brian; Groom, Jim

2010-01-01

Has the wave of the open web crested? What does "open educational technology" look like, and does it stand for anything? In this article, the authors discuss the rise of open educational technology. The present range of Web 2.0 service providers offers a self-evident strategic technology framework. Without much effort, online teachers and learners…

Framework for the Development of OER-Based Learning Materials in ODL Environment

ERIC Educational Resources Information Center

Teng, Khor Ean; Hung, Chung Sheng

2013-01-01

This paper describes the framework for the development of OER-based learning materials "TCC121/05 Programming Fundamentals with Java" for ODL learners in Wawasan Open University (WOU) using three main development phases mainly: creation, evaluation and production phases. The proposed framework has further been tested on ODL learners to…

Integration of genomic and medical data into a 3D atlas of human anatomy.

PubMed

Turinsky, Andrei L; Fanea, Elena; Trinh, Quang; Dong, Xiaoli; Stromer, Julie N; Shu, Xueling; Wat, Stephen; Hallgrímsson, Benedikt; Hill, Jonathan W; Edwards, Carol; Grosenick, Brenda; Yajima, Masumi; Sensen, Christoph W

2008-01-01

We have developed a framework for the visual integration and exploration of multi-scale biomedical data, which includes anatomical and molecular components. We have also created a Java-based software system that integrates molecular information, such as gene expression data, into a three-dimensional digital atlas of the male adult human anatomy. Our atlas is structured according to the Terminologia Anatomica. The underlying data-indexing mechanism uses open standards and semantic ontology-processing tools to establish the associations between heterogeneous data types. The software system makes an extensive use of virtual reality visualization.

External Modeling Framework And The OpenUTF

DTIC Science & Technology

2012-01-24

12S- SIW -034 WarpIV Technologies, Inc. 3/26/12 1 External Modeling Framework and the OpenUTF1 Jeffrey S. Steinman, Ph.D. Craig N. Lammers...unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 12S- SIW -034 WarpIV Technologies, Inc. 3/26/12...tracks. Full visualization was performed at the Naval Research Laboratory (NRL) in Washington DC. 12S- SIW -034 WarpIV Technologies, Inc. 3/26/12 3

Rechargeable Aluminum-Ion Batteries Based on an Open-Tunnel Framework.

PubMed

Kaveevivitchai, Watchareeya; Huq, Ashfia; Wang, Shaofei; Park, Min Je; Manthiram, Arumugam

2017-09-01

Rechargeable batteries based on an abundant metal such as aluminum with a three-electron transfer per atom are promising for large-scale electrochemical energy storage. Aluminum can be handled in air, thus offering superior safety, easy fabrication, and low cost. However, the development of Al-ion batteries has been challenging due to the difficulties in identifying suitable cathode materials. This study presents the use of a highly open framework Mo 2.5 +  y VO 9 +  z as a cathode for Al-ion batteries. The open-tunnel oxide allows a facile diffusion of the guest species and provides sufficient redox centers to help redistribute the charge within the local host lattice during the multivalent-ion insertion, thus leading to good rate capability with a specific capacity among the highest reported in the literature for Al-based batteries. This study also presents the use of Mo 2.5 +  y VO 9 +  z as a model host to develop a novel ultrafast technique for chemical insertion of Al ions into host structures. The microwave-assisted method employing diethylene glycol and aluminum diacetate (Al(OH)(C 2 H 3 O 2 ) 2 ) can be performed in air in as little as 30 min, which is far superior to the traditional chemical insertion techniques involving moisture-sensitive organometallic reagents. The Al-inserted Al x Mo 2.5 +  y VO 9 +  z obtained by the microwave-assisted chemical insertion can be used in Al-based rechargeable batteries. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Continuous integration for concurrent MOOSE framework and application development on GitHub

DOE PAGES

Slaughter, Andrew E.; Peterson, John W.; Gaston, Derek R.; ...

2015-11-20

For the past several years, Idaho National Laboratory’s MOOSE framework team has employed modern software engineering techniques (continuous integration, joint application/framework source code repos- itories, automated regression testing, etc.) in developing closed-source multiphysics simulation software (Gaston et al., Journal of Open Research Software vol. 2, article e10, 2014). In March 2014, the MOOSE framework was released under an open source license on GitHub, significantly expanding and diversifying the pool of current active and potential future contributors on the project. Despite this recent growth, the same philosophy of concurrent framework and application development continues to guide the project’s development roadmap. Severalmore » specific practices, including techniques for managing multiple repositories, conducting automated regression testing, and implementing a cascading build process are discussed in this short paper. Furthermore, special attention is given to describing the manner in which these practices naturally synergize with the GitHub API and GitHub-specific features such as issue tracking, Pull Requests, and project forks.« less

Continuous integration for concurrent MOOSE framework and application development on GitHub

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slaughter, Andrew E.; Peterson, John W.; Gaston, Derek R.

For the past several years, Idaho National Laboratory’s MOOSE framework team has employed modern software engineering techniques (continuous integration, joint application/framework source code repos- itories, automated regression testing, etc.) in developing closed-source multiphysics simulation software (Gaston et al., Journal of Open Research Software vol. 2, article e10, 2014). In March 2014, the MOOSE framework was released under an open source license on GitHub, significantly expanding and diversifying the pool of current active and potential future contributors on the project. Despite this recent growth, the same philosophy of concurrent framework and application development continues to guide the project’s development roadmap. Severalmore » specific practices, including techniques for managing multiple repositories, conducting automated regression testing, and implementing a cascading build process are discussed in this short paper. Furthermore, special attention is given to describing the manner in which these practices naturally synergize with the GitHub API and GitHub-specific features such as issue tracking, Pull Requests, and project forks.« less

Interim Open Source Software (OSS) Policy

EPA Pesticide Factsheets

This interim Policy establishes a framework to implement the requirements of the Office of Management and Budget's (OMB) Federal Source Code Policy to achieve efficiency, transparency and innovation through reusable and open source software.

Statistical Ring Opening Metathesis Copolymerization of Norbornene and Cyclopentene by Grubbs' 1st-Generation Catalyst.

PubMed

Nikovia, Christiana; Maroudas, Andreas-Philippos; Goulis, Panagiotis; Tzimis, Dionysios; Paraskevopoulou, Patrina; Pitsikalis, Marinos

2015-08-27

Statistical copolymers of norbornene (NBE) with cyclopentene (CP) were prepared by ring-opening metathesis polymerization, employing the 1st-generation Grubbs' catalyst, in the presence or absence of triphenylphosphine, PPh₃. The reactivity ratios were estimated using the Finemann-Ross, inverted Finemann-Ross, and Kelen-Tüdos graphical methods, along with the computer program COPOINT, which evaluates the parameters of binary copolymerizations from comonomer/copolymer composition data by integrating a given copolymerization equation in its differential form. Structural parameters of the copolymers were obtained by calculating the dyad sequence fractions and the mean sequence length, which were derived using the monomer reactivity ratios. The kinetics of thermal decomposition of the copolymers along with the respective homopolymers was studied by thermogravimetric analysis within the framework of the Ozawa-Flynn-Wall and Kissinger methodologies. Finally, the effect of triphenylphosphine on the kinetics of copolymerization, the reactivity ratios, and the kinetics of thermal decomposition were examined.

A reference architecture for integrated EHR in Colombia.

PubMed

de la Cruz, Edgar; Lopez, Diego M; Uribe, Gustavo; Gonzalez, Carolina; Blobel, Bernd

2011-01-01

The implementation of national EHR infrastructures has to start by a detailed definition of the overall structure and behavior of the EHR system (system architecture). Architectures have to be open, scalable, flexible, user accepted and user friendly, trustworthy, based on standards including terminologies and ontologies. The GCM provides an architectural framework created with the purpose of analyzing any kind of system, including EHR system´s architectures. The objective of this paper is to propose a reference architecture for the implementation of an integrated EHR in Colombia, based on the current state of system´s architectural models, and EHR standards. The proposed EHR architecture defines a set of services (elements) and their interfaces, to support the exchange of clinical documents, offering an open, scalable, flexible and semantically interoperable infrastructure. The architecture was tested in a pilot tele-consultation project in Colombia, where dental EHR are exchanged.

Frog: The fast & realistic OpenGL event displayer

NASA Astrophysics Data System (ADS)

Quertenmont, Loïc

2010-04-01

FROG [1] [2] is a generic framework dedicated to visualisation of events in high energy physics experiment. It is suitable to any particular physics experiment or detector design. The code is light (< 3 MB) and fast (browsing time ~ 20 events per second for a large High Energy Physics experiment) and can run on various operating systems, as its object-oriented structure (C++) relies on the cross-platform OpenGL[3] and Glut [4] libraries. Moreover, Frog does not require installation of heavy third party libraries for the visualisation. This documents describes the features and principles of Frog version 1.106, its working scheme and numerous functionalities such as: 3D and 2D visualisation, graphical user interface, mouse interface, configuration files, production of pictures of various format, integration of personal objects, etc. Finally the application of FROG for physic experiment/environement, such as Gastof, CMS, ILD, Delphes will be presented for illustration.

Quantum Brownian motion model for the stock market

NASA Astrophysics Data System (ADS)

Meng, Xiangyi; Zhang, Jian-Wei; Guo, Hong

2016-06-01

It is believed by the majority today that the efficient market hypothesis is imperfect because of market irrationality. Using the physical concepts and mathematical structures of quantum mechanics, we construct an econophysical framework for the stock market, based on which we analogously map massive numbers of single stocks into a reservoir consisting of many quantum harmonic oscillators and their stock index into a typical quantum open system-a quantum Brownian particle. In particular, the irrationality of stock transactions is quantitatively considered as the Planck constant within Heisenberg's uncertainty relationship of quantum mechanics in an analogous manner. We analyze real stock data of Shanghai Stock Exchange of China and investigate fat-tail phenomena and non-Markovian behaviors of the stock index with the assistance of the quantum Brownian motion model, thereby interpreting and studying the limitations of the classical Brownian motion model for the efficient market hypothesis from a new perspective of quantum open system dynamics.

Using OpenEHR in SICTI an electronic health record system for critical medicine

NASA Astrophysics Data System (ADS)

Filgueira, R.; Odriazola, A.; Simini, F.

2007-11-01

SICTI is a software tool for registering health records in critical medicine environments. Version 1.0 has been in use since 2003. The Biomedical Engineering Group (Núcleo de Ingeniería Biomédica), with support from the Technological Development Programme (Programa de Desarrollo Tecnológico), decided to develop a new version, to provide an aid for more critical medicine processes, based on a framework which would make the application domain change oriented. The team analyzed three alternatives: to develop an original product based on new research, to base the development on OpenEHR framework, or to use HL7 RIM as the reference model for SICTI. The team opted for OpenEHR. This work describes the use of OpenEHR, its strong and weak points, and states future work perspectives.

Modular heat exchanger

DOEpatents

Giardina, A.R.

1981-03-03

A shell and tube heat exchanger is described having a plurality of individually removable tube bundle modules. A lattice of structural steel forming rectangular openings therein is placed at each end of a cylindrical shell. Longitudinal structural members are placed in the shell between corners of the rectangular openings situated on opposite ends of the shell. Intermediate support members interconnect the longitudinal supports so as to increase the longitudinal supports rigidity. Rectangular parallelepiped tube bundle modules occupy the space defined by the longitudinal supports and end supports and each include a rectangular tube sheet situated on each end of a plurality of tubes extending there through, a plurality of rectangular tube supports located between the tube sheets, and a tube bundle module stiffening structure disposed about the bundle's periphery and being attached to the tube sheets and tube supports. The corners of each tube bundle module have longitudinal framework members which are mateable with and supported by the longitudinal support members. Intermediate support members constitute several lattices, each of which is situated in a plane between the end support members. The intermediate support members constituting the several lattices extend horizontally and vertically between longitudinal supports of adjacent tube module voids. An alternative embodiment for intermediate support members constitute a series of structural plates situated at the corners of the module voids and having recesses therein for receiving the respective longitudinal support members adjacent thereto, protrusions separating the recesses, and a plurality of struts situated between protrusions of adjacent structural plates. 12 figs.

Modular heat exchanger

DOEpatents

Giardina, Angelo R. [Marple Township, Delaware County, PA

1981-03-03

A shell and tube heat exchanger having a plurality of individually removable tube bundle modules. A lattice of structural steel forming rectangular openings therein is placed at each end of a cylindrical shell. Longitudinal structural members are placed in the shell between corners of the rectangular openings situated on opposite ends of the shell. Intermediate support members interconnect the longitudinal supports so as to increase the longitudinal supports rigidity. Rectangular parallelpiped tube bundle moldules occupy the space defined by the longitudinal supports and end supports and each include a rectangular tube sheet situated on each end of a plurality of tubes extending therethrough, a plurality of rectangular tube supports located between the tube sheets, and a tube bundle module stiffening structure disposed about the bundle's periphery and being attached to the tube sheets and tube supports. The corners of each tube bundle module have longitudinal framework members which are mateable with and supported by the longitudinal support members. Intermediate support members constitute several lattice, each of which is situate d in a plane between the end support members. The intermediate support members constituting the several lattice extend horizontally and vertically between longitudinal supports of adjacent tube module voids. An alternative embodiment for intermediate support members constitute a series of structural plates situated at the corners of the module voids and having recesses therein for receiving the respective longitudinal support members adjacent thereto, protrusions separating the recesses, and a plurality of struts situated between protrusions of adjacent structural plates.

From isosuperatoms to isosupermolecules: new concepts in cluster science

NASA Astrophysics Data System (ADS)

Liu, Liren; Li, Pai; Yuan, Lan-Feng; Cheng, Longjiu; Yang, Jinlong

2016-06-01

As an extension of the superatom concept, a new concept ``isosuperatom'' is proposed, reflecting the physical phenomenon that a superatom cluster can take multiple geometrical structures with their electronic structures topologically invariant. The icosahedral and cuboctahedral Au135+ units in the Au25(SCH2CH2Ph)18-, Au23(SC6H11)16- and Au24(SAdm)16 nanoclusters are found to be examples of this concept. Furthermore, two isosuperatoms can combine to form a supermolecule. For example, the structure of the {Ag32(DPPE)5(SC6H4CF3)24}2- nanocluster can be understood well in terms of a Ag2212+ supermolecule formed by two Ag138+ isosuperatoms. On the next level of complexity, various combinations of isosuperatoms can lead to supermolecules with different geometrical structures but similar electronic structures, i.e., ``isosupermolecules''. We take two synthesized nanoclusters Au20(PPhpy2)10Cl42+ and Au30S(StBu)18 to illustrate two Au206+ isosupermolecules. The proposed concepts of isosuperatom and isosupermolecule significantly enrich the superatom concept, give a new framework for understanding a wide range of nanoclusters, and open a new door for designing assembled materials.As an extension of the superatom concept, a new concept ``isosuperatom'' is proposed, reflecting the physical phenomenon that a superatom cluster can take multiple geometrical structures with their electronic structures topologically invariant. The icosahedral and cuboctahedral Au135+ units in the Au25(SCH2CH2Ph)18-, Au23(SC6H11)16- and Au24(SAdm)16 nanoclusters are found to be examples of this concept. Furthermore, two isosuperatoms can combine to form a supermolecule. For example, the structure of the {Ag32(DPPE)5(SC6H4CF3)24}2- nanocluster can be understood well in terms of a Ag2212+ supermolecule formed by two Ag138+ isosuperatoms. On the next level of complexity, various combinations of isosuperatoms can lead to supermolecules with different geometrical structures but similar electronic structures, i.e., ``isosupermolecules''. We take two synthesized nanoclusters Au20(PPhpy2)10Cl42+ and Au30S(StBu)18 to illustrate two Au206+ isosupermolecules. The proposed concepts of isosuperatom and isosupermolecule significantly enrich the superatom concept, give a new framework for understanding a wide range of nanoclusters, and open a new door for designing assembled materials. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01998f

Persistent electrochemical performance in epitaxial VO 2(B)

DOE PAGES

Lee, Shinbuhm; Sun, Xiao -Guang; Lubimtsev, Andrew A.; ...

2017-03-07

Discovering high-performance energy storage materials is indispensable for renewable energy, electric vehicle performance, and mobile computing. Owing to the open atomic framework and good room temperature conductivity, bronze-phase vanadium dioxide [VO 2(B)] has been regarded as a highly promising electrode material for Li ion batteries. However, previous attempts were unsuccessful to show the desired cycling performance and capacity without chemical modification. Here, we show with epitaxial VO 2(B) films that one can accomplish the theoretical limit for capacity with persistent charging–discharging cyclability owing to the high structural stability and unique open pathways for Li ion conduction. Atomic-scale characterization by scanningmore » transmission electron microscopy and density functional theory calculations also reveal that the unique open pathways in VO 2(B) provide the most stable sites for Li adsorption and diffusion. Furthermore, this work ultimately demonstrates that VO 2(B) is a highly promising energy storage material and has no intrinsic hindrance in achieving superior cyclability with a very high power and capacity in a Li-ion conductor.« less

An Open Source modular platform for hydrological model implementation

NASA Astrophysics Data System (ADS)

Kolberg, Sjur; Bruland, Oddbjørn

2010-05-01

An implementation framework for setup and evaluation of spatio-temporal models is developed, forming a highly modularized distributed model system. The ENKI framework allows building space-time models for hydrological or other environmental purposes, from a suite of separately compiled subroutine modules. The approach makes it easy for students, researchers and other model developers to implement, exchange, and test single routines in a fixed framework. The open-source license and modular design of ENKI will also facilitate rapid dissemination of new methods to institutions engaged in operational hydropower forecasting or other water resource management. Written in C++, ENKI uses a plug-in structure to build a complete model from separately compiled subroutine implementations. These modules contain very little code apart from the core process simulation, and are compiled as dynamic-link libraries (dll). A narrow interface allows the main executable to recognise the number and type of the different variables in each routine. The framework then exposes these variables to the user within the proper context, ensuring that time series exist for input variables, initialisation for states, GIS data sets for static map data, manually or automatically calibrated values for parameters etc. ENKI is designed to meet three different levels of involvement in model construction: • Model application: Running and evaluating a given model. Regional calibration against arbitrary data using a rich suite of objective functions, including likelihood and Bayesian estimation. Uncertainty analysis directed towards input or parameter uncertainty. o Need not: Know the model's composition of subroutines, or the internal variables in the model, or the creation of method modules. • Model analysis: Link together different process methods, including parallel setup of alternative methods for solving the same task. Investigate the effect of different spatial discretization schemes. o Need not: Write or compile computer code, handle file IO for each modules, • Routine implementation and testing. Implementation of new process-simulating methods/equations, specialised objective functions or quality control routines, testing of these in an existing framework. o Need not: Implement user or model interface for the new routine, IO handling, administration of model setup and run, calibration and validation routines etc. From being developed for Norway's largest hydropower producer Statkraft, ENKI is now being turned into an Open Source project. At the time of writing, the licence and the project administration is not established. Also, it remains to port the application to other compilers and computer platforms. However, we hope that ENKI will prove useful for both academic and operational users.

CJEP will offer open science badges.

PubMed

Pexman, Penny M

2017-03-01

This editorial announces the decision of the Canadian Journal of Experimental Psychology (CJEP) to offer Open Science Framework (OSF) Badges. The Centre for Open Science provides tools to facilitate open science practices. These include the OSF badges. The badges acknowledge papers that meet standards for openness of data, methods, or research process. They are now described in the CJEP Submission Guidelines, and are provided in the editorial. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Evaluation of a Framework to Implement Electronic Health Record Systems Based on the openEHR Standard

NASA Astrophysics Data System (ADS)

Orellana, Diego A.; Salas, Alberto A.; Solarz, Pablo F.; Medina Ruiz, Luis; Rotger, Viviana I.

2016-04-01

The production of clinical information about each patient is constantly increasing, and it is noteworthy that the information is created in different formats and at diverse points of care, resulting in fragmented, incomplete, inaccurate and isolated, health information. The use of health information technology has been promoted as having a decisive impact to improve the efficiency, cost-effectiveness, quality and safety of medical care delivery. However in developing countries the utilization of health information technology is insufficient and lacking of standards among other situations. In the present work we evaluate the framework EHRGen, based on the openEHR standard, as mean to reach generation and availability of patient centered information. The framework has been evaluated through the provided tools for final users, that is, without intervention of computer experts. It makes easier to adopt the openEHR ideas and provides an open source basis with a set of services, although some limitations in its current state conspire against interoperability and usability. However, despite the described limitations respect to usability and semantic interoperability, EHRGen is, at least regionally, a considerable step toward EHR adoption and interoperability, so that it should be supported from academic and administrative institutions.

A framework for conducting follow-up meetings with parents after a child's death in the pediatric intensive care unit.

PubMed

Eggly, Susan; Meert, Kathleen L; Berger, John; Zimmerman, Jerry; Anand, Kanwaljeet J S; Newth, Christopher J L; Harrison, Rick; Carcillo, Joseph; Dean, J Michael; Willson, Douglas F; Nicholson, Carol

2011-03-01

To describe a framework to assist pediatric intensive care unit physicians in conducting follow-up meetings with parents after their child's death. Many childhood deaths occur in pediatric intensive care units. Parents of children who die in pediatric intensive care units often desire a follow-up meeting with the physician(s) who cared for their child. Prior research conducted by the Collaborative Pediatric Critical Care Research Network on the experiences and perspectives of bereaved parents and pediatric intensive care unit physicians regarding the desirability, content, and conditions of follow-up meetings. The framework includes suggestions for inviting families to follow-up meetings (i.e., developing an institutional system, invitation timing, and format); preparing for the meeting (i.e., assessing family preferences; determining location, attendees, and discussion topics; reviewing medical and psychosocial history); structure of the meeting (i.e., opening, closing, and developing a meeting agenda); communicating effectively during the meeting; and follow-up for both parents and physicians. This framework is based on the experience and perspectives of bereaved parents and pediatric intensive care unit physicians. Future research should be conducted to determine the extent to which physician-parent follow-up meetings provide a benefit to parents, families, physicians, and other healthcare providers participating in these encounters.

A framework to simulate small shallow inland water bodies in semi-arid regions

NASA Astrophysics Data System (ADS)

Abbasi, Ali; Ohene Annor, Frank; van de Giesen, Nick

2017-12-01

In this study, a framework for simulating the flow field and heat transfer processes in small shallow inland water bodies has been developed. As the dynamics and thermal structure of these water bodies are crucial in studying the quality of stored water , and in assessing the heat fluxes from their surfaces as well, the heat transfer and temperature simulations were modeled. The proposed model is able to simulate the full 3-D water flow and heat transfer in the water body by applying complex and time varying boundary conditions. In this model, the continuity, momentum and temperature equations together with the turbulence equations, which comprise the buoyancy effect, have been solved. This model is built on the Reynolds Averaged Navier Stokes (RANS) equations with the widely used Boussinesq approach to solve the turbulence issues of the flow field. Micrometeorological data were obtained from an Automatic Weather Station (AWS) installed on the site and combined with field bathymetric measurements for the model. In the framework developed, a simple, applicable and generalizable approach is proposed for preparing the geometry of small shallow water bodies using coarsely measured bathymetry. All parts of the framework are based on open-source tools, which is essential for developing countries.

OpenGeoSys: Performance-Oriented Computational Methods for Numerical Modeling of Flow in Large Hydrogeological Systems

NASA Astrophysics Data System (ADS)

Naumov, D.; Fischer, T.; Böttcher, N.; Watanabe, N.; Walther, M.; Rink, K.; Bilke, L.; Shao, H.; Kolditz, O.

2014-12-01

OpenGeoSys (OGS) is a scientific open source code for numerical simulation of thermo-hydro-mechanical-chemical processes in porous and fractured media. Its basic concept is to provide a flexible numerical framework for solving multi-field problems for applications in geoscience and hydrology as e.g. for CO2 storage applications, geothermal power plant forecast simulation, salt water intrusion, water resources management, etc. Advances in computational mathematics have revolutionized the variety and nature of the problems that can be addressed by environmental scientists and engineers nowadays and an intensive code development in the last years enables in the meantime the solutions of much larger numerical problems and applications. However, solving environmental processes along the water cycle at large scales, like for complete catchment or reservoirs, stays computationally still a challenging task. Therefore, we started a new OGS code development with focus on execution speed and parallelization. In the new version, a local data structure concept improves the instruction and data cache performance by a tight bundling of data with an element-wise numerical integration loop. Dedicated analysis methods enable the investigation of memory-access patterns in the local and global assembler routines, which leads to further data structure optimization for an additional performance gain. The concept is presented together with a technical code analysis of the recent development and a large case study including transient flow simulation in the unsaturated / saturated zone of the Thuringian Syncline, Germany. The analysis is performed on a high-resolution mesh (up to 50M elements) with embedded fault structures.

A Real-Time Web of Things Framework with Customizable Openness Considering Legacy Devices

PubMed Central

Zhao, Shuai; Yu, Le; Cheng, Bo

2016-01-01

With the development of the Internet of Things (IoT), resources and applications based on it have emerged on a large scale. However, most efforts are “silo” solutions where devices and applications are tightly coupled. Infrastructures are needed to connect sensors to the Internet, open up and break the current application silos and move to a horizontal application mode. Based on the concept of Web of Things (WoT), many infrastructures have been proposed to integrate the physical world with the Web. However, issues such as no real-time guarantee, lack of fine-grained control of data, and the absence of explicit solutions for integrating heterogeneous legacy devices, hinder their widespread and practical use. To address these issues, this paper proposes a WoT resource framework that provides the infrastructures for the customizable openness and sharing of users’ data and resources under the premise of ensuring the real-time behavior of their own applications. The proposed framework is validated by actual systems and experimental evaluations. PMID:27690038

A Real-Time Web of Things Framework with Customizable Openness Considering Legacy Devices.

PubMed

Zhao, Shuai; Yu, Le; Cheng, Bo

2016-09-28

With the development of the Internet of Things (IoT), resources and applications based on it have emerged on a large scale. However, most efforts are "silo" solutions where devices and applications are tightly coupled. Infrastructures are needed to connect sensors to the Internet, open up and break the current application silos and move to a horizontal application mode. Based on the concept of Web of Things (WoT), many infrastructures have been proposed to integrate the physical world with the Web. However, issues such as no real-time guarantee, lack of fine-grained control of data, and the absence of explicit solutions for integrating heterogeneous legacy devices, hinder their widespread and practical use. To address these issues, this paper proposes a WoT resource framework that provides the infrastructures for the customizable openness and sharing of users' data and resources under the premise of ensuring the real-time behavior of their own applications. The proposed framework is validated by actual systems and experimental evaluations.

Structural study of Ni- or Mg-based complexes incorporated within UiO-66-NH{sub 2} framework and their impact on hydrogen sorption properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Žunkovič, E.; Mazaj, M.; Mali, G.

2015-05-15

Nickel and magnesium acetylacetonate molecular complexes were post-synthetically incorporated into microporous zirconium-based MOF (UiO-66-NH{sub 2}) in order to introduce active open-metal sites for hydrogen sorption. Elemental analysis, nitrogen physisorption and DFT calculations revealed that 5 molecules of Ni(acac){sub 2} or 2 molecules of Mg(acac){sub 2} were incorporated into one unit cell of UiO-66-NH{sub 2}. {sup 1}H–{sup 13}C CPMAS and {sup 1}H MAS NMR spectroscopy showed that, although embedded within the pores, both Ni- and Mg-complexes interacted with the UiO-66-NH{sub 2} framework only through weak van der Waals bonds. Inclusion of metal complexes led to the decrease of hydrogen sorption capacitiesmore » in Ni-modified as well as in Mg-modified samples in comparison with the parent UiO-66-NH{sub 2}. The isosteric hydrogen adsorption enthalpy slightly increased in the case of Ni-modified material, but not in the case of Mg-modified analogue. - Graphical abstract: A post-synthesis impregnation of Mg- and Ni-acetylacetonate complexes performed on zirconium-based MOF UiO-66-NH{sub 2} does influence the hydrogen sorption performance with respect to the parent matrix. The structural study revealed that Mg- and Ni-acetylacetonate molecules interact with zirconium-terephthalate framework only by weak interactions and they are not covalently bonded to aminoterephthalate ligand. Still, they remain confined into the pores even after hydrogen sorption experiments. - Highlights: • Mg- and Ni-acetylacetonate molecules embedded in the pores of UiO-66-NH{sub 2} by PSM. • Molecules of complexes interact with framework only by van der Waals interactions. • Type/structure of deposited metal-complex impact hydrogen enthalpy of adsorption.« less

PiCO QL: A software library for runtime interactive queries on program data

NASA Astrophysics Data System (ADS)

Fragkoulis, Marios; Spinellis, Diomidis; Louridas, Panos

PiCO QL is an open source C/C++ software whose scientific scope is real-time interactive analysis of in-memory data through SQL queries. It exposes a relational view of a system's or application's data structures, which is queryable through SQL. While the application or system is executing, users can input queries through a web-based interface or issue web service requests. Queries execute on the live data structures through the respective relational views. PiCO QL makes a good candidate for ad-hoc data analysis in applications and for diagnostics in systems settings. Applications of PiCO QL include the Linux kernel, the Valgrind instrumentation framework, a GIS application, a virtual real-time observatory of stellar objects, and a source code analyser.

[Scale Relativity Theory in living beings morphogenesis: fratal, determinism and chance].

PubMed

Chaline, J

2012-10-01

The Scale Relativity Theory has many biological applications from linear to non-linear and, from classical mechanics to quantum mechanics. Self-similar laws have been used as model for the description of a huge number of biological systems. Theses laws may explain the origin of basal life structures. Log-periodic behaviors of acceleration or deceleration can be applied to branching macroevolution, to the time sequences of major evolutionary leaps. The existence of such a law does not mean that the role of chance in evolution is reduced, but instead that randomness and contingency may occur within a framework which may itself be structured in a partly statistical way. The scale relativity theory can open new perspectives in evolution. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

RSA Opening Minds: A Curriculum for the 21st Century

ERIC Educational Resources Information Center

Candy, Sara

2011-01-01

This article discusses the RSA Opening Minds competence framework, an innovative curriculum to meet the needs of young people as future employees, lifelong learners and as citizens of the twenty-first century.

The Determination of Heat Capacity Ratios in a Simple Open System

ERIC Educational Resources Information Center

Holden, Glen L.

2007-01-01

A virtually closed system is treated as open and compared to known results. The classic experiment of Clement and Desormes provides the conceptual framework for this open system approach in determining the molar heat capacity ratios, lambda. This alternate view, extends the theoretical treatment beyond the first law of thermodynamics for closed…

75 FR 41102 - Energy Conservation Program: Re-Opening of the Public Comment Period for Commercial Refrigeration...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-15

... Conservation Program: Re-Opening of the Public Comment Period for Commercial Refrigeration Equipment AGENCY... document for commercial refrigeration equipment and provide notice of a public meeting. The NOPM provided... the framework document for commercial refrigeration equipment is to be re-opened from July 15, 2010 to...

A Numerical Modeling Framework for Cohesive Sediment Transport Driven by Waves and Tidal Currents

DTIC Science & Technology

2012-09-30

for sediment transport. The successful extension to multi-dimensions is benefited from an open-source CFD package, OpenFOAM (www.openfoam.org). This...linz.at/Drupal/), which couples the fluid solver OpenFOAM with the Discrete Element Model (DEM) solver LIGGGHTS (an improved LAMMPS for granular flow

A Framework for Open Textbooks Analytics System

ERIC Educational Resources Information Center

Prasad, Deepak; Totaram, Rajneel; Usagawa, Tsuyoshi

2016-01-01

In the last few years, open textbook development has picked up dramatically due both to the expense of commercially published textbooks and the increasing availability of high-quality OER alternatives. While this offers a tremendous benefit in terms of lowering student textbook costs, the question remains, to what extent (if any) do open textbooks…

A Framework for the Ethics of Open Education

ERIC Educational Resources Information Center

Farrow, Robert

2016-01-01

What difference does openness make to the ethics of teaching and research? This paper approaches this question both from the perspective of research into the use of open educational resources (OER) in teaching and learning. An outline of the nature and importance of ethics in education research is provided before the basic principles of research…

The Determinants of Interdistrict Open Enrollment Flows: Evidence from Two States

ERIC Educational Resources Information Center

Carlson, Deven; Lavery, Lesley; Witte, John F.

2011-01-01

Interdistrict open enrollment is the most widely used form of school choice in the United States. Through the theoretical lens of a utility maximization framework, this article analyzes the determinants of interdistrict open enrollment flows in Minnesota and Colorado. The authors' empirical analysis employs an original data set that details open…

Open source OCR framework using mobile devices

NASA Astrophysics Data System (ADS)

Zhou, Steven Zhiying; Gilani, Syed Omer; Winkler, Stefan

2008-02-01

Mobile phones have evolved from passive one-to-one communication device to powerful handheld computing device. Today most new mobile phones are capable of capturing images, recording video, and browsing internet and do much more. Exciting new social applications are emerging on mobile landscape, like, business card readers, sing detectors and translators. These applications help people quickly gather the information in digital format and interpret them without the need of carrying laptops or tablet PCs. However with all these advancements we find very few open source software available for mobile phones. For instance currently there are many open source OCR engines for desktop platform but, to our knowledge, none are available on mobile platform. Keeping this in perspective we propose a complete text detection and recognition system with speech synthesis ability, using existing desktop technology. In this work we developed a complete OCR framework with subsystems from open source desktop community. This includes a popular open source OCR engine named Tesseract for text detection & recognition and Flite speech synthesis module, for adding text-to-speech ability.

ImTK: an open source multi-center information management toolkit

NASA Astrophysics Data System (ADS)

Alaoui, Adil; Ingeholm, Mary Lou; Padh, Shilpa; Dorobantu, Mihai; Desai, Mihir; Cleary, Kevin; Mun, Seong K.

2008-03-01

The Information Management Toolkit (ImTK) Consortium is an open source initiative to develop robust, freely available tools related to the information management needs of basic, clinical, and translational research. An open source framework and agile programming methodology can enable distributed software development while an open architecture will encourage interoperability across different environments. The ISIS Center has conceptualized a prototype data sharing network that simulates a multi-center environment based on a federated data access model. This model includes the development of software tools to enable efficient exchange, sharing, management, and analysis of multimedia medical information such as clinical information, images, and bioinformatics data from multiple data sources. The envisioned ImTK data environment will include an open architecture and data model implementation that complies with existing standards such as Digital Imaging and Communications (DICOM), Health Level 7 (HL7), and the technical framework and workflow defined by the Integrating the Healthcare Enterprise (IHE) Information Technology Infrastructure initiative, mainly the Cross Enterprise Document Sharing (XDS) specifications.

Directing the breathing behavior of pillared-layered metal-organic frameworks via a systematic library of functionalized linkers bearing flexible substituents.

PubMed

Henke, Sebastian; Schneemann, Andreas; Wütscher, Annika; Fischer, Roland A

2012-06-06

Flexible metal-organic frameworks (MOFs), also referred to as soft porous crystals (SPCs), show reversible structural transitions dependent on the nature and quantity of adsorbed guest molecules. In recent studies it has been reported that covalent functionalization of the organic linker can influence or even integrate framework flexibility ("breathing") in MOFs. However, rational fine-tuning of such responsive properties is very desirable but challenging as well. Here we present a powerful approach for the targeted manipulation of responsiveness and framework flexibility of an important family of pillared-layered MOFs based on the parent structure [Zn(2)(bdc)(2)(dabco)](n) (bdc = 1,4-benzenedicarboxylate; dabco = 1,4-diazabicyclo[2.2.2]octane). A library of functionalized bdc-type linkers (fu-bdc), which bear additional dangling side groups at different positions of the benzene core (alkoxy groups of varying chain length with diverse functionalities and polarity), was generated. Synthesis of the materials [Zn(2)(fu-bdc)(2)(dabco)](n) yields the respective collection of highly responsive MOFs. The parent MOF is only weakly flexible; however, the substituted frameworks of [Zn(2)(fu-bdc)(2)(dabco)](n) contract drastically upon guest removal and expand again upon adsorption of DMF (N,N-dimethylformamide), EtOH, or CO(2), etc., while N(2) is hardly adsorbed and does not open the narrow-pored form. These "breathing" dynamics are attributed to the dangling side chains that act as immobilized "guests", which interact with mobile guest molecules as well as with themselves and with the framework backbone. The structural details of the guest-free, contracted form and the gas sorption behavior (phase transition pressure, hysteresis loop) are highly dependent on the nature of the substituent at the linker and can therefore be adjusted using our approach. Combining our library of functionalized linkers with the concept of mixed-component MOFs (solid solutions) offers very rich additional dimensions of tailoring the structural dynamics and responsiveness. Implementation of two differently functionalized linkers in varying ratios yields multicomponent single-phased [Zn(2)(fu-bdc')(2x)(fu-bdc″)(2-2x)(dabco)](n) MOFs (0 < x < 1) of increased inherent complexity, which feature a non-linear dependence of their gas sorption properties on the applied ratio of components. Hence, the responsive behavior of such pillared-layered MOFs can be extensively tuned via an intelligent combination of functionalized linkers.

Role of Sink Density in Nonequilibrium Chemical Redistribution in Alloys

DOE PAGES

Martinez, Enrique Saez; Senninger, Oriane; Caro, Alfredo; ...

2018-03-08

Nonequilibrium chemical redistribution in open systems submitted to external forces, such as particle irradiation, leads to changes in the structural properties of the material, potentially driving the system to failure. Such redistribution is controlled by the complex interplay between the production of point defects, atomic transport rates, and the sink character of the microstructure. In this work, we analyze this interplay by means of a kinetic Monte Carlo (KMC) framework with an underlying atomistic model for the Fe-Cr model alloy to study the effect of ideal defect sinks on Cr concentration profiles, with a particular focus on the role ofmore » interface density. We observe that the amount of segregation decreases linearly with decreasing interface spacing. Within the framework of the thermodynamics of irreversible processes, a general analytical model is derived and assessed against the KMC simulations to elucidate the structure-property relationship of this system. Interestingly, in the kinetic regime where elimination of point defects at sinks is dominant over bulk recombination, the solute segregation does not directly depend on the dose rate but only on the density of sinks. Furthermore, this model provides new insight into the design of microstructures that mitigate chemical redistribution and improve radiation tolerance.« less

In Situ, Time-Resolved, and Mechanistic Studies of Metal–Organic Framework Nucleation and Growth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Vleet, Mary J.; Weng, Tingting; Li, Xinyi

The vast chemical and structural diversity of metal–organic frameworks (MOFs) opens up the exciting possibility of “crystal engineering” MOFs tailored for particular catalytic or separation applications. Yet the process of reaction discovery, optimization, and scale-up of MOF synthesis remains extremely challenging, presenting significant obstacles to the synthetic realization of many otherwise promising MOF structures. Recently, significant new insights into the fundamental processes governing MOF nucleation and growth, as well as the relationship between reaction parameters and synthetic outcome, have been derived using powerful in situ, time-resolved and/or mechanistic studies of MOF crystallization. This Review provides a summary and associated criticalmore » analysis of the results of these and other related “direct” studies of MOF nucleation and growth, with a particular emphasis on the recent advances in instrument technologies that have enabled such studies and on the major hypotheses, theories, and models that have been used to explain MOF formation. We conclude with a summary of the major insights that have been gained from the work summarized in this Review, outlining our own perspective on potential fruitful new directions for investigation.« less

Polymer-Derived Silicoboron Carbonitride Foams for CO2 Capture: From Design to Application as Scaffolds for the in Situ Growth of Metal-Organic Frameworks.

PubMed

Sandra, Fabien; Depardieu, Martin; Mouline, Zineb; Vignoles, Gérard L; Iwamoto, Yuji; Miele, Philippe; Backov, Rénal; Bernard, Samuel

2016-06-06

A template-assisted polymer-derived ceramic route is investigated for preparing a series of silicoboron carbonitride (Si/B/C/N) foams with a hierarchical pore size distribution and tailorable interconnected porosity. A boron-modified polycarbosilazane was selected to impregnate monolithic silica and carbonaceous templates and form after pyrolysis and template removal Si/B/C/N foams. By changing the hard template nature and controlling the quantity of polymer to be impregnated, controlled micropore/macropore distributions with mesoscopic cell windows are generated. Specific surface areas from 29 to 239 m(2)  g(-1) and porosities from 51 to 77 % are achieved. These foams combine a low density with a thermal insulation and a relatively good thermostructural stability. Their particular structure allowed the in situ growth of metal-organic frameworks (MOFs) directly within the open-cell structure. MOFs offered a microporosity feature to the resulting Si/B/C/N@MOF composite foams that allowed increasing the specific surface area to provide CO2 uptake of 2.2 %. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Role of Sink Density in Nonequilibrium Chemical Redistribution in Alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martinez, Enrique Saez; Senninger, Oriane; Caro, Alfredo

Nonequilibrium chemical redistribution in open systems submitted to external forces, such as particle irradiation, leads to changes in the structural properties of the material, potentially driving the system to failure. Such redistribution is controlled by the complex interplay between the production of point defects, atomic transport rates, and the sink character of the microstructure. In this work, we analyze this interplay by means of a kinetic Monte Carlo (KMC) framework with an underlying atomistic model for the Fe-Cr model alloy to study the effect of ideal defect sinks on Cr concentration profiles, with a particular focus on the role ofmore » interface density. We observe that the amount of segregation decreases linearly with decreasing interface spacing. Within the framework of the thermodynamics of irreversible processes, a general analytical model is derived and assessed against the KMC simulations to elucidate the structure-property relationship of this system. Interestingly, in the kinetic regime where elimination of point defects at sinks is dominant over bulk recombination, the solute segregation does not directly depend on the dose rate but only on the density of sinks. Furthermore, this model provides new insight into the design of microstructures that mitigate chemical redistribution and improve radiation tolerance.« less

In Situ, Time-Resolved, and Mechanistic Studies of Metal–Organic Framework Nucleation and Growth

DOE PAGES

Van Vleet, Mary J.; Weng, Tingting; Li, Xinyi; ...

2018-03-07

The vast chemical and structural diversity of metal–organic frameworks (MOFs) opens up the exciting possibility of “crystal engineering” MOFs tailored for particular catalytic or separation applications. Yet the process of reaction discovery, optimization, and scale-up of MOF synthesis remains extremely challenging, presenting significant obstacles to the synthetic realization of many otherwise promising MOF structures. Recently, significant new insights into the fundamental processes governing MOF nucleation and growth, as well as the relationship between reaction parameters and synthetic outcome, have been derived using powerful in situ, time-resolved and/or mechanistic studies of MOF crystallization. This Review provides a summary and associated criticalmore » analysis of the results of these and other related “direct” studies of MOF nucleation and growth, with a particular emphasis on the recent advances in instrument technologies that have enabled such studies and on the major hypotheses, theories, and models that have been used to explain MOF formation. We conclude with a summary of the major insights that have been gained from the work summarized in this Review, outlining our own perspective on potential fruitful new directions for investigation.« less

Correlations between Community Structure and Link Formation in Complex Networks

PubMed Central

Liu, Zhen; He, Jia-Lin; Kapoor, Komal; Srivastava, Jaideep

2013-01-01

Background Links in complex networks commonly represent specific ties between pairs of nodes, such as protein-protein interactions in biological networks or friendships in social networks. However, understanding the mechanism of link formation in complex networks is a long standing challenge for network analysis and data mining. Methodology/Principal Findings Links in complex networks have a tendency to cluster locally and form so-called communities. This widely existed phenomenon reflects some underlying mechanism of link formation. To study the correlations between community structure and link formation, we present a general computational framework including a theory for network partitioning and link probability estimation. Our approach enables us to accurately identify missing links in partially observed networks in an efficient way. The links having high connection likelihoods in the communities reveal that links are formed preferentially to create cliques and accordingly promote the clustering level of the communities. The experimental results verify that such a mechanism can be well captured by our approach. Conclusions/Significance Our findings provide a new insight into understanding how links are created in the communities. The computational framework opens a wide range of possibilities to develop new approaches and applications, such as community detection and missing link prediction. PMID:24039818

Role of Sink Density in Nonequilibrium Chemical Redistribution in Alloys

NASA Astrophysics Data System (ADS)

Martínez, Enrique; Senninger, Oriane; Caro, Alfredo; Soisson, Frédéric; Nastar, Maylise; Uberuaga, Blas P.

2018-03-01

Nonequilibrium chemical redistribution in open systems submitted to external forces, such as particle irradiation, leads to changes in the structural properties of the material, potentially driving the system to failure. Such redistribution is controlled by the complex interplay between the production of point defects, atomic transport rates, and the sink character of the microstructure. In this work, we analyze this interplay by means of a kinetic Monte Carlo (KMC) framework with an underlying atomistic model for the Fe-Cr model alloy to study the effect of ideal defect sinks on Cr concentration profiles, with a particular focus on the role of interface density. We observe that the amount of segregation decreases linearly with decreasing interface spacing. Within the framework of the thermodynamics of irreversible processes, a general analytical model is derived and assessed against the KMC simulations to elucidate the structure-property relationship of this system. Interestingly, in the kinetic regime where elimination of point defects at sinks is dominant over bulk recombination, the solute segregation does not directly depend on the dose rate but only on the density of sinks. This model provides new insight into the design of microstructures that mitigate chemical redistribution and improve radiation tolerance.

Synthesis and Characterization of Novel Nonlinear Optical Materials

NASA Astrophysics Data System (ADS)

Liang, Cheryl Shuang

1992-01-01

Nonlinear optic materials are becoming increasingly important because of their many technological applications, such as second harmonic generation (SHG), optical switching, and waveguides for optical transmission. Currently, there is a demand for crystals transparent in the UV region, which would make the third and higher harmonic generations feasible. Compounds with the general stoichiometry ABCO _4 structural systems have shown to be promising candidates for frequency doubling into the UV region. The stuffed tridymite structure in which these ABCO_4 compounds crystallize is very tolerant to substitution, and over two hundred compounds have been synthesized up to date. While the presently available theories of optical nonlinearity have been applied to many inorganic solids, the threatened structure theory applied for ferroelectric properties can also be used to describe the structure/property relationship in the ABCO_4 structural family. Compounds synthesized for this study, ALiPO_4 (A = Sr, Ba, Pb) have shown that the SHG of these materials can be maximized by bringing each system close to its structural phase transition or by inducing stress in the pure phase structure. Studies have shown that the dielectric coefficients of KNbO_3 increase by more than tenfold with tantalum doping. This prompted the investigation of a mixed niobium/tantalum containing channelled tetrahedra/octahedra open framework, K_{2/3}Li _{1/3}Nb_ {rm 2-x}Ta_{ rm x}PO_8. These compounds are capable of ion exchange, where other cations are used to replace potassium. The cation-framework interaction mimics the guest-host relationship characteristic of many traditional zeolitic materials. This interaction also enables us to determine the role of the cation in framework polarizability, which can be measured by SHG intensities. Through ion exchange, many isostructural compounds can be made at low temperatures. A family of layered rubidium niobium/tantalum oxide compounds have been synthesized in an extension of the investigation of the above host-guest interaction. X -ray diffraction data have shown successful incorporation of n-butyl ammonium chloride followed by exchange of an organic salt which has very large SHG intensity, N-methylstilbazolium chloride, into the layers.

Synthesis, structure, and bonding in K12Au21Sn4. A polar intermetallic compound with dense Au20 and open AuSn4 layers.

PubMed

Li, Bin; Kim, Sung-Jin; Miller, Gordon J; Corbett, John D

2009-12-07

The new phase K(12)Au(21)Sn(4) has been synthesized by direct reaction of the elements at elevated temperatures. Single crystal X-ray diffraction established its orthorhombic structure, space group Pmmn (No. 59), a = 12.162(2); b = 18.058(4); c = 8.657(2) A, V = 1901.3(7) A(3), and Z = 2. The structure consists of infinite puckered sheets of vertex-sharing gold tetrahedra (Au(20)) that are tied together by thin layers of alternating four-bonded-Sn and -Au atoms (AuSn(4)). Remarkably, the dense but electron-poorer blocks of Au tetrahedra coexist with more open and saturated Au-Sn layers, which are fragments of a zinc blende type structure that maximize tetrahedral heteroatomic bonding outside of the network of gold tetrahedra. LMTO band structure calculations reveal metallic properties and a pseudogap at 256 valence electrons per formula unit, only three electrons fewer than in the title compound and at a point at which strong Au-Sn bonding is optimized. Additionally, the tight coordination of the Au framework atoms by K plays an important bonding role: each Au tetrahedra has 10 K neighbors and each K atom has 8-12 Au contacts. The appreciably different role of the p element Sn in this structure from that in the triel members in K(3)Au(5)In and Rb(2)Au(3)Tl appears to arise from its higher electron count which leads to better p-bonding (valence electron concentrations = 1.32 versus 1.22).

ESDORA: A Data Archive Infrastructure Using Digital Object Model and Open Source Frameworks

NASA Astrophysics Data System (ADS)

Shrestha, Biva; Pan, Jerry; Green, Jim; Palanisamy, Giriprakash; Wei, Yaxing; Lenhardt, W.; Cook, R. Bob; Wilson, B. E.; Leggott, M.

2011-12-01

There are an array of challenges associated with preserving, managing, and using contemporary scientific data. Large volume, multiple formats and data services, and the lack of a coherent mechanism for metadata/data management are some of the common issues across data centers. It is often difficult to preserve the data history and lineage information, along with other descriptive metadata, hindering the true science value for the archived data products. In this project, we use digital object abstraction architecture as the information/knowledge framework to address these challenges. We have used the following open-source frameworks: Fedora-Commons Repository, Drupal Content Management System, Islandora (Drupal Module) and Apache Solr Search Engine. The system is an active archive infrastructure for Earth Science data resources, which include ingestion, archiving, distribution, and discovery functionalities. We use an ingestion workflow to ingest the data and metadata, where many different aspects of data descriptions (including structured and non-structured metadata) are reviewed. The data and metadata are published after reviewing multiple times. They are staged during the reviewing phase. Each digital object is encoded in XML for long-term preservation of the content and relations among the digital items. The software architecture provides a flexible, modularized framework for adding pluggable user-oriented functionality. Solr is used to enable word search as well as faceted search. A home grown spatial search module is plugged in to allow user to make a spatial selection in a map view. A RDF semantic store within the Fedora-Commons Repository is used for storing information on data lineage, dissemination services, and text-based metadata. We use the semantic notion "isViewerFor" to register internally or externally referenced URLs, which are rendered within the same web browser when possible. With appropriate mapping of content into digital objects, many different data descriptions, including structured metadata, data history, auditing trails, are captured and coupled with the data content. The semantic store provides a foundation for possible further utilizations, including provide full-fledged Earth Science ontology for data interpretation or lineage tracking. Datasets from the NASA-sponsored Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) as well as from the Synthesis Thematic Data Center (MAST-DC) are used in a testing deployment with the system. The testing deployment allows us to validate the features and values described here for the integrated system, which will be presented here. Overall, we believe that the integrated system is valid, reusable data archive software that provides digital stewardship for Earth Sciences data content, now and in the future. References: [1] Devarakonda, Ranjeet, and Harold Shanafield. "Drupal: Collaborative framework for science research." Collaboration Technologies and Systems (CTS), 2011 International Conference on. IEEE, 2011. [2] Devarakonda, Ranjeet, et al. "Semantic search integration to climate data." Collaboration Technologies and Systems (CTS), 2014 International Conference on. IEEE, 2014.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.

PubMed

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry

PubMed Central

Röst, Hannes L.; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

Motivation In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Results Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Availability Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS. PMID:25927999

Entrapment of metal clusters in metal-organic framework channels by extended hooks anchored at open metal sites.

PubMed

Zheng, Shou-Tian; Zhao, Xiang; Lau, Samuel; Fuhr, Addis; Feng, Pingyun; Bu, Xianhui

2013-07-17

Reported here are the new concept of utilizing open metal sites (OMSs) for architectural pore design and its practical implementation. Specifically, it is shown here that OMSs can be used to run extended hooks (isonicotinates in this work) from the framework walls to the channel centers to effect the capture of single metal ions or clusters, with the concurrent partitioning of the large channel spaces into multiple domains, alteration of the host-guest charge relationship and associated guest-exchange properties, and transfer of OMSs from the walls to the channel centers. The concept of the extended hook, demonstrated here in the multicomponent dual-metal and dual-ligand system, should be generally applicable to a range of framework types.

MUFFSgenMC: An Open Source MUon Flexible Framework for Spectral GENeration for Monte Carlo Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chatzidakis, Stylianos; Greulich, Christopher

A cosmic ray Muon Flexible Framework for Spectral GENeration for Monte Carlo Applications (MUFFSgenMC) has been developed to support state-of-the-art cosmic ray muon tomographic applications. The flexible framework allows for easy and fast creation of source terms for popular Monte Carlo applications like GEANT4 and MCNP. This code framework simplifies the process of simulations used for cosmic ray muon tomography.

Study on spatial structure of retailing based on GIS in the city of Wuhan

NASA Astrophysics Data System (ADS)

Liu, Cheng-liang; Tian, Ying

2008-10-01

With the agility of market economy, the characteristic of market spatial structure becomes more complex since the reformation and open policy. The spatial structure has broken through the traditional framework which is non-equilibriums and scattered, and represented such modern development character as diversification, grade, network, and non-equilibrium. This paper chooses 200 stochastic retailing stores whose acreages all exceed 40m2 in the four circles of Wuhan city, after the analysis of spatial difference on acreages, number, population density, and manage forms with GIS spatial methods, and makes a conclusion that the retailing spatial structure of Wuhan city has took on figure of rating circle wholly and frame of centralization-diffusion and enchasing partially; as location is concerned, centralization and diffusion takes place simultaneously, has behaved that retailing concentrated in heartland of city with more favorable traffic and market location by the means of market infiltration, and distributed in suburb more dispersive by market monopoly.

Information Object Definition–based Unified Modeling Language Representation of DICOM Structured Reporting

PubMed Central

Tirado-Ramos, Alfredo; Hu, Jingkun; Lee, K.P.

2002-01-01

Supplement 23 to DICOM (Digital Imaging and Communications for Medicine), Structured Reporting, is a specification that supports a semantically rich representation of image and waveform content, enabling experts to share image and related patient information. DICOM SR supports the representation of textual and coded data linked to images and waveforms. Nevertheless, the medical information technology community needs models that work as bridges between the DICOM relational model and open object-oriented technologies. The authors assert that representations of the DICOM Structured Reporting standard, using object-oriented modeling languages such as the Unified Modeling Language, can provide a high-level reference view of the semantically rich framework of DICOM and its complex structures. They have produced an object-oriented model to represent the DICOM SR standard and have derived XML-exchangeable representations of this model using World Wide Web Consortium specifications. They expect the model to benefit developers and system architects who are interested in developing applications that are compliant with the DICOM SR specification. PMID:11751804

Transplant organizational structures: viewpoints from established centers.

PubMed

Abouljoud, M; Klintmalm, G; Whitehouse, S

2012-10-01

This personal viewpoint report summarizes the responses of a survey targeting established transplant programs with a structured framework, such as center, institute, or department, and stability of leadership to assure valuable experiential observations. The 18-item survey was sent to 20 US institutions that met inclusion criteria. The response rate was 100%. Seventeen institutions had a distinct transplant governance structure. A majority of respondents perceived that their type of transplant structure was associated with enhanced recognition within their institution (85%), improved regulatory compliance (85%), transplant volume growth (75%), improved quality outcomes (75%) and increased funding for transplant-related research (75%). The prevailing themes in respondents' remarks were the perceived need for autonomy of the transplant entity, alignment among services and finances and alignment of authority with responsibility. Many respondents suggested that a dialogue be opened about effective transplant infrastructure that overcomes the boundaries of traditional academic department silos. © Copyright 2012 The American Society of Transplantation and the American Society of Transplant Surgeons.

An Object-Oriented Serial DSMC Simulation Package

NASA Astrophysics Data System (ADS)

Liu, Hongli; Cai, Chunpei

2011-05-01

A newly developed three-dimensional direct simulation Monte Carlo (DSMC) simulation package, named GRASP ("Generalized Rarefied gAs Simulation Package"), is reported in this paper. This package utilizes the concept of simulation engine, many C++ features and software design patterns. The package has an open architecture which can benefit further development and maintenance of the code. In order to reduce the engineering time for three-dimensional models, a hybrid grid scheme, combined with a flexible data structure compiled by C++ language, are implemented in this package. This scheme utilizes a local data structure based on the computational cell to achieve high performance on workstation processors. This data structure allows the DSMC algorithm to be very efficiently parallelized with domain decomposition and it provides much flexibility in terms of grid types. This package can utilize traditional structured, unstructured or hybrid grids within the framework of a single code to model arbitrarily complex geometries and to simulate rarefied gas flows. Benchmark test cases indicate that this package has satisfactory accuracy for complex rarefied gas flows.

Highly Crystalline Multimetallic Nanoframes with Three-Dimensional Electrocatalytic Surfaces

DOE PAGES

Chen, Chen; Kang, Yijin; Huo, Ziyang; ...

2014-02-27

Control of structure at the atomic level can precisely and effectively tune catalytic properties of materials, enabling enhancement in both activity and durability. We synthesized a highly active and durable class of electrocatalysts by exploiting the structural evolution of platinum-nickel (Pt-Ni) bimetallic nanocrystals. The starting material, crystalline PtNi 3 polyhedra, transforms in solution by interior erosion into Pt 3Ni nanoframes with surfaces that offer three-dimensional molecular accessibility. The edges of the Pt-rich PtNi 3 polyhedra are maintained in the final Pt 3Ni nanoframes. Both the interior and exterior catalytic surfaces of this open-framework structure are composed of the nanosegregated Pt-skinmore » structure, which exhibits enhanced oxygen reduction reaction (ORR) activity. The Pt 3Ni nanoframe catalysts achieved a factor of 36 enhancement in mass activity and a factor of 22 enhancement in specific activity, respectively, for this reaction (relative to state-of-the-art platinum-carbon catalysts) during prolonged exposure to reaction conditions.« less

Syntheses and structural characterization of Co(II) and Cd(II) coordination polymers with 1,4-bis(imidazolyl)butane ligand

NASA Astrophysics Data System (ADS)

Lalegani, Arash; Khalaj, Mehdi; Sedaghat, Sajjad; Łyczko, Krzysztof; Lipkowski, Janusz

2017-11-01

Two new coordination polymers, {[Co(bib)3](PF6)2}n (1) and [Cd (bib) Cl2]n (2), were prepared at room temperature by the reaction of appropriate salts of cobalt (II) and cadmium (II) with the flexible linker ligands 1,4-bis(imidazolyl) butane (bib). The compounds were characterized by elemental analyses, IR spectroscopy and single crystal X-ray diffraction. In the polymeric structure of 1, the Co(II) ion lies on an inversion centre and adopts the CoN6 octahedral geometry, while in the structure of 2, the Cd(II) ions adopt the CdN2Cl4 pseudo-octahedral geometry. In compound 1, six bib ligands are coordinated to one central cobalt (II) to form an open 3D 2-fold interpenetrating framework of the α-polonium (pcu) type topology, while in compound 2 two bib ligands are coordinated to one central cadmium (II) to form 2D network structure.

A gel aging effect in the synthesis of open-framework gallium phosphates: structure solution and solid-state NMR of a large-pore, open-framework material† †Electronic supplementary information (ESI) available. CCDC 1577782 and 1577783. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7dt03709k

PubMed Central

Broom, Lucy K.; Clarkson, Guy J.; Guillou, Nathalie; Hooper, Joseph E.; Dawson, Daniel M.; Tang, Chiu C.; Ashbrook, Sharon E.

2017-01-01

The templated zeolite-analogue GaPO-34 (CHA structure type) crystallises from a gel precursor Ga2O3 : 2H3PO4 : 1HF : 1.7SDA : 70H2O (where SDA = structure directing agent), treated hydrothermally for 24 hours at 170 °C using either pyridine or 1-methylimizadole as SDA and one of either poorly crystalline ε-Ga2O3 or γ-Ga2O3 as gallium precursor. If the same gels are stirred for periods shorter than 2 hours but treated under identical hydrothermal conditions, then a second phase crystallises, free of GaPO-34. If β-Ga2O3 is used as a reagent only the second phase is found to crystallise, irrespective of gel aging time. The competing phase, which we denote GaPO-34A, has been structurally characterised using synchrotron powder X-ray diffraction for the pyridine material, GaPO-34A(pyr), and using single-crystal X-ray diffraction for the 1-methylimiazole material, GaPO-34A(mim). The structure of GaPO-34A(pyr), P1, a = 10.22682(6) Å, b = 12.09585(7) Å, c = 13.86713(8) Å, α = 104.6531(4)°, β = 100.8111(6)°, γ = 102.5228(6)°, contains 7 unique gallium sites and 6 phosphorus sites, with empirical formula [Ga7P6O24(OH)2F3(H2O)2]·2(C5NH6). GaPO-34A(mim) is isostructural but is modelled as a half volume unit cell, P1, a = 5.0991(2) Å, b = 12.0631(6) Å, c = 13.8405(9) Å, α = 104.626(5)°, β = 100.346(5)°, γ = 101.936(4)°, with a gallium and a bridging fluoride partially occupied and two partially occupied SDA sites. Solid-state 31P and 71Ga NMR spectroscopy confirms the structural complexity of GaPO-34A with signals resulting from overlapping lineshapes from multiple Ga and P sites, while 1H and 13C solid-state NMR spectra confirm the presence of the protonated SDA and provide evidence for disorder in the SDA. The protonated SDA is located in 14-ring one-dimensional channels with hydrogen bonding deduced from the SDA nitrogens to framework oxygen distances. Upon thermal treatment to investigate SDA removal, structure collapse occurs, which may be due the large number of bridging hydroxides and fluorides in the as-made material, and the unequal amounts of gallium and phosphorus present. PMID:29171855

On location of piezoelectric element in a smart-structure: numerical investigation and experiment

NASA Astrophysics Data System (ADS)

Oshmarin, D.; Iurlov, M.

2017-06-01

In this paper, based on some example problems it was demonstrated that in examining the possibilities of smart structure applications, the matter of considerable researchers’ concern is the problem of location of piezoelectric elements in the structure to allow effective realization of its smart functions in the framework of the specified strategy of structure control and target purposes (vibration damping, defectoscopy, etc.) The numerical and experimental investigations have shown that for structures with the elements made of piezoelectric materials, it is more convenient to use as a parameter, specifying the best location of the piezoelectric element for damping the vibrations at the prescribed frequency, the coefficient of electromechanical coupling, which is evaluated by the values of eigenfrequencies of the structure in the short-circuit and open-circuit regimes. The values of eigenfrequencies of vibrations are evaluated by solving the problem of natural vibrations of electromechanical systems by the finite element method using the applied ANSYS package. The investigation were conducted for a thin-walled aluminum shell in the form of half-cylinder.

Federated Space-Time Query for Earth Science Data Using OpenSearch Conventions

NASA Astrophysics Data System (ADS)

Lynnes, C.; Beaumont, B.; Duerr, R. E.; Hua, H.

2009-12-01

The past decade has seen a burgeoning of remote sensing and Earth science data providers, as evidenced in the growth of the Earth Science Information Partner (ESIP) federation. At the same time, the need to combine diverse data sets to enable understanding of the Earth as a system has also grown. While the expansion of data providers is in general a boon to such studies, the diversity presents a challenge to finding useful data for a given study. Locating all the data files with aerosol information for a particular volcanic eruption, for example, may involve learning and using several different search tools to execute the requisite space-time queries. To address this issue, the ESIP federation is developing a federated space-time query framework, based on the OpenSearch convention (www.opensearch.org), with Geo and Time extensions. In this framework, data providers publish OpenSearch Description Documents that describe in a machine-readable form how to execute queries against the provider. The novelty of OpenSearch is that the space-time query interface becomes both machine callable and easy enough to integrate into the web browser's search box. This flexibility, together with a simple REST (HTTP-get) interface, should allow a variety of data providers to participate in the federated search framework, from large institutional data centers to individual scientists. The simple interface enables trivial querying of multiple data sources and participation in recursive-like federated searches--all using the same common OpenSearch interface. This simplicity also makes the construction of clients easy, as does existing OpenSearch client libraries in a variety of languages. Moreover, a number of clients and aggregation services already exist and OpenSearch is already supported by a number of web browsers such as Firefox and Internet Explorer.

Agent-based large-scale emergency evacuation using real-time open government data.

DOT National Transportation Integrated Search

2014-01-01

The open government initiatives have provided tremendous data resources for the : transportation system and emergency services in urban areas. This paper proposes : a traffic simulation framework using high temporal resolution demographic data : and ...

Detection and attribution of climate change at regional scale: case study of Karkheh river basin in the west of Iran

NASA Astrophysics Data System (ADS)

Zohrabi, Narges; Goodarzi, Elahe; Massah Bavani, Alireza; Najafi, Husain

2017-11-01

This research aims at providing a statistical framework for detection and attribution of climate variability and change at regional scale when at least 30 years of observation data are available. While extensive research has been done on detecting significant observed trends in hydroclimate variables and attribution to anthropogenic greenhouse gas emissions in large continents, less attention has been paid for regional scale analysis. The latter is mainly important for adaptation to climate change in different sectors including but not limited to energy, agriculture, and water resources planning and management, and it is still an open discussion in many countries including the West Asian ones. In the absence of regional climate models, an informative framework is suggested providing useful insights for policymakers. It benefits from general flexibility, not being computationally expensive, and applying several trend tests to analyze temporal variations in temperature and precipitation (gradual and step changes). The framework is implemented for a very important river basin in the west of Iran. In general, some increasing and decreasing trends of the interannual precipitation and temperature have been detected. For precipitation annual time series, a reducing step was seen around 1996 compared with the gradual change in most of the stations, which have not experience a dramatical change. The range of natural forcing is found to be ±76 % for precipitation and ±1.4 °C for temperature considering a two-dimensional diagram of precipitation and temperature anomalies from 1000-year control run of global climate model (GCM). Findings out of applying the proposed framework may provide useful insights into how to approach structural and non-structural climate change adaptation strategies from central governments.

SHINE: Strategic Health Informatics Networks for Europe.

PubMed

Kruit, D; Cooper, P A

1994-10-01

The mission of SHINE is to construct an open systems framework for the development of regional community healthcare telematic services that support and add to the strategic business objectives of European healthcare providers and purchasers. This framework will contain a Methodology, that identifies healthcare business processes and develops a supporting IT strategy, and the Open Health Environment. This consists of an architecture and information standards that are 'open' and will be available to any organisation wishing to construct SHINE conform regional healthcare telematic services. Results are: generic models, e.g., regional healthcare business networks, IT strategies; demonstrable, e.g., pilot demonstrators, application and service prototypes; reports, e.g., SHINE Methodology, pilot specifications & evaluations; proposals, e.g., service/interface specifications, standards conformance.

PaaS for web applications with OpenShift Origin

NASA Astrophysics Data System (ADS)

Lossent, A.; Rodriguez Peon, A.; Wagner, A.

2017-10-01

The CERN Web Frameworks team has deployed OpenShift Origin to facilitate deployment of web applications and to improving efficiency in terms of computing resource usage. OpenShift leverages Docker containers and Kubernetes orchestration to provide a Platform-as-a-service solution oriented for web applications. We will review use cases and how OpenShift was integrated with other services such as source control, web site management and authentication services.

A new series of mixed oxalates MM'(C 2O 4) 3(H 2O) 3· nH 2O (M = Cd, Hg, Pb; M' = Zr, Hf) based on eight-fold coordinated metals: Synthesis, crystal structure from single-crystal and powder diffraction data and thermal behaviour

NASA Astrophysics Data System (ADS)

Gavilan, Elisabeth; Audebrand, Nathalie; Jeanneau, Erwann

2007-11-01

A new series of mixed oxalates MM'(C 2O 4) 3(H 2O) 3· nH 2O (M = Cd, Hg, Pb; M' = Zr, Hf) has been prepared. The crystal structures have been solved from single-crystal and powder diffraction data. The isotypical compounds crystallise with space group P2 1/ c (No. 14). The structures consist of honeycomb layers formed by eight-fold coordinated metals, in a distorted square-based antiprismatic conformation, connected together via oxalates which act as bidentate ligands and also as monodentate in a less-common μ3-bridging mode. Sheets are built from two shifted honeycomb layers and linked to each other through a hydrogen network. The resulting frameworks of the series display a compact two-dimensional arrangement of polyhedra MO 8 and M'O 8. Weakly-bonded water molecules are located between and within the sheets. Comparisons with the 3D open-framework structures of related metal oxalates are made. The dehydration processes occur in three or four steps. The final products are MO, M'O 2 and PbZrO 3 resulting from the sublimation of PbO in air. The size of PbZrO 3 crystallites, which are on average isotropic, has been evaluated to be 1055 Å from line-broadening analysis.

Tectonic framework of northeast Egypt and its bearing on hydrocarbon exploration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khalil, M.; Moustafa, A.R.

1995-08-01

Detailed structural study of northern and central Sinai, the northern Eastern Desert, and the northern Gulf of Suez clarified the tectonic framework of northeast Egypt. This framework is related to the movements between the African Plate and the Eurasian and Arabian Plates. Late Cretaceous folding and thrusting in response to oblique convergence between the African and Eurasian Plates formed NE-ENE oriented, doubly plunging, en echelon folds of the northern Egypt fold belt. This fold belt is well exposed in northern Sinai and a few other places but is concealed under younger sediments in the other parts of northern Egypt. Youngermore » folding of local importance is related to dextral slip on the Themed Fault (Central Sinai) in post Middle Eocene-pre Miocene time. Early Miocene rifting of the Afro-Arabian Plate led to the opening of the Suez rift and deposition of significant syn-rift facies. Half grabens and tilted fault blocks dominate the rift. Slightly tilted fault blocks characterize the competent Middle Eocene limestones of the Eastern Desert south of the Cairo-Suez road but north of this road, Middle Eocene rocks are locally dragged on nearby E-W and NW-SE oriented faults forming fault-drag folds. Ductile Upper Eocene and Miocene rocks are also folded about gentle NW-SE oriented doubly plunging folds. The different stages of tectonic activity in northern Egypt contributed to the development of different types of structural traps as well as different source, reservoir, and cap rocks. The sedimentary history of the region indicates well developed marine sediments of Jurassic, Cretaceous, Eocene, and Miocene ages. Basin development in structurally low areas provided good sites for hydrocarbon generation and maturation.« less

[Zn(INO) 2(DMF)]·DMF: A new three-dimensional supramolecular open framework containing one-dimensional channels

NASA Astrophysics Data System (ADS)

Hong, Jun

2006-02-01

A three-dimensional supramolecular compound, [Zn(INO) 2(DMF)]·DMF (1) (INO=isonicotinic acid N-oxide), has been prepared in the DMF solution at room temperature, and characterized by elemental analysis, TG and single crystal X-ray diffraction. The three-dimensional supramolecular open framework of 1 contains rectangular channels with the dimensions of 9.02×10.15 Å, assembled from one-dimensional helical chains via hydrogen-bonding and π-π stacking interactions. Furthermore, compound 1 shows blue photoluminescence at room temperature.

An open-source job management framework for parameter-space exploration: OACIS

NASA Astrophysics Data System (ADS)

Murase, Y.; Uchitane, T.; Ito, N.

2017-11-01

We present an open-source software framework for parameter-space exporation, named OACIS, which is useful to manage vast amount of simulation jobs and results in a systematic way. Recent development of high-performance computers enabled us to explore parameter spaces comprehensively, however, in such cases, manual management of the workflow is practically impossible. OACIS is developed aiming at reducing the cost of these repetitive tasks when conducting simulations by automating job submissions and data management. In this article, an overview of OACIS as well as a getting started guide are presented.

CONSTRUCTING A FLEXIBLE LIKELIHOOD FUNCTION FOR SPECTROSCOPIC INFERENCE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Czekala, Ian; Andrews, Sean M.; Mandel, Kaisey S.

2015-10-20

We present a modular, extensible likelihood framework for spectroscopic inference based on synthetic model spectra. The subtraction of an imperfect model from a continuously sampled spectrum introduces covariance between adjacent datapoints (pixels) into the residual spectrum. For the high signal-to-noise data with large spectral range that is commonly employed in stellar astrophysics, that covariant structure can lead to dramatically underestimated parameter uncertainties (and, in some cases, biases). We construct a likelihood function that accounts for the structure of the covariance matrix, utilizing the machinery of Gaussian process kernels. This framework specifically addresses the common problem of mismatches in model spectralmore » line strengths (with respect to data) due to intrinsic model imperfections (e.g., in the atomic/molecular databases or opacity prescriptions) by developing a novel local covariance kernel formalism that identifies and self-consistently downweights pathological spectral line “outliers.” By fitting many spectra in a hierarchical manner, these local kernels provide a mechanism to learn about and build data-driven corrections to synthetic spectral libraries. An open-source software implementation of this approach is available at http://iancze.github.io/Starfish, including a sophisticated probabilistic scheme for spectral interpolation when using model libraries that are sparsely sampled in the stellar parameters. We demonstrate some salient features of the framework by fitting the high-resolution V-band spectrum of WASP-14, an F5 dwarf with a transiting exoplanet, and the moderate-resolution K-band spectrum of Gliese 51, an M5 field dwarf.« less

A multimodal imaging framework for enhanced robot-assisted partial nephrectomy guidance

NASA Astrophysics Data System (ADS)

Halter, Ryan J.; Wu, Xiaotian; Hartov, Alex; Seigne, John; Khan, Shadab

2015-03-01

Robot-assisted laparoscopic partial nephrectomies (RALPN) are performed to treat patients with locally confined renal carcinoma. There are well-documented benefits to performing partial (opposed to radical) kidney resections and to using robot-assisted laparoscopic (opposed to open) approaches. However, there are challenges in identifying tumor margins and critical benign structures including blood vessels and collecting systems during current RALPN procedures. The primary objective of this effort is to couple multiple image and data streams together to augment visual information currently provided to surgeons performing RALPN and ultimately ensure complete tumor resection and minimal damage to functional structures (i.e. renal vasculature and collecting systems). To meet this challenge we have developed a framework and performed initial feasibility experiments to couple pre-operative high-resolution anatomic images with intraoperative MRI, ultrasound (US) and optical-based surface mapping and kidney tracking. With these registered images and data streams, we aim to overlay the high-resolution contrast-enhanced anatomic (CT or MR) images onto the surgeon's view screen for enhanced guidance. To date we have integrated the following components of our framework: 1) a method for tracking an intraoperative US probe to extract the kidney surface and a set of embedded kidney markers, 2) a method for co-registering intraoperative US scans with pre-operative MR scans, and 3) a method for deforming pre-op scans to match intraoperative scans. These components have been evaluated through phantom studies to demonstrate protocol feasibility.

Tablet computers in assessing performance in a high stakes exam: opinion matters.

PubMed

Currie, G P; Sinha, S; Thomson, F; Cleland, J; Denison, A R

2017-06-01

Background Tablet computers have emerged as a tool to capture, process and store data in examinations, yet evidence relating to their acceptability and usefulness in assessment is limited. Methods We performed an observational study to explore opinions and attitudes relating to tablet computer use in recording performance in a final year objective structured clinical examination at a single UK medical school. Examiners completed a short questionnaire encompassing background, forced-choice and open questions. Forced choice questions were analysed using descriptive statistics and open questions by framework analysis. Results Ninety-two (97% response rate) examiners completed the questionnaire of whom 85% had previous use of tablet computers. Ninety per cent felt checklist mark allocation was 'very/quite easy', while approximately half considered recording 'free-type' comments was 'easy/very easy'. Greater overall efficiency of marking and resource savings were considered the main advantages of tablet computers, while concerns relating to technological failure and ability to record free type comments were raised. Discussion In a context where examiners were familiar with tablet computers, they were preferred to paper checklists, although concerns were raised. This study adds to the limited literature underpinning the use of electronic devices as acceptable tools in objective structured clinical examinations.

Hearing voices: re/presenting the findings of narrative research into patient experience as poems.

PubMed

Stenhouse, R

2014-06-01

The study aimed to understand the experience of being a patient on an acute psychiatric inpatient ward. A further aim was to open up spaces for the voices of participants to be heard. Contemporary government policy places patient experience at the centre of healthcare policy and service development. Despite this, those who occupy marginalized discourses struggle to be heard within the dominant discourse of health care. A qualitative approach was used, and narrative was conceptualized as representing experience. Sociolinguistic theories informed the development of the analytic framework treating meaning as contextual and arising from both content and structure of narratives. Concepts of representation, voice and authorship were problematized. Thirteen people who had been inpatients on an acute psychiatric inpatient ward participated. Narrative data were gathered using unstructured interviews. The data were analysed holistically using a method that attended to both the structure and content of the narrative. The product of these holistic narratives was the development of a poem representing each participant's experience. This paper focuses on the development of these poems as a method of decentring the authorial voice and opening up spaces for the voices of the participants to be heard. © 2013 John Wiley & Sons Ltd.

The MOOC and Learning Analytics Innovation Cycle (MOLAC): A Reflective Summary of Ongoing Research and Its Challenges

ERIC Educational Resources Information Center

Drachsler, H.; Kalz, M.

2016-01-01

The article deals with the interplay between learning analytics and massive open online courses (MOOCs) and provides a conceptual framework to situate ongoing research in the MOOC and learning analytics innovation cycle (MOLAC framework). The MOLAC framework is organized on three levels: On the micro-level, the data collection and analytics…

OERScout Technology Framework: A Novel Approach to Open Educational Resources Search

ERIC Educational Resources Information Center

Abeywardena, Ishan Sudeera; Chan, Chee Seng; Tham, Choy Yoong

2013-01-01

The open educational resources (OER) movement has gained momentum in the past few years. With this new drive towards making knowledge open and accessible, a large number of OER repositories have been established and made available online throughout the world. However, the inability of existing search engines such as Google, Yahoo!, and Bing to…

A Requirements-Based Exploration of Open-Source Software Development Projects--Towards a Natural Language Processing Software Analysis Framework

ERIC Educational Resources Information Center

Vlas, Radu Eduard

2012-01-01

Open source projects do have requirements; they are, however, mostly informal, text descriptions found in requests, forums, and other correspondence. Understanding such requirements provides insight into the nature of open source projects. Unfortunately, manual analysis of natural language requirements is time-consuming, and for large projects,…

A Framework for Developing Competencies in Open and Distance Learning

ERIC Educational Resources Information Center

Arinto, Patricia B.

2013-01-01

Many open universities and distance education institutions have shifted from a predominantly print-based mode of delivery to an online mode characterised by the use of virtual learning environments and various web technologies. This paper describes the impact of the shift to open and distance e-learning (ODeL), as this trend might be called, on…

Migrations of the Mind: The Emergence of Open Source Education

ERIC Educational Resources Information Center

Glassman, Michael; Bartholomew, Mitchell; Jones, Travis

2011-01-01

The authors describe an Open Source approach to education. They define Open Source Education (OSE) as a teaching and learning framework where the use and presentation of information is non-hierarchical, malleable, and subject to the needs and contributions of students as they become "co-owners" of the course. The course transforms itself into an…

Cognitive Readiness Assessment and Reporting: An Open Source Mobile Framework for Operational Decision Support and Performance Improvement

ERIC Educational Resources Information Center

Heric, Matthew; Carter, Jenn

2011-01-01

Cognitive readiness (CR) and performance for operational time-critical environments are continuing points of focus for military and academic communities. In response to this need, we designed an open source interactive CR assessment application as a highly adaptive and efficient open source testing administration and analysis tool. It is capable…

Organizational Context and Capabilities for Integrating Care: A Framework for Improvement

PubMed Central

Grudniewicz, Agnes; Baker, G. Ross; Wodchis, Walter P.

2016-01-01

Background: Interventions aimed at integrating care have become widespread in healthcare; however, there is significant variability in their success. Differences in organizational contexts and associated capabilities may be responsible for some of this variability. Purpose: This study develops and validates a conceptual framework of organizational capabilities for integrating care, identifies which of these capabilities may be most important, and explores the mechanisms by which they influence integrated care efforts. Methods: The Context and Capabilities for Integrating Care (CCIC) Framework was developed through a literature review, and revised and validated through interviews with leaders and care providers engaged in integrated care networks in Ontario, Canada. Interviews involved open-ended questions and graphic elicitation. Quantitative content analysis was used to summarize the data. Results: The CCIC Framework consists of eighteen organizational factors in three categories: Basic Structures, People and Values, and Key Processes. The three most important capabilities shaping the capacity of organizations to implement integrated care interventions include Leadership Approach, Clinician Engagement and Leadership, and Readiness for Change. The majority of hypothesized relationships among organizational capabilities involved Readiness for Change and Partnering, emphasizing the complexity, interrelatedness and importance of these two factors to integrated care efforts. Conclusions: Organizational leaders can use the framework to determine readiness to integrate care, develop targeted change management strategies, and select appropriate partners with overlapping or complementary profiles on key capabilities. Researchers may use the results to test and refine the proposed framework, with a focus on the hypothesized relationships among organizational capabilities and between organizational capabilities and performance outcomes. PMID:28413366

The OpenEarth Framework (OEF) for the 3D Visualization of Integrated Earth Science Data

NASA Astrophysics Data System (ADS)

Nadeau, David; Moreland, John; Baru, Chaitan; Crosby, Chris

2010-05-01

Data integration is increasingly important as we strive to combine data from disparate sources and assemble better models of the complex processes operating at the Earth's surface and within its interior. These data are often large, multi-dimensional, and subject to differing conventions for data structures, file formats, coordinate spaces, and units of measure. When visualized, these data require differing, and sometimes conflicting, conventions for visual representations, dimensionality, symbology, and interaction. All of this makes the visualization of integrated Earth science data particularly difficult. The OpenEarth Framework (OEF) is an open-source data integration and visualization suite of applications and libraries being developed by the GEON project at the University of California, San Diego, USA. Funded by the NSF, the project is leveraging virtual globe technology from NASA's WorldWind to create interactive 3D visualization tools that combine and layer data from a wide variety of sources to create a holistic view of features at, above, and beneath the Earth's surface. The OEF architecture is open, cross-platform, modular, and based upon Java. The OEF's modular approach to software architecture yields an array of mix-and-match software components for assembling custom applications. Available modules support file format handling, web service communications, data management, user interaction, and 3D visualization. File parsers handle a variety of formal and de facto standard file formats used in the field. Each one imports data into a general-purpose common data model supporting multidimensional regular and irregular grids, topography, feature geometry, and more. Data within these data models may be manipulated, combined, reprojected, and visualized. The OEF's visualization features support a variety of conventional and new visualization techniques for looking at topography, tomography, point clouds, imagery, maps, and feature geometry. 3D data such as seismic tomography may be sliced by multiple oriented cutting planes and isosurfaced to create 3D skins that trace feature boundaries within the data. Topography may be overlaid with satellite imagery, maps, and data such as gravity and magnetics measurements. Multiple data sets may be visualized simultaneously using overlapping layers within a common 3D coordinate space. Data management within the OEF handles and hides the inevitable quirks of differing file formats, web protocols, storage structures, coordinate spaces, and metadata representations. Heuristics are used to extract necessary metadata used to guide data and visual operations. Derived data representations are computed to better support fluid interaction and visualization while the original data is left unchanged in its original form. Data is cached for better memory and network efficiency, and all visualization makes use of 3D graphics hardware support found on today's computers. The OpenEarth Framework project is currently prototyping the software for use in the visualization, and integration of continental scale geophysical data being produced by EarthScope-related research in the Western US. The OEF is providing researchers with new ways to display and interrogate their data and is anticipated to be a valuable tool for future EarthScope-related research.

Two Decades of Structure Building

PubMed Central

Gernsbacher, Morton Ann

2014-01-01

During the past decade I have been developing a very simple framework for describing the cognitive processes and mechanisms involved in discourse comprehension. I call this framework the Structure Building Framework, and it is based on evidence provided during the first decade of discourse processing research. According to the Structure Building Framework, the goal of comprehension is to build coherent mental representations or structures. Comprehenders build each structure by first laying a foundation. Comprehenders develop mental structures by mapping on new information when that information coheres or relates to previous information. However, when the incoming information is less related, comprehenders shift and attach a new substructure. The building blocks of mental structures are memory nodes, which are activated by incoming stimuli and controlled by two cognitive mechanisms: suppression and enhancement. In this article, first I review the seminal work on which the Structure Building Framework is based (the first decade of structure building research); then I recount the research I have conducted to test the Structure Building Framework (the second decade of structure building research). PMID:25484476

Hyperconnectivity, Attribute-Space Connectivity and Path Openings: Theoretical Relationships

NASA Astrophysics Data System (ADS)

Wilkinson, Michael H. F.

In this paper the relationship of hyperconnected filters with path openings and attribute-space connected filters is studied. Using a recently developed axiomatic framework based on hyperconnectivity operators, which are the hyperconnected equivalents of connectivity openings, it is shown that path openings are a special case of hyperconnected area openings. The new axiomatics also yield insight into the relationship between hyperconnectivity and attribute-space connectivity. It is shown any hyperconnectivity is an attribute-space connectivity, but that the reverse is not true.

Integration of electro-anatomical and imaging data of the left ventricle: An evaluation framework.

PubMed

Soto-Iglesias, David; Butakoff, Constantine; Andreu, David; Fernández-Armenta, Juan; Berruezo, Antonio; Camara, Oscar

2016-08-01

Integration of electrical and structural information for scar characterization in the left ventricle (LV) is a crucial step to better guide radio-frequency ablation therapies, which are usually performed in complex ventricular tachycardia (VT) cases. This integration requires finding a common representation where to map the electrical information from the electro-anatomical map (EAM) surfaces and tissue viability information from delay-enhancement magnetic resonance images (DE-MRI). However, the development of a consistent integration method is still an open problem due to the lack of a proper evaluation framework to assess its accuracy. In this paper we present both: (i) an evaluation framework to assess the accuracy of EAM and imaging integration strategies with simulated EAM data and a set of global and local measures; and (ii) a new integration methodology based on a planar disk representation where the LV surface meshes are quasi-conformally mapped (QCM) by flattening, allowing for simultaneous visualization and joint analysis of the multi-modal data. The developed evaluation framework was applied to estimate the accuracy of the QCM-based integration strategy on a benchmark dataset of 128 synthetically generated ground-truth cases presenting different scar configurations and EAM characteristics. The obtained results demonstrate a significant reduction in global overlap errors (50-100%) with respect to state-of-the-art integration techniques, also better preserving the local topology of small structures such as conduction channels in scars. Data from seventeen VT patients were also used to study the feasibility of the QCM technique in a clinical setting, consistently outperforming the alternative integration techniques in the presence of sparse and noisy clinical data. The proposed evaluation framework has allowed a rigorous comparison of different EAM and imaging data integration strategies, providing useful information to better guide clinical practice in complex cardiac interventions. Copyright © 2016 Elsevier B.V. All rights reserved.

CIM-EARTH: Community Integrated Model of Economic and Resource Trajectories for Humankind

NASA Astrophysics Data System (ADS)

Foster, I.; Elliott, J.; Munson, T.; Judd, K.; Moyer, E. J.; Sanstad, A. H.

2010-12-01

We report here on the development of an open source software framework termed CIM-EARTH that is intended to aid decision-making in climate and energy policy. Numerical modeling in support of evaluating policies to address climate change is difficult not only because of inherent uncertainties but because of the differences in scale and modeling approach required for various subcomponents of the system. Economic and climate models are structured quite differently, and while climate forcing can be assumed to be roughly global, climate impacts and the human response to them occur on small spatial scales. Mitigation policies likewise can be applied on scales ranging from the better part of a continent (e.g. a carbon cap-and-trade program for the entire U.S.) to a few hundred km (e.g. statewide renewable portfolio standards and local gasoline taxes). Both spatial and time resolution requirements can be challenging for global economic models. CIM-EARTH is a modular framework based around dynamic general equilibrium models. It is designed as a community tool that will enable study of the environmental benefits, transition costs, capitalization effects, and other consequences of both mitigation policies and unchecked climate change. Modularity enables both integration of highly resolved component sub-models for energy and other key systems and also user-directed choice of tradeoffs between e.g. spatial, sectoral, and time resolution. This poster describes the framework architecture, the current realized version, and plans for future releases. As with other open-source models familiar to the climate community (e.g. CCSM), deliverables will be made publicly available on a regular schedule, and community input is solicited for development of new features and modules.

Ordering of cations in the voids of the anionic framework of the crystal structure of catapleiite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yakubovich, O. V., E-mail: yakubol@geol.msu.ru; Karimova, O. V.; Ivanova, A. G.

2013-05-15

The pseudohexagonal crystal structure of the mineral catapleiite Na{sub 1.5}Ca{sub 0.2}[ZrSi{sub 3}(O,OH){sub 9}] {center_dot} 2(H{sub 2}O,F) from the Zhil'naya Valley in the central part of the Khibiny alkaline massif (Kola Peninsula, Russia) is studied by X-ray diffraction (XCalibur-S diffractometer, R = 0.0346): a = 20.100(4), b = 25.673(5), and c = 14.822(3) A; space group Fdd2, Z = 32, and {rho}{sub calcd} = 2.76 g/cm{sup 3}. Fluorine atoms substituting part of H{sub 2}O molecules in open channels of the crystal structure have been found for the first time in the catapleiite composition by microprobe analysis. The pattern of distribution ofmore » Na and Ca atoms over the voids of the mixed anionic framework consisting of Zr-octahedra and three-membered rings of Si-tetrahedra accounts for the pronounced pseudoperiodicity along the a and c axes of the pseudohexagonal unit cell and for the lowering of crystal symmetry to the orthorhombic one. It is shown that part of the hydrogen atoms of water molecules is statistically disordered; their distribution correlates with the pattern of the population of large eight-vertex polyhedra by Na and Ca atoms.« less